1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	\	\	SYM	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
4	0.15	0.15	CD	_	_	_
5	%	%	NN	_	_	_
6	Bile	Bile	NNP	_	_	_
7	Salt	Salt	NNP	_	_	_
8	Mix	Mix	NNP	_	_	_
9	Stress	stress	NN	_	_	_
10	,	,	,	_	_	_
11	90	90	CD	_	_	_
12	minutes	minute	NNS	_	_	_
13	,	,	,	_	_	_
14	static	static	JJ	_	_	_
15	,	,	,	_	_	_
16	5	5	CD	_	_	_
17	%	%	NN	_	_	_
18	CO2	co2	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	EHEC	ehec	NN	_	_	_
21	strain	strain	NN	_	_	_
22	:	:	:	_	_	_
23	86-24	86-24	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	0.2	0.2	CD	_	_	_
27	ppm	ppm	NN	_	_	_
28	deoxynivalenol	deoxynivalenol	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	0.2	0.2	CD	_	_	_
31	ppm	ppm	NN	_	_	_
32	nivalenol	nivalenol	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	0.5	0.5	CD	_	_	_
35	hour	hour	NN	_	_	_
36	expression	expression	NN	_	_	_
37	of	of	IN	_	_	_
38	synthetic	synthetic	JJ	_	_	_
39	protein	protein	NN	_	_	_
40	DX	dx	NN	_	_	_
41	in	in	IN	_	_	_
42	E.	e.	FW	_	_	_
43	coli	coli	FW	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	0.5	0.5	CD	_	_	_
46	mg/ml	mg/ml	NN	_	_	_
47	SHX	shx	NN	_	_	_
48	for	for	IN	_	_	_
49	20	20	CD	_	_	_
50	min	min	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	0.5	0.5	CD	_	_	_
53	MIC	mic	NN	_	_	_
54	of	of	IN	_	_	_
55	CYA	CYA	NNP	_	_	_
56	,	,	,	_	_	_
57	biological	biological	JJ	_	_	_
58	rep1	rep1	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	0.5	0.5	CD	_	_	_
61	MIC	mic	NN	_	_	_
62	of	of	IN	_	_	_
63	CYA	CYA	NNP	_	_	_
64	,	,	,	_	_	_
65	biological	biological	JJ	_	_	_
66	rep2	rep2	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	0.5	0.5	CD	_	_	_
69	MIC	mic	NN	_	_	_
70	of	of	IN	_	_	_
71	CYA	CYA	NNP	_	_	_
72	,	,	,	_	_	_
73	biological	biological	JJ	_	_	_
74	rep3	rep3	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	0.5	0.5	CD	_	_	_
77	%	%	NN	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	w/v	w/v	NN	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
82	_	_	NN	_	_	_
83	0	0	CD	_	_	_
84	min	min	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	0.5	0.5	CD	_	_	_
87	%	%	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	w/v	w/v	NN	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
92	_	_	SYM	_	_	_
93	15	15	CD	_	_	_
94	min	min	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	0.5	0.5	CD	_	_	_
97	%	%	NN	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	w/v	w/v	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
102	_	_	SYM	_	_	_
103	30	30	CD	_	_	_
104	min	min	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	0.5	0.5	CD	_	_	_
107	%	%	NN	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	w/v	w/v	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
112	_	_	SYM	_	_	_
113	5	5	CD	_	_	_
114	min	min	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	0.5	0.5	CD	_	_	_
117	%	%	NN	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	w/v	w/v	NN	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
122	_	_	NN	_	_	_
123	60	60	CD	_	_	_
124	min	min	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	0	0	CD	_	_	_
127	'	'	''	_	_	_
128	,	,	,	_	_	_
129	before	before	IN	_	_	_
130	UV	uv	NN	_	_	_
131	treatment	treatment	NN	_	_	_
132	,	,	,	_	_	_
133	25	25	CD	_	_	_
134	ug	ug	NN	_	_	_
135	total	total	JJ	_	_	_
136	RNA	rna	NN	_	_	_
137	,	,	,	_	_	_
138	2	2	CD	_	_	_
139	ug	ug	NN	_	_	_
140	pdN6	pdn6	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	0	0	CD	_	_	_
143	'	'	''	_	_	_
144	in	in	IN	_	_	_
145	minimal	minimal	JJ	_	_	_
146	medium	medium	NN	_	_	_
147	+0.2	+0.2	CD	_	_	_
148	%	%	NN	_	_	_
149	glu	glu	NN	_	_	_
150	,	,	,	_	_	_
151	25	25	CD	_	_	_
152	ug	ug	NN	_	_	_
153	total	total	JJ	_	_	_
154	RNA	rna	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	0	0	CD	_	_	_
157	'	'	''	_	_	_
158	in	in	IN	_	_	_
159	min	min	NN	_	_	_
160	med	med	VBD	_	_	_
161	+0.2	+0.2	CD	_	_	_
162	%	%	NN	_	_	_
163	glu	glu	NN	_	_	_
164	,	,	,	_	_	_
165	25ug	25ug	JJ	_	_	_
166	total	total	JJ	_	_	_
167	RNA	rna	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	0	0	CD	_	_	_
170	'	'	''	_	_	_
171	lexA	lexA	NNP	GEN	_	_
172	,	,	,	_	_	_
173	before	before	IN	_	_	_
174	UV	uv	NN	_	_	_
175	25	25	CD	_	_	_
176	ug	ug	NN	_	_	_
177	total	total	JJ	_	_	_
178	RNA	rna	NN	_	_	_
179	,	,	,	_	_	_
180	2	2	CD	_	_	_
181	ug	ug	NN	_	_	_
182	pdN6	pdn6	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	0	0	CD	_	_	_
185	min	min	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	0	0	CD	_	_	_
188	min	min	NN	_	_	_
189	,	,	,	_	_	_
190	0.8	0.8	CD	_	_	_
191	%	%	NN	_	_	_
192	butanol	butanol	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	0min-1	0min-1	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	0min-2	0min-2	JJ	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	0min-3	0min-3	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	0	0	CD	_	_	_
201	'	'	''	_	_	_
202	minimal	minimal	JJ	_	_	_
203	+	+	CC	_	_	_
204	0.2	0.2	CD	_	_	_
205	%	%	NN	_	_	_
206	glu	glu	NN	_	_	_
207	,	,	,	_	_	_
208	25	25	CD	_	_	_
209	ug	ug	NN	_	_	_
210	total	total	JJ	_	_	_
211	RNA	rna	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	0	0	CD	_	_	_
214	'	'	''	_	_	_
215	minimal	minimal	JJ	_	_	_
216	+02	+02	CD	_	_	_
217	%	%	NN	_	_	_
218	glu	glu	NN	_	_	_
219	,	,	,	_	_	_
220	25	25	CD	_	_	_
221	ug	ug	NN	_	_	_
222	total	total	JJ	_	_	_
223	RNA	rna	NN	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	0	0	CD	_	_	_
226	'	'	''	_	_	_
227	minimal	minimal	JJ	_	_	_
228	medium	medium	NN	_	_	_
229	+	+	CC	_	_	_
230	0.2	0.2	CD	_	_	_
231	%	%	NN	_	_	_
232	glu	glu	NN	_	_	_
233	,	,	,	_	_	_
234	25	25	CD	_	_	_
235	ug	ug	NN	_	_	_
236	total	total	JJ	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	0	0	CD	_	_	_
239	min	min	NN	_	_	_
240	minus	minus	CC	_	_	_
241	ciprofloxacin	ciprofloxacin	NN	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	0	0	CD	_	_	_
244	min	min	NN	_	_	_
245	Nov0	nov0	NN	_	_	_
246	ug/ml	ug/ml	NN	_	_	_
247	,	,	,	_	_	_
248	2	2	CD	_	_	_
249	ug	ug	NN	_	_	_
250	Say3AI	say3ai	NN	_	_	_
251	,	,	,	_	_	_
252	pdN6	pdn6	NN	_	_	_
253	RT	rt	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	0	0	CD	_	_	_
256	min	min	NN	_	_	_
257	Nov0	nov0	NN	_	_	_
258	ug/ml	ug/ml	NN	_	_	_
259	,	,	,	_	_	_
260	dnaCacrD	dnacacrd	NN	_	_	_
261	30	30	CD	_	_	_
262	min	min	NN	_	_	_
263	after	after	IN	_	_	_
264	synchr	synchr	NN	_	_	_
265	start	start	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	0	0	CD	_	_	_
268	min	min	NN	_	_	_
269	Nov500	nov500	NN	_	_	_
270	ug/ml	ug/ml	NN	_	_	_
271	,	,	,	_	_	_
272	2	2	CD	_	_	_
273	ug	ug	NN	_	_	_
274	Say3AI	say3ai	NN	_	_	_
275	,	,	,	_	_	_
276	pdN6	pdn6	NN	_	_	_
277	RT	rt	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	0	0	CD	_	_	_
280	min	min	NN	_	_	_
281	Nov500	nov500	NN	_	_	_
282	ug/ml	ug/ml	NN	_	_	_
283	,	,	,	_	_	_
284	dnaCacrD	dnacacrd	NN	_	_	_
285	30	30	CD	_	_	_
286	min	min	NN	_	_	_
287	after	after	IN	_	_	_
288	synchr	synchr	NN	_	_	_
289	start	start	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	0	0	CD	_	_	_
292	min	min	NN	_	_	_
293	plus	plus	CC	_	_	_
294	ciprofloxacin	ciprofloxacin	NN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	0	0	CD	_	_	_
297	min	min	NN	_	_	_
298	,	,	,	_	_	_
299	unstressed	unstressed	JJ	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	0	0	CD	_	_	_
302	%	%	NN	_	_	_
303	rep1	rep1	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	0	0	CD	_	_	_
306	%	%	NN	_	_	_
307	rep2	rep2	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	0	0	CD	_	_	_
310	%	%	NN	_	_	_
311	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
312	_	_	NN	_	_	_
313	0	0	CD	_	_	_
314	min	min	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	0	0	CD	_	_	_
317	%	%	NN	_	_	_
318	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
319	_	_	CD	_	_	_
320	15	15	CD	_	_	_
321	min	min	NN	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	0	0	CD	_	_	_
324	%	%	NN	_	_	_
325	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
326	_	_	CD	_	_	_
327	30	30	CD	_	_	_
328	min	min	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	0	0	CD	_	_	_
331	%	%	NN	_	_	_
332	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
333	_	_	CD	_	_	_
334	5	5	CD	_	_	_
335	min	min	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	0	0	CD	_	_	_
338	%	%	NN	_	_	_
339	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
340	_	_	CD	_	_	_
341	60	60	CD	_	_	_
342	min	min	NN	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	0	0	CD	_	_	_
345	'	'	''	_	_	_
346	wt	wt	JJ	_	_	_
347	,	,	,	_	_	_
348	before	before	IN	_	_	_
349	UV	uv	NN	_	_	_
350	treatment	treatment	NN	_	_	_
351	,	,	,	_	_	_
352	25	25	CD	_	_	_
353	ug	ug	NN	_	_	_
354	total	total	JJ	_	_	_
355	RNA	rna	NN	_	_	_
356	,	,	,	_	_	_
357	2	2	CD	_	_	_
358	ug	ug	NN	_	_	_
359	pdN6	pdn6	NN	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	0x58	0x58	NN	_	_	_
362	replicate	replicate	VBP	_	_	_
363	2	2	CD	_	_	_
364	state	state	NN	_	_	_
365	1	1	CD	_	_	_
366	-LRB-	-lrb-	-LRB-	_	_	_
367	IPTG	iptg	SYM	_	_	_
368	-	-	:	_	_	_
369	/	/	:	_	_	_
370	aTc	atc	SYM	_	_	_
371	-	-	:	_	_	_
372	/	/	:	_	_	_
373	Ara	Ara	NNP	_	_	_
374	-	-	:	_	_	_
375	-RRB-	-rrb-	-RRB-	_	_	_
376	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
377	0x58	0x58	NN	_	_	_
378	replicate	replicate	VBP	_	_	_
379	2	2	CD	_	_	_
380	state	state	NN	_	_	_
381	2	2	CD	_	_	_
382	-LRB-	-lrb-	-LRB-	_	_	_
383	IPTG	iptg	NN	_	_	_
384	+	+	CC	_	_	_
385	/	/	:	_	_	_
386	aTc	atc	SYM	_	_	_
387	-	-	:	_	_	_
388	/	/	:	_	_	_
389	Ara	Ara	NNP	_	_	_
390	-	-	:	_	_	_
391	-RRB-	-rrb-	-RRB-	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
393	0x58	0x58	NN	_	_	_
394	replicate	replicate	VBP	_	_	_
395	2	2	CD	_	_	_
396	state	state	NN	_	_	_
397	3	3	CD	_	_	_
398	-LRB-	-lrb-	-LRB-	_	_	_
399	IPTG	iptg	SYM	_	_	_
400	-	-	:	_	_	_
401	/	/	:	_	_	_
402	aTc	atc	NN	_	_	_
403	+	+	CC	_	_	_
404	/	/	:	_	_	_
405	Ara	Ara	NNP	_	_	_
406	-	-	:	_	_	_
407	-RRB-	-rrb-	-RRB-	_	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	0x58	0x58	NN	_	_	_
410	replicate	replicate	VBP	_	_	_
411	2	2	CD	_	_	_
412	state	state	NN	_	_	_
413	4	4	CD	_	_	_
414	-LRB-	-lrb-	-LRB-	_	_	_
415	IPTG	iptg	NN	_	_	_
416	+	+	CC	_	_	_
417	/	/	:	_	_	_
418	aTc	atc	NN	_	_	_
419	+	+	CC	_	_	_
420	/	/	:	_	_	_
421	Ara	Ara	NNP	_	_	_
422	-	-	:	_	_	_
423	-RRB-	-rrb-	-RRB-	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	0x58	0x58	NN	_	_	_
426	replicate	replicate	VBP	_	_	_
427	2	2	CD	_	_	_
428	state	state	NN	_	_	_
429	5	5	CD	_	_	_
430	-LRB-	-lrb-	-LRB-	_	_	_
431	IPTG	iptg	SYM	_	_	_
432	-	-	:	_	_	_
433	/	/	:	_	_	_
434	aTc	atc	SYM	_	_	_
435	-	-	:	_	_	_
436	/	/	:	_	_	_
437	Ara	Ara	NNP	_	_	_
438	+	+	CC	_	_	_
439	-RRB-	-rrb-	-RRB-	_	_	_
440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
441	0x58	0x58	NN	_	_	_
442	replicate	replicate	VBP	_	_	_
443	2	2	CD	_	_	_
444	state	state	NN	_	_	_
445	6	6	CD	_	_	_
446	-LRB-	-lrb-	-LRB-	_	_	_
447	IPTG	iptg	NN	_	_	_
448	+	+	CC	_	_	_
449	/	/	:	_	_	_
450	aTc	atc	SYM	_	_	_
451	-	-	:	_	_	_
452	/	/	:	_	_	_
453	Ara	Ara	NNP	_	_	_
454	+	+	CC	_	_	_
455	-RRB-	-rrb-	-RRB-	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	0x58	0x58	NN	_	_	_
458	replicate	replicate	VBP	_	_	_
459	2	2	CD	_	_	_
460	state	state	NN	_	_	_
461	7	7	CD	_	_	_
462	-LRB-	-lrb-	-LRB-	_	_	_
463	IPTG	iptg	SYM	_	_	_
464	-	-	:	_	_	_
465	/	/	:	_	_	_
466	aTc	atc	NN	_	_	_
467	+	+	CC	_	_	_
468	/	/	:	_	_	_
469	Ara	Ara	NNP	_	_	_
470	+	+	CC	_	_	_
471	-RRB-	-rrb-	-RRB-	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	0x58	0x58	NN	_	_	_
474	replicate	replicate	VBP	_	_	_
475	2	2	CD	_	_	_
476	state	state	NN	_	_	_
477	8	8	CD	_	_	_
478	-LRB-	-lrb-	-LRB-	_	_	_
479	IPTG	iptg	NN	_	_	_
480	+	+	CC	_	_	_
481	/	/	:	_	_	_
482	aTc	atc	NN	_	_	_
483	+	+	CC	_	_	_
484	/	/	:	_	_	_
485	Ara	Ara	NNP	_	_	_
486	+	+	CC	_	_	_
487	-RRB-	-rrb-	-RRB-	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
489	0x58	0x58	NN	_	_	_
490	replicate	replicate	VBP	_	_	_
491	3	3	CD	_	_	_
492	state	state	NN	_	_	_
493	1	1	CD	_	_	_
494	-LRB-	-lrb-	-LRB-	_	_	_
495	IPTG	iptg	SYM	_	_	_
496	-	-	:	_	_	_
497	/	/	:	_	_	_
498	aTc	atc	SYM	_	_	_
499	-	-	:	_	_	_
500	/	/	:	_	_	_
501	Ara	Ara	NNP	_	_	_
502	-	-	:	_	_	_
503	-RRB-	-rrb-	-RRB-	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	0x58	0x58	NN	_	_	_
506	replicate	replicate	VBP	_	_	_
507	3	3	CD	_	_	_
508	state	state	NN	_	_	_
509	2	2	CD	_	_	_
510	-LRB-	-lrb-	-LRB-	_	_	_
511	IPTG	iptg	NN	_	_	_
512	+	+	CC	_	_	_
513	/	/	:	_	_	_
514	aTc	atc	SYM	_	_	_
515	-	-	:	_	_	_
516	/	/	:	_	_	_
517	Ara	Ara	NNP	_	_	_
518	-	-	:	_	_	_
519	-RRB-	-rrb-	-RRB-	_	_	_
520	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
521	0x58	0x58	NN	_	_	_
522	replicate	replicate	VBP	_	_	_
523	3	3	CD	_	_	_
524	state	state	NN	_	_	_
525	3	3	CD	_	_	_
526	-LRB-	-lrb-	-LRB-	_	_	_
527	IPTG	iptg	SYM	_	_	_
528	-	-	:	_	_	_
529	/	/	:	_	_	_
530	aTc	atc	NN	_	_	_
531	+	+	CC	_	_	_
532	/	/	:	_	_	_
533	Ara	Ara	NNP	_	_	_
534	-	-	:	_	_	_
535	-RRB-	-rrb-	-RRB-	_	_	_
536	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
537	0x58	0x58	NN	_	_	_
538	replicate	replicate	VBP	_	_	_
539	3	3	CD	_	_	_
540	state	state	NN	_	_	_
541	4	4	CD	_	_	_
542	-LRB-	-lrb-	-LRB-	_	_	_
543	IPTG	iptg	NN	_	_	_
544	+	+	CC	_	_	_
545	/	/	:	_	_	_
546	aTc	atc	NN	_	_	_
547	+	+	CC	_	_	_
548	/	/	:	_	_	_
549	Ara	Ara	NNP	_	_	_
550	-	-	:	_	_	_
551	-RRB-	-rrb-	-RRB-	_	_	_
552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
553	0x58	0x58	NN	_	_	_
554	replicate	replicate	VBP	_	_	_
555	3	3	CD	_	_	_
556	state	state	NN	_	_	_
557	5	5	CD	_	_	_
558	-LRB-	-lrb-	-LRB-	_	_	_
559	IPTG	iptg	SYM	_	_	_
560	-	-	:	_	_	_
561	/	/	:	_	_	_
562	aTc	atc	SYM	_	_	_
563	-	-	:	_	_	_
564	/	/	:	_	_	_
565	Ara	Ara	NNP	_	_	_
566	+	+	CC	_	_	_
567	-RRB-	-rrb-	-RRB-	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	0x58	0x58	NN	_	_	_
570	replicate	replicate	VBP	_	_	_
571	3	3	CD	_	_	_
572	state	state	NN	_	_	_
573	6	6	CD	_	_	_
574	-LRB-	-lrb-	-LRB-	_	_	_
575	IPTG	iptg	NN	_	_	_
576	+	+	CC	_	_	_
577	/	/	:	_	_	_
578	aTc	atc	SYM	_	_	_
579	-	-	:	_	_	_
580	/	/	:	_	_	_
581	Ara	Ara	NNP	_	_	_
582	+	+	CC	_	_	_
583	-RRB-	-rrb-	-RRB-	_	_	_
584	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
585	0x58	0x58	NN	_	_	_
586	replicate	replicate	VBP	_	_	_
587	3	3	CD	_	_	_
588	state	state	NN	_	_	_
589	7	7	CD	_	_	_
590	-LRB-	-lrb-	-LRB-	_	_	_
591	IPTG	iptg	SYM	_	_	_
592	-	-	:	_	_	_
593	/	/	:	_	_	_
594	aTc	atc	NN	_	_	_
595	+	+	CC	_	_	_
596	/	/	:	_	_	_
597	Ara	Ara	NNP	_	_	_
598	+	+	CC	_	_	_
599	-RRB-	-rrb-	-RRB-	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
601	0x58	0x58	NN	_	_	_
602	replicate	replicate	VBP	_	_	_
603	3	3	CD	_	_	_
604	state	state	NN	_	_	_
605	8	8	CD	_	_	_
606	-LRB-	-lrb-	-LRB-	_	_	_
607	IPTG	iptg	NN	_	_	_
608	+	+	CC	_	_	_
609	/	/	:	_	_	_
610	aTc	atc	NN	_	_	_
611	+	+	CC	_	_	_
612	/	/	:	_	_	_
613	Ara	Ara	NNP	_	_	_
614	+	+	CC	_	_	_
615	-RRB-	-rrb-	-RRB-	_	_	_
616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
617	1	1	CD	_	_	_
618	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	10,000	10,000	CD	_	_	_
3	U	U	NNP	_	_	_
4	Pencillin	Pencillin	NNP	_	_	_
5	G	G	NNP	_	_	_
6	in	in	IN	_	_	_
7	media	media	NNS	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	1005	1005	CD	_	_	_
10	fork-blocking	fork-blocking	NN	_	_	_
11	strain	strain	NN	_	_	_
12	induced	induce	VBD	_	_	_
13	for	for	IN	_	_	_
14	Tus	Tus	NNP	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	1005	1005	CD	_	_	_
17	fork-blocking	fork-blocking	JJ	_	_	_
18	strain	strain	NN	_	_	_
19	induced	induce	VBN	_	_	_
20	for	for	IN	_	_	_
21	Tus	Tus	NNP	_	_	_
22	:	:	:	_	_	_
23	fork5	fork5	CD	_	_	_
24	_	_	NN	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	1005	1005	CD	_	_	_
28	fork-blocking	fork-blocking	JJ	_	_	_
29	strain	strain	NN	_	_	_
30	induced	induce	VBN	_	_	_
31	for	for	IN	_	_	_
32	Tus	Tus	NNP	_	_	_
33	:	:	:	_	_	_
34	fork5	fork5	CD	_	_	_
35	_	_	SYM	_	_	_
36	3	3	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	1005	1005	CD	_	_	_
39	,	,	,	_	_	_
40	LB	lb	NN	_	_	_
41	+	+	CC	_	_	_
42	0.2	0.2	CD	_	_	_
43	%	%	NN	_	_	_
44	glucose	glucose	NN	SUPP	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	tus	tus	NN	GEN	_	_
47	repressed	repress	VBN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	1005	1005	CD	_	_	_
51	,	,	,	_	_	_
52	LB	lb	NN	_	_	_
53	+	+	CC	_	_	_
54	0.4	0.4	CD	_	_	_
55	%	%	NN	_	_	_
56	arabinose	arabinose	NN	_	_	_
57	,	,	,	_	_	_
58	2.5	2.5	CD	_	_	_
59	hr	hr	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	tus	tus	NN	GEN	_	_
62	induced	induce	VBN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	1005	1005	CD	_	_	_
66	,	,	,	_	_	_
67	LB	lb	NN	_	_	_
68	+	+	CC	_	_	_
69	0.4	0.4	CD	_	_	_
70	%	%	NN	_	_	_
71	arabinose	arabinose	NN	_	_	_
72	,	,	,	_	_	_
73	3.5	3.5	CD	_	_	_
74	hr	hr	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	tus	tus	NN	GEN	_	_
77	induced	induce	VBN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
80	1005	1005	CD	_	_	_
81	,	,	,	_	_	_
82	LB	lb	NN	_	_	_
83	+	+	CC	_	_	_
84	0.4	0.4	CD	_	_	_
85	%	%	NN	_	_	_
86	arabinose	arabinose	NN	_	_	_
87	,	,	,	_	_	_
88	90	90	CD	_	_	_
89	'	'	''	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	tus	tus	FW	GEN	_	_
92	induced	induce	VBN	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	100ng	100ng	CD	_	_	_
96	16S	16s	NN	_	_	_
97	rRNA	rrna	NN	_	_	_
98	gene	gene	NN	_	_	_
99	amplicon	amplicon	NN	_	_	_
100	of	of	IN	_	_	_
101	a	a	DT	_	_	_
102	mock	mock	JJ	_	_	_
103	community	community	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	100	100	CD	_	_	_
106	%	%	NN	_	_	_
107	rep1	rep1	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	100	100	CD	_	_	_
110	%	%	NN	_	_	_
111	rep2	rep2	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	10A	10a	CD	_	_	_
114	_	_	NN	_	_	_
115	MG+PMA	mg+pma	NN	_	_	_
116	_	_	CD	_	_	_
117	t60	t60	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	10B	10b	NN	_	_	_
120	_	_	CD	_	_	_
121	MG+PMA	MG+PMA	NNP	_	_	_
122	_	_	CD	_	_	_
123	t60	t60	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	10C	10c	CD	_	_	_
126	_	_	NN	_	_	_
127	MG+PMA	mg+pma	NN	_	_	_
128	_	_	CD	_	_	_
129	t60	t60	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	10	10	CD	_	_	_
132	_	_	CD	_	_	_
133	ESBL019	esbl019	NN	_	_	_
134	Filamented	Filamented	NNP	_	_	_
135	Repl	Repl	NNP	_	_	_
136	3	3	CD	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	10	10	CD	_	_	_
139	.	.	.	_	_	_

1	FHI9.IND.HUS	fhi9.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	10	10	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	HP	HP	NNP	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	_	_	CD	_	_	_
11	noRh	norh	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	COPRO-Seq	copro-seq	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	10-HT874-PS-60min1	10-ht874-ps-60min1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	10J	10j	NN	_	_	_
19	.0	.0	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	10	10	CD	_	_	_
22	min	min	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	10	10	CD	_	_	_
25	min	min	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	10	10	CD	_	_	_
28	min	min	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	additional	additional	JJ	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	10	10	CD	_	_	_
34	min	min	NN	_	_	_
35	after	after	IN	_	_	_
36	UVtreatment	uvtreatment	NN	_	_	_
37	1	1	CD	_	_	_
38	'	'	''	_	_	_
39	,	,	,	_	_	_
40	40J	40j	NN	_	_	_
41	,	,	,	_	_	_
42	MG1655	mg1655	NN	_	_	_
43	in	in	IN	_	_	_
44	Davis	Davis	NNP	_	_	_
45	+0.4	+0.4	CD	_	_	_
46	%	%	NN	_	_	_
47	glu	glu	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	10	10	CD	_	_	_
50	min	min	NN	_	_	_
51	UV	uv	NN	_	_	_
52	treated	treat	VBN	_	_	_
53	cells	cell	NNS	_	_	_
54	,	,	,	_	_	_
55	25	25	CD	_	_	_
56	ug	ug	NN	_	_	_
57	total	total	JJ	_	_	_
58	RNA	rna	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	10	10	CD	_	_	_
61	ml	ml	NN	_	_	_
62	of	of	IN	_	_	_
63	cell	cell	NN	_	_	_
64	culture	culture	NN	_	_	_
65	was	be	VBD	_	_	_
66	mixed	mix	VBN	_	_	_
67	with	with	IN	_	_	_
68	5	5	CD	_	_	_
69	ml	ml	NN	_	_	_
70	ice	ice	NN	_	_	_
71	cold	cold	JJ	_	_	_
72	killing	killing	NN	_	_	_
73	buffer	buffer	NN	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	20mM	20mm	NN	_	_	_
76	Tris	tris	NN	_	_	_
77	and	and	CC	_	_	_
78	5mM	5mm	NN	_	_	_
79	MgCl2	mgcl2	NN	_	_	_
80	and	and	CC	_	_	_
81	20mM	20mm	NN	_	_	_
82	NaN3	nan3	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	and	and	CC	_	_	_
85	cells	cell	NNS	_	_	_
86	collected	collect	VBN	_	_	_
87	by	by	IN	_	_	_
88	centrifugation	centrifugation	NN	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	8000g	8000g	CD	_	_	_
91	,	,	,	_	_	_
92	4C	4c	NN	_	_	_
93	,	,	,	_	_	_
94	3	3	CD	_	_	_
95	min	min	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	.	.	.	_	_	_

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	25mg/ml	25mg/ml	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	was	be	VBD	_	_	_
16	added	add	VBN	_	_	_
17	and	and	CC	_	_	_
18	incubated	incubate	VBN	_	_	_
19	for	for	IN	_	_	_
20	30	30	CD	_	_	_
21	min	min	NN	_	_	_
22	at	at	IN	_	_	_
23	65	65	CD	_	_	_
24	°C	°c	NN	_	_	_
25	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	2μL	2μl	NN	_	_	_
4	proteinase	proteinase	NN	_	_	_
5	K	k	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	25	25	CD	_	_	_
8	mg/ml	mg/ml	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	added	add	VBN	_	_	_
12	and	and	CC	_	_	_
13	samples	sample	NNS	_	_	_
14	incubated	incubate	VBN	_	_	_
15	at	at	IN	_	_	_
16	37	37	CD	_	_	_
17	°C	°c	NN	_	_	_
18	for	for	IN	_	_	_
19	15	15	CD	_	_	_
20	min	min	NN	_	_	_
21	followed	follow	VBN	_	_	_
22	by	by	IN	_	_	_
23	phenol	phenol	NN	_	_	_
24	extraction	extraction	NN	_	_	_
25	and	and	CC	_	_	_
26	precipitation	precipitation	NN	_	_	_
27	with	with	IN	_	_	_
28	ethanol	ethanol	NN	_	_	_
29	and	and	CC	_	_	_
30	Na-acetate	na-acetate	NN	_	_	_
31	.	.	.	_	_	_

1	Precipitated	precipitate	VBN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	50μL	50μl	NN	_	_	_
7	dH2O	dh2o	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	10	10	CD	_	_	_
3	mM	mm	NN	KWSUPP	_	_
4	of	of	IN	_	_	_
5	sodium	sodium	NN	_	_	_
6	phosphate	phosphate	NN	_	_	_
7	and	and	CC	_	_	_
8	formaldehyde	formaldehyde	NN	_	_	_
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	were	be	VBD	_	_	_
17	then	then	RB	_	_	_
18	added	add	VBN	_	_	_
19	.	.	.	_	_	_

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	10	10	CD	_	_	_
20	ng	ng	NN	_	_	_
21	of	of	IN	_	_	_
22	DNA	dna	NN	_	_	_
23	were	be	VBD	_	_	_
24	submitted	submit	VBN	_	_	_
25	to	to	TO	_	_	_
26	the	the	DT	_	_	_
27	University	University	NNP	_	_	_
28	of	of	IN	_	_	_
29	Wisconsin-Madison	Wisconsin-Madison	NNP	_	_	_
30	DNA	DNA	NNP	_	_	_
31	Sequencing	sequencing	NN	_	_	_
32	Facility	facility	NN	_	_	_
33	for	for	IN	_	_	_
34	ChIP-seq	ChIP-seq	NNP	_	_	_
35	library	library	NN	_	_	_
36	preparation	preparation	NN	_	_	_
37	.	.	.	_	_	_

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	10	10	CD	_	_	_
3	ng	ng	NN	_	_	_
4	of	of	IN	_	_	_
5	DNA	dna	NN	_	_	_
6	were	be	VBD	_	_	_
7	submitted	submit	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	University	University	NNP	_	_	_
11	of	of	IN	_	_	_
12	Wisconsin-Madison	Wisconsin-Madison	NNP	_	_	_
13	DNA	DNA	NNP	_	_	_
14	Sequencing	sequencing	NN	_	_	_
15	Facility	facility	NN	_	_	_
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	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	NN	_	_	_
2	10	10	CD	_	_	_
3	pmol	pmol	NN	_	_	_
4	of	of	IN	_	_	_
5	a	a	DT	_	_	_
6	pre-adenylated	pre-adenylated	JJ	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	rApp	rapp	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	adapter	adapter	NN	_	_	_
11	were	be	VBD	_	_	_
12	ligated	ligate	VBN	_	_	_
13	to	to	TO	_	_	_
14	1	1	CD	_	_	_
15	μg	μg	NN	_	_	_
16	of	of	IN	_	_	_
17	nascent	nascent	JJ	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	or	or	CC	_	_	_
20	mature	mature	JJ	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	RNA	rna	NN	_	_	_
23	in	in	IN	_	_	_
24	a	a	DT	_	_	_
25	reaction	reaction	NN	_	_	_
26	volume	volume	NN	_	_	_
27	of	of	IN	_	_	_
28	20	20	CD	_	_	_
29	μl	μl	NN	_	_	_
30	,	,	,	_	_	_
31	using	use	VBG	_	_	_
32	400	400	CD	_	_	_
33	U	U	NNP	_	_	_
34	T4	t4	NN	_	_	_
35	RNA	rna	NN	_	_	_
36	Ligase	ligase	NN	_	_	_
37	2	2	CD	_	_	_
38	,	,	,	_	_	_
39	Deletion	deletion	NN	_	_	_
40	Mutant	mutant	JJ	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	Epicentre	Epicentre	NNP	_	_	_
43	,	,	,	_	_	_
44	cat	cat	NN	_	_	_
45	.	.	.	_	_	_

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/μl	μg/μl	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	resuspended	resuspend	VBN	_	_	_
22	in	in	IN	_	_	_
23	8.25	8.25	CD	_	_	_
24	μl	μl	NN	_	_	_
25	nuclease-free	nuclease-free	JJ	_	_	_
26	water	water	NN	_	_	_
27	.	.	.	_	_	_

1	10	10	CD	_	_	_
2	pmol	pmol	NN	_	_	_
3	of	of	IN	_	_	_
4	a	a	DT	_	_	_
5	5	5	CD	_	_	_
6	'	'	''	_	_	_
7	-	-	:	_	_	_
8	phosphorylated	phosphorylate	VBN	_	_	_
9	adapter	adapter	NN	_	_	_
10	were	be	VBD	_	_	_
11	ligated	ligate	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	3	3	CD	_	_	_
15	'	'	''	_	_	_
16	-	-	:	_	_	_
17	OH	oh	NN	_	_	_
18	of	of	IN	_	_	_
19	cDNA	cdna	NN	_	_	_
20	fragments	fragment	NNS	_	_	_
21	in	in	IN	_	_	_
22	a	a	DT	_	_	_
23	final	final	JJ	_	_	_
24	reaction	reaction	NN	_	_	_
25	volume	volume	NN	_	_	_
26	of	of	IN	_	_	_
27	25	25	CD	_	_	_
28	μl	μl	NN	_	_	_
29	,	,	,	_	_	_
30	in	in	IN	_	_	_
31	the	the	DT	_	_	_
32	presence	presence	NN	_	_	_
33	of	of	IN	_	_	_
34	0.05	0.05	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	ATP	atp	NN	SUPP	_	_
37	,	,	,	_	_	_
38	20	20	CD	_	_	_
39	%	%	NN	_	_	_
40	PEG-4000	peg-4000	NN	_	_	_
41	,	,	,	_	_	_
42	and	and	CC	_	_	_
43	100	100	CD	_	_	_
44	U	U	NNP	_	_	_
45	CircLigase	CircLigase	NNP	_	_	_
46	™	™	NNP	_	_	_
47	II	II	NNP	_	_	_
48	ssDNA	ssDNA	NNP	_	_	_
49	Ligase	Ligase	NNP	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Epicentre	Epicentre	NNP	_	_	_
52	,	,	,	_	_	_
53	cat	cat	NN	_	_	_
54	.	.	.	_	_	_

1	CL9025K	cl9025k	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	,	,	,	_	_	_
4	by	by	IN	_	_	_
5	incubation	incubation	NN	_	_	_
6	at	at	IN	_	_	_
7	60	60	CD	_	_	_
8	°C	°c	NN	_	_	_
9	for	for	IN	_	_	_
10	4	4	CD	_	_	_
11	hours	hour	NNS	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	68	68	CD	_	_	_
15	°C	°c	NN	_	_	_
16	for	for	IN	_	_	_
17	2	2	CD	_	_	_
18	hours	hour	NNS	_	_	_
19	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	fragments	fragment	NNS	_	_	_
4	were	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	from	from	IN	_	_	_
7	excess	excess	JJ	_	_	_
8	adapter	adapter	NN	_	_	_
9	using	use	VBG	_	_	_
10	1.8	1.8	CD	_	_	_
11	volumes	volume	NNS	_	_	_
12	of	of	IN	_	_	_
13	Agencourt	Agencourt	NNP	_	_	_
14	AMPure	AMPure	NNP	_	_	_
15	XP	xp	NN	_	_	_
16	beads	bead	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Beckman	Beckman	NNP	_	_	_
19	Coulter	Coulter	NNP	_	_	_
20	,	,	,	_	_	_
21	cat	cat	NN	_	_	_
22	.	.	.	_	_	_

1	A63881	a63881	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	,	,	,	_	_	_
4	following	follow	VBG	_	_	_
5	manufacturer	manufacturer	NN	_	_	_
6	's	's	POS	_	_	_
7	instructions	instruction	NNS	_	_	_
8	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	eluted	elute	VBN	_	_	_
4	in	in	IN	_	_	_
5	20	20	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	nuclease-free	nuclease-free	JJ	_	_	_
9	water	water	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	indexed	index	VBD	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	adapters	adapter	NNS	_	_	_
15	were	be	VBD	_	_	_
16	introduced	introduce	VBN	_	_	_
17	by	by	IN	_	_	_
18	15	15	CD	_	_	_
19	cycles	cycle	NNS	_	_	_
20	of	of	IN	_	_	_
21	PCR	pcr	NN	_	_	_
22	in	in	IN	_	_	_
23	the	the	DT	_	_	_
24	presence	presence	NN	_	_	_
25	of	of	IN	_	_	_
26	25	25	CD	_	_	_
27	pmol	pmol	NN	_	_	_
28	of	of	IN	_	_	_
29	each	each	DT	_	_	_
30	primer	primer	NN	_	_	_
31	,	,	,	_	_	_
32	and	and	CC	_	_	_
33	25	25	CD	_	_	_
34	μl	μl	NN	_	_	_
35	NEBNext	nebnext	NN	_	_	_
36	®	®	CD	_	_	_
37	High-Fidelity	high-fidelity	NN	_	_	_
38	2X	2x	NN	_	_	_
39	PCR	pcr	NN	_	_	_
40	Master	master	NN	_	_	_
41	Mix	Mix	NNP	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	NEB	NEB	NNP	_	_	_
44	,	,	,	_	_	_
45	cat	cat	NN	_	_	_
46	.	.	.	_	_	_

1	M0541L	m0541l	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	10	10	CD	_	_	_
3	pmol	pmol	NN	_	_	_
4	of	of	IN	_	_	_
5	a	a	DT	_	_	_
6	pre-adenylated	pre-adenylated	JJ	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	rApp	rapp	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	adapter	adapter	NN	_	_	_
11	were	be	VBD	_	_	_
12	ligated	ligate	VBN	_	_	_
13	to	to	TO	_	_	_
14	1	1	CD	_	_	_
15	μg	μg	NN	_	_	_
16	of	of	IN	_	_	_
17	nascent	nascent	JJ	_	_	_
18	RNA	rna	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	either	either	CC	_	_	_
21	total	total	NN	_	_	_
22	,	,	,	_	_	_
23	or	or	CC	_	_	_
24	rRNA-depleted	rrna-depleted	JJ	_	_	_
25	using	use	VBG	_	_	_
26	Ribo-Zero	Ribo-Zero	NNP	_	_	_
27	rRNA	rrna	NN	_	_	_
28	Removal	removal	NN	_	_	_
29	Kit	kit	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Illumina	Illumina	NNP	_	_	_
32	,	,	,	_	_	_
33	cat	cat	NN	_	_	_
34	.	.	.	_	_	_

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/μl	μg/μl	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	resuspended	resuspend	VBN	_	_	_
22	in	in	IN	_	_	_
23	8.25	8.25	CD	_	_	_
24	μl	μl	NN	_	_	_
25	nuclease-free	nuclease-free	JJ	_	_	_
26	water	water	NN	_	_	_
27	.	.	.	_	_	_

1	10	10	CD	_	_	_
2	pmol	pmol	NN	_	_	_
3	of	of	IN	_	_	_
4	a	a	DT	_	_	_
5	5	5	CD	_	_	_
6	'	'	''	_	_	_
7	-	-	:	_	_	_
8	phosphorilated	phosphorilate	VBN	_	_	_
9	adapter	adapter	NN	_	_	_
10	were	be	VBD	_	_	_
11	ligated	ligate	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	3	3	CD	_	_	_
15	'	'	''	_	_	_
16	-	-	:	_	_	_
17	OH	oh	NN	_	_	_
18	of	of	IN	_	_	_
19	cDNA	cdna	NN	_	_	_
20	fragments	fragment	NNS	_	_	_
21	in	in	IN	_	_	_
22	a	a	DT	_	_	_
23	final	final	JJ	_	_	_
24	reaction	reaction	NN	_	_	_
25	volume	volume	NN	_	_	_
26	of	of	IN	_	_	_
27	25	25	CD	_	_	_
28	μl	μl	NN	_	_	_
29	,	,	,	_	_	_
30	in	in	IN	_	_	_
31	the	the	DT	_	_	_
32	presence	presence	NN	_	_	_
33	of	of	IN	_	_	_
34	0.05	0.05	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	ATP	atp	NN	SUPP	_	_
37	,	,	,	_	_	_
38	20	20	CD	_	_	_
39	%	%	NN	_	_	_
40	PEG-4000	peg-4000	NN	_	_	_
41	,	,	,	_	_	_
42	and	and	CC	_	_	_
43	100	100	CD	_	_	_
44	U	U	NNP	_	_	_
45	CircLigase	CircLigase	NNP	_	_	_
46	™	™	NNP	_	_	_
47	II	II	NNP	_	_	_
48	ssDNA	ssDNA	NNP	_	_	_
49	Ligase	Ligase	NNP	_	_	_
50	,	,	,	_	_	_
51	by	by	IN	_	_	_
52	incubation	incubation	NN	_	_	_
53	at	at	IN	_	_	_
54	60	60	CD	_	_	_
55	°C	°c	NN	_	_	_
56	for	for	IN	_	_	_
57	4	4	CD	_	_	_
58	hours	hour	NNS	_	_	_
59	,	,	,	_	_	_
60	and	and	CC	_	_	_
61	68	68	CD	_	_	_
62	°C	°c	NN	_	_	_
63	for	for	IN	_	_	_
64	2	2	CD	_	_	_
65	hours	hour	NNS	_	_	_
66	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	fragments	fragment	NNS	_	_	_
4	were	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	from	from	IN	_	_	_
7	excess	excess	JJ	_	_	_
8	adapter	adapter	NN	_	_	_
9	using	use	VBG	_	_	_
10	1.8	1.8	CD	_	_	_
11	volumes	volume	NNS	_	_	_
12	of	of	IN	_	_	_
13	Agencourt	Agencourt	NNP	_	_	_
14	AMPure	AMPure	NNP	_	_	_
15	XP	xp	NN	_	_	_
16	beads	bead	NNS	_	_	_
17	,	,	,	_	_	_
18	following	follow	VBG	_	_	_
19	manufacturer	manufacturer	NN	_	_	_
20	's	's	POS	_	_	_
21	instructions	instruction	NNS	_	_	_
22	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	eluted	elute	VBN	_	_	_
4	in	in	IN	_	_	_
5	20	20	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	nuclease-free	nuclease-free	JJ	_	_	_
9	water	water	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	indexed	index	VBD	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	adapters	adapter	NNS	_	_	_
15	were	be	VBD	_	_	_
16	introduced	introduce	VBN	_	_	_
17	by	by	IN	_	_	_
18	15	15	CD	_	_	_
19	cycles	cycle	NNS	_	_	_
20	of	of	IN	_	_	_
21	PCR	pcr	NN	_	_	_
22	in	in	IN	_	_	_
23	the	the	DT	_	_	_
24	presence	presence	NN	_	_	_
25	of	of	IN	_	_	_
26	25	25	CD	_	_	_
27	pmol	pmol	NN	_	_	_
28	of	of	IN	_	_	_
29	each	each	DT	_	_	_
30	primer	primer	NN	_	_	_
31	,	,	,	_	_	_
32	and	and	CC	_	_	_
33	25	25	CD	_	_	_
34	μl	μl	NN	_	_	_
35	NEBNext	nebnext	NN	_	_	_
36	®	®	CD	_	_	_
37	High-Fidelity	high-fidelity	NN	_	_	_
38	2X	2x	NN	_	_	_
39	PCR	pcr	NN	_	_	_
40	Master	master	NN	_	_	_
41	Mix	Mix	NNP	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	10	10	CD	_	_	_
3	pmol	pmol	NN	_	_	_
4	of	of	IN	_	_	_
5	a	a	DT	_	_	_
6	pre-adenylated	pre-adenylated	JJ	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	rApp	rapp	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	adapter	adapter	NN	_	_	_
11	were	be	VBD	_	_	_
12	ligated	ligate	VBN	_	_	_
13	to	to	TO	_	_	_
14	rnpB	rnpb	NN	GEN	_	_
15	nascent	nascent	JJ	_	_	_
16	RNA	rna	NN	_	_	_
17	in	in	IN	_	_	_
18	a	a	DT	_	_	_
19	reaction	reaction	NN	_	_	_
20	volume	volume	NN	_	_	_
21	of	of	IN	_	_	_
22	20	20	CD	_	_	_
23	μl	μl	NN	_	_	_
24	,	,	,	_	_	_
25	using	use	VBG	_	_	_
26	400	400	CD	_	_	_
27	U	U	NNP	_	_	_
28	T4	t4	NN	_	_	_
29	RNA	rna	NN	_	_	_
30	Ligase	ligase	NN	_	_	_
31	2	2	CD	_	_	_
32	,	,	,	_	_	_
33	Deletion	deletion	NN	_	_	_
34	Mutant	mutant	JJ	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	presence	presence	NN	_	_	_
38	of	of	IN	_	_	_
39	20	20	CD	_	_	_
40	%	%	NN	_	_	_
41	PEG-8000	peg-8000	NN	_	_	_
42	,	,	,	_	_	_
43	by	by	IN	_	_	_
44	incubation	incubation	NN	_	_	_
45	at	at	IN	_	_	_
46	25	25	CD	_	_	_
47	°C	°c	NN	_	_	_
48	for	for	IN	_	_	_
49	2	2	CD	_	_	_
50	hours	hour	NNS	_	_	_
51	.	.	.	_	_	_

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/μl	μg/μl	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	resuspended	resuspend	VBN	_	_	_
22	in	in	IN	_	_	_
23	8.25	8.25	CD	_	_	_
24	μl	μl	NN	_	_	_
25	nuclease-free	nuclease-free	JJ	_	_	_
26	water	water	NN	_	_	_
27	.	.	.	_	_	_

1	10	10	CD	_	_	_
2	pmol	pmol	NN	_	_	_
3	of	of	IN	_	_	_
4	a	a	DT	_	_	_
5	5	5	CD	_	_	_
6	'	'	''	_	_	_
7	-	-	:	_	_	_
8	phosphorilated	phosphorilate	VBN	_	_	_
9	adapter	adapter	NN	_	_	_
10	were	be	VBD	_	_	_
11	ligated	ligate	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	3	3	CD	_	_	_
15	'	'	''	_	_	_
16	-	-	:	_	_	_
17	OH	oh	NN	_	_	_
18	of	of	IN	_	_	_
19	cDNA	cdna	NN	_	_	_
20	fragments	fragment	NNS	_	_	_
21	in	in	IN	_	_	_
22	a	a	DT	_	_	_
23	final	final	JJ	_	_	_
24	reaction	reaction	NN	_	_	_
25	volume	volume	NN	_	_	_
26	of	of	IN	_	_	_
27	25	25	CD	_	_	_
28	μl	μl	NN	_	_	_
29	,	,	,	_	_	_
30	in	in	IN	_	_	_
31	the	the	DT	_	_	_
32	presence	presence	NN	_	_	_
33	of	of	IN	_	_	_
34	0.05	0.05	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	ATP	atp	NN	SUPP	_	_
37	,	,	,	_	_	_
38	20	20	CD	_	_	_
39	%	%	NN	_	_	_
40	PEG-4000	peg-4000	NN	_	_	_
41	,	,	,	_	_	_
42	and	and	CC	_	_	_
43	100	100	CD	_	_	_
44	U	U	NNP	_	_	_
45	CircLigase	CircLigase	NNP	_	_	_
46	™	™	NNP	_	_	_
47	II	II	NNP	_	_	_
48	ssDNA	ssDNA	NNP	_	_	_
49	Ligase	Ligase	NNP	_	_	_
50	,	,	,	_	_	_
51	by	by	IN	_	_	_
52	incubation	incubation	NN	_	_	_
53	at	at	IN	_	_	_
54	60	60	CD	_	_	_
55	°C	°c	NN	_	_	_
56	for	for	IN	_	_	_
57	4	4	CD	_	_	_
58	hours	hour	NNS	_	_	_
59	,	,	,	_	_	_
60	and	and	CC	_	_	_
61	68	68	CD	_	_	_
62	°C	°c	NN	_	_	_
63	for	for	IN	_	_	_
64	2	2	CD	_	_	_
65	hours	hour	NNS	_	_	_
66	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	fragments	fragment	NNS	_	_	_
4	were	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	from	from	IN	_	_	_
7	excess	excess	JJ	_	_	_
8	adapter	adapter	NN	_	_	_
9	using	use	VBG	_	_	_
10	1.8	1.8	CD	_	_	_
11	volumes	volume	NNS	_	_	_
12	of	of	IN	_	_	_
13	Agencourt	Agencourt	NNP	_	_	_
14	AMPure	AMPure	NNP	_	_	_
15	XP	xp	NN	_	_	_
16	beads	bead	NNS	_	_	_
17	,	,	,	_	_	_
18	following	follow	VBG	_	_	_
19	manufacturer	manufacturer	NN	_	_	_
20	's	's	POS	_	_	_
21	instructions	instruction	NNS	_	_	_
22	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	eluted	elute	VBN	_	_	_
4	in	in	IN	_	_	_
5	20	20	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	nuclease-free	nuclease-free	JJ	_	_	_
9	water	water	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	indexed	index	VBD	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	adapters	adapter	NNS	_	_	_
15	were	be	VBD	_	_	_
16	introduced	introduce	VBN	_	_	_
17	by	by	IN	_	_	_
18	15	15	CD	_	_	_
19	cycles	cycle	NNS	_	_	_
20	of	of	IN	_	_	_
21	PCR	pcr	NN	_	_	_
22	in	in	IN	_	_	_
23	the	the	DT	_	_	_
24	presence	presence	NN	_	_	_
25	of	of	IN	_	_	_
26	25	25	CD	_	_	_
27	pmol	pmol	NN	_	_	_
28	of	of	IN	_	_	_
29	each	each	DT	_	_	_
30	primer	primer	NN	_	_	_
31	,	,	,	_	_	_
32	and	and	CC	_	_	_
33	25	25	CD	_	_	_
34	μl	μl	NN	_	_	_
35	NEBNext	nebnext	NN	_	_	_
36	®	®	CD	_	_	_
37	High-Fidelity	high-fidelity	NN	_	_	_
38	2X	2x	NN	_	_	_
39	PCR	pcr	NN	_	_	_
40	Master	master	NN	_	_	_
41	Mix	Mix	NNP	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	10	10	CD	_	_	_
3	μg	μg	NN	_	_	_
4	of	of	IN	_	_	_
5	total	total	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	sample	sample	NN	_	_	_
8	was	be	VBD	_	_	_
9	subjected	subject	VBN	_	_	_
10	to	to	TO	_	_	_
11	purification	purification	NN	_	_	_
12	for	for	IN	_	_	_
13	discarding	discard	VBG	_	_	_
14	rRNA	rrna	NN	_	_	_
15	via	via	IN	_	_	_
16	the	the	DT	_	_	_
17	MICROBExpress	microbexpress	NN	_	_	_
18	kit	kit	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Ambion	ambion	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	according	accord	VBG	_	_	_
23	to	to	TO	_	_	_
24	the	the	DT	_	_	_
25	manufacturer	manufacturer	NN	_	_	_
26	's	's	POS	_	_	_
27	protocol	protocol	NN	_	_	_
28	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	1.1	1.1	CD	_	_	_
3	A	a	DT	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	1.1	1.1	CD	_	_	_
6	A	a	DT	_	_	_
7	_	_	NN	_	_	_
8	Earth	Earth	NNP	_	_	_
9	_	_	SYM	_	_	_
10	25	25	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	11	11	CD	_	_	_
13	_	_	NN	_	_	_
14	ESBL019	esbl019	NN	_	_	_
15	Transition	transition	NN	_	_	_
16	Repl	repl	NN	_	_	_
17	3	3	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	11	11	CD	_	_	_
20	.	.	.	_	_	_

1	FHI12.nIND.HUS	fhi12.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	11-HT874-PS-60min2	11-ht874-ps-60min2	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	11K	11k	CD	_	_	_
6	.60	.60	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	1.2	1.2	CD	_	_	_
9	A	a	DT	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	1.2	1.2	CD	_	_	_
12	A	a	DT	_	_	_
13	_	_	NN	_	_	_
14	Space	space	NN	_	_	_
15	_	_	CD	_	_	_
16	25	25	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	12	12	CD	_	_	_
19	_	_	NN	_	_	_
20	ESBL019	esbl019	NN	_	_	_
21	Reverted	revert	VBD	_	_	_
22	Repl	repl	JJ	_	_	_
23	3	3	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	12	12	CD	_	_	_
26	.	.	.	_	_	_

1	FHI12.IND.HUS	fhi12.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	12	12	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	LP	lp	NN	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	COPRO-Seq	copro-seq	NN	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	12-HT874-PS-60min3	12-ht874-ps-60min3	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	12L	12l	NN	_	_	_
17	.120	.120	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	1.3	1.3	CD	_	_	_
20	A	a	DT	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	1.3	1.3	CD	_	_	_
23	A	a	DT	_	_	_
24	_	_	NN	_	_	_
25	Earth	Earth	NNP	_	_	_
26	_	_	SYM	_	_	_
27	25	25	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	13	13	CD	_	_	_
30	_	_	NN	_	_	_
31	ESBL019	esbl019	NN	_	_	_
32	Coliform	coliform	NN	_	_	_
33	Repl	repl	NN	_	_	_
34	4	4	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	13	13	CD	_	_	_
37	.	.	.	_	_	_

1	FHI24.nIND.HUS	fhi24.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	13	13	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	LP	lp	NN	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	COPRO-Seq	copro-seq	NN	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	1.4	1.4	CD	_	_	_
15	A	a	DT	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	1.4	1.4	CD	_	_	_
18	A	a	DT	_	_	_
19	_	_	NN	_	_	_
20	Space	space	NN	_	_	_
21	_	_	CD	_	_	_
22	25	25	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	14	14	CD	_	_	_
25	_	_	CD	_	_	_
26	ESBL019	esbl019	NN	_	_	_
27	Filamented	Filamented	NNP	_	_	_
28	Repl	Repl	NNP	_	_	_
29	4	4	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	14	14	CD	_	_	_
32	_	_	SYM	_	_	_
33	HF	hf	NNS	_	_	_
34	_	_	VBP	_	_	_
35	LP	lp	NN	_	_	_
36	_	_	SYM	_	_	_
37	noDP	nodp	NN	_	_	_
38	-LSB-	-lsb-	-LRB-	_	_	_
39	COPRO-Seq	copro-seq	NN	_	_	_
40	-RSB-	-rsb-	-RRB-	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	150	150	CD	_	_	_
43	minutes	minute	NNS	_	_	_
44	growth	growth	NN	_	_	_
45	in	in	IN	_	_	_
46	LB	LB	NNP	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	15	15	CD	_	_	_
49	'	'	''	_	_	_
50	10	10	CD	_	_	_
51	ug/ml	ug/ml	JJ	_	_	_
52	indole	indole	NN	_	_	_
53	aa	aa	NN	_	_	_
54	,	,	,	_	_	_
55	minimal	minimal	JJ	_	_	_
56	medium	medium	NN	_	_	_
57	+	+	CC	_	_	_
58	0.2	0.2	CD	_	_	_
59	%	%	NN	_	_	_
60	glu	glu	NN	_	_	_
61	,	,	,	_	_	_
62	25	25	CD	_	_	_
63	ug	ug	NN	_	_	_
64	total	total	JJ	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	15	15	CD	_	_	_
67	'	'	''	_	_	_
68	15	15	CD	_	_	_
69	ug/ml	ug/ml	JJ	_	_	_
70	indole	indole	NN	_	_	_
71	aa	aa	NN	_	_	_
72	,	,	,	_	_	_
73	minimal	minimal	JJ	_	_	_
74	medium	medium	NN	_	_	_
75	+	+	CC	_	_	_
76	0.2	0.2	CD	_	_	_
77	%	%	NN	_	_	_
78	glu	glu	NN	_	_	_
79	,	,	,	_	_	_
80	25	25	CD	_	_	_
81	ug	ug	NN	_	_	_
82	total	total	JJ	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	15	15	CD	_	_	_
85	'	'	''	_	_	_
86	+50	+50	CD	_	_	_
87	ug/ml	ug/ml	JJ	_	_	_
88	Trp	trp	NN	_	_	_
89	vs	vs	CC	_	_	_
90	0	0	CD	_	_	_
91	'	'	''	_	_	_
92	in	in	IN	_	_	_
93	min	min	NN	_	_	_
94	med	med	VBD	_	_	_
95	+0.2	+0.2	CD	_	_	_
96	%	%	NN	_	_	_
97	glu	glu	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	1.5	1.5	CD	_	_	_
100	A	a	DT	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	1.5	1.5	CD	_	_	_
103	A	a	DT	_	_	_
104	_	_	NN	_	_	_
105	Earth	Earth	NNP	_	_	_
106	_	_	SYM	_	_	_
107	50	50	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
109	15degrees	15degree	NNS	_	_	_
110	replicate	replicate	VBP	_	_	_
111	1	1	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	15degrees	15degree	NNS	_	_	_
114	replicate	replicate	VBP	_	_	_
115	2	2	CD	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
117	15degrees	15degree	NNS	_	_	_
118	replicate	replicate	VBP	_	_	_
119	3	3	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	15	15	CD	_	_	_
122	_	_	NN	_	_	_
123	ESBL019	esbl019	NN	_	_	_
124	Transition	transition	NN	_	_	_
125	Repl	repl	NN	_	_	_
126	4	4	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	15	15	CD	_	_	_
129	.	.	.	_	_	_

1	FHI25.nIND.HUS	fhi25.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	15	15	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	LP	lp	NN	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	COPRO-Seq	copro-seq	NN	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	1.5	1.5	CD	_	_	_
15	hour	hour	NN	_	_	_
16	expression	expression	NN	_	_	_
17	of	of	IN	_	_	_
18	synthetic	synthetic	JJ	_	_	_
19	protein	protein	NN	_	_	_
20	DX	dx	NN	_	_	_
21	in	in	IN	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	15	15	CD	_	_	_
26	'	'	''	_	_	_
27	in	in	IN	_	_	_
28	minimal	minimal	JJ	_	_	_
29	medium	medium	NN	_	_	_
30	+0.2	+0.2	CD	_	_	_
31	%	%	NN	_	_	_
32	glu	glu	NN	_	_	_
33	,	,	,	_	_	_
34	25	25	CD	_	_	_
35	ug	ug	NN	_	_	_
36	total	total	JJ	_	_	_
37	RNA	rna	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	15	15	CD	_	_	_
40	'	'	''	_	_	_
41	in	in	IN	_	_	_
42	min	min	NN	_	_	_
43	med	med	VBD	_	_	_
44	+0.2	+0.2	CD	_	_	_
45	%	%	NN	_	_	_
46	glu	glu	NN	_	_	_
47	+50	+50	CD	_	_	_
48	ug/ml	ug/ml	JJ	_	_	_
49	Trp	trp	NN	_	_	_
50	,25	,25	CD	_	_	_
51	ug	ug	NN	_	_	_
52	total	total	JJ	_	_	_
53	RNA	rna	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	15	15	CD	_	_	_
56	min	min	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	15	15	CD	_	_	_
59	min	min	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	additional	additional	JJ	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	15	15	CD	_	_	_
65	min	min	NN	_	_	_
66	after	after	IN	_	_	_
67	turning	turn	VBG	_	_	_
68	off	off	RP	_	_	_
69	oxygen	oxygen	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
71	15	15	CD	_	_	_
72	ml	ml	NN	_	_	_
73	of	of	IN	_	_	_
74	culture	culture	NN	_	_	_
75	was	be	VBD	_	_	_
76	mixed	mix	VBN	_	_	_
77	with	with	IN	_	_	_
78	30	30	CD	_	_	_
79	ml	ml	NN	_	_	_
80	of	of	IN	_	_	_
81	RNAprotect	rnaprotect	NN	_	_	_
82	bacterial	bacterial	JJ	_	_	_
83	reagent	reagent	NN	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	QIAGEN	QIAGEN	NNP	_	_	_
86	Ltd	Ltd	NNP	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1.5	1.5	CD	_	_	_
3	'	'	''	_	_	_
4	RNA	rna	NN	_	_	_
5	Decay	decay	NN	_	_	_
6	N-RNaseE	n-rnasee	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	BZ453	bz453	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	in	in	IN	_	_	_
11	M9	m9	NN	_	_	_
12	0.2	0.2	CD	_	_	_
13	%	%	NN	_	_	_
14	Glycerol	glycerol	NN	_	_	_
15	,	,	,	_	_	_
16	0.2	0.2	CD	_	_	_
17	%	%	NN	_	_	_
18	Tryptone	tryptone	NN	_	_	_
19	at	at	IN	_	_	_
20	30	30	CD	_	_	_
21	C	c	NN	_	_	_
22	Mid	Mid	NNP	_	_	_
23	Log	Log	NNP	_	_	_
24	Rep.	Rep.	NNP	_	_	_
25	A	A	NNP	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	1.5	1.5	CD	_	_	_
28	'	'	''	_	_	_
29	RNA	rna	NN	_	_	_
30	Decay	decay	NN	_	_	_
31	N-RNaseE	n-rnasee	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	BZ453	bz453	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	in	in	IN	_	_	_
36	M9	m9	NN	_	_	_
37	0.2	0.2	CD	_	_	_
38	%	%	NN	_	_	_
39	Glycerol	glycerol	NN	_	_	_
40	,	,	,	_	_	_
41	0.2	0.2	CD	_	_	_
42	%	%	NN	_	_	_
43	Tryptone	tryptone	NN	_	_	_
44	at	at	IN	_	_	_
45	30	30	CD	_	_	_
46	C	c	NN	_	_	_
47	Mid	Mid	NNP	_	_	_
48	Log	Log	NNP	_	_	_
49	Rep.	Rep.	NNP	_	_	_
50	A1	a1	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	1.5	1.5	CD	_	_	_
53	'	'	''	_	_	_
54	RNA	rna	NN	_	_	_
55	Decay	decay	NN	_	_	_
56	N-RNaseE	n-rnasee	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	BZ453	bz453	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	in	in	IN	_	_	_
61	M9	m9	NN	_	_	_
62	+	+	CC	_	_	_
63	0.2	0.2	CD	_	_	_
64	%	%	NN	_	_	_
65	Glycerol	glycerol	NN	_	_	_
66	,	,	,	_	_	_
67	0.2	0.2	CD	_	_	_
68	%	%	NN	_	_	_
69	Tryptone	tryptone	NN	_	_	_
70	at	at	IN	_	_	_
71	30	30	CD	_	_	_
72	C	c	NN	_	_	_
73	Mid	Mid	NNP	_	_	_
74	Log	Log	NNP	_	_	_
75	Rep.	Rep.	NNP	_	_	_
76	B	B	NNP	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	1.5	1.5	CD	_	_	_
79	'	'	''	_	_	_
80	RNA	rna	NN	_	_	_
81	Decay	decay	NN	_	_	_
82	N-RNaseE	n-rnasee	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	BZ453	bz453	NN	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	in	in	IN	_	_	_
87	M9	m9	NN	_	_	_
88	+	+	CC	_	_	_
89	0.2	0.2	CD	_	_	_
90	%	%	NN	_	_	_
91	Glycerol	glycerol	NN	_	_	_
92	,	,	,	_	_	_
93	0.2	0.2	CD	_	_	_
94	%	%	NN	_	_	_
95	Tryptone	tryptone	NN	_	_	_
96	at	at	IN	_	_	_
97	30	30	CD	_	_	_
98	C	c	NN	_	_	_
99	Mid	Mid	NNP	_	_	_
100	Log	Log	NNP	_	_	_
101	Rep.	Rep.	NNP	_	_	_
102	B1	b1	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	1.5	1.5	CD	_	_	_
105	'	'	''	_	_	_
106	RNA	rna	NN	_	_	_
107	Decay	decay	NN	_	_	_
108	of	of	IN	_	_	_
109	Eno	Eno	NNP	_	_	_
110	-	-	:	_	_	_
111	-LRB-	-lrb-	-LRB-	_	_	_
112	DF261	df261	NN	_	_	_
113	-RRB-	-rrb-	-RRB-	_	_	_
114	in	in	IN	_	_	_
115	M9	m9	NN	_	_	_
116	0.2	0.2	CD	_	_	_
117	%	%	NN	_	_	_
118	Glycerol	glycerol	NN	_	_	_
119	0.2	0.2	CD	_	_	_
120	%	%	NN	_	_	_
121	Tryptone	tryptone	NN	_	_	_
122	,	,	,	_	_	_
123	40	40	CD	_	_	_
124	mM	mm	NN	KWSUPP	_	_
125	Suc.at	suc.at	NN	_	_	_
126	30	30	CD	_	_	_
127	C	c	NN	_	_	_
128	Mid	Mid	NNP	_	_	_
129	Log	Log	NNP	_	_	_
130	Rep	Rep	NNP	_	_	_
131	A	A	NNP	_	_	_
132	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
133	1.5	1.5	CD	_	_	_
134	'	'	''	_	_	_
135	RNA	rna	NN	_	_	_
136	Decay	decay	NN	_	_	_
137	of	of	IN	_	_	_
138	Eno	Eno	NNP	_	_	_
139	-	-	:	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	DF261	df261	NN	_	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	in	in	IN	_	_	_
144	M9	m9	NN	_	_	_
145	0.2	0.2	CD	_	_	_
146	%	%	NN	_	_	_
147	Glycerol	glycerol	NN	_	_	_
148	0.2	0.2	CD	_	_	_
149	%	%	NN	_	_	_
150	Tryptone	tryptone	NN	_	_	_
151	40	40	CD	_	_	_
152	mM	mm	NN	KWSUPP	_	_
153	Suc	suc	NN	_	_	_
154	.	.	.	_	_	_

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	15	15	CD	_	_	_
189	'	'	''	_	_	_
190	vs	vs	CC	_	_	_
191	0	0	CD	_	_	_
192	'	'	''	_	_	_
193	in	in	IN	_	_	_
194	minimal	minimal	JJ	_	_	_
195	medium	medium	NN	_	_	_
196	+0.2	+0.2	CD	_	_	_
197	%	%	NN	_	_	_
198	glu	glu	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	16,000	16,000	CD	_	_	_
201	g	g	NN	_	_	_
202	for	for	IN	_	_	_
203	40	40	CD	_	_	_
204	s	s	NNS	_	_	_
205	at	at	IN	_	_	_
206	room	room	NN	_	_	_
207	temperature	temperature	NN	_	_	_
208	.	.	.	_	_	_

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	1.6	1.6	CD	_	_	_
11	A	a	DT	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	1.6	1.6	CD	_	_	_
14	A	a	DT	_	_	_
15	_	_	NN	_	_	_
16	Space	space	NN	_	_	_
17	_	_	CD	_	_	_
18	50	50	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	16	16	CD	_	_	_
21	_	_	CD	_	_	_
22	ESBL019	esbl019	NN	_	_	_
23	Reverted	revert	VBD	_	_	_
24	Repl	repl	JJ	_	_	_
25	4	4	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	16	16	CD	_	_	_
28	.	.	.	_	_	_

1	FHI25.IND.HUS	fhi25.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	170	170	CD	_	_	_
4	μl	μl	NN	_	_	_
5	were	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	from	from	IN	_	_	_
8	each	each	DT	_	_	_
9	of	of	IN	_	_	_
10	four	four	CD	_	_	_
11	wells	well	NNS	_	_	_
12	per	per	IN	_	_	_
13	time	time	NN	_	_	_
14	point	point	NN	_	_	_
15	and	and	CC	_	_	_
16	collected	collect	VBN	_	_	_
17	into	into	IN	_	_	_
18	a	a	DT	_	_	_
19	fresh	fresh	JJ	_	_	_
20	tube	tube	NN	_	_	_
21	were	be	VBD	_	_	_
22	1.360	1.360	CD	_	_	_
23	ml	ml	NN	_	_	_
24	of	of	IN	_	_	_
25	RNA	rna	NN	_	_	_
26	protection	protection	NN	_	_	_
27	buffer	buffer	NN	_	_	_
28	had	have	VBD	_	_	_
29	previously	previously	RB	_	_	_
30	been	be	VBN	_	_	_
31	added	add	VBN	_	_	_
32	.	.	.	_	_	_

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	NN	_	_	_
2	17.1	17.1	CD	_	_	_
3	A	a	DT	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	17.1	17.1	CD	_	_	_
6	A	a	DT	_	_	_
7	_	_	NN	_	_	_
8	Space	space	NN	_	_	_
9	_	_	CD	_	_	_
10	25	25	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	17.2	17.2	CD	_	_	_
13	A	a	DT	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	17.2	17.2	CD	_	_	_
16	A	a	DT	_	_	_
17	_	_	NN	_	_	_
18	Earth	Earth	NNP	_	_	_
19	_	_	SYM	_	_	_
20	25	25	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	172mM	172mm	NN	_	_	_
23	SCFA	scfa	NN	_	_	_
24	replicate	replicate	VBP	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	172mM	172mm	NN	_	_	_
28	SCFA	scfa	NN	_	_	_
29	replicate	replicate	VBP	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	17.3	17.3	CD	_	_	_
33	A	a	DT	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	17.3	17.3	CD	_	_	_
36	A	a	DT	_	_	_
37	_	_	NN	_	_	_
38	Space	space	NN	_	_	_
39	_	_	CD	_	_	_
40	25	25	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	17.4	17.4	CD	_	_	_
43	A	a	DT	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	17.4	17.4	CD	_	_	_
46	A	a	DT	_	_	_
47	_	_	NN	_	_	_
48	Earth	Earth	NNP	_	_	_
49	_	_	SYM	_	_	_
50	25	25	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	17.5	17.5	CD	_	_	_
53	A	a	DT	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	17.5	17.5	CD	_	_	_
56	A	a	DT	_	_	_
57	_	_	NN	_	_	_
58	Space	space	NN	_	_	_
59	_	_	CD	_	_	_
60	50	50	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	17.6	17.6	CD	_	_	_
63	A	a	DT	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	17.6	17.6	CD	_	_	_
66	A	a	DT	_	_	_
67	_	_	NN	_	_	_
68	Space	space	NN	_	_	_
69	_	_	CD	_	_	_
70	50	50	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
72	17.8	17.8	CD	_	_	_
73	A	a	DT	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	17.8	17.8	CD	_	_	_
76	A	a	DT	_	_	_
77	_	_	NN	_	_	_
78	Earth	Earth	NNP	_	_	_
79	_	_	SYM	_	_	_
80	50	50	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
82	1.7	1.7	CD	_	_	_
83	A	a	DT	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	1.7	1.7	CD	_	_	_
86	A	a	DT	_	_	_
87	_	_	NN	_	_	_
88	Earth	Earth	NNP	_	_	_
89	_	_	SYM	_	_	_
90	50	50	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	17	17	CD	_	_	_
93	.	.	.	_	_	_

1	FHI27.nIND.HUS	fhi27.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	17	17	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	HP	HP	NNP	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	COPRO-Seq	copro-seq	NN	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	18.2	18.2	CD	_	_	_
15	A	a	DT	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	18.2	18.2	CD	_	_	_
18	A	a	DT	_	_	_
19	_	_	NN	_	_	_
20	Earth	Earth	NNP	_	_	_
21	_	_	SYM	_	_	_
22	75	75	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	18.3	18.3	CD	_	_	_
25	A	a	DT	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	18.3	18.3	CD	_	_	_
28	A	a	DT	_	_	_
29	_	_	NN	_	_	_
30	Space	space	NN	_	_	_
31	_	_	CD	_	_	_
32	75	75	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	18.4	18.4	CD	_	_	_
35	A	a	DT	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	18.4	18.4	CD	_	_	_
38	A	a	DT	_	_	_
39	_	_	NN	_	_	_
40	Earth	Earth	NNP	_	_	_
41	_	_	SYM	_	_	_
42	75	75	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	18	18	CD	_	_	_
45	.	.	.	_	_	_

1	FHI27.IND.HUS	fhi27.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	18	18	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	HP	HP	NNP	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	COPRO-Seq	copro-seq	NN	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	1.8	1.8	CD	_	_	_
15	ml	ml	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	ca.	ca.	FW	_	_	_
18	3E	3e	FW	_	_	_
19	+9	+9	NN	_	_	_
20	cells	cell	NNS	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	were	be	VBD	_	_	_
23	pipetted	pipet	VBN	_	_	_
24	into	into	IN	_	_	_
25	2.0	2.0	CD	_	_	_
26	ml	ml	NN	_	_	_
27	tubes	tube	NNS	_	_	_
28	and	and	CC	_	_	_
29	immediately	immediately	RB	_	_	_
30	centrifuged	centrifuge	VBN	_	_	_
31	at	at	IN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	195	195	CD	_	_	_
34	min	min	NN	_	_	_
35	,	,	,	_	_	_
36	0.8	0.8	CD	_	_	_
37	%	%	NN	_	_	_
38	butanol	butanol	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	195min-1	195min-1	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	195min-2	195min-2	JJ	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	195min-3	195min-3	JJ	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	195	195	CD	_	_	_
47	min	min	NN	_	_	_
48	,	,	,	_	_	_
49	unstressed	unstressed	JJ	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	19	19	CD	_	_	_
52	.	.	.	_	_	_

1	FHI36.nIND.nHUS	fhi36.nind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	19	19	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	HP	HP	NNP	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	COPRO-Seq	copro-seq	NN	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	1A	1a	NN	_	_	_
15	1y	1y	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	1A	1a	NN	_	_	_
18	4y	4y	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	1A	1a	NN	_	_	_
21	_	_	CD	_	_	_
22	MG	mg	NN	_	_	_
23	_	_	NN	_	_	_
24	t0	t0	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	1A	1a	NN	_	_	_
27	T0	t0	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	1B	1b	NN	_	_	_
30	_	_	CD	_	_	_
31	MG	mg	NN	_	_	_
32	_	_	NN	_	_	_
33	t0	t0	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	1-butanol	1-butanol	NN	_	_	_
36	was	be	VBD	_	_	_
37	added	add	VBN	_	_	_
38	at	at	IN	_	_	_
39	a	a	DT	_	_	_
40	final	final	JJ	_	_	_
41	concentration	concentration	NN	_	_	_
42	of	of	IN	_	_	_
43	0.9	0.9	CD	_	_	_
44	%	%	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	vol/vol	vol/vol	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	and	and	CC	_	_	_
49	cells	cell	NNS	_	_	_
50	were	be	VBD	_	_	_
51	further	further	JJ	_	_	_
52	incubated	incubate	VBN	_	_	_
53	for	for	IN	_	_	_
54	30	30	CD	_	_	_
55	min	min	NN	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1C	1c	NN	_	_	_
3	_	_	CD	_	_	_
4	MG	mg	NN	_	_	_
5	_	_	NN	_	_	_
6	t0	t0	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	1	1	CD	_	_	_
9	_	_	NN	_	_	_
10	ESBL019	esbl019	NN	_	_	_
11	Coliform	coliform	NN	_	_	_
12	Repl	repl	NN	_	_	_
13	1	1	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	1	1	CD	_	_	_
16	.	.	.	_	_	_

1	FHI4.nIND.HUS	fhi4.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	1	1	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	LP	lp	NN	_	_	_
8	_	_	CD	_	_	_
9	noDP	nodp	NN	_	_	_
10	_	_	CD	_	_	_
11	noRh	norh	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	COPRO-Seq	copro-seq	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	1	1	CD	_	_	_
17	.	.	.	_	_	_

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	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-HT873-PA1	1-ht873-pa1	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	1-HT873-PA1	1-ht873-pa1	NN	_	_	_
16	-	-	:	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	1	1	CD	_	_	_
19	.	.	.	_	_	_

1	library	library	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	maanova	maanova	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	1	1	CD	_	_	_
7	min	min	NN	_	_	_
8	Nov0	nov0	NN	_	_	_
9	ug/ml	ug/ml	NN	_	_	_
10	,	,	,	_	_	_
11	2	2	CD	_	_	_
12	ug	ug	NN	_	_	_
13	Say3AI	say3ai	NN	_	_	_
14	,	,	,	_	_	_
15	pdN6	pdn6	NN	_	_	_
16	RT	rt	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	1	1	CD	_	_	_
19	min	min	NN	_	_	_
20	Nov0	nov0	NN	_	_	_
21	ug/ml	ug/ml	NN	_	_	_
22	,	,	,	_	_	_
23	dnaCacrD	dnacacrd	NN	_	_	_
24	30	30	CD	_	_	_
25	min	min	NN	_	_	_
26	after	after	IN	_	_	_
27	synchr	synchr	NN	_	_	_
28	start	start	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	1	1	CD	_	_	_
31	min	min	NN	_	_	_
32	Nov500	nov500	NN	_	_	_
33	ug/ml	ug/ml	NN	_	_	_
34	,	,	,	_	_	_
35	2	2	CD	_	_	_
36	ug	ug	NN	_	_	_
37	Say3AI	say3ai	NN	_	_	_
38	,	,	,	_	_	_
39	pdN6	pdn6	NN	_	_	_
40	RT	rt	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	1	1	CD	_	_	_
43	min	min	NN	_	_	_
44	Nov500	nov500	NN	_	_	_
45	ug/ml	ug/ml	NN	_	_	_
46	,	,	,	_	_	_
47	dnaCacrD	dnacacrd	NN	_	_	_
48	30	30	CD	_	_	_
49	min	min	NN	_	_	_
50	after	after	IN	_	_	_
51	synchr	synchr	NN	_	_	_
52	start	start	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	1	1	CD	_	_	_
55	ml	ml	NN	_	_	_
56	aliquot	aliquot	NN	_	_	_
57	of	of	IN	_	_	_
58	culture	culture	NN	_	_	_
59	was	be	VBD	_	_	_
60	transferred	transfer	VBN	_	_	_
61	to	to	TO	_	_	_
62	pressure	pressure	VB	_	_	_
63	vessel	vessel	NN	_	_	_
64	and	and	CC	_	_	_
65	pressurized	pressurize	VBD	_	_	_
66	at	at	IN	_	_	_
67	1MPa	1mpa	NN	_	_	_
68	for	for	IN	_	_	_
69	15	15	CD	_	_	_
70	min	min	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	1mL	1ml	NN	_	_	_
73	aliquots	aliquot	NNS	_	_	_
74	were	be	VBD	_	_	_
75	harvested	harvest	VBN	_	_	_
76	and	and	CC	_	_	_
77	mixed	mix	VBN	_	_	_
78	with	with	IN	_	_	_
79	0.5	0.5	CD	_	_	_
80	mL	ml	NN	_	_	_
81	Phenol/ethanol	phenol/ethanol	NN	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	5	5	CD	_	_	_
84	%	%	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	v/v	v/v	NN	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	Phenol	phenol	NN	_	_	_
89	in	in	IN	_	_	_
90	EtOHabs	etohab	NNS	_	_	_
91	-RRB-	-rrb-	-RRB-	_	_	_
92	.	.	.	_	_	_

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	stored	store	VBD	_	_	_
8	at	at	IN	_	_	_
9	-80	-80	CD	_	_	_
10	°C	°c	NN	_	_	_
11	until	until	IN	_	_	_
12	use	use	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1	1	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	each	each	DT	_	_	_
6	culture	culture	NN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	mycotoxin	mycotoxin	NN	_	_	_
10	was	be	VBD	_	_	_
11	centrifuged	centrifuge	VBN	_	_	_
12	and	and	CC	_	_	_
13	total	total	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	was	be	VBD	_	_	_
16	prepared	prepare	VBN	_	_	_
17	using	use	VBG	_	_	_
18	Hybrid-RTM	hybrid-rtm	JJ	_	_	_
19	kit	kit	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Gene	gene	NN	_	_	_
22	All	all	DT	_	_	_
23	,	,	,	_	_	_
24	Seoul	Seoul	NNP	_	_	_
25	,	,	,	_	_	_
26	Korea	Korea	NNP	_	_	_
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	protocols	protocol	NNS	_	_	_
34	.	.	.	_	_	_

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	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/ml	µg/ml	NN	_	_	_
33	for	for	IN	_	_	_
34	DY	dy	NN	_	_	_
35	330	330	CD	_	_	_
36	GyrA-SPA	gyra-spa	NN	_	_	_
37	and	and	CC	_	_	_
38	kanamycin	kanamycin	NN	_	_	_
39	50	50	CD	_	_	_
40	µg/ml	µg/ml	NN	_	_	_
41	,	,	,	_	_	_
42	chloramphenicol	chloramphenicol	NN	_	_	_
43	15	15	CD	_	_	_
44	µg/ml	µg/ml	NN	_	_	_
45	for	for	IN	_	_	_
46	DY	dy	NN	_	_	_
47	330	330	CD	_	_	_
48	GyrA-SPA	gyra-spa	NN	_	_	_
49	MuSGS	musgs	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	with	with	IN	_	_	_
52	cells	cell	NNS	_	_	_
53	from	from	IN	_	_	_
54	one	one	CD	_	_	_
55	isolate	isolate	JJ	_	_	_
56	colony	colony	NN	_	_	_
57	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	1	1	CD	_	_	_
13	ml	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	ethanol	ethanol	NN	_	_	_
16	20	20	CD	_	_	_
17	%	%	NN	_	_	_
18	and	and	CC	_	_	_
19	1	1	CD	_	_	_
20	ml	ml	NN	_	_	_
21	of	of	IN	_	_	_
22	LB	lb	NN	MED	_	_
23	broth	broth	NN	MED	_	_
24	were	be	VBD	_	_	_
25	added	add	VBN	_	_	_
26	when	when	WRB	_	_	_
27	the	the	DT	_	_	_
28	OD600	od600	NN	_	_	_
29	of	of	IN	_	_	_
30	each	each	DT	_	_	_
31	culture	culture	NN	_	_	_
32	reached	reach	VBD	_	_	_
33	0.4	0.4	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	1	1	CD	_	_	_
36	.	.	.	_	_	_

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/beta	pdi/beta	NN	_	_	_
20	subunit	subunit	NN	_	_	_
21	and	and	CC	_	_	_
22	repeated	repeat	VBN	_	_	_
23	addition	addition	NN	_	_	_
24	of	of	IN	_	_	_
25	the	the	DT	_	_	_
26	inducer	inducer	NN	_	_	_
27	anhydrotetracycline	anhydrotetracycline	NN	_	_	_
28	.	.	.	_	_	_

1	J	J	NNP	_	_	_
2	Biotechnol	Biotechnol	NNP	_	_	_
3	128:308-321	128:308-321	CD	_	_	_
4	.	.	.	_	_	_

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

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	pgcgrowthcondition	NNS	_	_	_
2	2003	2003	CD	_	_	_
3	,	,	,	_	_	_
4	PNAS	PNAS	NNP	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	.	.	.	_	_	_

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	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	200µl	200µl	NN	_	_	_
21	of	of	IN	_	_	_
22	prepared	prepared	JJ	_	_	_
23	E.coli	e.coli	NN	_	_	_
24	O157	o157	NN	_	_	_
25	cells	cell	NNS	_	_	_
26	within	within	IN	_	_	_
27	LB	lb	NN	MED	_	_
28	broth	broth	NN	MED	_	_
29	is	be	VBZ	_	_	_
30	spreaded	spread	VBN	_	_	_
31	to	to	TO	_	_	_
32	LB	LB	NNP	_	_	_
33	agar	agar	NN	_	_	_
34	plate	plate	NN	_	_	_
35	,	,	,	_	_	_
36	and	and	CC	_	_	_
37	sterilized	sterilize	VBN	_	_	_
38	6	6	CD	_	_	_
39	mm	mm	NN	_	_	_
40	filtered	filter	VBD	_	_	_
41	paper	paper	NN	_	_	_
42	disk	disk	NN	_	_	_
43	was	be	VBD	_	_	_
44	placed	place	VBN	_	_	_
45	on	on	IN	_	_	_
46	the	the	DT	_	_	_
47	plate	plate	NN	_	_	_
48	tightly	tightly	RB	_	_	_
49	,	,	,	_	_	_
50	where	where	WRB	_	_	_
51	E.coli	e.coli	JJ	_	_	_
52	O157	o157	NN	_	_	_
53	is	be	VBZ	_	_	_
54	spreaded	spread	VBN	_	_	_
55	.	.	.	_	_	_

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	20	20	CD	_	_	_
3	.	.	.	_	_	_

1	FHI36.IND.nHUS	fhi36.ind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	20	20	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	HP	HP	NNP	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	COPRO-Seq	copro-seq	NN	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	20	20	CD	_	_	_
15	min	min	NN	_	_	_
16	after	after	IN	_	_	_
17	UVtreatment	uvtreatment	NN	_	_	_
18	1	1	CD	_	_	_
19	'	'	''	_	_	_
20	,	,	,	_	_	_
21	40J	40j	NN	_	_	_
22	,	,	,	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	in	in	IN	_	_	_
25	Davis	Davis	NNP	_	_	_
26	+0.4	+0.4	CD	_	_	_
27	%	%	NN	_	_	_
28	glu	glu	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	20	20	CD	_	_	_
31	min	min	NN	_	_	_
32	Nov0	nov0	NN	_	_	_
33	ug/ml	ug/ml	NN	_	_	_
34	,	,	,	_	_	_
35	2	2	CD	_	_	_
36	ug	ug	NN	_	_	_
37	Say3AI	say3ai	NN	_	_	_
38	,	,	,	_	_	_
39	pdN6	pdn6	NN	_	_	_
40	RT	rt	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	20	20	CD	_	_	_
43	min	min	NN	_	_	_
44	Nov0	nov0	NN	_	_	_
45	ug/ml	ug/ml	NN	_	_	_
46	,	,	,	_	_	_
47	dnaCacrD	dnacacrd	NN	_	_	_
48	30	30	CD	_	_	_
49	min	min	NN	_	_	_
50	after	after	IN	_	_	_
51	synchr	synchr	NN	_	_	_
52	start	start	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	20	20	CD	_	_	_
55	min	min	NN	_	_	_
56	Nov500	nov500	NN	_	_	_
57	ug/ml	ug/ml	NN	_	_	_
58	,	,	,	_	_	_
59	2	2	CD	_	_	_
60	ug	ug	NN	_	_	_
61	Say3AI	say3ai	NN	_	_	_
62	,	,	,	_	_	_
63	pdN6	pdn6	NN	_	_	_
64	RT	rt	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	20	20	CD	_	_	_
67	min	min	NN	_	_	_
68	Nov500	nov500	NN	_	_	_
69	ug/ml	ug/ml	NN	_	_	_
70	,	,	,	_	_	_
71	dnaCacrD	dnacacrd	NN	_	_	_
72	30	30	CD	_	_	_
73	min	min	NN	_	_	_
74	after	after	IN	_	_	_
75	synchr	synchr	NN	_	_	_
76	start	start	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	20	20	CD	_	_	_
79	min	min	NN	_	_	_
80	Nov50	nov50	NN	_	_	_
81	ug/ml	ug/ml	NN	_	_	_
82	,	,	,	_	_	_
83	2	2	CD	_	_	_
84	ug	ug	NN	_	_	_
85	Say3AI	say3ai	NN	_	_	_
86	,	,	,	_	_	_
87	pdN6	pdn6	NN	_	_	_
88	RT	rt	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	20	20	CD	_	_	_
91	min	min	NN	_	_	_
92	Nov50	nov50	NN	_	_	_
93	ug/ml	ug/ml	NN	_	_	_
94	,	,	,	_	_	_
95	dnaCacrD	dnacacrd	NN	_	_	_
96	30	30	CD	_	_	_
97	min	min	NN	_	_	_
98	after	after	IN	_	_	_
99	synchr	synchr	NN	_	_	_
100	start	start	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	20	20	CD	_	_	_
103	min	min	NN	_	_	_
104	untreatedcells	untreatedcell	NNS	_	_	_
105	,	,	,	_	_	_
106	25	25	CD	_	_	_
107	ug	ug	NN	_	_	_
108	total	total	JJ	_	_	_
109	RNA	rna	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	20	20	CD	_	_	_
112	min	min	NN	_	_	_
113	UV	uv	NN	_	_	_
114	treated	treat	VBN	_	_	_
115	cells	cell	NNS	_	_	_
116	,	,	,	_	_	_
117	25	25	CD	_	_	_
118	ug	ug	NN	_	_	_
119	total	total	JJ	_	_	_
120	RNA	rna	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	20	20	CD	_	_	_
123	min	min	NN	_	_	_
124	UVtreatment	uvtreatment	NN	_	_	_
125	control	control	NN	_	_	_
126	,	,	,	_	_	_
127	MG1655	mg1655	NN	_	_	_
128	in	in	IN	_	_	_
129	Davis	Davis	NNP	_	_	_
130	+0.4	+0.4	CD	_	_	_
131	%	%	NN	_	_	_
132	glu	glu	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	20	20	CD	_	_	_
135	ug	ug	NN	_	_	_
136	of	of	IN	_	_	_
137	Total	total	JJ	_	_	_
138	RNA	rna	NN	_	_	_
139	from	from	IN	_	_	_
140	MG1655	mg1655	NN	_	_	_
141	-LRB-	-lrb-	-LRB-	_	_	_
142	Repaired	repair	VBN	_	_	_
143	NCM	NCM	NNP	_	_	_
144	3416	3416	CD	_	_	_
145	-RRB-	-rrb-	-RRB-	_	_	_
146	in	in	IN	_	_	_
147	LB	lb	NN	_	_	_
148	at	at	IN	_	_	_
149	30	30	CD	_	_	_
150	degrees	degree	NNS	_	_	_
151	OD	od	NN	_	_	_
152	600	600	CD	_	_	_
153	=	=	JJ	_	_	_
154	0.8	0.8	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	20	20	CD	_	_	_
157	ug	ug	NN	_	_	_
158	of	of	IN	_	_	_
159	Total	total	JJ	_	_	_
160	RNA	rna	NN	_	_	_
161	from	from	IN	_	_	_
162	MG1655	mg1655	NN	_	_	_
163	-LRB-	-lrb-	-LRB-	_	_	_
164	Repaired	repair	VBN	_	_	_
165	NCM	NCM	NNP	_	_	_
166	3416	3416	CD	_	_	_
167	-RRB-	-rrb-	-RRB-	_	_	_
168	in	in	IN	_	_	_
169	M9	m9	NN	_	_	_
170	at	at	IN	_	_	_
171	30	30	CD	_	_	_
172	degrees	degree	NNS	_	_	_
173	OD	od	NN	_	_	_
174	600	600	CD	_	_	_
175	=	=	JJ	_	_	_
176	0.8	0.8	CD	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	2.1	2.1	CD	_	_	_
179	A	a	DT	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	2.1	2.1	CD	_	_	_
182	A	a	DT	_	_	_
183	_	_	NN	_	_	_
184	Earth	Earth	NNP	_	_	_
185	_	_	SYM	_	_	_
186	75	75	CD	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	21	21	CD	_	_	_
189	.	.	.	_	_	_

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	2.3	2.3	CD	_	_	_
4	A	a	DT	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	23A1	23a1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	2.3	2.3	CD	_	_	_
9	A	a	DT	_	_	_
10	_	_	NN	_	_	_
11	Earth	Earth	NNP	_	_	_
12	_	_	SYM	_	_	_
13	75	75	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	23B1	23b1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	23C3	23c3	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	23	23	CD	_	_	_
20	.	.	.	_	_	_

1	FHI48.nIND.HUS	fhi48.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	23S	23s	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	240	240	CD	_	_	_
6	minutes	minute	NNS	_	_	_
7	growth	growth	NN	_	_	_
8	in	in	IN	_	_	_
9	LB	LB	NNP	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	2.4	2.4	CD	_	_	_
12	A	a	DT	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	2.4	2.4	CD	_	_	_
15	A	a	DT	_	_	_
16	_	_	NN	_	_	_
17	Space	space	NN	_	_	_
18	_	_	CD	_	_	_
19	75	75	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	252978410001	252978410001	CD	_	_	_
22	_	_	NN	_	_	_
23	B7A	b7a	NN	_	_	_
24	_	_	CD	_	_	_
25	CY5	cy5	NN	_	_	_
26	_	_	NN	_	_	_
27	BCE001MS16	bce001ms16	NN	_	_	_
28	_	_	CD	_	_	_
29	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	252978410001	252978410001	CD	_	_	_
32	_	_	NN	_	_	_
33	B7A	b7a	NN	_	_	_
34	_	_	CD	_	_	_
35	CY5	cy5	NN	_	_	_
36	_	_	NN	_	_	_
37	BCE022DS6	bce022ds6	NN	_	_	_
38	_	_	CD	_	_	_
39	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	252978410001	252978410001	CD	_	_	_
42	_	_	NN	_	_	_
43	B7A	b7a	NN	_	_	_
44	_	_	CD	_	_	_
45	CY5	cy5	NN	_	_	_
46	_	_	CD	_	_	_
47	BCE063MS14	bce063ms14	NN	_	_	_
48	_	_	CD	_	_	_
49	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	252978410001	252978410001	CD	_	_	_
52	_	_	NN	_	_	_
53	B7A	b7a	NN	_	_	_
54	_	_	CD	_	_	_
55	CY5	cy5	NN	_	_	_
56	_	_	SYM	_	_	_
57	ETP98015	etp98015	CD	_	_	_
58	_	_	SYM	_	_	_
59	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	252978410002	252978410002	CD	_	_	_
62	_	_	NN	_	_	_
63	B7A	b7a	NN	_	_	_
64	_	_	CD	_	_	_
65	CY5	cy5	NN	_	_	_
66	_	_	NN	_	_	_
67	BCE007	bce007	NN	_	_	_
68	_	_	CD	_	_	_
69	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	252978410002	252978410002	CD	_	_	_
72	_	_	NN	_	_	_
73	B7A	b7a	NN	_	_	_
74	_	_	CD	_	_	_
75	CY5	cy5	NN	_	_	_
76	_	_	CD	_	_	_
77	BCE041	bce041	NN	_	_	_
78	_	_	CD	_	_	_
79	MS11	ms11	NN	_	_	_
80	_	_	CD	_	_	_
81	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	252978410002	252978410002	CD	_	_	_
84	_	_	NN	_	_	_
85	B7A	b7a	NN	_	_	_
86	_	_	CD	_	_	_
87	CY5	cy5	NN	_	_	_
88	_	_	NN	_	_	_
89	BCE063	bce063	NN	_	_	_
90	_	_	CD	_	_	_
91	DS4	ds4	NN	_	_	_
92	_	_	CD	_	_	_
93	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	252978410002	252978410002	CD	_	_	_
96	_	_	NN	_	_	_
97	B7A	b7a	NN	_	_	_
98	_	_	CD	_	_	_
99	CY5	cy5	NN	_	_	_
100	_	_	SYM	_	_	_
101	ETP98028	etp98028	CD	_	_	_
102	_	_	SYM	_	_	_
103	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	252978410003	252978410003	CD	_	_	_
106	_	_	NN	_	_	_
107	B7A	b7a	NN	_	_	_
108	_	_	CD	_	_	_
109	CY5	cy5	NN	_	_	_
110	_	_	CD	_	_	_
111	C35662	c35662	NN	_	_	_
112	_	_	CD	_	_	_
113	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	252978410003	252978410003	CD	_	_	_
116	_	_	NN	_	_	_
117	B7A	b7a	NN	_	_	_
118	_	_	CD	_	_	_
119	CY5	cy5	NN	_	_	_
120	_	_	CD	_	_	_
121	ETP05	etp05	NN	_	_	_
122	_	_	NN	_	_	_
123	007	007	CD	_	_	_
124	_	_	SYM	_	_	_
125	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	252978410003	252978410003	CD	_	_	_
128	_	_	NN	_	_	_
129	B7A	b7a	NN	_	_	_
130	_	_	CD	_	_	_
131	CY5	cy5	NN	_	_	_
132	_	_	CD	_	_	_
133	ETP05	etp05	NN	_	_	_
134	_	_	NN	_	_	_
135	017	017	CD	_	_	_
136	_	_	SYM	_	_	_
137	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	252978410003	252978410003	CD	_	_	_
140	_	_	NN	_	_	_
141	B7A	b7a	NN	_	_	_
142	_	_	CD	_	_	_
143	CY5	cy5	NN	_	_	_
144	_	_	CD	_	_	_
145	ETP98062	etp98062	NN	_	_	_
146	_	_	CD	_	_	_
147	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	252978410004	252978410004	CD	_	_	_
150	_	_	NN	_	_	_
151	B7A	b7a	NN	_	_	_
152	_	_	CD	_	_	_
153	CY5	cy5	NN	_	_	_
154	_	_	NN	_	_	_
155	BCE003	bce003	NN	_	_	_
156	_	_	CD	_	_	_
157	DS5	ds5	NN	_	_	_
158	_	_	CD	_	_	_
159	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	252978410004	252978410004	CD	_	_	_
162	_	_	NN	_	_	_
163	B7A	b7a	NN	_	_	_
164	_	_	CD	_	_	_
165	CY5	cy5	NN	_	_	_
166	_	_	CD	_	_	_
167	BCE058	bce058	NN	_	_	_
168	_	_	CD	_	_	_
169	MS13	ms13	NN	_	_	_
170	_	_	CD	_	_	_
171	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	252978410004	252978410004	CD	_	_	_
174	_	_	NN	_	_	_
175	B7A	b7a	NN	_	_	_
176	_	_	CD	_	_	_
177	CY5	cy5	NN	_	_	_
178	_	_	NN	_	_	_
179	BCE069	bce069	NN	_	_	_
180	_	_	CD	_	_	_
181	MS9	ms9	NN	_	_	_
182	_	_	CD	_	_	_
183	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	252978410004	252978410004	CD	_	_	_
186	_	_	NN	_	_	_
187	B7A	b7a	NN	_	_	_
188	_	_	CD	_	_	_
189	CY5	cy5	NN	_	_	_
190	_	_	NN	_	_	_
191	BCE129	bce129	NN	_	_	_
192	_	_	CD	_	_	_
193	DS2	ds2	NN	_	_	_
194	_	_	CD	_	_	_
195	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	252978410005	252978410005	CD	_	_	_
198	_	_	NN	_	_	_
199	B7A	b7a	NN	_	_	_
200	_	_	CD	_	_	_
201	CY5	cy5	NN	_	_	_
202	_	_	CD	_	_	_
203	BCE008	bce008	NN	_	_	_
204	_	_	CD	_	_	_
205	MS13	ms13	NN	_	_	_
206	_	_	CD	_	_	_
207	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	252978410005	252978410005	CD	_	_	_
210	_	_	NN	_	_	_
211	B7A	b7a	NN	_	_	_
212	_	_	CD	_	_	_
213	CY5	cy5	NN	_	_	_
214	_	_	NN	_	_	_
215	BCE013	bce013	NN	_	_	_
216	_	_	CD	_	_	_
217	DS1	ds1	NN	_	_	_
218	_	_	CD	_	_	_
219	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	252978410005	252978410005	CD	_	_	_
222	_	_	NN	_	_	_
223	B7A	b7a	NN	_	_	_
224	_	_	CD	_	_	_
225	CY5	cy5	NN	_	_	_
226	_	_	NN	_	_	_
227	BCE035	bce035	NN	_	_	_
228	_	_	CD	_	_	_
229	MS8	ms8	NN	_	_	_
230	_	_	CD	_	_	_
231	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	252978410005	252978410005	CD	_	_	_
234	_	_	NN	_	_	_
235	B7A	b7a	NN	_	_	_
236	_	_	CD	_	_	_
237	CY5	cy5	NN	_	_	_
238	_	_	NN	_	_	_
239	BCE039	bce039	NN	_	_	_
240	_	_	CD	_	_	_
241	DS2	ds2	NN	_	_	_
242	_	_	CD	_	_	_
243	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	252978410006	252978410006	CD	_	_	_
246	_	_	NN	_	_	_
247	B7A	b7a	NN	_	_	_
248	_	_	CD	_	_	_
249	CY5	cy5	NN	_	_	_
250	_	_	CD	_	_	_
251	ETP05	etp05	NN	_	_	_
252	_	_	NN	_	_	_
253	012	012	CD	_	_	_
254	_	_	SYM	_	_	_
255	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	252978410006	252978410006	CD	_	_	_
258	_	_	NN	_	_	_
259	B7A	b7a	NN	_	_	_
260	_	_	CD	_	_	_
261	CY5	cy5	NN	_	_	_
262	_	_	CD	_	_	_
263	ETP05	etp05	NN	_	_	_
264	_	_	NN	_	_	_
265	019	019	CD	_	_	_
266	_	_	SYM	_	_	_
267	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	252978410006	252978410006	CD	_	_	_
270	_	_	NN	_	_	_
271	B7A	b7a	NN	_	_	_
272	_	_	CD	_	_	_
273	CY5	cy5	NN	_	_	_
274	_	_	CD	_	_	_
275	ETP05	etp05	NN	_	_	_
276	_	_	NN	_	_	_
277	026	026	CD	_	_	_
278	_	_	SYM	_	_	_
279	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	252978410006	252978410006	CD	_	_	_
282	_	_	NN	_	_	_
283	B7A	b7a	NN	_	_	_
284	_	_	CD	_	_	_
285	CY5	cy5	NN	_	_	_
286	_	_	CD	_	_	_
287	ETP05	etp05	NN	_	_	_
288	_	_	NN	_	_	_
289	044	044	CD	_	_	_
290	_	_	SYM	_	_	_
291	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	252978410007	252978410007	CD	_	_	_
294	_	_	NN	_	_	_
295	B7A	b7a	NN	_	_	_
296	_	_	CD	_	_	_
297	CY5	cy5	NN	_	_	_
298	_	_	CD	_	_	_
299	BCE002	bce002	NN	_	_	_
300	_	_	CD	_	_	_
301	MS12	ms12	NN	_	_	_
302	_	_	CD	_	_	_
303	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	252978410007	252978410007	CD	_	_	_
306	_	_	NN	_	_	_
307	B7A	b7a	NN	_	_	_
308	_	_	CD	_	_	_
309	CY5	cy5	NN	_	_	_
310	_	_	CD	_	_	_
311	BCE021	bce021	NN	_	_	_
312	_	_	CD	_	_	_
313	DS7	ds7	NN	_	_	_
314	_	_	CD	_	_	_
315	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	252978410007	252978410007	CD	_	_	_
318	_	_	NN	_	_	_
319	B7A	b7a	NN	_	_	_
320	_	_	CD	_	_	_
321	CY5	cy5	NN	_	_	_
322	_	_	NN	_	_	_
323	BCE049	bce049	NN	_	_	_
324	_	_	CD	_	_	_
325	MS9	ms9	NN	_	_	_
326	_	_	CD	_	_	_
327	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	252978410007	252978410007	CD	_	_	_
330	_	_	NN	_	_	_
331	B7A	b7a	NN	_	_	_
332	_	_	CD	_	_	_
333	CY5	cy5	NN	_	_	_
334	_	_	CD	_	_	_
335	ETP98061	etp98061	NN	_	_	_
336	_	_	CD	_	_	_
337	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	252978410008	252978410008	CD	_	_	_
340	_	_	NN	_	_	_
341	B7A	b7a	NN	_	_	_
342	_	_	CD	_	_	_
343	CY5	cy5	NN	_	_	_
344	_	_	SYM	_	_	_
345	180050	180050	CD	_	_	_
346	_	_	SYM	_	_	_
347	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	252978410008	252978410008	CD	_	_	_
350	_	_	NN	_	_	_
351	B7A	b7a	NN	_	_	_
352	_	_	CD	_	_	_
353	CY5	cy5	NN	_	_	_
354	_	_	CD	_	_	_
355	ETP98103	etp98103	NN	_	_	_
356	_	_	CD	_	_	_
357	CY3.mev.refIsIB.ou	cy3.mev.refisib.ou	NN	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	252978410008	252978410008	CD	_	_	_
360	_	_	NN	_	_	_
361	B7A	b7a	NN	_	_	_
362	_	_	CD	_	_	_
363	CY5	cy5	NN	_	_	_
364	_	_	CD	_	_	_
365	ETP98111	etp98111	NN	_	_	_
366	_	_	CD	_	_	_
367	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	252978410008	252978410008	CD	_	_	_
370	_	_	NN	_	_	_
371	B7A	b7a	NN	_	_	_
372	_	_	CD	_	_	_
373	CY5	cy5	NN	_	_	_
374	_	_	CD	_	_	_
375	TW03741	tw03741	NN	_	_	_
376	_	_	CD	_	_	_
377	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	252978410009	252978410009	CD	_	_	_
380	_	_	NN	_	_	_
381	B7A	b7a	NN	_	_	_
382	_	_	CD	_	_	_
383	CY5	cy5	NN	_	_	_
384	_	_	CD	_	_	_
385	E1787	e1787	NN	_	_	_
386	_	_	CD	_	_	_
387	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	252978410009	252978410009	CD	_	_	_
390	_	_	NN	_	_	_
391	B7A	b7a	NN	_	_	_
392	_	_	CD	_	_	_
393	CY5	cy5	NN	_	_	_
394	_	_	CD	_	_	_
395	E747	e747	NN	_	_	_
396	_	_	NN	_	_	_
397	0	0	CD	_	_	_
398	_	_	SYM	_	_	_
399	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	252978410009	252978410009	CD	_	_	_
402	_	_	NN	_	_	_
403	B7A	b7a	NN	_	_	_
404	_	_	CD	_	_	_
405	CY5	cy5	NN	_	_	_
406	_	_	CD	_	_	_
407	F595C	f595c	NN	_	_	_
408	_	_	CD	_	_	_
409	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
411	252978410009	252978410009	CD	_	_	_
412	_	_	NN	_	_	_
413	B7A	b7a	NN	_	_	_
414	_	_	CD	_	_	_
415	CY5	cy5	NN	_	_	_
416	_	_	CD	_	_	_
417	WS3572A1.mev.refIsIB.out	ws3572a1.mev.refisib.out	NN	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	252978410010	252978410010	CD	_	_	_
420	_	_	NN	_	_	_
421	B7A	b7a	NN	_	_	_
422	_	_	CD	_	_	_
423	CY5	cy5	NN	_	_	_
424	_	_	NN	_	_	_
425	229	229	CD	_	_	_
426	_	_	NN	_	_	_
427	1	1	CD	_	_	_
428	_	_	NN	_	_	_
429	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	252978410010	252978410010	CD	_	_	_
432	_	_	NN	_	_	_
433	B7A	b7a	NN	_	_	_
434	_	_	CD	_	_	_
435	CY5	cy5	NN	_	_	_
436	_	_	CD	_	_	_
437	ICDDR	icddr	NN	_	_	_
438	_	_	NN	_	_	_
439	B	b	NN	_	_	_
440	_	_	CD	_	_	_
441	p13	p13	NN	_	_	_
442	_	_	CD	_	_	_
443	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	252978410010	252978410010	CD	_	_	_
446	_	_	NN	_	_	_
447	B7A	b7a	NN	_	_	_
448	_	_	CD	_	_	_
449	CY5	cy5	NN	_	_	_
450	_	_	CD	_	_	_
451	ICDDR	icddr	NN	_	_	_
452	_	_	NN	_	_	_
453	B	b	NN	_	_	_
454	_	_	CD	_	_	_
455	p1	p1	NN	_	_	_
456	_	_	CD	_	_	_
457	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	252978410010	252978410010	CD	_	_	_
460	_	_	NN	_	_	_
461	B7A	b7a	NN	_	_	_
462	_	_	CD	_	_	_
463	CY5	cy5	NN	_	_	_
464	_	_	CD	_	_	_
465	ICDDR	icddr	NN	_	_	_
466	_	_	NN	_	_	_
467	B	b	NN	_	_	_
468	_	_	CD	_	_	_
469	p4	p4	NN	_	_	_
470	_	_	CD	_	_	_
471	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	252978410011	252978410011	CD	_	_	_
474	_	_	NN	_	_	_
475	B7A	b7a	NN	_	_	_
476	_	_	CD	_	_	_
477	CY5	cy5	NN	_	_	_
478	_	_	CD	_	_	_
479	DS26	ds26	NN	_	_	_
480	_	_	NN	_	_	_
481	1	1	CD	_	_	_
482	_	_	NN	_	_	_
483	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	252978410011	252978410011	CD	_	_	_
486	_	_	NN	_	_	_
487	B7A	b7a	NN	_	_	_
488	_	_	CD	_	_	_
489	CY5	cy5	NN	_	_	_
490	_	_	CD	_	_	_
491	E1777	e1777	NN	_	_	_
492	_	_	CD	_	_	_
493	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
494	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
495	252978410011	252978410011	CD	_	_	_
496	_	_	NN	_	_	_
497	B7A	b7a	NN	_	_	_
498	_	_	CD	_	_	_
499	CY5	cy5	NN	_	_	_
500	_	_	CD	_	_	_
501	E9034A	e9034a	NN	_	_	_
502	_	_	CD	_	_	_
503	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	252978410011	252978410011	CD	_	_	_
506	_	_	NN	_	_	_
507	B7A	b7a	NN	_	_	_
508	_	_	CD	_	_	_
509	CY5	cy5	NN	_	_	_
510	_	_	CD	_	_	_
511	NN	NN	NNP	_	_	_
512	_	_	SYM	_	_	_
513	34	34	CD	_	_	_
514	_	_	NN	_	_	_
515	1	1	CD	_	_	_
516	_	_	NN	_	_	_
517	3	3	CD	_	_	_
518	_	_	NN	_	_	_
519	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
520	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
521	252978410012	252978410012	CD	_	_	_
522	_	_	NN	_	_	_
523	B7A	b7a	NN	_	_	_
524	_	_	CD	_	_	_
525	CY5	cy5	NN	_	_	_
526	_	_	NN	_	_	_
527	42	42	CD	_	_	_
528	_	_	NN	_	_	_
529	1	1	CD	_	_	_
530	_	_	NN	_	_	_
531	C1	c1	NN	_	_	_
532	_	_	CD	_	_	_
533	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	252978410012	252978410012	CD	_	_	_
536	_	_	NN	_	_	_
537	B7A	b7a	NN	_	_	_
538	_	_	CD	_	_	_
539	CY5	cy5	NN	_	_	_
540	_	_	CD	_	_	_
541	ETEC	ETEC	NNP	_	_	_
542	_	_	SYM	_	_	_
543	18	18	CD	_	_	_
544	_	_	NN	_	_	_
545	2	2	CD	_	_	_
546	_	_	CD	_	_	_
547	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
548	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
549	252978410012	252978410012	CD	_	_	_
550	_	_	NN	_	_	_
551	B7A	b7a	NN	_	_	_
552	_	_	CD	_	_	_
553	CY5	cy5	NN	_	_	_
554	_	_	CD	_	_	_
555	ICDDR	icddr	NN	_	_	_
556	_	_	NN	_	_	_
557	B	b	NN	_	_	_
558	_	_	CD	_	_	_
559	p12	p12	NN	_	_	_
560	_	_	CD	_	_	_
561	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
562	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
563	252978410012	252978410012	CD	_	_	_
564	_	_	NN	_	_	_
565	B7A	b7a	NN	_	_	_
566	_	_	CD	_	_	_
567	CY5	cy5	NN	_	_	_
568	_	_	CD	_	_	_
569	LSN02	lsn02	NN	_	_	_
570	_	_	CD	_	_	_
571	012560	012560	CD	_	_	_
572	_	_	NN	_	_	_
573	A	a	DT	_	_	_
574	_	_	SYM	_	_	_
575	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
577	252978410013	252978410013	CD	_	_	_
578	_	_	NN	_	_	_
579	B7A	b7a	NN	_	_	_
580	_	_	CD	_	_	_
581	CY5	cy5	NN	_	_	_
582	_	_	SYM	_	_	_
583	180600	180600	CD	_	_	_
584	_	_	SYM	_	_	_
585	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
586	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
587	252978410013	252978410013	CD	_	_	_
588	_	_	NN	_	_	_
589	B7A	b7a	NN	_	_	_
590	_	_	CD	_	_	_
591	CY5	cy5	NN	_	_	_
592	_	_	SYM	_	_	_
593	ETEC	etec	NNS	_	_	_
594	_	_	VBP	_	_	_
595	10	10	CD	_	_	_
596	_	_	SYM	_	_	_
597	1	1	CD	_	_	_
598	_	_	CD	_	_	_
599	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
601	252978410013	252978410013	CD	_	_	_
602	_	_	NN	_	_	_
603	B7A	b7a	NN	_	_	_
604	_	_	CD	_	_	_
605	CY5	cy5	NN	_	_	_
606	_	_	CD	_	_	_
607	TW3574	tw3574	NN	_	_	_
608	_	_	CD	_	_	_
609	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
610	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
611	252978410013	252978410013	CD	_	_	_
612	_	_	NN	_	_	_
613	B7A	b7a	NN	_	_	_
614	_	_	CD	_	_	_
615	CY5	cy5	NN	_	_	_
616	_	_	NN	_	_	_
617	TW3585	tw3585	NN	_	_	_
618	_	_	CD	_	_	_
619	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
620	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
621	252978410014	252978410014	CD	_	_	_
622	_	_	NN	_	_	_
623	B7A	b7a	NN	_	_	_
624	_	_	CD	_	_	_
625	CY5	cy5	NN	_	_	_
626	_	_	CD	_	_	_
627	E20738A	e20738a	NN	_	_	_
628	_	_	CD	_	_	_
629	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
630	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
631	252978410014	252978410014	CD	_	_	_
632	_	_	NN	_	_	_
633	B7A	b7a	NN	_	_	_
634	_	_	CD	_	_	_
635	CY5	cy5	NN	_	_	_
636	_	_	CD	_	_	_
637	PUTI	PUTI	NNP	_	_	_
638	_	_	SYM	_	_	_
639	O26	o26	CD	_	_	_
640	_	_	SYM	_	_	_
641	UMN	UMN	NNP	_	_	_
642	_	_	SYM	_	_	_
643	O26	o26	CD	_	_	_
644	_	_	SYM	_	_	_
645	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
646	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
647	252978410014	252978410014	CD	_	_	_
648	_	_	NN	_	_	_
649	B7A	b7a	NN	_	_	_
650	_	_	CD	_	_	_
651	CY5	cy5	NN	_	_	_
652	_	_	CD	_	_	_
653	sPRH450	sprh450	NN	_	_	_
654	_	_	CD	_	_	_
655	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
656	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
657	252978410015	252978410015	CD	_	_	_
658	_	_	NN	_	_	_
659	B7A	b7a	NN	_	_	_
660	_	_	CD	_	_	_
661	CY5	cy5	NN	_	_	_
662	_	_	CD	_	_	_
663	E1392	e1392	NN	_	_	_
664	_	_	CD	_	_	_
665	75	75	CD	_	_	_
666	_	_	SYM	_	_	_
667	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
669	252978410015	252978410015	CD	_	_	_
670	_	_	NN	_	_	_
671	B7A	b7a	NN	_	_	_
672	_	_	CD	_	_	_
673	CY5	cy5	NN	_	_	_
674	_	_	CD	_	_	_
675	ICDDR	icddr	NN	_	_	_
676	_	_	NN	_	_	_
677	B	b	NN	_	_	_
678	_	_	CD	_	_	_
679	p5	p5	NN	_	_	_
680	_	_	CD	_	_	_
681	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
682	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
683	252978410015	252978410015	CD	_	_	_
684	_	_	NN	_	_	_
685	B7A	b7a	NN	_	_	_
686	_	_	CD	_	_	_
687	CY5	cy5	NN	_	_	_
688	_	_	CD	_	_	_
689	ICDDR	icddr	NN	_	_	_
690	_	_	NN	_	_	_
691	B	b	NN	_	_	_
692	_	_	CD	_	_	_
693	p8	p8	NN	_	_	_
694	_	_	CD	_	_	_
695	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
696	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
697	252978410015	252978410015	CD	_	_	_
698	_	_	NN	_	_	_
699	B7A	b7a	NN	_	_	_
700	_	_	CD	_	_	_
701	CY5	cy5	NN	_	_	_
702	_	_	CD	_	_	_
703	sPRH613	sprh613	NN	_	_	_
704	_	_	CD	_	_	_
705	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
706	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
707	252978410016	252978410016	CD	_	_	_
708	_	_	NN	_	_	_
709	B7A	b7a	NN	_	_	_
710	_	_	CD	_	_	_
711	CY5	cy5	NN	_	_	_
712	_	_	CD	_	_	_
713	D02	d02	NN	_	_	_
714	_	_	NN	_	_	_
715	2	2	CD	_	_	_
716	_	_	CD	_	_	_
717	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
718	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
719	252978410016	252978410016	CD	_	_	_
720	_	_	NN	_	_	_
721	B7A	b7a	NN	_	_	_
722	_	_	CD	_	_	_
723	CY5	cy5	NN	_	_	_
724	_	_	NN	_	_	_
725	E1785	e1785	NN	_	_	_
726	_	_	CD	_	_	_
727	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
729	252978410016	252978410016	CD	_	_	_
730	_	_	NN	_	_	_
731	B7A	b7a	NN	_	_	_
732	_	_	CD	_	_	_
733	CY5	cy5	NN	_	_	_
734	_	_	SYM	_	_	_
735	ETP98068	etp98068	CD	_	_	_
736	_	_	SYM	_	_	_
737	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
738	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
739	252978410016	252978410016	CD	_	_	_
740	_	_	NN	_	_	_
741	B7A	b7a	NN	_	_	_
742	_	_	CD	_	_	_
743	CY5	cy5	NN	_	_	_
744	_	_	CD	_	_	_
745	ICDDR	icddr	NN	_	_	_
746	_	_	NN	_	_	_
747	B	b	NN	_	_	_
748	_	_	CD	_	_	_
749	p11	p11	NN	_	_	_
750	_	_	CD	_	_	_
751	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
752	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
753	252978410017	252978410017	CD	_	_	_
754	_	_	NN	_	_	_
755	B7A	b7a	NN	_	_	_
756	_	_	CD	_	_	_
757	CY5	cy5	NN	_	_	_
758	_	_	NN	_	_	_
759	C35776	c35776	NN	_	_	_
760	_	_	CD	_	_	_
761	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
762	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
763	252978410017	252978410017	CD	_	_	_
764	_	_	NN	_	_	_
765	B7A	b7a	NN	_	_	_
766	_	_	CD	_	_	_
767	CY5	cy5	NN	_	_	_
768	_	_	CD	_	_	_
769	E1788	e1788	NN	_	_	_
770	_	_	CD	_	_	_
771	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
772	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
773	252978410017	252978410017	CD	_	_	_
774	_	_	NN	_	_	_
775	B7A	b7a	NN	_	_	_
776	_	_	CD	_	_	_
777	CY5	cy5	NN	_	_	_
778	_	_	CD	_	_	_
779	ETEC	ETEC	NNP	_	_	_
780	_	_	NNP	_	_	_
781	JURUA	JURUA	NNP	_	_	_
782	_	_	VBD	_	_	_
783	18	18	CD	_	_	_
784	_	_	SYM	_	_	_
785	11	11	CD	_	_	_
786	_	_	SYM	_	_	_
787	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
788	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
789	252978410017	252978410017	CD	_	_	_
790	_	_	NN	_	_	_
791	B7A	b7a	NN	_	_	_
792	_	_	CD	_	_	_
793	CY5	cy5	NN	_	_	_
794	_	_	CD	_	_	_
795	ICDDR	icddr	NN	_	_	_
796	_	_	NN	_	_	_
797	B	b	NN	_	_	_
798	_	_	CD	_	_	_
799	p9	p9	NN	_	_	_
800	_	_	CD	_	_	_
801	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
802	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
803	252978410018	252978410018	CD	_	_	_
804	_	_	NN	_	_	_
805	B7A	b7a	NN	_	_	_
806	_	_	CD	_	_	_
807	CY5	cy5	NN	_	_	_
808	_	_	CD	_	_	_
809	ARG3	arg3	NN	_	_	_
810	_	_	CD	_	_	_
811	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
812	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
813	252978410018	252978410018	CD	_	_	_
814	_	_	NN	_	_	_
815	B7A	b7a	NN	_	_	_
816	_	_	CD	_	_	_
817	CY5	cy5	NN	_	_	_
818	_	_	CD	_	_	_
819	E1792	e1792	NN	_	_	_
820	_	_	CD	_	_	_
821	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
823	252978410018	252978410018	CD	_	_	_
824	_	_	NN	_	_	_
825	B7A	b7a	NN	_	_	_
826	_	_	CD	_	_	_
827	CY5	cy5	NN	_	_	_
828	_	_	NN	_	_	_
829	MG1655	mg1655	NN	_	_	_
830	_	_	CD	_	_	_
831	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
832	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
833	252978410018	252978410018	CD	_	_	_
834	_	_	NN	_	_	_
835	B7A	b7a	NN	_	_	_
836	_	_	CD	_	_	_
837	CY5	cy5	NN	_	_	_
838	_	_	CD	_	_	_
839	sPRH21	sprh21	NN	_	_	_
840	_	_	CD	_	_	_
841	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
842	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
843	252978410019	252978410019	CD	_	_	_
844	_	_	NN	_	_	_
845	B7A	b7a	NN	_	_	_
846	_	_	CD	_	_	_
847	CY5	cy5	NN	_	_	_
848	_	_	CD	_	_	_
849	E1786	e1786	NN	_	_	_
850	_	_	CD	_	_	_
851	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
852	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
853	252978410019	252978410019	CD	_	_	_
854	_	_	NN	_	_	_
855	B7A	b7a	NN	_	_	_
856	_	_	CD	_	_	_
857	CY5	cy5	NN	_	_	_
858	_	_	CD	_	_	_
859	WS0115A	ws0115a	NN	_	_	_
860	_	_	CD	_	_	_
861	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
862	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
863	252978410020	252978410020	CD	_	_	_
864	_	_	NN	_	_	_
865	B7A	b7a	NN	_	_	_
866	_	_	CD	_	_	_
867	CY5	cy5	NN	_	_	_
868	_	_	SYM	_	_	_
869	179550	179550	CD	_	_	_
870	_	_	SYM	_	_	_
871	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
872	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
873	252978410020	252978410020	CD	_	_	_
874	_	_	NN	_	_	_
875	B7A	b7a	NN	_	_	_
876	_	_	CD	_	_	_
877	CY5	cy5	NN	_	_	_
878	_	_	NN	_	_	_
879	BCE046	bce046	NN	_	_	_
880	_	_	CD	_	_	_
881	DS2	ds2	NN	_	_	_
882	_	_	CD	_	_	_
883	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
884	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
885	252978410020	252978410020	CD	_	_	_
886	_	_	NN	_	_	_
887	B7A	b7a	NN	_	_	_
888	_	_	CD	_	_	_
889	CY5	cy5	NN	_	_	_
890	_	_	NN	_	_	_
891	BCE046	bce046	NN	_	_	_
892	_	_	CD	_	_	_
893	DS7	ds7	NN	_	_	_
894	_	_	CD	_	_	_
895	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
896	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
897	252978410020	252978410020	CD	_	_	_
898	_	_	NN	_	_	_
899	B7A	b7a	NN	_	_	_
900	_	_	CD	_	_	_
901	CY5	cy5	NN	_	_	_
902	_	_	CD	_	_	_
903	ETP98114	etp98114	NN	_	_	_
904	_	_	CD	_	_	_
905	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
907	252978410021	252978410021	CD	_	_	_
908	_	_	NN	_	_	_
909	B7A	b7a	NN	_	_	_
910	_	_	CD	_	_	_
911	CY5	cy5	NN	_	_	_
912	_	_	SYM	_	_	_
913	1080200	1080200	CD	_	_	_
914	_	_	SYM	_	_	_
915	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
916	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
917	252978410021	252978410021	CD	_	_	_
918	_	_	NN	_	_	_
919	B7A	b7a	NN	_	_	_
920	_	_	CD	_	_	_
921	CY5	cy5	NN	_	_	_
922	_	_	CD	_	_	_
923	BCE008	bce008	NN	_	_	_
924	_	_	CD	_	_	_
925	MS1	ms1	NN	_	_	_
926	_	_	CD	_	_	_
927	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
929	252978410021	252978410021	CD	_	_	_
930	_	_	NN	_	_	_
931	B7A	b7a	NN	_	_	_
932	_	_	CD	_	_	_
933	CY5	cy5	NN	_	_	_
934	_	_	CD	_	_	_
935	BCE054	bce054	NN	_	_	_
936	_	_	CD	_	_	_
937	MS24	ms24	NN	_	_	_
938	_	_	CD	_	_	_
939	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
940	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
941	252978410021	252978410021	CD	_	_	_
942	_	_	NN	_	_	_
943	B7A	b7a	NN	_	_	_
944	_	_	CD	_	_	_
945	CY5	cy5	NN	_	_	_
946	_	_	CD	_	_	_
947	ETP05	etp05	NN	_	_	_
948	_	_	NN	_	_	_
949	046	046	CD	_	_	_
950	_	_	SYM	_	_	_
951	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
952	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
953	252978410022	252978410022	CD	_	_	_
954	_	_	NN	_	_	_
955	B7A	b7a	NN	_	_	_
956	_	_	CD	_	_	_
957	CY5	cy5	NN	_	_	_
958	_	_	NN	_	_	_
959	BCE062	bce062	NN	_	_	_
960	_	_	CD	_	_	_
961	DS2	ds2	NN	_	_	_
962	_	_	CD	_	_	_
963	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
964	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
965	252978410022	252978410022	CD	_	_	_
966	_	_	NN	_	_	_
967	B7A	b7a	NN	_	_	_
968	_	_	CD	_	_	_
969	CY5	cy5	NN	_	_	_
970	_	_	NN	_	_	_
971	BCE069	bce069	NN	_	_	_
972	_	_	CD	_	_	_
973	DS2	ds2	NN	_	_	_
974	_	_	CD	_	_	_
975	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
976	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
977	252978410022	252978410022	CD	_	_	_
978	_	_	NN	_	_	_
979	B7A	b7a	NN	_	_	_
980	_	_	CD	_	_	_
981	CY5	cy5	NN	_	_	_
982	_	_	SYM	_	_	_
983	ETP98038	etp98038	CD	_	_	_
984	_	_	SYM	_	_	_
985	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
986	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
987	252978410022	252978410022	CD	_	_	_
988	_	_	NN	_	_	_
989	B7A	b7a	NN	_	_	_
990	_	_	CD	_	_	_
991	CY5	cy5	NN	_	_	_
992	_	_	CD	_	_	_
993	ETP98042	etp98042	NN	_	_	_
994	_	_	CD	_	_	_
995	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
996	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
997	252978410023	252978410023	CD	_	_	_
998	_	_	NN	_	_	_
999	B7A	b7a	NN	_	_	_
1000	_	_	CD	_	_	_
1001	CY5	cy5	NN	_	_	_
1002	_	_	SYM	_	_	_
1003	173150	173150	CD	_	_	_
1004	_	_	SYM	_	_	_
1005	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1006	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1007	252978410023	252978410023	CD	_	_	_
1008	_	_	NN	_	_	_
1009	B7A	b7a	NN	_	_	_
1010	_	_	CD	_	_	_
1011	CY5	cy5	NN	_	_	_
1012	_	_	SYM	_	_	_
1013	174750	174750	CD	_	_	_
1014	_	_	SYM	_	_	_
1015	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1016	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1017	252978410023	252978410023	CD	_	_	_
1018	_	_	NN	_	_	_
1019	B7A	b7a	NN	_	_	_
1020	_	_	CD	_	_	_
1021	CY5	cy5	NN	_	_	_
1022	_	_	SYM	_	_	_
1023	178850	178850	CD	_	_	_
1024	_	_	SYM	_	_	_
1025	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1026	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1027	252978410023	252978410023	CD	_	_	_
1028	_	_	NN	_	_	_
1029	B7A	b7a	NN	_	_	_
1030	_	_	CD	_	_	_
1031	CY5	cy5	NN	_	_	_
1032	_	_	SYM	_	_	_
1033	ETP98115	etp98115	CD	_	_	_
1034	_	_	SYM	_	_	_
1035	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1036	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1037	252978410024	252978410024	CD	_	_	_
1038	_	_	NN	_	_	_
1039	B7A	b7a	NN	_	_	_
1040	_	_	CD	_	_	_
1041	CY5	cy5	NN	_	_	_
1042	_	_	CD	_	_	_
1043	BCE018	bce018	NN	_	_	_
1044	_	_	CD	_	_	_
1045	DS6	ds6	NN	_	_	_
1046	_	_	CD	_	_	_
1047	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1048	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1049	252978410024	252978410024	CD	_	_	_
1050	_	_	NN	_	_	_
1051	B7A	b7a	NN	_	_	_
1052	_	_	CD	_	_	_
1053	CY5	cy5	NN	_	_	_
1054	_	_	CD	_	_	_
1055	BCE019	bce019	NN	_	_	_
1056	_	_	CD	_	_	_
1057	MS16	ms16	NN	_	_	_
1058	_	_	CD	_	_	_
1059	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1060	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1061	252978410024	252978410024	CD	_	_	_
1062	_	_	NN	_	_	_
1063	B7A	b7a	NN	_	_	_
1064	_	_	CD	_	_	_
1065	CY5	cy5	NN	_	_	_
1066	_	_	NN	_	_	_
1067	BCE046	bce046	NN	_	_	_
1068	_	_	CD	_	_	_
1069	MS16	ms16	NN	_	_	_
1070	_	_	CD	_	_	_
1071	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1072	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1073	252978410024	252978410024	CD	_	_	_
1074	_	_	NN	_	_	_
1075	B7A	b7a	NN	_	_	_
1076	_	_	CD	_	_	_
1077	CY5	cy5	NN	_	_	_
1078	_	_	NN	_	_	_
1079	BCE069	bce069	NN	_	_	_
1080	_	_	CD	_	_	_
1081	MS15	ms15	NN	_	_	_
1082	_	_	CD	_	_	_
1083	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1084	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1085	252978410025	252978410025	CD	_	_	_
1086	_	_	NN	_	_	_
1087	B7A	b7a	NN	_	_	_
1088	_	_	CD	_	_	_
1089	CY5	cy5	NN	_	_	_
1090	_	_	NN	_	_	_
1091	BCE007	bce007	NN	_	_	_
1092	_	_	CD	_	_	_
1093	MS11	ms11	NN	_	_	_
1094	_	_	CD	_	_	_
1095	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1096	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1097	252978410025	252978410025	CD	_	_	_
1098	_	_	NN	_	_	_
1099	B7A	b7a	NN	_	_	_
1100	_	_	CD	_	_	_
1101	CY5	cy5	NN	_	_	_
1102	_	_	NN	_	_	_
1103	BCE039	bce039	NN	_	_	_
1104	_	_	CD	_	_	_
1105	MS13	ms13	NN	_	_	_
1106	_	_	CD	_	_	_
1107	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1109	252978410025	252978410025	CD	_	_	_
1110	_	_	NN	_	_	_
1111	B7A	b7a	NN	_	_	_
1112	_	_	CD	_	_	_
1113	CY5	cy5	NN	_	_	_
1114	_	_	NN	_	_	_
1115	C35959	c35959	NN	_	_	_
1116	_	_	CD	_	_	_
1117	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1119	252978410025	252978410025	CD	_	_	_
1120	_	_	NN	_	_	_
1121	B7A	b7a	NN	_	_	_
1122	_	_	CD	_	_	_
1123	CY5	cy5	NN	_	_	_
1124	_	_	CD	_	_	_
1125	ETP05	etp05	NN	_	_	_
1126	_	_	NN	_	_	_
1127	050	050	CD	_	_	_
1128	_	_	SYM	_	_	_
1129	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1131	252978410026	252978410026	CD	_	_	_
1132	_	_	NN	_	_	_
1133	B7A	b7a	NN	_	_	_
1134	_	_	CD	_	_	_
1135	CY5	cy5	NN	_	_	_
1136	_	_	CD	_	_	_
1137	E24377A	e24377a	NN	_	_	_
1138	_	_	CD	_	_	_
1139	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1141	252978410026	252978410026	CD	_	_	_
1142	_	_	NN	_	_	_
1143	B7A	b7a	NN	_	_	_
1144	_	_	CD	_	_	_
1145	CY5	cy5	NN	_	_	_
1146	_	_	CD	_	_	_
1147	sPRH	sprh	NN	_	_	_
1148	_	_	NN	_	_	_
1149	418	418	CD	_	_	_
1150	_	_	SYM	_	_	_
1151	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1153	252978410026	252978410026	CD	_	_	_
1154	_	_	NN	_	_	_
1155	B7A	b7a	NN	_	_	_
1156	_	_	CD	_	_	_
1157	CY5	cy5	NN	_	_	_
1158	_	_	CD	_	_	_
1159	WS1896A	ws1896a	NN	_	_	_
1160	_	_	CD	_	_	_
1161	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1163	252978410026	252978410026	CD	_	_	_
1164	_	_	NN	_	_	_
1165	B7A	b7a	NN	_	_	_
1166	_	_	CD	_	_	_
1167	CY5	cy5	NN	_	_	_
1168	_	_	CD	_	_	_
1169	WS2068A	ws2068a	NN	_	_	_
1170	_	_	CD	_	_	_
1171	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1173	252978410027	252978410027	CD	_	_	_
1174	_	_	NN	_	_	_
1175	B7A	b7a	NN	_	_	_
1176	_	_	CD	_	_	_
1177	CY5	cy5	NN	_	_	_
1178	_	_	CD	_	_	_
1179	LSN03	lsn03	NN	_	_	_
1180	_	_	SYM	_	_	_
1181	016011	016011	CD	_	_	_
1182	_	_	CD	_	_	_
1183	A	a	DT	_	_	_
1184	_	_	NN	_	_	_
1185	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1187	252978410027	252978410027	CD	_	_	_
1188	_	_	NN	_	_	_
1189	B7A	b7a	NN	_	_	_
1190	_	_	CD	_	_	_
1191	CY5	cy5	NN	_	_	_
1192	_	_	CD	_	_	_
1193	sPRH	sprh	NN	_	_	_
1194	_	_	NN	_	_	_
1195	414	414	CD	_	_	_
1196	_	_	SYM	_	_	_
1197	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1199	252978410027	252978410027	CD	_	_	_
1200	_	_	NN	_	_	_
1201	B7A	b7a	NN	_	_	_
1202	_	_	CD	_	_	_
1203	CY5	cy5	NN	_	_	_
1204	_	_	CD	_	_	_
1205	sPRH	sprh	NN	_	_	_
1206	_	_	NN	_	_	_
1207	420	420	CD	_	_	_
1208	_	_	SYM	_	_	_
1209	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1211	252978410027	252978410027	CD	_	_	_
1212	_	_	NN	_	_	_
1213	B7A	b7a	NN	_	_	_
1214	_	_	CD	_	_	_
1215	ETEC20	etec20	NN	_	_	_
1216	_	_	SYM	_	_	_
1217	10	10	CD	_	_	_
1218	_	_	SYM	_	_	_
1219	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1221	252978410028	252978410028	CD	_	_	_
1222	_	_	NN	_	_	_
1223	B7A	b7a	NN	_	_	_
1224	_	_	CD	_	_	_
1225	CY5	cy5	NN	_	_	_
1226	_	_	CD	_	_	_
1227	ETP98073	etp98073	NN	_	_	_
1228	_	_	CD	_	_	_
1229	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1231	252978410028	252978410028	CD	_	_	_
1232	_	_	NN	_	_	_
1233	B7A	b7a	NN	_	_	_
1234	_	_	CD	_	_	_
1235	CY5	cy5	NN	_	_	_
1236	_	_	CD	_	_	_
1237	TW3439	tw3439	NN	_	_	_
1238	_	_	CD	_	_	_
1239	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1241	252978410028	252978410028	CD	_	_	_
1242	_	_	NN	_	_	_
1243	B7A	b7a	NN	_	_	_
1244	_	_	CD	_	_	_
1245	CY5	cy5	NN	_	_	_
1246	_	_	CD	_	_	_
1247	TW3576	tw3576	NN	_	_	_
1248	_	_	CD	_	_	_
1249	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1251	252978410028	252978410028	CD	_	_	_
1252	_	_	NN	_	_	_
1253	B7A	b7a	NN	_	_	_
1254	_	_	CD	_	_	_
1255	CY5	cy5	NN	_	_	_
1256	_	_	CD	_	_	_
1257	WS3080A	ws3080a	NN	_	_	_
1258	_	_	CD	_	_	_
1259	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1261	252978410029	252978410029	CD	_	_	_
1262	_	_	NN	_	_	_
1263	B7A	b7a	NN	_	_	_
1264	_	_	CD	_	_	_
1265	CY5	cy5	NN	_	_	_
1266	_	_	CD	_	_	_
1267	sPRH	sprh	NN	_	_	_
1268	_	_	NN	_	_	_
1269	403	403	CD	_	_	_
1270	_	_	SYM	_	_	_
1271	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1273	252978410029	252978410029	CD	_	_	_
1274	_	_	NN	_	_	_
1275	B7A	b7a	NN	_	_	_
1276	_	_	CD	_	_	_
1277	CY5	cy5	NN	_	_	_
1278	_	_	CD	_	_	_
1279	sPRH	sprh	NN	_	_	_
1280	_	_	NN	_	_	_
1281	443	443	CD	_	_	_
1282	_	_	SYM	_	_	_
1283	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1285	252978410029	252978410029	CD	_	_	_
1286	_	_	NN	_	_	_
1287	B7A	b7a	NN	_	_	_
1288	_	_	CD	_	_	_
1289	CY5	cy5	NN	_	_	_
1290	_	_	CD	_	_	_
1291	sPRH	sprh	NN	_	_	_
1292	_	_	NN	_	_	_
1293	604	604	CD	_	_	_
1294	_	_	SYM	_	_	_
1295	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1297	252978410029	252978410029	CD	_	_	_
1298	_	_	NN	_	_	_
1299	B7A	b7a	NN	_	_	_
1300	_	_	CD	_	_	_
1301	CY5	cy5	NN	_	_	_
1302	_	_	CD	_	_	_
1303	sPRH	sprh	NN	_	_	_
1304	_	_	NN	_	_	_
1305	606	606	CD	_	_	_
1306	_	_	SYM	_	_	_
1307	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1309	252978410030	252978410030	CD	_	_	_
1310	_	_	NN	_	_	_
1311	B7A	b7a	NN	_	_	_
1312	_	_	CD	_	_	_
1313	CY5	cy5	NN	_	_	_
1314	_	_	NN	_	_	_
1315	C36255	c36255	NN	_	_	_
1316	_	_	CD	_	_	_
1317	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1319	252978410030	252978410030	CD	_	_	_
1320	_	_	NN	_	_	_
1321	B7A	b7a	NN	_	_	_
1322	_	_	CD	_	_	_
1323	CY5	cy5	NN	_	_	_
1324	_	_	CD	_	_	_
1325	ETP05	etp05	NN	_	_	_
1326	_	_	NN	_	_	_
1327	008	008	CD	_	_	_
1328	_	_	SYM	_	_	_
1329	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1331	252978410030	252978410030	CD	_	_	_
1332	_	_	NN	_	_	_
1333	B7A	b7a	NN	_	_	_
1334	_	_	CD	_	_	_
1335	CY5	cy5	NN	_	_	_
1336	_	_	CD	_	_	_
1337	ETP98105	etp98105	NN	_	_	_
1338	_	_	CD	_	_	_
1339	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1341	252978410030	252978410030	CD	_	_	_
1342	_	_	NN	_	_	_
1343	B7A	b7a	NN	_	_	_
1344	_	_	CD	_	_	_
1345	ETP98066	etp98066	NN	_	_	_
1346	_	_	CD	_	_	_
1347	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1349	252978410031	252978410031	CD	_	_	_
1350	_	_	NN	_	_	_
1351	B7A	b7a	NN	_	_	_
1352	_	_	CD	_	_	_
1353	CY5	cy5	NN	_	_	_
1354	_	_	CD	_	_	_
1355	BCE054	bce054	NN	_	_	_
1356	_	_	CD	_	_	_
1357	DS4	ds4	NN	_	_	_
1358	_	_	CD	_	_	_
1359	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1361	252978410031	252978410031	CD	_	_	_
1362	_	_	NN	_	_	_
1363	B7A	b7a	NN	_	_	_
1364	_	_	CD	_	_	_
1365	CY5	cy5	NN	_	_	_
1366	_	_	CD	_	_	_
1367	BCE068	bce068	NN	_	_	_
1368	_	_	CD	_	_	_
1369	MS10	ms10	NN	_	_	_
1370	_	_	CD	_	_	_
1371	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1373	252978410031	252978410031	CD	_	_	_
1374	_	_	NN	_	_	_
1375	B7A	b7a	NN	_	_	_
1376	_	_	CD	_	_	_
1377	CY5	cy5	NN	_	_	_
1378	_	_	CD	_	_	_
1379	BCE068	bce068	NN	_	_	_
1380	_	_	CD	_	_	_
1381	MS23.mev.refIsIB.out	ms23.mev.refisib.out	NN	_	_	_
1382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1383	252978410031	252978410031	CD	_	_	_
1384	_	_	NN	_	_	_
1385	B7A	b7a	NN	_	_	_
1386	_	_	CD	_	_	_
1387	CY5	cy5	NN	_	_	_
1388	_	_	CD	_	_	_
1389	ETP05	etp05	NN	_	_	_
1390	_	_	NN	_	_	_
1391	015	015	CD	_	_	_
1392	_	_	SYM	_	_	_
1393	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1395	252978410032	252978410032	CD	_	_	_
1396	_	_	NN	_	_	_
1397	B7A	b7a	NN	_	_	_
1398	_	_	CD	_	_	_
1399	CY5	cy5	NN	_	_	_
1400	_	_	CD	_	_	_
1401	BCE011	bce011	NN	_	_	_
1402	_	_	CD	_	_	_
1403	DS3	ds3	NN	_	_	_
1404	_	_	CD	_	_	_
1405	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1407	252978410032	252978410032	CD	_	_	_
1408	_	_	NN	_	_	_
1409	B7A	b7a	NN	_	_	_
1410	_	_	CD	_	_	_
1411	CY5	cy5	NN	_	_	_
1412	_	_	NN	_	_	_
1413	BCE049	bce049	NN	_	_	_
1414	_	_	CD	_	_	_
1415	DS3	ds3	NN	_	_	_
1416	_	_	CD	_	_	_
1417	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1419	252978410032	252978410032	CD	_	_	_
1420	_	_	NN	_	_	_
1421	B7A	b7a	NN	_	_	_
1422	_	_	CD	_	_	_
1423	CY5	cy5	NN	_	_	_
1424	_	_	NN	_	_	_
1425	BCE062	bce062	NN	_	_	_
1426	_	_	CD	_	_	_
1427	MS24	ms24	NN	_	_	_
1428	_	_	CD	_	_	_
1429	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1431	252978410032	252978410032	CD	_	_	_
1432	_	_	NN	_	_	_
1433	B7A	b7a	NN	_	_	_
1434	_	_	CD	_	_	_
1435	CY5	cy5	NN	_	_	_
1436	_	_	NN	_	_	_
1437	BCE066	bce066	NN	_	_	_
1438	_	_	CD	_	_	_
1439	DS5	ds5	NN	_	_	_
1440	_	_	CD	_	_	_
1441	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1443	252978410033	252978410033	CD	_	_	_
1444	_	_	NN	_	_	_
1445	B7A	b7a	NN	_	_	_
1446	_	_	CD	_	_	_
1447	CY5	cy5	NN	_	_	_
1448	_	_	NN	_	_	_
1449	BCE035	bce035	NN	_	_	_
1450	_	_	CD	_	_	_
1451	DS6	ds6	NN	_	_	_
1452	_	_	CD	_	_	_
1453	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1455	252978410033	252978410033	CD	_	_	_
1456	_	_	NN	_	_	_
1457	B7A	b7a	NN	_	_	_
1458	_	_	CD	_	_	_
1459	CY5	cy5	NN	_	_	_
1460	_	_	NN	_	_	_
1461	C35209	c35209	NN	_	_	_
1462	_	_	CD	_	_	_
1463	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1465	252978410033	252978410033	CD	_	_	_
1466	_	_	NN	_	_	_
1467	B7A	b7a	NN	_	_	_
1468	_	_	CD	_	_	_
1469	CY5	cy5	NN	_	_	_
1470	_	_	CD	_	_	_
1471	ETP	etp	NN	_	_	_
1472	_	_	SYM	_	_	_
1473	98004	98004	CD	_	_	_
1474	_	_	SYM	_	_	_
1475	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1477	252978410033	252978410033	CD	_	_	_
1478	_	_	NN	_	_	_
1479	B7A	b7a	NN	_	_	_
1480	_	_	CD	_	_	_
1481	CY5	cy5	NN	_	_	_
1482	_	_	CD	_	_	_
1483	ETP98056	etp98056	NN	_	_	_
1484	_	_	CD	_	_	_
1485	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1487	252978410034	252978410034	CD	_	_	_
1488	_	_	NN	_	_	_
1489	B7A	b7a	NN	_	_	_
1490	_	_	CD	_	_	_
1491	CY5	cy5	NN	_	_	_
1492	_	_	NN	_	_	_
1493	BCE005	bce005	NN	_	_	_
1494	_	_	CD	_	_	_
1495	MS23	ms23	NN	_	_	_
1496	_	_	CD	_	_	_
1497	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1499	252978410034	252978410034	CD	_	_	_
1500	_	_	NN	_	_	_
1501	B7A	b7a	NN	_	_	_
1502	_	_	CD	_	_	_
1503	CY5	cy5	NN	_	_	_
1504	_	_	CD	_	_	_
1505	BCE061	bce061	NN	_	_	_
1506	_	_	CD	_	_	_
1507	DS1	ds1	NN	_	_	_
1508	_	_	CD	_	_	_
1509	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1510	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1511	252978410034	252978410034	CD	_	_	_
1512	_	_	NN	_	_	_
1513	B7A	b7a	NN	_	_	_
1514	_	_	CD	_	_	_
1515	CY5	cy5	NN	_	_	_
1516	_	_	CD	_	_	_
1517	ETP05	etp05	NN	_	_	_
1518	_	_	NN	_	_	_
1519	038	038	CD	_	_	_
1520	_	_	SYM	_	_	_
1521	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1523	252978410034	252978410034	CD	_	_	_
1524	_	_	NN	_	_	_
1525	B7A	b7a	NN	_	_	_
1526	_	_	CD	_	_	_
1527	CY5	cy5	NN	_	_	_
1528	_	_	CD	_	_	_
1529	ETP98053	etp98053	NN	_	_	_
1530	_	_	CD	_	_	_
1531	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1532	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1533	252978410035	252978410035	CD	_	_	_
1534	_	_	NN	_	_	_
1535	B7A	b7a	NN	_	_	_
1536	_	_	CD	_	_	_
1537	CY5	cy5	NN	_	_	_
1538	_	_	NN	_	_	_
1539	BCE055	bce055	NN	_	_	_
1540	_	_	CD	_	_	_
1541	DS1	ds1	NN	_	_	_
1542	_	_	CD	_	_	_
1543	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1545	252978410035	252978410035	CD	_	_	_
1546	_	_	NN	_	_	_
1547	B7A	b7a	NN	_	_	_
1548	_	_	CD	_	_	_
1549	CY5	cy5	NN	_	_	_
1550	_	_	CD	_	_	_
1551	ETP05	etp05	NN	_	_	_
1552	_	_	NN	_	_	_
1553	016	016	CD	_	_	_
1554	_	_	SYM	_	_	_
1555	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1556	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1557	252978410035	252978410035	CD	_	_	_
1558	_	_	NN	_	_	_
1559	B7A	b7a	NN	_	_	_
1560	_	_	CD	_	_	_
1561	CY5	cy5	NN	_	_	_
1562	_	_	CD	_	_	_
1563	ETP05	etp05	NN	_	_	_
1564	_	_	NN	_	_	_
1565	020	020	CD	_	_	_
1566	_	_	SYM	_	_	_
1567	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1569	252978410035	252978410035	CD	_	_	_
1570	_	_	NN	_	_	_
1571	B7A	b7a	NN	_	_	_
1572	_	_	CD	_	_	_
1573	CY5	cy5	NN	_	_	_
1574	_	_	CD	_	_	_
1575	ETP05	etp05	NN	_	_	_
1576	_	_	NN	_	_	_
1577	039	039	CD	_	_	_
1578	_	_	SYM	_	_	_
1579	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1581	252978410058	252978410058	CD	_	_	_
1582	_	_	NN	_	_	_
1583	B7A	b7a	NN	_	_	_
1584	_	_	CD	_	_	_
1585	CY5	cy5	NN	_	_	_
1586	_	_	SYM	_	_	_
1587	178900	178900	CD	_	_	_
1588	_	_	SYM	_	_	_
1589	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1590	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1591	252978410058	252978410058	CD	_	_	_
1592	_	_	NN	_	_	_
1593	B7A	b7a	NN	_	_	_
1594	_	_	CD	_	_	_
1595	CY5	cy5	NN	_	_	_
1596	_	_	SYM	_	_	_
1597	179100	179100	CD	_	_	_
1598	_	_	SYM	_	_	_
1599	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1601	252978410058	252978410058	CD	_	_	_
1602	_	_	NN	_	_	_
1603	B7A	b7a	NN	_	_	_
1604	_	_	CD	_	_	_
1605	CY5	cy5	NN	_	_	_
1606	_	_	CD	_	_	_
1607	ETP05	etp05	NN	_	_	_
1608	_	_	NN	_	_	_
1609	009	009	CD	_	_	_
1610	_	_	SYM	_	_	_
1611	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1612	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1613	252978410058	252978410058	CD	_	_	_
1614	_	_	NN	_	_	_
1615	B7A	b7a	NN	_	_	_
1616	_	_	CD	_	_	_
1617	CY5	cy5	NN	_	_	_
1618	_	_	CD	_	_	_
1619	ETP05	etp05	NN	_	_	_
1620	_	_	NN	_	_	_
1621	010	010	CD	_	_	_
1622	_	_	SYM	_	_	_
1623	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1624	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1625	252978410059	252978410059	CD	_	_	_
1626	_	_	NN	_	_	_
1627	B7A	b7a	NN	_	_	_
1628	_	_	CD	_	_	_
1629	CY5	cy5	NN	_	_	_
1630	_	_	NN	_	_	_
1631	532	532	CD	_	_	_
1632	_	_	NN	_	_	_
1633	WS6866B1	ws6866b1	NN	_	_	_
1634	_	_	CD	_	_	_
1635	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1637	252978410059	252978410059	CD	_	_	_
1638	_	_	NN	_	_	_
1639	B7A	b7a	NN	_	_	_
1640	_	_	CD	_	_	_
1641	CY5	cy5	NN	_	_	_
1642	_	_	CD	_	_	_
1643	ETP05	etp05	NN	_	_	_
1644	_	_	NN	_	_	_
1645	047	047	CD	_	_	_
1646	_	_	SYM	_	_	_
1647	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1648	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1649	252978410059	252978410059	CD	_	_	_
1650	_	_	NN	_	_	_
1651	B7A	b7a	NN	_	_	_
1652	_	_	CD	_	_	_
1653	CY5	cy5	NN	_	_	_
1654	_	_	CD	_	_	_
1655	ETP98097	etp98097	NN	_	_	_
1656	_	_	CD	_	_	_
1657	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1658	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1659	252978410059	252978410059	CD	_	_	_
1660	_	_	NN	_	_	_
1661	B7A	b7a	NN	_	_	_
1662	_	_	CD	_	_	_
1663	CY5	cy5	NN	_	_	_
1664	_	_	CD	_	_	_
1665	ETP98112	etp98112	NN	_	_	_
1666	_	_	CD	_	_	_
1667	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1669	252978410060	252978410060	CD	_	_	_
1670	_	_	NN	_	_	_
1671	B7A	b7a	NN	_	_	_
1672	_	_	CD	_	_	_
1673	CY5	cy5	NN	_	_	_
1674	_	_	CD	_	_	_
1675	ARG2	arg2	NN	_	_	_
1676	_	_	CD	_	_	_
1677	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1678	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1679	252978410060	252978410060	CD	_	_	_
1680	_	_	NN	_	_	_
1681	B7A	b7a	NN	_	_	_
1682	_	_	CD	_	_	_
1683	CY5	cy5	NN	_	_	_
1684	_	_	CD	_	_	_
1685	C35134	c35134	NN	_	_	_
1686	_	_	CD	_	_	_
1687	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1689	252978410060	252978410060	CD	_	_	_
1690	_	_	NN	_	_	_
1691	B7A	b7a	NN	_	_	_
1692	_	_	CD	_	_	_
1693	CY5	cy5	NN	_	_	_
1694	_	_	CD	_	_	_
1695	E1791	e1791	NN	_	_	_
1696	_	_	CD	_	_	_
1697	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1698	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1699	252978410060	252978410060	CD	_	_	_
1700	_	_	NN	_	_	_
1701	B7A	b7a	NN	_	_	_
1702	_	_	CD	_	_	_
1703	CY5	cy5	NN	_	_	_
1704	_	_	NN	_	_	_
1705	WS3596	ws3596	NN	_	_	_
1706	_	_	CD	_	_	_
1707	A4	a4	NN	_	_	_
1708	_	_	CD	_	_	_
1709	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1710	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1711	252978410061	252978410061	CD	_	_	_
1712	_	_	NN	_	_	_
1713	B7A	b7a	NN	_	_	_
1714	_	_	CD	_	_	_
1715	CY5	cy5	NN	_	_	_
1716	_	_	SYM	_	_	_
1717	COCAR07	cocar07	CD	_	_	_
1718	_	_	SYM	_	_	_
1719	40	40	CD	_	_	_
1720	_	_	SYM	_	_	_
1721	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1722	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1723	252978410061	252978410061	CD	_	_	_
1724	_	_	NN	_	_	_
1725	B7A	b7a	NN	_	_	_
1726	_	_	CD	_	_	_
1727	CY5	cy5	NN	_	_	_
1728	_	_	SYM	_	_	_
1729	COSIN07	cosin07	CD	_	_	_
1730	_	_	SYM	_	_	_
1731	88	88	CD	_	_	_
1732	_	_	SYM	_	_	_
1733	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1734	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1735	252978410061	252978410061	CD	_	_	_
1736	_	_	NN	_	_	_
1737	B7A	b7a	NN	_	_	_
1738	_	_	CD	_	_	_
1739	CY5	cy5	NN	_	_	_
1740	_	_	SYM	_	_	_
1741	COSIN07	cosin07	CD	_	_	_
1742	_	_	SYM	_	_	_
1743	92	92	CD	_	_	_
1744	_	_	SYM	_	_	_
1745	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1746	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1747	252978410062	252978410062	CD	_	_	_
1748	_	_	NN	_	_	_
1749	B7A	b7a	NN	_	_	_
1750	_	_	CD	_	_	_
1751	CY5	cy5	NN	_	_	_
1752	_	_	CD	_	_	_
1753	DS168	ds168	NN	_	_	_
1754	_	_	NN	_	_	_
1755	1	1	CD	_	_	_
1756	_	_	NN	_	_	_
1757	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1758	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1759	252978410062	252978410062	CD	_	_	_
1760	_	_	NN	_	_	_
1761	B7A	b7a	NN	_	_	_
1762	_	_	CD	_	_	_
1763	CY5	cy5	NN	_	_	_
1764	_	_	CD	_	_	_
1765	PE360	pe360	NN	_	_	_
1766	_	_	CD	_	_	_
1767	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1768	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1769	252978410062	252978410062	CD	_	_	_
1770	_	_	NN	_	_	_
1771	B7A	b7a	NN	_	_	_
1772	_	_	CD	_	_	_
1773	CY5	cy5	NN	_	_	_
1774	_	_	CD	_	_	_
1775	WS4087	ws4087	NN	_	_	_
1776	_	_	CD	_	_	_
1777	A1	a1	NN	_	_	_
1778	_	_	CD	_	_	_
1779	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1780	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1781	252978410062	252978410062	CD	_	_	_
1782	_	_	NN	_	_	_
1783	B7A	b7a	NN	_	_	_
1784	_	_	CD	_	_	_
1785	CY5	cy5	NN	_	_	_
1786	_	_	NN	_	_	_
1787	WS7179	ws7179	NN	_	_	_
1788	_	_	CD	_	_	_
1789	A2	a2	NN	_	_	_
1790	_	_	CD	_	_	_
1791	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1793	252978410063	252978410063	CD	_	_	_
1794	_	_	NN	_	_	_
1795	B7A	b7a	NN	_	_	_
1796	_	_	CD	_	_	_
1797	CY5	cy5	NN	_	_	_
1798	_	_	CD	_	_	_
1799	B7A	b7a	NN	_	_	_
1800	_	_	CD	_	_	_
1801	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1802	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1803	252978410063	252978410063	CD	_	_	_
1804	_	_	NN	_	_	_
1805	B7A	b7a	NN	_	_	_
1806	_	_	CD	_	_	_
1807	CY5	cy5	NN	_	_	_
1808	_	_	SYM	_	_	_
1809	COSIN07	cosin07	CD	_	_	_
1810	_	_	SYM	_	_	_
1811	14	14	CD	_	_	_
1812	_	_	SYM	_	_	_
1813	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1814	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1815	252978410063	252978410063	CD	_	_	_
1816	_	_	NN	_	_	_
1817	B7A	b7a	NN	_	_	_
1818	_	_	CD	_	_	_
1819	CY5	cy5	NN	_	_	_
1820	_	_	CD	_	_	_
1821	sPRH372	sprh372	NN	_	_	_
1822	_	_	CD	_	_	_
1823	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1824	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1825	252978410063	252978410063	CD	_	_	_
1826	_	_	NN	_	_	_
1827	B7A	b7a	NN	_	_	_
1828	_	_	CD	_	_	_
1829	CY5	cy5	NN	_	_	_
1830	_	_	CD	_	_	_
1831	TW3452	tw3452	NN	_	_	_
1832	_	_	CD	_	_	_
1833	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1834	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1835	252978410064	252978410064	CD	_	_	_
1836	_	_	NN	_	_	_
1837	B7A	b7a	NN	_	_	_
1838	_	_	CD	_	_	_
1839	CY5	cy5	NN	_	_	_
1840	_	_	CD	_	_	_
1841	E1789	e1789	NN	_	_	_
1842	_	_	CD	_	_	_
1843	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1844	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1845	252978410064	252978410064	CD	_	_	_
1846	_	_	NN	_	_	_
1847	B7A	b7a	NN	_	_	_
1848	_	_	CD	_	_	_
1849	CY5	cy5	NN	_	_	_
1850	_	_	CD	_	_	_
1851	E1790	e1790	NN	_	_	_
1852	_	_	CD	_	_	_
1853	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1854	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1855	252978410064	252978410064	CD	_	_	_
1856	_	_	NN	_	_	_
1857	B7A	b7a	NN	_	_	_
1858	_	_	CD	_	_	_
1859	CY5	cy5	NN	_	_	_
1860	_	_	CD	_	_	_
1861	HS	hs	NN	_	_	_
1862	_	_	CD	_	_	_
1863	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1864	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1865	252978410064	252978410064	CD	_	_	_
1866	_	_	NN	_	_	_
1867	B7A	b7a	NN	_	_	_
1868	_	_	CD	_	_	_
1869	CY5	cy5	NN	_	_	_
1870	_	_	CD	_	_	_
1871	sPRH609	sprh609	NN	_	_	_
1872	_	_	CD	_	_	_
1873	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1875	252978410065	252978410065	CD	_	_	_
1876	_	_	NN	_	_	_
1877	B7A	b7a	NN	_	_	_
1878	_	_	CD	_	_	_
1879	CY5	cy5	NN	_	_	_
1880	_	_	NN	_	_	_
1881	350C1A	350c1a	NN	_	_	_
1882	_	_	CD	_	_	_
1883	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1884	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1885	252978410065	252978410065	CD	_	_	_
1886	_	_	NN	_	_	_
1887	B7A	b7a	NN	_	_	_
1888	_	_	CD	_	_	_
1889	CY5	cy5	NN	_	_	_
1890	_	_	CD	_	_	_
1891	E2528	e2528	NN	_	_	_
1892	_	_	CD	_	_	_
1893	C1	c1	NN	_	_	_
1894	_	_	CD	_	_	_
1895	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1896	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1897	252978410065	252978410065	CD	_	_	_
1898	_	_	NN	_	_	_
1899	B7A	b7a	NN	_	_	_
1900	_	_	CD	_	_	_
1901	CY5	cy5	NN	_	_	_
1902	_	_	CD	_	_	_
1903	E8775	e8775	NN	_	_	_
1904	_	_	CD	_	_	_
1905	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1907	252978410065	252978410065	CD	_	_	_
1908	_	_	NN	_	_	_
1909	B7A	b7a	NN	_	_	_
1910	_	_	CD	_	_	_
1911	CY5	cy5	NN	_	_	_
1912	_	_	CD	_	_	_
1913	M424	m424	NN	_	_	_
1914	_	_	CD	_	_	_
1915	C1	c1	NN	_	_	_
1916	_	_	CD	_	_	_
1917	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1918	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1919	252978410066	252978410066	CD	_	_	_
1920	_	_	NN	_	_	_
1921	B7A	b7a	NN	_	_	_
1922	_	_	CD	_	_	_
1923	CY5	cy5	NN	_	_	_
1924	_	_	SYM	_	_	_
1925	2230	2230	CD	_	_	_
1926	_	_	SYM	_	_	_
1927	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1929	252978410066	252978410066	CD	_	_	_
1930	_	_	NN	_	_	_
1931	B7A	b7a	NN	_	_	_
1932	_	_	CD	_	_	_
1933	CY5	cy5	NN	_	_	_
1934	_	_	CD	_	_	_
1935	ICDDR	icddr	NN	_	_	_
1936	_	_	CD	_	_	_
1937	P	p	NN	_	_	_
1938	_	_	NN	_	_	_
1939	2	2	CD	_	_	_
1940	_	_	CD	_	_	_
1941	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1942	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1943	252978410066	252978410066	CD	_	_	_
1944	_	_	NN	_	_	_
1945	B7A	b7a	NN	_	_	_
1946	_	_	CD	_	_	_
1947	CY5	cy5	NN	_	_	_
1948	_	_	CD	_	_	_
1949	WS1933D	ws1933d	NN	_	_	_
1950	_	_	CD	_	_	_
1951	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1952	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1953	252978410066	252978410066	CD	_	_	_
1954	_	_	NN	_	_	_
1955	B7A	b7a	NN	_	_	_
1956	_	_	CD	_	_	_
1957	CY5	cy5	NN	_	_	_
1958	_	_	CD	_	_	_
1959	WS6582	ws6582	NN	_	_	_
1960	_	_	CD	_	_	_
1961	A1	a1	NN	_	_	_
1962	_	_	CD	_	_	_
1963	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1964	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1965	252978410067	252978410067	CD	_	_	_
1966	_	_	NN	_	_	_
1967	B7A	b7a	NN	_	_	_
1968	_	_	CD	_	_	_
1969	CY5	cy5	NN	_	_	_
1970	_	_	CD	_	_	_
1971	B2C	b2c	NN	_	_	_
1972	_	_	CD	_	_	_
1973	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1974	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1975	252978410067	252978410067	CD	_	_	_
1976	_	_	NN	_	_	_
1977	B7A	b7a	NN	_	_	_
1978	_	_	CD	_	_	_
1979	CY5	cy5	NN	_	_	_
1980	_	_	SYM	_	_	_
1981	ETEC	etec	NNS	_	_	_
1982	_	_	VBP	_	_	_
1983	8	8	CD	_	_	_
1984	_	_	SYM	_	_	_
1985	11	11	CD	_	_	_
1986	_	_	SYM	_	_	_
1987	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1988	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1989	252978410067	252978410067	CD	_	_	_
1990	_	_	NN	_	_	_
1991	B7A	b7a	NN	_	_	_
1992	_	_	CD	_	_	_
1993	CY5	cy5	NN	_	_	_
1994	_	_	CD	_	_	_
1995	F5656	f5656	NN	_	_	_
1996	_	_	CD	_	_	_
1997	C1	c1	NN	_	_	_
1998	_	_	CD	_	_	_
1999	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2000	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2001	252978410067	252978410067	CD	_	_	_
2002	_	_	NN	_	_	_
2003	B7A	b7a	NN	_	_	_
2004	_	_	CD	_	_	_
2005	CY5	cy5	NN	_	_	_
2006	_	_	CD	_	_	_
2007	WS7162	ws7162	NN	_	_	_
2008	_	_	CD	_	_	_
2009	A1	a1	NN	_	_	_
2010	_	_	CD	_	_	_
2011	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2012	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2013	252978410068	252978410068	CD	_	_	_
2014	_	_	NN	_	_	_
2015	B7A	b7a	NN	_	_	_
2016	_	_	CD	_	_	_
2017	CY5	cy5	NN	_	_	_
2018	_	_	NN	_	_	_
2019	CFT073	cft073	NN	_	_	_
2020	_	_	CD	_	_	_
2021	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2022	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2023	252978410068	252978410068	CD	_	_	_
2024	_	_	NN	_	_	_
2025	B7A	b7a	NN	_	_	_
2026	_	_	CD	_	_	_
2027	CY5	cy5	NN	_	_	_
2028	_	_	CD	_	_	_
2029	ICDDR	icddr	NN	_	_	_
2030	_	_	NN	_	_	_
2031	B	b	NN	_	_	_
2032	_	_	CD	_	_	_
2033	p	p	NN	_	_	_
2034	_	_	SYM	_	_	_
2035	10	10	CD	_	_	_
2036	_	_	SYM	_	_	_
2037	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2038	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2039	252978410068	252978410068	CD	_	_	_
2040	_	_	NN	_	_	_
2041	B7A	b7a	NN	_	_	_
2042	_	_	CD	_	_	_
2043	CY5	cy5	NN	_	_	_
2044	_	_	CD	_	_	_
2045	M408C1	m408c1	NN	_	_	_
2046	_	_	CD	_	_	_
2047	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2048	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2049	252978410068	252978410068	CD	_	_	_
2050	_	_	NN	_	_	_
2051	B7A	b7a	NN	_	_	_
2052	_	_	CD	_	_	_
2053	CY5	cy5	NN	_	_	_
2054	_	_	CD	_	_	_
2055	WS3294A	ws3294a	NN	_	_	_
2056	_	_	CD	_	_	_
2057	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2058	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2059	252978410069	252978410069	CD	_	_	_
2060	_	_	NN	_	_	_
2061	B7A	b7a	NN	_	_	_
2062	_	_	CD	_	_	_
2063	CY5	cy5	NN	_	_	_
2064	_	_	CD	_	_	_
2065	278485	278485	CD	_	_	_
2066	_	_	NN	_	_	_
2067	1	1	CD	_	_	_
2068	_	_	NN	_	_	_
2069	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2070	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2071	252978410069	252978410069	CD	_	_	_
2072	_	_	NN	_	_	_
2073	B7A	b7a	NN	_	_	_
2074	_	_	CD	_	_	_
2075	CY5	cy5	NN	_	_	_
2076	_	_	CD	_	_	_
2077	sPRH25	sprh25	NN	_	_	_
2078	_	_	CD	_	_	_
2079	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2080	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2081	252978410069	252978410069	CD	_	_	_
2082	_	_	NN	_	_	_
2083	B7A	b7a	NN	_	_	_
2084	_	_	CD	_	_	_
2085	CY5	cy5	NN	_	_	_
2086	_	_	CD	_	_	_
2087	sPRH421	sprh421	NN	_	_	_
2088	_	_	CD	_	_	_
2089	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2090	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2091	252978410069	252978410069	CD	_	_	_
2092	_	_	NN	_	_	_
2093	B7A	b7a	NN	_	_	_
2094	_	_	CD	_	_	_
2095	CY5	cy5	NN	_	_	_
2096	_	_	CD	_	_	_
2097	sPRH610	sprh610	NN	_	_	_
2098	_	_	CD	_	_	_
2099	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2101	252978410070	252978410070	CD	_	_	_
2102	_	_	NN	_	_	_
2103	B7A	b7a	NN	_	_	_
2104	_	_	CD	_	_	_
2105	CY5	cy5	NN	_	_	_
2106	_	_	CD	_	_	_
2107	ICDDR	icddr	NN	_	_	_
2108	_	_	NN	_	_	_
2109	B	b	NN	_	_	_
2110	_	_	CD	_	_	_
2111	p7	p7	NN	_	_	_
2112	_	_	CD	_	_	_
2113	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2115	252978410070	252978410070	CD	_	_	_
2116	_	_	NN	_	_	_
2117	B7A	b7a	NN	_	_	_
2118	_	_	CD	_	_	_
2119	CY5	cy5	NN	_	_	_
2120	_	_	CD	_	_	_
2121	NR	nr	NN	_	_	_
2122	_	_	SYM	_	_	_
2123	12	12	CD	_	_	_
2124	_	_	SYM	_	_	_
2125	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2127	252978410070	252978410070	CD	_	_	_
2128	_	_	NN	_	_	_
2129	B7A	b7a	NN	_	_	_
2130	_	_	CD	_	_	_
2131	CY5	cy5	NN	_	_	_
2132	_	_	CD	_	_	_
2133	sPRH20	sprh20	NN	_	_	_
2134	_	_	CD	_	_	_
2135	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2137	252978410070	252978410070	CD	_	_	_
2138	_	_	NN	_	_	_
2139	B7A	b7a	NN	_	_	_
2140	_	_	CD	_	_	_
2141	CY5	cy5	NN	_	_	_
2142	_	_	CD	_	_	_
2143	sPRH612	sprh612	NN	_	_	_
2144	_	_	CD	_	_	_
2145	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2147	252978410071	252978410071	CD	_	_	_
2148	_	_	NN	_	_	_
2149	B7A	b7a	NN	_	_	_
2150	_	_	CD	_	_	_
2151	CY5	cy5	NN	_	_	_
2152	_	_	NN	_	_	_
2153	292	292	CD	_	_	_
2154	_	_	NN	_	_	_
2155	1	1	CD	_	_	_
2156	_	_	NN	_	_	_
2157	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2159	252978410071	252978410071	CD	_	_	_
2160	_	_	NN	_	_	_
2161	B7A	b7a	NN	_	_	_
2162	_	_	CD	_	_	_
2163	CY5	cy5	NN	_	_	_
2164	_	_	CD	_	_	_
2165	COCAR07	cocar07	NN	_	_	_
2166	_	_	NN	_	_	_
2167	043	043	CD	_	_	_
2168	_	_	SYM	_	_	_
2169	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2171	252978410071	252978410071	CD	_	_	_
2172	_	_	NN	_	_	_
2173	B7A	b7a	NN	_	_	_
2174	_	_	CD	_	_	_
2175	CY5	cy5	NN	_	_	_
2176	_	_	SYM	_	_	_
2177	COSIN07	cosin07	CD	_	_	_
2178	_	_	SYM	_	_	_
2179	61	61	CD	_	_	_
2180	_	_	SYM	_	_	_
2181	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2183	252978410071	252978410071	CD	_	_	_
2184	_	_	NN	_	_	_
2185	B7A	b7a	NN	_	_	_
2186	_	_	CD	_	_	_
2187	CY5	cy5	NN	_	_	_
2188	_	_	CD	_	_	_
2189	O157	o157	NN	_	_	_
2190	_	_	CD	_	_	_
2191	h7	h7	NN	_	_	_
2192	_	_	CD	_	_	_
2193	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2195	252978410072	252978410072	CD	_	_	_
2196	_	_	NN	_	_	_
2197	B7A	b7a	NN	_	_	_
2198	_	_	CD	_	_	_
2199	CY5	cy5	NN	_	_	_
2200	_	_	SYM	_	_	_
2201	COSIN07	cosin07	CD	_	_	_
2202	_	_	SYM	_	_	_
2203	36	36	CD	_	_	_
2204	_	_	SYM	_	_	_
2205	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2207	252978410072	252978410072	CD	_	_	_
2208	_	_	NN	_	_	_
2209	B7A	b7a	NN	_	_	_
2210	_	_	CD	_	_	_
2211	CY5	cy5	NN	_	_	_
2212	_	_	CD	_	_	_
2213	ICDDR	icddr	NN	_	_	_
2214	_	_	NN	_	_	_
2215	B	b	NN	_	_	_
2216	_	_	CD	_	_	_
2217	p6	p6	NN	_	_	_
2218	_	_	CD	_	_	_
2219	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2221	252978410072	252978410072	CD	_	_	_
2222	_	_	NN	_	_	_
2223	B7A	b7a	NN	_	_	_
2224	_	_	CD	_	_	_
2225	CY5	cy5	NN	_	_	_
2226	_	_	CD	_	_	_
2227	O63	o63	NN	_	_	_
2228	_	_	CD	_	_	_
2229	nm	nm	NN	_	_	_
2230	_	_	NN	_	_	_
2231	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2233	252978410072	252978410072	CD	_	_	_
2234	_	_	NN	_	_	_
2235	B7A	b7a	NN	_	_	_
2236	_	_	CD	_	_	_
2237	CY5	cy5	NN	_	_	_
2238	_	_	CD	_	_	_
2239	sPRH605	sprh605	NN	_	_	_
2240	_	_	CD	_	_	_
2241	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2243	252978410073	252978410073	CD	_	_	_
2244	_	_	NN	_	_	_
2245	B7A	b7a	NN	_	_	_
2246	_	_	CD	_	_	_
2247	CY5	cy5	NN	_	_	_
2248	_	_	NN	_	_	_
2249	214	214	CD	_	_	_
2250	_	_	NN	_	_	_
2251	4	4	CD	_	_	_
2252	_	_	SYM	_	_	_
2253	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2255	252978410073	252978410073	CD	_	_	_
2256	_	_	NN	_	_	_
2257	B7A	b7a	NN	_	_	_
2258	_	_	CD	_	_	_
2259	CY5	cy5	NN	_	_	_
2260	_	_	CD	_	_	_
2261	E7476A	e7476a	NN	_	_	_
2262	_	_	CD	_	_	_
2263	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2265	252978410073	252978410073	CD	_	_	_
2266	_	_	NN	_	_	_
2267	B7A	b7a	NN	_	_	_
2268	_	_	CD	_	_	_
2269	CY5	cy5	NN	_	_	_
2270	_	_	NN	_	_	_
2271	WS1896	ws1896	NN	_	_	_
2272	_	_	CD	_	_	_
2273	A1	a1	NN	_	_	_
2274	_	_	CD	_	_	_
2275	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2277	252978410073	252978410073	CD	_	_	_
2278	_	_	NN	_	_	_
2279	B7A	b7a	NN	_	_	_
2280	_	_	CD	_	_	_
2281	CY5	cy5	NN	_	_	_
2282	_	_	CD	_	_	_
2283	WS2173A	ws2173a	NN	_	_	_
2284	_	_	CD	_	_	_
2285	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2287	252978410075	252978410075	CD	_	_	_
2288	_	_	NN	_	_	_
2289	B7A	b7a	NN	_	_	_
2290	_	_	CD	_	_	_
2291	CY5	cy5	NN	_	_	_
2292	_	_	CD	_	_	_
2293	ETP05	etp05	NN	_	_	_
2294	_	_	NN	_	_	_
2295	011	011	CD	_	_	_
2296	_	_	SYM	_	_	_
2297	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2299	252978410075	252978410075	CD	_	_	_
2300	_	_	NN	_	_	_
2301	B7A	b7a	NN	_	_	_
2302	_	_	CD	_	_	_
2303	CY5	cy5	NN	_	_	_
2304	_	_	CD	_	_	_
2305	ETP05	etp05	NN	_	_	_
2306	_	_	NN	_	_	_
2307	035	035	CD	_	_	_
2308	_	_	SYM	_	_	_
2309	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2311	252978410075	252978410075	CD	_	_	_
2312	_	_	NN	_	_	_
2313	B7A	b7a	NN	_	_	_
2314	_	_	CD	_	_	_
2315	CY5	cy5	NN	_	_	_
2316	_	_	SYM	_	_	_
2317	O78	o78	CD	_	_	_
2318	_	_	CD	_	_	_
2319	h11	h11	NN	_	_	_
2320	_	_	CD	_	_	_
2321	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2323	252978410075	252978410075	CD	_	_	_
2324	_	_	NN	_	_	_
2325	B7A	b7a	NN	_	_	_
2326	_	_	CD	_	_	_
2327	CY5	cy5	NN	_	_	_
2328	_	_	CD	_	_	_
2329	sPRH445	sprh445	NN	_	_	_
2330	_	_	CD	_	_	_
2331	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2333	252978410076	252978410076	CD	_	_	_
2334	_	_	NN	_	_	_
2335	B7A	b7a	NN	_	_	_
2336	_	_	CD	_	_	_
2337	CY5	cy5	NN	_	_	_
2338	_	_	SYM	_	_	_
2339	178200	178200	CD	_	_	_
2340	_	_	SYM	_	_	_
2341	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2343	252978410076	252978410076	CD	_	_	_
2344	_	_	NN	_	_	_
2345	B7A	b7a	NN	_	_	_
2346	_	_	CD	_	_	_
2347	CY5	cy5	NN	_	_	_
2348	_	_	NN	_	_	_
2349	C35213	c35213	NN	_	_	_
2350	_	_	CD	_	_	_
2351	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2353	252978410076	252978410076	CD	_	_	_
2354	_	_	NN	_	_	_
2355	B7A	b7a	NN	_	_	_
2356	_	_	CD	_	_	_
2357	CY5	cy5	NN	_	_	_
2358	_	_	NN	_	_	_
2359	C35605	c35605	NN	_	_	_
2360	_	_	CD	_	_	_
2361	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2363	252978410076	252978410076	CD	_	_	_
2364	_	_	NN	_	_	_
2365	B7A	b7a	NN	_	_	_
2366	_	_	CD	_	_	_
2367	CY5	cy5	NN	_	_	_
2368	_	_	CD	_	_	_
2369	ETP98109	etp98109	NN	_	_	_
2370	_	_	CD	_	_	_
2371	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2373	252978410077	252978410077	CD	_	_	_
2374	_	_	NN	_	_	_
2375	B7A	b7a	NN	_	_	_
2376	_	_	CD	_	_	_
2377	CY5	cy5	NN	_	_	_
2378	_	_	SYM	_	_	_
2379	174900	174900	CD	_	_	_
2380	_	_	SYM	_	_	_
2381	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2383	252978410077	252978410077	CD	_	_	_
2384	_	_	NN	_	_	_
2385	B7A	b7a	NN	_	_	_
2386	_	_	CD	_	_	_
2387	CY5	cy5	NN	_	_	_
2388	_	_	NN	_	_	_
2389	C34666	c34666	NN	_	_	_
2390	_	_	CD	_	_	_
2391	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2393	252978410077	252978410077	CD	_	_	_
2394	_	_	NN	_	_	_
2395	B7A	b7a	NN	_	_	_
2396	_	_	CD	_	_	_
2397	CY5	cy5	NN	_	_	_
2398	_	_	CD	_	_	_
2399	ETP05	etp05	NN	_	_	_
2400	_	_	NN	_	_	_
2401	002	002	CD	_	_	_
2402	_	_	SYM	_	_	_
2403	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2405	252978410077	252978410077	CD	_	_	_
2406	_	_	NN	_	_	_
2407	B7A	b7a	NN	_	_	_
2408	_	_	CD	_	_	_
2409	CY5	cy5	NN	_	_	_
2410	_	_	CD	_	_	_
2411	ETP05	etp05	NN	_	_	_
2412	_	_	NN	_	_	_
2413	003	003	CD	_	_	_
2414	_	_	SYM	_	_	_
2415	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2417	252978410078	252978410078	CD	_	_	_
2418	_	_	NN	_	_	_
2419	B7A	b7a	NN	_	_	_
2420	_	_	CD	_	_	_
2421	CY5	cy5	NN	_	_	_
2422	_	_	NN	_	_	_
2423	2	2	CD	_	_	_
2424	_	_	NN	_	_	_
2425	1	1	CD	_	_	_
2426	_	_	NN	_	_	_
2427	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2429	252978410078	252978410078	CD	_	_	_
2430	_	_	NN	_	_	_
2431	B7A	b7a	NN	_	_	_
2432	_	_	CD	_	_	_
2433	CY5	cy5	NN	_	_	_
2434	_	_	CD	_	_	_
2435	WS2741	ws2741	NN	_	_	_
2436	_	_	CD	_	_	_
2437	A1	a1	NN	_	_	_
2438	_	_	CD	_	_	_
2439	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2441	252978410078	252978410078	CD	_	_	_
2442	_	_	NN	_	_	_
2443	B7A	b7a	NN	_	_	_
2444	_	_	CD	_	_	_
2445	CY5	cy5	NN	_	_	_
2446	_	_	CD	_	_	_
2447	WS4264	ws4264	NN	_	_	_
2448	_	_	CD	_	_	_
2449	A1	a1	NN	_	_	_
2450	_	_	CD	_	_	_
2451	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2452	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2453	252978410078	252978410078	CD	_	_	_
2454	_	_	NN	_	_	_
2455	B7A	b7a	NN	_	_	_
2456	_	_	CD	_	_	_
2457	CY5	cy5	NN	_	_	_
2458	_	_	CD	_	_	_
2459	WS5874	ws5874	NN	_	_	_
2460	_	_	CD	_	_	_
2461	A1	a1	NN	_	_	_
2462	_	_	CD	_	_	_
2463	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2465	25	25	CD	_	_	_
2466	.	.	.	_	_	_

1	FHI79.nIND.HUS	fhi79.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	25	25	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	turning	turn	VBG	_	_	_
7	off	off	RP	_	_	_
8	oxygen	oxygen	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	26	26	CD	_	_	_
11	.	.	.	_	_	_

1	FHI79.IND.HUS	fhi79.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	26	26	CD	_	_	_
4	%	%	NN	_	_	_
5	rep1	rep1	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	26	26	CD	_	_	_
8	%	%	NN	_	_	_
9	rep2	rep2	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	27	27	CD	_	_	_
12	.	.	.	_	_	_

1	FHI95.nIND.nHUS	fhi95.nind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	285c/control	285c/control	NN	_	_	_
4	vector	vector	NN	_	_	_
5	at	at	IN	_	_	_
6	30	30	CD	_	_	_
7	C	c	NN	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	285c/control	285c/control	NN	_	_	_
11	vector	vector	NN	_	_	_
12	at	at	IN	_	_	_
13	30	30	CD	_	_	_
14	C	c	NN	_	_	_
15	2	2	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	285c/control	285c/control	NN	_	_	_
18	vector	vector	NN	_	_	_
19	at	at	IN	_	_	_
20	30	30	CD	_	_	_
21	C	c	NN	_	_	_
22	3	3	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	28	28	CD	_	_	_
25	.	.	.	_	_	_

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	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	2A	2a	NN	_	_	_
5	1y	1y	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	2A	2a	NN	_	_	_
8	4y	4y	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	2A	2a	NN	_	_	_
11	_	_	CD	_	_	_
12	MG	mg	NN	_	_	_
13	_	_	NN	_	_	_
14	t10	t10	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	2B	2b	NN	_	_	_
17	_	_	CD	_	_	_
18	MG	mg	NN	_	_	_
19	_	_	NN	_	_	_
20	t10	t10	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	2C	2c	NN	_	_	_
23	_	_	CD	_	_	_
24	MG	mg	NN	_	_	_
25	_	_	NN	_	_	_
26	t10	t10	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	2	2	CD	_	_	_
29	_	_	CD	_	_	_
30	ESBL019	esbl019	NN	_	_	_
31	Filamented	Filamented	NNP	_	_	_
32	Repl	Repl	NNP	_	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	2	2	CD	_	_	_
36	.	.	.	_	_	_

1	FHI4.IND.HUS	fhi4.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	2	2	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	LP	lp	NN	_	_	_
8	_	_	CD	_	_	_
9	noDP	nodp	NN	_	_	_
10	_	_	CD	_	_	_
11	noRh	norh	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	COPRO-Seq	copro-seq	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	2	2	CD	_	_	_
17	hour	hour	NN	_	_	_
18	expression	expression	NN	_	_	_
19	of	of	IN	_	_	_
20	synthetic	synthetic	JJ	_	_	_
21	protein	protein	NN	_	_	_
22	DX	dx	NN	_	_	_
23	in	in	IN	_	_	_
24	E.	e.	FW	_	_	_
25	coli	coli	FW	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	2-HT873-PA2	2-ht873-pa2	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	2-HT873-PA2	2-ht873-pa2	NN	_	_	_
30	-	-	:	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	2	2	CD	_	_	_
33	min	min	NN	_	_	_
34	after	after	IN	_	_	_
35	turning	turn	VBG	_	_	_
36	off	off	RP	_	_	_
37	oxygen	oxygen	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	2	2	CD	_	_	_
40	min	min	NN	_	_	_
41	Nov10	nov10	NN	_	_	_
42	ug/ml	ug/ml	NN	_	_	_
43	,	,	,	_	_	_
44	2	2	CD	_	_	_
45	ug	ug	NN	_	_	_
46	Sau3AI	sau3ai	NN	_	_	_
47	,	,	,	_	_	_
48	pdN6	pdn6	NN	_	_	_
49	RT	rt	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	2	2	CD	_	_	_
52	min	min	NN	_	_	_
53	Nov10	nov10	NN	_	_	_
54	ug/ml	ug/ml	NN	_	_	_
55	,	,	,	_	_	_
56	dnaCacrD	dnacacrd	NN	_	_	_
57	30	30	CD	_	_	_
58	min	min	NN	_	_	_
59	after	after	IN	_	_	_
60	synchr	synchr	NN	_	_	_
61	start	start	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	2	2	CD	_	_	_
64	min	min	NN	_	_	_
65	Nov2	nov2	NN	_	_	_
66	ug/ml	ug/ml	NN	_	_	_
67	,	,	,	_	_	_
68	2	2	CD	_	_	_
69	ug	ug	NN	_	_	_
70	Say3AI	say3ai	NN	_	_	_
71	,	,	,	_	_	_
72	pdN6	pdn6	NN	_	_	_
73	RT	rt	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	2	2	CD	_	_	_
76	min	min	NN	_	_	_
77	Nov2	nov2	NN	_	_	_
78	ug/ml	ug/ml	NN	_	_	_
79	,	,	,	_	_	_
80	dnaCacrD	dnacacrd	NN	_	_	_
81	30	30	CD	_	_	_
82	min	min	NN	_	_	_
83	after	after	IN	_	_	_
84	synchr	synchr	NN	_	_	_
85	start	start	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	2	2	CD	_	_	_
88	min	min	NN	_	_	_
89	Nov5	nov5	NN	_	_	_
90	ug/ml	ug/ml	NN	_	_	_
91	,	,	,	_	_	_
92	2	2	CD	_	_	_
93	ug	ug	NN	_	_	_
94	Say3AI	say3ai	NN	_	_	_
95	,	,	,	_	_	_
96	pdN6	pdn6	NN	_	_	_
97	RT	rt	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	2	2	CD	_	_	_
100	min	min	NN	_	_	_
101	Nov5	nov5	NN	_	_	_
102	ug/ml	ug/ml	NN	_	_	_
103	,	,	,	_	_	_
104	dnaCacrD	dnacacrd	NN	_	_	_
105	30	30	CD	_	_	_
106	min	min	NN	_	_	_
107	after	after	IN	_	_	_
108	synchr	synchr	NN	_	_	_
109	start	start	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	2	2	CD	_	_	_
112	ppm	ppm	NN	_	_	_
113	deoxynivalenol	deoxynivalenol	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	2	2	CD	_	_	_
116	ppm	ppm	NN	_	_	_
117	nivalenol	nivalenol	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	2	2	CD	_	_	_
120	.	.	.	_	_	_

1	Read	Read	NNP	_	_	_
2	data	datum	NNS	_	_	_
3	:	:	:	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	2	2	CD	_	_	_
6	'	'	''	_	_	_
7	RNA	rna	NN	_	_	_
8	Decay	decay	NN	_	_	_
9	of	of	IN	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Repaired	repair	VBN	_	_	_
13	NCM	NCM	NNP	_	_	_
14	3416	3416	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	in	in	IN	_	_	_
17	LB	lb	NN	_	_	_
18	at	at	IN	_	_	_
19	30	30	CD	_	_	_
20	C	c	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	2	2	CD	_	_	_
23	'	'	''	_	_	_
24	RNA	rna	NN	_	_	_
25	Decay	decay	NN	_	_	_
26	of	of	IN	_	_	_
27	MG1655	mg1655	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Repaired	repair	VBN	_	_	_
30	NCM	NCM	NNP	_	_	_
31	3416	3416	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	in	in	IN	_	_	_
34	M9	m9	NN	_	_	_
35	+	+	CC	_	_	_
36	0.2	0.2	CD	_	_	_
37	%	%	NN	_	_	_
38	Glucose	glucose	NN	_	_	_
39	Trial	trial	NN	_	_	_
40	A	a	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	2	2	CD	_	_	_
43	'	'	''	_	_	_
44	RNA	rna	NN	_	_	_
45	Decay	decay	NN	_	_	_
46	of	of	IN	_	_	_
47	MG1655	mg1655	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	Repaired	repair	VBN	_	_	_
50	NCM	NCM	NNP	_	_	_
51	3416	3416	CD	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	in	in	IN	_	_	_
54	M9	m9	NN	_	_	_
55	+	+	CC	_	_	_
56	0.2	0.2	CD	_	_	_
57	%	%	NN	_	_	_
58	Glucose	glucose	NN	_	_	_
59	Trial	trial	NN	_	_	_
60	B	b	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	2	2	CD	_	_	_
63	ug	ug	NN	_	_	_
64	of	of	IN	_	_	_
65	Genomic	genomic	JJ	_	_	_
66	MG	mg	NN	_	_	_
67	1655	1655	CD	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	Repaired	repair	VBN	_	_	_
70	NCM	NCM	NNP	_	_	_
71	3416	3416	CD	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	DNA	dna	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	2	2	CD	_	_	_
76	ug	ug	NN	_	_	_
77	of	of	IN	_	_	_
78	MG1655	mg1655	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	Repaired	repair	VBN	_	_	_
81	NCM	NCM	NNP	_	_	_
82	3416	3416	CD	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	Genomic	genomic	JJ	_	_	_
85	DNA	dna	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	2	2	CD	_	_	_
88	.	.	.	_	_	_

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	2xOriT	2xorit	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	2	2	CD	_	_	_
5	μg	μg	NN	_	_	_
6	of	of	IN	_	_	_
7	RNA	rna	NN	_	_	_
8	from	from	IN	_	_	_
9	the	the	DT	_	_	_
10	cytoplasmic	cytoplasmic	JJ	_	_	_
11	fraction	fraction	NN	_	_	_
12	were	be	VBD	_	_	_
13	diluted	dilute	VBN	_	_	_
14	in	in	IN	_	_	_
15	20	20	CD	_	_	_
16	μl	μl	NN	_	_	_
17	of	of	IN	_	_	_
18	Fragmentation	fragmentation	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	fragmented	fragmented	JJ	_	_	_
23	by	by	IN	_	_	_
24	incubation	incubation	NN	_	_	_
25	at	at	IN	_	_	_
26	95	95	CD	_	_	_
27	°C	°c	NN	_	_	_
28	for	for	IN	_	_	_
29	5	5	CD	_	_	_
30	minutes	minute	NNS	_	_	_
31	.	.	.	_	_	_

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/μl	μg/μl	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	resuspended	resuspend	VBN	_	_	_
22	in	in	IN	_	_	_
23	6	6	CD	_	_	_
24	μl	μl	NN	_	_	_
25	nuclease-free	nuclease-free	JJ	_	_	_
26	water	water	NN	_	_	_
27	.	.	.	_	_	_

1	10	10	CD	_	_	_
2	pmol	pmol	NN	_	_	_
3	of	of	IN	_	_	_
4	a	a	DT	_	_	_
5	pre-adenylated	pre-adenylated	JJ	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	rApp	rapp	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	adapter	adapter	NN	_	_	_
10	were	be	VBD	_	_	_
11	ligated	ligate	VBN	_	_	_
12	to	to	TO	_	_	_
13	size-selected	size-selected	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	fragments	fragment	NNS	_	_	_
16	in	in	IN	_	_	_
17	a	a	DT	_	_	_
18	reaction	reaction	NN	_	_	_
19	volume	volume	NN	_	_	_
20	of	of	IN	_	_	_
21	20	20	CD	_	_	_
22	μl	μl	NN	_	_	_
23	,	,	,	_	_	_
24	using	use	VBG	_	_	_
25	400	400	CD	_	_	_
26	U	U	NNP	_	_	_
27	T4	t4	NN	_	_	_
28	RNA	rna	NN	_	_	_
29	Ligase	ligase	NN	_	_	_
30	2	2	CD	_	_	_
31	,	,	,	_	_	_
32	Deletion	deletion	NN	_	_	_
33	Mutant	mutant	JJ	_	_	_
34	in	in	IN	_	_	_
35	the	the	DT	_	_	_
36	presence	presence	NN	_	_	_
37	of	of	IN	_	_	_
38	20	20	CD	_	_	_
39	%	%	NN	_	_	_
40	PEG-8000	peg-8000	NN	_	_	_
41	,	,	,	_	_	_
42	by	by	IN	_	_	_
43	incubation	incubation	NN	_	_	_
44	at	at	IN	_	_	_
45	25	25	CD	_	_	_
46	°C	°c	NN	_	_	_
47	for	for	IN	_	_	_
48	2	2	CD	_	_	_
49	hours	hour	NNS	_	_	_
50	.	.	.	_	_	_

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	40-150	40-150	CD	_	_	_
25	nt	nt	NNS	_	_	_
26	was	be	VBD	_	_	_
27	cut	cut	VBN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	corresponding	correspond	VBG	_	_	_
30	to	to	TO	_	_	_
31	truncated	truncate	VBN	_	_	_
32	cDNA	cdna	NN	_	_	_
33	products	product	NNS	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
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/μl	μg/μl	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	resuspended	resuspend	VBN	_	_	_
22	in	in	IN	_	_	_
23	8.25	8.25	CD	_	_	_
24	μl	μl	NN	_	_	_
25	nuclease-free	nuclease-free	JJ	_	_	_
26	water	water	NN	_	_	_
27	.	.	.	_	_	_

1	10	10	CD	_	_	_
2	pmol	pmol	NN	_	_	_
3	of	of	IN	_	_	_
4	a	a	DT	_	_	_
5	5	5	CD	_	_	_
6	'	'	''	_	_	_
7	-	-	:	_	_	_
8	phosphorilated	phosphorilate	VBN	_	_	_
9	adapter	adapter	NN	_	_	_
10	were	be	VBD	_	_	_
11	ligated	ligate	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	3	3	CD	_	_	_
15	'	'	''	_	_	_
16	-	-	:	_	_	_
17	OH	oh	NN	_	_	_
18	of	of	IN	_	_	_
19	cDNA	cdna	NN	_	_	_
20	fragments	fragment	NNS	_	_	_
21	in	in	IN	_	_	_
22	a	a	DT	_	_	_
23	final	final	JJ	_	_	_
24	reaction	reaction	NN	_	_	_
25	volume	volume	NN	_	_	_
26	of	of	IN	_	_	_
27	25	25	CD	_	_	_
28	μl	μl	NN	_	_	_
29	,	,	,	_	_	_
30	in	in	IN	_	_	_
31	the	the	DT	_	_	_
32	presence	presence	NN	_	_	_
33	of	of	IN	_	_	_
34	0.05	0.05	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	ATP	atp	NN	SUPP	_	_
37	,	,	,	_	_	_
38	20	20	CD	_	_	_
39	%	%	NN	_	_	_
40	PEG-4000	peg-4000	NN	_	_	_
41	,	,	,	_	_	_
42	and	and	CC	_	_	_
43	100	100	CD	_	_	_
44	U	U	NNP	_	_	_
45	CircLigase	CircLigase	NNP	_	_	_
46	™	™	NNP	_	_	_
47	II	II	NNP	_	_	_
48	ssDNA	ssDNA	NNP	_	_	_
49	Ligase	Ligase	NNP	_	_	_
50	,	,	,	_	_	_
51	by	by	IN	_	_	_
52	incubation	incubation	NN	_	_	_
53	at	at	IN	_	_	_
54	60	60	CD	_	_	_
55	°C	°c	NN	_	_	_
56	for	for	IN	_	_	_
57	4	4	CD	_	_	_
58	hours	hour	NNS	_	_	_
59	,	,	,	_	_	_
60	and	and	CC	_	_	_
61	68	68	CD	_	_	_
62	°C	°c	NN	_	_	_
63	for	for	IN	_	_	_
64	2	2	CD	_	_	_
65	hours	hour	NNS	_	_	_
66	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	fragments	fragment	NNS	_	_	_
4	were	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	from	from	IN	_	_	_
7	excess	excess	JJ	_	_	_
8	adapter	adapter	NN	_	_	_
9	using	use	VBG	_	_	_
10	1.8	1.8	CD	_	_	_
11	volumes	volume	NNS	_	_	_
12	of	of	IN	_	_	_
13	Agencourt	Agencourt	NNP	_	_	_
14	AMPure	AMPure	NNP	_	_	_
15	XP	xp	NN	_	_	_
16	beads	bead	NNS	_	_	_
17	,	,	,	_	_	_
18	following	follow	VBG	_	_	_
19	manufacturer	manufacturer	NN	_	_	_
20	's	's	POS	_	_	_
21	instructions	instruction	NNS	_	_	_
22	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	eluted	elute	VBN	_	_	_
4	in	in	IN	_	_	_
5	20	20	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	nuclease-free	nuclease-free	JJ	_	_	_
9	water	water	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	indexed	index	VBD	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	adapters	adapter	NNS	_	_	_
15	were	be	VBD	_	_	_
16	introduced	introduce	VBN	_	_	_
17	by	by	IN	_	_	_
18	15	15	CD	_	_	_
19	cycles	cycle	NNS	_	_	_
20	of	of	IN	_	_	_
21	PCR	pcr	NN	_	_	_
22	in	in	IN	_	_	_
23	the	the	DT	_	_	_
24	presence	presence	NN	_	_	_
25	of	of	IN	_	_	_
26	25	25	CD	_	_	_
27	pmol	pmol	NN	_	_	_
28	of	of	IN	_	_	_
29	each	each	DT	_	_	_
30	primer	primer	NN	_	_	_
31	,	,	,	_	_	_
32	and	and	CC	_	_	_
33	25	25	CD	_	_	_
34	μl	μl	NN	_	_	_
35	NEBNext	nebnext	NN	_	_	_
36	®	®	CD	_	_	_
37	High-Fidelity	high-fidelity	NN	_	_	_
38	2X	2x	NN	_	_	_
39	PCR	pcr	NN	_	_	_
40	Master	master	NN	_	_	_
41	Mix	Mix	NNP	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	30	30	CD	_	_	_
3	'	'	''	_	_	_
4	10	10	CD	_	_	_
5	ug/ml	ug/ml	JJ	_	_	_
6	indole	indole	NN	_	_	_
7	aa	aa	NN	_	_	_
8	,	,	,	_	_	_
9	minimal	minimal	JJ	_	_	_
10	medium	medium	NN	_	_	_
11	+	+	CC	_	_	_
12	0.2	0.2	CD	_	_	_
13	%	%	NN	_	_	_
14	glu	glu	NN	_	_	_
15	,	,	,	_	_	_
16	25	25	CD	_	_	_
17	ug	ug	NN	_	_	_
18	total	total	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	30	30	CD	_	_	_
21	'	'	''	_	_	_
22	15	15	CD	_	_	_
23	ug/ml	ug/ml	JJ	_	_	_
24	indole	indole	NN	_	_	_
25	aa	aa	NN	_	_	_
26	,	,	,	_	_	_
27	25	25	CD	_	_	_
28	ug	ug	NN	_	_	_
29	total	total	JJ	_	_	_
30	RNA	rna	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	30	30	CD	_	_	_
33	'	'	''	_	_	_
34	+50	+50	CD	_	_	_
35	ug/ml	ug/ml	JJ	_	_	_
36	Trp	trp	NN	_	_	_
37	vs	vs	CC	_	_	_
38	0	0	CD	_	_	_
39	'	'	''	_	_	_
40	in	in	IN	_	_	_
41	min	min	NN	_	_	_
42	med	med	VBD	_	_	_
43	+0.2	+0.2	CD	_	_	_
44	%	%	NN	_	_	_
45	glu	glu	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	30	30	CD	_	_	_
48	'	'	''	_	_	_
49	in	in	IN	_	_	_
50	minimal	minimal	JJ	_	_	_
51	medium	medium	NN	_	_	_
52	+0.2	+0.2	CD	_	_	_
53	%	%	NN	_	_	_
54	glu	glu	NN	_	_	_
55	,	,	,	_	_	_
56	25	25	CD	_	_	_
57	ug	ug	NN	_	_	_
58	total	total	JJ	_	_	_
59	RNA	rna	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	30	30	CD	_	_	_
62	'	'	''	_	_	_
63	in	in	IN	_	_	_
64	min	min	NN	_	_	_
65	med	med	VBD	_	_	_
66	+0.2	+0.2	CD	_	_	_
67	%	%	NN	_	_	_
68	glu	glu	NN	_	_	_
69	+50	+50	CD	_	_	_
70	ug/ml	ug/ml	JJ	_	_	_
71	Trp	trp	NN	_	_	_
72	,25	,25	CD	_	_	_
73	ug	ug	NN	_	_	_
74	tot	tot	NN	_	_	_
75	RNA	rna	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	30	30	CD	_	_	_
78	min	min	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	30	30	CD	_	_	_
81	min	min	NN	_	_	_
82	,	,	,	_	_	_
83	0.8	0.8	CD	_	_	_
84	%	%	NN	_	_	_
85	butanol	butanol	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	30min-1	30min-1	JJ	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	30min-2	30min-2	JJ	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	30min-3	30min-3	JJ	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	30	30	CD	_	_	_
94	min	min	NN	_	_	_
95	minus	minus	CC	_	_	_
96	ciprofloxacin	ciprofloxacin	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	30	30	CD	_	_	_
99	min	min	NN	_	_	_
100	plus	plus	CC	_	_	_
101	ciprofloxacin	ciprofloxacin	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	30	30	CD	_	_	_
104	min	min	NN	_	_	_
105	,	,	,	_	_	_
106	unstressed	unstressed	JJ	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	30mM	30mm	NN	_	_	_
109	SCFA	scfa	NN	_	_	_
110	replicate	replicate	VBP	_	_	_
111	1	1	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	30mM	30mm	NN	_	_	_
114	SCFA	scfa	NN	_	_	_
115	replicate	replicate	VBP	_	_	_
116	2	2	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
118	30mM	30mm	NN	_	_	_
119	SCFA	scfa	NN	_	_	_
120	replicate	replicate	VBP	_	_	_
121	3	3	CD	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	30mM	30mm	NN	_	_	_
124	SCFA	scfa	NN	_	_	_
125	replicate	replicate	VB	_	_	_
126	4	4	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
128	30	30	CD	_	_	_
129	'	'	''	_	_	_
130	vs	vs	CC	_	_	_
131	0	0	CD	_	_	_
132	'	'	''	_	_	_
133	in	in	IN	_	_	_
134	minimal	minimal	JJ	_	_	_
135	medium	medium	NN	_	_	_
136	+0.2	+0.2	CD	_	_	_
137	%	%	NN	_	_	_
138	glu	glu	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	31	31	CD	_	_	_
141	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav104.nIND.nHUS	olav104.nind.nhus	JJ	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	32D	32d	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	32	32	CD	_	_	_
7	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav104.IND.nHUS	olav104.ind.nhus	JJ	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	33D	33d	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	33	33	CD	_	_	_
7	.	.	.	_	_	_

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	35381	35381	CD	_	_	_
5	_	_	SYM	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	35382	35382	CD	_	_	_
9	_	_	NN	_	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	35B	35b	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	3.5	3.5	CD	_	_	_
15	hour	hour	NN	_	_	_
16	expression	expression	NN	_	_	_
17	of	of	IN	_	_	_
18	synthetic	synthetic	JJ	_	_	_
19	protein	protein	NN	_	_	_
20	DX	dx	NN	_	_	_
21	in	in	IN	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	35	35	CD	_	_	_
26	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav172.nIND.nHUS	olav172.nind.nhus	JJ	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	360	360	CD	_	_	_
5	minutes	minute	NNS	_	_	_
6	growth	growth	NN	_	_	_
7	in	in	IN	_	_	_
8	LB	LB	NNP	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	37	37	CD	_	_	_
11	.	.	.	_	_	_

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	39A1	39a1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	39B1	39b1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	39C1	39c1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	39	39	CD	_	_	_
11	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav178.nIND.nHUS	Olav178.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	3A	3a	NN	_	_	_
5	1m	1m	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	3A	3a	NN	_	_	_
8	1y	1y	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	3A	3a	NN	_	_	_
11	4y	4y	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	3a	3a	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

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	\	\	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	3A	3a	NN	_	_	_
26	_	_	CD	_	_	_
27	MG	mg	NN	_	_	_
28	_	_	NN	_	_	_
29	t30	t30	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	3b	3b	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

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/REF	intensity/ref	NN	_	_	_
34	_	_	CD	_	_	_
35	MEDIAN	MEDIAN	NNP	_	_	_
36	_	_	CD	_	_	_
37	INTENSITY	intensity	NN	_	_	_
38	to	to	TO	_	_	_
39	VALUE	VALUE	NNP	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	3B	3b	NN	_	_	_
42	_	_	CD	_	_	_
43	MG	mg	NN	_	_	_
44	_	_	NN	_	_	_
45	t30	t30	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	3	3	CD	_	_	_
48	.	.	.	_	_	_

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/Query	reference/query	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	from	from	IN	_	_	_
11	the	the	DT	_	_	_
12	normalized	normalize	VBN	_	_	_
13	.	.	.	_	_	_

1	mev	mev	NN	_	_	_
2	file	file	NN	_	_	_
3	:	:	:	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	3c	3c	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	.	.	.	_	_	_

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/REF	intensity/ref	NN	_	_	_
17	_	_	CD	_	_	_
18	MEDIAN	MEDIAN	NNP	_	_	_
19	_	_	CD	_	_	_
20	INTENSITY	intensity	NN	_	_	_
21	to	to	TO	_	_	_
22	VALUE	VALUE	NNP	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	3C	3c	NN	_	_	_
3	_	_	CD	_	_	_
4	MG	mg	NN	_	_	_
5	_	_	NN	_	_	_
6	t30	t30	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	3C-seq	3c-seq	NN	_	_	_
9	:	:	:	_	_	_
10	5	5	CD	_	_	_
11	µg	µg	NN	_	_	_
12	of	of	IN	_	_	_
13	a	a	DT	_	_	_
14	3C	3c	NN	_	_	_
15	library	library	NN	_	_	_
16	was	be	VBD	_	_	_
17	suspended	suspend	VBN	_	_	_
18	in	in	IN	_	_	_
19	water	water	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	final	final	JJ	_	_	_
22	volume	volume	NN	_	_	_
23	130	130	CD	_	_	_
24	µL	µl	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	sheared	shear	VBD	_	_	_
28	using	use	VBG	_	_	_
29	a	a	DT	_	_	_
30	Covaris	Covaris	NNP	_	_	_
31	S220	s220	NN	_	_	_
32	instrument	instrument	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Duty	duty	NN	_	_	_
35	cycle	cycle	NN	_	_	_
36	5	5	CD	_	_	_
37	,	,	,	_	_	_
38	Intensity	intensity	NN	_	_	_
39	5	5	CD	_	_	_
40	,	,	,	_	_	_
41	cycles/burst	cycles/burst	NN	_	_	_
42	200	200	CD	_	_	_
43	,	,	,	_	_	_
44	time	time	NN	_	_	_
45	60	60	CD	_	_	_
46	sec	sec	NN	_	_	_
47	for	for	IN	_	_	_
48	4	4	CD	_	_	_
49	cycles	cycle	NNS	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	and	and	CC	_	_	_
6	processed	process	VBN	_	_	_
7	according	accord	VBG	_	_	_
8	to	to	TO	_	_	_
9	manufacturer	manufacturer	NN	_	_	_
10	instructions	instruction	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Paired-End	paired-end	NN	_	_	_
13	DNA	dna	NN	_	_	_
14	sample	sample	NN	_	_	_
15	Prep	Prep	NNP	_	_	_
16	Kit	kit	NN	_	_	_
17	--	--	:	_	_	_
18	Illumina	Illumina	NNP	_	_	_
19	--	--	:	_	_	_
20	PE-930-1001	pe-930-1001	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	except	except	IN	_	_	_
24	that	that	DT	_	_	_
25	DNA	dna	NN	_	_	_
26	was	be	VBD	_	_	_
27	ligated	ligate	VBN	_	_	_
28	to	to	TO	_	_	_
29	custom-made	custom-made	JJ	_	_	_
30	adapters	adapter	NNS	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	see	see	VB	_	_	_
33	Marbouty	Marbouty	NNP	_	_	_
34	M.	M.	NNP	_	_	_
35	et	et	NNP	_	_	_
36	al	al	NNP	_	_	_
37	,	,	,	_	_	_
38	2015	2015	CD	_	_	_
39	,	,	,	_	_	_
40	Mol	Mol	NNP	_	_	_
41	Cell	cell	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	for	for	IN	_	_	_
44	4	4	CD	_	_	_
45	hours	hour	NNS	_	_	_
46	at	at	IN	_	_	_
47	room	room	NN	_	_	_
48	temperature	temperature	NN	_	_	_
49	.	.	.	_	_	_

1	Tubes	tube	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	65	65	CD	_	_	_
7	°C	°c	NN	_	_	_
8	for	for	IN	_	_	_
9	20	20	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	fragments	fragment	NNS	_	_	_
3	ranging	range	VBG	_	_	_
4	in	in	IN	_	_	_
5	size	size	NN	_	_	_
6	from	from	IN	_	_	_
7	400	400	CD	_	_	_
8	to	to	TO	_	_	_
9	900	900	CD	_	_	_
10	pb	pb	NN	_	_	_
11	were	be	VBD	_	_	_
12	purified	purify	VBN	_	_	_
13	using	use	VBG	_	_	_
14	a	a	DT	_	_	_
15	PippinPrep	PippinPrep	NNP	_	_	_
16	apparatus	apparatus	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	SAGE	sage	NN	_	_	_
19	Science	science	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	library	library	NN	_	_	_
4	,	,	,	_	_	_
5	four	four	CD	_	_	_
6	test	test	NN	_	_	_
7	PCR	pcr	NN	_	_	_
8	reactions	reaction	NNS	_	_	_
9	were	be	VBD	_	_	_
10	performed	perform	VBN	_	_	_
11	to	to	TO	_	_	_
12	determine	determine	VB	_	_	_
13	the	the	DT	_	_	_
14	optimal	optimal	JJ	_	_	_
15	number	number	NN	_	_	_
16	of	of	IN	_	_	_
17	PCR	pcr	NN	_	_	_
18	cycles	cycle	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	1	1	CD	_	_	_
21	or	or	CC	_	_	_
22	2	2	CD	_	_	_
23	µL	µl	NN	_	_	_
24	of	of	IN	_	_	_
25	the	the	DT	_	_	_
26	collected	collect	VBN	_	_	_
27	DNA	dna	NN	_	_	_
28	,	,	,	_	_	_
29	Illumina	Illumina	NNP	_	_	_
30	primers	primer	NNS	_	_	_
31	PE1	pe1	NN	_	_	_
32	.0	.0	NN	_	_	_
33	and	and	CC	_	_	_
34	PE2	pe2	NN	_	_	_
35	.0	.0	CD	_	_	_
36	using	use	VBG	_	_	_
37	Taq	taq	NN	_	_	_
38	Phusion	phusion	NN	_	_	_
39	-LSB-	-lsb-	-LRB-	_	_	_
40	Finnzymes	finnzyme	NNS	_	_	_
41	-RSB-	-rsb-	-RRB-	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	large-scale	large-scale	JJ	_	_	_
3	PCR	pcr	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	8	8	CD	_	_	_
6	reactions	reaction	NNS	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	then	then	RB	_	_	_
10	set-up	set-up	JJ	_	_	_
11	with	with	IN	_	_	_
12	the	the	DT	_	_	_
13	number	number	NN	_	_	_
14	of	of	IN	_	_	_
15	PCR	pcr	NN	_	_	_
16	cycles	cycle	NNS	_	_	_
17	determined	determine	VBN	_	_	_
18	previously	previously	RB	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	PCR	pcr	NN	_	_	_
3	product	product	NN	_	_	_
4	was	be	VBD	_	_	_
5	finally	finally	RB	_	_	_
6	purified	purify	VBN	_	_	_
7	on	on	IN	_	_	_
8	Qiagen	Qiagen	NNP	_	_	_
9	MinElute	MinElute	NNP	_	_	_
10	columns	column	NNS	_	_	_
11	and	and	CC	_	_	_
12	subject	subject	JJ	_	_	_
13	to	to	TO	_	_	_
14	paired-end	paired-end	NN	_	_	_
15	sequenced	sequence	VBN	_	_	_
16	on	on	IN	_	_	_
17	an	a	DT	_	_	_
18	Illumina	Illumina	NNP	_	_	_
19	sequencer	sequencer	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	3C-seq	3c-seq	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	proccessed	proccess	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	3C-seq	3c-seq	JJ	_	_	_
9	pipeline	pipeline	NN	_	_	_
10	available	available	JJ	_	_	_
11	at	at	IN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	https://github.com/koszullab/	https://github.com/koszullab/	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	3C-seq	3c-seq	NN	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	fis	fis	NN	GEN	_	_
7	cells	cell	NNS	_	_	_
8	in	in	IN	_	_	_
9	exponential	exponential	JJ	GrowthPhase	_	_
10	phase	phase	NN	GrowthPhase	_	_
11	30	30	CD	_	_	_
12	°C	°c	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	3C-seq	3c-seq	NN	_	_	_
15	of	of	IN	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	fis	fis	NN	GEN	_	_
19	cells	cell	NNS	_	_	_
20	in	in	IN	_	_	_
21	exponential	exponential	JJ	GrowthPhase	_	_
22	phase	phase	NN	GrowthPhase	_	_
23	30	30	CD	_	_	_
24	°C	°c	NN	_	_	_
25	-	-	:	_	_	_
26	Replicate	replicate	VB	_	_	_
27	1	1	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	3C-seq	3c-seq	NN	_	_	_
30	of	of	IN	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	hns	hns	NN	GEN	_	_
34	cells	cell	NNS	_	_	_
35	in	in	IN	_	_	_
36	exponential	exponential	JJ	GrowthPhase	_	_
37	phase	phase	NN	GrowthPhase	_	_
38	30	30	CD	_	_	_
39	°C	°c	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	3C-seq	3c-seq	NN	_	_	_
42	of	of	IN	_	_	_
43	E.	e.	FW	_	_	_
44	coli	coli	FW	_	_	_
45	hns	hns	NN	GEN	_	_
46	cells	cell	NNS	_	_	_
47	in	in	IN	_	_	_
48	exponential	exponential	JJ	GrowthPhase	_	_
49	phase	phase	NN	GrowthPhase	_	_
50	30	30	CD	_	_	_
51	°C	°c	NN	_	_	_
52	-	-	:	_	_	_
53	Replicate	replicate	VB	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	3C-seq	3c-seq	NN	_	_	_
57	of	of	IN	_	_	_
58	E.	e.	FW	_	_	_
59	coli	coli	FW	_	_	_
60	hupAB	hupab	NN	_	_	_
61	cells	cell	NNS	_	_	_
62	in	in	IN	_	_	_
63	exponential	exponential	JJ	GrowthPhase	_	_
64	phase	phase	NN	GrowthPhase	_	_
65	37	37	CD	_	_	_
66	°C	°c	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	3C-seq	3c-seq	NN	_	_	_
69	of	of	IN	_	_	_
70	E.	e.	FW	_	_	_
71	coli	coli	FW	_	_	_
72	hupAB	hupab	NN	_	_	_
73	cells	cell	NNS	_	_	_
74	in	in	IN	_	_	_
75	exponential	exponential	JJ	GrowthPhase	_	_
76	phase	phase	NN	GrowthPhase	_	_
77	37	37	CD	_	_	_
78	°C	°c	SYM	_	_	_
79	-	-	:	_	_	_
80	Replicate	replicate	VB	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	3C-seq	3c-seq	NN	_	_	_
84	of	of	IN	_	_	_
85	E.	e.	FW	_	_	_
86	coli	coli	FW	_	_	_
87	matP	matp	NN	GEN	_	_
88	cells	cell	NNS	_	_	_
89	in	in	IN	_	_	_
90	exponential	exponential	JJ	GrowthPhase	_	_
91	phase	phase	NN	GrowthPhase	_	_
92	22	22	CD	_	_	_
93	°C	°c	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	3C-seq	3c-seq	NN	_	_	_
96	of	of	IN	_	_	_
97	E.	e.	FW	_	_	_
98	coli	coli	FW	_	_	_
99	matP	matp	NN	GEN	_	_
100	cells	cell	NNS	_	_	_
101	in	in	IN	_	_	_
102	exponential	exponential	JJ	GrowthPhase	_	_
103	phase	phase	NN	GrowthPhase	_	_
104	30	30	CD	_	_	_
105	°C	°c	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	3C-seq	3c-seq	NN	_	_	_
108	of	of	IN	_	_	_
109	E.	e.	FW	_	_	_
110	coli	coli	FW	_	_	_
111	matP	matp	NN	GEN	_	_
112	cells	cell	NNS	_	_	_
113	in	in	IN	_	_	_
114	exponential	exponential	JJ	GrowthPhase	_	_
115	phase	phase	NN	GrowthPhase	_	_
116	30	30	CD	_	_	_
117	°C	°c	NN	_	_	_
118	-	-	:	_	_	_
119	Replicate	replicate	VB	_	_	_
120	1	1	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	3C-seq	3c-seq	NN	_	_	_
123	of	of	IN	_	_	_
124	E.	e.	FW	_	_	_
125	coli	coli	FW	_	_	_
126	matPDC20	matpdc20	NN	_	_	_
127	cells	cell	NNS	_	_	_
128	harbouring	harbour	VBG	_	_	_
129	plasmid	plasmid	NN	_	_	_
130	pGBM2-5xmatS	pgbm2-5xmats	NN	_	_	_
131	in	in	IN	_	_	_
132	exponential	exponential	JJ	GrowthPhase	_	_
133	phase	phase	NN	GrowthPhase	_	_
134	30	30	CD	_	_	_
135	°C	°c	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	3C-seq	3c-seq	NN	_	_	_
138	of	of	IN	_	_	_
139	E.	e.	FW	_	_	_
140	coli	coli	FW	_	_	_
141	matPDC20	matpdc20	NN	_	_	_
142	cells	cell	NNS	_	_	_
143	harbouring	harbour	VBG	_	_	_
144	plasmid	plasmid	NN	_	_	_
145	pGBM2	pgbm2	NN	_	_	_
146	in	in	IN	_	_	_
147	exponential	exponential	JJ	GrowthPhase	_	_
148	phase	phase	NN	GrowthPhase	_	_
149	30	30	CD	_	_	_
150	°C	°c	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	3C-seq	3c-seq	NN	_	_	_
153	of	of	IN	_	_	_
154	E.	e.	FW	_	_	_
155	coli	coli	FW	_	_	_
156	matPDC20	matpdc20	NN	_	_	_
157	cells	cell	NNS	_	_	_
158	in	in	IN	_	_	_
159	exponential	exponential	JJ	GrowthPhase	_	_
160	phase	phase	NN	GrowthPhase	_	_
161	30	30	CD	_	_	_
162	°C	°c	NN	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	3C-seq	3c-seq	NN	_	_	_
165	of	of	IN	_	_	_
166	E.	e.	FW	_	_	_
167	coli	coli	FW	_	_	_
168	mukB	mukb	NN	GEN	_	_
169	cells	cell	NNS	_	_	_
170	in	in	IN	_	_	_
171	exponential	exponential	JJ	GrowthPhase	_	_
172	phase	phase	NN	GrowthPhase	_	_
173	22	22	CD	_	_	_
174	°C	°c	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	3C-seq	3c-seq	NN	_	_	_
177	of	of	IN	_	_	_
178	E.	e.	FW	_	_	_
179	coli	coli	FW	_	_	_
180	mukB	mukb	NN	GEN	_	_
181	cells	cell	NNS	_	_	_
182	in	in	IN	_	_	_
183	exponential	exponential	JJ	GrowthPhase	_	_
184	phase	phase	NN	GrowthPhase	_	_
185	22	22	CD	_	_	_
186	°C	°c	NN	_	_	_
187	-	-	:	_	_	_
188	Replicate	replicate	VB	_	_	_
189	1	1	CD	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	3C-seq	3c-seq	NN	_	_	_
192	of	of	IN	_	_	_
193	E.	e.	FW	_	_	_
194	coli	coli	FW	_	_	_
195	mukBmatP	mukbmatp	NN	_	_	_
196	cells	cell	NNS	_	_	_
197	in	in	IN	_	_	_
198	exponential	exponential	JJ	GrowthPhase	_	_
199	phase	phase	NN	GrowthPhase	_	_
200	22	22	CD	_	_	_
201	°C	°c	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	3C-seq	3c-seq	NN	_	_	_
204	of	of	IN	_	_	_
205	E.	e.	FW	_	_	_
206	coli	coli	FW	_	_	_
207	wt	wt	JJ	_	_	_
208	cells	cell	NNS	_	_	_
209	harbouring	harbour	VBG	_	_	_
210	plasmid	plasmid	NN	_	_	_
211	pGBM2-5xmatS	pgbm2-5xmats	NN	_	_	_
212	in	in	IN	_	_	_
213	exponential	exponential	JJ	GrowthPhase	_	_
214	phase	phase	NN	GrowthPhase	_	_
215	30	30	CD	_	_	_
216	°C	°c	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	3C-seq	3c-seq	NN	_	_	_
219	of	of	IN	_	_	_
220	E.	e.	FW	_	_	_
221	coli	coli	FW	_	_	_
222	wt	wt	JJ	_	_	_
223	cells	cell	NNS	_	_	_
224	harbouring	harbour	VBG	_	_	_
225	plasmid	plasmid	NN	_	_	_
226	pGBM2-5xmatS	pgbm2-5xmats	NN	_	_	_
227	in	in	IN	_	_	_
228	exponential	exponential	JJ	GrowthPhase	_	_
229	phase	phase	NN	GrowthPhase	_	_
230	30	30	CD	_	_	_
231	°C	°c	NN	_	_	_
232	-	-	:	_	_	_
233	Replicate	replicate	VB	_	_	_
234	1	1	CD	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	3C-seq	3c-seq	NN	_	_	_
237	of	of	IN	_	_	_
238	E.	e.	FW	_	_	_
239	coli	coli	FW	_	_	_
240	wt	wt	JJ	_	_	_
241	cells	cell	NNS	_	_	_
242	harbouring	harbour	VBG	_	_	_
243	plasmid	plasmid	NN	_	_	_
244	pGBM2	pgbm2	NN	_	_	_
245	in	in	IN	_	_	_
246	exponential	exponential	JJ	GrowthPhase	_	_
247	phase	phase	NN	GrowthPhase	_	_
248	30	30	CD	_	_	_
249	°C	°c	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	3C-seq	3c-seq	NN	_	_	_
252	of	of	IN	_	_	_
253	E.	e.	FW	_	_	_
254	coli	coli	FW	_	_	_
255	wt	wt	JJ	_	_	_
256	cells	cell	NNS	_	_	_
257	harbouring	harbour	VBG	_	_	_
258	plasmid	plasmid	NN	_	_	_
259	pGBM2	pgbm2	NN	_	_	_
260	in	in	IN	_	_	_
261	exponential	exponential	JJ	GrowthPhase	_	_
262	phase	phase	NN	GrowthPhase	_	_
263	30	30	CD	_	_	_
264	°C	°c	NN	_	_	_
265	-	-	:	_	_	_
266	Replicate	replicate	VB	_	_	_
267	1	1	CD	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	3C-seq	3c-seq	NN	_	_	_
270	of	of	IN	_	_	_
271	E.	e.	FW	_	_	_
272	coli	coli	FW	_	_	_
273	wt	wt	JJ	_	_	_
274	cells	cell	NNS	_	_	_
275	in	in	IN	_	_	_
276	exponential	exponential	JJ	GrowthPhase	_	_
277	phase	phase	NN	GrowthPhase	_	_
278	22	22	CD	_	_	_
279	°C	°c	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	3C-seq	3c-seq	NN	_	_	_
282	of	of	IN	_	_	_
283	E.	e.	FW	_	_	_
284	coli	coli	FW	_	_	_
285	wt	wt	JJ	_	_	_
286	cells	cell	NNS	_	_	_
287	in	in	IN	_	_	_
288	exponential	exponential	JJ	GrowthPhase	_	_
289	phase	phase	NN	GrowthPhase	_	_
290	22	22	CD	_	_	_
291	°C	°c	NN	_	_	_
292	-	-	:	_	_	_
293	Replicate	replicate	VB	_	_	_
294	1	1	CD	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	3C-seq	3c-seq	NN	_	_	_
297	of	of	IN	_	_	_
298	E.	e.	FW	_	_	_
299	coli	coli	FW	_	_	_
300	wt	wt	JJ	_	_	_
301	cells	cell	NNS	_	_	_
302	in	in	IN	_	_	_
303	exponential	exponential	JJ	GrowthPhase	_	_
304	phase	phase	NN	GrowthPhase	_	_
305	30	30	CD	_	_	_
306	°C	°c	NN	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	3C-seq	3c-seq	NN	_	_	_
309	of	of	IN	_	_	_
310	E.	e.	FW	_	_	_
311	coli	coli	FW	_	_	_
312	wt	wt	JJ	_	_	_
313	cells	cell	NNS	_	_	_
314	in	in	IN	_	_	_
315	exponential	exponential	JJ	GrowthPhase	_	_
316	phase	phase	NN	GrowthPhase	_	_
317	30	30	CD	_	_	_
318	°C	°c	NN	_	_	_
319	-	-	:	_	_	_
320	Replicate	replicate	VB	_	_	_
321	1	1	CD	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	3C-seq	3c-seq	NN	_	_	_
324	of	of	IN	_	_	_
325	E.	e.	FW	_	_	_
326	coli	coli	FW	_	_	_
327	wt	wt	JJ	_	_	_
328	cells	cell	NNS	_	_	_
329	in	in	IN	_	_	_
330	exponential	exponential	JJ	GrowthPhase	_	_
331	phase	phase	NN	GrowthPhase	_	_
332	30	30	CD	_	_	_
333	°C	°c	NN	_	_	_
334	-	-	:	_	_	_
335	Replicate	replicate	VB	_	_	_
336	2	2	CD	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
338	3C-seq	3c-seq	NN	_	_	_
339	of	of	IN	_	_	_
340	E.	e.	FW	_	_	_
341	coli	coli	FW	_	_	_
342	wt	wt	JJ	_	_	_
343	cells	cell	NNS	_	_	_
344	in	in	IN	_	_	_
345	exponential	exponential	JJ	GrowthPhase	_	_
346	phase	phase	NN	GrowthPhase	_	_
347	37	37	CD	_	_	_
348	°C	°c	NN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	3C-seq	3c-seq	NN	_	_	_
351	of	of	IN	_	_	_
352	E.	e.	FW	_	_	_
353	coli	coli	FW	_	_	_
354	wt	wt	JJ	_	_	_
355	cells	cell	NNS	_	_	_
356	in	in	IN	_	_	_
357	exponential	exponential	JJ	GrowthPhase	_	_
358	phase	phase	NN	GrowthPhase	_	_
359	37	37	CD	_	_	_
360	°C	°c	SYM	_	_	_
361	-	-	:	_	_	_
362	Replicate	replicate	VB	_	_	_
363	1	1	CD	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	3C-seq	3c-seq	NN	_	_	_
366	of	of	IN	_	_	_
367	E.	e.	FW	_	_	_
368	coli	coli	FW	_	_	_
369	wt	wt	JJ	_	_	_
370	cells	cell	NNS	_	_	_
371	in	in	IN	_	_	_
372	exponential	exponential	JJ	GrowthPhase	_	_
373	phase	phase	NN	GrowthPhase	_	_
374	LB	lb	NN	_	_	_
375	30	30	CD	_	_	_
376	°C	°c	NN	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	3C-seq	3c-seq	NN	_	_	_
379	of	of	IN	_	_	_
380	E.	e.	FW	_	_	_
381	coli	coli	FW	_	_	_
382	wt	wt	JJ	_	_	_
383	cells	cell	NNS	_	_	_
384	in	in	IN	_	_	_
385	exponential	exponential	JJ	GrowthPhase	_	_
386	phase	phase	NN	GrowthPhase	_	_
387	LB	lb	NN	_	_	_
388	30	30	CD	_	_	_
389	°C	°c	NN	_	_	_
390	-	-	:	_	_	_
391	Replicate	replicate	VB	_	_	_
392	1	1	CD	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	3C-seq	3c-seq	NN	_	_	_
395	of	of	IN	_	_	_
396	E.	e.	FW	_	_	_
397	coli	coli	FW	_	_	_
398	wt	wt	JJ	_	_	_
399	cells	cell	NNS	_	_	_
400	in	in	IN	_	_	_
401	stationary	stationary	JJ	GrowthPhase	_	_
402	phase	phase	NN	GrowthPhase	_	_
403	30	30	CD	_	_	_
404	°C	°c	NN	_	_	_
405	-LRB-	-lrb-	-LRB-	_	_	_
406	30h	30h	NN	_	_	_
407	-RRB-	-rrb-	-RRB-	_	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	3C-seq	3c-seq	NN	_	_	_
410	of	of	IN	_	_	_
411	E.	e.	FW	_	_	_
412	coli	coli	FW	_	_	_
413	wt	wt	JJ	_	_	_
414	cells	cell	NNS	_	_	_
415	in	in	IN	_	_	_
416	stationary	stationary	JJ	GrowthPhase	_	_
417	phase	phase	NN	GrowthPhase	_	_
418	30	30	CD	_	_	_
419	°C	°c	NN	_	_	_
420	-LRB-	-lrb-	-LRB-	_	_	_
421	30h	30h	NN	_	_	_
422	-RRB-	-rrb-	-RRB-	_	_	_
423	-	-	:	_	_	_
424	Replicate	replicate	VB	_	_	_
425	1	1	CD	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	3C-seq	3c-seq	NN	_	_	_
428	of	of	IN	_	_	_
429	E.	e.	FW	_	_	_
430	coli	coli	FW	_	_	_
431	zapB	zapb	NN	GEN	_	_
432	cells	cell	NNS	_	_	_
433	harbouring	harbour	VBG	_	_	_
434	plasmid	plasmid	NN	_	_	_
435	pGBM2-5xmatS	pgbm2-5xmats	NN	_	_	_
436	in	in	IN	_	_	_
437	exponential	exponential	JJ	GrowthPhase	_	_
438	phase	phase	NN	GrowthPhase	_	_
439	30	30	CD	_	_	_
440	°C	°c	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	3C-seq	3c-seq	NN	_	_	_
443	of	of	IN	_	_	_
444	E.	e.	FW	_	_	_
445	coli	coli	FW	_	_	_
446	zapB	zapb	NN	GEN	_	_
447	cells	cell	NNS	_	_	_
448	harbouring	harbour	VBG	_	_	_
449	plasmid	plasmid	NN	_	_	_
450	pGBM2	pgbm2	NN	_	_	_
451	in	in	IN	_	_	_
452	exponential	exponential	JJ	GrowthPhase	_	_
453	phase	phase	NN	GrowthPhase	_	_
454	30	30	CD	_	_	_
455	°C	°c	NN	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	3C-seq	3c-seq	NN	_	_	_
458	of	of	IN	_	_	_
459	E.	e.	FW	_	_	_
460	coli	coli	FW	_	_	_
461	zapB	zapb	NN	GEN	_	_
462	cells	cell	NNS	_	_	_
463	in	in	IN	_	_	_
464	exponential	exponential	JJ	GrowthPhase	_	_
465	phase	phase	NN	GrowthPhase	_	_
466	30	30	CD	_	_	_
467	°C	°c	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	3	3	CD	_	_	_
470	'	'	''	_	_	_
471	-	-	:	_	_	_
472	end	end	NN	_	_	_
473	RNA-seq	rna-seq	NN	_	_	_
474	,	,	,	_	_	_
475	Cytosolic	cytosolic	JJ	_	_	_
476	fraction	fraction	NN	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	3	3	CD	_	_	_
479	'	'	''	_	_	_
480	-	-	:	_	_	_
481	end	end	NN	_	_	_
482	RNA-seq	rna-seq	NN	_	_	_
483	,	,	,	_	_	_
484	Cytosolic	cytosolic	JJ	_	_	_
485	fraction	fraction	NN	_	_	_
486	,	,	,	_	_	_
487	Replicate	replicate	VB	_	_	_
488	#	#	#	_	_	_
489	1	1	CD	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	3	3	CD	_	_	_
492	'	'	''	_	_	_
493	-	-	:	_	_	_
494	end	end	NN	_	_	_
495	RNA-seq	rna-seq	NN	_	_	_
496	,	,	,	_	_	_
497	Cytosolic	cytosolic	JJ	_	_	_
498	fraction	fraction	NN	_	_	_
499	,	,	,	_	_	_
500	Replicate	replicate	VB	_	_	_
501	#	#	#	_	_	_
502	2	2	CD	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	3	3	CD	_	_	_
505	'	'	''	_	_	_
506	-	-	:	_	_	_
507	end	end	NN	_	_	_
508	RNA-seq	rna-seq	NN	_	_	_
509	,	,	,	_	_	_
510	Nucleoid	nucleoid	NN	_	_	_
511	fraction	fraction	NN	_	_	_
512	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
513	3	3	CD	_	_	_
514	'	'	''	_	_	_
515	-	-	:	_	_	_
516	end	end	NN	_	_	_
517	RNA-seq	rna-seq	NN	_	_	_
518	,	,	,	_	_	_
519	Nucleoid	nucleoid	NN	_	_	_
520	fraction	fraction	NN	_	_	_
521	,	,	,	_	_	_
522	Replicate	replicate	VB	_	_	_
523	#	#	#	_	_	_
524	1	1	CD	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	3	3	CD	_	_	_
527	'	'	''	_	_	_
528	-	-	:	_	_	_
529	end	end	NN	_	_	_
530	RNA-seq	rna-seq	NN	_	_	_
531	,	,	,	_	_	_
532	Nucleoid	nucleoid	NN	_	_	_
533	fraction	fraction	NN	_	_	_
534	,	,	,	_	_	_
535	Replicate	replicate	VB	_	_	_
536	#	#	#	_	_	_
537	2	2	CD	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
539	3	3	CD	_	_	_
540	_	_	NN	_	_	_
541	ESBL019	esbl019	NN	_	_	_
542	Transition	transition	NN	_	_	_
543	Repl	repl	NN	_	_	_
544	1	1	CD	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	3	3	CD	_	_	_
547	.	.	.	_	_	_

1	FHI6.nIND.HUS	fhi6.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	3	3	CD	_	_	_
4	_	_	NN	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	LP	lp	NN	_	_	_
8	_	_	CD	_	_	_
9	noDP	nodp	NN	_	_	_
10	_	_	CD	_	_	_
11	noRh	norh	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	COPRO-Seq	copro-seq	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	3	3	CD	_	_	_
17	hour	hour	NN	_	_	_
18	expression	expression	NN	_	_	_
19	of	of	IN	_	_	_
20	synthetic	synthetic	JJ	_	_	_
21	protein	protein	NN	_	_	_
22	DX	dx	NN	_	_	_
23	in	in	IN	_	_	_
24	E.	e.	FW	_	_	_
25	coli	coli	FW	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	3-HT873-PA3	3-ht873-pa3	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	3-HT873-PA3	3-ht873-pa3	NN	_	_	_
30	-	-	:	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	3	3	CD	_	_	_
33	.	.	.	_	_	_

1	Log	log	VB	_	_	_
2	transformation	transformation	NN	_	_	_
3	:	:	:	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	3	3	CD	_	_	_
6	'	'	''	_	_	_
7	RNA	rna	NN	_	_	_
8	Decay	decay	NN	_	_	_
9	N-RNaseE	n-rnasee	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	BZ453	bz453	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	in	in	IN	_	_	_
14	M9	m9	NN	_	_	_
15	+	+	CC	_	_	_
16	0.2	0.2	CD	_	_	_
17	%	%	NN	_	_	_
18	Glycerol	glycerol	NN	_	_	_
19	,	,	,	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	Tryptone	tryptone	NN	_	_	_
23	at	at	IN	_	_	_
24	30	30	CD	_	_	_
25	C	c	NN	_	_	_
26	Mid	Mid	NNP	_	_	_
27	Log	Log	NNP	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	3	3	CD	_	_	_
30	'	'	''	_	_	_
31	RNA	rna	NN	_	_	_
32	Decay	decay	NN	_	_	_
33	N-RNaseE	n-rnasee	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	BZ453	bz453	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	in	in	IN	_	_	_
38	M9	m9	NN	_	_	_
39	+	+	CC	_	_	_
40	0.2	0.2	CD	_	_	_
41	%	%	NN	_	_	_
42	Glycerol	glycerol	NN	_	_	_
43	,	,	,	_	_	_
44	0.2	0.2	CD	_	_	_
45	%	%	NN	_	_	_
46	Tryptone	tryptone	NN	_	_	_
47	at	at	IN	_	_	_
48	30	30	CD	_	_	_
49	C	c	NN	_	_	_
50	Mid	Mid	NNP	_	_	_
51	Log	Log	NNP	_	_	_
52	1	1	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	3	3	CD	_	_	_
55	'	'	''	_	_	_
56	RNA	rna	NN	_	_	_
57	Decay	decay	NN	_	_	_
58	of	of	IN	_	_	_
59	Eno	Eno	NNP	_	_	_
60	-	-	:	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	DF261	df261	NN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	in	in	IN	_	_	_
65	M9	m9	NN	_	_	_
66	0.2	0.2	CD	_	_	_
67	%	%	NN	_	_	_
68	Glycerol	glycerol	NN	_	_	_
69	0.2	0.2	CD	_	_	_
70	%	%	NN	_	_	_
71	Tryptone	tryptone	NN	_	_	_
72	40	40	CD	_	_	_
73	mM	mm	NN	KWSUPP	_	_
74	Suc	suc	NN	_	_	_
75	.	.	.	_	_	_

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	3XSCOTS	3xscots	CD	_	_	_
84	cDNA	cdna	NN	_	_	_
85	24	24	CD	_	_	_
86	h	h	NN	_	_	_
87	post-infection	post-infection	JJ	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	3XSCOTS	3xscot	NNS	_	_	_
90	cDNA	cdna	NN	_	_	_
91	in	in	IN	_	_	_
92	RPMI	rpmi	NN	_	_	_
93	medium	medium	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	3XSCOTS	3xscots	CD	_	_	_
96	cDNA	cdna	NN	_	_	_
97	obtained	obtain	VBN	_	_	_
98	24	24	CD	_	_	_
99	h	h	NN	_	_	_
100	post-infection	post-infection	JJ	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	3XSCOTS	3xscot	NNS	_	_	_
103	cDNA	cdna	NN	_	_	_
104	obtained	obtain	VBN	_	_	_
105	2h	2h	JJ	_	_	_
106	post-infection	post-infection	JJ	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	3XSCOTS	3xscot	NNS	_	_	_
109	cDNA	cdna	NN	_	_	_
110	obtained	obtain	VBN	_	_	_
111	8h	8h	JJ	_	_	_
112	post-infection	post-infection	JJ	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	3XSCOTS	3xscot	NNS	_	_	_
115	cDNA	cdna	NN	_	_	_
116	obtained	obtain	VBN	_	_	_
117	8h	8h	JJ	_	_	_
118	post-infection	post-infection	JJ	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	3XSCOTS	3xscot	NNS	_	_	_
121	cDNA	cdna	NN	_	_	_
122	obtained	obtain	VBN	_	_	_
123	after	after	IN	_	_	_
124	8h	8h	JJ	_	_	_
125	post-infection	post-infection	JJ	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	3XSCOTS	3xscot	NNS	_	_	_
128	cDNA	cdna	NN	_	_	_
129	obtained	obtain	VBN	_	_	_
130	in	in	IN	_	_	_
131	RPMI	rpmi	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	3XSCOTS	3xscots	CD	_	_	_
134	cDNA	cdna	NN	_	_	_
135	obtained	obtain	VBN	_	_	_
136	in	in	IN	_	_	_
137	RPMI	rpmi	NN	_	_	_
138	medium	medium	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	40	40	CD	_	_	_
141	hours	hour	NNS	_	_	_
142	1	1	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	40	40	CD	_	_	_
145	hours	hour	NNS	_	_	_
146	2	2	CD	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
148	40	40	CD	_	_	_
149	hours	hour	NNS	_	_	_
150	3	3	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	40	40	CD	_	_	_
153	hours	hour	NNS	_	_	_
154	cultivation	cultivation	NN	_	_	_
155	in	in	IN	_	_	_
156	continuous	continuous	JJ	_	_	_
157	culture	culture	NN	_	_	_
158	-LRB-	-lrb-	-LRB-	_	_	_
159	mineral	mineral	JJ	_	_	_
160	medium	medium	NN	_	_	_
161	with	with	IN	_	_	_
162	100	100	CD	_	_	_
163	mg/l	mg/l	NN	_	_	_
164	glucose	glucose	NN	SUPP	_	_
165	-RRB-	-rrb-	-RRB-	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	40	40	CD	_	_	_
168	hours	hour	NNS	_	_	_
169	of	of	IN	_	_	_
170	cultivation	cultivation	NN	_	_	_
171	in	in	IN	_	_	_
172	continuous	continuous	JJ	_	_	_
173	colture	colture	NN	_	_	_
174	-LRB-	-lrb-	-LRB-	_	_	_
175	mineral	mineral	JJ	_	_	_
176	medium	medium	NN	_	_	_
177	with	with	IN	_	_	_
178	100	100	CD	_	_	_
179	mg/l	mg/l	NN	_	_	_
180	glucose	glucose	NN	SUPP	_	_
181	-RRB-	-rrb-	-RRB-	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	40	40	CD	_	_	_
184	min	min	NN	_	_	_
185	after	after	IN	_	_	_
186	UVtreatment	uvtreatment	NN	_	_	_
187	1	1	CD	_	_	_
188	,	,	,	_	_	_
189	40J	40j	NN	_	_	_
190	,	,	,	_	_	_
191	MG1655	mg1655	NN	_	_	_
192	in	in	IN	_	_	_
193	Davis	Davis	NNP	_	_	_
194	+0.4	+0.4	CD	_	_	_
195	%	%	NN	_	_	_
196	glu	glu	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	40	40	CD	_	_	_
199	min	min	NN	_	_	_
200	Nov10	nov10	NN	_	_	_
201	ug/ml	ug/ml	NN	_	_	_
202	,	,	,	_	_	_
203	2	2	CD	_	_	_
204	ug	ug	NN	_	_	_
205	Sau3AI	sau3ai	NN	_	_	_
206	,	,	,	_	_	_
207	pdN6	pdn6	NN	_	_	_
208	RT	rt	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	40	40	CD	_	_	_
211	min	min	NN	_	_	_
212	Nov10	nov10	NN	_	_	_
213	ug/ml	ug/ml	NN	_	_	_
214	,	,	,	_	_	_
215	dnaCacrD	dnacacrd	NN	_	_	_
216	30	30	CD	_	_	_
217	min	min	NN	_	_	_
218	after	after	IN	_	_	_
219	synchr	synchr	NN	_	_	_
220	start	start	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	40	40	CD	_	_	_
223	min	min	NN	_	_	_
224	Nov2	nov2	NN	_	_	_
225	ug/ml	ug/ml	NN	_	_	_
226	,	,	,	_	_	_
227	2	2	CD	_	_	_
228	ug	ug	NN	_	_	_
229	Say3AI	say3ai	NN	_	_	_
230	,	,	,	_	_	_
231	pdN6	pdn6	NN	_	_	_
232	RT	rt	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	40	40	CD	_	_	_
235	min	min	NN	_	_	_
236	Nov2	nov2	NN	_	_	_
237	ug/ml	ug/ml	NN	_	_	_
238	,	,	,	_	_	_
239	dnaCacrD	dnacacrd	NN	_	_	_
240	30	30	CD	_	_	_
241	min	min	NN	_	_	_
242	after	after	IN	_	_	_
243	synchr	synchr	NN	_	_	_
244	start	start	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	40	40	CD	_	_	_
247	min	min	NN	_	_	_
248	Nov5	nov5	NN	_	_	_
249	ug/ml	ug/ml	NN	_	_	_
250	,	,	,	_	_	_
251	2	2	CD	_	_	_
252	ug	ug	NN	_	_	_
253	Sau3AI	sau3ai	NN	_	_	_
254	,	,	,	_	_	_
255	pdN6	pdn6	NN	_	_	_
256	RT	rt	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	40	40	CD	_	_	_
259	min	min	NN	_	_	_
260	Nov5	nov5	NN	_	_	_
261	ug/ml	ug/ml	NN	_	_	_
262	,	,	,	_	_	_
263	dnaCacrD	dnacacrd	NN	_	_	_
264	30	30	CD	_	_	_
265	min	min	NN	_	_	_
266	after	after	IN	_	_	_
267	synchr	synchr	NN	_	_	_
268	start	start	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	40	40	CD	_	_	_
271	min	min	NN	_	_	_
272	untreatedcells	untreatedcell	NNS	_	_	_
273	,	,	,	_	_	_
274	25	25	CD	_	_	_
275	ug	ug	NN	_	_	_
276	total	total	JJ	_	_	_
277	RNA	rna	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	40	40	CD	_	_	_
280	.	.	.	_	_	_

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	4.5	4.5	CD	_	_	_
4	'	'	''	_	_	_
5	RNA	rna	NN	_	_	_
6	Decay	decay	NN	_	_	_
7	N-RNaseE	n-rnasee	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	BZ453	bz453	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	in	in	IN	_	_	_
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	at	at	IN	_	_	_
22	30	30	CD	_	_	_
23	C	c	NN	_	_	_
24	Mid	Mid	NNP	_	_	_
25	Log	Log	NNP	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	4.5	4.5	CD	_	_	_
28	'	'	''	_	_	_
29	RNA	rna	NN	_	_	_
30	Decay	decay	NN	_	_	_
31	N-RNaseE	n-rnasee	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	BZ453	bz453	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	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	4.5	4.5	CD	_	_	_
53	'	'	''	_	_	_
54	RNA	rna	NN	_	_	_
55	Decay	decay	NN	_	_	_
56	of	of	IN	_	_	_
57	Eno	Eno	NNP	_	_	_
58	-	-	:	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	DF261	df261	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	in	in	IN	_	_	_
63	M9	m9	NN	_	_	_
64	0.2	0.2	CD	_	_	_
65	%	%	NN	_	_	_
66	Glycerol	glycerol	NN	_	_	_
67	0.2	0.2	CD	_	_	_
68	%	%	NN	_	_	_
69	Tryptone	tryptone	NN	_	_	_
70	40	40	CD	_	_	_
71	mM	mm	NN	KWSUPP	_	_
72	Suc	suc	NN	_	_	_
73	.	.	.	_	_	_

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	46degrees	46degree	NNS	_	_	_
84	replicate	replicate	VBP	_	_	_
85	1	1	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	46degrees	46degree	NNS	_	_	_
88	replicate	replicate	VBP	_	_	_
89	2	2	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
91	46degrees	46degree	NNS	_	_	_
92	replicate	replicate	VBP	_	_	_
93	3	3	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	46	46	CD	_	_	_
96	.	.	.	_	_	_

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	4A	4a	NN	_	_	_
5	1m	1m	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	4A	4a	NN	_	_	_
8	1y	1y	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	4A	4a	NN	_	_	_
11	4y	4y	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	4A	4a	NN	_	_	_
14	_	_	CD	_	_	_
15	MG	mg	NN	_	_	_
16	_	_	NN	_	_	_
17	t60	t60	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	4B	4b	NN	_	_	_
20	_	_	CD	_	_	_
21	MG	mg	NN	_	_	_
22	_	_	NN	_	_	_
23	t60	t60	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	4C	4c	NN	_	_	_
26	_	_	CD	_	_	_
27	MG	mg	NN	_	_	_
28	_	_	NN	_	_	_
29	t60	t60	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	4	4	CD	_	_	_
32	_	_	NN	_	_	_
33	ESBL019	esbl019	NN	_	_	_
34	Reverted	revert	VBD	_	_	_
35	Repl	repl	NN	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	4	4	CD	_	_	_
39	.	.	.	_	_	_

1	FHI6.IND.HUS	fhi6.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	4	4	CD	_	_	_
4	hour	hour	NN	_	_	_
5	expression	expression	NN	_	_	_
6	of	of	IN	_	_	_
7	synthetic	synthetic	JJ	_	_	_
8	protein	protein	NN	_	_	_
9	DX	dx	NN	_	_	_
10	in	in	IN	_	_	_
11	E.	e.	FW	_	_	_
12	coli	coli	FW	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	4-HT873-PS-60min1	4-ht873-ps-60min1	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	4	4	CD	_	_	_
17	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	by	by	IN	_	_	_
3	Glowess	glowess	NN	_	_	_
4	method	method	NN	_	_	_
5	:	:	:	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	4	4	CD	_	_	_
8	'	'	''	_	_	_
9	RNA	rna	NN	_	_	_
10	Decay	decay	NN	_	_	_
11	of	of	IN	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Repaired	repair	VBN	_	_	_
15	NCM	NCM	NNP	_	_	_
16	3416	3416	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	in	in	IN	_	_	_
19	LB	lb	NN	_	_	_
20	at	at	IN	_	_	_
21	30	30	CD	_	_	_
22	C	c	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	4	4	CD	_	_	_
25	'	'	''	_	_	_
26	RNA	rna	NN	_	_	_
27	Decay	decay	NN	_	_	_
28	of	of	IN	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Repaired	repair	VBN	_	_	_
32	NCM	NCM	NNP	_	_	_
33	3416	3416	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	in	in	IN	_	_	_
36	M9	m9	NN	_	_	_
37	+	+	CC	_	_	_
38	0.2	0.2	CD	_	_	_
39	%	%	NN	_	_	_
40	Glucose	glucose	NN	_	_	_
41	Trial	trial	NN	_	_	_
42	A	a	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	4	4	CD	_	_	_
45	'	'	''	_	_	_
46	RNA	rna	NN	_	_	_
47	Decay	decay	NN	_	_	_
48	of	of	IN	_	_	_
49	MG1655	mg1655	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Repaired	repair	VBN	_	_	_
52	NCM	NCM	NNP	_	_	_
53	3416	3416	CD	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	in	in	IN	_	_	_
56	M9	m9	NN	_	_	_
57	+	+	CC	_	_	_
58	0.2	0.2	CD	_	_	_
59	%	%	NN	_	_	_
60	Glucose	glucose	NN	_	_	_
61	Trial	trial	NN	_	_	_
62	B	b	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	500	500	CD	_	_	_
65	hours	hour	NNS	_	_	_
66	1	1	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	500	500	CD	_	_	_
69	hours	hour	NNS	_	_	_
70	2	2	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	500	500	CD	_	_	_
73	hours	hour	NNS	_	_	_
74	3	3	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	500	500	CD	_	_	_
77	hours	hour	NNS	_	_	_
78	of	of	IN	_	_	_
79	cultivation	cultivation	NN	_	_	_
80	in	in	IN	_	_	_
81	continuous	continuous	JJ	_	_	_
82	colture	colture	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	mineral	mineral	JJ	_	_	_
85	medium	medium	NN	_	_	_
86	with	with	IN	_	_	_
87	100	100	CD	_	_	_
88	mg/l	mg/l	NN	_	_	_
89	glucose	glucose	NN	SUPP	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	500	500	CD	_	_	_
93	ng	ng	NN	_	_	_
94	chrom	chrom	NN	_	_	_
95	.	.	.	_	_	_

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	50	50	CD	_	_	_
3	bp	bp	NN	_	_	_
4	single-end	single-end	JJ	_	_	_
5	reads	read	VBZ	_	_	_
6	,	,	,	_	_	_
7	were	be	VBD	_	_	_
8	mapped	map	VBN	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	genome	genome	NN	_	_	_
12	with	with	IN	_	_	_
13	using	use	VBG	_	_	_
14	bowtie2	bowtie2	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Langmead	langmead	NN	_	_	_
17	and	and	CC	_	_	_
18	Salzberg	Salzberg	NNP	_	_	_
19	,	,	,	_	_	_
20	2012	2012	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	using	use	VBG	_	_	_
23	default	default	NN	_	_	_
24	parameters	parameter	NNS	_	_	_
25	.	.	.	_	_	_

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	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/ml	mg/ml	NN	_	_	_
12	lysozyme	lysozyme	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Fisher	Fisher	NNP	_	_	_
15	Scientific	Scientific	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	in	in	IN	_	_	_
6	50	50	CD	_	_	_
7	ml	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	RNase	rnase	NN	_	_	_
10	free	free	JJ	_	_	_
11	water	water	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Ambion	Ambion	NNP	_	_	_
14	Inc.	Inc.	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	using	use	VBG	_	_	_
17	the	the	DT	_	_	_
18	NanoDrop	NanoDrop	NNP	_	_	_
19	Spectrophotometer	Spectrophotometer	NNP	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	NanoDrop	NanoDrop	NNP	_	_	_
22	Technologies	Technologies	NNPS	_	_	_
23	,	,	,	_	_	_
24	Inc.	Inc.	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	examined	examine	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	RNA	rna	NN	_	_	_
8	6000	6000	CD	_	_	_
9	Nano	Nano	NNP	_	_	_
10	Labchip	labchip	NN	_	_	_
11	with	with	IN	_	_	_
12	an	a	DT	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	2100	2100	CD	_	_	_
15	Bioanalyzer	Bioanalyzer	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Agilent	Agilent	NNP	_	_	_
18	Technologies	Technologies	NNPS	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	50	50	CD	_	_	_
3	ng	ng	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	fragmented	fragmented	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	converted	convert	VBN	_	_	_
10	to	to	TO	_	_	_
11	sequencing	sequencing	NN	_	_	_
12	library	library	NN	_	_	_
13	using	use	VBG	_	_	_
14	TruSeq	TruSeq	NNP	_	_	_
15	®	®	NNP	_	_	_
16	Stranded	Stranded	NNP	_	_	_
17	mRNA	mrna	NN	_	_	_
18	Sample	Sample	NNP	_	_	_
19	Prep	Prep	NNP	_	_	_
20	Kit	kit	NN	_	_	_
21	in	in	IN	_	_	_
22	accordance	accordance	NN	_	_	_
23	with	with	IN	_	_	_
24	manufacturer	manufacturer	NN	_	_	_
25	's	's	POS	_	_	_
26	instruction	instruction	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Illumina	Illumina	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	50	50	CD	_	_	_
3	OD600	od600	NN	_	_	_
4	of	of	IN	_	_	_
5	bacteria	bacterium	NNS	_	_	_
6	have	have	VBP	_	_	_
7	been	be	VBN	_	_	_
8	grown	grow	VBN	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	desired	desire	VBN	_	_	_
12	growth	growth	NN	_	_	_
13	stage	stage	NN	_	_	_
14	and	and	CC	_	_	_
15	harvested	harvest	VBN	_	_	_
16	by	by	IN	_	_	_
17	centrifugation	centrifugation	NN	_	_	_
18	.	.	.	_	_	_

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/ml	u/ml	NN	_	_	_
42	DNase	dnase	NN	_	_	_
43	I	i	CD	_	_	_
44	,	,	,	_	_	_
45	Thermo	Thermo	NNP	_	_	_
46	Scientific	Scientific	NNP	_	_	_
47	,	,	,	_	_	_
48	200	200	CD	_	_	_
49	U/ml	u/ml	NN	_	_	_
50	SUPERase-IN	superase-in	NN	_	_	_
51	,	,	,	_	_	_
52	Life	Life	NNP	_	_	_
53	Technologies	Technologies	NNPS	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	.	.	.	_	_	_

1	Lysis	lysis	NN	_	_	_
2	was	be	VBD	_	_	_
3	carried	carry	VBN	_	_	_
4	out	out	RP	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	Retsch	retsch	JJ	_	_	_
8	MM400	mm400	NN	_	_	_
9	machine	machine	NN	_	_	_
10	at	at	IN	_	_	_
11	30	30	CD	_	_	_
12	Hz	hz	NN	_	_	_
13	for	for	IN	_	_	_
14	10	10	CD	_	_	_
15	min	min	NN	_	_	_
16	in	in	IN	_	_	_
17	the	the	DT	_	_	_
18	presence	presence	NN	_	_	_
19	of	of	IN	_	_	_
20	750	750	CD	_	_	_
21	µl	µl	NN	_	_	_
22	0.1	0.1	CD	_	_	_
23	mm	mm	NN	_	_	_
24	glass	glass	NN	_	_	_
25	beads	bead	NNS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	cleared	clear	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	14,000	14,000	CD	_	_	_
9	g	g	NN	_	_	_
10	at	at	IN	_	_	_
11	4	4	CD	_	_	_
12	°C	°c	NN	_	_	_
13	for	for	IN	_	_	_
14	10	10	CD	_	_	_
15	min	min	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	35	35	CD	_	_	_
6	µl	µl	NN	_	_	_
7	of	of	IN	_	_	_
8	monoclonal	monoclonal	JJ	_	_	_
9	anti-FLAG	anti-flag	JJ	_	_	_
10	M2	m2	NN	_	_	_
11	antibody	antibody	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Sigma	Sigma	NNP	_	_	_
14	,	,	,	_	_	_
15	#F1804	#f1804	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	rocked	rock	VBD	_	_	_
19	for	for	IN	_	_	_
20	30	30	CD	_	_	_
21	min	min	NN	_	_	_
22	at	at	IN	_	_	_
23	4	4	CD	_	_	_
24	°C	°c	NN	_	_	_
25	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	75	75	CD	_	_	_
3	µl	µl	NN	_	_	_
4	of	of	IN	_	_	_
5	pre-washed	pre-washed	JJ	_	_	_
6	Protein	protein	NN	_	_	_
7	A	a	DT	_	_	_
8	sepharose	sepharose	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Sigma	Sigma	NNP	_	_	_
11	,	,	,	_	_	_
12	#P6649	#p6649	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	were	be	VBD	_	_	_
15	added	add	VBN	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	mixture	mixture	NN	_	_	_
19	was	be	VBD	_	_	_
20	rocked	rock	VBN	_	_	_
21	for	for	IN	_	_	_
22	additional	additional	JJ	_	_	_
23	30	30	CD	_	_	_
24	min	min	NN	_	_	_
25	.	.	.	_	_	_

1	Afterwards	afterwards	RB	_	_	_
2	,	,	,	_	_	_
3	beads	bead	NNS	_	_	_
4	were	be	VBD	_	_	_
5	washed	wash	VBN	_	_	_
6	extensively	extensively	RB	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	similar	similar	JJ	_	_	_
14	flow-through	flow-through	JJ	_	_	_
15	and	and	CC	_	_	_
16	wash	wash	NN	_	_	_
17	protein	protein	NN	_	_	_
18	and	and	CC	_	_	_
19	RNA	rna	NN	_	_	_
20	samples	sample	NNS	_	_	_
21	were	be	VBD	_	_	_
22	collected	collect	VBN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	50	50	CD	_	_	_
3	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav17.IND.nHUS	Olav17.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	5	5	CD	_	_	_
5	'	'	''	_	_	_
6	10	10	CD	_	_	_
7	ug/ml	ug/ml	JJ	_	_	_
8	indole	indole	NN	_	_	_
9	aa	aa	NN	_	_	_
10	,	,	,	_	_	_
11	minimal	minimal	JJ	_	_	_
12	medium	medium	NN	_	_	_
13	+	+	CC	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	glu	glu	NN	_	_	_
17	,	,	,	_	_	_
18	25	25	CD	_	_	_
19	ug	ug	NN	_	_	_
20	total	total	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	5	5	CD	_	_	_
23	'	'	''	_	_	_
24	15	15	CD	_	_	_
25	ug/ml	ug/ml	JJ	_	_	_
26	indole	indole	NN	_	_	_
27	aa	aa	NN	_	_	_
28	,	,	,	_	_	_
29	minimal	minimal	JJ	_	_	_
30	medium	medium	NN	_	_	_
31	+	+	CC	_	_	_
32	0.2	0.2	CD	_	_	_
33	%	%	NN	_	_	_
34	glu	glu	NN	_	_	_
35	,	,	,	_	_	_
36	25	25	CD	_	_	_
37	ug	ug	NN	_	_	_
38	total	total	JJ	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	51	51	CD	_	_	_
41	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
3	5	5	CD	_	_	_
4	'	'	''	_	_	_
5	+50	+50	CD	_	_	_
6	ug/ml	ug/ml	JJ	_	_	_
7	Trp	trp	NN	_	_	_
8	vs	vs	CC	_	_	_
9	0	0	CD	_	_	_
10	'	'	''	_	_	_
11	in	in	IN	_	_	_
12	min	min	NN	_	_	_
13	med	med	VBD	_	_	_
14	+0.2	+0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	glu	glu	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	55	55	CD	_	_	_
19	min	min	NN	_	_	_
20	after	after	IN	_	_	_
21	turning	turn	VBG	_	_	_
22	off	off	RP	_	_	_
23	oxygen	oxygen	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	55	55	CD	_	_	_
26	.	.	.	_	_	_

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	5A	5a	NN	_	_	_
5	1m	1m	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	5A	5a	NN	_	_	_
8	_	_	CD	_	_	_
9	MG+H	mg+h	NN	_	_	_
10	g	g	NN	_	_	_
11	_	_	CD	_	_	_
12	t10	t10	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	5-azacytidine-treated	5-azacytidine-treated	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	5B	5b	NN	_	_	_
17	_	_	CD	_	_	_
18	MG+H	mg+h	NN	_	_	_
19	g	g	NN	_	_	_
20	_	_	CD	_	_	_
21	t10	t10	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	5C	5c	NN	_	_	_
24	_	_	CD	_	_	_
25	MG+H	mg+h	NN	_	_	_
26	g	g	NN	_	_	_
27	_	_	CD	_	_	_
28	t10	t10	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	5	5	CD	_	_	_
31	_	_	NN	_	_	_
32	ESBL019	esbl019	NN	_	_	_
33	Coliform	coliform	NN	_	_	_
34	Repl	repl	NN	_	_	_
35	2	2	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	5	5	CD	_	_	_
38	.	.	.	_	_	_

1	FHI7.nIND.HUS	fhi7.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	5	5	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	LP	lp	NN	_	_	_
8	_	_	CD	_	_	_
9	noDP	nodp	NN	_	_	_
10	_	_	CD	_	_	_
11	noRh	norh	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	COPRO-Seq	copro-seq	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	5-HT873-PS-60min2	5-ht873-ps-60min2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	5	5	CD	_	_	_
19	'	'	''	_	_	_
20	in	in	IN	_	_	_
21	minimal	minimal	JJ	_	_	_
22	medium	medium	NN	_	_	_
23	+0.2	+0.2	CD	_	_	_
24	%	%	NN	_	_	_
25	glu	glu	NN	_	_	_
26	,	,	,	_	_	_
27	25	25	CD	_	_	_
28	ug	ug	NN	_	_	_
29	total	total	JJ	_	_	_
30	RNA	rna	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	5	5	CD	_	_	_
33	'	'	''	_	_	_
34	in	in	IN	_	_	_
35	min	min	NN	_	_	_
36	med	med	VBD	_	_	_
37	+0.2	+0.2	CD	_	_	_
38	%	%	NN	_	_	_
39	glu	glu	NN	_	_	_
40	+50	+50	CD	_	_	_
41	ug/ml	ug/ml	JJ	_	_	_
42	Trp	trp	NN	_	_	_
43	,25	,25	CD	_	_	_
44	ug	ug	NN	_	_	_
45	total	total	JJ	_	_	_
46	RNA	rna	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	5	5	CD	_	_	_
49	'	'	''	_	_	_
50	linker	linker	NN	_	_	_
51	and	and	CC	_	_	_
52	poly	poly	NN	_	_	_
53	A-tail	a-tail	NN	_	_	_
54	removal	removal	NN	_	_	_
55	using	use	VBG	_	_	_
56	READemption	reademption	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	5	5	CD	_	_	_
59	min	min	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	5	5	CD	_	_	_
62	min	min	NN	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	additional	additional	JJ	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	5	5	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	5	5	CD	_	_	_
75	min	min	NN	_	_	_
76	after	after	IN	_	_	_
77	turning	turn	VBG	_	_	_
78	off	off	RP	_	_	_
79	oxygen	oxygen	NN	_	_	_
80	first	first	RB	_	_	_
81	replicate	replicate	VB	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	5	5	CD	_	_	_
84	min	min	NN	_	_	_
85	after	after	IN	_	_	_
86	UVtreatment	uvtreatment	NN	_	_	_
87	1	1	CD	_	_	_
88	,	,	,	_	_	_
89	40J	40j	NN	_	_	_
90	,	,	,	_	_	_
91	MG1655	mg1655	NN	_	_	_
92	in	in	IN	_	_	_
93	Davis	Davis	NNP	_	_	_
94	+0.4	+0.4	CD	_	_	_
95	%	%	NN	_	_	_
96	glu	glu	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	5	5	CD	_	_	_
99	min	min	NN	_	_	_
100	untreatedcells	untreatedcell	NNS	_	_	_
101	,	,	,	_	_	_
102	25	25	CD	_	_	_
103	ug	ug	NN	_	_	_
104	total	total	JJ	_	_	_
105	RNA	rna	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	5	5	CD	_	_	_
108	ml	ml	NN	_	_	_
109	bacterial	bacterial	JJ	_	_	_
110	cultures	culture	NNS	_	_	_
111	with	with	IN	_	_	_
112	a	a	DT	_	_	_
113	known	known	JJ	_	_	_
114	inoculum	inoculum	NN	_	_	_
115	of	of	IN	_	_	_
116	E.	e.	FW	_	_	_
117	coli	coli	FW	_	_	_
118	cells	cell	NNS	_	_	_
119	-LRB-	-lrb-	-LRB-	_	_	_
120	1.0	1.0	CD	_	_	_
121	×	×	NN	_	_	_
122	109	109	CD	_	_	_
123	cfu/ml	cfu/ml	NN	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	was	be	VBD	_	_	_
126	added	add	VBN	_	_	_
127	at	at	IN	_	_	_
128	1:1	1:1	CD	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	v/v	v/v	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	to	to	TO	_	_	_
133	the	the	DT	_	_	_
134	microemulsion	microemulsion	NN	_	_	_
135	and	and	CC	_	_	_
136	incubated	incubate	VBN	_	_	_
137	on	on	IN	_	_	_
138	a	a	DT	_	_	_
139	tube	tube	NN	_	_	_
140	rotator	rotator	NN	_	_	_
141	at	at	IN	_	_	_
142	200	200	CD	_	_	_
143	rpm	rpm	NN	_	_	_
144	for	for	IN	_	_	_
145	4	4	CD	_	_	_
146	h	h	NN	_	_	_
147	at	at	IN	_	_	_
148	37	37	CD	_	_	_
149	°C	°c	NN	_	_	_
150	for	for	IN	_	_	_
151	the	the	DT	_	_	_
152	subsequent	subsequent	JJ	_	_	_
153	DNA	dna	NN	_	_	_
154	microarray	microarray	NN	_	_	_
155	analysis	analysis	NN	_	_	_
156	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	the	the	DT	_	_	_
3	preliminary	preliminary	JJ	_	_	_
4	experiment	experiment	NN	_	_	_
5	,	,	,	_	_	_
6	a	a	DT	_	_	_
7	complete	complete	JJ	_	_	_
8	loss	loss	NN	_	_	_
9	of	of	IN	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	viability	viability	NN	_	_	_
13	was	be	VBD	_	_	_
14	achieved	achieve	VBN	_	_	_
15	after	after	IN	_	_	_
16	8	8	CD	_	_	_
17	h	h	NN	_	_	_
18	by	by	IN	_	_	_
19	the	the	DT	_	_	_
20	aforementioned	aforementioned	JJ	_	_	_
21	treatment	treatment	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	prepared	prepared	JJ	_	_	_
3	microemulsion	microemulsion	NN	_	_	_
4	has	have	VBZ	_	_	_
5	an	a	DT	_	_	_
6	oil	oil	NN	_	_	_
7	phase	phase	NN	_	_	_
8	of	of	IN	_	_	_
9	glycerol	glycerol	NN	SUPP	_	_
10	monolaurate	monolaurate	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	5.5	5.5	CD	_	_	_
13	%	%	NN	_	_	_
14	w/w	w/w	NN	_	_	_
15	of	of	IN	_	_	_
16	the	the	DT	_	_	_
17	total	total	JJ	_	_	_
18	emulsion	emulsion	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	ethanol	ethanol	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	5.5	5.5	CD	_	_	_
24	%	%	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	a	a	DT	_	_	_
29	surfactant	surfactant	JJ	_	_	_
30	phase	phase	NN	_	_	_
31	of	of	IN	_	_	_
32	Tween	Tween	NNP	_	_	_
33	20	20	CD	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	43	43	CD	_	_	_
36	%	%	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	Mixtures	mixture	NNS	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	surfactant-oil	surfactant-oil	JJ	_	_	_
5	phase	phase	NN	_	_	_
6	were	be	VBD	_	_	_
7	prepared	prepare	VBN	_	_	_
8	in	in	IN	_	_	_
9	stoppered	stoppered	JJ	_	_	_
10	flasks	flask	NNS	_	_	_
11	and	and	CC	_	_	_
12	kept	keep	VBD	_	_	_
13	in	in	IN	_	_	_
14	a	a	DT	_	_	_
15	25	25	CD	_	_	_
16	°C	°c	NN	_	_	_
17	water	water	NN	_	_	_
18	bath	bath	NN	_	_	_
19	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	water	water	NN	_	_	_
5	phase	phase	NN	_	_	_
6	was	be	VBD	_	_	_
7	added	add	VBN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	treated	treat	VBN	_	_	_
14	in	in	IN	_	_	_
15	an	a	DT	_	_	_
16	ultrasonic	ultrasonic	JJ	_	_	_
17	bath	bath	NN	_	_	_
18	until	until	IN	_	_	_
19	the	the	DT	_	_	_
20	system	system	NN	_	_	_
21	became	become	VBD	_	_	_
22	optically	optically	RB	_	_	_
23	clear	clear	JJ	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	allowed	allow	VBN	_	_	_
27	to	to	TO	_	_	_
28	equilibrate	equilibrate	VB	_	_	_
29	at	at	IN	_	_	_
30	25	25	CD	_	_	_
31	°C	°c	NN	_	_	_
32	for	for	IN	_	_	_
33	at	at	IN	_	_	_
34	least	least	JJS	_	_	_
35	24	24	CD	_	_	_
36	h	h	NN	_	_	_
37	to	to	TO	_	_	_
38	guarantee	guarantee	VB	_	_	_
39	steady-state	steady-state	JJ	_	_	_
40	conditions	condition	NNS	_	_	_
41	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	5	5	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	cell	cell	NN	_	_	_
6	suspension	suspension	NN	_	_	_
7	were	be	VBD	_	_	_
8	added	add	VBN	_	_	_
9	to	to	TO	_	_	_
10	0.625	0.625	CD	_	_	_
11	ml	ml	NN	_	_	_
12	of	of	IN	_	_	_
13	pre-chilled	pre-chilled	JJ	_	_	_
14	stop	stop	NN	_	_	_
15	solution	solution	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	5	5	CD	_	_	_
18	%	%	NN	_	_	_
19	phenol/95	phenol/95	CD	_	_	_
20	%	%	NN	_	_	_
21	ethanol	ethanol	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	vortexed	vortexed	JJ	_	_	_
25	and	and	CC	_	_	_
26	incubated	incubate	VBN	_	_	_
27	for	for	IN	_	_	_
28	5	5	CD	_	_	_
29	min	min	NN	_	_	_
30	on	on	IN	_	_	_
31	ice	ice	NN	_	_	_
32	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	pelleted	pellete	VBN	_	_	_
4	for	for	IN	_	_	_
5	5	5	CD	_	_	_
6	min	min	NN	_	_	_
7	at	at	IN	_	_	_
8	5000	5000	CD	_	_	_
9	g	g	NN	_	_	_
10	,	,	,	_	_	_
11	flash	flash	NN	_	_	_
12	frozen	freeze	VBN	_	_	_
13	in	in	IN	_	_	_
14	a	a	DT	_	_	_
15	dry	dry	JJ	_	_	_
16	ice-ethanol	ice-ethanol	NN	_	_	_
17	bath	bath	NN	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBD	_	_	_
20	at	at	IN	_	_	_
21	-80	-80	CD	_	_	_
22	oC	oc	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	5mL	5ml	NN	_	_	_
3	of	of	IN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	mixed	mix	VBN	_	_	_
7	with	with	IN	_	_	_
8	5mL	5ml	NN	_	_	_
9	of	of	IN	_	_	_
10	hot	hot	JJ	_	_	_
11	acid	acid	NN	_	_	_
12	phenol	phenol	NN	_	_	_
13	:	:	:	_	_	_
14	chloroform	chloroform	NN	_	_	_
15	.	.	.	_	_	_

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	1/10V	1/10v	NN	_	_	_
16	3M	3M	NNP	_	_	_
17	sodium	sodium	NN	SUPP	_	_
18	acetate	acetate	NN	SUPP	_	_
19	pH	ph	NN	_	_	_
20	5.2	5.2	CD	_	_	_
21	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	and	and	CC	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	DNase	dnase	NN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	Rneasy	Rneasy	NNP	_	_	_
12	kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Qiagen	qiagen	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	5	5	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	1/10V	1/10v	NN	_	_	_
11	10	10	CD	_	_	_
12	%	%	NN	_	_	_
13	phenol	phenol	NN	_	_	_
14	:	:	:	_	_	_
15	ethanol	ethanol	NN	_	_	_
16	buffer	buffer	NN	_	_	_
17	to	to	TO	_	_	_
18	stabilize	stabilize	VB	_	_	_
19	the	the	DT	_	_	_
20	RNA	rna	NN	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	centrifuged	centrifuge	VBD	_	_	_
24	at	at	IN	_	_	_
25	4	4	CD	_	_	_
26	oC	oc	NN	_	_	_
27	,	,	,	_	_	_
28	4300	4300	CD	_	_	_
29	×	×	CD	_	_	_
30	g	g	NN	_	_	_
31	for	for	IN	_	_	_
32	30	30	CD	_	_	_
33	min	min	NN	_	_	_
34	to	to	TO	_	_	_
35	pellet	pellet	NN	_	_	_
36	cells	cell	NNS	_	_	_
37	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	and	and	CC	_	_	_
6	cell	cell	NN	_	_	_
7	pellets	pellet	NNS	_	_	_
8	were	be	VBD	_	_	_
9	suspended	suspend	VBN	_	_	_
10	in	in	IN	_	_	_
11	5	5	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	buffer	buffer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	2	2	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	EDTA	edta	NN	_	_	_
19	,	,	,	_	_	_
20	20	20	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	NaOAc	naoac	NN	_	_	_
23	,	,	,	_	_	_
24	pH	ph	NN	_	_	_
25	5.2	5.2	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	before	before	IN	_	_	_
28	mixing	mix	VBG	_	_	_
29	with	with	IN	_	_	_
30	equal	equal	JJ	_	_	_
31	volume	volume	NN	_	_	_
32	of	of	IN	_	_	_
33	hot	hot	JJ	_	_	_
34	acid-phenol	acid-phenol	NN	_	_	_
35	:	:	:	_	_	_
36	chloroform	chloroform	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	pH	ph	NN	_	_	_
39	4.5	4.5	CD	_	_	_
40	with	with	IN	_	_	_
41	Iso	Iso	NNP	_	_	_
42	Amyl	Amyl	NNP	_	_	_
43	Alcohol	Alcohol	NNP	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	IAA	IAA	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	,	,	,	_	_	_
48	125:25:1	125:25:1	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Ambion	Ambion	NNP	_	_	_
52	,	,	,	_	_	_
53	Austin	Austin	NNP	_	_	_
54	,	,	,	_	_	_
55	TX	TX	NNP	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	and	and	CC	_	_	_
58	incubating	incubate	VBG	_	_	_
59	at	at	IN	_	_	_
60	65	65	CD	_	_	_
61	oC	oc	NN	_	_	_
62	with	with	IN	_	_	_
63	periodic	periodic	JJ	_	_	_
64	shaking	shake	VBG	_	_	_
65	for	for	IN	_	_	_
66	10	10	CD	_	_	_
67	min	min	NN	_	_	_
68	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	at	at	IN	_	_	_
6	3220	3220	CD	_	_	_
7	×	×	CD	_	_	_
8	g	g	NN	_	_	_
9	for	for	IN	_	_	_
10	20	20	CD	_	_	_
11	min	min	NN	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	supernatant	supernatant	NN	_	_	_
15	was	be	VBD	_	_	_
16	subjected	subject	VBN	_	_	_
17	to	to	TO	_	_	_
18	further	further	JJ	_	_	_
19	extractions	extraction	NNS	_	_	_
20	with	with	IN	_	_	_
21	phenol	phenol	NN	_	_	_
22	:	:	:	_	_	_
23	chloroform	chloroform	NN	_	_	_
24	and	and	CC	_	_	_
25	chloroform	chloroform	NN	_	_	_
26	:	:	:	_	_	_
27	IAA	iaa	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	3	3	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitated	JJ	_	_	_
4	overnight	overnight	JJ	_	_	_
5	at	at	IN	_	_	_
6	-70	-70	CD	_	_	_
7	oC	oc	NN	_	_	_
8	in	in	IN	_	_	_
9	2.5	2.5	CD	_	_	_
10	volume	volume	NN	_	_	_
11	100	100	CD	_	_	_
12	%	%	NN	_	_	_
13	ethanol	ethanol	NN	_	_	_
14	and	and	CC	_	_	_
15	1/10	1/10	CD	_	_	_
16	volume	volume	NN	_	_	_
17	3	3	CD	_	_	_
18	M	m	NN	_	_	_
19	sodium	sodium	NN	SUPP	_	_
20	acetate	acetate	NN	SUPP	_	_
21	pH	ph	NN	_	_	_
22	5.2	5.2	CD	_	_	_
23	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	purification	purification	NN	_	_	_
3	and	and	CC	_	_	_
4	DNase	dnase	NN	_	_	_
5	treatment	treatment	NN	_	_	_
6	of	of	IN	_	_	_
7	RNA	rna	NN	_	_	_
8	samples	sample	NNS	_	_	_
9	were	be	VBD	_	_	_
10	done	do	VBN	_	_	_
11	with	with	IN	_	_	_
12	the	the	DT	_	_	_
13	Rneasy	Rneasy	NNP	_	_	_
14	kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Qiagen	Qiagen	NNP	_	_	_
17	,	,	,	_	_	_
18	Valencia	Valencia	NNP	_	_	_
19	,	,	,	_	_	_
20	CA	CA	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	RNA	rna	NN	_	_	_
24	quality	quality	NN	_	_	_
25	was	be	VBD	_	_	_
26	assessed	assess	VBN	_	_	_
27	on	on	IN	_	_	_
28	a	a	DT	_	_	_
29	formaldehyde-agarose	formaldehyde-agarose	NN	_	_	_
30	gel	gel	NN	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	5	5	CD	_	_	_
3	.	.	.	_	_	_

1	Save	save	VB	_	_	_
2	the	the	DT	_	_	_
3	plot	plot	NN	_	_	_
4	files	file	VBZ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	5	5	CD	_	_	_
7	'	'	''	_	_	_
8	vs	vs	CC	_	_	_
9	0	0	CD	_	_	_
10	'	'	''	_	_	_
11	in	in	IN	_	_	_
12	minimal	minimal	JJ	_	_	_
13	medium	medium	NN	_	_	_
14	+0.2	+0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	glu	glu	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	60	60	CD	_	_	_
19	'	'	''	_	_	_
20	10	10	CD	_	_	_
21	ug/ml	ug/ml	JJ	_	_	_
22	indole	indole	NN	_	_	_
23	aa	aa	NN	_	_	_
24	,	,	,	_	_	_
25	minimal	minimal	JJ	_	_	_
26	medium	medium	NN	_	_	_
27	+	+	CC	_	_	_
28	0.2	0.2	CD	_	_	_
29	%	%	NN	_	_	_
30	glu	glu	NN	_	_	_
31	,	,	,	_	_	_
32	25	25	CD	_	_	_
33	ug	ug	NN	_	_	_
34	total	total	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	60	60	CD	_	_	_
37	'	'	''	_	_	_
38	15	15	CD	_	_	_
39	ug/ml	ug/ml	JJ	_	_	_
40	indole	indole	NN	_	_	_
41	aa	aa	NN	_	_	_
42	,	,	,	_	_	_
43	minimal	minimal	JJ	_	_	_
44	medium	medium	NN	_	_	_
45	+	+	CC	_	_	_
46	0.2	0.2	CD	_	_	_
47	%	%	NN	_	_	_
48	glu	glu	NN	_	_	_
49	,	,	,	_	_	_
50	25	25	CD	_	_	_
51	ug	ug	NN	_	_	_
52	total	total	JJ	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	60	60	CD	_	_	_
55	'	'	''	_	_	_
56	+	+	CC	_	_	_
57	50	50	CD	_	_	_
58	ug/ml	ug/ml	JJ	_	_	_
59	Trp	trp	NN	_	_	_
60	in	in	IN	_	_	_
61	min	min	NN	_	_	_
62	+.2	+.2	CD	_	_	_
63	%	%	NN	_	_	_
64	glu	glu	NN	_	_	_
65	,	,	,	_	_	_
66	25	25	CD	_	_	_
67	ug	ug	NN	_	_	_
68	RNA	rna	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	60	60	CD	_	_	_
71	'	'	''	_	_	_
72	+50	+50	CD	_	_	_
73	ug/ml	ug/ml	JJ	_	_	_
74	Trp	trp	NN	_	_	_
75	vs	vs	CC	_	_	_
76	0	0	CD	_	_	_
77	'	'	''	_	_	_
78	in	in	IN	_	_	_
79	min	min	NN	_	_	_
80	med	med	VBD	_	_	_
81	+0.2	+0.2	CD	_	_	_
82	%	%	NN	_	_	_
83	glu	glu	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	60	60	CD	_	_	_
86	'	'	''	_	_	_
87	50	50	CD	_	_	_
88	ug/ml	ug/ml	JJ	_	_	_
89	tryptophan	tryptophan	NN	_	_	_
90	,	,	,	_	_	_
91	minimal	minimal	JJ	_	_	_
92	+02	+02	CD	_	_	_
93	%	%	NN	_	_	_
94	glu	glu	NN	_	_	_
95	,	,	,	_	_	_
96	25	25	CD	_	_	_
97	ug	ug	NN	_	_	_
98	total	total	JJ	_	_	_
99	RNA	rna	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	60	60	CD	_	_	_
102	'	'	''	_	_	_
103	in	in	IN	_	_	_
104	min	min	NN	_	_	_
105	+.2	+.2	CD	_	_	_
106	%	%	NN	_	_	_
107	glu	glu	NN	_	_	_
108	,	,	,	_	_	_
109	25	25	CD	_	_	_
110	ug	ug	NN	_	_	_
111	RNA	rna	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	60	60	CD	_	_	_
114	'	'	''	_	_	_
115	in	in	IN	_	_	_
116	minimal	minimal	JJ	_	_	_
117	medium	medium	NN	_	_	_
118	+0.2	+0.2	CD	_	_	_
119	%	%	NN	_	_	_
120	glu	glu	NN	_	_	_
121	,	,	,	_	_	_
122	25	25	CD	_	_	_
123	ug	ug	NN	_	_	_
124	total	total	JJ	_	_	_
125	RNA	rna	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	60	60	CD	_	_	_
128	'	'	''	_	_	_
129	in	in	IN	_	_	_
130	min	min	NN	_	_	_
131	med	med	VBD	_	_	_
132	+0.2	+0.2	CD	_	_	_
133	%	%	NN	_	_	_
134	glu	glu	NN	_	_	_
135	+50	+50	CD	_	_	_
136	ug/ml	ug/ml	JJ	_	_	_
137	Trp	trp	NN	_	_	_
138	,25	,25	CD	_	_	_
139	ug	ug	NN	_	_	_
140	tot	tot	NN	_	_	_
141	RNA	rna	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	60	60	CD	_	_	_
144	min	min	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	60	60	CD	_	_	_
147	min	min	NN	_	_	_
148	after	after	IN	_	_	_
149	UVtreatment	uvtreatment	NN	_	_	_
150	1	1	CD	_	_	_
151	,	,	,	_	_	_
152	40J	40j	NN	_	_	_
153	,	,	,	_	_	_
154	MG1655	mg1655	NN	_	_	_
155	in	in	IN	_	_	_
156	Davis	Davis	NNP	_	_	_
157	+0.4	+0.4	CD	_	_	_
158	%	%	NN	_	_	_
159	glu	glu	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	60	60	CD	_	_	_
162	min	min	NN	_	_	_
163	untreatedcells	untreatedcell	NNS	_	_	_
164	,	,	,	_	_	_
165	25	25	CD	_	_	_
166	ug	ug	NN	_	_	_
167	total	total	JJ	_	_	_
168	RNA	rna	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	60	60	CD	_	_	_
171	min	min	NN	_	_	_
172	UV	uv	NN	_	_	_
173	treated	treat	VBN	_	_	_
174	cells	cell	NNS	_	_	_
175	,	,	,	_	_	_
176	25	25	CD	_	_	_
177	ug	ug	NN	_	_	_
178	total	total	JJ	_	_	_
179	RNA	rna	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	60	60	CD	_	_	_
182	min	min	NN	_	_	_
183	UVtreatment	uvtreatment	NN	_	_	_
184	control	control	NN	_	_	_
185	,	,	,	_	_	_
186	MG1655	mg1655	NN	_	_	_
187	in	in	IN	_	_	_
188	Davis	Davis	NNP	_	_	_
189	+0.4	+0.4	CD	_	_	_
190	%	%	NN	_	_	_
191	glu	glu	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	60	60	CD	_	_	_
194	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav176.nIND.HUS	olav176.nind.hus	JJ	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	60	60	CD	_	_	_
5	'	'	''	_	_	_
6	vs.	vs.	CC	_	_	_
7	0	0	CD	_	_	_
8	'	'	''	_	_	_
9	,	,	,	_	_	_
10	50	50	CD	_	_	_
11	ug/ml	ug/ml	JJ	_	_	_
12	tryptophan	tryptophan	NN	_	_	_
13	,	,	,	_	_	_
14	minimal	minimal	JJ	_	_	_
15	+02	+02	CD	_	_	_
16	%	%	NN	_	_	_
17	glu	glu	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	60	60	CD	_	_	_
20	'	'	''	_	_	_
21	vs	vs	CC	_	_	_
22	0	0	CD	_	_	_
23	'	'	''	_	_	_
24	in	in	IN	_	_	_
25	minimal	minimal	JJ	_	_	_
26	medium	medium	NN	_	_	_
27	+0.2	+0.2	CD	_	_	_
28	%	%	NN	_	_	_
29	glu	glu	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	60	60	CD	_	_	_
32	'	'	''	_	_	_
33	vs	vs	CC	_	_	_
34	0	0	CD	_	_	_
35	'	'	''	_	_	_
36	in	in	IN	_	_	_
37	minimal	minimal	JJ	_	_	_
38	medium	medium	NN	_	_	_
39	+0.2	+0.2	CD	_	_	_
40	%	%	NN	_	_	_
41	glu	glu	NN	_	_	_
42	,	,	,	_	_	_
43	II	ii	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	68908	68908	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	68909	68909	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	68910	68910	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	68911	68911	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	68912	68912	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	68913	68913	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	68915	68915	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	68916	68916	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	68917	68917	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	68919	68919	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	68920	68920	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	68921	68921	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	68922	68922	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	68923	68923	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	68924	68924	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	68925	68925	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	68926	68926	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	68927	68927	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	68928	68928	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	68929	68929	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	68930	68930	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	68931	68931	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	68932	68932	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	68933	68933	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	6A	6a	NN	_	_	_
94	1m	1m	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	6A	6a	NN	_	_	_
97	_	_	CD	_	_	_
98	MG+H	mg+h	NN	_	_	_
99	g	g	NN	_	_	_
100	_	_	CD	_	_	_
101	t30	t30	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	6B	6b	NN	_	_	_
104	_	_	CD	_	_	_
105	MG+H	mg+h	NN	_	_	_
106	g	g	NN	_	_	_
107	_	_	CD	_	_	_
108	t30	t30	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	6	6	CD	_	_	_
111	.	.	.	_	_	_

1	close	close	RB	_	_	_
2	the	the	DT	_	_	_
3	graph	graph	NN	_	_	_
4	:	:	:	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	6C	6c	NN	_	_	_
7	_	_	CD	_	_	_
8	MG+H	mg+h	NN	_	_	_
9	g	g	NN	_	_	_
10	_	_	CD	_	_	_
11	t30	t30	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	6	6	CD	_	_	_
14	_	_	NN	_	_	_
15	ESBL019	esbl019	NN	_	_	_
16	Filamented	Filamented	NNP	_	_	_
17	Repl	Repl	NNP	_	_	_
18	2	2	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	6	6	CD	_	_	_
21	.	.	.	_	_	_

1	FHI7.IND.HUS	fhi7.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	6	6	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	HP	HP	NNP	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	_	_	CD	_	_	_
11	noRh	norh	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	COPRO-Seq	copro-seq	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	6-HT873-PS-60min3	6-ht873-ps-60min3	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	6	6	CD	_	_	_
19	'	'	''	_	_	_
20	RNA	rna	NN	_	_	_
21	Decay	decay	NN	_	_	_
22	N-RNaseE	n-rnasee	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	BZ453	bz453	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	in	in	IN	_	_	_
27	M9	m9	NN	_	_	_
28	+	+	CC	_	_	_
29	0.2	0.2	CD	_	_	_
30	%	%	NN	_	_	_
31	Glycerol	glycerol	NN	_	_	_
32	,	,	,	_	_	_
33	0.2	0.2	CD	_	_	_
34	%	%	NN	_	_	_
35	Tryptone	tryptone	NN	_	_	_
36	at	at	IN	_	_	_
37	30	30	CD	_	_	_
38	C	c	NN	_	_	_
39	Mid	Mid	NNP	_	_	_
40	Log	Log	NNP	_	_	_
41	Rep.	Rep.	NNP	_	_	_
42	A	A	NNP	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	6	6	CD	_	_	_
45	'	'	''	_	_	_
46	RNA	rna	NN	_	_	_
47	Decay	decay	NN	_	_	_
48	N-RNaseE	n-rnasee	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	BZ453	bz453	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	in	in	IN	_	_	_
53	M9	m9	NN	_	_	_
54	+	+	CC	_	_	_
55	0.2	0.2	CD	_	_	_
56	%	%	NN	_	_	_
57	Glycerol	glycerol	NN	_	_	_
58	,	,	,	_	_	_
59	0.2	0.2	CD	_	_	_
60	%	%	NN	_	_	_
61	Tryptone	tryptone	NN	_	_	_
62	at	at	IN	_	_	_
63	30	30	CD	_	_	_
64	C	c	NN	_	_	_
65	Mid	Mid	NNP	_	_	_
66	Log	Log	NNP	_	_	_
67	Rep.	Rep.	NNP	_	_	_
68	A1	a1	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	6	6	CD	_	_	_
71	'	'	''	_	_	_
72	RNA	rna	NN	_	_	_
73	Decay	decay	NN	_	_	_
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	Rep.	Rep.	NNP	_	_	_
94	B	B	NNP	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	6	6	CD	_	_	_
97	'	'	''	_	_	_
98	RNA	rna	NN	_	_	_
99	Decay	decay	NN	_	_	_
100	N-RNaseE	n-rnasee	NN	_	_	_
101	-LRB-	-lrb-	-LRB-	_	_	_
102	BZ453	bz453	NN	_	_	_
103	-RRB-	-rrb-	-RRB-	_	_	_
104	in	in	IN	_	_	_
105	M9	m9	NN	_	_	_
106	+	+	CC	_	_	_
107	0.2	0.2	CD	_	_	_
108	%	%	NN	_	_	_
109	Glycerol	glycerol	NN	_	_	_
110	,	,	,	_	_	_
111	0.2	0.2	CD	_	_	_
112	%	%	NN	_	_	_
113	Tryptone	tryptone	NN	_	_	_
114	at	at	IN	_	_	_
115	30	30	CD	_	_	_
116	C	c	NN	_	_	_
117	Mid	Mid	NNP	_	_	_
118	Log	Log	NNP	_	_	_
119	Rep.	Rep.	NNP	_	_	_
120	B1	b1	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	6	6	CD	_	_	_
123	'	'	''	_	_	_
124	RNA	rna	NN	_	_	_
125	Decay	decay	NN	_	_	_
126	of	of	IN	_	_	_
127	Eno	Eno	NNP	_	_	_
128	-	-	:	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	DF261	df261	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	in	in	IN	_	_	_
133	M9	m9	NN	_	_	_
134	0.2	0.2	CD	_	_	_
135	%	%	NN	_	_	_
136	Glycerol	glycerol	NN	_	_	_
137	0.2	0.2	CD	_	_	_
138	%	%	NN	_	_	_
139	Tryptone	tryptone	NN	_	_	_
140	40	40	CD	_	_	_
141	mM	mm	NN	KWSUPP	_	_
142	Suc	suc	NN	_	_	_
143	.	.	.	_	_	_

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	MG1655	mg1655	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Repaired	repair	VBN	_	_	_
17	NCM	NCM	NNP	_	_	_
18	3416	3416	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	in	in	IN	_	_	_
21	LB	lb	NN	_	_	_
22	at	at	IN	_	_	_
23	30	30	CD	_	_	_
24	C	c	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	6	6	CD	_	_	_
27	'	'	''	_	_	_
28	RNA	rna	NN	_	_	_
29	Decay	decay	NN	_	_	_
30	of	of	IN	_	_	_
31	MG1655	mg1655	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Repaired	repair	VBN	_	_	_
34	NCM	NCM	NNP	_	_	_
35	3416	3416	CD	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	in	in	IN	_	_	_
38	M9	m9	NN	_	_	_
39	+	+	CC	_	_	_
40	0.2	0.2	CD	_	_	_
41	%	%	NN	_	_	_
42	Glucose	glucose	NN	_	_	_
43	Trial	trial	NN	_	_	_
44	A	a	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	6	6	CD	_	_	_
47	'	'	''	_	_	_
48	RNA	rna	NN	_	_	_
49	Decay	decay	NN	_	_	_
50	of	of	IN	_	_	_
51	MG1655	mg1655	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	Repaired	repair	VBN	_	_	_
54	NCM	NCM	NNP	_	_	_
55	3416	3416	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	in	in	IN	_	_	_
58	M9	m9	NN	_	_	_
59	+	+	CC	_	_	_
60	0.2	0.2	CD	_	_	_
61	%	%	NN	_	_	_
62	Glucose	glucose	NN	_	_	_
63	Trial	trial	NN	_	_	_
64	B	b	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	6	6	CD	_	_	_
67	'	'	''	_	_	_
68	RNA	rna	NN	_	_	_
69	Decay	decay	NN	_	_	_
70	of	of	IN	_	_	_
71	Pnp	pnp	NN	_	_	_
72	-	-	:	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	YHC012	yhc012	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	at	at	IN	_	_	_
87	30	30	CD	_	_	_
88	C	c	NN	_	_	_
89	Mid	Mid	NNP	_	_	_
90	Log	Log	NNP	_	_	_
91	Rep.	Rep.	NNP	_	_	_
92	A2	a2	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	6	6	CD	_	_	_
95	'	'	''	_	_	_
96	RNA	rna	NN	_	_	_
97	Decay	decay	NN	_	_	_
98	of	of	IN	_	_	_
99	Pnp	pnp	NN	_	_	_
100	-	-	:	_	_	_
101	-LRB-	-lrb-	-LRB-	_	_	_
102	YHC012	yhc012	NN	_	_	_
103	-RRB-	-rrb-	-RRB-	_	_	_
104	in	in	IN	_	_	_
105	M9	m9	NN	_	_	_
106	+	+	CC	_	_	_
107	0.2	0.2	CD	_	_	_
108	%	%	NN	_	_	_
109	Glycerol	glycerol	NN	_	_	_
110	,	,	,	_	_	_
111	0.2	0.2	CD	_	_	_
112	%	%	NN	_	_	_
113	Tryptone	tryptone	NN	_	_	_
114	at	at	IN	_	_	_
115	30	30	CD	_	_	_
116	C	c	NN	_	_	_
117	Mid	Mid	NNP	_	_	_
118	Log	Log	NNP	_	_	_
119	Rep.	Rep.	NNP	_	_	_
120	B2	b2	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	6	6	CD	_	_	_
123	'	'	''	_	_	_
124	RNA	rna	NN	_	_	_
125	Decay	decay	NN	_	_	_
126	of	of	IN	_	_	_
127	RhlB	rhlb	NN	_	_	_
128	-	-	:	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	SU02	su02	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	in	in	IN	_	_	_
133	M9	m9	NN	_	_	_
134	+	+	CC	_	_	_
135	0.2	0.2	CD	_	_	_
136	%	%	NN	_	_	_
137	Glycerol	glycerol	NN	_	_	_
138	,	,	,	_	_	_
139	0.2	0.2	CD	_	_	_
140	%	%	NN	_	_	_
141	Tryptone	tryptone	NN	_	_	_
142	at	at	IN	_	_	_
143	30	30	CD	_	_	_
144	C	c	NN	_	_	_
145	Mid	Mid	NNP	_	_	_
146	Log	Log	NNP	_	_	_
147	Replicate	replicate	VB	_	_	_
148	A	a	DT	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	6	6	CD	_	_	_
151	'	'	''	_	_	_
152	RNA	rna	NN	_	_	_
153	Decay	decay	NN	_	_	_
154	of	of	IN	_	_	_
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	Replicate	replicate	VB	_	_	_
176	A1	a1	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	6	6	CD	_	_	_
179	'	'	''	_	_	_
180	RNA	rna	NN	_	_	_
181	Decay	decay	NN	_	_	_
182	of	of	IN	_	_	_
183	RhlB	rhlb	NN	_	_	_
184	-	-	:	_	_	_
185	-LRB-	-lrb-	-LRB-	_	_	_
186	SU02	su02	NN	_	_	_
187	-RRB-	-rrb-	-RRB-	_	_	_
188	in	in	IN	_	_	_
189	M9	m9	NN	_	_	_
190	+	+	CC	_	_	_
191	0.2	0.2	CD	_	_	_
192	%	%	NN	_	_	_
193	Glycerol	glycerol	NN	_	_	_
194	,	,	,	_	_	_
195	0.2	0.2	CD	_	_	_
196	%	%	NN	_	_	_
197	Tryptone	tryptone	NN	_	_	_
198	at	at	IN	_	_	_
199	30	30	CD	_	_	_
200	C	c	NN	_	_	_
201	Mid	Mid	NNP	_	_	_
202	Log	Log	NNP	_	_	_
203	Replicate	replicate	VB	_	_	_
204	B	b	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	6	6	CD	_	_	_
207	'	'	''	_	_	_
208	RNA	rna	NN	_	_	_
209	Decay	decay	NN	_	_	_
210	of	of	IN	_	_	_
211	RhlB	rhlb	NN	_	_	_
212	-	-	:	_	_	_
213	-LRB-	-lrb-	-LRB-	_	_	_
214	SU02	su02	NN	_	_	_
215	-RRB-	-rrb-	-RRB-	_	_	_
216	in	in	IN	_	_	_
217	M9	m9	NN	_	_	_
218	+	+	CC	_	_	_
219	0.2	0.2	CD	_	_	_
220	%	%	NN	_	_	_
221	Glycerol	glycerol	NN	_	_	_
222	,	,	,	_	_	_
223	0.2	0.2	CD	_	_	_
224	%	%	NN	_	_	_
225	Tryptone	tryptone	NN	_	_	_
226	at	at	IN	_	_	_
227	30	30	CD	_	_	_
228	C	c	NN	_	_	_
229	Mid	Mid	NNP	_	_	_
230	Log	Log	NNP	_	_	_
231	Replicate	replicate	VB	_	_	_
232	B1	b1	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	6	6	CD	_	_	_
235	'	'	''	_	_	_
236	RNA	rna	NN	_	_	_
237	Decay	decay	NN	_	_	_
238	of	of	IN	_	_	_
239	WT	WT	NNP	_	_	_
240	-LRB-	-lrb-	-LRB-	_	_	_
241	K10	k10	NN	_	_	_
242	-RRB-	-rrb-	-RRB-	_	_	_
243	in	in	IN	_	_	_
244	M9	m9	NN	_	_	_
245	0.2	0.2	CD	_	_	_
246	%	%	NN	_	_	_
247	Glycerol	glycerol	NN	_	_	_
248	0.2	0.2	CD	_	_	_
249	%	%	NN	_	_	_
250	Tryptone	tryptone	NN	_	_	_
251	40	40	CD	_	_	_
252	mM	mm	NN	KWSUPP	_	_
253	Suc	suc	NN	_	_	_
254	.	.	.	_	_	_

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	NN	_	_	_
169	72	72	CD	_	_	_
170	hr	hr	NN	_	_	_
171	colony	colony	NN	_	_	_
172	growth	growth	NN	_	_	_
173	equiv	equiv	NN	_	_	_
174	.	.	.	_	_	_

1	to	to	TO	_	_	_
2	wildtype	wildtype	JJ	_	_	_
3	colony	colony	NN	_	_	_
4	size	size	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	75th	75th	JJ	_	_	_
7	percentile	percentile	NN	_	_	_
8	shift	shift	NN	_	_	_
9	normalisation	normalisation	NN	_	_	_
10	and	and	CC	_	_	_
11	baseline	baseline	NN	_	_	_
12	adjusted	adjusted	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	7A	7a	NN	_	_	_
15	_	_	CD	_	_	_
16	MG+H	mg+h	NN	_	_	_
17	g	g	NN	_	_	_
18	_	_	CD	_	_	_
19	t60	t60	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	7B	7b	NN	_	_	_
22	_	_	CD	_	_	_
23	MG+H	mg+h	NN	_	_	_
24	g	g	NN	_	_	_
25	_	_	CD	_	_	_
26	t60	t60	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	7C	7c	NN	_	_	_
29	_	_	CD	_	_	_
30	MG+H	mg+h	NN	_	_	_
31	g	g	NN	_	_	_
32	_	_	CD	_	_	_
33	t60	t60	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	7	7	CD	_	_	_
36	_	_	NN	_	_	_
37	ESBL019	esbl019	NN	_	_	_
38	Transition	transition	NN	_	_	_
39	Repl	repl	NN	_	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	7	7	CD	_	_	_
43	.	.	.	_	_	_

1	FHI8.nIND.HUS	fhi8.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	7G	7g	NN	_	_	_
4	.0	.0	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	7	7	CD	_	_	_
7	h	h	NN	_	_	_
8	7HI	7HI	NNP	_	_	_
9	biofilm	biofilm	NN	_	_	_
10	cells	cell	NNS	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	7	7	CD	_	_	_
13	h	h	NN	_	_	_
14	biofilm	biofilm	NN	_	_	_
15	cells	cell	NNS	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	7	7	CD	_	_	_
18	_	_	SYM	_	_	_
19	HF	hf	NNS	_	_	_
20	_	_	VBP	_	_	_
21	HP	HP	NNP	_	_	_
22	_	_	SYM	_	_	_
23	noDP	nodp	NN	_	_	_
24	_	_	CD	_	_	_
25	noRh	norh	NN	_	_	_
26	-LSB-	-lsb-	-LRB-	_	_	_
27	COPRO-Seq	copro-seq	NN	_	_	_
28	-RSB-	-rsb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	7	7	CD	_	_	_
31	h	h	NN	_	_	_
32	isatin	isatin	NN	_	_	_
33	biofilm	biofilm	NN	_	_	_
34	cells	cell	NNS	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	7	7	CD	_	_	_
37	h	h	NN	_	_	_
38	suspension	suspension	NN	_	_	_
39	cells	cell	NNS	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	7-HT874-PA1	7-ht874-pa1	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	7-HT874-PA1	7-ht874-pa1	NN	_	_	_
44	-	-	:	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	7	7	CD	_	_	_
47	min	min	NN	_	_	_
48	Nov0	nov0	NN	_	_	_
49	ug/ml	ug/ml	NN	_	_	_
50	,	,	,	_	_	_
51	2	2	CD	_	_	_
52	ug	ug	NN	_	_	_
53	Say3AI	say3ai	NN	_	_	_
54	,	,	,	_	_	_
55	pdN6	pdn6	NN	_	_	_
56	RT	rt	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	7	7	CD	_	_	_
59	min	min	NN	_	_	_
60	Nov0	nov0	NN	_	_	_
61	ug/ml	ug/ml	NN	_	_	_
62	,	,	,	_	_	_
63	dnaCacrD	dnacacrd	NN	_	_	_
64	30	30	CD	_	_	_
65	min	min	NN	_	_	_
66	after	after	IN	_	_	_
67	synchr	synchr	NN	_	_	_
68	start	start	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	7	7	CD	_	_	_
71	min	min	NN	_	_	_
72	Nov500	nov500	NN	_	_	_
73	ug/ml	ug/ml	NN	_	_	_
74	,	,	,	_	_	_
75	2	2	CD	_	_	_
76	ug	ug	NN	_	_	_
77	Say3AI	say3ai	NN	_	_	_
78	,	,	,	_	_	_
79	pdN6	pdn6	NN	_	_	_
80	RT	rt	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	7	7	CD	_	_	_
83	min	min	NN	_	_	_
84	Nov500	nov500	NN	_	_	_
85	ug/ml	ug/ml	NN	_	_	_
86	,	,	,	_	_	_
87	dnaCacrD	dnacacrd	NN	_	_	_
88	30	30	CD	_	_	_
89	min	min	NN	_	_	_
90	after	after	IN	_	_	_
91	synchr	synchr	NN	_	_	_
92	start	start	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	7	7	CD	_	_	_
95	.	.	.	_	_	_

1	output	output	NN	_	_	_
2	:	:	:	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	80	80	CD	_	_	_
5	min	min	NN	_	_	_
6	,	,	,	_	_	_
7	0.8	0.8	CD	_	_	_
8	%	%	NN	_	_	_
9	butanol	butanol	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	80min-1	80min-1	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	80min-2	80min-2	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	80min-3	80min-3	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	80	80	CD	_	_	_
18	min	min	NN	_	_	_
19	Nov10	nov10	NN	_	_	_
20	ug/ml	ug/ml	NN	_	_	_
21	,	,	,	_	_	_
22	2	2	CD	_	_	_
23	ug	ug	NN	_	_	_
24	Sau3AI	sau3ai	NN	_	_	_
25	,	,	,	_	_	_
26	pdN6	pdn6	NN	_	_	_
27	RT	rt	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	80	80	CD	_	_	_
30	min	min	NN	_	_	_
31	Nov10	nov10	NN	_	_	_
32	ug/ml	ug/ml	NN	_	_	_
33	,	,	,	_	_	_
34	dnaCacrD	dnacacrd	NN	_	_	_
35	30	30	CD	_	_	_
36	min	min	NN	_	_	_
37	after	after	IN	_	_	_
38	synchr	synchr	NN	_	_	_
39	start	start	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	80	80	CD	_	_	_
42	min	min	NN	_	_	_
43	Nov5	nov5	NN	_	_	_
44	ug/ml	ug/ml	NN	_	_	_
45	,	,	,	_	_	_
46	2	2	CD	_	_	_
47	ug	ug	NN	_	_	_
48	Sau3AI	sau3ai	NN	_	_	_
49	,	,	,	_	_	_
50	pdN6	pdn6	NN	_	_	_
51	RT	rt	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	80	80	CD	_	_	_
54	min	min	NN	_	_	_
55	Nov5	nov5	NN	_	_	_
56	ug/ml	ug/ml	NN	_	_	_
57	,	,	,	_	_	_
58	dnaCacrD	dnacacrd	NN	_	_	_
59	30	30	CD	_	_	_
60	min	min	NN	_	_	_
61	after	after	IN	_	_	_
62	synchr	synchr	NN	_	_	_
63	start	start	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	80	80	CD	_	_	_
66	min	min	NN	_	_	_
67	,	,	,	_	_	_
68	unstressed	unstressed	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	81-4420	81-4420	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	83-2315	83-2315	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	86-1390	86-1390	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	86-4220	86-4220	CD	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	873-Con1	873-con1	NN	_	_	_
79	--	--	:	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	873-Con2	873-con2	NN	_	_	_
82	--	--	:	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	873-Con3	873-con3	NN	_	_	_
85	--	--	:	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	873-PA1	873-pa1	NN	_	_	_
88	--	--	:	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	873-PA2	873-pa2	NN	_	_	_
91	--	--	:	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	873-PA3	873-pa3	NN	_	_	_
94	--	--	:	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	87-4725	87-4725	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	875-Con1	875-con1	NN	_	_	_
99	--	--	:	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	875-Con2	875-con2	NN	_	_	_
102	--	--	:	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	875-Con3	875-con3	NN	_	_	_
105	--	--	:	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	875-PA1	875-pa1	NN	_	_	_
108	--	--	:	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	875-PA2	875-pa2	NN	_	_	_
111	--	--	:	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	875-PA3	875-pa3	NN	_	_	_
114	--	--	:	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	88-1861	88-1861	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	88-4299	88-4299	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	89-56-196	89-56-196	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	8A	8a	NN	_	_	_
123	_	_	CD	_	_	_
124	MG+PMA	MG+PMA	NNP	_	_	_
125	_	_	CD	_	_	_
126	t10	t10	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	8B	8b	NN	_	_	_
129	_	_	CD	_	_	_
130	MG+PMA	MG+PMA	NNP	_	_	_
131	_	_	CD	_	_	_
132	t10	t10	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	8C	8c	NN	_	_	_
135	_	_	CD	_	_	_
136	MG+PMA	MG+PMA	NNP	_	_	_
137	_	_	CD	_	_	_
138	t10	t10	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	8	8	CD	_	_	_
141	_	_	NN	_	_	_
142	ESBL019	esbl019	NN	_	_	_
143	Reverted	revert	VBD	_	_	_
144	Repl	repl	NN	_	_	_
145	2	2	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	8	8	CD	_	_	_
148	.	.	.	_	_	_

1	FHI8.IND.HUS	fhi8.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	8-HT874-PA2	8-ht874-pa2	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	8-HT874-PA2	8-ht874-pa2	NN	_	_	_
6	-	-	:	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	8	8	CD	_	_	_
9	ml	ml	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	culture	culture	NN	_	_	_
13	was	be	VBD	_	_	_
14	mixed	mix	VBN	_	_	_
15	with	with	IN	_	_	_
16	1/10V	1/10v	NN	_	_	_
17	10	10	CD	_	_	_
18	%	%	NN	_	_	_
19	phenol	phenol	NN	_	_	_
20	:	:	:	_	_	_
21	ethanol	ethanol	NN	_	_	_
22	buffer	buffer	NN	_	_	_
23	to	to	TO	_	_	_
24	stabilize	stabilize	VB	_	_	_
25	the	the	DT	_	_	_
26	RNA	rna	NN	_	_	_
27	,	,	,	_	_	_
28	and	and	CC	_	_	_
29	centrifuged	centrifuge	VBD	_	_	_
30	at	at	IN	_	_	_
31	4	4	CD	_	_	_
32	oC	oc	NN	_	_	_
33	,	,	,	_	_	_
34	4300	4300	CD	_	_	_
35	×	×	CD	_	_	_
36	g	g	NN	_	_	_
37	for	for	IN	_	_	_
38	30	30	CD	_	_	_
39	min	min	NN	_	_	_
40	to	to	TO	_	_	_
41	pellet	pellet	NN	_	_	_
42	cells	cell	NNS	_	_	_
43	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	and	and	CC	_	_	_
6	cell	cell	NN	_	_	_
7	pellets	pellet	NNS	_	_	_
8	were	be	VBD	_	_	_
9	suspended	suspend	VBN	_	_	_
10	in	in	IN	_	_	_
11	5	5	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	buffer	buffer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	2	2	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	EDTA	edta	NN	_	_	_
19	,	,	,	_	_	_
20	20	20	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	NaOAc	naoac	NN	_	_	_
23	,	,	,	_	_	_
24	pH	ph	NN	_	_	_
25	5.2	5.2	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	before	before	IN	_	_	_
28	mixing	mix	VBG	_	_	_
29	with	with	IN	_	_	_
30	equal	equal	JJ	_	_	_
31	volume	volume	NN	_	_	_
32	of	of	IN	_	_	_
33	hot	hot	JJ	_	_	_
34	acid-phenol	acid-phenol	NN	_	_	_
35	:	:	:	_	_	_
36	chloroform	chloroform	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	pH	ph	NN	_	_	_
39	4.5	4.5	CD	_	_	_
40	with	with	IN	_	_	_
41	Iso	Iso	NNP	_	_	_
42	Amyl	Amyl	NNP	_	_	_
43	Alcohol	Alcohol	NNP	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	IAA	IAA	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	,	,	,	_	_	_
48	125:25:1	125:25:1	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Ambion	Ambion	NNP	_	_	_
52	,	,	,	_	_	_
53	Austin	Austin	NNP	_	_	_
54	,	,	,	_	_	_
55	TX	TX	NNP	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	and	and	CC	_	_	_
58	incubating	incubate	VBG	_	_	_
59	at	at	IN	_	_	_
60	65	65	CD	_	_	_
61	oC	oc	NN	_	_	_
62	with	with	IN	_	_	_
63	periodic	periodic	JJ	_	_	_
64	shaking	shake	VBG	_	_	_
65	for	for	IN	_	_	_
66	10	10	CD	_	_	_
67	min	min	NN	_	_	_
68	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	at	at	IN	_	_	_
6	3220	3220	CD	_	_	_
7	×	×	CD	_	_	_
8	g	g	NN	_	_	_
9	for	for	IN	_	_	_
10	20	20	CD	_	_	_
11	min	min	NN	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	supernatant	supernatant	NN	_	_	_
15	was	be	VBD	_	_	_
16	subjected	subject	VBN	_	_	_
17	to	to	TO	_	_	_
18	further	further	JJ	_	_	_
19	extractions	extraction	NNS	_	_	_
20	with	with	IN	_	_	_
21	phenol	phenol	NN	_	_	_
22	:	:	:	_	_	_
23	chloroform	chloroform	NN	_	_	_
24	and	and	CC	_	_	_
25	chloroform	chloroform	NN	_	_	_
26	:	:	:	_	_	_
27	IAA	iaa	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	3	3	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitated	JJ	_	_	_
4	overnight	overnight	JJ	_	_	_
5	at	at	IN	_	_	_
6	-70	-70	CD	_	_	_
7	oC	oc	NN	_	_	_
8	in	in	IN	_	_	_
9	2.5	2.5	CD	_	_	_
10	volume	volume	NN	_	_	_
11	100	100	CD	_	_	_
12	%	%	NN	_	_	_
13	ethanol	ethanol	NN	_	_	_
14	and	and	CC	_	_	_
15	1/10	1/10	CD	_	_	_
16	volume	volume	NN	_	_	_
17	3	3	CD	_	_	_
18	M	m	NN	_	_	_
19	sodium	sodium	NN	SUPP	_	_
20	acetate	acetate	NN	SUPP	_	_
21	pH	ph	NN	_	_	_
22	5.2	5.2	CD	_	_	_
23	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	purification	purification	NN	_	_	_
3	and	and	CC	_	_	_
4	DNase	dnase	NN	_	_	_
5	treatment	treatment	NN	_	_	_
6	of	of	IN	_	_	_
7	RNA	rna	NN	_	_	_
8	samples	sample	NNS	_	_	_
9	were	be	VBD	_	_	_
10	done	do	VBN	_	_	_
11	with	with	IN	_	_	_
12	the	the	DT	_	_	_
13	Rneasy	Rneasy	NNP	_	_	_
14	kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Qiagen	Qiagen	NNP	_	_	_
17	,	,	,	_	_	_
18	Valencia	Valencia	NNP	_	_	_
19	,	,	,	_	_	_
20	CA	CA	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	RNA	rna	NN	_	_	_
24	quality	quality	NN	_	_	_
25	was	be	VBD	_	_	_
26	assessed	assess	VBN	_	_	_
27	on	on	IN	_	_	_
28	a	a	DT	_	_	_
29	formaldehyde-agarose	formaldehyde-agarose	NN	_	_	_
30	gel	gel	NN	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	8	8	CD	_	_	_
3	'	'	''	_	_	_
4	RNA	rna	NN	_	_	_
5	Decay	decay	NN	_	_	_
6	of	of	IN	_	_	_
7	MG1655	mg1655	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Repaired	repair	VBN	_	_	_
10	MCM	mcm	NN	_	_	_
11	3416	3416	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	in	in	IN	_	_	_
14	M9	m9	NN	_	_	_
15	+	+	CC	_	_	_
16	0.2	0.2	CD	_	_	_
17	%	%	NN	_	_	_
18	Glucose	glucose	NN	_	_	_
19	Trial	trial	NN	_	_	_
20	A	a	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	8	8	CD	_	_	_
23	'	'	''	_	_	_
24	RNA	rna	NN	_	_	_
25	Decay	decay	NN	_	_	_
26	of	of	IN	_	_	_
27	MG1655	mg1655	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Repaired	repair	VBN	_	_	_
30	NCM	NCM	NNP	_	_	_
31	3416	3416	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	in	in	IN	_	_	_
34	LB	lb	NN	_	_	_
35	at	at	IN	_	_	_
36	30	30	CD	_	_	_
37	C	c	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	8	8	CD	_	_	_
40	'	'	''	_	_	_
41	RNA	rna	NN	_	_	_
42	Decay	decay	NN	_	_	_
43	of	of	IN	_	_	_
44	MG1655	mg1655	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	Repaired	repair	VBN	_	_	_
47	NCM	NCM	NNP	_	_	_
48	3416	3416	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	in	in	IN	_	_	_
51	M9	m9	NN	_	_	_
52	+	+	CC	_	_	_
53	0.2	0.2	CD	_	_	_
54	%	%	NN	_	_	_
55	Glucose	glucose	NN	_	_	_
56	Trial	trial	NN	_	_	_
57	B	b	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	90	90	CD	_	_	_
60	min	min	NN	_	_	_
61	minus	minus	CC	_	_	_
62	ciprofloxacin	ciprofloxacin	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	90	90	CD	_	_	_
65	min	min	NN	_	_	_
66	plus	plus	CC	_	_	_
67	ciprofloxacin	ciprofloxacin	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	90	90	CD	_	_	_
70	minutes	minute	NNS	_	_	_
71	growth	growth	NN	_	_	_
72	in	in	IN	_	_	_
73	LB	LB	NNP	_	_	_
74	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
75	91-19-172	91-19-172	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
77	9A	9a	NN	_	_	_
78	3y	3y	JJ	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	9A	9a	NN	_	_	_
81	5y	5y	JJ	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	9A	9a	NN	_	_	_
84	_	_	CD	_	_	_
85	MG+PMA	mg+pma	NN	_	_	_
86	_	_	CD	_	_	_
87	t30	t30	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	9A	9a	NN	_	_	_
90	T0	t0	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	9B	9b	NN	_	_	_
93	_	_	CD	_	_	_
94	MG+PMA	mg+pma	NN	_	_	_
95	_	_	CD	_	_	_
96	t30	t30	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	9C	9c	NN	_	_	_
99	_	_	NN	_	_	_
100	MG+PMA	mg+pma	NN	_	_	_
101	_	_	CD	_	_	_
102	t30	t30	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	9	9	CD	_	_	_
105	_	_	NN	_	_	_
106	ESBL019	esbl019	NN	_	_	_
107	Coliform	coliform	NN	_	_	_
108	Repl	repl	NN	_	_	_
109	3	3	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	9	9	CD	_	_	_
112	.	.	.	_	_	_

1	FHI9.nIND.HUS	fhi9.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	9	9	CD	_	_	_
4	_	_	SYM	_	_	_
5	HF	hf	NNS	_	_	_
6	_	_	VBP	_	_	_
7	HP	HP	NNP	_	_	_
8	_	_	SYM	_	_	_
9	noDP	nodp	NN	_	_	_
10	_	_	CD	_	_	_
11	noRh	norh	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	COPRO-Seq	copro-seq	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	9-HT874-PA3	9-ht874-pa3	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	9-HT874-PA3	9-ht874-pa3	NN	_	_	_
19	-	-	:	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	A0-A1	a0-a1	NN	_	_	_
22	_	_	CD	_	_	_
23	rep1	rep1	NN	_	_	_
24	_	_	VBD	_	_	_
25	a	a	DT	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	A0-A1	a0-a1	NN	_	_	_
28	_	_	CD	_	_	_
29	rep1	rep1	NN	_	_	_
30	_	_	NN	_	_	_
31	b	b	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	A0-A1	a0-a1	NN	_	_	_
34	_	_	CD	_	_	_
35	rep2	rep2	NN	_	_	_
36	_	_	VBD	_	_	_
37	a	a	DT	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	A0-A1	a0-a1	NN	_	_	_
40	_	_	CD	_	_	_
41	rep2	rep2	NN	_	_	_
42	_	_	NN	_	_	_
43	b	b	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	A0-A1	a0-a1	NN	_	_	_
46	_	_	CD	_	_	_
47	rep3	rep3	NN	_	_	_
48	_	_	VBD	_	_	_
49	a	a	DT	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	A0-A1	a0-a1	NN	_	_	_
52	_	_	CD	_	_	_
53	rep3	rep3	NN	_	_	_
54	_	_	NN	_	_	_
55	b	b	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	A0-E0	a0-e0	NN	_	_	_
58	_	_	CD	_	_	_
59	rep1	rep1	NN	_	_	_
60	_	_	VBD	_	_	_
61	a	a	DT	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	A0-E0	a0-e0	NN	_	_	_
64	_	_	CD	_	_	_
65	rep1	rep1	NN	_	_	_
66	_	_	NN	_	_	_
67	b	b	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	A0-E0	a0-e0	NN	_	_	_
70	_	_	CD	_	_	_
71	rep2	rep2	NN	_	_	_
72	_	_	VBD	_	_	_
73	a	a	DT	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	A0-E0	a0-e0	NN	_	_	_
76	_	_	CD	_	_	_
77	rep2	rep2	NN	_	_	_
78	_	_	NN	_	_	_
79	b	b	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	A0-E0	a0-e0	NN	_	_	_
82	_	_	CD	_	_	_
83	rep3	rep3	NN	_	_	_
84	_	_	VBD	_	_	_
85	a	a	DT	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	A0-E0	a0-e0	NN	_	_	_
88	_	_	CD	_	_	_
89	rep3	rep3	NN	_	_	_
90	_	_	NN	_	_	_
91	b	b	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	A10	a10	NN	_	_	_
94	:	:	:	_	_	_
95	LJ110	lj110	NN	_	_	_
96	del	del	FW	_	_	_
97	pdhr	pdhr	FW	_	_	_
98	MMAcetat	mmacetat	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	A11	a11	NN	_	_	_
101	:	:	:	_	_	_
102	LJ110	lj110	NN	_	_	_
103	pTM30	ptm30	NN	_	_	_
104	MMAcetat	mmacetat	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	A12	a12	NN	_	_	_
107	:	:	:	_	_	_
108	LJ110	lj110	NN	_	_	_
109	pTM30pdhr	ptm30pdhr	NN	_	_	_
110	MMAcetat	mmacetat	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	A1	a1	NN	_	_	_
113	:	:	:	_	_	_
114	LJ110	lj110	NN	_	_	_
115	LBo	lbo	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	A2	a2	NN	_	_	_
118	:	:	:	_	_	_
119	LJ110	lj110	NN	_	_	_
120	del	del	FW	_	_	_
121	pdhr	pdhr	FW	_	_	_
122	LBo	lbo	FW	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	A2	a2	NN	_	_	_
125	,	,	,	_	_	_
126	osmotolerant	osmotolerant	JJ	_	_	_
127	mutant	mutant	JJ	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	A2	a2	NN	_	_	_
130	Replicate	replicate	VB	_	_	_
131	1	1	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	A2	a2	NN	_	_	_
134	Replicate	replicate	VB	_	_	_
135	2	2	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
137	A3	a3	NN	_	_	_
138	:	:	:	_	_	_
139	LJ110	lj110	NN	_	_	_
140	pTM30	ptm30	NN	_	_	_
141	LBo	lbo	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	A4	a4	NN	_	_	_
144	:	:	:	_	_	_
145	LJ110	lj110	NN	_	_	_
146	pTM30pdhr	ptm30pdhr	NN	_	_	_
147	LBo	lbo	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	A4	a4	NN	_	_	_
150	,	,	,	_	_	_
151	osmotolerant	osmotolerant	JJ	_	_	_
152	mutant	mutant	JJ	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	A4	a4	NN	_	_	_
155	Replicate	replicate	VB	_	_	_
156	1	1	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	A4	a4	NN	_	_	_
159	Replicate	replicate	VB	_	_	_
160	2	2	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
162	A5	a5	NN	_	_	_
163	:	:	:	_	_	_
164	LJ110	lj110	NN	_	_	_
165	MMPyruvat	mmpyruvat	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	A	a	DT	_	_	_
168	5	5	CD	_	_	_
169	ml	ml	NN	_	_	_
170	overnight	overnight	JJ	_	_	_
171	culture	culture	NN	_	_	_
172	of	of	IN	_	_	_
173	E.	e.	FW	_	_	_
174	coli	coli	FW	_	_	_
175	O157	o157	NN	_	_	_
176	:	:	:	_	_	_
177	H7	h7	NN	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	Sakai	Sakai	NNP	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	was	be	VBD	_	_	_
182	grown	grow	VBN	_	_	_
183	in	in	IN	_	_	_
184	Neidhardt	Neidhardt	NNP	_	_	_
185	's	's	POS	_	_	_
186	EZ	EZ	NNP	_	_	_
187	Rich	Rich	NNP	_	_	_
188	Defined	Defined	NNP	_	_	_
189	Medium	medium	NN	_	_	_
190	for	for	IN	_	_	_
191	18	18	CD	_	_	_
192	h	h	NN	_	_	_
193	at	at	IN	_	_	_
194	37C	37c	NN	_	_	_
195	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	shaken	shake	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	further	further	JJ	_	_	_
8	10	10	CD	_	_	_
9	min	min	NN	_	_	_
10	before	before	IN	_	_	_
11	2	2	CD	_	_	_
12	volumes	volume	NNS	_	_	_
13	of	of	IN	_	_	_
14	RNAprotect	rnaprotect	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	TM	tm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Ltd	Ltd	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	were	be	VBD	_	_	_
23	added	add	VBN	_	_	_
24	to	to	TO	_	_	_
25	stabilise	stabilise	VB	_	_	_
26	the	the	DT	_	_	_
27	RNA	rna	NN	_	_	_
28	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	sample	sample	NN	_	_	_
3	corresponds	correspond	VBZ	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	culture	culture	NN	_	_	_
7	that	that	WDT	_	_	_
8	was	be	VBD	_	_	_
9	not	not	RB	_	_	_
10	treated	treat	VBN	_	_	_
11	with	with	IN	_	_	_
12	menadione	menadione	NN	_	_	_
13	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	on	on	IN	_	_	_
7	different	different	JJ	_	_	_
8	occasions	occasion	NNS	_	_	_
9	to	to	TO	_	_	_
10	make	make	VB	_	_	_
11	the	the	DT	_	_	_
12	3	3	CD	_	_	_
13	replicates	replicate	VBZ	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	this	this	DT	_	_	_
17	study	study	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	5	5	CD	_	_	_
4	ml	ml	NN	_	_	_
5	overnight	overnight	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	of	of	IN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	O157	o157	NN	_	_	_
11	:	:	:	_	_	_
12	H7	h7	NN	_	_	_
13	was	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	in	in	IN	_	_	_
16	Neidhardt	Neidhardt	NNP	_	_	_
17	's	's	POS	_	_	_
18	EZ	EZ	NNP	_	_	_
19	Rich	Rich	NNP	_	_	_
20	Defined	Defined	NNP	_	_	_
21	Medium	medium	NN	_	_	_
22	for	for	IN	_	_	_
23	18	18	CD	_	_	_
24	h	h	NN	_	_	_
25	at	at	IN	_	_	_
26	37C	37c	NN	_	_	_
27	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	this	this	DT	_	_	_
24	sample	sample	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	shaken	shake	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	further	further	JJ	_	_	_
8	10	10	CD	_	_	_
9	min	min	NN	_	_	_
10	before	before	IN	_	_	_
11	2	2	CD	_	_	_
12	volumes	volume	NNS	_	_	_
13	of	of	IN	_	_	_
14	RNAprotect	rnaprotect	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	TM	tm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Ltd	Ltd	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	were	be	VBD	_	_	_
23	added	add	VBN	_	_	_
24	to	to	TO	_	_	_
25	stabilise	stabilise	VB	_	_	_
26	the	the	DT	_	_	_
27	RNA	rna	NN	_	_	_
28	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	on	on	IN	_	_	_
7	different	different	JJ	_	_	_
8	occasions	occasion	NNS	_	_	_
9	to	to	TO	_	_	_
10	make	make	VB	_	_	_
11	the	the	DT	_	_	_
12	3	3	CD	_	_	_
13	replicates	replicate	VBZ	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	this	this	DT	_	_	_
17	study	study	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	5	5	CD	_	_	_
4	ml	ml	NN	_	_	_
5	overnight	overnight	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	of	of	IN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	was	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	in	in	IN	_	_	_
12	Neidhardt	Neidhardt	NNP	_	_	_
13	's	's	POS	_	_	_
14	EZ	EZ	NNP	_	_	_
15	Rich	Rich	NNP	_	_	_
16	Defined	Defined	NNP	_	_	_
17	Medium	medium	NN	_	_	_
18	for	for	IN	_	_	_
19	18	18	CD	_	_	_
20	h	h	NN	_	_	_
21	at	at	IN	_	_	_
22	37C	37c	NN	_	_	_
23	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	shaken	shake	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	further	further	JJ	_	_	_
8	10	10	CD	_	_	_
9	min	min	NN	_	_	_
10	before	before	IN	_	_	_
11	2	2	CD	_	_	_
12	volumes	volume	NNS	_	_	_
13	of	of	IN	_	_	_
14	RNAprotect	rnaprotect	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	TM	tm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Ltd	Ltd	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	were	be	VBD	_	_	_
23	added	add	VBN	_	_	_
24	to	to	TO	_	_	_
25	stabilise	stabilise	VB	_	_	_
26	the	the	DT	_	_	_
27	RNA	rna	NN	_	_	_
28	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	sample	sample	NN	_	_	_
3	corresponds	correspond	VBZ	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	culture	culture	NN	_	_	_
7	that	that	WDT	_	_	_
8	was	be	VBD	_	_	_
9	not	not	RB	_	_	_
10	treated	treat	VBN	_	_	_
11	with	with	IN	_	_	_
12	menadione	menadione	NN	_	_	_
13	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	on	on	IN	_	_	_
7	different	different	JJ	_	_	_
8	occasions	occasion	NNS	_	_	_
9	to	to	TO	_	_	_
10	make	make	VB	_	_	_
11	the	the	DT	_	_	_
12	3	3	CD	_	_	_
13	replicates	replicate	VBZ	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	this	this	DT	_	_	_
17	study	study	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	5	5	CD	_	_	_
4	ml	ml	NN	_	_	_
5	overnight	overnight	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	of	of	IN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	was	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	in	in	IN	_	_	_
12	Neidhardt	Neidhardt	NNP	_	_	_
13	's	's	POS	_	_	_
14	EZ	EZ	NNP	_	_	_
15	Rich	Rich	NNP	_	_	_
16	Defined	Defined	NNP	_	_	_
17	Medium	medium	NN	_	_	_
18	for	for	IN	_	_	_
19	18	18	CD	_	_	_
20	h	h	NN	_	_	_
21	at	at	IN	_	_	_
22	37C	37c	NN	_	_	_
23	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
22	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	sample	sample	NN	_	_	_
3	corresponds	correspond	VBZ	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	culture	culture	NN	_	_	_
7	that	that	WDT	_	_	_
8	was	be	VBD	_	_	_
9	not	not	RB	_	_	_
10	treated	treat	VBN	_	_	_
11	with	with	IN	_	_	_
12	menadione	menadione	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	shaken	shake	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	further	further	JJ	_	_	_
8	10	10	CD	_	_	_
9	min	min	NN	_	_	_
10	before	before	IN	_	_	_
11	2	2	CD	_	_	_
12	volumes	volume	NNS	_	_	_
13	of	of	IN	_	_	_
14	RNAprotect	rnaprotect	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	TM	tm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Ltd	Ltd	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	were	be	VBD	_	_	_
23	added	add	VBN	_	_	_
24	to	to	TO	_	_	_
25	stabilise	stabilise	VB	_	_	_
26	the	the	DT	_	_	_
27	RNA	rna	NN	_	_	_
28	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	on	on	IN	_	_	_
7	different	different	JJ	_	_	_
8	occasions	occasion	NNS	_	_	_
9	to	to	TO	_	_	_
10	make	make	VB	_	_	_
11	the	the	DT	_	_	_
12	3	3	CD	_	_	_
13	replicates	replicate	VBZ	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	this	this	DT	_	_	_
17	study	study	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	5	5	CD	_	_	_
4	ml	ml	NN	_	_	_
5	overnight	overnight	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	of	of	IN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	was	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	in	in	IN	_	_	_
12	Neidhardt	Neidhardt	NNP	_	_	_
13	's	's	POS	_	_	_
14	EZ	EZ	NNP	_	_	_
15	Rich	Rich	NNP	_	_	_
16	Defined	Defined	NNP	_	_	_
17	Medium	medium	NN	_	_	_
18	for	for	IN	_	_	_
19	18	18	CD	_	_	_
20	h	h	NN	_	_	_
21	at	at	IN	_	_	_
22	37C	37c	NN	_	_	_
23	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	this	this	DT	_	_	_
24	sample	sample	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	shaken	shake	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	further	further	JJ	_	_	_
8	10	10	CD	_	_	_
9	min	min	NN	_	_	_
10	before	before	IN	_	_	_
11	2	2	CD	_	_	_
12	volumes	volume	NNS	_	_	_
13	of	of	IN	_	_	_
14	RNAprotect	rnaprotect	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	TM	tm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Ltd	Ltd	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	were	be	VBD	_	_	_
23	added	add	VBN	_	_	_
24	to	to	TO	_	_	_
25	stabilise	stabilise	VB	_	_	_
26	the	the	DT	_	_	_
27	RNA	rna	NN	_	_	_
28	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	on	on	IN	_	_	_
7	different	different	JJ	_	_	_
8	occasions	occasion	NNS	_	_	_
9	to	to	TO	_	_	_
10	make	make	VB	_	_	_
11	the	the	DT	_	_	_
12	3	3	CD	_	_	_
13	replicates	replicate	VBZ	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	this	this	DT	_	_	_
17	study	study	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	5	5	CD	_	_	_
4	ml	ml	NN	_	_	_
5	overnight	overnight	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	of	of	IN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	was	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	in	in	IN	_	_	_
12	Neidhardt	Neidhardt	NNP	_	_	_
13	's	's	POS	_	_	_
14	EZ	EZ	NNP	_	_	_
15	Rich	Rich	NNP	_	_	_
16	Defined	Defined	NNP	_	_	_
17	Medium	medium	NN	_	_	_
18	for	for	IN	_	_	_
19	18	18	CD	_	_	_
20	h	h	NN	_	_	_
21	at	at	IN	_	_	_
22	37C	37c	NN	_	_	_
23	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	this	this	DT	_	_	_
24	sample	sample	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	shaken	shake	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	further	further	JJ	_	_	_
8	10	10	CD	_	_	_
9	min	min	NN	_	_	_
10	before	before	IN	_	_	_
11	2	2	CD	_	_	_
12	volumes	volume	NNS	_	_	_
13	of	of	IN	_	_	_
14	RNAprotect	rnaprotect	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	TM	tm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Ltd	Ltd	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	were	be	VBD	_	_	_
23	added	add	VBN	_	_	_
24	to	to	TO	_	_	_
25	stabilise	stabilise	VB	_	_	_
26	the	the	DT	_	_	_
27	RNA	rna	NN	_	_	_
28	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	on	on	IN	_	_	_
7	different	different	JJ	_	_	_
8	occasions	occasion	NNS	_	_	_
9	to	to	TO	_	_	_
10	make	make	VB	_	_	_
11	the	the	DT	_	_	_
12	3	3	CD	_	_	_
13	replicates	replicate	VBZ	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	this	this	DT	_	_	_
17	study	study	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	5	5	CD	_	_	_
4	ml	ml	NN	_	_	_
5	overnight	overnight	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	of	of	IN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	was	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	in	in	IN	_	_	_
12	Neidhardt	Neidhardt	NNP	_	_	_
13	's	's	POS	_	_	_
14	EZ	EZ	NNP	_	_	_
15	Rich	Rich	NNP	_	_	_
16	Defined	Defined	NNP	_	_	_
17	Medium	medium	NN	_	_	_
18	for	for	IN	_	_	_
19	18	18	CD	_	_	_
20	h	h	NN	_	_	_
21	at	at	IN	_	_	_
22	37C	37c	NN	_	_	_
23	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
22	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	sample	sample	NN	_	_	_
3	corresponds	correspond	VBZ	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	culture	culture	NN	_	_	_
7	that	that	WDT	_	_	_
8	was	be	VBD	_	_	_
9	not	not	RB	_	_	_
10	treated	treat	VBN	_	_	_
11	with	with	IN	_	_	_
12	menadione	menadione	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	shaken	shake	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	further	further	JJ	_	_	_
8	10	10	CD	_	_	_
9	min	min	NN	_	_	_
10	before	before	IN	_	_	_
11	2	2	CD	_	_	_
12	volumes	volume	NNS	_	_	_
13	of	of	IN	_	_	_
14	RNAprotect	rnaprotect	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	TM	tm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Ltd	Ltd	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	were	be	VBD	_	_	_
23	added	add	VBN	_	_	_
24	to	to	TO	_	_	_
25	stabilise	stabilise	VB	_	_	_
26	the	the	DT	_	_	_
27	RNA	rna	NN	_	_	_
28	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	on	on	IN	_	_	_
7	different	different	JJ	_	_	_
8	occasions	occasion	NNS	_	_	_
9	to	to	TO	_	_	_
10	make	make	VB	_	_	_
11	the	the	DT	_	_	_
12	3	3	CD	_	_	_
13	replicates	replicate	VBZ	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	this	this	DT	_	_	_
17	study	study	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A6	a6	NN	_	_	_
3	:	:	:	_	_	_
4	LJ110	lj110	NN	_	_	_
5	del	del	FW	_	_	_
6	pdhr	pdhr	FW	_	_	_
7	MMPyruvat	mmpyruvat	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	A7	a7	NN	_	_	_
10	:	:	:	_	_	_
11	LJ110	lj110	NN	_	_	_
12	pTM30	ptm30	NN	_	_	_
13	MMPyruvat	mmpyruvat	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	A8	a8	NN	_	_	_
16	:	:	:	_	_	_
17	LJ110	lj110	NN	_	_	_
18	pTM30pdhr	ptm30pdhr	NN	_	_	_
19	MMPyruvat	mmpyruvat	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	A9	a9	NN	_	_	_
22	:	:	:	_	_	_
23	LJ110	lj110	NN	_	_	_
24	MMAcetat	mmacetat	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	accession	accession	NN	_	_	_
27	:	:	:	_	_	_
28	NC	nc	NN	_	_	_
29	_	_	SYM	_	_	_
30	000913.2	000913.2	CD	_	_	_
31	+	+	CC	_	_	_
32	NC	NC	NNP	_	_	_
33	_	_	SYM	_	_	_
34	000913.3	000913.3	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	accession	accession	NN	_	_	_
37	:	:	:	_	_	_
38	U00006	u00006	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	According	accord	VBG	_	_	_
41	to	to	TO	_	_	_
42	Invitrogen	Invitrogen	NNP	_	_	_
43	PureLink	PureLink	NNP	_	_	_
44	Micro-to-Midi	Micro-to-Midi	NNP	_	_	_
45	Total	Total	NNP	_	_	_
46	RNA	rna	NN	_	_	_
47	Purification	purification	NN	_	_	_
48	System	System	NNP	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	acetate	acetate	NN	SUPP	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	acetonitrile	acetonitrile	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Acid	acid	NN	_	_	_
55	adaptation	adaptation	NN	_	_	_
56	was	be	VBD	_	_	_
57	done	do	VBN	_	_	_
58	in	in	IN	_	_	_
59	DMEM	dmem	NN	_	_	_
60	at	at	IN	_	_	_
61	pH	ph	NN	_	_	_
62	5.0	5.0	CD	_	_	_
63	at	at	IN	_	_	_
64	room	room	NN	_	_	_
65	temperature	temperature	NN	_	_	_
66	,	,	,	_	_	_
67	followed	follow	VBN	_	_	_
68	by	by	IN	_	_	_
69	acid-stress	acid-stress	NN	_	_	_
70	at	at	IN	_	_	_
71	pH	ph	NN	_	_	_
72	3.0	3.0	CD	_	_	_
73	for	for	IN	_	_	_
74	30	30	CD	_	_	_
75	minutes	minute	NNS	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Acidic	Acidic	NNP	_	_	_
78	Hot	Hot	NNP	_	_	_
79	Phenol	Phenol	NNP	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Acid	Acid	NNP	_	_	_
82	shocking	shocking	JJ	_	_	_
83	was	be	VBD	_	_	_
84	done	do	VBN	_	_	_
85	in	in	IN	_	_	_
86	DMEM	dmem	NN	_	_	_
87	at	at	IN	_	_	_
88	pH	ph	NN	_	_	_
89	3.0	3.0	CD	_	_	_
90	at	at	IN	_	_	_
91	room	room	NN	_	_	_
92	temperature	temperature	NN	_	_	_
93	for	for	IN	_	_	_
94	30	30	CD	_	_	_
95	minutes	minute	NNS	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Acid	acid	NN	_	_	_
98	shocking	shocking	JJ	_	_	_
99	was	be	VBD	_	_	_
100	done	do	VBN	_	_	_
101	in	in	IN	_	_	_
102	DMEM	dmem	NN	_	_	_
103	at	at	IN	_	_	_
104	pH	ph	NN	_	_	_
105	3.0	3.0	CD	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	unbuffered	unbuffered	JJ	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	at	at	IN	_	_	_
110	room	room	NN	_	_	_
111	temperature	temperature	NN	_	_	_
112	for	for	IN	_	_	_
113	15	15	CD	_	_	_
114	minutes	minute	NNS	_	_	_
115	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
116	AcrA-Negative	AcrA-Negative	NNP	_	_	_
117	,	,	,	_	_	_
118	Multidrug	Multidrug	NNP	_	_	_
119	Efflux	Efflux	NNP	_	_	_
120	Mutant	Mutant	NNP	_	_	_
121	Strain	Strain	NNP	_	_	_
122	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
123	AcrB	acrb	NN	_	_	_
124	-	-	:	_	_	_
125	and	and	CC	_	_	_
126	EmrAB-Negative	emrab-negative	JJ	_	_	_
127	,	,	,	_	_	_
128	Multidrug	multidrug	JJ	_	_	_
129	Efflux	Efflux	NNP	_	_	_
130	Mutant	Mutant	NNP	_	_	_
131	Strain	Strain	NNP	_	_	_
132	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
133	AcrB-Negative	AcrB-Negative	NNP	_	_	_
134	,	,	,	_	_	_
135	Multidrug	Multidrug	NNP	_	_	_
136	Efflux	Efflux	NNP	_	_	_
137	Mutant	Mutant	NNP	_	_	_
138	Strain	Strain	NNP	_	_	_
139	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
140	ACSH	ACSH	NNP	_	_	_
141	_	_	VBD	_	_	_
142	Exp	Exp	NNP	_	_	_
143	_	_	NNP	_	_	_
144	CIYS	CIYS	NNP	_	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	ACSH	ACSH	NNP	_	_	_
147	_	_	VBD	_	_	_
148	Exp	Exp	NNP	_	_	_
149	_	_	NNP	_	_	_
150	CNFT	CNFT	NNP	_	_	_
151	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
152	ACSH	ACSH	NNP	_	_	_
153	_	_	VBD	_	_	_
154	Stat1	stat1	NN	_	_	_
155	_	_	CD	_	_	_
156	CNFW	CNFW	NNP	_	_	_
157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
158	ACSH	ACSH	NNP	_	_	_
159	_	_	VBD	_	_	_
160	Stat1	stat1	NN	_	_	_
161	_	_	CD	_	_	_
162	CNGG	CNGG	NNP	_	_	_
163	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
164	ACSH	ACSH	NNP	_	_	_
165	_	_	VBD	_	_	_
166	Trans	Trans	NNP	_	_	_
167	_	_	NNP	_	_	_
168	CIYT	CIYT	NNP	_	_	_
169	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
170	ACSH	ACSH	NNP	_	_	_
171	_	_	VBD	_	_	_
172	Trans	Trans	NNP	_	_	_
173	_	_	NNP	_	_	_
174	CNFU	CNFU	NNP	_	_	_
175	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
176	A	a	DT	_	_	_
177	culture	culture	NN	_	_	_
178	volume	volume	NN	_	_	_
179	of	of	IN	_	_	_
180	7	7	CD	_	_	_
181	ml	ml	NN	_	_	_
182	was	be	VBD	_	_	_
183	mixed	mix	VBN	_	_	_
184	with	with	IN	_	_	_
185	the	the	DT	_	_	_
186	same	same	JJ	_	_	_
187	volume	volume	NN	_	_	_
188	of	of	IN	_	_	_
189	boiling	boil	VBG	_	_	_
190	2	2	CD	_	_	_
191	%	%	NN	_	_	_
192	SDS	sds	NN	_	_	_
193	,	,	,	_	_	_
194	4mM	4mm	NN	_	_	_
195	EDTA	edta	NN	_	_	_
196	and	and	CC	_	_	_
197	heated	heat	VBN	_	_	_
198	at	at	IN	_	_	_
199	100	100	CD	_	_	_
200	°C	°c	NN	_	_	_
201	for	for	IN	_	_	_
202	3	3	CD	_	_	_
203	to	to	TO	_	_	_
204	5	5	CD	_	_	_
205	minutes	minute	NNS	_	_	_
206	then	then	RB	_	_	_
207	vortexed	vortex	VBD	_	_	_
208	.	.	.	_	_	_

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	NN	_	_	_
2	Adapted	adapt	VBD	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	DST160	dst160	NN	_	_	_
7	,	,	,	_	_	_
8	tolerant	tolerant	JJ	_	_	_
9	to	to	TO	_	_	_
10	high	high	JJ	_	_	_
11	succinic	succinic	JJ	_	_	_
12	acid	acid	NN	_	_	_
13	concentration	concentration	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Adapter	adapter	NN	_	_	_
17	cutting	cut	VBG	_	_	_
18	using	use	VBG	_	_	_
19	cutadapt	cutadapt	NN	_	_	_
20	,	,	,	_	_	_
21	version	version	NN	_	_	_
22	1.2.1	1.2.1	CD	_	_	_
23	,	,	,	_	_	_
24	parameters	parameter	NNS	_	_	_
25	-	-	:	_	_	_
26	e	e	SYM	_	_	_
27	0.1	0.1	CD	_	_	_
28	-	-	:	_	_	_
29	O	o	NN	_	_	_
30	1	1	CD	_	_	_
31	-	-	:	_	_	_
32	m	m	NN	_	_	_
33	12	12	CD	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	Adapter	Adapter	NNP	_	_	_
36	cutting	cut	VBG	_	_	_
37	using	use	VBG	_	_	_
38	cutadapt	cutadapt	NN	_	_	_
39	,	,	,	_	_	_
40	version	version	NN	_	_	_
41	1.8.3	1.8.3	CD	_	_	_
42	,	,	,	_	_	_
43	parameters	parameter	NNS	_	_	_
44	-	-	:	_	_	_
45	e	e	SYM	_	_	_
46	0.1	0.1	CD	_	_	_
47	-	-	:	_	_	_
48	O	o	NN	_	_	_
49	1	1	CD	_	_	_
50	-	-	:	_	_	_
51	m	m	NN	_	_	_
52	12	12	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Adapters	adapter	NNS	_	_	_
55	trimmed	trim	VBD	_	_	_
56	with	with	IN	_	_	_
57	Cutadapt	cutadapt	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	v1	v1	NN	_	_	_
60	.12	.12	CD	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Adaptive	adaptive	JJ	_	_	_
64	threshold	threshold	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	quantitation	quantitation	NN	_	_	_
67	method	method	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	uses	use	VBZ	_	_	_
70	the	the	DT	_	_	_
71	parameters	parameter	NNS	_	_	_
72	of	of	IN	_	_	_
73	the	the	DT	_	_	_
74	spot	spot	NN	_	_	_
75	diameter	diameter	NN	_	_	_
76	and	and	CC	_	_	_
77	background	background	NN	_	_	_
78	inner	inner	JJ	_	_	_
79	and	and	CC	_	_	_
80	outer	outer	JJ	_	_	_
81	dimensions	dimension	NNS	_	_	_
82	to	to	TO	_	_	_
83	create	create	VB	_	_	_
84	a	a	DT	_	_	_
85	spot	spot	NN	_	_	_
86	mask	mask	NN	_	_	_
87	and	and	CC	_	_	_
88	background	background	NN	_	_	_
89	mask	mask	NN	_	_	_
90	,	,	,	_	_	_
91	then	then	RB	_	_	_
92	refines	refine	VBZ	_	_	_
93	the	the	DT	_	_	_
94	mask	mask	NN	_	_	_
95	on	on	IN	_	_	_
96	a	a	DT	_	_	_
97	pixel-by-pixel	pixel-by-pixel	JJ	_	_	_
98	basis	basis	NN	_	_	_
99	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Adaptor	adaptor	NN	_	_	_
3	Sequences	sequence	NNS	_	_	_
4	were	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	using	use	VBG	_	_	_
7	fastx	fastx	NN	_	_	_
8	_	_	NN	_	_	_
9	clipper	clipper	NN	_	_	_
10	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	http://hannonlab.cshl.edu/fastx_toolkit/index.html	http://hannonlab.cshl.edu/fastx_toolkit/index.html	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	-	-	:	_	_	_
5	Example	example	NN	_	_	_
6	:	:	:	_	_	_
7	fastx	fastx	NN	_	_	_
8	_	_	NN	_	_	_
9	clipper	clipper	NN	_	_	_
10	-	-	:	_	_	_
11	a	a	DT	_	_	_
12	GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATG	gatcggaagagcacacgtctgaactccagtcaccgatgtatctcgtatg	NN	_	_	_
13	-	-	:	_	_	_
14	i	i	FW	_	_	_
15	DL4900	dl4900	FW	_	_	_
16	_	_	SYM	_	_	_
17	raw.fasta	raw.fasta	SYM	_	_	_
18	-	-	:	_	_	_
19	o	o	NN	_	_	_
20	DL4900	dl4900	NN	_	_	_
21	_	_	CD	_	_	_
22	clipped.fasta	clipped.fasta	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	Add	add	VBP	_	_	_
25	100	100	CD	_	_	_
26	μl	μl	NN	_	_	_
27	1	1	CD	_	_	_
28	mg/ml	mg/ml	NN	_	_	_
29	lysozyme	lysozyme	NN	_	_	_
30	buffer	buffer	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	TE	te	NN	_	_	_
33	buffer	buffer	NN	_	_	_
34	:	:	:	_	_	_
35	10	10	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	Tris-HCL	tris-hcl	NN	_	_	_
38	,	,	,	_	_	_
39	1	1	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	EDTA	edta	NN	_	_	_
42	pH	ph	NN	_	_	_
43	=	=	JJ	_	_	_
44	8.0	8.0	CD	_	_	_
45	containing	contain	VBG	_	_	_
46	1	1	CD	_	_	_
47	mg/ml	mg/ml	NN	_	_	_
48	lysozyme	lysozyme	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	.	.	.	_	_	_

1	Vortex	Vortex	NNP	_	_	_
2	for	for	IN	_	_	_
3	10	10	CD	_	_	_
4	s	s	NNS	_	_	_
5	and	and	CC	_	_	_
6	incubate	incubate	VB	_	_	_
7	at	at	IN	_	_	_
8	RT	rt	NN	_	_	_
9	for	for	IN	_	_	_
10	at	at	IN	_	_	_
11	least	least	JJS	_	_	_
12	15	15	CD	_	_	_
13	min	min	NN	_	_	_
14	.	.	.	_	_	_

1	Add	add	VB	_	_	_
2	350	350	CD	_	_	_
3	μl	μl	NN	_	_	_
4	Buffer	buffer	NN	_	_	_
5	RLT	rlt	NN	_	_	_
6	and	and	CC	_	_	_
7	vortex	vortex	NN	_	_	_
8	vigorously	vigorously	RB	_	_	_
9	.	.	.	_	_	_

1	Add	add	VB	_	_	_
2	250	250	CD	_	_	_
3	μl	μl	NN	_	_	_
4	100	100	CD	_	_	_
5	%	%	NN	_	_	_
6	ethanol	ethanol	NN	_	_	_
7	,	,	,	_	_	_
8	mix	mix	NN	_	_	_
9	by	by	IN	_	_	_
10	pipetting	pipetting	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Adenosine	Adenosine	NNP	_	_	_
3	addition	addition	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Adpater	adpater	NN	_	_	_
6	sequences	sequence	NNS	_	_	_
7	were	be	VBD	_	_	_
8	clipped	clip	VBN	_	_	_
9	with	with	IN	_	_	_
10	CutAdapt	CutAdapt	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Aeration	Aeration	NNP	_	_	_
13	was	be	VBD	_	_	_
14	initiated	initiate	VBN	_	_	_
15	at	at	IN	_	_	_
16	1	1	CD	_	_	_
17	l/min	l/min	NN	_	_	_
18	when	when	WRB	_	_	_
19	the	the	DT	_	_	_
20	culture	culture	NN	_	_	_
21	reached	reach	VBD	_	_	_
22	an	a	DT	_	_	_
23	OD	od	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	600nm	600nm	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	of	of	IN	_	_	_
28	3	3	CD	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Aerobic	Aerobic	NNP	_	_	_
3	1	1	CD	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	Aerobic	Aerobic	NNP	_	_	_
6	2	2	CD	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Aerobic	Aerobic	NNP	_	_	_
9	3	3	CD	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Aerobic	Aerobic	NNP	_	_	_
12	and	and	CC	_	_	_
13	anaerobic	anaerobic	JJ	_	_	_
14	cultures	culture	NNS	_	_	_
15	were	be	VBD	_	_	_
16	grown	grow	VBN	_	_	_
17	in	in	IN	_	_	_
18	600	600	CD	_	_	_
19	mL	ml	NN	_	_	_
20	aliquots	aliquot	NNS	_	_	_
21	of	of	IN	_	_	_
22	DM25	dm25	NN	_	_	_
23	and	and	CC	_	_	_
24	incubated	incubate	VBN	_	_	_
25	at	at	IN	_	_	_
26	37	37	CD	_	_	_
27	°C	°c	NN	_	_	_
28	with	with	IN	_	_	_
29	an	a	DT	_	_	_
30	orbital	orbital	JJ	_	_	_
31	shaking	shake	VBG	_	_	_
32	of	of	IN	_	_	_
33	150	150	CD	_	_	_
34	RPM	rpm	NN	_	_	_
35	and	and	CC	_	_	_
36	inoculated	inoculate	VBN	_	_	_
37	with	with	IN	_	_	_
38	1/100th	1/100th	JJ	_	_	_
39	volume	volume	NN	_	_	_
40	of	of	IN	_	_	_
41	overnight	overnight	JJ	_	_	_
42	culture	culture	NN	_	_	_
43	.	.	.	_	_	_

1	Aerobic	aerobic	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	for	for	IN	_	_	_
6	9	9	CD	_	_	_
7	h	h	NN	_	_	_
8	while	while	IN	_	_	_
9	anaerobic	anaerobic	JJ	_	_	_
10	cultures	culture	NNS	_	_	_
11	were	be	VBD	_	_	_
12	grown	grow	VBN	_	_	_
13	for	for	IN	_	_	_
14	16	16	CD	_	_	_
15	h.	h.	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Aerobic	aerobic	JJ	_	_	_
18	culture	culture	NN	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Aerobic	aerobic	JJ	_	_	_
21	cultures	culture	NNS	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Aerobic	Aerobic	NNP	_	_	_
24	Cultures	Cultures	NNP	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Aerobic	Aerobic	NNP	_	_	_
27	E.	E.	NNP	_	_	_
28	coli	coli	NN	_	_	_
29	exposed	expose	VBN	_	_	_
30	to	to	TO	_	_	_
31	CO-RMs	co-rm	NNS	_	_	_
32	for	for	IN	_	_	_
33	15	15	CD	_	_	_
34	minutes	minute	NNS	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	Aerobic	Aerobic	NNP	_	_	_
37	E.	E.	NNP	_	_	_
38	coli	coli	NN	_	_	_
39	not	not	RB	_	_	_
40	exposed	expose	VBN	_	_	_
41	to	to	TO	_	_	_
42	CO-RMs	co-rm	NNS	_	_	_
43	for	for	IN	_	_	_
44	15	15	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	control	control	NN	_	_	_
48	cells	cell	NNS	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
51	Aerobic	aerobic	JJ	_	_	_
52	growth	growth	NN	_	_	_
53	at	at	IN	_	_	_
54	37	37	CD	_	_	_
55	°C	°c	NN	_	_	_
56	in	in	IN	_	_	_
57	specified	specify	VBN	_	_	_
58	media	media	NNS	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	aerobic	aerobic	JJ	_	_	_
61	INPUT	input	NN	_	_	_
62	DNA	dna	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Aerobic	aerobic	JJ	_	_	_
65	MG1655	mg1655	NN	_	_	_
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	Aerobic	aerobic	JJ	_	_	_
74	MG1655	mg1655	NN	_	_	_
75	not	not	RB	_	_	_
76	exposed	expose	VBN	_	_	_
77	to	to	TO	_	_	_
78	CO-RMs	co-rm	NNS	_	_	_
79	for	for	IN	_	_	_
80	15	15	CD	_	_	_
81	minutes	minute	NNS	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	control	control	NN	_	_	_
84	cells	cell	NNS	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
87	aerobic	aerobic	JJ	_	_	_
88	reference	reference	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	affyexp	affyexp	JJ	_	_	_
91	_	_	NN	_	_	_
92	delta-arcA	delta-arca	NN	_	_	_
93	_	_	NN	_	_	_
94	glucose	glucose	NN	SUPP	_	_
95	_	_	CD	_	_	_
96	NH4CL	nh4cl	NN	_	_	_
97	_	_	NN	_	_	_
98	anaerobic	anaerobic	JJ	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	affyexp	affyexp	NN	_	_	_
101	_	_	CD	_	_	_
102	delta-arcA	delta-arca	NN	_	_	_
103	_	_	NN	_	_	_
104	glucose	glucose	NN	SUPP	_	_
105	_	_	CD	_	_	_
106	NH4CL	nh4cl	NN	_	_	_
107	_	_	NN	_	_	_
108	anaerobic	anaerobic	JJ	_	_	_
109	_	_	NN	_	_	_
110	1	1	CD	_	_	_
111	.	.	.	_	_	_

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	Affymetrix	Affymetrix	NNP	_	_	_
4	.	.	.	_	_	_

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/MM	PM/MM	NNP	_	_	_
14	difference	difference	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Affymetrix	Affymetrix	NNP	_	_	_
18	GeneChip	GeneChip	NNP	_	_	_
19	Operating	Operating	NNP	_	_	_
20	Software	Software	NNP	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	GCOS	GCOS	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	Version	Version	NNP	_	_	_
25	1.4	1.4	CD	_	_	_
26	Details	detail	NNS	_	_	_
27	:	:	:	_	_	_
28	Intra-chip	intra-chip	JJ	_	_	_
29	normalizations	normalization	NNS	_	_	_
30	were	be	VBD	_	_	_
31	performed	perform	VBN	_	_	_
32	using	use	VBG	_	_	_
33	Affymetrix	Affymetrix	NNP	_	_	_
34	Gene	Gene	NNP	_	_	_
35	Chip	Chip	NNP	_	_	_
36	Operating	Operating	NNP	_	_	_
37	Software	Software	NNP	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	GCOS	GCOS	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

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	NNP	_	_	_
2	Affymetrix	Affymetrix	NNP	_	_	_
3	Microarray	Microarray	NNP	_	_	_
4	Suite	Suite	NNP	_	_	_
5	5.0	5.0	CD	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Affymetrix	Affymetrix	NNP	_	_	_
8	Microarray	Microarray	NNP	_	_	_
9	Suite/GCOS	Suite/GCOS	NNP	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	After	after	IN	_	_	_
12	0.5	0.5	CD	_	_	_
13	M	m	NN	_	_	_
14	NaCl	nacl	NN	_	_	_
15	treatment	treatment	NN	_	_	_
16	for	for	IN	_	_	_
17	10	10	CD	_	_	_
18	min	min	NN	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	early-exponential	early-exponential	JJ	_	_	_
22	phase	phase	NN	_	_	_
23	cells	cell	NNS	_	_	_
24	,	,	,	_	_	_
25	samples	sample	NNS	_	_	_
26	were	be	VBD	_	_	_
27	collected	collect	VBN	_	_	_
28	.	.	.	_	_	_

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	NNP	_	_	_
2	After	after	IN	_	_	_
3	50	50	CD	_	_	_
4	hours	hour	NNS	_	_	_
5	,	,	,	_	_	_
6	samples	sample	NNS	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	10	10	CD	_	_	_
9	ml	ml	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	were	be	VBD	_	_	_
12	harvested	harvest	VBN	_	_	_
13	directly	directly	RB	_	_	_
14	into	into	IN	_	_	_
15	RNA	rna	NN	_	_	_
16	Protect	protect	VB	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	Qiagen	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	to	to	TO	_	_	_
21	stabilize	stabilize	VB	_	_	_
22	RNA	rna	NN	_	_	_
23	,	,	,	_	_	_
24	and	and	CC	_	_	_
25	total	total	JJ	_	_	_
26	RNA	rna	NN	_	_	_
27	was	be	VBD	_	_	_
28	purified	purify	VBN	_	_	_
29	using	use	VBG	_	_	_
30	Qiagen	Qiagen	NNP	_	_	_
31	's	's	POS	_	_	_
32	RNeasy	RNeasy	NNP	_	_	_
33	Mini	Mini	NNP	_	_	_
34	kit	kit	NN	_	_	_
35	as	as	IN	_	_	_
36	recommended	recommend	VBN	_	_	_
37	by	by	IN	_	_	_
38	the	the	DT	_	_	_
39	suppliers	supplier	NNS	_	_	_
40	.	.	.	_	_	_

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	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	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	NNP	_	_	_
2	After	after	IN	_	_	_
3	6	6	CD	_	_	_
4	hours	hour	NNS	_	_	_
5	of	of	IN	_	_	_
6	growth	growth	NN	_	_	_
7	both	both	CC	_	_	_
8	control	control	NN	_	_	_
9	and	and	CC	_	_	_
10	test	test	NN	_	_	_
11	strains	strain	NNS	_	_	_
12	were	be	VBD	_	_	_
13	induced	induce	VBN	_	_	_
14	with	with	IN	_	_	_
15	0.5	0.5	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	IPTG	iptg	NN	_	_	_
18	and	and	CC	_	_	_
19	harvested	harvest	VBN	_	_	_
20	2	2	CD	_	_	_
21	hours	hour	NNS	_	_	_
22	post-induction	post-induction	JJ	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	backgroud	backgroud	NN	_	_	_
4	correction	correction	NN	_	_	_
5	and	and	CC	_	_	_
6	total	total	JJ	_	_	_
7	intensity	intensity	NN	_	_	_
8	normalization	normalization	NN	_	_	_
9	,	,	,	_	_	_
10	ratio	ratio	NN	_	_	_
11	to	to	TO	_	_	_
12	reference	reference	NN	_	_	_
13	were	be	VBD	_	_	_
14	calculated	calculate	VBN	_	_	_
15	and	and	CC	_	_	_
16	log	log	NN	_	_	_
17	base	base	NN	_	_	_
18	2	2	CD	_	_	_
19	transformed	transform	VBN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	After	after	IN	_	_	_
22	chilling	chill	VBG	_	_	_
23	on	on	IN	_	_	_
24	ice	ice	NN	_	_	_
25	,	,	,	_	_	_
26	each	each	DT	_	_	_
27	100-ml	100-ml	JJ	_	_	_
28	culture	culture	NN	_	_	_
29	was	be	VBD	_	_	_
30	mixed	mix	VBN	_	_	_
31	with	with	IN	_	_	_
32	25	25	CD	_	_	_
33	ml	ml	NN	_	_	_
34	ice-cold	ice-cold	JJ	_	_	_
35	ethanol/phenol	ethanol/phenol	NN	_	_	_
36	solution	solution	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	5	5	CD	_	_	_
39	%	%	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	v/v	v/v	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	,	,	,	_	_	_
44	water-saturated	water-saturated	JJ	_	_	_
45	phenol	phenol	NN	_	_	_
46	in	in	IN	_	_	_
47	95	95	CD	_	_	_
48	%	%	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	v/v	v/v	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	ethanol	ethanol	NN	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	.	.	.	_	_	_

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	7,000	7,000	CD	_	_	_
8	g	g	NN	_	_	_
9	for	for	IN	_	_	_
10	2	2	CD	_	_	_
11	min	min	NN	_	_	_
12	at	at	IN	_	_	_
13	4	4	CD	_	_	_
14	°C	°c	NN	_	_	_
15	,	,	,	_	_	_
16	flash-frozen	flash-frozen	JJ	_	_	_
17	with	with	IN	_	_	_
18	dry	dry	JJ	_	_	_
19	ice	ice	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	stored	store	VBD	_	_	_
23	at	at	IN	_	_	_
24	--	--	:	_	_	_
25	80	80	CD	_	_	_
26	°C	°c	NN	_	_	_
27	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	for	for	IN	_	_	_
5	each	each	DT	_	_	_
6	sample	sample	NN	_	_	_
7	were	be	VBD	_	_	_
8	mixed	mix	VBN	_	_	_
9	together	together	RB	_	_	_
10	for	for	IN	_	_	_
11	determination	determination	NN	_	_	_
12	of	of	IN	_	_	_
13	transcriptional	transcriptional	JJ	_	_	_
14	profiles	profile	NNS	_	_	_
15	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	collected	collect	VBN	_	_	_
8	bacterial	bacterial	JJ	_	_	_
9	cells	cell	NNS	_	_	_
10	using	use	VBG	_	_	_
11	TRIzol	trizol	NN	_	_	_
12	reagent	reagent	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Thermo	Thermo	NNP	_	_	_
15	Fisher	Fisher	NNP	_	_	_
16	Scientifc	Scientifc	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	at	at	IN	_	_	_
26	42	42	CD	_	_	_
27	°C	°c	NN	_	_	_
28	for	for	IN	_	_	_
29	1	1	CD	_	_	_
30	h.	h.	NNP	_	_	_
31	Next	Next	NNP	_	_	_
32	,	,	,	_	_	_
33	200	200	CD	_	_	_
34	µl	µl	NN	_	_	_
35	proteinase	proteinase	NN	_	_	_
36	K	k	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	20	20	CD	_	_	_
39	mg/ml	mg/ml	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	were	be	VBD	_	_	_
42	added	add	VBN	_	_	_
43	and	and	CC	_	_	_
44	samples	sample	NNS	_	_	_
45	incubated	incubate	VBN	_	_	_
46	for	for	IN	_	_	_
47	2	2	CD	_	_	_
48	h	h	NN	_	_	_
49	at	at	IN	_	_	_
50	42	42	CD	_	_	_
51	and	and	CC	_	_	_
52	6	6	CD	_	_	_
53	h	h	NN	_	_	_
54	at	at	IN	_	_	_
55	65	65	CD	_	_	_
56	°C	°c	NN	_	_	_
57	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	with	with	IN	_	_	_
5	phenol	phenol	NN	_	_	_
6	and	and	CC	_	_	_
7	chlorophorm	chlorophorm	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	After	after	IN	_	_	_
10	dividing	divide	VBG	_	_	_
11	sequence	sequence	NN	_	_	_
12	runs	run	NNS	_	_	_
13	by	by	IN	_	_	_
14	barcode	barcode	NN	_	_	_
15	,	,	,	_	_	_
16	we	we	PRP	_	_	_
17	mapped	map	VBD	_	_	_
18	the	the	DT	_	_	_
19	reads	read	VBZ	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	relevant	relevant	JJ	_	_	_
23	genomes	genome	NNS	_	_	_
24	using	use	VBG	_	_	_
25	the	the	DT	_	_	_
26	ssaha2	ssaha2	NN	_	_	_
27	algorithm	algorithm	NN	_	_	_
28	.	.	.	_	_	_

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	After	after	IN	_	_	_
3	each	each	DT	_	_	_
4	sequenced	sequence	VBN	_	_	_
5	fragments	fragment	NNS	_	_	_
6	were	be	VBD	_	_	_
7	aligned	align	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	reference	reference	NN	_	_	_
11	genome	genome	NN	_	_	_
12	using	use	VBG	_	_	_
13	Bowtie	Bowtie	NNP	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	position	position	NN	_	_	_
17	of	of	IN	_	_	_
18	each	each	DT	_	_	_
19	alignment	alignment	NN	_	_	_
20	is	be	VBZ	_	_	_
21	distributed	distribute	VBN	_	_	_
22	into	into	IN	_	_	_
23	several	several	JJ	_	_	_
24	nucleotides	nucleotide	NNS	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	center	center	NN	_	_	_
28	of	of	IN	_	_	_
29	the	the	DT	_	_	_
30	footprint	footprint	NN	_	_	_
31	.	.	.	_	_	_

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	After	after	IN	_	_	_
20	exposed	expose	VBN	_	_	_
21	under	under	IN	_	_	_
22	the	the	DT	_	_	_
23	red	red	JJ	_	_	_
24	light	light	NN	_	_	_
25	with	with	IN	_	_	_
26	a	a	DT	_	_	_
27	specific	specific	JJ	_	_	_
28	ON/OFF	on/off	NN	_	_	_
29	frequency	frequency	NN	_	_	_
30	for	for	IN	_	_	_
31	10	10	CD	_	_	_
32	hours	hour	NNS	_	_	_
33	,	,	,	_	_	_
34	1	1	CD	_	_	_
35	ml	ml	NN	_	_	_
36	bacterial	bacterial	JJ	_	_	_
37	culture	culture	NN	_	_	_
38	was	be	VBD	_	_	_
39	sampled	sample	VBN	_	_	_
40	and	and	CC	_	_	_
41	the	the	DT	_	_	_
42	bacterial	bacterial	JJ	_	_	_
43	cells	cell	NNS	_	_	_
44	were	be	VBD	_	_	_
45	collected	collect	VBN	_	_	_
46	at	at	IN	_	_	_
47	4	4	CD	_	_	_
48	°C	°c	NN	_	_	_
49	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	of	of	IN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	was	be	VBD	_	_	_
8	extracted	extract	VBN	_	_	_
9	using	use	VBG	_	_	_
10	RNAprep	rnaprep	NN	_	_	_
11	pure	pure	JJ	_	_	_
12	Cell/Bacteria	Cell/Bacteria	NNP	_	_	_
13	Kit	kit	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	TIANGEN	TIANGEN	NNP	_	_	_
16	,	,	,	_	_	_
17	DP430	dp430	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	preserved	preserve	VBN	_	_	_
21	at	at	IN	_	_	_
22	-80	-80	CD	_	_	_
23	°C	°c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	normalization	normalization	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	expression	expression	NN	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	gene	gene	NN	_	_	_
10	was	be	VBD	_	_	_
11	calculated	calculate	VBN	_	_	_
12	by	by	IN	_	_	_
13	a	a	DT	_	_	_
14	RMA-summarization	rma-summarization	NN	_	_	_
15	procedure	procedure	NN	_	_	_
16	within	within	IN	_	_	_
17	each	each	DT	_	_	_
18	growth	growth	NN	_	_	_
19	condition	condition	NN	_	_	_
20	.	.	.	_	_	_

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	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://www.bioinformatica.unito.it/oneChannelGUI/	http://www.bioinformatica.unito.it/onechannelgui/	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	perform	perform	VB	_	_	_
14	a	a	DT	_	_	_
15	differential	differential	JJ	_	_	_
16	expression	expression	NN	_	_	_
17	analysis	analysis	NN	_	_	_
18	.	.	.	_	_	_

1	As	as	IN	_	_	_
2	the	the	DT	_	_	_
3	dataset	dataset	NN	_	_	_
4	is	be	VBZ	_	_	_
5	limited	limit	VBN	_	_	_
6	in	in	IN	_	_	_
7	number	number	NN	_	_	_
8	of	of	IN	_	_	_
9	samples	sample	NNS	_	_	_
10	and	and	CC	_	_	_
11	replicates	replicate	VBZ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	4	4	CD	_	_	_
14	GeneChips	genechip	NNS	_	_	_
15	hybridized	hybridize	VBD	_	_	_
16	,	,	,	_	_	_
17	2	2	CD	_	_	_
18	replicates	replicate	VBZ	_	_	_
19	for	for	IN	_	_	_
20	each	each	DT	_	_	_
21	condition	condition	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	we	we	PRP	_	_	_
24	decided	decide	VBD	_	_	_
25	to	to	TO	_	_	_
26	apply	apply	VB	_	_	_
27	a	a	DT	_	_	_
28	simple	simple	JJ	_	_	_
29	non-parametric	non-parametric	JJ	_	_	_
30	statistical	statistical	JJ	_	_	_
31	method	method	NN	_	_	_
32	based	base	VBN	_	_	_
33	on	on	IN	_	_	_
34	ranks	rank	NNS	_	_	_
35	of	of	IN	_	_	_
36	fold	fold	JJ	_	_	_
37	changes	change	NNS	_	_	_
38	to	to	TO	_	_	_
39	perform	perform	VB	_	_	_
40	a	a	DT	_	_	_
41	two-class	two-class	JJ	_	_	_
42	paired	paired	JJ	_	_	_
43	differential	differential	JJ	_	_	_
44	analysis	analysis	NN	_	_	_
45	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	select	select	VB	_	_	_
3	only	only	RB	_	_	_
4	significatively	significatively	RB	_	_	_
5	differentially	differentially	RB	_	_	_
6	expressed	express	VBN	_	_	_
7	genes	gene	NNS	_	_	_
8	we	we	PRP	_	_	_
9	set	set	VBD	_	_	_
10	the	the	DT	_	_	_
11	following	follow	VBG	_	_	_
12	parameters	parameter	NNS	_	_	_
13	for	for	IN	_	_	_
14	the	the	DT	_	_	_
15	Rank	Rank	NNP	_	_	_
16	Product	product	NN	_	_	_
17	analysis	analysis	NN	_	_	_
18	:	:	:	_	_	_
19	100	100	CD	_	_	_
20	permutations	permutation	NNS	_	_	_
21	and	and	CC	_	_	_
22	0.1	0.1	CD	_	_	_
23	cut-off	cut-off	JJ	_	_	_
24	percentage	percentage	NN	_	_	_
25	of	of	IN	_	_	_
26	false	false	JJ	_	_	_
27	positives	positive	NNS	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	pfp	pfp	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	which	which	WDT	_	_	_
32	corresponds	correspond	VBZ	_	_	_
33	to	to	TO	_	_	_
34	a	a	DT	_	_	_
35	p-value	p-value	NN	_	_	_
36	<	<	JJR	_	_	_
37	0.01	0.01	CD	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	reaching	reach	VBG	_	_	_
4	an	a	DT	_	_	_
5	OD600nm	od600nm	NN	_	_	_
6	of	of	IN	_	_	_
7	0.9	0.9	CD	_	_	_
8	,	,	,	_	_	_
9	cell	cell	NN	_	_	_
10	cultures	culture	NNS	_	_	_
11	were	be	VBD	_	_	_
12	placed	place	VBN	_	_	_
13	immediately	immediately	RB	_	_	_
14	in	in	IN	_	_	_
15	a	a	DT	_	_	_
16	shaking	shake	VBG	_	_	_
17	water	water	NN	_	_	_
18	bath	bath	NN	_	_	_
19	along	along	IN	_	_	_
20	with	with	IN	_	_	_
21	another	another	DT	_	_	_
22	BHI	BHI	NNP	_	_	_
23	flask	flask	NN	_	_	_
24	carrying	carry	VBG	_	_	_
25	a	a	DT	_	_	_
26	type	type	NN	_	_	_
27	T	t	NN	_	_	_
28	thermocouple	thermocouple	NN	_	_	_
29	connected	connect	VBN	_	_	_
30	to	to	TO	_	_	_
31	a	a	DT	_	_	_
32	MultiPaq	MultiPaq	NNP	_	_	_
33	21	21	CD	_	_	_
34	datalogger	datalogger	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Datapaq	Datapaq	NNP	_	_	_
37	Inc.	Inc.	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	for	for	IN	_	_	_
40	temperature	temperature	NN	_	_	_
41	profile	profile	NN	_	_	_
42	and	and	CC	_	_	_
43	the	the	DT	_	_	_
44	process	process	NN	_	_	_
45	lethality	lethality	NN	_	_	_
46	values	value	NNS	_	_	_
47	monitoring	monitor	VBG	_	_	_
48	in	in	IN	_	_	_
49	real	real	JJ	_	_	_
50	time	time	NN	_	_	_
51	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	the	the	DT	_	_	_
4	final	final	JJ	_	_	_
5	wash	wash	NN	_	_	_
6	&	&	CC	_	_	_
7	staining	staining	NN	_	_	_
8	step	step	NN	_	_	_
9	,	,	,	_	_	_
10	Affymetrix	Affymetrix	NNP	_	_	_
11	GeneChip	GeneChip	NNP	_	_	_
12	®	®	NNP	_	_	_
13	E.coli	E.coli	NNP	_	_	_
14	Genome	Genome	NNP	_	_	_
15	array	array	NN	_	_	_
16	was	be	VBD	_	_	_
17	scanned	scan	VBN	_	_	_
18	using	use	VBG	_	_	_
19	Affymetrix	Affymetrix	NNP	_	_	_
20	Model	Model	NNP	_	_	_
21	3000	3000	CD	_	_	_
22	G7	G7	NNP	_	_	_
23	scanner	scanner	NN	_	_	_
24	and	and	CC	_	_	_
25	the	the	DT	_	_	_
26	image	image	NN	_	_	_
27	data	datum	NNS	_	_	_
28	was	be	VBD	_	_	_
29	extracted	extract	VBN	_	_	_
30	through	through	IN	_	_	_
31	Affymetrix	Affymetrix	NNP	_	_	_
32	Commnad	Commnad	NNP	_	_	_
33	Console	Console	NNP	_	_	_
34	software	software	NN	_	_	_
35	.	.	.	_	_	_

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	AG102MB	ag102mb	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	hyper-resistant	hyper-resistant	JJ	_	_	_
10	AG102	ag102	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	marR1	marr1	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

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	AG102	ag102	NN	_	_	_
3	was	be	VBD	_	_	_
4	previously	previously	RB	_	_	_
5	derived	derive	VBN	_	_	_
6	from	from	IN	_	_	_
7	AG100	ag100	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	K-12	k-12	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	.	.	.	_	_	_

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	A	a	NN	_	_	_
3	generalized	generalize	VBN	_	_	_
4	linear	linear	JJ	_	_	_
5	model	model	NN	_	_	_
6	likelihood	likelihood	NN	_	_	_
7	ratio	ratio	NN	_	_	_
8	test	test	NN	_	_	_
9	was	be	VBD	_	_	_
10	performed	perform	VBN	_	_	_
11	to	to	TO	_	_	_
12	test	test	VB	_	_	_
13	for	for	IN	_	_	_
14	differential	differential	JJ	_	_	_
15	expression	expression	NN	_	_	_
16	between	between	IN	_	_	_
17	groups	group	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	HUS	hus	NNS	_	_	_
20	vs.	vs.	CC	_	_	_
21	non-HUS	non-hus	JJ	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	condition	condition	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	induced	induce	VBN	_	_	_
27	vs.	vs.	CC	_	_	_
28	non-induced	non-induced	JJ	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	with	with	IN	_	_	_
32	FDR-adjusted	fdr-adjusted	JJ	_	_	_
33	p-values	p-values	NN	_	_	_
34	<	<	JJR	_	_	_
35	0.05	0.05	CD	_	_	_
36	regarded	regard	VBN	_	_	_
37	as	as	IN	_	_	_
38	statistically	statistically	RB	_	_	_
39	significant	significant	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	agent	agent	NN	_	_	_
42	:	:	:	_	_	_
43	0.05	0.05	CD	_	_	_
44	mg/ml	mg/ml	NN	_	_	_
45	Phloretin	phloretin	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	agent	agent	NN	_	_	_
48	:	:	:	_	_	_
49	0.5	0.5	CD	_	_	_
50	%	%	NN	_	_	_
51	honey	honey	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	agent	agent	NN	_	_	_
54	:	:	:	_	_	_
55	1x	1x	NN	_	_	_
56	CORM2	corm2	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	agent	agent	NN	_	_	_
59	:	:	:	_	_	_
60	1x	1x	NN	_	_	_
61	vehicle	vehicle	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	agent	agent	NN	_	_	_
64	:	:	:	_	_	_
65	20x	20x	CD	_	_	_
66	CORM2	corm2	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	agent	agent	NN	_	_	_
69	:	:	:	_	_	_
70	20x	20x	CD	_	_	_
71	vehicle	vehicle	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	agent	agent	NN	_	_	_
74	:	:	:	_	_	_
75	control	control	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
77	agent	agent	NN	_	_	_
78	:	:	:	_	_	_
79	control	control	NN	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	1	1	CD	_	_	_
82	ml	ml	NN	_	_	_
83	of	of	IN	_	_	_
84	LB	lb	NN	MED	_	_
85	broth	broth	NN	MED	_	_
86	added	add	VBD	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	agent	agent	NN	_	_	_
90	:	:	:	_	_	_
91	CORM-401	corm-401	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	agent	agent	NN	_	_	_
94	:	:	:	_	_	_
95	DPD	dpd	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
97	agent	agent	NN	_	_	_
98	:	:	:	_	_	_
99	DPD	dpd	NN	_	_	_
100	and	and	CC	_	_	_
101	rifampicin	rifampicin	NN	SUPP	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	agent	agent	NN	_	_	_
104	:	:	:	_	_	_
105	ethanol	ethanol	NN	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	1	1	CD	_	_	_
108	ml	ml	NN	_	_	_
109	of	of	IN	_	_	_
110	ethanol	ethanol	NN	_	_	_
111	20	20	CD	_	_	_
112	%	%	NN	_	_	_
113	added	add	VBD	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	agent	agent	NN	_	_	_
117	:	:	:	_	_	_
118	Fe	Fe	NNP	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
120	agent	agent	NN	_	_	_
121	:	:	:	_	_	_
122	Fe	Fe	NNP	_	_	_
123	and	and	CC	_	_	_
124	rifampicin	rifampicin	NN	SUPP	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	agent	agent	NN	_	_	_
127	:	:	:	_	_	_
128	glycolaldehyde	glycolaldehyde	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	agent	agent	NN	_	_	_
131	:	:	:	_	_	_
132	H2O	h2o	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	agent	agent	NN	_	_	_
135	:	:	:	_	_	_
136	no	no	DT	_	_	_
137	triclosan	triclosan	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	agent	agent	NN	_	_	_
140	:	:	:	_	_	_
141	polyphenols	polyphenol	NNS	_	_	_
142	-LRB-	-lrb-	-LRB-	_	_	_
143	1	1	CD	_	_	_
144	ml	ml	NN	_	_	_
145	of	of	IN	_	_	_
146	OVWPE	ovwpe	NN	_	_	_
147	diluted	dilute	VBN	_	_	_
148	in	in	IN	_	_	_
149	ethanol	ethanol	NN	_	_	_
150	20	20	CD	_	_	_
151	%	%	NN	_	_	_
152	added	add	VBD	_	_	_
153	-RRB-	-rrb-	-RRB-	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	agent	agent	NN	_	_	_
156	:	:	:	_	_	_
157	triclosan	triclosan	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	agent	agent	NN	_	_	_
160	:	:	:	_	_	_
161	ZnSO4	znso4	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	Agilent	Agilent	NNP	_	_	_
164	Feature	Feature	NNP	_	_	_
165	Extraction	Extraction	NNP	_	_	_
166	Software	Software	NNP	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	v	v	LS	_	_	_
169	10.10.1.1	10.10.1.1	CD	_	_	_
170	-RRB-	-rrb-	-RRB-	_	_	_
171	was	be	VBD	_	_	_
172	used	use	VBN	_	_	_
173	for	for	IN	_	_	_
174	background	background	NN	_	_	_
175	subtraction	subtraction	NN	_	_	_
176	and	and	CC	_	_	_
177	LOWESS	lowess	NN	_	_	_
178	normalization	normalization	NN	_	_	_
179	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Agilent	Agilent	NNP	_	_	_
3	Feature	Feature	NNP	_	_	_
4	Extraction	Extraction	NNP	_	_	_
5	Software	Software	NNP	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	v	v	LS	_	_	_
8	8.5.1.1	8.5.1.1	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	for	for	IN	_	_	_
13	background	background	NN	_	_	_
14	subtraction	subtraction	NN	_	_	_
15	and	and	CC	_	_	_
16	LOWESS	lowess	NN	_	_	_
17	normalization	normalization	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Agilent	Agilent	NNP	_	_	_
3	Feature	Feature	NNP	_	_	_
4	Extraction	Extraction	NNP	_	_	_
5	Software	Software	NNP	_	_	_
6	v.	v.	CC	_	_	_
7	9.5.3.1	9.5.3.1	CD	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	background	background	NN	_	_	_
12	subtraction	subtraction	NN	_	_	_
13	and	and	CC	_	_	_
14	LOWESS	lowess	NN	_	_	_
15	normalization	normalization	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Agilent	Agilent	NNP	_	_	_
3	Feature	Feature	NNP	_	_	_
4	Extraction	Extraction	NNP	_	_	_
5	Software	Software	NNP	_	_	_
6	v.	v.	CC	_	_	_
7	9.5.3.1	9.5.3.1	CD	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	background	background	NN	_	_	_
12	subtraction	subtraction	NN	_	_	_
13	and	and	CC	_	_	_
14	LOWESS	lowess	NN	_	_	_
15	normalization	normalization	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Agilent	Agilent	NNP	_	_	_
3	Feature	Feature	NNP	_	_	_
4	Extraction	Extraction	NNP	_	_	_
5	Software	Software	NNP	_	_	_
6	version	version	NN	_	_	_
7	10.5.1.1	10.5.1.1	CD	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Agilent	Agilent	NNP	_	_	_
3	Feature	Feature	NNP	_	_	_
4	Extract	extract	NN	_	_	_
5	software	software	NN	_	_	_
6	performed	perform	VBN	_	_	_
7	background	background	NN	_	_	_
8	normalization	normalization	NN	_	_	_
9	and	and	CC	_	_	_
10	LOWESS	lowess	NN	_	_	_
11	correction	correction	NN	_	_	_
12	for	for	IN	_	_	_
13	dye	dye	VB	_	_	_
14	bias	bias	NN	_	_	_
15	.	.	.	_	_	_

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	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	agitation	agitation	NN	_	_	_
14	speed	speed	NN	_	_	_
15	:	:	:	_	_	_
16	1200	1200	CD	_	_	_
17	rpm	rpm	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	agitation	agitation	NN	_	_	_
20	speed	speed	NN	_	_	_
21	:	:	:	_	_	_
22	600	600	CD	_	_	_
23	rpm	rpm	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	agno3	agno3	NN	_	_	_
26	concentration	concentration	NN	_	_	_
27	in	in	IN	_	_	_
28	µm	µm	NN	_	_	_
29	:	:	:	_	_	_
30	0	0	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	agno3	agno3	NN	_	_	_
33	concentration	concentration	NN	_	_	_
34	in	in	IN	_	_	_
35	µm	µm	NN	_	_	_
36	:	:	:	_	_	_
37	5	5	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	agno3	agno3	NN	_	_	_
40	concentration	concentration	NN	_	_	_
41	in	in	IN	_	_	_
42	µm	µm	NN	_	_	_
43	:	:	:	_	_	_
44	6.5	6.5	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	agno3	agno3	NN	_	_	_
47	concentration	concentration	NN	_	_	_
48	in	in	IN	_	_	_
49	µm	µm	NN	_	_	_
50	:	:	:	_	_	_
51	8.5	8.5	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
53	Alanine	alanine	NN	_	_	_
54	addition	addition	NN	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Alert	Alert	NNP	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Algorithm	Algorithm	NNP	_	_	_
59	:	:	:	_	_	_
60	ExpressionStat	ExpressionStat	NNP	_	_	_
61	5.0	5.0	CD	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Affymetrix	Affymetrix	NNP	_	_	_
64	Microarray	Microarray	NNP	_	_	_
65	Suite	Suite	NNP	_	_	_
66	Version	Version	NNP	_	_	_
67	5.0	5.0	CD	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Aligned	Aligned	NNP	_	_	_
71	reads	read	VBZ	_	_	_
72	were	be	VBD	_	_	_
73	designated	designate	VBN	_	_	_
74	to	to	TO	_	_	_
75	top	top	JJ	_	_	_
76	and	and	CC	_	_	_
77	bottom	bottom	JJ	_	_	_
78	strands	strand	NNS	_	_	_
79	using	use	VBG	_	_	_
80	Samtools	Samtools	NNP	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	Aligned	Aligned	NNP	_	_	_
83	to	to	TO	_	_	_
84	NC	NC	NNP	_	_	_
85	_	_	SYM	_	_	_
86	000913.3	000913.3	CD	_	_	_
87	with	with	IN	_	_	_
88	bwa	bwa	NN	_	_	_
89	version	version	NN	_	_	_
90	0.7.7	0.7.7	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
92	Alignment	alignment	NN	_	_	_
93	,	,	,	_	_	_
94	Quantiatino	quantiatino	NN	_	_	_
95	and	and	CC	_	_	_
96	Normalization	normalization	NN	_	_	_
97	,	,	,	_	_	_
98	Differential	differential	JJ	_	_	_
99	Expression	expression	NN	_	_	_
100	:	:	:	_	_	_
101	We	we	PRP	_	_	_
102	used	use	VBD	_	_	_
103	the	the	DT	_	_	_
104	SPARTA	SPARTA	NNP	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	version	version	NN	_	_	_
107	1	1	CD	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	software	software	NN	_	_	_
110	package	package	NN	_	_	_
111	for	for	IN	_	_	_
112	alignment	alignment	NN	_	_	_
113	,	,	,	_	_	_
114	differential	differential	JJ	_	_	_
115	expression	expression	NN	_	_	_
116	analysis	analysis	NN	_	_	_
117	,	,	,	_	_	_
118	and	and	CC	_	_	_
119	post-analysis	post-analysis	JJ	_	_	_
120	diagnostics	diagnostic	NNS	_	_	_
121	.	.	.	_	_	_

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	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	NN	_	_	_
2	alignment	alignment	NN	_	_	_
3	:	:	:	_	_	_
4	STAR	star	NN	_	_	_
5	2.4.0	2.4.0	CD	_	_	_
6	i	i	FW	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
8	Alignment	alignment	NN	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	E.	e.	FW	_	_	_
12	coli	coli	FW	_	_	_
13	K12	k12	NN	_	_	_
14	MG1655	mg1655	NN	_	_	_
15	genome	genome	NN	_	_	_
16	sequence	sequence	NN	_	_	_
17	was	be	VBD	_	_	_
18	performed	perform	VBN	_	_	_
19	using	use	VBG	_	_	_
20	TMAP	tmap	NN	_	_	_
21	map4	map4	NN	_	_	_
22	algorithm	algorithm	NN	_	_	_
23	with	with	IN	_	_	_
24	5	5	CD	_	_	_
25	'	'	''	_	_	_
26	and	and	CC	_	_	_
27	3	3	CD	_	_	_
28	'	'	''	_	_	_
29	soft-clipping	soft-clipping	JJ	_	_	_
30	and	and	CC	_	_	_
31	a	a	DT	_	_	_
32	minimum	minimum	JJ	_	_	_
33	seed	seed	NN	_	_	_
34	length	length	NN	_	_	_
35	of	of	IN	_	_	_
36	20	20	CD	_	_	_
37	nt	nt	NNS	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	A	a	DT	_	_	_
40	Linker-1	linker-1	NN	_	_	_
41	adapter	adapter	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	IDT	idt	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	was	be	VBD	_	_	_
46	ligated	ligate	VBN	_	_	_
47	onto	onto	IN	_	_	_
48	the	the	DT	_	_	_
49	3	3	CD	_	_	_
50	'	'	''	_	_	_
51	end	end	NN	_	_	_
52	of	of	IN	_	_	_
53	size	size	NN	_	_	_
54	selected	select	VBN	_	_	_
55	RNA	rna	NN	_	_	_
56	fragments	fragment	NNS	_	_	_
57	,	,	,	_	_	_
58	either	either	CC	_	_	_
59	ribosome	ribosome	NN	_	_	_
60	footprints	footprint	NNS	_	_	_
61	or	or	CC	_	_	_
62	fragmented	fragmented	JJ	_	_	_
63	total	total	JJ	_	_	_
64	RNA	rna	NN	_	_	_
65	.	.	.	_	_	_

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	culture	culture	NN	_	_	_
4	experiments	experiment	NNS	_	_	_
5	were	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	in	in	IN	_	_	_
8	MOPS	MOPS	NNP	MED	_	_
9	medium	medium	NN	_	_	_
10	supplemented	supplement	VBN	_	_	_
11	with	with	IN	_	_	_
12	0.2	0.2	CD	_	_	_
13	%	%	NN	_	_	_
14	glucose	glucose	NN	SUPP	_	_
15	,	,	,	_	_	_
16	19	19	CD	_	_	_
17	amino	amino	NN	SUPP	_	_
18	acids	acid	NNS	SUPP	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	without	without	IN	_	_	_
21	methionine	methionine	NN	SUPP	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	vitamins	vitamin	NNS	_	_	_
25	,	,	,	_	_	_
26	bases	basis	NNS	_	_	_
27	and	and	CC	_	_	_
28	micronutrients	micronutrient	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	MOPS	mop	NNS	MED	_	_
31	rich	rich	JJ	_	_	_
32	defined	define	VBN	_	_	_
33	medium	medium	NN	_	_	_
34	minus	minus	CC	_	_	_
35	methionine	methionine	NN	SUPP	_	_
36	,	,	,	_	_	_
37	Teknova	teknova	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

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	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	NNP	_	_	_
2	All	All	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	based	base	VBN	_	_	_
6	on	on	IN	_	_	_
7	MOPS	mop	NNS	MED	_	_
8	media	media	NNS	_	_	_
9	with	with	IN	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Teknova	teknova	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	with	with	IN	_	_	_
18	either	either	CC	_	_	_
19	full	full	JJ	_	_	_
20	supplement	supplement	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Neidhardt	Neidhardt	NNP	_	_	_
23	et	et	FW	_	_	_
24	al.	al.	FW	_	_	_
25	,	,	,	_	_	_
26	1974	1974	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	based	base	VBN	_	_	_
6	on	on	IN	_	_	_
7	MOPS	mop	NNS	MED	_	_
8	media	media	NNS	_	_	_
9	with	with	IN	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Teknova	teknova	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	with	with	IN	_	_	_
18	full	full	JJ	_	_	_
19	supplement	supplement	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Neidhardt	Neidhardt	NNP	_	_	_
22	et	et	FW	_	_	_
23	al.	al.	FW	_	_	_
24	,	,	,	_	_	_
25	1974	1974	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	minus	minus	CC	_	_	_
28	methionine	methionine	NN	SUPP	_	_
29	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	carried	carry	VBN	_	_	_
6	out	out	RP	_	_	_
7	in	in	IN	_	_	_
8	a	a	DT	_	_	_
9	5	5	CD	_	_	_
10	l	l	NN	_	_	_
11	fermentor	fermentor	JJ	_	_	_
12	BIOSTAT	biostat	NN	_	_	_
13	B-DCU	b-dcu	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Sartorius	Sartorius	NNP	_	_	_
16	BBI	BBI	NNP	_	_	_
17	Systems	Systems	NNPS	_	_	_
18	Inc.	Inc.	NNP	_	_	_
19	.	.	.	_	_	_

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	NNP	_	_	_
11	All	All	NNP	_	_	_
12	cultures	culture	NNS	_	_	_
13	were	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	aerobically	aerobically	RB	_	_	_
16	in	in	IN	_	_	_
17	a	a	DT	_	_	_
18	thermostatically	thermostatically	RB	_	_	_
19	controlled	control	VBN	_	_	_
20	37oC	37oc	NN	_	_	_
21	culture	culture	NN	_	_	_
22	room	room	NN	_	_	_
23	.	.	.	_	_	_

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	All	All	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	at	at	IN	_	_	_
7	37C	37c	NN	_	_	_
8	in	in	IN	_	_	_
9	well-mixed	well-mixed	JJ	_	_	_
10	minimal	minimal	JJ	_	_	_
11	media	media	NNS	_	_	_
12	modified	modify	VBN	_	_	_
13	with	with	IN	_	_	_
14	M63	m63	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	mM63	mm63	NN	_	_	_
17	:	:	:	_	_	_
18	pH	ph	NN	_	_	_
19	7.0	7.0	CD	_	_	_
20	,	,	,	_	_	_
21	62	62	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	K2HPO4	k2hpo4	NN	_	_	_
24	,	,	,	_	_	_
25	39	39	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	KH2PO4	kh2po4	NN	_	_	_
28	,	,	,	_	_	_
29	15	15	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	ammonium	ammonium	NN	SUPP	_	_
32	sulfate	sulfate	NN	SUPP	_	_
33	,	,	,	_	_	_
34	1.8	1.8	CD	_	_	_
35	µM	µm	NN	_	_	_
36	FeSO4-7H2O	feso4-7h2o	NN	_	_	_
37	,	,	,	_	_	_
38	15	15	CD	_	_	_
39	µM	µm	NN	_	_	_
40	thiamine	thiamine	NN	SUPP	_	_
41	hydrochloride	hydrochloride	NN	SUPP	_	_
42	,	,	,	_	_	_
43	0.2	0.2	CD	_	_	_
44	mM	mm	NN	KWSUPP	_	_
45	MgSO4-7H2O	mgso4-7h2o	NN	_	_	_
46	and	and	CC	_	_	_
47	22	22	CD	_	_	_
48	mM	mm	NN	KWSUPP	_	_
49	glucose	glucose	NN	SUPP	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	.	.	.	_	_	_

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/cm	8/cm	NN	_	_	_
24	^	^	NN	_	_	_
25	2	2	CD	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	used	use	VBN	_	_	_
29	six-well	six-well	JJ	_	_	_
30	cell	cell	NN	_	_	_
31	culture	culture	NN	_	_	_
32	companion	companion	NN	_	_	_
33	plates	plate	NNS	_	_	_
34	for	for	IN	_	_	_
35	the	the	DT	_	_	_
36	inserts	insert	NNS	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	BD	BD	NNP	_	_	_
39	Falcon	Falcon	NNP	_	_	_
40	,	,	,	_	_	_
41	Franklin	Franklin	NNP	_	_	_
42	Lakes	Lakes	NNP	_	_	_
43	,	,	,	_	_	_
44	NJ	NJ	NNP	_	_	_
45	,	,	,	_	_	_
46	USA	USA	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	,	,	,	_	_	_
49	to	to	TO	_	_	_
50	separately	separately	RB	_	_	_
51	harvest	harvest	VB	_	_	_
52	I	I	PRP	_	_	_
53	--	--	:	_	_	_
54	and	and	CC	_	_	_
55	L	l	NN	_	_	_
56	--	--	:	_	_	_
57	populations	population	NNS	_	_	_
58	from	from	IN	_	_	_
59	cocultures	coculture	NNS	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	Hosoda	Hosoda	NNP	_	_	_
62	et	et	FW	_	_	_
63	al.	al.	FW	_	_	_
64	,	,	,	_	_	_
65	\	\	SYM	_	_	_
66	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
67	all	all	DT	_	_	_
68	cultures	culture	NNS	_	_	_
69	were	be	VBD	_	_	_
70	grown	grow	VBN	_	_	_
71	in	in	IN	_	_	_
72	10	10	CD	_	_	_
73	ml	ml	NN	_	_	_
74	LB	lb	NN	MED	_	_
75	broth	broth	NN	MED	_	_
76	at	at	IN	_	_	_
77	37C/180rpm	37c/180rpm	NN	_	_	_
78	for	for	IN	_	_	_
79	24	24	CD	_	_	_
80	hours	hour	NNS	_	_	_
81	and	and	CC	_	_	_
82	flash-frozen	flash-frozen	JJ	_	_	_
83	with	with	IN	_	_	_
84	liquid	liquid	JJ	_	_	_
85	nitrogen	nitrogen	NN	_	_	_
86	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	data	data	NN	_	_	_
4	analysis	analysis	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Rockhopper	Rockhopper	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	McClure	McClure	NNP	_	_	_
11	et	et	FW	_	_	_
12	al.	al.	FW	_	_	_
13	,	,	,	_	_	_
14	2013	2013	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	Escherichia	escherichia	FW	Organism	_	_
18	coli	coli	FW	Organism	_	_
19	str	str	FW	_	_	_
20	.	.	.	_	_	_

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	All	all	DT	_	_	_
3	data	datum	NNS	_	_	_
4	was	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Rockhopper	Rockhopper	NNP	_	_	_
8	Ver	Ver	NNP	_	_	_
9	.2.03	.2.03	CD	_	_	_
10	.	.	.	_	_	_

1	Rockhopper	Rockhopper	NNP	_	_	_
2	is	be	VBZ	_	_	_
3	an	a	DT	_	_	_
4	\	\	JJ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	All	all	DT	_	_	_
7	raw	raw	JJ	_	_	_
8	FastQ	fastq	NN	_	_	_
9	files	file	NNS	_	_	_
10	generated	generate	VBN	_	_	_
11	were	be	VBD	_	_	_
12	filtered	filter	VBN	_	_	_
13	using	use	VBG	_	_	_
14	FASTX-Toolkit	fastx-toolkit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	http://hannonlab.cshl.edu/fastx_toolkit/	http://hannonlab.cshl.edu/fastx_toolkit/	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	All	all	DT	_	_	_
3	RNA	rna	NN	_	_	_
4	data	datum	NNS	_	_	_
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	Xuzhou21	xuzhou21	NN	_	_	_
12	using	use	VBG	_	_	_
13	SOAP2	soap2	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	hot	hot	JJ	_	_	_
9	phenol	phenol	NN	_	_	_
10	extraction	extraction	NN	_	_	_
11	with	with	IN	_	_	_
12	DNA	dna	NN	_	_	_
13	digestion	digestion	NN	_	_	_
14	,	,	,	_	_	_
15	following	follow	VBG	_	_	_
16	standard	standard	JJ	_	_	_
17	protocol	protocol	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	All	all	DT	_	_	_
20	samples	sample	NNS	_	_	_
21	were	be	VBD	_	_	_
22	extracted	extract	VBN	_	_	_
23	using	use	VBG	_	_	_
24	the	the	DT	_	_	_
25	Qiagen	Qiagen	NNP	_	_	_
26	Rnasey	Rnasey	NNP	_	_	_
27	Mini	Mini	NNP	_	_	_
28	Kit	kit	NN	_	_	_
29	,	,	,	_	_	_
30	following	follow	VBG	_	_	_
31	standard	standard	JJ	_	_	_
32	protocol	protocol	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	All	all	DT	_	_	_
35	samples	sample	NNS	_	_	_
36	were	be	VBD	_	_	_
37	processed	process	VBN	_	_	_
38	following	follow	VBG	_	_	_
39	NEB	NEB	NNP	_	_	_
40	's	's	POS	_	_	_
41	protocol	protocol	NN	_	_	_
42	from	from	IN	_	_	_
43	the	the	DT	_	_	_
44	NEBNext	nebnext	NN	_	_	_
45	®	®	NN	_	_	_
46	ChIP-Seq	chip-seq	JJ	_	_	_
47	library	library	NN	_	_	_
48	preparation	preparation	NN	_	_	_
49	kit	kit	NN	_	_	_
50	.	.	.	_	_	_

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	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	NNP	_	_	_
2	All	All	NNP	_	_	_
3	strains	strain	NNS	_	_	_
4	used	use	VBN	_	_	_
5	in	in	IN	_	_	_
6	this	this	DT	_	_	_
7	study	study	NN	_	_	_
8	were	be	VBD	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	K-12	k-12	NN	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	and	and	CC	_	_	_
14	its	its	PRP$	_	_	_
15	derivatives	derivative	NNS	_	_	_
16	.	.	.	_	_	_

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/v	w/v	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	carbon	carbon	NN	_	_	_
20	source	source	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	glucose	glucose	NN	SUPP	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	0.1	0.1	CD	_	_	_
26	%	%	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	w/v	w/v	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	nitrogen	nitrogen	NN	_	_	_
31	source	source	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	NH4Cl	nh4cl	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	and	and	CC	_	_	_
37	cultured	culture	VBN	_	_	_
38	overnight	overnight	JJ	_	_	_
39	at	at	IN	_	_	_
40	37	37	CD	_	_	_
41	°C	°c	NN	_	_	_
42	with	with	IN	_	_	_
43	constant	constant	JJ	_	_	_
44	agitation	agitation	NN	_	_	_
45	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:100	1:100	CD	_	_	_
6	into	into	IN	_	_	_
7	fresh	fresh	JJ	_	_	_
8	minimal	minimal	JJ	_	_	_
9	medium	medium	NN	_	_	_
10	and	and	CC	_	_	_
11	then	then	RB	_	_	_
12	cultured	culture	VBN	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	to	to	TO	_	_	_
17	an	a	DT	_	_	_
18	appropriate	appropriate	JJ	_	_	_
19	cell	cell	NN	_	_	_
20	density	density	NN	_	_	_
21	with	with	IN	_	_	_
22	constant	constant	JJ	_	_	_
23	agitation	agitation	NN	_	_	_
24	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	anaerobic	anaerobic	JJ	_	_	_
4	cultures	culture	NNS	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	minimal	minimal	JJ	_	_	_
8	medium	medium	NN	_	_	_
9	were	be	VBD	_	_	_
10	flushed	flush	VBN	_	_	_
11	with	with	IN	_	_	_
12	nitrogen	nitrogen	NN	_	_	_
13	and	and	CC	_	_	_
14	then	then	RB	_	_	_
15	continuously	continuously	RB	_	_	_
16	monitored	monitor	VBN	_	_	_
17	using	use	VBG	_	_	_
18	a	a	DT	_	_	_
19	polarographic-dissolved	polarographic-dissolved	JJ	_	_	_
20	oxygen	oxygen	NN	_	_	_
21	probe	probe	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Cole-Parmer	Cole-Parmer	NNP	_	_	_
24	Instruments	Instruments	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	to	to	TO	_	_	_
27	ensure	ensure	VB	_	_	_
28	anaerobicity	anaerobicity	NN	_	_	_
29	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	nitrate	nitrate	JJ	SUPP	_	_
3	respiration	respiration	NN	_	_	_
4	20	20	CD	_	_	_
5	mmol	mmol	NN	_	_	_
6	potassium	potassium	NN	_	_	_
7	nitrate	nitrate	NN	SUPP	_	_
8	was	be	VBD	_	_	_
9	added	add	VBN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	strains	strain	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	M9	m9	NN	MED	_	_
8	minimal	minimal	JJ	MED	_	_
9	media	media	NNS	MED	_	_
10	supplemented	supplement	VBN	_	_	_
11	with	with	IN	_	_	_
12	25	25	CD	_	_	_
13	ug/ml	ug/ml	NN	_	_	_
14	streptomycin	streptomycin	NN	_	_	_
15	and	and	CC	_	_	_
16	0.52	0.52	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	arginine	arginine	NN	SUPP	_	_
19	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	to	to	TO	_	_	_
5	OD	od	NN	_	_	_
6	=	=	JJ	_	_	_
7	0.5	0.5	CD	_	_	_
8	@	@	SYM	_	_	_
9	30	30	CD	_	_	_
10	C	c	NN	_	_	_
11	;	;	:	_	_	_
12	experimental	experimental	JJ	_	_	_
13	samples	sample	NNS	_	_	_
14	were	be	VBD	_	_	_
15	then	then	RB	_	_	_
16	transferred	transfer	VBN	_	_	_
17	to	to	TO	_	_	_
18	a	a	DT	_	_	_
19	shaking	shake	VBG	_	_	_
20	water	water	NN	_	_	_
21	bath	bath	NN	_	_	_
22	@	@	SYM	_	_	_
23	42	42	CD	_	_	_
24	C.	C.	NNP	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	All	All	NNP	_	_	_
27	strains	strain	NNS	_	_	_
28	were	be	VBD	_	_	_
29	grown	grow	VBN	_	_	_
30	shaking	shake	VBG	_	_	_
31	at	at	IN	_	_	_
32	37	37	CD	_	_	_
33	°C	°c	NN	_	_	_
34	in	in	IN	_	_	_
35	200mL	200ml	NN	_	_	_
36	cultures	culture	NNS	_	_	_
37	of	of	IN	_	_	_
38	MOPS	mop	NNS	MED	_	_
39	complete-glucose	complete-glucose	JJ	_	_	_
40	liquid	liquid	JJ	_	_	_
41	media	media	NNS	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	unless	unless	IN	_	_	_
44	otherwise	otherwise	RB	_	_	_
45	annotated	annotated	JJ	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	in	in	IN	_	_	_
48	1L	1l	NN	_	_	_
49	flasks	flask	NNS	_	_	_
50	and	and	CC	_	_	_
51	cells	cell	NNS	_	_	_
52	were	be	VBD	_	_	_
53	harvested	harvest	VBN	_	_	_
54	at	at	IN	_	_	_
55	OD	od	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	420nm	420nm	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	between	between	IN	_	_	_
60	0.4	0.4	CD	_	_	_
61	-	-	:	_	_	_
62	0.6	0.6	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
64	All	all	PDT	_	_	_
65	those	those	DT	_	_	_
66	uniquely	uniquely	RB	_	_	_
67	mapped	map	VBN	_	_	_
68	reads	read	VBZ	_	_	_
69	were	be	VBD	_	_	_
70	used	use	VBN	_	_	_
71	to	to	TO	_	_	_
72	calculate	calculate	VB	_	_	_
73	the	the	DT	_	_	_
74	gene	gene	NN	_	_	_
75	expression	expression	NN	_	_	_
76	level	level	NN	_	_	_
77	by	by	IN	_	_	_
78	the	the	DT	_	_	_
79	RPKM	rpkm	NN	_	_	_
80	method	method	NN	_	_	_
81	,	,	,	_	_	_
82	which	which	WDT	_	_	_
83	is	be	VBZ	_	_	_
84	able	able	JJ	_	_	_
85	to	to	TO	_	_	_
86	eliminate	eliminate	VB	_	_	_
87	the	the	DT	_	_	_
88	influence	influence	NN	_	_	_
89	of	of	IN	_	_	_
90	different	different	JJ	_	_	_
91	gene	gene	NN	_	_	_
92	length	length	NN	_	_	_
93	and	and	CC	_	_	_
94	sequencing	sequencing	NN	_	_	_
95	discrepancy	discrepancy	NN	_	_	_
96	on	on	IN	_	_	_
97	the	the	DT	_	_	_
98	calculation	calculation	NN	_	_	_
99	of	of	IN	_	_	_
100	gene	gene	NN	_	_	_
101	expression	expression	NN	_	_	_
102	and	and	CC	_	_	_
103	thus	thus	RB	_	_	_
104	the	the	DT	_	_	_
105	calculated	calculate	VBN	_	_	_
106	gene	gene	NN	_	_	_
107	expression	expression	NN	_	_	_
108	level	level	NN	_	_	_
109	can	can	MD	GEN	_	_
110	be	be	VB	_	_	_
111	directly	directly	RB	_	_	_
112	used	use	VBN	_	_	_
113	for	for	IN	_	_	_
114	comparing	compare	VBG	_	_	_
115	the	the	DT	_	_	_
116	difference	difference	NN	_	_	_
117	of	of	IN	_	_	_
118	gene	gene	NN	_	_	_
119	expression	expression	NN	_	_	_
120	among	among	IN	_	_	_
121	samples	sample	NNS	_	_	_
122	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Ambion	Ambion	NNP	_	_	_
3	RiboPure	RiboPure	NNP	_	_	_
4	RNA	rna	NN	_	_	_
5	Isolation	isolation	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Ambion	Ambion	NNP	_	_	_
8	RiboPure	RiboPure	NNP	_	_	_
9	RNA	rna	NN	_	_	_
10	Isolation	isolation	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	A	a	NN	_	_	_
13	minimal	minimal	JJ	_	_	_
14	growth	growth	NN	_	_	_
15	medium	medium	NN	_	_	_
16	as	as	IN	_	_	_
17	described	describe	VBN	_	_	_
18	in	in	IN	_	_	_
19	the	the	DT	_	_	_
20	study	study	NN	_	_	_
21	by	by	IN	_	_	_
22	Ihssen	Ihssen	NNP	_	_	_
23	and	and	CC	_	_	_
24	Egli	Egli	NNP	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	2004	2004	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	used	use	VBN	_	_	_
30	for	for	IN	_	_	_
31	all	all	DT	_	_	_
32	experiments	experiment	NNS	_	_	_
33	.	.	.	_	_	_

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	Amino	amino	NN	_	_	_
3	acid	acid	NN	_	_	_
4	or	or	CC	_	_	_
5	nucleotide	nucleotide	NN	_	_	_
6	added	add	VBD	_	_	_
7	to	to	TO	_	_	_
8	final	final	JJ	_	_	_
9	concentration	concentration	NN	_	_	_
10	of	of	IN	_	_	_
11	1	1	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	not	not	RB	_	_	_
14	exceeding	exceed	VBG	_	_	_
15	1/100th	1/100th	JJ	_	_	_
16	volume	volume	NN	_	_	_
17	of	of	IN	_	_	_
18	culture	culture	NN	_	_	_
19	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	10	10	CD	_	_	_
3	mins	min	NNS	_	_	_
4	,	,	,	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	spun	spin	VBN	_	_	_
8	down	down	RB	_	_	_
9	and	and	CC	_	_	_
10	snap	snap	VB	_	_	_
11	frozen	freeze	VBN	_	_	_
12	in	in	IN	_	_	_
13	liquid	liquid	JJ	_	_	_
14	nitrogen	nitrogen	NN	_	_	_
15	and	and	CC	_	_	_
16	stored	store	VBD	_	_	_
17	at	at	IN	_	_	_
18	-80	-80	CD	_	_	_
19	C	c	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Among	among	IN	_	_	_
22	potential	potential	JJ	_	_	_
23	TSSs	tsss	NNS	_	_	_
24	,	,	,	_	_	_
25	only	only	RB	_	_	_
26	TSSs	tsss	NNS	_	_	_
27	with	with	IN	_	_	_
28	the	the	DT	_	_	_
29	strongest	strongest	JJS	_	_	_
30	signal	signal	NN	_	_	_
31	within	within	IN	_	_	_
32	10	10	CD	_	_	_
33	bp	bp	NN	_	_	_
34	window	window	NN	_	_	_
35	were	be	VBD	_	_	_
36	kept	keep	VBN	_	_	_
37	to	to	TO	_	_	_
38	remove	remove	VB	_	_	_
39	possible	possible	JJ	_	_	_
40	noise	noise	NN	_	_	_
41	signals	signal	NNS	_	_	_
42	,	,	,	_	_	_
43	and	and	CC	_	_	_
44	TSSs	tsss	NNS	_	_	_
45	with	with	IN	_	_	_
46	greater	greater	JJR	_	_	_
47	than	than	IN	_	_	_
48	or	or	CC	_	_	_
49	equal	equal	JJ	_	_	_
50	to	to	TO	_	_	_
51	40	40	CD	_	_	_
52	%	%	NN	_	_	_
53	of	of	IN	_	_	_
54	the	the	DT	_	_	_
55	strongest	strongest	JJS	_	_	_
56	signal	signal	NN	_	_	_
57	upstream	upstream	RB	_	_	_
58	of	of	IN	_	_	_
59	an	a	DT	_	_	_
60	annotated	annotated	JJ	_	_	_
61	gene	gene	NN	_	_	_
62	were	be	VBD	_	_	_
63	considered	consider	VBN	_	_	_
64	as	as	IN	_	_	_
65	multiple	multiple	JJ	_	_	_
66	TSSs	tsss	NNS	_	_	_
67	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ampicilin	ampicilin	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Ampicilin	ampicilin	NN	_	_	_
6	_	_	NN	_	_	_
7	treatment	treatment	NN	_	_	_
8	_	_	NN	_	_	_
9	plasmidmappedreads	plasmidmappedread	NNS	_	_	_
10	_	_	VBP	_	_	_
11	statistical	statistical	JJ	_	_	_
12	_	_	NN	_	_	_
13	output.txt	output.txt	NN	_	_	_
14	:	:	:	_	_	_
15	NC	NC	NNP	_	_	_
16	_	_	NNP	_	_	_
17	012692.1	012692.1	CD	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Amp	Amp	NNP	_	_	_
20	_	_	NNP	_	_	_
21	Treatment	treatment	NN	_	_	_
22	_	_	NN	_	_	_
23	genomemappedreads	genomemappedread	NNS	_	_	_
24	_	_	VBP	_	_	_
25	statistical	statistical	JJ	_	_	_
26	_	_	NN	_	_	_
27	output.txt	output.txt	NN	_	_	_
28	:	:	:	_	_	_
29	NC	nc	NN	_	_	_
30	_	_	SYM	_	_	_
31	000913.2	000913.2	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	Anaerobic	anaerobic	JJ	_	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Anaerobic	anaerobic	JJ	_	_	_
37	3	3	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	Anaerobic	anaerobic	JJ	_	_	_
40	cultures	culture	NNS	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	Anaerobic	anaerobic	JJ	_	_	_
43	Cultures	culture	NNS	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
45	Anaerobic	anaerobic	JJ	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	exposed	expose	VBN	_	_	_
49	to	to	TO	_	_	_
50	CO-RMs	co-rm	NNS	_	_	_
51	for	for	IN	_	_	_
52	15	15	CD	_	_	_
53	minutes	minute	NNS	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	Anaerobic	anaerobic	JJ	_	_	_
56	E.	e.	FW	_	_	_
57	coli	coli	FW	_	_	_
58	not	not	RB	_	_	_
59	exposed	expose	VBN	_	_	_
60	to	to	TO	_	_	_
61	CO-RMs	co-rm	NNS	_	_	_
62	for	for	IN	_	_	_
63	15	15	CD	_	_	_
64	minutes	minute	NNS	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	control	control	NN	_	_	_
67	cells	cell	NNS	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	Anaerobic	anaerobic	JJ	_	_	_
71	E.	e.	FW	_	_	_
72	coli	coli	FW	_	_	_
73	were	be	VBD	_	_	_
74	exposed	expose	VBN	_	_	_
75	to	to	TO	_	_	_
76	CO-RMs	co-rm	NNS	_	_	_
77	for	for	IN	_	_	_
78	15	15	CD	_	_	_
79	minutes	minute	NNS	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
81	anaerobic	anaerobic	JJ	_	_	_
82	INPUT	input	NN	_	_	_
83	DNA	dna	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	Anaerobic	anaerobic	JJ	_	_	_
86	,	,	,	_	_	_
87	Iron	iron	JJ	_	_	_
88	Deficient	deficient	JJ	_	_	_
89	cultures	culture	NNS	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
91	Anaerobic	anaerobic	JJ	_	_	_
92	MG1655	mg1655	NN	_	_	_
93	exposed	expose	VBN	_	_	_
94	to	to	TO	_	_	_
95	CO-RMs	co-rm	NNS	_	_	_
96	for	for	IN	_	_	_
97	15	15	CD	_	_	_
98	minutes	minute	NNS	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Anaerobic	anaerobic	JJ	_	_	_
101	MG1655	mg1655	NN	_	_	_
102	not	not	RB	_	_	_
103	exposed	expose	VBN	_	_	_
104	to	to	TO	_	_	_
105	CO-RMs	co-rm	NNS	_	_	_
106	for	for	IN	_	_	_
107	15	15	CD	_	_	_
108	minutes	minute	NNS	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	control	control	NN	_	_	_
111	cells	cell	NNS	_	_	_
112	-RRB-	-rrb-	-RRB-	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
114	Anaerobic	anaerobic	JJ	_	_	_
115	MG1655	mg1655	NN	_	_	_
116	were	be	VBD	_	_	_
117	exposed	expose	VBN	_	_	_
118	to	to	TO	_	_	_
119	CO-RMs	co-rm	NNS	_	_	_
120	for	for	IN	_	_	_
121	15	15	CD	_	_	_
122	minutes	minute	NNS	_	_	_
123	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
124	Anaerobic	Anaerobic	NNP	_	_	_
125	,	,	,	_	_	_
126	minus	minus	CC	_	_	_
127	nitrate	nitrate	NN	SUPP	_	_
128	,	,	,	_	_	_
129	IP	IP	NNP	_	_	_
130	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
131	Anaerobic	Anaerobic	NNP	_	_	_
132	,	,	,	_	_	_
133	plus	plus	CC	_	_	_
134	nitrate	nitrate	NN	SUPP	_	_
135	,	,	,	_	_	_
136	IP	IP	NNP	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	anaerobic	anaerobic	JJ	_	_	_
139	reference	reference	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	analysis	analysis	NN	_	_	_
142	:	:	:	_	_	_
143	in	in	FW	_	_	_
144	vitro	vitro	FW	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	analysis	analysis	NN	_	_	_
147	:	:	:	_	_	_
148	in	in	FW	_	_	_
149	vivo	vivo	FW	_	_	_
150	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
151	Ancestral	ancestral	JJ	_	_	_
152	E.	e.	FW	_	_	_
153	coli	coli	FW	_	_	_
154	B	b	NN	_	_	_
155	REL606	rel606	NN	_	_	_
156	strain	strain	NN	_	_	_
157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
158	Ancestral	ancestral	JJ	_	_	_
159	I	I	PRP	_	_	_
160	-	-	:	_	_	_
161	cells	cell	NNS	_	_	_
162	at	at	IN	_	_	_
163	amino	amino	NN	_	_	_
164	acid	acid	NN	_	_	_
165	starvation	starvation	NN	_	_	_
166	in	in	IN	_	_	_
167	monoculture	monoculture	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
169	Ancestral	ancestral	JJ	_	_	_
170	I	I	PRP	_	_	_
171	-	-	:	_	_	_
172	cells	cell	NNS	_	_	_
173	at	at	IN	_	_	_
174	log	log	NN	_	_	_
175	phase	phase	NN	_	_	_
176	in	in	IN	_	_	_
177	monoculture	monoculture	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
179	Ancestral	ancestral	JJ	_	_	_
180	I	I	PRP	_	_	_
181	-	-	:	_	_	_
182	cells	cell	NNS	_	_	_
183	in	in	IN	_	_	_
184	coculture	coculture	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	Ancestral	ancestral	JJ	_	_	_
187	I	I	PRP	_	_	_
188	-	-	:	_	_	_
189	cells	cell	NNS	_	_	_
190	in	in	IN	_	_	_
191	coculture	coculture	NN	_	_	_
192	,	,	,	_	_	_
193	a	a	DT	_	_	_
194	biological	biological	JJ	_	_	_
195	replicate	replicate	VB	_	_	_
196	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
197	Ancestral	ancestral	JJ	_	_	_
198	L	l	NN	_	_	_
199	-	-	:	_	_	_
200	cells	cell	NNS	_	_	_
201	at	at	IN	_	_	_
202	amino	amino	NN	_	_	_
203	acid	acid	NN	_	_	_
204	starvation	starvation	NN	_	_	_
205	in	in	IN	_	_	_
206	monoculture	monoculture	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	Ancestral	ancestral	JJ	_	_	_
209	L	l	NN	_	_	_
210	-	-	:	_	_	_
211	cells	cell	NNS	_	_	_
212	at	at	IN	_	_	_
213	log	log	NN	_	_	_
214	phase	phase	NN	_	_	_
215	in	in	IN	_	_	_
216	monoculture	monoculture	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	Ancestral	ancestral	JJ	_	_	_
219	L	l	NN	_	_	_
220	-	-	:	_	_	_
221	cells	cell	NNS	_	_	_
222	at	at	IN	_	_	_
223	log	log	NN	_	_	_
224	phase	phase	NN	_	_	_
225	in	in	IN	_	_	_
226	monoculture	monoculture	NN	_	_	_
227	,	,	,	_	_	_
228	a	a	DT	_	_	_
229	technical	technical	JJ	_	_	_
230	replicate	replicate	VB	_	_	_
231	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
232	Ancestral	ancestral	JJ	_	_	_
233	L	l	NN	_	_	_
234	-	-	:	_	_	_
235	cells	cell	NNS	_	_	_
236	in	in	IN	_	_	_
237	coculture	coculture	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	Ancestral	ancestral	JJ	_	_	_
240	L	l	NN	_	_	_
241	-	-	:	_	_	_
242	cells	cell	NNS	_	_	_
243	in	in	IN	_	_	_
244	coculture	coculture	NN	_	_	_
245	,	,	,	_	_	_
246	a	a	DT	_	_	_
247	biological	biological	JJ	_	_	_
248	replicate	replicate	VB	_	_	_
249	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
250	Annotation	Annotation	NNP	_	_	_
251	:	:	:	_	_	_
252	The	the	DT	_	_	_
253	reference	reference	NN	_	_	_
254	genome	genome	NN	_	_	_
255	-LRB-	-lrb-	-LRB-	_	_	_
256	Escherichia	escherichia	FW	_	_	_
257	_	_	FW	_	_	_
258	coli	coli	FW	_	_	_
259	_	_	SYM	_	_	_
260	cft073.ASM744v1.dna.chromosome.Chromosome.fa	cft073.asm744v1.dna.chromosome.chromosome.fa	NN	_	_	_
261	-RRB-	-rrb-	-RRB-	_	_	_
262	and	and	CC	_	_	_
263	annotations	annotation	NNS	_	_	_
264	-LRB-	-lrb-	-LRB-	_	_	_
265	Escherichia	escherichia	FW	_	_	_
266	_	_	FW	_	_	_
267	coli	coli	FW	_	_	_
268	_	_	SYM	_	_	_
269	cft073.ASM744v1	cft073.asm744v1	NN	_	_	_
270	.32	.32	CD	_	_	_
271	.	.	.	_	_	_

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	An	a	DT	_	_	_
9	o/n	o/n	JJ	_	_	_
10	culture	culture	NN	_	_	_
11	of	of	IN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	TolC	tolc	NN	_	_	_
15	was	be	VBD	_	_	_
16	diluted	dilute	VBN	_	_	_
17	to	to	TO	_	_	_
18	an	a	DT	_	_	_
19	OD600	od600	NN	_	_	_
20	of	of	IN	_	_	_
21	0.1	0.1	CD	_	_	_
22	and	and	CC	_	_	_
23	supplied	supply	VBN	_	_	_
24	with	with	IN	_	_	_
25	a	a	DT	_	_	_
26	final	final	JJ	_	_	_
27	concentration	concentration	NN	_	_	_
28	of	of	IN	_	_	_
29	0.5	0.5	CD	_	_	_
30	µg/ml	µg/ml	NN	_	_	_
31	Carolacton	carolacton	NN	_	_	_
32	in	in	IN	_	_	_
33	MeOH	meoh	NN	_	_	_
34	.	.	.	_	_	_

1	Controls	Controls	NNP	_	_	_
2	received	receive	VBD	_	_	_
3	the	the	DT	_	_	_
4	same	same	JJ	_	_	_
5	volume	volume	NN	_	_	_
6	MeOH	meoh	NN	_	_	_
7	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	early	early	JJ	_	_	_
3	time-points	time-point	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	t	t	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	were	be	VBD	_	_	_
8	chosen	choose	VBN	_	_	_
9	to	to	TO	_	_	_
10	be	be	VB	_	_	_
11	analyzed	analyze	VBN	_	_	_
12	by	by	IN	_	_	_
13	RNA-seq	rna-seq	NN	_	_	_
14	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	addition	addition	NN	_	_	_
4	of	of	IN	_	_	_
5	Carolacton	carolacton	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	t0	t0	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	t5	t5	NN	_	_	_
11	,	,	,	_	_	_
12	t15	t15	NN	_	_	_
13	and	and	CC	_	_	_
14	t30	t30	NN	_	_	_
15	min	min	NN	_	_	_
16	after	after	IN	_	_	_
17	addition	addition	NN	_	_	_
18	of	of	IN	_	_	_
19	Carolacton	Carolacton	NNP	_	_	_
20	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	each	each	DT	_	_	_
3	point	point	NN	_	_	_
4	,	,	,	_	_	_
5	5	5	CD	_	_	_
6	ml	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	culture	culture	NN	_	_	_
9	were	be	VBD	_	_	_
10	mixed	mix	VBN	_	_	_
11	with	with	IN	_	_	_
12	an	a	DT	_	_	_
13	equal	equal	JJ	_	_	_
14	volume	volume	NN	_	_	_
15	RNAprotect	rnaprotect	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	qiagen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	incubated	incubate	VBN	_	_	_
21	at	at	IN	_	_	_
22	room	room	NN	_	_	_
23	temperature	temperature	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	RT	rt	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	for	for	IN	_	_	_
28	5	5	CD	_	_	_
29	min	min	NN	_	_	_
30	,	,	,	_	_	_
31	the	the	DT	_	_	_
32	cells	cell	NNS	_	_	_
33	harvested	harvest	VBN	_	_	_
34	by	by	IN	_	_	_
35	centrifugation	centrifugation	NN	_	_	_
36	,	,	,	_	_	_
37	and	and	CC	_	_	_
38	the	the	DT	_	_	_
39	pellet	pellet	NN	_	_	_
40	frozen	frozen	JJ	_	_	_
41	and	and	CC	_	_	_
42	stored	store	VBN	_	_	_
43	at	at	IN	_	_	_
44	-80	-80	CD	_	_	_
45	°C	°c	NN	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	An	a	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	of	of	IN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	O104	o104	NN	_	_	_
9	:	:	:	_	_	_
10	H4	h4	NN	_	_	_
11	strain	strain	NN	_	_	_
12	LB226692	lb226692	NN	_	_	_
13	was	be	VBD	_	_	_
14	diluted	dilute	VBN	_	_	_
15	1:10,000	1:10,000	CD	_	_	_
16	in	in	IN	_	_	_
17	pre-warmed	pre-warmed	JJ	_	_	_
18	LB	lb	NN	MED	_	_
19	medium	medium	NN	MED	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	10	10	CD	_	_	_
22	g/L	g/l	NN	_	_	_
23	tryptone	tryptone	NN	SUPP	_	_
24	,	,	,	_	_	_
25	5	5	CD	_	_	_
26	g/L	g/l	NN	_	_	_
27	yeast	yeast	NN	SUPP	_	_
28	extract	extract	NN	SUPP	_	_
29	,	,	,	_	_	_
30	5	5	CD	_	_	_
31	g/L	g/l	NN	_	_	_
32	NaCl	nacl	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	and	and	CC	_	_	_
35	cells	cell	NNS	_	_	_
36	were	be	VBD	_	_	_
37	grown	grow	VBN	_	_	_
38	at	at	IN	_	_	_
39	37oC	37oc	NN	_	_	_
40	,	,	,	_	_	_
41	180	180	CD	_	_	_
42	rpm	rpm	NN	_	_	_
43	for	for	IN	_	_	_
44	3.5	3.5	CD	_	_	_
45	h	h	NN	_	_	_
46	to	to	TO	_	_	_
47	an	a	DT	_	_	_
48	OD600	od600	NN	_	_	_
49	of	of	IN	_	_	_
50	0.52	0.52	CD	_	_	_
51	.	.	.	_	_	_

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/ml	µg/ml	NN	_	_	_
19	of	of	IN	_	_	_
20	carbenicillin	carbenicillin	NN	_	_	_
21	,	,	,	_	_	_
22	40	40	CD	_	_	_
23	µg/ml	µg/ml	NN	_	_	_
24	biotin	biotin	NN	SUPP	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	70	70	CD	_	_	_
28	µM	µm	NN	_	_	_
29	IPTG	iptg	NN	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	back	back	JJ	_	_	_
3	diluted	diluted	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	until	until	IN	_	_	_
11	reaching	reach	VBG	_	_	_
12	an	a	DT	_	_	_
13	OD600	od600	NN	_	_	_
14	of	of	IN	_	_	_
15	0.45	0.45	CD	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	An	a	DT	_	_	_
3	RNeasy	rneasy	JJ	_	_	_
4	kit	kit	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Qiagen	Qiagen	NNP	_	_	_
7	Ltd	Ltd	NNP	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	extract	extract	VB	_	_	_
13	the	the	DT	_	_	_
14	total	total	JJ	_	_	_
15	RNA	rna	NN	_	_	_
16	according	accord	VBG	_	_	_
17	to	to	TO	_	_	_
18	manufacturers	manufacturer	NNS	_	_	_
19	'	'	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	An	a	DT	_	_	_
3	RNeasy	rneasy	NN	_	_	_
4	minikit	minikit	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	pgcgrowthcondition	NNS	_	_	_
2	Antibodies	antibody	NNS	_	_	_
3	for	for	IN	_	_	_
4	beta	beta	NN	_	_	_
5	of	of	IN	_	_	_
6	RNAP	rnap	NN	_	_	_
7	-	-	:	_	_	_
8	NeoClone	NeoClone	NNP	_	_	_
9	,	,	,	_	_	_
10	Cat	Cat	NNP	_	_	_
11	Number	number	NN	_	_	_
12	:	:	:	_	_	_
13	W0002	w0002	NN	_	_	_
14	,	,	,	_	_	_
15	Lot	lot	NN	_	_	_
16	Number	number	NN	_	_	_
17	:	:	:	_	_	_
18	2008L10-001	2008l10-001	NN	_	_	_
19	Antibodies	antibody	NNS	_	_	_
20	for	for	IN	_	_	_
21	sigma70	sigma70	NN	_	_	_
22	of	of	IN	_	_	_
23	RNAP	rnap	NN	_	_	_
24	-	-	:	_	_	_
25	NeoClone	NeoClone	NNP	_	_	_
26	,	,	,	_	_	_
27	Cat	Cat	NNP	_	_	_
28	Number	number	NN	_	_	_
29	:	:	:	_	_	_
30	W0004	w0004	NN	_	_	_
31	,	,	,	_	_	_
32	Lot	lot	NN	_	_	_
33	Number	number	NN	_	_	_
34	:	:	:	_	_	_
35	2008K12-001	2008k12-001	NN	_	_	_
36	All	all	DT	_	_	_
37	other	other	JJ	_	_	_
38	antibodies	antibody	NNS	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	FNR	fnr	NN	TF	_	_
41	,	,	,	_	_	_
42	H-NS	h-ns	NN	_	_	_
43	,	,	,	_	_	_
44	IHF	ihf	NN	TF	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	were	be	VBD	_	_	_
47	produced	produce	VBN	_	_	_
48	in	in	IN	_	_	_
49	this	this	DT	_	_	_
50	study	study	NN	_	_	_
51	and	and	CC	_	_	_
52	are	be	VBP	_	_	_
53	not	not	RB	_	_	_
54	commercially	commercially	RB	_	_	_
55	available	available	JJ	_	_	_
56	.	.	.	_	_	_

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	:	:	:	_	_	_
11	Affinity	affinity	NN	_	_	_
12	Purified	purify	VBN	_	_	_
13	FNR	fnr	NN	TF	_	_
14	antibody	antibody	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	antibody	antibody	NN	_	_	_
17	:	:	:	_	_	_
18	Affinity	affinity	NN	_	_	_
19	purified	purify	VBN	_	_	_
20	FNR	fnr	NN	TF	_	_
21	polyclonal	polyclonal	JJ	_	_	_
22	antibody	antibody	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	antibody	antibody	NN	_	_	_
25	:	:	:	_	_	_
26	anti-DksA	anti-dksa	JJ	_	_	_
27	rabbit	rabbit	NN	_	_	_
28	polyclonal	polyclonal	JJ	_	_	_
29	antisera	antisera	NNS	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
31	antibody	antibody	NN	_	_	_
32	:	:	:	_	_	_
33	Anti-Dps	anti-dps	JJ	_	_	_
34	antibodies	antibody	NNS	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
36	antibody	antibody	NN	_	_	_
37	:	:	:	_	_	_
38	anti-FLAG	anti-flag	JJ	_	_	_
39	mAb	mab	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	antibody	antibody	NN	_	_	_
42	:	:	:	_	_	_
43	anti-RNAP	anti-rnap	JJ	_	_	_
44	b	b	NN	_	_	_
45	subunit	subunit	NN	_	_	_
46	NT63	nt63	NN	_	_	_
47	monoclonal	monoclonal	JJ	_	_	_
48	antibodies	antibody	NNS	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
50	antibody	antibody	NN	_	_	_
51	:	:	:	_	_	_
52	anti-s70	anti-s70	JJ	_	_	_
53	monoclonal	monoclonal	JJ	_	_	_
54	antibodies	antibody	NNS	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
56	antibody	antibody	NN	_	_	_
57	:	:	:	_	_	_
58	Flag	flag	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	antibody	antibody	NN	_	_	_
61	:	:	:	_	_	_
62	IgG	igg	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	antibody	antibody	NN	_	_	_
65	:	:	:	_	_	_
66	INPUT	INPUT	NNP	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
68	antibody	antibody	NN	_	_	_
69	manufacturer	manufacturer	NN	_	_	_
70	:	:	:	_	_	_
71	Upstate	upstate	JJ	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	antibody	antibody	NN	_	_	_
74	:	:	:	_	_	_
75	Monoclonal	monoclonal	JJ	_	_	_
76	antibody	antibody	NN	_	_	_
77	for	for	IN	_	_	_
78	RNA	rna	NN	_	_	_
79	polymerase	polymerase	NN	_	_	_
80	Beta	beta	NN	_	_	_
81	'	'	''	_	_	_
82	subunit	subunit	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	NT73	nt73	NN	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	antibody	antibody	NN	_	_	_
88	:	:	:	_	_	_
89	Monoclonal	monoclonal	JJ	_	_	_
90	antibody	antibody	NN	_	_	_
91	for	for	IN	_	_	_
92	RNA	rna	NN	_	_	_
93	polymerase	polymerase	NN	_	_	_
94	Beta	beta	NN	_	_	_
95	subunit	subunit	NN	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	W0002	w0002	NN	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	antibody	antibody	NN	_	_	_
101	:	:	:	_	_	_
102	Monoclonal	monoclonal	JJ	_	_	_
103	ANTI-FLAG	anti-flag	NN	_	_	_
104	M2	m2	NN	_	_	_
105	antibody	antibody	NN	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	F3165	f3165	NN	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	-	-	:	_	_	_
110	Sigma	Sigma	NNP	_	_	_
111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
112	antibody	antibody	NN	_	_	_
113	:	:	:	_	_	_
114	None	none	NN	_	_	_
115	,	,	,	_	_	_
116	input	input	NN	_	_	_
117	DNA	dna	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	antibody	antibody	NN	_	_	_
120	:	:	:	_	_	_
121	normal	normal	JJ	_	_	_
122	mouse	mouse	NN	_	_	_
123	IgG	igg	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	antibody	antibody	NN	_	_	_
126	:	:	:	_	_	_
127	normal	normal	JJ	_	_	_
128	mouse	mouse	NN	_	_	_
129	IgG	igg	NN	_	_	_
130	-LRB-	-lrb-	-LRB-	_	_	_
131	Upstate	upstate	JJ	_	_	_
132	-RRB-	-rrb-	-RRB-	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	antibody	antibody	NN	_	_	_
135	:	:	:	_	_	_
136	polyclonal	polyclonal	JJ	_	_	_
137	antiserum	antiserum	NN	_	_	_
138	was	be	VBD	_	_	_
139	raised	raise	VBN	_	_	_
140	against	against	IN	_	_	_
141	His6-ArcA	his6-arca	NN	_	_	_
142	then	then	RB	_	_	_
143	Affinity	Affinity	NNP	_	_	_
144	Purified	purify	VBN	_	_	_
145	using	use	VBG	_	_	_
146	purified	purify	VBN	_	_	_
147	ArcA	arca	NN	TF	_	_
148	to	to	TO	_	_	_
149	yield	yield	VB	_	_	_
150	the	the	DT	_	_	_
151	polyclonal	polyclonal	JJ	_	_	_
152	antibodies	antibody	NNS	_	_	_
153	used	use	VBN	_	_	_
154	for	for	IN	_	_	_
155	ChIP	chip	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	antibody	antibody	NN	_	_	_
158	:	:	:	_	_	_
159	polycolonal	polycolonal	JJ	_	_	_
160	antiserum	antiserum	NN	_	_	_
161	was	be	VBD	_	_	_
162	raised	raise	VBN	_	_	_
163	against	against	IN	_	_	_
164	His6-ArcA	his6-arca	NN	_	_	_
165	then	then	RB	_	_	_
166	Affinity	Affinity	NNP	_	_	_
167	Purified	purify	VBN	_	_	_
168	against	against	IN	_	_	_
169	ArcA	arca	NN	TF	_	_
170	to	to	TO	_	_	_
171	yield	yield	VB	_	_	_
172	the	the	DT	_	_	_
173	polyclonal	polyclonal	JJ	_	_	_
174	antibodies	antibody	NNS	_	_	_
175	used	use	VBN	_	_	_
176	for	for	IN	_	_	_
177	ChIP	chip	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	antibody	antibody	NN	_	_	_
180	:	:	:	_	_	_
181	Pre-cleared	pre-cleared	JJ	_	_	_
182	FNR	fnr	NN	TF	_	_
183	antibody	antibody	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	antibody	antibody	NN	_	_	_
186	:	:	:	_	_	_
187	Pre-cleared	pre-cleared	JJ	_	_	_
188	H-NS	h-ns	NN	_	_	_
189	polyclonal	polyclonal	JJ	_	_	_
190	antibody	antibody	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	antibody	antibody	NN	_	_	_
193	:	:	:	_	_	_
194	Pre-cleared	pre-cleared	JJ	_	_	_
195	IHF	ihf	NN	TF	_	_
196	polyclonal	polyclonal	JJ	_	_	_
197	antibody	antibody	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	antibody	antibody	NN	_	_	_
200	:	:	:	_	_	_
201	rabbit	rabbit	NN	_	_	_
202	pre-immune	pre-immune	JJ	_	_	_
203	IgG	igg	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	antibody	antibody	NN	_	_	_
206	:	:	:	_	_	_
207	RNAP	rnap	NN	_	_	_
208	beta	beta	NN	_	_	_
209	subunit	subunit	NN	_	_	_
210	-LRB-	-lrb-	-LRB-	_	_	_
211	NT63	nt63	NN	_	_	_
212	-RRB-	-rrb-	-RRB-	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	antibody	antibody	NN	_	_	_
215	:	:	:	_	_	_
216	RNA	rna	NN	_	_	_
217	Polymerase	polymerase	NN	_	_	_
218	ß	ß	NN	_	_	_
219	monoclonal	monoclonal	JJ	_	_	_
220	antibody	antibody	NN	_	_	_
221	from	from	IN	_	_	_
222	NeoClone	NeoClone	NNP	_	_	_
223	-LRB-	-lrb-	-LRB-	_	_	_
224	W0002	w0002	NN	_	_	_
225	-RRB-	-rrb-	-RRB-	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	antibody	antibody	NN	_	_	_
228	:	:	:	_	_	_
229	RNA	rna	NN	_	_	_
230	Polymerase	polymerase	NN	_	_	_
231	σ70	σ70	NN	_	_	_
232	monoclonal	monoclonal	JJ	_	_	_
233	antibody	antibody	NN	_	_	_
234	from	from	IN	_	_	_
235	NeoClone	NeoClone	NNP	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	W0004	w0004	NN	_	_	_
238	-RRB-	-rrb-	-RRB-	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	antibody	antibody	NN	_	_	_
241	vendor/catalog	vendor/catalog	NN	_	_	_
242	#	#	#	_	_	_
243	:	:	:	_	_	_
244	Sigma/Cat	sigma/cat	NN	_	_	_
245	.	.	.	_	_	_

1	No	no	DT	_	_	_
2	.	.	.	_	_	_

1	F1804	f1804	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	APEC	apec	NN	_	_	_
4	strain	strain	NN	_	_	_
5	O08	o08	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	APEC	apec	NN	_	_	_
8	strain	strain	NN	_	_	_
9	SCI-07	sci-07	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	A	a	NN	_	_	_
12	pool	pool	NN	_	_	_
13	of	of	IN	_	_	_
14	3	3	CD	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	clones	clone	NNS	_	_	_
18	forming	form	VBG	_	_	_
19	large	large	JJ	_	_	_
20	colonies	colony	NNS	_	_	_
21	when	when	WRB	_	_	_
22	plated	plate	VBN	_	_	_
23	on	on	IN	_	_	_
24	TTagar	ttagar	NN	_	_	_
25	and	and	CC	_	_	_
26	derived	derive	VBN	_	_	_
27	from	from	IN	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	B	b	NN	_	_	_
31	REL606	rel606	NN	_	_	_
32	after	after	IN	_	_	_
33	150	150	CD	_	_	_
34	days	day	NNS	_	_	_
35	of	of	IN	_	_	_
36	seasonal	seasonal	JJ	_	_	_
37	evolution	evolution	NN	_	_	_
38	experiment	experiment	NN	_	_	_
39	in	in	IN	_	_	_
40	18	18	CD	_	_	_
41	mm	mm	NN	_	_	_
42	test	test	NN	_	_	_
43	tubes	tube	NNS	_	_	_
44	in	in	IN	_	_	_
45	DMga	dmga	JJ	_	_	_
46	medium	medium	NN	_	_	_
47	.	.	.	_	_	_

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	AR1	ar1	SYM	_	_	_
3	-	-	:	_	_	_
4	/	/	:	_	_	_
5	AR2	ar2	SYM	_	_	_
6	-	-	:	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	AR1	ar1	NN	_	_	_
9	-	-	:	_	_	_
10	/	/	:	_	_	_
11	AR2	ar2	SYM	_	_	_
12	-	-	:	_	_	_
13	rep	rep	NN	GEN	_	_
14	1	1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	AR1	ar1	NN	_	_	_
17	-	-	:	_	_	_
18	/	/	:	_	_	_
19	AR2	ar2	SYM	_	_	_
20	-	-	:	_	_	_
21	rep	rep	NN	GEN	_	_
22	2	2	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	AR1	ar1	NN	_	_	_
25	-	-	:	_	_	_
26	/	/	:	_	_	_
27	AR2	ar2	SYM	_	_	_
28	-	-	:	_	_	_
29	rep	rep	NN	GEN	_	_
30	3	3	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	ArcA	arca	NN	TF	_	_
33	-	-	:	_	_	_
34	Aerobic	aerobic	JJ	_	_	_
35	-	-	:	_	_	_
36	Affinity	affinity	NN	_	_	_
37	Purified	purify	VBN	_	_	_
38	-	-	:	_	_	_
39	A	a	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	ArcA	arca	NN	TF	_	_
42	-	-	:	_	_	_
43	Anaerobic	anaerobic	JJ	_	_	_
44	-	-	:	_	_	_
45	Affinity	affinity	NN	_	_	_
46	Purified	purify	VBN	_	_	_
47	-	-	:	_	_	_
48	biological	biological	JJ	_	_	_
49	rep	rep	NN	GEN	_	_
50	A	a	DT	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	ArcA	arca	NN	TF	_	_
53	-	-	:	_	_	_
54	Anaerobic	anaerobic	JJ	_	_	_
55	-	-	:	_	_	_
56	Affinity	affinity	NN	_	_	_
57	Purified	purify	VBN	_	_	_
58	-	-	:	_	_	_
59	biological	biological	JJ	_	_	_
60	rep	rep	NN	GEN	_	_
61	B	b	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	∆	∆	CD	_	_	_
64	ArcA	arca	NN	TF	_	_
65	-	-	:	_	_	_
66	Anaerobic	anaerobic	JJ	_	_	_
67	-	-	:	_	_	_
68	Affinity	affinity	NN	_	_	_
69	Purified	purify	VBN	_	_	_
70	-	-	:	_	_	_
71	technical	technical	JJ	_	_	_
72	rep	rep	NN	GEN	_	_
73	A	a	DT	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	∆	∆	CD	_	_	_
76	ArcA	arca	NN	TF	_	_
77	-	-	:	_	_	_
78	Anaerobic	anaerobic	JJ	_	_	_
79	-	-	:	_	_	_
80	Affinity	affinity	NN	_	_	_
81	Purified	purify	VBN	_	_	_
82	-	-	:	_	_	_
83	technical	technical	JJ	_	_	_
84	rep	rep	NN	GEN	_	_
85	B	b	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	ArcA	arca	NN	TF	_	_
88	_	_	NN	_	_	_
89	anaerobic	anaerobic	JJ	_	_	_
90	_	_	NN	_	_	_
91	ChIP-seq	ChIP-seq	NNP	_	_	_
92	_	_	NNP	_	_	_
93	IP	IP	NNP	_	_	_
94	_	_	SYM	_	_	_
95	A.wig	A.wig	NNP	_	_	_
96	:	:	:	_	_	_
97	U00096	u00096	NN	_	_	_
98	.2	.2	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	ArcA	arca	NN	TF	_	_
101	_	_	NN	_	_	_
102	anaerobic	anaerobic	JJ	_	_	_
103	_	_	NN	_	_	_
104	ChIP-seq	ChIP-seq	NNP	_	_	_
105	_	_	NNP	_	_	_
106	IP	IP	NNP	_	_	_
107	_	_	NNP	_	_	_
108	B.wig	B.wig	NNP	_	_	_
109	:	:	:	_	_	_
110	U00096	u00096	NN	_	_	_
111	.2	.2	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	ArcA	arca	NN	TF	_	_
114	INPUT	input	NN	_	_	_
115	DNA	dna	NN	_	_	_
116	from	from	IN	_	_	_
117	WT	WT	NNP	_	_	_
118	Escherchia	Escherchia	NNP	_	_	_
119	coli	coli	NN	_	_	_
120	MG1655	mg1655	NN	_	_	_
121	K-12	k-12	NN	_	_	_
122	,	,	,	_	_	_
123	no	no	DT	_	_	_
124	antibody	antibody	NN	_	_	_
125	control	control	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
127	ArcA	arca	NN	TF	_	_
128	INPUT	input	NN	_	_	_
129	from	from	IN	_	_	_
130	WT	WT	NNP	_	_	_
131	Escherichia	escherichia	FW	Organism	_	_
132	coli	coli	FW	Organism	_	_
133	MG1655	mg1655	NN	_	_	_
134	K-12	k-12	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	ArcA	arca	NN	TF	_	_
137	IP	IP	NNP	_	_	_
138	ChIP-seq	ChIP-seq	NNP	_	_	_
139	Anaerobic	Anaerobic	NNP	_	_	_
140	Biological	Biological	NNP	_	_	_
141	replicate	replicate	VB	_	_	_
142	1	1	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	ArcA	arca	NN	TF	_	_
145	IP	IP	NNP	_	_	_
146	ChIP-seq	ChIP-seq	NNP	_	_	_
147	Anaerobic	Anaerobic	NNP	_	_	_
148	Biological	Biological	NNP	_	_	_
149	replicate	replicate	VB	_	_	_
150	2	2	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
152	∆	∆	SYM	_	_	_
153	arcA	arcA	NNP	GEN	_	_
154	IP	IP	NNP	_	_	_
155	DNA	dna	NN	_	_	_
156	from	from	IN	_	_	_
157	PK9416	pk9416	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	ArcA	arca	NN	TF	_	_
160	IP	IP	NNP	_	_	_
161	DNA	dna	NN	_	_	_
162	from	from	IN	_	_	_
163	WT	WT	NNP	_	_	_
164	Escherichia	escherichia	FW	Organism	_	_
165	coli	coli	FW	Organism	_	_
166	MG1655	mg1655	NN	_	_	_
167	K-12	k-12	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	ArcA	arca	NN	TF	_	_
170	IP	IP	NNP	_	_	_
171	from	from	IN	_	_	_
172	WT	WT	NNP	_	_	_
173	Escherichia	escherichia	FW	Organism	_	_
174	coli	coli	FW	Organism	_	_
175	MG1655	mg1655	NN	_	_	_
176	K-12	k-12	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	Archaea	archaea	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	Arginine	arginine	NN	_	_	_
181	addition	addition	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	ArgR	argr	NN	TF	_	_
184	_	_	CD	_	_	_
185	Arginine	arginine	NN	_	_	_
186	_	_	NN	_	_	_
187	1	1	CD	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	ArgR	argr	NN	TF	_	_
190	_	_	CD	_	_	_
191	Arginine	arginine	NN	_	_	_
192	_	_	NN	_	_	_
193	2	2	CD	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	ArgR	argr	NN	TF	_	_
196	-LRB-	-lrb-	-LRB-	_	_	_
197	-	-	:	_	_	_
198	arg	arg	NN	_	_	_
199	-RRB-	-rrb-	-RRB-	_	_	_
200	rep1	rep1	NN	_	_	_
201	and	and	CC	_	_	_
202	rep2	rep2	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	ArgR	argr	NN	TF	_	_
205	-LRB-	-lrb-	-LRB-	_	_	_
206	+	+	CC	_	_	_
207	arg	arg	NN	_	_	_
208	-RRB-	-rrb-	-RRB-	_	_	_
209	rep1	rep1	NN	_	_	_
210	and	and	CC	_	_	_
211	rep2	rep2	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	ArgR	argr	NN	TF	_	_
214	_	_	CD	_	_	_
215	NH4Cl	nh4cl	NN	_	_	_
216	_	_	NN	_	_	_
217	1	1	CD	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	ArgR	argr	NN	TF	_	_
220	_	_	CD	_	_	_
221	NH4Cl	nh4cl	NN	_	_	_
222	_	_	NN	_	_	_
223	2	2	CD	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	Arrays	array	NNS	_	_	_
226	were	be	VBD	_	_	_
227	processed	process	VBN	_	_	_
228	using	use	VBG	_	_	_
229	Nimblegen	Nimblegen	NNP	_	_	_
230	's	's	POS	_	_	_
231	standard	standard	JJ	_	_	_
232	protocol	protocol	NN	_	_	_
233	for	for	IN	_	_	_
234	Nimblescan	nimblescan	JJ	_	_	_
235	2.4	2.4	CD	_	_	_
236	ChIP	chip	NN	_	_	_
237	data	datum	NNS	_	_	_
238	extraction	extraction	NN	_	_	_
239	.	.	.	_	_	_

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	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	NN	_	_	_
13	A	a	NN	_	_	_
14	single	single	JJ	_	_	_
15	colony	colony	NN	_	_	_
16	of	of	IN	_	_	_
17	Escherichia	escherichia	FW	Organism	_	_
18	coli	coli	FW	Organism	_	_
19	was	be	VBD	_	_	_
20	inoculated	inoculate	VBN	_	_	_
21	into	into	IN	_	_	_
22	250	250	CD	_	_	_
23	ml	ml	NN	_	_	_
24	of	of	IN	_	_	_
25	LB	lb	NN	MED	_	_
26	medium	medium	NN	MED	_	_
27	without	without	IN	_	_	_
28	antibiotics	antibiotic	NNS	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	grown	grow	VBN	_	_	_
32	at	at	IN	_	_	_
33	37C	37c	NN	_	_	_
34	with	with	IN	_	_	_
35	shaking	shake	VBG	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	150	150	CD	_	_	_
38	RPM	rpm	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	for	for	IN	_	_	_
41	approximately	approximately	RB	_	_	_
42	4	4	CD	_	_	_
43	hours	hour	NNS	_	_	_
44	,	,	,	_	_	_
45	until	until	IN	_	_	_
46	OD600	od600	NN	_	_	_
47	was	be	VBD	_	_	_
48	~	~	CD	_	_	_
49	0.3	0.3	CD	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	log	log	NN	_	_	_
52	phase	phase	NN	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	.	.	.	_	_	_

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/ml	g/ml	NN	_	_	_
38	,	,	,	_	_	_
39	and	and	CC	_	_	_
40	bacteria	bacterium	NNS	_	_	_
41	were	be	VBD	_	_	_
42	incubated	incubate	VBN	_	_	_
43	for	for	IN	_	_	_
44	additional	additional	JJ	_	_	_
45	2	2	CD	_	_	_
46	minutes	minute	NNS	_	_	_
47	to	to	TO	_	_	_
48	block	block	VB	_	_	_
49	transcription	transcription	NN	_	_	_
50	.	.	.	_	_	_

1	25	25	CD	_	_	_
2	ml	ml	NN	_	_	_
3	aliquots	aliquot	NNS	_	_	_
4	of	of	IN	_	_	_
5	bacteria	bacterium	NNS	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	rapidly	rapidly	RB	_	_	_
9	pelleted	pellete	VBN	_	_	_
10	by	by	IN	_	_	_
11	centrifugation	centrifugation	NN	_	_	_
12	at	at	IN	_	_	_
13	4C	4c	NN	_	_	_
14	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	,	,	,	_	_	_
4	medium	medium	NN	_	_	_
5	was	be	VBD	_	_	_
6	decanted	decant	VBN	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	cells	cell	NNS	_	_	_
10	from	from	IN	_	_	_
11	each	each	DT	_	_	_
12	25	25	CD	_	_	_
13	ml	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	culture	culture	NN	_	_	_
16	were	be	VBD	_	_	_
17	resuspended	resuspend	VBN	_	_	_
18	in	in	IN	_	_	_
19	1	1	CD	_	_	_
20	ml	ml	NN	_	_	_
21	of	of	IN	_	_	_
22	structure	structure	NN	_	_	_
23	probing	probe	VBG	_	_	_
24	buffer	buffer	NN	_	_	_
25	-LSB-	-lsb-	-LRB-	_	_	_
26	10	10	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	HEPES-KOH	hepes-koh	NN	_	_	_
29	pH	ph	NN	_	_	_
30	7.9	7.9	CD	_	_	_
31	;	;	:	_	_	_
32	140	140	CD	_	_	_
33	mM	mm	NN	KWSUPP	_	_
34	NaCl	nacl	NN	_	_	_
35	;	;	:	_	_	_
36	3	3	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	KCl	kcl	NN	_	_	_
39	-RSB-	-rsb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	DMS	dms	NN	_	_	_
2	was	be	VBD	_	_	_
3	diluted	dilute	VBN	_	_	_
4	1:6	1:6	CD	_	_	_
5	in	in	IN	_	_	_
6	100	100	CD	_	_	_
7	%	%	NN	_	_	_
8	Ethanol	ethanol	NN	_	_	_
9	to	to	TO	_	_	_
10	a	a	DT	_	_	_
11	final	final	JJ	_	_	_
12	concentration	concentration	NN	_	_	_
13	of	of	IN	_	_	_
14	1.76	1.76	CD	_	_	_
15	M.	m.	NN	_	_	_
16	Diluted	Diluted	NNP	_	_	_
17	DMS	DMS	NNP	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	to	to	TO	_	_	_
21	bacteria	bacterium	NNS	_	_	_
22	to	to	TO	_	_	_
23	a	a	DT	_	_	_
24	final	final	JJ	_	_	_
25	concentration	concentration	NN	_	_	_
26	of	of	IN	_	_	_
27	~	~	NN	_	_	_
28	105	105	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	incubated	incubate	VBN	_	_	_
4	with	with	IN	_	_	_
5	moderate	moderate	JJ	_	_	_
6	shaking	shake	VBG	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	800	800	CD	_	_	_
9	RPM	rpm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	at	at	IN	_	_	_
12	25C	25c	NN	_	_	_
13	for	for	IN	_	_	_
14	2	2	CD	_	_	_
15	minutes	minute	NNS	_	_	_
16	,	,	,	_	_	_
17	after	after	IN	_	_	_
18	which	which	WDT	_	_	_
19	reactions	reaction	NNS	_	_	_
20	were	be	VBD	_	_	_
21	immediately	immediately	RB	_	_	_
22	transferred	transfer	VBN	_	_	_
23	to	to	TO	_	_	_
24	ice	ice	NN	_	_	_
25	.	.	.	_	_	_

1	DTT	dtt	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	0.7	0.7	CD	_	_	_
10	M	m	NN	_	_	_
11	to	to	TO	_	_	_
12	quench	quench	VB	_	_	_
13	DMS	DMS	NNP	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	vigorously	vigorously	RB	_	_	_
19	vortexed	vortex	VBN	_	_	_
20	for	for	IN	_	_	_
21	10	10	CD	_	_	_
22	seconds	seconds	NNS	_	_	_
23	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	pelleted	pellete	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	10,000	10,000	CD	_	_	_
9	g	g	NN	_	_	_
10	for	for	IN	_	_	_
11	30	30	CD	_	_	_
12	seconds	seconds	NNS	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	4C	4c	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	supernatant	supernatant	NN	_	_	_
20	was	be	VBD	_	_	_
21	decanted	decant	VBN	_	_	_
22	.	.	.	_	_	_

1	Pellets	pellet	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	Isoamyl	Isoamyl	NNP	_	_	_
10	alcohol	alcohol	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Sigma	Sigma	NNP	_	_	_
13	Aldrich	Aldrich	NNP	_	_	_
14	,	,	,	_	_	_
15	cat	cat	NN	_	_	_
16	.	.	.	_	_	_

1	W205702	w205702	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	to	to	TO	_	_	_
4	remove	remove	VB	_	_	_
5	traces	trace	NNS	_	_	_
6	of	of	IN	_	_	_
7	water-insoluble	water-insoluble	JJ	_	_	_
8	DMS	dms	NN	_	_	_
9	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	pelleted	pellete	VBN	_	_	_
5	by	by	IN	_	_	_
6	additional	additional	JJ	_	_	_
7	centrifugation	centrifugation	NN	_	_	_
8	at	at	IN	_	_	_
9	10,000	10,000	CD	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	30	30	CD	_	_	_
13	seconds	seconds	NNS	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	4C	4c	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	supernatant	supernatant	NN	_	_	_
19	was	be	VBD	_	_	_
20	decanted	decant	VBN	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	samples	sample	NNS	_	_	_
24	were	be	VBD	_	_	_
25	snap-frozen	snap-frozen	JJ	_	_	_
26	in	in	IN	_	_	_
27	liquid	liquid	JJ	_	_	_
28	nitrogen	nitrogen	NN	_	_	_
29	.	.	.	_	_	_

1	Pellets	pellet	NNS	_	_	_
2	were	be	VBD	_	_	_
3	stored	store	VBN	_	_	_
4	at	at	IN	_	_	_
5	-80	-80	CD	_	_	_
6	C.	C.	NNP	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	A	A	NNP	_	_	_
9	single	single	JJ	_	_	_
10	large	large	JJ	_	_	_
11	fastq	fastq	NN	_	_	_
12	format	format	NN	_	_	_
13	file	file	NN	_	_	_
14	of	of	IN	_	_	_
15	high	high	JJ	_	_	_
16	quality	quality	NN	_	_	_
17	reads	read	VBZ	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Q	Q	NNP	_	_	_
20	≥	≥	SYM	_	_	_
21	30	30	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	was	be	VBD	_	_	_
24	split	split	VBN	_	_	_
25	into	into	IN	_	_	_
26	about	about	IN	_	_	_
27	10	10	CD	_	_	_
28	smaller	smaller	JJR	_	_	_
29	files	file	NNS	_	_	_
30	by	by	IN	_	_	_
31	using	use	VBG	_	_	_
32	a	a	DT	_	_	_
33	shell	shell	NN	_	_	_
34	script	script	NN	_	_	_
35	splitReads.sh	splitreads.sh	JJ	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Aspartate	aspartate	NN	_	_	_
38	addition	addition	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	aspC	aspc	NN	GEN	_	_
41	KO	ko	NN	_	_	_
42	rep1	rep1	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	aspC	aspc	NN	GEN	_	_
45	KO	ko	NN	_	_	_
46	rep2	rep2	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	aspC	aspc	NN	GEN	_	_
49	KO	ko	NN	_	_	_
50	rep3	rep3	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Assignment	assignment	NN	_	_	_
53	to	to	TO	_	_	_
54	restriction	restriction	NN	_	_	_
55	fragment	fragment	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Astat	astat	NN	_	_	_
58	_	_	NN	_	_	_
59	chemostat	chemostat	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	A-stat	a-stat	NN	_	_	_
62	gene	gene	NN	_	_	_
63	expression	expression	NN	_	_	_
64	changes	change	NNS	_	_	_
65	0.3	0.3	CD	_	_	_
66	/	/	:	_	_	_
67	0.47	0.47	CD	_	_	_
68	h-1	h-1	NN	_	_	_
69	dye-flip	dye-flip	JJ	_	_	_
70	repl	repl	NN	_	_	_
71	.3	.3	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	A-stat	a-stat	NN	_	_	_
74	gene	gene	NN	_	_	_
75	expression	expression	NN	_	_	_
76	changes	change	NNS	_	_	_
77	0.47	0.47	CD	_	_	_
78	/	/	:	_	_	_
79	0.3	0.3	CD	_	_	_
80	h-1	h-1	NN	_	_	_
81	repl	repl	NN	_	_	_
82	.1	.1	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	A-stat	a-stat	NN	_	_	_
85	gene	gene	NN	_	_	_
86	expression	expression	NN	_	_	_
87	changes	change	NNS	_	_	_
88	0.47	0.47	CD	_	_	_
89	/	/	:	_	_	_
90	0.3	0.3	CD	_	_	_
91	h-1	h-1	NN	_	_	_
92	repl	repl	NN	_	_	_
93	.2.1	.2.1	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	A-stat	a-stat	NN	_	_	_
96	gene	gene	NN	_	_	_
97	expression	expression	NN	_	_	_
98	changes	change	NNS	_	_	_
99	0.47	0.47	CD	_	_	_
100	/	/	:	_	_	_
101	0.3	0.3	CD	_	_	_
102	h-1	h-1	NN	_	_	_
103	repl	repl	NN	_	_	_
104	.2.2	.2.2	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	A-stat	a-stat	NN	_	_	_
107	,	,	,	_	_	_
108	specific	specific	JJ	_	_	_
109	growth	growth	NN	_	_	_
110	rate	rate	NN	_	_	_
111	0.48	0.48	CD	_	_	_
112	1/h	1/h	JJ	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	AT1	at1	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	AT1	at1	NN	_	_	_
117	biological	biological	JJ	_	_	_
118	replicate	replicate	VBP	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
120	At	at	IN	_	_	_
121	3	3	CD	_	_	_
122	h	h	NN	_	_	_
123	of	of	IN	_	_	_
124	culture	culture	NN	_	_	_
125	,	,	,	_	_	_
126	60	60	CD	_	_	_
127	mL	ml	NN	_	_	_
128	of	of	IN	_	_	_
129	culture	culture	NN	_	_	_
130	-LRB-	-lrb-	-LRB-	_	_	_
131	at	at	IN	_	_	_
132	OD595	od595	CD	_	_	_
133	nm	nm	NN	_	_	_
134	=	=	JJ	_	_	_
135	0.73	0.73	CD	_	_	_
136	±	±	SYM	_	_	_
137	0.07	0.07	CD	_	_	_
138	,	,	,	_	_	_
139	0.63	0.63	CD	_	_	_
140	±	±	SYM	_	_	_
141	0.02	0.02	CD	_	_	_
142	,	,	,	_	_	_
143	0.12	0.12	CD	_	_	_
144	±	±	SYM	_	_	_
145	0.01	0.01	CD	_	_	_
146	and	and	CC	_	_	_
147	0.11	0.11	CD	_	_	_
148	±	±	NN	_	_	_
149	0.02	0.02	CD	_	_	_
150	for	for	IN	_	_	_
151	cultures	culture	NNS	_	_	_
152	subjected	subject	VBN	_	_	_
153	to	to	TO	_	_	_
154	0	0	CD	_	_	_
155	,	,	,	_	_	_
156	5.0	5.0	CD	_	_	_
157	,	,	,	_	_	_
158	6.5	6.5	CD	_	_	_
159	and	and	CC	_	_	_
160	8.5	8.5	CD	_	_	_
161	µM	µm	NN	_	_	_
162	AgNO3	agno3	NN	_	_	_
163	,	,	,	_	_	_
164	respectively	respectively	RB	_	_	_
165	-RRB-	-rrb-	-RRB-	_	_	_
166	were	be	VBD	_	_	_
167	sampled	sample	VBN	_	_	_
168	and	and	CC	_	_	_
169	centrifuged	centrifuge	VBN	_	_	_
170	-LRB-	-lrb-	-LRB-	_	_	_
171	4000	4000	CD	_	_	_
172	rpm	rpm	NN	_	_	_
173	,	,	,	_	_	_
174	5	5	CD	_	_	_
175	min	min	NN	_	_	_
176	,	,	,	_	_	_
177	4	4	CD	_	_	_
178	°C	°c	NN	_	_	_
179	-RRB-	-rrb-	-RRB-	_	_	_
180	,	,	,	_	_	_
181	then	then	RB	_	_	_
182	the	the	DT	_	_	_
183	pellet	pellet	NN	_	_	_
184	was	be	VBD	_	_	_
185	frozen	freeze	VBN	_	_	_
186	in	in	IN	_	_	_
187	liquid	liquid	JJ	_	_	_
188	nitrogen	nitrogen	NN	_	_	_
189	.	.	.	_	_	_

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	NN	_	_	_
2	ATCACG-D1	atcacg-d1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	ATCC2	atcc2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	ATCC3	atcc3	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	each	each	DT	_	_	_
10	time	time	NN	_	_	_
11	point	point	NN	_	_	_
12	,	,	,	_	_	_
13	15	15	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	each	each	DT	_	_	_
17	culture	culture	NN	_	_	_
18	was	be	VBD	_	_	_
19	mixed	mix	VBN	_	_	_
20	with	with	IN	_	_	_
21	30	30	CD	_	_	_
22	ml	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	RNAprotect	rnaprotect	NN	_	_	_
25	Bacteria	bacterium	NNS	_	_	_
26	Reagent	reagent	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Qiagen	qiagen	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	vortexed	vortex	VBN	_	_	_
32	for	for	IN	_	_	_
33	5s	5	NNS	_	_	_
34	,	,	,	_	_	_
35	incubated	incubate	VBN	_	_	_
36	for	for	IN	_	_	_
37	5	5	CD	_	_	_
38	min	min	NN	_	_	_
39	at	at	IN	_	_	_
40	room	room	NN	_	_	_
41	temperature	temperature	NN	_	_	_
42	,	,	,	_	_	_
43	and	and	CC	_	_	_
44	centrifuged	centrifuge	VBN	_	_	_
45	for	for	IN	_	_	_
46	10	10	CD	_	_	_
47	min	min	NN	_	_	_
48	at	at	IN	_	_	_
49	5000g	5000g	CD	_	_	_
50	.	.	.	_	_	_

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	OD	od	NN	_	_	_
4	~	~	NN	_	_	_
5	0.3	0.3	CD	_	_	_
6	,	,	,	_	_	_
7	cultures	culture	NNS	_	_	_
8	were	be	VBD	_	_	_
9	induced	induce	VBN	_	_	_
10	with	with	IN	_	_	_
11	1mM	1mm	NN	_	_	_
12	IPTG	iptg	NN	_	_	_
13	for	for	IN	_	_	_
14	the	the	DT	_	_	_
15	appropriate	appropriate	JJ	_	_	_
16	length	length	NN	_	_	_
17	of	of	IN	_	_	_
18	time	time	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	At	at	IN	_	_	_
3	OD450	od450	NN	_	_	_
4	=	=	JJ	_	_	_
5	0.3	0.3	CD	_	_	_
6	,	,	,	_	_	_
7	cultures	culture	NNS	_	_	_
8	induced	induce	VBN	_	_	_
9	with	with	IN	_	_	_
10	1	1	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	IPTG	iptg	NN	_	_	_
13	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD600	od600	NN	_	_	_
10	~	~	NN	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	serine	serine	NN	_	_	_
14	hydroxamate	hydroxamate	NN	_	_	_
15	was	be	VBD	_	_	_
16	added	add	VBN	_	_	_
17	to	to	TO	_	_	_
18	a	a	DT	_	_	_
19	final	final	JJ	_	_	_
20	concentration	concentration	NN	_	_	_
21	of	of	IN	_	_	_
22	0.5	0.5	CD	_	_	_
23	mg/ml	mg/ml	NN	_	_	_
24	,	,	,	_	_	_
25	cells	cell	NNS	_	_	_
26	were	be	VBD	_	_	_
27	collected	collect	VBN	_	_	_
28	40	40	CD	_	_	_
29	minutes	minute	NNS	_	_	_
30	later	later	RB	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	At	at	IN	_	_	_
3	OD600	od600	NN	_	_	_
4	of	of	IN	_	_	_
5	0.5	0.5	CD	_	_	_
6	,	,	,	_	_	_
7	cell	cell	NN	_	_	_
8	cultures	culture	NNS	_	_	_
9	were	be	VBD	_	_	_
10	separated	separate	VBN	_	_	_
11	into	into	IN	_	_	_
12	two	two	CD	_	_	_
13	flasks	flask	NNS	_	_	_
14	.	.	.	_	_	_

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	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	A	a	NN	_	_	_
3	total	total	NN	_	_	_
4	of	of	IN	_	_	_
5	six	six	CD	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	analyzed	analyze	VBN	_	_	_
9	.	.	.	_	_	_

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	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	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	pgcgrowthcondition	NNS	_	_	_
18	At	at	IN	_	_	_
19	the	the	DT	_	_	_
20	appropriate	appropriate	JJ	_	_	_
21	optical	optical	JJ	_	_	_
22	density	density	NN	_	_	_
23	,	,	,	_	_	_
24	culture	culture	NN	_	_	_
25	growth	growth	NN	_	_	_
26	was	be	VBD	_	_	_
27	instantaneously	instantaneously	RB	_	_	_
28	arrested	arrest	VBN	_	_	_
29	by	by	IN	_	_	_
30	addition	addition	NN	_	_	_
31	of	of	IN	_	_	_
32	an	a	DT	_	_	_
33	equal	equal	JJ	_	_	_
34	volume	volume	NN	_	_	_
35	of	of	IN	_	_	_
36	chilled	chill	VBN	_	_	_
37	100	100	CD	_	_	_
38	%	%	NN	_	_	_
39	ethanol	ethanol	NN	_	_	_
40	,	,	,	_	_	_
41	and	and	CC	_	_	_
42	the	the	DT	_	_	_
43	cells	cell	NNS	_	_	_
44	were	be	VBD	_	_	_
45	stored	store	VBN	_	_	_
46	at	at	IN	_	_	_
47	--	--	:	_	_	_
48	80	80	CD	_	_	_
49	°C	°c	NN	_	_	_
50	until	until	IN	_	_	_
51	they	they	PRP	_	_	_
52	were	be	VBD	_	_	_
53	processed	process	VBN	_	_	_
54	for	for	IN	_	_	_
55	RNA	rna	NN	_	_	_
56	extraction	extraction	NN	_	_	_
57	.	.	.	_	_	_

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	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	v/v	NN	_	_	_
20	-RSB-	-rsb-	-RRB-	_	_	_
21	ethanol	ethanol	NN	_	_	_
22	;	;	:	_	_	_
23	5	5	CD	_	_	_
24	%	%	NN	_	_	_
25	-LSB-	-lsb-	-LRB-	_	_	_
26	v/v	v/v	NN	_	_	_
27	-RSB-	-rsb-	-RRB-	_	_	_
28	phenol	phenol	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	was	be	VBD	_	_	_
31	added	add	VBN	_	_	_
32	to	to	TO	_	_	_
33	a	a	DT	_	_	_
34	culture	culture	NN	_	_	_
35	to	to	TO	_	_	_
36	inhibit	inhibit	VB	_	_	_
37	cell	cell	NN	_	_	_
38	metabolism	metabolism	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Kime	Kime	NNP	_	_	_
41	et	et	FW	_	_	_
42	al.	al.	FW	_	_	_
43	2008	2008	CD	_	_	_
44	.	.	.	_	_	_

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	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	harvested	harvest	VBN	_	_	_
17	by	by	IN	_	_	_
18	centrifugation	centrifugation	NN	_	_	_
19	.	.	.	_	_	_

1	When	when	WRB	_	_	_
2	necessary	necessary	JJ	_	_	_
3	,	,	,	_	_	_
4	cell	cell	NN	_	_	_
5	pellets	pellet	NNS	_	_	_
6	were	be	VBD	_	_	_
7	stored	store	VBN	_	_	_
8	frozen	freeze	VBN	_	_	_
9	at	at	IN	_	_	_
10	-80	-80	CD	_	_	_
11	C.	C.	NNP	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	At	at	IN	_	_	_
14	time	time	NN	_	_	_
15	point	point	NN	_	_	_
16	0	0	CD	_	_	_
17	,	,	,	_	_	_
18	rifampicin	rifampicin	NN	SUPP	_	_
19	was	be	VBD	_	_	_
20	added	add	VBN	_	_	_
21	to	to	TO	_	_	_
22	a	a	DT	_	_	_
23	final	final	JJ	_	_	_
24	concentration	concentration	NN	_	_	_
25	of	of	IN	_	_	_
26	500ug/ml	500ug/ml	NN	_	_	_
27	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	at	at	IN	_	_	_
5	0	0	CD	_	_	_
6	,	,	,	_	_	_
7	2	2	CD	_	_	_
8	,	,	,	_	_	_
9	4	4	CD	_	_	_
10	,	,	,	_	_	_
11	6	6	CD	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	8	8	CD	_	_	_
15	minutes	minute	NNS	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Automatic	Automatic	NNP	_	_	_
3	extractor	extractor	NN	_	_	_
4	in	in	IN	_	_	_
5	Verigene	verigene	JJ	_	_	_
6	system	system	NN	_	_	_
7	of	of	IN	_	_	_
8	genomic	genomic	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	average	average	JJ	_	_	_
12	fitness	fitness	NN	_	_	_
13	:	:	:	_	_	_
14	0.196851676684606	0.196851676684606	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	average	average	JJ	_	_	_
17	fitness	fitness	NN	_	_	_
18	:	:	:	_	_	_
19	0.296737932583603	0.296737932583603	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
21	average	average	JJ	_	_	_
22	fitness	fitness	NN	_	_	_
23	:	:	:	_	_	_
24	0.344592279464807	0.344592279464807	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	average	average	JJ	_	_	_
27	fitness	fitness	NN	_	_	_
28	:	:	:	_	_	_
29	0.353076289611459	0.353076289611459	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	average	average	JJ	_	_	_
32	fitness	fitness	NN	_	_	_
33	:	:	:	_	_	_
34	0.434286415079969	0.434286415079969	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	average	average	JJ	_	_	_
37	fitness	fitness	NN	_	_	_
38	:	:	:	_	_	_
39	0.502711019240335	0.502711019240335	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	Average	average	JJ	_	_	_
42	Normalization	normalization	NN	_	_	_
43	using	use	VBG	_	_	_
44	GeneChip	GeneChip	NNP	_	_	_
45	Operating	Operating	NNP	_	_	_
46	Software	Software	NNP	_	_	_
47	Version	Version	NNP	_	_	_
48	1.4	1.4	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	AW1	aw1	NN	_	_	_
51	.7	.7	CD	_	_	_
52	,	,	,	_	_	_
53	steady-state	steady-state	JJ	_	_	_
54	continuous	continuous	JJ	_	_	_
55	cultured	culture	VBN	_	_	_
56	experimental	experimental	JJ	_	_	_
57	samples	sample	NNS	_	_	_
58	at	at	IN	_	_	_
59	37	37	CD	_	_	_
60	°C	°c	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	AW1	aw1	NN	_	_	_
63	.7	.7	CD	_	_	_
64	,	,	,	_	_	_
65	steady-state	steady-state	JJ	_	_	_
66	continuous	continuous	JJ	_	_	_
67	cultured	culture	VBN	_	_	_
68	experimental	experimental	JJ	_	_	_
69	samples	sample	NNS	_	_	_
70	at	at	IN	_	_	_
71	37	37	CD	_	_	_
72	°C	°c	NN	_	_	_
73	and	and	CC	_	_	_
74	then	then	RB	_	_	_
75	15	15	CD	_	_	_
76	minutes	minute	NNS	_	_	_
77	heatshock	heatshock	NN	_	_	_
78	at	at	IN	_	_	_
79	50	50	CD	_	_	_
80	°C	°c	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	azide	azide	NN	_	_	_
83	treated	treat	VBN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	B10	b10	NN	_	_	_
86	DH10BGFP	dh10bgfp	NN	_	_	_
87	_	_	CD	_	_	_
88	pSB1C3	psb1c3	NN	_	_	_
89	_	_	NN	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	B10	b10	NN	_	_	_
93	:	:	:	_	_	_
94	LJ110	lj110	NN	_	_	_
95	del	del	FW	_	_	_
96	pdhr	pdhr	FW	_	_	_
97	MMAcetat	mmacetat	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	B11	b11	NN	_	_	_
100	:	:	:	_	_	_
101	LJ110	lj110	NN	_	_	_
102	pTM30	ptm30	NN	_	_	_
103	MMAcetat	mmacetat	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	B12	b12	NN	_	_	_
106	:	:	:	_	_	_
107	LJ110	lj110	NN	_	_	_
108	pTM30pdhr	ptm30pdhr	NN	_	_	_
109	MMAcetat	mmacetat	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	B17	b17	NN	_	_	_
112	MG1655GFP	mg1655gfp	NN	_	_	_
113	_	_	CD	_	_	_
114	pSB1C3	psb1c3	NN	_	_	_
115	_	_	NN	_	_	_
116	2	2	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	B1	b1	NN	_	_	_
119	:	:	:	_	_	_
120	LJ110	lj110	NN	_	_	_
121	LBo	lbo	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	B22	b22	NN	_	_	_
124	MG1655GFP	mg1655gfp	NN	_	_	_
125	_	_	CD	_	_	_
126	pSB1C3	psb1c3	NN	_	_	_
127	_	_	CD	_	_	_
128	H3	h3	NN	_	_	_
129	_	_	NN	_	_	_
130	2	2	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	b2618	b2618	NN	_	_	_
133	_	_	CD	_	_	_
134	U	U	NNP	_	_	_
135	_	_	NNP	_	_	_
136	N0075	N0075	NNP	_	_	_
137	_	_	VBD	_	_	_
138	r1	r1	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	b2618	b2618	NN	_	_	_
141	_	_	CD	_	_	_
142	U	U	NNP	_	_	_
143	_	_	NNP	_	_	_
144	N0075	N0075	NNP	_	_	_
145	_	_	VBD	_	_	_
146	r2	r2	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	b2618	b2618	NN	_	_	_
149	_	_	CD	_	_	_
150	U	U	NNP	_	_	_
151	_	_	NNP	_	_	_
152	N0075	N0075	NNP	_	_	_
153	_	_	VBD	_	_	_
154	r3	r3	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	b2618	b2618	NN	_	_	_
157	upregulation	upregulation	NN	_	_	_
158	,	,	,	_	_	_
159	0.075	0.075	CD	_	_	_
160	ug/ml	ug/ml	NN	_	_	_
161	norfloxacin	norfloxacin	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	B26	b26	NN	_	_	_
164	MG1655GFP	mg1655gfp	NN	_	_	_
165	_	_	CD	_	_	_
166	Lux	lux	FW	_	_	_
167	_	_	FW	_	_	_
168	2	2	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	B2	b2	NN	_	_	_
171	:	:	:	_	_	_
172	LJ110	lj110	NN	_	_	_
173	del	del	FW	_	_	_
174	pdhr	pdhr	FW	_	_	_
175	LBo	lbo	FW	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	B3	b3	NN	_	_	_
178	DH10BGFP	dh10bgfp	NN	_	_	_
179	_	_	CD	_	_	_
180	pSB1C3	psb1c3	NN	_	_	_
181	_	_	NN	_	_	_
182	2	2	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	B3	b3	NN	_	_	_
185	:	:	:	_	_	_
186	LJ110	lj110	NN	_	_	_
187	pTM30	ptm30	NN	_	_	_
188	LBo	lbo	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	B4	b4	NN	_	_	_
191	DH10BGFP	dh10bgfp	NN	_	_	_
192	_	_	CD	_	_	_
193	pLys	ply	VBZ	_	_	_
194	_	_	SYM	_	_	_
195	2	2	CD	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	B4	b4	NN	_	_	_
198	:	:	:	_	_	_
199	LJ110	lj110	NN	_	_	_
200	pTM30pdhr	ptm30pdhr	NN	_	_	_
201	LBo	lbo	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	B500	b500	CD	_	_	_
204	_	_	NN	_	_	_
205	1	1	CD	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	B5	b5	NN	_	_	_
208	:	:	:	_	_	_
209	LJ110	lj110	NN	_	_	_
210	MMPyruvat	mmpyruvat	NN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	B6	b6	NN	_	_	_
213	:	:	:	_	_	_
214	LJ110	lj110	NN	_	_	_
215	del	del	FW	_	_	_
216	pdhr	pdhr	FW	_	_	_
217	MMPyruvat	mmpyruvat	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	B7	b7	NN	_	_	_
220	DH10BGFP	dh10bgfp	NN	_	_	_
221	_	_	CD	_	_	_
222	pD864	pd864	NN	_	_	_
223	_	_	NN	_	_	_
224	2	2	CD	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	B7	b7	NN	_	_	_
227	:	:	:	_	_	_
228	LJ110	lj110	NN	_	_	_
229	pTM30	ptm30	NN	_	_	_
230	MMPyruvat	mmpyruvat	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	B8	b8	NN	_	_	_
233	:	:	:	_	_	_
234	LJ110	lj110	NN	_	_	_
235	pTM30pdhr	ptm30pdhr	NN	_	_	_
236	MMPyruvat	mmpyruvat	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	B9	b9	NN	_	_	_
239	DH10BGFP	dh10bgfp	NN	_	_	_
240	_	_	CD	_	_	_
241	pLys	ply	VBZ	_	_	_
242	_	_	SYM	_	_	_
243	M1	m1	NN	_	_	_
244	_	_	NN	_	_	_
245	2	2	CD	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	B9	b9	NN	_	_	_
248	:	:	:	_	_	_
249	LJ110	lj110	NN	_	_	_
250	MMAcetat	mmacetat	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	Background	background	NN	_	_	_
253	correction	correction	NN	_	_	_
254	and	and	CC	_	_	_
255	normalization	normalization	NN	_	_	_
256	-LRB-	-lrb-	-LRB-	_	_	_
257	print-tip	print-tip	JJ	_	_	_
258	loess	loess	NN	_	_	_
259	and	and	CC	_	_	_
260	quantile	quantile	NN	_	_	_
261	-RRB-	-rrb-	-RRB-	_	_	_
262	were	be	VBD	_	_	_
263	performed	perform	VBN	_	_	_
264	using	use	VBG	_	_	_
265	the	the	DT	_	_	_
266	limma	limma	NN	_	_	_
267	R	r	NN	_	_	_
268	package	package	NN	_	_	_
269	.	.	.	_	_	_

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://bioinformatics.skcc.org/webarray/	http://bioinformatics.skcc.org/webarray/	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	the	the	DT	_	_	_
3	program	program	NN	_	_	_
4	EDGE	edge	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	http://www.biostat.washington.edu/software/jstorey/edge/	http://www.biostat.washington.edu/software/jstorey/edge/	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	to	to	TO	_	_	_
11	estimate	estimate	VB	_	_	_
12	the	the	DT	_	_	_
13	conditional	conditional	JJ	_	_	_
14	false	false	JJ	_	_	_
15	discovery	discovery	NN	_	_	_
16	rate	rate	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	FDR	FDR	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	the	the	DT	_	_	_
22	expected	expect	VBN	_	_	_
23	proportion	proportion	NN	_	_	_
24	of	of	IN	_	_	_
25	false	false	JJ	_	_	_
26	positives	positive	NNS	_	_	_
27	conditioned	condition	VBN	_	_	_
28	on	on	IN	_	_	_
29	having	have	VBG	_	_	_
30	k	k	NN	_	_	_
31	`	`	``	_	_	_
32	significant	significant	JJ	_	_	_
33	'	'	''	_	_	_
34	findings	finding	NNS	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	background	background	NN	_	_	_
3	:	:	:	_	_	_
4	crp	crp	NN	GEN	_	_
5	mutant	mutant	JJ	_	_	_
6	background	background	NN	_	_	_
7	,	,	,	_	_	_
8	fis	fi	VBZ	GEN	_	_
9	flag	flag	NN	_	_	_
10	tag	tag	NN	GEN	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	background	background	NN	_	_	_
13	:	:	:	_	_	_
14	fis	fis	NN	GEN	_	_
15	mutant	mutant	JJ	_	_	_
16	background	background	NN	_	_	_
17	,	,	,	_	_	_
18	crp	crp	NN	GEN	_	_
19	flag	flag	NN	_	_	_
20	tag	tag	NN	GEN	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	background	background	NN	_	_	_
23	strain	strain	NN	_	_	_
24	:	:	:	_	_	_
25	BW25113	bw25113	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	background	background	NN	_	_	_
28	strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	BW27784	bw27784	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	background	background	NN	_	_	_
33	strain	strain	NN	_	_	_
34	:	:	:	_	_	_
35	LJ110	lj110	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Background	background	NN	_	_	_
38	subtractions	subtraction	NNS	_	_	_
39	and	and	CC	_	_	_
40	normalization	normalization	NN	_	_	_
41	of	of	IN	_	_	_
42	extracted	extract	VBN	_	_	_
43	data	datum	NNS	_	_	_
44	were	be	VBD	_	_	_
45	performed	perform	VBN	_	_	_
46	through	through	IN	_	_	_
47	R	r	NN	_	_	_
48	using	use	VBG	_	_	_
49	the	the	DT	_	_	_
50	Bioconductor	Bioconductor	NNP	_	_	_
51	package	package	NN	_	_	_
52	as	as	IN	_	_	_
53	described	describe	VBN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	Yang	Yang	NNP	_	_	_
56	,	,	,	_	_	_
57	Y.H.	Y.H.	NNP	_	_	_
58	et	et	FW	_	_	_
59	al.	al.	FW	_	_	_
60	.	.	.	_	_	_

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	background	background	NN	_	_	_
3	:	:	:	_	_	_
4	wild	wild	JJ	_	_	_
5	type	type	NN	_	_	_
6	,	,	,	_	_	_
7	crp	crp	NN	GEN	_	_
8	flag	flag	NN	_	_	_
9	tag	tag	NN	GEN	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	background	background	NN	_	_	_
12	:	:	:	_	_	_
13	wild	wild	JJ	_	_	_
14	type	type	NN	_	_	_
15	,	,	,	_	_	_
16	fis	fi	VBZ	GEN	_	_
17	flag	flag	NN	_	_	_
18	tag	tag	NN	GEN	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	bacteria	bacterium	NNS	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Bacteria	bacterium	NNS	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Bacteria	bacterium	NNS	_	_	_
25	at	at	IN	_	_	_
26	58	58	CD	_	_	_
27	°C	°c	NN	_	_	_
28	F	f	NN	_	_	_
29	=	=	JJ	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Bacteria	bacterium	NNS	_	_	_
33	at	at	IN	_	_	_
34	58	58	CD	_	_	_
35	°C	°c	NN	_	_	_
36	F	f	NN	_	_	_
37	=	=	JJ	_	_	_
38	3	3	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Bacteria	bacterium	NNS	_	_	_
41	at	at	IN	_	_	_
42	60	60	CD	_	_	_
43	°C	°c	NN	_	_	_
44	F	f	NN	_	_	_
45	=	=	JJ	_	_	_
46	3	3	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Bacteria	bacterium	NNS	_	_	_
49	at	at	IN	_	_	_
50	71	71	CD	_	_	_
51	°C	°c	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Bacteria	bacterium	NNS	_	_	_
54	cells	cell	NNS	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	bacteria	bacterium	NNS	_	_	_
57	grown	grow	VBN	_	_	_
58	at	at	IN	_	_	_
59	37	37	CD	_	_	_
60	°	°	CD	_	_	_
61	C	c	NN	_	_	_
62	with	with	IN	_	_	_
63	shaking	shake	VBG	_	_	_
64	until	until	IN	_	_	_
65	log	log	NN	_	_	_
66	phase	phase	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	bacteria	bacterium	NNS	_	_	_
69	grown	grow	VBN	_	_	_
70	at	at	IN	_	_	_
71	37	37	CD	_	_	_
72	°	°	CD	_	_	_
73	C	c	NN	_	_	_
74	with	with	IN	_	_	_
75	shaking	shake	VBG	_	_	_
76	until	until	IN	_	_	_
77	log	log	NN	_	_	_
78	phase	phase	NN	_	_	_
79	with	with	IN	_	_	_
80	ampicilin	ampicilin	NN	_	_	_
81	treatment	treatment	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	bacteria	bacterium	NNS	_	_	_
84	grown	grow	VBN	_	_	_
85	at	at	IN	_	_	_
86	37	37	CD	_	_	_
87	°	°	CD	_	_	_
88	C	c	NN	_	_	_
89	with	with	IN	_	_	_
90	shaking	shake	VBG	_	_	_
91	until	until	IN	_	_	_
92	log	log	NN	_	_	_
93	phase	phase	NN	_	_	_
94	with	with	IN	_	_	_
95	florfenicol	florfenicol	NN	_	_	_
96	treatment	treatment	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	bacteria	bacterium	NNS	_	_	_
99	grown	grow	VBN	_	_	_
100	at	at	IN	_	_	_
101	37	37	CD	_	_	_
102	°	°	CD	_	_	_
103	C	c	NN	_	_	_
104	with	with	IN	_	_	_
105	shaking	shake	VBG	_	_	_
106	until	until	IN	_	_	_
107	log	log	NN	_	_	_
108	phase	phase	NN	_	_	_
109	with	with	IN	_	_	_
110	streptomycin	streptomycin	NN	_	_	_
111	treatment	treatment	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	bacteria	bacterium	NNS	_	_	_
114	grown	grow	VBN	_	_	_
115	in	in	IN	_	_	_
116	LB	lb	NN	_	_	_
117	in	in	FW	_	_	_
118	vitro	vitro	FW	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	bacteria	bacterium	NNS	_	_	_
121	harvested	harvest	VBN	_	_	_
122	from	from	IN	_	_	_
123	blood	blood	NN	_	_	_
124	of	of	IN	_	_	_
125	chickens	chicken	NNS	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Bacterial	bacterial	JJ	_	_	_
128	cell	cell	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	bacterial	bacterial	JJ	_	_	_
131	cell	cell	NN	_	_	_
132	culture	culture	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	Bacterial	bacterial	JJ	_	_	_
135	Cell	cell	NN	_	_	_
136	Lysates	lysate	NNS	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	bacterial	bacterial	JJ	_	_	_
139	cell	cell	NN	_	_	_
140	lysates	lysate	NNS	_	_	_
141	_	_	VBP	_	_	_
142	input	input	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	bacterial	bacterial	JJ	_	_	_
145	cell	cell	NN	_	_	_
146	lysates	lysate	NNS	_	_	_
147	_	_	VBP	_	_	_
148	RecA-ChIP-seq	reca-chip-seq	JJ	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	Bacterial	bacterial	JJ	_	_	_
151	cell	cell	NN	_	_	_
152	pellet	pellet	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	bacterial	bacterial	JJ	_	_	_
155	cells	cell	NNS	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
157	Bacterial	bacterial	JJ	_	_	_
158	cells	cell	NNS	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
160	Bacterial	bacterial	JJ	_	_	_
161	cells	cell	NNS	_	_	_
162	from	from	IN	_	_	_
163	an	a	DT	_	_	_
164	overnight	overnight	JJ	_	_	_
165	culture	culture	NN	_	_	_
166	were	be	VBD	_	_	_
167	washed	wash	VBN	_	_	_
168	and	and	CC	_	_	_
169	diluted	dilute	VBN	_	_	_
170	in	in	IN	_	_	_
171	fresh	fresh	JJ	_	_	_
172	SILAC	silac	NN	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	stable	stable	JJ	_	_	_
175	isotope	isotope	NN	_	_	_
176	labeling	labeling	NN	_	_	_
177	with	with	IN	_	_	_
178	amino	amino	NN	SUPP	_	_
179	acids	acid	NNS	SUPP	_	_
180	in	in	IN	_	_	_
181	cell	cell	NN	_	_	_
182	culture	culture	NN	_	_	_
183	-RRB-	-rrb-	-RRB-	_	_	_
184	medium	medium	NN	_	_	_
185	optimized	optimize	VBN	_	_	_
186	for	for	IN	_	_	_
187	non-auxotrophic	non-auxotrophic	JJ	_	_	_
188	E.	e.	FW	_	_	_
189	coli	coli	FW	_	_	_
190	-LRB-	-lrb-	-LRB-	_	_	_
191	Ping	ping	VB	_	_	_
192	LY	LY	NNP	_	_	_
193	et	et	FW	_	_	_
194	al.	al.	FW	_	_	_
195	.	.	.	_	_	_

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	NN	_	_	_
2	bacterial	bacterial	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	OD600	od600	NN	_	_	_
7	=	=	JJ	_	_	_
8	0.5	0.5	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Bacterial	bacterial	JJ	_	_	_
11	cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	aerobically	aerobically	RB	_	_	_
15	in	in	IN	_	_	_
16	M9	m9	NN	_	_	_
17	medium	medium	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	glucose	glucose	NN	SUPP	_	_
23	and	and	CC	_	_	_
24	5	5	CD	_	_	_
25	%	%	NN	_	_	_
26	LB	lb	NN	_	_	_
27	at	at	IN	_	_	_
28	37	37	CD	_	_	_
29	°C	°c	NN	_	_	_
30	under	under	IN	_	_	_
31	constant	constant	JJ	_	_	_
32	shaking	shake	VBG	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	~	~	NN	_	_	_
35	120	120	CD	_	_	_
36	rpm	rpm	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	in	in	IN	_	_	_
39	a	a	DT	_	_	_
40	water	water	NN	_	_	_
41	bath	bath	NN	_	_	_
42	and	and	CC	_	_	_
43	harvested	harvest	VBN	_	_	_
44	at	at	IN	_	_	_
45	OD	od	NN	_	_	_
46	~	~	NN	_	_	_
47	0.6	0.6	CD	_	_	_
48	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacterial	bacterial	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	dYT	dyt	JJ	_	_	_
8	medium	medium	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Miller	Miller	NNP	_	_	_
11	,	,	,	_	_	_
12	JH	JH	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	1972	1972	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	Experiments	experiment	NNS	_	_	_
17	in	in	IN	_	_	_
18	Molecular	molecular	JJ	_	_	_
19	Genetics	Genetics	NNP	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Cold	Cold	NNP	_	_	_
22	Spring	Spring	NNP	_	_	_
23	Harbor	Harbor	NNP	_	_	_
24	Laboratory	Laboratory	NNP	_	_	_
25	,	,	,	_	_	_
26	Cold	Cold	NNP	_	_	_
27	Spring	Spring	NNP	_	_	_
28	Harbor	Harbor	NNP	_	_	_
29	,	,	,	_	_	_
30	NY	NY	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	supplemented	supplement	VBN	_	_	_
33	with	with	IN	_	_	_
34	kanamycin	kanamycin	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	10	10	CD	_	_	_
37	mg/L	mg/l	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	,	,	,	_	_	_
40	ampicillin	ampicillin	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	100	100	CD	_	_	_
43	mg/L	mg/l	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	and	and	CC	_	_	_
46	IPTG	iptg	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	0.1	0.1	CD	_	_	_
49	mM	mm	NN	KWSUPP	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	at	at	IN	_	_	_
52	30	30	CD	_	_	_
53	°C	°c	NN	_	_	_
54	in	in	IN	_	_	_
55	a	a	DT	_	_	_
56	shaking	shake	VBG	_	_	_
57	water	water	NN	_	_	_
58	bath	bath	NN	_	_	_
59	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	a	a	DT	_	_	_
3	turbidity	turbidity	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	measured	measure	VBN	_	_	_
6	at	at	IN	_	_	_
7	OD536	od536	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	of	of	IN	_	_	_
10	approximately	approximately	RB	_	_	_
11	0.1	0.1	CD	_	_	_
12	bacteria	bacterium	NNS	_	_	_
13	were	be	VBD	_	_	_
14	harvested	harvest	VBN	_	_	_
15	by	by	IN	_	_	_
16	centrifugation	centrifugation	NN	_	_	_
17	at	at	IN	_	_	_
18	ambient	ambient	JJ	_	_	_
19	temperature	temperature	NN	_	_	_
20	and	and	CC	_	_	_
21	resuspended	resuspend	VBN	_	_	_
22	in	in	IN	_	_	_
23	fresh	fresh	JJ	_	_	_
24	dYT	dyt	NN	_	_	_
25	medium	medium	NN	_	_	_
26	containing	contain	VBG	_	_	_
27	antibiotics	antibiotic	NNS	_	_	_
28	and	and	CC	_	_	_
29	0.2	0.2	CD	_	_	_
30	%	%	NN	_	_	_
31	arabinose	arabinose	NN	_	_	_
32	.	.	.	_	_	_

1	Growth	growth	NN	_	_	_
2	was	be	VBD	_	_	_
3	continued	continue	VBN	_	_	_
4	at	at	IN	_	_	_
5	30	30	CD	_	_	_
6	°C	°c	NN	_	_	_
7	and	and	CC	_	_	_
8	10	10	CD	_	_	_
9	hours	hour	NNS	_	_	_
10	after	after	IN	_	_	_
11	inducer	inducer	NN	_	_	_
12	shift	shift	NN	_	_	_
13	3	3	CD	_	_	_
14	ml	ml	NN	_	_	_
15	sample	sample	NN	_	_	_
16	were	be	VBD	_	_	_
17	withdrawn	withdraw	VBN	_	_	_
18	,	,	,	_	_	_
19	treated	treat	VBN	_	_	_
20	with	with	IN	_	_	_
21	RNAPROTECT	rnaprotect	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Qiagen	Qiagen	NNP	_	_	_
24	,	,	,	_	_	_
25	Ballerup	Ballerup	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	,	,	,	_	_	_
28	harvested	harvest	VBN	_	_	_
29	by	by	IN	_	_	_
30	centrifugation	centrifugation	NN	_	_	_
31	and	and	CC	_	_	_
32	frozen	freeze	VBN	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacterial	bacterial	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	grown	grow	VBN	_	_	_
5	overnight	overnight	RB	_	_	_
6	at	at	IN	_	_	_
7	37C	37c	NN	_	_	_
8	,	,	,	_	_	_
9	given	give	VBN	_	_	_
10	1	1	CD	_	_	_
11	%	%	NN	_	_	_
12	sub-culturing	sub-culturing	JJ	_	_	_
13	till	till	IN	_	_	_
14	OD	od	NN	_	_	_
15	at	at	IN	_	_	_
16	600nm	600nm	NN	_	_	_
17	was	be	VBD	_	_	_
18	0.4	0.4	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	Bacterial	bacterial	JJ	_	_	_
21	cultures	culture	NNS	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Bacterial	bacterial	JJ	_	_	_
24	culture	culture	NN	_	_	_
25	with	with	IN	_	_	_
26	0.2	0.2	CD	_	_	_
27	ppm	ppm	NN	_	_	_
28	deoxynivalenol	deoxynivalenol	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Bacterial	bacterial	JJ	_	_	_
31	culture	culture	NN	_	_	_
32	with	with	IN	_	_	_
33	0.2	0.2	CD	_	_	_
34	ppm	ppm	NN	_	_	_
35	nivalenol	nivalenol	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Bacterial	bacterial	JJ	_	_	_
38	culture	culture	NN	_	_	_
39	with	with	IN	_	_	_
40	2	2	CD	_	_	_
41	ppm	ppm	NN	_	_	_
42	deoxynivalenol	deoxynivalenol	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Bacterial	bacterial	JJ	_	_	_
45	culture	culture	NN	_	_	_
46	with	with	IN	_	_	_
47	2	2	CD	_	_	_
48	ppm	ppm	NN	_	_	_
49	nivalenol	nivalenol	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Bacterial	bacterial	JJ	_	_	_
52	culture	culture	NN	_	_	_
53	with	with	IN	_	_	_
54	acetonitrile	acetonitrile	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Bacterial	bacterial	JJ	_	_	_
57	liquid	liquid	JJ	_	_	_
58	culture	culture	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Bacterial	bacterial	JJ	_	_	_
61	lysis	lysis	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	bacterial	bacterial	JJ	_	_	_
64	pellet	pellet	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Bacterial	bacterial	JJ	_	_	_
67	pellets	pellet	NNS	_	_	_
68	were	be	VBD	_	_	_
69	resuspended	resuspend	VBN	_	_	_
70	in	in	IN	_	_	_
71	350µl	350µl	CD	_	_	_
72	RNAwiz	rnawiz	NN	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	Ambion	Ambion	NNP	_	_	_
75	,	,	,	_	_	_
76	Austin	Austin	NNP	_	_	_
77	,	,	,	_	_	_
78	TX	TX	NNP	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	and	and	CC	_	_	_
81	kept	keep	VBD	_	_	_
82	at	at	IN	_	_	_
83	-80	-80	CD	_	_	_
84	°C	°c	NN	_	_	_
85	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacterial	bacterial	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	with	with	IN	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	with	with	IN	_	_	_
16	RNA	rna	NN	_	_	_
17	Integrity	integrity	NN	_	_	_
18	Number	number	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	RIN	rin	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	>	>	JJR	_	_	_
23	9	9	CD	_	_	_
24	were	be	VBD	_	_	_
25	used	use	VBN	_	_	_
26	for	for	IN	_	_	_
27	labeling	label	VBG	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Bacterial	bacterial	JJ	_	_	_
30	RNA	rna	NN	_	_	_
31	was	be	VBD	_	_	_
32	stabilized	stabilize	VBN	_	_	_
33	in	in	FW	_	_	_
34	vivo	vivo	FW	_	_	_
35	,	,	,	_	_	_
36	by	by	IN	_	_	_
37	using	use	VBG	_	_	_
38	RNA	rna	NN	_	_	_
39	protect	protect	VBP	_	_	_
40	Bacteria	bacterium	NNS	_	_	_
41	Reagent	reagent	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	Qiagen	qiagen	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

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	Bacterial	bacterial	JJ	_	_	_
3	strains	strain	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	LB	lb	NN	_	_	_
8	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Bacteria	bacterium	NNS	_	_	_
3	suspension	suspension	NN	_	_	_
4	heated	heat	VBN	_	_	_
5	at	at	IN	_	_	_
6	58	58	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	a	a	DT	_	_	_
10	process	process	NN	_	_	_
11	lethality	lethality	NN	_	_	_
12	value	value	NN	_	_	_
13	of	of	IN	_	_	_
14	2	2	CD	_	_	_
15	-	-	:	_	_	_
16	Replicate	replicate	VB	_	_	_
17	1	1	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Bacteria	bacterium	NNS	_	_	_
20	suspension	suspension	NN	_	_	_
21	heated	heat	VBN	_	_	_
22	at	at	IN	_	_	_
23	58	58	CD	_	_	_
24	°C	°c	NN	_	_	_
25	to	to	TO	_	_	_
26	a	a	DT	_	_	_
27	process	process	NN	_	_	_
28	lethality	lethality	NN	_	_	_
29	value	value	NN	_	_	_
30	of	of	IN	_	_	_
31	2	2	CD	_	_	_
32	-	-	:	_	_	_
33	Replicate	replicate	VB	_	_	_
34	2	2	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	Bacteria	bacterium	NNS	_	_	_
37	suspension	suspension	NN	_	_	_
38	heated	heat	VBN	_	_	_
39	at	at	IN	_	_	_
40	58	58	CD	_	_	_
41	°C	°c	NN	_	_	_
42	to	to	TO	_	_	_
43	a	a	DT	_	_	_
44	process	process	NN	_	_	_
45	lethality	lethality	NN	_	_	_
46	value	value	NN	_	_	_
47	of	of	IN	_	_	_
48	2	2	CD	_	_	_
49	-	-	:	_	_	_
50	Replicate	replicate	VB	_	_	_
51	3	3	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Bacteria	bacterium	NNS	_	_	_
54	suspension	suspension	NN	_	_	_
55	heated	heat	VBN	_	_	_
56	at	at	IN	_	_	_
57	58	58	CD	_	_	_
58	°C	°c	NN	_	_	_
59	to	to	TO	_	_	_
60	a	a	DT	_	_	_
61	process	process	NN	_	_	_
62	lethality	lethality	NN	_	_	_
63	value	value	NN	_	_	_
64	of	of	IN	_	_	_
65	2	2	CD	_	_	_
66	-	-	:	_	_	_
67	Replicate	replicate	VB	_	_	_
68	4	4	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	Bacteria	bacterium	NNS	_	_	_
71	suspension	suspension	NN	_	_	_
72	heated	heat	VBN	_	_	_
73	at	at	IN	_	_	_
74	58	58	CD	_	_	_
75	°C	°c	NN	_	_	_
76	to	to	TO	_	_	_
77	a	a	DT	_	_	_
78	process	process	NN	_	_	_
79	lethality	lethality	NN	_	_	_
80	value	value	NN	_	_	_
81	of	of	IN	_	_	_
82	2	2	CD	_	_	_
83	-	-	:	_	_	_
84	Replicate	replicate	VB	_	_	_
85	5	5	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
87	Bacteria	bacterium	NNS	_	_	_
88	suspension	suspension	NN	_	_	_
89	heated	heat	VBN	_	_	_
90	at	at	IN	_	_	_
91	58	58	CD	_	_	_
92	°C	°c	NN	_	_	_
93	to	to	TO	_	_	_
94	a	a	DT	_	_	_
95	process	process	NN	_	_	_
96	lethality	lethality	NN	_	_	_
97	value	value	NN	_	_	_
98	of	of	IN	_	_	_
99	3	3	CD	_	_	_
100	-	-	:	_	_	_
101	Replicate	replicate	VB	_	_	_
102	1	1	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Bacteria	bacterium	NNS	_	_	_
105	suspension	suspension	NN	_	_	_
106	heated	heat	VBN	_	_	_
107	at	at	IN	_	_	_
108	58	58	CD	_	_	_
109	°C	°c	NN	_	_	_
110	to	to	TO	_	_	_
111	a	a	DT	_	_	_
112	process	process	NN	_	_	_
113	lethality	lethality	NN	_	_	_
114	value	value	NN	_	_	_
115	of	of	IN	_	_	_
116	3	3	CD	_	_	_
117	-	-	:	_	_	_
118	Replicate	replicate	VB	_	_	_
119	2	2	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
121	Bacteria	bacterium	NNS	_	_	_
122	suspension	suspension	NN	_	_	_
123	heated	heat	VBN	_	_	_
124	at	at	IN	_	_	_
125	58	58	CD	_	_	_
126	°C	°c	NN	_	_	_
127	to	to	TO	_	_	_
128	a	a	DT	_	_	_
129	process	process	NN	_	_	_
130	lethality	lethality	NN	_	_	_
131	value	value	NN	_	_	_
132	of	of	IN	_	_	_
133	3	3	CD	_	_	_
134	-	-	:	_	_	_
135	Replicate	replicate	VB	_	_	_
136	3	3	CD	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	Bacteria	bacterium	NNS	_	_	_
139	suspension	suspension	NN	_	_	_
140	heated	heat	VBN	_	_	_
141	at	at	IN	_	_	_
142	58	58	CD	_	_	_
143	°C	°c	NN	_	_	_
144	to	to	TO	_	_	_
145	a	a	DT	_	_	_
146	process	process	NN	_	_	_
147	lethality	lethality	NN	_	_	_
148	value	value	NN	_	_	_
149	of	of	IN	_	_	_
150	3	3	CD	_	_	_
151	-	-	:	_	_	_
152	Replicate	replicate	VB	_	_	_
153	4	4	CD	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
155	Bacteria	bacterium	NNS	_	_	_
156	suspension	suspension	NN	_	_	_
157	heated	heat	VBN	_	_	_
158	at	at	IN	_	_	_
159	60	60	CD	_	_	_
160	°C	°c	NN	_	_	_
161	to	to	TO	_	_	_
162	a	a	DT	_	_	_
163	process	process	NN	_	_	_
164	lethality	lethality	NN	_	_	_
165	value	value	NN	_	_	_
166	of	of	IN	_	_	_
167	3	3	CD	_	_	_
168	-	-	:	_	_	_
169	Replicate	replicate	VB	_	_	_
170	1	1	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	Bacteria	bacterium	NNS	_	_	_
173	suspension	suspension	NN	_	_	_
174	heated	heat	VBN	_	_	_
175	at	at	IN	_	_	_
176	60	60	CD	_	_	_
177	°C	°c	NN	_	_	_
178	to	to	TO	_	_	_
179	a	a	DT	_	_	_
180	process	process	NN	_	_	_
181	lethality	lethality	NN	_	_	_
182	value	value	NN	_	_	_
183	of	of	IN	_	_	_
184	3	3	CD	_	_	_
185	-	-	:	_	_	_
186	Replicate	replicate	VB	_	_	_
187	2	2	CD	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
189	Bacteria	bacterium	NNS	_	_	_
190	suspension	suspension	NN	_	_	_
191	heated	heat	VBN	_	_	_
192	at	at	IN	_	_	_
193	60	60	CD	_	_	_
194	°C	°c	NN	_	_	_
195	to	to	TO	_	_	_
196	a	a	DT	_	_	_
197	process	process	NN	_	_	_
198	lethality	lethality	NN	_	_	_
199	value	value	NN	_	_	_
200	of	of	IN	_	_	_
201	3	3	CD	_	_	_
202	-	-	:	_	_	_
203	Replicate	replicate	VB	_	_	_
204	3	3	CD	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	Bacteria	bacterium	NNS	_	_	_
207	suspension	suspension	NN	_	_	_
208	heated	heat	VBN	_	_	_
209	at	at	IN	_	_	_
210	60	60	CD	_	_	_
211	°C	°c	NN	_	_	_
212	to	to	TO	_	_	_
213	a	a	DT	_	_	_
214	process	process	NN	_	_	_
215	lethality	lethality	NN	_	_	_
216	value	value	NN	_	_	_
217	of	of	IN	_	_	_
218	3	3	CD	_	_	_
219	-	-	:	_	_	_
220	Replicate	replicate	VB	_	_	_
221	4	4	CD	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
223	Bacteria	bacterium	NNS	_	_	_
224	suspension	suspension	NN	_	_	_
225	heated	heat	VBN	_	_	_
226	to	to	TO	_	_	_
227	a	a	DT	_	_	_
228	core	core	NN	_	_	_
229	temperature	temperature	NN	_	_	_
230	of	of	IN	_	_	_
231	71	71	CD	_	_	_
232	°C	°c	NN	_	_	_
233	-	-	:	_	_	_
234	Replicate	replicate	VB	_	_	_
235	1	1	CD	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	Bacteria	bacterium	NNS	_	_	_
238	suspension	suspension	NN	_	_	_
239	heated	heat	VBN	_	_	_
240	to	to	TO	_	_	_
241	a	a	DT	_	_	_
242	core	core	NN	_	_	_
243	temperature	temperature	NN	_	_	_
244	of	of	IN	_	_	_
245	71	71	CD	_	_	_
246	°C	°c	NN	_	_	_
247	-	-	:	_	_	_
248	Replicate	replicate	VB	_	_	_
249	2	2	CD	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
251	Bacteria	bacterium	NNS	_	_	_
252	suspension	suspension	NN	_	_	_
253	heated	heat	VBN	_	_	_
254	to	to	TO	_	_	_
255	a	a	DT	_	_	_
256	core	core	NN	_	_	_
257	temperature	temperature	NN	_	_	_
258	of	of	IN	_	_	_
259	71	71	CD	_	_	_
260	°C	°c	NN	_	_	_
261	-	-	:	_	_	_
262	Replicate	replicate	VB	_	_	_
263	3	3	CD	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	Bacteria	bacterium	NNS	_	_	_
266	suspension	suspension	NN	_	_	_
267	heated	heat	VBN	_	_	_
268	to	to	TO	_	_	_
269	a	a	DT	_	_	_
270	core	core	NN	_	_	_
271	temperature	temperature	NN	_	_	_
272	of	of	IN	_	_	_
273	71	71	CD	_	_	_
274	°C	°c	NN	_	_	_
275	-	-	:	_	_	_
276	Replicate	replicate	VB	_	_	_
277	4	4	CD	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
279	Bacteria	bacterium	NNS	_	_	_
280	suspension	suspension	NN	_	_	_
281	heated	heat	VBN	_	_	_
282	to	to	TO	_	_	_
283	a	a	DT	_	_	_
284	core	core	NN	_	_	_
285	temperature	temperature	NN	_	_	_
286	of	of	IN	_	_	_
287	71	71	CD	_	_	_
288	°C	°c	NN	_	_	_
289	-	-	:	_	_	_
290	Replicate	replicate	VB	_	_	_
291	5	5	CD	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
293	Bacteria	bacterium	NNS	_	_	_
294	were	be	VBD	_	_	_
295	cultured	culture	VBN	_	_	_
296	in	in	IN	_	_	_
297	an	a	DT	_	_	_
298	M9	m9	NN	MED	_	_
299	minimal	minimal	JJ	MED	_	_
300	medium	medium	NN	MED	_	_
301	supplemented	supplement	VBN	_	_	_
302	with	with	IN	_	_	_
303	2	2	CD	_	_	_
304	g/L	g/l	NN	_	_	_
305	lactose	lactose	NN	_	_	_
306	and	and	CC	_	_	_
307	5	5	CD	_	_	_
308	mM	mm	NN	KWSUPP	_	_
309	phenylethylamine	phenylethylamine	NN	_	_	_
310	-LRB-	-lrb-	-LRB-	_	_	_
311	PEA	pea	NN	_	_	_
312	,	,	,	_	_	_
313	M9	m9	NN	_	_	_
314	+	+	CC	_	_	_
315	L+PEA	l+pea	NN	_	_	_
316	-RRB-	-rrb-	-RRB-	_	_	_
317	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	induce	induce	VB	_	_	_
3	ECAO	ecao	NN	_	_	_
4	expression	expression	NN	_	_	_
5	from	from	IN	_	_	_
6	tynA	tyna	NN	GEN	_	_
7	gene	gene	NN	_	_	_
8	,	,	,	_	_	_
9	o/n	o/n	JJ	_	_	_
10	culture	culture	NN	_	_	_
11	of	of	IN	_	_	_
12	wt	wt	JJ	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	in	in	IN	_	_	_
16	M9-lactose	m9-lactose	JJ	_	_	_
17	medium	medium	NN	_	_	_
18	was	be	VBD	_	_	_
19	diluted	dilute	VBN	_	_	_
20	1:20	1:20	CD	_	_	_
21	in	in	IN	_	_	_
22	M9	m9	NN	_	_	_
23	+	+	CC	_	_	_
24	L+PEA	l+pea	NN	_	_	_
25	with	with	IN	_	_	_
26	5	5	CD	_	_	_
27	μM	μm	NN	_	_	_
28	CuSO4	cuso4	NN	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	aerobically	aerobically	RB	_	_	_
6	at	at	IN	_	_	_
7	+30	+30	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	250	250	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	shaking	shake	VBG	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	30C	30c	NN	_	_	_
7	with	with	IN	_	_	_
8	shaking	shake	VBG	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	~	~	NN	_	_	_
11	200	200	CD	_	_	_
12	rpm	rpm	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	fully	fully	RB	_	_	_
16	supplemented	supplement	VBN	_	_	_
17	MOPS	mop	NNS	MED	_	_
18	glucose	glucose	NN	SUPP	_	_
19	media	media	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Teknova	teknova	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	to	to	TO	_	_	_
24	OD420	od420	NN	_	_	_
25	~	~	NN	_	_	_
26	0.4	0.4	CD	_	_	_
27	.	.	.	_	_	_

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	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	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	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
14	Bacteria	bacterium	NNS	_	_	_
15	were	be	VBD	_	_	_
16	grown	grow	VBN	_	_	_
17	in	in	IN	_	_	_
18	LB	lb	NN	MED	_	_
19	broth	broth	NN	MED	_	_
20	overnight	overnight	JJ	_	_	_
21	and	and	CC	_	_	_
22	subcultured	subculture	VBN	_	_	_
23	in	in	IN	_	_	_
24	DMEM	DMEM	NNP	_	_	_
25	prior	prior	RB	_	_	_
26	to	to	TO	_	_	_
27	acid	acid	NN	_	_	_
28	stress	stress	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Bacteria	bacterium	NNS	_	_	_
31	were	be	VBD	_	_	_
32	grown	grow	VBN	_	_	_
33	in	in	IN	_	_	_
34	LB	lb	NN	MED	_	_
35	broth	broth	NN	MED	_	_
36	overnight	overnight	JJ	_	_	_
37	and	and	CC	_	_	_
38	subcultured	subculture	VBN	_	_	_
39	in	in	IN	_	_	_
40	DMEM	dmem	NN	_	_	_
41	to	to	TO	_	_	_
42	OD600	od600	NN	_	_	_
43	of	of	IN	_	_	_
44	0.4	0.4	CD	_	_	_
45	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	with	with	IN	_	_	_
6	0.5	0.5	CD	_	_	_
7	Vol	vol	NN	_	_	_
8	of	of	IN	_	_	_
9	5	5	CD	_	_	_
10	%	%	NN	_	_	_
11	phenol	phenol	NN	_	_	_
12	in	in	IN	_	_	_
13	ethanol	ethanol	NN	_	_	_
14	and	and	CC	_	_	_
15	frozen	freeze	VBN	_	_	_
16	at	at	IN	_	_	_
17	-80	-80	CD	_	_	_
18	C.	C.	NNP	_	_	_
19	Total	Total	NNP	_	_	_
20	RNA	rna	NN	_	_	_
21	was	be	VBD	_	_	_
22	extracted	extract	VBN	_	_	_
23	from	from	IN	_	_	_
24	frozen	frozen	JJ	_	_	_
25	cultures	culture	NNS	_	_	_
26	using	use	VBG	_	_	_
27	RNeasy	RNeasy	NNP	_	_	_
28	kit	kit	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Qiagen	qiagen	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	by	by	IN	_	_	_
6	direct	direct	JJ	_	_	_
7	injection	injection	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	mouse	mouse	NN	_	_	_
11	bladder	bladder	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	kidney	kidney	NN	_	_	_
15	samples	sample	NNS	_	_	_
16	were	be	VBD	_	_	_
17	taken	take	VBN	_	_	_
18	at	at	IN	_	_	_
19	day	day	NN	_	_	_
20	2	2	CD	_	_	_
21	post-infection	post-infection	JJ	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Bacteria	bacterium	NNS	_	_	_
24	were	be	VBD	_	_	_
25	lyzed	lyze	VBN	_	_	_
26	with	with	IN	_	_	_
27	lyzozyme	lyzozyme	NN	_	_	_
28	and	and	CC	_	_	_
29	sonicated	sonicate	VBN	_	_	_
30	to	to	TO	_	_	_
31	shear	shear	NN	_	_	_
32	DNA	dna	NN	_	_	_
33	.	.	.	_	_	_

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	NNP	_	_	_
2	Bacterium	Bacterium	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	Bacteroides	Bacteroides	NNPS	_	_	_
5	caccae	caccae	FW	_	_	_
6	ATCC	atcc	NN	_	_	_
7	43185	43185	CD	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Bacteroides	Bacteroides	NNPS	_	_	_
10	fragilis	fragili	VBZ	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Bacteroides	Bacteroides	NNPS	_	_	_
13	ovatus	ovatus	NN	_	_	_
14	ATCC	atcc	NN	_	_	_
15	8483	8483	CD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Bacteroides	Bacteroides	NNPS	_	_	_
18	thetaiotaomicron	thetaiotaomicron	RB	_	_	_
19	VPI-5482	vpi-5482	JJ	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	BAM	bam	NN	_	_	_
22	files	file	NNS	_	_	_
23	of	of	IN	_	_	_
24	each	each	DT	_	_	_
25	ChIP	chip	NN	_	_	_
26	biological	biological	JJ	_	_	_
27	replicate	replicate	VB	_	_	_
28	and	and	CC	_	_	_
29	the	the	DT	_	_	_
30	input	input	NN	_	_	_
31	replicate	replicate	VB	_	_	_
32	samples	sample	NNS	_	_	_
33	were	be	VBD	_	_	_
34	used	use	VBN	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	MACS	macs	NN	_	_	_
38	peak	peak	NN	_	_	_
39	calling	call	VBG	_	_	_
40	program	program	NN	_	_	_
41	with	with	IN	_	_	_
42	the	the	DT	_	_	_
43	-	-	:	_	_	_
44	f	f	LS	_	_	_
45	BAMPE	bampe	NN	_	_	_
46	parameter	parameter	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	BAM	bam	NN	_	_	_
49	files	file	NNS	_	_	_
50	of	of	IN	_	_	_
51	the	the	DT	_	_	_
52	resulting	result	VBG	_	_	_
53	assembly	assembly	NN	_	_	_
54	data	datum	NNS	_	_	_
55	were	be	VBD	_	_	_
56	exported	export	VBN	_	_	_
57	to	to	TO	_	_	_
58	JMP	JMP	NNP	_	_	_
59	Genomics	Genomics	NNP	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	SAS	SAS	NNP	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	.	.	.	_	_	_

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	NN	_	_	_
16	basal	basal	JJ	_	_	_
17	media	media	NNS	_	_	_
18	:	:	:	_	_	_
19	M9	m9	NN	_	_	_
20	+	+	CC	_	_	_
21	4	4	CD	_	_	_
22	g/L	g/l	NN	_	_	_
23	glc	glc	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	glucose	glucose	NN	SUPP	_	_
26	minimal	minimal	JJ	_	_	_
27	media	media	NNS	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Basecalling	basecalling	NN	_	_	_
31	performed	perform	VBN	_	_	_
32	by	by	IN	_	_	_
33	MiSeq	miseq	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	RTA	rta	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Base	base	NN	_	_	_
39	calling	call	VBG	_	_	_
40	performed	perform	VBN	_	_	_
41	using	use	VBG	_	_	_
42	Illumina	Illumina	NNP	_	_	_
43	GA	GA	NNP	_	_	_
44	pipeline	pipeline	NN	_	_	_
45	1.6	1.6	CD	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Basecalling	basecalling	NN	_	_	_
3	was	be	VBD	_	_	_
4	done	do	VBN	_	_	_
5	on	on	IN	_	_	_
6	the	the	DT	_	_	_
7	sequencers	sequencer	NNS	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	sequencer	sequencer	NN	_	_	_
11	's	's	POS	_	_	_
12	Real-Time	Real-Time	NNP	_	_	_
13	Analysis	analysis	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	RTA	rta	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	software	software	NN	_	_	_
18	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Base	Base	NNP	_	_	_
3	calling	call	VBG	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	by	by	IN	_	_	_
7	the	the	DT	_	_	_
8	DOE	DOE	NNP	_	_	_
9	Joint	Joint	NNP	_	_	_
10	Genome	Genome	NNP	_	_	_
11	Institute	Institute	NNP	_	_	_
12	using	use	VBG	_	_	_
13	Illumina	Illumina	NNP	_	_	_
14	software	software	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Basecalling	basecalling	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	by	by	IN	_	_	_
6	Torrent	Torrent	NNP	_	_	_
7	Suite	Suite	NNP	_	_	_
8	version	version	NN	_	_	_
9	5	5	CD	_	_	_
10	software	software	NN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	default	default	NN	_	_	_
14	settings	setting	NNS	_	_	_
15	.	.	.	_	_	_

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	Basecalls	basecall	NNS	_	_	_
10	performed	perform	VBN	_	_	_
11	using	use	VBG	_	_	_
12	CASAVA	CASAVA	NNP	_	_	_
13	version	version	NN	_	_	_
14	1.7	1.7	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Basecalls	basecall	NNS	_	_	_
17	performed	perform	VBN	_	_	_
18	using	use	VBG	_	_	_
19	CASAVA	CASAVA	NNP	_	_	_
20	version	version	NN	_	_	_
21	1.8	1.8	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Basecalls	basecall	NNS	_	_	_
24	performed	perform	VBN	_	_	_
25	using	use	VBG	_	_	_
26	CASAVA	CASAVA	NNP	_	_	_
27	version	version	NN	_	_	_
28	1.8.2	1.8.2	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Basecalls	basecall	NNS	_	_	_
31	performed	perform	VBN	_	_	_
32	using	use	VBG	_	_	_
33	CASAVA	CASAVA	NNP	_	_	_
34	version	version	NN	_	_	_
35	1.8.2	1.8.2	CD	_	_	_
36	.	.	.	_	_	_

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	NN	_	_	_
2	Basecalls	basecall	NNS	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	HCS	hcs	NN	_	_	_
6	2.0.5	2.0.5	CD	_	_	_
7	and	and	CC	_	_	_
8	RTA	RTA	NNP	_	_	_
9	1.17.20	1.17.20	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Basecalls	basecall	NNS	_	_	_
12	performed	perform	VBN	_	_	_
13	using	use	VBG	_	_	_
14	Illumina	Illumina	NNP	_	_	_
15	CASAVA	CASAVA	NNP	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Base	Base	NNP	_	_	_
3	calls	call	VBZ	_	_	_
4	performed	perform	VBN	_	_	_
5	with	with	IN	_	_	_
6	RTA	rta	NN	_	_	_
7	v1	v1	NN	_	_	_
8	.18.5	.18.5	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Base	base	NN	_	_	_
11	calls	call	NNS	_	_	_
12	were	be	VBD	_	_	_
13	made	make	VBN	_	_	_
14	using	use	VBG	_	_	_
15	MiSeq	MiSeq	NNP	_	_	_
16	Reporter	reporter	NN	_	_	_
17	v.	v.	CC	_	_	_
18	2.6.2.1	2.6.2.1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Basecalls	basecall	NNS	_	_	_
21	were	be	VBD	_	_	_
22	performed	perform	VBN	_	_	_
23	using	use	VBG	_	_	_
24	CASAVA	CASAVA	NNP	_	_	_
25	.1.8	.1.8	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	base	base	NN	_	_	_
28	calls	call	VBZ	_	_	_
29	with	with	IN	_	_	_
30	quality	quality	NN	_	_	_
31	metrics	metric	NNS	_	_	_
32	were	be	VBD	_	_	_
33	generated	generate	VBN	_	_	_
34	using	use	VBG	_	_	_
35	the	the	DT	_	_	_
36	HiSeq	HiSeq	NNP	_	_	_
37	2500	2500	CD	_	_	_
38	Control	Control	NNP	_	_	_
39	software	software	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	batch	batch	NN	_	_	_
42	:	:	:	_	_	_
43	10	10	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	batch	batch	NN	_	_	_
46	:	:	:	_	_	_
47	11	11	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	batch	batch	NN	_	_	_
50	:	:	:	_	_	_
51	12	12	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	batch	batch	NN	_	_	_
54	:	:	:	_	_	_
55	13	13	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	batch	batch	NN	_	_	_
58	:	:	:	_	_	_
59	14	14	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	batch	batch	NN	_	_	_
62	:	:	:	_	_	_
63	15	15	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	batch	batch	NN	_	_	_
66	:	:	:	_	_	_
67	16	16	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	batch	batch	NN	_	_	_
70	:	:	:	_	_	_
71	17	17	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	batch	batch	NN	_	_	_
74	:	:	:	_	_	_
75	18	18	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	batch	batch	NN	_	_	_
78	:	:	:	_	_	_
79	19	19	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	batch	batch	NN	_	_	_
82	:	:	:	_	_	_
83	20	20	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	batch	batch	NN	_	_	_
86	:	:	:	_	_	_
87	21	21	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	batch	batch	NN	_	_	_
90	:	:	:	_	_	_
91	22	22	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	batch	batch	NN	_	_	_
94	:	:	:	_	_	_
95	23	23	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	batch	batch	NN	_	_	_
98	:	:	:	_	_	_
99	24	24	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	batch	batch	NN	_	_	_
102	:	:	:	_	_	_
103	25	25	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	batch	batch	NN	_	_	_
106	:	:	:	_	_	_
107	26	26	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	batch	batch	NN	_	_	_
110	:	:	:	_	_	_
111	27	27	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	batch	batch	NN	_	_	_
114	:	:	:	_	_	_
115	7	7	CD	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	batch	batch	NN	_	_	_
118	:	:	:	_	_	_
119	8	8	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	batch	batch	NN	_	_	_
122	:	:	:	_	_	_
123	9	9	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Batch	batch	NN	_	_	_
126	anaerobically	anaerobically	RB	_	_	_
127	grown	grow	VBN	_	_	_
128	cultures	culture	NNS	_	_	_
129	in	in	IN	_	_	_
130	hemA	hema	NN	GEN	_	_
131	defined	define	VBN	_	_	_
132	medium	medium	NN	_	_	_
133	,	,	,	_	_	_
134	exposed	expose	VBN	_	_	_
135	to	to	TO	_	_	_
136	100uM	100um	VB	_	_	_
137	CORM-3	corm-3	NN	_	_	_
138	for	for	IN	_	_	_
139	10	10	CD	_	_	_
140	min	min	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	Batch	batch	NN	_	_	_
143	anaerobically	anaerobically	RB	_	_	_
144	grown	grow	VBN	_	_	_
145	cultures	culture	NNS	_	_	_
146	in	in	IN	_	_	_
147	hemA	hema	NN	GEN	_	_
148	defined	define	VBN	_	_	_
149	medium	medium	NN	_	_	_
150	,	,	,	_	_	_
151	exposed	expose	VBN	_	_	_
152	to	to	TO	_	_	_
153	100uM	100um	VB	_	_	_
154	CORM-3	corm-3	NN	_	_	_
155	for	for	IN	_	_	_
156	120	120	CD	_	_	_
157	min	min	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	Batch	batch	NN	_	_	_
160	anaerobically	anaerobically	RB	_	_	_
161	grown	grow	VBN	_	_	_
162	cultures	culture	NNS	_	_	_
163	in	in	IN	_	_	_
164	hemA	hema	NN	GEN	_	_
165	defined	define	VBN	_	_	_
166	medium	medium	NN	_	_	_
167	,	,	,	_	_	_
168	exposed	expose	VBN	_	_	_
169	to	to	TO	_	_	_
170	100uM	100um	VB	_	_	_
171	CORM-3	corm-3	NN	_	_	_
172	for	for	IN	_	_	_
173	20	20	CD	_	_	_
174	min	min	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	Batch	batch	NN	_	_	_
177	anaerobically	anaerobically	RB	_	_	_
178	grown	grow	VBN	_	_	_
179	cultures	culture	NNS	_	_	_
180	in	in	IN	_	_	_
181	hemA	hema	NN	GEN	_	_
182	defined	define	VBN	_	_	_
183	medium	medium	NN	_	_	_
184	,	,	,	_	_	_
185	exposed	expose	VBN	_	_	_
186	to	to	TO	_	_	_
187	100uM	100um	VB	_	_	_
188	CORM-3	corm-3	NN	_	_	_
189	for	for	IN	_	_	_
190	40	40	CD	_	_	_
191	min	min	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	Batch	batch	NN	_	_	_
194	anaerobically	anaerobically	RB	_	_	_
195	grown	grow	VBN	_	_	_
196	cultures	culture	NNS	_	_	_
197	in	in	IN	_	_	_
198	hemA	hema	NN	GEN	_	_
199	defined	define	VBN	_	_	_
200	medium	medium	NN	_	_	_
201	,	,	,	_	_	_
202	exposed	expose	VBN	_	_	_
203	to	to	TO	_	_	_
204	100uM	100um	VB	_	_	_
205	CORM-3	corm-3	NN	_	_	_
206	for	for	IN	_	_	_
207	60	60	CD	_	_	_
208	min	min	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	Batch	batch	NN	_	_	_
211	anaerobically	anaerobically	RB	_	_	_
212	grown	grow	VBN	_	_	_
213	cultures	culture	NNS	_	_	_
214	in	in	IN	_	_	_
215	hemA	hema	NN	GEN	_	_
216	defined	define	VBN	_	_	_
217	medium	medium	NN	_	_	_
218	,	,	,	_	_	_
219	exposed	expose	VBN	_	_	_
220	to	to	TO	_	_	_
221	100uM	100um	VB	_	_	_
222	iCORM-3	icorm-3	NN	_	_	_
223	for	for	IN	_	_	_
224	10	10	CD	_	_	_
225	min	min	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	Batch	batch	NN	_	_	_
228	anaerobically	anaerobically	RB	_	_	_
229	grown	grow	VBN	_	_	_
230	cultures	culture	NNS	_	_	_
231	in	in	IN	_	_	_
232	hemA	hema	NN	GEN	_	_
233	defined	define	VBN	_	_	_
234	medium	medium	NN	_	_	_
235	,	,	,	_	_	_
236	exposed	expose	VBN	_	_	_
237	to	to	TO	_	_	_
238	100uM	100um	VB	_	_	_
239	iCORM-3	icorm-3	NN	_	_	_
240	for	for	IN	_	_	_
241	120	120	CD	_	_	_
242	min	min	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	Batch	batch	NN	_	_	_
245	anaerobically	anaerobically	RB	_	_	_
246	grown	grow	VBN	_	_	_
247	cultures	culture	NNS	_	_	_
248	in	in	IN	_	_	_
249	hemA	hema	NN	GEN	_	_
250	defined	define	VBN	_	_	_
251	medium	medium	NN	_	_	_
252	,	,	,	_	_	_
253	exposed	expose	VBN	_	_	_
254	to	to	TO	_	_	_
255	100uM	100um	VB	_	_	_
256	iCORM-3	icorm-3	NN	_	_	_
257	for	for	IN	_	_	_
258	20	20	CD	_	_	_
259	min	min	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	Batch	batch	NN	_	_	_
262	anaerobically	anaerobically	RB	_	_	_
263	grown	grow	VBN	_	_	_
264	cultures	culture	NNS	_	_	_
265	in	in	IN	_	_	_
266	hemA	hema	NN	GEN	_	_
267	defined	define	VBN	_	_	_
268	medium	medium	NN	_	_	_
269	,	,	,	_	_	_
270	exposed	expose	VBN	_	_	_
271	to	to	TO	_	_	_
272	100uM	100um	VB	_	_	_
273	iCORM-3	icorm-3	NN	_	_	_
274	for	for	IN	_	_	_
275	40	40	CD	_	_	_
276	min	min	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	Batch	batch	NN	_	_	_
279	anaerobically	anaerobically	RB	_	_	_
280	grown	grow	VBN	_	_	_
281	cultures	culture	NNS	_	_	_
282	in	in	IN	_	_	_
283	hemA	hema	NN	GEN	_	_
284	defined	define	VBN	_	_	_
285	medium	medium	NN	_	_	_
286	,	,	,	_	_	_
287	exposed	expose	VBN	_	_	_
288	to	to	TO	_	_	_
289	100uM	100um	VB	_	_	_
290	iCORM-3	icorm-3	NN	_	_	_
291	for	for	IN	_	_	_
292	60	60	CD	_	_	_
293	min	min	NN	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	Batch	batch	NN	_	_	_
296	anaerobically	anaerobically	RB	_	_	_
297	grown	grow	VBN	_	_	_
298	cultures	culture	NNS	_	_	_
299	in	in	IN	_	_	_
300	hemA	hema	NN	GEN	_	_
301	defined	define	VBN	_	_	_
302	medium	medium	NN	_	_	_
303	,	,	,	_	_	_
304	prior	prior	RB	_	_	_
305	to	to	TO	_	_	_
306	CORM-3	corm-3	NN	_	_	_
307	addition	addition	NN	_	_	_
308	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
309	Batch	batch	NN	_	_	_
310	anaerobically	anaerobically	RB	_	_	_
311	grown	grow	VBN	_	_	_
312	cultures	culture	NNS	_	_	_
313	in	in	IN	_	_	_
314	hemA	hema	NN	GEN	_	_
315	defined	define	VBN	_	_	_
316	medium	medium	NN	_	_	_
317	,	,	,	_	_	_
318	prior	prior	RB	_	_	_
319	to	to	TO	_	_	_
320	CORM-3	corm-3	NN	_	_	_
321	addition	addition	NN	_	_	_
322	-LRB-	-lrb-	-LRB-	_	_	_
323	t	t	NN	_	_	_
324	=	=	JJ	_	_	_
325	0	0	CD	_	_	_
326	-RRB-	-rrb-	-RRB-	_	_	_
327	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
328	Batch	batch	NN	_	_	_
329	anaerobically	anaerobically	RB	_	_	_
330	grown	grow	VBN	_	_	_
331	cultures	culture	NNS	_	_	_
332	in	in	IN	_	_	_
333	hemA	hema	NN	GEN	_	_
334	defined	define	VBN	_	_	_
335	medium	medium	NN	_	_	_
336	,	,	,	_	_	_
337	prior	prior	RB	_	_	_
338	to	to	TO	_	_	_
339	iCORM-3	icorm-3	NN	_	_	_
340	addition	addition	NN	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	batch	batch	NN	_	_	_
343	culture	culture	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	batch	batch	NN	_	_	_
346	culture	culture	NN	_	_	_
347	rep1	rep1	NN	_	_	_
348	,	,	,	_	_	_
349	0.5	0.5	CD	_	_	_
350	min	min	NN	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	batch	batch	NN	_	_	_
353	culture	culture	NN	_	_	_
354	rep1	rep1	NN	_	_	_
355	,	,	,	_	_	_
356	0	0	CD	_	_	_
357	min	min	NN	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	batch	batch	NN	_	_	_
360	culture	culture	NN	_	_	_
361	rep1	rep1	NN	_	_	_
362	,	,	,	_	_	_
363	10	10	CD	_	_	_
364	min	min	NN	_	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
366	batch	batch	NN	_	_	_
367	culture	culture	NN	_	_	_
368	rep1	rep1	NN	_	_	_
369	,	,	,	_	_	_
370	1	1	CD	_	_	_
371	min	min	NN	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	batch	batch	NN	_	_	_
374	culture	culture	NN	_	_	_
375	rep1	rep1	NN	_	_	_
376	,	,	,	_	_	_
377	2	2	CD	_	_	_
378	min	min	NN	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	batch	batch	NN	_	_	_
381	culture	culture	NN	_	_	_
382	rep1	rep1	NN	_	_	_
383	,	,	,	_	_	_
384	5	5	CD	_	_	_
385	min	min	NN	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	batch	batch	NN	_	_	_
388	culture	culture	NN	_	_	_
389	rep2	rep2	NN	_	_	_
390	,	,	,	_	_	_
391	0.5	0.5	CD	_	_	_
392	min	min	NN	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	batch	batch	NN	_	_	_
395	culture	culture	NN	_	_	_
396	rep2	rep2	NN	_	_	_
397	,	,	,	_	_	_
398	0	0	CD	_	_	_
399	min	min	NN	_	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	batch	batch	NN	_	_	_
402	culture	culture	NN	_	_	_
403	rep2	rep2	NN	_	_	_
404	,	,	,	_	_	_
405	10	10	CD	_	_	_
406	min	min	NN	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	batch	batch	NN	_	_	_
409	culture	culture	NN	_	_	_
410	rep2	rep2	NN	_	_	_
411	,	,	,	_	_	_
412	1	1	CD	_	_	_
413	min	min	NN	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	batch	batch	NN	_	_	_
416	culture	culture	NN	_	_	_
417	rep2	rep2	NN	_	_	_
418	,	,	,	_	_	_
419	2	2	CD	_	_	_
420	min	min	NN	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	batch	batch	NN	_	_	_
423	culture	culture	NN	_	_	_
424	rep2	rep2	NN	_	_	_
425	,	,	,	_	_	_
426	5	5	CD	_	_	_
427	min	min	NN	_	_	_
428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
429	batch	batch	NN	_	_	_
430	culture	culture	NN	_	_	_
431	rep3	rep3	NN	_	_	_
432	,	,	,	_	_	_
433	0.5	0.5	CD	_	_	_
434	min	min	NN	_	_	_
435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
436	batch	batch	NN	_	_	_
437	culture	culture	NN	_	_	_
438	rep3	rep3	NN	_	_	_
439	,	,	,	_	_	_
440	0	0	CD	_	_	_
441	min	min	NN	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	batch	batch	NN	_	_	_
444	culture	culture	NN	_	_	_
445	rep3	rep3	NN	_	_	_
446	,	,	,	_	_	_
447	10	10	CD	_	_	_
448	min	min	NN	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	batch	batch	NN	_	_	_
451	culture	culture	NN	_	_	_
452	rep3	rep3	NN	_	_	_
453	,	,	,	_	_	_
454	1	1	CD	_	_	_
455	min	min	NN	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	batch	batch	NN	_	_	_
458	culture	culture	NN	_	_	_
459	rep3	rep3	NN	_	_	_
460	,	,	,	_	_	_
461	2	2	CD	_	_	_
462	min	min	NN	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	batch	batch	NN	_	_	_
465	culture	culture	NN	_	_	_
466	rep3	rep3	NN	_	_	_
467	,	,	,	_	_	_
468	5	5	CD	_	_	_
469	min	min	NN	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	Batch	batch	NN	_	_	_
472	cultures	culture	NNS	_	_	_
473	of	of	IN	_	_	_
474	E.	e.	FW	_	_	_
475	coli	coli	FW	_	_	_
476	MG1655	mg1655	NN	_	_	_
477	were	be	VBD	_	_	_
478	grown	grow	VBN	_	_	_
479	at	at	IN	_	_	_
480	37	37	CD	_	_	_
481	°C	°c	NN	_	_	_
482	with	with	IN	_	_	_
483	shaking	shake	VBG	_	_	_
484	in	in	IN	_	_	_
485	Luria-Bertani	luria-bertani	JJ	_	_	_
486	medium	medium	NN	_	_	_
487	-LRB-	-lrb-	-LRB-	_	_	_
488	0.1	0.1	CD	_	_	_
489	%	%	NN	_	_	_
490	Bacto	bacto	NN	_	_	_
491	Tryptone	tryptone	NN	_	_	_
492	,	,	,	_	_	_
493	0.05	0.05	CD	_	_	_
494	%	%	NN	_	_	_
495	yeast	yeast	NN	SUPP	_	_
496	extract	extract	NN	SUPP	_	_
497	,	,	,	_	_	_
498	0.05	0.05	CD	_	_	_
499	%	%	NN	_	_	_
500	NaCl	nacl	NN	_	_	_
501	-RRB-	-rrb-	-RRB-	_	_	_
502	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Batch	batch	NN	_	_	_
3	growth	growth	NN	_	_	_
4	in	in	IN	_	_	_
5	mineral	mineral	JJ	_	_	_
6	medium	medium	NN	_	_	_
7	supplied	supply	VBN	_	_	_
8	with	with	IN	_	_	_
9	4	4	CD	_	_	_
10	g/l	g/l	NN	_	_	_
11	glucose	glucose	NN	SUPP	_	_
12	as	as	IN	_	_	_
13	sole	sole	JJ	_	_	_
14	carbon	carbon	NN	_	_	_
15	source	source	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	optical	optical	JJ	_	_	_
18	density	density	NN	_	_	_
19	0.4	0.4	CD	_	_	_
20	at	at	IN	_	_	_
21	546nm	546nm	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Batch	batch	NN	_	_	_
25	growth	growth	NN	_	_	_
26	in	in	IN	_	_	_
27	mineral	mineral	JJ	_	_	_
28	medium	medium	NN	_	_	_
29	supplied	supply	VBN	_	_	_
30	with	with	IN	_	_	_
31	4	4	CD	_	_	_
32	g/l	g/l	NN	_	_	_
33	glucose	glucose	NN	SUPP	_	_
34	as	as	IN	_	_	_
35	sole	sole	JJ	_	_	_
36	carbon	carbon	NN	_	_	_
37	source	source	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	optical	optical	JJ	_	_	_
40	density	density	NN	_	_	_
41	of	of	IN	_	_	_
42	0.4	0.4	CD	_	_	_
43	at	at	IN	_	_	_
44	546	546	CD	_	_	_
45	nm	nm	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	BC-7ppm	bc-7ppm	JJ	_	_	_
49	replicate	replicate	VB	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	BC-7ppm	bc-7ppm	JJ	_	_	_
53	replicate	replicate	VB	_	_	_
54	2	2	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
56	BC-7ppm	bc-7ppm	JJ	_	_	_
57	replicate	replicate	VB	_	_	_
58	3	3	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	BC-9ppm	bc-9ppm	JJ	_	_	_
61	replicate	replicate	VB	_	_	_
62	1	1	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	BC-9ppm	bc-9ppm	JJ	_	_	_
65	replicate	replicate	VB	_	_	_
66	2	2	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	BC-9ppm	bc-9ppm	JJ	_	_	_
69	replicate	replicate	VB	_	_	_
70	3	3	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	bcl2fastq2	bcl2fastq2	NN	_	_	_
73	v2	v2	NN	_	_	_
74	.15.0	.15.0	CD	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	Demultiplexing	demultiplexing	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	,	,	,	_	_	_
79	Fastqc	fastqc	NN	_	_	_
80	0.11.5	0.11.5	CD	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	read	read	VB	_	_	_
83	quality	quality	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	,	,	,	_	_	_
86	Cutadapt-1.9.1	cutadapt-1.9.1	NN	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	adaptor	adaptor	NN	_	_	_
89	trimming	trim	VBG	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	B	b	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	,	,	,	_	_	_
96	column	column	NN	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	X	x	NN	_	_	_
99	-RRB-	-rrb-	-RRB-	_	_	_
100	,	,	,	_	_	_
101	and	and	CC	_	_	_
102	row	row	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	Y	y	NN	_	_	_
105	-RRB-	-rrb-	-RRB-	_	_	_
106	number	number	NN	_	_	_
107	,	,	,	_	_	_
108	red	red	JJ	_	_	_
109	foreground	foreground	NN	_	_	_
110	-LRB-	-lrb-	-LRB-	_	_	_
111	f	f	FW	_	_	_
112	_	_	FW	_	_	_
113	r	r	NN	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	and	and	CC	_	_	_
116	background	background	NN	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	b	b	NN	_	_	_
119	_	_	CD	_	_	_
120	r	r	NN	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	,	,	,	_	_	_
123	green	green	JJ	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	bcp	bcp	NN	GEN	_	_
126	___	___	CD	_	_	_
127	U	U	NNP	_	_	_
128	_	_	NNP	_	_	_
129	N0075	N0075	NNP	_	_	_
130	_	_	NNP	_	_	_
131	r1	r1	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	bcp	bcp	NN	GEN	_	_
134	___	___	CD	_	_	_
135	U	U	NNP	_	_	_
136	_	_	NNP	_	_	_
137	N0075	N0075	NNP	_	_	_
138	_	_	NNP	_	_	_
139	r2	r2	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	bcp	bcp	NN	GEN	_	_
142	___	___	CD	_	_	_
143	U	U	NNP	_	_	_
144	_	_	NNP	_	_	_
145	N0075	N0075	NNP	_	_	_
146	_	_	NNP	_	_	_
147	r3	r3	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	bcp	bcp	NN	GEN	_	_
150	upregulation	upregulation	NN	_	_	_
151	,	,	,	_	_	_
152	0.075	0.075	CD	_	_	_
153	ug/ml	ug/ml	NN	_	_	_
154	norfloxacin	norfloxacin	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	Bear	Bear	NNP	_	_	_
157	feces	fece	NNS	_	_	_
158	isolate	isolate	VBP	_	_	_
159	B1	b1	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
161	Bear	Bear	NNP	_	_	_
162	feces	fece	VBZ	_	_	_
163	isolate	isolate	JJ	_	_	_
164	B3	b3	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
166	Bear	Bear	NNP	_	_	_
167	feces	fece	VBZ	_	_	_
168	isolate	isolate	JJ	_	_	_
169	B5	b5	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	Bear	Bear	NNP	_	_	_
172	III	III	NNP	_	_	_
173	versus	versus	CC	_	_	_
174	MG1655	MG1655	NNP	_	_	_
175	technical	technical	JJ	_	_	_
176	replicate	replicate	VB	_	_	_
177	1	1	CD	_	_	_
178	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
179	Bear	Bear	NNP	_	_	_
180	III	III	NNP	_	_	_
181	versus	versus	CC	_	_	_
182	MG1655	MG1655	NNP	_	_	_
183	technical	technical	JJ	_	_	_
184	replicate	replicate	VBP	_	_	_
185	2	2	CD	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
187	Bear	Bear	NNP	_	_	_
188	II	II	NNP	_	_	_
189	versus	versus	CC	_	_	_
190	MG1655	MG1655	NNP	_	_	_
191	technical	technical	JJ	_	_	_
192	replicate	replicate	VB	_	_	_
193	1	1	CD	_	_	_
194	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
195	Bear	Bear	NNP	_	_	_
196	II	II	NNP	_	_	_
197	versus	versus	CC	_	_	_
198	MG1655	MG1655	NNP	_	_	_
199	technical	technical	JJ	_	_	_
200	replicate	replicate	VB	_	_	_
201	2	2	CD	_	_	_
202	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
203	Bear	Bear	NNP	_	_	_
204	I	I	NNP	_	_	_
205	versus	versus	CC	_	_	_
206	MG1655	MG1655	NNP	_	_	_
207	technical	technical	JJ	_	_	_
208	replicate	replicate	VB	_	_	_
209	1	1	CD	_	_	_
210	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
211	Bear	Bear	NNP	_	_	_
212	I	I	NNP	_	_	_
213	versus	versus	CC	_	_	_
214	MG1655	MG1655	NNP	_	_	_
215	technical	technical	JJ	_	_	_
216	replicate	replicate	VBP	_	_	_
217	2	2	CD	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
219	Beta	beta	JJ	_	_	_
220	_	_	NN	_	_	_
221	ChIP	chip	NN	_	_	_
222	_	_	CD	_	_	_
223	A	a	DT	_	_	_
224	_	_	NN	_	_	_
225	cy5	cy5	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	Beta	beta	NN	_	_	_
228	_	_	CD	_	_	_
229	ChIP	chip	NN	_	_	_
230	_	_	NN	_	_	_
231	B	b	NN	_	_	_
232	_	_	CD	_	_	_
233	cy5	cy5	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	Beta	beta	NN	_	_	_
236	_	_	CD	_	_	_
237	ChIP	chip	NN	_	_	_
238	_	_	NN	_	_	_
239	control	control	NN	_	_	_
240	_	_	CD	_	_	_
241	A	a	DT	_	_	_
242	_	_	NN	_	_	_
243	cy3	cy3	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	Beta	beta	NN	_	_	_
246	_	_	CD	_	_	_
247	ChIP	chip	NN	_	_	_
248	_	_	NN	_	_	_
249	control	control	NN	_	_	_
250	_	_	NN	_	_	_
251	B	b	NN	_	_	_
252	_	_	CD	_	_	_
253	cy3	cy3	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	Bexp	bexp	NN	_	_	_
256	_	_	CD	_	_	_
257	Bstat	Bstat	NNP	_	_	_
258	_	_	SYM	_	_	_
259	dyeswap1	dyeswap1	CD	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	Bexp	bexp	NN	_	_	_
262	_	_	CD	_	_	_
263	Bstat	Bstat	NNP	_	_	_
264	_	_	SYM	_	_	_
265	dyeswap2	dyeswap2	CD	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	Bexp	bexp	NN	_	_	_
268	_	_	CD	_	_	_
269	Bstat	Bstat	NNP	_	_	_
270	_	_	CD	_	_	_
271	rep1	rep1	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	Bexp	bexp	NN	_	_	_
274	_	_	CD	_	_	_
275	Bstat	Bstat	NNP	_	_	_
276	_	_	CD	_	_	_
277	rep2	rep2	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	Bexp	bexp	NN	_	_	_
280	_	_	CD	_	_	_
281	Kexp	Kexp	NNP	_	_	_
282	_	_	SYM	_	_	_
283	dyeswap1	dyeswap1	CD	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	Bexp	bexp	NN	_	_	_
286	_	_	CD	_	_	_
287	Kexp	Kexp	NNP	_	_	_
288	_	_	SYM	_	_	_
289	dyeswap2	dyeswap2	CD	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	Bexp	bexp	NN	_	_	_
292	_	_	CD	_	_	_
293	Kexp	Kexp	NNP	_	_	_
294	_	_	CD	_	_	_
295	rep1	rep1	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	Bexp	bexp	NN	_	_	_
298	_	_	CD	_	_	_
299	Kexp	Kexp	NNP	_	_	_
300	_	_	CD	_	_	_
301	rep2	rep2	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	Bexp	bexp	NN	_	_	_
304	_	_	CD	_	_	_
305	Kstat	Kstat	NNP	_	_	_
306	_	_	SYM	_	_	_
307	dyeswap1	dyeswap1	CD	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	Bexp	bexp	NN	_	_	_
310	_	_	CD	_	_	_
311	Kstat	Kstat	NNP	_	_	_
312	_	_	SYM	_	_	_
313	dyeswap2	dyeswap2	CD	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	Bexp	bexp	NN	_	_	_
316	_	_	CD	_	_	_
317	Kstat	Kstat	NNP	_	_	_
318	_	_	CD	_	_	_
319	rep1	rep1	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	Bexp	bexp	NN	_	_	_
322	_	_	CD	_	_	_
323	Kstat	Kstat	NNP	_	_	_
324	_	_	CD	_	_	_
325	rep2	rep2	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	BGI	bgi	NN	_	_	_
328	inhouse	inhouse	NN	_	_	_
329	software	software	NN	_	_	_
330	``	``	``	_	_	_
331	filter	filter	NN	_	_	_
332	_	_	NN	_	_	_
333	fq	fq	NN	_	_	_
334	''	''	''	_	_	_
335	for	for	IN	_	_	_
336	basecalling	basecalling	NN	_	_	_
337	and	and	CC	_	_	_
338	trimming	trim	VBG	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	Bicyclomycin	bicyclomycin	NN	_	_	_
341	-LRB-	-lrb-	-LRB-	_	_	_
342	BCM	bcm	NN	_	_	_
343	,	,	,	_	_	_
344	gift	gift	NN	_	_	_
345	of	of	IN	_	_	_
346	Schering-Plough	Schering-Plough	NNP	_	_	_
347	Animal	Animal	NNP	_	_	_
348	Health	Health	NNP	_	_	_
349	-RRB-	-rrb-	-RRB-	_	_	_
350	was	be	VBD	_	_	_
351	added	add	VBN	_	_	_
352	to	to	TO	_	_	_
353	the	the	DT	_	_	_
354	culture	culture	NN	_	_	_
355	at	at	IN	_	_	_
356	the	the	DT	_	_	_
357	indicated	indicate	VBN	_	_	_
358	dose	dose	NN	_	_	_
359	for	for	IN	_	_	_
360	20	20	CD	_	_	_
361	minutes	minute	NNS	_	_	_
362	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	BigWIG	bigwig	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	NN	_	_	_
2	bile	bile	NN	_	_	_
3	+1	+1	CD	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	bile	bile	NN	_	_	_
6	+2	+2	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	bile	bile	NN	_	_	_
9	+3	+3	CD	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Bile	Bile	NNP	_	_	_
12	salt	salt	NN	_	_	_
13	stress	stress	NN	_	_	_
14	was	be	VBD	_	_	_
15	done	do	VBN	_	_	_
16	in	in	IN	_	_	_
17	DMEM	dmem	NN	_	_	_
18	at	at	IN	_	_	_
19	pH	ph	NN	_	_	_
20	7.4	7.4	CD	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	unbuffered	unbuffered	JJ	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	at	at	IN	_	_	_
25	37C	37c	NN	_	_	_
26	,	,	,	_	_	_
27	5	5	CD	_	_	_
28	%	%	NN	_	_	_
29	CO2	co2	NN	_	_	_
30	,	,	,	_	_	_
31	static	static	JJ	_	_	_
32	incubation	incubation	NN	_	_	_
33	for	for	IN	_	_	_
34	90	90	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Binning	binning	NN	_	_	_
38	at	at	IN	_	_	_
39	5kb	5kb	JJ	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Bio1	bio1	NN	_	_	_
3	1m	1m	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Bio1	bio1	NN	_	_	_
6	1y	1y	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Bio2	bio2	NN	_	_	_
9	1m	1m	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Bio2	bio2	NN	_	_	_
12	1y	1y	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Bio3	bio3	NN	_	_	_
15	1m	1m	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Bio3	bio3	NN	_	_	_
18	1y	1y	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Bio4	bio4	NN	_	_	_
21	1m	1m	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Bio4	bio4	NN	_	_	_
24	1y	1y	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Bio-6	bio-6	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Bio	bio	NN	_	_	_
29	Contro	contro	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Biofilms	biofilm	NNS	_	_	_
32	were	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	on	on	IN	_	_	_
35	nylon	nylon	NN	_	_	_
36	membranes	membrane	NNS	_	_	_
37	using	use	VBG	_	_	_
38	agar	agar	NN	_	_	_
39	as	as	IN	_	_	_
40	the	the	DT	_	_	_
41	source	source	NN	_	_	_
42	of	of	IN	_	_	_
43	nutrients	nutrient	NNS	_	_	_
44	and	and	CC	_	_	_
45	water	water	NN	_	_	_
46	.	.	.	_	_	_

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	biological	biological	JJ	_	_	_
3	replicate	replicate	VB	_	_	_
4	:	:	:	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	biological	biological	JJ	_	_	_
8	replicate	replicate	VB	_	_	_
9	:	:	:	_	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	biological	biological	JJ	_	_	_
13	replicate	replicate	VB	_	_	_
14	:	:	:	_	_	_
15	318	318	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	biological	biological	JJ	_	_	_
18	replicate	replicate	VB	_	_	_
19	:	:	:	_	_	_
20	320	320	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	biological	biological	JJ	_	_	_
23	replicate	replicate	VB	_	_	_
24	:	:	:	_	_	_
25	327	327	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	biological	biological	JJ	_	_	_
28	replicate	replicate	VB	_	_	_
29	:	:	:	_	_	_
30	Replicate	replicate	VB	_	_	_
31	1	1	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Biological	Biological	NNP	_	_	_
34	replicates	replicate	VBZ	_	_	_
35	per	per	IN	_	_	_
36	genotype	genotype	NN	_	_	_
37	were	be	VBD	_	_	_
38	incubated	incubate	VBN	_	_	_
39	at	at	IN	_	_	_
40	1	1	CD	_	_	_
41	mg/L	mg/l	NN	_	_	_
42	of	of	IN	_	_	_
43	ciprofloxacin	ciprofloxacin	NN	_	_	_
44	during	during	IN	_	_	_
45	60	60	CD	_	_	_
46	minutes	minute	NNS	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	that	that	WDT	_	_	_
49	means	mean	VBZ	_	_	_
50	250xMIC	250xmic	NN	_	_	_
51	for	for	IN	_	_	_
52	E.	e.	FW	_	_	_
53	coli	coli	FW	_	_	_
54	ATCC	atcc	NN	_	_	_
55	25922	25922	CD	_	_	_
56	,	,	,	_	_	_
57	8xMIC	8xmic	NN	_	_	_
58	for	for	IN	_	_	_
59	EC14	ec14	NN	_	_	_
60	,	,	,	_	_	_
61	2xMIC	2xmic	NN	_	_	_
62	for	for	IN	_	_	_
63	EC19	ec19	NN	_	_	_
64	and	and	CC	_	_	_
65	1xMIC	1xmic	NN	_	_	_
66	for	for	IN	_	_	_
67	EC24	ec24	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	biological	biological	JJ	_	_	_
3	replicate	replicate	VB	_	_	_
4	:	:	:	_	_	_
5	t	t	NN	_	_	_
6	=	=	JJ	_	_	_
7	0	0	CD	_	_	_
8	Replicate	replicate	NN	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	biological	biological	JJ	_	_	_
12	replicate	replicate	VB	_	_	_
13	:	:	:	_	_	_
14	t	t	NN	_	_	_
15	=	=	JJ	_	_	_
16	0	0	CD	_	_	_
17	replicate	replicate	VBP	_	_	_
18	2	2	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	biomass	biomass	VBP	_	_	_
21	collected	collect	VBN	_	_	_
22	in	in	IN	_	_	_
23	the	the	DT	_	_	_
24	transition	transition	NN	_	_	_
25	between	between	IN	_	_	_
26	exponential	exponential	JJ	_	_	_
27	to	to	TO	_	_	_
28	stationary	stationary	JJ	GrowthPhase	_	_
29	phase	phase	NN	GrowthPhase	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Biomass	Biomass	NNP	_	_	_
32	was	be	VBD	_	_	_
33	snap	snap	JJ	_	_	_
34	frozen	freeze	VBN	_	_	_
35	in	in	IN	_	_	_
36	liquid	liquid	JJ	_	_	_
37	nitrogen	nitrogen	NN	_	_	_
38	and	and	CC	_	_	_
39	stored	store	VBD	_	_	_
40	at	at	IN	_	_	_
41	-80	-80	CD	_	_	_
42	C	c	NN	_	_	_
43	prior	prior	JJ	_	_	_
44	to	to	TO	_	_	_
45	extraction	extraction	NN	_	_	_
46	with	with	IN	_	_	_
47	Qiagen	Qiagen	NNP	_	_	_
48	RNeasy	RNeasy	NNP	_	_	_
49	Midi	Midi	NNP	_	_	_
50	kits	kit	NNS	_	_	_
51	.	.	.	_	_	_

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	NN	_	_	_
2	bioremediation	bioremediation	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	:	:	:	_	_	_
5	Alert	Alert	NNP	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	ex	ex	FW	_	_	_
8	situ	situ	FW	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	bioremediation	bioremediation	NN	_	_	_
12	treatment	treatment	NN	_	_	_
13	:	:	:	_	_	_
14	Eureka	Eureka	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	in	in	FW	_	_	_
17	situ	situ	FW	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Biotinylated	biotinylate	VBN	_	_	_
21	GST	gst	NN	_	_	_
22	protein	protein	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	BL21	bl21	NN	_	_	_
25	_	_	NN	_	_	_
26	1	1	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	BL21	bl21	NN	_	_	_
29	_	_	NN	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	BL21	bl21	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	DE3	de3	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	_	_	CD	_	_	_
37	adhE	adhe	NN	GEN	_	_
38	mutant	mutant	JJ	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	BL21	bl21	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	DE3	de3	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	,	,	,	_	_	_
45	adhE	adhe	NN	GEN	_	_
46	mutant	mutant	JJ	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	BL21	bl21	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	DE3	de3	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	HPA	hpa	NN	_	_	_
53	0mM	0mm	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	BL21	bl21	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	DE3	de3	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	HPA	hpa	NN	_	_	_
60	3mM	3mm	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	BL21	bl21	NN	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	DE3	de3	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	with	with	IN	_	_	_
67	3	3	CD	_	_	_
68	mM	mm	NN	KWSUPP	_	_
69	of	of	IN	_	_	_
70	heptanoic	heptanoic	JJ	_	_	_
71	acid	acid	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	BL21	bl21	NN	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	DE3	de3	NN	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	without	without	IN	_	_	_
78	heptanoic	heptanoic	JJ	_	_	_
79	acid	acid	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	BL21	bl21	NN	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	mu	mu	NN	_	_	_
84	=	=	JJ	_	_	_
85	0.20	0.20	CD	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	1	1	LS	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	BL21	bl21	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	mu	mu	NN	_	_	_
94	=	=	JJ	_	_	_
95	0.20	0.20	CD	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	2	2	LS	_	_	_
99	-RRB-	-rrb-	-RRB-	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	BL21	bl21	NN	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	mu	mu	NN	_	_	_
104	=	=	JJ	_	_	_
105	0.20	0.20	CD	_	_	_
106	-RRB-	-rrb-	-RRB-	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	3	3	LS	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	BL21	bl21	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	mu	mu	NN	_	_	_
114	=	=	JJ	_	_	_
115	0.20	0.20	CD	_	_	_
116	-RRB-	-rrb-	-RRB-	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	4	4	LS	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	BL21	bl21	NN	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	mu	mu	NN	_	_	_
124	=	=	JJ	_	_	_
125	0.46	0.46	CD	_	_	_
126	-RRB-	-rrb-	-RRB-	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	1	1	LS	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	BL21	bl21	NN	_	_	_
132	-LRB-	-lrb-	-LRB-	_	_	_
133	mu	mu	NN	_	_	_
134	=	=	JJ	_	_	_
135	0.46	0.46	CD	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	-LRB-	-lrb-	-LRB-	_	_	_
138	2	2	LS	_	_	_
139	-RRB-	-rrb-	-RRB-	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	BL21	bl21	NN	_	_	_
142	-LRB-	-lrb-	-LRB-	_	_	_
143	mu	mu	NN	_	_	_
144	=	=	JJ	_	_	_
145	0.46	0.46	CD	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	-LRB-	-lrb-	-LRB-	_	_	_
148	3	3	LS	_	_	_
149	-RRB-	-rrb-	-RRB-	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	BL21	bl21	NN	_	_	_
152	-LRB-	-lrb-	-LRB-	_	_	_
153	mu	mu	NN	_	_	_
154	=	=	JJ	_	_	_
155	0.46	0.46	CD	_	_	_
156	-RRB-	-rrb-	-RRB-	_	_	_
157	-LRB-	-lrb-	-LRB-	_	_	_
158	4	4	LS	_	_	_
159	-RRB-	-rrb-	-RRB-	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	BL21/pOri1	bl21/pori1	NN	_	_	_
162	-LRB-	-lrb-	-LRB-	_	_	_
163	mu	mu	NN	_	_	_
164	=	=	JJ	_	_	_
165	0.20	0.20	CD	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	1	1	LS	_	_	_
169	-RRB-	-rrb-	-RRB-	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	BL21/pOri1	bl21/pori1	NN	_	_	_
172	-LRB-	-lrb-	-LRB-	_	_	_
173	mu	mu	NN	_	_	_
174	=	=	JJ	_	_	_
175	0.20	0.20	CD	_	_	_
176	-RRB-	-rrb-	-RRB-	_	_	_
177	-LRB-	-lrb-	-LRB-	_	_	_
178	2	2	LS	_	_	_
179	-RRB-	-rrb-	-RRB-	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	BL21/pOri1	bl21/pori1	NN	_	_	_
182	-LRB-	-lrb-	-LRB-	_	_	_
183	mu	mu	NN	_	_	_
184	=	=	JJ	_	_	_
185	0.20	0.20	CD	_	_	_
186	-RRB-	-rrb-	-RRB-	_	_	_
187	-LRB-	-lrb-	-LRB-	_	_	_
188	3	3	LS	_	_	_
189	-RRB-	-rrb-	-RRB-	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	BL21/pOri1	bl21/pori1	NN	_	_	_
192	-LRB-	-lrb-	-LRB-	_	_	_
193	mu	mu	NN	_	_	_
194	=	=	JJ	_	_	_
195	0.20	0.20	CD	_	_	_
196	-RRB-	-rrb-	-RRB-	_	_	_
197	-LRB-	-lrb-	-LRB-	_	_	_
198	4	4	LS	_	_	_
199	-RRB-	-rrb-	-RRB-	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	BL21/pOri1	bl21/pori1	NN	_	_	_
202	-LRB-	-lrb-	-LRB-	_	_	_
203	mu	mu	NN	_	_	_
204	=	=	JJ	_	_	_
205	0.39	0.39	CD	_	_	_
206	-RRB-	-rrb-	-RRB-	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	1	1	LS	_	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	BL21/pOri1	bl21/pori1	NN	_	_	_
212	-LRB-	-lrb-	-LRB-	_	_	_
213	mu	mu	NN	_	_	_
214	=	=	JJ	_	_	_
215	0.39	0.39	CD	_	_	_
216	-RRB-	-rrb-	-RRB-	_	_	_
217	-LRB-	-lrb-	-LRB-	_	_	_
218	2	2	LS	_	_	_
219	-RRB-	-rrb-	-RRB-	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	BL21/pOri1	bl21/pori1	NN	_	_	_
222	-LRB-	-lrb-	-LRB-	_	_	_
223	mu	mu	NN	_	_	_
224	=	=	JJ	_	_	_
225	0.39	0.39	CD	_	_	_
226	-RRB-	-rrb-	-RRB-	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	3	3	LS	_	_	_
229	-RRB-	-rrb-	-RRB-	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	BL21/pOri1	bl21/pori1	NN	_	_	_
232	-LRB-	-lrb-	-LRB-	_	_	_
233	mu	mu	NN	_	_	_
234	=	=	JJ	_	_	_
235	0.39	0.39	CD	_	_	_
236	-RRB-	-rrb-	-RRB-	_	_	_
237	-LRB-	-lrb-	-LRB-	_	_	_
238	4	4	LS	_	_	_
239	-RRB-	-rrb-	-RRB-	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	BL21/pOri2	bl21/pori2	NN	_	_	_
242	-LRB-	-lrb-	-LRB-	_	_	_
243	mu	mu	NN	_	_	_
244	=	=	JJ	_	_	_
245	0.20	0.20	CD	_	_	_
246	-RRB-	-rrb-	-RRB-	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	1	1	LS	_	_	_
249	-RRB-	-rrb-	-RRB-	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	BL21/pOri2	bl21/pori2	NN	_	_	_
252	-LRB-	-lrb-	-LRB-	_	_	_
253	mu	mu	NN	_	_	_
254	=	=	JJ	_	_	_
255	0.20	0.20	CD	_	_	_
256	-RRB-	-rrb-	-RRB-	_	_	_
257	-LRB-	-lrb-	-LRB-	_	_	_
258	2	2	LS	_	_	_
259	-RRB-	-rrb-	-RRB-	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	BL21/pOri2	bl21/pori2	NN	_	_	_
262	-LRB-	-lrb-	-LRB-	_	_	_
263	mu	mu	NN	_	_	_
264	=	=	JJ	_	_	_
265	0.20	0.20	CD	_	_	_
266	-RRB-	-rrb-	-RRB-	_	_	_
267	-LRB-	-lrb-	-LRB-	_	_	_
268	3	3	LS	_	_	_
269	-RRB-	-rrb-	-RRB-	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	BL21/pOri2	bl21/pori2	NN	_	_	_
272	-LRB-	-lrb-	-LRB-	_	_	_
273	mu	mu	NN	_	_	_
274	=	=	JJ	_	_	_
275	0.20	0.20	CD	_	_	_
276	-RRB-	-rrb-	-RRB-	_	_	_
277	-LRB-	-lrb-	-LRB-	_	_	_
278	4	4	LS	_	_	_
279	-RRB-	-rrb-	-RRB-	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	BL21/pOri2	bl21/pori2	NN	_	_	_
282	-LRB-	-lrb-	-LRB-	_	_	_
283	mu	mu	NN	_	_	_
284	=	=	JJ	_	_	_
285	0.29	0.29	CD	_	_	_
286	-RRB-	-rrb-	-RRB-	_	_	_
287	-LRB-	-lrb-	-LRB-	_	_	_
288	1	1	LS	_	_	_
289	-RRB-	-rrb-	-RRB-	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	BL21/pOri2	bl21/pori2	NN	_	_	_
292	-LRB-	-lrb-	-LRB-	_	_	_
293	mu	mu	NN	_	_	_
294	=	=	JJ	_	_	_
295	0.29	0.29	CD	_	_	_
296	-RRB-	-rrb-	-RRB-	_	_	_
297	-LRB-	-lrb-	-LRB-	_	_	_
298	2	2	LS	_	_	_
299	-RRB-	-rrb-	-RRB-	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	BL21/pOri2	bl21/pori2	NN	_	_	_
302	-LRB-	-lrb-	-LRB-	_	_	_
303	mu	mu	NN	_	_	_
304	=	=	JJ	_	_	_
305	0.29	0.29	CD	_	_	_
306	-RRB-	-rrb-	-RRB-	_	_	_
307	-LRB-	-lrb-	-LRB-	_	_	_
308	3	3	LS	_	_	_
309	-RRB-	-rrb-	-RRB-	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	BL21/pOri2	bl21/pori2	NN	_	_	_
312	-LRB-	-lrb-	-LRB-	_	_	_
313	mu	mu	NN	_	_	_
314	=	=	JJ	_	_	_
315	0.29	0.29	CD	_	_	_
316	-RRB-	-rrb-	-RRB-	_	_	_
317	-LRB-	-lrb-	-LRB-	_	_	_
318	4	4	LS	_	_	_
319	-RRB-	-rrb-	-RRB-	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	bla	bla	NN	_	_	_
322	_	_	NN	_	_	_
323	0	0	CD	_	_	_
324	min	min	NN	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	bla	bla	NN	_	_	_
327	_	_	CD	_	_	_
328	10	10	CD	_	_	_
329	min	min	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	bla	bla	NN	_	_	_
332	_	_	CD	_	_	_
333	15	15	CD	_	_	_
334	min	min	NN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	bla	bla	NN	_	_	_
337	_	_	NN	_	_	_
338	1	1	CD	_	_	_
339	min	min	NN	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	bla	bla	NN	_	_	_
342	_	_	NN	_	_	_
343	2	2	CD	_	_	_
344	min	min	NN	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	bla	bla	NN	_	_	_
347	_	_	CD	_	_	_
348	4	4	CD	_	_	_
349	min	min	NN	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	bla	bla	NN	_	_	_
352	_	_	CD	_	_	_
353	6	6	CD	_	_	_
354	min	min	NN	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	bla	bla	NN	_	_	_
357	_	_	CD	_	_	_
358	8	8	CD	_	_	_
359	min	min	NN	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	Blautia	blautia	NN	_	_	_
362	coccoides	coccoide	NNS	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	Blautia	blautia	NN	_	_	_
365	hydrogenotrophica	hydrogenotrophica	NN	_	_	_
366	DSM	DSM	NNP	_	_	_
367	10507	10507	CD	_	_	_
368	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
369	Blood	Blood	NNP	_	_	_
370	culture	culture	NN	_	_	_
371	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
372	Blood	Blood	NNP	_	_	_
373	culture	culture	NN	_	_	_
374	bottle	bottle	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	Blue	blue	JJ	_	_	_
377	_	_	NN	_	_	_
378	1	1	CD	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	Blue	blue	JJ	_	_	_
381	_	_	NN	_	_	_
382	2	2	CD	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	BnTR1	bntr1	NN	_	_	_
385	,	,	,	_	_	_
386	37	37	CD	_	_	_
387	°C	°c	NN	_	_	_
388	,	,	,	_	_	_
389	replicate	replicate	VB	_	_	_
390	1	1	CD	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	BnTR1	bntr1	NN	_	_	_
393	,	,	,	_	_	_
394	37	37	CD	_	_	_
395	°C	°c	NN	_	_	_
396	,	,	,	_	_	_
397	replicate	replicate	VB	_	_	_
398	2	2	CD	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
400	BnTR1	bntr1	NN	_	_	_
401	,	,	,	_	_	_
402	37	37	CD	_	_	_
403	°C	°c	NN	_	_	_
404	,	,	,	_	_	_
405	replicate	replicate	VB	_	_	_
406	3	3	CD	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	BnTR1	bntr1	NN	_	_	_
409	_	_	NN	_	_	_
410	37	37	CD	_	_	_
411	_	_	CD	_	_	_
412	rep1	rep1	NN	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	BnTR1	bntr1	NN	_	_	_
415	_	_	NN	_	_	_
416	37	37	CD	_	_	_
417	_	_	CD	_	_	_
418	rep2	rep2	NN	_	_	_
419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
420	BnTR1	bntr1	NN	_	_	_
421	_	_	NN	_	_	_
422	37	37	CD	_	_	_
423	_	_	CD	_	_	_
424	rep3	rep3	NN	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	BnTR1	bntr1	NN	_	_	_
427	,	,	,	_	_	_
428	42	42	CD	_	_	_
429	°C	°c	NN	_	_	_
430	,	,	,	_	_	_
431	replicate	replicate	VB	_	_	_
432	1	1	CD	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	BnTR1	bntr1	NN	_	_	_
435	,	,	,	_	_	_
436	42	42	CD	_	_	_
437	°C	°c	NN	_	_	_
438	,	,	,	_	_	_
439	replicate	replicate	VB	_	_	_
440	2	2	CD	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
442	BnTR1	bntr1	NN	_	_	_
443	,	,	,	_	_	_
444	42	42	CD	_	_	_
445	°C	°c	NN	_	_	_
446	,	,	,	_	_	_
447	replicate	replicate	VB	_	_	_
448	3	3	CD	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	BnTR1	bntr1	NN	_	_	_
451	_	_	CD	_	_	_
452	42	42	CD	_	_	_
453	_	_	NN	_	_	_
454	rep1	rep1	NN	_	_	_
455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
456	BnTR1	bntr1	NN	_	_	_
457	_	_	CD	_	_	_
458	42	42	CD	_	_	_
459	_	_	NN	_	_	_
460	rep2	rep2	NN	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	BnTR1	bntr1	NN	_	_	_
463	_	_	CD	_	_	_
464	42	42	CD	_	_	_
465	_	_	NN	_	_	_
466	rep3	rep3	NN	_	_	_
467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
468	Bordetella	bordetella	NN	_	_	_
469	sp.	sp.	NN	_	_	_
470	.	.	.	_	_	_

1	IITR-02	iitr-02	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	bovine-biased-1	bovine-biased-1	NN	_	_	_
4	strain	strain	NN	_	_	_
5	grown	grow	VBN	_	_	_
6	to	to	TO	_	_	_
7	exponential	exponential	JJ	GrowthPhase	_	_
8	phase	phase	NN	GrowthPhase	_	_
9	of	of	IN	_	_	_
10	growth	growth	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	bovine-biased-2	bovine-biased-2	NN	_	_	_
13	strain	strain	NN	_	_	_
14	grown	grow	VBN	_	_	_
15	to	to	TO	_	_	_
16	exponential	exponential	JJ	GrowthPhase	_	_
17	phase	phase	NN	GrowthPhase	_	_
18	of	of	IN	_	_	_
19	growth	growth	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	bovine-biased-3	bovine-biased-3	NN	_	_	_
22	strain	strain	NN	_	_	_
23	grown	grow	VBN	_	_	_
24	to	to	TO	_	_	_
25	exponential	exponential	JJ	GrowthPhase	_	_
26	phase	phase	NN	GrowthPhase	_	_
27	of	of	IN	_	_	_
28	growth	growth	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	bovine-biased-4	bovine-biased-4	NN	_	_	_
31	strain	strain	NN	_	_	_
32	grown	grow	VBN	_	_	_
33	to	to	TO	_	_	_
34	exponential	exponential	JJ	GrowthPhase	_	_
35	phase	phase	NN	GrowthPhase	_	_
36	of	of	IN	_	_	_
37	growth	growth	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	bowtie2-build	bowtie2-build	JJ	_	_	_
40	final	final	JJ	_	_	_
41	_	_	NN	_	_	_
42	reference	reference	NN	_	_	_
43	_	_	CD	_	_	_
44	seqs/REL606	seqs/rel606	NN	_	_	_
45	.	.	.	_	_	_

1	fa	fa	NN	_	_	_
2	indexes/REL606	indexes/rel606	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Bowtie	bowtie	NN	_	_	_
5	2	2	CD	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Langmead	langmead	NN	_	_	_
8	B	b	NN	_	_	_
9	&	&	CC	_	_	_
10	Salzberg	Salzberg	NNP	_	_	_
11	SL	SL	NNP	_	_	_
12	,	,	,	_	_	_
13	2012	2012	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	was	be	VBD	_	_	_
16	used	use	VBN	_	_	_
17	with	with	IN	_	_	_
18	default	default	NN	_	_	_
19	parameters	parameter	NNS	_	_	_
20	,	,	,	_	_	_
21	to	to	TO	_	_	_
22	remove	remove	VB	_	_	_
23	any	any	DT	_	_	_
24	sequence	sequence	NN	_	_	_
25	reads	read	VBZ	_	_	_
26	aligning	align	VBG	_	_	_
27	to	to	TO	_	_	_
28	ribosomal	ribosomal	JJ	_	_	_
29	RNA	rna	NN	_	_	_
30	,	,	,	_	_	_
31	transfer	transfer	NN	_	_	_
32	RNA	rna	NN	_	_	_
33	and	and	CC	_	_	_
34	non-coding	non-coding	JJ	_	_	_
35	RNA	rna	NN	_	_	_
36	sequences	sequence	NNS	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	bowtie2	bowtie2	NN	_	_	_
3	v2	v2	NN	_	_	_
4	.2.3	.2.3	CD	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	alignment	alignment	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Bowtie	bowtie	NN	_	_	_
11	alignments	alignment	NNS	_	_	_
12	against	against	IN	_	_	_
13	the	the	DT	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	genome	genome	NN	_	_	_
17	were	be	VBD	_	_	_
18	converted	convert	VBN	_	_	_
19	to	to	TO	_	_	_
20	wiggle	wiggle	VB	_	_	_
21	files	file	NNS	_	_	_
22	.	.	.	_	_	_

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	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	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	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/chloroform	phenol/chloroform	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	pH	ph	NN	_	_	_
16	4.5	4.5	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	once	once	RB	_	_	_
20	in	in	IN	_	_	_
21	chloroform/isoamyl	chloroform/isoamyl	JJ	_	_	_
22	alcohol	alcohol	NN	_	_	_
23	,	,	,	_	_	_
24	and	and	CC	_	_	_
25	precipitated	precipitate	VBD	_	_	_
26	with	with	IN	_	_	_
27	isopropanol	isopropanol	NN	_	_	_
28	.	.	.	_	_	_

1	Pellets	pellet	NNS	_	_	_
2	were	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	with	with	IN	_	_	_
5	1	1	CD	_	_	_
6	mL	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	70	70	CD	_	_	_
9	%	%	NN	_	_	_
10	ethanol	ethanol	NN	_	_	_
11	,	,	,	_	_	_
12	dried	dry	VBD	_	_	_
13	and	and	CC	_	_	_
14	purified	purify	VBN	_	_	_
15	using	use	VBG	_	_	_
16	QIAGEN	QIAGEN	NNP	_	_	_
17	RNeasy	RNeasy	NNP	_	_	_
18	kit	kit	NN	_	_	_
19	.	.	.	_	_	_

1	Final	final	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	with	with	IN	_	_	_
6	100	100	CD	_	_	_
7	µL	µl	NN	_	_	_
8	of	of	IN	_	_	_
9	nuclease-free	nuclease-free	JJ	_	_	_
10	water	water	NN	_	_	_
11	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	purification	purification	NN	_	_	_
3	,	,	,	_	_	_
4	DNAse	dnase	NN	_	_	_
5	treatment	treatment	NN	_	_	_
6	with	with	IN	_	_	_
7	TURBO	TURBO	NNP	_	_	_
8	DNase	dnase	NN	_	_	_
9	kit	kit	NN	_	_	_
10	was	be	VBD	_	_	_
11	performed	perform	VBN	_	_	_
12	according	accord	VBG	_	_	_
13	to	to	TO	_	_	_
14	manufacturer	manufacturer	NN	_	_	_
15	's	's	POS	_	_	_
16	manual	manual	NN	_	_	_
17	,	,	,	_	_	_
18	except	except	IN	_	_	_
19	that	that	DT	_	_	_
20	twice	twice	JJ	_	_	_
21	amount	amount	NN	_	_	_
22	of	of	IN	_	_	_
23	recommended	recommend	VBN	_	_	_
24	DNase	dnase	NN	_	_	_
25	inactivation	inactivation	NN	_	_	_
26	reagent	reagent	NN	_	_	_
27	was	be	VBD	_	_	_
28	used	use	VBN	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	integrity	integrity	NN	_	_	_
3	of	of	IN	_	_	_
4	DNA-free	dna-free	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	analyzed	analyze	VBN	_	_	_
8	on	on	IN	_	_	_
9	either	either	CC	_	_	_
10	native	native	JJ	_	_	_
11	agarose	agarose	NN	_	_	_
12	gel	gel	NN	_	_	_
13	or	or	CC	_	_	_
14	on	on	IN	_	_	_
15	Agilent	Agilent	NNP	_	_	_
16	Bioanalyzer	Bioanalyzer	NNP	_	_	_
17	RNA	rna	NN	_	_	_
18	6000	6000	CD	_	_	_
19	Nano	Nano	NNP	_	_	_
20	chip	chip	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Briefly	briefly	RB	_	_	_
3	,	,	,	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	were	be	VBD	_	_	_
7	isolated	isolate	VBN	_	_	_
8	from	from	IN	_	_	_
9	cell	cell	NN	_	_	_
10	culture	culture	NN	_	_	_
11	with	with	IN	_	_	_
12	Total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	Extraction	extraction	NN	_	_	_
15	Kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	RBC	rbc	NN	_	_	_
18	Bioscience	bioscience	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	according	accord	VBG	_	_	_
21	to	to	TO	_	_	_
22	manufacturer	manufacturer	NN	_	_	_
23	's	's	POS	_	_	_
24	specifications	specification	NNS	_	_	_
25	.	.	.	_	_	_

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	NNP	_	_	_
2	Broiler	broiler	NN	_	_	_
3	Fecal	fecal	JJ	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	BRP	brp	NN	_	_	_
6	Induction	induction	NN	_	_	_
7	10	10	CD	_	_	_
8	Minutes	Minutes	NNPS	_	_	_
9	against	against	IN	_	_	_
10	5	5	CD	_	_	_
11	Minutes	Minutes	NNPS	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	BRP	BRP	NNP	_	_	_
14	Induction	induction	NN	_	_	_
15	-10	-10	CD	_	_	_
16	minutes	minute	NNS	_	_	_
17	against	against	IN	_	_	_
18	60	60	CD	_	_	_
19	minutes	minute	NNS	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	BRP	BRP	NNP	_	_	_
22	Induction	induction	NN	_	_	_
23	20	20	CD	_	_	_
24	minutes	minute	NNS	_	_	_
25	against	against	IN	_	_	_
26	10	10	CD	_	_	_
27	minutes	minute	NNS	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	BRP	BRP	NNP	_	_	_
30	Induction	induction	NN	_	_	_
31	30	30	CD	_	_	_
32	minutes	minute	NNS	_	_	_
33	against	against	IN	_	_	_
34	20	20	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	BRP	BRP	NNP	_	_	_
38	Induction	induction	NN	_	_	_
39	45	45	CD	_	_	_
40	minutes	minute	NNS	_	_	_
41	against	against	IN	_	_	_
42	30	30	CD	_	_	_
43	minutes	minute	NNS	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	BRP	BRP	NNP	_	_	_
46	Induction	induction	NN	_	_	_
47	5	5	CD	_	_	_
48	minutes	minute	NNS	_	_	_
49	against	against	IN	_	_	_
50	2	2	CD	_	_	_
51	minutes	minute	NNS	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	BRP	BRP	NNP	_	_	_
54	Induction	induction	NN	_	_	_
55	60	60	CD	_	_	_
56	minutes	minute	NNS	_	_	_
57	against	against	IN	_	_	_
58	45	45	CD	_	_	_
59	minutes	minute	NNS	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	B	b	NN	_	_	_
62	strain	strain	NN	_	_	_
63	_	_	RB	_	_	_
64	wild	wild	JJ	_	_	_
65	type	type	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	B	b	NN	_	_	_
68	strain	strain	NN	_	_	_
69	,	,	,	_	_	_
70	wild	wild	JJ	_	_	_
71	type	type	NN	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Butanol	Butanol	NNP	_	_	_
74	_	_	NNP	_	_	_
75	Challenge	Challenge	NNP	_	_	_
76	_	_	VBD	_	_	_
77	Step	step	NN	_	_	_
78	_	_	SYM	_	_	_
79	1-1	1-1	CD	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Butanol	Butanol	NNP	_	_	_
82	_	_	NNP	_	_	_
83	Challenge	Challenge	NNP	_	_	_
84	_	_	VBD	_	_	_
85	Step	step	NN	_	_	_
86	_	_	NN	_	_	_
87	1-2	1-2	CD	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	Butanol	Butanol	NNP	_	_	_
90	_	_	NNP	_	_	_
91	Challenge	Challenge	NNP	_	_	_
92	_	_	VBD	_	_	_
93	Step	step	NN	_	_	_
94	_	_	SYM	_	_	_
95	2-1	2-1	CD	_	_	_
96	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
97	Butanol	Butanol	NNP	_	_	_
98	_	_	NNP	_	_	_
99	Challenge	Challenge	NNP	_	_	_
100	_	_	VBD	_	_	_
101	Step	step	NN	_	_	_
102	_	_	SYM	_	_	_
103	2-2	2-2	CD	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Butanol	Butanol	NNP	_	_	_
106	_	_	NNP	_	_	_
107	Challenge	Challenge	NNP	_	_	_
108	_	_	VBD	_	_	_
109	Step	step	NN	_	_	_
110	_	_	SYM	_	_	_
111	3-1	3-1	CD	_	_	_
112	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
113	Butanol	Butanol	NNP	_	_	_
114	_	_	NNP	_	_	_
115	Challenge	Challenge	NNP	_	_	_
116	_	_	VBD	_	_	_
117	Step	step	NN	_	_	_
118	_	_	SYM	_	_	_
119	3-2	3-2	CD	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	Butanol	Butanol	NNP	_	_	_
122	_	_	NNP	_	_	_
123	Challenge	Challenge	NNP	_	_	_
124	_	_	VBD	_	_	_
125	Step	step	NN	_	_	_
126	_	_	SYM	_	_	_
127	4-1	4-1	CD	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	Butanol	Butanol	NNP	_	_	_
130	_	_	NNP	_	_	_
131	Challenge	Challenge	NNP	_	_	_
132	_	_	VBD	_	_	_
133	Step	step	NN	_	_	_
134	_	_	SYM	_	_	_
135	4-2	4-2	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	BW25113	bw25113	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	BW25113	bw25113	NN	_	_	_
140	_	_	CD	_	_	_
141	adhE	adhe	NN	GEN	_	_
142	mutant	mutant	JJ	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	BW25113	bw25113	NN	_	_	_
145	,	,	,	_	_	_
146	adhE	adhe	NN	GEN	_	_
147	mutant	mutant	JJ	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	BW25113	bw25113	NN	_	_	_
150	,	,	,	_	_	_
151	H2O2	h2o2	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	BW25113	bw25113	NN	_	_	_
154	HEPES-glu	hepes-glu	NN	_	_	_
155	30	30	CD	_	_	_
156	min	min	NN	_	_	_
157	4.5	4.5	CD	_	_	_
158	%	%	NN	_	_	_
159	deoxycholate	deoxycholate	NN	SUPP	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	BW25113	bw25113	NN	_	_	_
162	hha	hha	NN	GEN	_	_
163	deletion	deletion	NN	_	_	_
164	mutant	mutant	JJ	_	_	_
165	LB	lb	NN	_	_	_
166	4	4	CD	_	_	_
167	hr	hr	NN	_	_	_
168	biofilm	biofilm	NN	_	_	_
169	cells	cell	NNS	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
171	BW25113	bw25113	NN	_	_	_
172	hha	hha	NN	GEN	_	_
173	mutant	mutant	JJ	_	_	_
174	LB	lb	NN	_	_	_
175	glu	glu	NN	_	_	_
176	15	15	CD	_	_	_
177	hr	hr	NN	_	_	_
178	biofilm	biofilm	NN	_	_	_
179	cells	cell	NNS	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
181	BW25113	bw25113	NN	_	_	_
182	hha	hha	NN	GEN	_	_
183	mutant	mutant	JJ	_	_	_
184	LB	lb	NN	_	_	_
185	glu	glu	NN	_	_	_
186	24	24	CD	_	_	_
187	hr	hr	NN	_	_	_
188	biofilm	biofilm	NN	_	_	_
189	cells	cell	NNS	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
191	BW25113	bw25113	NN	_	_	_
192	hha	hha	NN	GEN	_	_
193	mutant	mutant	JJ	_	_	_
194	LB	lb	NN	_	_	_
195	glu	glu	NN	_	_	_
196	4	4	CD	_	_	_
197	hr	hr	NN	_	_	_
198	biofilm	biofilm	NN	_	_	_
199	cells	cell	NNS	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
201	BW25113	bw25113	NN	_	_	_
202	luxS	luxs	NN	GEN	_	_
203	LB	lb	NN	_	_	_
204	30C	30c	CD	_	_	_
205	free-living	free-living	JJ	_	_	_
206	cells	cell	NNS	_	_	_
207	100	100	CD	_	_	_
208	uM	um	NN	_	_	_
209	AI2	ai2	NN	_	_	_
210	3h	3h	VBP	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	BW25113	bw25113	NN	_	_	_
213	luxS	luxs	NN	GEN	_	_
214	LB	lb	NN	_	_	_
215	30C	30c	CD	_	_	_
216	free-living	free-living	JJ	_	_	_
217	cells	cell	NNS	_	_	_
218	no	no	DT	_	_	_
219	AI2	ai2	NN	_	_	_
220	for	for	IN	_	_	_
221	3h	3h	JJ	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	BW25113	bw25113	NN	_	_	_
224	luxS	luxs	NN	GEN	_	_
225	LB	lb	NN	_	_	_
226	37C	37c	NN	_	_	_
227	free-living	free-living	JJ	_	_	_
228	cells	cell	NNS	_	_	_
229	100	100	CD	_	_	_
230	uM	um	NN	_	_	_
231	AI2	ai2	NN	_	_	_
232	3h	3h	VBP	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	BW25113	bw25113	NN	_	_	_
235	luxS	luxs	NN	GEN	_	_
236	LB	lb	NN	_	_	_
237	37C	37c	NN	_	_	_
238	free-living	free-living	JJ	_	_	_
239	cells	cell	NNS	_	_	_
240	no	no	DT	_	_	_
241	AI2	ai2	NN	_	_	_
242	3h	3h	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	BW25113	bw25113	NN	_	_	_
245	mqsR	mqsr	NN	GEN	_	_
246	mutant	mutant	NN	_	_	_
247	at	at	IN	_	_	_
248	OD600	od600	NN	_	_	_
249	=	=	JJ	_	_	_
250	0.5	0.5	CD	_	_	_
251	LB	lb	NN	_	_	_
252	37C	37c	NN	_	_	_
253	suspension	suspension	NN	_	_	_
254	cell	cell	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	BW25113	bw25113	NN	_	_	_
257	mqsR/pBS	mqsr/pbs	NN	_	_	_
258	-LRB-	-lrb-	-LRB-	_	_	_
259	Kan	Kan	NNP	_	_	_
260	-RRB-	-rrb-	-RRB-	_	_	_
261	-	-	:	_	_	_
262	mqsR	mqsr	NN	GEN	_	_
263	2-1	2-1	CD	_	_	_
264	in	in	IN	_	_	_
265	LB	lb	NN	_	_	_
266	with	with	IN	_	_	_
267	ampicillin	ampicillin	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	BW25113	bw25113	NN	_	_	_
270	mqsR/pBS	mqsr/pbs	NN	_	_	_
271	-LRB-	-lrb-	-LRB-	_	_	_
272	Kan	Kan	NNP	_	_	_
273	-RRB-	-rrb-	-RRB-	_	_	_
274	-	-	:	_	_	_
275	mqsR	mqsr	NN	GEN	_	_
276	in	in	IN	_	_	_
277	LB	lb	NN	_	_	_
278	with	with	IN	_	_	_
279	ampicillin	ampicillin	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	BW25113-pCA24N	bw25113-pca24n	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	BW25113-pCA24N	bw25113-pca24n	NN	_	_	_
284	_	_	CD	_	_	_
285	arT	art	NN	_	_	_
286	LB	lb	NN	_	_	_
287	90	90	CD	_	_	_
288	min	min	NN	_	_	_
289	1	1	CD	_	_	_
290	mM	mm	NN	KWSUPP	_	_
291	IPTG	iptg	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
294	at	at	IN	_	_	_
295	OD600	od600	NN	_	_	_
296	=	=	JJ	_	_	_
297	0.5	0.5	CD	_	_	_
298	LB	lb	NN	_	_	_
299	37C	37c	NN	_	_	_
300	2	2	CD	_	_	_
301	mM	mm	NN	KWSUPP	_	_
302	IPTG	iptg	NN	_	_	_
303	suspension	suspension	NN	_	_	_
304	cell	cell	NN	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
307	at	at	IN	_	_	_
308	OD600	od600	NN	_	_	_
309	=	=	JJ	_	_	_
310	0.5	0.5	CD	_	_	_
311	LB	lb	NN	_	_	_
312	37C	37c	NN	_	_	_
313	then	then	RB	_	_	_
314	2	2	CD	_	_	_
315	mM	mm	NN	KWSUPP	_	_
316	IPTG	iptg	NN	_	_	_
317	for	for	IN	_	_	_
318	15	15	CD	_	_	_
319	min	min	NN	_	_	_
320	short	short	JJ	_	_	_
321	time	time	NN	_	_	_
322	suspension	suspension	NN	_	_	_
323	cell	cell	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	BW25113-pCA24N	bw25113-pca24n	NN	_	_	_
326	_	_	CD	_	_	_
327	dosP	dosp	NN	GEN	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	BW25113-pCA24N	bw25113-pca24n	NN	_	_	_
330	LB	lb	NN	_	_	_
331	90	90	CD	_	_	_
332	min	min	NN	_	_	_
333	1	1	CD	_	_	_
334	mM	mm	NN	KWSUPP	_	_
335	IPTG	iptg	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
338	at	at	IN	_	_	_
339	OD600	od600	NN	_	_	_
340	=	=	JJ	_	_	_
341	0.5	0.5	CD	_	_	_
342	LB	lb	NN	_	_	_
343	37C	37c	NN	_	_	_
344	2	2	CD	_	_	_
345	mM	mm	NN	KWSUPP	_	_
346	IPTG	iptg	NN	_	_	_
347	suspension	suspension	NN	_	_	_
348	cell	cell	NN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
351	at	at	IN	_	_	_
352	OD600	od600	NN	_	_	_
353	=	=	JJ	_	_	_
354	0.5	0.5	CD	_	_	_
355	LB	lb	NN	_	_	_
356	37C	37c	NN	_	_	_
357	then	then	RB	_	_	_
358	2	2	CD	_	_	_
359	mM	mm	NN	KWSUPP	_	_
360	IPTG	iptg	NN	_	_	_
361	for	for	IN	_	_	_
362	15	15	CD	_	_	_
363	min	min	NN	_	_	_
364	short	short	JJ	_	_	_
365	time	time	NN	_	_	_
366	suspension	suspension	NN	_	_	_
367	cell	cell	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	BW25113	bw25113	NN	_	_	_
370	sdiA-empty	sdia-empty	JJ	_	_	_
371	vector	vector	NN	_	_	_
372	12h	12h	NN	_	_	_
373	biofilm	biofilm	NN	_	_	_
374	cells	cell	NNS	_	_	_
375	at	at	IN	_	_	_
376	30oC	30oC	NNP	_	_	_
377	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
378	BW25113	bw25113	NN	_	_	_
379	sdiA	sdia	NN	GEN	_	_
380	LB	lb	NN	_	_	_
381	30C	30c	NN	_	_	_
382	OD	od	NN	_	_	_
383	4.0	4.0	CD	_	_	_
384	free-living	free-living	JJ	_	_	_
385	cells	cell	NNS	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	BW25113	bw25113	NN	_	_	_
388	sdiA	sdia	NN	GEN	_	_
389	mutant	mutant	JJ	_	_	_
390	LB	lb	NN	_	_	_
391	with	with	IN	_	_	_
392	1	1	CD	_	_	_
393	mM	mm	NN	KWSUPP	_	_
394	indole	indole	NN	_	_	_
395	7-h	7-h	JJ	_	_	_
396	30C	30c	NN	_	_	_
397	biofilm	biofilm	NN	_	_	_
398	cell	cell	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	BW25113	bw25113	NN	_	_	_
401	sdiA	sdia	NN	GEN	_	_
402	mutant	mutant	JJ	_	_	_
403	LB	lb	NN	_	_	_
404	with	with	IN	_	_	_
405	DMF	dmf	NN	_	_	_
406	7-h	7-h	JJ	_	_	_
407	30C	30c	NN	_	_	_
408	biofilm	biofilm	NN	_	_	_
409	cell	cell	NN	_	_	_
410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
411	BW25113	bw25113	NN	_	_	_
412	sdiA-SdiA1E11	sdia-sdia1e11	NN	_	_	_
413	12h	12h	NN	_	_	_
414	biofilm	biofilm	NN	_	_	_
415	cells	cell	NNS	_	_	_
416	at	at	IN	_	_	_
417	30oC	30oC	NNP	_	_	_
418	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
419	BW25113	bw25113	NN	_	_	_
420	sdiA-WTSdiA	sdia-wtsdia	NN	_	_	_
421	12h	12h	NN	_	_	_
422	biofilm	biofilm	NN	_	_	_
423	cells	cell	NNS	_	_	_
424	at	at	IN	_	_	_
425	30oC	30oC	NNP	_	_	_
426	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
427	BW25113	bw25113	NN	_	_	_
428	tnaA	tnaa	NN	GEN	_	_
429	Biofilm	biofilm	NN	_	_	_
430	100	100	CD	_	_	_
431	uM	um	NN	_	_	_
432	indole	indole	FW	_	_	_
433	7h	7h	FW	_	_	_
434	LB	lb	NN	_	_	_
435	30C	30c	NN	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	BW25113	bw25113	NN	_	_	_
438	tnaA	tnaa	NN	GEN	_	_
439	Biofilm	biofilm	NN	_	_	_
440	100	100	CD	_	_	_
441	uM	um	NN	_	_	_
442	indole	indole	FW	_	_	_
443	7h	7h	FW	_	_	_
444	LB	lb	NN	_	_	_
445	37C	37c	NN	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	BW25113	bw25113	NN	_	_	_
448	tnaA	tnaa	NN	GEN	_	_
449	Biofilm	biofilm	NN	_	_	_
450	DMF	dmf	NN	_	_	_
451	7h	7h	VBP	_	_	_
452	LB	lb	NN	_	_	_
453	37C	37c	NN	_	_	_
454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
455	BW25113	bw25113	NN	_	_	_
456	tnaA	tnaa	NN	GEN	_	_
457	LB	lb	NN	_	_	_
458	30C	30c	NN	_	_	_
459	biofilm	biofilm	NN	_	_	_
460	cells	cell	NNS	_	_	_
461	with	with	IN	_	_	_
462	DMF	dmf	NN	_	_	_
463	7h	7h	VBP	_	_	_
464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
465	BW25113	bw25113	NN	_	_	_
466	,	,	,	_	_	_
467	water	water	NN	_	_	_
468	-LRB-	-lrb-	-LRB-	_	_	_
469	negative	negative	JJ	_	_	_
470	control	control	NN	_	_	_
471	-RRB-	-rrb-	-RRB-	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	BW25113	bw25113	NN	_	_	_
474	with	with	IN	_	_	_
475	deoxycholate	deoxycholate	NN	SUPP	_	_
476	stress	stress	NN	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	BW25113	bw25113	NN	_	_	_
479	w/t	w/t	NN	_	_	_
480	7h	7h	VBP	_	_	_
481	LB	lb	NN	_	_	_
482	30C	30c	NN	_	_	_
483	biofilm	biofilm	NN	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	BW25113	bw25113	NN	_	_	_
486	w/t	w/t	NN	_	_	_
487	7h	7h	VBP	_	_	_
488	LB	lb	NN	_	_	_
489	30C	30c	NN	_	_	_
490	free-living	free-living	JJ	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	BW25113	bw25113	NN	_	_	_
493	wt	wt	JJ	_	_	_
494	at	at	IN	_	_	_
495	OD600	od600	NN	_	_	_
496	=	=	JJ	_	_	_
497	0.5	0.5	CD	_	_	_
498	LB	lb	NN	_	_	_
499	37C	37c	NN	_	_	_
500	suspension	suspension	NN	_	_	_
501	cell	cell	NN	_	_	_
502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
503	BW25113	bw25113	NN	_	_	_
504	w/t	w/t	NN	_	_	_
505	LB	lb	NN	_	_	_
506	30C	30c	NN	_	_	_
507	OD	od	NN	_	_	_
508	4.0	4.0	CD	_	_	_
509	free-living	free-living	JJ	_	_	_
510	cells	cell	NNS	_	_	_
511	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
512	BW25113	bw25113	NN	_	_	_
513	w/t	w/t	NN	_	_	_
514	LB	lb	NN	_	_	_
515	4	4	CD	_	_	_
516	hr	hr	NN	_	_	_
517	biofilm	biofilm	NN	_	_	_
518	cells	cell	NNS	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
520	BW25113	bw25113	NN	_	_	_
521	w/t	w/t	NN	_	_	_
522	LB	lb	NN	_	_	_
523	glu	glu	NN	_	_	_
524	15	15	CD	_	_	_
525	hr	hr	NN	_	_	_
526	biofilm	biofilm	NN	_	_	_
527	cells	cell	NNS	_	_	_
528	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
529	BW25113	bw25113	NN	_	_	_
530	W/T	w/t	NN	_	_	_
531	LBglu	lbglu	NN	_	_	_
532	24h	24h	JJ	_	_	_
533	biofilm	biofilm	NN	_	_	_
534	cells	cell	NNS	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
536	BW25113	bw25113	NN	_	_	_
537	w/t	w/t	NN	_	_	_
538	LB	lb	NN	_	_	_
539	glu	glu	NN	_	_	_
540	24	24	CD	_	_	_
541	hr	hr	NN	_	_	_
542	biofilm	biofilm	NN	_	_	_
543	cells	cell	NNS	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
545	BW25113	bw25113	NN	_	_	_
546	w/t	w/t	NN	_	_	_
547	LB	lb	NN	_	_	_
548	glu	glu	NN	_	_	_
549	4	4	CD	_	_	_
550	hr	hr	NN	_	_	_
551	biofilm	biofilm	NN	_	_	_
552	cells	cell	NNS	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
554	BW25113	bw25113	NN	_	_	_
555	ychH	ychh	NN	GEN	_	_
556	,	,	,	_	_	_
557	H2O2	h2o2	NN	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
559	BW25113	bw25113	NN	_	_	_
560	ychH	ychh	NN	GEN	_	_
561	,	,	,	_	_	_
562	water	water	NN	_	_	_
563	-LRB-	-lrb-	-LRB-	_	_	_
564	negative	negative	JJ	_	_	_
565	control	control	NN	_	_	_
566	-RRB-	-rrb-	-RRB-	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	BW25113	bw25113	NN	_	_	_
569	ygiW	ygiw	NN	GEN	_	_
570	,	,	,	_	_	_
571	H2O2	h2o2	NN	_	_	_
572	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
573	BW25113	bw25113	NN	_	_	_
574	ygiW	ygiw	NN	GEN	_	_
575	,	,	,	_	_	_
576	water	water	NN	_	_	_
577	-LRB-	-lrb-	-LRB-	_	_	_
578	negative	negative	JJ	_	_	_
579	control	control	NN	_	_	_
580	-RRB-	-rrb-	-RRB-	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	BW25113	bw25113	NN	_	_	_
583	ymgB	ymgb	NN	_	_	_
584	LBglu	lbglu	NN	_	_	_
585	24h	24h	JJ	_	_	_
586	biofilm	biofilm	NN	_	_	_
587	cells	cell	NNS	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
589	BW25113	bw25113	NN	_	_	_
590	ΔmqsRA	δmqsra	NN	_	_	_
591	HEPES-glu	hepes-glu	NN	_	_	_
592	30	30	CD	_	_	_
593	min	min	NN	_	_	_
594	4.5	4.5	CD	_	_	_
595	%	%	NN	_	_	_
596	deoxycholate	deoxycholate	NN	SUPP	_	_
597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
598	BW25113	bw25113	NN	_	_	_
599	ΔmqsRA	δmqsra	NN	_	_	_
600	with	with	IN	_	_	_
601	deoxycholate	deoxycholate	NN	SUPP	_	_
602	stress	stress	NN	_	_	_
603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
604	BWG	bwg	NN	_	_	_
605	_	_	CD	_	_	_
606	butanol	butanol	NN	_	_	_
607	_	_	CD	_	_	_
608	3passages	3passage	NNS	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	BWG	bwg	NN	_	_	_
611	_	_	NN	_	_	_
612	replicated	replicate	VBN	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	BWY	bwy	NN	_	_	_
615	_	_	NN	_	_	_
616	butanol	butanol	NN	_	_	_
617	_	_	CD	_	_	_
618	3passages	3passage	NNS	_	_	_
619	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
620	BWY	bwy	NN	_	_	_
621	_	_	NN	_	_	_
622	replicated	replicate	VBN	_	_	_
623	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
624	BZNT	bznt	JJ	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	C1	c1	NN	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	C2	c2	NN	_	_	_
629	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
630	Call	call	VB	_	_	_
631	peaks	peak	NNS	_	_	_
632	to	to	TO	_	_	_
633	and	and	CC	_	_	_
634	FDR	FDR	NNP	_	_	_
635	0.1	0.1	CD	_	_	_
636	,	,	,	_	_	_
637	MOSAiCs	MOSAiCs	NNP	_	_	_
638	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
639	CAR005	car005	NN	_	_	_
640	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
641	CAR005	car005	NN	_	_	_
642	strain	strain	NN	_	_	_
643	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
644	carbon	carbon	NN	_	_	_
645	source	source	NN	_	_	_
646	:	:	:	_	_	_
647	acetate	acetate	NN	SUPP	_	_
648	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
649	carbon	carbon	NN	_	_	_
650	source	source	NN	_	_	_
651	:	:	:	_	_	_
652	fructose	fructose	NN	_	_	_
653	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
654	carbon	carbon	NN	_	_	_
655	source	source	NN	_	_	_
656	:	:	:	_	_	_
657	gluconate	gluconate	NN	_	_	_
658	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
659	carbon	carbon	NN	_	_	_
660	source	source	NN	_	_	_
661	:	:	:	_	_	_
662	glucose	glucose	NN	SUPP	_	_
663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
664	carbon	carbon	NN	_	_	_
665	source	source	NN	_	_	_
666	:	:	:	_	_	_
667	Glucose	glucose	NN	_	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
669	carbon	carbon	NN	_	_	_
670	source	source	NN	_	_	_
671	:	:	:	_	_	_
672	glycerol	glycerol	NN	SUPP	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
674	carbon	carbon	NN	_	_	_
675	source	source	NN	_	_	_
676	:	:	:	_	_	_
677	Glycerol	glycerol	NN	_	_	_
678	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
679	carbon	carbon	NN	_	_	_
680	source	source	NN	_	_	_
681	:	:	:	_	_	_
682	glycerol	glycerol	NN	SUPP	_	_
683	+	+	CC	_	_	_
684	propionate	propionate	NN	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
686	carbon	carbon	NN	_	_	_
687	source	source	NN	_	_	_
688	:	:	:	_	_	_
689	lactate	lactate	NN	_	_	_
690	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
691	CASAVA	CASAVA	NNP	_	_	_
692	version	version	NN	_	_	_
693	1.4	1.4	CD	_	_	_
694	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
695	cas	ca	VBZ	_	_	_
696	_	_	SYM	_	_	_
697	RNAA	RNAA	NNP	_	_	_
698	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
699	Cattle	Cattle	NNP	_	_	_
700	feces	fece	NNS	_	_	_
701	isolate	isolate	VBP	_	_	_
702	C1A	c1a	NN	_	_	_
703	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
704	Cattle	cattle	JJ	_	_	_
705	feces	fece	NNS	_	_	_
706	isolate	isolate	VBP	_	_	_
707	C4A	c4a	NN	_	_	_
708	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
709	Cattle	cattle	JJ	_	_	_
710	feces	fece	NNS	_	_	_
711	isolate	isolate	VBP	_	_	_
712	C6D	c6d	NN	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
714	Cattle	Cattle	NNP	_	_	_
715	III	III	NNP	_	_	_
716	versus	versus	CC	_	_	_
717	MG1655	MG1655	NNP	_	_	_
718	technical	technical	JJ	_	_	_
719	replicate	replicate	VB	_	_	_
720	1	1	CD	_	_	_
721	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
722	Cattle	Cattle	NNP	_	_	_
723	III	III	NNP	_	_	_
724	versus	versus	CC	_	_	_
725	MG1655	MG1655	NNP	_	_	_
726	technical	technical	JJ	_	_	_
727	replicate	replicate	VB	_	_	_
728	2	2	CD	_	_	_
729	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
730	Cattle	Cattle	NNP	_	_	_
731	II	II	NNP	_	_	_
732	versus	versus	CC	_	_	_
733	MG1655	MG1655	NNP	_	_	_
734	technical	technical	JJ	_	_	_
735	replicate	replicate	VB	_	_	_
736	1	1	CD	_	_	_
737	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
738	Cattle	Cattle	NNP	_	_	_
739	II	II	NNP	_	_	_
740	versus	versus	CC	_	_	_
741	MG1655	MG1655	NNP	_	_	_
742	technical	technical	JJ	_	_	_
743	replicate	replicate	VB	_	_	_
744	2	2	CD	_	_	_
745	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
746	Cattle	Cattle	NNP	_	_	_
747	I	I	PRP	_	_	_
748	versus	versus	CC	_	_	_
749	MG1655	mg1655	NN	_	_	_
750	technical	technical	JJ	_	_	_
751	replicate	replicate	VB	_	_	_
752	1	1	CD	_	_	_
753	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
754	Cattle	Cattle	NNP	_	_	_
755	I	I	PRP	_	_	_
756	versus	versus	CC	_	_	_
757	MG1655	mg1655	NN	_	_	_
758	technical	technical	JJ	_	_	_
759	replicate	replicate	VBP	_	_	_
760	2	2	CD	_	_	_
761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
762	Caulobacter	caulobacter	NN	_	_	_
763	crescentus	crescentus	NN	_	_	_
764	and	and	CC	_	_	_
765	derivatives	derivative	NNS	_	_	_
766	were	be	VBD	_	_	_
767	grown	grow	VBN	_	_	_
768	at	at	IN	_	_	_
769	30	30	CD	_	_	_
770	°C	°c	NN	_	_	_
771	in	in	IN	_	_	_
772	PYE	pye	NN	_	_	_
773	-LRB-	-lrb-	-LRB-	_	_	_
774	Peptone	peptone	NN	_	_	_
775	yeast	yeast	NN	SUPP	_	_
776	extract	extract	NN	SUPP	_	_
777	-RRB-	-rrb-	-RRB-	_	_	_
778	or	or	CC	_	_	_
779	LB	lb	NN	_	_	_
780	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
781	CCCP-1	cccp-1	NN	_	_	_
782	,	,	,	_	_	_
783	biological	biological	JJ	_	_	_
784	rep1	rep1	NN	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	CCCP-2	cccp-2	NN	_	_	_
787	,	,	,	_	_	_
788	biological	biological	JJ	_	_	_
789	rep2	rep2	NN	_	_	_
790	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
791	CCCP-3	cccp-3	NN	_	_	_
792	,	,	,	_	_	_
793	biological	biological	JJ	_	_	_
794	rep3	rep3	NN	_	_	_
795	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
796	ccdB	ccdb	NN	_	_	_
797	_	_	CD	_	_	_
798	K12	k12	NN	_	_	_
799	_	_	NN	_	_	_
800	0	0	CD	_	_	_
801	_	_	NN	_	_	_
802	r1	r1	NN	_	_	_
803	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
804	ccdB	ccdb	NN	_	_	_
805	_	_	CD	_	_	_
806	K12	k12	NN	_	_	_
807	_	_	NN	_	_	_
808	120	120	CD	_	_	_
809	_	_	NN	_	_	_
810	r1	r1	NN	_	_	_
811	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
812	ccdB	ccdb	NN	_	_	_
813	_	_	CD	_	_	_
814	K12	k12	NN	_	_	_
815	_	_	CD	_	_	_
816	30	30	CD	_	_	_
817	_	_	NN	_	_	_
818	r1	r1	NN	_	_	_
819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
820	ccdB	ccdb	NN	_	_	_
821	_	_	CD	_	_	_
822	K12	k12	NN	_	_	_
823	_	_	NN	_	_	_
824	60	60	CD	_	_	_
825	_	_	NN	_	_	_
826	r1	r1	NN	_	_	_
827	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
828	ccdB	ccdb	NN	_	_	_
829	_	_	CD	_	_	_
830	K12	k12	NN	_	_	_
831	_	_	NN	_	_	_
832	90	90	CD	_	_	_
833	_	_	NN	_	_	_
834	r1	r1	NN	_	_	_
835	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
836	ccdB	ccdb	NN	_	_	_
837	_	_	CD	_	_	_
838	MG1063	mg1063	NN	_	_	_
839	_	_	NN	_	_	_
840	0	0	CD	_	_	_
841	_	_	NN	_	_	_
842	r1	r1	NN	_	_	_
843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
844	ccdB	ccdb	NN	_	_	_
845	_	_	CD	_	_	_
846	MG1063	mg1063	NN	_	_	_
847	_	_	NN	_	_	_
848	0	0	CD	_	_	_
849	_	_	NN	_	_	_
850	r2	r2	NN	_	_	_
851	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
852	ccdB	ccdb	NN	_	_	_
853	_	_	CD	_	_	_
854	MG1063	mg1063	NN	_	_	_
855	_	_	NN	_	_	_
856	120	120	CD	_	_	_
857	_	_	NN	_	_	_
858	r1	r1	NN	_	_	_
859	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
860	ccdB	ccdb	NN	_	_	_
861	_	_	CD	_	_	_
862	MG1063	mg1063	NN	_	_	_
863	_	_	CD	_	_	_
864	30	30	CD	_	_	_
865	_	_	NN	_	_	_
866	r1	r1	NN	_	_	_
867	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
868	ccdB	ccdb	NN	_	_	_
869	_	_	CD	_	_	_
870	MG1063	mg1063	NN	_	_	_
871	_	_	CD	_	_	_
872	30	30	CD	_	_	_
873	_	_	NN	_	_	_
874	r2	r2	NN	_	_	_
875	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
876	ccdB	ccdb	NN	_	_	_
877	_	_	CD	_	_	_
878	MG1063	mg1063	NN	_	_	_
879	_	_	NN	_	_	_
880	60	60	CD	_	_	_
881	_	_	NN	_	_	_
882	r1	r1	NN	_	_	_
883	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
884	ccdB	ccdb	NN	_	_	_
885	_	_	CD	_	_	_
886	MG1063	mg1063	NN	_	_	_
887	_	_	NN	_	_	_
888	60	60	CD	_	_	_
889	_	_	NN	_	_	_
890	r2	r2	NN	_	_	_
891	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
892	ccdB	ccdb	NN	_	_	_
893	_	_	CD	_	_	_
894	MG1063	mg1063	NN	_	_	_
895	_	_	NN	_	_	_
896	90	90	CD	_	_	_
897	_	_	NN	_	_	_
898	r1	r1	NN	_	_	_
899	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
900	ccdB	ccdb	NN	_	_	_
901	_	_	CD	_	_	_
902	MG1063	mg1063	NN	_	_	_
903	_	_	NN	_	_	_
904	90	90	CD	_	_	_
905	_	_	NN	_	_	_
906	r2	r2	NN	_	_	_
907	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
908	ccdB	ccdb	NN	_	_	_
909	_	_	CD	_	_	_
910	W1863	w1863	NN	_	_	_
911	_	_	NN	_	_	_
912	0	0	CD	_	_	_
913	_	_	NN	_	_	_
914	r1	r1	NN	_	_	_
915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
916	ccdB	ccdb	NN	_	_	_
917	_	_	CD	_	_	_
918	W1863	w1863	NN	_	_	_
919	_	_	CD	_	_	_
920	30	30	CD	_	_	_
921	_	_	NN	_	_	_
922	r1	r1	NN	_	_	_
923	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
924	ccdB	ccdb	NN	_	_	_
925	_	_	CD	_	_	_
926	W1863	w1863	NN	_	_	_
927	_	_	NN	_	_	_
928	60	60	CD	_	_	_
929	_	_	NN	_	_	_
930	r1	r1	NN	_	_	_
931	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
932	ccdB	ccdb	NN	_	_	_
933	_	_	CD	_	_	_
934	W1863	w1863	NN	_	_	_
935	_	_	NN	_	_	_
936	90	90	CD	_	_	_
937	_	_	CD	_	_	_
938	r1	r1	NN	_	_	_
939	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
940	cDNA	cdna	NN	_	_	_
941	_	_	NN	_	_	_
942	A	a	NN	_	_	_
943	_	_	CD	_	_	_
944	cy3	cy3	NN	_	_	_
945	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
946	cDNA	cdna	NN	_	_	_
947	_	_	NN	_	_	_
948	B	b	NN	_	_	_
949	_	_	CD	_	_	_
950	cy5	cy5	NN	_	_	_
951	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
952	cDNA	cdna	NN	_	_	_
953	libraries	library	NNS	_	_	_
954	for	for	IN	_	_	_
955	the	the	DT	_	_	_
956	Illumina	Illumina	NNP	_	_	_
957	sequencing	sequencing	NN	_	_	_
958	platform	platform	NN	_	_	_
959	were	be	VBD	_	_	_
960	constructed	construct	VBN	_	_	_
961	by	by	IN	_	_	_
962	vertis	vertis	NN	_	_	_
963	Biotechnology	Biotechnology	NNP	_	_	_
964	AG	AG	NNP	_	_	_
965	,	,	,	_	_	_
966	Germany	Germany	NNP	_	_	_
967	,	,	,	_	_	_
968	as	as	IN	_	_	_
969	described	describe	VBN	_	_	_
970	previously	previously	RB	_	_	_
971	-LRB-	-lrb-	-LRB-	_	_	_
972	Berezikov	Berezikov	NNP	_	_	_
973	et	et	FW	_	_	_
974	al.	al.	FW	_	_	_
975	,2006	,2006	CD	_	_	_
976	-RRB-	-rrb-	-RRB-	_	_	_
977	,	,	,	_	_	_
978	without	without	IN	_	_	_
979	the	the	DT	_	_	_
980	RNA	rna	NN	_	_	_
981	size-fractionation	size-fractionation	NN	_	_	_
982	step	step	NN	_	_	_
983	prior	prior	RB	_	_	_
984	to	to	TO	_	_	_
985	cDNA	cdna	NN	_	_	_
986	synthesis	synthesis	NN	_	_	_
987	.	.	.	_	_	_

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/µl	ng/µl	NN	_	_	_
20	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	library-specific	library-specific	JJ	_	_	_
3	barcode	barcode	NN	_	_	_
4	for	for	IN	_	_	_
5	multiplex	multiplex	JJ	_	_	_
6	sequencing	sequencing	NN	_	_	_
7	was	be	VBD	_	_	_
8	part	part	NN	_	_	_
9	of	of	IN	_	_	_
10	a	a	DT	_	_	_
11	3	3	CD	_	_	_
12	'	'	''	_	_	_
13	-	-	:	_	_	_
14	sequencing	sequencing	NN	_	_	_
15	adapter	adapter	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cDNA	cdna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	barcoded	barcode	VBN	_	_	_
6	with	with	IN	_	_	_
7	the	the	DT	_	_	_
8	TruSeq	TruSeq	NNP	_	_	_
9	RNA	rna	NN	_	_	_
10	Sample	sample	NN	_	_	_
11	Prep	Prep	NNP	_	_	_
12	Kit	kit	NN	_	_	_
13	v2	v2	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Illumina	Illumina	NNP	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	,	,	,	_	_	_
18	San	San	NNP	_	_	_
19	Diego	Diego	NNP	_	_	_
20	,	,	,	_	_	_
21	CA	CA	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

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	cDNA	cdna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	constructed	construct	VBN	_	_	_
6	at	at	IN	_	_	_
7	Purdue	Purdue	NNP	_	_	_
8	using	use	VBG	_	_	_
9	an	a	DT	_	_	_
10	adapted	adapt	VBN	_	_	_
11	SOLiD	SOLiD	NNP	_	_	_
12	Total	Total	NNP	_	_	_
13	RNA-Seq	RNA-Seq	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	.	.	.	_	_	_

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	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	cDNA	cdna	NN	_	_	_
3	library	library	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	nascent	nascent	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	constructed	construct	VBN	_	_	_
10	according	accord	VBG	_	_	_
11	to	to	TO	_	_	_
12	Churchman	Churchman	NNP	_	_	_
13	and	and	CC	_	_	_
14	Weissman	Weissman	NNP	_	_	_
15	,	,	,	_	_	_
16	Nature	Nature	NNP	_	_	_
17	2011	2011	CD	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	PMID	pmid	NN	_	_	_
20	:	:	:	_	_	_
21	21248844	21248844	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cDNA	cdna	NN	_	_	_
3	made	make	VBN	_	_	_
4	from	from	IN	_	_	_
5	strain	strain	NN	_	_	_
6	KMD	kmd	NN	_	_	_
7	extracted	extract	VBN	_	_	_
8	from	from	IN	_	_	_
9	mouse	mouse	NN	_	_	_
10	kidney	kidney	NN	_	_	_
11	on	on	IN	_	_	_
12	day	day	NN	_	_	_
13	2	2	CD	_	_	_
14	post	post	NN	_	_	_
15	infection	infection	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	cDNA	cdna	NN	_	_	_
18	made	make	VBN	_	_	_
19	from	from	IN	_	_	_
20	strain	strain	NN	_	_	_
21	PC1012	pc1012	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	marArobsoxS	mararobsoxs	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	extracted	extract	VBN	_	_	_
26	from	from	IN	_	_	_
27	mouse	mouse	NN	_	_	_
28	kidney	kidney	NN	_	_	_
29	on	on	IN	_	_	_
30	day	day	NN	_	_	_
31	2	2	CD	_	_	_
32	post	post	NN	_	_	_
33	infection	infection	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	cDNA	cdna	NN	_	_	_
36	of	of	IN	_	_	_
37	EPEC	epec	NN	_	_	_
38	strain	strain	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	cDNA	cdna	NN	_	_	_
41	reads	read	VBZ	_	_	_
42	were	be	VBD	_	_	_
43	trimmed	trim	VBN	_	_	_
44	so	so	RB	_	_	_
45	that	that	IN	_	_	_
46	the	the	DT	_	_	_
47	quality	quality	NN	_	_	_
48	at	at	IN	_	_	_
49	each	each	DT	_	_	_
50	base	base	NN	_	_	_
51	position	position	NN	_	_	_
52	was	be	VBD	_	_	_
53	above	above	IN	_	_	_
54	30	30	CD	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	~	~	CD	_	_	_
57	15-20	15-20	CD	_	_	_
58	bp	bp	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	and	and	CC	_	_	_
61	then	then	RB	_	_	_
62	mapped	map	VBD	_	_	_
63	either	either	CC	_	_	_
64	to	to	TO	_	_	_
65	the	the	DT	_	_	_
66	E.	e.	FW	_	_	_
67	coli	coli	FW	_	_	_
68	K-12	k-12	NN	_	_	_
69	MG1655	mg1655	NN	_	_	_
70	published	publish	VBN	_	_	_
71	genome	genome	NN	_	_	_
72	sequence	sequence	NN	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	Genbank	Genbank	NNP	_	_	_
75	accession	accession	NN	_	_	_
76	no	no	DT	_	_	_
77	.	.	.	_	_	_

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://www.iayork.com/XPlasMap/	http://www.iayork.com/xplasmap/	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	and	and	CC	_	_	_
10	IGV	igv	NN	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	reads	read	VBZ	_	_	_
3	mapped	map	VBN	_	_	_
4	per	per	IN	_	_	_
5	kilobase	kilobase	NN	_	_	_
6	of	of	IN	_	_	_
7	gene	gene	NN	_	_	_
8	per	per	IN	_	_	_
9	million	million	CD	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	RPKM	rpkm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	reads	read	VBZ	_	_	_
14	was	be	VBD	_	_	_
15	calculated	calculate	VBN	_	_	_
16	using	use	VBG	_	_	_
17	either	either	CC	_	_	_
18	the	the	DT	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	chromosome	chromosome	NN	_	_	_
22	or	or	CC	_	_	_
23	the	the	DT	_	_	_
24	pAR060302	par060302	NN	_	_	_
25	annotation	annotation	NN	_	_	_
26	and	and	CC	_	_	_
27	was	be	VBD	_	_	_
28	used	use	VBN	_	_	_
29	for	for	IN	_	_	_
30	global	global	JJ	_	_	_
31	normalization	normalization	NN	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	per	per	IN	_	_	_
3	kilobase	kilobase	NN	_	_	_
4	cDNA	cdna	NN	_	_	_
5	length	length	NN	_	_	_
6	normalized	normalize	VBD	_	_	_
7	the	the	DT	_	_	_
8	effect	effect	NN	_	_	_
9	of	of	IN	_	_	_
10	different	different	JJ	_	_	_
11	length	length	NN	_	_	_
12	of	of	IN	_	_	_
13	cDNAs	cdna	NNS	_	_	_
14	such	such	JJ	_	_	_
15	that	that	IN	_	_	_
16	the	the	DT	_	_	_
17	sequence	sequence	NN	_	_	_
18	reads	read	VBZ	_	_	_
19	have	have	VB	_	_	_
20	a	a	DT	_	_	_
21	equal	equal	JJ	_	_	_
22	chance	chance	NN	_	_	_
23	to	to	TO	_	_	_
24	map	map	VB	GEN	_	_
25	on	on	IN	_	_	_
26	the	the	DT	_	_	_
27	long	long	JJ	_	_	_
28	cDNA	cdna	NN	_	_	_
29	regions	region	NNS	_	_	_
30	and	and	CC	_	_	_
31	the	the	DT	_	_	_
32	short	short	JJ	_	_	_
33	cDNA	cdna	NN	_	_	_
34	regions	region	NNS	_	_	_
35	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	RPKM	rpkm	NN	_	_	_
3	normalization	normalization	NN	_	_	_
4	,	,	,	_	_	_
5	each	each	DT	_	_	_
6	sample	sample	NN	_	_	_
7	is	be	VBZ	_	_	_
8	comparable	comparable	JJ	_	_	_
9	to	to	TO	_	_	_
10	each	each	DT	_	_	_
11	other	other	JJ	_	_	_
12	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	R	r	NN	_	_	_
3	package	package	NN	_	_	_
4	,	,	,	_	_	_
5	DEGseq	degseq	NN	_	_	_
6	,	,	,	_	_	_
7	was	be	VBD	_	_	_
8	used	use	VBN	_	_	_
9	to	to	TO	_	_	_
10	identify	identify	VB	_	_	_
11	differentially	differentially	RB	_	_	_
12	expressed	express	VBN	_	_	_
13	genes	gene	NNS	_	_	_
14	between	between	IN	_	_	_
15	the	the	DT	_	_	_
16	control	control	NN	_	_	_
17	and	and	CC	_	_	_
18	each	each	DT	_	_	_
19	antibiotic	antibiotic	JJ	_	_	_
20	treatment	treatment	NN	_	_	_
21	condition	condition	NN	_	_	_
22	.	.	.	_	_	_

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	NN	_	_	_
22	CEL	cel	NN	_	_	_
23	files	file	NNS	_	_	_
24	were	be	VBD	_	_	_
25	quantified	quantify	VBN	_	_	_
26	with	with	IN	_	_	_
27	Distribution	distribution	NN	_	_	_
28	Free	Free	NNP	_	_	_
29	Weighted	Weighted	NNP	_	_	_
30	method	method	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	DFW	dfw	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	,	,	,	_	_	_
35	using	use	VBG	_	_	_
36	the	the	DT	_	_	_
37	statistical	statistical	JJ	_	_	_
38	language	language	NN	_	_	_
39	R	r	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	R-2.7.2	r-2.7.2	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	and	and	CC	_	_	_
44	Bioconductor	Bioconductor	NNP	_	_	_
45	2.2	2.2	CD	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cell	cell	NN	_	_	_
3	culture	culture	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Cell	cell	NN	_	_	_
6	culture	culture	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Cell	cell	NN	_	_	_
9	cultures	culture	NNS	_	_	_
10	were	be	VBD	_	_	_
11	cross	cross	JJ	_	_	_
12	linked	link	VBN	_	_	_
13	by	by	IN	_	_	_
14	addition	addition	NN	_	_	_
15	of	of	IN	_	_	_
16	27	27	CD	_	_	_
17	µl	µl	NN	_	_	_
18	of	of	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	37	37	CD	_	_	_
22	%	%	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
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	1	1	CD	_	_	_
31	%	%	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

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	25mg/ml	25mg/ml	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	was	be	VBD	_	_	_
16	added	add	VBN	_	_	_
17	and	and	CC	_	_	_
18	incubated	incubate	VBN	_	_	_
19	for	for	IN	_	_	_
20	30	30	CD	_	_	_
21	min	min	NN	_	_	_
22	at	at	IN	_	_	_
23	65	65	CD	_	_	_
24	°C	°c	NN	_	_	_
25	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	100μL	100μl	NN	_	_	_
4	proteinase	proteinase	NN	_	_	_
5	K	k	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	25	25	CD	_	_	_
8	mg/ml	mg/ml	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	added	add	VBN	_	_	_
12	and	and	CC	_	_	_
13	samples	sample	NNS	_	_	_
14	incubated	incubate	VBN	_	_	_
15	at	at	IN	_	_	_
16	42	42	CD	_	_	_
17	°C	°c	NN	_	_	_
18	for	for	IN	_	_	_
19	2	2	CD	_	_	_
20	h	h	NN	_	_	_
21	and	and	CC	_	_	_
22	65	65	CD	_	_	_
23	°C	°c	NN	_	_	_
24	for	for	IN	_	_	_
25	6	6	CD	_	_	_
26	h	h	NN	_	_	_
27	to	to	TO	_	_	_
28	reverse	reverse	VB	_	_	_
29	the	the	DT	_	_	_
30	crosslink	crosslink	NN	_	_	_
31	followed	follow	VBN	_	_	_
32	by	by	IN	_	_	_
33	phenol	phenol	NN	_	_	_
34	extraction	extraction	NN	_	_	_
35	and	and	CC	_	_	_
36	precipitation	precipitation	NN	_	_	_
37	with	with	IN	_	_	_
38	ethanol	ethanol	NN	_	_	_
39	and	and	CC	_	_	_
40	Na-acetate	na-acetate	NN	_	_	_
41	.	.	.	_	_	_

1	Precipitated	precipitate	VBN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	50μL	50μl	NN	_	_	_
7	dH2O	dh2o	NN	_	_	_
8	.	.	.	_	_	_

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/mL	u/ml	NN	_	_	_
55	SUPERase	superase	NN	_	_	_
56	•	•	SYM	_	_	_
57	In	in	IN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	Ambion	Ambion	NNP	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	and	and	CC	_	_	_
63	1X	1x	NN	_	_	_
64	protease	protease	NN	_	_	_
65	inhibitor	inhibitor	NN	_	_	_
66	cocktail	cocktail	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Complete	complete	JJ	_	_	_
69	,	,	,	_	_	_
70	EDTA-free	edta-free	NN	_	_	_
71	,	,	,	_	_	_
72	Roche	Roche	NNP	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	,	,	,	_	_	_
75	supplemented	supplement	VBN	_	_	_
76	with	with	IN	_	_	_
77	10	10	CD	_	_	_
78	mM	mm	NN	KWSUPP	_	_
79	MnCl2	mncl2	NN	SUPP	_	_
80	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	by	by	IN	_	_	_
8	pipetting	pipetting	NN	_	_	_
9	.	.	.	_	_	_

1	RQ1	rq1	NN	_	_	_
2	DNase	dnase	NN	_	_	_
3	I	i	CD	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	110	110	CD	_	_	_
6	U	U	NNP	_	_	_
7	total	total	NN	_	_	_
8	,	,	,	_	_	_
9	Promega	Promega	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	and	and	CC	_	_	_
14	incubated	incubate	VBN	_	_	_
15	for	for	IN	_	_	_
16	20	20	CD	_	_	_
17	min	min	NN	_	_	_
18	on	on	IN	_	_	_
19	ice	ice	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	reaction	reaction	NN	_	_	_
3	was	be	VBD	_	_	_
4	quenched	quench	VBN	_	_	_
5	with	with	IN	_	_	_
6	EDTA	edta	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	25	25	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	final	final	JJ	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	,	,	,	_	_	_
13	which	which	WDT	_	_	_
14	releases	release	VBZ	_	_	_
15	polysomes	polysome	NNS	_	_	_
16	from	from	IN	_	_	_
17	the	the	DT	_	_	_
18	transcript	transcript	NN	_	_	_
19	and	and	CC	_	_	_
20	reduces	reduce	VBZ	_	_	_
21	contamination	contamination	NN	_	_	_
22	from	from	IN	_	_	_
23	ribosomal	ribosomal	JJ	_	_	_
24	RNA	rna	NN	_	_	_
25	and	and	CC	_	_	_
26	ribosome-associated	ribosome-associated	JJ	_	_	_
27	tRNAs	trna	NNS	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	clarified	clarify	VBN	_	_	_
5	at	at	IN	_	_	_
6	4	4	CD	_	_	_
7	°C	°c	NN	_	_	_
8	by	by	IN	_	_	_
9	centrifugation	centrifugation	NN	_	_	_
10	at	at	IN	_	_	_
11	20,000	20,000	CD	_	_	_
12	g	g	NN	_	_	_
13	for	for	IN	_	_	_
14	10	10	CD	_	_	_
15	min	min	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	loaded	load	VBN	_	_	_
5	onto	onto	IN	_	_	_
6	a	a	DT	_	_	_
7	PD	pd	NN	_	_	_
8	MiniTrap	MiniTrap	NNP	_	_	_
9	G-25	G-25	NNP	_	_	_
10	column	column	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	GE	GE	NNP	_	_	_
13	Healthcare	Healthcare	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	eluted	elute	VBN	_	_	_
17	with	with	IN	_	_	_
18	lysis	lysis	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	supplemented	supplement	VBN	_	_	_
21	with	with	IN	_	_	_
22	1	1	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	EDTA	edta	NN	_	_	_
25	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	clarified	clarify	VBN	_	_	_
8	lysate	lysate	NN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	miRNeasy	miRNeasy	NNP	_	_	_
12	kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Qiagen	qiagen	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

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	CD	_	_	_
45	cells/ml	cells/ml	NNS	_	_	_
46	and	and	CC	_	_	_
47	100	100	CD	_	_	_
48	mg/l	mg/l	NN	_	_	_
49	of	of	IN	_	_	_
50	TiO2	tio2	NN	_	_	_
51	nanoparticles	nanoparticle	NNS	_	_	_
52	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	at	at	IN	_	_	_
7	20	20	CD	_	_	_
8	°C	°c	NN	_	_	_
9	on	on	IN	_	_	_
10	a	a	DT	_	_	_
11	dark	dark	JJ	_	_	_
12	rotary	rotary	JJ	_	_	_
13	shaker	shaker	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	150	150	CD	_	_	_
16	rpm	rpm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	5	5	CD	_	_	_
20	h.	h.	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	cell	cell	NN	_	_	_
23	pellets	pellet	NNS	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Cell	Cell	NNP	_	_	_
26	pellets	pellet	NNS	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	from	from	IN	_	_	_
29	initial	initial	JJ	_	_	_
30	250	250	CD	_	_	_
31	mL	ml	NN	_	_	_
32	of	of	IN	_	_	_
33	culture	culture	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	were	be	VBD	_	_	_
36	thawed	thaw	VBN	_	_	_
37	and	and	CC	_	_	_
38	resuspended	resuspend	VBN	_	_	_
39	in	in	IN	_	_	_
40	250	250	CD	_	_	_
41	μL	μl	NN	_	_	_
42	of	of	IN	_	_	_
43	IP	IP	NNP	_	_	_
44	buffer	buffer	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	100	100	CD	_	_	_
47	mM	mm	NN	KWSUPP	_	_
48	Tris	Tris	NNP	_	_	_
49	pH	ph	NN	_	_	_
50	8	8	CD	_	_	_
51	,	,	,	_	_	_
52	300	300	CD	_	_	_
53	mM	mm	NN	KWSUPP	_	_
54	NaCl	nacl	NN	_	_	_
55	,	,	,	_	_	_
56	1	1	CD	_	_	_
57	%	%	NN	_	_	_
58	TritonX-100	tritonx-100	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	and	and	CC	_	_	_
61	sonicated	sonicate	VBN	_	_	_
62	using	use	VBG	_	_	_
63	a	a	DT	_	_	_
64	microtip	microtip	NN	_	_	_
65	sonicator	sonicator	NN	_	_	_
66	set	set	VBN	_	_	_
67	at	at	IN	_	_	_
68	10	10	CD	_	_	_
69	%	%	NN	_	_	_
70	output	output	NN	_	_	_
71	for	for	IN	_	_	_
72	20	20	CD	_	_	_
73	second	second	JJ	_	_	_
74	intervals	interval	NNS	_	_	_
75	with	with	IN	_	_	_
76	periods	period	NNS	_	_	_
77	of	of	IN	_	_	_
78	cooling	cool	VBG	_	_	_
79	in	in	IN	_	_	_
80	between	between	IN	_	_	_
81	.	.	.	_	_	_

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/ml	ng/ml	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	micrococcal	micrococcal	JJ	_	_	_
20	nuclease	nuclease	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	50	50	CD	_	_	_
23	units	unit	NNS	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	20	20	CD	_	_	_
27	μM	μm	NN	_	_	_
28	CaCl2	cacl2	NN	_	_	_
29	,1.2	,1.2	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	KCl	kcl	NN	_	_	_
32	,	,	,	_	_	_
33	0.3	0.3	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	,	,	,	_	_	_
37	6	6	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	sucrose	sucrose	NN	_	_	_
40	,	,	,	_	_	_
41	and	and	CC	_	_	_
42	10	10	CD	_	_	_
43	μM	μm	NN	_	_	_
44	DTT	dtt	NN	_	_	_
45	.	.	.	_	_	_

1	EDTA	edta	NN	_	_	_
2	was	be	VBD	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	mM	mm	NN	KWSUPP	_	_
7	to	to	TO	_	_	_
8	stop	stop	VB	_	_	_
9	the	the	DT	_	_	_
10	micrococcal	micrococcal	JJ	_	_	_
11	nuclease	nuclease	NN	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	were	be	VBD	_	_	_
16	spun	spin	VBN	_	_	_
17	down	down	RP	_	_	_
18	to	to	TO	_	_	_
19	remove	remove	VB	_	_	_
20	cell	cell	NN	_	_	_
21	debris	debris	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	precleared	preclear	VBN	_	_	_
6	through	through	IN	_	_	_
7	incubation	incubation	NN	_	_	_
8	with	with	IN	_	_	_
9	a	a	DT	_	_	_
10	50/50	50/50	CD	_	_	_
11	slurry	slurry	NN	_	_	_
12	of	of	IN	_	_	_
13	sepharose	sepharose	NN	_	_	_
14	protein	protein	NN	_	_	_
15	A	a	NN	_	_	_
16	beads	bead	NNS	_	_	_
17	in	in	IN	_	_	_
18	IP	IP	NNP	_	_	_
19	buffer	buffer	NN	_	_	_
20	for	for	IN	_	_	_
21	2-3	2-3	CD	_	_	_
22	hours	hour	NNS	_	_	_
23	at	at	IN	_	_	_
24	4	4	CD	_	_	_
25	°C	°c	NN	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	and	and	CC	_	_	_
8	antibody	antibody	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	pre-cleared	pre-cleared	JJ	_	_	_
14	lysate	lysate	NN	_	_	_
15	for	for	IN	_	_	_
16	an	a	DT	_	_	_
17	overnight	overnight	JJ	_	_	_
18	incubation	incubation	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	next	next	JJ	_	_	_
3	day	day	NN	_	_	_
4	,	,	,	_	_	_
5	30	30	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	50/50	50/50	CD	_	_	_
10	slurry	slurry	NN	_	_	_
11	of	of	IN	_	_	_
12	sepharose	sepharose	NN	_	_	_
13	protein	protein	NN	_	_	_
14	A	a	NN	_	_	_
15	beads	bead	NNS	_	_	_
16	in	in	IN	_	_	_
17	IP	IP	NNP	_	_	_
18	buffer	buffer	NN	_	_	_
19	was	be	VBD	_	_	_
20	added	add	VBN	_	_	_
21	to	to	TO	_	_	_
22	the	the	DT	_	_	_
23	lysate	lysate	NN	_	_	_
24	to	to	TO	_	_	_
25	capture	capture	VB	_	_	_
26	antibody-protein-DNA	antibody-protein-dna	JJ	_	_	_
27	complex	complex	NN	_	_	_
28	for	for	IN	_	_	_
29	one	one	CD	_	_	_
30	hour	hour	NN	_	_	_
31	at	at	IN	_	_	_
32	4	4	CD	_	_	_
33	°C	°c	NN	_	_	_
34	.	.	.	_	_	_

1	Beads	bead	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	LiCl	licl	NN	_	_	_
11	wash	wash	NN	_	_	_
12	buffer	buffer	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	100	100	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	Tris	Tris	NNP	_	_	_
17	pH	ph	NN	_	_	_
18	8	8	CD	_	_	_
19	,	,	,	_	_	_
20	250	250	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	LiCl	licl	NN	_	_	_
23	,	,	,	_	_	_
24	2	2	CD	_	_	_
25	%	%	NN	_	_	_
26	TritonX-100	tritonx-100	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	,	,	,	_	_	_
29	twice	twice	RB	_	_	_
30	with	with	IN	_	_	_
31	600	600	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	NaCl	nacl	NN	_	_	_
34	wash	wash	NN	_	_	_
35	buffer	buffer	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	100	100	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	Tris	Tris	NNP	_	_	_
40	pH	ph	NN	_	_	_
41	8	8	CD	_	_	_
42	,	,	,	_	_	_
43	600	600	CD	_	_	_
44	mM	mm	NN	KWSUPP	_	_
45	NaCl	nacl	NN	_	_	_
46	,	,	,	_	_	_
47	2	2	CD	_	_	_
48	%	%	NN	_	_	_
49	TritonX-100	tritonx-100	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	,	,	,	_	_	_
52	twice	twice	RB	_	_	_
53	with	with	IN	_	_	_
54	300	300	CD	_	_	_
55	mM	mm	NN	KWSUPP	_	_
56	NaCl	nacl	NN	_	_	_
57	wash	wash	NN	_	_	_
58	buffer	buffer	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	100	100	CD	_	_	_
61	mM	mm	NN	KWSUPP	_	_
62	Tris	Tris	NNP	_	_	_
63	pH	ph	NN	_	_	_
64	8	8	CD	_	_	_
65	,	,	,	_	_	_
66	300	300	CD	_	_	_
67	mM	mm	NN	KWSUPP	_	_
68	NaCl	nacl	NN	_	_	_
69	,	,	,	_	_	_
70	2	2	CD	_	_	_
71	%	%	NN	_	_	_
72	TritonX-100	tritonx-100	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	,	,	,	_	_	_
75	and	and	CC	_	_	_
76	twice	twice	RB	_	_	_
77	with	with	IN	_	_	_
78	TE	te	NN	_	_	_
79	.	.	.	_	_	_

1	Elution	elution	NN	_	_	_
2	buffer	buffer	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	50	50	CD	_	_	_
5	mM	mm	NN	KWSUPP	_	_
6	Tris	Tris	NNP	_	_	_
7	pH	ph	NN	_	_	_
8	8	8	CD	_	_	_
9	,	,	,	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	EDTA	edta	NN	_	_	_
13	,	,	,	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	SDS	sds	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	after	after	IN	_	_	_
21	the	the	DT	_	_	_
22	final	final	JJ	_	_	_
23	wash	wash	NN	_	_	_
24	step	step	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	beads	bead	NNS	_	_	_
28	were	be	VBD	_	_	_
29	incubated	incubate	VBN	_	_	_
30	at	at	IN	_	_	_
31	65	65	CD	_	_	_
32	°C	°c	NN	_	_	_
33	for	for	IN	_	_	_
34	30	30	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	to	to	TO	_	_	_
37	remove	remove	VB	_	_	_
38	the	the	DT	_	_	_
39	crosslinked	crosslink	VBN	_	_	_
40	protein-DNA	protein-dna	JJ	_	_	_
41	complexes	complex	NNS	_	_	_
42	from	from	IN	_	_	_
43	the	the	DT	_	_	_
44	beads	bead	NNS	_	_	_
45	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	to	to	TO	_	_	_
4	remove	remove	VB	_	_	_
5	the	the	DT	_	_	_
6	beads	bead	NNS	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	samples	sample	NNS	_	_	_
10	were	be	VBD	_	_	_
11	incubated	incubate	VBN	_	_	_
12	overnight	overnight	RB	_	_	_
13	at	at	IN	_	_	_
14	65	65	CD	_	_	_
15	°C	°c	NN	_	_	_
16	to	to	TO	_	_	_
17	reverse	reverse	VB	_	_	_
18	the	the	DT	_	_	_
19	protein-DNA	protein-dna	JJ	_	_	_
20	formaldehyde	formaldehyde	NN	_	_	_
21	crosslinks	crosslink	NNS	_	_	_
22	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	's	's	POS	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	and	and	CC	_	_	_
11	eluted	elute	VBN	_	_	_
12	to	to	TO	_	_	_
13	a	a	DT	_	_	_
14	final	final	JJ	_	_	_
15	volume	volume	NN	_	_	_
16	of	of	IN	_	_	_
17	50	50	CD	_	_	_
18	μl	μl	NN	_	_	_
19	with	with	IN	_	_	_
20	EB	EB	NNP	_	_	_
21	.	.	.	_	_	_

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/ml	ng/ml	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	micrococcal	micrococcal	JJ	_	_	_
19	nuclease	nuclease	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	50	50	CD	_	_	_
22	units	unit	NNS	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	20	20	CD	_	_	_
26	µM	µm	NN	_	_	_
27	CaCl2	cacl2	NN	_	_	_
28	,1.2	,1.2	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	KCl	kcl	NN	_	_	_
31	,	,	,	_	_	_
32	0.3	0.3	CD	_	_	_
33	mM	mm	NN	KWSUPP	_	_
34	NaCl	nacl	NN	_	_	_
35	,	,	,	_	_	_
36	6	6	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	sucrose	sucrose	NN	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	10	10	CD	_	_	_
42	µM	µm	NN	_	_	_
43	DTT	dtt	NN	_	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	treatment	treatment	NN	_	_	_
3	,	,	,	_	_	_
4	a	a	DT	_	_	_
5	distribution	distribution	NN	_	_	_
6	of	of	IN	_	_	_
7	DNA	dna	NN	_	_	_
8	fragments	fragment	NNS	_	_	_
9	ranging	range	VBG	_	_	_
10	from	from	IN	_	_	_
11	200-600	200-600	CD	_	_	_
12	bp	bp	NN	_	_	_
13	was	be	VBD	_	_	_
14	detected	detect	VBN	_	_	_
15	by	by	IN	_	_	_
16	agarose-gel	agarose-gel	JJ	_	_	_
17	electrophoretic	electrophoretic	JJ	_	_	_
18	separation	separation	NN	_	_	_
19	of	of	IN	_	_	_
20	a	a	DT	_	_	_
21	small	small	JJ	_	_	_
22	sample	sample	NN	_	_	_
23	that	that	WDT	_	_	_
24	was	be	VBD	_	_	_
25	de-crosslinked	de-crosslinked	JJ	_	_	_
26	by	by	IN	_	_	_
27	incubation	incubation	NN	_	_	_
28	at	at	IN	_	_	_
29	65	65	CD	_	_	_
30	°C	°c	NN	_	_	_
31	for	for	IN	_	_	_
32	>	>	JJR	_	_	_
33	4	4	CD	_	_	_
34	hr	hr	NN	_	_	_
35	.	.	.	_	_	_

1	EDTA	edta	NN	_	_	_
2	was	be	VBD	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	mM	mm	NN	KWSUPP	_	_
7	to	to	TO	_	_	_
8	stop	stop	VB	_	_	_
9	the	the	DT	_	_	_
10	micrococcal	micrococcal	JJ	_	_	_
11	nuclease	nuclease	NN	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	were	be	VBD	_	_	_
16	spun	spin	VBN	_	_	_
17	down	down	RP	_	_	_
18	to	to	TO	_	_	_
19	remove	remove	VB	_	_	_
20	cell	cell	NN	_	_	_
21	debris	debris	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	50/50	50/50	CD	_	_	_
9	slurry	slurry	NN	_	_	_
10	of	of	IN	_	_	_
11	Sepharose	sepharose	NN	_	_	_
12	protein	protein	NN	_	_	_
13	A	a	NN	_	_	_
14	beads	bead	NNS	_	_	_
15	and	and	CC	_	_	_
16	protein	protein	NN	_	_	_
17	G	g	NN	_	_	_
18	beads	bead	NNS	_	_	_
19	in	in	IN	_	_	_
20	IP	IP	NNP	_	_	_
21	buffer	buffer	NN	_	_	_
22	for	for	IN	_	_	_
23	2-3	2-3	CD	_	_	_
24	hours	hour	NNS	_	_	_
25	at	at	IN	_	_	_
26	4	4	CD	_	_	_
27	°C	°c	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	and	and	CC	_	_	_
8	antibody	antibody	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	pre-cleared	pre-cleared	JJ	_	_	_
14	lysate	lysate	NN	_	_	_
15	for	for	IN	_	_	_
16	an	a	DT	_	_	_
17	overnight	overnight	JJ	_	_	_
18	incubation	incubation	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	next	next	JJ	_	_	_
3	day	day	NN	_	_	_
4	,	,	,	_	_	_
5	30	30	CD	_	_	_
6	µl	µl	NN	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	50/50	50/50	CD	_	_	_
10	slurry	slurry	NN	_	_	_
11	of	of	IN	_	_	_
12	Sepharose	sepharose	NN	_	_	_
13	protein	protein	NN	_	_	_
14	A	a	NN	_	_	_
15	and	and	CC	_	_	_
16	G	g	NN	_	_	_
17	beads	bead	NNS	_	_	_
18	in	in	IN	_	_	_
19	IP	IP	NNP	_	_	_
20	buffer	buffer	NN	_	_	_
21	was	be	VBD	_	_	_
22	added	add	VBN	_	_	_
23	to	to	TO	_	_	_
24	the	the	DT	_	_	_
25	lysate	lysate	NN	_	_	_
26	to	to	TO	_	_	_
27	capture	capture	VB	_	_	_
28	antibody-protein-DNA	antibody-protein-dna	JJ	_	_	_
29	complex	complex	NN	_	_	_
30	for	for	IN	_	_	_
31	one	one	CD	_	_	_
32	hour	hour	NN	_	_	_
33	at	at	IN	_	_	_
34	4	4	CD	_	_	_
35	°C	°c	NN	_	_	_
36	.	.	.	_	_	_

1	Beads	bead	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	250	250	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	LiCl	licl	NN	_	_	_
13	wash	wash	NN	_	_	_
14	buffer	buffer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	100	100	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	Tris	Tris	NNP	_	_	_
19	pH	ph	NN	_	_	_
20	8	8	CD	_	_	_
21	,	,	,	_	_	_
22	250	250	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	LiCl	licl	NN	_	_	_
25	,	,	,	_	_	_
26	2	2	CD	_	_	_
27	%	%	NN	_	_	_
28	TritonX-100	tritonx-100	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	twice	twice	RB	_	_	_
32	with	with	IN	_	_	_
33	600	600	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	wash	wash	NN	_	_	_
37	buffer	buffer	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	100	100	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	Tris	Tris	NNP	_	_	_
42	pH	ph	NN	_	_	_
43	8	8	CD	_	_	_
44	,	,	,	_	_	_
45	600	600	CD	_	_	_
46	mM	mm	NN	KWSUPP	_	_
47	NaCl	nacl	NN	_	_	_
48	,	,	,	_	_	_
49	2	2	CD	_	_	_
50	%	%	NN	_	_	_
51	SDS	sds	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	,	,	,	_	_	_
54	twice	twice	RB	_	_	_
55	with	with	IN	_	_	_
56	300	300	CD	_	_	_
57	mM	mm	NN	KWSUPP	_	_
58	NaCl	nacl	NN	_	_	_
59	wash	wash	NN	_	_	_
60	buffer	buffer	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	100	100	CD	_	_	_
63	mM	mm	NN	KWSUPP	_	_
64	Tris	Tris	NNP	_	_	_
65	pH	ph	NN	_	_	_
66	8	8	CD	_	_	_
67	,	,	,	_	_	_
68	300	300	CD	_	_	_
69	mM	mm	NN	KWSUPP	_	_
70	NaCl	nacl	NN	_	_	_
71	,	,	,	_	_	_
72	2	2	CD	_	_	_
73	%	%	NN	_	_	_
74	SDS	sds	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	,	,	,	_	_	_
77	and	and	CC	_	_	_
78	twice	twice	RB	_	_	_
79	with	with	IN	_	_	_
80	TE	te	NN	_	_	_
81	.	.	.	_	_	_

1	Elution	elution	NN	_	_	_
2	buffer	buffer	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	50	50	CD	_	_	_
5	mM	mm	NN	KWSUPP	_	_
6	Tris	Tris	NNP	_	_	_
7	pH	ph	NN	_	_	_
8	8	8	CD	_	_	_
9	,	,	,	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	EDTA	edta	NN	_	_	_
13	,	,	,	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	SDS	sds	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	after	after	IN	_	_	_
21	the	the	DT	_	_	_
22	final	final	JJ	_	_	_
23	wash	wash	NN	_	_	_
24	step	step	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	beads	bead	NNS	_	_	_
28	were	be	VBD	_	_	_
29	incubated	incubate	VBN	_	_	_
30	at	at	IN	_	_	_
31	65	65	CD	_	_	_
32	°C	°c	NN	_	_	_
33	for	for	IN	_	_	_
34	30	30	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	toremove	toremove	VBP	_	_	_
37	the	the	DT	_	_	_
38	crosslinked	crosslink	VBN	_	_	_
39	protein-DNA	protein-dna	JJ	_	_	_
40	complexes	complex	NNS	_	_	_
41	from	from	IN	_	_	_
42	the	the	DT	_	_	_
43	beads	bead	NNS	_	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	to	to	TO	_	_	_
4	remove	remove	VB	_	_	_
5	the	the	DT	_	_	_
6	beads	bead	NNS	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	samples	sample	NNS	_	_	_
10	were	be	VBD	_	_	_
11	incubated	incubate	VBN	_	_	_
12	overnight	overnight	RB	_	_	_
13	at	at	IN	_	_	_
14	65	65	CD	_	_	_
15	°C	°c	NN	_	_	_
16	to	to	TO	_	_	_
17	reverse	reverse	VB	_	_	_
18	the	the	DT	_	_	_
19	protein-DNA	protein-dna	JJ	_	_	_
20	formaldehyde	formaldehyde	NN	_	_	_
21	crosslinks	crosslink	NNS	_	_	_
22	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	's	's	POS	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	and	and	CC	_	_	_
11	eluted	elute	VBN	_	_	_
12	to	to	TO	_	_	_
13	a	a	DT	_	_	_
14	final	final	JJ	_	_	_
15	volume	volume	NN	_	_	_
16	of	of	IN	_	_	_
17	50ul	50ul	JJ	_	_	_
18	with	with	IN	_	_	_
19	EB	EB	NNP	_	_	_
20	.	.	.	_	_	_

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/ml	ng/ml	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	micrococcal	micrococcal	JJ	_	_	_
19	nuclease	nuclease	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	50	50	CD	_	_	_
22	units	unit	NNS	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	20	20	CD	_	_	_
26	μM	μm	NN	_	_	_
27	CaCl2	cacl2	NN	_	_	_
28	,1.2	,1.2	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	KCl	kcl	NN	_	_	_
31	,	,	,	_	_	_
32	0.3	0.3	CD	_	_	_
33	mM	mm	NN	KWSUPP	_	_
34	NaCl	nacl	NN	_	_	_
35	,	,	,	_	_	_
36	6	6	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	sucrose	sucrose	NN	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	10	10	CD	_	_	_
42	μM	μm	NN	_	_	_
43	DTT	dtt	NN	_	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	treatment	treatment	NN	_	_	_
3	,	,	,	_	_	_
4	a	a	DT	_	_	_
5	distribution	distribution	NN	_	_	_
6	of	of	IN	_	_	_
7	DNA	dna	NN	_	_	_
8	fragments	fragment	NNS	_	_	_
9	ranging	range	VBG	_	_	_
10	from	from	IN	_	_	_
11	200-600	200-600	CD	_	_	_
12	bp	bp	NN	_	_	_
13	was	be	VBD	_	_	_
14	detected	detect	VBN	_	_	_
15	by	by	IN	_	_	_
16	agarose-gel	agarose-gel	JJ	_	_	_
17	electrophoretic	electrophoretic	JJ	_	_	_
18	separation	separation	NN	_	_	_
19	of	of	IN	_	_	_
20	a	a	DT	_	_	_
21	small	small	JJ	_	_	_
22	sample	sample	NN	_	_	_
23	that	that	WDT	_	_	_
24	was	be	VBD	_	_	_
25	de-crosslinked	de-crosslinked	JJ	_	_	_
26	by	by	IN	_	_	_
27	incubation	incubation	NN	_	_	_
28	at	at	IN	_	_	_
29	65	65	CD	_	_	_
30	°C	°c	NN	_	_	_
31	for	for	IN	_	_	_
32	>	>	JJR	_	_	_
33	4	4	CD	_	_	_
34	hr	hr	NN	_	_	_
35	.	.	.	_	_	_

1	EDTA	edta	NN	_	_	_
2	was	be	VBD	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	mM	mm	NN	KWSUPP	_	_
7	to	to	TO	_	_	_
8	stop	stop	VB	_	_	_
9	the	the	DT	_	_	_
10	micrococcal	micrococcal	JJ	_	_	_
11	nuclease	nuclease	NN	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	were	be	VBD	_	_	_
16	spun	spin	VBN	_	_	_
17	down	down	RP	_	_	_
18	to	to	TO	_	_	_
19	remove	remove	VB	_	_	_
20	cell	cell	NN	_	_	_
21	debris	debris	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	50/50	50/50	CD	_	_	_
9	slurry	slurry	NN	_	_	_
10	of	of	IN	_	_	_
11	Sepharose	sepharose	NN	_	_	_
12	protein	protein	NN	_	_	_
13	A	a	NN	_	_	_
14	beads	bead	NNS	_	_	_
15	and	and	CC	_	_	_
16	protein	protein	NN	_	_	_
17	G	g	NN	_	_	_
18	beads	bead	NNS	_	_	_
19	in	in	IN	_	_	_
20	IP	IP	NNP	_	_	_
21	buffer	buffer	NN	_	_	_
22	for	for	IN	_	_	_
23	2-3	2-3	CD	_	_	_
24	hours	hour	NNS	_	_	_
25	at	at	IN	_	_	_
26	4	4	CD	_	_	_
27	°C	°c	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	and	and	CC	_	_	_
8	antibody	antibody	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	pre-cleared	pre-cleared	JJ	_	_	_
14	lysate	lysate	NN	_	_	_
15	for	for	IN	_	_	_
16	an	a	DT	_	_	_
17	overnight	overnight	JJ	_	_	_
18	incubation	incubation	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	next	next	JJ	_	_	_
3	day	day	NN	_	_	_
4	,	,	,	_	_	_
5	30	30	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	50/50	50/50	CD	_	_	_
10	slurry	slurry	NN	_	_	_
11	of	of	IN	_	_	_
12	Sepharose	sepharose	NN	_	_	_
13	protein	protein	NN	_	_	_
14	A	a	NN	_	_	_
15	and	and	CC	_	_	_
16	G	g	NN	_	_	_
17	beads	bead	NNS	_	_	_
18	in	in	IN	_	_	_
19	IP	IP	NNP	_	_	_
20	buffer	buffer	NN	_	_	_
21	was	be	VBD	_	_	_
22	added	add	VBN	_	_	_
23	to	to	TO	_	_	_
24	the	the	DT	_	_	_
25	lysate	lysate	NN	_	_	_
26	to	to	TO	_	_	_
27	capture	capture	VB	_	_	_
28	antibody-protein-DNA	antibody-protein-dna	JJ	_	_	_
29	complex	complex	NN	_	_	_
30	for	for	IN	_	_	_
31	one	one	CD	_	_	_
32	hour	hour	NN	_	_	_
33	at	at	IN	_	_	_
34	4	4	CD	_	_	_
35	°C	°c	NN	_	_	_
36	.	.	.	_	_	_

1	Beads	bead	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	250	250	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	LiCl	licl	NN	_	_	_
13	wash	wash	NN	_	_	_
14	buffer	buffer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	100	100	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	Tris	Tris	NNP	_	_	_
19	pH	ph	NN	_	_	_
20	8	8	CD	_	_	_
21	,	,	,	_	_	_
22	250	250	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	LiCl	licl	NN	_	_	_
25	,	,	,	_	_	_
26	2	2	CD	_	_	_
27	%	%	NN	_	_	_
28	TritonX-100	tritonx-100	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	twice	twice	RB	_	_	_
32	with	with	IN	_	_	_
33	600	600	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	wash	wash	NN	_	_	_
37	buffer	buffer	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	100	100	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	Tris	Tris	NNP	_	_	_
42	pH	ph	NN	_	_	_
43	8	8	CD	_	_	_
44	,	,	,	_	_	_
45	600	600	CD	_	_	_
46	mM	mm	NN	KWSUPP	_	_
47	NaCl	nacl	NN	_	_	_
48	,	,	,	_	_	_
49	2	2	CD	_	_	_
50	%	%	NN	_	_	_
51	SDS	sds	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	,	,	,	_	_	_
54	twice	twice	RB	_	_	_
55	with	with	IN	_	_	_
56	300	300	CD	_	_	_
57	mM	mm	NN	KWSUPP	_	_
58	NaCl	nacl	NN	_	_	_
59	wash	wash	NN	_	_	_
60	buffer	buffer	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	100	100	CD	_	_	_
63	mM	mm	NN	KWSUPP	_	_
64	Tris	Tris	NNP	_	_	_
65	pH	ph	NN	_	_	_
66	8	8	CD	_	_	_
67	,	,	,	_	_	_
68	300	300	CD	_	_	_
69	mM	mm	NN	KWSUPP	_	_
70	NaCl	nacl	NN	_	_	_
71	,	,	,	_	_	_
72	2	2	CD	_	_	_
73	%	%	NN	_	_	_
74	SDS	sds	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	,	,	,	_	_	_
77	and	and	CC	_	_	_
78	twice	twice	RB	_	_	_
79	with	with	IN	_	_	_
80	TE	te	NN	_	_	_
81	.	.	.	_	_	_

1	Elution	elution	NN	_	_	_
2	buffer	buffer	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	50	50	CD	_	_	_
5	mM	mm	NN	KWSUPP	_	_
6	Tris	Tris	NNP	_	_	_
7	pH	ph	NN	_	_	_
8	8	8	CD	_	_	_
9	,	,	,	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	EDTA	edta	NN	_	_	_
13	,	,	,	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	SDS	sds	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	after	after	IN	_	_	_
21	the	the	DT	_	_	_
22	final	final	JJ	_	_	_
23	wash	wash	NN	_	_	_
24	step	step	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	beads	bead	NNS	_	_	_
28	were	be	VBD	_	_	_
29	incubated	incubate	VBN	_	_	_
30	at	at	IN	_	_	_
31	65	65	CD	_	_	_
32	°C	°c	NN	_	_	_
33	for	for	IN	_	_	_
34	30	30	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	toremove	toremove	VBP	_	_	_
37	the	the	DT	_	_	_
38	crosslinked	crosslink	VBN	_	_	_
39	protein-DNA	protein-dna	JJ	_	_	_
40	complexes	complex	NNS	_	_	_
41	from	from	IN	_	_	_
42	the	the	DT	_	_	_
43	beads	bead	NNS	_	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	to	to	TO	_	_	_
4	remove	remove	VB	_	_	_
5	the	the	DT	_	_	_
6	beads	bead	NNS	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	samples	sample	NNS	_	_	_
10	were	be	VBD	_	_	_
11	incubated	incubate	VBN	_	_	_
12	overnight	overnight	RB	_	_	_
13	at	at	IN	_	_	_
14	65	65	CD	_	_	_
15	°C	°c	NN	_	_	_
16	to	to	TO	_	_	_
17	reverse	reverse	VB	_	_	_
18	the	the	DT	_	_	_
19	protein-DNA	protein-dna	JJ	_	_	_
20	formaldehyde	formaldehyde	NN	_	_	_
21	crosslinks	crosslink	NNS	_	_	_
22	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	's	's	POS	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	and	and	CC	_	_	_
11	eluted	elute	VBN	_	_	_
12	to	to	TO	_	_	_
13	a	a	DT	_	_	_
14	final	final	JJ	_	_	_
15	volume	volume	NN	_	_	_
16	of	of	IN	_	_	_
17	50ul	50ul	JJ	_	_	_
18	with	with	IN	_	_	_
19	EB	EB	NNP	_	_	_
20	.	.	.	_	_	_

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/ml	ng/ml	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	micrococcal	micrococcal	JJ	_	_	_
19	nuclease	nuclease	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	50	50	CD	_	_	_
22	units	unit	NNS	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	20	20	CD	_	_	_
26	μM	μm	NN	_	_	_
27	CaCl2	cacl2	NN	_	_	_
28	,1.2	,1.2	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	KCl	kcl	NN	_	_	_
31	,	,	,	_	_	_
32	0.3	0.3	CD	_	_	_
33	mM	mm	NN	KWSUPP	_	_
34	NaCl	nacl	NN	_	_	_
35	,	,	,	_	_	_
36	6	6	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	sucrose	sucrose	NN	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	10	10	CD	_	_	_
42	μM	μm	NN	_	_	_
43	DTT	dtt	NN	_	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	treatment	treatment	NN	_	_	_
3	,	,	,	_	_	_
4	a	a	DT	_	_	_
5	distribution	distribution	NN	_	_	_
6	of	of	IN	_	_	_
7	DNA	dna	NN	_	_	_
8	fragments	fragment	NNS	_	_	_
9	ranging	range	VBG	_	_	_
10	from	from	IN	_	_	_
11	200-600	200-600	CD	_	_	_
12	bp	bp	NN	_	_	_
13	was	be	VBD	_	_	_
14	detected	detect	VBN	_	_	_
15	by	by	IN	_	_	_
16	agarose-gel	agarose-gel	JJ	_	_	_
17	electrophoretic	electrophoretic	JJ	_	_	_
18	separation	separation	NN	_	_	_
19	of	of	IN	_	_	_
20	a	a	DT	_	_	_
21	small	small	JJ	_	_	_
22	sample	sample	NN	_	_	_
23	that	that	WDT	_	_	_
24	was	be	VBD	_	_	_
25	de-crosslinked	de-crosslinked	JJ	_	_	_
26	by	by	IN	_	_	_
27	incubation	incubation	NN	_	_	_
28	at	at	IN	_	_	_
29	65	65	CD	_	_	_
30	°C	°c	NN	_	_	_
31	for	for	IN	_	_	_
32	>	>	JJR	_	_	_
33	4	4	CD	_	_	_
34	hr	hr	NN	_	_	_
35	.	.	.	_	_	_

1	EDTA	edta	NN	_	_	_
2	was	be	VBD	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	mM	mm	NN	KWSUPP	_	_
7	to	to	TO	_	_	_
8	stop	stop	VB	_	_	_
9	the	the	DT	_	_	_
10	micrococcal	micrococcal	JJ	_	_	_
11	nuclease	nuclease	NN	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	were	be	VBD	_	_	_
16	spun	spin	VBN	_	_	_
17	down	down	RP	_	_	_
18	to	to	TO	_	_	_
19	remove	remove	VB	_	_	_
20	cell	cell	NN	_	_	_
21	debris	debris	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	50/50	50/50	CD	_	_	_
9	slurry	slurry	NN	_	_	_
10	of	of	IN	_	_	_
11	Sepharose	sepharose	NN	_	_	_
12	protein	protein	NN	_	_	_
13	A	a	NN	_	_	_
14	beads	bead	NNS	_	_	_
15	and	and	CC	_	_	_
16	protein	protein	NN	_	_	_
17	G	g	NN	_	_	_
18	beads	bead	NNS	_	_	_
19	in	in	IN	_	_	_
20	IP	IP	NNP	_	_	_
21	buffer	buffer	NN	_	_	_
22	for	for	IN	_	_	_
23	2-3	2-3	CD	_	_	_
24	hours	hour	NNS	_	_	_
25	at	at	IN	_	_	_
26	4	4	CD	_	_	_
27	°C	°c	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	and	and	CC	_	_	_
8	no	no	DT	_	_	_
9	antibody	antibody	NN	_	_	_
10	was	be	VBD	_	_	_
11	added	add	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	pre-cleared	pre-cleared	JJ	_	_	_
15	lysate	lysate	NN	_	_	_
16	for	for	IN	_	_	_
17	an	a	DT	_	_	_
18	overnight	overnight	JJ	_	_	_
19	incubation	incubation	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	next	next	JJ	_	_	_
3	day	day	NN	_	_	_
4	,	,	,	_	_	_
5	30	30	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	50/50	50/50	CD	_	_	_
10	slurry	slurry	NN	_	_	_
11	of	of	IN	_	_	_
12	Sepharose	sepharose	NN	_	_	_
13	protein	protein	NN	_	_	_
14	A	a	NN	_	_	_
15	and	and	CC	_	_	_
16	G	g	NN	_	_	_
17	beads	bead	NNS	_	_	_
18	in	in	IN	_	_	_
19	IP	IP	NNP	_	_	_
20	buffer	buffer	NN	_	_	_
21	was	be	VBD	_	_	_
22	added	add	VBN	_	_	_
23	to	to	TO	_	_	_
24	the	the	DT	_	_	_
25	lysate	lysate	NN	_	_	_
26	to	to	TO	_	_	_
27	capture	capture	VB	_	_	_
28	antibody-protein-DNA	antibody-protein-dna	JJ	_	_	_
29	complex	complex	NN	_	_	_
30	for	for	IN	_	_	_
31	one	one	CD	_	_	_
32	hour	hour	NN	_	_	_
33	at	at	IN	_	_	_
34	4	4	CD	_	_	_
35	°C	°c	NN	_	_	_
36	.	.	.	_	_	_

1	Beads	bead	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	250	250	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	LiCl	licl	NN	_	_	_
13	wash	wash	NN	_	_	_
14	buffer	buffer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	100	100	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	Tris	Tris	NNP	_	_	_
19	pH	ph	NN	_	_	_
20	8	8	CD	_	_	_
21	,	,	,	_	_	_
22	250	250	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	LiCl	licl	NN	_	_	_
25	,	,	,	_	_	_
26	2	2	CD	_	_	_
27	%	%	NN	_	_	_
28	TritonX-100	tritonx-100	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	twice	twice	RB	_	_	_
32	with	with	IN	_	_	_
33	600	600	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	wash	wash	NN	_	_	_
37	buffer	buffer	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	100	100	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	Tris	Tris	NNP	_	_	_
42	pH	ph	NN	_	_	_
43	8	8	CD	_	_	_
44	,	,	,	_	_	_
45	600	600	CD	_	_	_
46	mM	mm	NN	KWSUPP	_	_
47	NaCl	nacl	NN	_	_	_
48	,	,	,	_	_	_
49	2	2	CD	_	_	_
50	%	%	NN	_	_	_
51	SDS	sds	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	,	,	,	_	_	_
54	twice	twice	RB	_	_	_
55	with	with	IN	_	_	_
56	300	300	CD	_	_	_
57	mM	mm	NN	KWSUPP	_	_
58	NaCl	nacl	NN	_	_	_
59	wash	wash	NN	_	_	_
60	buffer	buffer	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	100	100	CD	_	_	_
63	mM	mm	NN	KWSUPP	_	_
64	Tris	Tris	NNP	_	_	_
65	pH	ph	NN	_	_	_
66	8	8	CD	_	_	_
67	,	,	,	_	_	_
68	300	300	CD	_	_	_
69	mM	mm	NN	KWSUPP	_	_
70	NaCl	nacl	NN	_	_	_
71	,	,	,	_	_	_
72	2	2	CD	_	_	_
73	%	%	NN	_	_	_
74	SDS	sds	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	,	,	,	_	_	_
77	and	and	CC	_	_	_
78	twice	twice	RB	_	_	_
79	with	with	IN	_	_	_
80	TE	te	NN	_	_	_
81	.	.	.	_	_	_

1	Elution	elution	NN	_	_	_
2	buffer	buffer	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	50	50	CD	_	_	_
5	mM	mm	NN	KWSUPP	_	_
6	Tris	Tris	NNP	_	_	_
7	pH	ph	NN	_	_	_
8	8	8	CD	_	_	_
9	,	,	,	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	EDTA	edta	NN	_	_	_
13	,	,	,	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	SDS	sds	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	after	after	IN	_	_	_
21	the	the	DT	_	_	_
22	final	final	JJ	_	_	_
23	wash	wash	NN	_	_	_
24	step	step	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	beads	bead	NNS	_	_	_
28	were	be	VBD	_	_	_
29	incubated	incubate	VBN	_	_	_
30	at	at	IN	_	_	_
31	65	65	CD	_	_	_
32	°C	°c	NN	_	_	_
33	for	for	IN	_	_	_
34	30	30	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	toremove	toremove	VBP	_	_	_
37	the	the	DT	_	_	_
38	crosslinked	crosslink	VBN	_	_	_
39	protein-DNA	protein-dna	JJ	_	_	_
40	complexes	complex	NNS	_	_	_
41	from	from	IN	_	_	_
42	the	the	DT	_	_	_
43	beads	bead	NNS	_	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	to	to	TO	_	_	_
4	remove	remove	VB	_	_	_
5	the	the	DT	_	_	_
6	beads	bead	NNS	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	samples	sample	NNS	_	_	_
10	were	be	VBD	_	_	_
11	incubated	incubate	VBN	_	_	_
12	overnight	overnight	RB	_	_	_
13	at	at	IN	_	_	_
14	65	65	CD	_	_	_
15	°C	°c	NN	_	_	_
16	to	to	TO	_	_	_
17	reverse	reverse	VB	_	_	_
18	the	the	DT	_	_	_
19	protein-DNA	protein-dna	JJ	_	_	_
20	formaldehyde	formaldehyde	NN	_	_	_
21	crosslinks	crosslink	NNS	_	_	_
22	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	's	's	POS	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	and	and	CC	_	_	_
11	eluted	elute	VBN	_	_	_
12	to	to	TO	_	_	_
13	a	a	DT	_	_	_
14	final	final	JJ	_	_	_
15	volume	volume	NN	_	_	_
16	of	of	IN	_	_	_
17	50ul	50ul	JJ	_	_	_
18	with	with	IN	_	_	_
19	EB	EB	NNP	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	pellets	pellet	NNS	_	_	_
4	were	be	VBD	_	_	_
5	lysed	lyse	VBN	_	_	_
6	and	and	CC	_	_	_
7	RNA	rna	NN	_	_	_
8	collected	collect	VBN	_	_	_
9	using	use	VBG	_	_	_
10	Qiagen	Qiagen	NNP	_	_	_
11	's	's	POS	_	_	_
12	RNeasy	RNeasy	NNP	_	_	_
13	Plus	Plus	NNP	_	_	_
14	Mini	Mini	NNP	_	_	_
15	Kit	kit	NN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	Bacteria	bacterium	NNS	_	_	_
19	Protect	protect	VB	_	_	_
20	RNA	rna	NN	_	_	_
21	kit	kit	NN	_	_	_
22	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	pellets	pellet	NNS	_	_	_
4	were	be	VBD	_	_	_
5	lysed	lyse	VBN	_	_	_
6	in	in	IN	_	_	_
7	Tissue	tissue	NN	_	_	_
8	and	and	CC	_	_	_
9	Cell	cell	NN	_	_	_
10	lysis	lysis	NN	_	_	_
11	solution	solution	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	EpiCentre	EpiCentre	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	proteinase	proteinase	NN	_	_	_
17	K.	K.	NNP	_	_	_
18	RNA	rna	NN	_	_	_
19	was	be	VBD	_	_	_
20	isolated	isolate	VBN	_	_	_
21	and	and	CC	_	_	_
22	DNase	dnase	NN	_	_	_
23	treated	treat	VBN	_	_	_
24	using	use	VBG	_	_	_
25	the	the	DT	_	_	_
26	RNeasy	RNeasy	NNP	_	_	_
27	Kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Qiagen	qiagen	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	using	use	VBG	_	_	_
32	the	the	DT	_	_	_
33	manufacturer	manufacturer	NN	_	_	_
34	's	's	POS	_	_	_
35	protocol	protocol	NN	_	_	_
36	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
4	Cells	cell	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	10	10	CD	_	_	_
7	ml	ml	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	for	for	IN	_	_	_
10	transcriptomic	transcriptomic	JJ	_	_	_
11	analysis	analysis	NN	_	_	_
12	were	be	VBD	_	_	_
13	collected	collect	VBN	_	_	_
14	into	into	IN	_	_	_
15	tubes	tube	NNS	_	_	_
16	containing	contain	VBG	_	_	_
17	1.25	1.25	CD	_	_	_
18	ml	ml	NN	_	_	_
19	ice-cold	ice-cold	JJ	_	_	_
20	5	5	CD	_	_	_
21	%	%	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	vol/vol	vol/vol	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	unbuffered	unbuffered	JJ	_	_	_
26	phenol	phenol	NN	_	_	_
27	in	in	IN	_	_	_
28	ethanol	ethanol	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	EP	ep	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	and	and	CC	_	_	_
33	pelleted	pellete	VBN	_	_	_
34	by	by	IN	_	_	_
35	centrifugation	centrifugation	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	10,000	10,000	CD	_	_	_
38	g	g	NN	_	_	_
39	,	,	,	_	_	_
40	4	4	CD	_	_	_
41	°C	°c	NN	_	_	_
42	,	,	,	_	_	_
43	3	3	CD	_	_	_
44	min	min	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	remove	remove	VB	_	_	_
3	residual	residual	JJ	_	_	_
4	traces	trace	NNS	_	_	_
5	of	of	IN	_	_	_
6	hydrolysate	hydrolysate	NN	_	_	_
7	,	,	,	_	_	_
8	cell	cell	NN	_	_	_
9	pellets	pellet	NNS	_	_	_
10	were	be	VBD	_	_	_
11	twice	twice	RB	_	_	_
12	resuspended	resuspend	VBN	_	_	_
13	in	in	IN	_	_	_
14	ice-cold	ice-cold	JJ	_	_	_
15	GMM	gmm	NN	_	_	_
16	plus	plus	CC	_	_	_
17	0.125	0.125	CD	_	_	_
18	volume	volume	NN	_	_	_
19	of	of	IN	_	_	_
20	EP	ep	NN	_	_	_
21	,	,	,	_	_	_
22	repelleted	repellete	VBN	_	_	_
23	,	,	,	_	_	_
24	then	then	RB	_	_	_
25	flash	flash	VBP	_	_	_
26	frozen	freeze	VBN	_	_	_
27	in	in	IN	_	_	_
28	dry	dry	JJ	_	_	_
29	ice-ethanol	ice-ethanol	NN	_	_	_
30	,	,	,	_	_	_
31	and	and	CC	_	_	_
32	stored	store	VBD	_	_	_
33	at	at	IN	_	_	_
34	-80	-80	CD	_	_	_
35	°C	°c	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	12	12	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	treatment	treatment	NN	_	_	_
7	by	by	IN	_	_	_
8	norfloxacin	norfloxacin	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	cells	cell	NNS	_	_	_
11	24	24	CD	_	_	_
12	min	min	NN	_	_	_
13	after	after	IN	_	_	_
14	treatment	treatment	NN	_	_	_
15	by	by	IN	_	_	_
16	norfloxacin	norfloxacin	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	cells	cell	NNS	_	_	_
19	36	36	CD	_	_	_
20	min	min	NN	_	_	_
21	after	after	IN	_	_	_
22	treatment	treatment	NN	_	_	_
23	by	by	IN	_	_	_
24	norfloxacin	norfloxacin	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	cells	cell	NNS	_	_	_
27	48	48	CD	_	_	_
28	min	min	NN	_	_	_
29	after	after	IN	_	_	_
30	treatment	treatment	NN	_	_	_
31	by	by	IN	_	_	_
32	norfloxacin	norfloxacin	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	cells	cell	NNS	_	_	_
35	60	60	CD	_	_	_
36	min	min	NN	_	_	_
37	after	after	IN	_	_	_
38	treatment	treatment	NN	_	_	_
39	by	by	IN	_	_	_
40	norfloxacin	norfloxacin	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Cells	cell	NNS	_	_	_
43	aerobically	aerobically	RB	_	_	_
44	grown	grow	VBN	_	_	_
45	to	to	TO	_	_	_
46	mid-log	mid-log	JJ	_	_	_
47	phase	phase	NN	_	_	_
48	in	in	IN	_	_	_
49	MOPS/0	mops/0	NN	_	_	_
50	.5	.5	CD	_	_	_
51	%	%	NN	_	_	_
52	glucose	glucose	NN	SUPP	_	_
53	at	at	IN	_	_	_
54	37C	37c	NN	_	_	_
55	and	and	CC	_	_	_
56	~	~	NN	_	_	_
57	250	250	CD	_	_	_
58	RPM	rpm	NNS	_	_	_
59	.	.	.	_	_	_

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/mL	ug/ml	NN	_	_	_
31	RNaseA	rnasea	NN	_	_	_
32	,	,	,	_	_	_
33	protease	protease	NN	_	_	_
34	inhibitor	inhibitor	NN	_	_	_
35	cocktail	cocktail	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Sigma	Sigma	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	and	and	CC	_	_	_
40	1	1	CD	_	_	_
41	kU	ku	NN	_	_	_
42	Ready-LyseTM	ready-lysetm	NN	_	_	_
43	lysozyme	lysozyme	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Epicentre	Epicentre	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	room	room	NN	_	_	_
7	temperature	temperature	NN	_	_	_
8	for	for	IN	_	_	_
9	30	30	CD	_	_	_
10	min	min	NN	_	_	_
11	and	and	CC	_	_	_
12	then	then	RB	_	_	_
13	treated	treat	VBN	_	_	_
14	with	with	IN	_	_	_
15	0.5	0.5	CD	_	_	_
16	mL	ml	NN	_	_	_
17	of	of	IN	_	_	_
18	2XIP	2xip	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	with	with	IN	_	_	_
21	the	the	DT	_	_	_
22	protease	protease	NN	_	_	_
23	inhibitor	inhibitor	NN	_	_	_
24	cocktail	cocktail	NN	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	sonicated	sonicate	VBN	_	_	_
6	four	four	CD	_	_	_
7	times	time	NNS	_	_	_
8	for	for	IN	_	_	_
9	20	20	CD	_	_	_
10	sec	sec	NN	_	_	_
11	each	each	DT	_	_	_
12	in	in	IN	_	_	_
13	an	a	DT	_	_	_
14	ice	ice	NN	_	_	_
15	bath	bath	NN	_	_	_
16	to	to	TO	_	_	_
17	fragment	fragment	NN	_	_	_
18	the	the	DT	_	_	_
19	chromatin	chromatin	NN	_	_	_
20	complexes	complex	NNS	_	_	_
21	using	use	VBG	_	_	_
22	Misonix	Misonix	NNP	_	_	_
23	sonicator	sonicator	NN	_	_	_
24	3000	3000	CD	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	output	output	NN	_	_	_
27	level	level	NN	_	_	_
28	=	=	JJ	_	_	_
29	2.5	2.5	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	range	range	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	DNA	dna	NN	_	_	_
6	size	size	NN	_	_	_
7	resulting	result	VBG	_	_	_
8	from	from	IN	_	_	_
9	the	the	DT	_	_	_
10	sonication	sonication	NN	_	_	_
11	procedure	procedure	NN	_	_	_
12	was	be	VBD	_	_	_
13	300	300	CD	_	_	_
14	--	--	:	_	_	_
15	1000	1000	CD	_	_	_
16	bp	bp	NN	_	_	_
17	.	.	.	_	_	_

1	6	6	CD	_	_	_
2	uL	ul	NN	_	_	_
3	of	of	IN	_	_	_
4	mouse	mouse	NN	_	_	_
5	antibody	antibody	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	NT63	nt63	NN	_	_	_
8	,	,	,	_	_	_
9	Neoclone	neoclone	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	used	use	VBN	_	_	_
13	to	to	TO	_	_	_
14	immunoprecipitate	immunoprecipitate	NN	_	_	_
15	the	the	DT	_	_	_
16	chromatin	chromatin	NN	_	_	_
17	complex	complex	NN	_	_	_
18	of	of	IN	_	_	_
19	RNA	rna	NN	_	_	_
20	polymerase	polymerase	NN	_	_	_
21	subunit	subunit	NN	_	_	_
22	and	and	CC	_	_	_
23	DNA	dna	NN	_	_	_
24	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	control	control	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	mock-IP	mock-ip	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	,	,	,	_	_	_
8	2	2	CD	_	_	_
9	ug	ug	NN	_	_	_
10	of	of	IN	_	_	_
11	normal	normal	JJ	_	_	_
12	mouse	mouse	NN	_	_	_
13	IgG	igg	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Upstate	upstate	JJ	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	was	be	VBD	_	_	_
18	added	add	VBN	_	_	_
19	into	into	IN	_	_	_
20	the	the	DT	_	_	_
21	cell	cell	NN	_	_	_
22	extract	extract	NN	_	_	_
23	.	.	.	_	_	_

1	IP	IP	NNP	_	_	_
2	DNAs	dna	NNS	_	_	_
3	were	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	with	with	IN	_	_	_
6	QIAquick	qiaquick	NN	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	Kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	then	then	RB	_	_	_
14	amplified	amplify	VBD	_	_	_
15	PCR	pcr	NN	_	_	_
16	.	.	.	_	_	_

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/mL	ug/ml	NN	_	_	_
31	RNaseA	rnasea	NN	_	_	_
32	,	,	,	_	_	_
33	protease	protease	NN	_	_	_
34	inhibitor	inhibitor	NN	_	_	_
35	cocktail	cocktail	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Sigma	Sigma	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	and	and	CC	_	_	_
40	1	1	CD	_	_	_
41	kU	ku	NN	_	_	_
42	Ready-LyseTM	ready-lysetm	NN	_	_	_
43	lysozyme	lysozyme	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Epicentre	Epicentre	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	room	room	NN	_	_	_
7	temperature	temperature	NN	_	_	_
8	for	for	IN	_	_	_
9	30	30	CD	_	_	_
10	min	min	NN	_	_	_
11	and	and	CC	_	_	_
12	then	then	RB	_	_	_
13	treated	treat	VBN	_	_	_
14	with	with	IN	_	_	_
15	0.5	0.5	CD	_	_	_
16	mL	ml	NN	_	_	_
17	of	of	IN	_	_	_
18	2XIP	2xip	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	with	with	IN	_	_	_
21	the	the	DT	_	_	_
22	protease	protease	NN	_	_	_
23	inhibitor	inhibitor	NN	_	_	_
24	cocktail	cocktail	NN	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	sonicated	sonicate	VBN	_	_	_
6	four	four	CD	_	_	_
7	times	time	NNS	_	_	_
8	for	for	IN	_	_	_
9	20	20	CD	_	_	_
10	sec	sec	NN	_	_	_
11	each	each	DT	_	_	_
12	in	in	IN	_	_	_
13	an	a	DT	_	_	_
14	ice	ice	NN	_	_	_
15	bath	bath	NN	_	_	_
16	to	to	TO	_	_	_
17	fragment	fragment	NN	_	_	_
18	the	the	DT	_	_	_
19	chromatin	chromatin	NN	_	_	_
20	complexes	complex	NNS	_	_	_
21	using	use	VBG	_	_	_
22	Misonix	Misonix	NNP	_	_	_
23	sonicator	sonicator	NN	_	_	_
24	3000	3000	CD	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	output	output	NN	_	_	_
27	level	level	NN	_	_	_
28	=	=	JJ	_	_	_
29	2.5	2.5	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	range	range	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	DNA	dna	NN	_	_	_
6	size	size	NN	_	_	_
7	resulting	result	VBG	_	_	_
8	from	from	IN	_	_	_
9	the	the	DT	_	_	_
10	sonication	sonication	NN	_	_	_
11	procedure	procedure	NN	_	_	_
12	was	be	VBD	_	_	_
13	300	300	CD	_	_	_
14	--	--	:	_	_	_
15	1000	1000	CD	_	_	_
16	bp	bp	NN	_	_	_
17	.	.	.	_	_	_

1	6	6	CD	_	_	_
2	uL	ul	NN	_	_	_
3	of	of	IN	_	_	_
4	mouse	mouse	NN	_	_	_
5	antibody	antibody	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	NT63	nt63	NN	_	_	_
8	,	,	,	_	_	_
9	Neoclone	neoclone	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	used	use	VBN	_	_	_
13	to	to	TO	_	_	_
14	immunoprecipitate	immunoprecipitate	NN	_	_	_
15	the	the	DT	_	_	_
16	chromatin	chromatin	NN	_	_	_
17	complex	complex	NN	_	_	_
18	of	of	IN	_	_	_
19	RNA	rna	NN	_	_	_
20	polymerase	polymerase	NN	_	_	_
21	subunit	subunit	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	rpoB	rpob	NN	GEN	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	DNA	dna	NN	_	_	_
27	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	control	control	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	mock-IP	mock-ip	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	,	,	,	_	_	_
8	2	2	CD	_	_	_
9	ug	ug	NN	_	_	_
10	of	of	IN	_	_	_
11	normal	normal	JJ	_	_	_
12	mouse	mouse	NN	_	_	_
13	IgG	igg	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Upstate	upstate	JJ	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	was	be	VBD	_	_	_
18	added	add	VBN	_	_	_
19	into	into	IN	_	_	_
20	the	the	DT	_	_	_
21	cell	cell	NN	_	_	_
22	extract	extract	NN	_	_	_
23	.	.	.	_	_	_

1	IP	IP	NNP	_	_	_
2	DNAs	dna	NNS	_	_	_
3	were	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	with	with	IN	_	_	_
6	QIAquick	qiaquick	NN	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	Kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	then	then	RB	_	_	_
14	amplified	amplify	VBD	_	_	_
15	PCR	pcr	NN	_	_	_
16	.	.	.	_	_	_

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/mL	ug/ml	NN	_	_	_
31	RNaseA	rnasea	NN	_	_	_
32	,	,	,	_	_	_
33	protease	protease	NN	_	_	_
34	inhibitor	inhibitor	NN	_	_	_
35	cocktail	cocktail	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Sigma	Sigma	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	and	and	CC	_	_	_
40	1	1	CD	_	_	_
41	kU	ku	NN	_	_	_
42	Ready-LyseTM	ready-lysetm	NN	_	_	_
43	lysozyme	lysozyme	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Epicentre	Epicentre	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	room	room	NN	_	_	_
7	temperature	temperature	NN	_	_	_
8	for	for	IN	_	_	_
9	30	30	CD	_	_	_
10	min	min	NN	_	_	_
11	and	and	CC	_	_	_
12	then	then	RB	_	_	_
13	treated	treat	VBN	_	_	_
14	with	with	IN	_	_	_
15	0.5	0.5	CD	_	_	_
16	mL	ml	NN	_	_	_
17	of	of	IN	_	_	_
18	2XIP	2xip	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	with	with	IN	_	_	_
21	the	the	DT	_	_	_
22	protease	protease	NN	_	_	_
23	inhibitor	inhibitor	NN	_	_	_
24	cocktail	cocktail	NN	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	sonicated	sonicate	VBN	_	_	_
6	four	four	CD	_	_	_
7	times	time	NNS	_	_	_
8	for	for	IN	_	_	_
9	20	20	CD	_	_	_
10	sec	sec	NN	_	_	_
11	each	each	DT	_	_	_
12	in	in	IN	_	_	_
13	an	a	DT	_	_	_
14	ice	ice	NN	_	_	_
15	bath	bath	NN	_	_	_
16	to	to	TO	_	_	_
17	fragment	fragment	NN	_	_	_
18	the	the	DT	_	_	_
19	chromatin	chromatin	NN	_	_	_
20	complexes	complex	NNS	_	_	_
21	using	use	VBG	_	_	_
22	Misonix	Misonix	NNP	_	_	_
23	sonicator	sonicator	NN	_	_	_
24	3000	3000	CD	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	output	output	NN	_	_	_
27	level	level	NN	_	_	_
28	=	=	JJ	_	_	_
29	2.5	2.5	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	range	range	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	DNA	dna	NN	_	_	_
6	size	size	NN	_	_	_
7	resulting	result	VBG	_	_	_
8	from	from	IN	_	_	_
9	the	the	DT	_	_	_
10	sonication	sonication	NN	_	_	_
11	procedure	procedure	NN	_	_	_
12	was	be	VBD	_	_	_
13	300	300	CD	_	_	_
14	-	-	:	_	_	_
15	1000	1000	CD	_	_	_
16	bp	bp	NN	_	_	_
17	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	control	control	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	mock-IP	mock-ip	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	,	,	,	_	_	_
8	2	2	CD	_	_	_
9	ug	ug	NN	_	_	_
10	of	of	IN	_	_	_
11	normal	normal	JJ	_	_	_
12	mouse	mouse	NN	_	_	_
13	IgG	igg	NN	_	_	_
14	was	be	VBD	_	_	_
15	added	add	VBN	_	_	_
16	into	into	IN	_	_	_
17	the	the	DT	_	_	_
18	cell	cell	NN	_	_	_
19	extract	extract	NN	_	_	_
20	.	.	.	_	_	_

1	IP	IP	NNP	_	_	_
2	DNAs	dna	NNS	_	_	_
3	were	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	with	with	IN	_	_	_
6	QIAquick	qiaquick	NN	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	Kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	then	then	RB	_	_	_
14	amplified	amplify	VBD	_	_	_
15	PCR	pcr	NN	_	_	_
16	.	.	.	_	_	_

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	Cells	cell	NNS	_	_	_
37	corresponding	correspond	VBG	_	_	_
38	to	to	TO	_	_	_
39	10	10	CD	_	_	_
40	ml	ml	NN	_	_	_
41	culture	culture	NN	_	_	_
42	volume	volume	NN	_	_	_
43	were	be	VBD	_	_	_
44	harvested	harvest	VBN	_	_	_
45	at	at	IN	_	_	_
46	0	0	CD	_	_	_
47	hrs	hr	NNS	_	_	_
48	using	use	VBG	_	_	_
49	centrifugation	centrifugation	NN	_	_	_
50	.	.	.	_	_	_

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	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	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	for	for	IN	_	_	_
24	inoculation	inoculation	NN	_	_	_
25	were	be	VBD	_	_	_
26	from	from	IN	_	_	_
27	overnight	overnight	JJ	_	_	_
28	planktonic	planktonic	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	in	in	IN	_	_	_
31	10	10	CD	_	_	_
32	%	%	NN	_	_	_
33	Luria-Bertani	luria-bertani	JJ	_	_	_
34	broth	broth	NN	_	_	_
35	at	at	IN	_	_	_
36	30	30	CD	_	_	_
37	degree	degree	NN	_	_	_
38	Celsius	Celsius	NNP	_	_	_
39	.	.	.	_	_	_

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	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	.	.	.	_	_	_

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	Cells	cell	NNS	_	_	_
19	from	from	IN	_	_	_
20	each	each	DT	_	_	_
21	strain	strain	NN	_	_	_
22	were	be	VBD	_	_	_
23	rapidly	rapidly	RB	_	_	_
24	harvested	harvest	VBN	_	_	_
25	by	by	IN	_	_	_
26	filtration	filtration	NN	_	_	_
27	and	and	CC	_	_	_
28	lysate	lysate	NN	_	_	_
29	was	be	VBD	_	_	_
30	produced	produce	VBN	_	_	_
31	by	by	IN	_	_	_
32	pulverization	pulverization	NN	_	_	_
33	of	of	IN	_	_	_
34	liquid	liquid	JJ	_	_	_
35	nitrogen	nitrogen	NN	_	_	_
36	cooled	cool	VBN	_	_	_
37	samples	sample	NNS	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	from	from	IN	_	_	_
4	single	single	JJ	_	_	_
5	colonies	colony	NNS	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	on	on	IN	_	_	_
9	LB	LB	NNP	_	_	_
10	agar	agar	NN	_	_	_
11	and	and	CC	_	_	_
12	then	then	RB	_	_	_
13	inoculated	inoculate	VBN	_	_	_
14	into	into	IN	_	_	_
15	liquid	liquid	JJ	_	_	_
16	LB	lb	NN	_	_	_
17	and	and	CC	_	_	_
18	grown	grow	VBN	_	_	_
19	to	to	TO	_	_	_
20	saturation	saturation	NN	_	_	_
21	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	grew	grow	VBD	_	_	_
4	in	in	IN	_	_	_
5	MOPS	MOPS	NNP	MED	_	_
6	minimal	minimal	JJ	_	_	_
7	medium	medium	NN	_	_	_
8	with	with	IN	_	_	_
9	0.4	0.4	CD	_	_	_
10	%	%	NN	_	_	_
11	glucose	glucose	NN	SUPP	_	_
12	and	and	CC	_	_	_
13	0.2	0.2	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	K2HPO4	k2hpo4	NN	_	_	_
16	and	and	CC	_	_	_
17	harvested	harvest	VBN	_	_	_
18	at	at	IN	_	_	_
19	the	the	DT	_	_	_
20	OD600	od600	NN	_	_	_
21	value	value	NN	_	_	_
22	of	of	IN	_	_	_
23	1.0	1.0	CD	_	_	_
24	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	harvested	harvest	VBN	_	_	_
4	at	at	IN	_	_	_
5	OD450	od450	NN	_	_	_
6	=	=	JJ	_	_	_
7	0.3	0.3	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Cells	cell	NNS	_	_	_
10	in	in	IN	_	_	_
11	log	log	NN	_	_	_
12	phase	phase	NN	_	_	_
13	under	under	IN	_	_	_
14	ethanol	ethanol	NN	_	_	_
15	stress	stress	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Cells	cell	NNS	_	_	_
18	in	in	IN	_	_	_
19	log	log	NN	_	_	_
20	phase	phase	NN	_	_	_
21	under	under	IN	_	_	_
22	furfural	furfural	JJ	_	_	_
23	stress	stress	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Cells	cell	NNS	_	_	_
26	in	in	IN	_	_	_
27	RNAlater	rnalater	NN	_	_	_
28	were	be	VBD	_	_	_
29	aliquoted	aliquote	VBN	_	_	_
30	into	into	IN	_	_	_
31	two	two	CD	_	_	_
32	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	evolved	evolve	VBD	_	_	_
6	colony	colony	NN	_	_	_
7	type	type	NN	_	_	_
8	were	be	VBD	_	_	_
9	collected	collect	VBN	_	_	_
10	by	by	IN	_	_	_
11	centrifugation	centrifugation	NN	_	_	_
12	at	at	IN	_	_	_
13	13,000	13,000	CD	_	_	_
14	×	×	CD	_	_	_
15	g	g	NN	_	_	_
16	for	for	IN	_	_	_
17	1	1	CD	_	_	_
18	min	min	NN	_	_	_
19	at	at	IN	_	_	_
20	4	4	CD	_	_	_
21	°C	°c	NN	_	_	_
22	and	and	CC	_	_	_
23	were	be	VBD	_	_	_
24	immediately	immediately	RB	_	_	_
25	used	use	VBN	_	_	_
26	for	for	IN	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	isolation	isolation	NN	_	_	_
30	with	with	IN	_	_	_
31	NucleoSpin	nucleospin	NN	_	_	_
32	RNA	rna	NN	_	_	_
33	II	ii	CD	_	_	_
34	isolation	isolation	NN	_	_	_
35	kit	kit	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Macherey	macherey	NN	_	_	_
38	--	--	:	_	_	_
39	Nagel	Nagel	NNP	_	_	_
40	,	,	,	_	_	_
41	Biokè	Biokè	NNP	_	_	_
42	,	,	,	_	_	_
43	Leiden	Leiden	NNP	_	_	_
44	,	,	,	_	_	_
45	the	the	DT	_	_	_
46	Netherlands	Netherlands	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	prior	prior	RB	_	_	_
4	to	to	TO	_	_	_
5	treatment	treatment	NN	_	_	_
6	by	by	IN	_	_	_
7	norfloxacin	norfloxacin	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Cells	cell	NNS	_	_	_
10	treated	treat	VBN	_	_	_
11	during	during	IN	_	_	_
12	mid-exponential	mid-exponential	JJ	_	_	_
13	growth	growth	NN	_	_	_
14	phase	phase	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Cells	cell	NNS	_	_	_
17	treated	treat	VBN	_	_	_
18	with	with	IN	_	_	_
19	bacterial	bacterial	JJ	_	_	_
20	protect	protect	VBP	_	_	_
21	reagent	reagent	NN	_	_	_
22	and	and	CC	_	_	_
23	freeze	freeze	NN	_	_	_
24	at	at	IN	_	_	_
25	-70	-70	CD	_	_	_
26	C	c	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Cells	cell	NNS	_	_	_
29	used	use	VBN	_	_	_
30	for	for	IN	_	_	_
31	expression	expression	NN	_	_	_
32	analysis	analysis	NN	_	_	_
33	were	be	VBD	_	_	_
34	grown	grow	VBN	_	_	_
35	in	in	IN	_	_	_
36	minimal	minimal	JJ	_	_	_
37	medium	medium	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	Glansdorff	glansdorff	FW	_	_	_
40	,	,	,	_	_	_
41	1965	1965	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	supplemented	supplement	VBN	_	_	_
44	with	with	IN	_	_	_
45	0.5	0.5	CD	_	_	_
46	%	%	NN	_	_	_
47	glucose	glucose	NN	SUPP	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	w/v	w/v	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	,	,	,	_	_	_
52	L-methionine	l-methionine	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	100	100	CD	_	_	_
55	mg	mg	NN	_	_	_
56	ml-1	ml-1	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	and	and	CC	_	_	_
59	with	with	IN	_	_	_
60	L-arginine	l-arginine	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	100ug	100ug	CD	_	_	_
63	ml-1	ml-1	NN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	expression	expression	NN	_	_	_
3	analysis	analysis	NN	_	_	_
4	,	,	,	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	in	in	IN	_	_	_
9	a	a	DT	_	_	_
10	rotary	rotary	JJ	_	_	_
11	shaker	shaker	NN	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	and	and	CC	_	_	_
16	harvested	harvest	VBN	_	_	_
17	by	by	IN	_	_	_
18	centrifugation	centrifugation	NN	_	_	_
19	at	at	IN	_	_	_
20	mid-log	mid-log	JJ	_	_	_
21	phase	phase	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	OD	od	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	660nm	660nm	NN	_	_	_
27	=	=	JJ	_	_	_
28	0.5	0.5	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	the	the	DT	_	_	_
32	metabolism	metabolism	NN	_	_	_
33	was	be	VBD	_	_	_
34	quenched	quench	VBN	_	_	_
35	in	in	IN	_	_	_
36	liquid	liquid	JJ	_	_	_
37	nitrogen	nitrogen	NN	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	used	use	VBN	_	_	_
4	for	for	IN	_	_	_
5	expression	expression	NN	_	_	_
6	analysis	analysis	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	minimal	minimal	JJ	_	_	_
11	medium	medium	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Glansdorff	glansdorff	FW	_	_	_
14	,	,	,	_	_	_
15	1965	1965	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	supplemented	supplement	VBN	_	_	_
18	with	with	IN	_	_	_
19	0.5	0.5	CD	_	_	_
20	%	%	NN	_	_	_
21	glucose	glucose	NN	SUPP	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	w/v	w/v	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	L-methionine	l-methionine	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	100ug	100ug	CD	_	_	_
29	ml-1	ml-1	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	and	and	CC	_	_	_
32	with	with	IN	_	_	_
33	L-arginine	l-arginine	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	100ug	100ug	CD	_	_	_
36	ml-1	ml-1	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	expression	expression	NN	_	_	_
3	analysis	analysis	NN	_	_	_
4	,	,	,	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	in	in	IN	_	_	_
9	a	a	DT	_	_	_
10	rotary	rotary	JJ	_	_	_
11	shaker	shaker	NN	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	and	and	CC	_	_	_
16	harvested	harvest	VBN	_	_	_
17	by	by	IN	_	_	_
18	centrifugation	centrifugation	NN	_	_	_
19	at	at	IN	_	_	_
20	mid-log	mid-log	JJ	_	_	_
21	phase	phase	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	OD	od	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	660nm	660nm	NN	_	_	_
27	=	=	JJ	_	_	_
28	0.5	0.5	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	the	the	DT	_	_	_
32	metabolism	metabolism	NN	_	_	_
33	was	be	VBD	_	_	_
34	quenched	quench	VBN	_	_	_
35	in	in	IN	_	_	_
36	liquid	liquid	JJ	_	_	_
37	nitrogen	nitrogen	NN	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	used	use	VBN	_	_	_
4	for	for	IN	_	_	_
5	expression	expression	NN	_	_	_
6	analysis	analysis	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	minimal	minimal	JJ	_	_	_
11	medium	medium	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Glansdorff	glansdorff	FW	_	_	_
14	,	,	,	_	_	_
15	1965	1965	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	supplemented	supplement	VBN	_	_	_
18	with	with	IN	_	_	_
19	0.5	0.5	CD	_	_	_
20	%	%	NN	_	_	_
21	glucose	glucose	NN	SUPP	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	w/v	w/v	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	L-methionine	l-methionine	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	100ug	100ug	CD	_	_	_
29	ml-1	ml-1	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	expression	expression	NN	_	_	_
3	analysis	analysis	NN	_	_	_
4	,	,	,	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	in	in	IN	_	_	_
9	a	a	DT	_	_	_
10	rotary	rotary	JJ	_	_	_
11	shaker	shaker	NN	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	and	and	CC	_	_	_
16	harvested	harvest	VBN	_	_	_
17	by	by	IN	_	_	_
18	centrifugation	centrifugation	NN	_	_	_
19	at	at	IN	_	_	_
20	mid-log	mid-log	JJ	_	_	_
21	phase	phase	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	OD	od	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	660nm	660nm	NN	_	_	_
27	=	=	JJ	_	_	_
28	0.5	0.5	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	the	the	DT	_	_	_
32	metabolism	metabolism	NN	_	_	_
33	was	be	VBD	_	_	_
34	quenched	quench	VBN	_	_	_
35	in	in	IN	_	_	_
36	liquid	liquid	JJ	_	_	_
37	nitrogen	nitrogen	NN	_	_	_
38	.	.	.	_	_	_

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	1.25	1.25	CD	_	_	_
8	M	m	NN	_	_	_
9	sucrose	sucrose	NN	_	_	_
10	to	to	TO	_	_	_
11	an	a	DT	_	_	_
12	osmotic	osmotic	JJ	_	_	_
13	pressure	pressure	NN	_	_	_
14	of	of	IN	_	_	_
15	2.7	2.7	CD	_	_	_
16	Os	os	NNS	_	_	_
17	kg-1	kg-1	NN	_	_	_
18	for	for	IN	_	_	_
19	10	10	CD	_	_	_
20	minutes	minute	NNS	_	_	_
21	.	.	.	_	_	_

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	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/chloroform	phenol/chloroform	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	pH	ph	NN	_	_	_
10	=	=	JJ	_	_	_
11	4.5	4.5	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Life	Life	NNP	_	_	_
15	Technologies	Technologies	NNPS	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	precipitated	precipitated	JJ	_	_	_
19	with	with	IN	_	_	_
20	ethanol	ethanol	NN	_	_	_
21	and	and	CC	_	_	_
22	30	30	CD	_	_	_
23	µL	µl	NN	_	_	_
24	,	,	,	_	_	_
25	3	3	CD	_	_	_
26	M	m	NN	_	_	_
27	sodium	sodium	NN	SUPP	_	_
28	acetate	acetate	NN	SUPP	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	pH	ph	NN	_	_	_
31	=	=	JJ	_	_	_
32	5.5	5.5	CD	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Fisher	Fisher	NNP	_	_	_
36	Scientific	Scientific	NNP	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	,	,	,	_	_	_
39	overnight	overnight	JJ	_	_	_
40	at	at	IN	_	_	_
41	-80	-80	CD	_	_	_
42	ºC	ºc	NN	_	_	_
43	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	precipitation	precipitation	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	tubes	tube	NNS	_	_	_
6	were	be	VBD	_	_	_
7	centrifuged	centrifuge	VBN	_	_	_
8	and	and	CC	_	_	_
9	the	the	DT	_	_	_
10	RNA	rna	NN	_	_	_
11	pellet	pellet	NN	_	_	_
12	was	be	VBD	_	_	_
13	washed	wash	VBN	_	_	_
14	twice	twice	RB	_	_	_
15	with	with	IN	_	_	_
16	70	70	CD	_	_	_
17	%	%	NN	_	_	_
18	ethanol	ethanol	NN	_	_	_
19	and	and	CC	_	_	_
20	dried	dry	VBN	_	_	_
21	under	under	IN	_	_	_
22	vacuum	vacuum	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	as	as	IN	_	_	_
6	a	a	DT	_	_	_
7	function	function	NN	_	_	_
8	of	of	IN	_	_	_
9	time	time	NN	_	_	_
10	after	after	IN	_	_	_
11	rifampicin	rifampicin	NN	SUPP	_	_
12	treatment	treatment	NN	_	_	_
13	at	at	IN	_	_	_
14	the	the	DT	_	_	_
15	specified	specify	VBN	_	_	_
16	times	time	NNS	_	_	_
17	.	.	.	_	_	_

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	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	and	and	CC	_	_	_
8	washed	wash	VBN	_	_	_
9	three	three	CD	_	_	_
10	times	time	NNS	_	_	_
11	in	in	IN	_	_	_
12	ice-cold	ice-cold	JJ	_	_	_
13	1X	1x	NN	_	_	_
14	PBS	PBS	NNP	_	_	_
15	.	.	.	_	_	_

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	1/100	1/100	CD	_	_	_
10	anti-RecA	anti-reca	JJ	_	_	_
11	antibody	antibody	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Abcam	abcam	NN	_	_	_
14	,	,	,	_	_	_
15	ab63797	ab63797	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	IP	IP	NNP	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	with	with	IN	_	_	_
7	Protein	protein	NN	_	_	_
8	G	g	NN	_	_	_
9	Dynabeads	dynabead	NNS	_	_	_
10	®	®	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Life	Life	NNP	_	_	_
13	Technologies	Technologies	NNPS	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	for	for	IN	_	_	_
16	2	2	CD	_	_	_
17	h	h	NN	_	_	_
18	at	at	IN	_	_	_
19	room	room	NN	_	_	_
20	temperature	temperature	NN	_	_	_
21	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	3	3	CD	_	_	_
6	times	time	NNS	_	_	_
7	with	with	IN	_	_	_
8	1	1	CD	_	_	_
9	X	x	NN	_	_	_
10	PBS	PBS	NNP	_	_	_
11	+	+	CC	_	_	_
12	0.02	0.02	CD	_	_	_
13	%	%	NN	_	_	_
14	Tween-20	tween-20	NN	_	_	_
15	before	before	IN	_	_	_
16	re-suspending	re-suspend	VBG	_	_	_
17	the	the	DT	_	_	_
18	Protein	protein	NN	_	_	_
19	G	g	NN	_	_	_
20	dynabeads	dynabead	NNS	_	_	_
21	in	in	IN	_	_	_
22	200	200	CD	_	_	_
23	μl	μl	NN	_	_	_
24	of	of	IN	_	_	_
25	TE	TE	NNP	_	_	_
26	buffer	buffer	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	10	10	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	Tris	tris	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	pH	ph	NN	_	_	_
33	7.4	7.4	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	1	1	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	EDTA	edta	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	+	+	CC	_	_	_
41	1	1	CD	_	_	_
42	%	%	NN	_	_	_
43	SDS	sds	NN	_	_	_
44	.	.	.	_	_	_

1	100	100	CD	_	_	_
2	μl	μl	NN	_	_	_
3	of	of	IN	_	_	_
4	TE	TE	NNP	_	_	_
5	buffer	buffer	NN	_	_	_
6	was	be	VBD	_	_	_
7	added	add	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	input	input	NN	_	_	_
11	samples	sample	NNS	_	_	_
12	and	and	CC	_	_	_
13	all	all	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	were	be	VBD	_	_	_
16	then	then	RB	_	_	_
17	incubated	incubate	VBN	_	_	_
18	at	at	IN	_	_	_
19	65	65	CD	_	_	_
20	°C	°c	NN	_	_	_
21	for	for	IN	_	_	_
22	10	10	CD	_	_	_
23	h	h	NN	_	_	_
24	to	to	TO	_	_	_
25	reverse	reverse	VB	_	_	_
26	formaldehyde	formaldehyde	NN	_	_	_
27	crosslinks	crosslink	NNS	_	_	_
28	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	MinElute	MinElute	NNP	_	_	_
7	PCR	pcr	NN	_	_	_
8	purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	eluted	elute	VBN	_	_	_
4	in	in	IN	_	_	_
5	50	50	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	TE	TE	NNP	_	_	_
9	buffer	buffer	NN	_	_	_
10	using	use	VBG	_	_	_
11	a	a	DT	_	_	_
12	2-step	2-step	JJ	_	_	_
13	elution	elution	NN	_	_	_
14	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	stored	store	VBN	_	_	_
4	at	at	IN	_	_	_
5	-20	-20	CD	_	_	_
6	°C	°c	NN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	cross-linked	cross-link	VBN	_	_	_
5	by	by	IN	_	_	_
6	the	the	DT	_	_	_
7	addition	addition	NN	_	_	_
8	of	of	IN	_	_	_
9	formaldehyde	formaldehyde	NN	_	_	_
10	at	at	IN	_	_	_
11	1	1	CD	_	_	_
12	%	%	NN	_	_	_
13	final	final	JJ	_	_	_
14	concentration	concentration	NN	_	_	_
15	with	with	IN	_	_	_
16	continued	continued	JJ	_	_	_
17	shaking	shake	VBG	_	_	_
18	at	at	IN	_	_	_
19	37	37	CD	_	_	_
20	°C	°c	NN	_	_	_
21	for	for	IN	_	_	_
22	5	5	CD	_	_	_
23	min	min	NN	_	_	_
24	before	before	IN	_	_	_
25	quenching	quench	VBG	_	_	_
26	with	with	IN	_	_	_
27	glycine	glycine	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	100	100	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	final	final	JJ	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	crosslinked	crosslink	VBN	_	_	_
5	in	in	IN	_	_	_
6	1	1	CD	_	_	_
7	%	%	NN	_	_	_
8	formadehyde	formadehyde	NN	_	_	_
9	for	for	IN	_	_	_
10	25	25	CD	_	_	_
11	min	min	NN	_	_	_
12	at	at	IN	_	_	_
13	room	room	NN	_	_	_
14	temperature	temperature	NN	_	_	_
15	followed	follow	VBN	_	_	_
16	by	by	IN	_	_	_
17	5	5	CD	_	_	_
18	minutes	minute	NNS	_	_	_
19	of	of	IN	_	_	_
20	quenching	quench	VBG	_	_	_
21	with	with	IN	_	_	_
22	glycine	glycine	NN	_	_	_
23	.	.	.	_	_	_

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	cultured	culture	VBN	_	_	_
12	in	in	IN	_	_	_
13	LB	lb	NN	MED	_	_
14	medium	medium	NN	MED	_	_
15	containing	contain	VBG	_	_	_
16	ampicillin	ampicillin	NN	_	_	_
17	at	at	IN	_	_	_
18	28	28	CD	_	_	_
19	˚C	˚c	NN	_	_	_
20	.	.	.	_	_	_

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	1/70	1/70	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	v/v	v/v	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	was	be	VBD	_	_	_
18	incubated	incubate	VBN	_	_	_
19	for	for	IN	_	_	_
20	2	2	CD	_	_	_
21	hr	hr	NN	_	_	_
22	at	at	IN	_	_	_
23	28	28	CD	_	_	_
24	˚C	˚c	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	OD600	od600	NN	_	_	_
27	reached	reach	VBN	_	_	_
28	0.35	0.35	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	then	then	RB	_	_	_
32	for	for	IN	_	_	_
33	2	2	CD	_	_	_
34	hr	hr	NN	_	_	_
35	at	at	IN	_	_	_
36	42	42	CD	_	_	_
37	˚C	˚c	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	OD600	od600	NN	_	_	_
40	reached	reach	VBN	_	_	_
41	2.3	2.3	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	to	to	TO	_	_	_
44	induce	induce	VB	_	_	_
45	the	the	DT	_	_	_
46	PR	pr	NN	_	_	_
47	promoter	promoter	NN	_	_	_
48	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	disrupted	disrupt	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonication	sonication	NN	_	_	_
7	and	and	CC	_	_	_
8	NsrR	nsrr	NN	TF	_	_
9	bound	bind	VBD	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	isolated	isolate	VBN	_	_	_
13	with	with	IN	_	_	_
14	anti-Flag	anti-flag	JJ	_	_	_
15	antibody	antibody	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	enyzmatically	enyzmatically	RB	_	_	_
5	lysed	lyse	VBN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	presence	presence	NN	_	_	_
9	of	of	IN	_	_	_
10	protease	protease	NN	_	_	_
11	inhibitors	inhibitor	NNS	_	_	_
12	prior	prior	RB	_	_	_
13	to	to	TO	_	_	_
14	fragmentation	fragmentation	NN	_	_	_
15	using	use	VBG	_	_	_
16	sonication	sonication	NN	_	_	_
17	.	.	.	_	_	_

1	Protein/DNA	protein/dna	NN	_	_	_
2	complexes	complex	NNS	_	_	_
3	were	be	VBD	_	_	_
4	recovered	recover	VBN	_	_	_
5	using	use	VBG	_	_	_
6	an	a	DT	_	_	_
7	appropriate	appropriate	JJ	_	_	_
8	mouse	mouse	NN	_	_	_
9	monoclonal	monoclonal	JJ	_	_	_
10	antibody	antibody	NN	_	_	_
11	followed	follow	VBN	_	_	_
12	by	by	IN	_	_	_
13	recovery	recovery	NN	_	_	_
14	using	use	VBG	_	_	_
15	Pan	pan	NN	_	_	_
16	Mouse	mouse	NN	_	_	_
17	IgG	igg	NN	_	_	_
18	Dynabeads	dynabead	NNS	_	_	_
19	.	.	.	_	_	_

1	While	while	IN	_	_	_
2	complexed	complex	VBN	_	_	_
3	on	on	IN	_	_	_
4	the	the	DT	_	_	_
5	magnetic	magnetic	JJ	_	_	_
6	bead	bead	NN	_	_	_
7	,	,	,	_	_	_
8	a	a	DT	_	_	_
9	series	series	NN	_	_	_
10	of	of	IN	_	_	_
11	enzymatic	enzymatic	JJ	_	_	_
12	reactions	reaction	NNS	_	_	_
13	were	be	VBD	_	_	_
14	performed	perform	VBN	_	_	_
15	to	to	TO	_	_	_
16	1	1	LS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	end	end	VB	_	_	_
19	repair	repair	NN	_	_	_
20	,	,	,	_	_	_
21	fragmented	fragmented	JJ	_	_	_
22	DNA	dna	NN	_	_	_
23	,	,	,	_	_	_
24	2	2	LS	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	ligate	ligate	NN	_	_	_
27	sequencing	sequencing	NN	_	_	_
28	adpator	adpator	NN	_	_	_
29	2	2	CD	_	_	_
30	,	,	,	_	_	_
31	3	3	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	nick	nick	NN	_	_	_
34	repair	repair	NN	_	_	_
35	,	,	,	_	_	_
36	4	4	LS	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	lambda	lambda	NN	_	_	_
39	exonuclease	exonuclease	NN	_	_	_
40	treatment	treatment	NN	_	_	_
41	,	,	,	_	_	_
42	5	5	CD	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	RecJ	recj	NN	_	_	_
45	nuclease	nuclease	NN	_	_	_
46	treatment	treatment	NN	_	_	_
47	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	based	base	VBN	_	_	_
4	on	on	IN	_	_	_
5	the	the	DT	_	_	_
6	method	method	NN	_	_	_
7	developed	develop	VBN	_	_	_
8	by	by	IN	_	_	_
9	Rhee	Rhee	NNP	_	_	_
10	et	et	FW	_	_	_
11	al.	al.	FW	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	doi	doi	FW	_	_	_
14	:	:	:	_	_	_
15	10.1016	10.1016	CD	_	_	_
16	/	/	:	_	_	_
17	j.cell	j.cell	JJ	_	_	_
18	.2011.11.013	.2011.11.013	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	IP	IP	NNP	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	rleased	rlease	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	complex	complex	NN	_	_	_
9	and	and	CC	_	_	_
10	recovered	recover	VBD	_	_	_
11	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	fixed	fix	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	required	require	VBN	_	_	_
8	growth	growth	NN	_	_	_
9	phase	phase	NN	_	_	_
10	in	in	IN	_	_	_
11	formaldehyde	formaldehyde	NN	_	_	_
12	,	,	,	_	_	_
13	quenched	quench	VBN	_	_	_
14	,	,	,	_	_	_
15	washed	wash	VBN	_	_	_
16	and	and	CC	_	_	_
17	lysed	lyse	VBN	_	_	_
18	.	.	.	_	_	_

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	fixed	fix	VBN	_	_	_
5	with	with	IN	_	_	_
6	1	1	CD	_	_	_
7	%	%	NN	_	_	_
8	formaldehyde	formaldehyde	NN	_	_	_
9	for	for	IN	_	_	_
10	5	5	CD	_	_	_
11	min	min	NN	_	_	_
12	before	before	IN	_	_	_
13	quenching	quench	VBG	_	_	_
14	with	with	IN	_	_	_
15	ice-cold	ice-cold	JJ	_	_	_
16	glycine	glycine	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	100mM	100mm	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

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/ml	ng/ml	NN	_	_	_
17	;	;	:	_	_	_
18	USB	usb	JJ	_	_	_
19	,	,	,	_	_	_
20	Inc.	Inc.	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	the	the	DT	_	_	_
24	samples	sample	NNS	_	_	_
25	were	be	VBD	_	_	_
26	centrifuged	centrifuge	VBN	_	_	_
27	at	at	IN	_	_	_
28	20,000	20,000	CD	_	_	_
29	x	x	CC	_	_	_
30	g	g	NN	_	_	_
31	for	for	IN	_	_	_
32	10	10	CD	_	_	_
33	min	min	NN	_	_	_
34	at	at	IN	_	_	_
35	4	4	CD	_	_	_
36	°C	°c	NN	_	_	_
37	to	to	TO	_	_	_
38	remove	remove	VB	_	_	_
39	cell	cell	NN	_	_	_
40	debris	debris	NN	_	_	_
41	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	50/50	50/50	CD	_	_	_
9	slurry	slurry	NN	_	_	_
10	of	of	IN	_	_	_
11	Sepharose	sepharose	NN	_	_	_
12	protein	protein	NN	_	_	_
13	A	a	NN	_	_	_
14	beads	bead	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Upstate	upstate	NN	_	_	_
17	;	;	:	_	_	_
18	now	now	RB	_	_	_
19	Millipore	Millipore	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	protein	protein	NN	_	_	_
23	G	g	NN	_	_	_
24	beads	bead	NNS	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	GE	GE	NNP	_	_	_
27	Healthcare	Healthcare	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	in	in	IN	_	_	_
30	IP	IP	NNP	_	_	_
31	buffer	buffer	NN	_	_	_
32	for	for	IN	_	_	_
33	3	3	CD	_	_	_
34	hours	hour	NNS	_	_	_
35	at	at	IN	_	_	_
36	4	4	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	1000	1000	CD	_	_	_
9	x	x	CC	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	2	2	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	antibodies	antibody	NNS	_	_	_
20	were	be	VBD	_	_	_
21	added	add	VBN	_	_	_
22	to	to	TO	_	_	_
23	the	the	DT	_	_	_
24	pre-cleared	pre-cleared	JJ	_	_	_
25	lysate	lysate	NN	_	_	_
26	for	for	IN	_	_	_
27	an	a	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	incubation	incubation	NN	_	_	_
30	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	ChIP	chip	NN	_	_	_
3	,	,	,	_	_	_
4	we	we	PRP	_	_	_
5	used	use	VBD	_	_	_
6	anti-RNAP	anti-rnap	JJ	_	_	_
7	b	b	NN	_	_	_
8	subunit	subunit	NN	_	_	_
9	NT63	nt63	NN	_	_	_
10	monoclonal	monoclonal	JJ	_	_	_
11	antibodies	antibody	NNS	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Neoclone	neoclone	JJ	_	_	_
14	W0002	w0002	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	anti-RNAP	anti-rnap	JJ	_	_	_
18	s70	s70	NN	_	_	_
19	subunit	subunit	NN	_	_	_
20	monoclonal	monoclonal	JJ	_	_	_
21	antibodies	antibody	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Neoclone	neoclone	JJ	_	_	_
24	W0004	w0004	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	or	or	CC	_	_	_
28	anti-DksA	anti-dksa	JJ	_	_	_
29	rabbit	rabbit	NN	_	_	_
30	polyclonal	polyclonal	JJ	_	_	_
31	antisera	antisera	NNS	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	a	a	DT	_	_	_
34	kind	kind	NN	_	_	_
35	gift	gift	NN	_	_	_
36	from	from	IN	_	_	_
37	Diana	Diana	NNP	_	_	_
38	Downs	Downs	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	next	next	JJ	_	_	_
3	day	day	NN	_	_	_
4	,	,	,	_	_	_
5	30	30	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	50/50	50/50	CD	_	_	_
10	slurry	slurry	NN	_	_	_
11	of	of	IN	_	_	_
12	Sepharose	sepharose	NN	_	_	_
13	protein	protein	NN	_	_	_
14	A	a	NN	_	_	_
15	and	and	CC	_	_	_
16	G	g	NN	_	_	_
17	beads	bead	NNS	_	_	_
18	in	in	IN	_	_	_
19	250	250	CD	_	_	_
20	μl	μl	NN	_	_	_
21	IP	IP	NNP	_	_	_
22	buffer	buffer	NN	_	_	_
23	was	be	VBD	_	_	_
24	added	add	VBN	_	_	_
25	to	to	TO	_	_	_
26	the	the	DT	_	_	_
27	lysate	lysate	NN	_	_	_
28	to	to	TO	_	_	_
29	capture	capture	VB	_	_	_
30	antibody-protein-DNA	antibody-protein-dna	JJ	_	_	_
31	complex	complex	NN	_	_	_
32	for	for	IN	_	_	_
33	one	one	CD	_	_	_
34	hour	hour	NN	_	_	_
35	at	at	IN	_	_	_
36	4	4	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Beads	bead	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	250	250	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	LiCl	licl	NN	_	_	_
13	wash	wash	NN	_	_	_
14	buffer	buffer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	100	100	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	Tris	Tris	NNP	_	_	_
19	pH	ph	NN	_	_	_
20	8	8	CD	_	_	_
21	,	,	,	_	_	_
22	250	250	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	LiCl	licl	NN	_	_	_
25	,	,	,	_	_	_
26	2	2	CD	_	_	_
27	%	%	NN	_	_	_
28	Triton	Triton	NNP	_	_	_
29	X-100	x-100	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	twice	twice	RB	_	_	_
33	with	with	IN	_	_	_
34	1	1	CD	_	_	_
35	ml	ml	NN	_	_	_
36	600	600	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	NaCl	nacl	NN	_	_	_
39	wash	wash	NN	_	_	_
40	buffer	buffer	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	100	100	CD	_	_	_
43	mM	mm	NN	KWSUPP	_	_
44	Tris	Tris	NNP	_	_	_
45	pH	ph	NN	_	_	_
46	8	8	CD	_	_	_
47	,	,	,	_	_	_
48	600	600	CD	_	_	_
49	mM	mm	NN	KWSUPP	_	_
50	NaCl	nacl	NN	_	_	_
51	,	,	,	_	_	_
52	2	2	CD	_	_	_
53	%	%	NN	_	_	_
54	SDS	sds	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	,	,	,	_	_	_
57	twice	twice	RB	_	_	_
58	with	with	IN	_	_	_
59	1	1	CD	_	_	_
60	ml	ml	NN	_	_	_
61	300	300	CD	_	_	_
62	mM	mm	NN	KWSUPP	_	_
63	NaCl	nacl	NN	_	_	_
64	wash	wash	NN	_	_	_
65	buffer	buffer	NN	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	100	100	CD	_	_	_
68	mM	mm	NN	KWSUPP	_	_
69	Tris	Tris	NNP	_	_	_
70	pH	ph	NN	_	_	_
71	8	8	CD	_	_	_
72	,	,	,	_	_	_
73	300	300	CD	_	_	_
74	mM	mm	NN	KWSUPP	_	_
75	NaCl	nacl	NN	_	_	_
76	,	,	,	_	_	_
77	2	2	CD	_	_	_
78	%	%	NN	_	_	_
79	SDS	sds	NN	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	,	,	,	_	_	_
82	and	and	CC	_	_	_
83	twice	twice	RB	_	_	_
84	with	with	IN	_	_	_
85	1	1	CD	_	_	_
86	ml	ml	NN	_	_	_
87	TE	te	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	10	10	CD	_	_	_
90	mM	mm	NN	KWSUPP	_	_
91	Tris	Tris	NNP	_	_	_
92	pH	ph	NN	_	_	_
93	8	8	CD	_	_	_
94	,	,	,	_	_	_
95	1	1	CD	_	_	_
96	mM	mm	NN	KWSUPP	_	_
97	EDTA	edta	NN	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	.	.	.	_	_	_

1	Elution	elution	NN	_	_	_
2	buffer	buffer	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	50	50	CD	_	_	_
5	mM	mm	NN	KWSUPP	_	_
6	Tris	Tris	NNP	_	_	_
7	pH	ph	NN	_	_	_
8	8	8	CD	_	_	_
9	,	,	,	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	EDTA	edta	NN	_	_	_
13	,	,	,	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	SDS	sds	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	after	after	IN	_	_	_
21	the	the	DT	_	_	_
22	final	final	JJ	_	_	_
23	wash	wash	NN	_	_	_
24	step	step	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	beads	bead	NNS	_	_	_
28	were	be	VBD	_	_	_
29	incubated	incubate	VBN	_	_	_
30	at	at	IN	_	_	_
31	65	65	CD	_	_	_
32	°C	°c	NN	_	_	_
33	for	for	IN	_	_	_
34	30	30	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	to	to	TO	_	_	_
37	remove	remove	VB	_	_	_
38	the	the	DT	_	_	_
39	crosslinked	crosslink	VBN	_	_	_
40	protein-DNA	protein-dna	JJ	_	_	_
41	complexes	complex	NNS	_	_	_
42	from	from	IN	_	_	_
43	the	the	DT	_	_	_
44	beads	bead	NNS	_	_	_
45	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1000	1000	CD	_	_	_
5	x	x	CC	_	_	_
6	g	g	NN	_	_	_
7	for	for	IN	_	_	_
8	2	2	CD	_	_	_
9	min	min	NN	_	_	_
10	at	at	IN	_	_	_
11	25	25	CD	_	_	_
12	°C	°c	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	to	to	TO	_	_	_
15	remove	remove	VB	_	_	_
16	the	the	DT	_	_	_
17	beads	bead	NNS	_	_	_
18	,	,	,	_	_	_
19	the	the	DT	_	_	_
20	samples	sample	NNS	_	_	_
21	were	be	VBD	_	_	_
22	incubated	incubate	VBN	_	_	_
23	overnight	overnight	RB	_	_	_
24	at	at	IN	_	_	_
25	65	65	CD	_	_	_
26	°C	°c	NN	_	_	_
27	to	to	TO	_	_	_
28	reverse	reverse	VB	_	_	_
29	the	the	DT	_	_	_
30	protein-DNA	protein-dna	JJ	_	_	_
31	formaldehyde	formaldehyde	NN	_	_	_
32	crosslinks	crosslink	NNS	_	_	_
33	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	's	's	POS	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	and	and	CC	_	_	_
11	eluted	elute	VBN	_	_	_
12	in	in	IN	_	_	_
13	a	a	DT	_	_	_
14	final	final	JJ	_	_	_
15	volume	volume	NN	_	_	_
16	of	of	IN	_	_	_
17	65	65	CD	_	_	_
18	μl	μl	NN	_	_	_
19	with	with	IN	_	_	_
20	10	10	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	Tris	Tris	NNP	_	_	_
23	pH	ph	NN	_	_	_
24	8	8	CD	_	_	_
25	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	aerobically	aerobically	RB	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	25	25	CD	_	_	_
8	%	%	NN	_	_	_
9	O2	o2	CD	_	_	_
10	,	,	,	_	_	_
11	70	70	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	0.35	0.35	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	1/100	1/100	CD	_	_	_
5	vol	vol	NN	_	_	_
6	.	.	.	_	_	_

1	of	of	IN	_	_	_
2	1M	1m	NN	_	_	_
3	,	,	,	_	_	_
4	pH	ph	NN	_	_	_
5	7.6	7.6	CD	_	_	_
6	;	;	:	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	final	final	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	mid-log	mid-log	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	to	to	TO	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	final	final	JJ	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	anaerobic	anaerobic	JJ	_	_	_
27	sparging	sparging	NN	_	_	_
28	was	be	VBD	_	_	_
29	continued	continue	VBN	_	_	_
30	for	for	IN	_	_	_
31	10	10	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	2.5	2.5	CD	_	_	_
3	M	m	NN	_	_	_
4	glycine	glycine	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	100mM	100mm	NN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	anaerobic	anaerobic	JJ	_	_	_
19	sparging	sparging	NN	_	_	_
20	for	for	IN	_	_	_
21	30	30	CD	_	_	_
22	minutes	minute	NNS	_	_	_
23	to	to	TO	_	_	_
24	stop	stop	VB	_	_	_
25	the	the	DT	_	_	_
26	crosslinking	crosslinking	NN	_	_	_
27	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	spun	spin	VBN	_	_	_
4	at	at	IN	_	_	_
5	5000	5000	CD	_	_	_
6	x	x	CC	_	_	_
7	g	g	NN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	repeatedly	repeatedly	RB	_	_	_
12	with	with	IN	_	_	_
13	phosphate	phosphate	NN	_	_	_
14	buffered	buffer	VBN	_	_	_
15	saline	saline	NN	_	_	_
16	before	before	IN	_	_	_
17	being	be	VBG	_	_	_
18	frozen	freeze	VBN	_	_	_
19	at	at	IN	_	_	_
20	-80	-80	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	aerobically	aerobically	RB	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	70	70	CD	_	_	_
8	%	%	NN	_	_	_
9	N2	n2	NN	_	_	_
10	,	,	,	_	_	_
11	25	25	CD	_	_	_
12	%	%	NN	_	_	_
13	O2	o2	CD	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	5	5	CD	_	_	_
17	%	%	NN	_	_	_
18	CO2	co2	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	or	or	CC	_	_	_
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	~	~	NN	_	_	_
38	0.3-0.35	0.3-0.35	CD	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	aerobically	aerobically	RB	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	70	70	CD	_	_	_
8	%	%	NN	_	_	_
9	N2	n2	NN	_	_	_
10	,	,	,	_	_	_
11	25	25	CD	_	_	_
12	%	%	NN	_	_	_
13	O2	o2	CD	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	5	5	CD	_	_	_
17	%	%	NN	_	_	_
18	CO2	co2	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	or	or	CC	_	_	_
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	~	~	NN	_	_	_
38	0.3-0.35	0.3-0.35	CD	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	in	in	IN	_	_	_
41	MOPS	mop	NNS	MED	_	_
42	minimal	minimal	JJ	_	_	_
43	glucose	glucose	NN	SUPP	_	_
44	media	media	NNS	_	_	_
45	containing	contain	VBG	_	_	_
46	10	10	CD	_	_	_
47	µM	µm	NN	_	_	_
48	FeSO4	feso4	NN	_	_	_
49	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	anaerobically	anaerobically	RB	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	95	95	CD	_	_	_
8	%	%	NN	_	_	_
9	N2	n2	NN	_	_	_
10	and	and	CC	_	_	_
11	5	5	CD	_	_	_
12	%	%	NN	_	_	_
13	CO2	co2	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	until	until	IN	_	_	_
16	mid-log	mid-log	JJ	_	_	_
17	phase	phase	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	OD600	od600	NN	_	_	_
20	of	of	IN	_	_	_
21	0.3	0.3	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	treated	treat	VBN	_	_	_
25	with	with	IN	_	_	_
26	1	1	CD	_	_	_
27	%	%	NN	_	_	_
28	final	final	JJ	_	_	_
29	volumen	voluman	NNS	_	_	_
30	formaldehyde	formaldehyde	NN	_	_	_
31	for	for	IN	_	_	_
32	ten	ten	CD	_	_	_
33	minutes	minute	NNS	_	_	_
34	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1/100	1/100	CD	_	_	_
5	vol	vol	NN	_	_	_
6	.	.	.	_	_	_

1	of	of	IN	_	_	_
2	1M	1m	NN	_	_	_
3	,	,	,	_	_	_
4	pH	ph	NN	_	_	_
5	7.6	7.6	CD	_	_	_
6	;	;	:	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	final	final	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	mid-log	mid-log	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	to	to	TO	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	final	final	JJ	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	anaerobic	anaerobic	JJ	_	_	_
27	sparging	sparging	NN	_	_	_
28	was	be	VBD	_	_	_
29	continued	continue	VBN	_	_	_
30	for	for	IN	_	_	_
31	10	10	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	2.5	2.5	CD	_	_	_
3	M	m	NN	_	_	_
4	glycine	glycine	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	100mM	100mm	NN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	anaerobic	anaerobic	JJ	_	_	_
19	sparging	sparging	NN	_	_	_
20	for	for	IN	_	_	_
21	30	30	CD	_	_	_
22	minutes	minute	NNS	_	_	_
23	to	to	TO	_	_	_
24	stop	stop	VB	_	_	_
25	the	the	DT	_	_	_
26	crosslinking	crosslinking	NN	_	_	_
27	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	spun	spin	VBN	_	_	_
4	at	at	IN	_	_	_
5	5000	5000	CD	_	_	_
6	x	x	CC	_	_	_
7	g	g	NN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	repeatedly	repeatedly	RB	_	_	_
12	with	with	IN	_	_	_
13	phosphate	phosphate	NN	_	_	_
14	buffered	buffer	VBN	_	_	_
15	saline	saline	NN	_	_	_
16	before	before	IN	_	_	_
17	being	be	VBG	_	_	_
18	frozen	freeze	VBN	_	_	_
19	at	at	IN	_	_	_
20	-80	-80	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

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	in	in	IN	_	_	_
9	LB	lb	NN	MED	_	_
10	medium	medium	NN	MED	_	_
11	to	to	TO	_	_	_
12	an	a	DT	_	_	_
13	OD600	od600	NN	_	_	_
14	of	of	IN	_	_	_
15	0.55-0.6	0.55-0.6	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	Cells	cell	NNS	_	_	_
18	were	be	VBD	_	_	_
19	grown	grow	VBN	_	_	_
20	at	at	IN	_	_	_
21	30	30	CD	_	_	_
22	°C	°c	NN	_	_	_
23	to	to	TO	_	_	_
24	an	a	DT	_	_	_
25	OD450	od450	NN	_	_	_
26	of	of	IN	_	_	_
27	about	about	IN	_	_	_
28	0.07	0.07	CD	_	_	_
29	in	in	IN	_	_	_
30	AB	AB	NNP	_	_	_
31	glucose	glucose	NN	SUPP	_	_
32	CAA	CAA	NNP	_	_	_
33	medium	medium	NN	_	_	_
34	,	,	,	_	_	_
35	shifted	shift	VBD	_	_	_
36	to	to	TO	_	_	_
37	39	39	CD	_	_	_
38	°C	°c	NN	_	_	_
39	for	for	IN	_	_	_
40	70	70	CD	_	_	_
41	min	min	NN	_	_	_
42	and	and	CC	_	_	_
43	back	back	RB	_	_	_
44	to	to	TO	_	_	_
45	30	30	CD	_	_	_
46	°C	°c	NN	_	_	_
47	for	for	IN	_	_	_
48	0	0	CD	_	_	_
49	min	min	NN	_	_	_
50	before	before	IN	_	_	_
51	crosslinking	crosslink	VBG	_	_	_
52	.	.	.	_	_	_

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	,	,	,	_	_	_
9	200	200	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	in	in	IN	_	_	_
12	M9	m9	NN	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	,	,	,	_	_	_
15	for	for	IN	_	_	_
16	16	16	CD	_	_	_
17	hours	hour	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	stationary	stationary	JJ	GrowthPhase	_	_
20	phase	phase	NN	GrowthPhase	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
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	in	in	IN	_	_	_
9	Luria-Bertani	Luria-Bertani	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	LB	LB	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	medium	medium	NN	_	_	_
14	containing	contain	VBG	_	_	_
15	50	50	CD	_	_	_
16	μg/ml	μg/ml	NN	_	_	_
17	ampicillin	ampicillin	NN	_	_	_
18	overnight	overnight	RB	_	_	_
19	,	,	,	_	_	_
20	then	then	RB	_	_	_
21	diluted	dilute	VBN	_	_	_
22	at	at	IN	_	_	_
23	a	a	DT	_	_	_
24	ratio	ratio	NN	_	_	_
25	of	of	IN	_	_	_
26	1:100	1:100	CD	_	_	_
27	into	into	IN	_	_	_
28	LB	lb	NN	MED	_	_
29	medium	medium	NN	MED	_	_
30	containing	contain	VBG	_	_	_
31	1.5	1.5	CD	_	_	_
32	%	%	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	v/v	v/v	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	ethanol	ethanol	NN	_	_	_
37	and	and	CC	_	_	_
38	50	50	CD	_	_	_
39	μg/ml	μg/ml	NN	_	_	_
40	ampicillin	ampicillin	NN	_	_	_
41	,	,	,	_	_	_
42	and	and	CC	_	_	_
43	grown	grow	VBN	_	_	_
44	at	at	IN	_	_	_
45	37	37	CD	_	_	_
46	°C	°c	NN	_	_	_
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	in	in	IN	_	_	_
9	Luria-Bertani	Luria-Bertani	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	LB	LB	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	medium	medium	NN	_	_	_
14	supplemented	supplement	VBN	_	_	_
15	with	with	IN	_	_	_
16	50	50	CD	_	_	_
17	μg/ml	μg/ml	NN	_	_	_
18	ampicillin	ampicillin	NN	_	_	_
19	overnight	overnight	RB	_	_	_
20	,	,	,	_	_	_
21	then	then	RB	_	_	_
22	inoculated	inoculate	VBN	_	_	_
23	into	into	IN	_	_	_
24	LB	lb	NN	MED	_	_
25	medium	medium	NN	MED	_	_
26	supplemented	supplement	VBN	_	_	_
27	with	with	IN	_	_	_
28	0.095	0.095	CD	_	_	_
29	%	%	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	v/v	v/v	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	furfural	furfural	NN	_	_	_
34	and	and	CC	_	_	_
35	50	50	CD	_	_	_
36	μg/ml	μg/ml	NN	_	_	_
37	ampicillin	ampicillin	NN	_	_	_
38	at	at	IN	_	_	_
39	an	a	DT	_	_	_
40	initial	initial	JJ	_	_	_
41	OD600	od600	NN	_	_	_
42	value	value	NN	_	_	_
43	of	of	IN	_	_	_
44	0.02	0.02	CD	_	_	_
45	,	,	,	_	_	_
46	and	and	CC	_	_	_
47	grown	grow	VBN	_	_	_
48	at	at	IN	_	_	_
49	37	37	CD	_	_	_
50	°C	°c	NN	_	_	_
51	.	.	.	_	_	_

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	in	in	IN	_	_	_
9	M4	m4	NN	_	_	_
10	minimal	minimal	JJ	_	_	_
11	medium	medium	NN	_	_	_
12	under	under	IN	_	_	_
13	oxic	oxic	JJ	_	_	_
14	and	and	CC	_	_	_
15	anoxic	anoxic	JJ	_	_	_
16	conditions	condition	NNS	_	_	_
17	.	.	.	_	_	_

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/l	g/l	NN	_	_	_
34	caseinhydrolysate	caseinhydrolysate	NN	_	_	_
35	1	1	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	MgSO4	mgso4	NN	_	_	_
38	,	,	,	_	_	_
39	0.1	0.1	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	CaCl2	cacl2	NN	_	_	_
42	and	and	CC	_	_	_
43	trace	trace	NN	_	_	_
44	elements	element	NNS	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	5	5	CD	_	_	_
47	μM	μm	NN	_	_	_
48	CoCl2	cocl2	NN	_	_	_
49	,	,	,	_	_	_
50	0.2	0.2	CD	_	_	_
51	μM	μm	NN	_	_	_
52	CuSO4	cuso4	NN	_	_	_
53	,	,	,	_	_	_
54	57	57	CD	_	_	_
55	μM	μm	NN	_	_	_
56	H3BO3	h3bo3	NN	_	_	_
57	,	,	,	_	_	_
58	5.4	5.4	CD	_	_	_
59	μM	μm	NN	_	_	_
60	FeCl2	fecl2	NN	_	_	_
61	,	,	,	_	_	_
62	1.3	1.3	CD	_	_	_
63	μM	μm	NN	_	_	_
64	MnSO4	mnso4	NN	_	_	_
65	,	,	,	_	_	_
66	67.2	67.2	CD	_	_	_
67	μM	μm	NN	_	_	_
68	Na2EDTA	na2edta	NN	_	_	_
69	,	,	,	_	_	_
70	3.9	3.9	CD	_	_	_
71	μM	μm	NN	_	_	_
72	Na2MoO4	na2moo4	NN	_	_	_
73	,	,	,	_	_	_
74	1.5	1.5	CD	_	_	_
75	μM	μm	NN	_	_	_
76	Na2SeO4	na2seo4	NN	_	_	_
77	,	,	,	_	_	_
78	5	5	CD	_	_	_
79	μM	μm	NN	_	_	_
80	NiCl2	nicl2	NN	_	_	_
81	,	,	,	_	_	_
82	and	and	CC	_	_	_
83	1	1	CD	_	_	_
84	μM	μm	NN	_	_	_
85	ZnSO4	znso4	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pH	ph	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	media	media	NNS	_	_	_
6	was	be	VBD	_	_	_
7	adjusted	adjust	VBN	_	_	_
8	to	to	TO	_	_	_
9	7.2	7.2	CD	_	_	_
10	.	.	.	_	_	_

1	Glycerol	glycerol	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	50	50	CD	_	_	_
4	mM	mm	NN	KWSUPP	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	or	or	CC	_	_	_
7	glycerol	glycerol	NN	SUPP	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	50mM	50mm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	plus	plus	CC	_	_	_
12	propionate	propionate	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	10	10	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	served	serve	VBD	_	_	_
18	as	as	IN	_	_	_
19	the	the	DT	_	_	_
20	carbon	carbon	NN	_	_	_
21	and	and	CC	_	_	_
22	electron	electron	NN	_	_	_
23	sources	source	NNS	_	_	_
24	,	,	,	_	_	_
25	respectively	respectively	RB	_	_	_
26	.	.	.	_	_	_

1	Potassium	potassium	NN	_	_	_
2	nitrate	nitrate	NN	SUPP	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	50	50	CD	_	_	_
5	mM	mm	NN	KWSUPP	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	the	the	DT	_	_	_
9	electron	electron	NN	_	_	_
10	acceptor	acceptor	NN	_	_	_
11	under	under	IN	_	_	_
12	anoxic	anoxic	JJ	_	_	_
13	conditions	condition	NNS	_	_	_
14	.	.	.	_	_	_

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	100	100	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	.	.	.	_	_	_

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	at	at	IN	_	_	_
6	37oC	37oc	NN	_	_	_
7	without	without	IN	_	_	_
8	shaking	shake	VBG	_	_	_
9	in	in	IN	_	_	_
10	18	18	CD	_	_	_
11	mm	mm	NN	_	_	_
12	test	test	NN	_	_	_
13	tubes	tube	NNS	_	_	_
14	containing	contain	VBG	_	_	_
15	5	5	CD	_	_	_
16	ml	ml	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	MOPS-based	mops-based	JJ	_	_	_
20	culture	culture	NN	_	_	_
21	medium	medium	NN	_	_	_
22	designed	design	VBN	_	_	_
23	by	by	IN	_	_	_
24	Neidhardt	Neidhardt	NNP	_	_	_
25	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
24	of	of	IN	_	_	_
25	lyophilized	lyophilized	JJ	_	_	_
26	mucus	mucus	NN	_	_	_
27	at	at	IN	_	_	_
28	A600	a600	NN	_	_	_
29	=	=	JJ	_	_	_
30	0.2	0.2	CD	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	P1	p1	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	or	or	CC	_	_	_
35	0.5	0.5	CD	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	P2	p2	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	250	250	CD	_	_	_
8	ml	ml	NN	_	_	_
9	fermenter	fermenter	NN	_	_	_
10	containing	contain	VBG	_	_	_
11	100	100	CD	_	_	_
12	ml	ml	NN	_	_	_
13	LB	lb	NN	MED	_	_
14	medium	medium	NN	MED	_	_
15	supplemented	supplement	VBN	_	_	_
16	with	with	IN	_	_	_
17	3	3	CD	_	_	_
18	g/L	g/l	NN	_	_	_
19	glucose	glucose	NN	SUPP	_	_
20	,	,	,	_	_	_
21	0.1	0.1	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	IPTG	iptg	NN	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	50	50	CD	_	_	_
27	μg/mL	μg/ml	NN	_	_	_
28	antibiotics	antibiotic	NNS	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	fermentors	fermentor	NNS	_	_	_
3	were	be	VBD	_	_	_
4	operated	operate	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	and	and	CC	_	_	_
9	250	250	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	with	with	IN	_	_	_
12	aeration	aeration	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	200	200	CD	_	_	_
15	mL/min	ml/min	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	Flow	flow	NN	_	_	_
2	rate	rate	NN	_	_	_
3	was	be	VBD	_	_	_
4	1.162	1.162	CD	_	_	_
5	ml/min	ml/min	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	dilution	dilution	NN	_	_	_
8	rate	rate	NN	_	_	_
9	0,7	0,7	CD	_	_	_
10	/	/	:	_	_	_
11	h	h	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	for	for	IN	_	_	_
6	RNA	rna	NN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	anaerobic	anaerobic	JJ	_	_	_
7	incubator	incubator	NN	_	_	_
8	for	for	IN	_	_	_
9	1h	1h	NN	_	_	_
10	at	at	IN	_	_	_
11	37	37	CD	_	_	_
12	℃	℃	NN	_	_	_
13	and	and	CC	_	_	_
14	drugs	drug	NNS	_	_	_
15	were	be	VBD	_	_	_
16	added	add	VBN	_	_	_
17	according	accord	VBG	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	different	different	JJ	_	_	_
21	concentrations	concentration	NNS	_	_	_
22	.	.	.	_	_	_

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	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	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	LB	lb	NN	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	degrees	degree	NNS	_	_	_
10	celsius	celsius	NN	_	_	_
11	with	with	IN	_	_	_
12	shaking	shake	VBG	_	_	_
13	for	for	IN	_	_	_
14	150	150	CD	_	_	_
15	minutes	minute	NNS	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Cells	cell	NNS	_	_	_
18	were	be	VBD	_	_	_
19	grown	grow	VBN	_	_	_
20	in	in	IN	_	_	_
21	LB	lb	NN	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	degrees	degree	NNS	_	_	_
25	celsius	celsius	NN	_	_	_
26	with	with	IN	_	_	_
27	shaking	shake	VBG	_	_	_
28	for	for	IN	_	_	_
29	240	240	CD	_	_	_
30	minutes	minute	NNS	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Cells	cell	NNS	_	_	_
33	were	be	VBD	_	_	_
34	grown	grow	VBN	_	_	_
35	in	in	IN	_	_	_
36	LB	lb	NN	_	_	_
37	at	at	IN	_	_	_
38	37	37	CD	_	_	_
39	degrees	degree	NNS	_	_	_
40	celsius	celsius	NN	_	_	_
41	with	with	IN	_	_	_
42	shaking	shake	VBG	_	_	_
43	for	for	IN	_	_	_
44	360	360	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Cells	cell	NNS	_	_	_
48	were	be	VBD	_	_	_
49	grown	grow	VBN	_	_	_
50	in	in	IN	_	_	_
51	LB	lb	NN	_	_	_
52	at	at	IN	_	_	_
53	37	37	CD	_	_	_
54	degrees	degree	NNS	_	_	_
55	celsius	celsius	NN	_	_	_
56	with	with	IN	_	_	_
57	shaking	shake	VBG	_	_	_
58	for	for	IN	_	_	_
59	90	90	CD	_	_	_
60	minutes	minute	NNS	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Cells	cell	NNS	_	_	_
63	were	be	VBD	_	_	_
64	grown	grow	VBN	_	_	_
65	in	in	IN	_	_	_
66	LB	LB	NNP	MED	_	_
67	media	media	NNS	MED	_	_
68	supplemented	supplement	VBN	_	_	_
69	with	with	IN	_	_	_
70	0.2	0.2	CD	_	_	_
71	%	%	NN	_	_	_
72	arabinose	arabinose	NN	_	_	_
73	at	at	IN	_	_	_
74	37	37	CD	_	_	_
75	°C	°c	NN	_	_	_
76	to	to	TO	_	_	_
77	and	and	CC	_	_	_
78	OD600nm	od600nm	NN	_	_	_
79	of	of	IN	_	_	_
80	0.2-0.25	0.2-0.25	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
82	Cells	cell	NNS	_	_	_
83	were	be	VBD	_	_	_
84	grown	grow	VBN	_	_	_
85	in	in	IN	_	_	_
86	LB	LB	NNP	MED	_	_
87	media	media	NNS	MED	_	_
88	with	with	IN	_	_	_
89	1mM	1mm	NN	_	_	_
90	IPTG	iptg	NN	_	_	_
91	at	at	IN	_	_	_
92	37	37	CD	_	_	_
93	°C	°c	NN	_	_	_
94	with	with	IN	_	_	_
95	shaking	shake	VBG	_	_	_
96	for	for	IN	_	_	_
97	2	2	CD	_	_	_
98	hours	hour	NNS	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	cells	cell	NNS	_	_	_
101	were	be	VBD	_	_	_
102	grown	grow	VBN	_	_	_
103	in	in	IN	_	_	_
104	LB	lb	NN	_	_	_
105	overnight	overnight	JJ	_	_	_
106	at	at	IN	_	_	_
107	37	37	CD	_	_	_
108	degrees	degree	NNS	_	_	_
109	celcius	celcius	NN	_	_	_
110	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	Luria	Luria	NNP	_	_	_
7	Bertani	Bertani	NNP	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	LB	LB	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	media	media	NNS	_	_	_
12	at	at	IN	_	_	_
13	37C	37c	NN	_	_	_
14	at	at	IN	_	_	_
15	200	200	CD	_	_	_
16	rpm	rpm	NN	_	_	_
17	.	.	.	_	_	_

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	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	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	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	M9	m9	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	0.4	0.4	CD	_	_	_
10	%	%	NN	_	_	_
11	w/v	w/v	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	grown	grow	VBN	_	_	_
17	in	in	IN	_	_	_
18	M9	m9	NN	_	_	_
19	medium	medium	NN	_	_	_
20	supplemented	supplement	VBN	_	_	_
21	with	with	IN	_	_	_
22	0.2	0.2	CD	_	_	_
23	%	%	NN	_	_	_
24	glucose	glucose	NN	SUPP	_	_
25	and	and	CC	_	_	_
26	0.4	0.4	CD	_	_	_
27	%	%	NN	_	_	_
28	casamino	casamino	NN	_	_	_
29	acid	acid	NN	_	_	_
30	at	at	IN	_	_	_
31	37	37	CD	_	_	_
32	℃	℃	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	Cells	cell	NNS	_	_	_
35	were	be	VBD	_	_	_
36	grown	grow	VBN	_	_	_
37	in	in	IN	_	_	_
38	M9	m9	NN	MED	_	_
39	minimal	minimal	JJ	MED	_	_
40	media	media	NNS	MED	_	_
41	supplemented	supplement	VBN	_	_	_
42	with	with	IN	_	_	_
43	0.2	0.2	CD	_	_	_
44	%	%	NN	_	_	_
45	casamino	casamino	NN	SUPP	_	_
46	acids	acid	NNS	SUPP	_	_
47	,	,	,	_	_	_
48	0.5	0.5	CD	_	_	_
49	%	%	NN	_	_	_
50	glucose	glucose	NN	SUPP	_	_
51	5μM	5μm	NN	_	_	_
52	CaCl2	cacl2	NN	_	_	_
53	and	and	CC	_	_	_
54	1mM	1mm	NN	_	_	_
55	MgSO4	mgso4	NN	_	_	_
56	at	at	IN	_	_	_
57	37	37	CD	_	_	_
58	°C	°c	NN	_	_	_
59	to	to	TO	_	_	_
60	and	and	CC	_	_	_
61	OD600nm	od600nm	NN	_	_	_
62	of	of	IN	_	_	_
63	0.2-0.25	0.2-0.25	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	Cells	cell	NNS	_	_	_
66	were	be	VBD	_	_	_
67	grown	grow	VBN	_	_	_
68	in	in	IN	_	_	_
69	MOPS	mop	NNS	MED	_	_
70	minimal	minimal	JJ	_	_	_
71	medium	medium	NN	_	_	_
72	with	with	IN	_	_	_
73	0.2	0.2	CD	_	_	_
74	%	%	NN	_	_	_
75	glucose	glucose	NN	SUPP	_	_
76	at	at	IN	_	_	_
77	37	37	CD	_	_	_
78	degrees	degree	NNS	_	_	_
79	C	c	NN	_	_	_
80	in	in	IN	_	_	_
81	gas-sparged	gas-sparged	JJ	_	_	_
82	Roux	Roux	NNP	_	_	_
83	bottles	bottle	NNS	_	_	_
84	to	to	TO	_	_	_
85	mid-log	mid-log	JJ	_	_	_
86	phase	phase	NN	_	_	_
87	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	shake	shake	NN	_	_	_
7	flasks	flask	NNS	_	_	_
8	to	to	TO	_	_	_
9	mid-exponential	mid-exponential	JJ	_	_	_
10	phase	phase	NN	_	_	_
11	under	under	IN	_	_	_
12	either	either	CC	_	_	_
13	aerobic	aerobic	JJ	_	_	_
14	or	or	CC	_	_	_
15	anaerobic	anaerobic	JJ	_	_	_
16	conditions	condition	NNS	_	_	_
17	depending	depend	VBG	_	_	_
18	on	on	IN	_	_	_
19	the	the	DT	_	_	_
20	sample	sample	NN	_	_	_
21	.	.	.	_	_	_

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	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	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/mL	mg/ml	NN	_	_	_
13	5-azacytidine	5-azacytidine	NN	_	_	_
14	to	to	TO	_	_	_
15	logarithmic	logarithmic	JJ	_	_	_
16	phase	phase	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	2	2	CD	_	_	_
19	hours	hour	NNS	_	_	_
20	,	,	,	_	_	_
21	A600	a600	NN	_	_	_
22	=	=	JJ	_	_	_
23	~	~	NN	_	_	_
24	0.45	0.45	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	or	or	CC	_	_	_
27	early	early	JJ	GrowthPhase	_	_
28	stationary	stationary	JJ	GrowthPhase	_	_
29	phase	phase	NN	GrowthPhase	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	8	8	CD	_	_	_
32	hours	hour	NNS	_	_	_
33	,	,	,	_	_	_
34	A600	a600	NN	_	_	_
35	=	=	JJ	_	_	_
36	~	~	NN	_	_	_
37	2.7	2.7	CD	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Cells	cell	NNS	_	_	_
41	were	be	VBD	_	_	_
42	grown	grow	VBN	_	_	_
43	in	in	IN	_	_	_
44	the	the	DT	_	_	_
45	minimal	minimal	JJ	_	_	_
46	media	media	NNS	_	_	_
47	,	,	,	_	_	_
48	M63	m63	NN	_	_	_
49	.	.	.	_	_	_

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/mL	cells/ml	NN	_	_	_
12	within	within	IN	_	_	_
13	the	the	DT	_	_	_
14	exponential	exponential	JJ	_	_	_
15	growth	growth	NN	_	_	_
16	phase	phase	NN	_	_	_
17	.	.	.	_	_	_

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/mL	cells/ml	NN	_	_	_
10	within	within	IN	_	_	_
11	the	the	DT	_	_	_
12	exponential	exponential	JJ	_	_	_
13	growth	growth	NN	_	_	_
14	phase	phase	NN	_	_	_
15	.	.	.	_	_	_

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	modified	modify	VBN	_	_	_
11	M63	m63	NN	_	_	_
12	.	.	.	_	_	_

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/mL	cells/ml	NN	_	_	_
12	within	within	IN	_	_	_
13	the	the	DT	_	_	_
14	exponential	exponential	JJ	_	_	_
15	growth	growth	NN	_	_	_
16	phase	phase	NN	_	_	_
17	.	.	.	_	_	_

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	grown	grow	VBN	_	_	_
20	to	to	TO	_	_	_
21	an	a	DT	_	_	_
22	OD	od	NN	_	_	_
23	of	of	IN	_	_	_
24	0.4	0.4	CD	_	_	_
25	and	and	CC	_	_	_
26	then	then	RB	_	_	_
27	0.5	0.5	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	IPTG	iptg	NN	_	_	_
30	was	be	VBD	_	_	_
31	added	add	VBN	_	_	_
32	to	to	TO	_	_	_
33	induce	induce	VB	_	_	_
34	the	the	DT	_	_	_
35	protein	protein	NN	_	_	_
36	expression	expression	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Cells	cell	NNS	_	_	_
39	were	be	VBD	_	_	_
40	grown	grow	VBN	_	_	_
41	to	to	TO	_	_	_
42	approximately	approximately	RB	_	_	_
43	mid-log	mid-log	JJ	_	_	_
44	phase	phase	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	OD560	od560	NN	_	_	_
47	=	=	JJ	_	_	_
48	approximately	approximately	RB	_	_	_
49	0.5	0.5	CD	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	in	in	IN	_	_	_
52	LB	lb	NN	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	exponential	exponential	JJ	GrowthPhase	_	_
7	phase	phase	NN	GrowthPhase	_	_
8	in	in	IN	_	_	_
9	Lysogeny	Lysogeny	NNP	_	_	_
10	broth	broth	NN	_	_	_
11	,	,	,	_	_	_
12	37oC	37oc	NN	_	_	_
13	with	with	IN	_	_	_
14	shaking	shake	VBG	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Cells	cell	NNS	_	_	_
17	were	be	VBD	_	_	_
18	grown	grow	VBN	_	_	_
19	to	to	TO	_	_	_
20	the	the	DT	_	_	_
21	stationary	stationary	JJ	GrowthPhase	_	_
22	phase	phase	NN	GrowthPhase	_	_
23	at	at	IN	_	_	_
24	37ºC	37ºc	NN	_	_	_
25	in	in	IN	_	_	_
26	Luria-Bertani	luria-bertani	JJ	_	_	_
27	medium	medium	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	with	with	IN	_	_	_
6	16	16	CD	_	_	_
7	µM	µm	NN	_	_	_
8	IPTG	iptg	NN	_	_	_
9	and	and	CC	_	_	_
10	300	300	CD	_	_	_
11	µL	µl	NN	_	_	_
12	Cm20	cm20	NN	_	_	_
13	anaerobically	anaerobically	RB	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	95	95	CD	_	_	_
16	%	%	NN	_	_	_
17	N2	n2	NN	_	_	_
18	and	and	CC	_	_	_
19	5	5	CD	_	_	_
20	%	%	NN	_	_	_
21	CO2	co2	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	until	until	IN	_	_	_
24	mid-log	mid-log	JJ	_	_	_
25	phase	phase	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600	od600	NN	_	_	_
28	of	of	IN	_	_	_
29	0.3	0.3	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	and	and	CC	_	_	_
32	treated	treat	VBN	_	_	_
33	with	with	IN	_	_	_
34	1	1	CD	_	_	_
35	%	%	NN	_	_	_
36	final	final	JJ	_	_	_
37	volumen	voluman	NNS	_	_	_
38	formaldehyde	formaldehyde	NN	_	_	_
39	for	for	IN	_	_	_
40	ten	ten	CD	_	_	_
41	minutes	minute	NNS	_	_	_
42	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1/100	1/100	CD	_	_	_
5	vol	vol	NN	_	_	_
6	.	.	.	_	_	_

1	of	of	IN	_	_	_
2	1M	1m	NN	_	_	_
3	,	,	,	_	_	_
4	pH	ph	NN	_	_	_
5	7.6	7.6	CD	_	_	_
6	;	;	:	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	final	final	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	mid-log	mid-log	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	to	to	TO	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	final	final	JJ	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	anaerobic	anaerobic	JJ	_	_	_
27	sparging	sparging	NN	_	_	_
28	was	be	VBD	_	_	_
29	continued	continue	VBN	_	_	_
30	for	for	IN	_	_	_
31	10	10	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	2.5	2.5	CD	_	_	_
3	M	m	NN	_	_	_
4	glycine	glycine	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	100mM	100mm	NN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	anaerobic	anaerobic	JJ	_	_	_
19	sparging	sparging	NN	_	_	_
20	for	for	IN	_	_	_
21	30	30	CD	_	_	_
22	minutes	minute	NNS	_	_	_
23	to	to	TO	_	_	_
24	stop	stop	VB	_	_	_
25	the	the	DT	_	_	_
26	crosslinking	crosslinking	NN	_	_	_
27	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	spun	spin	VBN	_	_	_
4	at	at	IN	_	_	_
5	5000	5000	CD	_	_	_
6	x	x	CC	_	_	_
7	g	g	NN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	repeatedly	repeatedly	RB	_	_	_
12	with	with	IN	_	_	_
13	phosphate	phosphate	NN	_	_	_
14	buffered	buffer	VBN	_	_	_
15	saline	saline	NN	_	_	_
16	before	before	IN	_	_	_
17	being	be	VBG	_	_	_
18	frozen	freeze	VBN	_	_	_
19	at	at	IN	_	_	_
20	-80	-80	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	with	with	IN	_	_	_
6	4	4	CD	_	_	_
7	µM	µm	NN	_	_	_
8	IPTG	iptg	NN	_	_	_
9	and	and	CC	_	_	_
10	300	300	CD	_	_	_
11	µL	µl	NN	_	_	_
12	Cm20	cm20	NN	_	_	_
13	anaerobically	anaerobically	RB	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	95	95	CD	_	_	_
16	%	%	NN	_	_	_
17	N2	n2	NN	_	_	_
18	and	and	CC	_	_	_
19	5	5	CD	_	_	_
20	%	%	NN	_	_	_
21	CO2	co2	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	until	until	IN	_	_	_
24	mid-log	mid-log	JJ	_	_	_
25	phase	phase	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600	od600	NN	_	_	_
28	of	of	IN	_	_	_
29	0.3	0.3	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	and	and	CC	_	_	_
32	treated	treat	VBN	_	_	_
33	with	with	IN	_	_	_
34	1	1	CD	_	_	_
35	%	%	NN	_	_	_
36	final	final	JJ	_	_	_
37	volumen	voluman	NNS	_	_	_
38	formaldehyde	formaldehyde	NN	_	_	_
39	for	for	IN	_	_	_
40	ten	ten	CD	_	_	_
41	minutes	minute	NNS	_	_	_
42	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1/100	1/100	CD	_	_	_
5	vol	vol	NN	_	_	_
6	.	.	.	_	_	_

1	of	of	IN	_	_	_
2	1M	1m	NN	_	_	_
3	,	,	,	_	_	_
4	pH	ph	NN	_	_	_
5	7.6	7.6	CD	_	_	_
6	;	;	:	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	final	final	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	mid-log	mid-log	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	to	to	TO	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	final	final	JJ	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	anaerobic	anaerobic	JJ	_	_	_
27	sparging	sparging	NN	_	_	_
28	was	be	VBD	_	_	_
29	continued	continue	VBN	_	_	_
30	for	for	IN	_	_	_
31	10	10	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	2.5	2.5	CD	_	_	_
3	M	m	NN	_	_	_
4	glycine	glycine	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	100mM	100mm	NN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	anaerobic	anaerobic	JJ	_	_	_
19	sparging	sparging	NN	_	_	_
20	for	for	IN	_	_	_
21	30	30	CD	_	_	_
22	minutes	minute	NNS	_	_	_
23	to	to	TO	_	_	_
24	stop	stop	VB	_	_	_
25	the	the	DT	_	_	_
26	crosslinking	crosslinking	NN	_	_	_
27	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	spun	spin	VBN	_	_	_
4	at	at	IN	_	_	_
5	5000	5000	CD	_	_	_
6	x	x	CC	_	_	_
7	g	g	NN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	repeatedly	repeatedly	RB	_	_	_
12	with	with	IN	_	_	_
13	phosphate	phosphate	NN	_	_	_
14	buffered	buffer	VBN	_	_	_
15	saline	saline	NN	_	_	_
16	before	before	IN	_	_	_
17	being	be	VBG	_	_	_
18	frozen	freeze	VBN	_	_	_
19	at	at	IN	_	_	_
20	-80	-80	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	with	with	IN	_	_	_
6	8	8	CD	_	_	_
7	µM	µm	NN	_	_	_
8	IPTG	iptg	NN	_	_	_
9	and	and	CC	_	_	_
10	300	300	CD	_	_	_
11	µL	µl	NN	_	_	_
12	Cm20	cm20	NN	_	_	_
13	anaerobically	anaerobically	RB	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	95	95	CD	_	_	_
16	%	%	NN	_	_	_
17	N2	n2	NN	_	_	_
18	and	and	CC	_	_	_
19	5	5	CD	_	_	_
20	%	%	NN	_	_	_
21	CO2	co2	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	until	until	IN	_	_	_
24	mid-log	mid-log	JJ	_	_	_
25	phase	phase	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600	od600	NN	_	_	_
28	of	of	IN	_	_	_
29	0.3	0.3	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	and	and	CC	_	_	_
32	treated	treat	VBN	_	_	_
33	with	with	IN	_	_	_
34	1	1	CD	_	_	_
35	%	%	NN	_	_	_
36	final	final	JJ	_	_	_
37	volumen	voluman	NNS	_	_	_
38	formaldehyde	formaldehyde	NN	_	_	_
39	for	for	IN	_	_	_
40	ten	ten	CD	_	_	_
41	minutes	minute	NNS	_	_	_
42	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1/100	1/100	CD	_	_	_
5	vol	vol	NN	_	_	_
6	.	.	.	_	_	_

1	of	of	IN	_	_	_
2	1M	1m	NN	_	_	_
3	,	,	,	_	_	_
4	pH	ph	NN	_	_	_
5	7.6	7.6	CD	_	_	_
6	;	;	:	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	final	final	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	mid-log	mid-log	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	to	to	TO	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	final	final	JJ	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	anaerobic	anaerobic	JJ	_	_	_
27	sparging	sparging	NN	_	_	_
28	was	be	VBD	_	_	_
29	continued	continue	VBN	_	_	_
30	for	for	IN	_	_	_
31	10	10	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	2.5	2.5	CD	_	_	_
3	M	m	NN	_	_	_
4	glycine	glycine	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	100mM	100mm	NN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	anaerobic	anaerobic	JJ	_	_	_
19	sparging	sparging	NN	_	_	_
20	for	for	IN	_	_	_
21	30	30	CD	_	_	_
22	minutes	minute	NNS	_	_	_
23	to	to	TO	_	_	_
24	stop	stop	VB	_	_	_
25	the	the	DT	_	_	_
26	crosslinking	crosslinking	NN	_	_	_
27	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	spun	spin	VBN	_	_	_
4	at	at	IN	_	_	_
5	5000	5000	CD	_	_	_
6	x	x	CC	_	_	_
7	g	g	NN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	repeatedly	repeatedly	RB	_	_	_
12	with	with	IN	_	_	_
13	phosphate	phosphate	NN	_	_	_
14	buffered	buffer	VBN	_	_	_
15	saline	saline	NN	_	_	_
16	before	before	IN	_	_	_
17	being	be	VBG	_	_	_
18	frozen	freeze	VBN	_	_	_
19	at	at	IN	_	_	_
20	-80	-80	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	with	with	IN	_	_	_
6	vigorous	vigorous	JJ	_	_	_
7	shaking	shake	VBG	_	_	_
8	at	at	IN	_	_	_
9	37	37	CD	_	_	_
10	°C	°c	NN	_	_	_
11	to	to	TO	_	_	_
12	mid-log	mid-log	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	light	light	JJ	_	_	_
15	scattering	scattering	NN	_	_	_
16	at	at	IN	_	_	_
17	600	600	CD	_	_	_
18	nm	nm	NN	_	_	_
19	equivalent	equivalent	NN	_	_	_
20	to	to	TO	_	_	_
21	0.4	0.4	CD	_	_	_
22	OD	od	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1/100	1/100	CD	_	_	_
5	vol	vol	NN	_	_	_
6	.	.	.	_	_	_

1	of	of	IN	_	_	_
2	1M	1m	NN	_	_	_
3	,	,	,	_	_	_
4	pH	ph	NN	_	_	_
5	7.6	7.6	CD	_	_	_
6	;	;	:	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	final	final	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	mid-log	mid-log	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	to	to	TO	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	final	final	JJ	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	shaking	shake	VBG	_	_	_
27	was	be	VBD	_	_	_
28	continued	continue	VBN	_	_	_
29	for	for	IN	_	_	_
30	5	5	CD	_	_	_
31	min	min	NN	_	_	_
32	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	2.5	2.5	CD	_	_	_
3	M	m	NN	_	_	_
4	glycine	glycine	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	100mM	100mm	NN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	agitation	agitation	NN	_	_	_
19	for	for	IN	_	_	_
20	30	30	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	to	to	TO	_	_	_
23	stop	stop	VB	_	_	_
24	the	the	DT	_	_	_
25	crosslinking	crosslinking	NN	_	_	_
26	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	spun	spin	VBN	_	_	_
4	at	at	IN	_	_	_
5	5000	5000	CD	_	_	_
6	x	x	CC	_	_	_
7	g	g	NN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	repeatedly	repeatedly	RB	_	_	_
12	with	with	IN	_	_	_
13	phosphate	phosphate	NN	_	_	_
14	buffered	buffer	VBN	_	_	_
15	saline	saline	NN	_	_	_
16	before	before	IN	_	_	_
17	being	be	VBG	_	_	_
18	frozen	freeze	VBN	_	_	_
19	at	at	IN	_	_	_
20	-80	-80	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	after	after	IN	_	_	_
6	the	the	DT	_	_	_
7	addition	addition	NN	_	_	_
8	of	of	IN	_	_	_
9	rifampicin	rifampicin	NN	SUPP	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	250	250	CD	_	_	_
12	μg/ml	μg/ml	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	to	to	TO	_	_	_
15	stop	stop	VB	_	_	_
16	nascent	nascent	JJ	_	_	_
17	transcription	transcription	NN	_	_	_
18	and	and	CC	_	_	_
19	quenched	quench	VBN	_	_	_
20	with	with	IN	_	_	_
21	stop	stop	NN	_	_	_
22	solution	solution	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	10	10	CD	_	_	_
25	%	%	NN	_	_	_
26	phenol	phenol	NN	_	_	_
27	in	in	IN	_	_	_
28	ethanol	ethanol	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	first	first	JJ	_	_	_
3	timepoint	timepoint	NN	_	_	_
4	was	be	VBD	_	_	_
5	taken	take	VBN	_	_	_
6	3.5	3.5	CD	_	_	_
7	minutes	minute	NNS	_	_	_
8	after	after	IN	_	_	_
9	addition	addition	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	antibiotic	antibiotic	JJ	_	_	_
13	to	to	TO	_	_	_
14	give	give	VB	_	_	_
15	time	time	NN	_	_	_
16	for	for	IN	_	_	_
17	the	the	DT	_	_	_
18	diffusion	diffusion	NN	_	_	_
19	of	of	IN	_	_	_
20	rifampicin	rifampicin	NN	SUPP	_	_
21	into	into	IN	_	_	_
22	the	the	DT	_	_	_
23	cells	cell	NNS	_	_	_
24	and	and	CC	_	_	_
25	binding	binding	NN	_	_	_
26	of	of	IN	_	_	_
27	the	the	DT	_	_	_
28	antibiotic	antibiotic	JJ	_	_	_
29	to	to	TO	_	_	_
30	RNA	rna	NN	_	_	_
31	polymerase	polymerase	NN	_	_	_
32	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	called	call	VBN	_	_	_
5	0	0	CD	_	_	_
6	minutes	minute	NNS	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	further	further	RB	_	_	_
10	samples	sample	NNS	_	_	_
11	were	be	VBD	_	_	_
12	taken	take	VBN	_	_	_
13	at	at	IN	_	_	_
14	2.5	2.5	CD	_	_	_
15	,	,	,	_	_	_
16	5	5	CD	_	_	_
17	,	,	,	_	_	_
18	7.5	7.5	CD	_	_	_
19	,	,	,	_	_	_
20	10	10	CD	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	20	20	CD	_	_	_
24	minutes	minute	NNS	_	_	_
25	from	from	IN	_	_	_
26	wild-type	wild-type	JJ	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	and	and	CC	_	_	_
30	the	the	DT	_	_	_
31	RNase	rnase	NN	_	_	_
32	III	iii	CD	_	_	_
33	mutant	mutant	NN	_	_	_
34	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	partial	partial	JJ	_	_	_
3	biological	biological	JJ	_	_	_
4	replicate	replicate	VB	_	_	_
5	of	of	IN	_	_	_
6	wild-type	wild-type	JJ	_	_	_
7	was	be	VBD	_	_	_
8	taken	take	VBN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	0	0	CD	_	_	_
11	,	,	,	_	_	_
12	2.5	2.5	CD	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	7.5	7.5	CD	_	_	_
16	minutes	minute	NNS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	to	to	TO	_	_	_
20	examine	examine	VB	_	_	_
21	the	the	DT	_	_	_
22	reproducibility	reproducibility	NN	_	_	_
23	between	between	IN	_	_	_
24	samples	sample	NNS	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	and	and	CC	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	RNAlater	rnalater	NN	_	_	_
9	and	and	CC	_	_	_
10	kept	keep	VBD	_	_	_
11	in	in	IN	_	_	_
12	4C	4c	NN	_	_	_
13	fridge	fridge	NN	_	_	_
14	overnight	overnight	JJ	_	_	_
15	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	directly	directly	RB	_	_	_
6	into	into	IN	_	_	_
7	phenol	phenol	NN	_	_	_
8	:	:	:	_	_	_
9	ethanol	ethanol	NN	_	_	_
10	to	to	TO	_	_	_
11	stabilize	stabilize	VB	_	_	_
12	RNA	rna	NN	_	_	_
13	and	and	CC	_	_	_
14	total	total	JJ	_	_	_
15	RNA	rna	NN	_	_	_
16	was	be	VBD	_	_	_
17	purified	purify	VBN	_	_	_
18	using	use	VBG	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	's	's	POS	_	_	_
21	RNeasy	RNeasy	NNP	_	_	_
22	Mini	Mini	NNP	_	_	_
23	Kit	kit	NN	_	_	_
24	,	,	,	_	_	_
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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	from	from	IN	_	_	_
6	aerobic	aerobic	JJ	_	_	_
7	and	and	CC	_	_	_
8	anaerobic	anaerobic	JJ	_	_	_
9	cultures	culture	NNS	_	_	_
10	of	of	IN	_	_	_
11	seven	seven	CD	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	strains	strain	NNS	_	_	_
15	grown	grow	VBN	_	_	_
16	to	to	TO	_	_	_
17	an	a	DT	_	_	_
18	OD600	od600	NN	_	_	_
19	of	of	IN	_	_	_
20	0.6	0.6	CD	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	exponential	exponential	JJ	GrowthPhase	_	_
23	phase	phase	NN	GrowthPhase	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	on	on	IN	_	_	_
6	days	day	NNS	_	_	_
7	1	1	CD	_	_	_
8	and	and	CC	_	_	_
9	3	3	CD	_	_	_
10	of	of	IN	_	_	_
11	glucose	glucose	NN	SUPP	_	_
12	starvation	starvation	NN	_	_	_
13	,	,	,	_	_	_
14	with	with	IN	_	_	_
15	samples	sample	NNS	_	_	_
16	taken	take	VBN	_	_	_
17	from	from	IN	_	_	_
18	the	the	DT	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Cells	cell	NNS	_	_	_
21	were	be	VBD	_	_	_
22	harvested	harvest	VBN	_	_	_
23	using	use	VBG	_	_	_
24	RNAprotect	rnaprotect	NN	_	_	_
25	Bacteria	bacterium	NNS	_	_	_
26	Reagent	reagent	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Qiagen	Qiagen	NNP	_	_	_
29	,	,	,	_	_	_
30	Hilden	Hilden	NNP	_	_	_
31	,	,	,	_	_	_
32	Germany	Germany	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	for	for	IN	_	_	_
35	stabilization	stabilization	NN	_	_	_
36	of	of	IN	_	_	_
37	RNA	rna	NN	_	_	_
38	.	.	.	_	_	_

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	260/280	260/280	CD	_	_	_
17	nm	nm	NN	_	_	_
18	in	in	IN	_	_	_
19	a	a	DT	_	_	_
20	GeneQuant	GeneQuant	NNP	_	_	_
21	II	II	NNP	_	_	_
22	spectrophotometer	spectrophotometer	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Amersham	amersham	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	concentration	concentration	NN	_	_	_
3	was	be	VBD	_	_	_
4	determined	determine	VBN	_	_	_
5	by	by	IN	_	_	_
6	measuring	measure	VBG	_	_	_
7	UV	uv	NN	_	_	_
8	light	light	NN	_	_	_
9	absorption	absorption	NN	_	_	_
10	at	at	IN	_	_	_
11	260	260	CD	_	_	_
12	nm	nm	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	37C	37c	NN	_	_	_
7	prior	prior	RB	_	_	_
8	to	to	TO	_	_	_
9	extraction	extraction	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	induced	induce	VBN	_	_	_
14	with	with	IN	_	_	_
15	arabinose	arabinose	NN	_	_	_
16	or	or	CC	_	_	_
17	heat	heat	NN	_	_	_
18	shocked	shocked	JJ	_	_	_
19	,	,	,	_	_	_
20	then	then	RB	_	_	_
21	harvested	harvest	VBN	_	_	_
22	and	and	CC	_	_	_
23	flash	flash	VB	_	_	_
24	frozen	frozen	JJ	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	from	from	IN	_	_	_
6	frozen	frozen	JJ	_	_	_
7	cultures	culture	NNS	_	_	_
8	into	into	IN	_	_	_
9	5	5	CD	_	_	_
10	mL	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	LB	lb	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	grown	grow	VBN	_	_	_
16	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	from	from	IN	_	_	_
6	overnight	overnight	JJ	_	_	_
7	grown	grown	JJ	_	_	_
8	culture	culture	NN	_	_	_
9	in	in	IN	_	_	_
10	Lysogeny	Lysogeny	NNP	_	_	_
11	Broth	Broth	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	LB	LB	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	then	then	RB	_	_	_
17	harvested	harvest	VBN	_	_	_
18	in	in	IN	_	_	_
19	the	the	DT	_	_	_
20	early	early	JJ	_	_	_
21	exponential	exponential	JJ	_	_	_
22	growth	growth	NN	_	_	_
23	phase	phase	NN	_	_	_
24	and	and	CC	_	_	_
25	mid	mid	JJ	_	_	_
26	exponential	exponential	JJ	_	_	_
27	growth	growth	NN	_	_	_
28	phase	phase	NN	_	_	_
29	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	lysed	lyse	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Biospec	biospec	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	mRNA	mrna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	using	use	VBG	_	_	_
17	a	a	DT	_	_	_
18	Qiagen	Qiagen	NNP	_	_	_
19	RNeasy	RNeasy	NNP	_	_	_
20	mini	minus	NNS	_	_	_
21	kit	kit	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Cat	cat	NN	_	_	_
24	#	#	#	_	_	_
25	74104	74104	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pelleted	pelleted	JJ	_	_	_
5	and	and	CC	_	_	_
6	RNA	rna	NN	_	_	_
7	was	be	VBD	_	_	_
8	purified	purify	VBN	_	_	_
9	using	use	VBG	_	_	_
10	a	a	DT	_	_	_
11	commercially	commercially	RB	_	_	_
12	available	available	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	extraction	extraction	NN	_	_	_
15	kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	qiagen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

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	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	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	10mg/ml	10mg/ml	JJ	_	_	_
23	lysosyme	lysosyme	NN	_	_	_
24	,	,	,	_	_	_
25	0.1	0.1	CD	_	_	_
26	mg/ml	mg/ml	JJ	_	_	_
27	EDTA	edta	NN	_	_	_
28	,	,	,	_	_	_
29	0.1	0.1	CD	_	_	_
30	mg/ml	mg/ml	NN	_	_	_
31	RNaseA	rnasea	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	and	and	CC	_	_	_
34	subsequently	subsequently	RB	_	_	_
35	incubated	incubate	VBN	_	_	_
36	for	for	IN	_	_	_
37	30	30	CD	_	_	_
38	min	min	NN	_	_	_
39	at	at	IN	_	_	_
40	37C	37c	NN	_	_	_
41	.	.	.	_	_	_

1	Next	next	RB	_	_	_
2	,	,	,	_	_	_
3	IP	IP	NNP	_	_	_
4	buffer	buffer	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	50mM	50mm	NN	_	_	_
9	Hepes	hepe	NNS	_	_	_
10	,	,	,	_	_	_
11	150mM	150mm	NN	_	_	_
12	NaCl	nacl	NN	_	_	_
13	,	,	,	_	_	_
14	1mM	1mm	NN	_	_	_
15	EDTA	edta	NN	_	_	_
16	,	,	,	_	_	_
17	1	1	CD	_	_	_
18	%	%	NN	_	_	_
19	triton	triton	NN	_	_	_
20	,	,	,	_	_	_
21	0.1	0.1	CD	_	_	_
22	%	%	NN	_	_	_
23	sodium	sodium	NN	_	_	_
24	deoxycholate	deoxycholate	NN	SUPP	_	_
25	,	,	,	_	_	_
26	0.1	0.1	CD	_	_	_
27	%	%	NN	_	_	_
28	SDS	sds	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	have	have	VBP	_	_	_
3	been	be	VBN	_	_	_
4	sonicated	sonicate	VBN	_	_	_
5	,	,	,	_	_	_
6	centrifugated	centrifugate	VBN	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	the	the	DT	_	_	_
10	supernatent	supernatent	NN	_	_	_
11	was	be	VBD	_	_	_
12	used	use	VBN	_	_	_
13	for	for	IN	_	_	_
14	the	the	DT	_	_	_
15	immunoprecipitation	immunoprecipitation	NN	_	_	_
16	.	.	.	_	_	_

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

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	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	/	/	:	_	_	_
19	g	g	NN	_	_	_
20	of	of	IN	_	_	_
21	DNase	dnase	NN	_	_	_
22	I	i	CD	_	_	_
23	,	,	,	_	_	_
24	27	27	CD	_	_	_
25	--	--	:	_	_	_
26	0514-01	0514-01	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Amersham	Amersham	NNP	_	_	_
29	Biosciences	Biosciences	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	for	for	IN	_	_	_
32	10	10	CD	_	_	_
33	min	min	NN	_	_	_
34	at	at	IN	_	_	_
35	37	37	CD	_	_	_
36	°C	°c	NN	_	_	_
37	in	in	IN	_	_	_
38	1	1	CD	_	_	_
39	One-Phor-All	one-phor-all	NN	_	_	_
40	buffer	buffer	NN	_	_	_
41	,	,	,	_	_	_
42	27	27	CD	_	_	_
43	--	--	:	_	_	_
44	0901-02	0901-02	CD	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	Amersham	Amersham	NNP	_	_	_
47	Biosciences	Biosciences	NNP	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	.	.	.	_	_	_

1	Heat	heat	NN	_	_	_
2	inactivation	inactivation	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	DNase	dnase	NN	_	_	_
6	I	i	CD	_	_	_
7	enzyme	enzyme	NN	_	_	_
8	was	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	at	at	IN	_	_	_
11	98	98	CD	_	_	_
12	°C	°c	NN	_	_	_
13	for	for	IN	_	_	_
14	10	10	CD	_	_	_
15	min	min	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	transferred	transfer	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	fresh	fresh	JJ	_	_	_
8	minimal	minimal	JJ	_	_	_
9	media	media	NNS	_	_	_
10	,	,	,	_	_	_
11	mM63	mm63	NN	_	_	_
12	,	,	,	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	presence	presence	NN	_	_	_
16	or	or	CC	_	_	_
17	absence	absence	NN	_	_	_
18	of	of	IN	_	_	_
19	histidine	histidine	NN	_	_	_
20	.	.	.	_	_	_

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/mL	cells/ml	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	the	the	DT	_	_	_
13	final	final	JJ	_	_	_
14	ones	one	NNS	_	_	_
15	~	~	VBP	_	_	_
16	108	108	CD	_	_	_
17	cells/mL	cells/ml	NN	_	_	_
18	within	within	IN	_	_	_
19	the	the	DT	_	_	_
20	exponential	exponential	JJ	_	_	_
21	growth	growth	NN	_	_	_
22	phase	phase	NN	_	_	_
23	.	.	.	_	_	_

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	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	,	,	,	_	_	_
14	spun	spin	VBD	_	_	_
15	down	down	RB	_	_	_
16	and	and	CC	_	_	_
17	flash	flash	VB	_	_	_
18	frozen	frozen	JJ	_	_	_
19	and	and	CC	_	_	_
20	stored	store	VBN	_	_	_
21	at	at	IN	_	_	_
22	-80	-80	CD	_	_	_
23	°C	°c	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	ref	ref	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	rifampicin	rifampicin	NN	SUPP	_	_
7	before	before	IN	_	_	_
8	sample	sample	NN	_	_	_
9	collection	collection	NN	_	_	_
10	.	.	.	_	_	_

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	cell	cell	NN	_	_	_
3	type	type	NN	_	_	_
4	:	:	:	_	_	_
5	Ancestral	ancestral	JJ	_	_	_
6	I	I	PRP	_	_	_
7	-	-	:	_	_	_
8	cells	cell	NNS	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	cell	cell	NN	_	_	_
11	type	type	NN	_	_	_
12	:	:	:	_	_	_
13	Ancestral	ancestral	JJ	_	_	_
14	L	l	NN	_	_	_
15	-	-	:	_	_	_
16	cells	cell	NNS	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	cell	cell	NN	_	_	_
19	type	type	NN	_	_	_
20	:	:	:	_	_	_
21	bacterial	bacterial	JJ	_	_	_
22	cells	cell	NNS	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	cell	cell	NN	_	_	_
25	type	type	NN	_	_	_
26	:	:	:	_	_	_
27	bacterial	bacterial	JJ	_	_	_
28	liquid	liquid	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	cell	cell	NN	_	_	_
32	type	type	NN	_	_	_
33	:	:	:	_	_	_
34	biofilm	biofilm	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	cell	cell	NN	_	_	_
37	type	type	NN	_	_	_
38	:	:	:	_	_	_
39	Escherichia	escherichia	FW	Organism	_	_
40	coli	coli	FW	Organism	_	_
41	str	str	FW	_	_	_
42	.	.	.	_	_	_

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

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	cell	cell	NN	_	_	_
4	type	type	NN	_	_	_
5	:	:	:	_	_	_
6	Evolved	evolve	VBN	_	_	_
7	I	I	PRP	_	_	_
8	-	-	:	_	_	_
9	cells	cell	NNS	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	cell	cell	NN	_	_	_
12	type	type	NN	_	_	_
13	:	:	:	_	_	_
14	Evolved	evolve	VBN	_	_	_
15	L	l	NN	_	_	_
16	-	-	:	_	_	_
17	cells	cell	NNS	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	cell	cell	NN	_	_	_
20	type	type	NN	_	_	_
21	:	:	:	_	_	_
22	Original	original	JJ	_	_	_
23	prototroph	prototroph	NN	_	_	_
24	DH1	dh1	NN	_	_	_
25	cells	cell	NNS	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
27	cell	cell	NN	_	_	_
28	type	type	NN	_	_	_
29	:	:	:	_	_	_
30	Persister	persister	NN	_	_	_
31	cells	cell	NNS	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
33	cell	cell	NN	_	_	_
34	type	type	NN	_	_	_
35	:	:	:	_	_	_
36	Planktonic	planktonic	JJ	_	_	_
37	cells	cell	NNS	_	_	_
38	harvested	harvest	VBN	_	_	_
39	at	at	IN	_	_	_
40	a	a	DT	_	_	_
41	turbidity	turbidity	NN	_	_	_
42	of	of	IN	_	_	_
43	0.5	0.5	CD	_	_	_
44	at	at	IN	_	_	_
45	600	600	CD	_	_	_
46	nm	nm	NN	_	_	_
47	,	,	,	_	_	_
48	adjusted	adjust	VBN	_	_	_
49	to	to	TO	_	_	_
50	the	the	DT	_	_	_
51	turbidity	turbidity	NN	_	_	_
52	at	at	IN	_	_	_
53	1	1	CD	_	_	_
54	,	,	,	_	_	_
55	and	and	CC	_	_	_
56	then	then	RB	_	_	_
57	exposed	expose	VBN	_	_	_
58	to	to	TO	_	_	_
59	20	20	CD	_	_	_
60	μg/mL	μg/ml	NN	_	_	_
61	ampicillin	ampicillin	NN	_	_	_
62	for	for	IN	_	_	_
63	1	1	CD	_	_	_
64	h.	h.	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Cell	cell	NN	_	_	_
67	were	be	VBD	_	_	_
68	grown	grow	VBN	_	_	_
69	in	in	IN	_	_	_
70	3-liter	3-liter	NN	_	_	_
71	stirred	stir	VBD	_	_	_
72	tank	tank	NN	_	_	_
73	bioreactor	bioreactor	NN	_	_	_
74	anaerobically	anaerobically	RB	_	_	_
75	.	.	.	_	_	_

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/l	g/l	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	,	,	,	_	_	_
11	K2HPO4	k2hpo4	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	2.5	2.5	CD	_	_	_
14	g/l	g/l	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	NH4	nh4	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	2SO4	2so4	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	9.0	9.0	CD	_	_	_
23	g/l	g/l	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	Glucose	glucose	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	15.0	15.0	CD	_	_	_
29	g/l	g/l	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	CaCl2	cacl2	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	2.2	2.2	CD	_	_	_
35	mg/l	mg/l	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	,	,	,	_	_	_
38	MgSO4	mgso4	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	0.55	0.55	CD	_	_	_
41	g/l	g/l	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	,	,	,	_	_	_
44	NaH2-Citrate	nah2-citrate	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	234	234	CD	_	_	_
47	mg/l	mg/l	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	,	,	,	_	_	_
50	FeCl3	fecl3	NN	_	_	_
51	*	*	SYM	_	_	_
52	6	6	CD	_	_	_
53	H2O	h2o	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	25.0	25.0	CD	_	_	_
56	mg/l	mg/l	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	,	,	,	_	_	_
59	ZnSO4	znso4	NN	_	_	_
60	*	*	SYM	_	_	_
61	7	7	CD	_	_	_
62	H2O	h2o	NN	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	0.18	0.18	CD	_	_	_
65	mg/l	mg/l	NN	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	,	,	,	_	_	_
68	MnSO4	mnso4	NN	_	_	_
69	*	*	SYM	_	_	_
70	7	7	CD	_	_	_
71	H2O	h2o	NN	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	0.1	0.1	CD	_	_	_
74	mg/l	mg/l	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	,	,	,	_	_	_
77	CuSO4	cuso4	NN	_	_	_
78	*	*	SYM	_	_	_
79	5	5	CD	_	_	_
80	H2O	h2o	NN	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	0.16	0.16	CD	_	_	_
83	mg/l	mg/l	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	,	,	,	_	_	_
86	CoCl2	cocl2	NN	_	_	_
87	*	*	SYM	_	_	_
88	6	6	CD	_	_	_
89	H2O	h2o	NN	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	0.18	0.18	CD	_	_	_
92	mg/l	mg/l	NN	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	.	.	.	_	_	_

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	CFT073	cft073	NN	_	_	_
47	in	in	IN	_	_	_
48	K-med	k-med	JJ	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	CFT073	cft073	NN	_	_	_
51	in	in	IN	_	_	_
52	LB	LB	NNP	_	_	_
53	,	,	,	_	_	_
54	after	after	IN	_	_	_
55	5	5	CD	_	_	_
56	hours	hour	NNS	_	_	_
57	of	of	IN	_	_	_
58	growth	growth	NN	_	_	_
59	.	.	.	_	_	_

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/mL	µg/ml	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	,	,	,	_	_	_
11	after	after	IN	_	_	_
12	5	5	CD	_	_	_
13	hours	hour	NNS	_	_	_
14	of	of	IN	_	_	_
15	growth	growth	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	CFT073	cft073	NN	_	_	_
3	in	in	IN	_	_	_
4	NaCl	nacl	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	CFT073	cft073	NN	_	_	_
7	in	in	IN	_	_	_
8	urea	urea	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	CFT073	cft073	NN	_	_	_
11	K-med	k-med	JJ	_	_	_
12	biological	biological	JJ	_	_	_
13	rep	rep	NN	GEN	_	_
14	1	1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	CFT073	cft073	NN	_	_	_
17	K-med	k-med	JJ	_	_	_
18	biological	biological	JJ	_	_	_
19	rep	rep	NN	GEN	_	_
20	2	2	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	CFT073	cft073	NN	_	_	_
23	K-med	k-med	JJ	_	_	_
24	biological	biological	JJ	_	_	_
25	rep	rep	NN	GEN	_	_
26	3	3	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	CFT073	cft073	NN	_	_	_
29	_	_	CD	_	_	_
30	LB+PAC	lb+pac	NN	_	_	_
31	s	s	NNS	_	_	_
32	_	_	VBP	_	_	_
33	rep1	rep1	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	CFT073	cft073	NN	_	_	_
36	_	_	CD	_	_	_
37	LB+PAC	lb+pac	NN	_	_	_
38	s	s	NNS	_	_	_
39	_	_	VBP	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	CFT073	cft073	NN	_	_	_
43	_	_	CD	_	_	_
44	LB+PAC	lb+pac	NN	_	_	_
45	s	s	NNS	_	_	_
46	_	_	VBP	_	_	_
47	rep3	rep3	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	CFT073	cft073	NN	_	_	_
50	_	_	CD	_	_	_
51	LB	lb	NN	_	_	_
52	_	_	CD	_	_	_
53	rep1	rep1	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	CFT073	cft073	NN	_	_	_
56	_	_	CD	_	_	_
57	LB	lb	NN	_	_	_
58	_	_	CD	_	_	_
59	rep2	rep2	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	CFT073	cft073	NN	_	_	_
62	_	_	CD	_	_	_
63	LB	lb	NN	_	_	_
64	_	_	CD	_	_	_
65	rep3	rep3	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	CFT073	cft073	NN	_	_	_
68	NaCl	nacl	NN	_	_	_
69	biological	biological	JJ	_	_	_
70	rep	rep	NN	GEN	_	_
71	1	1	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	CFT073	cft073	NN	_	_	_
74	NaCl	nacl	NN	_	_	_
75	biological	biological	JJ	_	_	_
76	rep	rep	NN	GEN	_	_
77	2	2	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	CFT073	cft073	NN	_	_	_
80	NaCl	nacl	NN	_	_	_
81	biological	biological	JJ	_	_	_
82	rep	rep	NN	GEN	_	_
83	3	3	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	CFT073	cft073	NN	_	_	_
86	+	+	CC	_	_	_
87	pBAD	pbad	NN	_	_	_
88	rep	rep	NN	GEN	_	_
89	1	1	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	CFT073	cft073	NN	_	_	_
92	+	+	CC	_	_	_
93	pBAD	pbad	NN	_	_	_
94	rep	rep	NN	GEN	_	_
95	2	2	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	CFT073	cft073	NN	_	_	_
98	+	+	CC	_	_	_
99	pBAD	pbad	NN	_	_	_
100	rep	rep	NN	GEN	_	_
101	3	3	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	CFT073	cft073	NN	_	_	_
104	+	+	CC	_	_	_
105	pBAD-tosR	pbad-tosr	NN	_	_	_
106	rep	rep	NN	GEN	_	_
107	1	1	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	CFT073	cft073	NN	_	_	_
110	+	+	CC	_	_	_
111	pBAD-tosR	pbad-tosr	NN	_	_	_
112	rep	rep	NN	GEN	_	_
113	2	2	CD	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	CFT073	cft073	NN	_	_	_
116	+	+	CC	_	_	_
117	pBAD-tosR	pbad-tosr	NN	_	_	_
118	rep	rep	NN	GEN	_	_
119	3	3	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	CFT073	cft073	NN	_	_	_
122	urea	urea	NN	_	_	_
123	biological	biological	JJ	_	_	_
124	rep	rep	NN	GEN	_	_
125	1	1	CD	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	CFT073	cft073	NN	_	_	_
128	urea	urea	NN	_	_	_
129	biological	biological	JJ	_	_	_
130	rep	rep	NN	GEN	_	_
131	2	2	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	CFT073	cft073	NN	_	_	_
134	urea	urea	NN	_	_	_
135	biological	biological	JJ	_	_	_
136	rep	rep	NN	GEN	_	_
137	3	3	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	Cfx	Cfx	NNP	_	_	_
140	_	_	NNP	_	_	_
141	IN	in	IN	_	_	_
142	_	_	CD	_	_	_
143	10mkM	10mkm	NN	_	_	_
144	_	_	NN	_	_	_
145	3	3	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	Cfx	Cfx	NNP	_	_	_
148	_	_	NNP	_	_	_
149	IN	in	IN	_	_	_
150	_	_	SYM	_	_	_
151	Mu	mu	FW	_	_	_
152	_	_	FW	_	_	_
153	10mkM	10mkm	NN	_	_	_
154	_	_	NN	_	_	_
155	1	1	CD	_	_	_
156	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
157	Cfx	Cfx	NNP	_	_	_
158	_	_	NNP	_	_	_
159	IN	in	IN	_	_	_
160	_	_	SYM	_	_	_
161	Mu	mu	FW	_	_	_
162	_	_	FW	_	_	_
163	10mkM	10mkm	NN	_	_	_
164	_	_	NN	_	_	_
165	2	2	CD	_	_	_
166	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
167	Cfx	Cfx	NNP	_	_	_
168	_	_	NNP	_	_	_
169	IP	IP	NNP	_	_	_
170	_	_	NNP	_	_	_
171	10mkM	10mkM	NNP	_	_	_
172	_	_	SYM	_	_	_
173	3	3	CD	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	Cfx	Cfx	NNP	_	_	_
176	_	_	NNP	_	_	_
177	IP	IP	NNP	_	_	_
178	_	_	SYM	_	_	_
179	Mu	mu	FW	_	_	_
180	_	_	FW	_	_	_
181	10mkM	10mkm	NN	_	_	_
182	_	_	NN	_	_	_
183	1	1	CD	_	_	_
184	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
185	Cfx	Cfx	NNP	_	_	_
186	_	_	NNP	_	_	_
187	IP	IP	NNP	_	_	_
188	_	_	SYM	_	_	_
189	Mu	mu	FW	_	_	_
190	_	_	FW	_	_	_
191	10mkM	10mkm	NN	_	_	_
192	_	_	NN	_	_	_
193	2	2	CD	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	CGATGT-D2	cgatgt-d2	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	CH3COOH	ch3cooh	NN	_	_	_
198	-LRB-	-lrb-	-LRB-	_	_	_
199	pH	ph	NN	_	_	_
200	5.9	5.9	CD	_	_	_
201	±	±	SYM	_	_	_
202	0.05	0.05	CD	_	_	_
203	-RRB-	-rrb-	-RRB-	_	_	_
204	;	;	:	_	_	_
205	HCl	hcl	NN	_	_	_
206	-LRB-	-lrb-	-LRB-	_	_	_
207	pH	ph	NN	_	_	_
208	4.75	4.75	CD	_	_	_
209	±	±	SYM	_	_	_
210	0.05	0.05	CD	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	;	;	:	_	_	_
213	NaOH	naoh	NN	_	_	_
214	-LRB-	-lrb-	-LRB-	_	_	_
215	pH	ph	NN	_	_	_
216	9.6	9.6	CD	_	_	_
217	±	±	SYM	_	_	_
218	0.05	0.05	CD	_	_	_
219	-RRB-	-rrb-	-RRB-	_	_	_
220	;	;	:	_	_	_
221	EtOH	etoh	NN	_	_	_
222	-LRB-	-lrb-	-LRB-	_	_	_
223	5	5	CD	_	_	_
224	%	%	NN	_	_	_
225	-RRB-	-rrb-	-RRB-	_	_	_
226	;	;	:	_	_	_
227	NaCl	nacl	NN	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	4.5	4.5	CD	_	_	_
230	%	%	NN	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	;	;	:	_	_	_
233	Glycerol	glycerol	NN	_	_	_
234	-LRB-	-lrb-	-LRB-	_	_	_
235	15	15	CD	_	_	_
236	%	%	NN	_	_	_
237	-RRB-	-rrb-	-RRB-	_	_	_
238	;	;	:	_	_	_
239	BC	bc	NN	_	_	_
240	-LRB-	-lrb-	-LRB-	_	_	_
241	7	7	CD	_	_	_
242	and	and	CC	_	_	_
243	9	9	CD	_	_	_
244	mg/ml	mg/ml	NN	_	_	_
245	-RRB-	-rrb-	-RRB-	_	_	_
246	;	;	:	_	_	_
247	EtBr	etbr	NN	_	_	_
248	-LRB-	-lrb-	-LRB-	_	_	_
249	150	150	CD	_	_	_
250	mg/ml	mg/ml	NN	_	_	_
251	-RRB-	-rrb-	-RRB-	_	_	_
252	;	;	:	_	_	_
253	46	46	CD	_	_	_
254	°C	°c	NN	_	_	_
255	;	;	:	_	_	_
256	15	15	CD	_	_	_
257	°C	°c	NN	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	CH3COOH	ch3cooh	NN	_	_	_
260	replicate	replicate	VBP	_	_	_
261	1	1	CD	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	CH3COOH	ch3cooh	NN	_	_	_
264	replicate	replicate	VBP	_	_	_
265	2	2	CD	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	CH3COOH	ch3cooh	NN	_	_	_
268	replicate	replicate	VBP	_	_	_
269	3	3	CD	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	channel	channel	NN	_	_	_
272	1	1	CD	_	_	_
273	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
274	Channel	Channel	NNP	_	_	_
275	1	1	CD	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	Chemostat	chemostat	NN	_	_	_
278	1	1	CD	_	_	_
279	h	h	NN	_	_	_
280	irradiated	irradiated	JJ	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Chemostat	chemostat	NN	_	_	_
283	1h	1h	NN	_	_	_
284	irradiated	irradiated	JJ	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	Chemostat	chemostat	NN	_	_	_
287	50	50	CD	_	_	_
288	h	h	NN	_	_	_
289	irradiated	irradiated	JJ	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	chemostat	chemostat	NN	_	_	_
292	,	,	,	_	_	_
293	specific	specific	JJ	_	_	_
294	growth	growth	NN	_	_	_
295	rate	rate	NN	_	_	_
296	0.51	0.51	CD	_	_	_
297	1/h	1/h	JJ	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	chemostat	chemostat	NN	_	_	_
300	STR	str	NN	_	_	_
301	culture	culture	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	chemostat	chemostat	NN	_	_	_
304	STR	str	NN	_	_	_
305	culture	culture	NN	_	_	_
306	STR	str	NN	_	_	_
307	reference	reference	NN	_	_	_
308	1	1	CD	_	_	_
309	,	,	,	_	_	_
310	rep1	rep1	NN	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	chemostat	chemostat	NN	_	_	_
313	STR	str	NN	_	_	_
314	culture	culture	NN	_	_	_
315	STR	str	NN	_	_	_
316	reference	reference	NN	_	_	_
317	1	1	CD	_	_	_
318	,	,	,	_	_	_
319	rep2	rep2	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	chemostat	chemostat	NN	_	_	_
322	STR	str	NN	_	_	_
323	culture	culture	NN	_	_	_
324	STR	str	NN	_	_	_
325	reference	reference	NN	_	_	_
326	2	2	CD	_	_	_
327	,	,	,	_	_	_
328	rep1	rep1	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	chemostat	chemostat	NN	_	_	_
331	STR	str	NN	_	_	_
332	culture	culture	NN	_	_	_
333	STR	str	NN	_	_	_
334	reference	reference	NN	_	_	_
335	2	2	CD	_	_	_
336	,	,	,	_	_	_
337	rep2	rep2	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	chemostat	chemostat	NN	_	_	_
340	STR	str	NN	_	_	_
341	culture	culture	NN	_	_	_
342	STR	str	NN	_	_	_
343	reference	reference	NN	_	_	_
344	3	3	CD	_	_	_
345	,	,	,	_	_	_
346	rep1	rep1	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	chemostat	chemostat	NN	_	_	_
349	STR	str	NN	_	_	_
350	culture	culture	NN	_	_	_
351	STR	str	NN	_	_	_
352	reference	reference	NN	_	_	_
353	3	3	CD	_	_	_
354	,	,	,	_	_	_
355	rep2	rep2	NN	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	chemostat	chemostat	NN	_	_	_
358	STR-PFR	str-pfr	NN	_	_	_
359	culture	culture	NN	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	chemostat	chemostat	NN	_	_	_
362	STR-PFR	str-pfr	NN	_	_	_
363	culture	culture	NN	_	_	_
364	PFR	pfr	NN	_	_	_
365	P1	p1	NN	_	_	_
366	120	120	CD	_	_	_
367	min	min	NN	_	_	_
368	,	,	,	_	_	_
369	rep1	rep1	NN	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	chemostat	chemostat	NN	_	_	_
372	STR-PFR	str-pfr	NN	_	_	_
373	culture	culture	NN	_	_	_
374	PFR	pfr	NN	_	_	_
375	P1	p1	NN	_	_	_
376	120	120	CD	_	_	_
377	min	min	NN	_	_	_
378	,	,	,	_	_	_
379	rep2	rep2	NN	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
381	chemostat	chemostat	NN	_	_	_
382	STR-PFR	str-pfr	NN	_	_	_
383	culture	culture	NN	_	_	_
384	PFR	pfr	NN	_	_	_
385	P1	p1	NN	_	_	_
386	25	25	CD	_	_	_
387	min	min	NN	_	_	_
388	,	,	,	_	_	_
389	rep1	rep1	NN	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	chemostat	chemostat	NN	_	_	_
392	STR-PFR	str-pfr	NN	_	_	_
393	culture	culture	NN	_	_	_
394	PFR	pfr	NN	_	_	_
395	P1	p1	NN	_	_	_
396	25	25	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	PFR	pfr	NN	_	_	_
405	P1	p1	NN	_	_	_
406	28h	28h	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	PFR	pfr	NN	_	_	_
414	P1	p1	NN	_	_	_
415	28h	28h	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	PFR	pfr	NN	_	_	_
423	P3	p3	NN	_	_	_
424	120	120	CD	_	_	_
425	min	min	NN	_	_	_
426	,	,	,	_	_	_
427	rep1	rep1	NN	_	_	_
428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
429	chemostat	chemostat	NN	_	_	_
430	STR-PFR	str-pfr	NN	_	_	_
431	culture	culture	NN	_	_	_
432	PFR	pfr	NN	_	_	_
433	P3	p3	NN	_	_	_
434	120	120	CD	_	_	_
435	min	min	NN	_	_	_
436	,	,	,	_	_	_
437	rep2	rep2	NN	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	chemostat	chemostat	NN	_	_	_
440	STR-PFR	str-pfr	NN	_	_	_
441	culture	culture	NN	_	_	_
442	PFR	pfr	NN	_	_	_
443	P3	p3	NN	_	_	_
444	25	25	CD	_	_	_
445	min	min	NN	_	_	_
446	,	,	,	_	_	_
447	rep1	rep1	NN	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	chemostat	chemostat	NN	_	_	_
450	STR-PFR	str-pfr	NN	_	_	_
451	culture	culture	NN	_	_	_
452	PFR	pfr	NN	_	_	_
453	P3	p3	NN	_	_	_
454	25	25	CD	_	_	_
455	min	min	NN	_	_	_
456	,	,	,	_	_	_
457	rep2	rep2	NN	_	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	chemostat	chemostat	NN	_	_	_
460	STR-PFR	str-pfr	NN	_	_	_
461	culture	culture	NN	_	_	_
462	PFR	pfr	NN	_	_	_
463	P3	p3	NN	_	_	_
464	28h	28h	NN	_	_	_
465	,	,	,	_	_	_
466	rep1	rep1	NN	_	_	_
467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
468	chemostat	chemostat	NN	_	_	_
469	STR-PFR	str-pfr	NN	_	_	_
470	culture	culture	NN	_	_	_
471	PFR	pfr	NN	_	_	_
472	P3	p3	NN	_	_	_
473	28h	28h	NN	_	_	_
474	,	,	,	_	_	_
475	rep2	rep2	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	chemostat	chemostat	NN	_	_	_
478	STR-PFR	str-pfr	NN	_	_	_
479	culture	culture	NN	_	_	_
480	PFR	pfr	NN	_	_	_
481	P5	p5	NN	_	_	_
482	10	10	CD	_	_	_
483	min	min	NN	_	_	_
484	,	,	,	_	_	_
485	rep1	rep1	NN	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	chemostat	chemostat	NN	_	_	_
488	STR-PFR	str-pfr	NN	_	_	_
489	culture	culture	NN	_	_	_
490	PFR	pfr	NN	_	_	_
491	P5	p5	NN	_	_	_
492	10	10	CD	_	_	_
493	min	min	NN	_	_	_
494	,	,	,	_	_	_
495	rep2	rep2	NN	_	_	_
496	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
497	chemostat	chemostat	NN	_	_	_
498	STR-PFR	str-pfr	NN	_	_	_
499	culture	culture	NN	_	_	_
500	PFR	pfr	NN	_	_	_
501	P5	p5	NN	_	_	_
502	120	120	CD	_	_	_
503	min	min	NN	_	_	_
504	,	,	,	_	_	_
505	rep1	rep1	NN	_	_	_
506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
507	chemostat	chemostat	NN	_	_	_
508	STR-PFR	str-pfr	NN	_	_	_
509	culture	culture	NN	_	_	_
510	PFR	pfr	NN	_	_	_
511	P5	p5	NN	_	_	_
512	120	120	CD	_	_	_
513	min	min	NN	_	_	_
514	,	,	,	_	_	_
515	rep2	rep2	NN	_	_	_
516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
517	chemostat	chemostat	NN	_	_	_
518	STR-PFR	str-pfr	NN	_	_	_
519	culture	culture	NN	_	_	_
520	PFR	pfr	NN	_	_	_
521	P5	p5	NN	_	_	_
522	210	210	CD	_	_	_
523	min	min	NN	_	_	_
524	,	,	,	_	_	_
525	rep1	rep1	NN	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	chemostat	chemostat	NN	_	_	_
528	STR-PFR	str-pfr	NN	_	_	_
529	culture	culture	NN	_	_	_
530	PFR	pfr	NN	_	_	_
531	P5	p5	NN	_	_	_
532	210	210	CD	_	_	_
533	min	min	NN	_	_	_
534	,	,	,	_	_	_
535	rep2	rep2	NN	_	_	_
536	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
537	chemostat	chemostat	NN	_	_	_
538	STR-PFR	str-pfr	NN	_	_	_
539	culture	culture	NN	_	_	_
540	PFR	pfr	NN	_	_	_
541	P5	p5	NN	_	_	_
542	25h	25h	NN	_	_	_
543	,	,	,	_	_	_
544	rep1	rep1	NN	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	chemostat	chemostat	NN	_	_	_
547	STR-PFR	str-pfr	NN	_	_	_
548	culture	culture	NN	_	_	_
549	PFR	pfr	NN	_	_	_
550	P5	p5	NN	_	_	_
551	25h	25h	NN	_	_	_
552	,	,	,	_	_	_
553	rep2	rep2	NN	_	_	_
554	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
555	chemostat	chemostat	NN	_	_	_
556	STR-PFR	str-pfr	NN	_	_	_
557	culture	culture	NN	_	_	_
558	PFR	pfr	NN	_	_	_
559	P5	p5	NN	_	_	_
560	25	25	CD	_	_	_
561	min	min	NN	_	_	_
562	,	,	,	_	_	_
563	rep1	rep1	NN	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	chemostat	chemostat	NN	_	_	_
566	STR-PFR	str-pfr	NN	_	_	_
567	culture	culture	NN	_	_	_
568	PFR	pfr	NN	_	_	_
569	P5	p5	NN	_	_	_
570	25	25	CD	_	_	_
571	min	min	NN	_	_	_
572	,	,	,	_	_	_
573	rep2	rep2	NN	_	_	_
574	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
575	chemostat	chemostat	NN	_	_	_
576	STR-PFR	str-pfr	NN	_	_	_
577	culture	culture	NN	_	_	_
578	PFR	pfr	NN	_	_	_
579	P5	p5	NN	_	_	_
580	26h	26h	NN	_	_	_
581	,	,	,	_	_	_
582	rep2	rep2	NN	_	_	_
583	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
584	chemostat	chemostat	NN	_	_	_
585	STR-PFR	str-pfr	NN	_	_	_
586	culture	culture	NN	_	_	_
587	PFR	pfr	NN	_	_	_
588	P5	p5	NN	_	_	_
589	28h	28h	NN	_	_	_
590	,	,	,	_	_	_
591	rep1	rep1	NN	_	_	_
592	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
593	chemostat	chemostat	NN	_	_	_
594	STR-PFR	str-pfr	NN	_	_	_
595	culture	culture	NN	_	_	_
596	PFR	pfr	NN	_	_	_
597	P5	p5	NN	_	_	_
598	28h	28h	NN	_	_	_
599	,	,	,	_	_	_
600	rep2	rep2	NN	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	chemostat	chemostat	NN	_	_	_
603	STR-PFR	str-pfr	NN	_	_	_
604	culture	culture	NN	_	_	_
605	PFR	pfr	NN	_	_	_
606	P5	p5	NN	_	_	_
607	330	330	CD	_	_	_
608	min	min	NN	_	_	_
609	,	,	,	_	_	_
610	rep2	rep2	NN	_	_	_
611	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
612	chemostat	chemostat	NN	_	_	_
613	STR-PFR	str-pfr	NN	_	_	_
614	culture	culture	NN	_	_	_
615	PFR	pfr	NN	_	_	_
616	P5	p5	NN	_	_	_
617	45	45	CD	_	_	_
618	min	min	NN	_	_	_
619	,	,	,	_	_	_
620	rep1	rep1	NN	_	_	_
621	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
622	chemostat	chemostat	NN	_	_	_
623	STR-PFR	str-pfr	NN	_	_	_
624	culture	culture	NN	_	_	_
625	PFR	pfr	NN	_	_	_
626	P5	p5	NN	_	_	_
627	45	45	CD	_	_	_
628	min	min	NN	_	_	_
629	,	,	,	_	_	_
630	rep2	rep2	NN	_	_	_
631	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
632	chemostat	chemostat	NN	_	_	_
633	STR-PFR	str-pfr	NN	_	_	_
634	culture	culture	NN	_	_	_
635	PFR	pfr	NN	_	_	_
636	P5	p5	NN	_	_	_
637	5	5	CD	_	_	_
638	min	min	NN	_	_	_
639	,	,	,	_	_	_
640	rep1	rep1	NN	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
642	chemostat	chemostat	NN	_	_	_
643	STR-PFR	str-pfr	NN	_	_	_
644	culture	culture	NN	_	_	_
645	PFR	pfr	NN	_	_	_
646	P5	p5	NN	_	_	_
647	5	5	CD	_	_	_
648	min	min	NN	_	_	_
649	,	,	,	_	_	_
650	rep2	rep2	NN	_	_	_
651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
652	chemostat	chemostat	NN	_	_	_
653	STR-PFR	str-pfr	NN	_	_	_
654	culture	culture	NN	_	_	_
655	PFR	pfr	NN	_	_	_
656	P5	p5	NN	_	_	_
657	75	75	CD	_	_	_
658	min	min	NN	_	_	_
659	,	,	,	_	_	_
660	rep2	rep2	NN	_	_	_
661	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
662	chemostat	chemostat	NN	_	_	_
663	STR-PFR	str-pfr	NN	_	_	_
664	culture	culture	NN	_	_	_
665	STR	str	NN	_	_	_
666	10	10	CD	_	_	_
667	min	min	NN	_	_	_
668	,	,	,	_	_	_
669	rep1	rep1	NN	_	_	_
670	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
671	chemostat	chemostat	NN	_	_	_
672	STR-PFR	str-pfr	NN	_	_	_
673	culture	culture	NN	_	_	_
674	STR	str	NN	_	_	_
675	10	10	CD	_	_	_
676	min	min	NN	_	_	_
677	,	,	,	_	_	_
678	rep2	rep2	NN	_	_	_
679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
680	chemostat	chemostat	NN	_	_	_
681	STR-PFR	str-pfr	NN	_	_	_
682	culture	culture	NN	_	_	_
683	STR	str	NN	_	_	_
684	120	120	CD	_	_	_
685	min	min	NN	_	_	_
686	,	,	,	_	_	_
687	rep1	rep1	NN	_	_	_
688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
689	chemostat	chemostat	NN	_	_	_
690	STR-PFR	str-pfr	NN	_	_	_
691	culture	culture	NN	_	_	_
692	STR	str	NN	_	_	_
693	120	120	CD	_	_	_
694	min	min	NN	_	_	_
695	,	,	,	_	_	_
696	rep2	rep2	NN	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
698	chemostat	chemostat	NN	_	_	_
699	STR-PFR	str-pfr	NN	_	_	_
700	culture	culture	NN	_	_	_
701	STR	str	NN	_	_	_
702	210	210	CD	_	_	_
703	min	min	NN	_	_	_
704	,	,	,	_	_	_
705	rep1	rep1	NN	_	_	_
706	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
707	chemostat	chemostat	NN	_	_	_
708	STR-PFR	str-pfr	NN	_	_	_
709	culture	culture	NN	_	_	_
710	STR	str	NN	_	_	_
711	210	210	CD	_	_	_
712	min	min	NN	_	_	_
713	,	,	,	_	_	_
714	rep2	rep2	NN	_	_	_
715	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
716	chemostat	chemostat	NN	_	_	_
717	STR-PFR	str-pfr	NN	_	_	_
718	culture	culture	NN	_	_	_
719	STR	str	NN	_	_	_
720	25h	25h	NN	_	_	_
721	,	,	,	_	_	_
722	rep1	rep1	NN	_	_	_
723	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
724	chemostat	chemostat	NN	_	_	_
725	STR-PFR	str-pfr	NN	_	_	_
726	culture	culture	NN	_	_	_
727	STR	str	NN	_	_	_
728	25h	25h	NN	_	_	_
729	,	,	,	_	_	_
730	rep2	rep2	NN	_	_	_
731	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
732	chemostat	chemostat	NN	_	_	_
733	STR-PFR	str-pfr	NN	_	_	_
734	culture	culture	NN	_	_	_
735	STR	str	NN	_	_	_
736	25	25	CD	_	_	_
737	min	min	NN	_	_	_
738	,	,	,	_	_	_
739	rep1	rep1	NN	_	_	_
740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
741	chemostat	chemostat	NN	_	_	_
742	STR-PFR	str-pfr	NN	_	_	_
743	culture	culture	NN	_	_	_
744	STR	str	NN	_	_	_
745	25	25	CD	_	_	_
746	min	min	NN	_	_	_
747	,	,	,	_	_	_
748	rep2	rep2	NN	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
750	chemostat	chemostat	NN	_	_	_
751	STR-PFR	str-pfr	NN	_	_	_
752	culture	culture	NN	_	_	_
753	STR	str	NN	_	_	_
754	26h	26h	NN	_	_	_
755	,	,	,	_	_	_
756	rep1	rep1	NN	_	_	_
757	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
758	chemostat	chemostat	NN	_	_	_
759	STR-PFR	str-pfr	NN	_	_	_
760	culture	culture	NN	_	_	_
761	STR	str	NN	_	_	_
762	26h	26h	NN	_	_	_
763	,	,	,	_	_	_
764	rep2	rep2	NN	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
766	chemostat	chemostat	NN	_	_	_
767	STR-PFR	str-pfr	NN	_	_	_
768	culture	culture	NN	_	_	_
769	STR	str	NN	_	_	_
770	28h	28h	NN	_	_	_
771	,	,	,	_	_	_
772	rep1	rep1	NN	_	_	_
773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
774	chemostat	chemostat	NN	_	_	_
775	STR-PFR	str-pfr	NN	_	_	_
776	culture	culture	NN	_	_	_
777	STR	str	NN	_	_	_
778	28h	28h	NN	_	_	_
779	,	,	,	_	_	_
780	rep2	rep2	NN	_	_	_
781	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
782	chemostat	chemostat	NN	_	_	_
783	STR-PFR	str-pfr	NN	_	_	_
784	culture	culture	NN	_	_	_
785	STR	str	NN	_	_	_
786	330	330	CD	_	_	_
787	min	min	NN	_	_	_
788	,	,	,	_	_	_
789	rep1	rep1	NN	_	_	_
790	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
791	chemostat	chemostat	NN	_	_	_
792	STR-PFR	str-pfr	NN	_	_	_
793	culture	culture	NN	_	_	_
794	STR	str	NN	_	_	_
795	330	330	CD	_	_	_
796	min	min	NN	_	_	_
797	,	,	,	_	_	_
798	rep2	rep2	NN	_	_	_
799	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
800	chemostat	chemostat	NN	_	_	_
801	STR-PFR	str-pfr	NN	_	_	_
802	culture	culture	NN	_	_	_
803	STR	str	NN	_	_	_
804	45	45	CD	_	_	_
805	min	min	NN	_	_	_
806	,	,	,	_	_	_
807	rep1	rep1	NN	_	_	_
808	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
809	chemostat	chemostat	NN	_	_	_
810	STR-PFR	str-pfr	NN	_	_	_
811	culture	culture	NN	_	_	_
812	STR	str	NN	_	_	_
813	45	45	CD	_	_	_
814	min	min	NN	_	_	_
815	,	,	,	_	_	_
816	rep2	rep2	NN	_	_	_
817	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
818	chemostat	chemostat	NN	_	_	_
819	STR-PFR	str-pfr	NN	_	_	_
820	culture	culture	NN	_	_	_
821	STR	str	NN	_	_	_
822	5	5	CD	_	_	_
823	min	min	NN	_	_	_
824	,	,	,	_	_	_
825	rep1	rep1	NN	_	_	_
826	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
827	chemostat	chemostat	NN	_	_	_
828	STR-PFR	str-pfr	NN	_	_	_
829	culture	culture	NN	_	_	_
830	STR	str	NN	_	_	_
831	5	5	CD	_	_	_
832	min	min	NN	_	_	_
833	,	,	,	_	_	_
834	rep2	rep2	NN	_	_	_
835	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
836	chemostat	chemostat	NN	_	_	_
837	STR-PFR	str-pfr	NN	_	_	_
838	culture	culture	NN	_	_	_
839	STR	str	NN	_	_	_
840	75	75	CD	_	_	_
841	min	min	NN	_	_	_
842	,	,	,	_	_	_
843	rep1	rep1	NN	_	_	_
844	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
845	chemostat	chemostat	NN	_	_	_
846	STR-PFR	str-pfr	NN	_	_	_
847	culture	culture	NN	_	_	_
848	STR	str	NN	_	_	_
849	75	75	CD	_	_	_
850	min	min	NN	_	_	_
851	,	,	,	_	_	_
852	rep2	rep2	NN	_	_	_
853	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
854	chilled	chill	VBN	_	_	_
855	in	in	IN	_	_	_
856	a	a	DT	_	_	_
857	dry	dry	JJ	_	_	_
858	ice/ethanol	ice/ethanol	NN	_	_	_
859	.	.	.	_	_	_

1	bath	bath	NN	_	_	_
2	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	homogenization	homogenization	NN	_	_	_
3	with	with	IN	_	_	_
4	glass	glass	NN	_	_	_
5	beads	bead	NNS	_	_	_
6	,	,	,	_	_	_
7	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	chip	chip	NN	_	_	_
5	antibody	antibody	NN	_	_	_
6	:	:	:	_	_	_
7	9E10	9e10	NN	_	_	_
8	Myc	myc	NN	_	_	_
9	tag	tag	NN	GEN	_	_
10	antibody	antibody	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	chip	chip	NN	_	_	_
13	antibody	antibody	NN	_	_	_
14	:	:	:	_	_	_
15	anti-b	anti-b	JJ	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	RNAP	rnap	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	NT63	nt63	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
21	chip	chip	NN	_	_	_
22	antibody	antibody	NN	_	_	_
23	:	:	:	_	_	_
24	anti-c-myc	anti-c-myc	JJ	_	_	_
25	antibody	antibody	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	chip	chip	NN	_	_	_
28	antibody	antibody	NN	_	_	_
29	:	:	:	_	_	_
30	anti-FecI	anti-feci	JJ	_	_	_
31	antibody	antibody	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	chip	chip	NN	_	_	_
34	antibody	antibody	NN	_	_	_
35	:	:	:	_	_	_
36	anti-Flag	anti-flag	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	chip	chip	NN	_	_	_
39	antibody	antibody	NN	_	_	_
40	:	:	:	_	_	_
41	anti-FLAG	anti-flag	JJ	_	_	_
42	antibody	antibody	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	Sigma	Sigma	NNP	_	_	_
45	Cat	Cat	NNP	_	_	_
46	#	#	#	_	_	_
47	:	:	:	_	_	_
48	F3165-1MG	f3165-1mg	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	chip	chip	NN	_	_	_
52	antibody	antibody	NN	_	_	_
53	:	:	:	_	_	_
54	antiFlag	antiflag	NN	_	_	_
55	M2	m2	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	chip	chip	NN	_	_	_
58	antibody	antibody	NN	_	_	_
59	:	:	:	_	_	_
60	anti-Flag	anti-flag	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Sigma	Sigma	NNP	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
65	chip	chip	NN	_	_	_
66	antibody	antibody	NN	_	_	_
67	:	:	:	_	_	_
68	Anti-FLAG	anti-flag	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	sigma-aldrich	sigma-aldrich	JJ	_	_	_
71	cat	cat	NN	_	_	_
72	no	no	DT	_	_	_
73	F3165	f3165	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	chip	chip	NN	_	_	_
77	antibody	antibody	NN	_	_	_
78	:	:	:	_	_	_
79	anti-H-NS	anti-h-ns	JJ	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
81	chip	chip	NN	_	_	_
82	antibody	antibody	NN	_	_	_
83	:	:	:	_	_	_
84	anti-myc	anti-myc	JJ	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
86	chip	chip	NN	_	_	_
87	antibody	antibody	NN	_	_	_
88	:	:	:	_	_	_
89	Anti-myc	anti-myc	NN	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	9E10	9e10	NN	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	Santa	Santa	NNP	_	_	_
95	Cruz	Cruz	NNP	_	_	_
96	,	,	,	_	_	_
97	Dallas	Dallas	NNP	_	_	_
98	,	,	,	_	_	_
99	TX	TX	NNP	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	chip	chip	NN	_	_	_
103	antibody	antibody	NN	_	_	_
104	:	:	:	_	_	_
105	anti-myc	anti-myc	JJ	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	Santa	Santa	NNP	_	_	_
108	Cruz	Cruz	NNP	_	_	_
109	Biotech	Biotech	NNP	_	_	_
110	,	,	,	_	_	_
111	sc-28207	sc-28207	NN	_	_	_
112	-RRB-	-rrb-	-RRB-	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	chip	chip	NN	_	_	_
115	antibody	antibody	NN	_	_	_
116	:	:	:	_	_	_
117	anti-RecA	anti-reca	JJ	_	_	_
118	antibody	antibody	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
120	chip	chip	NN	_	_	_
121	antibody	antibody	NN	_	_	_
122	:	:	:	_	_	_
123	anti-RpoB	anti-rpob	JJ	_	_	_
124	antibody	antibody	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
126	chip	chip	NN	_	_	_
127	antibody	antibody	NN	_	_	_
128	:	:	:	_	_	_
129	anti-RpoB	anti-rpob	NN	_	_	_
130	-LRB-	-lrb-	-LRB-	_	_	_
131	Neoclone	Neoclone	NNP	_	_	_
132	,	,	,	_	_	_
133	WP002	wp002	NN	_	_	_
134	-RRB-	-rrb-	-RRB-	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	chip	chip	NN	_	_	_
137	antibody	antibody	NN	_	_	_
138	:	:	:	_	_	_
139	anti-rpoB	anti-rpob	NN	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	Santa	Santa	NNP	_	_	_
142	Cruz	Cruz	NNP	_	_	_
143	Biotech	Biotech	NNP	_	_	_
144	,	,	,	_	_	_
145	sc-56766	sc-56766	NN	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	chip	chip	NN	_	_	_
149	antibody	antibody	NN	_	_	_
150	:	:	:	_	_	_
151	anti-RpoD	anti-rpod	JJ	_	_	_
152	antibody	antibody	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
154	chip	chip	NN	_	_	_
155	antibody	antibody	NN	_	_	_
156	:	:	:	_	_	_
157	anti-RpoF	anti-rpof	JJ	_	_	_
158	antibody	antibody	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
160	chip	chip	NN	_	_	_
161	antibody	antibody	NN	_	_	_
162	:	:	:	_	_	_
163	anti-RpoN	anti-rpon	JJ	_	_	_
164	antibody	antibody	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
166	chip	chip	NN	_	_	_
167	antibody	antibody	NN	_	_	_
168	:	:	:	_	_	_
169	anti-RpoS	anti-rpos	JJ	_	_	_
170	antibody	antibody	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
172	chip	chip	NN	_	_	_
173	antibody	antibody	NN	_	_	_
174	:	:	:	_	_	_
175	anti-RpoS	anti-rpos	NN	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	neoclone	neoclone	NN	_	_	_
178	,	,	,	_	_	_
179	WP009	wp009	NN	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	chip	chip	NN	_	_	_
183	antibody	antibody	NN	_	_	_
184	:	:	:	_	_	_
185	biotin	biotin	NN	SUPP	_	_
186	conjugated	conjugate	VBN	_	_	_
187	anti-c-myc	anti-c-myc	JJ	_	_	_
188	antibody	antibody	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
190	chip	chip	NN	_	_	_
191	antibody	antibody	NN	_	_	_
192	cat	cat	NN	_	_	_
193	.	.	.	_	_	_

1	#	#	#	_	_	_
2	:	:	:	_	_	_
3	ab63797	ab63797	CD	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	chip	chip	NN	_	_	_
6	antibody	antibody	NN	_	_	_
7	cat	cat	NN	_	_	_
8	.	.	.	_	_	_

1	#	#	#	_	_	_
2	:	:	:	_	_	_
3	sc-28207	sc-28207	JJ	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	chip	chip	NN	_	_	_
6	antibody	antibody	NN	_	_	_
7	cat	cat	NN	_	_	_
8	.	.	.	_	_	_

1	#	#	#	_	_	_
2	:	:	:	_	_	_
3	W0002	w0002	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	chip	chip	NN	_	_	_
6	antibody	antibody	NN	_	_	_
7	:	:	:	_	_	_
8	c-Myc	c-myc	NN	_	_	_
9	Antibody	antibody	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	9E10	9e10	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	Santa	Santa	NNP	_	_	_
15	Cruz	Cruz	NNP	_	_	_
16	Biotech	Biotech	NNP	_	_	_
17	,	,	,	_	_	_
18	sc-40	sc-40	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	chip	chip	NN	_	_	_
21	antibody	antibody	NN	_	_	_
22	:	:	:	_	_	_
23	Custom	Custom	NNP	_	_	_
24	anti-Fur	anti-fur	JJ	_	_	_
25	polyclonal	polyclonal	JJ	_	_	_
26	antibody	antibody	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	chip	chip	NN	_	_	_
29	antibody	antibody	NN	_	_	_
30	:	:	:	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	CRP	crp	NN	TF	_	_
34	Monoclonal	monoclonal	JJ	_	_	_
35	Antibody	antibody	NN	_	_	_
36	,	,	,	_	_	_
37	Neoclone	neoclone	NN	_	_	_
38	,	,	,	_	_	_
39	#N0004	#n0004	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	chip	chip	NN	_	_	_
42	antibody	antibody	NN	_	_	_
43	:	:	:	_	_	_
44	E.	e.	FW	_	_	_
45	coli	coli	FW	_	_	_
46	RNA	rna	NN	_	_	_
47	Sigma	Sigma	NNP	_	_	_
48	70	70	CD	_	_	_
49	Monoclonal	monoclonal	JJ	_	_	_
50	Antibody	antibody	NN	_	_	_
51	,	,	,	_	_	_
52	Neoclone	neoclone	NN	_	_	_
53	,	,	,	_	_	_
54	#WP004	#wp004	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
56	chip	chip	NN	_	_	_
57	antibody	antibody	NN	_	_	_
58	:	:	:	_	_	_
59	FLAG	flag	NN	_	_	_
60	antibody	antibody	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	chip	chip	NN	_	_	_
63	antibody	antibody	NN	_	_	_
64	:	:	:	_	_	_
65	HRP-conjugated	hrp-conjugated	JJ	_	_	_
66	sheep	sheep	NN	_	_	_
67	anti-mouse	anti-mouse	JJ	_	_	_
68	IgG	igg	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	chip	chip	NN	_	_	_
71	antibody	antibody	NN	_	_	_
72	manufacturer/lot	manufacturer/lot	NN	_	_	_
73	#	#	#	_	_	_
74	:	:	:	_	_	_
75	Sigma-Aldrich	Sigma-Aldrich	NNP	_	_	_
76	,	,	,	_	_	_
77	M8823-1ML	m8823-1ml	NN	_	_	_
78	,	,	,	_	_	_
79	Lot	lot	NN	_	_	_
80	#	#	#	_	_	_
81	SLBD7244V	slbd7244v	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
83	chip	chip	NN	_	_	_
84	antibody	antibody	NN	_	_	_
85	manufacturer	manufacturer	NN	_	_	_
86	:	:	:	_	_	_
87	Upstate	upstate	JJ	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
89	chip	chip	NN	_	_	_
90	antibody	antibody	NN	_	_	_
91	:	:	:	_	_	_
92	Monoclonal	monoclonal	JJ	_	_	_
93	anti-FLAG	anti-flag	JJ	_	_	_
94	antibody	antibody	NN	_	_	_
95	,	,	,	_	_	_
96	Murine	murine	JJ	_	_	_
97	IgG	igg	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
99	chip	chip	NN	_	_	_
100	antibody	antibody	NN	_	_	_
101	:	:	:	_	_	_
102	Monoclonal	monoclonal	JJ	_	_	_
103	ANTI-FLAG	anti-flag	NN	_	_	_
104	M5	m5	NN	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	Sigma-Aldrich	Sigma-Aldrich	NNP	_	_	_
107	,	,	,	_	_	_
108	catalog	catalog	NN	_	_	_
109	number	number	NN	_	_	_
110	:	:	:	_	_	_
111	F4042	f4042	NN	_	_	_
112	-RRB-	-rrb-	-RRB-	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	chip	chip	NN	_	_	_
115	antibody	antibody	NN	_	_	_
116	:	:	:	_	_	_
117	none	none	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
119	chip	chip	NN	_	_	_
120	antibody	antibody	NN	_	_	_
121	:	:	:	_	_	_
122	None	none	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	chip	chip	NN	_	_	_
125	antibody	antibody	NN	_	_	_
126	:	:	:	_	_	_
127	none	none	NN	_	_	_
128	,	,	,	_	_	_
129	input	input	NN	_	_	_
130	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
131	chip	chip	NN	_	_	_
132	antibody	antibody	NN	_	_	_
133	:	:	:	_	_	_
134	normal	normal	JJ	_	_	_
135	mouse	mouse	NN	_	_	_
136	IgG	igg	NN	_	_	_
137	-LRB-	-lrb-	-LRB-	_	_	_
138	Upstate	upstate	JJ	_	_	_
139	-RRB-	-rrb-	-RRB-	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
141	chip	chip	NN	_	_	_
142	antibody	antibody	NN	_	_	_
143	:	:	:	_	_	_
144	normal	normal	JJ	_	_	_
145	rabbit	rabbit	NN	_	_	_
146	IgG	igg	NN	_	_	_
147	-LRB-	-lrb-	-LRB-	_	_	_
148	Upstate	upstate	JJ	_	_	_
149	Biotechnology	biotechnology	NN	_	_	_
150	,	,	,	_	_	_
151	Cat	cat	NN	_	_	_
152	.	.	.	_	_	_

1	no.	no.	RB	_	_	_
2	12-370	12-370	CD	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	chip	chip	NN	_	_	_
6	antibody	antibody	NN	_	_	_
7	:	:	:	_	_	_
8	RNAP	rnap	NN	_	_	_
9	beta	beta	NN	_	_	_
10	subunit	subunit	NN	_	_	_
11	antibody	antibody	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	chip	chip	NN	_	_	_
14	antibody	antibody	NN	_	_	_
15	:	:	:	_	_	_
16	RNA	rna	NN	_	_	_
17	polymerase	polymerase	NN	_	_	_
18	subunit	subunit	NN	_	_	_
19	β	β	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
21	chip	chip	NN	_	_	_
22	antibody	antibody	NN	_	_	_
23	:	:	:	_	_	_
24	RpoS	rpos	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Neoclone	neoclone	JJ	_	_	_
27	cat	cat	NN	_	_	_
28	.	.	.	_	_	_

1	no	no	DT	_	_	_
2	.	.	.	_	_	_

1	WP009	wp009	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	chip	chip	NN	_	_	_
5	antibody	antibody	NN	_	_	_
6	:	:	:	_	_	_
7	SeqA	seqa	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	chip	chip	NN	_	_	_
10	antibody	antibody	NN	_	_	_
11	vendor	vendor	NN	_	_	_
12	:	:	:	_	_	_
13	Abcam	Abcam	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	chip	chip	NN	_	_	_
16	antibody	antibody	NN	_	_	_
17	vendor	vendor	NN	_	_	_
18	:	:	:	_	_	_
19	Amersham	Amersham	NNP	_	_	_
20	Biosciences	Biosciences	NNP	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	chip	chip	NN	_	_	_
23	antibody	antibody	NN	_	_	_
24	vendor	vendor	NN	_	_	_
25	:	:	:	_	_	_
26	Neoclone	Neoclone	NNP	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	chip	chip	NN	_	_	_
29	antibody	antibody	NN	_	_	_
30	vendor	vendor	NN	_	_	_
31	:	:	:	_	_	_
32	Santa	Santa	NNP	_	_	_
33	Cruz	Cruz	NNP	_	_	_
34	Biotech	Biotech	NNP	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	chip	chip	NN	_	_	_
37	antibody	antibody	NN	_	_	_
38	vendor	vendor	NN	_	_	_
39	:	:	:	_	_	_
40	Santa	Santa	NNP	_	_	_
41	Cruz	Cruz	NNP	_	_	_
42	Biotechnology	Biotechnology	NNP	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	chip	chip	NN	_	_	_
45	antibody	antibody	NN	_	_	_
46	:	:	:	_	_	_
47	σ32	σ32	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	chip-ArcA	chip-arca	NN	_	_	_
50	_	_	CD	_	_	_
51	ArcA8myc	arca8myc	NN	_	_	_
52	_	_	NN	_	_	_
53	glucose	glucose	NN	SUPP	_	_
54	_	_	CD	_	_	_
55	NH4CL	nh4cl	NN	_	_	_
56	_	_	NN	_	_	_
57	anaerobic	anaerobic	JJ	_	_	_
58	_	_	NN	_	_	_
59	1	1	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	chip-ArcA	chip-arca	NN	_	_	_
62	_	_	CD	_	_	_
63	ArcA8myc	arca8myc	NN	_	_	_
64	_	_	NN	_	_	_
65	glucose	glucose	NN	SUPP	_	_
66	_	_	CD	_	_	_
67	NH4CL	nh4cl	NN	_	_	_
68	_	_	NN	_	_	_
69	anaerobic	anaerobic	JJ	_	_	_
70	_	_	NN	_	_	_
71	2	2	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	chip-ArcA	chip-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	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	chip-ArcA	chip-arca	NN	_	_	_
86	_	_	CD	_	_	_
87	ArcA8myc	arca8myc	NN	_	_	_
88	_	_	NN	_	_	_
89	glucose	glucose	NN	SUPP	_	_
90	_	_	CD	_	_	_
91	NH4CL	nh4cl	NN	_	_	_
92	_	_	CD	_	_	_
93	NO3	no3	NN	_	_	_
94	_	_	NN	_	_	_
95	1	1	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	chip-ArcA	chip-arca	NN	_	_	_
98	_	_	CD	_	_	_
99	ArcA8myc	arca8myc	NN	_	_	_
100	_	_	NN	_	_	_
101	glucose	glucose	NN	SUPP	_	_
102	_	_	CD	_	_	_
103	NH4CL	nh4cl	NN	_	_	_
104	_	_	CD	_	_	_
105	NO3	no3	NN	_	_	_
106	_	_	NN	_	_	_
107	2	2	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	chip-ArcA	chip-arca	NN	_	_	_
110	_	_	CD	_	_	_
111	ArcA8myc	arca8myc	NN	_	_	_
112	_	_	NN	_	_	_
113	glucose	glucose	NN	SUPP	_	_
114	_	_	CD	_	_	_
115	NH4CL	nh4cl	NN	_	_	_
116	_	_	CD	_	_	_
117	NO3	no3	NN	_	_	_
118	_	_	NN	_	_	_
119	3	3	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Chipchip	chipchip	NN	_	_	_
122	BW25113/pBAD-Myc-His	bw25113/pbad-myc-his	NN	_	_	_
123	C	c	NN	_	_	_
124	in	in	IN	_	_	_
125	LB	lb	NN	_	_	_
126	for	for	IN	_	_	_
127	24	24	CD	_	_	_
128	h	h	NN	_	_	_
129	37oC	37oc	NN	_	_	_
130	with	with	IN	_	_	_
131	0.5	0.5	CD	_	_	_
132	%	%	NN	_	_	_
133	L-arabinose	l-arabinose	JJ	_	_	_
134	suspension	suspension	NN	_	_	_
135	cell	cell	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	Chipchip	chipchip	NN	_	_	_
138	BW25113/pBAD-Myc-His	bw25113/pbad-myc-his	NN	_	_	_
139	C-mqsA	c-mqsa	NN	_	_	_
140	in	in	IN	_	_	_
141	LB	lb	NN	_	_	_
142	for	for	IN	_	_	_
143	24	24	CD	_	_	_
144	h	h	NN	_	_	_
145	37oC	37oc	NN	_	_	_
146	with	with	IN	_	_	_
147	0.5	0.5	CD	_	_	_
148	%	%	NN	_	_	_
149	L-arabinose	l-arabinose	JJ	_	_	_
150	suspension	suspension	NN	_	_	_
151	cell	cell	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	Chipchip	chipchip	NN	_	_	_
154	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
155	in	in	IN	_	_	_
156	LB	lb	NN	_	_	_
157	for	for	IN	_	_	_
158	24	24	CD	_	_	_
159	h	h	NN	_	_	_
160	37oC	37oc	NN	_	_	_
161	with	with	IN	_	_	_
162	2	2	CD	_	_	_
163	mM	mm	NN	KWSUPP	_	_
164	IPTG	iptg	NN	_	_	_
165	biofilm	biofilm	NN	_	_	_
166	cell	cell	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	Chipchip	chipchip	NN	_	_	_
169	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
170	in	in	IN	_	_	_
171	LB	lb	NN	_	_	_
172	for	for	IN	_	_	_
173	24	24	CD	_	_	_
174	h	h	NN	_	_	_
175	37oC	37oc	NN	_	_	_
176	with	with	IN	_	_	_
177	2	2	CD	_	_	_
178	mM	mm	NN	KWSUPP	_	_
179	IPTG	iptg	NN	_	_	_
180	biofilm	biofilm	NN	_	_	_
181	cell	cell	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	ChIP	chip	NN	_	_	_
184	DNA	dna	NN	_	_	_
185	from	from	IN	_	_	_
186	MG1655	mg1655	NN	_	_	_
187	_	_	CD	_	_	_
188	PhoB	phob	NN	TF	_	_
189	_	_	CD	_	_	_
190	FLAG	flag	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	ChIP	chip	NN	_	_	_
193	DNA	dna	NN	_	_	_
194	from	from	IN	_	_	_
195	MG1655	mg1655	NN	_	_	_
196	wild	wild	JJ	_	_	_
197	type	type	NN	_	_	_
198	strain	strain	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	ChIPExo-ArcA	chipexo-arca	NN	_	_	_
201	_	_	CD	_	_	_
202	ArcA8myc	arca8myc	NN	_	_	_
203	_	_	NN	_	_	_
204	glucose	glucose	NN	SUPP	_	_
205	_	_	CD	_	_	_
206	NH4Cl	nh4cl	NN	_	_	_
207	_	_	NN	_	_	_
208	anaerobic	anaerobic	JJ	_	_	_
209	_	_	NN	_	_	_
210	1	1	CD	_	_	_
211	_	_	NN	_	_	_
212	anti-myc	anti-myc	JJ	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	ChIPExo-ArcA	chipexo-arca	NN	_	_	_
215	_	_	CD	_	_	_
216	ArcA8myc	arca8myc	NN	_	_	_
217	_	_	NN	_	_	_
218	glucose	glucose	NN	SUPP	_	_
219	_	_	CD	_	_	_
220	NH4Cl	nh4cl	NN	_	_	_
221	_	_	NN	_	_	_
222	anaerobic	anaerobic	JJ	_	_	_
223	_	_	NN	_	_	_
224	2	2	CD	_	_	_
225	_	_	SYM	_	_	_
226	anti-myc	anti-myc	JJ	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	ChIPExo-ArcA	chipexo-arca	NN	_	_	_
229	_	_	CD	_	_	_
230	ArcA8myc	arca8myc	NN	_	_	_
231	_	_	NN	_	_	_
232	glucose	glucose	NN	SUPP	_	_
233	_	_	CD	_	_	_
234	NH4Cl	nh4cl	NN	_	_	_
235	_	_	NN	_	_	_
236	anaerobic	anaerobic	JJ	_	_	_
237	_	_	NN	_	_	_
238	3	3	CD	_	_	_
239	_	_	NN	_	_	_
240	anti-myc	anti-myc	JJ	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
243	_	_	NN	_	_	_
244	delAr1delAr2	delar1delar2	NN	_	_	_
245	_	_	CD	_	_	_
246	glycerol	glycerol	NN	SUPP	_	_
247	_	_	NN	_	_	_
248	NH4Cl	nh4cl	NN	_	_	_
249	_	_	CD	_	_	_
250	O2	o2	CD	_	_	_
251	_	_	NN	_	_	_
252	1	1	CD	_	_	_
253	_	_	NN	_	_	_
254	anti-crp	anti-crp	JJ	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
257	_	_	NN	_	_	_
258	delAr1delAr2	delar1delar2	NN	_	_	_
259	_	_	CD	_	_	_
260	glycerol	glycerol	NN	SUPP	_	_
261	_	_	NN	_	_	_
262	NH4Cl	nh4cl	NN	_	_	_
263	_	_	CD	_	_	_
264	O2	o2	CD	_	_	_
265	_	_	NN	_	_	_
266	2	2	CD	_	_	_
267	_	_	SYM	_	_	_
268	anti-crp	anti-crp	JJ	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
271	_	_	NN	_	_	_
272	delAr1delAr2	delar1delar2	NN	_	_	_
273	_	_	CD	_	_	_
274	glycerol	glycerol	NN	SUPP	_	_
275	_	_	NN	_	_	_
276	NH4Cl	nh4cl	NN	_	_	_
277	_	_	CD	_	_	_
278	O2	o2	CD	_	_	_
279	_	_	NN	_	_	_
280	3	3	CD	_	_	_
281	_	_	NN	_	_	_
282	anti-crp	anti-crp	JJ	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
285	_	_	NN	_	_	_
286	delAr1	delar1	NN	_	_	_
287	_	_	CD	_	_	_
288	glycerol	glycerol	NN	SUPP	_	_
289	_	_	NN	_	_	_
290	NH4Cl	nh4cl	NN	_	_	_
291	_	_	CD	_	_	_
292	O2	o2	CD	_	_	_
293	_	_	NN	_	_	_
294	1	1	CD	_	_	_
295	_	_	NN	_	_	_
296	anti-crp	anti-crp	JJ	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
299	_	_	NN	_	_	_
300	delAr1	delar1	NN	_	_	_
301	_	_	CD	_	_	_
302	glycerol	glycerol	NN	SUPP	_	_
303	_	_	NN	_	_	_
304	NH4Cl	nh4cl	NN	_	_	_
305	_	_	CD	_	_	_
306	O2	o2	CD	_	_	_
307	_	_	NN	_	_	_
308	2	2	CD	_	_	_
309	_	_	SYM	_	_	_
310	anti-crp	anti-crp	JJ	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
313	_	_	NN	_	_	_
314	delAr1	delar1	NN	_	_	_
315	_	_	CD	_	_	_
316	glycerol	glycerol	NN	SUPP	_	_
317	_	_	NN	_	_	_
318	NH4Cl	nh4cl	NN	_	_	_
319	_	_	CD	_	_	_
320	O2	o2	CD	_	_	_
321	_	_	NN	_	_	_
322	3	3	CD	_	_	_
323	_	_	NN	_	_	_
324	anti-crp	anti-crp	JJ	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
327	_	_	NN	_	_	_
328	delAr2	delar2	NN	_	_	_
329	_	_	CD	_	_	_
330	glycerol	glycerol	NN	SUPP	_	_
331	_	_	NN	_	_	_
332	NH4Cl	nh4cl	NN	_	_	_
333	_	_	CD	_	_	_
334	O2	o2	CD	_	_	_
335	_	_	NN	_	_	_
336	1	1	CD	_	_	_
337	_	_	NN	_	_	_
338	anti-crp	anti-crp	JJ	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
341	_	_	NN	_	_	_
342	delAr2	delar2	NN	_	_	_
343	_	_	CD	_	_	_
344	glycerol	glycerol	NN	SUPP	_	_
345	_	_	NN	_	_	_
346	NH4Cl	nh4cl	NN	_	_	_
347	_	_	CD	_	_	_
348	O2	o2	CD	_	_	_
349	_	_	NN	_	_	_
350	2	2	CD	_	_	_
351	_	_	SYM	_	_	_
352	anti-crp	anti-crp	JJ	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
355	_	_	NN	_	_	_
356	delAr2	delar2	NN	_	_	_
357	_	_	CD	_	_	_
358	glycerol	glycerol	NN	SUPP	_	_
359	_	_	NN	_	_	_
360	NH4Cl	nh4cl	NN	_	_	_
361	_	_	CD	_	_	_
362	O2	o2	CD	_	_	_
363	_	_	NN	_	_	_
364	3	3	CD	_	_	_
365	_	_	NN	_	_	_
366	anti-crp	anti-crp	JJ	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
369	_	_	NN	_	_	_
370	delta-crp	delta-crp	JJ	_	_	_
371	_	_	NN	_	_	_
372	glycerol	glycerol	NN	SUPP	_	_
373	_	_	CD	_	_	_
374	NH4Cl	nh4cl	NN	_	_	_
375	_	_	CD	_	_	_
376	O2	o2	CD	_	_	_
377	_	_	NN	_	_	_
378	1	1	CD	_	_	_
379	_	_	NN	_	_	_
380	anti-crp	anti-crp	JJ	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
383	_	_	NN	_	_	_
384	delta-crp	delta-crp	JJ	_	_	_
385	_	_	NN	_	_	_
386	glycerol	glycerol	NN	SUPP	_	_
387	_	_	CD	_	_	_
388	NH4Cl	nh4cl	NN	_	_	_
389	_	_	CD	_	_	_
390	O2	o2	CD	_	_	_
391	_	_	NN	_	_	_
392	2	2	CD	_	_	_
393	_	_	SYM	_	_	_
394	anti-crp	anti-crp	JJ	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
397	_	_	NN	_	_	_
398	delta-crp	delta-crp	JJ	_	_	_
399	_	_	NN	_	_	_
400	glycerol	glycerol	NN	SUPP	_	_
401	_	_	CD	_	_	_
402	NH4Cl	nh4cl	NN	_	_	_
403	_	_	CD	_	_	_
404	O2	o2	CD	_	_	_
405	_	_	NN	_	_	_
406	3	3	CD	_	_	_
407	_	_	NN	_	_	_
408	anti-crp	anti-crp	JJ	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
411	_	_	NN	_	_	_
412	wt	wt	JJ	_	_	_
413	_	_	NN	_	_	_
414	fructose	fructose	NN	_	_	_
415	_	_	CD	_	_	_
416	NH4Cl	nh4cl	NN	_	_	_
417	_	_	CD	_	_	_
418	O2	o2	CD	_	_	_
419	_	_	NN	_	_	_
420	1	1	CD	_	_	_
421	_	_	CD	_	_	_
422	anti-crp	anti-crp	JJ	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
424	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
425	_	_	NN	_	_	_
426	wt	wt	JJ	_	_	_
427	_	_	NN	_	_	_
428	fructose	fructose	NN	_	_	_
429	_	_	CD	_	_	_
430	NH4Cl	nh4cl	NN	_	_	_
431	_	_	CD	_	_	_
432	O2	o2	CD	_	_	_
433	_	_	NN	_	_	_
434	2	2	CD	_	_	_
435	_	_	CD	_	_	_
436	anti-crp	anti-crp	JJ	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
438	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
439	_	_	NN	_	_	_
440	wt	wt	JJ	_	_	_
441	_	_	NN	_	_	_
442	fructose	fructose	NN	_	_	_
443	_	_	CD	_	_	_
444	NH4Cl	nh4cl	NN	_	_	_
445	_	_	CD	_	_	_
446	O2	o2	CD	_	_	_
447	_	_	NN	_	_	_
448	3	3	CD	_	_	_
449	_	_	NN	_	_	_
450	anti-crp	anti-crp	JJ	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
453	_	_	NN	_	_	_
454	wt	wt	JJ	_	_	_
455	_	_	NN	_	_	_
456	fructose	fructose	NN	_	_	_
457	_	_	CD	_	_	_
458	NH4Cl	nh4cl	NN	_	_	_
459	_	_	CD	_	_	_
460	O2	o2	CD	_	_	_
461	_	_	NN	_	_	_
462	4	4	CD	_	_	_
463	_	_	SYM	_	_	_
464	anti-crp	anti-crp	JJ	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
467	_	_	NN	_	_	_
468	wt	wt	JJ	_	_	_
469	_	_	NN	_	_	_
470	fructose	fructose	NN	_	_	_
471	_	_	CD	_	_	_
472	NH4Cl	nh4cl	NN	_	_	_
473	_	_	SYM	_	_	_
474	O2	o2	CD	_	_	_
475	_	_	SYM	_	_	_
476	5	5	CD	_	_	_
477	_	_	SYM	_	_	_
478	anti-crp	anti-crp	JJ	_	_	_
479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
480	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
481	_	_	NN	_	_	_
482	wt	wt	JJ	_	_	_
483	_	_	NN	_	_	_
484	glucose	glucose	NN	SUPP	_	_
485	_	_	CD	_	_	_
486	NH4Cl	nh4cl	NN	_	_	_
487	_	_	CD	_	_	_
488	O2	o2	CD	_	_	_
489	_	_	NN	_	_	_
490	1	1	CD	_	_	_
491	_	_	CD	_	_	_
492	anti-crp	anti-crp	JJ	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
494	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
495	_	_	NN	_	_	_
496	wt	wt	JJ	_	_	_
497	_	_	NN	_	_	_
498	glucose	glucose	NN	SUPP	_	_
499	_	_	CD	_	_	_
500	NH4Cl	nh4cl	NN	_	_	_
501	_	_	CD	_	_	_
502	O2	o2	CD	_	_	_
503	_	_	NN	_	_	_
504	2	2	CD	_	_	_
505	_	_	CD	_	_	_
506	anti-crp	anti-crp	JJ	_	_	_
507	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
508	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
509	_	_	NN	_	_	_
510	wt	wt	JJ	_	_	_
511	_	_	NN	_	_	_
512	glycerol	glycerol	NN	SUPP	_	_
513	_	_	CD	_	_	_
514	NH4Cl	nh4cl	NN	_	_	_
515	_	_	CD	_	_	_
516	O2	o2	CD	_	_	_
517	_	_	NN	_	_	_
518	1	1	CD	_	_	_
519	_	_	CD	_	_	_
520	anti-crp	anti-crp	JJ	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
522	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
523	_	_	NN	_	_	_
524	wt	wt	JJ	_	_	_
525	_	_	NN	_	_	_
526	glycerol	glycerol	NN	SUPP	_	_
527	_	_	CD	_	_	_
528	NH4Cl	nh4cl	NN	_	_	_
529	_	_	CD	_	_	_
530	O2	o2	CD	_	_	_
531	_	_	NN	_	_	_
532	1	1	CD	_	_	_
533	_	_	CD	_	_	_
534	anti-crp	anti-crp	JJ	_	_	_
535	_	_	NN	_	_	_
536	rif	rif	NN	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
539	_	_	NN	_	_	_
540	wt	wt	JJ	_	_	_
541	_	_	NN	_	_	_
542	glycerol	glycerol	NN	SUPP	_	_
543	_	_	CD	_	_	_
544	NH4Cl	nh4cl	NN	_	_	_
545	_	_	CD	_	_	_
546	O2	o2	CD	_	_	_
547	_	_	NN	_	_	_
548	2	2	CD	_	_	_
549	_	_	CD	_	_	_
550	anti-crp	anti-crp	JJ	_	_	_
551	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
552	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
553	_	_	NN	_	_	_
554	wt	wt	JJ	_	_	_
555	_	_	NN	_	_	_
556	glycerol	glycerol	NN	SUPP	_	_
557	_	_	CD	_	_	_
558	NH4Cl	nh4cl	NN	_	_	_
559	_	_	CD	_	_	_
560	O2	o2	CD	_	_	_
561	_	_	NN	_	_	_
562	2	2	CD	_	_	_
563	_	_	CD	_	_	_
564	anti-crp	anti-crp	JJ	_	_	_
565	_	_	NN	_	_	_
566	rif	rif	NN	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
569	_	_	NN	_	_	_
570	wt	wt	JJ	_	_	_
571	_	_	NN	_	_	_
572	glycerol	glycerol	NN	SUPP	_	_
573	_	_	CD	_	_	_
574	NH4Cl	nh4cl	NN	_	_	_
575	_	_	CD	_	_	_
576	O2	o2	CD	_	_	_
577	_	_	NN	_	_	_
578	3	3	CD	_	_	_
579	_	_	NN	_	_	_
580	anti-crp	anti-crp	JJ	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
583	_	_	NN	_	_	_
584	wt	wt	JJ	_	_	_
585	_	_	NN	_	_	_
586	glycerol	glycerol	NN	SUPP	_	_
587	_	_	CD	_	_	_
588	NH4Cl	nh4cl	NN	_	_	_
589	_	_	CD	_	_	_
590	O2	o2	CD	_	_	_
591	_	_	NN	_	_	_
592	3	3	CD	_	_	_
593	_	_	NN	_	_	_
594	anti-crp	anti-crp	JJ	_	_	_
595	_	_	NN	_	_	_
596	rif	rif	NN	_	_	_
597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
598	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
599	_	_	NN	_	_	_
600	wt	wt	JJ	_	_	_
601	_	_	NN	_	_	_
602	glycerol	glycerol	NN	SUPP	_	_
603	_	_	CD	_	_	_
604	NH4Cl	nh4cl	NN	_	_	_
605	_	_	CD	_	_	_
606	O2	o2	CD	_	_	_
607	_	_	NN	_	_	_
608	4	4	CD	_	_	_
609	_	_	SYM	_	_	_
610	anti-crp	anti-crp	JJ	_	_	_
611	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
612	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
613	_	_	NN	_	_	_
614	wt	wt	JJ	_	_	_
615	_	_	NN	_	_	_
616	glycerol	glycerol	NN	SUPP	_	_
617	_	_	CD	_	_	_
618	NH4Cl	nh4cl	NN	_	_	_
619	_	_	SYM	_	_	_
620	O2	o2	CD	_	_	_
621	_	_	SYM	_	_	_
622	5	5	CD	_	_	_
623	_	_	SYM	_	_	_
624	anti-crp	anti-crp	JJ	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
627	_	_	NN	_	_	_
628	wt	wt	JJ	_	_	_
629	_	_	NN	_	_	_
630	glycerol	glycerol	NN	SUPP	_	_
631	_	_	CD	_	_	_
632	NH4Cl	nh4cl	NN	_	_	_
633	_	_	CD	_	_	_
634	O2	o2	CD	_	_	_
635	_	_	NN	_	_	_
636	6	6	CD	_	_	_
637	_	_	NN	_	_	_
638	anti-crp	anti-crp	JJ	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	ChIPExo-Fnr	chipexo-fnr	JJ	_	_	_
641	_	_	NN	_	_	_
642	Fnr8myc	fnr8myc	NN	_	_	_
643	_	_	NN	_	_	_
644	glucose	glucose	NN	SUPP	_	_
645	_	_	CD	_	_	_
646	NH4Cl	nh4cl	NN	_	_	_
647	_	_	NN	_	_	_
648	anaerobic	anaerobic	JJ	_	_	_
649	_	_	NN	_	_	_
650	1	1	CD	_	_	_
651	_	_	CD	_	_	_
652	anti-myc	anti-myc	JJ	_	_	_
653	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
654	ChIPExo-Fnr	chipexo-fnr	JJ	_	_	_
655	_	_	NN	_	_	_
656	Fnr8myc	fnr8myc	NN	_	_	_
657	_	_	NN	_	_	_
658	glucose	glucose	NN	SUPP	_	_
659	_	_	CD	_	_	_
660	NH4Cl	nh4cl	NN	_	_	_
661	_	_	NN	_	_	_
662	anaerobic	anaerobic	JJ	_	_	_
663	_	_	NN	_	_	_
664	2	2	CD	_	_	_
665	_	_	CD	_	_	_
666	anti-myc	anti-myc	JJ	_	_	_
667	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
668	ChIPExo-Fnr	chipexo-fnr	JJ	_	_	_
669	_	_	NN	_	_	_
670	Fnr8myc	fnr8myc	NN	_	_	_
671	_	_	NN	_	_	_
672	glucose	glucose	NN	SUPP	_	_
673	_	_	CD	_	_	_
674	NH4Cl	nh4cl	NN	_	_	_
675	_	_	NN	_	_	_
676	anaerobic	anaerobic	JJ	_	_	_
677	_	_	NN	_	_	_
678	3	3	CD	_	_	_
679	_	_	NN	_	_	_
680	anti-myc	anti-myc	JJ	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	ChIP-exo	ChIP-exo	NNP	_	_	_
683	GadE	GadE	NNP	TF	_	_
684	pH5	ph5	NN	_	_	_
685	.5	.5	CD	_	_	_
686	1	1	CD	_	_	_
687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
688	ChIP-exo	ChIP-exo	NNP	_	_	_
689	GadE	GadE	NNP	TF	_	_
690	pH5	ph5	NN	_	_	_
691	.5	.5	CD	_	_	_
692	2	2	CD	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
694	ChIP-exo	chip-exo	JJ	_	_	_
695	GadW	gadw	NN	TF	_	_
696	pH5	ph5	NN	_	_	_
697	.5	.5	CD	_	_	_
698	1	1	CD	_	_	_
699	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
700	ChIP-exo	chip-exo	JJ	_	_	_
701	GadW	gadw	NN	TF	_	_
702	pH5	ph5	NN	_	_	_
703	.5	.5	CD	_	_	_
704	2	2	CD	_	_	_
705	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
706	ChIP-exo	chip-exo	JJ	_	_	_
707	GadX	gadx	NN	TF	_	_
708	pH5	ph5	NN	_	_	_
709	.5	.5	CD	_	_	_
710	1	1	CD	_	_	_
711	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
712	ChIP-exo	chip-exo	JJ	_	_	_
713	GadX	gadx	NN	TF	_	_
714	pH5	ph5	NN	_	_	_
715	.5	.5	CD	_	_	_
716	2	2	CD	_	_	_
717	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
718	ChIP-exo	chip-exo	NN	_	_	_
719	reads	read	VBZ	_	_	_
720	were	be	VBD	_	_	_
721	aligned	align	VBN	_	_	_
722	to	to	TO	_	_	_
723	the	the	DT	_	_	_
724	ASM584v2	asm584v2	NN	_	_	_
725	genome	genome	NN	_	_	_
726	reference	reference	NN	_	_	_
727	sequence	sequence	NN	_	_	_
728	using	use	VBG	_	_	_
729	using	use	VBG	_	_	_
730	bowtie	bowtie	NN	_	_	_
731	v1	v1	NN	_	_	_
732	.0.0	.0.0	CD	_	_	_
733	with	with	IN	_	_	_
734	parameters	parameter	NNS	_	_	_
735	-	-	:	_	_	_
736	S	s	NN	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
738	ChIP-exo	chip-exo	NN	_	_	_
739	reads	read	VBZ	_	_	_
740	were	be	VBD	_	_	_
741	aligned	align	VBN	_	_	_
742	to	to	TO	_	_	_
743	the	the	DT	_	_	_
744	NC	NC	NNP	_	_	_
745	_	_	SYM	_	_	_
746	000913	000913	CD	_	_	_
747	genome	genome	NN	_	_	_
748	reference	reference	NN	_	_	_
749	sequence	sequence	NN	_	_	_
750	using	use	VBG	_	_	_
751	using	use	VBG	_	_	_
752	bowtie	bowtie	NN	_	_	_
753	v1	v1	NN	_	_	_
754	.0.0	.0.0	CD	_	_	_
755	with	with	IN	_	_	_
756	parameters	parameter	NNS	_	_	_
757	-	-	:	_	_	_
758	S	s	NN	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
760	ChIP-exo	chip-exo	NN	_	_	_
761	reads	read	VBZ	_	_	_
762	were	be	VBD	_	_	_
763	aligned	align	VBN	_	_	_
764	using	use	VBG	_	_	_
765	BWA	bwa	NN	_	_	_
766	with	with	IN	_	_	_
767	default	default	NN	_	_	_
768	parameters	parameter	NNS	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
770	ChIPExo-RpoD	chipexo-rpod	JJ	_	_	_
771	_	_	NN	_	_	_
772	wt	wt	JJ	_	_	_
773	_	_	NN	_	_	_
774	fructose	fructose	NN	_	_	_
775	_	_	CD	_	_	_
776	NH4Cl	nh4cl	NN	_	_	_
777	_	_	CD	_	_	_
778	O2	o2	CD	_	_	_
779	_	_	NN	_	_	_
780	1	1	CD	_	_	_
781	_	_	NN	_	_	_
782	anti-rpod	anti-rpod	JJ	_	_	_
783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
784	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
785	_	_	CD	_	_	_
786	wt	wt	JJ	_	_	_
787	_	_	NN	_	_	_
788	fructose	fructose	NN	_	_	_
789	_	_	CD	_	_	_
790	NH4Cl	nh4cl	NN	_	_	_
791	_	_	CD	_	_	_
792	O2	o2	CD	_	_	_
793	_	_	NN	_	_	_
794	2	2	CD	_	_	_
795	_	_	SYM	_	_	_
796	anti-rpod	anti-rpod	JJ	_	_	_
797	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
798	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
799	_	_	CD	_	_	_
800	wt	wt	JJ	_	_	_
801	_	_	NN	_	_	_
802	fructose	fructose	NN	_	_	_
803	_	_	CD	_	_	_
804	NH4Cl	nh4cl	NN	_	_	_
805	_	_	CD	_	_	_
806	O2	o2	CD	_	_	_
807	_	_	NN	_	_	_
808	3	3	CD	_	_	_
809	_	_	NN	_	_	_
810	anti-rpod	anti-rpod	JJ	_	_	_
811	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
812	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
813	_	_	CD	_	_	_
814	wt	wt	JJ	_	_	_
815	_	_	NN	_	_	_
816	glucose	glucose	NN	SUPP	_	_
817	_	_	CD	_	_	_
818	NH4Cl	nh4cl	NN	_	_	_
819	_	_	CD	_	_	_
820	O2	o2	CD	_	_	_
821	_	_	NN	_	_	_
822	1	1	CD	_	_	_
823	_	_	NN	_	_	_
824	anti-rpod	anti-rpod	JJ	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
827	_	_	CD	_	_	_
828	wt	wt	JJ	_	_	_
829	_	_	NN	_	_	_
830	glucose	glucose	NN	SUPP	_	_
831	_	_	CD	_	_	_
832	NH4Cl	nh4cl	NN	_	_	_
833	_	_	CD	_	_	_
834	O2	o2	CD	_	_	_
835	_	_	NN	_	_	_
836	2	2	CD	_	_	_
837	_	_	SYM	_	_	_
838	anti-rpod	anti-rpod	JJ	_	_	_
839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
840	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
841	_	_	CD	_	_	_
842	wt	wt	JJ	_	_	_
843	_	_	NN	_	_	_
844	glucose	glucose	NN	SUPP	_	_
845	_	_	CD	_	_	_
846	NH4Cl	nh4cl	NN	_	_	_
847	_	_	CD	_	_	_
848	O2	o2	CD	_	_	_
849	_	_	NN	_	_	_
850	3	3	CD	_	_	_
851	_	_	NN	_	_	_
852	anti-rpod	anti-rpod	JJ	_	_	_
853	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
854	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
855	_	_	CD	_	_	_
856	wt	wt	JJ	_	_	_
857	_	_	NN	_	_	_
858	glycerol	glycerol	NN	SUPP	_	_
859	_	_	CD	_	_	_
860	NH4Cl	nh4cl	NN	_	_	_
861	_	_	CD	_	_	_
862	O2	o2	CD	_	_	_
863	_	_	NN	_	_	_
864	1	1	CD	_	_	_
865	_	_	NN	_	_	_
866	anti-rpod	anti-rpod	JJ	_	_	_
867	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
868	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
869	_	_	CD	_	_	_
870	wt	wt	JJ	_	_	_
871	_	_	NN	_	_	_
872	glycerol	glycerol	NN	SUPP	_	_
873	_	_	CD	_	_	_
874	NH4Cl	nh4cl	NN	_	_	_
875	_	_	CD	_	_	_
876	O2	o2	CD	_	_	_
877	_	_	NN	_	_	_
878	2	2	CD	_	_	_
879	_	_	SYM	_	_	_
880	anti-rpod	anti-rpod	JJ	_	_	_
881	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
882	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
883	_	_	CD	_	_	_
884	wt	wt	JJ	_	_	_
885	_	_	NN	_	_	_
886	glycerol	glycerol	NN	SUPP	_	_
887	_	_	CD	_	_	_
888	NH4Cl	nh4cl	NN	_	_	_
889	_	_	CD	_	_	_
890	O2	o2	CD	_	_	_
891	_	_	NN	_	_	_
892	3	3	CD	_	_	_
893	_	_	NN	_	_	_
894	anti-rpod	anti-rpod	JJ	_	_	_
895	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
896	ChIP-exo	chip-exo	NN	_	_	_
897	RpoS	rpos	NN	_	_	_
898	pH5	ph5	NN	_	_	_
899	.5	.5	CD	_	_	_
900	1	1	CD	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	ChIP-exo	chip-exo	JJ	_	_	_
903	RpoS	rpos	NN	_	_	_
904	pH5	ph5	NN	_	_	_
905	.5	.5	CD	_	_	_
906	2	2	CD	_	_	_
907	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
908	chip-Fnr	chip-fnr	JJ	_	_	_
909	_	_	NN	_	_	_
910	Fnr8myc	fnr8myc	NN	_	_	_
911	_	_	NN	_	_	_
912	glucose	glucose	NN	SUPP	_	_
913	_	_	CD	_	_	_
914	NH4CL	nh4cl	NN	_	_	_
915	_	_	NN	_	_	_
916	anaerobic	anaerobic	JJ	_	_	_
917	_	_	NN	_	_	_
918	1	1	CD	_	_	_
919	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
920	chip-Fnr	chip-fnr	JJ	_	_	_
921	_	_	NN	_	_	_
922	Fnr8myc	fnr8myc	NN	_	_	_
923	_	_	NN	_	_	_
924	glucose	glucose	NN	SUPP	_	_
925	_	_	CD	_	_	_
926	NH4CL	nh4cl	NN	_	_	_
927	_	_	NN	_	_	_
928	anaerobic	anaerobic	JJ	_	_	_
929	_	_	NN	_	_	_
930	2	2	CD	_	_	_
931	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
932	chip-Fnr	chip-fnr	JJ	_	_	_
933	_	_	NN	_	_	_
934	Fnr8myc	fnr8myc	NN	_	_	_
935	_	_	NN	_	_	_
936	glucose	glucose	NN	SUPP	_	_
937	_	_	CD	_	_	_
938	NH4CL	nh4cl	NN	_	_	_
939	_	_	NN	_	_	_
940	anaerobic	anaerobic	JJ	_	_	_
941	_	_	NN	_	_	_
942	3	3	CD	_	_	_
943	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
944	chip-Fnr	chip-fnr	JJ	_	_	_
945	_	_	NN	_	_	_
946	Fnr8myc	fnr8myc	NN	_	_	_
947	_	_	NN	_	_	_
948	glucose	glucose	NN	SUPP	_	_
949	_	_	CD	_	_	_
950	NH4CL	nh4cl	NN	_	_	_
951	_	_	CD	_	_	_
952	NO3	no3	NN	_	_	_
953	_	_	NN	_	_	_
954	1	1	CD	_	_	_
955	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
956	chip-Fnr	chip-fnr	JJ	_	_	_
957	_	_	NN	_	_	_
958	Fnr8myc	fnr8myc	NN	_	_	_
959	_	_	NN	_	_	_
960	glucose	glucose	NN	SUPP	_	_
961	_	_	CD	_	_	_
962	NH4CL	nh4cl	NN	_	_	_
963	_	_	CD	_	_	_
964	NO3	no3	NN	_	_	_
965	_	_	NN	_	_	_
966	2	2	CD	_	_	_
967	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
968	chip-Fnr	chip-fnr	JJ	_	_	_
969	_	_	NN	_	_	_
970	Fnr8myc	fnr8myc	NN	_	_	_
971	_	_	NN	_	_	_
972	glucose	glucose	NN	SUPP	_	_
973	_	_	CD	_	_	_
974	NH4CL	nh4cl	NN	_	_	_
975	_	_	CD	_	_	_
976	NO3	no3	NN	_	_	_
977	_	_	NN	_	_	_
978	3	3	CD	_	_	_
979	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
980	ChIP	chip	NN	_	_	_
981	_	_	CD	_	_	_
982	hns-F	hns-f	NN	_	_	_
983	_	_	SYM	_	_	_
984	bcm	bcm	SYM	_	_	_
985	-	-	:	_	_	_
986	#	#	#	_	_	_
987	1	1	CD	_	_	_
988	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
989	ChIP	chip	NN	_	_	_
990	_	_	CD	_	_	_
991	hns-F	hns-f	NN	_	_	_
992	_	_	CD	_	_	_
993	bcm	bcm	NN	_	_	_
994	+	+	CC	_	_	_
995	#	#	#	_	_	_
996	1	1	CD	_	_	_
997	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
998	ChIP	chip	NN	_	_	_
999	_	_	CD	_	_	_
1000	hns-F	hns-f	NN	_	_	_
1001	_	_	SYM	_	_	_
1002	bcm	bcm	SYM	_	_	_
1003	-	-	:	_	_	_
1004	#	#	#	_	_	_
1005	2	2	CD	_	_	_
1006	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1007	ChIP	chip	NN	_	_	_
1008	_	_	SYM	_	_	_
1009	hns-F	hns-f	JJ	_	_	_
1010	_	_	NN	_	_	_
1011	bcm	bcm	NN	_	_	_
1012	+	+	CC	_	_	_
1013	#	#	#	_	_	_
1014	2	2	CD	_	_	_
1015	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1016	ChIP-Seq	chip-seq	JJ	_	_	_
1017	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1018	ChIP-seq	chip-seq	NN	_	_	_
1019	experiments	experiment	NNS	_	_	_
1020	were	be	VBD	_	_	_
1021	performed	perform	VBN	_	_	_
1022	in	in	IN	_	_	_
1023	duplicate	duplicate	VB	_	_	_
1024	using	use	VBG	_	_	_
1025	similar	similar	JJ	_	_	_
1026	growth	growth	NN	_	_	_
1027	condition	condition	NN	_	_	_
1028	and	and	CC	_	_	_
1029	protocols	protocol	NNS	_	_	_
1030	for	for	IN	_	_	_
1031	chromatin	chromatin	NN	_	_	_
1032	immunoprecipitation	immunoprecipitation	NN	_	_	_
1033	.	.	.	_	_	_

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	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	ChIP-seq	ChIP-seq	NNP	_	_	_
14	libraries	library	NNS	_	_	_
15	were	be	VBD	_	_	_
16	prepared	prepare	VBN	_	_	_
17	from	from	IN	_	_	_
18	5-10	5-10	CD	_	_	_
19	ng	ng	NN	_	_	_
20	of	of	IN	_	_	_
21	the	the	DT	_	_	_
22	DNA	dna	NN	_	_	_
23	samples	sample	NNS	_	_	_
24	with	with	IN	_	_	_
25	the	the	DT	_	_	_
26	NebNext	NebNext	NNP	_	_	_
27	®	®	SYM	_	_	_
28	Ultra	ultra	FW	_	_	_
29	™	™	FW	_	_	_
30	DNA	dna	NN	_	_	_
31	Library	Library	NNP	_	_	_
32	Prep	Prep	NNP	_	_	_
33	Kit	kit	NN	_	_	_
34	for	for	IN	_	_	_
35	Illumina	Illumina	NNP	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	New	New	NNP	_	_	_
38	England	England	NNP	_	_	_
39	Biolabs	Biolabs	NNP	_	_	_
40	,	,	,	_	_	_
41	MA	MA	NNP	_	_	_
42	,	,	,	_	_	_
43	USA	USA	NNP	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	following	follow	VBG	_	_	_
46	the	the	DT	_	_	_
47	manufacturer	manufacturer	NN	_	_	_
48	's	's	POS	_	_	_
49	instructions	instruction	NNS	_	_	_
50	.	.	.	_	_	_

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	NN	_	_	_
2	ChIP-seq	chip-seq	NN	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	aligned	align	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	CFT073	cft073	NN	_	_	_
9	genome	genome	NN	_	_	_
10	using	use	VBG	_	_	_
11	bowtie	bowtie	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	version	version	NN	_	_	_
14	0.12.8	0.12.8	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	ChIP-seq	chip-seq	NN	_	_	_
18	reads	read	VBZ	_	_	_
19	were	be	VBD	_	_	_
20	aligned	align	VBN	_	_	_
21	to	to	TO	_	_	_
22	the	the	DT	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	NC	nc	FW	_	_	_
26	_	_	SYM	_	_	_
27	000913	000913	CD	_	_	_
28	genome	genome	NN	_	_	_
29	using	use	VBG	_	_	_
30	BWA	BWA	NNP	_	_	_
31	0.6.2	0.6.2	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Cholic	Cholic	NNP	_	_	_
34	Acid	Acid	NNP	_	_	_
35	Treatment	treatment	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	CHP	chp	NN	_	_	_
38	files	file	NNS	_	_	_
39	were	be	VBD	_	_	_
40	generated	generate	VBN	_	_	_
41	using	use	VBG	_	_	_
42	Affymetrix	Affymetrix	NNP	_	_	_
43	Expression	expression	NN	_	_	_
44	Control	control	NN	_	_	_
45	.	.	.	_	_	_

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	NNP	_	_	_
2	Chromatin	Chromatin	NNP	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	and	and	CC	_	_	_
6	processed	process	VBN	_	_	_
7	according	accord	VBG	_	_	_
8	to	to	TO	_	_	_
9	Oxford	Oxford	NNP	_	_	_
10	Gene	Gene	NNP	_	_	_
11	Technology	Technology	NNP	_	_	_
12	protocols	protocol	NNS	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	www.ogt.co.uk	www.ogt.co.uk	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Chromosomal	chromosomal	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	CIP2G	cip2g	NN	_	_	_
6	_	_	CD	_	_	_
7	00000	00000	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	CIP2G	cip2g	NN	_	_	_
10	_	_	CD	_	_	_
11	00045	00045	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	CIP2G	cip2g	NN	_	_	_
14	_	_	CD	_	_	_
15	00090	00090	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	CIP2G	cip2g	NN	_	_	_
18	_	_	CD	_	_	_
19	00135	00135	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	CIP2G	cip2g	NN	_	_	_
22	_	_	CD	_	_	_
23	00180	00180	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	CIP4G	cip4g	NN	_	_	_
26	_	_	CD	_	_	_
27	00000	00000	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	CIP4G	cip4g	NN	_	_	_
30	_	_	CD	_	_	_
31	00045	00045	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	CIP4G	cip4g	NN	_	_	_
34	_	_	CD	_	_	_
35	00090	00090	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	CIP4G	cip4g	NN	_	_	_
38	_	_	CD	_	_	_
39	00135	00135	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	CIP4G	cip4g	NN	_	_	_
42	_	_	CD	_	_	_
43	00180	00180	CD	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
46	Rep	Rep	NNP	_	_	_
47	1	1	CD	_	_	_
48	+	+	CC	_	_	_
49	A-IP	a-ip	JJ	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Ciprofloxacin	ciprofloxacin	NN	_	_	_
52	Rep	Rep	NNP	_	_	_
53	1	1	CD	_	_	_
54	+	+	CC	_	_	_
55	A+IP	A+IP	NNP	_	_	_
56	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
57	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
58	Rep	Rep	NNP	_	_	_
59	2	2	CD	_	_	_
60	+	+	CC	_	_	_
61	A-IP	a-ip	JJ	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Ciprofloxacin	ciprofloxacin	NN	_	_	_
64	Rep	Rep	NNP	_	_	_
65	2	2	CD	_	_	_
66	+	+	CC	_	_	_
67	A+IP	A+IP	NNP	_	_	_
68	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
69	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
70	Rep	Rep	NNP	_	_	_
71	3	3	CD	_	_	_
72	+	+	CC	_	_	_
73	A-IP	a-ip	JJ	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	Ciprofloxacin	ciprofloxacin	NN	_	_	_
76	Rep	Rep	NNP	_	_	_
77	3	3	CD	_	_	_
78	+	+	CC	_	_	_
79	A+IP	A+IP	NNP	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	CIPSG	CIPSG	NNP	_	_	_
82	_	_	SYM	_	_	_
83	00000	00000	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	CIPSG	cipsg	NN	_	_	_
86	_	_	CD	_	_	_
87	00045	00045	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	CIPSG	cipsg	NN	_	_	_
90	_	_	CD	_	_	_
91	00090	00090	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	CIPSG	cipsg	NN	_	_	_
94	_	_	CD	_	_	_
95	00135	00135	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	CIPSG	cipsg	NN	_	_	_
98	_	_	CD	_	_	_
99	00180	00180	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	Cirpofloxacin	cirpofloxacin	NN	_	_	_
102	treated	treat	VBN	_	_	_
103	fur	fur	NN	GEN	_	_
104	mutant	mutant	JJ	_	_	_
105	sample	sample	NN	_	_	_
106	at	at	IN	_	_	_
107	T1h	t1h	NN	_	_	_
108	,	,	,	_	_	_
109	biological	biological	JJ	_	_	_
110	rep	rep	NN	GEN	_	_
111	1	1	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	Cirpofloxacin	cirpofloxacin	NN	_	_	_
114	treated	treat	VBN	_	_	_
115	fur	fur	NN	GEN	_	_
116	mutant	mutant	JJ	_	_	_
117	sample	sample	NN	_	_	_
118	at	at	IN	_	_	_
119	T1h	t1h	NN	_	_	_
120	,	,	,	_	_	_
121	biological	biological	JJ	_	_	_
122	rep	rep	NN	GEN	_	_
123	2	2	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Cirpofloxacin	cirpofloxacin	NN	_	_	_
126	treated	treat	VBN	_	_	_
127	WT	wt	JJ	_	_	_
128	sample	sample	NN	_	_	_
129	at	at	IN	_	_	_
130	T1h	t1h	NN	_	_	_
131	,	,	,	_	_	_
132	biological	biological	JJ	_	_	_
133	rep	rep	NN	GEN	_	_
134	1	1	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	Cirpofloxacin	cirpofloxacin	NN	_	_	_
137	treated	treat	VBN	_	_	_
138	WT	wt	JJ	_	_	_
139	sample	sample	NN	_	_	_
140	at	at	IN	_	_	_
141	T1h	t1h	NN	_	_	_
142	,	,	,	_	_	_
143	biological	biological	JJ	_	_	_
144	rep	rep	NN	GEN	_	_
145	2	2	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	Clarified	clarify	VBN	_	_	_
148	extracts	extract	NNS	_	_	_
149	were	be	VBD	_	_	_
150	treated	treat	VBN	_	_	_
151	with	with	IN	_	_	_
152	microccocal	microccocal	JJ	_	_	_
153	nuclease	nuclease	NN	_	_	_
154	-LRB-	-lrb-	-LRB-	_	_	_
155	45	45	CD	_	_	_
156	enzyme	enzyme	NN	_	_	_
157	units	unit	NNS	_	_	_
158	per	per	IN	_	_	_
159	absorbance	absorbance	NN	_	_	_
160	unit	unit	NN	_	_	_
161	of	of	IN	_	_	_
162	lysate	lysate	NN	_	_	_
163	at	at	IN	_	_	_
164	260	260	CD	_	_	_
165	nm	nm	NN	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	,	,	,	_	_	_
168	purified	purify	VBN	_	_	_
169	through	through	IN	_	_	_
170	a	a	DT	_	_	_
171	sucrose	sucrose	NN	_	_	_
172	cushion	cushion	NN	_	_	_
173	,	,	,	_	_	_
174	and	and	CC	_	_	_
175	affinity	affinity	NN	_	_	_
176	purified	purify	VBN	_	_	_
177	via	via	IN	_	_	_
178	TF	tf	NN	_	_	_
179	.	.	.	_	_	_

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	NNP	_	_	_
2	Clindamycin	Clindamycin	NNP	_	_	_
3	_	_	NNP	_	_	_
4	replicate	replicate	VB	_	_	_
5	_	_	SYM	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Clindamycin	clindamycin	NN	_	_	_
9	_	_	NN	_	_	_
10	replicate	replicate	VBP	_	_	_
11	_	_	NN	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Clindamycin	Clindamycin	NNP	_	_	_
15	_	_	NNP	_	_	_
16	replicate	replicate	VB	_	_	_
17	_	_	SYM	_	_	_
18	3	3	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	clinical-1	clinical-1	NN	_	_	_
21	strain	strain	NN	_	_	_
22	grown	grow	VBN	_	_	_
23	to	to	TO	_	_	_
24	exponential	exponential	JJ	GrowthPhase	_	_
25	phase	phase	NN	GrowthPhase	_	_
26	of	of	IN	_	_	_
27	growth	growth	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Clinical-1	clinical-1	NN	_	_	_
30	vs	vs	CC	_	_	_
31	Bovine-biased-1	bovine-biased-1	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Clinical-1	clinical-1	NN	_	_	_
34	vs	vs	CC	_	_	_
35	Bovine-biased-2	bovine-biased-2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Clinical-1	clinical-1	NN	_	_	_
38	vs	vs	CC	_	_	_
39	Bovine-biased-3	bovine-biased-3	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Clinical-1	clinical-1	NN	_	_	_
42	vs	vs	CC	_	_	_
43	Bovine-biased-4	bovine-biased-4	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	clinical-2	clinical-2	NN	_	_	_
46	strain	strain	NN	_	_	_
47	grown	grow	VBN	_	_	_
48	to	to	TO	_	_	_
49	exponential	exponential	JJ	GrowthPhase	_	_
50	phase	phase	NN	GrowthPhase	_	_
51	of	of	IN	_	_	_
52	growth	growth	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Clinical-2	clinical-2	NN	_	_	_
55	vs	vs	CC	_	_	_
56	Bovine-biased-1	bovine-biased-1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Clinical-2	clinical-2	NN	_	_	_
59	vs	vs	CC	_	_	_
60	Bovine-biased-2	bovine-biased-2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Clinical-2	clinical-2	NN	_	_	_
63	vs	vs	CC	_	_	_
64	Bovine-biased-3	bovine-biased-3	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Clinical-2	clinical-2	NN	_	_	_
67	vs	vs	CC	_	_	_
68	Bovine-biased-4	bovine-biased-4	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	clinical-3	clinical-3	NN	_	_	_
71	strain	strain	NN	_	_	_
72	grown	grow	VBN	_	_	_
73	to	to	TO	_	_	_
74	exponential	exponential	JJ	GrowthPhase	_	_
75	phase	phase	NN	GrowthPhase	_	_
76	of	of	IN	_	_	_
77	growth	growth	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	Clinical-3	clinical-3	NN	_	_	_
80	vs	vs	CC	_	_	_
81	Bovine-biased-1	bovine-biased-1	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	Clinical-3	clinical-3	NN	_	_	_
84	vs	vs	CC	_	_	_
85	Bovine-biased-2	bovine-biased-2	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Clinical-3	clinical-3	NN	_	_	_
88	vs	vs	CC	_	_	_
89	Bovine-biased-3	bovine-biased-3	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	Clinical-3	clinical-3	NN	_	_	_
92	vs	vs	CC	_	_	_
93	Bovine-biased-4	bovine-biased-4	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	clinical-4	clinical-4	NN	_	_	_
96	strain	strain	NN	_	_	_
97	grown	grow	VBN	_	_	_
98	to	to	TO	_	_	_
99	exponential	exponential	JJ	GrowthPhase	_	_
100	phase	phase	NN	GrowthPhase	_	_
101	of	of	IN	_	_	_
102	growth	growth	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Clinical-4	clinical-4	NN	_	_	_
105	vs	vs	CC	_	_	_
106	Bovine-biased-1	bovine-biased-1	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	Clinical-4	clinical-4	NN	_	_	_
109	vs	vs	CC	_	_	_
110	Bovine-biased-2	bovine-biased-2	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Clinical-4	clinical-4	NN	_	_	_
113	vs	vs	CC	_	_	_
114	Bovine-biased-3	bovine-biased-3	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Clinical-4	clinical-4	NN	_	_	_
117	vs	vs	CC	_	_	_
118	Bovine-biased-4	bovine-biased-4	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
120	Clinical	clinical	JJ	_	_	_
121	isolate	isolate	NN	_	_	_
122	,	,	,	_	_	_
123	minus	minus	CC	_	_	_
124	ciprofloxacin	ciprofloxacin	NN	_	_	_
125	,	,	,	_	_	_
126	0	0	CD	_	_	_
127	min	min	NN	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	Clinical	clinical	JJ	_	_	_
130	isolate	isolate	NN	_	_	_
131	,	,	,	_	_	_
132	minus	minus	CC	_	_	_
133	ciprofloxacin	ciprofloxacin	NN	_	_	_
134	,	,	,	_	_	_
135	30	30	CD	_	_	_
136	min	min	NN	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	Clinical	clinical	JJ	_	_	_
139	isolate	isolate	NN	_	_	_
140	,	,	,	_	_	_
141	minus	minus	CC	_	_	_
142	ciprofloxacin	ciprofloxacin	NN	_	_	_
143	,	,	,	_	_	_
144	90	90	CD	_	_	_
145	min	min	NN	_	_	_
146	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
147	Clinical	clinical	JJ	_	_	_
148	isolate	isolate	NN	_	_	_
149	,	,	,	_	_	_
150	plus	plus	CC	_	_	_
151	ciprofloxacin	ciprofloxacin	NN	_	_	_
152	,	,	,	_	_	_
153	0	0	CD	_	_	_
154	min	min	NN	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	Clinical	clinical	JJ	_	_	_
157	isolate	isolate	NN	_	_	_
158	,	,	,	_	_	_
159	plus	plus	CC	_	_	_
160	ciprofloxacin	ciprofloxacin	NN	_	_	_
161	,	,	,	_	_	_
162	30	30	CD	_	_	_
163	min	min	NN	_	_	_
164	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
165	Clinical	clinical	JJ	_	_	_
166	isolate	isolate	NN	_	_	_
167	,	,	,	_	_	_
168	plus	plus	CC	_	_	_
169	ciprofloxacin	ciprofloxacin	NN	_	_	_
170	,	,	,	_	_	_
171	90	90	CD	_	_	_
172	min	min	NN	_	_	_
173	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
174	Clones	clone	NNS	_	_	_
175	were	be	VBD	_	_	_
176	grown	grow	VBN	_	_	_
177	in	in	IN	_	_	_
178	M9	m9	NN	_	_	_
179	with	with	IN	_	_	_
180	0.4	0.4	CD	_	_	_
181	%	%	NN	_	_	_
182	-LRB-	-lrb-	-LRB-	_	_	_
183	w/v	w/v	NN	_	_	_
184	-RRB-	-rrb-	-RRB-	_	_	_
185	glucose	glucose	NN	SUPP	_	_
186	as	as	IN	_	_	_
187	carbon	carbon	NN	_	_	_
188	source	source	NN	_	_	_
189	minimal	minimal	JJ	_	_	_
190	medium	medium	NN	_	_	_
191	with	with	IN	_	_	_
192	0.3	0.3	CD	_	_	_
193	M	m	NN	_	_	_
194	NaCl	nacl	NN	_	_	_
195	-LRB-	-lrb-	-LRB-	_	_	_
196	osmotic	osmotic	JJ	_	_	_
197	stress	stress	NN	_	_	_
198	medium	medium	NN	_	_	_
199	-RRB-	-rrb-	-RRB-	_	_	_
200	to	to	TO	_	_	_
201	mid-log	mid-log	JJ	_	_	_
202	phase	phase	NN	_	_	_
203	-LRB-	-lrb-	-LRB-	_	_	_
204	OD600	od600	NN	_	_	_
205	approx.	approx.	RB	_	_	_
206	0.8	0.8	CD	_	_	_
207	-RRB-	-rrb-	-RRB-	_	_	_
208	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	-LSB-	-lsb-	-LRB-	_	_	_
3	Clostridium	clostridium	NN	_	_	_
4	-RSB-	-rsb-	-RRB-	_	_	_
5	leptum	leptum	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	-LSB-	-lsb-	-LRB-	_	_	_
8	Clostridium	clostridium	NN	_	_	_
9	-RSB-	-rsb-	-RRB-	_	_	_
10	symbiosum	symbiosum	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Cluster	cluster	NN	_	_	_
13	detection	detection	NN	_	_	_
14	and	and	CC	_	_	_
15	base	base	NN	_	_	_
16	calling	calling	NN	_	_	_
17	were	be	VBD	_	_	_
18	performed	perform	VBN	_	_	_
19	using	use	VBG	_	_	_
20	RTA	RTA	NNP	_	_	_
21	v1	v1	NN	_	_	_
22	.13	.13	CD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Illumina	Illumina	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	the	the	DT	_	_	_
29	quality	quality	NN	_	_	_
30	of	of	IN	_	_	_
31	the	the	DT	_	_	_
32	reads	read	VBZ	_	_	_
33	was	be	VBD	_	_	_
34	assessed	assess	VBN	_	_	_
35	with	with	IN	_	_	_
36	CASAVA	casava	NN	_	_	_
37	v1	v1	NN	_	_	_
38	.8.1	.8.1	CD	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Illumina	Illumina	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Co-hybridization	co-hybridization	NN	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	G	g	NN	_	_	_
7	1/2	1/2	CD	_	_	_
8	isolate	isolate	NN	_	_	_
9	with	with	IN	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	K-12	k-12	NN	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Co-hybridization	co-hybridization	NN	_	_	_
16	of	of	IN	_	_	_
17	E.	e.	FW	_	_	_
18	coli	coli	FW	_	_	_
19	G	g	NN	_	_	_
20	1/2	1/2	CD	_	_	_
21	isolate	isolate	NN	_	_	_
22	with	with	IN	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	O157	o157	NN	_	_	_
26	:	:	:	_	_	_
27	H7	h7	NN	_	_	_
28	EDL933	edl933	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Co-hybridization	co-hybridization	NN	_	_	_
31	of	of	IN	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	G	g	NN	_	_	_
35	3/10	3/10	CD	_	_	_
36	isolate	isolate	NN	_	_	_
37	with	with	IN	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	O157	o157	NN	_	_	_
41	:	:	:	_	_	_
42	H7	h7	NN	_	_	_
43	EDL933	edl933	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Co-hybridization	co-hybridization	NN	_	_	_
46	of	of	IN	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	G	g	NN	_	_	_
50	4/9	4/9	CD	_	_	_
51	isolate	isolate	NN	_	_	_
52	with	with	IN	_	_	_
53	E.	e.	FW	_	_	_
54	coli	coli	FW	_	_	_
55	K-12	k-12	NN	_	_	_
56	MG1655	mg1655	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Co-hybridization	co-hybridization	NN	_	_	_
59	of	of	IN	_	_	_
60	E.	e.	FW	_	_	_
61	coli	coli	FW	_	_	_
62	G5	g5	NN	_	_	_
63	isolate	isolate	NN	_	_	_
64	with	with	IN	_	_	_
65	E.	e.	FW	_	_	_
66	coli	coli	FW	_	_	_
67	K-12	k-12	NN	_	_	_
68	MG1655	mg1655	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Co-hybridization	co-hybridization	NN	_	_	_
71	of	of	IN	_	_	_
72	E.	e.	FW	_	_	_
73	coli	coli	FW	_	_	_
74	G5	g5	NN	_	_	_
75	isolate	isolate	NN	_	_	_
76	with	with	IN	_	_	_
77	E.	e.	FW	_	_	_
78	coli	coli	FW	_	_	_
79	O157	o157	NN	_	_	_
80	:	:	:	_	_	_
81	H7	h7	NN	_	_	_
82	EDL933	edl933	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Co-hybridization	co-hybridization	NN	_	_	_
85	of	of	IN	_	_	_
86	E.	e.	FW	_	_	_
87	coli	coli	FW	_	_	_
88	isolate	isolate	NN	_	_	_
89	G	g	NN	_	_	_
90	3/10	3/10	CD	_	_	_
91	with	with	IN	_	_	_
92	control	control	NN	_	_	_
93	strain	strain	NN	_	_	_
94	K-12	k-12	NN	_	_	_
95	MG1655	mg1655	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Co-hybridization	co-hybridization	NN	_	_	_
98	of	of	IN	_	_	_
99	E.	e.	FW	_	_	_
100	coli	coli	FW	_	_	_
101	isolate	isolate	NN	_	_	_
102	G	g	NN	_	_	_
103	4/9	4/9	CD	_	_	_
104	with	with	IN	_	_	_
105	E.	e.	FW	_	_	_
106	coli	coli	FW	_	_	_
107	O157	o157	NN	_	_	_
108	:	:	:	_	_	_
109	H7	h7	NN	_	_	_
110	EDL933	edl933	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Co-hybridization	co-hybridization	NN	_	_	_
113	of	of	IN	_	_	_
114	E.	e.	FW	_	_	_
115	coli	coli	FW	_	_	_
116	O157	o157	NN	_	_	_
117	:	:	:	_	_	_
118	H7	h7	NN	_	_	_
119	EDL933	edl933	NN	_	_	_
120	with	with	IN	_	_	_
121	E.	e.	FW	_	_	_
122	coli	coli	FW	_	_	_
123	K-12	k-12	NN	_	_	_
124	M1655	m1655	NN	_	_	_
125	#	#	#	_	_	_
126	1	1	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Co-hybridization	co-hybridization	NN	_	_	_
129	of	of	IN	_	_	_
130	E.	e.	FW	_	_	_
131	coli	coli	FW	_	_	_
132	O157	o157	NN	_	_	_
133	:	:	:	_	_	_
134	H7	h7	NN	_	_	_
135	EDL933	edl933	NN	_	_	_
136	with	with	IN	_	_	_
137	E.	e.	FW	_	_	_
138	coli	coli	FW	_	_	_
139	K-12	k-12	NN	_	_	_
140	M1655	m1655	NN	_	_	_
141	#	#	#	_	_	_
142	2	2	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	coli	coli	NN	_	_	_
145	_	_	NN	_	_	_
146	coldstress	coldstress	VBP	_	_	_
147	_	_	SYM	_	_	_
148	timepoint1	timepoint1	CD	_	_	_
149	_	_	CD	_	_	_
150	rep1	rep1	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	coli	coli	NN	_	_	_
153	_	_	NN	_	_	_
154	coldstress	coldstress	VBP	_	_	_
155	_	_	SYM	_	_	_
156	timepoint1	timepoint1	CD	_	_	_
157	_	_	CD	_	_	_
158	rep2	rep2	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	coli	coli	NN	_	_	_
161	_	_	NN	_	_	_
162	coldstress	coldstress	VBP	_	_	_
163	_	_	SYM	_	_	_
164	timepoint1	timepoint1	CD	_	_	_
165	_	_	CD	_	_	_
166	rep3	rep3	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	coli	coli	NN	_	_	_
169	_	_	NN	_	_	_
170	coldstress	coldstress	VBP	_	_	_
171	_	_	SYM	_	_	_
172	timepoint2	timepoint2	CD	_	_	_
173	_	_	CD	_	_	_
174	rep1	rep1	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	coli	coli	NN	_	_	_
177	_	_	NN	_	_	_
178	coldstress	coldstress	VBP	_	_	_
179	_	_	SYM	_	_	_
180	timepoint2	timepoint2	CD	_	_	_
181	_	_	CD	_	_	_
182	rep2	rep2	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	coli	coli	NN	_	_	_
185	_	_	NN	_	_	_
186	coldstress	coldstress	VBP	_	_	_
187	_	_	SYM	_	_	_
188	timepoint2	timepoint2	CD	_	_	_
189	_	_	CD	_	_	_
190	rep3	rep3	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	coli	coli	NN	_	_	_
193	_	_	NN	_	_	_
194	coldstress	coldstress	VBP	_	_	_
195	_	_	SYM	_	_	_
196	timepoint3	timepoint3	CD	_	_	_
197	_	_	CD	_	_	_
198	rep1	rep1	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	coli	coli	NN	_	_	_
201	_	_	NN	_	_	_
202	coldstress	coldstress	VBP	_	_	_
203	_	_	SYM	_	_	_
204	timepoint3	timepoint3	CD	_	_	_
205	_	_	CD	_	_	_
206	rep2	rep2	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	coli	coli	NN	_	_	_
209	_	_	NN	_	_	_
210	coldstress	coldstress	VBP	_	_	_
211	_	_	SYM	_	_	_
212	timepoint3	timepoint3	CD	_	_	_
213	_	_	CD	_	_	_
214	rep3	rep3	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	coli	coli	NN	_	_	_
217	_	_	NN	_	_	_
218	coldstress	coldstress	VBP	_	_	_
219	_	_	SYM	_	_	_
220	timepoint4	timepoint4	CD	_	_	_
221	_	_	CD	_	_	_
222	rep1	rep1	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	coli	coli	NN	_	_	_
225	_	_	NN	_	_	_
226	coldstress	coldstress	VBP	_	_	_
227	_	_	SYM	_	_	_
228	timepoint4	timepoint4	CD	_	_	_
229	_	_	CD	_	_	_
230	rep2	rep2	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	coli	coli	NN	_	_	_
233	_	_	NN	_	_	_
234	coldstress	coldstress	VBP	_	_	_
235	_	_	SYM	_	_	_
236	timepoint4	timepoint4	CD	_	_	_
237	_	_	CD	_	_	_
238	rep3	rep3	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	coli	coli	NN	_	_	_
241	_	_	NN	_	_	_
242	coldstress	coldstress	VBP	_	_	_
243	_	_	SYM	_	_	_
244	timepoint5	timepoint5	CD	_	_	_
245	_	_	CD	_	_	_
246	rep1	rep1	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	coli	coli	NN	_	_	_
249	_	_	NN	_	_	_
250	coldstress	coldstress	VBP	_	_	_
251	_	_	SYM	_	_	_
252	timepoint5	timepoint5	CD	_	_	_
253	_	_	CD	_	_	_
254	rep2	rep2	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	coli	coli	NN	_	_	_
257	_	_	NN	_	_	_
258	coldstress	coldstress	VBP	_	_	_
259	_	_	SYM	_	_	_
260	timepoint5	timepoint5	CD	_	_	_
261	_	_	CD	_	_	_
262	rep3	rep3	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	coli	coli	NN	_	_	_
265	_	_	NN	_	_	_
266	coldstress	coldstress	VBP	_	_	_
267	_	_	SYM	_	_	_
268	timepoint6	timepoint6	CD	_	_	_
269	_	_	CD	_	_	_
270	rep1	rep1	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	coli	coli	NN	_	_	_
273	_	_	NN	_	_	_
274	coldstress	coldstress	VBP	_	_	_
275	_	_	SYM	_	_	_
276	timepoint6	timepoint6	CD	_	_	_
277	_	_	CD	_	_	_
278	rep2	rep2	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	coli	coli	NN	_	_	_
281	_	_	NN	_	_	_
282	coldstress	coldstress	VBP	_	_	_
283	_	_	SYM	_	_	_
284	timepoint6	timepoint6	CD	_	_	_
285	_	_	CD	_	_	_
286	rep3	rep3	NN	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	coli	coli	NN	_	_	_
289	_	_	NN	_	_	_
290	coldstress	coldstress	VBP	_	_	_
291	_	_	SYM	_	_	_
292	timepoint7	timepoint7	CD	_	_	_
293	_	_	CD	_	_	_
294	rep1	rep1	NN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	coli	coli	NN	_	_	_
297	_	_	NN	_	_	_
298	coldstress	coldstress	VBP	_	_	_
299	_	_	SYM	_	_	_
300	timepoint7	timepoint7	CD	_	_	_
301	_	_	CD	_	_	_
302	rep2	rep2	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	coli	coli	NN	_	_	_
305	_	_	NN	_	_	_
306	coldstress	coldstress	VBP	_	_	_
307	_	_	SYM	_	_	_
308	timepoint7	timepoint7	CD	_	_	_
309	_	_	CD	_	_	_
310	rep3	rep3	NN	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	coli	coli	NN	_	_	_
313	_	_	NN	_	_	_
314	coldstress	coldstress	VBP	_	_	_
315	_	_	SYM	_	_	_
316	timepoint8	timepoint8	CD	_	_	_
317	_	_	CD	_	_	_
318	rep1	rep1	NN	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	coli	coli	NN	_	_	_
321	_	_	NN	_	_	_
322	coldstress	coldstress	VBP	_	_	_
323	_	_	SYM	_	_	_
324	timepoint8	timepoint8	CD	_	_	_
325	_	_	CD	_	_	_
326	rep2	rep2	NN	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	coli	coli	NN	_	_	_
329	_	_	NN	_	_	_
330	coldstress	coldstress	VBP	_	_	_
331	_	_	SYM	_	_	_
332	timepoint8	timepoint8	CD	_	_	_
333	_	_	CD	_	_	_
334	rep3	rep3	NN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	coli	coli	NN	_	_	_
337	_	_	NN	_	_	_
338	control	control	NN	_	_	_
339	_	_	CD	_	_	_
340	timepoint1	timepoint1	NN	_	_	_
341	_	_	CD	_	_	_
342	rep1	rep1	NN	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	coli	coli	NN	_	_	_
345	_	_	NN	_	_	_
346	control	control	NN	_	_	_
347	_	_	CD	_	_	_
348	timepoint1	timepoint1	NN	_	_	_
349	_	_	CD	_	_	_
350	rep2	rep2	NN	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	coli	coli	NN	_	_	_
353	_	_	NN	_	_	_
354	control	control	NN	_	_	_
355	_	_	CD	_	_	_
356	timepoint1	timepoint1	NN	_	_	_
357	_	_	CD	_	_	_
358	rep3	rep3	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	coli	coli	NN	_	_	_
361	_	_	NN	_	_	_
362	control	control	NN	_	_	_
363	_	_	CD	_	_	_
364	timepoint2	timepoint2	NN	_	_	_
365	_	_	CD	_	_	_
366	rep1	rep1	NN	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	coli	coli	NN	_	_	_
369	_	_	NN	_	_	_
370	control	control	NN	_	_	_
371	_	_	CD	_	_	_
372	timepoint2	timepoint2	NN	_	_	_
373	_	_	CD	_	_	_
374	rep2	rep2	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	coli	coli	NN	_	_	_
377	_	_	NN	_	_	_
378	control	control	NN	_	_	_
379	_	_	CD	_	_	_
380	timepoint2	timepoint2	NN	_	_	_
381	_	_	CD	_	_	_
382	rep3	rep3	NN	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	coli	coli	NN	_	_	_
385	_	_	NN	_	_	_
386	control	control	NN	_	_	_
387	_	_	CD	_	_	_
388	timepoint3	timepoint3	NN	_	_	_
389	_	_	CD	_	_	_
390	rep1	rep1	NN	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	coli	coli	NN	_	_	_
393	_	_	NN	_	_	_
394	control	control	NN	_	_	_
395	_	_	CD	_	_	_
396	timepoint3	timepoint3	NN	_	_	_
397	_	_	CD	_	_	_
398	rep2	rep2	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	coli	coli	NN	_	_	_
401	_	_	NN	_	_	_
402	control	control	NN	_	_	_
403	_	_	CD	_	_	_
404	timepoint3	timepoint3	NN	_	_	_
405	_	_	CD	_	_	_
406	rep3	rep3	NN	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	coli	coli	NN	_	_	_
409	_	_	NN	_	_	_
410	control	control	NN	_	_	_
411	_	_	CD	_	_	_
412	timepoint4	timepoint4	NN	_	_	_
413	_	_	CD	_	_	_
414	rep1	rep1	NN	_	_	_
415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
416	coli	coli	NN	_	_	_
417	_	_	NN	_	_	_
418	control	control	NN	_	_	_
419	_	_	CD	_	_	_
420	timepoint4	timepoint4	NN	_	_	_
421	_	_	CD	_	_	_
422	rep2	rep2	NN	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	coli	coli	NN	_	_	_
425	_	_	NN	_	_	_
426	control	control	NN	_	_	_
427	_	_	CD	_	_	_
428	timepoint4	timepoint4	NN	_	_	_
429	_	_	CD	_	_	_
430	rep3	rep3	NN	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	coli	coli	NN	_	_	_
433	_	_	NN	_	_	_
434	control	control	NN	_	_	_
435	_	_	CD	_	_	_
436	timepoint5	timepoint5	NN	_	_	_
437	_	_	CD	_	_	_
438	rep1	rep1	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	coli	coli	NN	_	_	_
441	_	_	NN	_	_	_
442	control	control	NN	_	_	_
443	_	_	CD	_	_	_
444	timepoint5	timepoint5	NN	_	_	_
445	_	_	CD	_	_	_
446	rep2	rep2	NN	_	_	_
447	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
448	coli	coli	NN	_	_	_
449	_	_	NN	_	_	_
450	control	control	NN	_	_	_
451	_	_	CD	_	_	_
452	timepoint5	timepoint5	NN	_	_	_
453	_	_	CD	_	_	_
454	rep3	rep3	NN	_	_	_
455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
456	coli	coli	NN	_	_	_
457	_	_	NN	_	_	_
458	control	control	NN	_	_	_
459	_	_	CD	_	_	_
460	timepoint6	timepoint6	NN	_	_	_
461	_	_	CD	_	_	_
462	rep1	rep1	NN	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	coli	coli	NN	_	_	_
465	_	_	NN	_	_	_
466	control	control	NN	_	_	_
467	_	_	CD	_	_	_
468	timepoint6	timepoint6	NN	_	_	_
469	_	_	CD	_	_	_
470	rep2	rep2	NN	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	coli	coli	NN	_	_	_
473	_	_	NN	_	_	_
474	control	control	NN	_	_	_
475	_	_	CD	_	_	_
476	timepoint6	timepoint6	NN	_	_	_
477	_	_	CD	_	_	_
478	rep3	rep3	NN	_	_	_
479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
480	coli	coli	NN	_	_	_
481	_	_	NN	_	_	_
482	control	control	NN	_	_	_
483	_	_	CD	_	_	_
484	timepoint7	timepoint7	NN	_	_	_
485	_	_	CD	_	_	_
486	rep1	rep1	NN	_	_	_
487	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
488	coli	coli	NN	_	_	_
489	_	_	NN	_	_	_
490	control	control	NN	_	_	_
491	_	_	CD	_	_	_
492	timepoint7	timepoint7	NN	_	_	_
493	_	_	CD	_	_	_
494	rep2	rep2	NN	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
496	coli	coli	NN	_	_	_
497	_	_	NN	_	_	_
498	control	control	NN	_	_	_
499	_	_	CD	_	_	_
500	timepoint7	timepoint7	NN	_	_	_
501	_	_	CD	_	_	_
502	rep3	rep3	NN	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	coli	coli	NN	_	_	_
505	_	_	NN	_	_	_
506	control	control	NN	_	_	_
507	_	_	SYM	_	_	_
508	timepoint8	timepoint8	CD	_	_	_
509	_	_	CD	_	_	_
510	rep1	rep1	NN	_	_	_
511	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
512	coli	coli	NN	_	_	_
513	_	_	NN	_	_	_
514	control	control	NN	_	_	_
515	_	_	SYM	_	_	_
516	timepoint8	timepoint8	CD	_	_	_
517	_	_	CD	_	_	_
518	rep2	rep2	NN	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	coli	coli	NN	_	_	_
521	_	_	NN	_	_	_
522	control	control	NN	_	_	_
523	_	_	SYM	_	_	_
524	timepoint8	timepoint8	CD	_	_	_
525	_	_	CD	_	_	_
526	rep3	rep3	NN	_	_	_
527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
528	coli	coli	NN	_	_	_
529	_	_	NN	_	_	_
530	heatstress	heatstress	VBP	_	_	_
531	_	_	SYM	_	_	_
532	timepoint1	timepoint1	CD	_	_	_
533	_	_	CD	_	_	_
534	rep1	rep1	NN	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	coli	coli	NN	_	_	_
537	_	_	NN	_	_	_
538	heatstress	heatstress	VBP	_	_	_
539	_	_	SYM	_	_	_
540	timepoint1	timepoint1	CD	_	_	_
541	_	_	CD	_	_	_
542	rep2	rep2	NN	_	_	_
543	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
544	coli	coli	NN	_	_	_
545	_	_	NN	_	_	_
546	heatstress	heatstress	VBP	_	_	_
547	_	_	SYM	_	_	_
548	timepoint1	timepoint1	CD	_	_	_
549	_	_	CD	_	_	_
550	rep3	rep3	NN	_	_	_
551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
552	coli	coli	NN	_	_	_
553	_	_	NN	_	_	_
554	heatstress	heatstress	VBP	_	_	_
555	_	_	SYM	_	_	_
556	timepoint2	timepoint2	CD	_	_	_
557	_	_	CD	_	_	_
558	rep1	rep1	NN	_	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
560	coli	coli	NN	_	_	_
561	_	_	NN	_	_	_
562	heatstress	heatstress	VBP	_	_	_
563	_	_	SYM	_	_	_
564	timepoint2	timepoint2	CD	_	_	_
565	_	_	CD	_	_	_
566	rep2	rep2	NN	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	coli	coli	NN	_	_	_
569	_	_	NN	_	_	_
570	heatstress	heatstress	VBP	_	_	_
571	_	_	SYM	_	_	_
572	timepoint2	timepoint2	CD	_	_	_
573	_	_	CD	_	_	_
574	rep3	rep3	NN	_	_	_
575	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
576	coli	coli	NN	_	_	_
577	_	_	NN	_	_	_
578	heatstress	heatstress	VBP	_	_	_
579	_	_	SYM	_	_	_
580	timepoint3	timepoint3	CD	_	_	_
581	_	_	CD	_	_	_
582	rep1	rep1	NN	_	_	_
583	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
584	coli	coli	NN	_	_	_
585	_	_	NN	_	_	_
586	heatstress	heatstress	VBP	_	_	_
587	_	_	SYM	_	_	_
588	timepoint3	timepoint3	CD	_	_	_
589	_	_	CD	_	_	_
590	rep2	rep2	NN	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	coli	coli	NN	_	_	_
593	_	_	NN	_	_	_
594	heatstress	heatstress	VBP	_	_	_
595	_	_	SYM	_	_	_
596	timepoint3	timepoint3	CD	_	_	_
597	_	_	CD	_	_	_
598	rep3	rep3	NN	_	_	_
599	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
600	coli	coli	NN	_	_	_
601	_	_	NN	_	_	_
602	heatstress	heatstress	VBP	_	_	_
603	_	_	SYM	_	_	_
604	timepoint4	timepoint4	CD	_	_	_
605	_	_	CD	_	_	_
606	rep1	rep1	NN	_	_	_
607	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
608	coli	coli	NN	_	_	_
609	_	_	NN	_	_	_
610	heatstress	heatstress	VBP	_	_	_
611	_	_	SYM	_	_	_
612	timepoint4	timepoint4	CD	_	_	_
613	_	_	CD	_	_	_
614	rep2	rep2	NN	_	_	_
615	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
616	coli	coli	NN	_	_	_
617	_	_	NN	_	_	_
618	heatstress	heatstress	VBP	_	_	_
619	_	_	SYM	_	_	_
620	timepoint4	timepoint4	CD	_	_	_
621	_	_	CD	_	_	_
622	rep3	rep3	NN	_	_	_
623	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
624	coli	coli	NN	_	_	_
625	_	_	NN	_	_	_
626	heatstress	heatstress	VBP	_	_	_
627	_	_	SYM	_	_	_
628	timepoint5	timepoint5	CD	_	_	_
629	_	_	CD	_	_	_
630	rep1	rep1	NN	_	_	_
631	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
632	coli	coli	NN	_	_	_
633	_	_	NN	_	_	_
634	heatstress	heatstress	VBP	_	_	_
635	_	_	SYM	_	_	_
636	timepoint5	timepoint5	CD	_	_	_
637	_	_	CD	_	_	_
638	rep2	rep2	NN	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	coli	coli	NN	_	_	_
641	_	_	NN	_	_	_
642	heatstress	heatstress	VBP	_	_	_
643	_	_	SYM	_	_	_
644	timepoint5	timepoint5	CD	_	_	_
645	_	_	CD	_	_	_
646	rep3	rep3	NN	_	_	_
647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
648	coli	coli	NN	_	_	_
649	_	_	NN	_	_	_
650	heatstress	heatstress	VBP	_	_	_
651	_	_	SYM	_	_	_
652	timepoint6	timepoint6	CD	_	_	_
653	_	_	CD	_	_	_
654	rep1	rep1	NN	_	_	_
655	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
656	coli	coli	NN	_	_	_
657	_	_	NN	_	_	_
658	heatstress	heatstress	VBP	_	_	_
659	_	_	SYM	_	_	_
660	timepoint6	timepoint6	CD	_	_	_
661	_	_	CD	_	_	_
662	rep2	rep2	NN	_	_	_
663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
664	coli	coli	NN	_	_	_
665	_	_	NN	_	_	_
666	heatstress	heatstress	VBP	_	_	_
667	_	_	SYM	_	_	_
668	timepoint6	timepoint6	CD	_	_	_
669	_	_	CD	_	_	_
670	rep3	rep3	NN	_	_	_
671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
672	coli	coli	NN	_	_	_
673	_	_	NN	_	_	_
674	heatstress	heatstress	VBP	_	_	_
675	_	_	SYM	_	_	_
676	timepoint7	timepoint7	CD	_	_	_
677	_	_	CD	_	_	_
678	rep1	rep1	NN	_	_	_
679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
680	coli	coli	NN	_	_	_
681	_	_	NN	_	_	_
682	heatstress	heatstress	VBP	_	_	_
683	_	_	SYM	_	_	_
684	timepoint7	timepoint7	CD	_	_	_
685	_	_	CD	_	_	_
686	rep2	rep2	NN	_	_	_
687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
688	coli	coli	NN	_	_	_
689	_	_	NN	_	_	_
690	heatstress	heatstress	VBP	_	_	_
691	_	_	SYM	_	_	_
692	timepoint7	timepoint7	CD	_	_	_
693	_	_	CD	_	_	_
694	rep3	rep3	NN	_	_	_
695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
696	coli	coli	NN	_	_	_
697	_	_	NN	_	_	_
698	heatstress	heatstress	VBP	_	_	_
699	_	_	SYM	_	_	_
700	timepoint8	timepoint8	CD	_	_	_
701	_	_	CD	_	_	_
702	rep1	rep1	NN	_	_	_
703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
704	coli	coli	NN	_	_	_
705	_	_	NN	_	_	_
706	heatstress	heatstress	VBP	_	_	_
707	_	_	SYM	_	_	_
708	timepoint8	timepoint8	CD	_	_	_
709	_	_	CD	_	_	_
710	rep2	rep2	NN	_	_	_
711	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
712	coli	coli	NN	_	_	_
713	_	_	NN	_	_	_
714	heatstress	heatstress	VBP	_	_	_
715	_	_	SYM	_	_	_
716	timepoint8	timepoint8	CD	_	_	_
717	_	_	CD	_	_	_
718	rep3	rep3	NN	_	_	_
719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
720	coli	coli	NN	_	_	_
721	_	_	NN	_	_	_
722	lactose	lactose	NN	_	_	_
723	_	_	CD	_	_	_
724	timepoint2	timepoint2	NN	_	_	_
725	_	_	CD	_	_	_
726	rep1	rep1	NN	_	_	_
727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
728	coli	coli	NN	_	_	_
729	_	_	NN	_	_	_
730	lactose	lactose	NN	_	_	_
731	_	_	CD	_	_	_
732	timepoint2	timepoint2	NN	_	_	_
733	_	_	CD	_	_	_
734	rep2	rep2	NN	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
736	coli	coli	NN	_	_	_
737	_	_	NN	_	_	_
738	lactose	lactose	NN	_	_	_
739	_	_	CD	_	_	_
740	timepoint2	timepoint2	NN	_	_	_
741	_	_	CD	_	_	_
742	rep3	rep3	NN	_	_	_
743	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
744	coli	coli	NN	_	_	_
745	_	_	NN	_	_	_
746	lactose	lactose	NN	_	_	_
747	_	_	CD	_	_	_
748	timepoint3	timepoint3	NN	_	_	_
749	_	_	CD	_	_	_
750	rep1	rep1	NN	_	_	_
751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
752	coli	coli	NN	_	_	_
753	_	_	NN	_	_	_
754	lactose	lactose	NN	_	_	_
755	_	_	CD	_	_	_
756	timepoint3	timepoint3	NN	_	_	_
757	_	_	CD	_	_	_
758	rep3	rep3	NN	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
760	coli	coli	NN	_	_	_
761	_	_	NN	_	_	_
762	lactose	lactose	NN	_	_	_
763	_	_	CD	_	_	_
764	timepoint4	timepoint4	NN	_	_	_
765	_	_	CD	_	_	_
766	rep1	rep1	NN	_	_	_
767	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
768	coli	coli	NN	_	_	_
769	_	_	NN	_	_	_
770	lactose	lactose	NN	_	_	_
771	_	_	CD	_	_	_
772	timepoint4	timepoint4	NN	_	_	_
773	_	_	CD	_	_	_
774	rep2	rep2	NN	_	_	_
775	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
776	coli	coli	NN	_	_	_
777	_	_	NN	_	_	_
778	lactose	lactose	NN	_	_	_
779	_	_	CD	_	_	_
780	timepoint4	timepoint4	NN	_	_	_
781	_	_	CD	_	_	_
782	rep3	rep3	NN	_	_	_
783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
784	coli	coli	NN	_	_	_
785	_	_	NN	_	_	_
786	lactose	lactose	NN	_	_	_
787	_	_	CD	_	_	_
788	timepoint5	timepoint5	NN	_	_	_
789	_	_	CD	_	_	_
790	rep1	rep1	NN	_	_	_
791	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
792	coli	coli	NN	_	_	_
793	_	_	NN	_	_	_
794	lactose	lactose	NN	_	_	_
795	_	_	CD	_	_	_
796	timepoint5	timepoint5	NN	_	_	_
797	_	_	CD	_	_	_
798	rep2	rep2	NN	_	_	_
799	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
800	coli	coli	NN	_	_	_
801	_	_	NN	_	_	_
802	lactose	lactose	NN	_	_	_
803	_	_	CD	_	_	_
804	timepoint5	timepoint5	NN	_	_	_
805	_	_	CD	_	_	_
806	rep3	rep3	NN	_	_	_
807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
808	coli	coli	NN	_	_	_
809	_	_	NN	_	_	_
810	lactose	lactose	NN	_	_	_
811	_	_	CD	_	_	_
812	timepoint6	timepoint6	NN	_	_	_
813	_	_	CD	_	_	_
814	rep1	rep1	NN	_	_	_
815	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
816	coli	coli	NN	_	_	_
817	_	_	NN	_	_	_
818	lactose	lactose	NN	_	_	_
819	_	_	CD	_	_	_
820	timepoint6	timepoint6	NN	_	_	_
821	_	_	CD	_	_	_
822	rep2	rep2	NN	_	_	_
823	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
824	coli	coli	NN	_	_	_
825	_	_	NN	_	_	_
826	lactose	lactose	NN	_	_	_
827	_	_	CD	_	_	_
828	timepoint6	timepoint6	NN	_	_	_
829	_	_	CD	_	_	_
830	rep3	rep3	NN	_	_	_
831	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
832	coli	coli	NN	_	_	_
833	_	_	NN	_	_	_
834	lactose	lactose	NN	_	_	_
835	_	_	CD	_	_	_
836	timepoint7	timepoint7	NN	_	_	_
837	_	_	CD	_	_	_
838	rep1	rep1	NN	_	_	_
839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
840	coli	coli	NN	_	_	_
841	_	_	NN	_	_	_
842	lactose	lactose	NN	_	_	_
843	_	_	CD	_	_	_
844	timepoint7	timepoint7	NN	_	_	_
845	_	_	CD	_	_	_
846	rep2	rep2	NN	_	_	_
847	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
848	Coli-MDS42	coli-mds42	NN	_	_	_
849	_	_	CD	_	_	_
850	bcm-100mcg	bcm-100mcg	NN	_	_	_
851	/	/	:	_	_	_
852	ml	ml	NN	_	_	_
853	_	_	NN	_	_	_
854	rep1	rep1	NN	_	_	_
855	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
856	Coli-MDS42	coli-mds42	NN	_	_	_
857	_	_	CD	_	_	_
858	bcm-100mcg	bcm-100mcg	NN	_	_	_
859	/	/	:	_	_	_
860	ml	ml	NN	_	_	_
861	_	_	NN	_	_	_
862	rep2	rep2	NN	_	_	_
863	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
864	Coli-MDS42	coli-mds42	NN	_	_	_
865	_	_	CD	_	_	_
866	del-nusA	del-nusa	NN	_	_	_
867	_	_	CD	_	_	_
868	rep1	rep1	NN	_	_	_
869	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
870	Coli-MDS42	coli-mds42	NN	_	_	_
871	_	_	CD	_	_	_
872	del-nusA	del-nusa	NN	_	_	_
873	_	_	CD	_	_	_
874	rep2	rep2	NN	_	_	_
875	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
876	Coli-MDS42	coli-mds42	NN	_	_	_
877	_	_	CD	_	_	_
878	del-nusG	del-nusg	NN	_	_	_
879	_	_	CD	_	_	_
880	rep1	rep1	NN	_	_	_
881	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
882	Coli-MDS42	coli-mds42	NN	_	_	_
883	_	_	CD	_	_	_
884	del-nusG	del-nusg	NN	_	_	_
885	_	_	CD	_	_	_
886	rep2	rep2	NN	_	_	_
887	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
888	Coli-MDS42	coli-mds42	NN	_	_	_
889	_	_	CD	_	_	_
890	no-drug	no-drug	JJ	_	_	_
891	_	_	NN	_	_	_
892	rep1	rep1	NN	_	_	_
893	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
894	Coli-MDS42	coli-mds42	NN	_	_	_
895	_	_	CD	_	_	_
896	no-drug	no-drug	JJ	_	_	_
897	_	_	NN	_	_	_
898	rep2	rep2	NN	_	_	_
899	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
900	Coli-MG1655	coli-mg1655	NN	_	_	_
901	_	_	CD	_	_	_
902	bcm-100mcg	bcm-100mcg	NN	_	_	_
903	/	/	:	_	_	_
904	ml	ml	NN	_	_	_
905	_	_	NN	_	_	_
906	rep1	rep1	NN	_	_	_
907	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
908	Coli-MG1655	coli-mg1655	NN	_	_	_
909	_	_	CD	_	_	_
910	bcm-100mcg	bcm-100mcg	NN	_	_	_
911	/	/	:	_	_	_
912	ml	ml	NN	_	_	_
913	_	_	NN	_	_	_
914	rep2	rep2	NN	_	_	_
915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
916	Coli-MG1655	coli-mg1655	NN	_	_	_
917	_	_	CD	_	_	_
918	bcm-10mcg	bcm-10mcg	NN	_	_	_
919	/	/	:	_	_	_
920	ml	ml	NN	_	_	_
921	_	_	NN	_	_	_
922	rep1	rep1	NN	_	_	_
923	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
924	Coli-MG1655	coli-mg1655	NN	_	_	_
925	_	_	CD	_	_	_
926	bcm-10mcg	bcm-10mcg	NN	_	_	_
927	/	/	:	_	_	_
928	ml	ml	NN	_	_	_
929	_	_	NN	_	_	_
930	rep2	rep2	NN	_	_	_
931	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
932	Coli-MG1655	coli-mg1655	NN	_	_	_
933	_	_	CD	_	_	_
934	bcm-25mcg	bcm-25mcg	NN	_	_	_
935	/	/	:	_	_	_
936	ml	ml	NN	_	_	_
937	_	_	NN	_	_	_
938	rep1	rep1	NN	_	_	_
939	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
940	Coli-MG1655	coli-mg1655	NN	_	_	_
941	_	_	CD	_	_	_
942	bcm-25mcg	bcm-25mcg	NN	_	_	_
943	/	/	:	_	_	_
944	ml	ml	NN	_	_	_
945	_	_	NN	_	_	_
946	rep2	rep2	NN	_	_	_
947	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
948	Coli-MG1655	coli-mg1655	NN	_	_	_
949	_	_	CD	_	_	_
950	no-drug	no-drug	JJ	_	_	_
951	_	_	NN	_	_	_
952	rep1	rep1	NN	_	_	_
953	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
954	Coli-MG1655	coli-mg1655	NN	_	_	_
955	_	_	CD	_	_	_
956	no-drug	no-drug	JJ	_	_	_
957	_	_	NN	_	_	_
958	rep2	rep2	NN	_	_	_
959	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
960	Coli-O157H7	coli-o157h7	NN	_	_	_
961	_	_	CD	_	_	_
962	bcm-100mcg	bcm-100mcg	NN	_	_	_
963	/	/	:	_	_	_
964	ml	ml	NN	_	_	_
965	_	_	NN	_	_	_
966	rep1	rep1	NN	_	_	_
967	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
968	Coli-O157H7	coli-o157h7	NN	_	_	_
969	_	_	CD	_	_	_
970	bcm-100mcg	bcm-100mcg	NN	_	_	_
971	/	/	:	_	_	_
972	ml	ml	NN	_	_	_
973	_	_	NN	_	_	_
974	rep2	rep2	NN	_	_	_
975	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
976	Coli-O157H7	coli-o157h7	NN	_	_	_
977	_	_	CD	_	_	_
978	no-drug	no-drug	JJ	_	_	_
979	_	_	NN	_	_	_
980	rep1	rep1	NN	_	_	_
981	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
982	Coli-O157H7	coli-o157h7	NN	_	_	_
983	_	_	CD	_	_	_
984	no-drug	no-drug	JJ	_	_	_
985	_	_	NN	_	_	_
986	rep2	rep2	NN	_	_	_
987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
988	coli	coli	NN	_	_	_
989	_	_	NN	_	_	_
990	oxidativestress	oxidativestress	NN	_	_	_
991	_	_	CD	_	_	_
992	timepoint10	timepoint10	NN	_	_	_
993	_	_	CD	_	_	_
994	rep1	rep1	NN	_	_	_
995	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
996	coli	coli	NN	_	_	_
997	_	_	NN	_	_	_
998	oxidativestress	oxidativestress	NN	_	_	_
999	_	_	CD	_	_	_
1000	timepoint10	timepoint10	NN	_	_	_
1001	_	_	CD	_	_	_
1002	rep2	rep2	NN	_	_	_
1003	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1004	coli	coli	NN	_	_	_
1005	_	_	NN	_	_	_
1006	oxidativestress	oxidativestress	NN	_	_	_
1007	_	_	CD	_	_	_
1008	timepoint10	timepoint10	NN	_	_	_
1009	_	_	CD	_	_	_
1010	rep4	rep4	NN	_	_	_
1011	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1012	coli	coli	NN	_	_	_
1013	_	_	NN	_	_	_
1014	oxidativestress	oxidativestress	NN	_	_	_
1015	_	_	CD	_	_	_
1016	timepoint11	timepoint11	NN	_	_	_
1017	_	_	CD	_	_	_
1018	rep1	rep1	NN	_	_	_
1019	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1020	coli	coli	NN	_	_	_
1021	_	_	NN	_	_	_
1022	oxidativestress	oxidativestress	NN	_	_	_
1023	_	_	CD	_	_	_
1024	timepoint11	timepoint11	NN	_	_	_
1025	_	_	CD	_	_	_
1026	rep2	rep2	NN	_	_	_
1027	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1028	coli	coli	NN	_	_	_
1029	_	_	NN	_	_	_
1030	oxidativestress	oxidativestress	NN	_	_	_
1031	_	_	CD	_	_	_
1032	timepoint11	timepoint11	NN	_	_	_
1033	_	_	CD	_	_	_
1034	rep4	rep4	NN	_	_	_
1035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1036	coli	coli	NN	_	_	_
1037	_	_	NN	_	_	_
1038	oxidativestress	oxidativestress	NN	_	_	_
1039	_	_	CD	_	_	_
1040	timepoint12	timepoint12	NN	_	_	_
1041	_	_	CD	_	_	_
1042	rep2	rep2	NN	_	_	_
1043	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1044	coli	coli	NN	_	_	_
1045	_	_	NN	_	_	_
1046	oxidativestress	oxidativestress	NN	_	_	_
1047	_	_	CD	_	_	_
1048	timepoint1	timepoint1	NN	_	_	_
1049	_	_	CD	_	_	_
1050	rep1	rep1	NN	_	_	_
1051	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1052	coli	coli	NN	_	_	_
1053	_	_	NN	_	_	_
1054	oxidativestress	oxidativestress	NN	_	_	_
1055	_	_	CD	_	_	_
1056	timepoint1	timepoint1	NN	_	_	_
1057	_	_	CD	_	_	_
1058	rep2	rep2	NN	_	_	_
1059	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1060	coli	coli	NN	_	_	_
1061	_	_	NN	_	_	_
1062	oxidativestress	oxidativestress	NN	_	_	_
1063	_	_	CD	_	_	_
1064	timepoint1	timepoint1	NN	_	_	_
1065	_	_	CD	_	_	_
1066	rep4	rep4	NN	_	_	_
1067	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1068	coli	coli	NN	_	_	_
1069	_	_	NN	_	_	_
1070	oxidativestress	oxidativestress	NN	_	_	_
1071	_	_	CD	_	_	_
1072	timepoint2	timepoint2	NN	_	_	_
1073	_	_	CD	_	_	_
1074	rep1	rep1	NN	_	_	_
1075	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1076	coli	coli	NN	_	_	_
1077	_	_	NN	_	_	_
1078	oxidativestress	oxidativestress	NN	_	_	_
1079	_	_	CD	_	_	_
1080	timepoint2	timepoint2	NN	_	_	_
1081	_	_	CD	_	_	_
1082	rep2	rep2	NN	_	_	_
1083	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1084	coli	coli	NN	_	_	_
1085	_	_	NN	_	_	_
1086	oxidativestress	oxidativestress	NN	_	_	_
1087	_	_	CD	_	_	_
1088	timepoint2	timepoint2	NN	_	_	_
1089	_	_	CD	_	_	_
1090	rep4	rep4	NN	_	_	_
1091	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1092	coli	coli	NN	_	_	_
1093	_	_	NN	_	_	_
1094	oxidativestress	oxidativestress	NN	_	_	_
1095	_	_	CD	_	_	_
1096	timepoint3	timepoint3	NN	_	_	_
1097	_	_	CD	_	_	_
1098	rep1	rep1	NN	_	_	_
1099	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1100	coli	coli	NN	_	_	_
1101	_	_	NN	_	_	_
1102	oxidativestress	oxidativestress	NN	_	_	_
1103	_	_	CD	_	_	_
1104	timepoint3	timepoint3	NN	_	_	_
1105	_	_	CD	_	_	_
1106	rep2	rep2	NN	_	_	_
1107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1108	coli	coli	NN	_	_	_
1109	_	_	NN	_	_	_
1110	oxidativestress	oxidativestress	NN	_	_	_
1111	_	_	CD	_	_	_
1112	timepoint3	timepoint3	NN	_	_	_
1113	_	_	CD	_	_	_
1114	rep4	rep4	NN	_	_	_
1115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1116	coli	coli	NN	_	_	_
1117	_	_	NN	_	_	_
1118	oxidativestress	oxidativestress	NN	_	_	_
1119	_	_	CD	_	_	_
1120	timepoint4	timepoint4	NN	_	_	_
1121	_	_	CD	_	_	_
1122	rep1	rep1	NN	_	_	_
1123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1124	coli	coli	NN	_	_	_
1125	_	_	NN	_	_	_
1126	oxidativestress	oxidativestress	NN	_	_	_
1127	_	_	CD	_	_	_
1128	timepoint4	timepoint4	NN	_	_	_
1129	_	_	CD	_	_	_
1130	rep2	rep2	NN	_	_	_
1131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1132	coli	coli	NN	_	_	_
1133	_	_	NN	_	_	_
1134	oxidativestress	oxidativestress	NN	_	_	_
1135	_	_	CD	_	_	_
1136	timepoint4	timepoint4	NN	_	_	_
1137	_	_	CD	_	_	_
1138	rep4	rep4	NN	_	_	_
1139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1140	coli	coli	NN	_	_	_
1141	_	_	NN	_	_	_
1142	oxidativestress	oxidativestress	NN	_	_	_
1143	_	_	CD	_	_	_
1144	timepoint5	timepoint5	NN	_	_	_
1145	_	_	CD	_	_	_
1146	rep1	rep1	NN	_	_	_
1147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1148	coli	coli	NN	_	_	_
1149	_	_	NN	_	_	_
1150	oxidativestress	oxidativestress	NN	_	_	_
1151	_	_	CD	_	_	_
1152	timepoint5	timepoint5	NN	_	_	_
1153	_	_	CD	_	_	_
1154	rep2	rep2	NN	_	_	_
1155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1156	coli	coli	NN	_	_	_
1157	_	_	NN	_	_	_
1158	oxidativestress	oxidativestress	NN	_	_	_
1159	_	_	CD	_	_	_
1160	timepoint5	timepoint5	NN	_	_	_
1161	_	_	CD	_	_	_
1162	rep4	rep4	NN	_	_	_
1163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1164	coli	coli	NN	_	_	_
1165	_	_	NN	_	_	_
1166	oxidativestress	oxidativestress	NN	_	_	_
1167	_	_	CD	_	_	_
1168	timepoint6	timepoint6	NN	_	_	_
1169	_	_	CD	_	_	_
1170	rep1	rep1	NN	_	_	_
1171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1172	coli	coli	NN	_	_	_
1173	_	_	NN	_	_	_
1174	oxidativestress	oxidativestress	NN	_	_	_
1175	_	_	CD	_	_	_
1176	timepoint6	timepoint6	NN	_	_	_
1177	_	_	CD	_	_	_
1178	rep2	rep2	NN	_	_	_
1179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1180	coli	coli	NN	_	_	_
1181	_	_	NN	_	_	_
1182	oxidativestress	oxidativestress	NN	_	_	_
1183	_	_	CD	_	_	_
1184	timepoint6	timepoint6	NN	_	_	_
1185	_	_	CD	_	_	_
1186	rep4	rep4	NN	_	_	_
1187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1188	coli	coli	NN	_	_	_
1189	_	_	NN	_	_	_
1190	oxidativestress	oxidativestress	NN	_	_	_
1191	_	_	CD	_	_	_
1192	timepoint7	timepoint7	NN	_	_	_
1193	_	_	CD	_	_	_
1194	rep1	rep1	NN	_	_	_
1195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1196	coli	coli	NN	_	_	_
1197	_	_	NN	_	_	_
1198	oxidativestress	oxidativestress	NN	_	_	_
1199	_	_	CD	_	_	_
1200	timepoint7	timepoint7	NN	_	_	_
1201	_	_	CD	_	_	_
1202	rep2	rep2	NN	_	_	_
1203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1204	coli	coli	NN	_	_	_
1205	_	_	NN	_	_	_
1206	oxidativestress	oxidativestress	NN	_	_	_
1207	_	_	CD	_	_	_
1208	timepoint7	timepoint7	NN	_	_	_
1209	_	_	CD	_	_	_
1210	rep4	rep4	NN	_	_	_
1211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1212	coli	coli	NN	_	_	_
1213	_	_	NN	_	_	_
1214	oxidativestress	oxidativestress	VBP	_	_	_
1215	_	_	SYM	_	_	_
1216	timepoint8	timepoint8	CD	_	_	_
1217	_	_	CD	_	_	_
1218	rep1	rep1	NN	_	_	_
1219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1220	coli	coli	NN	_	_	_
1221	_	_	NN	_	_	_
1222	oxidativestress	oxidativestress	VBP	_	_	_
1223	_	_	SYM	_	_	_
1224	timepoint8	timepoint8	CD	_	_	_
1225	_	_	CD	_	_	_
1226	rep2	rep2	NN	_	_	_
1227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1228	coli	coli	NN	_	_	_
1229	_	_	NN	_	_	_
1230	oxidativestress	oxidativestress	VBP	_	_	_
1231	_	_	SYM	_	_	_
1232	timepoint8	timepoint8	CD	_	_	_
1233	_	_	CD	_	_	_
1234	rep4	rep4	NN	_	_	_
1235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1236	coli	coli	NN	_	_	_
1237	_	_	NN	_	_	_
1238	oxidativestress	oxidativestress	NN	_	_	_
1239	_	_	CD	_	_	_
1240	timepoint9	timepoint9	NN	_	_	_
1241	_	_	CD	_	_	_
1242	rep1	rep1	NN	_	_	_
1243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1244	coli	coli	NN	_	_	_
1245	_	_	NN	_	_	_
1246	oxidativestress	oxidativestress	NN	_	_	_
1247	_	_	CD	_	_	_
1248	timepoint9	timepoint9	NN	_	_	_
1249	_	_	CD	_	_	_
1250	rep2	rep2	NN	_	_	_
1251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1252	coli	coli	NN	_	_	_
1253	_	_	NN	_	_	_
1254	oxidativestress	oxidativestress	NN	_	_	_
1255	_	_	CD	_	_	_
1256	timepoint9	timepoint9	NN	_	_	_
1257	_	_	CD	_	_	_
1258	rep4	rep4	NN	_	_	_
1259	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1260	Collected	collect	VBN	_	_	_
1261	cells	cell	NNS	_	_	_
1262	were	be	VBD	_	_	_
1263	lysed	lyse	VBN	_	_	_
1264	using	use	VBG	_	_	_
1265	Trizol	Trizol	NNP	_	_	_
1266	-LRB-	-lrb-	-LRB-	_	_	_
1267	Invitrogen	Invitrogen	NNP	_	_	_
1268	-RRB-	-rrb-	-RRB-	_	_	_
1269	,	,	,	_	_	_
1270	and	and	CC	_	_	_
1271	total	total	JJ	_	_	_
1272	RNA	rna	NN	_	_	_
1273	was	be	VBD	_	_	_
1274	isolated	isolate	VBN	_	_	_
1275	using	use	VBG	_	_	_
1276	phenol-chloroform	phenol-chloroform	JJ	_	_	_
1277	and	and	CC	_	_	_
1278	precipitated	precipitated	JJ	_	_	_
1279	with	with	IN	_	_	_
1280	ice	ice	NN	_	_	_
1281	cold	cold	JJ	_	_	_
1282	isopropanol	isopropanol	NN	_	_	_
1283	.	.	.	_	_	_

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	NN	_	_	_
2	Collinsella	collinsella	NN	_	_	_
3	aerofaciens	aerofacien	NNS	_	_	_
4	ATCC	atcc	NN	_	_	_
5	25986	25986	CD	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Colony	Colony	NNP	_	_	_
8	Biofilm	Biofilm	NNP	_	_	_
9	Replicate	replicate	VB	_	_	_
10	1	1	CD	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Colony	Colony	NNP	_	_	_
13	Biofilm	Biofilm	NNP	_	_	_
14	Replicate	replicate	VB	_	_	_
15	2	2	CD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Colony	Colony	NNP	_	_	_
18	Biofilm	Biofilm	NNP	_	_	_
19	Replicate	replicate	VB	_	_	_
20	3	3	CD	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Colony	Colony	NNP	_	_	_
23	Biofilm	Biofilm	NNP	_	_	_
24	Replicate	replicate	VB	_	_	_
25	4	4	CD	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Column	Column	NNP	_	_	_
28	purification	purification	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Combined	Combined	NNP	_	_	_
31	input	input	NN	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	common	common	JJ	_	_	_
34	reference	reference	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	OD600	od600	NN	_	_	_
37	=	=	JJ	_	_	_
38	0.5	0.5	CD	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	CompA	compa	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Comparison	comparison	NN	_	_	_
44	cya	cya	NN	_	_	_
45	mutant	mutant	NN	_	_	_
46	with	with	IN	_	_	_
47	wt	wt	JJ	_	_	_
48	under	under	IN	_	_	_
49	glucose-limited	glucose-limited	JJ	_	_	_
50	conditions	condition	NNS	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	replicate	replicate	VB	_	_	_
53	1	1	LS	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Comparison	comparison	NN	_	_	_
57	cya	cya	NN	_	_	_
58	mutant	mutant	NN	_	_	_
59	with	with	IN	_	_	_
60	wt	wt	JJ	_	_	_
61	under	under	IN	_	_	_
62	glucose-limited	glucose-limited	JJ	_	_	_
63	conditions	condition	NNS	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	replicate	replicate	VB	_	_	_
66	2	2	LS	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Comparison	comparison	NN	_	_	_
70	cya	cya	NN	_	_	_
71	mutant	mutant	NN	_	_	_
72	with	with	IN	_	_	_
73	wt	wt	JJ	_	_	_
74	under	under	IN	_	_	_
75	glucose-limited	glucose-limited	JJ	_	_	_
76	conditions	condition	NNS	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	replicate	replicate	VB	_	_	_
79	3	3	LS	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Comparison	comparison	NN	_	_	_
83	rpoS	rpos	NN	GEN	_	_
84	mutant	mutant	NN	_	_	_
85	with	with	IN	_	_	_
86	wt	wt	JJ	_	_	_
87	under	under	IN	_	_	_
88	glucose-limited	glucose-limited	JJ	_	_	_
89	conditions	condition	NNS	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	replicate	replicate	VB	_	_	_
92	1	1	LS	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Comparison	comparison	NN	_	_	_
96	rpoS	rpos	NN	GEN	_	_
97	mutant	mutant	NN	_	_	_
98	with	with	IN	_	_	_
99	wt	wt	JJ	_	_	_
100	under	under	IN	_	_	_
101	glucose-limited	glucose-limited	JJ	_	_	_
102	conditions	condition	NNS	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	replicate	replicate	VB	_	_	_
105	2	2	LS	_	_	_
106	-RRB-	-rrb-	-RRB-	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	Comparison	comparison	NN	_	_	_
109	rpoS	rpos	NN	GEN	_	_
110	mutant	mutant	NN	_	_	_
111	with	with	IN	_	_	_
112	wt	wt	JJ	_	_	_
113	under	under	IN	_	_	_
114	glucose-limited	glucose-limited	JJ	_	_	_
115	conditions	condition	NNS	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	replicate	replicate	VB	_	_	_
118	3	3	LS	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	CompB	compb	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	Compile	compile	VB	_	_	_
124	annotated	annotated	JJ	_	_	_
125	counts	count	NNS	_	_	_
126	using	use	VBG	_	_	_
127	custom	custom	NN	_	_	_
128	Python	Python	NNP	_	_	_
129	script	script	NN	_	_	_
130	-LRB-	-lrb-	-LRB-	_	_	_
131	ExtractMapCounts	extractmapcount	NNS	_	_	_
132	from	from	IN	_	_	_
133	http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz	http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz	NN	_	_	_
134	-RRB-	-rrb-	-RRB-	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	completely	completely	RB	_	_	_
137	aerobic	aerobic	JJ	_	_	_
138	conditions	condition	NNS	_	_	_
139	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
140	Computation	Computation	NNP	_	_	_
141	of	of	IN	_	_	_
142	genomic	genomic	JJ	_	_	_
143	intervals	interval	NNS	_	_	_
144	based	base	VBN	_	_	_
145	on	on	IN	_	_	_
146	computed	computed	JJ	_	_	_
147	signal	signal	NN	_	_	_
148	and	and	CC	_	_	_
149	p-values	p-values	JJ	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	Computation	computation	NN	_	_	_
152	of	of	IN	_	_	_
153	summary	summary	NN	_	_	_
154	statistics	statistics	NNS	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	CON206	con206	NN	_	_	_
157	.3	.3	NN	_	_	_
158	A	a	NN	_	_	_
159	_	_	NN	_	_	_
160	u1	u1	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	CON206	con206	NN	_	_	_
163	.3	.3	NN	_	_	_
164	A	a	NN	_	_	_
165	_	_	NN	_	_	_
166	u2	u2	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	CON206	con206	NN	_	_	_
169	.3	.3	NN	_	_	_
170	A	a	NN	_	_	_
171	_	_	NN	_	_	_
172	y1	y1	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	CON206	con206	NN	_	_	_
175	.3	.3	NN	_	_	_
176	A	a	NN	_	_	_
177	_	_	NN	_	_	_
178	y2	y2	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	CON208	con208	NN	_	_	_
181	.3	.3	NN	_	_	_
182	A	a	NN	_	_	_
183	_	_	NN	_	_	_
184	u1	u1	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	CON208	con208	NN	_	_	_
187	.3	.3	NN	_	_	_
188	A	a	NN	_	_	_
189	_	_	NN	_	_	_
190	u8	u8	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	CON208	con208	NN	_	_	_
193	.3	.3	NN	_	_	_
194	A	a	NN	_	_	_
195	_	_	NN	_	_	_
196	y2	y2	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	CON208	con208	NN	_	_	_
199	.3	.3	NN	_	_	_
200	A	a	NN	_	_	_
201	_	_	NN	_	_	_
202	y6	y6	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	concentration	concentration	NN	_	_	_
205	:	:	:	_	_	_
206	0.2	0.2	CD	_	_	_
207	ppm	ppm	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	concentration	concentration	NN	_	_	_
210	:	:	:	_	_	_
211	2	2	CD	_	_	_
212	ppm	ppm	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	condition	condition	NN	_	_	_
215	:	:	:	_	_	_
216	37ºC	37ºc	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	condition	condition	NN	_	_	_
219	:	:	:	_	_	_
220	45ºC	45ºc	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	condition	condition	NN	_	_	_
223	:	:	:	_	_	_
224	acetonitrile	acetonitrile	NN	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	control	control	NN	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	condition	condition	NN	_	_	_
230	:	:	:	_	_	_
231	exponential	exponential	JJ	_	_	_
232	growth	growth	NN	_	_	_
233	,	,	,	_	_	_
234	36.9	36.9	CD	_	_	_
235	ºC	ºc	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	condition	condition	NN	_	_	_
238	:	:	:	_	_	_
239	exponential	exponential	JJ	_	_	_
240	growth	growth	NN	_	_	_
241	,	,	,	_	_	_
242	41.2	41.2	CD	_	_	_
243	ºC	ºc	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	condition	condition	NN	_	_	_
246	:	:	:	_	_	_
247	exponential	exponential	JJ	_	_	_
248	growth	growth	NN	_	_	_
249	,	,	,	_	_	_
250	43.2	43.2	CD	_	_	_
251	ºC	ºc	NN	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	condition	condition	NN	_	_	_
254	:	:	:	_	_	_
255	exponential	exponential	JJ	_	_	_
256	growth	growth	NN	_	_	_
257	,	,	,	_	_	_
258	44.8	44.8	CD	_	_	_
259	ºC	ºc	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	condition	condition	NN	_	_	_
262	:	:	:	_	_	_
263	glucose	glucose	NN	SUPP	_	_
264	limited	limited	JJ	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	condition	condition	NN	_	_	_
267	:	:	:	_	_	_
268	heat-shocked	heat-shocked	JJ	_	_	_
269	condition	condition	NN	_	_	_
270	without	without	IN	_	_	_
271	rifampicin	rifampicin	NN	SUPP	_	_
272	treatment	treatment	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	condition	condition	NN	_	_	_
275	:	:	:	_	_	_
276	heat	heat	NN	_	_	_
277	shock	shock	NN	_	_	_
278	response	response	NN	_	_	_
279	,	,	,	_	_	_
280	44.8	44.8	CD	_	_	_
281	ºC	ºc	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	condition	condition	NN	_	_	_
284	:	:	:	_	_	_
285	histidine	histidine	NN	_	_	_
286	depleted	deplete	VBD	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	condition	condition	NN	_	_	_
289	:	:	:	_	_	_
290	histidine	histidine	NN	_	_	_
291	supplied	supply	VBD	_	_	_
292	,	,	,	_	_	_
293	1	1	CD	_	_	_
294	mM	mm	NN	KWSUPP	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	condition	condition	NN	_	_	_
297	:	:	:	_	_	_
298	in	in	FW	_	_	_
299	vitro	vitro	FW	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	condition	condition	NN	_	_	_
302	:	:	:	_	_	_
303	in	in	FW	_	_	_
304	vivo	vivo	FW	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	condition	condition	NN	_	_	_
307	:	:	:	_	_	_
308	LB	lb	NN	_	_	_
309	+3	+3	CD	_	_	_
310	g/L	g/L	NNP	_	_	_
311	Glc	Glc	NNP	_	_	_
312	+0.1	+0.1	CD	_	_	_
313	mM	mm	NN	KWSUPP	_	_
314	IPTG	iptg	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	condition	condition	NN	_	_	_
317	:	:	:	_	_	_
318	LB	lb	NN	_	_	_
319	+3	+3	CD	_	_	_
320	g/L	g/L	NNP	_	_	_
321	Glc	Glc	NNP	_	_	_
322	+0.1	+0.1	CD	_	_	_
323	mM	mm	NN	KWSUPP	_	_
324	IPTG	iptg	NN	_	_	_
325	+	+	CC	_	_	_
326	50μg/ml	50μg/ml	JJ	_	_	_
327	Amp	amp	NN	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	condition	condition	NN	_	_	_
330	:	:	:	_	_	_
331	mid-exponential	mid-exponential	JJ	_	_	_
332	condition	condition	NN	_	_	_
333	without	without	IN	_	_	_
334	rifampicin	rifampicin	NN	SUPP	_	_
335	treatment	treatment	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	condition	condition	NN	_	_	_
338	:	:	:	_	_	_
339	mid-exponential	mid-exponential	JJ	_	_	_
340	condition	condition	NN	_	_	_
341	with	with	IN	_	_	_
342	rifampicin	rifampicin	NN	SUPP	_	_
343	treatment	treatment	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	condition	condition	NN	_	_	_
346	:	:	:	_	_	_
347	myxotoxin	myxotoxin	NN	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	condition	condition	NN	_	_	_
350	:	:	:	_	_	_
351	nitrogen-limiting	nitrogen-limiting	JJ	_	_	_
352	condition	condition	NN	_	_	_
353	without	without	IN	_	_	_
354	rifampicin	rifampicin	NN	SUPP	_	_
355	treatment	treatment	NN	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	condition	condition	NN	_	_	_
358	:	:	:	_	_	_
359	osmotic	osmotic	JJ	_	_	_
360	pressure	pressure	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	condition	condition	NN	_	_	_
363	:	:	:	_	_	_
364	regular	regular	JJ	_	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
366	condition	condition	NN	_	_	_
367	:	:	:	_	_	_
368	starvation	starvation	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	condition	condition	NN	_	_	_
371	:	:	:	_	_	_
372	stationary	stationary	JJ	_	_	_
373	condition	condition	NN	_	_	_
374	without	without	IN	_	_	_
375	rifampicin	rifampicin	NN	SUPP	_	_
376	treatment	treatment	NN	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	condition	condition	NN	_	_	_
379	:	:	:	_	_	_
380	temperature	temperature	NN	_	_	_
381	change	change	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	conducted	conduct	VBN	_	_	_
384	by	by	IN	_	_	_
385	CeGaT	cegat	NN	_	_	_
386	-LRB-	-lrb-	-LRB-	_	_	_
387	Tübingen	tübingen	NN	_	_	_
388	,	,	,	_	_	_
389	Germany	Germany	NNP	_	_	_
390	-RRB-	-rrb-	-RRB-	_	_	_
391	according	accord	VBG	_	_	_
392	to	to	TO	_	_	_
393	SOLiD	solid	JJ	_	_	_
394	standard	standard	JJ	_	_	_
395	protocols	protocol	NNS	_	_	_
396	for	for	IN	_	_	_
397	RNA-seq	rna-seq	JJ	_	_	_
398	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
399	con	con	NN	_	_	_
400	_	_	CD	_	_	_
401	RNAA	rnaa	NN	_	_	_
402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
403	consensus	consensus	NN	_	_	_
404	binding	binding	NN	_	_	_
405	regions	region	NNS	_	_	_
406	were	be	VBD	_	_	_
407	obtained	obtain	VBN	_	_	_
408	as	as	IN	_	_	_
409	the	the	DT	_	_	_
410	portion	portion	NN	_	_	_
411	which	which	WDT	_	_	_
412	was	be	VBD	_	_	_
413	covered	cover	VBN	_	_	_
414	by	by	IN	_	_	_
415	replicate	replicate	VB	_	_	_
416	samples	sample	NNS	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	contamination	contamination	NN	_	_	_
419	status	status	NN	_	_	_
420	:	:	:	_	_	_
421	hydrocarbon	hydrocarbon	NN	_	_	_
422	contaminated	contaminate	VBN	_	_	_
423	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
424	Continuous	continuous	JJ	_	_	_
425	aerobically	aerobically	RB	_	_	_
426	grown	grow	VBN	_	_	_
427	cultures	culture	NNS	_	_	_
428	in	in	IN	_	_	_
429	Evans	Evans	NNP	_	_	_
430	medium	medium	NN	_	_	_
431	,	,	,	_	_	_
432	CORM-401	corm-401	NN	_	_	_
433	samples	sample	NNS	_	_	_
434	or	or	CC	_	_	_
435	samples	sample	NNS	_	_	_
436	prior	prior	RB	_	_	_
437	to	to	TO	_	_	_
438	addition	addition	NN	_	_	_
439	of	of	IN	_	_	_
440	CORM-401	corm-401	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
442	Continuous	continuous	JJ	_	_	_
443	aerobically	aerobically	RB	_	_	_
444	grown	grow	VBN	_	_	_
445	cultures	culture	NNS	_	_	_
446	in	in	IN	_	_	_
447	Evans	Evans	NNP	_	_	_
448	medium	medium	NN	_	_	_
449	,	,	,	_	_	_
450	exposed	expose	VBN	_	_	_
451	to	to	TO	_	_	_
452	0.1	0.1	CD	_	_	_
453	L/min	l/min	NN	_	_	_
454	CO	co	NN	_	_	_
455	gas	gas	NN	_	_	_
456	for	for	IN	_	_	_
457	10	10	CD	_	_	_
458	min	min	NN	_	_	_
459	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
460	Continuous	continuous	JJ	_	_	_
461	aerobically	aerobically	RB	_	_	_
462	grown	grow	VBN	_	_	_
463	cultures	culture	NNS	_	_	_
464	in	in	IN	_	_	_
465	Evans	Evans	NNP	_	_	_
466	medium	medium	NN	_	_	_
467	,	,	,	_	_	_
468	exposed	expose	VBN	_	_	_
469	to	to	TO	_	_	_
470	0.1	0.1	CD	_	_	_
471	L/min	l/min	NN	_	_	_
472	CO	co	NN	_	_	_
473	gas	gas	NN	_	_	_
474	for	for	IN	_	_	_
475	10	10	CD	_	_	_
476	min	min	NN	_	_	_
477	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
478	Continuous	continuous	JJ	_	_	_
479	aerobically	aerobically	RB	_	_	_
480	grown	grow	VBN	_	_	_
481	cultures	culture	NNS	_	_	_
482	in	in	IN	_	_	_
483	Evans	Evans	NNP	_	_	_
484	medium	medium	NN	_	_	_
485	,	,	,	_	_	_
486	exposed	expose	VBN	_	_	_
487	to	to	TO	_	_	_
488	0.1	0.1	CD	_	_	_
489	L/min	l/min	NN	_	_	_
490	CO	co	NN	_	_	_
491	gas	gas	NN	_	_	_
492	for	for	IN	_	_	_
493	20	20	CD	_	_	_
494	min	min	NN	_	_	_
495	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
496	Continuous	continuous	JJ	_	_	_
497	aerobically	aerobically	RB	_	_	_
498	grown	grow	VBN	_	_	_
499	cultures	culture	NNS	_	_	_
500	in	in	IN	_	_	_
501	Evans	Evans	NNP	_	_	_
502	medium	medium	NN	_	_	_
503	,	,	,	_	_	_
504	exposed	expose	VBN	_	_	_
505	to	to	TO	_	_	_
506	0.1	0.1	CD	_	_	_
507	L/min	l/min	NN	_	_	_
508	CO	co	NN	_	_	_
509	gas	gas	NN	_	_	_
510	for	for	IN	_	_	_
511	2.5	2.5	CD	_	_	_
512	min	min	NN	_	_	_
513	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
514	Continuous	continuous	JJ	_	_	_
515	aerobically	aerobically	RB	_	_	_
516	grown	grow	VBN	_	_	_
517	cultures	culture	NNS	_	_	_
518	in	in	IN	_	_	_
519	Evans	Evans	NNP	_	_	_
520	medium	medium	NN	_	_	_
521	,	,	,	_	_	_
522	exposed	expose	VBN	_	_	_
523	to	to	TO	_	_	_
524	0.1	0.1	CD	_	_	_
525	L/min	l/min	NN	_	_	_
526	CO	co	NN	_	_	_
527	gas	gas	NN	_	_	_
528	for	for	IN	_	_	_
529	40	40	CD	_	_	_
530	min	min	NN	_	_	_
531	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
532	Continuous	continuous	JJ	_	_	_
533	aerobically	aerobically	RB	_	_	_
534	grown	grow	VBN	_	_	_
535	cultures	culture	NNS	_	_	_
536	in	in	IN	_	_	_
537	Evans	Evans	NNP	_	_	_
538	medium	medium	NN	_	_	_
539	,	,	,	_	_	_
540	exposed	expose	VBN	_	_	_
541	to	to	TO	_	_	_
542	0.1	0.1	CD	_	_	_
543	L/min	l/min	NN	_	_	_
544	CO	co	NN	_	_	_
545	gas	gas	NN	_	_	_
546	for	for	IN	_	_	_
547	5	5	CD	_	_	_
548	min	min	NN	_	_	_
549	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
550	Continuous	continuous	JJ	_	_	_
551	aerobically	aerobically	RB	_	_	_
552	grown	grow	VBN	_	_	_
553	cultures	culture	NNS	_	_	_
554	in	in	IN	_	_	_
555	Evans	Evans	NNP	_	_	_
556	medium	medium	NN	_	_	_
557	,	,	,	_	_	_
558	exposed	expose	VBN	_	_	_
559	to	to	TO	_	_	_
560	0.1	0.1	CD	_	_	_
561	L/min	l/min	NN	_	_	_
562	CO	co	NN	_	_	_
563	gas	gas	NN	_	_	_
564	for	for	IN	_	_	_
565	80	80	CD	_	_	_
566	min	min	NN	_	_	_
567	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
568	Continuous	continuous	JJ	_	_	_
569	aerobically	aerobically	RB	_	_	_
570	grown	grow	VBN	_	_	_
571	cultures	culture	NNS	_	_	_
572	in	in	IN	_	_	_
573	Evans	Evans	NNP	_	_	_
574	medium	medium	NN	_	_	_
575	,	,	,	_	_	_
576	exposed	expose	VBN	_	_	_
577	to	to	TO	_	_	_
578	40uM	40um	NN	_	_	_
579	CORM-3	corm-3	NN	_	_	_
580	for	for	IN	_	_	_
581	10	10	CD	_	_	_
582	min	min	NN	_	_	_
583	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
584	Continuous	continuous	JJ	_	_	_
585	aerobically	aerobically	RB	_	_	_
586	grown	grow	VBN	_	_	_
587	cultures	culture	NNS	_	_	_
588	in	in	IN	_	_	_
589	Evans	Evans	NNP	_	_	_
590	medium	medium	NN	_	_	_
591	,	,	,	_	_	_
592	exposed	expose	VBN	_	_	_
593	to	to	TO	_	_	_
594	40uM	40um	NN	_	_	_
595	CORM-3	corm-3	NN	_	_	_
596	for	for	IN	_	_	_
597	20	20	CD	_	_	_
598	min	min	NN	_	_	_
599	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
600	Continuous	continuous	JJ	_	_	_
601	aerobically	aerobically	RB	_	_	_
602	grown	grow	VBN	_	_	_
603	cultures	culture	NNS	_	_	_
604	in	in	IN	_	_	_
605	Evans	Evans	NNP	_	_	_
606	medium	medium	NN	_	_	_
607	,	,	,	_	_	_
608	exposed	expose	VBN	_	_	_
609	to	to	TO	_	_	_
610	40uM	40um	NN	_	_	_
611	CORM-3	corm-3	NN	_	_	_
612	for	for	IN	_	_	_
613	2.5	2.5	CD	_	_	_
614	min	min	NN	_	_	_
615	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
616	Continuous	continuous	JJ	_	_	_
617	aerobically	aerobically	RB	_	_	_
618	grown	grow	VBN	_	_	_
619	cultures	culture	NNS	_	_	_
620	in	in	IN	_	_	_
621	Evans	Evans	NNP	_	_	_
622	medium	medium	NN	_	_	_
623	,	,	,	_	_	_
624	exposed	expose	VBN	_	_	_
625	to	to	TO	_	_	_
626	40uM	40um	NN	_	_	_
627	CORM-3	corm-3	NN	_	_	_
628	for	for	IN	_	_	_
629	40	40	CD	_	_	_
630	min	min	NN	_	_	_
631	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
632	Continuous	continuous	JJ	_	_	_
633	aerobically	aerobically	RB	_	_	_
634	grown	grow	VBN	_	_	_
635	cultures	culture	NNS	_	_	_
636	in	in	IN	_	_	_
637	Evans	Evans	NNP	_	_	_
638	medium	medium	NN	_	_	_
639	,	,	,	_	_	_
640	exposed	expose	VBN	_	_	_
641	to	to	TO	_	_	_
642	40uM	40um	NN	_	_	_
643	CORM-3	corm-3	NN	_	_	_
644	for	for	IN	_	_	_
645	5	5	CD	_	_	_
646	min	min	NN	_	_	_
647	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
648	Continuous	continuous	JJ	_	_	_
649	aerobically	aerobically	RB	_	_	_
650	grown	grow	VBN	_	_	_
651	cultures	culture	NNS	_	_	_
652	in	in	IN	_	_	_
653	Evans	Evans	NNP	_	_	_
654	medium	medium	NN	_	_	_
655	,	,	,	_	_	_
656	exposed	expose	VBN	_	_	_
657	to	to	TO	_	_	_
658	40uM	40um	NN	_	_	_
659	CORM-3	corm-3	NN	_	_	_
660	for	for	IN	_	_	_
661	80	80	CD	_	_	_
662	min	min	NN	_	_	_
663	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
664	Continuous	continuous	JJ	_	_	_
665	aerobically	aerobically	RB	_	_	_
666	grown	grow	VBN	_	_	_
667	cultures	culture	NNS	_	_	_
668	in	in	IN	_	_	_
669	Evans	Evans	NNP	_	_	_
670	medium	medium	NN	_	_	_
671	,	,	,	_	_	_
672	exposed	expose	VBN	_	_	_
673	to	to	TO	_	_	_
674	40uM	40um	NN	_	_	_
675	iCORM-3	icorm-3	NN	_	_	_
676	for	for	IN	_	_	_
677	10	10	CD	_	_	_
678	min	min	NN	_	_	_
679	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
680	Continuous	continuous	JJ	_	_	_
681	aerobically	aerobically	RB	_	_	_
682	grown	grow	VBN	_	_	_
683	cultures	culture	NNS	_	_	_
684	in	in	IN	_	_	_
685	Evans	Evans	NNP	_	_	_
686	medium	medium	NN	_	_	_
687	,	,	,	_	_	_
688	exposed	expose	VBN	_	_	_
689	to	to	TO	_	_	_
690	40uM	40um	NN	_	_	_
691	iCORM-3	icorm-3	NN	_	_	_
692	for	for	IN	_	_	_
693	20	20	CD	_	_	_
694	min	min	NN	_	_	_
695	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
696	Continuous	continuous	JJ	_	_	_
697	aerobically	aerobically	RB	_	_	_
698	grown	grow	VBN	_	_	_
699	cultures	culture	NNS	_	_	_
700	in	in	IN	_	_	_
701	Evans	Evans	NNP	_	_	_
702	medium	medium	NN	_	_	_
703	,	,	,	_	_	_
704	exposed	expose	VBN	_	_	_
705	to	to	TO	_	_	_
706	40uM	40um	NN	_	_	_
707	iCORM-3	icorm-3	NN	_	_	_
708	for	for	IN	_	_	_
709	2.5	2.5	CD	_	_	_
710	min	min	NN	_	_	_
711	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
712	Continuous	continuous	JJ	_	_	_
713	aerobically	aerobically	RB	_	_	_
714	grown	grow	VBN	_	_	_
715	cultures	culture	NNS	_	_	_
716	in	in	IN	_	_	_
717	Evans	Evans	NNP	_	_	_
718	medium	medium	NN	_	_	_
719	,	,	,	_	_	_
720	exposed	expose	VBN	_	_	_
721	to	to	TO	_	_	_
722	40uM	40um	NN	_	_	_
723	iCORM-3	icorm-3	NN	_	_	_
724	for	for	IN	_	_	_
725	40	40	CD	_	_	_
726	min	min	NN	_	_	_
727	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
728	Continuous	continuous	JJ	_	_	_
729	aerobically	aerobically	RB	_	_	_
730	grown	grow	VBN	_	_	_
731	cultures	culture	NNS	_	_	_
732	in	in	IN	_	_	_
733	Evans	Evans	NNP	_	_	_
734	medium	medium	NN	_	_	_
735	,	,	,	_	_	_
736	exposed	expose	VBN	_	_	_
737	to	to	TO	_	_	_
738	40uM	40um	NN	_	_	_
739	iCORM-3	icorm-3	NN	_	_	_
740	for	for	IN	_	_	_
741	5	5	CD	_	_	_
742	min	min	NN	_	_	_
743	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
744	Continuous	continuous	JJ	_	_	_
745	aerobically	aerobically	RB	_	_	_
746	grown	grow	VBN	_	_	_
747	cultures	culture	NNS	_	_	_
748	in	in	IN	_	_	_
749	Evans	Evans	NNP	_	_	_
750	medium	medium	NN	_	_	_
751	,	,	,	_	_	_
752	exposed	expose	VBN	_	_	_
753	to	to	TO	_	_	_
754	40uM	40um	NN	_	_	_
755	iCORM-3	icorm-3	NN	_	_	_
756	for	for	IN	_	_	_
757	80	80	CD	_	_	_
758	min	min	NN	_	_	_
759	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
760	Continuous	continuous	JJ	_	_	_
761	aerobically	aerobically	RB	_	_	_
762	grown	grow	VBN	_	_	_
763	cultures	culture	NNS	_	_	_
764	in	in	IN	_	_	_
765	Evans	Evans	NNP	_	_	_
766	medium	medium	NN	_	_	_
767	,	,	,	_	_	_
768	prior	prior	RB	_	_	_
769	to	to	TO	_	_	_
770	CORM-3	corm-3	NN	_	_	_
771	addition	addition	NN	_	_	_
772	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
773	Continuous	continuous	JJ	_	_	_
774	anaerobically	anaerobically	RB	_	_	_
775	grown	grow	VBN	_	_	_
776	cultures	culture	NNS	_	_	_
777	in	in	IN	_	_	_
778	Evans	Evans	NNP	_	_	_
779	medium	medium	NN	_	_	_
780	,	,	,	_	_	_
781	CORM-401	corm-401	NN	_	_	_
782	samples	sample	NNS	_	_	_
783	or	or	CC	_	_	_
784	samples	sample	NNS	_	_	_
785	prior	prior	RB	_	_	_
786	to	to	TO	_	_	_
787	addition	addition	NN	_	_	_
788	of	of	IN	_	_	_
789	CORM-401	corm-401	NN	_	_	_
790	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
791	Continuous	continuous	JJ	_	_	_
792	anaerobically	anaerobically	RB	_	_	_
793	grown	grow	VBN	_	_	_
794	cultures	culture	NNS	_	_	_
795	in	in	IN	_	_	_
796	Evans	Evans	NNP	_	_	_
797	medium	medium	NN	_	_	_
798	,	,	,	_	_	_
799	exposed	expose	VBN	_	_	_
800	to	to	TO	_	_	_
801	40uM	40um	NN	_	_	_
802	CORM-3	corm-3	NN	_	_	_
803	for	for	IN	_	_	_
804	10	10	CD	_	_	_
805	min	min	NN	_	_	_
806	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
807	Continuous	continuous	JJ	_	_	_
808	anaerobically	anaerobically	RB	_	_	_
809	grown	grow	VBN	_	_	_
810	cultures	culture	NNS	_	_	_
811	in	in	IN	_	_	_
812	Evans	Evans	NNP	_	_	_
813	medium	medium	NN	_	_	_
814	,	,	,	_	_	_
815	exposed	expose	VBN	_	_	_
816	to	to	TO	_	_	_
817	40uM	40um	NN	_	_	_
818	CORM-3	corm-3	NN	_	_	_
819	for	for	IN	_	_	_
820	20	20	CD	_	_	_
821	min	min	NN	_	_	_
822	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
823	Continuous	continuous	JJ	_	_	_
824	anaerobically	anaerobically	RB	_	_	_
825	grown	grow	VBN	_	_	_
826	cultures	culture	NNS	_	_	_
827	in	in	IN	_	_	_
828	Evans	Evans	NNP	_	_	_
829	medium	medium	NN	_	_	_
830	,	,	,	_	_	_
831	exposed	expose	VBN	_	_	_
832	to	to	TO	_	_	_
833	40uM	40um	NN	_	_	_
834	CORM-3	corm-3	NN	_	_	_
835	for	for	IN	_	_	_
836	2.5	2.5	CD	_	_	_
837	min	min	NN	_	_	_
838	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
839	Continuous	continuous	JJ	_	_	_
840	anaerobically	anaerobically	RB	_	_	_
841	grown	grow	VBN	_	_	_
842	cultures	culture	NNS	_	_	_
843	in	in	IN	_	_	_
844	Evans	Evans	NNP	_	_	_
845	medium	medium	NN	_	_	_
846	,	,	,	_	_	_
847	exposed	expose	VBN	_	_	_
848	to	to	TO	_	_	_
849	40uM	40um	NN	_	_	_
850	CORM-3	corm-3	NN	_	_	_
851	for	for	IN	_	_	_
852	40	40	CD	_	_	_
853	min	min	NN	_	_	_
854	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
855	Continuous	continuous	JJ	_	_	_
856	anaerobically	anaerobically	RB	_	_	_
857	grown	grow	VBN	_	_	_
858	cultures	culture	NNS	_	_	_
859	in	in	IN	_	_	_
860	Evans	Evans	NNP	_	_	_
861	medium	medium	NN	_	_	_
862	,	,	,	_	_	_
863	exposed	expose	VBN	_	_	_
864	to	to	TO	_	_	_
865	40uM	40um	NN	_	_	_
866	CORM-3	corm-3	NN	_	_	_
867	for	for	IN	_	_	_
868	5	5	CD	_	_	_
869	min	min	NN	_	_	_
870	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
871	Continuous	continuous	JJ	_	_	_
872	anaerobically	anaerobically	RB	_	_	_
873	grown	grow	VBN	_	_	_
874	cultures	culture	NNS	_	_	_
875	in	in	IN	_	_	_
876	Evans	Evans	NNP	_	_	_
877	medium	medium	NN	_	_	_
878	,	,	,	_	_	_
879	exposed	expose	VBN	_	_	_
880	to	to	TO	_	_	_
881	40uM	40um	NN	_	_	_
882	CORM-3	corm-3	NN	_	_	_
883	for	for	IN	_	_	_
884	80	80	CD	_	_	_
885	min	min	NN	_	_	_
886	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
887	Continuous	continuous	JJ	_	_	_
888	anaerobically	anaerobically	RB	_	_	_
889	grown	grow	VBN	_	_	_
890	cultures	culture	NNS	_	_	_
891	in	in	IN	_	_	_
892	Evans	Evans	NNP	_	_	_
893	medium	medium	NN	_	_	_
894	,	,	,	_	_	_
895	exposed	expose	VBN	_	_	_
896	to	to	TO	_	_	_
897	40uM	40um	NN	_	_	_
898	iCORM-3	icorm-3	NN	_	_	_
899	for	for	IN	_	_	_
900	10	10	CD	_	_	_
901	min	min	NN	_	_	_
902	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
903	Continuous	continuous	JJ	_	_	_
904	anaerobically	anaerobically	RB	_	_	_
905	grown	grow	VBN	_	_	_
906	cultures	culture	NNS	_	_	_
907	in	in	IN	_	_	_
908	Evans	Evans	NNP	_	_	_
909	medium	medium	NN	_	_	_
910	,	,	,	_	_	_
911	exposed	expose	VBN	_	_	_
912	to	to	TO	_	_	_
913	40uM	40um	NN	_	_	_
914	iCORM-3	icorm-3	NN	_	_	_
915	for	for	IN	_	_	_
916	20	20	CD	_	_	_
917	min	min	NN	_	_	_
918	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
919	Continuous	continuous	JJ	_	_	_
920	anaerobically	anaerobically	RB	_	_	_
921	grown	grow	VBN	_	_	_
922	cultures	culture	NNS	_	_	_
923	in	in	IN	_	_	_
924	Evans	Evans	NNP	_	_	_
925	medium	medium	NN	_	_	_
926	,	,	,	_	_	_
927	exposed	expose	VBN	_	_	_
928	to	to	TO	_	_	_
929	40uM	40um	NN	_	_	_
930	iCORM-3	icorm-3	NN	_	_	_
931	for	for	IN	_	_	_
932	2.5	2.5	CD	_	_	_
933	min	min	NN	_	_	_
934	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
935	Continuous	continuous	JJ	_	_	_
936	anaerobically	anaerobically	RB	_	_	_
937	grown	grow	VBN	_	_	_
938	cultures	culture	NNS	_	_	_
939	in	in	IN	_	_	_
940	Evans	Evans	NNP	_	_	_
941	medium	medium	NN	_	_	_
942	,	,	,	_	_	_
943	exposed	expose	VBN	_	_	_
944	to	to	TO	_	_	_
945	40uM	40um	NN	_	_	_
946	iCORM-3	icorm-3	NN	_	_	_
947	for	for	IN	_	_	_
948	40	40	CD	_	_	_
949	min	min	NN	_	_	_
950	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
951	Continuous	continuous	JJ	_	_	_
952	anaerobically	anaerobically	RB	_	_	_
953	grown	grow	VBN	_	_	_
954	cultures	culture	NNS	_	_	_
955	in	in	IN	_	_	_
956	Evans	Evans	NNP	_	_	_
957	medium	medium	NN	_	_	_
958	,	,	,	_	_	_
959	exposed	expose	VBN	_	_	_
960	to	to	TO	_	_	_
961	40uM	40um	NN	_	_	_
962	iCORM-3	icorm-3	NN	_	_	_
963	for	for	IN	_	_	_
964	5	5	CD	_	_	_
965	min	min	NN	_	_	_
966	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
967	Continuous	continuous	JJ	_	_	_
968	anaerobically	anaerobically	RB	_	_	_
969	grown	grow	VBN	_	_	_
970	cultures	culture	NNS	_	_	_
971	in	in	IN	_	_	_
972	Evans	Evans	NNP	_	_	_
973	medium	medium	NN	_	_	_
974	,	,	,	_	_	_
975	exposed	expose	VBN	_	_	_
976	to	to	TO	_	_	_
977	40uM	40um	NN	_	_	_
978	iCORM-3	icorm-3	NN	_	_	_
979	for	for	IN	_	_	_
980	80	80	CD	_	_	_
981	min	min	NN	_	_	_
982	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
983	Continuous	continuous	JJ	_	_	_
984	anaerobically	anaerobically	RB	_	_	_
985	grown	grow	VBN	_	_	_
986	cultures	culture	NNS	_	_	_
987	in	in	IN	_	_	_
988	Evans	Evans	NNP	_	_	_
989	medium	medium	NN	_	_	_
990	,	,	,	_	_	_
991	exposed	expose	VBN	_	_	_
992	to	to	TO	_	_	_
993	CO	CO	NNP	_	_	_
994	gas	gas	NN	_	_	_
995	at	at	IN	_	_	_
996	0.1	0.1	CD	_	_	_
997	L/min	l/min	NN	_	_	_
998	for	for	IN	_	_	_
999	10	10	CD	_	_	_
1000	min	min	NN	_	_	_
1001	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1002	Continuous	continuous	JJ	_	_	_
1003	anaerobically	anaerobically	RB	_	_	_
1004	grown	grow	VBN	_	_	_
1005	cultures	culture	NNS	_	_	_
1006	in	in	IN	_	_	_
1007	Evans	Evans	NNP	_	_	_
1008	medium	medium	NN	_	_	_
1009	,	,	,	_	_	_
1010	exposed	expose	VBN	_	_	_
1011	to	to	TO	_	_	_
1012	CO	CO	NNP	_	_	_
1013	gas	gas	NN	_	_	_
1014	at	at	IN	_	_	_
1015	0.1	0.1	CD	_	_	_
1016	L/min	l/min	NN	_	_	_
1017	for	for	IN	_	_	_
1018	20	20	CD	_	_	_
1019	min	min	NN	_	_	_
1020	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1021	Continuous	continuous	JJ	_	_	_
1022	anaerobically	anaerobically	RB	_	_	_
1023	grown	grow	VBN	_	_	_
1024	cultures	culture	NNS	_	_	_
1025	in	in	IN	_	_	_
1026	Evans	Evans	NNP	_	_	_
1027	medium	medium	NN	_	_	_
1028	,	,	,	_	_	_
1029	exposed	expose	VBN	_	_	_
1030	to	to	TO	_	_	_
1031	CO	CO	NNP	_	_	_
1032	gas	gas	NN	_	_	_
1033	at	at	IN	_	_	_
1034	0.1	0.1	CD	_	_	_
1035	L/min	l/min	NN	_	_	_
1036	for	for	IN	_	_	_
1037	2.5	2.5	CD	_	_	_
1038	min	min	NN	_	_	_
1039	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1040	Continuous	continuous	JJ	_	_	_
1041	anaerobically	anaerobically	RB	_	_	_
1042	grown	grow	VBN	_	_	_
1043	cultures	culture	NNS	_	_	_
1044	in	in	IN	_	_	_
1045	Evans	Evans	NNP	_	_	_
1046	medium	medium	NN	_	_	_
1047	,	,	,	_	_	_
1048	exposed	expose	VBN	_	_	_
1049	to	to	TO	_	_	_
1050	CO	CO	NNP	_	_	_
1051	gas	gas	NN	_	_	_
1052	at	at	IN	_	_	_
1053	0.1	0.1	CD	_	_	_
1054	L/min	l/min	NN	_	_	_
1055	for	for	IN	_	_	_
1056	40	40	CD	_	_	_
1057	min	min	NN	_	_	_
1058	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1059	Continuous	continuous	JJ	_	_	_
1060	anaerobically	anaerobically	RB	_	_	_
1061	grown	grow	VBN	_	_	_
1062	cultures	culture	NNS	_	_	_
1063	in	in	IN	_	_	_
1064	Evans	Evans	NNP	_	_	_
1065	medium	medium	NN	_	_	_
1066	,	,	,	_	_	_
1067	exposed	expose	VBN	_	_	_
1068	to	to	TO	_	_	_
1069	CO	CO	NNP	_	_	_
1070	gas	gas	NN	_	_	_
1071	at	at	IN	_	_	_
1072	0.1	0.1	CD	_	_	_
1073	L/min	l/min	NN	_	_	_
1074	for	for	IN	_	_	_
1075	5	5	CD	_	_	_
1076	min	min	NN	_	_	_
1077	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1078	Continuous	continuous	JJ	_	_	_
1079	anaerobically	anaerobically	RB	_	_	_
1080	grown	grow	VBN	_	_	_
1081	cultures	culture	NNS	_	_	_
1082	in	in	IN	_	_	_
1083	Evans	Evans	NNP	_	_	_
1084	medium	medium	NN	_	_	_
1085	,	,	,	_	_	_
1086	exposed	expose	VBN	_	_	_
1087	to	to	TO	_	_	_
1088	CO	CO	NNP	_	_	_
1089	gas	gas	NN	_	_	_
1090	at	at	IN	_	_	_
1091	0.1	0.1	CD	_	_	_
1092	L/min	l/min	NN	_	_	_
1093	for	for	IN	_	_	_
1094	80	80	CD	_	_	_
1095	min	min	NN	_	_	_
1096	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1097	Continuous	continuous	JJ	_	_	_
1098	anaerobically	anaerobically	RB	_	_	_
1099	grown	grow	VBN	_	_	_
1100	cultures	culture	NNS	_	_	_
1101	in	in	IN	_	_	_
1102	Evans	Evans	NNP	_	_	_
1103	medium	medium	NN	_	_	_
1104	,	,	,	_	_	_
1105	prior	prior	RB	_	_	_
1106	to	to	TO	_	_	_
1107	CORM-3	corm-3	NN	_	_	_
1108	addition	addition	NN	_	_	_
1109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1110	control	control	NN	_	_	_
1111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1112	Control	Control	NNP	_	_	_
1113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1114	Control	Control	NNP	_	_	_
1115	,	,	,	_	_	_
1116	0.8	0.8	CD	_	_	_
1117	%	%	NN	_	_	_
1118	butanol	butanol	NN	_	_	_
1119	,1.5	,1.5	CD	_	_	_
1120	h	h	NN	_	_	_
1121	,	,	,	_	_	_
1122	replicate	replicate	VB	_	_	_
1123	1	1	CD	_	_	_
1124	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1125	Control	Control	NNP	_	_	_
1126	,	,	,	_	_	_
1127	0.8	0.8	CD	_	_	_
1128	%	%	NN	_	_	_
1129	butanol	butanol	NN	_	_	_
1130	,1.5	,1.5	CD	_	_	_
1131	h	h	NN	_	_	_
1132	,	,	,	_	_	_
1133	replicate	replicate	VB	_	_	_
1134	2	2	CD	_	_	_
1135	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1136	Control	Control	NNP	_	_	_
1137	,	,	,	_	_	_
1138	0.8	0.8	CD	_	_	_
1139	%	%	NN	_	_	_
1140	butanol	butanol	NN	_	_	_
1141	,1.5	,1.5	CD	_	_	_
1142	h	h	NN	_	_	_
1143	,	,	,	_	_	_
1144	replicate	replicate	VB	_	_	_
1145	3	3	CD	_	_	_
1146	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1147	Control	Control	NNP	_	_	_
1148	_	_	NNP	_	_	_
1149	1	1	CD	_	_	_
1150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1151	Control109	control109	NN	_	_	_
1152	_	_	CD	_	_	_
1153	0.8	0.8	CD	_	_	_
1154	%	%	NN	_	_	_
1155	Bu	bu	NN	_	_	_
1156	_	_	CD	_	_	_
1157	1.5	1.5	CD	_	_	_
1158	h	h	NN	_	_	_
1159	_	_	CD	_	_	_
1160	rep1	rep1	NN	_	_	_
1161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1162	Control109	control109	NN	_	_	_
1163	_	_	CD	_	_	_
1164	0.8	0.8	CD	_	_	_
1165	%	%	NN	_	_	_
1166	Bu	bu	NN	_	_	_
1167	_	_	CD	_	_	_
1168	1.5	1.5	CD	_	_	_
1169	h	h	NN	_	_	_
1170	_	_	CD	_	_	_
1171	rep2	rep2	NN	_	_	_
1172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1173	Control109	control109	NN	_	_	_
1174	_	_	CD	_	_	_
1175	0.8	0.8	CD	_	_	_
1176	%	%	NN	_	_	_
1177	Bu	bu	NN	_	_	_
1178	_	_	CD	_	_	_
1179	1.5	1.5	CD	_	_	_
1180	h	h	NN	_	_	_
1181	_	_	CD	_	_	_
1182	rep3	rep3	NN	_	_	_
1183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1184	control	control	NN	_	_	_
1185	12h	12h	VBP	_	_	_
1186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1187	Control-1	control-1	NN	_	_	_
1188	,	,	,	_	_	_
1189	biological	biological	JJ	_	_	_
1190	rep1	rep1	NN	_	_	_
1191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1192	Control	Control	NNP	_	_	_
1193	_	_	NN	_	_	_
1194	2	2	CD	_	_	_
1195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1196	control	control	NN	_	_	_
1197	24h	24h	JJ	_	_	_
1198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1199	Control-2	control-2	NN	_	_	_
1200	,	,	,	_	_	_
1201	biological	biological	JJ	_	_	_
1202	rep2	rep2	NN	_	_	_
1203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1204	Control-3	control-3	NN	_	_	_
1205	,	,	,	_	_	_
1206	biological	biological	JJ	_	_	_
1207	rep3	rep3	NN	_	_	_
1208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1209	control	control	NN	_	_	_
1210	6h	6h	VBP	_	_	_
1211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1212	control	control	NN	_	_	_
1213	-LRB-	-lrb-	-LRB-	_	_	_
1214	additional	additional	JJ	_	_	_
1215	-RRB-	-rrb-	-RRB-	_	_	_
1216	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1217	Control	Control	NNP	_	_	_
1218	bacteria	bacterium	NNS	_	_	_
1219	at	at	IN	_	_	_
1220	37	37	CD	_	_	_
1221	°C	°c	NN	_	_	_
1222	-LRB-	-lrb-	-LRB-	_	_	_
1223	common	common	JJ	_	_	_
1224	reference	reference	NN	_	_	_
1225	-RRB-	-rrb-	-RRB-	_	_	_
1226	.	.	.	_	_	_

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	NN	_	_	_
2	control	control	NN	_	_	_
3	,	,	,	_	_	_
4	biological	biological	JJ	_	_	_
5	rep1	rep1	NN	_	_	_
6	C1	c1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	control	control	NN	_	_	_
9	,	,	,	_	_	_
10	biological	biological	JJ	_	_	_
11	rep1	rep1	NN	_	_	_
12	C2	c2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	control	control	NN	_	_	_
15	,	,	,	_	_	_
16	biological	biological	JJ	_	_	_
17	rep1	rep1	NN	_	_	_
18	C3	c3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	control	control	NN	_	_	_
21	,	,	,	_	_	_
22	biological	biological	JJ	_	_	_
23	rep2	rep2	NN	_	_	_
24	C4	c4	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	control	control	NN	_	_	_
27	,	,	,	_	_	_
28	biological	biological	JJ	_	_	_
29	rep2	rep2	NN	_	_	_
30	C5	c5	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	control	control	NN	_	_	_
33	,	,	,	_	_	_
34	biological	biological	JJ	_	_	_
35	rep2	rep2	NN	_	_	_
36	C6	c6	NN	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Control	Control	NNP	_	_	_
39	chemostat	chemostat	NN	_	_	_
40	1	1	CD	_	_	_
41	h	h	NN	_	_	_
42	not	not	RB	_	_	_
43	irradiated	irradiated	JJ	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	Control	Control	NNP	_	_	_
46	chemostat	chemostat	NN	_	_	_
47	1h	1h	NN	_	_	_
48	not	not	RB	_	_	_
49	irradiated	irradiated	JJ	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Control	Control	NNP	_	_	_
52	chemostat	chemostat	NN	_	_	_
53	50	50	CD	_	_	_
54	h	h	NN	_	_	_
55	not	not	RB	_	_	_
56	irradiated	irradiated	JJ	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Control	Control	NNP	_	_	_
59	pAN1201	pan1201	NN	_	_	_
60	replicate	replicate	VB	_	_	_
61	1	1	CD	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	IPTG	iptg	SYM	_	_	_
64	-	-	:	_	_	_
65	/	/	:	_	_	_
66	aTc	atc	SYM	_	_	_
67	-	-	:	_	_	_
68	/	/	:	_	_	_
69	Ara	Ara	NNP	_	_	_
70	-	-	:	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Control	Control	NNP	_	_	_
74	pAN1201	pan1201	NN	_	_	_
75	replicate	replicate	VB	_	_	_
76	2	2	CD	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	IPTG	iptg	SYM	_	_	_
79	-	-	:	_	_	_
80	/	/	:	_	_	_
81	aTc	atc	SYM	_	_	_
82	-	-	:	_	_	_
83	/	/	:	_	_	_
84	Ara	Ara	NNP	_	_	_
85	-	-	:	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Control	Control	NNP	_	_	_
89	replicate	replicate	VB	_	_	_
90	1	1	CD	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	Control	Control	NNP	_	_	_
93	replicate	replicate	VB	_	_	_
94	2	2	CD	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	Control	Control	NNP	_	_	_
97	replicate	replicate	VB	_	_	_
98	3	3	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	control	control	NN	_	_	_
101	sample	sample	NN	_	_	_
102	at	at	IN	_	_	_
103	30	30	CD	_	_	_
104	min	min	NN	_	_	_
105	,	,	,	_	_	_
106	biological	biological	JJ	_	_	_
107	rep1	rep1	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	control	control	NN	_	_	_
110	sample	sample	NN	_	_	_
111	at	at	IN	_	_	_
112	30	30	CD	_	_	_
113	min	min	NN	_	_	_
114	,	,	,	_	_	_
115	biological	biological	JJ	_	_	_
116	rep2	rep2	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	control	control	NN	_	_	_
119	sample	sample	NN	_	_	_
120	at	at	IN	_	_	_
121	60	60	CD	_	_	_
122	min	min	NN	_	_	_
123	,	,	,	_	_	_
124	biological	biological	JJ	_	_	_
125	rep1	rep1	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	control	control	NN	_	_	_
128	sample	sample	NN	_	_	_
129	at	at	IN	_	_	_
130	60	60	CD	_	_	_
131	min	min	NN	_	_	_
132	,	,	,	_	_	_
133	biological	biological	JJ	_	_	_
134	rep2	rep2	NN	_	_	_
135	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
136	Control	Control	NNP	_	_	_
137	samples	sample	NNS	_	_	_
138	-LRB-	-lrb-	-LRB-	_	_	_
139	285c/empty	285c/empty	JJ	_	_	_
140	vector	vector	NN	_	_	_
141	-RRB-	-rrb-	-RRB-	_	_	_
142	were	be	VBD	_	_	_
143	harvested	harvest	VBN	_	_	_
144	via	via	IN	_	_	_
145	filtration	filtration	NN	_	_	_
146	and	and	CC	_	_	_
147	resuspended	resuspend	VBN	_	_	_
148	in	in	IN	_	_	_
149	RNALater	rnalater	NN	_	_	_
150	once	once	IN	_	_	_
151	they	they	PRP	_	_	_
152	had	have	VBD	_	_	_
153	reached	reach	VBN	_	_	_
154	OD	od	NN	_	_	_
155	=	=	JJ	_	_	_
156	0.5	0.5	CD	_	_	_
157	.	.	.	_	_	_

1	Experimental	experimental	JJ	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	after	after	IN	_	_	_
6	1	1	CD	_	_	_
7	hour	hour	NN	_	_	_
8	of	of	IN	_	_	_
9	heat	heat	NN	_	_	_
10	shock	shock	NN	_	_	_
11	at	at	IN	_	_	_
12	42	42	CD	_	_	_
13	C	c	NN	_	_	_
14	in	in	IN	_	_	_
15	an	a	DT	_	_	_
16	analogous	analogous	JJ	_	_	_
17	procedure	procedure	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Control	Control	NNP	_	_	_
3	_	_	NNP	_	_	_
4	Step	step	VB	_	_	_
5	_	_	SYM	_	_	_
6	1-1	1-1	CD	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Control	Control	NNP	_	_	_
9	_	_	NNP	_	_	_
10	Step	step	VB	_	_	_
11	_	_	SYM	_	_	_
12	1-2	1-2	CD	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Control	Control	NNP	_	_	_
15	_	_	NNP	_	_	_
16	Step	step	VB	_	_	_
17	_	_	SYM	_	_	_
18	2-1	2-1	CD	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Control	Control	NNP	_	_	_
21	_	_	NNP	_	_	_
22	Step	step	VB	_	_	_
23	_	_	SYM	_	_	_
24	2-2	2-2	CD	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Control	Control	NNP	_	_	_
27	_	_	NNP	_	_	_
28	Step	step	VB	_	_	_
29	_	_	SYM	_	_	_
30	3-1	3-1	CD	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Control	Control	NNP	_	_	_
33	_	_	NNP	_	_	_
34	Step	step	VB	_	_	_
35	_	_	SYM	_	_	_
36	3-2	3-2	CD	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Control	Control	NNP	_	_	_
39	_	_	NNP	_	_	_
40	Step	step	VB	_	_	_
41	_	_	SYM	_	_	_
42	4-1	4-1	CD	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	Control	Control	NNP	_	_	_
45	_	_	NNP	_	_	_
46	Step	step	VB	_	_	_
47	_	_	SYM	_	_	_
48	4-2	4-2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	control	control	NN	_	_	_
51	strain	strain	NN	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	Control	Control	NNP	_	_	_
54	Strain	Strain	NNP	_	_	_
55	at	at	IN	_	_	_
56	specific	specific	JJ	_	_	_
57	growth	growth	NN	_	_	_
58	rate	rate	NN	_	_	_
59	0.5h-1	0.5h-1	JJ	_	_	_
60	0h	0h	NN	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Control	Control	NNP	_	_	_
63	Strain	Strain	NNP	_	_	_
64	at	at	IN	_	_	_
65	specific	specific	JJ	_	_	_
66	growth	growth	NN	_	_	_
67	rate	rate	NN	_	_	_
68	0.5h-1	0.5h-1	JJ	_	_	_
69	10h	10h	CD	_	_	_
70	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
71	Control	Control	NNP	_	_	_
72	Strain	Strain	NNP	_	_	_
73	at	at	IN	_	_	_
74	specific	specific	JJ	_	_	_
75	growth	growth	NN	_	_	_
76	rate	rate	NN	_	_	_
77	0.5h-1	0.5h-1	JJ	_	_	_
78	16h	16h	NN	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	Control	Control	NNP	_	_	_
81	Strain	Strain	NNP	_	_	_
82	at	at	IN	_	_	_
83	specific	specific	JJ	_	_	_
84	growth	growth	NN	_	_	_
85	rate	rate	NN	_	_	_
86	0.5h-1	0.5h-1	JJ	_	_	_
87	20h	20h	JJ	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	Control	Control	NNP	_	_	_
90	Strain	Strain	NNP	_	_	_
91	at	at	IN	_	_	_
92	specific	specific	JJ	_	_	_
93	growth	growth	NN	_	_	_
94	rate	rate	NN	_	_	_
95	0.5h-1	0.5h-1	JJ	_	_	_
96	6h	6h	JJ	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	Control	Control	NNP	_	_	_
99	Strain	Strain	NNP	_	_	_
100	at	at	IN	_	_	_
101	specific	specific	JJ	_	_	_
102	growth	growth	NN	_	_	_
103	rate	rate	NN	_	_	_
104	0.5h-1	0.5h-1	JJ	_	_	_
105	8h	8h	NN	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	Control	Control	NNP	_	_	_
108	strain	strain	NN	_	_	_
109	exponentially	exponentially	RB	_	_	_
110	grown	grow	VBN	_	_	_
111	in	in	IN	_	_	_
112	the	the	DT	_	_	_
113	absence	absence	NN	_	_	_
114	of	of	IN	_	_	_
115	histidine	histidine	NN	_	_	_
116	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
117	Control	Control	NNP	_	_	_
118	strain	strain	NN	_	_	_
119	exponentially	exponentially	RB	_	_	_
120	grown	grow	VBN	_	_	_
121	in	in	IN	_	_	_
122	the	the	DT	_	_	_
123	presence	presence	NN	_	_	_
124	of	of	IN	_	_	_
125	histidine	histidine	NN	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	1	1	CD	_	_	_
128	mM	mm	NN	KWSUPP	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	control	control	NN	_	_	_
132	strain	strain	NN	_	_	_
133	K-12	k-12	NN	_	_	_
134	MG1655	mg1655	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	control	control	NN	_	_	_
137	strain	strain	NN	_	_	_
138	O157	o157	NN	_	_	_
139	:	:	:	_	_	_
140	H7	h7	NN	_	_	_
141	EDL933	edl933	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	control	control	NN	_	_	_
144	strain	strain	NN	_	_	_
145	with	with	IN	_	_	_
146	hypoxanthine	hypoxanthine	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	control	control	NN	_	_	_
149	strain	strain	NN	_	_	_
150	w/o	w/o	NN	_	_	_
151	hypoxanthine	hypoxanthine	NN	_	_	_
152	120	120	CD	_	_	_
153	min	min	NN	_	_	_
154	at	at	IN	_	_	_
155	low	low	JJ	_	_	_
156	dilution	dilution	NN	_	_	_
157	protocol	protocol	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	control	control	NN	_	_	_
160	strain	strain	NN	_	_	_
161	w/o	w/o	NN	_	_	_
162	hypoxanthine	hypoxanthine	NN	_	_	_
163	15	15	CD	_	_	_
164	min	min	NN	_	_	_
165	at	at	IN	_	_	_
166	low	low	JJ	_	_	_
167	dilution	dilution	NN	_	_	_
168	protocol	protocol	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	control	control	NN	_	_	_
171	strain	strain	NN	_	_	_
172	w/o	w/o	NN	_	_	_
173	hypoxanthine	hypoxanthine	NN	_	_	_
174	30	30	CD	_	_	_
175	min	min	NN	_	_	_
176	at	at	IN	_	_	_
177	low	low	JJ	_	_	_
178	dilution	dilution	NN	_	_	_
179	protocol	protocol	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	control	control	NN	_	_	_
182	strain	strain	NN	_	_	_
183	w/o	w/o	NN	_	_	_
184	hypoxanthine	hypoxanthine	NN	_	_	_
185	45	45	CD	_	_	_
186	min	min	NN	_	_	_
187	at	at	IN	_	_	_
188	low	low	JJ	_	_	_
189	dilution	dilution	NN	_	_	_
190	protocol	protocol	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	control	control	NN	_	_	_
193	strain	strain	NN	_	_	_
194	w/o	w/o	NN	_	_	_
195	hypoxanthine	hypoxanthine	NN	_	_	_
196	60	60	CD	_	_	_
197	min	min	NN	_	_	_
198	at	at	IN	_	_	_
199	low	low	JJ	_	_	_
200	dilution	dilution	NN	_	_	_
201	protocol	protocol	NN	_	_	_
202	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
203	Control	Control	NNP	_	_	_
204	treatment	treatment	NN	_	_	_
205	.	.	.	_	_	_

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	NNP	_	_	_
23	Control	Control	NNP	_	_	_
24	treatment	treatment	NN	_	_	_
25	.	.	.	_	_	_

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	NNP	_	_	_
12	Control	Control	NNP	_	_	_
13	Wild	Wild	NNP	_	_	_
14	type	type	NN	_	_	_
15	E.coli	e.coli	NN	_	_	_
16	SE15	se15	NN	_	_	_
17	vs.	vs.	CC	_	_	_
18	LuxS	luxs	NN	_	_	_
19	mutant	mutant	JJ	_	_	_
20	E.coli	e.coli	NN	_	_	_
21	SE15	se15	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	conversion	conversion	NN	_	_	_
24	:	:	:	_	_	_
25	Convert	convert	VB	_	_	_
26	SOLiD	solid	JJ	_	_	_
27	output	output	NN	_	_	_
28	to	to	TO	_	_	_
29	fastq	fastq	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Galaxy	galaxy	NN	_	_	_
32	Version	version	NN	_	_	_
33	1.0.0	1.0.0	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	;	;	:	_	_	_
36	default	default	NN	_	_	_
37	parameters	parameter	NNS	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	convert	convert	VBP	_	_	_
3	back	back	RB	_	_	_
4	to	to	TO	_	_	_
5	sorted.sam	sorted.sam	NN	_	_	_
6	with	with	IN	_	_	_
7	samtools	samtool	NNS	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	convert	convert	VBP	_	_	_
10	bowtie	bowtie	NN	_	_	_
11	output	output	NN	_	_	_
12	.	.	.	_	_	_

1	sam	sam	NN	_	_	_
2	to	to	TO	_	_	_
3	.	.	.	_	_	_

1	bam	bam	NN	_	_	_
2	with	with	IN	_	_	_
3	samtools	samtool	NNS	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	corresponding	correspond	VBG	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	same	same	JJ	_	_	_
9	tip	tip	NN	_	_	_
10	.	.	.	_	_	_

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	counting	counting	NN	_	_	_
16	:	:	:	_	_	_
17	countOverlaps	countoverlap	NNS	_	_	_
18	of	of	IN	_	_	_
19	Iranges	irange	NNS	_	_	_
20	;	;	:	_	_	_
21	default	default	NN	_	_	_
22	parameters	parameter	NNS	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	Count	count	NN	_	_	_
25	reads	read	VBZ	_	_	_
26	aligned	align	VBN	_	_	_
27	to	to	TO	_	_	_
28	each	each	DT	_	_	_
29	base	base	NN	_	_	_
30	IGVtools	igvtools	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	version	version	NN	_	_	_
33	2.3.71	2.3.71	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	window	window	NN	_	_	_
37	size	size	NN	_	_	_
38	=	=	JJ	_	_	_
39	1	1	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Counts	count	VBZ	_	_	_
42	per	per	IN	_	_	_
43	million	million	CD	_	_	_
44	unique	unique	JJ	_	_	_
45	reads	read	VBZ	_	_	_
46	were	be	VBD	_	_	_
47	calculated	calculate	VBN	_	_	_
48	for	for	IN	_	_	_
49	each	each	DT	_	_	_
50	gene	gene	NN	_	_	_
51	.	.	.	_	_	_

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

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Coverage	Coverage	NNP	_	_	_
3	calculation	calculation	NN	_	_	_
4	and	and	CC	_	_	_
5	normalisation	normalisation	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	TRAPL	trapl	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Coverage	Coverage	NNP	_	_	_
11	calculation	calculation	NN	_	_	_
12	and	and	CC	_	_	_
13	normalisation	normalisation	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	via	via	IN	_	_	_
16	READemption	reademption	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	cpxA-ala-1	cpxa-ala-1	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	cpxA-ala-2	cpxa-ala-2	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	cpxA	cpxa	NN	GEN	_	_
24	mutant	mutant	NN	_	_	_
25	in	in	IN	_	_	_
26	Ala	Ala	NNP	_	_	_
27	media	media	NNS	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	cpxA	cpxa	NN	GEN	_	_
30	mutant	mutant	NN	_	_	_
31	in	in	IN	_	_	_
32	Gln	gln	NN	_	_	_
33	media	media	NNS	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	cpxR	cpxr	NN	GEN	_	_
36	__	__	CD	_	_	_
37	U	U	NNP	_	_	_
38	_	_	NNP	_	_	_
39	N0075	N0075	NNP	_	_	_
40	_	_	VBD	_	_	_
41	r1	r1	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	cpxR	cpxr	NN	GEN	_	_
44	__	__	CD	_	_	_
45	U	U	NNP	_	_	_
46	_	_	NNP	_	_	_
47	N0075	N0075	NNP	_	_	_
48	_	_	VBD	_	_	_
49	r2	r2	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	cpxR	cpxr	NN	GEN	_	_
52	__	__	CD	_	_	_
53	U	U	NNP	_	_	_
54	_	_	NNP	_	_	_
55	N0075	N0075	NNP	_	_	_
56	_	_	SYM	_	_	_
57	r3	r3	FW	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
59	cpxR	cpxr	NN	GEN	_	_
60	upregulation	upregulation	NN	_	_	_
61	,	,	,	_	_	_
62	0.075	0.075	CD	_	_	_
63	ug/ml	ug/ml	NN	_	_	_
64	norfloxacin	norfloxacin	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	cra-8myc	cra-8myc	NN	_	_	_
67	tagged	tag	VBD	_	_	_
68	strain	strain	NN	_	_	_
69	_	_	NN	_	_	_
70	acetate	acetate	NN	SUPP	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	cra-8myc	cra-8myc	NN	_	_	_
73	tagged	tag	VBD	_	_	_
74	strain	strain	NN	_	_	_
75	_	_	NN	_	_	_
76	fructose	fructose	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	cra-8myc	cra-8myc	NN	_	_	_
79	tagged	tag	VBD	_	_	_
80	strain	strain	NN	_	_	_
81	_	_	NN	_	_	_
82	glucose	glucose	NN	SUPP	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
84	Cra	Cra	NNP	TF	_	_
85	acetate	acetate	NN	SUPP	_	_
86	1	1	CD	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Cra	Cra	NNP	TF	_	_
89	acetate	acetate	NN	SUPP	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
92	Cra	Cra	NNP	TF	_	_
93	fructose	fructose	NN	_	_	_
94	1	1	CD	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	Cra	Cra	NNP	TF	_	_
97	fructose	fructose	NN	_	_	_
98	2	2	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
100	Cra	cra	NN	TF	_	_
101	glucose	glucose	NN	SUPP	_	_
102	1	1	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Cra	cra	NN	TF	_	_
105	glucose	glucose	NN	SUPP	_	_
106	2	2	CD	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	cra	cra	NN	GEN	_	_
109	KO	ko	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	cra	cra	NN	GEN	_	_
112	KO	ko	NN	_	_	_
113	+	+	CC	_	_	_
114	L-trp	l-trp	JJ	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	crcB	crcb	NN	GEN	_	_
117	__	__	CD	_	_	_
118	U	U	NNP	_	_	_
119	_	_	NNP	_	_	_
120	N0075	N0075	NNP	_	_	_
121	_	_	VBD	_	_	_
122	r1	r1	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	crcB	crcb	NN	GEN	_	_
125	__	__	CD	_	_	_
126	U	U	NNP	_	_	_
127	_	_	NNP	_	_	_
128	N0075	N0075	NNP	_	_	_
129	_	_	VBD	_	_	_
130	r2	r2	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	crcB	crcb	NN	GEN	_	_
133	__	__	CD	_	_	_
134	U	U	NNP	_	_	_
135	_	_	NNP	_	_	_
136	N0075	N0075	NNP	_	_	_
137	_	_	SYM	_	_	_
138	r3	r3	FW	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
140	crcB	crcb	NN	GEN	_	_
141	upregulation	upregulation	NN	_	_	_
142	,	,	,	_	_	_
143	0.075	0.075	CD	_	_	_
144	ug/ml	ug/ml	NN	_	_	_
145	norfloxacin	norfloxacin	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
147	CRE	cre	NN	_	_	_
148	Multi	multi	JJ	_	_	_
149	0uM	0um	NN	_	_	_
150	Rep1	rep1	NN	_	_	_
151	Plasmid	plasmid	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	CRE	cre	NN	_	_	_
154	Multi	multi	JJ	_	_	_
155	0uM	0um	NN	_	_	_
156	Rep2	rep2	NN	_	_	_
157	Plasmid	plasmid	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	CRE	cre	NN	_	_	_
160	Multi	multi	JJ	_	_	_
161	100uM	100um	NN	_	_	_
162	Rep1	rep1	NN	_	_	_
163	Plasmid	plasmid	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	CRE	cre	NN	_	_	_
166	Multi	multi	JJ	_	_	_
167	100uM	100um	NN	_	_	_
168	Rep2	rep2	NN	_	_	_
169	Plasmid	plasmid	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	CRE	cre	NN	_	_	_
172	Single	single	JJ	_	_	_
173	100uM	100um	NN	_	_	_
174	Rep1	rep1	NN	_	_	_
175	Plasmid	plasmid	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	CRE	cre	NN	_	_	_
178	Single	single	JJ	_	_	_
179	100uM	100um	NN	_	_	_
180	Rep2	rep2	NN	_	_	_
181	Plasmid	plasmid	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	Crooks	crook	NNS	_	_	_
184	_	_	VBP	_	_	_
185	aero	aero	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	Crooks	crook	NNS	_	_	_
188	_	_	VBP	_	_	_
189	anaero	anaero	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	Crosslink	Crosslink	NNP	_	_	_
192	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
193	Cross-linked	cross-linked	JJ	_	_	_
194	and	and	CC	_	_	_
195	sonicated	sonicated	JJ	_	_	_
196	chromatin	chromatin	NN	_	_	_
197	complex	complex	NN	_	_	_
198	of	of	IN	_	_	_
199	ArcA-8myc	arca-8myc	NN	_	_	_
200	and	and	CC	_	_	_
201	DNA	dna	NN	_	_	_
202	was	be	VBD	_	_	_
203	immunoprecipitated	immunoprecipitate	VBN	_	_	_
204	by	by	IN	_	_	_
205	rabbit	rabbit	NN	_	_	_
206	serum	serum	NN	_	_	_
207	containing	contain	VBG	_	_	_
208	myc	myc	NN	_	_	_
209	antibody	antibody	NN	_	_	_
210	.	.	.	_	_	_

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	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	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	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	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	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	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	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	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	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	anti-RpoB	anti-rpob	JJ	_	_	_
15	antibody	antibody	NN	_	_	_
16	.	.	.	_	_	_

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	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	normal	normal	JJ	_	_	_
16	mouse	mouse	NN	_	_	_
17	IgG	igg	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Upstate	upstate	JJ	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	for	for	IN	_	_	_
22	the	the	DT	_	_	_
23	control	control	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	mock-IP	mock-ip	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
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	two	two	CD	_	_	_
9	times	time	NNS	_	_	_
10	with	with	IN	_	_	_
11	ice-cold	ice-cold	JJ	_	_	_
12	PBS	PBS	NNP	_	_	_
13	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
26	lysozyme	lysozyme	NN	_	_	_
27	,	,	,	_	_	_
28	50	50	CD	_	_	_
29	%	%	NN	_	_	_
30	glycerol	glycerol	NN	SUPP	_	_
31	,	,	,	_	_	_
32	50mM	50mm	NN	_	_	_
33	Tris-HCl	tris-hcl	NN	_	_	_
34	pH7	ph7	NN	_	_	_
35	.5	.5	CD	_	_	_
36	,	,	,	_	_	_
37	100mM	100mm	NN	_	_	_
38	NaCl	nacl	NN	_	_	_
39	,	,	,	_	_	_
40	1mM	1mm	NN	_	_	_
41	DTT	dtt	NN	_	_	_
42	,	,	,	_	_	_
43	0.1	0.1	CD	_	_	_
44	%	%	NN	_	_	_
45	Triton	Triton	NNP	_	_	_
46	X-100	x-100	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	followed	follow	VBD	_	_	_
49	of	of	IN	_	_	_
50	a	a	DT	_	_	_
51	5	5	CD	_	_	_
52	min	min	NN	_	_	_
53	incubation	incubation	NN	_	_	_
54	at	at	IN	_	_	_
55	room	room	NN	_	_	_
56	temperature	temperature	NN	_	_	_
57	.	.	.	_	_	_

1	10μl	10μl	NN	_	_	_
2	of	of	IN	_	_	_
3	cOmplete	complete	JJ	_	_	_
4	EDTA	edta	NN	_	_	_
5	free	free	JJ	_	_	_
6	protease	protease	NN	_	_	_
7	inhibitor	inhibitor	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Roche	Roche	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	were	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	and	and	CC	_	_	_
14	incubated	incubate	VBN	_	_	_
15	10	10	CD	_	_	_
16	min	min	NN	_	_	_
17	at	at	IN	_	_	_
18	room	room	NN	_	_	_
19	temperature	temperature	NN	_	_	_
20	.	.	.	_	_	_

1	550μl	550μl	NN	_	_	_
2	of	of	IN	_	_	_
3	ChIP	chip	NN	_	_	_
4	buffer	buffer	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	1.1	1.1	CD	_	_	_
7	%	%	NN	_	_	_
8	Triton	Triton	NNP	_	_	_
9	X-100	x-100	NN	_	_	_
10	,	,	,	_	_	_
11	1.2	1.2	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	EDTA	edta	NN	_	_	_
14	,	,	,	_	_	_
15	16.7	16.7	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	Tris-HCl	tris-hcl	NN	_	_	_
18	,	,	,	_	_	_
19	167mM	167mm	NN	_	_	_
20	NaCl	nacl	NN	_	_	_
21	,	,	,	_	_	_
22	20μl/ml	20μl/ml	NN	_	_	_
23	of	of	IN	_	_	_
24	cOmplete	complete	JJ	_	_	_
25	EDTA	edta	NN	_	_	_
26	free	free	JJ	_	_	_
27	protease	protease	NN	_	_	_
28	inhibitor	inhibitor	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Roche	Roche	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	were	be	VBD	_	_	_
33	added	add	VBN	_	_	_
34	followed	follow	VBN	_	_	_
35	of	of	IN	_	_	_
36	10	10	CD	_	_	_
37	min	min	NN	_	_	_
38	incubation	incubation	NN	_	_	_
39	at	at	IN	_	_	_
40	37ºC	37ºc	NN	_	_	_
41	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	sonicated	sonicate	VBN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	UP200S-Hielscher	up200s-hielscher	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	to	to	TO	_	_	_
10	an	a	DT	_	_	_
11	average	average	JJ	_	_	_
12	size	size	NN	_	_	_
13	between	between	IN	_	_	_
14	300bp	300bp	JJ	_	_	_
15	and	and	CC	_	_	_
16	700bp	700bp	JJ	_	_	_
17	with	with	IN	_	_	_
18	5	5	CD	_	_	_
19	cycles	cycle	NNS	_	_	_
20	of	of	IN	_	_	_
21	and	and	CC	_	_	_
22	amplitude	amplitude	NN	_	_	_
23	of	of	IN	_	_	_
24	55	55	CD	_	_	_
25	%	%	NN	_	_	_
26	,	,	,	_	_	_
27	0.45	0.45	CD	_	_	_
28	sec	sec	NN	_	_	_
29	pulse	pulse	NN	_	_	_
30	during	during	IN	_	_	_
31	10sec	10sec	CD	_	_	_
32	and	and	CC	_	_	_
33	50sec	50sec	CD	_	_	_
34	in	in	IN	_	_	_
35	ice	ice	NN	_	_	_
36	.	.	.	_	_	_

1	Insoluble	insoluble	JJ	_	_	_
2	cell	cell	NN	_	_	_
3	debris	debris	NN	_	_	_
4	were	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	by	by	IN	_	_	_
7	centrifugation	centrifugation	NN	_	_	_
8	at	at	IN	_	_	_
9	20000g	20000g	NN	_	_	_
10	for	for	IN	_	_	_
11	3	3	CD	_	_	_
12	min	min	NN	_	_	_
13	at	at	IN	_	_	_
14	4ºC	4ºc	NN	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	supernatant	supernatant	JJ	_	_	_
18	collected	collect	VBN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	α-Flag-agarose	α-flag-agarose	NN	_	_	_
7	beads	bead	NNS	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Sigma	Sigma	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	and	and	CC	_	_	_
12	incubated	incubate	VBN	_	_	_
13	at	at	IN	_	_	_
14	4ºC	4ºc	NN	_	_	_
15	under	under	IN	_	_	_
16	rotation	rotation	NN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	washed	wash	VBN	_	_	_
6	once	once	RB	_	_	_
7	with	with	IN	_	_	_
8	low	low	JJ	_	_	_
9	salt	salt	NN	_	_	_
10	wash	wash	NN	_	_	_
11	buffer	buffer	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	0.1	0.1	CD	_	_	_
14	%	%	NN	_	_	_
15	SDS	sds	NN	_	_	_
16	,	,	,	_	_	_
17	1	1	CD	_	_	_
18	%	%	NN	_	_	_
19	Triton	Triton	NNP	_	_	_
20	X-100	x-100	NN	_	_	_
21	,	,	,	_	_	_
22	2mM	2mm	NN	_	_	_
23	EDTA	edta	NN	_	_	_
24	,	,	,	_	_	_
25	20mM	20mm	NN	_	_	_
26	Tris-HCl	tris-hcl	NN	_	_	_
27	pH	ph	NN	_	_	_
28	8.1	8.1	CD	_	_	_
29	,	,	,	_	_	_
30	150mM	150mm	NN	_	_	_
31	NaCl	nacl	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	,	,	,	_	_	_
34	once	once	RB	_	_	_
35	with	with	IN	_	_	_
36	high	high	JJ	_	_	_
37	salt	salt	NN	_	_	_
38	wash	wash	NN	_	_	_
39	buffer	buffer	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	0.1	0.1	CD	_	_	_
42	%	%	NN	_	_	_
43	SDS	sds	NN	_	_	_
44	,	,	,	_	_	_
45	1	1	CD	_	_	_
46	%	%	NN	_	_	_
47	Triton	Triton	NNP	_	_	_
48	X-100	x-100	NN	_	_	_
49	,	,	,	_	_	_
50	2mM	2mm	NN	_	_	_
51	EDTA	edta	NN	_	_	_
52	,	,	,	_	_	_
53	20mM	20mm	NN	_	_	_
54	Tris-HCl	tris-hcl	NN	_	_	_
55	pH	ph	NN	_	_	_
56	8.1	8.1	CD	_	_	_
57	,	,	,	_	_	_
58	500mM	500mm	NN	_	_	_
59	NaCl	nacl	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	,	,	,	_	_	_
62	once	once	RB	_	_	_
63	with	with	IN	_	_	_
64	LiCl	licl	NN	_	_	_
65	wash	wash	NN	_	_	_
66	buffer	buffer	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	250mM	250mm	NN	_	_	_
69	LiCl	licl	NN	_	_	_
70	,	,	,	_	_	_
71	1	1	CD	_	_	_
72	%	%	NN	_	_	_
73	NP-40	np-40	NN	_	_	_
74	,	,	,	_	_	_
75	1	1	CD	_	_	_
76	%	%	NN	_	_	_
77	deoxycholate	deoxycholate	NN	SUPP	_	_
78	,	,	,	_	_	_
79	1mM	1mm	NN	_	_	_
80	EDTA	edta	NN	_	_	_
81	,	,	,	_	_	_
82	10mM	10mm	NN	_	_	_
83	Tris-HCl	tris-hcl	NN	_	_	_
84	pH	ph	NN	_	_	_
85	8.1	8.1	CD	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	,	,	,	_	_	_
88	and	and	CC	_	_	_
89	twice	twice	RB	_	_	_
90	with	with	IN	_	_	_
91	TE	te	NN	_	_	_
92	buffer	buffer	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	10mM	10mm	NN	_	_	_
95	Tris-HCl	tris-hcl	NN	_	_	_
96	pH	ph	NN	_	_	_
97	8.1	8.1	CD	_	_	_
98	,	,	,	_	_	_
99	1mM	1mm	NN	_	_	_
100	EDTA	edta	NN	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	washes	wash	VBZ	_	_	_
3	with	with	IN	_	_	_
4	250μl	250μl	NN	_	_	_
5	of	of	IN	_	_	_
6	freshly	freshly	RB	_	_	_
7	prepared	prepared	JJ	_	_	_
8	elution	elution	NN	_	_	_
9	buffer	buffer	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	1	1	CD	_	_	_
12	%	%	NN	_	_	_
13	SDS	sds	NN	_	_	_
14	,	,	,	_	_	_
15	100mM	100mm	NN	_	_	_
16	NaHCO3	nahco3	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	were	be	VBD	_	_	_
19	done	do	VBN	_	_	_
20	followed	follow	VBN	_	_	_
21	by	by	IN	_	_	_
22	vortexing	vortex	VBG	_	_	_
23	and	and	CC	_	_	_
24	incubation	incubation	NN	_	_	_
25	under	under	IN	_	_	_
26	rotation	rotation	NN	_	_	_
27	at	at	IN	_	_	_
28	room	room	NN	_	_	_
29	temperature	temperature	NN	_	_	_
30	for	for	IN	_	_	_
31	15	15	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	reverse	reverse	VB	_	_	_
3	the	the	DT	_	_	_
4	cross-link	cross-link	NN	_	_	_
5	30μl	30μl	NN	_	_	_
6	of	of	IN	_	_	_
7	5M	5m	NN	_	_	_
8	NaCl	nacl	NN	_	_	_
9	were	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	elute	elute	NN	_	_	_
14	and	and	CC	_	_	_
15	incubated	incubate	VBN	_	_	_
16	over	over	IN	_	_	_
17	night	night	NN	_	_	_
18	at	at	IN	_	_	_
19	65ºC	65ºc	NN	_	_	_
20	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	,	,	,	_	_	_
3	4μl	4μl	NN	_	_	_
4	of	of	IN	_	_	_
5	0.5	0.5	CD	_	_	_
6	M	m	NN	_	_	_
7	EDTA	edta	NN	_	_	_
8	,	,	,	_	_	_
9	20μl	20μl	NN	_	_	_
10	of	of	IN	_	_	_
11	1M	1m	NN	_	_	_
12	Tris-HCl	tris-hcl	NN	_	_	_
13	pH	ph	NN	_	_	_
14	6.5	6.5	CD	_	_	_
15	and	and	CC	_	_	_
16	2μl	2μl	CD	_	_	_
17	of	of	IN	_	_	_
18	10mg/ml	10mg/ml	CD	_	_	_
19	Proteinase-K	proteinase-k	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Sigma	Sigma	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	were	be	VBD	_	_	_
24	added	add	VBN	_	_	_
25	and	and	CC	_	_	_
26	the	the	DT	_	_	_
27	suspension	suspension	NN	_	_	_
28	incubated	incubate	VBN	_	_	_
29	at	at	IN	_	_	_
30	45ºC	45ºc	NN	_	_	_
31	for	for	IN	_	_	_
32	2h	2h	NN	_	_	_
33	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	and	and	CC	_	_	_
5	recovered	recover	VBN	_	_	_
6	by	by	IN	_	_	_
7	standard	standard	JJ	_	_	_
8	phenol-chloroform	phenol-chloroform	JJ	_	_	_
9	extraction	extraction	NN	_	_	_
10	and	and	CC	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	precipitation	precipitation	NN	_	_	_
13	with	with	IN	_	_	_
14	20μg	20μg	NN	_	_	_
15	of	of	IN	_	_	_
16	glycogen	glycogen	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	harvested	harvest	VBN	_	_	_
6	by	by	IN	_	_	_
7	centrifugation	centrifugation	NN	_	_	_
8	,	,	,	_	_	_
9	washed	wash	VBN	_	_	_
10	thrice	thrice	RB	_	_	_
11	with	with	IN	_	_	_
12	ice-cold	ice-cold	JJ	_	_	_
13	TBS	tbs	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	pH	ph	NN	_	_	_
16	7.5	7.5	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	resuspended	resuspend	VBN	_	_	_
20	in	in	IN	_	_	_
21	1	1	CD	_	_	_
22	ml	ml	NN	_	_	_
23	lysis	lysis	NN	_	_	_
24	buffer	buffer	NN	_	_	_
25	-LSB-	-lsb-	-LRB-	_	_	_
26	10	10	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	Tris	tris	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	pH	ph	NN	_	_	_
31	8.0	8.0	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	,	,	,	_	_	_
34	20	20	CD	_	_	_
35	%	%	NN	_	_	_
36	sucrose	sucrose	NN	_	_	_
37	,	,	,	_	_	_
38	50	50	CD	_	_	_
39	mM	mm	NN	KWSUPP	_	_
40	NaCl	nacl	NN	_	_	_
41	,	,	,	_	_	_
42	10	10	CD	_	_	_
43	mM	mm	NN	KWSUPP	_	_
44	EDTA	edta	NN	_	_	_
45	,	,	,	_	_	_
46	20	20	CD	_	_	_
47	mg/ml	mg/ml	NN	_	_	_
48	lysozyme	lysozyme	NN	_	_	_
49	and	and	CC	_	_	_
50	0.1	0.1	CD	_	_	_
51	mg/ml	mg/ml	NN	_	_	_
52	RNase	rnase	NN	_	_	_
53	A	a	NN	_	_	_
54	-RSB-	-rsb-	-RRB-	_	_	_
55	and	and	CC	_	_	_
56	incubated	incubate	VBN	_	_	_
57	at	at	IN	_	_	_
58	37	37	CD	_	_	_
59	°C	°c	NN	_	_	_
60	for	for	IN	_	_	_
61	30	30	CD	_	_	_
62	min	min	NN	_	_	_
63	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	lysis	lysis	NN	_	_	_
3	,	,	,	_	_	_
4	3	3	CD	_	_	_
5	ml	ml	NN	_	_	_
6	immunoprecipitation	immunoprecipitation	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	IP	IP	NNP	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LSB-	-lsb-	-LRB-	_	_	_
12	50	50	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	HEPES	hepe	NNS	_	_	_
15	--	--	:	_	_	_
16	KOH	koh	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	pH	ph	NN	_	_	_
19	7.5	7.5	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	150	150	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	NaCl	nacl	NN	_	_	_
25	,	,	,	_	_	_
26	1	1	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	EDTA	edta	NN	_	_	_
29	,	,	,	_	_	_
30	1	1	CD	_	_	_
31	%	%	NN	_	_	_
32	Triton	Triton	NNP	_	_	_
33	X-100	x-100	NN	_	_	_
34	,	,	,	_	_	_
35	0.1	0.1	CD	_	_	_
36	%	%	NN	_	_	_
37	sodium	sodium	NN	_	_	_
38	deoxycholate	deoxycholate	NN	SUPP	_	_
39	,	,	,	_	_	_
40	0.1	0.1	CD	_	_	_
41	%	%	NN	_	_	_
42	sodium	sodium	NN	_	_	_
43	dodecyl	dodecyl	NN	_	_	_
44	sulphate	sulphate	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	SDS	sds	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	and	and	CC	_	_	_
49	PMSF	pmsf	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	final	final	JJ	_	_	_
52	1	1	CD	_	_	_
53	mM	mm	NN	KWSUPP	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	-RSB-	-rsb-	-RRB-	_	_	_
56	was	be	VBD	_	_	_
57	added	add	VBN	_	_	_
58	and	and	CC	_	_	_
59	the	the	DT	_	_	_
60	DNA	dna	NN	_	_	_
61	sheared	shear	VBD	_	_	_
62	to	to	TO	_	_	_
63	an	a	DT	_	_	_
64	average	average	JJ	_	_	_
65	size	size	NN	_	_	_
66	of	of	IN	_	_	_
67	~	~	NN	_	_	_
68	250	250	CD	_	_	_
69	bp	bp	NN	_	_	_
70	using	use	VBG	_	_	_
71	a	a	DT	_	_	_
72	Bioruptor	bioruptor	NN	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	Diagenode	diagenode	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	.	.	.	_	_	_

1	Insoluble	insoluble	JJ	_	_	_
2	cellular	cellular	JJ	_	_	_
3	matter	matter	NN	_	_	_
4	was	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	by	by	IN	_	_	_
7	centrifugation	centrifugation	NN	_	_	_
8	for	for	IN	_	_	_
9	10	10	CD	_	_	_
10	min	min	NN	_	_	_
11	at	at	IN	_	_	_
12	4	4	CD	_	_	_
13	°C	°c	NN	_	_	_
14	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	800	800	CD	_	_	_
3	μl	μl	NN	_	_	_
4	aliquot	aliquot	NN	_	_	_
5	was	be	VBD	_	_	_
6	incubated	incubate	VBN	_	_	_
7	with	with	IN	_	_	_
8	20	20	CD	_	_	_
9	μl	μl	NN	_	_	_
10	Protein	protein	NN	_	_	_
11	A/G	a/g	NN	_	_	_
12	UltraLink	UltraLink	NNP	_	_	_
13	Resin	Resin	NNP	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Pierce	Pierce	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	on	on	IN	_	_	_
18	a	a	DT	_	_	_
19	rotary	rotary	JJ	_	_	_
20	shaker	shaker	NN	_	_	_
21	for	for	IN	_	_	_
22	45	45	CD	_	_	_
23	minutes	minute	NNS	_	_	_
24	at	at	IN	_	_	_
25	room	room	NN	_	_	_
26	temperature	temperature	NN	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	and	and	CC	_	_	_
6	incubated	incubate	VBN	_	_	_
7	with	with	IN	_	_	_
8	mouse	mouse	NN	_	_	_
9	monoclonal	monoclonal	JJ	_	_	_
10	antibody	antibody	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	and	and	CC	_	_	_
4	30	30	CD	_	_	_
5	μl	μl	NN	_	_	_
6	Protein	protein	NN	_	_	_
7	A/G	a/g	NN	_	_	_
8	UltraLink	UltraLink	NNP	_	_	_
9	Resin	Resin	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	pre-incubated	pre-incubated	JJ	_	_	_
12	with	with	IN	_	_	_
13	1mg/ml	1mg/ml	JJ	_	_	_
14	BSA	bsa	NN	_	_	_
15	in	in	IN	_	_	_
16	TBS	tbs	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	on	on	IN	_	_	_
20	a	a	DT	_	_	_
21	rotary	rotary	JJ	_	_	_
22	shaker	shaker	NN	_	_	_
23	at	at	IN	_	_	_
24	room	room	NN	_	_	_
25	temperature	temperature	NN	_	_	_
26	for	for	IN	_	_	_
27	90	90	CD	_	_	_
28	min	min	NN	_	_	_
29	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	once	once	RB	_	_	_
5	with	with	IN	_	_	_
6	IP	IP	NNP	_	_	_
7	buffer	buffer	NN	_	_	_
8	,	,	,	_	_	_
9	twice	twice	RB	_	_	_
10	with	with	IN	_	_	_
11	IP	IP	NNP	_	_	_
12	buffer	buffer	NN	_	_	_
13	+	+	CC	_	_	_
14	500	500	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	NaCl	nacl	NN	_	_	_
17	,	,	,	_	_	_
18	once	once	RB	_	_	_
19	with	with	IN	_	_	_
20	wash	wash	NN	_	_	_
21	buffer	buffer	NN	_	_	_
22	-LSB-	-lsb-	-LRB-	_	_	_
23	10	10	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	Tris	tris	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	pH	ph	NN	_	_	_
28	8.0	8.0	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	250	250	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	LiCl	licl	NN	_	_	_
34	,	,	,	_	_	_
35	1	1	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	EDTA	edta	NN	_	_	_
38	,	,	,	_	_	_
39	0.5	0.5	CD	_	_	_
40	%	%	NN	_	_	_
41	Nonidet	Nonidet	NNP	_	_	_
42	P-40	P-40	NNP	_	_	_
43	and	and	CC	_	_	_
44	0.5	0.5	CD	_	_	_
45	%	%	NN	_	_	_
46	sodium	sodium	NN	_	_	_
47	deoxycholate	deoxycholate	NN	SUPP	_	_
48	-RSB-	-rsb-	-RRB-	_	_	_
49	and	and	CC	_	_	_
50	once	once	RB	_	_	_
51	with	with	IN	_	_	_
52	TE	te	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	pH	ph	NN	_	_	_
55	7.5	7.5	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	.	.	.	_	_	_

1	Immunoprecipitated	immunoprecipitate	VBN	_	_	_
2	complexes	complex	NNS	_	_	_
3	were	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	in	in	IN	_	_	_
6	100	100	CD	_	_	_
7	μl	μl	NN	_	_	_
8	elution	elution	NN	_	_	_
9	buffer	buffer	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	10	10	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	Tris	tris	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	pH	ph	NN	_	_	_
16	7.5	7.5	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	10	10	CD	_	_	_
20	mM	mm	NN	KWSUPP	_	_
21	EDTA	edta	NN	_	_	_
22	and	and	CC	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	SDS	sds	NN	_	_	_
26	-RSB-	-rsb-	-RRB-	_	_	_
27	at	at	IN	_	_	_
28	65	65	CD	_	_	_
29	°C	°c	NN	_	_	_
30	for	for	IN	_	_	_
31	20	20	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

1	Immunoprecipitated	immunoprecipitate	VBN	_	_	_
2	samples	sample	NNS	_	_	_
3	and	and	CC	_	_	_
4	the	the	DT	_	_	_
5	sheared	sheared	JJ	_	_	_
6	DNA	dna	NN	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	Bioruptor	Bioruptor	NNP	_	_	_
10	were	be	VBD	_	_	_
11	uncrosslinked	uncrosslinked	JJ	_	_	_
12	in	in	IN	_	_	_
13	elution	elution	NN	_	_	_
14	buffer	buffer	NN	_	_	_
15	containing	contain	VBG	_	_	_
16	0.8	0.8	CD	_	_	_
17	mg/ml	mg/ml	NN	_	_	_
18	Pronase	Pronase	NNP	_	_	_
19	at	at	IN	_	_	_
20	42	42	CD	_	_	_
21	°C	°c	NN	_	_	_
22	for	for	IN	_	_	_
23	2	2	CD	_	_	_
24	h	h	NN	_	_	_
25	followed	follow	VBN	_	_	_
26	by	by	IN	_	_	_
27	65	65	CD	_	_	_
28	°C	°c	NN	_	_	_
29	for	for	IN	_	_	_
30	6	6	CD	_	_	_
31	h.	h.	NN	_	_	_
32	DNA	dna	NN	_	_	_
33	was	be	VBD	_	_	_
34	purified	purify	VBN	_	_	_
35	using	use	VBG	_	_	_
36	the	the	DT	_	_	_
37	phenol-chloroform	phenol-chloroform	JJ	_	_	_
38	method	method	NN	_	_	_
39	.	.	.	_	_	_

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	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	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	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	NN	_	_	_
2	Crosslinked/reversed	crosslinked/reversed	VBD	_	_	_
3	DNA	dna	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Crosslinking	crosslinking	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	using	use	VBG	_	_	_
9	1	1	CD	_	_	_
10	%	%	NN	_	_	_
11	of	of	IN	_	_	_
12	forlmaldehyde	forlmaldehyde	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	crp.ee.chipseq	crp.ee.chipseq	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	crp.ee.input	crp.ee.input	JJ	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	crpfis.rep1.ee	crpfis.rep1.ee	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	crpfis.rep1.me	crpfis.rep1.me	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	crpfis.rep2.ee	crpfis.rep2.ee	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	crpfis.rep2.me	crpfis.rep2.me	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	crp.me.chipseq	crp.me.chipseq	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	crp.me	crp.me	NN	_	_	_
29	,	,	,	_	_	_
30	input	input	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	crp.me.input	crp.me.input	JJ	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	crpmutant.fis.ee.chipseq	crpmutant.fis.ee.chipseq	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	crpmutant.fis.ee.input	crpmutant.fis.ee.input	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	crpmutant.fis.me.chipseq	crpmutant.fis.me.chipseq	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	crpmutant.fis.me.input	crpmutant.fis.me.input	JJ	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	crp.rep1.ee	crp.rep1.ee	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	crp.rep1.me	crp.rep1.me	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	crp.rep2.ee	crp.rep2.ee	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	crp.rep2.me	crp.rep2.me	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	crp	crp	VBP	GEN	_	_
51	___	___	CD	_	_	_
52	U	U	NNP	_	_	_
53	_	_	NNP	_	_	_
54	N0075	N0075	NNP	_	_	_
55	_	_	VBD	_	_	_
56	r1	r1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	crp	crp	VBP	GEN	_	_
59	___	___	CD	_	_	_
60	U	U	NNP	_	_	_
61	_	_	NNP	_	_	_
62	N0075	N0075	NNP	_	_	_
63	_	_	VBD	_	_	_
64	r2	r2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
66	crp	crp	VBP	GEN	_	_
67	___	___	CD	_	_	_
68	U	U	NNP	_	_	_
69	_	_	NNP	_	_	_
70	N0075	N0075	NNP	_	_	_
71	_	_	SYM	_	_	_
72	r3	r3	FW	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
74	crp	crp	NN	GEN	_	_
75	upregulation	upregulation	NN	_	_	_
76	,	,	,	_	_	_
77	0.075	0.075	CD	_	_	_
78	ug/ml	ug/ml	NN	_	_	_
79	norfloxacin	norfloxacin	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	CSH50	csh50	NN	_	_	_
82	control	control	NN	_	_	_
83	E-minimal	e-minimal	JJ	_	_	_
84	medium	medium	NN	_	_	_
85	90	90	CD	_	_	_
86	min	min	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	CSH50	csh50	NN	_	_	_
89	control	control	NN	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	mock	mock	JJ	_	_	_
92	igG	igg	NN	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	E-minimal	e-minimal	JJ	_	_	_
95	medium	medium	NN	_	_	_
96	replicate	replicate	VB	_	_	_
97	1	1	CD	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	CSH50	csh50	NN	_	_	_
100	control	control	NN	_	_	_
101	-LRB-	-lrb-	-LRB-	_	_	_
102	mock	mock	JJ	_	_	_
103	igG	igg	NN	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	E-minimal	e-minimal	JJ	_	_	_
106	medium	medium	NN	_	_	_
107	replicate	replicate	VB	_	_	_
108	2	2	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
110	CSH50	csh50	NN	_	_	_
111	E-minimal	e-minimal	JJ	_	_	_
112	medium	medium	NN	_	_	_
113	pH	ph	NN	_	_	_
114	4.5	4.5	CD	_	_	_
115	90	90	CD	_	_	_
116	min	min	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	CSH50	csh50	NN	_	_	_
119	E-minimal	e-minimal	JJ	_	_	_
120	medium	medium	NN	_	_	_
121	pH	ph	NN	_	_	_
122	4.5	4.5	CD	_	_	_
123	90	90	CD	_	_	_
124	min	min	NN	_	_	_
125	replicate	replicate	VBP	_	_	_
126	1	1	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	CSH50	csh50	NN	_	_	_
129	E-minimal	e-minimal	JJ	_	_	_
130	medium	medium	NN	_	_	_
131	pH	ph	NN	_	_	_
132	4.5	4.5	CD	_	_	_
133	90	90	CD	_	_	_
134	min	min	NN	_	_	_
135	replicate	replicate	VBP	_	_	_
136	2	2	CD	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
138	CSH50	csh50	NN	_	_	_
139	E-minimal	e-minimal	JJ	_	_	_
140	medium	medium	NN	_	_	_
141	pH	ph	NN	_	_	_
142	4.5	4.5	CD	_	_	_
143	90	90	CD	_	_	_
144	min	min	NN	_	_	_
145	replicate	replicate	VBP	_	_	_
146	3	3	CD	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	CSH50	csh50	NN	_	_	_
149	E-minimal	e-minimal	JJ	_	_	_
150	medium	medium	NN	_	_	_
151	pH	ph	NN	_	_	_
152	7	7	CD	_	_	_
153	90	90	CD	_	_	_
154	min	min	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	CSH50	csh50	NN	_	_	_
157	E-minimal	e-minimal	JJ	_	_	_
158	medium	medium	NN	_	_	_
159	pH	ph	NN	_	_	_
160	7	7	CD	_	_	_
161	90	90	CD	_	_	_
162	min	min	NN	_	_	_
163	replicate	replicate	VBP	_	_	_
164	1	1	CD	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	CSH50	csh50	NN	_	_	_
167	E-minimal	e-minimal	JJ	_	_	_
168	medium	medium	NN	_	_	_
169	pH	ph	NN	_	_	_
170	7	7	CD	_	_	_
171	90	90	CD	_	_	_
172	min	min	NN	_	_	_
173	replicate	replicate	VBP	_	_	_
174	2	2	CD	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
176	CSH50	csh50	NN	_	_	_
177	E-minimal	e-minimal	JJ	_	_	_
178	medium	medium	NN	_	_	_
179	pH	ph	NN	_	_	_
180	7	7	CD	_	_	_
181	90	90	CD	_	_	_
182	min	min	NN	_	_	_
183	replicate	replicate	VBP	_	_	_
184	3	3	CD	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
186	CsiR	csir	NN	TF	_	_
187	_	_	CD	_	_	_
188	ChIPSeq	chipseq	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
190	CsiR	csir	NN	TF	_	_
191	_	_	CD	_	_	_
192	RNASeq	rnaseq	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	cspF	cspf	NN	GEN	_	_
195	__	__	CD	_	_	_
196	U	U	NNP	_	_	_
197	_	_	NNP	_	_	_
198	N0075	N0075	NNP	_	_	_
199	_	_	VBD	_	_	_
200	r1	r1	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	cspF	cspf	NN	GEN	_	_
203	__	__	CD	_	_	_
204	U	U	NNP	_	_	_
205	_	_	NNP	_	_	_
206	N0075	N0075	NNP	_	_	_
207	_	_	VBD	_	_	_
208	r2	r2	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	cspF	cspf	NN	GEN	_	_
211	__	__	CD	_	_	_
212	U	U	NNP	_	_	_
213	_	_	NNP	_	_	_
214	N0075	N0075	NNP	_	_	_
215	_	_	SYM	_	_	_
216	r3	r3	FW	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
218	cspF	cspf	NN	GEN	_	_
219	upregulation	upregulation	NN	_	_	_
220	,	,	,	_	_	_
221	0.075	0.075	CD	_	_	_
222	ug/ml	ug/ml	NN	_	_	_
223	norfloxacin	norfloxacin	NN	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
225	csv	csv	VBP	_	_	_
226	files	file	NNS	_	_	_
227	contain	contain	VBP	_	_	_
228	16	16	CD	_	_	_
229	columns	column	NNS	_	_	_
230	of	of	IN	_	_	_
231	the	the	DT	_	_	_
232	data	datum	NNS	_	_	_
233	,	,	,	_	_	_
234	each	each	DT	_	_	_
235	pair	pair	NN	_	_	_
236	corresponds	correspond	VBZ	_	_	_
237	to	to	TO	_	_	_
238	the	the	DT	_	_	_
239	counts	count	NNS	_	_	_
240	from	from	IN	_	_	_
241	the	the	DT	_	_	_
242	top	top	NN	_	_	_
243	-LRB-	-lrb-	-LRB-	_	_	_
244	odd	odd	JJ	_	_	_
245	numbers	number	NNS	_	_	_
246	-RRB-	-rrb-	-RRB-	_	_	_
247	and	and	CC	_	_	_
248	bottom	bottom	NN	_	_	_
249	-LRB-	-lrb-	-LRB-	_	_	_
250	even	even	RB	_	_	_
251	numbers	number	NNS	_	_	_
252	-RRB-	-rrb-	-RRB-	_	_	_
253	strand	strand	NN	_	_	_
254	.	.	.	_	_	_

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	ctrl1	ctrl1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	ctrl2	ctrl2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	ctrl3	ctrl3	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	cultivation	cultivation	NN	_	_	_
9	:	:	:	_	_	_
10	continuous	continuous	JJ	_	_	_
11	cultivation	cultivation	NN	_	_	_
12	,	,	,	_	_	_
13	A-stat	a-stat	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	cultivation	cultivation	NN	_	_	_
16	:	:	:	_	_	_
17	continuous	continuous	JJ	_	_	_
18	cultivation	cultivation	NN	_	_	_
19	,	,	,	_	_	_
20	chemostat	chemostat	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	culture	culture	NN	_	_	_
23	:	:	:	_	_	_
24	18	18	CD	_	_	_
25	h	h	NN	_	_	_
26	at	at	IN	_	_	_
27	37	37	CD	_	_	_
28	°C	°c	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Culture	culture	NN	_	_	_
31	cells	cell	NNS	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
33	culture	culture	NN	_	_	_
34	condition	condition	NN	_	_	_
35	:	:	:	_	_	_
36	Aerobic	aerobic	JJ	_	_	_
37	cultures	culture	NNS	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
39	culture	culture	NN	_	_	_
40	condition	condition	NN	_	_	_
41	:	:	:	_	_	_
42	Anaerobic	anaerobic	JJ	_	_	_
43	cultures	culture	NNS	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
45	culture	culture	NN	_	_	_
46	condition	condition	NN	_	_	_
47	:	:	:	_	_	_
48	Anaerobic	anaerobic	JJ	_	_	_
49	Cultures	culture	NNS	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
51	culture	culture	NN	_	_	_
52	condition	condition	NN	_	_	_
53	:	:	:	_	_	_
54	anaerobic	anaerobic	JJ	_	_	_
55	fermentive	fermentive	JJ	_	_	_
56	condition	condition	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	culture	culture	NN	_	_	_
59	condition	condition	NN	_	_	_
60	:	:	:	_	_	_
61	nitrate	nitrate	VB	SUPP	_	_
62	respiratory	respiratory	JJ	_	_	_
63	condition	condition	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Culture	culture	NN	_	_	_
66	conditions	condition	NNS	_	_	_
67	:	:	:	_	_	_
68	37	37	CD	_	_	_
69	C	c	NN	_	_	_
70	with	with	IN	_	_	_
71	shaking	shake	VBG	_	_	_
72	at	at	IN	_	_	_
73	220	220	CD	_	_	_
74	RPM	rpm	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	culture	culture	NN	_	_	_
77	conditions	condition	NNS	_	_	_
78	:	:	:	_	_	_
79	aerobic	aerobic	JJ	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	culture	culture	NN	_	_	_
82	conditions	condition	NNS	_	_	_
83	:	:	:	_	_	_
84	anaerobic	anaerobic	JJ	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	Cultured	culture	VBN	_	_	_
87	cells	cell	NNS	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
89	Cultured	culture	VBN	_	_	_
90	cells	cell	NNS	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	50	50	CD	_	_	_
93	mL	ml	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	were	be	VBD	_	_	_
96	cross-linked	cross-link	VBN	_	_	_
97	with	with	IN	_	_	_
98	1	1	CD	_	_	_
99	%	%	NN	_	_	_
100	formaldehyde	formaldehyde	NN	_	_	_
101	at	at	IN	_	_	_
102	room	room	NN	_	_	_
103	temperature	temperature	NN	_	_	_
104	for	for	IN	_	_	_
105	30	30	CD	_	_	_
106	min	min	NN	_	_	_
107	and	and	CC	_	_	_
108	added	add	VBD	_	_	_
109	2	2	CD	_	_	_
110	mL	ml	NN	_	_	_
111	of	of	IN	_	_	_
112	2.5	2.5	CD	_	_	_
113	M	m	NN	_	_	_
114	glycine	glycine	NN	_	_	_
115	to	to	TO	_	_	_
116	quench	quench	VB	_	_	_
117	the	the	DT	_	_	_
118	unused	unused	JJ	_	_	_
119	formaldehyde	formaldehyde	NN	_	_	_
120	.	.	.	_	_	_

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/mL	μg/ml	NN	_	_	_
47	RNaseA	rnasea	NN	_	_	_
48	,	,	,	_	_	_
49	protease	protease	NN	_	_	_
50	inhibitor	inhibitor	NN	_	_	_
51	cocktail	cocktail	NN	_	_	_
52	and	and	CC	_	_	_
53	1	1	CD	_	_	_
54	kU	ku	NN	_	_	_
55	Ready-Lyse	ready-lyse	NN	_	_	_
56	lysozyme	lysozyme	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	Epicentre	Epicentre	NNP	_	_	_
59	,	,	,	_	_	_
60	Madison	Madison	NNP	_	_	_
61	,	,	,	_	_	_
62	WI	WI	NNP	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	and	and	CC	_	_	_
65	incubated	incubate	VBN	_	_	_
66	at	at	IN	_	_	_
67	37oC	37oc	NN	_	_	_
68	for	for	IN	_	_	_
69	30	30	CD	_	_	_
70	min	min	NN	_	_	_
71	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	0.5	0.5	CD	_	_	_
8	mL	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	2	2	CD	_	_	_
11	×	×	CD	_	_	_
12	IP	IP	NNP	_	_	_
13	buffer	buffer	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	100	100	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	Tris-HCl	tris-hcl	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	pH	ph	NN	_	_	_
20	7.5	7.5	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	100	100	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	NaCl	nacl	NN	_	_	_
26	,	,	,	_	_	_
27	1	1	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	EDTA	edta	NN	_	_	_
30	,	,	,	_	_	_
31	2	2	CD	_	_	_
32	%	%	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	v/v	v/v	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	Triton	Triton	NNP	_	_	_
37	X-100	x-100	NN	_	_	_
38	,	,	,	_	_	_
39	and	and	CC	_	_	_
40	protease	protease	NN	_	_	_
41	inhibitor	inhibitor	NN	_	_	_
42	cocktail	cocktail	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	,	,	,	_	_	_
45	followed	follow	VBN	_	_	_
46	by	by	IN	_	_	_
47	incubation	incubation	NN	_	_	_
48	on	on	IN	_	_	_
49	ice	ice	NN	_	_	_
50	for	for	IN	_	_	_
51	30	30	CD	_	_	_
52	min	min	NN	_	_	_
53	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	sonicated	sonicate	VBN	_	_	_
6	in	in	IN	_	_	_
7	an	a	DT	_	_	_
8	ice	ice	NN	_	_	_
9	bath	bath	NN	_	_	_
10	using	use	VBG	_	_	_
11	Sonic	Sonic	NNP	_	_	_
12	Dismembrator	Dismembrator	NNP	_	_	_
13	Model	Model	NNP	_	_	_
14	500	500	CD	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	four	four	CD	_	_	_
17	times	time	NNS	_	_	_
18	for	for	IN	_	_	_
19	20	20	CD	_	_	_
20	s	s	NNS	_	_	_
21	each	each	DT	_	_	_
22	,	,	,	_	_	_
23	output	output	NN	_	_	_
24	level	level	NN	_	_	_
25	,	,	,	_	_	_
26	2.5	2.5	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	Size	size	NN	_	_	_
2	distribution	distribution	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	fragmented	fragmented	JJ	_	_	_
6	DNAs	dna	NNS	_	_	_
7	was	be	VBD	_	_	_
8	confirmed	confirm	VBN	_	_	_
9	using	use	VBG	_	_	_
10	agarose	agarose	NN	_	_	_
11	gel	gel	NN	_	_	_
12	electrophoresis	electrophoresis	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	200-400	200-400	CD	_	_	_
15	bp	bp	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	after	after	IN	_	_	_
18	removing	remove	VBG	_	_	_
19	cell	cell	NN	_	_	_
20	debris	debris	NN	_	_	_
21	by	by	IN	_	_	_
22	centrifugation	centrifugation	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	denity	denity	NN	_	_	_
4	:	:	:	_	_	_
5	OD600	od600	NN	_	_	_
6	=	=	JJ	_	_	_
7	0.55-0.6	0.55-0.6	CD	_	_	_
8	culture	culture	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	cultured	culture	VBN	_	_	_
11	in	in	IN	_	_	_
12	:	:	:	_	_	_
13	M9	m9	NN	MED	_	_
14	minimal	minimal	JJ	MED	_	_
15	media	media	NNS	MED	_	_
16	with	with	IN	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	acetate	acetate	NN	SUPP	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	cultured	culture	VBN	_	_	_
22	in	in	IN	_	_	_
23	:	:	:	_	_	_
24	M9	m9	NN	MED	_	_
25	minimal	minimal	JJ	MED	_	_
26	media	media	NNS	MED	_	_
27	with	with	IN	_	_	_
28	0.2	0.2	CD	_	_	_
29	%	%	NN	_	_	_
30	fructose	fructose	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	cultured	culture	VBN	_	_	_
33	in	in	IN	_	_	_
34	:	:	:	_	_	_
35	M9	m9	NN	MED	_	_
36	minimal	minimal	JJ	MED	_	_
37	media	media	NNS	MED	_	_
38	with	with	IN	_	_	_
39	0.2	0.2	CD	_	_	_
40	%	%	NN	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Culture	culture	NN	_	_	_
44	grown	grow	VBN	_	_	_
45	in	in	IN	_	_	_
46	14	14	CD	_	_	_
47	ml	ml	NN	_	_	_
48	tube	tube	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Culture	culture	NN	_	_	_
51	grown	grow	VBN	_	_	_
52	in	in	IN	_	_	_
53	250	250	CD	_	_	_
54	ml	ml	NN	_	_	_
55	Erlenmeyer	erlenmeyer	NN	_	_	_
56	flask	flask	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	culture/growth	culture/growth	NN	_	_	_
59	condition	condition	NN	_	_	_
60	:	:	:	_	_	_
61	Heatshock	Heatshock	NNP	_	_	_
62	15	15	CD	_	_	_
63	min	min	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	culture/growth	culture/growth	NN	_	_	_
66	condition	condition	NN	_	_	_
67	:	:	:	_	_	_
68	Heatshock	heatshock	NN	_	_	_
69	30	30	CD	_	_	_
70	min	min	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	culture/growth	culture/growth	NN	_	_	_
73	condition	condition	NN	_	_	_
74	:	:	:	_	_	_
75	Heatshock	heatshock	NN	_	_	_
76	60	60	CD	_	_	_
77	min	min	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	culture/growth	culture/growth	NN	_	_	_
80	condition	condition	NN	_	_	_
81	:	:	:	_	_	_
82	LB	lb	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	OD	od	NN	_	_	_
85	=	=	JJ	_	_	_
86	0.87	0.87	CD	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	culture/growth	culture/growth	NN	_	_	_
90	condition	condition	NN	_	_	_
91	:	:	:	_	_	_
92	MOPS-P	mops-p	NN	_	_	_
93	0h	0h	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	culture/growth	culture/growth	NN	_	_	_
96	condition	condition	NN	_	_	_
97	:	:	:	_	_	_
98	MOPS-P	mops-p	NN	_	_	_
99	2h	2h	JJ	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	culture/growth	culture/growth	NN	_	_	_
102	condition	condition	NN	_	_	_
103	:	:	:	_	_	_
104	MOPS-P	mops-p	NN	_	_	_
105	4h	4h	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	culture	culture	NN	_	_	_
108	media	media	NNS	_	_	_
109	:	:	:	_	_	_
110	10	10	CD	_	_	_
111	%	%	NN	_	_	_
112	Luria	Luria	NNP	MED	_	_
113	broth	broth	NN	MED	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	culture	culture	NN	_	_	_
116	media	media	NNS	_	_	_
117	:	:	:	_	_	_
118	LB	lb	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	culture	culture	NN	_	_	_
121	media	media	NNS	_	_	_
122	:	:	:	_	_	_
123	LB	lb	NN	_	_	_
124	with	with	IN	_	_	_
125	2.5	2.5	CD	_	_	_
126	mM	mm	NN	KWSUPP	_	_
127	Fumaric	fumaric	JJ	_	_	_
128	acid	acid	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	Culture	culture	NN	_	_	_
131	of	of	IN	_	_	_
132	bacterial	bacterial	JJ	_	_	_
133	strains	strain	NNS	_	_	_
134	-LRB-	-lrb-	-LRB-	_	_	_
135	10	10	CD	_	_	_
136	mL	ml	NN	_	_	_
137	-RRB-	-rrb-	-RRB-	_	_	_
138	were	be	VBD	_	_	_
139	centrifuged	centrifuge	VBN	_	_	_
140	20	20	CD	_	_	_
141	min	min	NN	_	_	_
142	at	at	IN	_	_	_
143	10,000	10,000	CD	_	_	_
144	g	g	NN	_	_	_
145	and	and	CC	_	_	_
146	bacterial	bacterial	JJ	_	_	_
147	pellets	pellet	NNS	_	_	_
148	were	be	VBD	_	_	_
149	washed	wash	VBN	_	_	_
150	3	3	CD	_	_	_
151	times	time	NNS	_	_	_
152	with	with	IN	_	_	_
153	2	2	CD	_	_	_
154	mL	ml	NN	_	_	_
155	of	of	IN	_	_	_
156	phosphate	phosphate	NN	_	_	_
157	buffered	buffer	VBN	_	_	_
158	saline	saline	NN	_	_	_
159	-LRB-	-lrb-	-LRB-	_	_	_
160	PBS	PBS	NNP	_	_	_
161	-RRB-	-rrb-	-RRB-	_	_	_
162	.	.	.	_	_	_

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/mL	mg/ml	NN	_	_	_
24	,	,	,	_	_	_
25	Invitrogen	Invitrogen	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grinded	grind	VBN	_	_	_
6	3	3	CD	_	_	_
7	min	min	NN	_	_	_
8	with	with	IN	_	_	_
9	~	~	NN	_	_	_
10	100	100	CD	_	_	_
11	mg	mg	NN	_	_	_
12	of	of	IN	_	_	_
13	0.1	0.1	CD	_	_	_
14	mm	mm	NN	_	_	_
15	zirconia	zirconia	NN	_	_	_
16	beads	bead	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	BioSpec	BioSpec	NNP	_	_	_
19	Products	Products	NNPS	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	using	use	VBG	_	_	_
22	the	the	DT	_	_	_
23	model	model	NN	_	_	_
24	MM2000	mm2000	NN	_	_	_
25	BeadBeater	beadbeater	NN	_	_	_
26	instrument	instrument	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Retsch	retsch	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	Concentration	concentration	NN	_	_	_
2	and	and	CC	_	_	_
3	quality	quality	NN	_	_	_
4	of	of	IN	_	_	_
5	isolated	isolate	VBN	_	_	_
6	gDNA	gdna	NN	_	_	_
7	were	be	VBD	_	_	_
8	checked	check	VBN	_	_	_
9	with	with	IN	_	_	_
10	the	the	DT	_	_	_
11	spectrophotometer	spectrophotometer	NN	_	_	_
12	Nanodrop	Nanodrop	NNP	_	_	_
13	1000	1000	CD	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Thermo	Thermo	NNP	_	_	_
16	Fisher	Fisher	NNP	_	_	_
17	Scientific	Scientific	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Their	they	PRP$	_	_	_
2	integrity	integrity	NN	_	_	_
3	was	be	VBD	_	_	_
4	verified	verify	VBN	_	_	_
5	by	by	IN	_	_	_
6	1	1	CD	_	_	_
7	%	%	NN	_	_	_
8	agarose	agarose	NN	_	_	_
9	gel	gel	NN	_	_	_
10	electrophoresis	electrophoresis	NN	_	_	_
11	.	.	.	_	_	_

1	gDNA	gdna	NN	_	_	_
2	were	be	VBD	_	_	_
3	kept	keep	VBN	_	_	_
4	at	at	IN	_	_	_
5	-20	-20	CD	_	_	_
6	°C	°c	NN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	+	+	CC	_	_	_
5	A	a	DT	_	_	_
6	and	and	CC	_	_	_
7	-	-	:	_	_	_
8	A	a	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	were	be	VBD	_	_	_
11	incubated	incubate	VBN	_	_	_
12	at	at	IN	_	_	_
13	32	32	CD	_	_	_
14	°C	°c	NN	_	_	_
15	with	with	IN	_	_	_
16	shaking	shake	VBG	_	_	_
17	for	for	IN	_	_	_
18	additional	additional	JJ	_	_	_
19	15	15	CD	_	_	_
20	min	min	NN	_	_	_
21	,	,	,	_	_	_
22	then	then	RB	_	_	_
23	cells	cell	NNS	_	_	_
24	were	be	VBD	_	_	_
25	pelleted	pellete	VBN	_	_	_
26	by	by	IN	_	_	_
27	centrifugation	centrifugation	NN	_	_	_
28	at	at	IN	_	_	_
29	10	10	CD	_	_	_
30	°C	°c	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	4500xg	4500xg	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	and	and	CC	_	_	_
35	resuspended	resuspend	VBN	_	_	_
36	in	in	IN	_	_	_
37	10	10	CD	_	_	_
38	ml	ml	NN	_	_	_
39	of	of	IN	_	_	_
40	TES	tes	NN	_	_	_
41	buffer	buffer	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	10	10	CD	_	_	_
44	mM	mm	NN	KWSUPP	_	_
45	Tris-Cl	tris-cl	NN	_	_	_
46	pH7	ph7	NN	_	_	_
47	.5	.5	CD	_	_	_
48	,	,	,	_	_	_
49	1	1	CD	_	_	_
50	mM	mm	NN	KWSUPP	_	_
51	EDTA	edta	NN	_	_	_
52	,	,	,	_	_	_
53	250	250	CD	_	_	_
54	mM	mm	NN	KWSUPP	_	_
55	NaCl	nacl	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	.	.	.	_	_	_

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	NNP	_	_	_
2	Culture	culture	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	for	for	IN	_	_	_
5	microarray	microarray	NN	_	_	_
6	analysis	analysis	NN	_	_	_
7	were	be	VBD	_	_	_
8	added	add	VBN	_	_	_
9	to	to	TO	_	_	_
10	ice-cold	ice-cold	JJ	_	_	_
11	5	5	CD	_	_	_
12	%	%	NN	_	_	_
13	water-saturated	water-saturated	JJ	_	_	_
14	phenol	phenol	NN	_	_	_
15	in	in	IN	_	_	_
16	ethanol	ethanol	NN	_	_	_
17	solution	solution	NN	_	_	_
18	,	,	,	_	_	_
19	centrifuged	centrifuge	VBN	_	_	_
20	at	at	IN	_	_	_
21	6,600	6,600	CD	_	_	_
22	g	g	NN	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	cell	cell	NN	_	_	_
26	pellets	pellet	NNS	_	_	_
27	flash	flash	VBP	_	_	_
28	frozen	freeze	VBN	_	_	_
29	in	in	IN	_	_	_
30	liquid	liquid	JJ	_	_	_
31	N2	n2	NN	_	_	_
32	before	before	IN	_	_	_
33	storing	store	VBG	_	_	_
34	at	at	IN	_	_	_
35	-80	-80	CD	_	_	_
36	degrees	degree	NNS	_	_	_
37	C	c	NN	_	_	_
38	until	until	IN	_	_	_
39	required	require	VBN	_	_	_
40	.	.	.	_	_	_

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	Culture	culture	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	frozen	freeze	VBN	_	_	_
5	in	in	IN	_	_	_
6	liquid	liquid	JJ	_	_	_
7	methanol	methanol	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	Culture	culture	NN	_	_	_
10	samples	sample	NNS	_	_	_
11	were	be	VBD	_	_	_
12	transferred	transfer	VBN	_	_	_
13	directly	directly	RB	_	_	_
14	into	into	IN	_	_	_
15	an	a	DT	_	_	_
16	ice-cold	ice-cold	JJ	_	_	_
17	ethanol/phenol	ethanol/phenol	NN	_	_	_
18	stop	stop	VB	_	_	_
19	solution	solution	NN	_	_	_
20	,	,	,	_	_	_
21	then	then	RB	_	_	_
22	collected	collect	VBN	_	_	_
23	by	by	IN	_	_	_
24	centrifugation	centrifugation	NN	_	_	_
25	and	and	CC	_	_	_
26	stored	store	VBD	_	_	_
27	at	at	IN	_	_	_
28	-80	-80	CD	_	_	_
29	°C	°c	NN	_	_	_
30	until	until	IN	_	_	_
31	RNA	rna	NN	_	_	_
32	extraction	extraction	NN	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	for	for	IN	_	_	_
4	samples	sample	NNS	_	_	_
5	1	1	CD	_	_	_
6	and	and	CC	_	_	_
7	2	2	CD	_	_	_
8	were	be	VBD	_	_	_
9	incubated	incubate	VBN	_	_	_
10	at	at	IN	_	_	_
11	44	44	CD	_	_	_
12	°C	°c	NN	_	_	_
13	for	for	IN	_	_	_
14	45	45	CD	_	_	_
15	min	min	NN	_	_	_
16	after	after	IN	_	_	_
17	growth	growth	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	grown	grow	VBN	_	_	_
4	in	in	IN	_	_	_
5	MOPS	mop	NNS	MED	_	_
6	minimal	minimal	JJ	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	media	media	NNS	_	_	_
9	containing	contain	VBG	_	_	_
10	10	10	CD	_	_	_
11	µM	µm	NN	_	_	_
12	FeSO4	feso4	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Cultures	culture	NNS	_	_	_
15	of	of	IN	_	_	_
16	both	both	DT	_	_	_
17	strains	strain	NNS	_	_	_
18	were	be	VBD	_	_	_
19	started	start	VBN	_	_	_
20	with	with	IN	_	_	_
21	a	a	DT	_	_	_
22	2	2	CD	_	_	_
23	%	%	NN	_	_	_
24	overnight	overnight	JJ	_	_	_
25	inoculum	inoculum	NN	_	_	_
26	in	in	IN	_	_	_
27	LB	LB	NNP	MED	_	_
28	media	media	NNS	MED	_	_
29	containing	contain	VBG	_	_	_
30	35ug/ml	35ug/ml	JJ	_	_	_
31	chloramphenicol	chloramphenicol	NN	_	_	_
32	.	.	.	_	_	_

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

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/R104A	g101s/r104a	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	for	for	IN	_	_	_
23	an	a	DT	_	_	_
24	hour	hour	NN	_	_	_
25	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	of	of	IN	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	TLS1637-TLS1650	tls1637-tls1650	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	were	be	VBD	_	_	_
9	grown	grow	VBN	_	_	_
10	at	at	IN	_	_	_
11	30oC	30oC	NNP	_	_	_
12	in	in	IN	_	_	_
13	LB	LB	NNP	_	_	_
14	and	and	CC	_	_	_
15	supplemented	supplement	VBN	_	_	_
16	with	with	IN	_	_	_
17	antibiotics	antibiotic	NNS	_	_	_
18	,	,	,	_	_	_
19	as	as	RB	_	_	_
20	necessary	necessary	JJ	_	_	_
21	,	,	,	_	_	_
22	at	at	IN	_	_	_
23	appropriate	appropriate	JJ	_	_	_
24	concentrations	concentration	NNS	_	_	_
25	.	.	.	_	_	_

1	IPTG	iptg	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	0.5	0.5	CD	_	_	_
4	mM	mm	NN	KWSUPP	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	was	be	VBD	_	_	_
7	added	add	VBN	_	_	_
8	to	to	TO	_	_	_
9	induce	induce	VB	_	_	_
10	the	the	DT	_	_	_
11	production	production	NN	_	_	_
12	of	of	IN	_	_	_
13	T18-ParB	t18-parb	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	WT	wt	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	or	or	CC	_	_	_
18	T18-ParB	t18-parb	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	G101S	g101s	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	an	a	DT	_	_	_
3	hour	hour	NN	_	_	_
4	,	,	,	_	_	_
5	formadehyde	formadehyde	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	1	1	CD	_	_	_
8	%	%	NN	_	_	_
9	final	final	JJ	_	_	_
10	concentration	concentration	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	were	be	VBD	_	_	_
13	added	add	VBN	_	_	_
14	to	to	TO	_	_	_
15	fix	fix	VB	_	_	_
16	cells	cell	NNS	_	_	_
17	for	for	IN	_	_	_
18	ChIP-seq	ChIP-seq	NNP	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	CFT073	cft073	NN	_	_	_
7	were	be	VBD	_	_	_
8	maintained	maintain	VBN	_	_	_
9	at	at	IN	_	_	_
10	--	--	:	_	_	_
11	80ºC	80ºc	NN	_	_	_
12	in	in	IN	_	_	_
13	Luria-Bertani	luria-bertani	JJ	_	_	_
14	broth	broth	NN	_	_	_
15	with	with	IN	_	_	_
16	15	15	CD	_	_	_
17	%	%	NN	_	_	_
18	glycerol	glycerol	NN	SUPP	_	_
19	.	.	.	_	_	_

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/mL	µg/ml	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	were	be	VBD	_	_	_
3	incubated	incubate	VBN	_	_	_
4	at	at	IN	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	,	,	,	_	_	_
8	5	5	CD	_	_	_
9	h	h	NN	_	_	_
10	,	,	,	_	_	_
11	200	200	CD	_	_	_
12	rpm	rpm	NN	_	_	_
13	to	to	TO	_	_	_
14	mid-log	mid-log	JJ	_	_	_
15	growth	growth	NN	_	_	_
16	phase	phase	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	MG1655	mg1655	NN	_	_	_
7	and	and	CC	_	_	_
8	its	its	PRP$	_	_	_
9	derivates	derivate	NNS	_	_	_
10	were	be	VBD	_	_	_
11	cross	cross	JJ	_	_	_
12	linked	link	VBN	_	_	_
13	by	by	IN	_	_	_
14	addition	addition	NN	_	_	_
15	of	of	IN	_	_	_
16	27	27	CD	_	_	_
17	µl	µl	NN	_	_	_
18	of	of	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	37	37	CD	_	_	_
22	%	%	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
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	1	1	CD	_	_	_
31	%	%	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
28	lysozyme	lysozyme	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	incubation	incubation	NN	_	_	_
32	at	at	IN	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	for	for	IN	_	_	_
36	30	30	CD	_	_	_
37	min	min	NN	_	_	_
38	C	c	NN	_	_	_
39	followed	follow	VBN	_	_	_
40	by	by	IN	_	_	_
41	addition	addition	NN	_	_	_
42	of	of	IN	_	_	_
43	4	4	CD	_	_	_
44	ml	ml	NN	_	_	_
45	IP	IP	NNP	_	_	_
46	buffer	buffer	NN	_	_	_
47	cells	cell	NNS	_	_	_
48	were	be	VBD	_	_	_
49	sonicated	sonicate	VBN	_	_	_
50	on	on	IN	_	_	_
51	ice	ice	NN	_	_	_
52	with	with	IN	_	_	_
53	12	12	CD	_	_	_
54	times	time	NNS	_	_	_
55	30	30	CD	_	_	_
56	sec	sec	NN	_	_	_
57	and	and	CC	_	_	_
58	30	30	CD	_	_	_
59	sec	sec	NN	_	_	_
60	breaks	break	NNS	_	_	_
61	at	at	IN	_	_	_
62	an	a	DT	_	_	_
63	UP	up	NN	_	_	_
64	400s	400s	CD	_	_	_
65	Ultrasonic	ultrasonic	JJ	_	_	_
66	processor	processor	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Dr.	Dr.	NNP	_	_	_
69	Hielscher	Hielscher	NNP	_	_	_
70	GmbH	gmbh	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	with	with	IN	_	_	_
73	100	100	CD	_	_	_
74	%	%	NN	_	_	_
75	power	power	NN	_	_	_
76	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	for	for	IN	_	_	_
4	10	10	CD	_	_	_
5	min	min	NN	_	_	_
6	at	at	IN	_	_	_
7	9000	9000	CD	_	_	_
8	g	g	NN	_	_	_
9	,	,	,	_	_	_
10	800	800	CD	_	_	_
11	µl	µl	NN	_	_	_
12	aliquotes	aliquote	NNS	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	supernatant	supernatant	NN	_	_	_
16	were	be	VBD	_	_	_
17	stored	store	VBN	_	_	_
18	at	at	IN	_	_	_
19	-20	-20	CD	_	_	_
20	°C	°c	NN	_	_	_
21	.	.	.	_	_	_

1	800	800	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	cell	cell	NN	_	_	_
6	extract	extract	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	see	see	VB	_	_	_
9	above	above	IN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	were	be	VBD	_	_	_
12	incubated	incubate	VBN	_	_	_
13	with	with	IN	_	_	_
14	20	20	CD	_	_	_
15	µl	µl	NN	_	_	_
16	protein	protein	NN	_	_	_
17	A/G	a/g	NN	_	_	_
18	agarose	agarose	NN	_	_	_
19	beads	bead	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Ultralink	ultralink	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	antibody	antibody	NN	_	_	_
25	rotating	rotate	VBG	_	_	_
26	at	at	IN	_	_	_
27	4	4	CD	_	_	_
28	°C	°c	NN	_	_	_
29	.	.	.	_	_	_

1	Washing	wash	VBG	_	_	_
2	was	be	VBD	_	_	_
3	done	do	VBN	_	_	_
4	with	with	IN	_	_	_
5	500	500	CD	_	_	_
6	µl	µl	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	2	2	CD	_	_	_
10	x	x	CC	_	_	_
11	500	500	CD	_	_	_
12	µl	µl	NN	_	_	_
13	IP	IP	NNP	_	_	_
14	buffer	buffer	NN	_	_	_
15	-LSB-	-lsb-	-LRB-	_	_	_
16	50	50	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	HEPES-KOH	hepes-koh	NN	_	_	_
19	pH	ph	NN	_	_	_
20	7.5	7.5	CD	_	_	_
21	,	,	,	_	_	_
22	150	150	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	NaCl	nacl	NN	_	_	_
25	,	,	,	_	_	_
26	1	1	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	EDTA	edta	NN	_	_	_
29	,	,	,	_	_	_
30	1	1	CD	_	_	_
31	%	%	NN	_	_	_
32	Triton	Triton	NNP	_	_	_
33	X	X	NNP	_	_	_
34	100	100	CD	_	_	_
35	,	,	,	_	_	_
36	0.1	0.1	CD	_	_	_
37	%	%	NN	_	_	_
38	Sodium	sodium	NN	_	_	_
39	deoxycholate	deoxycholate	NN	SUPP	_	_
40	,	,	,	_	_	_
41	0.1	0.1	CD	_	_	_
42	%	%	NN	_	_	_
43	SDS	sds	NN	_	_	_
44	-RSB-	-rsb-	-RRB-	_	_	_
45	,	,	,	_	_	_
46	1	1	CD	_	_	_
47	x	x	CC	_	_	_
48	IP	IP	NNP	_	_	_
49	buffer	buffer	NN	_	_	_
50	with	with	IN	_	_	_
51	500mM	500mm	NN	_	_	_
52	NaCl	nacl	NN	_	_	_
53	,	,	,	_	_	_
54	1	1	CD	_	_	_
55	x	x	NN	_	_	_
56	wash	wash	NN	_	_	_
57	buffer	buffer	NN	_	_	_
58	-LSB-	-lsb-	-LRB-	_	_	_
59	10mM	10mm	NN	_	_	_
60	Tris	Tris	NNP	_	_	_
61	pH	ph	NN	_	_	_
62	8.0	8.0	CD	_	_	_
63	,	,	,	_	_	_
64	250	250	CD	_	_	_
65	mM	mm	NN	KWSUPP	_	_
66	LiCl	licl	NN	_	_	_
67	,	,	,	_	_	_
68	1	1	CD	_	_	_
69	mM	mm	NN	KWSUPP	_	_
70	EDTA	edta	NN	_	_	_
71	,	,	,	_	_	_
72	0.5	0.5	CD	_	_	_
73	%	%	NN	_	_	_
74	Nonidet-P40	nonidet-p40	NN	_	_	_
75	,	,	,	_	_	_
76	0.5	0.5	CD	_	_	_
77	%	%	NN	_	_	_
78	Sodium	sodium	NN	_	_	_
79	deoxycholate	deoxycholate	NN	SUPP	_	_
80	-RSB-	-rsb-	-RRB-	_	_	_
81	and	and	CC	_	_	_
82	1	1	CD	_	_	_
83	x	x	CC	_	_	_
84	TE	TE	NNP	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	followed	follow	VBN	_	_	_
87	by	by	IN	_	_	_
88	rotation	rotation	NN	_	_	_
89	at	at	IN	_	_	_
90	room	room	NN	_	_	_
91	temperature	temperature	NN	_	_	_
92	for	for	IN	_	_	_
93	three	three	CD	_	_	_
94	minutes	minute	NNS	_	_	_
95	with	with	IN	_	_	_
96	subsequent	subsequent	JJ	_	_	_
97	collection	collection	NN	_	_	_
98	of	of	IN	_	_	_
99	the	the	DT	_	_	_
100	beads	bead	NNS	_	_	_
101	by	by	IN	_	_	_
102	centrifugation	centrifugation	NN	_	_	_
103	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	elution	elution	NN	_	_	_
3	,	,	,	_	_	_
4	100	100	CD	_	_	_
5	µl	µl	NN	_	_	_
6	elution	elution	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	50	50	CD	_	_	_
10	mM	mm	NN	KWSUPP	_	_
11	Tris	tris	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	pH	ph	NN	_	_	_
14	7.5	7.5	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	10	10	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	EDTA	edta	NN	_	_	_
20	,	,	,	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	SDS	sds	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	was	be	VBD	_	_	_
26	added	add	VBN	_	_	_
27	to	to	TO	_	_	_
28	the	the	DT	_	_	_
29	beads	bead	NNS	_	_	_
30	,	,	,	_	_	_
31	incubated	incubate	VBN	_	_	_
32	in	in	IN	_	_	_
33	a	a	DT	_	_	_
34	65	65	CD	_	_	_
35	°C	°c	NN	_	_	_
36	water	water	NN	_	_	_
37	bath	bath	NN	_	_	_
38	for	for	IN	_	_	_
39	10	10	CD	_	_	_
40	min	min	NN	_	_	_
41	and	and	CC	_	_	_
42	centrifuged	centrifuge	VBN	_	_	_
43	as	as	IN	_	_	_
44	above	above	JJ	_	_	_
45	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	reversion	reversion	NN	_	_	_
3	of	of	IN	_	_	_
4	crosslink	crosslink	NNP	_	_	_
5	the	the	DT	_	_	_
6	DNA	dna	NN	_	_	_
7	was	be	VBD	_	_	_
8	purified	purify	VBN	_	_	_
9	with	with	IN	_	_	_
10	phenol/chloroform	phenol/chloroform	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	MG1655	mg1655	NN	_	_	_
7	and	and	CC	_	_	_
8	its	its	PRP$	_	_	_
9	derivates	derivate	NNS	_	_	_
10	were	be	VBD	_	_	_
11	cross	cross	JJ	_	_	_
12	linked	link	VBN	_	_	_
13	by	by	IN	_	_	_
14	addition	addition	NN	_	_	_
15	of	of	IN	_	_	_
16	27	27	CD	_	_	_
17	µl	µl	NN	_	_	_
18	of	of	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	37	37	CD	_	_	_
22	%	%	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
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	1	1	CD	_	_	_
31	%	%	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
28	lysozyme	lysozyme	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	incubation	incubation	NN	_	_	_
32	at	at	IN	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	for	for	IN	_	_	_
36	30	30	CD	_	_	_
37	min	min	NN	_	_	_
38	C	c	NN	_	_	_
39	followed	follow	VBN	_	_	_
40	by	by	IN	_	_	_
41	addition	addition	NN	_	_	_
42	of	of	IN	_	_	_
43	4	4	CD	_	_	_
44	ml	ml	NN	_	_	_
45	IP	IP	NNP	_	_	_
46	buffer	buffer	NN	_	_	_
47	cells	cell	NNS	_	_	_
48	were	be	VBD	_	_	_
49	sonicated	sonicate	VBN	_	_	_
50	on	on	IN	_	_	_
51	ice	ice	NN	_	_	_
52	with	with	IN	_	_	_
53	12	12	CD	_	_	_
54	times	time	NNS	_	_	_
55	30	30	CD	_	_	_
56	sec	sec	NN	_	_	_
57	and	and	CC	_	_	_
58	30	30	CD	_	_	_
59	sec	sec	NN	_	_	_
60	breaks	break	NNS	_	_	_
61	at	at	IN	_	_	_
62	an	a	DT	_	_	_
63	UP	up	NN	_	_	_
64	400s	400s	CD	_	_	_
65	Ultrasonic	ultrasonic	JJ	_	_	_
66	processor	processor	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Dr.	Dr.	NNP	_	_	_
69	Hielscher	Hielscher	NNP	_	_	_
70	GmbH	gmbh	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	with	with	IN	_	_	_
73	100	100	CD	_	_	_
74	%	%	NN	_	_	_
75	power	power	NN	_	_	_
76	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	for	for	IN	_	_	_
4	10	10	CD	_	_	_
5	min	min	NN	_	_	_
6	at	at	IN	_	_	_
7	9000	9000	CD	_	_	_
8	g	g	NN	_	_	_
9	,	,	,	_	_	_
10	800	800	CD	_	_	_
11	µl	µl	NN	_	_	_
12	aliquotes	aliquote	NNS	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	supernatant	supernatant	NN	_	_	_
16	were	be	VBD	_	_	_
17	stored	store	VBN	_	_	_
18	at	at	IN	_	_	_
19	-20	-20	CD	_	_	_
20	°C	°c	NN	_	_	_
21	.	.	.	_	_	_

1	800	800	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	cell	cell	NN	_	_	_
6	extract	extract	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	see	see	VB	_	_	_
9	above	above	IN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	were	be	VBD	_	_	_
12	incubated	incubate	VBN	_	_	_
13	with	with	IN	_	_	_
14	20	20	CD	_	_	_
15	µl	µl	NN	_	_	_
16	protein	protein	NN	_	_	_
17	A/G	a/g	NN	_	_	_
18	agarose	agarose	NN	_	_	_
19	beads	bead	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Ultralink	ultralink	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	antibody	antibody	NN	_	_	_
25	rotating	rotate	VBG	_	_	_
26	at	at	IN	_	_	_
27	4	4	CD	_	_	_
28	°C	°c	NN	_	_	_
29	.	.	.	_	_	_

1	Washing	wash	VBG	_	_	_
2	was	be	VBD	_	_	_
3	done	do	VBN	_	_	_
4	with	with	IN	_	_	_
5	500	500	CD	_	_	_
6	µl	µl	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	2	2	CD	_	_	_
10	x	x	CC	_	_	_
11	500	500	CD	_	_	_
12	µl	µl	NN	_	_	_
13	IP	IP	NNP	_	_	_
14	buffer	buffer	NN	_	_	_
15	-LSB-	-lsb-	-LRB-	_	_	_
16	50	50	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	HEPES-KOH	hepes-koh	NN	_	_	_
19	pH	ph	NN	_	_	_
20	7.5	7.5	CD	_	_	_
21	,	,	,	_	_	_
22	150	150	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	NaCl	nacl	NN	_	_	_
25	,	,	,	_	_	_
26	1	1	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	EDTA	edta	NN	_	_	_
29	,	,	,	_	_	_
30	1	1	CD	_	_	_
31	%	%	NN	_	_	_
32	Triton	Triton	NNP	_	_	_
33	X	X	NNP	_	_	_
34	100	100	CD	_	_	_
35	,	,	,	_	_	_
36	0.1	0.1	CD	_	_	_
37	%	%	NN	_	_	_
38	Sodium	sodium	NN	_	_	_
39	deoxycholate	deoxycholate	NN	SUPP	_	_
40	,	,	,	_	_	_
41	0.1	0.1	CD	_	_	_
42	%	%	NN	_	_	_
43	SDS	sds	NN	_	_	_
44	-RSB-	-rsb-	-RRB-	_	_	_
45	,	,	,	_	_	_
46	1	1	CD	_	_	_
47	x	x	CC	_	_	_
48	IP	IP	NNP	_	_	_
49	buffer	buffer	NN	_	_	_
50	with	with	IN	_	_	_
51	500mM	500mm	NN	_	_	_
52	NaCl	nacl	NN	_	_	_
53	,	,	,	_	_	_
54	1	1	CD	_	_	_
55	x	x	NN	_	_	_
56	wash	wash	NN	_	_	_
57	buffer	buffer	NN	_	_	_
58	-LSB-	-lsb-	-LRB-	_	_	_
59	10mM	10mm	NN	_	_	_
60	Tris	Tris	NNP	_	_	_
61	pH	ph	NN	_	_	_
62	8.0	8.0	CD	_	_	_
63	,	,	,	_	_	_
64	250	250	CD	_	_	_
65	mM	mm	NN	KWSUPP	_	_
66	LiCl	licl	NN	_	_	_
67	,	,	,	_	_	_
68	1	1	CD	_	_	_
69	mM	mm	NN	KWSUPP	_	_
70	EDTA	edta	NN	_	_	_
71	,	,	,	_	_	_
72	0.5	0.5	CD	_	_	_
73	%	%	NN	_	_	_
74	Nonidet-P40	nonidet-p40	NN	_	_	_
75	,	,	,	_	_	_
76	0.5	0.5	CD	_	_	_
77	%	%	NN	_	_	_
78	Sodium	sodium	NN	_	_	_
79	deoxycholate	deoxycholate	NN	SUPP	_	_
80	-RSB-	-rsb-	-RRB-	_	_	_
81	and	and	CC	_	_	_
82	1	1	CD	_	_	_
83	x	x	CC	_	_	_
84	TE	TE	NNP	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	followed	follow	VBN	_	_	_
87	by	by	IN	_	_	_
88	rotation	rotation	NN	_	_	_
89	at	at	IN	_	_	_
90	room	room	NN	_	_	_
91	temperature	temperature	NN	_	_	_
92	for	for	IN	_	_	_
93	three	three	CD	_	_	_
94	minutes	minute	NNS	_	_	_
95	with	with	IN	_	_	_
96	subsequent	subsequent	JJ	_	_	_
97	collection	collection	NN	_	_	_
98	of	of	IN	_	_	_
99	the	the	DT	_	_	_
100	beads	bead	NNS	_	_	_
101	by	by	IN	_	_	_
102	centrifugation	centrifugation	NN	_	_	_
103	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	elution	elution	NN	_	_	_
3	,	,	,	_	_	_
4	100	100	CD	_	_	_
5	µl	µl	NN	_	_	_
6	elution	elution	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	50	50	CD	_	_	_
10	mM	mm	NN	KWSUPP	_	_
11	Tris	tris	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	pH	ph	NN	_	_	_
14	7.5	7.5	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	10	10	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	EDTA	edta	NN	_	_	_
20	,	,	,	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	SDS	sds	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	was	be	VBD	_	_	_
26	added	add	VBN	_	_	_
27	to	to	TO	_	_	_
28	the	the	DT	_	_	_
29	beads	bead	NNS	_	_	_
30	,	,	,	_	_	_
31	incubated	incubate	VBN	_	_	_
32	in	in	IN	_	_	_
33	a	a	DT	_	_	_
34	65	65	CD	_	_	_
35	°C	°c	NN	_	_	_
36	water	water	NN	_	_	_
37	bath	bath	NN	_	_	_
38	for	for	IN	_	_	_
39	10	10	CD	_	_	_
40	min	min	NN	_	_	_
41	and	and	CC	_	_	_
42	centrifuged	centrifuge	VBN	_	_	_
43	as	as	IN	_	_	_
44	above	above	JJ	_	_	_
45	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	reversion	reversion	NN	_	_	_
3	of	of	IN	_	_	_
4	crosslink	crosslink	NNP	_	_	_
5	the	the	DT	_	_	_
6	DNA	dna	NN	_	_	_
7	was	be	VBD	_	_	_
8	purified	purify	VBN	_	_	_
9	with	with	IN	_	_	_
10	phenol/chloroform	phenol/chloroform	NN	_	_	_
11	.	.	.	_	_	_

1	METHOD	method	NN	_	_	_
2	DETAILS	detail	NNS	_	_	_
3	are	be	VBP	_	_	_
4	given	give	VBN	_	_	_
5	and	and	CC	_	_	_
6	are	be	VBP	_	_	_
7	important	important	JJ	_	_	_
8	for	for	IN	_	_	_
9	the	the	DT	_	_	_
10	different	different	JJ	_	_	_
11	arrays	array	NNS	_	_	_
12	.	.	.	_	_	_

1	METHOD	method	NN	_	_	_
2	DETAILS	detail	NNS	_	_	_
3	:	:	:	_	_	_
4	For	for	IN	_	_	_
5	RNAP	rnap	NN	_	_	_
6	old	old	JJ	_	_	_
7	,	,	,	_	_	_
8	SeqA	seqa	NN	_	_	_
9	old	old	JJ	_	_	_
10	and	and	CC	_	_	_
11	SeqA	seqa	NN	_	_	_
12	old	old	JJ	_	_	_
13	deltaSeqA	deltaseqa	NN	_	_	_
14	:	:	:	_	_	_
15	Cell	cell	NN	_	_	_
16	extracts	extract	NNS	_	_	_
17	were	be	VBD	_	_	_
18	incubated	incubate	VBN	_	_	_
19	with	with	IN	_	_	_
20	agarose	agarose	NN	_	_	_
21	beads	bead	NNS	_	_	_
22	and	and	CC	_	_	_
23	antibody	antibody	NN	_	_	_
24	over	over	IN	_	_	_
25	night	night	NN	_	_	_
26	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	transferred	transfer	VBN	_	_	_
4	to	to	TO	_	_	_
5	a	a	DT	_	_	_
6	Spin-X	spin-x	NN	_	_	_
7	centrifuge	centrifuge	NN	_	_	_
8	column	column	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Costar	costar	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	,	,	,	_	_	_
13	centrifuged	centrifuge	VBN	_	_	_
14	for	for	IN	_	_	_
15	2	2	CD	_	_	_
16	min	min	NN	_	_	_
17	at	at	IN	_	_	_
18	4.000	4.000	CD	_	_	_
19	rpm	rpm	NN	_	_	_
20	to	to	TO	_	_	_
21	collect	collect	VB	_	_	_
22	the	the	DT	_	_	_
23	beads	bead	NNS	_	_	_
24	on	on	IN	_	_	_
25	the	the	DT	_	_	_
26	column	column	NN	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flow	flow	NN	_	_	_
3	through	through	IN	_	_	_
4	was	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	.	.	.	_	_	_

1	Washing	wash	VBG	_	_	_
2	was	be	VBD	_	_	_
3	by	by	IN	_	_	_
4	adding	add	VBG	_	_	_
5	the	the	DT	_	_	_
6	described	describe	VBN	_	_	_
7	buffers	buffer	NNS	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	beads	bead	NNS	_	_	_
11	on	on	IN	_	_	_
12	the	the	DT	_	_	_
13	spin	spin	NN	_	_	_
14	column	column	NN	_	_	_
15	and	and	CC	_	_	_
16	rotation	rotation	NN	_	_	_
17	at	at	IN	_	_	_
18	room	room	NN	_	_	_
19	temperature	temperature	NN	_	_	_
20	for	for	IN	_	_	_
21	three	three	CD	_	_	_
22	minutes	minute	NNS	_	_	_
23	with	with	IN	_	_	_
24	subsequent	subsequent	JJ	_	_	_
25	collection	collection	NN	_	_	_
26	of	of	IN	_	_	_
27	the	the	DT	_	_	_
28	beads	bead	NNS	_	_	_
29	by	by	IN	_	_	_
30	centrifugation	centrifugation	NN	_	_	_
31	as	as	IN	_	_	_
32	above	above	JJ	_	_	_
33	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	elution	elution	NN	_	_	_
3	,	,	,	_	_	_
4	100	100	CD	_	_	_
5	µl	µl	NN	_	_	_
6	elution	elution	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	was	be	VBD	_	_	_
9	added	add	VBN	_	_	_
10	to	to	TO	_	_	_
11	the	the	DT	_	_	_
12	column	column	NN	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	beads	bead	NNS	_	_	_
16	,	,	,	_	_	_
17	incubated	incubate	VBN	_	_	_
18	in	in	IN	_	_	_
19	a	a	DT	_	_	_
20	65	65	CD	_	_	_
21	°C	°c	NN	_	_	_
22	water	water	NN	_	_	_
23	bath	bath	NN	_	_	_
24	for	for	IN	_	_	_
25	10	10	CD	_	_	_
26	min	min	NN	_	_	_
27	and	and	CC	_	_	_
28	centrifuged	centrifuge	VBN	_	_	_
29	as	as	IN	_	_	_
30	above	above	JJ	_	_	_
31	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	prepare	prepare	VB	_	_	_
3	the	the	DT	_	_	_
4	control	control	NN	_	_	_
5	DNA	dna	NN	_	_	_
6	,	,	,	_	_	_
7	800	800	CD	_	_	_
8	µl	µl	NN	_	_	_
9	of	of	IN	_	_	_
10	sonicated	sonicated	JJ	_	_	_
11	cell	cell	NN	_	_	_
12	extract	extract	NN	_	_	_
13	was	be	VBD	_	_	_
14	incubated	incubate	VBN	_	_	_
15	at	at	IN	_	_	_
16	65	65	CD	_	_	_
17	°C	°c	NN	_	_	_
18	over	over	IN	_	_	_
19	night	night	NN	_	_	_
20	followed	follow	VBN	_	_	_
21	by	by	IN	_	_	_
22	30	30	CD	_	_	_
23	min	min	NN	_	_	_
24	after	after	IN	_	_	_
25	addition	addition	NN	_	_	_
26	of	of	IN	_	_	_
27	1	1	CD	_	_	_
28	µl	µl	NN	_	_	_
29	RNase	rnase	NN	_	_	_
30	A	a	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	20	20	CD	_	_	_
33	mg/ml	mg/ml	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	extraction	extraction	NN	_	_	_
37	with	with	IN	_	_	_
38	phenol/chloroform	phenol/chloroform	NN	_	_	_
39	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	SeqA	seqa	NN	_	_	_
3	new	new	JJ	_	_	_
4	,	,	,	_	_	_
5	SeqA	seqa	NN	_	_	_
6	new	new	JJ	_	_	_
7	deltaSeqA	deltaseqa	NN	_	_	_
8	,	,	,	_	_	_
9	sigma32	sigma32	NN	_	_	_
10	30	30	CD	_	_	_
11	°C	°c	NN	_	_	_
12	and	and	CC	_	_	_
13	sigma	sigma	NN	_	_	_
14	32	32	CD	_	_	_
15	43	43	CD	_	_	_
16	°C	°c	NN	_	_	_
17	:	:	:	_	_	_
18	The	the	DT	_	_	_
19	ChIP	chip	NN	_	_	_
20	protocol	protocol	NN	_	_	_
21	as	as	IN	_	_	_
22	described	describe	VBN	_	_	_
23	above	above	IN	_	_	_
24	resulted	result	VBN	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	high	high	JJ	_	_	_
28	background	background	NN	_	_	_
29	signal	signal	NN	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	following	follow	VBG	_	_	_
3	modifications	modification	NNS	_	_	_
4	were	be	VBD	_	_	_
5	applied	apply	VBN	_	_	_
6	.	.	.	_	_	_

1	First	first	RB	_	_	_
2	,	,	,	_	_	_
3	agarose	agarose	NN	_	_	_
4	beads	bead	NNS	_	_	_
5	were	be	VBD	_	_	_
6	not	not	RB	_	_	_
7	collected	collect	VBN	_	_	_
8	on	on	IN	_	_	_
9	a	a	DT	_	_	_
10	spin	spin	NN	_	_	_
11	column	column	NN	_	_	_
12	but	but	CC	_	_	_
13	instead	instead	RB	_	_	_
14	at	at	IN	_	_	_
15	the	the	DT	_	_	_
16	bottom	bottom	NN	_	_	_
17	of	of	IN	_	_	_
18	a	a	DT	_	_	_
19	usual	usual	JJ	_	_	_
20	1.5	1.5	CD	_	_	_
21	ml	ml	NN	_	_	_
22	reaction	reaction	NN	_	_	_
23	tube	tube	NN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	than	than	IN	_	_	_
5	removed	remove	VBN	_	_	_
6	by	by	IN	_	_	_
7	pipetting	pipetting	NN	_	_	_
8	.	.	.	_	_	_

1	Second	second	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	control	control	NN	_	_	_
5	DNA	dna	NN	_	_	_
6	was	be	VBD	_	_	_
7	taken	take	VBN	_	_	_
8	from	from	IN	_	_	_
9	the	the	DT	_	_	_
10	supernatant	supernatant	JJ	_	_	_
11	resulting	result	VBG	_	_	_
12	from	from	IN	_	_	_
13	centrifugation	centrifugation	NN	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	precipitated	precipitated	JJ	_	_	_
17	chromatin	chromatin	NN	_	_	_
18	beads	bead	NNS	_	_	_
19	processed	process	VBN	_	_	_
20	further	further	RB	_	_	_
21	as	as	IN	_	_	_
22	the	the	DT	_	_	_
23	immuno	immuno	NN	_	_	_
24	precipitated	precipitated	JJ	_	_	_
25	DNA	dna	NN	_	_	_
26	after	after	IN	_	_	_
27	elution	elution	NN	_	_	_
28	.	.	.	_	_	_

1	Third	Third	NNP	_	_	_
2	,	,	,	_	_	_
3	before	before	IN	_	_	_
4	addition	addition	NN	_	_	_
5	of	of	IN	_	_	_
6	proteinase	proteinase	NN	_	_	_
7	K	k	NN	_	_	_
8	sample	sample	NN	_	_	_
9	and	and	CC	_	_	_
10	control	control	NN	_	_	_
11	DNA	dna	NN	_	_	_
12	were	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	with	with	IN	_	_	_
15	RNase	rnase	NN	_	_	_
16	A	a	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	50	50	CD	_	_	_
19	µg/ml	µg/ml	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	for	for	IN	_	_	_
22	at	at	IN	_	_	_
23	least	least	JJS	_	_	_
24	90	90	CD	_	_	_
25	min	min	NN	_	_	_
26	at	at	IN	_	_	_
27	42	42	CD	_	_	_
28	°C	°c	NN	_	_	_
29	.	.	.	_	_	_

1	Incubation	incubation	NN	_	_	_
2	of	of	IN	_	_	_
3	800	800	CD	_	_	_
4	µl	µl	NN	_	_	_
5	cell	cell	NN	_	_	_
6	extract	extract	NN	_	_	_
7	with	with	IN	_	_	_
8	σ32	σ32	NN	_	_	_
9	-	-	:	_	_	_
10	or	or	CC	_	_	_
11	SeqA	seqa	NN	_	_	_
12	antiserum	antiserum	NN	_	_	_
13	was	be	VBD	_	_	_
14	for	for	IN	_	_	_
15	1	1	CD	_	_	_
16	h	h	NN	_	_	_
17	at	at	IN	_	_	_
18	4	4	CD	_	_	_
19	°C	°c	NN	_	_	_
20	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	sigma32	sigma32	CD	_	_	_
3	30	30	CD	_	_	_
4	°C	°c	NN	_	_	_
5	short	short	JJ	_	_	_
6	RNase	rnase	NN	_	_	_
7	and	and	CC	_	_	_
8	sigma32	sigma32	NN	_	_	_
9	30	30	CD	_	_	_
10	°C	°c	NN	_	_	_
11	short	short	JJ	_	_	_
12	RNase	rnase	NN	_	_	_
13	:	:	:	_	_	_
14	The	the	DT	_	_	_
15	ChIP	chip	NN	_	_	_
16	protocol	protocol	NN	_	_	_
17	was	be	VBD	_	_	_
18	as	as	IN	_	_	_
19	described	describe	VBN	_	_	_
20	for	for	IN	_	_	_
21	sigma	sigma	NN	_	_	_
22	32	32	CD	_	_	_
23	30	30	CD	_	_	_
24	°C	°c	NN	_	_	_
25	and	and	CC	_	_	_
26	sigma	sigma	NN	_	_	_
27	32	32	CD	_	_	_
28	43	43	CD	_	_	_
29	°C	°c	NN	_	_	_
30	but	but	CC	_	_	_
31	with	with	IN	_	_	_
32	a	a	DT	_	_	_
33	shorter	shorter	JJR	_	_	_
34	RNase	rnase	NN	_	_	_
35	A	a	DT	_	_	_
36	incubation	incubation	NN	_	_	_
37	for	for	IN	_	_	_
38	only	only	RB	_	_	_
39	30	30	CD	_	_	_
40	instead	instead	RB	_	_	_
41	of	of	IN	_	_	_
42	90	90	CD	_	_	_
43	min	min	NN	_	_	_
44	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	into	into	IN	_	_	_
6	DNA-RNA	DNA-RNA	NNP	_	_	_
7	Protect	Protect	NNP	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Sierra	Sierra	NNP	_	_	_
10	Diagnostics	Diagnostics	NNPS	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	inhibit	inhibit	VB	_	_	_
14	RNA	rna	NN	_	_	_
15	degradation	degradation	NN	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	RNA	rna	NN	_	_	_
19	was	be	VBD	_	_	_
20	purified	purify	VBN	_	_	_
21	using	use	VBG	_	_	_
22	RNeasy	rneasy	NN	_	_	_
23	minkits	minkit	NNS	_	_	_
24	with	with	IN	_	_	_
25	the	the	DT	_	_	_
26	optional	optional	JJ	_	_	_
27	DNase	dnase	NN	_	_	_
28	treatment	treatment	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Qiagen	qiagen	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

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/L	g/l	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	in	in	IN	_	_	_
39	vigorously	vigorously	RB	_	_	_
40	shaken	shake	VBN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	225	225	CD	_	_	_
43	rpm	rpm	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	Fernbach	fernbach	NN	_	_	_
46	flasks	flask	NNS	_	_	_
47	.	.	.	_	_	_

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/ml	ug/ml	JJ	_	_	_
7	chloramphenicol	chloramphenicol	NN	_	_	_
8	to	to	TO	_	_	_
9	maintain	maintain	VB	_	_	_
10	selection	selection	NN	_	_	_
11	.	.	.	_	_	_

1	However	however	RB	_	_	_
2	,	,	,	_	_	_
3	this	this	DT	_	_	_
4	genomic	genomic	JJ	_	_	_
5	mutation	mutation	NN	_	_	_
6	is	be	VBZ	_	_	_
7	stable	stable	JJ	_	_	_
8	and	and	CC	_	_	_
9	RNA	rna	NN	_	_	_
10	was	be	VBD	_	_	_
11	prepared	prepare	VBN	_	_	_
12	from	from	IN	_	_	_
13	non-selectively	non-selectively	JJ	_	_	_
14	grown	grown	JJ	_	_	_
15	cultures	culture	NNS	_	_	_
16	inoculated	inoculate	VBN	_	_	_
17	with	with	IN	_	_	_
18	overnight	overnight	JJ	_	_	_
19	stocks	stock	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	grown	grow	VBN	_	_	_
22	with	with	IN	_	_	_
23	selection	selection	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	to	to	TO	_	_	_
26	eliminate	eliminate	VB	_	_	_
27	any	any	DT	_	_	_
28	unrelated	unrelated	JJ	_	_	_
29	effects	effect	NNS	_	_	_
30	of	of	IN	_	_	_
31	exogenous	exogenous	JJ	_	_	_
32	drugs	drug	NNS	_	_	_
33	on	on	IN	_	_	_
34	gene	gene	NN	_	_	_
35	expression	expression	NN	_	_	_
36	.	.	.	_	_	_

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/ml	ug/ml	NN	_	_	_
7	kanamycin	kanamycin	NN	_	_	_
8	to	to	TO	_	_	_
9	maintain	maintain	VB	_	_	_
10	selection	selection	NN	_	_	_
11	.	.	.	_	_	_

1	However	however	RB	_	_	_
2	,	,	,	_	_	_
3	this	this	DT	_	_	_
4	genomic	genomic	JJ	_	_	_
5	mutation	mutation	NN	_	_	_
6	is	be	VBZ	_	_	_
7	stable	stable	JJ	_	_	_
8	and	and	CC	_	_	_
9	RNA	rna	NN	_	_	_
10	was	be	VBD	_	_	_
11	prepared	prepare	VBN	_	_	_
12	from	from	IN	_	_	_
13	non-selectively	non-selectively	JJ	_	_	_
14	grown	grown	JJ	_	_	_
15	cultures	culture	NNS	_	_	_
16	inoculated	inoculate	VBN	_	_	_
17	with	with	IN	_	_	_
18	overnight	overnight	JJ	_	_	_
19	stocks	stock	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	grown	grow	VBN	_	_	_
22	with	with	IN	_	_	_
23	selection	selection	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	to	to	TO	_	_	_
26	eliminate	eliminate	VB	_	_	_
27	any	any	DT	_	_	_
28	unrelated	unrelated	JJ	_	_	_
29	effects	effect	NNS	_	_	_
30	of	of	IN	_	_	_
31	exogenous	exogenous	JJ	_	_	_
32	drugs	drug	NNS	_	_	_
33	on	on	IN	_	_	_
34	gene	gene	NN	_	_	_
35	expression	expression	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	OD600	od600	NN	_	_	_
8	value	value	NN	_	_	_
9	of	of	IN	_	_	_
10	1.0	1.0	CD	_	_	_
11	and	and	CC	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	formaldehyde	formaldehyde	NN	_	_	_
17	for	for	IN	_	_	_
18	10	10	CD	_	_	_
19	min	min	NN	_	_	_
20	.	.	.	_	_	_

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/ml	ku/ml	NN	_	_	_
14	lysozyme	lysozyme	NN	_	_	_
15	,	,	,	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	PMSF	pmsf	NN	_	_	_
19	and	and	CC	_	_	_
20	protease	protease	NN	_	_	_
21	inhibitor	inhibitor	NN	_	_	_
22	cocktail	cocktail	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Sigma	Sigma	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	for	for	IN	_	_	_
27	30	30	CD	_	_	_
28	min	min	NN	_	_	_
29	at	at	IN	_	_	_
30	4	4	CD	_	_	_
31	℃	℃	NN	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysates	lysate	NNS	_	_	_
3	were	be	VBD	_	_	_
4	sonicated	sonicate	VBN	_	_	_
5	by	by	IN	_	_	_
6	a	a	DT	_	_	_
7	sonicator	sonicator	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Bioruptor	bioruptor	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	and	and	CC	_	_	_
12	this	this	DT	_	_	_
13	sonication	sonication	NN	_	_	_
14	resulted	result	VBD	_	_	_
15	in	in	IN	_	_	_
16	the	the	DT	_	_	_
17	size	size	NN	_	_	_
18	of	of	IN	_	_	_
19	DNA	dna	NN	_	_	_
20	ranged	range	VBD	_	_	_
21	from	from	IN	_	_	_
22	100	100	CD	_	_	_
23	bps	bp	NNS	_	_	_
24	to	to	TO	_	_	_
25	1000	1000	CD	_	_	_
26	bps	bp	NNS	_	_	_
27	with	with	IN	_	_	_
28	the	the	DT	_	_	_
29	average	average	JJ	_	_	_
30	size	size	NN	_	_	_
31	of	of	IN	_	_	_
32	500	500	CD	_	_	_
33	bps	bp	NNS	_	_	_
34	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	sonication	sonication	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	lysates	lysate	NNS	_	_	_
6	were	be	VBD	_	_	_
7	centrifuged	centrifuge	VBN	_	_	_
8	at	at	IN	_	_	_
9	12,000	12,000	CD	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	20	20	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	℃	℃	NN	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	resulting	result	VBG	_	_	_
20	supernatant	supernatant	NN	_	_	_
21	was	be	VBD	_	_	_
22	used	use	VBN	_	_	_
23	for	for	IN	_	_	_
24	immunoprecipitation	immunoprecipitation	NN	_	_	_
25	.	.	.	_	_	_

1	Before	before	IN	_	_	_
2	immunoprecipitation	immunoprecipitation	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	magnetic	magnetic	JJ	_	_	_
6	beads	bead	NNS	_	_	_
7	coated	coat	VBN	_	_	_
8	with	with	IN	_	_	_
9	Dynabeads	Dynabeads	NNPS	_	_	_
10	Protein	protein	NN	_	_	_
11	G	g	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Invitrogen	invitrogen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	were	be	VBD	_	_	_
16	pre-incubated	pre-incubated	JJ	_	_	_
17	with	with	IN	_	_	_
18	0.05	0.05	CD	_	_	_
19	mg/ml	mg/ml	NN	_	_	_
20	anti-FLAG	anti-flag	JJ	_	_	_
21	antibody	antibody	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Sigma	Sigma	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	the	the	DT	_	_	_
27	lysates	lysate	NNS	_	_	_
28	were	be	VBD	_	_	_
29	also	also	RB	_	_	_
30	pre-cleared	pre-clear	VBN	_	_	_
31	by	by	IN	_	_	_
32	incubating	incubate	VBG	_	_	_
33	with	with	IN	_	_	_
34	the	the	DT	_	_	_
35	beads	bead	NNS	_	_	_
36	only	only	RB	_	_	_
37	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	immunoprecipitate	immunoprecipitate	NN	_	_	_
3	the	the	DT	_	_	_
4	PhoB-FLAG-DNA	phob-flag-dna	JJ	_	_	_
5	complex	complex	NN	_	_	_
6	,	,	,	_	_	_
7	beads	bead	NNS	_	_	_
8	pre-incubated	pre-incubated	JJ	_	_	_
9	with	with	IN	_	_	_
10	antibody	antibody	NN	_	_	_
11	were	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	in	in	IN	_	_	_
14	both	both	CC	_	_	_
15	lysates	lysate	NNS	_	_	_
16	of	of	IN	_	_	_
17	MG1655	mg1655	NN	_	_	_
18	_	_	CD	_	_	_
19	PhoB	phob	NN	TF	_	_
20	_	_	CD	_	_	_
21	FLAG	flag	NN	_	_	_
22	and	and	CC	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	strains	strain	NNS	_	_	_
25	at	at	IN	_	_	_
26	4	4	CD	_	_	_
27	℃	℃	CD	_	_	_
28	overnight	overnight	JJ	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	IP	IP	NNP	_	_	_
8	buffer	buffer	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	Tris-HCl	tris-hcl	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	pH	ph	NN	_	_	_
15	7.4	7.4	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	0.1	0.1	CD	_	_	_
19	M	m	NN	_	_	_
20	NaCl	nacl	NN	_	_	_
21	,	,	,	_	_	_
22	1	1	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	EDTA	edta	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	0.05	0.05	CD	_	_	_
28	%	%	NN	_	_	_
29	-LSB-	-lsb-	-LRB-	_	_	_
30	v/v	v/v	NN	_	_	_
31	-RSB-	-rsb-	-RRB-	_	_	_
32	Tween-20	tween-20	NN	_	_	_
33	and	and	CC	_	_	_
34	1	1	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	fresh	fresh	JJ	_	_	_
37	PMSF	pmsf	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	,	,	,	_	_	_
40	twice	twice	RB	_	_	_
41	with	with	IN	_	_	_
42	ChIP	chip	NN	_	_	_
43	wash	wash	NN	_	_	_
44	buffer	buffer	NN	_	_	_
45	I	i	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	10	10	CD	_	_	_
48	mM	mm	NN	KWSUPP	_	_
49	Tris	Tris	NNP	_	_	_
50	HCl	hcl	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	pH	ph	NN	_	_	_
53	7.4	7.4	CD	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	,	,	,	_	_	_
56	300	300	CD	_	_	_
57	mM	mm	NN	KWSUPP	_	_
58	NaCl	nacl	NN	_	_	_
59	,	,	,	_	_	_
60	1	1	CD	_	_	_
61	mM	mm	NN	KWSUPP	_	_
62	EDTA	edta	NN	_	_	_
63	,	,	,	_	_	_
64	0.1	0.1	CD	_	_	_
65	%	%	NN	_	_	_
66	Tween-20	tween-20	NN	_	_	_
67	and	and	CC	_	_	_
68	1	1	CD	_	_	_
69	mM	mm	NN	KWSUPP	_	_
70	fresh	fresh	JJ	_	_	_
71	PMSF	pmsf	NN	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	,	,	,	_	_	_
74	three	three	CD	_	_	_
75	times	time	NNS	_	_	_
76	with	with	IN	_	_	_
77	ChIP	chip	NN	_	_	_
78	wash	wash	NN	_	_	_
79	buffer	buffer	NN	_	_	_
80	II	ii	CD	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	10	10	CD	_	_	_
83	mM	mm	NN	KWSUPP	_	_
84	Tris-HCl	tris-hcl	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	pH	ph	NN	_	_	_
87	7.4	7.4	CD	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	,	,	,	_	_	_
90	500	500	CD	_	_	_
91	mM	mm	NN	KWSUPP	_	_
92	NaCl	nacl	NN	_	_	_
93	,	,	,	_	_	_
94	1	1	CD	_	_	_
95	mM	mm	NN	KWSUPP	_	_
96	EDTA	edta	NN	_	_	_
97	,	,	,	_	_	_
98	0.1	0.1	CD	_	_	_
99	%	%	NN	_	_	_
100	-LSB-	-lsb-	-LRB-	_	_	_
101	v/v	v/v	NN	_	_	_
102	-RSB-	-rsb-	-RRB-	_	_	_
103	Tween-20	tween-20	NN	_	_	_
104	and	and	CC	_	_	_
105	1	1	CD	_	_	_
106	mM	mm	NN	KWSUPP	_	_
107	fresh	fresh	JJ	_	_	_
108	PMSF	pmsf	NN	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	,	,	,	_	_	_
111	once	once	RB	_	_	_
112	with	with	IN	_	_	_
113	ChIP	chip	NN	_	_	_
114	wash	wash	NN	_	_	_
115	buffer	buffer	NN	_	_	_
116	III	iii	CD	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	10	10	CD	_	_	_
119	mM	mm	NN	KWSUPP	_	_
120	Tris-HCl	tris-hcl	NN	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	pH	ph	NN	_	_	_
123	7.4	7.4	CD	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	,	,	,	_	_	_
126	250	250	CD	_	_	_
127	mM	mm	NN	KWSUPP	_	_
128	LiCl	licl	NN	_	_	_
129	,	,	,	_	_	_
130	1	1	CD	_	_	_
131	mM	mm	NN	KWSUPP	_	_
132	EDTA	edta	NN	_	_	_
133	,	,	,	_	_	_
134	0.1	0.1	CD	_	_	_
135	%	%	NN	_	_	_
136	-LSB-	-lsb-	-LRB-	_	_	_
137	v/v	v/v	NN	_	_	_
138	-RSB-	-rsb-	-RRB-	_	_	_
139	Tween-20	tween-20	NN	_	_	_
140	and	and	CC	_	_	_
141	1	1	CD	_	_	_
142	mM	mm	NN	KWSUPP	_	_
143	fresh	fresh	JJ	_	_	_
144	PMSF	pmsf	NN	_	_	_
145	-RRB-	-rrb-	-RRB-	_	_	_
146	and	and	CC	_	_	_
147	once	once	RB	_	_	_
148	with	with	IN	_	_	_
149	TE	te	NN	_	_	_
150	buffer	buffer	NN	_	_	_
151	-LRB-	-lrb-	-LRB-	_	_	_
152	10	10	CD	_	_	_
153	mM	mm	NN	KWSUPP	_	_
154	Tris-HCl	tris-hcl	NN	_	_	_
155	-LRB-	-lrb-	-LRB-	_	_	_
156	pH	ph	NN	_	_	_
157	7.4	7.4	CD	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	and	and	CC	_	_	_
160	1	1	CD	_	_	_
161	mM	mm	NN	KWSUPP	_	_
162	EDTA	edta	NN	_	_	_
163	-RRB-	-rrb-	-RRB-	_	_	_
164	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	removing	remove	VBG	_	_	_
3	the	the	DT	_	_	_
4	TE	TE	NNP	_	_	_
5	buffer	buffer	NN	_	_	_
6	,	,	,	_	_	_
7	beads	bead	NNS	_	_	_
8	were	be	VBD	_	_	_
9	incubated	incubate	VBN	_	_	_
10	with	with	IN	_	_	_
11	elution	elution	NN	_	_	_
12	buffer	buffer	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	50	50	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	Tris-HCl	tris-hcl	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	pH	ph	NN	_	_	_
19	7.4	7.4	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	10	10	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	EDTA	edta	NN	_	_	_
25	and	and	CC	_	_	_
26	1	1	CD	_	_	_
27	%	%	NN	_	_	_
28	SDS	sds	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	at	at	IN	_	_	_
31	65	65	CD	_	_	_
32	℃	℃	NN	_	_	_
33	for	for	IN	_	_	_
34	15	15	CD	_	_	_
35	min	min	NN	_	_	_
36	twice	twice	RB	_	_	_
37	and	and	CC	_	_	_
38	then	then	RB	_	_	_
39	the	the	DT	_	_	_
40	resulting	result	VBG	_	_	_
41	eluted	elute	VBN	_	_	_
42	solutions	solution	NNS	_	_	_
43	combined	combine	VBN	_	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubating	incubate	VBG	_	_	_
3	with	with	IN	_	_	_
4	the	the	DT	_	_	_
5	final	final	JJ	_	_	_
6	concentration	concentration	NN	_	_	_
7	of	of	IN	_	_	_
8	10.5	10.5	CD	_	_	_
9	U/ml	u/ml	NN	_	_	_
10	proteinase	proteinase	NN	_	_	_
11	K	k	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Sigma	Sigma	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	at	at	IN	_	_	_
16	42	42	CD	_	_	_
17	℃	℃	NN	_	_	_
18	for	for	IN	_	_	_
19	2	2	CD	_	_	_
20	hours	hour	NNS	_	_	_
21	,	,	,	_	_	_
22	the	the	DT	_	_	_
23	reverse	reverse	JJ	_	_	_
24	cross-link	cross-link	NN	_	_	_
25	procedure	procedure	NN	_	_	_
26	was	be	VBD	_	_	_
27	performed	perform	VBN	_	_	_
28	by	by	IN	_	_	_
29	incubating	incubate	VBG	_	_	_
30	at	at	IN	_	_	_
31	65	65	CD	_	_	_
32	℃	℃	CD	_	_	_
33	overnight	overnight	JJ	_	_	_
34	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	the	the	DT	_	_	_
7	final	final	JJ	_	_	_
8	concentration	concentration	NN	_	_	_
9	of	of	IN	_	_	_
10	26	26	CD	_	_	_
11	μg/ml	μg/ml	NN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Sigma	Sigma	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	PCR	pcr	NN	_	_	_
3	purification	purification	NN	_	_	_
4	kit	kit	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Qiagen	qiagen	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	to	to	TO	_	_	_
11	purify	purify	VB	_	_	_
12	DNA	dna	NN	_	_	_
13	from	from	IN	_	_	_
14	the	the	DT	_	_	_
15	RNase	rnase	NN	_	_	_
16	A-treated	a-treated	JJ	_	_	_
17	samples	sample	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
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	,	,	,	_	_	_
10	incubated	incubate	VBN	_	_	_
11	overnight	overnight	RB	_	_	_
12	,	,	,	_	_	_
13	sub-cultured	sub-cultured	JJ	_	_	_
14	with	with	IN	_	_	_
15	a	a	DT	_	_	_
16	1	1	CD	_	_	_
17	%	%	NN	_	_	_
18	inoculum	inoculum	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	grown	grow	VBN	_	_	_
22	to	to	TO	_	_	_
23	the	the	DT	_	_	_
24	late	late	JJ	_	_	_
25	exponential	exponential	JJ	_	_	_
26	growth	growth	NN	_	_	_
27	phase	phase	NN	_	_	_
28	,	,	,	_	_	_
29	corresponding	correspond	VBG	_	_	_
30	to	to	TO	_	_	_
31	an	a	DT	_	_	_
32	OD600	od600	NN	_	_	_
33	nm	nm	NN	_	_	_
34	of	of	IN	_	_	_
35	0.6	0.6	CD	_	_	_
36	--	--	:	_	_	_
37	0.7	0.7	CD	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	maintained	maintain	VBN	_	_	_
5	on	on	IN	_	_	_
6	tryptic	tryptic	JJ	_	_	_
7	soy	soy	NN	_	_	_
8	agar	agar	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	TSA	tsa	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Becton	Becton	NNP	_	_	_
14	Dickinson	Dickinson	NNP	_	_	_
15	,	,	,	_	_	_
16	Le	Le	NNP	_	_	_
17	Pont	Pont	NNP	_	_	_
18	Claix	Claix	NNP	_	_	_
19	,	,	,	_	_	_
20	France	France	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

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/ml	cfu/ml	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	suspension	suspension	NN	_	_	_
3	was	be	VBD	_	_	_
4	exposed	expose	VBN	_	_	_
5	to	to	TO	_	_	_
6	CORM-2	corm-2	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	250	250	CD	_	_	_
9	µM	µm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	or	or	CC	_	_	_
12	vehicle	vehicle	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	2.5	2.5	CD	_	_	_
15	%	%	NN	_	_	_
16	DMSO	dmso	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	4	4	CD	_	_	_
20	hours	hour	NNS	_	_	_
21	at	at	IN	_	_	_
22	37	37	CD	_	_	_
23	°C	°c	NN	_	_	_
24	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	volume	volume	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	10	10	CD	_	_	_
5	µl	µl	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	spread	spread	VBN	_	_	_
9	onto	onto	IN	_	_	_
10	TSA-agar	tsa-agar	JJ	_	_	_
11	plates	plate	NNS	_	_	_
12	and	and	CC	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	37	37	CD	_	_	_
16	°C	°c	NN	_	_	_
17	overnight	overnight	JJ	_	_	_
18	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	procedure	procedure	NN	_	_	_
3	was	be	VBD	_	_	_
4	repeated	repeat	VBN	_	_	_
5	10	10	CD	_	_	_
6	times	time	NNS	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	10x	10x	CD	_	_	_
9	,	,	,	_	_	_
10	~	~	CD	_	_	_
11	45	45	CD	_	_	_
12	generations	generation	NNS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	or	or	CC	_	_	_
15	20	20	CD	_	_	_
16	times	time	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	20x	20x	NN	_	_	_
19	,	,	,	_	_	_
20	~	~	NN	_	_	_
21	90	90	CD	_	_	_
22	generations	generation	NNS	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	split	split	VBN	_	_	_
5	into	into	IN	_	_	_
6	two	two	CD	_	_	_
7	10	10	CD	_	_	_
8	ml	ml	NN	_	_	_
9	cultures	culture	NNS	_	_	_
10	.	.	.	_	_	_

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	NN	_	_	_
20	Cultures	culture	NNS	_	_	_
21	were	be	VBD	_	_	_
22	spun	spin	VBN	_	_	_
23	down	down	RP	_	_	_
24	at	at	IN	_	_	_
25	4	4	CD	_	_	_
26	°C	°c	NN	_	_	_
27	,	,	,	_	_	_
28	15,000	15,000	CD	_	_	_
29	×	×	CD	_	_	_
30	g	g	NN	_	_	_
31	for	for	IN	_	_	_
32	3	3	CD	_	_	_
33	minutes	minute	NNS	_	_	_
34	.	.	.	_	_	_

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	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/phenol	ethanol/phenol	NN	_	_	_
10	stop	stop	VB	_	_	_
11	solution	solution	NN	_	_	_
12	,	,	,	_	_	_
13	which	which	WDT	_	_	_
14	immediately	immediately	RB	_	_	_
15	inactivated	inactivate	VBD	_	_	_
16	cellular	cellular	JJ	_	_	_
17	RNases	rnase	NNS	_	_	_
18	.	.	.	_	_	_

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	stored	store	VBD	_	_	_
8	at	at	IN	_	_	_
9	-80	-80	CD	_	_	_
10	oC	oc	NN	_	_	_
11	until	until	IN	_	_	_
12	RNA	rna	NN	_	_	_
13	extraction	extraction	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	system	system	NN	_	_	_
4	:	:	:	_	_	_
5	BACTEC	bactec	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	culture	culture	NN	_	_	_
8	system	system	NN	_	_	_
9	:	:	:	_	_	_
10	flask	flask	NN	_	_	_
11	with	with	IN	_	_	_
12	continous	continous	JJ	_	_	_
13	shaking	shake	VBG	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	250	250	CD	_	_	_
16	rpm	rpm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	culture	culture	NN	_	_	_
20	system	system	NN	_	_	_
21	:	:	:	_	_	_
22	flask	flask	NN	_	_	_
23	with	with	IN	_	_	_
24	continuous	continuous	JJ	_	_	_
25	shaking	shake	VBG	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	250	250	CD	_	_	_
28	rpm	rpm	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	culture	culture	NN	_	_	_
32	system	system	NN	_	_	_
33	:	:	:	_	_	_
34	static	static	JJ	_	_	_
35	petri	petri	JJ	_	_	_
36	dish	dish	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	disposable	disposable	JJ	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
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	37	37	CD	_	_	_
54	°C	°c	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	culture	culture	NN	_	_	_
57	temperature	temperature	NN	_	_	_
58	:	:	:	_	_	_
59	42	42	CD	_	_	_
60	°C	°c	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	culture	culture	NN	_	_	_
63	temperature	temperature	NN	_	_	_
64	:	:	:	_	_	_
65	42	42	CD	_	_	_
66	°C	°c	NN	_	_	_
67	for	for	IN	_	_	_
68	60	60	CD	_	_	_
69	min	min	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	culture	culture	NN	_	_	_
72	temperature	temperature	NN	_	_	_
73	:	:	:	_	_	_
74	room	room	NN	_	_	_
75	temperature	temperature	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	20	20	CD	_	_	_
78	C	c	NN	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	culture	culture	NN	_	_	_
82	time	time	NN	_	_	_
83	:	:	:	_	_	_
84	18	18	CD	_	_	_
85	h	h	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	culture	culture	NN	_	_	_
88	type	type	NN	_	_	_
89	:	:	:	_	_	_
90	Ancestor	Ancestor	NNP	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	culture	culture	NN	_	_	_
93	type	type	NN	_	_	_
94	:	:	:	_	_	_
95	coculture	coculture	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	culture	culture	NN	_	_	_
98	type	type	NN	_	_	_
99	:	:	:	_	_	_
100	evolved	evolve	VBD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
102	culture	culture	NN	_	_	_
103	type	type	NN	_	_	_
104	:	:	:	_	_	_
105	monoculture	monoculture	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	Custom	Custom	NNP	_	_	_
108	anti-Fur	anti-fur	JJ	_	_	_
109	antibodies	antibody	NNS	_	_	_
110	were	be	VBD	_	_	_
111	purified	purify	VBN	_	_	_
112	over	over	IN	_	_	_
113	a	a	DT	_	_	_
114	His6-Fur	his6-fur	NN	_	_	_
115	bound	bind	VBD	_	_	_
116	HiTrap	HiTrap	NNP	_	_	_
117	NHS-activated	NHS-activated	NNP	_	_	_
118	HP	HP	NNP	_	_	_
119	column	column	NN	_	_	_
120	-LRB-	-lrb-	-LRB-	_	_	_
121	GE	GE	NNP	_	_	_
122	Healthcare	Healthcare	NNP	_	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	as	as	IN	_	_	_
125	previously	previously	RB	_	_	_
126	described	describe	VBN	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	PMID	pmid	NN	_	_	_
129	:	:	:	_	_	_
130	21478858	21478858	CD	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	.	.	.	_	_	_

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	CV108	cv108	NN	_	_	_
3	_	_	CD	_	_	_
4	minus	minus	CC	_	_	_
5	_	_	SYM	_	_	_
6	aMG	aMG	NNP	_	_	_
7	_	_	SYM	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	CV108	cv108	NN	_	_	_
11	_	_	CD	_	_	_
12	minus	minus	CC	_	_	_
13	_	_	SYM	_	_	_
14	aMG	aMG	NNP	_	_	_
15	_	_	SYM	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	CV108	cv108	NN	_	_	_
19	_	_	CD	_	_	_
20	minus	minus	CC	_	_	_
21	_	_	SYM	_	_	_
22	aMG	aMG	NNP	_	_	_
23	_	_	SYM	_	_	_
24	3	3	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	CV108	cv108	NN	_	_	_
27	_	_	NN	_	_	_
28	plus	plus	CC	_	_	_
29	_	_	SYM	_	_	_
30	aMG	aMG	NNP	_	_	_
31	_	_	SYM	_	_	_
32	1	1	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	CV108	cv108	NN	_	_	_
35	_	_	NN	_	_	_
36	plus	plus	CC	_	_	_
37	_	_	SYM	_	_	_
38	aMG	aMG	NNP	_	_	_
39	_	_	SYM	_	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	CV108	cv108	NN	_	_	_
43	_	_	NN	_	_	_
44	plus	plus	CC	_	_	_
45	_	_	SYM	_	_	_
46	aMG	aMG	NNP	_	_	_
47	_	_	SYM	_	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Cy3	cy3	NN	_	_	_
51	and	and	CC	_	_	_
52	Cy5	cy5	NN	_	_	_
53	intensities	intensity	NNS	_	_	_
54	were	be	VBD	_	_	_
55	normalized	normalize	VBN	_	_	_
56	by	by	IN	_	_	_
57	scaling	scale	VBG	_	_	_
58	so	so	RB	_	_	_
59	that	that	IN	_	_	_
60	the	the	DT	_	_	_
61	75th	75th	JJ	_	_	_
62	percentile	percentile	NN	_	_	_
63	in	in	IN	_	_	_
64	the	the	DT	_	_	_
65	Cy3	cy3	NN	_	_	_
66	and	and	CC	_	_	_
67	Cy5	cy5	NN	_	_	_
68	channels	channel	NNS	_	_	_
69	were	be	VBD	_	_	_
70	equal	equal	JJ	_	_	_
71	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cy3	cy3	NN	_	_	_
3	labeled	label	VBN	_	_	_
4	EHEC	EHEC	NNP	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	pH	ph	NN	_	_	_
9	7.4	7.4	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Cy3	cy3	NN	_	_	_
12	labeled	label	VBN	_	_	_
13	EHEC	EHEC	NNP	_	_	_
14	grown	grow	VBN	_	_	_
15	in	in	IN	_	_	_
16	DMEM	DMEM	NNP	_	_	_
17	pH	ph	NN	_	_	_
18	7.4	7.4	CD	_	_	_
19	,	,	,	_	_	_
20	15	15	CD	_	_	_
21	minutes	minute	NNS	_	_	_
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	NN	_	_	_
38	acid-adapted	acid-adapted	JJ	_	_	_
39	in	in	IN	_	_	_
40	DMEM	DMEM	NNP	_	_	_
41	pH	ph	NN	_	_	_
42	5	5	CD	_	_	_
43	,	,	,	_	_	_
44	followed	follow	VBN	_	_	_
45	by	by	IN	_	_	_
46	30	30	CD	_	_	_
47	minutes	minute	NNS	_	_	_
48	pH	ph	NN	_	_	_
49	3	3	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Cy5	cy5	NN	_	_	_
52	labeled	label	VBN	_	_	_
53	EHEC	EHEC	NNP	_	_	_
54	acid-stressed	acid-stressed	JJ	_	_	_
55	in	in	IN	_	_	_
56	DMEM	DMEM	NNP	_	_	_
57	pH	ph	NN	_	_	_
58	3	3	CD	_	_	_
59	,	,	,	_	_	_
60	15	15	CD	_	_	_
61	minutes	minute	NNS	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Cy5	cy5	NN	_	_	_
64	labeled	label	VBN	_	_	_
65	EHEC	EHEC	NNP	_	_	_
66	acid-stressed	acid-stressed	JJ	_	_	_
67	in	in	IN	_	_	_
68	DMEM	DMEM	NNP	_	_	_
69	pH	ph	NN	_	_	_
70	3	3	CD	_	_	_
71	,	,	,	_	_	_
72	30minutes	30minutes	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Cy5	cy5	NN	_	_	_
75	labeled	label	VBN	_	_	_
76	EHEC	EHEC	NNP	_	_	_
77	bile	bile	NN	_	_	_
78	salt-stressed	salt-stressed	JJ	_	_	_
79	in	in	IN	_	_	_
80	DMEM	DMEM	NNP	_	_	_
81	,	,	,	_	_	_
82	90	90	CD	_	_	_
83	minutes	minute	NNS	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	cy	cy	NN	_	_	_
86	_	_	CD	_	_	_
87	a4	a4	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	cya	cya	NN	_	_	_
90	mutant	mutant	JJ	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	cya.rep1.ee	cya.rep1.ee	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	cya.rep1.me	cya.rep1.me	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	cya.rep2.ee	cya.rep2.ee	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	cya.rep2.me	cya.rep2.me	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	cy	cy	NN	_	_	_
101	_	_	CD	_	_	_
102	b4	b4	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	cyc1	cyc1	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	cyc2	cyc2	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	cyc3	cyc3	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	cyc4	cyc4	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	cyd1	cyd1	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	cyd2	cyd2	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	cyd3	cyd3	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	cyd4	cyd4	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	cysA	cysa	NN	GEN	_	_
121	KO	ko	NN	_	_	_
122	rep1	rep1	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	cysA	cysa	NN	GEN	_	_
125	KO	ko	NN	_	_	_
126	rep2	rep2	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	cysA	cysa	NN	GEN	_	_
129	KO	ko	NN	_	_	_
130	rep3	rep3	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	cysG	cysg	NN	GEN	_	_
133	KO	ko	NN	_	_	_
134	LB	lb	NN	_	_	_
135	rep1	rep1	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	cysG	cysg	NN	GEN	_	_
138	KO	ko	NN	_	_	_
139	LB	lb	NN	_	_	_
140	rep2	rep2	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	cysH	cysh	NN	GEN	_	_
143	KO	ko	NN	_	_	_
144	LB	lb	NN	_	_	_
145	rep1	rep1	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	cysH	cysh	NN	GEN	_	_
148	KO	ko	NN	_	_	_
149	LB	lb	NN	_	_	_
150	rep2	rep2	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	cysQ-gln-1	cysq-gln-1	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	cysQ-gln-2	cysq-gln-2	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	cysQ	cysq	NN	GEN	_	_
157	mutantin	mutantin	NN	_	_	_
158	Ala	ala	NN	_	_	_
159	media	media	NNS	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	cysQ	cysq	NN	GEN	_	_
162	mutantin	mutantin	NN	_	_	_
163	Gln	gln	NN	_	_	_
164	media	media	NNS	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	Cysteine	cysteine	NN	_	_	_
167	addition	addition	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	Cytidine	cytidine	NN	_	_	_
170	addition	addition	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	D1-ae10	d1-ae10	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	D1-ae11	d1-ae11	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	D1-ae12	d1-ae12	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	D1	d1	NN	_	_	_
179	+	+	CC	_	_	_
180	ae7	ae7	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	D1	d1	NN	_	_	_
183	+	+	CC	_	_	_
184	ae8	ae8	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	D1	d1	NN	_	_	_
187	+	+	CC	_	_	_
188	ae9	ae9	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	D1	d1	NN	_	_	_
191	+	+	CC	_	_	_
192	AN	a	DT	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	D1	d1	NN	_	_	_
195	+	+	CC	_	_	_
196	AN2	an2	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	D1	d1	NN	_	_	_
199	+	+	CC	_	_	_
200	AN3	an3	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	D1-AN4	d1-an4	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	D1-AN5	d1-an5	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	D1-AN6	d1-an6	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	D2	d2	NN	_	_	_
209	_	_	CD	_	_	_
210	14	14	CD	_	_	_
211	_	_	NN	_	_	_
212	m10	m10	NN	_	_	_
213	-LSB-	-lsb-	-LRB-	_	_	_
214	COPRO-Seq	copro-seq	NN	_	_	_
215	-RSB-	-rsb-	-RRB-	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	D2	d2	NN	_	_	_
218	_	_	CD	_	_	_
219	14	14	CD	_	_	_
220	_	_	SYM	_	_	_
221	m11	m11	NN	_	_	_
222	-LSB-	-lsb-	-LRB-	_	_	_
223	COPRO-Seq	copro-seq	NN	_	_	_
224	-RSB-	-rsb-	-RRB-	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	D2	d2	NN	_	_	_
227	_	_	CD	_	_	_
228	14	14	CD	_	_	_
229	_	_	SYM	_	_	_
230	m12	m12	NN	_	_	_
231	-LSB-	-lsb-	-LRB-	_	_	_
232	COPRO-Seq	copro-seq	NN	_	_	_
233	-RSB-	-rsb-	-RRB-	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	D2	d2	NN	_	_	_
236	_	_	CD	_	_	_
237	14	14	CD	_	_	_
238	_	_	SYM	_	_	_
239	m13	m13	NN	_	_	_
240	-LSB-	-lsb-	-LRB-	_	_	_
241	COPRO-Seq	copro-seq	NN	_	_	_
242	-RSB-	-rsb-	-RRB-	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	D2	d2	NN	_	_	_
245	_	_	CD	_	_	_
246	14	14	CD	_	_	_
247	_	_	SYM	_	_	_
248	m1	m1	NN	_	_	_
249	-LSB-	-lsb-	-LRB-	_	_	_
250	COPRO-Seq	copro-seq	NN	_	_	_
251	-RSB-	-rsb-	-RRB-	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	D2	d2	NN	_	_	_
254	_	_	CD	_	_	_
255	14	14	CD	_	_	_
256	_	_	NN	_	_	_
257	m2	m2	NN	_	_	_
258	-LSB-	-lsb-	-LRB-	_	_	_
259	COPRO-Seq	copro-seq	NN	_	_	_
260	-RSB-	-rsb-	-RRB-	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	D2	d2	NN	_	_	_
263	_	_	CD	_	_	_
264	14	14	CD	_	_	_
265	_	_	NN	_	_	_
266	m3	m3	NN	_	_	_
267	-LSB-	-lsb-	-LRB-	_	_	_
268	COPRO-Seq	copro-seq	NN	_	_	_
269	-RSB-	-rsb-	-RRB-	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	D2	d2	NN	_	_	_
272	_	_	CD	_	_	_
273	14	14	CD	_	_	_
274	_	_	NN	_	_	_
275	m4	m4	NN	_	_	_
276	-LSB-	-lsb-	-LRB-	_	_	_
277	COPRO-Seq	copro-seq	NN	_	_	_
278	-RSB-	-rsb-	-RRB-	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	D2	d2	NN	_	_	_
281	_	_	CD	_	_	_
282	14	14	CD	_	_	_
283	_	_	NN	_	_	_
284	m5	m5	NN	_	_	_
285	-LSB-	-lsb-	-LRB-	_	_	_
286	COPRO-Seq	copro-seq	NN	_	_	_
287	-RSB-	-rsb-	-RRB-	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	D2	d2	NN	_	_	_
290	_	_	CD	_	_	_
291	14	14	CD	_	_	_
292	_	_	NN	_	_	_
293	m7	m7	NN	_	_	_
294	-LSB-	-lsb-	-LRB-	_	_	_
295	COPRO-Seq	copro-seq	NN	_	_	_
296	-RSB-	-rsb-	-RRB-	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	D2	d2	NN	_	_	_
299	_	_	CD	_	_	_
300	14	14	CD	_	_	_
301	_	_	NN	_	_	_
302	m8	m8	NN	_	_	_
303	-LSB-	-lsb-	-LRB-	_	_	_
304	COPRO-Seq	copro-seq	NN	_	_	_
305	-RSB-	-rsb-	-RRB-	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	D2	d2	NN	_	_	_
308	_	_	CD	_	_	_
309	14	14	CD	_	_	_
310	_	_	NN	_	_	_
311	m9	m9	NN	_	_	_
312	-LSB-	-lsb-	-LRB-	_	_	_
313	COPRO-Seq	copro-seq	NN	_	_	_
314	-RSB-	-rsb-	-RRB-	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	D2	d2	NN	_	_	_
317	_	_	NN	_	_	_
318	1	1	CD	_	_	_
319	_	_	CD	_	_	_
320	m12	m12	NN	_	_	_
321	-LSB-	-lsb-	-LRB-	_	_	_
322	COPRO-Seq	copro-seq	NN	_	_	_
323	-RSB-	-rsb-	-RRB-	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	D2	d2	NN	_	_	_
326	_	_	NN	_	_	_
327	1	1	CD	_	_	_
328	_	_	CD	_	_	_
329	m13	m13	NN	_	_	_
330	-LSB-	-lsb-	-LRB-	_	_	_
331	COPRO-Seq	copro-seq	NN	_	_	_
332	-RSB-	-rsb-	-RRB-	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	D2	d2	NN	_	_	_
335	_	_	NN	_	_	_
336	1	1	CD	_	_	_
337	_	_	SYM	_	_	_
338	m1	m1	NN	_	_	_
339	-LSB-	-lsb-	-LRB-	_	_	_
340	COPRO-Seq	copro-seq	NN	_	_	_
341	-RSB-	-rsb-	-RRB-	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	D2	d2	NN	_	_	_
344	_	_	NN	_	_	_
345	1	1	CD	_	_	_
346	_	_	CD	_	_	_
347	m2	m2	NN	_	_	_
348	-LSB-	-lsb-	-LRB-	_	_	_
349	COPRO-Seq	copro-seq	NN	_	_	_
350	-RSB-	-rsb-	-RRB-	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	D2	d2	NN	_	_	_
353	_	_	NN	_	_	_
354	1	1	CD	_	_	_
355	_	_	CD	_	_	_
356	m3	m3	NN	_	_	_
357	-LSB-	-lsb-	-LRB-	_	_	_
358	COPRO-Seq	copro-seq	NN	_	_	_
359	-RSB-	-rsb-	-RRB-	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	D2	d2	NN	_	_	_
362	_	_	NN	_	_	_
363	1	1	CD	_	_	_
364	_	_	CD	_	_	_
365	m4	m4	NN	_	_	_
366	-LSB-	-lsb-	-LRB-	_	_	_
367	COPRO-Seq	copro-seq	NN	_	_	_
368	-RSB-	-rsb-	-RRB-	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	D2	d2	NN	_	_	_
371	_	_	NN	_	_	_
372	1	1	CD	_	_	_
373	_	_	CD	_	_	_
374	m5	m5	NN	_	_	_
375	-LSB-	-lsb-	-LRB-	_	_	_
376	COPRO-Seq	copro-seq	NN	_	_	_
377	-RSB-	-rsb-	-RRB-	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	D2	d2	NN	_	_	_
380	_	_	NN	_	_	_
381	1	1	CD	_	_	_
382	_	_	CD	_	_	_
383	m6	m6	NN	_	_	_
384	-LSB-	-lsb-	-LRB-	_	_	_
385	COPRO-Seq	copro-seq	NN	_	_	_
386	-RSB-	-rsb-	-RRB-	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	D2	d2	NN	_	_	_
389	_	_	NN	_	_	_
390	1	1	CD	_	_	_
391	_	_	CD	_	_	_
392	m7	m7	NN	_	_	_
393	-LSB-	-lsb-	-LRB-	_	_	_
394	COPRO-Seq	copro-seq	NN	_	_	_
395	-RSB-	-rsb-	-RRB-	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
397	D2	d2	NN	_	_	_
398	_	_	NN	_	_	_
399	1	1	CD	_	_	_
400	_	_	CD	_	_	_
401	m8	m8	NN	_	_	_
402	-LSB-	-lsb-	-LRB-	_	_	_
403	COPRO-Seq	copro-seq	NN	_	_	_
404	-RSB-	-rsb-	-RRB-	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	D2	d2	NN	_	_	_
407	_	_	NN	_	_	_
408	1	1	CD	_	_	_
409	_	_	CD	_	_	_
410	m9	m9	NN	_	_	_
411	-LSB-	-lsb-	-LRB-	_	_	_
412	COPRO-Seq	copro-seq	NN	_	_	_
413	-RSB-	-rsb-	-RRB-	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	D2	d2	NN	_	_	_
416	_	_	NN	_	_	_
417	2	2	CD	_	_	_
418	_	_	CD	_	_	_
419	m10	m10	NN	_	_	_
420	-LSB-	-lsb-	-LRB-	_	_	_
421	COPRO-Seq	copro-seq	NN	_	_	_
422	-RSB-	-rsb-	-RRB-	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	D2	d2	NN	_	_	_
425	_	_	NN	_	_	_
426	2	2	CD	_	_	_
427	_	_	CD	_	_	_
428	m12	m12	NN	_	_	_
429	-LSB-	-lsb-	-LRB-	_	_	_
430	COPRO-Seq	copro-seq	NN	_	_	_
431	-RSB-	-rsb-	-RRB-	_	_	_
432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
433	D2	d2	NN	_	_	_
434	_	_	NN	_	_	_
435	2	2	CD	_	_	_
436	_	_	CD	_	_	_
437	m13	m13	NN	_	_	_
438	-LSB-	-lsb-	-LRB-	_	_	_
439	COPRO-Seq	copro-seq	NN	_	_	_
440	-RSB-	-rsb-	-RRB-	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	D2	d2	NN	_	_	_
443	_	_	NN	_	_	_
444	2	2	CD	_	_	_
445	_	_	SYM	_	_	_
446	m1	m1	NN	_	_	_
447	-LSB-	-lsb-	-LRB-	_	_	_
448	COPRO-Seq	copro-seq	NN	_	_	_
449	-RSB-	-rsb-	-RRB-	_	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
451	D2	d2	NN	_	_	_
452	_	_	NN	_	_	_
453	2	2	CD	_	_	_
454	_	_	CD	_	_	_
455	m2	m2	NN	_	_	_
456	-LSB-	-lsb-	-LRB-	_	_	_
457	COPRO-Seq	copro-seq	NN	_	_	_
458	-RSB-	-rsb-	-RRB-	_	_	_
459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
460	D2	d2	NN	_	_	_
461	_	_	NN	_	_	_
462	2	2	CD	_	_	_
463	_	_	CD	_	_	_
464	m3	m3	NN	_	_	_
465	-LSB-	-lsb-	-LRB-	_	_	_
466	COPRO-Seq	copro-seq	NN	_	_	_
467	-RSB-	-rsb-	-RRB-	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	D2	d2	NN	_	_	_
470	_	_	NN	_	_	_
471	2	2	CD	_	_	_
472	_	_	CD	_	_	_
473	m4	m4	NN	_	_	_
474	-LSB-	-lsb-	-LRB-	_	_	_
475	COPRO-Seq	copro-seq	NN	_	_	_
476	-RSB-	-rsb-	-RRB-	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	D2	d2	NN	_	_	_
479	_	_	NN	_	_	_
480	2	2	CD	_	_	_
481	_	_	CD	_	_	_
482	m5	m5	NN	_	_	_
483	-LSB-	-lsb-	-LRB-	_	_	_
484	COPRO-Seq	copro-seq	NN	_	_	_
485	-RSB-	-rsb-	-RRB-	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	D2	d2	NN	_	_	_
488	_	_	NN	_	_	_
489	2	2	CD	_	_	_
490	_	_	CD	_	_	_
491	m6	m6	NN	_	_	_
492	-LSB-	-lsb-	-LRB-	_	_	_
493	COPRO-Seq	copro-seq	NN	_	_	_
494	-RSB-	-rsb-	-RRB-	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
496	D2	d2	NN	_	_	_
497	_	_	NN	_	_	_
498	2	2	CD	_	_	_
499	_	_	CD	_	_	_
500	m7	m7	NN	_	_	_
501	-LSB-	-lsb-	-LRB-	_	_	_
502	COPRO-Seq	copro-seq	NN	_	_	_
503	-RSB-	-rsb-	-RRB-	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	D2	d2	NN	_	_	_
506	_	_	NN	_	_	_
507	2	2	CD	_	_	_
508	_	_	CD	_	_	_
509	m8	m8	NN	_	_	_
510	-LSB-	-lsb-	-LRB-	_	_	_
511	COPRO-Seq	copro-seq	NN	_	_	_
512	-RSB-	-rsb-	-RRB-	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	D2	d2	NN	_	_	_
515	_	_	NN	_	_	_
516	2	2	CD	_	_	_
517	_	_	CD	_	_	_
518	m9	m9	NN	_	_	_
519	-LSB-	-lsb-	-LRB-	_	_	_
520	COPRO-Seq	copro-seq	NN	_	_	_
521	-RSB-	-rsb-	-RRB-	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
523	D2	d2	NN	_	_	_
524	_	_	CD	_	_	_
525	4	4	CD	_	_	_
526	_	_	NN	_	_	_
527	m10	m10	NN	_	_	_
528	-LSB-	-lsb-	-LRB-	_	_	_
529	COPRO-Seq	copro-seq	NN	_	_	_
530	-RSB-	-rsb-	-RRB-	_	_	_
531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
532	D2	d2	NN	_	_	_
533	_	_	CD	_	_	_
534	4	4	CD	_	_	_
535	_	_	SYM	_	_	_
536	m11	m11	NN	_	_	_
537	-LSB-	-lsb-	-LRB-	_	_	_
538	COPRO-Seq	copro-seq	NN	_	_	_
539	-RSB-	-rsb-	-RRB-	_	_	_
540	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
541	D2	d2	NN	_	_	_
542	_	_	CD	_	_	_
543	4	4	CD	_	_	_
544	_	_	SYM	_	_	_
545	m12	m12	NN	_	_	_
546	-LSB-	-lsb-	-LRB-	_	_	_
547	COPRO-Seq	copro-seq	NN	_	_	_
548	-RSB-	-rsb-	-RRB-	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	D2	d2	NN	_	_	_
551	_	_	CD	_	_	_
552	4	4	CD	_	_	_
553	_	_	SYM	_	_	_
554	m13	m13	NN	_	_	_
555	-LSB-	-lsb-	-LRB-	_	_	_
556	COPRO-Seq	copro-seq	NN	_	_	_
557	-RSB-	-rsb-	-RRB-	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
559	D2	d2	NN	_	_	_
560	_	_	CD	_	_	_
561	4	4	CD	_	_	_
562	_	_	SYM	_	_	_
563	m1	m1	NN	_	_	_
564	-LSB-	-lsb-	-LRB-	_	_	_
565	COPRO-Seq	copro-seq	NN	_	_	_
566	-RSB-	-rsb-	-RRB-	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	D2	d2	NN	_	_	_
569	_	_	CD	_	_	_
570	4	4	CD	_	_	_
571	_	_	NN	_	_	_
572	m3	m3	NN	_	_	_
573	-LSB-	-lsb-	-LRB-	_	_	_
574	COPRO-Seq	copro-seq	NN	_	_	_
575	-RSB-	-rsb-	-RRB-	_	_	_
576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
577	D2	d2	NN	_	_	_
578	_	_	CD	_	_	_
579	4	4	CD	_	_	_
580	_	_	NN	_	_	_
581	m4	m4	NN	_	_	_
582	-LSB-	-lsb-	-LRB-	_	_	_
583	COPRO-Seq	copro-seq	NN	_	_	_
584	-RSB-	-rsb-	-RRB-	_	_	_
585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
586	D2	d2	NN	_	_	_
587	_	_	CD	_	_	_
588	4	4	CD	_	_	_
589	_	_	NN	_	_	_
590	m5	m5	NN	_	_	_
591	-LSB-	-lsb-	-LRB-	_	_	_
592	COPRO-Seq	copro-seq	NN	_	_	_
593	-RSB-	-rsb-	-RRB-	_	_	_
594	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
595	D2	d2	NN	_	_	_
596	_	_	CD	_	_	_
597	4	4	CD	_	_	_
598	_	_	NN	_	_	_
599	m6	m6	NN	_	_	_
600	-LSB-	-lsb-	-LRB-	_	_	_
601	COPRO-Seq	copro-seq	NN	_	_	_
602	-RSB-	-rsb-	-RRB-	_	_	_
603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
604	D2	d2	NN	_	_	_
605	_	_	CD	_	_	_
606	4	4	CD	_	_	_
607	_	_	NN	_	_	_
608	m7	m7	NN	_	_	_
609	-LSB-	-lsb-	-LRB-	_	_	_
610	COPRO-Seq	copro-seq	NN	_	_	_
611	-RSB-	-rsb-	-RRB-	_	_	_
612	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
613	D2	d2	NN	_	_	_
614	_	_	CD	_	_	_
615	4	4	CD	_	_	_
616	_	_	NN	_	_	_
617	m8	m8	NN	_	_	_
618	-LSB-	-lsb-	-LRB-	_	_	_
619	COPRO-Seq	copro-seq	NN	_	_	_
620	-RSB-	-rsb-	-RRB-	_	_	_
621	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
622	D2	d2	NN	_	_	_
623	_	_	NN	_	_	_
624	4	4	CD	_	_	_
625	_	_	CD	_	_	_
626	m9	m9	NN	_	_	_
627	-LSB-	-lsb-	-LRB-	_	_	_
628	COPRO-Seq	copro-seq	NN	_	_	_
629	-RSB-	-rsb-	-RRB-	_	_	_
630	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
631	D2	d2	NN	_	_	_
632	_	_	NN	_	_	_
633	7	7	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	D2	d2	NN	_	_	_
641	_	_	NN	_	_	_
642	7	7	CD	_	_	_
643	_	_	NN	_	_	_
644	m11	m11	NN	_	_	_
645	-LSB-	-lsb-	-LRB-	_	_	_
646	COPRO-Seq	copro-seq	NN	_	_	_
647	-RSB-	-rsb-	-RRB-	_	_	_
648	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
649	D2	d2	NN	_	_	_
650	_	_	NN	_	_	_
651	7	7	CD	_	_	_
652	_	_	NN	_	_	_
653	m12	m12	NN	_	_	_
654	-LSB-	-lsb-	-LRB-	_	_	_
655	COPRO-Seq	copro-seq	NN	_	_	_
656	-RSB-	-rsb-	-RRB-	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
658	D2	d2	NN	_	_	_
659	_	_	NN	_	_	_
660	7	7	CD	_	_	_
661	_	_	NN	_	_	_
662	m13	m13	NN	_	_	_
663	-LSB-	-lsb-	-LRB-	_	_	_
664	COPRO-Seq	copro-seq	NN	_	_	_
665	-RSB-	-rsb-	-RRB-	_	_	_
666	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
667	D2	d2	NN	_	_	_
668	_	_	NN	_	_	_
669	7	7	CD	_	_	_
670	_	_	SYM	_	_	_
671	m1	m1	NN	_	_	_
672	-LSB-	-lsb-	-LRB-	_	_	_
673	COPRO-Seq	copro-seq	NN	_	_	_
674	-RSB-	-rsb-	-RRB-	_	_	_
675	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
676	D2	d2	NN	_	_	_
677	_	_	NN	_	_	_
678	7	7	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	D2	d2	NN	_	_	_
686	_	_	NN	_	_	_
687	7	7	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	D2	d2	NN	_	_	_
695	_	_	NN	_	_	_
696	7	7	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	D2	d2	NN	_	_	_
704	_	_	NN	_	_	_
705	7	7	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	D2	d2	NN	_	_	_
713	_	_	NN	_	_	_
714	7	7	CD	_	_	_
715	_	_	NN	_	_	_
716	m8	m8	NN	_	_	_
717	-LSB-	-lsb-	-LRB-	_	_	_
718	COPRO-Seq	copro-seq	NN	_	_	_
719	-RSB-	-rsb-	-RRB-	_	_	_
720	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
721	D2	d2	NN	_	_	_
722	_	_	NN	_	_	_
723	7	7	CD	_	_	_
724	_	_	NN	_	_	_
725	m9	m9	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	10	10	CD	_	_	_
733	_	_	SYM	_	_	_
734	m1	m1	NN	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
736	D3	d3	NN	_	_	_
737	_	_	CD	_	_	_
738	10	10	CD	_	_	_
739	_	_	NN	_	_	_
740	m10	m10	NN	_	_	_
741	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
742	D3	d3	NN	_	_	_
743	_	_	CD	_	_	_
744	10	10	CD	_	_	_
745	_	_	NN	_	_	_
746	m11	m11	NN	_	_	_
747	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
748	D3	d3	NN	_	_	_
749	_	_	CD	_	_	_
750	10	10	CD	_	_	_
751	_	_	NN	_	_	_
752	m12	m12	NN	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	D3	d3	NN	_	_	_
755	_	_	CD	_	_	_
756	10	10	CD	_	_	_
757	_	_	NN	_	_	_
758	m13	m13	NN	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
760	D3	d3	NN	_	_	_
761	_	_	CD	_	_	_
762	10	10	CD	_	_	_
763	_	_	NN	_	_	_
764	m2	m2	NN	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
766	D3	d3	NN	_	_	_
767	_	_	CD	_	_	_
768	10	10	CD	_	_	_
769	_	_	NN	_	_	_
770	m3	m3	NN	_	_	_
771	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
772	D3	d3	NN	_	_	_
773	_	_	CD	_	_	_
774	10	10	CD	_	_	_
775	_	_	NN	_	_	_
776	m4	m4	NN	_	_	_
777	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
778	D3	d3	NN	_	_	_
779	_	_	CD	_	_	_
780	10	10	CD	_	_	_
781	_	_	NN	_	_	_
782	m5	m5	NN	_	_	_
783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
784	D3	d3	NN	_	_	_
785	_	_	CD	_	_	_
786	10	10	CD	_	_	_
787	_	_	NN	_	_	_
788	m6	m6	NN	_	_	_
789	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
790	D3	d3	NN	_	_	_
791	_	_	CD	_	_	_
792	10	10	CD	_	_	_
793	_	_	NN	_	_	_
794	m7	m7	NN	_	_	_
795	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
796	D3	d3	NN	_	_	_
797	_	_	CD	_	_	_
798	10	10	CD	_	_	_
799	_	_	NN	_	_	_
800	m8	m8	NN	_	_	_
801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
802	D3	d3	NN	_	_	_
803	_	_	CD	_	_	_
804	10	10	CD	_	_	_
805	_	_	NN	_	_	_
806	m9	m9	NN	_	_	_
807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
808	D3	d3	NN	_	_	_
809	_	_	CD	_	_	_
810	14	14	CD	_	_	_
811	_	_	NN	_	_	_
812	m10	m10	NN	_	_	_
813	-LSB-	-lsb-	-LRB-	_	_	_
814	COPRO-Seq	copro-seq	NN	_	_	_
815	-RSB-	-rsb-	-RRB-	_	_	_
816	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
817	D3	d3	NN	_	_	_
818	_	_	CD	_	_	_
819	14	14	CD	_	_	_
820	_	_	SYM	_	_	_
821	m11	m11	NN	_	_	_
822	-LSB-	-lsb-	-LRB-	_	_	_
823	COPRO-Seq	copro-seq	NN	_	_	_
824	-RSB-	-rsb-	-RRB-	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	D3	d3	NN	_	_	_
827	_	_	CD	_	_	_
828	14	14	CD	_	_	_
829	_	_	SYM	_	_	_
830	m12	m12	NN	_	_	_
831	-LSB-	-lsb-	-LRB-	_	_	_
832	COPRO-Seq	copro-seq	NN	_	_	_
833	-RSB-	-rsb-	-RRB-	_	_	_
834	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
835	D3	d3	NN	_	_	_
836	_	_	CD	_	_	_
837	14	14	CD	_	_	_
838	_	_	SYM	_	_	_
839	m13	m13	NN	_	_	_
840	-LSB-	-lsb-	-LRB-	_	_	_
841	COPRO-Seq	copro-seq	NN	_	_	_
842	-RSB-	-rsb-	-RRB-	_	_	_
843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
844	D3	d3	NN	_	_	_
845	_	_	CD	_	_	_
846	14	14	CD	_	_	_
847	_	_	NN	_	_	_
848	m2	m2	NN	_	_	_
849	-LSB-	-lsb-	-LRB-	_	_	_
850	COPRO-Seq	copro-seq	NN	_	_	_
851	-RSB-	-rsb-	-RRB-	_	_	_
852	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
853	D3	d3	NN	_	_	_
854	_	_	CD	_	_	_
855	14	14	CD	_	_	_
856	_	_	NN	_	_	_
857	m3	m3	NN	_	_	_
858	-LSB-	-lsb-	-LRB-	_	_	_
859	COPRO-Seq	copro-seq	NN	_	_	_
860	-RSB-	-rsb-	-RRB-	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
862	D3	d3	NN	_	_	_
863	_	_	CD	_	_	_
864	14	14	CD	_	_	_
865	_	_	NN	_	_	_
866	m4	m4	NN	_	_	_
867	-LSB-	-lsb-	-LRB-	_	_	_
868	COPRO-Seq	copro-seq	NN	_	_	_
869	-RSB-	-rsb-	-RRB-	_	_	_
870	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
871	D3	d3	NN	_	_	_
872	_	_	CD	_	_	_
873	14	14	CD	_	_	_
874	_	_	NN	_	_	_
875	m5	m5	NN	_	_	_
876	-LSB-	-lsb-	-LRB-	_	_	_
877	COPRO-Seq	copro-seq	NN	_	_	_
878	-RSB-	-rsb-	-RRB-	_	_	_
879	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
880	D3	d3	NN	_	_	_
881	_	_	CD	_	_	_
882	14	14	CD	_	_	_
883	_	_	NN	_	_	_
884	m6	m6	NN	_	_	_
885	-LSB-	-lsb-	-LRB-	_	_	_
886	COPRO-Seq	copro-seq	NN	_	_	_
887	-RSB-	-rsb-	-RRB-	_	_	_
888	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
889	D3	d3	NN	_	_	_
890	_	_	CD	_	_	_
891	14	14	CD	_	_	_
892	_	_	NN	_	_	_
893	m7	m7	NN	_	_	_
894	-LSB-	-lsb-	-LRB-	_	_	_
895	COPRO-Seq	copro-seq	NN	_	_	_
896	-RSB-	-rsb-	-RRB-	_	_	_
897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
898	D3	d3	NN	_	_	_
899	_	_	CD	_	_	_
900	14	14	CD	_	_	_
901	_	_	NN	_	_	_
902	m8	m8	NN	_	_	_
903	-LSB-	-lsb-	-LRB-	_	_	_
904	COPRO-Seq	copro-seq	NN	_	_	_
905	-RSB-	-rsb-	-RRB-	_	_	_
906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
907	D3	d3	NN	_	_	_
908	_	_	CD	_	_	_
909	14	14	CD	_	_	_
910	_	_	NN	_	_	_
911	m9	m9	NN	_	_	_
912	-LSB-	-lsb-	-LRB-	_	_	_
913	COPRO-Seq	copro-seq	NN	_	_	_
914	-RSB-	-rsb-	-RRB-	_	_	_
915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
916	D3	d3	NN	_	_	_
917	_	_	NN	_	_	_
918	1	1	CD	_	_	_
919	_	_	CD	_	_	_
920	m10	m10	NN	_	_	_
921	-LSB-	-lsb-	-LRB-	_	_	_
922	COPRO-Seq	copro-seq	NN	_	_	_
923	-RSB-	-rsb-	-RRB-	_	_	_
924	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
925	D3	d3	NN	_	_	_
926	_	_	NN	_	_	_
927	1	1	CD	_	_	_
928	_	_	CD	_	_	_
929	m11	m11	NN	_	_	_
930	-LSB-	-lsb-	-LRB-	_	_	_
931	COPRO-Seq	copro-seq	NN	_	_	_
932	-RSB-	-rsb-	-RRB-	_	_	_
933	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
934	D3	d3	NN	_	_	_
935	_	_	NN	_	_	_
936	1	1	CD	_	_	_
937	_	_	CD	_	_	_
938	m13	m13	NN	_	_	_
939	-LSB-	-lsb-	-LRB-	_	_	_
940	COPRO-Seq	copro-seq	NN	_	_	_
941	-RSB-	-rsb-	-RRB-	_	_	_
942	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
943	D3	d3	NN	_	_	_
944	_	_	NN	_	_	_
945	1	1	CD	_	_	_
946	_	_	SYM	_	_	_
947	m1	m1	NN	_	_	_
948	-LSB-	-lsb-	-LRB-	_	_	_
949	COPRO-Seq	copro-seq	NN	_	_	_
950	-RSB-	-rsb-	-RRB-	_	_	_
951	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
952	D3	d3	NN	_	_	_
953	_	_	NN	_	_	_
954	1	1	CD	_	_	_
955	_	_	CD	_	_	_
956	m2	m2	NN	_	_	_
957	-LSB-	-lsb-	-LRB-	_	_	_
958	COPRO-Seq	copro-seq	NN	_	_	_
959	-RSB-	-rsb-	-RRB-	_	_	_
960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
961	D3	d3	NN	_	_	_
962	_	_	NN	_	_	_
963	1	1	CD	_	_	_
964	_	_	CD	_	_	_
965	m3	m3	NN	_	_	_
966	-LSB-	-lsb-	-LRB-	_	_	_
967	COPRO-Seq	copro-seq	NN	_	_	_
968	-RSB-	-rsb-	-RRB-	_	_	_
969	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
970	D3	d3	NN	_	_	_
971	_	_	NN	_	_	_
972	1	1	CD	_	_	_
973	_	_	CD	_	_	_
974	m4	m4	NN	_	_	_
975	-LSB-	-lsb-	-LRB-	_	_	_
976	COPRO-Seq	copro-seq	NN	_	_	_
977	-RSB-	-rsb-	-RRB-	_	_	_
978	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
979	D3	d3	NN	_	_	_
980	_	_	NN	_	_	_
981	1	1	CD	_	_	_
982	_	_	CD	_	_	_
983	m5	m5	NN	_	_	_
984	-LSB-	-lsb-	-LRB-	_	_	_
985	COPRO-Seq	copro-seq	NN	_	_	_
986	-RSB-	-rsb-	-RRB-	_	_	_
987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
988	D3	d3	NN	_	_	_
989	_	_	NN	_	_	_
990	1	1	CD	_	_	_
991	_	_	CD	_	_	_
992	m6	m6	NN	_	_	_
993	-LSB-	-lsb-	-LRB-	_	_	_
994	COPRO-Seq	copro-seq	NN	_	_	_
995	-RSB-	-rsb-	-RRB-	_	_	_
996	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
997	D3	d3	NN	_	_	_
998	_	_	NN	_	_	_
999	1	1	CD	_	_	_
1000	_	_	CD	_	_	_
1001	m7	m7	NN	_	_	_
1002	-LSB-	-lsb-	-LRB-	_	_	_
1003	COPRO-Seq	copro-seq	NN	_	_	_
1004	-RSB-	-rsb-	-RRB-	_	_	_
1005	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1006	D3	d3	NN	_	_	_
1007	_	_	NN	_	_	_
1008	1	1	CD	_	_	_
1009	_	_	CD	_	_	_
1010	m8	m8	NN	_	_	_
1011	-LSB-	-lsb-	-LRB-	_	_	_
1012	COPRO-Seq	copro-seq	NN	_	_	_
1013	-RSB-	-rsb-	-RRB-	_	_	_
1014	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1015	D3	d3	NN	_	_	_
1016	_	_	NN	_	_	_
1017	2	2	CD	_	_	_
1018	_	_	CD	_	_	_
1019	m10	m10	NN	_	_	_
1020	-LSB-	-lsb-	-LRB-	_	_	_
1021	COPRO-Seq	copro-seq	NN	_	_	_
1022	-RSB-	-rsb-	-RRB-	_	_	_
1023	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1024	D3	d3	NN	_	_	_
1025	_	_	NN	_	_	_
1026	2	2	CD	_	_	_
1027	_	_	CD	_	_	_
1028	m11	m11	NN	_	_	_
1029	-LSB-	-lsb-	-LRB-	_	_	_
1030	COPRO-Seq	copro-seq	NN	_	_	_
1031	-RSB-	-rsb-	-RRB-	_	_	_
1032	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1033	D3	d3	NN	_	_	_
1034	_	_	NN	_	_	_
1035	2	2	CD	_	_	_
1036	_	_	CD	_	_	_
1037	m12	m12	NN	_	_	_
1038	-LSB-	-lsb-	-LRB-	_	_	_
1039	COPRO-Seq	copro-seq	NN	_	_	_
1040	-RSB-	-rsb-	-RRB-	_	_	_
1041	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1042	D3	d3	NN	_	_	_
1043	_	_	NN	_	_	_
1044	2	2	CD	_	_	_
1045	_	_	CD	_	_	_
1046	m13	m13	NN	_	_	_
1047	-LSB-	-lsb-	-LRB-	_	_	_
1048	COPRO-Seq	copro-seq	NN	_	_	_
1049	-RSB-	-rsb-	-RRB-	_	_	_
1050	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1051	D3	d3	NN	_	_	_
1052	_	_	NN	_	_	_
1053	2	2	CD	_	_	_
1054	_	_	CD	_	_	_
1055	m2	m2	NN	_	_	_
1056	-LSB-	-lsb-	-LRB-	_	_	_
1057	COPRO-Seq	copro-seq	NN	_	_	_
1058	-RSB-	-rsb-	-RRB-	_	_	_
1059	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1060	D3	d3	NN	_	_	_
1061	_	_	NN	_	_	_
1062	2	2	CD	_	_	_
1063	_	_	CD	_	_	_
1064	m4	m4	NN	_	_	_
1065	-LSB-	-lsb-	-LRB-	_	_	_
1066	COPRO-Seq	copro-seq	NN	_	_	_
1067	-RSB-	-rsb-	-RRB-	_	_	_
1068	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1069	D3	d3	NN	_	_	_
1070	_	_	NN	_	_	_
1071	2	2	CD	_	_	_
1072	_	_	CD	_	_	_
1073	m5	m5	NN	_	_	_
1074	-LSB-	-lsb-	-LRB-	_	_	_
1075	COPRO-Seq	copro-seq	NN	_	_	_
1076	-RSB-	-rsb-	-RRB-	_	_	_
1077	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1078	D3	d3	NN	_	_	_
1079	_	_	NN	_	_	_
1080	2	2	CD	_	_	_
1081	_	_	CD	_	_	_
1082	m6	m6	NN	_	_	_
1083	-LSB-	-lsb-	-LRB-	_	_	_
1084	COPRO-Seq	copro-seq	NN	_	_	_
1085	-RSB-	-rsb-	-RRB-	_	_	_
1086	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1087	D3	d3	NN	_	_	_
1088	_	_	NN	_	_	_
1089	2	2	CD	_	_	_
1090	_	_	CD	_	_	_
1091	m7	m7	NN	_	_	_
1092	-LSB-	-lsb-	-LRB-	_	_	_
1093	COPRO-Seq	copro-seq	NN	_	_	_
1094	-RSB-	-rsb-	-RRB-	_	_	_
1095	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1096	D3	d3	NN	_	_	_
1097	_	_	CD	_	_	_
1098	4	4	CD	_	_	_
1099	_	_	NN	_	_	_
1100	m10	m10	NN	_	_	_
1101	-LSB-	-lsb-	-LRB-	_	_	_
1102	COPRO-Seq	copro-seq	NN	_	_	_
1103	-RSB-	-rsb-	-RRB-	_	_	_
1104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1105	D3	d3	NN	_	_	_
1106	_	_	CD	_	_	_
1107	4	4	CD	_	_	_
1108	_	_	SYM	_	_	_
1109	m11	m11	NN	_	_	_
1110	-LSB-	-lsb-	-LRB-	_	_	_
1111	COPRO-Seq	copro-seq	NN	_	_	_
1112	-RSB-	-rsb-	-RRB-	_	_	_
1113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1114	D3	d3	NN	_	_	_
1115	_	_	CD	_	_	_
1116	4	4	CD	_	_	_
1117	_	_	SYM	_	_	_
1118	m12	m12	NN	_	_	_
1119	-LSB-	-lsb-	-LRB-	_	_	_
1120	COPRO-Seq	copro-seq	NN	_	_	_
1121	-RSB-	-rsb-	-RRB-	_	_	_
1122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1123	D3	d3	NN	_	_	_
1124	_	_	CD	_	_	_
1125	4	4	CD	_	_	_
1126	_	_	SYM	_	_	_
1127	m13	m13	NN	_	_	_
1128	-LSB-	-lsb-	-LRB-	_	_	_
1129	COPRO-Seq	copro-seq	NN	_	_	_
1130	-RSB-	-rsb-	-RRB-	_	_	_
1131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1132	D3	d3	NN	_	_	_
1133	_	_	CD	_	_	_
1134	4	4	CD	_	_	_
1135	_	_	SYM	_	_	_
1136	m1	m1	NN	_	_	_
1137	-LSB-	-lsb-	-LRB-	_	_	_
1138	COPRO-Seq	copro-seq	NN	_	_	_
1139	-RSB-	-rsb-	-RRB-	_	_	_
1140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1141	D3	d3	NN	_	_	_
1142	_	_	CD	_	_	_
1143	4	4	CD	_	_	_
1144	_	_	NN	_	_	_
1145	m2	m2	NN	_	_	_
1146	-LSB-	-lsb-	-LRB-	_	_	_
1147	COPRO-Seq	copro-seq	NN	_	_	_
1148	-RSB-	-rsb-	-RRB-	_	_	_
1149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1150	D3	d3	NN	_	_	_
1151	_	_	CD	_	_	_
1152	4	4	CD	_	_	_
1153	_	_	NN	_	_	_
1154	m3	m3	NN	_	_	_
1155	-LSB-	-lsb-	-LRB-	_	_	_
1156	COPRO-Seq	copro-seq	NN	_	_	_
1157	-RSB-	-rsb-	-RRB-	_	_	_
1158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1159	D3	d3	NN	_	_	_
1160	_	_	CD	_	_	_
1161	4	4	CD	_	_	_
1162	_	_	NN	_	_	_
1163	m4	m4	NN	_	_	_
1164	-LSB-	-lsb-	-LRB-	_	_	_
1165	COPRO-Seq	copro-seq	NN	_	_	_
1166	-RSB-	-rsb-	-RRB-	_	_	_
1167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1168	D3	d3	NN	_	_	_
1169	_	_	CD	_	_	_
1170	4	4	CD	_	_	_
1171	_	_	NN	_	_	_
1172	m5	m5	NN	_	_	_
1173	-LSB-	-lsb-	-LRB-	_	_	_
1174	COPRO-Seq	copro-seq	NN	_	_	_
1175	-RSB-	-rsb-	-RRB-	_	_	_
1176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1177	D3	d3	NN	_	_	_
1178	_	_	CD	_	_	_
1179	4	4	CD	_	_	_
1180	_	_	NN	_	_	_
1181	m6	m6	NN	_	_	_
1182	-LSB-	-lsb-	-LRB-	_	_	_
1183	COPRO-Seq	copro-seq	NN	_	_	_
1184	-RSB-	-rsb-	-RRB-	_	_	_
1185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1186	D3	d3	NN	_	_	_
1187	_	_	CD	_	_	_
1188	4	4	CD	_	_	_
1189	_	_	NN	_	_	_
1190	m7	m7	NN	_	_	_
1191	-LSB-	-lsb-	-LRB-	_	_	_
1192	COPRO-Seq	copro-seq	NN	_	_	_
1193	-RSB-	-rsb-	-RRB-	_	_	_
1194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1195	D3	d3	NN	_	_	_
1196	_	_	CD	_	_	_
1197	4	4	CD	_	_	_
1198	_	_	NN	_	_	_
1199	m8	m8	NN	_	_	_
1200	-LSB-	-lsb-	-LRB-	_	_	_
1201	COPRO-Seq	copro-seq	NN	_	_	_
1202	-RSB-	-rsb-	-RRB-	_	_	_
1203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1204	D3	d3	NN	_	_	_
1205	_	_	NN	_	_	_
1206	4	4	CD	_	_	_
1207	_	_	CD	_	_	_
1208	m9	m9	NN	_	_	_
1209	-LSB-	-lsb-	-LRB-	_	_	_
1210	COPRO-Seq	copro-seq	NN	_	_	_
1211	-RSB-	-rsb-	-RRB-	_	_	_
1212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1213	D3	d3	NN	_	_	_
1214	_	_	NN	_	_	_
1215	7	7	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	D3	d3	NN	_	_	_
1223	_	_	NN	_	_	_
1224	7	7	CD	_	_	_
1225	_	_	NN	_	_	_
1226	m11	m11	NN	_	_	_
1227	-LSB-	-lsb-	-LRB-	_	_	_
1228	COPRO-Seq	copro-seq	NN	_	_	_
1229	-RSB-	-rsb-	-RRB-	_	_	_
1230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1231	D3	d3	NN	_	_	_
1232	_	_	NN	_	_	_
1233	7	7	CD	_	_	_
1234	_	_	NN	_	_	_
1235	m12	m12	NN	_	_	_
1236	-LSB-	-lsb-	-LRB-	_	_	_
1237	COPRO-Seq	copro-seq	NN	_	_	_
1238	-RSB-	-rsb-	-RRB-	_	_	_
1239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1240	D3	d3	NN	_	_	_
1241	_	_	NN	_	_	_
1242	7	7	CD	_	_	_
1243	_	_	NN	_	_	_
1244	m13	m13	NN	_	_	_
1245	-LSB-	-lsb-	-LRB-	_	_	_
1246	COPRO-Seq	copro-seq	NN	_	_	_
1247	-RSB-	-rsb-	-RRB-	_	_	_
1248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1249	D3	d3	NN	_	_	_
1250	_	_	NN	_	_	_
1251	7	7	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	D3	d3	NN	_	_	_
1259	_	_	NN	_	_	_
1260	7	7	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	D3	d3	NN	_	_	_
1268	_	_	NN	_	_	_
1269	7	7	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	D3	d3	NN	_	_	_
1277	_	_	NN	_	_	_
1278	7	7	CD	_	_	_
1279	_	_	NN	_	_	_
1280	m4	m4	NN	_	_	_
1281	-LSB-	-lsb-	-LRB-	_	_	_
1282	COPRO-Seq	copro-seq	NN	_	_	_
1283	-RSB-	-rsb-	-RRB-	_	_	_
1284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1285	D3	d3	NN	_	_	_
1286	_	_	NN	_	_	_
1287	7	7	CD	_	_	_
1288	_	_	NN	_	_	_
1289	m5	m5	NN	_	_	_
1290	-LSB-	-lsb-	-LRB-	_	_	_
1291	COPRO-Seq	copro-seq	NN	_	_	_
1292	-RSB-	-rsb-	-RRB-	_	_	_
1293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1294	D3	d3	NN	_	_	_
1295	_	_	NN	_	_	_
1296	7	7	CD	_	_	_
1297	_	_	NN	_	_	_
1298	m6	m6	NN	_	_	_
1299	-LSB-	-lsb-	-LRB-	_	_	_
1300	COPRO-Seq	copro-seq	NN	_	_	_
1301	-RSB-	-rsb-	-RRB-	_	_	_
1302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1303	D3	d3	NN	_	_	_
1304	_	_	NN	_	_	_
1305	7	7	CD	_	_	_
1306	_	_	NN	_	_	_
1307	m9	m9	NN	_	_	_
1308	-LSB-	-lsb-	-LRB-	_	_	_
1309	COPRO-Seq	copro-seq	NN	_	_	_
1310	-RSB-	-rsb-	-RRB-	_	_	_
1311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1312	D3	d3	NN	_	_	_
1313	+	+	CC	_	_	_
1314	ae19	ae19	NN	_	_	_
1315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1316	D3	d3	NN	_	_	_
1317	+	+	CC	_	_	_
1318	ae20	ae20	NN	_	_	_
1319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1320	D3	d3	NN	_	_	_
1321	+	+	CC	_	_	_
1322	ae21	ae21	NN	_	_	_
1323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1324	D3-ae22	d3-ae22	NN	_	_	_
1325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1326	D3-ae23	d3-ae23	NN	_	_	_
1327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1328	D3-ae24	d3-ae24	NN	_	_	_
1329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1330	D3	d3	NN	_	_	_
1331	+	+	CC	_	_	_
1332	AN13	an13	NN	_	_	_
1333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1334	D3	d3	NN	_	_	_
1335	+	+	CC	_	_	_
1336	AN14	an14	NN	_	_	_
1337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1338	D3	d3	NN	_	_	_
1339	+	+	CC	_	_	_
1340	AN15	an15	NN	_	_	_
1341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1342	D3-AN16	d3-an16	NN	_	_	_
1343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1344	D3-AN17	d3-an17	NN	_	_	_
1345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1346	D3-AN18	d3-an18	NN	_	_	_
1347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1348	D4	d4	NN	_	_	_
1349	_	_	CD	_	_	_
1350	10	10	CD	_	_	_
1351	_	_	SYM	_	_	_
1352	m1	m1	NN	_	_	_
1353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1354	D4	d4	NN	_	_	_
1355	_	_	CD	_	_	_
1356	10	10	CD	_	_	_
1357	_	_	NN	_	_	_
1358	m10	m10	NN	_	_	_
1359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1360	D4	d4	NN	_	_	_
1361	_	_	CD	_	_	_
1362	10	10	CD	_	_	_
1363	_	_	NN	_	_	_
1364	m11	m11	NN	_	_	_
1365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1366	D4	d4	NN	_	_	_
1367	_	_	CD	_	_	_
1368	10	10	CD	_	_	_
1369	_	_	NN	_	_	_
1370	m12	m12	NN	_	_	_
1371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1372	D4	d4	NN	_	_	_
1373	_	_	CD	_	_	_
1374	10	10	CD	_	_	_
1375	_	_	NN	_	_	_
1376	m13	m13	NN	_	_	_
1377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1378	D4	d4	NN	_	_	_
1379	_	_	CD	_	_	_
1380	10	10	CD	_	_	_
1381	_	_	NN	_	_	_
1382	m2	m2	NN	_	_	_
1383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1384	D4	d4	NN	_	_	_
1385	_	_	CD	_	_	_
1386	10	10	CD	_	_	_
1387	_	_	NN	_	_	_
1388	m3	m3	NN	_	_	_
1389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1390	D4	d4	NN	_	_	_
1391	_	_	CD	_	_	_
1392	10	10	CD	_	_	_
1393	_	_	NN	_	_	_
1394	m4	m4	NN	_	_	_
1395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1396	D4	d4	NN	_	_	_
1397	_	_	CD	_	_	_
1398	10	10	CD	_	_	_
1399	_	_	NN	_	_	_
1400	m5	m5	NN	_	_	_
1401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1402	D4	d4	NN	_	_	_
1403	_	_	CD	_	_	_
1404	10	10	CD	_	_	_
1405	_	_	NN	_	_	_
1406	m6	m6	NN	_	_	_
1407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1408	D4	d4	NN	_	_	_
1409	_	_	CD	_	_	_
1410	10	10	CD	_	_	_
1411	_	_	NN	_	_	_
1412	m7	m7	NN	_	_	_
1413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1414	D4	d4	NN	_	_	_
1415	_	_	CD	_	_	_
1416	10	10	CD	_	_	_
1417	_	_	NN	_	_	_
1418	m8	m8	NN	_	_	_
1419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1420	D4	d4	NN	_	_	_
1421	_	_	CD	_	_	_
1422	10	10	CD	_	_	_
1423	_	_	NN	_	_	_
1424	m9	m9	NN	_	_	_
1425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1426	D4	d4	NN	_	_	_
1427	_	_	CD	_	_	_
1428	14	14	CD	_	_	_
1429	_	_	NN	_	_	_
1430	m10	m10	NN	_	_	_
1431	-LSB-	-lsb-	-LRB-	_	_	_
1432	COPRO-Seq	copro-seq	NN	_	_	_
1433	-RSB-	-rsb-	-RRB-	_	_	_
1434	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1435	D4	d4	NN	_	_	_
1436	_	_	CD	_	_	_
1437	14	14	CD	_	_	_
1438	_	_	SYM	_	_	_
1439	m11	m11	NN	_	_	_
1440	-LSB-	-lsb-	-LRB-	_	_	_
1441	COPRO-Seq	copro-seq	NN	_	_	_
1442	-RSB-	-rsb-	-RRB-	_	_	_
1443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1444	D4	d4	NN	_	_	_
1445	_	_	CD	_	_	_
1446	14	14	CD	_	_	_
1447	_	_	SYM	_	_	_
1448	m12	m12	NN	_	_	_
1449	-LSB-	-lsb-	-LRB-	_	_	_
1450	COPRO-Seq	copro-seq	NN	_	_	_
1451	-RSB-	-rsb-	-RRB-	_	_	_
1452	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1453	D4	d4	NN	_	_	_
1454	_	_	CD	_	_	_
1455	14	14	CD	_	_	_
1456	_	_	SYM	_	_	_
1457	m13	m13	NN	_	_	_
1458	-LSB-	-lsb-	-LRB-	_	_	_
1459	COPRO-Seq	copro-seq	NN	_	_	_
1460	-RSB-	-rsb-	-RRB-	_	_	_
1461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1462	D4	d4	NN	_	_	_
1463	_	_	CD	_	_	_
1464	14	14	CD	_	_	_
1465	_	_	SYM	_	_	_
1466	m1	m1	NN	_	_	_
1467	-LSB-	-lsb-	-LRB-	_	_	_
1468	COPRO-Seq	copro-seq	NN	_	_	_
1469	-RSB-	-rsb-	-RRB-	_	_	_
1470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1471	D4	d4	NN	_	_	_
1472	_	_	CD	_	_	_
1473	14	14	CD	_	_	_
1474	_	_	NN	_	_	_
1475	m2	m2	NN	_	_	_
1476	-LSB-	-lsb-	-LRB-	_	_	_
1477	COPRO-Seq	copro-seq	NN	_	_	_
1478	-RSB-	-rsb-	-RRB-	_	_	_
1479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1480	D4	d4	NN	_	_	_
1481	_	_	CD	_	_	_
1482	14	14	CD	_	_	_
1483	_	_	NN	_	_	_
1484	m3	m3	NN	_	_	_
1485	-LSB-	-lsb-	-LRB-	_	_	_
1486	COPRO-Seq	copro-seq	NN	_	_	_
1487	-RSB-	-rsb-	-RRB-	_	_	_
1488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1489	D4	d4	NN	_	_	_
1490	_	_	CD	_	_	_
1491	14	14	CD	_	_	_
1492	_	_	NN	_	_	_
1493	m5	m5	NN	_	_	_
1494	-LSB-	-lsb-	-LRB-	_	_	_
1495	COPRO-Seq	copro-seq	NN	_	_	_
1496	-RSB-	-rsb-	-RRB-	_	_	_
1497	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1498	D4	d4	NN	_	_	_
1499	_	_	CD	_	_	_
1500	14	14	CD	_	_	_
1501	_	_	NN	_	_	_
1502	m6	m6	NN	_	_	_
1503	-LSB-	-lsb-	-LRB-	_	_	_
1504	COPRO-Seq	copro-seq	NN	_	_	_
1505	-RSB-	-rsb-	-RRB-	_	_	_
1506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1507	D4	d4	NN	_	_	_
1508	_	_	CD	_	_	_
1509	14	14	CD	_	_	_
1510	_	_	NN	_	_	_
1511	m7	m7	NN	_	_	_
1512	-LSB-	-lsb-	-LRB-	_	_	_
1513	COPRO-Seq	copro-seq	NN	_	_	_
1514	-RSB-	-rsb-	-RRB-	_	_	_
1515	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1516	D4	d4	NN	_	_	_
1517	_	_	CD	_	_	_
1518	14	14	CD	_	_	_
1519	_	_	NN	_	_	_
1520	m8	m8	NN	_	_	_
1521	-LSB-	-lsb-	-LRB-	_	_	_
1522	COPRO-Seq	copro-seq	NN	_	_	_
1523	-RSB-	-rsb-	-RRB-	_	_	_
1524	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1525	D4	d4	NN	_	_	_
1526	_	_	CD	_	_	_
1527	14	14	CD	_	_	_
1528	_	_	NN	_	_	_
1529	m9	m9	NN	_	_	_
1530	-LSB-	-lsb-	-LRB-	_	_	_
1531	COPRO-Seq	copro-seq	NN	_	_	_
1532	-RSB-	-rsb-	-RRB-	_	_	_
1533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1534	D4	d4	NN	_	_	_
1535	_	_	NN	_	_	_
1536	1	1	CD	_	_	_
1537	_	_	CD	_	_	_
1538	m10	m10	NN	_	_	_
1539	-LSB-	-lsb-	-LRB-	_	_	_
1540	COPRO-Seq	copro-seq	NN	_	_	_
1541	-RSB-	-rsb-	-RRB-	_	_	_
1542	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1543	D4	d4	NN	_	_	_
1544	_	_	NN	_	_	_
1545	1	1	CD	_	_	_
1546	_	_	CD	_	_	_
1547	m11	m11	NN	_	_	_
1548	-LSB-	-lsb-	-LRB-	_	_	_
1549	COPRO-Seq	copro-seq	NN	_	_	_
1550	-RSB-	-rsb-	-RRB-	_	_	_
1551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1552	D4	d4	NN	_	_	_
1553	_	_	NN	_	_	_
1554	1	1	CD	_	_	_
1555	_	_	CD	_	_	_
1556	m12	m12	NN	_	_	_
1557	-LSB-	-lsb-	-LRB-	_	_	_
1558	COPRO-Seq	copro-seq	NN	_	_	_
1559	-RSB-	-rsb-	-RRB-	_	_	_
1560	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1561	D4	d4	NN	_	_	_
1562	_	_	NN	_	_	_
1563	1	1	CD	_	_	_
1564	_	_	CD	_	_	_
1565	m13	m13	NN	_	_	_
1566	-LSB-	-lsb-	-LRB-	_	_	_
1567	COPRO-Seq	copro-seq	NN	_	_	_
1568	-RSB-	-rsb-	-RRB-	_	_	_
1569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1570	D4	d4	NN	_	_	_
1571	_	_	NN	_	_	_
1572	1	1	CD	_	_	_
1573	_	_	CD	_	_	_
1574	m7	m7	NN	_	_	_
1575	-LSB-	-lsb-	-LRB-	_	_	_
1576	COPRO-Seq	copro-seq	NN	_	_	_
1577	-RSB-	-rsb-	-RRB-	_	_	_
1578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1579	D4	d4	NN	_	_	_
1580	_	_	NN	_	_	_
1581	1	1	CD	_	_	_
1582	_	_	CD	_	_	_
1583	m8	m8	NN	_	_	_
1584	-LSB-	-lsb-	-LRB-	_	_	_
1585	COPRO-Seq	copro-seq	NN	_	_	_
1586	-RSB-	-rsb-	-RRB-	_	_	_
1587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1588	D4	d4	NN	_	_	_
1589	_	_	NN	_	_	_
1590	1	1	CD	_	_	_
1591	_	_	CD	_	_	_
1592	m9	m9	NN	_	_	_
1593	-LSB-	-lsb-	-LRB-	_	_	_
1594	COPRO-Seq	copro-seq	NN	_	_	_
1595	-RSB-	-rsb-	-RRB-	_	_	_
1596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1597	D4	d4	NN	_	_	_
1598	_	_	NN	_	_	_
1599	2	2	CD	_	_	_
1600	_	_	CD	_	_	_
1601	m10	m10	NN	_	_	_
1602	-LSB-	-lsb-	-LRB-	_	_	_
1603	COPRO-Seq	copro-seq	NN	_	_	_
1604	-RSB-	-rsb-	-RRB-	_	_	_
1605	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1606	D4	d4	NN	_	_	_
1607	_	_	NN	_	_	_
1608	2	2	CD	_	_	_
1609	_	_	CD	_	_	_
1610	m11	m11	NN	_	_	_
1611	-LSB-	-lsb-	-LRB-	_	_	_
1612	COPRO-Seq	copro-seq	NN	_	_	_
1613	-RSB-	-rsb-	-RRB-	_	_	_
1614	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1615	D4	d4	NN	_	_	_
1616	_	_	NN	_	_	_
1617	2	2	CD	_	_	_
1618	_	_	CD	_	_	_
1619	m12	m12	NN	_	_	_
1620	-LSB-	-lsb-	-LRB-	_	_	_
1621	COPRO-Seq	copro-seq	NN	_	_	_
1622	-RSB-	-rsb-	-RRB-	_	_	_
1623	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1624	D4	d4	NN	_	_	_
1625	_	_	NN	_	_	_
1626	2	2	CD	_	_	_
1627	_	_	CD	_	_	_
1628	m13	m13	NN	_	_	_
1629	-LSB-	-lsb-	-LRB-	_	_	_
1630	COPRO-Seq	copro-seq	NN	_	_	_
1631	-RSB-	-rsb-	-RRB-	_	_	_
1632	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1633	D4	d4	NN	_	_	_
1634	_	_	NN	_	_	_
1635	2	2	CD	_	_	_
1636	_	_	CD	_	_	_
1637	m2	m2	NN	_	_	_
1638	-LSB-	-lsb-	-LRB-	_	_	_
1639	COPRO-Seq	copro-seq	NN	_	_	_
1640	-RSB-	-rsb-	-RRB-	_	_	_
1641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1642	D4	d4	NN	_	_	_
1643	_	_	NN	_	_	_
1644	2	2	CD	_	_	_
1645	_	_	CD	_	_	_
1646	m3	m3	NN	_	_	_
1647	-LSB-	-lsb-	-LRB-	_	_	_
1648	COPRO-Seq	copro-seq	NN	_	_	_
1649	-RSB-	-rsb-	-RRB-	_	_	_
1650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1651	D4	d4	NN	_	_	_
1652	_	_	NN	_	_	_
1653	2	2	CD	_	_	_
1654	_	_	CD	_	_	_
1655	m4	m4	NN	_	_	_
1656	-LSB-	-lsb-	-LRB-	_	_	_
1657	COPRO-Seq	copro-seq	NN	_	_	_
1658	-RSB-	-rsb-	-RRB-	_	_	_
1659	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1660	D4	d4	NN	_	_	_
1661	_	_	NN	_	_	_
1662	2	2	CD	_	_	_
1663	_	_	CD	_	_	_
1664	m5	m5	NN	_	_	_
1665	-LSB-	-lsb-	-LRB-	_	_	_
1666	COPRO-Seq	copro-seq	NN	_	_	_
1667	-RSB-	-rsb-	-RRB-	_	_	_
1668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1669	D4	d4	NN	_	_	_
1670	_	_	NN	_	_	_
1671	2	2	CD	_	_	_
1672	_	_	CD	_	_	_
1673	m6	m6	NN	_	_	_
1674	-LSB-	-lsb-	-LRB-	_	_	_
1675	COPRO-Seq	copro-seq	NN	_	_	_
1676	-RSB-	-rsb-	-RRB-	_	_	_
1677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1678	D4	d4	NN	_	_	_
1679	_	_	NN	_	_	_
1680	2	2	CD	_	_	_
1681	_	_	CD	_	_	_
1682	m7	m7	NN	_	_	_
1683	-LSB-	-lsb-	-LRB-	_	_	_
1684	COPRO-Seq	copro-seq	NN	_	_	_
1685	-RSB-	-rsb-	-RRB-	_	_	_
1686	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1687	D4	d4	NN	_	_	_
1688	_	_	NN	_	_	_
1689	2	2	CD	_	_	_
1690	_	_	CD	_	_	_
1691	m8	m8	NN	_	_	_
1692	-LSB-	-lsb-	-LRB-	_	_	_
1693	COPRO-Seq	copro-seq	NN	_	_	_
1694	-RSB-	-rsb-	-RRB-	_	_	_
1695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1696	D4	d4	NN	_	_	_
1697	_	_	NN	_	_	_
1698	2	2	CD	_	_	_
1699	_	_	CD	_	_	_
1700	m9	m9	NN	_	_	_
1701	-LSB-	-lsb-	-LRB-	_	_	_
1702	COPRO-Seq	copro-seq	NN	_	_	_
1703	-RSB-	-rsb-	-RRB-	_	_	_
1704	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1705	D4	d4	NN	_	_	_
1706	_	_	CD	_	_	_
1707	4	4	CD	_	_	_
1708	_	_	NN	_	_	_
1709	m10	m10	NN	_	_	_
1710	-LSB-	-lsb-	-LRB-	_	_	_
1711	COPRO-Seq	copro-seq	NN	_	_	_
1712	-RSB-	-rsb-	-RRB-	_	_	_
1713	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1714	D4	d4	NN	_	_	_
1715	_	_	CD	_	_	_
1716	4	4	CD	_	_	_
1717	_	_	SYM	_	_	_
1718	m12	m12	NN	_	_	_
1719	-LSB-	-lsb-	-LRB-	_	_	_
1720	COPRO-Seq	copro-seq	NN	_	_	_
1721	-RSB-	-rsb-	-RRB-	_	_	_
1722	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1723	D4	d4	NN	_	_	_
1724	_	_	CD	_	_	_
1725	4	4	CD	_	_	_
1726	_	_	SYM	_	_	_
1727	m13	m13	NN	_	_	_
1728	-LSB-	-lsb-	-LRB-	_	_	_
1729	COPRO-Seq	copro-seq	NN	_	_	_
1730	-RSB-	-rsb-	-RRB-	_	_	_
1731	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1732	D4	d4	NN	_	_	_
1733	_	_	CD	_	_	_
1734	4	4	CD	_	_	_
1735	_	_	NN	_	_	_
1736	m2	m2	NN	_	_	_
1737	-LSB-	-lsb-	-LRB-	_	_	_
1738	COPRO-Seq	copro-seq	NN	_	_	_
1739	-RSB-	-rsb-	-RRB-	_	_	_
1740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1741	D4	d4	NN	_	_	_
1742	_	_	CD	_	_	_
1743	4	4	CD	_	_	_
1744	_	_	NN	_	_	_
1745	m4	m4	NN	_	_	_
1746	-LSB-	-lsb-	-LRB-	_	_	_
1747	COPRO-Seq	copro-seq	NN	_	_	_
1748	-RSB-	-rsb-	-RRB-	_	_	_
1749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1750	D4	d4	NN	_	_	_
1751	_	_	CD	_	_	_
1752	4	4	CD	_	_	_
1753	_	_	NN	_	_	_
1754	m5	m5	NN	_	_	_
1755	-LSB-	-lsb-	-LRB-	_	_	_
1756	COPRO-Seq	copro-seq	NN	_	_	_
1757	-RSB-	-rsb-	-RRB-	_	_	_
1758	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1759	D4	d4	NN	_	_	_
1760	_	_	CD	_	_	_
1761	4	4	CD	_	_	_
1762	_	_	NN	_	_	_
1763	m6	m6	NN	_	_	_
1764	-LSB-	-lsb-	-LRB-	_	_	_
1765	COPRO-Seq	copro-seq	NN	_	_	_
1766	-RSB-	-rsb-	-RRB-	_	_	_
1767	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1768	D4	d4	NN	_	_	_
1769	_	_	CD	_	_	_
1770	4	4	CD	_	_	_
1771	_	_	NN	_	_	_
1772	m7	m7	NN	_	_	_
1773	-LSB-	-lsb-	-LRB-	_	_	_
1774	COPRO-Seq	copro-seq	NN	_	_	_
1775	-RSB-	-rsb-	-RRB-	_	_	_
1776	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1777	D4	d4	NN	_	_	_
1778	_	_	CD	_	_	_
1779	4	4	CD	_	_	_
1780	_	_	NN	_	_	_
1781	m8	m8	NN	_	_	_
1782	-LSB-	-lsb-	-LRB-	_	_	_
1783	COPRO-Seq	copro-seq	NN	_	_	_
1784	-RSB-	-rsb-	-RRB-	_	_	_
1785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1786	D4	d4	NN	_	_	_
1787	_	_	NN	_	_	_
1788	4	4	CD	_	_	_
1789	_	_	CD	_	_	_
1790	m9	m9	NN	_	_	_
1791	-LSB-	-lsb-	-LRB-	_	_	_
1792	COPRO-Seq	copro-seq	NN	_	_	_
1793	-RSB-	-rsb-	-RRB-	_	_	_
1794	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1795	D4	d4	NN	_	_	_
1796	_	_	NN	_	_	_
1797	7	7	CD	_	_	_
1798	_	_	SYM	_	_	_
1799	m1	m1	NN	_	_	_
1800	-LSB-	-lsb-	-LRB-	_	_	_
1801	COPRO-Seq	copro-seq	NN	_	_	_
1802	-RSB-	-rsb-	-RRB-	_	_	_
1803	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1804	D4	d4	NN	_	_	_
1805	_	_	NN	_	_	_
1806	7	7	CD	_	_	_
1807	_	_	NN	_	_	_
1808	m2	m2	NN	_	_	_
1809	-LSB-	-lsb-	-LRB-	_	_	_
1810	COPRO-Seq	copro-seq	NN	_	_	_
1811	-RSB-	-rsb-	-RRB-	_	_	_
1812	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1813	D4	d4	NN	_	_	_
1814	_	_	NN	_	_	_
1815	7	7	CD	_	_	_
1816	_	_	NN	_	_	_
1817	m3	m3	NN	_	_	_
1818	-LSB-	-lsb-	-LRB-	_	_	_
1819	COPRO-Seq	copro-seq	NN	_	_	_
1820	-RSB-	-rsb-	-RRB-	_	_	_
1821	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1822	D4	d4	NN	_	_	_
1823	_	_	NN	_	_	_
1824	7	7	CD	_	_	_
1825	_	_	NN	_	_	_
1826	m4	m4	NN	_	_	_
1827	-LSB-	-lsb-	-LRB-	_	_	_
1828	COPRO-Seq	copro-seq	NN	_	_	_
1829	-RSB-	-rsb-	-RRB-	_	_	_
1830	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1831	D4	d4	NN	_	_	_
1832	_	_	NN	_	_	_
1833	7	7	CD	_	_	_
1834	_	_	NN	_	_	_
1835	m5	m5	NN	_	_	_
1836	-LSB-	-lsb-	-LRB-	_	_	_
1837	COPRO-Seq	copro-seq	NN	_	_	_
1838	-RSB-	-rsb-	-RRB-	_	_	_
1839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1840	D4	d4	NN	_	_	_
1841	_	_	NN	_	_	_
1842	7	7	CD	_	_	_
1843	_	_	NN	_	_	_
1844	m6	m6	NN	_	_	_
1845	-LSB-	-lsb-	-LRB-	_	_	_
1846	COPRO-Seq	copro-seq	NN	_	_	_
1847	-RSB-	-rsb-	-RRB-	_	_	_
1848	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1849	dam	dam	NN	GEN	_	_
1850	___	___	CD	_	_	_
1851	U	U	NNP	_	_	_
1852	_	_	NNP	_	_	_
1853	N0075	N0075	NNP	_	_	_
1854	_	_	NNP	_	_	_
1855	r1	r1	NN	_	_	_
1856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1857	dam	dam	NN	GEN	_	_
1858	___	___	CD	_	_	_
1859	U	U	NNP	_	_	_
1860	_	_	NNP	_	_	_
1861	N0075	N0075	NNP	_	_	_
1862	_	_	NNP	_	_	_
1863	r2	r2	NN	_	_	_
1864	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1865	dam	dam	NN	GEN	_	_
1866	___	___	CD	_	_	_
1867	U	U	NNP	_	_	_
1868	_	_	NNP	_	_	_
1869	N0075	N0075	NNP	_	_	_
1870	_	_	NNP	_	_	_
1871	r3	r3	NN	_	_	_
1872	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1873	dam	dam	NN	GEN	_	_
1874	upregulation	upregulation	NN	_	_	_
1875	,	,	,	_	_	_
1876	0.075	0.075	CD	_	_	_
1877	ug/ml	ug/ml	NN	_	_	_
1878	norfloxacin	norfloxacin	NN	_	_	_
1879	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1880	∆	∆	CD	_	_	_
1881	dapF	dapf	NN	GEN	_	_
1882	parent	parent	NN	_	_	_
1883	Sample	sample	NN	_	_	_
1884	28	28	CD	_	_	_
1885	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1886	∆	∆	CD	_	_	_
1887	dapF	dapf	NN	GEN	_	_
1888	parent	parent	NN	_	_	_
1889	Sample	sample	NN	_	_	_
1890	47	47	CD	_	_	_
1891	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1892	∆	∆	CD	_	_	_
1893	dapF	dapf	NN	GEN	_	_
1894	parent	parent	NN	_	_	_
1895	Sample	Sample	NNP	_	_	_
1896	9	9	CD	_	_	_
1897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1898	dapF	dapf	NN	GEN	_	_
1899	suppressor	suppressor	NN	_	_	_
1900	1-1	1-1	CD	_	_	_
1901	Sample	sample	NN	_	_	_
1902	10	10	CD	_	_	_
1903	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1904	dapF	dapf	NN	GEN	_	_
1905	suppressor	suppressor	NN	_	_	_
1906	1-1	1-1	CD	_	_	_
1907	Sample	sample	NN	_	_	_
1908	29	29	CD	_	_	_
1909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1910	dapF	dapf	NN	GEN	_	_
1911	suppressor	suppressor	NN	_	_	_
1912	1-1	1-1	CD	_	_	_
1913	Sample	sample	NN	_	_	_
1914	48	48	CD	_	_	_
1915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1916	dapF	dapf	NN	GEN	_	_
1917	suppressor	suppressor	NN	_	_	_
1918	3-1	3-1	CD	_	_	_
1919	Sample	Sample	NNP	_	_	_
1920	11	11	CD	_	_	_
1921	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1922	dapF	dapf	NN	GEN	_	_
1923	suppressor	suppressor	NN	_	_	_
1924	3-1	3-1	CD	_	_	_
1925	Sample	Sample	NNP	_	_	_
1926	30	30	CD	_	_	_
1927	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1928	dapF	dapf	NN	GEN	_	_
1929	suppressor	suppressor	NN	_	_	_
1930	3-1	3-1	CD	_	_	_
1931	Sample	Sample	NNP	_	_	_
1932	49	49	CD	_	_	_
1933	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1934	Data	Data	NNP	_	_	_
1935	analysis	analysis	NN	_	_	_
1936	was	be	VBD	_	_	_
1937	carried	carry	VBN	_	_	_
1938	out	out	RP	_	_	_
1939	using	use	VBG	_	_	_
1940	the	the	DT	_	_	_
1941	Agilent	Agilent	NNP	_	_	_
1942	GeneSpring	GeneSpring	NNP	_	_	_
1943	GX	GX	NNP	_	_	_
1944	.	.	.	_	_	_

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	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	analysis	analysis	NN	_	_	_
4	was	be	VBD	_	_	_
5	done	do	VBN	_	_	_
6	using	use	VBG	_	_	_
7	R	r	NN	_	_	_
8	language	language	NN	_	_	_
9	and	and	CC	_	_	_
10	environment	environment	NN	_	_	_
11	for	for	IN	_	_	_
12	a	a	DT	_	_	_
13	statistical	statistical	JJ	_	_	_
14	computing	computing	NN	_	_	_
15	and	and	CC	_	_	_
16	Bioconductor	bioconductor	NN	_	_	_
17	.	.	.	_	_	_

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	Data	Data	NNP	_	_	_
3	collapsed	collapse	VBD	_	_	_
4	using	use	VBG	_	_	_
5	fastx	fastx	NN	_	_	_
6	collapser	collapser	NN	_	_	_
7	to	to	TO	_	_	_
8	remove	remove	VB	_	_	_
9	identical	identical	JJ	_	_	_
10	sequencing	sequencing	NN	_	_	_
11	reads	read	VBZ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	http://hannonlab.cshl.edu/fastx_toolkit/index.html	http://hannonlab.cshl.edu/fastx_toolkit/index.html	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	-	-	:	_	_	_
16	Example	example	NN	_	_	_
17	:	:	:	_	_	_
18	fastx	fastx	NN	_	_	_
19	_	_	NN	_	_	_
20	collapser	collapser	NN	_	_	_
21	-	-	:	_	_	_
22	i	i	FW	_	_	_
23	DL4900	dl4900	FW	_	_	_
24	_	_	SYM	_	_	_
25	clipped.fasta	clipped.fasta	SYM	_	_	_
26	-	-	:	_	_	_
27	o	o	NN	_	_	_
28	DL4900	dl4900	NN	_	_	_
29	_	_	CD	_	_	_
30	clip	clip	NN	_	_	_
31	_	_	SYM	_	_	_
32	clp.fasta	clp.fasta	FW	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Data	Data	NNP	_	_	_
35	extraction	extraction	NN	_	_	_
36	from	from	IN	_	_	_
37	Images	image	NNS	_	_	_
38	was	be	VBD	_	_	_
39	done	do	VBN	_	_	_
40	using	use	VBG	_	_	_
41	Feature	Feature	NNP	_	_	_
42	Extraction	Extraction	NNP	_	_	_
43	software	software	NN	_	_	_
44	v	v	LS	_	_	_
45	9.5.1	9.5.1	CD	_	_	_
46	of	of	IN	_	_	_
47	Agilent	Agilent	NNP	_	_	_
48	.	.	.	_	_	_

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	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	NNP	_	_	_
9	Data	Data	NNP	_	_	_
10	filtering	filter	VBG	_	_	_
11	was	be	VBD	_	_	_
12	done	do	VBN	_	_	_
13	with	with	IN	_	_	_
14	in-house	in-house	JJ	_	_	_
15	script	script	NN	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	set	set	VBN	_	_	_
19	value	value	NN	_	_	_
20	as	as	IN	_	_	_
21	follows	follow	VBZ	_	_	_
22	:	:	:	_	_	_
23	Removal	removal	NN	_	_	_
24	if	if	IN	_	_	_
25	%	%	NN	_	_	_
26	of	of	IN	_	_	_
27	N	n	NN	_	_	_
28	nucleotide	nucleotide	NN	_	_	_
29	is	be	VBZ	_	_	_
30	more	more	JJR	_	_	_
31	than	than	IN	_	_	_
32	10	10	CD	_	_	_
33	%	%	NN	_	_	_
34	,	,	,	_	_	_
35	if	if	IN	_	_	_
36	more	more	JJR	_	_	_
37	than	than	IN	_	_	_
38	40	40	CD	_	_	_
39	%	%	NN	_	_	_
40	of	of	IN	_	_	_
41	the	the	DT	_	_	_
42	nucleotide	nucleotide	NN	_	_	_
43	is	be	VBZ	_	_	_
44	Q20	q20	NN	_	_	_
45	or	or	CC	_	_	_
46	less	less	JJR	_	_	_
47	,	,	,	_	_	_
48	if	if	IN	_	_	_
49	average	average	JJ	_	_	_
50	quality	quality	NN	_	_	_
51	of	of	IN	_	_	_
52	the	the	DT	_	_	_
53	reads	read	VBZ	_	_	_
54	is	be	VBZ	_	_	_
55	less	less	JJR	_	_	_
56	than	than	IN	_	_	_
57	Q20	q20	NN	_	_	_
58	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	from	from	IN	_	_	_
4	two	two	CD	_	_	_
5	independent	independent	JJ	_	_	_
6	experiments	experiment	NNS	_	_	_
7	were	be	VBD	_	_	_
8	normalized	normalize	VBN	_	_	_
9	and	and	CC	_	_	_
10	then	then	RB	_	_	_
11	analyzed	analyze	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	GenePix	GenePix	NNP	_	_	_
15	Pro	pro	FW	_	_	_
16	3.0	3.0	CD	_	_	_
17	software	software	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Axon	Axon	NNP	_	_	_
20	Instruments	Instruments	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	has	have	VBZ	_	_	_
4	not	not	RB	_	_	_
5	been	be	VBN	_	_	_
6	processed	process	VBN	_	_	_
7	other	other	JJ	_	_	_
8	than	than	IN	_	_	_
9	those	those	DT	_	_	_
10	protocols	protocol	NNS	_	_	_
11	within	within	IN	_	_	_
12	GCOSv1	gcosv1	NN	_	_	_
13	.4	.4	CD	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Data	datum	NNS	_	_	_
16	included	include	VBD	_	_	_
17	in	in	IN	_	_	_
18	file	file	NN	_	_	_
19	has	have	VBZ	_	_	_
20	not	not	RB	_	_	_
21	been	be	VBN	_	_	_
22	processed	process	VBN	_	_	_
23	other	other	JJ	_	_	_
24	than	than	IN	_	_	_
25	those	those	DT	_	_	_
26	protocols	protocol	NNS	_	_	_
27	within	within	IN	_	_	_
28	GCOSv1	gcosv1	NN	_	_	_
29	.4	.4	CD	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Data	Data	NNP	_	_	_
32	obtained	obtain	VBN	_	_	_
33	from	from	IN	_	_	_
34	E.	e.	FW	_	_	_
35	coli	coli	FW	_	_	_
36	O157	o157	NN	_	_	_
37	:	:	:	_	_	_
38	H7	h7	NN	_	_	_
39	microarrays	microarray	NNS	_	_	_
40	were	be	VBD	_	_	_
41	normalized	normalize	VBN	_	_	_
42	using	use	VBG	_	_	_
43	the	the	DT	_	_	_
44	Ratio-based	ratio-based	JJ	_	_	_
45	and	and	CC	_	_	_
46	Lowess	lowess	JJ	_	_	_
47	methods	method	NNS	_	_	_
48	in	in	IN	_	_	_
49	Acuity	acuity	NN	_	_	_
50	3.1	3.1	CD	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Axon	axon	NN	_	_	_
53	instruments	instrument	NNS	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	before	before	IN	_	_	_
56	analysis	analysis	NN	_	_	_
57	.	.	.	_	_	_

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/Fluor	647/Fluor	NNP	_	_	_
14	546	546	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	in	in	IN	_	_	_
17	Acuity	acuity	NN	_	_	_
18	3.1	3.1	CD	_	_	_
19	and	and	CC	_	_	_
20	subsequently	subsequently	RB	_	_	_
21	analyzed	analyze	VBN	_	_	_
22	in	in	IN	_	_	_
23	Microsoft	Microsoft	NNP	_	_	_
24	Excel	Excel	NNP	_	_	_
25	.	.	.	_	_	_

1	Control	control	NN	_	_	_
2	,	,	,	_	_	_
3	blank	blank	JJ	_	_	_
4	,	,	,	_	_	_
5	and	and	CC	_	_	_
6	test	test	NN	_	_	_
7	spots	spot	NNS	_	_	_
8	with	with	IN	_	_	_
9	a	a	DT	_	_	_
10	mean	mean	JJ	_	_	_
11	intensity	intensity	NN	_	_	_
12	below	below	IN	_	_	_
13	that	that	DT	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	mean	mean	NN	_	_	_
17	of	of	IN	_	_	_
18	all	all	DT	_	_	_
19	negative	negative	JJ	_	_	_
20	controls	control	NNS	_	_	_
21	were	be	VBD	_	_	_
22	removed	remove	VBN	_	_	_
23	from	from	IN	_	_	_
24	the	the	DT	_	_	_
25	analysis	analysis	NN	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	arithmetic	arithmetic	NN	_	_	_
3	mean	mean	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	remaining	remain	VBG	_	_	_
7	spots	spot	NNS	_	_	_
8	across	across	IN	_	_	_
9	the	the	DT	_	_	_
10	duplicates	duplicate	NNS	_	_	_
11	was	be	VBD	_	_	_
12	taken	take	VBN	_	_	_
13	to	to	TO	_	_	_
14	construct	construct	VB	_	_	_
15	the	the	DT	_	_	_
16	dataset	dataset	NN	_	_	_
17	.	.	.	_	_	_

1	GACK	gack	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	Genomotyping	genomotyping	JJ	_	_	_
4	Analysis	analysis	NN	_	_	_
5	by	by	IN	_	_	_
6	Charles	Charles	NNP	_	_	_
7	Kim	Kim	NNP	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	was	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	to	to	TO	_	_	_
13	generate	generate	VB	_	_	_
14	a	a	DT	_	_	_
15	cut	cut	NN	_	_	_
16	off	off	IN	_	_	_
17	value	value	NN	_	_	_
18	determining	determine	VBG	_	_	_
19	the	the	DT	_	_	_
20	presence	presence	NN	_	_	_
21	or	or	CC	_	_	_
22	absence	absence	NN	_	_	_
23	of	of	IN	_	_	_
24	genes	gene	NNS	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	a	a	DT	_	_	_
28	dendrogram	dendrogram	NN	_	_	_
29	using	use	VBG	_	_	_
30	the	the	DT	_	_	_
31	Euclidean	euclidean	JJ	_	_	_
32	distance	distance	NN	_	_	_
33	metric	metric	JJ	_	_	_
34	with	with	IN	_	_	_
35	average	average	JJ	_	_	_
36	linkage	linkage	NN	_	_	_
37	was	be	VBD	_	_	_
38	created	create	VBN	_	_	_
39	with	with	IN	_	_	_
40	tMEV	tmev	NN	_	_	_
41	v4	v4	NN	_	_	_
42	.1	.1	NN	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	processed	process	VBN	_	_	_
4	with	with	IN	_	_	_
5	FeatureExtraction	FeatureExtraction	NNP	_	_	_
6	v9	v9	NN	_	_	_
7	.5.1	.5.1	NN	_	_	_
8	and	and	CC	_	_	_
9	quantile	quantile	NN	_	_	_
10	normalized	normalize	VBD	_	_	_
11	using	use	VBG	_	_	_
12	R2	r2	NN	_	_	_
13	.6.1	.6.1	CD	_	_	_
14	statistical	statistical	JJ	_	_	_
15	software	software	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Data	Data	NNP	_	_	_
18	quantification	quantification	NN	_	_	_
19	was	be	VBD	_	_	_
20	performed	perform	VBN	_	_	_
21	using	use	VBG	_	_	_
22	Agilent	Agilent	NNP	_	_	_
23	Feature	Feature	NNP	_	_	_
24	Extraction	Extraction	NNP	_	_	_
25	software	software	NN	_	_	_
26	9.3.2.1	9.3.2.1	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Agilent	Agilent	NNP	_	_	_
29	Technology	Technology	NNP	_	_	_
30	,	,	,	_	_	_
31	USA	USA	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

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	Data	Data	NNP	_	_	_
3	=	=	JJ	_	_	_
4	read.madata	read.madata	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	\	\	CD	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Data	Data	NNP	_	_	_
9	selection	selection	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Datasets	dataset	NNS	_	_	_
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	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	analysed	analyse	VBN	_	_	_
5	using	use	VBG	_	_	_
6	GeneSpring	GeneSpring	NNP	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Data	Data	NNP	_	_	_
9	was	be	VBD	_	_	_
10	analyzed	analyze	VBN	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	Affymetrix	Affymetrix	NNP	_	_	_
14	GenomeChipOperating	GenomeChipOperating	NNP	_	_	_
15	Software	Software	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	GCOS	GCOS	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

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	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/Cy5	cy3/cy5	NN	_	_	_
32	channels	channel	NNS	_	_	_
33	were	be	VBD	_	_	_
34	chosen	choose	VBN	_	_	_
35	for	for	IN	_	_	_
36	analysis	analysis	NN	_	_	_
37	.	.	.	_	_	_

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	One	one	CD	_	_	_
2	sample	sample	NN	_	_	_
3	t-tests	t-test	NNS	_	_	_
4	were	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	across	across	IN	_	_	_
7	replicates	replicate	VBZ	_	_	_
8	.	.	.	_	_	_

1	P-value	p-value	NN	_	_	_
2	of	of	IN	_	_	_
3	0.05	0.05	CD	_	_	_
4	was	be	VBD	_	_	_
5	chosen	choose	VBN	_	_	_
6	as	as	IN	_	_	_
7	the	the	DT	_	_	_
8	significant	significant	JJ	_	_	_
9	level	level	NN	_	_	_
10	.	.	.	_	_	_

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/Cy5	cy3/cy5	NN	_	_	_
28	channels	channel	NNS	_	_	_
29	were	be	VBD	_	_	_
30	chosen	choose	VBN	_	_	_
31	for	for	IN	_	_	_
32	further	further	JJ	_	_	_
33	analysis	analysis	NN	_	_	_
34	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	sample	sample	NN	_	_	_
3	t-tests	t-test	NNS	_	_	_
4	were	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	across	across	IN	_	_	_
7	replicates	replicate	VBZ	_	_	_
8	.	.	.	_	_	_

1	Step-down	step-down	JJ	_	_	_
2	Bonferroni-Holm	Bonferroni-Holm	NNP	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	for	for	IN	_	_	_
6	the	the	DT	_	_	_
7	correction	correction	NN	_	_	_
8	of	of	IN	_	_	_
9	multiple	multiple	JJ	_	_	_
10	hypotheses	hypothesis	NNS	_	_	_
11	testing	testing	NN	_	_	_
12	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	oligonucleotides	oligonucleotide	NNS	_	_	_
3	for	for	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	K12	k12	NN	_	_	_
7	were	be	VBD	_	_	_
8	choosen	choosen	VBN	_	_	_
9	to	to	TO	_	_	_
10	draw	draw	VB	_	_	_
11	conclusion	conclusion	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	with	with	IN	_	_	_
6	RMA	rma	NN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	program	program	NN	_	_	_
10	Partek	Partek	NNP	_	_	_
11	6.6	6.6	CD	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Data	Data	NNP	_	_	_
14	was	be	VBD	_	_	_
15	extracted	extract	VBN	_	_	_
16	with	with	IN	_	_	_
17	Agilent	Agilent	NNP	_	_	_
18	Feature	Feature	NNP	_	_	_
19	Extraction	Extraction	NNP	_	_	_
20	software	software	NN	_	_	_
21	10.7	10.7	CD	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Agilent	Agilent	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	using	use	VBG	_	_	_
26	default	default	NN	_	_	_
27	parameters	parameter	NNS	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	protocol	protocol	NN	_	_	_
30	GE1-v1	ge1-v1	NN	_	_	_
31	_	_	CD	_	_	_
32	91	91	CD	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	to	to	TO	_	_	_
35	obtain	obtain	VB	_	_	_
36	background	background	NN	_	_	_
37	subtracted	subtract	VBN	_	_	_
38	and	and	CC	_	_	_
39	spatially	spatially	RB	_	_	_
40	detrended	detrend	VBD	_	_	_
41	Processed	processed	JJ	_	_	_
42	Signal	signal	NN	_	_	_
43	intensities	intensity	NNS	_	_	_
44	.	.	.	_	_	_

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	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	obtained	obtain	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	GeneChip	GeneChip	NNP	_	_	_
8	®	®	NNP	_	_	_
9	Command	command	NN	_	_	_
10	Console	console	NN	_	_	_
11	and	and	CC	_	_	_
12	Expression	expression	NN	_	_	_
13	Console	Console	NNP	_	_	_
14	Software	Software	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	AGCC	AGCC	NNP	_	_	_
17	;	;	:	_	_	_
18	Version	Version	NNP	_	_	_
19	3.2	3.2	CD	_	_	_
20	and	and	CC	_	_	_
21	Expression	expression	NN	_	_	_
22	Console	console	NN	_	_	_
23	;	;	:	_	_	_
24	Version	Version	NNP	_	_	_
25	1.2	1.2	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	using	use	VBG	_	_	_
28	the	the	DT	_	_	_
29	MAS5	mas5	NN	_	_	_
30	algorithm	algorithm	NN	_	_	_
31	to	to	TO	_	_	_
32	generate	generate	VB	_	_	_
33	.	.	.	_	_	_

1	CHP	chp	NN	_	_	_
2	files	file	NNS	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	processed	process	VBN	_	_	_
5	by	by	IN	_	_	_
6	MATLAB	MATLAB	NNP	_	_	_
7	to	to	TO	_	_	_
8	median	median	JJ	_	_	_
9	normalize	normalize	VB	_	_	_
10	each	each	DT	_	_	_
11	channel	channel	NN	_	_	_
12	and	and	CC	_	_	_
13	lowess	lowess	NN	_	_	_
14	normalize	normalize	VBP	_	_	_
15	the	the	DT	_	_	_
16	sample	sample	NN	_	_	_
17	set	set	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	were	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	by	by	IN	_	_	_
6	Feature	Feature	NNP	_	_	_
7	Extraction	Extraction	NNP	_	_	_
8	V.	V.	NNP	_	_	_
9	11.5.1.1	11.5.1.1	CD	_	_	_
10	.	.	.	_	_	_

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

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	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	were	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	using	use	VBG	_	_	_
6	GeneChip	GeneChip	NNP	_	_	_
7	Operating	Operating	NNP	_	_	_
8	Software	Software	NNP	_	_	_
9	Version	Version	NNP	_	_	_
10	1.4	1.4	CD	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Affymetrix	Affymetrix	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Data	datum	NNS	_	_	_
16	were	be	VBD	_	_	_
17	analyzed	analyze	VBN	_	_	_
18	with	with	IN	_	_	_
19	RMA	rma	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Robust	robust	JJ	_	_	_
22	Multiarray	Multiarray	NNP	_	_	_
23	Analysis	analysis	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	using	use	VBG	_	_	_
26	Affymetrix	Affymetrix	NNP	_	_	_
27	default	default	NN	_	_	_
28	analysis	analysis	NN	_	_	_
29	settings	setting	NNS	_	_	_
30	and	and	CC	_	_	_
31	global	global	JJ	_	_	_
32	scaling	scaling	NN	_	_	_
33	as	as	IN	_	_	_
34	normalization	normalization	NN	_	_	_
35	method	method	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	were	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	in	in	IN	_	_	_
6	GenePix	GenePix	NNP	_	_	_
7	4100A	4100a	CD	_	_	_
8	scanning	scanning	NN	_	_	_
9	software	software	NN	_	_	_
10	and	and	CC	_	_	_
11	normalized	normalize	VBD	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	lowess	lowess	NN	_	_	_
15	method	method	NN	_	_	_
16	implemented	implement	VBN	_	_	_
17	in	in	IN	_	_	_
18	TM4	tm4	NN	_	_	_
19	MIDAS	midas	NN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Data	Data	NNP	_	_	_
22	were	be	VBD	_	_	_
23	extracted	extract	VBN	_	_	_
24	with	with	IN	_	_	_
25	Feature	feature	NN	_	_	_
26	Extraction	extraction	NN	_	_	_
27	software	software	NN	_	_	_
28	10.7	10.7	CD	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Agilent	agilent	JJ	_	_	_
31	technologies	technology	NNS	_	_	_
32	,	,	,	_	_	_
33	Santa	Santa	NNP	_	_	_
34	Clara	Clara	NNP	_	_	_
35	,	,	,	_	_	_
36	CA	CA	NNP	_	_	_
37	,	,	,	_	_	_
38	US	US	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

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	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	were	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	using	use	VBG	_	_	_
6	LOWESS	lowess	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	MIDAS	midas	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	and	and	CC	_	_	_
11	analyzed	analyze	VBN	_	_	_
12	for	for	IN	_	_	_
13	statistical	statistical	JJ	_	_	_
14	significance	significance	NN	_	_	_
15	using	use	VBG	_	_	_
16	the	the	DT	_	_	_
17	Rank	Rank	NNP	_	_	_
18	Product	Product	NNP	_	_	_
19	method	method	NN	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	MultiExperimentViewer	MultiExperimentViewer	NNP	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Data	Data	NNP	_	_	_
25	were	be	VBD	_	_	_
26	normalized	normalize	VBN	_	_	_
27	using	use	VBG	_	_	_
28	RMA	RMA	NNP	_	_	_
29	algorithm	algorithm	NN	_	_	_
30	from	from	IN	_	_	_
31	R/Bioconductor/XPS	r/bioconductor/xps	NN	_	_	_
32	package	package	NN	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	were	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	LOWESS	LOWESS	NNP	_	_	_
8	algorithm	algorithm	NN	_	_	_
9	and	and	CC	_	_	_
10	analyzed	analyze	VBN	_	_	_
11	for	for	IN	_	_	_
12	statistical	statistical	JJ	_	_	_
13	significance	significance	NN	_	_	_
14	using	use	VBG	_	_	_
15	the	the	DT	_	_	_
16	MeV	mev	NN	_	_	_
17	package	package	NN	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Data	Data	NNP	_	_	_
20	were	be	VBD	_	_	_
21	processed	process	VBN	_	_	_
22	using	use	VBG	_	_	_
23	Affymetrix	Affymetrix	NNP	_	_	_
24	apt-probeset-summarize	apt-probeset-summarize	JJ	_	_	_
25	software	software	NN	_	_	_
26	version	version	NN	_	_	_
27	1.10	1.10	CD	_	_	_
28	and	and	CC	_	_	_
29	RMA	RMA	NNP	_	_	_
30	algorithm	algorithm	NN	_	_	_
31	.	.	.	_	_	_

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	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	Data	Data	NNP	_	_	_
22	were	be	VBD	_	_	_
23	visualized	visualize	VBN	_	_	_
24	in	in	IN	_	_	_
25	the	the	DT	_	_	_
26	Rockhopper	Rockhopper	NNP	_	_	_
27	IGV	igv	NN	_	_	_
28	genome	genome	NN	_	_	_
29	browser	browser	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	McClure	McClure	NNP	_	_	_
32	et	et	FW	_	_	_
33	al.	al.	FW	_	_	_
34	,	,	,	_	_	_
35	2013	2013	CD	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	and	and	CC	_	_	_
38	TreeView	TreeView	NNP	_	_	_
39	3.0	3.0	CD	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Saldana	Saldana	NNP	_	_	_
42	et	et	FW	_	_	_
43	al.	al.	FW	_	_	_
44	,	,	,	_	_	_
45	2004	2004	CD	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	day	day	NN	_	_	_
3	:	:	:	_	_	_
4	.	.	.	_	_	_

1	strain	strain	NN	_	_	_
2	:	:	:	_	_	_
3	.	.	.	_	_	_

1	oxygen	oxygen	NN	_	_	_
2	:	:	:	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	dcd	dcd	VBD	GEN	_	_
3	KO	KO	NNP	_	_	_
4	LB	LB	NNP	_	_	_
5	rep1	rep1	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	dcd	dcd	NN	GEN	_	_
8	KO	KO	NNP	_	_	_
9	LB	LB	NNP	_	_	_
10	rep2	rep2	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	dcd	dcd	NN	GEN	_	_
13	KO	ko	NN	_	_	_
14	M9	m9	NN	_	_	_
15	rep1	rep1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	dcd	dcd	NN	GEN	_	_
18	KO	ko	NN	_	_	_
19	M9	m9	NN	_	_	_
20	rep2	rep2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	DdksA	ddksa	NN	_	_	_
23	cells	cell	NNS	_	_	_
24	were	be	VBD	_	_	_
25	grown	grow	VBN	_	_	_
26	in	in	IN	_	_	_
27	MOPS	MOPS	NNP	MED	_	_
28	medium	medium	NN	_	_	_
29	with	with	IN	_	_	_
30	0.2	0.2	CD	_	_	_
31	%	%	NN	_	_	_
32	glucose	glucose	NN	SUPP	_	_
33	,	,	,	_	_	_
34	leucine	leucine	NN	SUPP	_	_
35	,	,	,	_	_	_
36	isoleucine	isoleucine	NN	_	_	_
37	,	,	,	_	_	_
38	valine	valine	NN	_	_	_
39	,	,	,	_	_	_
40	glycine	glycine	NN	_	_	_
41	,	,	,	_	_	_
42	phenylalanine	phenylalanine	NN	SUPP	_	_
43	,	,	,	_	_	_
44	threonine	threonine	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	40	40	CD	_	_	_
47	mg/ml	mg/ml	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	and	and	CC	_	_	_
50	uracil	uracil	NN	SUPP	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	50	50	CD	_	_	_
53	mg/ml	mg/ml	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	until	until	IN	_	_	_
56	mid-log	mid-log	JJ	_	_	_
57	phase	phase	NN	_	_	_
58	and	and	CC	_	_	_
59	treated	treat	VBN	_	_	_
60	with	with	IN	_	_	_
61	0.5	0.5	CD	_	_	_
62	mg/ml	mg/ml	NN	_	_	_
63	serine	serine	NN	_	_	_
64	hydroxamate	hydroxamate	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	SHX	shx	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	for	for	IN	_	_	_
69	20	20	CD	_	_	_
70	min	min	NN	_	_	_
71	at	at	IN	_	_	_
72	37	37	CD	_	_	_
73	°C	°c	NN	_	_	_
74	with	with	IN	_	_	_
75	vigorous	vigorous	JJ	_	_	_
76	shaking	shake	VBG	_	_	_
77	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DdksA	ddksa	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	MOPS	MOPS	NNP	MED	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	,	,	,	_	_	_
14	leucine	leucine	NN	SUPP	_	_
15	,	,	,	_	_	_
16	isoleucine	isoleucine	NN	_	_	_
17	,	,	,	_	_	_
18	valine	valine	NN	_	_	_
19	,	,	,	_	_	_
20	glycine	glycine	NN	_	_	_
21	,	,	,	_	_	_
22	phenylalanine	phenylalanine	NN	SUPP	_	_
23	,	,	,	_	_	_
24	threonine	threonine	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	40	40	CD	_	_	_
27	mg/ml	mg/ml	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	uracil	uracil	NN	SUPP	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	50	50	CD	_	_	_
33	mg/ml	mg/ml	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	until	until	IN	_	_	_
36	mid-log	mid-log	JJ	_	_	_
37	phase	phase	NN	_	_	_
38	at	at	IN	_	_	_
39	37	37	CD	_	_	_
40	°C	°c	NN	_	_	_
41	with	with	IN	_	_	_
42	vigorous	vigorous	JJ	_	_	_
43	shaking	shake	VBG	_	_	_
44	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DdksA	ddksa	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	MOPS	MOPS	NNP	MED	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	,	,	,	_	_	_
14	leucine	leucine	NN	SUPP	_	_
15	,	,	,	_	_	_
16	isoleucine	isoleucine	NN	_	_	_
17	,	,	,	_	_	_
18	valine	valine	NN	_	_	_
19	,	,	,	_	_	_
20	glycine	glycine	NN	_	_	_
21	,	,	,	_	_	_
22	phenylalanine	phenylalanine	NN	SUPP	_	_
23	,	,	,	_	_	_
24	threonine	threonine	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	40	40	CD	_	_	_
27	mg/ml	mg/ml	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	uracil	uracil	NN	SUPP	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	50	50	CD	_	_	_
33	mg/ml	mg/ml	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	~	~	NN	_	_	_
41	0.4	0.4	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	at	at	IN	_	_	_
44	37	37	CD	_	_	_
45	°C	°c	NN	_	_	_
46	with	with	IN	_	_	_
47	vigorous	vigorous	JJ	_	_	_
48	shaking	shake	VBG	_	_	_
49	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
10	Deer	deer	NNS	_	_	_
11	feces	fece	NNS	_	_	_
12	isolate	isolate	VBP	_	_	_
13	D1	d1	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	Deer	deer	NNS	_	_	_
16	feces	fece	NNS	_	_	_
17	isolate	isolate	NN	_	_	_
18	D3	d3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	Deer	deer	NNS	_	_	_
21	feces	fece	NNS	_	_	_
22	isolate	isolate	VBP	_	_	_
23	W6A	w6a	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	Deer	deer	NNS	_	_	_
26	III	iii	CD	_	_	_
27	versus	versus	CC	_	_	_
28	MG1655	mg1655	CD	_	_	_
29	technical	technical	JJ	_	_	_
30	replicate	replicate	VB	_	_	_
31	1	1	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Deer	deer	NNS	_	_	_
34	III	iii	CD	_	_	_
35	versus	versus	CC	_	_	_
36	MG1655	mg1655	CD	_	_	_
37	technical	technical	JJ	_	_	_
38	replicate	replicate	VB	_	_	_
39	2	2	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	Deer	deer	NNS	_	_	_
42	II	ii	CD	_	_	_
43	versus	versus	CC	_	_	_
44	MG1655	mg1655	CD	_	_	_
45	technical	technical	JJ	_	_	_
46	replicate	replicate	VB	_	_	_
47	1	1	CD	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	Deer	deer	NNS	_	_	_
50	II	ii	CD	_	_	_
51	versus	versus	CC	_	_	_
52	MG1655	mg1655	CD	_	_	_
53	technical	technical	JJ	_	_	_
54	replicate	replicate	VB	_	_	_
55	2	2	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	Deer	deer	NNS	_	_	_
58	I	I	PRP	_	_	_
59	versus	versus	CC	_	_	_
60	MG1655	mg1655	NN	_	_	_
61	technical	technical	JJ	_	_	_
62	replicate	replicate	VB	_	_	_
63	1	1	CD	_	_	_
64	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
65	Deer	deer	NNS	_	_	_
66	I	I	PRP	_	_	_
67	versus	versus	CC	_	_	_
68	MG1655	mg1655	NN	_	_	_
69	technical	technical	JJ	_	_	_
70	replicate	replicate	VB	_	_	_
71	2	2	CD	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Delta	Delta	NNP	_	_	_
74	dksA	dksA	NNP	GEN	_	_
75	Cells	cell	NNS	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Delta	Delta	NNP	_	_	_
78	dksA	dksA	NNP	GEN	_	_
79	Cells	cell	NNS	_	_	_
80	Replicate	replicate	VB	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Delta	Delta	NNP	_	_	_
84	dksA	dksA	NNP	GEN	_	_
85	Cells	cell	NNS	_	_	_
86	Replicate	replicate	VB	_	_	_
87	2	2	CD	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	Delta	Delta	NNP	_	_	_
90	dksA	dksA	NNP	GEN	_	_
91	Cells	cell	NNS	_	_	_
92	Replicate	replicate	VB	_	_	_
93	3	3	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	delta	delta	NN	_	_	_
96	hfq	hfq	NN	GEN	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Delta	delta	NN	_	_	_
99	hfq	hfq	NN	GEN	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	deltamatP	deltamatp	NN	_	_	_
102	22	22	CD	_	_	_
103	°C	°c	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	delta-rnr	delta-rnr	JJ	_	_	_
106	mutant	mutant	JJ	_	_	_
107	_	_	NN	_	_	_
108	anoxic	anoxic	JJ	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	NO3	no3	NN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	_	_	SYM	_	_	_
113	glycerol	glycerol	NN	SUPP	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	delta-rnr	delta-rnr	JJ	_	_	_
116	mutant	mutant	JJ	_	_	_
117	_	_	NN	_	_	_
118	anoxic	anoxic	JJ	_	_	_
119	-LRB-	-lrb-	-LRB-	_	_	_
120	NO3	no3	NN	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	_	_	SYM	_	_	_
123	glycerol	glycerol	NN	SUPP	_	_
124	+	+	CC	_	_	_
125	propionate	propionate	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	delta-rnr	delta-rnr	JJ	_	_	_
128	mutant	mutant	JJ	_	_	_
129	_	_	NN	_	_	_
130	oxic	oxic	JJ	_	_	_
131	_	_	NN	_	_	_
132	glycerol	glycerol	NN	SUPP	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	delta-rnr	delta-rnr	JJ	_	_	_
135	mutant	mutant	JJ	_	_	_
136	_	_	NN	_	_	_
137	oxic	oxic	JJ	_	_	_
138	_	_	NN	_	_	_
139	glycerol	glycerol	NN	SUPP	_	_
140	+	+	CC	_	_	_
141	propionate	propionate	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
143	Delta	Delta	NNP	_	_	_
144	rseA	rseA	NNP	GEN	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	Demultiplexing	Demultiplexing	NNP	_	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	Depletion	depletion	NN	_	_	_
149	of	of	IN	_	_	_
150	ribosomal	ribosomal	JJ	_	_	_
151	RNA	rna	NN	_	_	_
152	was	be	VBD	_	_	_
153	accomplished	accomplish	VBN	_	_	_
154	with	with	IN	_	_	_
155	the	the	DT	_	_	_
156	Ribominus	Ribominus	NNP	_	_	_
157	Transcriptome	Transcriptome	NNP	_	_	_
158	Isolation	isolation	NN	_	_	_
159	Kit	kit	NN	_	_	_
160	-LRB-	-lrb-	-LRB-	_	_	_
161	Thermo	Thermo	NNP	_	_	_
162	Fisher	Fisher	NNP	_	_	_
163	-RRB-	-rrb-	-RRB-	_	_	_
164	followed	follow	VBN	_	_	_
165	by	by	IN	_	_	_
166	ethanol	ethanol	NN	_	_	_
167	precipitation	precipitation	NN	_	_	_
168	.	.	.	_	_	_

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	NN	_	_	_
2	Desulfovibrio	desulfovibrio	NN	_	_	_
3	piger	piger	NN	_	_	_
4	GOR1	gor1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	Detailed	detailed	JJ	_	_	_
7	parameters	parameter	NNS	_	_	_
8	for	for	IN	_	_	_
9	reads	read	VBZ	_	_	_
10	mapping	mapping	NN	_	_	_
11	:	:	:	_	_	_
12	bowtie2	bowtie2	NN	_	_	_
13	-	-	:	_	_	_
14	x	x	CC	_	_	_
15	ATCC8739	atcc8739	NN	_	_	_
16	-1	-1	CD	_	_	_
17	X	x	NN	_	_	_
18	_	_	NN	_	_	_
19	1	1	CD	_	_	_
20	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
11	developmental	developmental	JJ	_	_	_
12	stage	stage	NN	_	_	_
13	:	:	:	_	_	_
14	mixed	mixed	JJ	_	_	_
15	population	population	NN	_	_	_
16	,	,	,	_	_	_
17	exponential	exponential	JJ	GrowthPhase	_	_
18	phase	phase	NN	GrowthPhase	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	DGE	dge	NN	_	_	_
21	analysis	analysis	NN	_	_	_
22	used	use	VBD	_	_	_
23	a	a	DT	_	_	_
24	false-discovery	false-discovery	JJ	_	_	_
25	rate	rate	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	FDR	FDR	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	of	of	IN	_	_	_
30	0.10	0.10	CD	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	∆	∆	SYM	_	_	_
3	dgk	dgk	FW	_	_	_
4	parent	parent	NN	_	_	_
5	Sample	sample	NN	_	_	_
6	16	16	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	∆	∆	CD	_	_	_
9	dgk	dgk	NN	_	_	_
10	parent	parent	NN	_	_	_
11	Sample	sample	NN	_	_	_
12	35	35	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	∆	∆	CD	_	_	_
15	dgk	dgk	NN	_	_	_
16	parent	parent	NN	_	_	_
17	Sample	sample	NN	_	_	_
18	54	54	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	dgk	dgk	NN	_	_	_
21	suppressor	suppressor	NN	_	_	_
22	1-1	1-1	CD	_	_	_
23	Sample	sample	NN	_	_	_
24	17	17	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	dgk	dgk	NN	_	_	_
27	suppressor	suppressor	NN	_	_	_
28	1-1	1-1	CD	_	_	_
29	Sample	sample	NN	_	_	_
30	36	36	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	dgk	dgk	NN	_	_	_
33	suppressor	suppressor	NN	_	_	_
34	1-1	1-1	CD	_	_	_
35	Sample	sample	NN	_	_	_
36	55	55	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	dgk	dgk	NN	_	_	_
39	suppressor	suppressor	NN	_	_	_
40	2-1	2-1	CD	_	_	_
41	Sample	sample	NN	_	_	_
42	18	18	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	dgk	dgk	NN	_	_	_
45	suppressor	suppressor	NN	_	_	_
46	2-1	2-1	CD	_	_	_
47	Sample	sample	NN	_	_	_
48	37	37	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	dgk	dgk	NN	_	_	_
51	suppressor	suppressor	NN	_	_	_
52	2-1	2-1	CD	_	_	_
53	Sample	sample	NN	_	_	_
54	56	56	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	dgk	dgk	NN	_	_	_
57	suppressor	suppressor	NN	_	_	_
58	3-1	3-1	CD	_	_	_
59	Sample	sample	NN	_	_	_
60	19	19	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	dgk	dgk	NN	_	_	_
63	suppressor	suppressor	NN	_	_	_
64	3-1	3-1	CD	_	_	_
65	Sample	sample	NN	_	_	_
66	38	38	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	dgk	dgk	NN	_	_	_
69	suppressor	suppressor	NN	_	_	_
70	3-1	3-1	CD	_	_	_
71	Sample	sample	NN	_	_	_
72	57	57	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	DH1-log	dh1-log	JJ	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	DH1-log-tr	dh1-log-tr	JJ	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	DicF	dicf	NN	_	_	_
79	rep1	rep1	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	DicF	dicf	NN	_	_	_
82	rep2	rep2	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	DicF	dicf	NN	_	_	_
85	rep3	rep3	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	diet	diet	NN	_	_	_
88	:	:	:	_	_	_
89	Mouse	mouse	NN	_	_	_
90	was	be	VBD	_	_	_
91	fed	feed	VBN	_	_	_
92	a	a	DT	_	_	_
93	meal	meal	NN	_	_	_
94	of	of	IN	_	_	_
95	human	human	JJ	_	_	_
96	pureed	pureed	NN	_	_	_
97	food	food	NN	_	_	_
98	in	in	IN	_	_	_
99	the	the	DT	_	_	_
100	following	follow	VBG	_	_	_
101	concentrations	concentration	NNS	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	g/kg	g/kg	NN	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	=	=	JJ	_	_	_
106	>	>	JJR	_	_	_
107	APPLE	APPLE	NNP	_	_	_
108	:	:	:	_	_	_
109	250	250	CD	_	_	_
110	,	,	,	_	_	_
111	OAT	oat	NN	_	_	_
112	:	:	:	_	_	_
113	250	250	CD	_	_	_
114	,	,	,	_	_	_
115	RICE	RICE	NNP	_	_	_
116	:	:	:	_	_	_
117	250	250	CD	_	_	_
118	,	,	,	_	_	_
119	BEEF	beef	NN	_	_	_
120	:	:	:	_	_	_
121	250	250	CD	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
123	diet	diet	NN	_	_	_
124	:	:	:	_	_	_
125	Mouse	mouse	NN	_	_	_
126	was	be	VBD	_	_	_
127	fed	feed	VBN	_	_	_
128	a	a	DT	_	_	_
129	meal	meal	NN	_	_	_
130	of	of	IN	_	_	_
131	human	human	JJ	_	_	_
132	pureed	pureed	NN	_	_	_
133	food	food	NN	_	_	_
134	in	in	IN	_	_	_
135	the	the	DT	_	_	_
136	following	follow	VBG	_	_	_
137	concentrations	concentration	NNS	_	_	_
138	-LRB-	-lrb-	-LRB-	_	_	_
139	g/kg	g/kg	NN	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	=	=	JJ	_	_	_
142	>	>	JJR	_	_	_
143	APPLE	APPLE	NNP	_	_	_
144	:	:	:	_	_	_
145	250	250	CD	_	_	_
146	,	,	,	_	_	_
147	RICE	RICE	NNP	_	_	_
148	:	:	:	_	_	_
149	250	250	CD	_	_	_
150	,	,	,	_	_	_
151	OAT	oat	NN	_	_	_
152	:	:	:	_	_	_
153	250	250	CD	_	_	_
154	,	,	,	_	_	_
155	BEEF	beef	NN	_	_	_
156	:	:	:	_	_	_
157	250	250	CD	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
159	diet	diet	NN	_	_	_
160	:	:	:	_	_	_
161	Mouse	mouse	NN	_	_	_
162	was	be	VBD	_	_	_
163	fed	feed	VBN	_	_	_
164	a	a	DT	_	_	_
165	meal	meal	NN	_	_	_
166	of	of	IN	_	_	_
167	human	human	JJ	_	_	_
168	pureed	pureed	NN	_	_	_
169	food	food	NN	_	_	_
170	in	in	IN	_	_	_
171	the	the	DT	_	_	_
172	following	follow	VBG	_	_	_
173	concentrations	concentration	NNS	_	_	_
174	-LRB-	-lrb-	-LRB-	_	_	_
175	g/kg	g/kg	NN	_	_	_
176	-RRB-	-rrb-	-RRB-	_	_	_
177	=	=	JJ	_	_	_
178	>	>	JJR	_	_	_
179	APPLE	APPLE	NNP	_	_	_
180	:	:	:	_	_	_
181	250	250	CD	_	_	_
182	,	,	,	_	_	_
183	RICE	RICE	NNP	_	_	_
184	:	:	:	_	_	_
185	250	250	CD	_	_	_
186	,	,	,	_	_	_
187	PEACH	PEACH	NNP	_	_	_
188	:	:	:	_	_	_
189	250	250	CD	_	_	_
190	,	,	,	_	_	_
191	CHICK	CHICK	NNP	_	_	_
192	:	:	:	_	_	_
193	250	250	CD	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
195	diet	diet	NN	_	_	_
196	:	:	:	_	_	_
197	Mouse	mouse	NN	_	_	_
198	was	be	VBD	_	_	_
199	fed	feed	VBN	_	_	_
200	a	a	DT	_	_	_
201	meal	meal	NN	_	_	_
202	of	of	IN	_	_	_
203	human	human	JJ	_	_	_
204	pureed	pureed	NN	_	_	_
205	food	food	NN	_	_	_
206	in	in	IN	_	_	_
207	the	the	DT	_	_	_
208	following	follow	VBG	_	_	_
209	concentrations	concentration	NNS	_	_	_
210	-LRB-	-lrb-	-LRB-	_	_	_
211	g/kg	g/kg	NN	_	_	_
212	-RRB-	-rrb-	-RRB-	_	_	_
213	=	=	JJ	_	_	_
214	>	>	JJR	_	_	_
215	APPLE	APPLE	NNP	_	_	_
216	:	:	:	_	_	_
217	666.7	666.7	CD	_	_	_
218	,	,	,	_	_	_
219	BEEF	beef	NN	_	_	_
220	:	:	:	_	_	_
221	222.2	222.2	CD	_	_	_
222	,	,	,	_	_	_
223	CHICK	CHICK	NNP	_	_	_
224	:	:	:	_	_	_
225	55.6	55.6	CD	_	_	_
226	,	,	,	_	_	_
227	PEACH	PEACH	NNP	_	_	_
228	:	:	:	_	_	_
229	55.6	55.6	CD	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
231	diet	diet	NN	_	_	_
232	:	:	:	_	_	_
233	Mouse	mouse	NN	_	_	_
234	was	be	VBD	_	_	_
235	fed	feed	VBN	_	_	_
236	a	a	DT	_	_	_
237	meal	meal	NN	_	_	_
238	of	of	IN	_	_	_
239	human	human	JJ	_	_	_
240	pureed	pureed	NN	_	_	_
241	food	food	NN	_	_	_
242	in	in	IN	_	_	_
243	the	the	DT	_	_	_
244	following	follow	VBG	_	_	_
245	concentrations	concentration	NNS	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	g/kg	g/kg	NN	_	_	_
248	-RRB-	-rrb-	-RRB-	_	_	_
249	=	=	JJ	_	_	_
250	>	>	JJR	_	_	_
251	APPLE	APPLE	NNP	_	_	_
252	:	:	:	_	_	_
253	666.7	666.7	CD	_	_	_
254	,	,	,	_	_	_
255	OAT	oat	NN	_	_	_
256	:	:	:	_	_	_
257	222.2	222.2	CD	_	_	_
258	,	,	,	_	_	_
259	CHICK	CHICK	NNP	_	_	_
260	:	:	:	_	_	_
261	55.6	55.6	CD	_	_	_
262	,	,	,	_	_	_
263	BEEF	beef	NN	_	_	_
264	:	:	:	_	_	_
265	55.6	55.6	CD	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
267	diet	diet	NN	_	_	_
268	:	:	:	_	_	_
269	Mouse	mouse	NN	_	_	_
270	was	be	VBD	_	_	_
271	fed	feed	VBN	_	_	_
272	a	a	DT	_	_	_
273	meal	meal	NN	_	_	_
274	of	of	IN	_	_	_
275	human	human	JJ	_	_	_
276	pureed	pureed	NN	_	_	_
277	food	food	NN	_	_	_
278	in	in	IN	_	_	_
279	the	the	DT	_	_	_
280	following	follow	VBG	_	_	_
281	concentrations	concentration	NNS	_	_	_
282	-LRB-	-lrb-	-LRB-	_	_	_
283	g/kg	g/kg	NN	_	_	_
284	-RRB-	-rrb-	-RRB-	_	_	_
285	=	=	JJ	_	_	_
286	>	>	JJR	_	_	_
287	APPLE	APPLE	NNP	_	_	_
288	:	:	:	_	_	_
289	666.7	666.7	CD	_	_	_
290	,	,	,	_	_	_
291	PEACH	PEACH	NNP	_	_	_
292	:	:	:	_	_	_
293	222.2	222.2	CD	_	_	_
294	,	,	,	_	_	_
295	CHICK	CHICK	NNP	_	_	_
296	:	:	:	_	_	_
297	55.6	55.6	CD	_	_	_
298	,	,	,	_	_	_
299	RICE	RICE	NNP	_	_	_
300	:	:	:	_	_	_
301	55.6	55.6	CD	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
303	diet	diet	NN	_	_	_
304	:	:	:	_	_	_
305	Mouse	mouse	NN	_	_	_
306	was	be	VBD	_	_	_
307	fed	feed	VBN	_	_	_
308	a	a	DT	_	_	_
309	meal	meal	NN	_	_	_
310	of	of	IN	_	_	_
311	human	human	JJ	_	_	_
312	pureed	pureed	NN	_	_	_
313	food	food	NN	_	_	_
314	in	in	IN	_	_	_
315	the	the	DT	_	_	_
316	following	follow	VBG	_	_	_
317	concentrations	concentration	NNS	_	_	_
318	-LRB-	-lrb-	-LRB-	_	_	_
319	g/kg	g/kg	NN	_	_	_
320	-RRB-	-rrb-	-RRB-	_	_	_
321	=	=	JJ	_	_	_
322	>	>	JJR	_	_	_
323	APPLE	APPLE	NNP	_	_	_
324	:	:	:	_	_	_
325	666.7	666.7	CD	_	_	_
326	,	,	,	_	_	_
327	PEACH	PEACH	NNP	_	_	_
328	:	:	:	_	_	_
329	222.2	222.2	CD	_	_	_
330	,	,	,	_	_	_
331	CHICK	CHICK	NNP	_	_	_
332	:	:	:	_	_	_
333	55.6	55.6	CD	_	_	_
334	,	,	,	_	_	_
335	SWEET	SWEET	NNP	_	_	_
336	_	_	NNP	_	_	_
337	POTATO	POTATO	NNP	_	_	_
338	:	:	:	_	_	_
339	55.6	55.6	CD	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
341	diet	diet	NN	_	_	_
342	:	:	:	_	_	_
343	Mouse	mouse	NN	_	_	_
344	was	be	VBD	_	_	_
345	fed	feed	VBN	_	_	_
346	a	a	DT	_	_	_
347	meal	meal	NN	_	_	_
348	of	of	IN	_	_	_
349	human	human	JJ	_	_	_
350	pureed	pureed	NN	_	_	_
351	food	food	NN	_	_	_
352	in	in	IN	_	_	_
353	the	the	DT	_	_	_
354	following	follow	VBG	_	_	_
355	concentrations	concentration	NNS	_	_	_
356	-LRB-	-lrb-	-LRB-	_	_	_
357	g/kg	g/kg	NN	_	_	_
358	-RRB-	-rrb-	-RRB-	_	_	_
359	=	=	JJ	_	_	_
360	>	>	JJR	_	_	_
361	BEEF	beef	NN	_	_	_
362	:	:	:	_	_	_
363	250	250	CD	_	_	_
364	,	,	,	_	_	_
365	PEA	PEA	NNP	_	_	_
366	:	:	:	_	_	_
367	250	250	CD	_	_	_
368	,	,	,	_	_	_
369	CHICK	CHICK	NNP	_	_	_
370	:	:	:	_	_	_
371	250	250	CD	_	_	_
372	,	,	,	_	_	_
373	OAT	oat	NN	_	_	_
374	:	:	:	_	_	_
375	250	250	CD	_	_	_
376	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
377	diet	diet	NN	_	_	_
378	:	:	:	_	_	_
379	Mouse	mouse	NN	_	_	_
380	was	be	VBD	_	_	_
381	fed	feed	VBN	_	_	_
382	a	a	DT	_	_	_
383	meal	meal	NN	_	_	_
384	of	of	IN	_	_	_
385	human	human	JJ	_	_	_
386	pureed	pureed	NN	_	_	_
387	food	food	NN	_	_	_
388	in	in	IN	_	_	_
389	the	the	DT	_	_	_
390	following	follow	VBG	_	_	_
391	concentrations	concentration	NNS	_	_	_
392	-LRB-	-lrb-	-LRB-	_	_	_
393	g/kg	g/kg	NN	_	_	_
394	-RRB-	-rrb-	-RRB-	_	_	_
395	=	=	JJ	_	_	_
396	>	>	JJR	_	_	_
397	BEEF	beef	NN	_	_	_
398	:	:	:	_	_	_
399	666.7	666.7	CD	_	_	_
400	,	,	,	_	_	_
401	PEACH	PEACH	NNP	_	_	_
402	:	:	:	_	_	_
403	222.2	222.2	CD	_	_	_
404	,	,	,	_	_	_
405	SWEET	SWEET	NNP	_	_	_
406	_	_	NNP	_	_	_
407	POTATO	POTATO	NNP	_	_	_
408	:	:	:	_	_	_
409	55.6	55.6	CD	_	_	_
410	,	,	,	_	_	_
411	RICE	RICE	NNP	_	_	_
412	:	:	:	_	_	_
413	55.6	55.6	CD	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
415	diet	diet	NN	_	_	_
416	:	:	:	_	_	_
417	Mouse	mouse	NN	_	_	_
418	was	be	VBD	_	_	_
419	fed	feed	VBN	_	_	_
420	a	a	DT	_	_	_
421	meal	meal	NN	_	_	_
422	of	of	IN	_	_	_
423	human	human	JJ	_	_	_
424	pureed	pureed	NN	_	_	_
425	food	food	NN	_	_	_
426	in	in	IN	_	_	_
427	the	the	DT	_	_	_
428	following	follow	VBG	_	_	_
429	concentrations	concentration	NNS	_	_	_
430	-LRB-	-lrb-	-LRB-	_	_	_
431	g/kg	g/kg	NN	_	_	_
432	-RRB-	-rrb-	-RRB-	_	_	_
433	=	=	JJ	_	_	_
434	>	>	JJR	_	_	_
435	BEEF	beef	NN	_	_	_
436	:	:	:	_	_	_
437	666.7	666.7	CD	_	_	_
438	,	,	,	_	_	_
439	RICE	RICE	NNP	_	_	_
440	:	:	:	_	_	_
441	222.2	222.2	CD	_	_	_
442	,	,	,	_	_	_
443	PEA	PEA	NNP	_	_	_
444	:	:	:	_	_	_
445	55.6	55.6	CD	_	_	_
446	,	,	,	_	_	_
447	CHICK	CHICK	NNP	_	_	_
448	:	:	:	_	_	_
449	55.6	55.6	CD	_	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
451	diet	diet	NN	_	_	_
452	:	:	:	_	_	_
453	Mouse	mouse	NN	_	_	_
454	was	be	VBD	_	_	_
455	fed	feed	VBN	_	_	_
456	a	a	DT	_	_	_
457	meal	meal	NN	_	_	_
458	of	of	IN	_	_	_
459	human	human	JJ	_	_	_
460	pureed	pureed	NN	_	_	_
461	food	food	NN	_	_	_
462	in	in	IN	_	_	_
463	the	the	DT	_	_	_
464	following	follow	VBG	_	_	_
465	concentrations	concentration	NNS	_	_	_
466	-LRB-	-lrb-	-LRB-	_	_	_
467	g/kg	g/kg	NN	_	_	_
468	-RRB-	-rrb-	-RRB-	_	_	_
469	=	=	JJ	_	_	_
470	>	>	JJR	_	_	_
471	CHICK	chick	NN	_	_	_
472	:	:	:	_	_	_
473	421.1	421.1	CD	_	_	_
474	,	,	,	_	_	_
475	BEEF	beef	NN	_	_	_
476	:	:	:	_	_	_
477	421.1	421.1	CD	_	_	_
478	,	,	,	_	_	_
479	PEA	PEA	NNP	_	_	_
480	:	:	:	_	_	_
481	105.3	105.3	CD	_	_	_
482	,	,	,	_	_	_
483	APPLE	APPLE	NNP	_	_	_
484	:	:	:	_	_	_
485	52.6	52.6	CD	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
487	diet	diet	NN	_	_	_
488	:	:	:	_	_	_
489	Mouse	mouse	NN	_	_	_
490	was	be	VBD	_	_	_
491	fed	feed	VBN	_	_	_
492	a	a	DT	_	_	_
493	meal	meal	NN	_	_	_
494	of	of	IN	_	_	_
495	human	human	JJ	_	_	_
496	pureed	pureed	NN	_	_	_
497	food	food	NN	_	_	_
498	in	in	IN	_	_	_
499	the	the	DT	_	_	_
500	following	follow	VBG	_	_	_
501	concentrations	concentration	NNS	_	_	_
502	-LRB-	-lrb-	-LRB-	_	_	_
503	g/kg	g/kg	NN	_	_	_
504	-RRB-	-rrb-	-RRB-	_	_	_
505	=	=	JJ	_	_	_
506	>	>	JJR	_	_	_
507	CHICK	chick	NN	_	_	_
508	:	:	:	_	_	_
509	666.7	666.7	CD	_	_	_
510	,	,	,	_	_	_
511	PEACH	PEACH	NNP	_	_	_
512	:	:	:	_	_	_
513	222.2	222.2	CD	_	_	_
514	,	,	,	_	_	_
515	BEEF	beef	NN	_	_	_
516	:	:	:	_	_	_
517	55.6	55.6	CD	_	_	_
518	,	,	,	_	_	_
519	RICE	RICE	NNP	_	_	_
520	:	:	:	_	_	_
521	55.6	55.6	CD	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
523	diet	diet	NN	_	_	_
524	:	:	:	_	_	_
525	Mouse	mouse	NN	_	_	_
526	was	be	VBD	_	_	_
527	fed	feed	VBN	_	_	_
528	a	a	DT	_	_	_
529	meal	meal	NN	_	_	_
530	of	of	IN	_	_	_
531	human	human	JJ	_	_	_
532	pureed	pureed	NN	_	_	_
533	food	food	NN	_	_	_
534	in	in	IN	_	_	_
535	the	the	DT	_	_	_
536	following	follow	VBG	_	_	_
537	concentrations	concentration	NNS	_	_	_
538	-LRB-	-lrb-	-LRB-	_	_	_
539	g/kg	g/kg	NN	_	_	_
540	-RRB-	-rrb-	-RRB-	_	_	_
541	=	=	JJ	_	_	_
542	>	>	JJR	_	_	_
543	CHICK	chick	NN	_	_	_
544	:	:	:	_	_	_
545	666.7	666.7	CD	_	_	_
546	,	,	,	_	_	_
547	PEACH	PEACH	NNP	_	_	_
548	:	:	:	_	_	_
549	222.2	222.2	CD	_	_	_
550	,	,	,	_	_	_
551	RICE	RICE	NNP	_	_	_
552	:	:	:	_	_	_
553	55.6	55.6	CD	_	_	_
554	,	,	,	_	_	_
555	OAT	oat	NN	_	_	_
556	:	:	:	_	_	_
557	55.6	55.6	CD	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
559	diet	diet	NN	_	_	_
560	:	:	:	_	_	_
561	Mouse	mouse	NN	_	_	_
562	was	be	VBD	_	_	_
563	fed	feed	VBN	_	_	_
564	a	a	DT	_	_	_
565	meal	meal	NN	_	_	_
566	of	of	IN	_	_	_
567	human	human	JJ	_	_	_
568	pureed	pureed	NN	_	_	_
569	food	food	NN	_	_	_
570	in	in	IN	_	_	_
571	the	the	DT	_	_	_
572	following	follow	VBG	_	_	_
573	concentrations	concentration	NNS	_	_	_
574	-LRB-	-lrb-	-LRB-	_	_	_
575	g/kg	g/kg	NN	_	_	_
576	-RRB-	-rrb-	-RRB-	_	_	_
577	=	=	JJ	_	_	_
578	>	>	JJR	_	_	_
579	CHICK	chick	NN	_	_	_
580	:	:	:	_	_	_
581	666.7	666.7	CD	_	_	_
582	,	,	,	_	_	_
583	SWEET	SWEET	NNP	_	_	_
584	_	_	NNP	_	_	_
585	POTATO	POTATO	NNP	_	_	_
586	:	:	:	_	_	_
587	222.2	222.2	CD	_	_	_
588	,	,	,	_	_	_
589	RICE	RICE	NNP	_	_	_
590	:	:	:	_	_	_
591	55.6	55.6	CD	_	_	_
592	,	,	,	_	_	_
593	OAT	oat	NN	_	_	_
594	:	:	:	_	_	_
595	55.6	55.6	CD	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
597	diet	diet	NN	_	_	_
598	:	:	:	_	_	_
599	Mouse	mouse	NN	_	_	_
600	was	be	VBD	_	_	_
601	fed	feed	VBN	_	_	_
602	a	a	DT	_	_	_
603	meal	meal	NN	_	_	_
604	of	of	IN	_	_	_
605	human	human	JJ	_	_	_
606	pureed	pureed	NN	_	_	_
607	food	food	NN	_	_	_
608	in	in	IN	_	_	_
609	the	the	DT	_	_	_
610	following	follow	VBG	_	_	_
611	concentrations	concentration	NNS	_	_	_
612	-LRB-	-lrb-	-LRB-	_	_	_
613	g/kg	g/kg	NN	_	_	_
614	-RRB-	-rrb-	-RRB-	_	_	_
615	=	=	JJ	_	_	_
616	>	>	JJR	_	_	_
617	OAT	oat	NN	_	_	_
618	:	:	:	_	_	_
619	421.1	421.1	CD	_	_	_
620	,	,	,	_	_	_
621	APPLE	APPLE	NNP	_	_	_
622	:	:	:	_	_	_
623	421.1	421.1	CD	_	_	_
624	,	,	,	_	_	_
625	BEEF	beef	NN	_	_	_
626	:	:	:	_	_	_
627	105.3	105.3	CD	_	_	_
628	,	,	,	_	_	_
629	RICE	RICE	NNP	_	_	_
630	:	:	:	_	_	_
631	52.6	52.6	CD	_	_	_
632	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
633	diet	diet	NN	_	_	_
634	:	:	:	_	_	_
635	Mouse	mouse	NN	_	_	_
636	was	be	VBD	_	_	_
637	fed	feed	VBN	_	_	_
638	a	a	DT	_	_	_
639	meal	meal	NN	_	_	_
640	of	of	IN	_	_	_
641	human	human	JJ	_	_	_
642	pureed	pureed	NN	_	_	_
643	food	food	NN	_	_	_
644	in	in	IN	_	_	_
645	the	the	DT	_	_	_
646	following	follow	VBG	_	_	_
647	concentrations	concentration	NNS	_	_	_
648	-LRB-	-lrb-	-LRB-	_	_	_
649	g/kg	g/kg	NN	_	_	_
650	-RRB-	-rrb-	-RRB-	_	_	_
651	=	=	JJ	_	_	_
652	>	>	JJR	_	_	_
653	OAT	oat	NN	_	_	_
654	:	:	:	_	_	_
655	421.1	421.1	CD	_	_	_
656	,	,	,	_	_	_
657	RICE	RICE	NNP	_	_	_
658	:	:	:	_	_	_
659	421.1	421.1	CD	_	_	_
660	,	,	,	_	_	_
661	CHICK	CHICK	NNP	_	_	_
662	:	:	:	_	_	_
663	105.3	105.3	CD	_	_	_
664	:	:	:	_	_	_
665	APPLE	APPLE	NNP	_	_	_
666	:	:	:	_	_	_
667	52.6	52.6	CD	_	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
669	diet	diet	NN	_	_	_
670	:	:	:	_	_	_
671	Mouse	mouse	NN	_	_	_
672	was	be	VBD	_	_	_
673	fed	feed	VBN	_	_	_
674	a	a	DT	_	_	_
675	meal	meal	NN	_	_	_
676	of	of	IN	_	_	_
677	human	human	JJ	_	_	_
678	pureed	pureed	NN	_	_	_
679	food	food	NN	_	_	_
680	in	in	IN	_	_	_
681	the	the	DT	_	_	_
682	following	follow	VBG	_	_	_
683	concentrations	concentration	NNS	_	_	_
684	-LRB-	-lrb-	-LRB-	_	_	_
685	g/kg	g/kg	NN	_	_	_
686	-RRB-	-rrb-	-RRB-	_	_	_
687	=	=	JJ	_	_	_
688	>	>	JJR	_	_	_
689	OAT	oat	NN	_	_	_
690	:	:	:	_	_	_
691	666.7	666.7	CD	_	_	_
692	,	,	,	_	_	_
693	RICE	RICE	NNP	_	_	_
694	:	:	:	_	_	_
695	222.2	222.2	CD	_	_	_
696	,	,	,	_	_	_
697	BEEF	beef	NN	_	_	_
698	:	:	:	_	_	_
699	55.6	55.6	CD	_	_	_
700	,	,	,	_	_	_
701	SWEET	SWEET	NNP	_	_	_
702	_	_	NNP	_	_	_
703	POTATO	POTATO	NNP	_	_	_
704	:	:	:	_	_	_
705	55.6	55.6	CD	_	_	_
706	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
707	diet	diet	NN	_	_	_
708	:	:	:	_	_	_
709	Mouse	mouse	NN	_	_	_
710	was	be	VBD	_	_	_
711	fed	feed	VBN	_	_	_
712	a	a	DT	_	_	_
713	meal	meal	NN	_	_	_
714	of	of	IN	_	_	_
715	human	human	JJ	_	_	_
716	pureed	pureed	NN	_	_	_
717	food	food	NN	_	_	_
718	in	in	IN	_	_	_
719	the	the	DT	_	_	_
720	following	follow	VBG	_	_	_
721	concentrations	concentration	NNS	_	_	_
722	-LRB-	-lrb-	-LRB-	_	_	_
723	g/kg	g/kg	NN	_	_	_
724	-RRB-	-rrb-	-RRB-	_	_	_
725	=	=	JJ	_	_	_
726	>	>	JJR	_	_	_
727	PEA	pea	NN	_	_	_
728	:	:	:	_	_	_
729	250	250	CD	_	_	_
730	,	,	,	_	_	_
731	OAT	oat	NN	_	_	_
732	:	:	:	_	_	_
733	250	250	CD	_	_	_
734	,	,	,	_	_	_
735	BEEF	beef	NN	_	_	_
736	:	:	:	_	_	_
737	250	250	CD	_	_	_
738	,	,	,	_	_	_
739	CHICK	CHICK	NNP	_	_	_
740	:	:	:	_	_	_
741	250	250	CD	_	_	_
742	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
743	diet	diet	NN	_	_	_
744	:	:	:	_	_	_
745	Mouse	mouse	NN	_	_	_
746	was	be	VBD	_	_	_
747	fed	feed	VBN	_	_	_
748	a	a	DT	_	_	_
749	meal	meal	NN	_	_	_
750	of	of	IN	_	_	_
751	human	human	JJ	_	_	_
752	pureed	pureed	NN	_	_	_
753	food	food	NN	_	_	_
754	in	in	IN	_	_	_
755	the	the	DT	_	_	_
756	following	follow	VBG	_	_	_
757	concentrations	concentration	NNS	_	_	_
758	-LRB-	-lrb-	-LRB-	_	_	_
759	g/kg	g/kg	NN	_	_	_
760	-RRB-	-rrb-	-RRB-	_	_	_
761	=	=	JJ	_	_	_
762	>	>	JJR	_	_	_
763	PEA	pea	NN	_	_	_
764	:	:	:	_	_	_
765	421.1	421.1	CD	_	_	_
766	,	,	,	_	_	_
767	CHICK	CHICK	NNP	_	_	_
768	:	:	:	_	_	_
769	421.1	421.1	CD	_	_	_
770	,	,	,	_	_	_
771	RICE	RICE	NNP	_	_	_
772	:	:	:	_	_	_
773	105.3	105.3	CD	_	_	_
774	,	,	,	_	_	_
775	PEACH	PEACH	NNP	_	_	_
776	:	:	:	_	_	_
777	52.6	52.6	CD	_	_	_
778	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
779	diet	diet	NN	_	_	_
780	:	:	:	_	_	_
781	Mouse	mouse	NN	_	_	_
782	was	be	VBD	_	_	_
783	fed	feed	VBN	_	_	_
784	a	a	DT	_	_	_
785	meal	meal	NN	_	_	_
786	of	of	IN	_	_	_
787	human	human	JJ	_	_	_
788	pureed	pureed	NN	_	_	_
789	food	food	NN	_	_	_
790	in	in	IN	_	_	_
791	the	the	DT	_	_	_
792	following	follow	VBG	_	_	_
793	concentrations	concentration	NNS	_	_	_
794	-LRB-	-lrb-	-LRB-	_	_	_
795	g/kg	g/kg	NN	_	_	_
796	-RRB-	-rrb-	-RRB-	_	_	_
797	=	=	JJ	_	_	_
798	>	>	JJR	_	_	_
799	PEA	pea	NN	_	_	_
800	:	:	:	_	_	_
801	666.7	666.7	CD	_	_	_
802	,	,	,	_	_	_
803	APPLE	APPLE	NNP	_	_	_
804	:	:	:	_	_	_
805	222.2	222.2	CD	_	_	_
806	,	,	,	_	_	_
807	SWEET	SWEET	NNP	_	_	_
808	_	_	NNP	_	_	_
809	POTATO	POTATO	NNP	_	_	_
810	:	:	:	_	_	_
811	55.6	55.6	CD	_	_	_
812	,	,	,	_	_	_
813	PEACH	PEACH	NNP	_	_	_
814	:	:	:	_	_	_
815	55.6	55.6	CD	_	_	_
816	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
817	diet	diet	NN	_	_	_
818	:	:	:	_	_	_
819	Mouse	mouse	NN	_	_	_
820	was	be	VBD	_	_	_
821	fed	feed	VBN	_	_	_
822	a	a	DT	_	_	_
823	meal	meal	NN	_	_	_
824	of	of	IN	_	_	_
825	human	human	JJ	_	_	_
826	pureed	pureed	NN	_	_	_
827	food	food	NN	_	_	_
828	in	in	IN	_	_	_
829	the	the	DT	_	_	_
830	following	follow	VBG	_	_	_
831	concentrations	concentration	NNS	_	_	_
832	-LRB-	-lrb-	-LRB-	_	_	_
833	g/kg	g/kg	NN	_	_	_
834	-RRB-	-rrb-	-RRB-	_	_	_
835	=	=	JJ	_	_	_
836	>	>	JJR	_	_	_
837	PEA	pea	NN	_	_	_
838	:	:	:	_	_	_
839	666.7	666.7	CD	_	_	_
840	,	,	,	_	_	_
841	CHICK	CHICK	NNP	_	_	_
842	:	:	:	_	_	_
843	222.2	222.2	CD	_	_	_
844	,	,	,	_	_	_
845	OAT	oat	NN	_	_	_
846	:	:	:	_	_	_
847	55.6	55.6	CD	_	_	_
848	,	,	,	_	_	_
849	SWEET	SWEET	NNP	_	_	_
850	_	_	NNP	_	_	_
851	POTATO	POTATO	NNP	_	_	_
852	:	:	:	_	_	_
853	55.6	55.6	CD	_	_	_
854	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
855	diet	diet	NN	_	_	_
856	:	:	:	_	_	_
857	Mouse	mouse	NN	_	_	_
858	was	be	VBD	_	_	_
859	fed	feed	VBN	_	_	_
860	a	a	DT	_	_	_
861	meal	meal	NN	_	_	_
862	of	of	IN	_	_	_
863	human	human	JJ	_	_	_
864	pureed	pureed	NN	_	_	_
865	food	food	NN	_	_	_
866	in	in	IN	_	_	_
867	the	the	DT	_	_	_
868	following	follow	VBG	_	_	_
869	concentrations	concentration	NNS	_	_	_
870	-LRB-	-lrb-	-LRB-	_	_	_
871	g/kg	g/kg	NN	_	_	_
872	-RRB-	-rrb-	-RRB-	_	_	_
873	=	=	JJ	_	_	_
874	>	>	JJR	_	_	_
875	PEA	pea	NN	_	_	_
876	:	:	:	_	_	_
877	666.7	666.7	CD	_	_	_
878	,	,	,	_	_	_
879	PEACH	PEACH	NNP	_	_	_
880	:	:	:	_	_	_
881	222.2	222.2	CD	_	_	_
882	,	,	,	_	_	_
883	CHICK	CHICK	NNP	_	_	_
884	:	:	:	_	_	_
885	55.6	55.6	CD	_	_	_
886	,	,	,	_	_	_
887	OAT	oat	NN	_	_	_
888	:	:	:	_	_	_
889	55.6	55.6	CD	_	_	_
890	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
891	diet	diet	NN	_	_	_
892	:	:	:	_	_	_
893	Mouse	mouse	NN	_	_	_
894	was	be	VBD	_	_	_
895	fed	feed	VBN	_	_	_
896	a	a	DT	_	_	_
897	meal	meal	NN	_	_	_
898	of	of	IN	_	_	_
899	human	human	JJ	_	_	_
900	pureed	pureed	NN	_	_	_
901	food	food	NN	_	_	_
902	in	in	IN	_	_	_
903	the	the	DT	_	_	_
904	following	follow	VBG	_	_	_
905	concentrations	concentration	NNS	_	_	_
906	-LRB-	-lrb-	-LRB-	_	_	_
907	g/kg	g/kg	NN	_	_	_
908	-RRB-	-rrb-	-RRB-	_	_	_
909	=	=	JJ	_	_	_
910	>	>	JJR	_	_	_
911	PEA	pea	NN	_	_	_
912	:	:	:	_	_	_
913	666.7	666.7	CD	_	_	_
914	,	,	,	_	_	_
915	RICE	RICE	NNP	_	_	_
916	:	:	:	_	_	_
917	222.2	222.2	CD	_	_	_
918	,	,	,	_	_	_
919	APPLE	APPLE	NNP	_	_	_
920	:	:	:	_	_	_
921	55.6	55.6	CD	_	_	_
922	,	,	,	_	_	_
923	BEEF	beef	NN	_	_	_
924	:	:	:	_	_	_
925	55.6	55.6	CD	_	_	_
926	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
927	diet	diet	NN	_	_	_
928	:	:	:	_	_	_
929	Mouse	mouse	NN	_	_	_
930	was	be	VBD	_	_	_
931	fed	feed	VBN	_	_	_
932	a	a	DT	_	_	_
933	meal	meal	NN	_	_	_
934	of	of	IN	_	_	_
935	human	human	JJ	_	_	_
936	pureed	pureed	NN	_	_	_
937	food	food	NN	_	_	_
938	in	in	IN	_	_	_
939	the	the	DT	_	_	_
940	following	follow	VBG	_	_	_
941	concentrations	concentration	NNS	_	_	_
942	-LRB-	-lrb-	-LRB-	_	_	_
943	g/kg	g/kg	NN	_	_	_
944	-RRB-	-rrb-	-RRB-	_	_	_
945	=	=	JJ	_	_	_
946	>	>	JJR	_	_	_
947	PEA	pea	NN	_	_	_
948	:	:	:	_	_	_
949	666.7	666.7	CD	_	_	_
950	,	,	,	_	_	_
951	RICE	RICE	NNP	_	_	_
952	:	:	:	_	_	_
953	222.2	222.2	CD	_	_	_
954	,	,	,	_	_	_
955	SWEET	SWEET	NNP	_	_	_
956	_	_	NNP	_	_	_
957	POTATO	POTATO	NNP	_	_	_
958	:	:	:	_	_	_
959	55.6	55.6	CD	_	_	_
960	,	,	,	_	_	_
961	PEACH	PEACH	NNP	_	_	_
962	:	:	:	_	_	_
963	55.6	55.6	CD	_	_	_
964	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
965	diet	diet	NN	_	_	_
966	:	:	:	_	_	_
967	Mouse	mouse	NN	_	_	_
968	was	be	VBD	_	_	_
969	fed	feed	VBN	_	_	_
970	a	a	DT	_	_	_
971	meal	meal	NN	_	_	_
972	of	of	IN	_	_	_
973	human	human	JJ	_	_	_
974	pureed	pureed	NN	_	_	_
975	food	food	NN	_	_	_
976	in	in	IN	_	_	_
977	the	the	DT	_	_	_
978	following	follow	VBG	_	_	_
979	concentrations	concentration	NNS	_	_	_
980	-LRB-	-lrb-	-LRB-	_	_	_
981	g/kg	g/kg	NN	_	_	_
982	-RRB-	-rrb-	-RRB-	_	_	_
983	=	=	JJ	_	_	_
984	>	>	JJR	_	_	_
985	PEACH	peach	NN	_	_	_
986	:	:	:	_	_	_
987	250	250	CD	_	_	_
988	,	,	,	_	_	_
989	OAT	oat	NN	_	_	_
990	:	:	:	_	_	_
991	250	250	CD	_	_	_
992	,	,	,	_	_	_
993	RICE	RICE	NNP	_	_	_
994	:	:	:	_	_	_
995	250	250	CD	_	_	_
996	,	,	,	_	_	_
997	SWEET	SWEET	NNP	_	_	_
998	_	_	NNP	_	_	_
999	POTATO	POTATO	NNP	_	_	_
1000	:	:	:	_	_	_
1001	250	250	CD	_	_	_
1002	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1003	diet	diet	NN	_	_	_
1004	:	:	:	_	_	_
1005	Mouse	mouse	NN	_	_	_
1006	was	be	VBD	_	_	_
1007	fed	feed	VBN	_	_	_
1008	a	a	DT	_	_	_
1009	meal	meal	NN	_	_	_
1010	of	of	IN	_	_	_
1011	human	human	JJ	_	_	_
1012	pureed	pureed	NN	_	_	_
1013	food	food	NN	_	_	_
1014	in	in	IN	_	_	_
1015	the	the	DT	_	_	_
1016	following	follow	VBG	_	_	_
1017	concentrations	concentration	NNS	_	_	_
1018	-LRB-	-lrb-	-LRB-	_	_	_
1019	g/kg	g/kg	NN	_	_	_
1020	-RRB-	-rrb-	-RRB-	_	_	_
1021	=	=	JJ	_	_	_
1022	>	>	JJR	_	_	_
1023	PEACH	peach	NN	_	_	_
1024	:	:	:	_	_	_
1025	421.1	421.1	CD	_	_	_
1026	,	,	,	_	_	_
1027	BEEF	beef	NN	_	_	_
1028	:	:	:	_	_	_
1029	421.1	421.1	CD	_	_	_
1030	,	,	,	_	_	_
1031	OAT	oat	NN	_	_	_
1032	:	:	:	_	_	_
1033	105.3	105.3	CD	_	_	_
1034	,	,	,	_	_	_
1035	RICE	RICE	NNP	_	_	_
1036	:	:	:	_	_	_
1037	52.6	52.6	CD	_	_	_
1038	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1039	diet	diet	NN	_	_	_
1040	:	:	:	_	_	_
1041	Mouse	mouse	NN	_	_	_
1042	was	be	VBD	_	_	_
1043	fed	feed	VBN	_	_	_
1044	a	a	DT	_	_	_
1045	meal	meal	NN	_	_	_
1046	of	of	IN	_	_	_
1047	human	human	JJ	_	_	_
1048	pureed	pureed	NN	_	_	_
1049	food	food	NN	_	_	_
1050	in	in	IN	_	_	_
1051	the	the	DT	_	_	_
1052	following	follow	VBG	_	_	_
1053	concentrations	concentration	NNS	_	_	_
1054	-LRB-	-lrb-	-LRB-	_	_	_
1055	g/kg	g/kg	NN	_	_	_
1056	-RRB-	-rrb-	-RRB-	_	_	_
1057	=	=	JJ	_	_	_
1058	>	>	JJR	_	_	_
1059	PEACH	peach	NN	_	_	_
1060	:	:	:	_	_	_
1061	421.1	421.1	CD	_	_	_
1062	,	,	,	_	_	_
1063	OAT	oat	NN	_	_	_
1064	:	:	:	_	_	_
1065	421.1	421.1	CD	_	_	_
1066	,	,	,	_	_	_
1067	SWEET	SWEET	NNP	_	_	_
1068	_	_	NNP	_	_	_
1069	POTATO	POTATO	NNP	_	_	_
1070	:	:	:	_	_	_
1071	105.3	105.3	CD	_	_	_
1072	,	,	,	_	_	_
1073	BEEF	beef	NN	_	_	_
1074	:	:	:	_	_	_
1075	52.6	52.6	CD	_	_	_
1076	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1077	diet	diet	NN	_	_	_
1078	:	:	:	_	_	_
1079	Mouse	mouse	NN	_	_	_
1080	was	be	VBD	_	_	_
1081	fed	feed	VBN	_	_	_
1082	a	a	DT	_	_	_
1083	meal	meal	NN	_	_	_
1084	of	of	IN	_	_	_
1085	human	human	JJ	_	_	_
1086	pureed	pureed	NN	_	_	_
1087	food	food	NN	_	_	_
1088	in	in	IN	_	_	_
1089	the	the	DT	_	_	_
1090	following	follow	VBG	_	_	_
1091	concentrations	concentration	NNS	_	_	_
1092	-LRB-	-lrb-	-LRB-	_	_	_
1093	g/kg	g/kg	NN	_	_	_
1094	-RRB-	-rrb-	-RRB-	_	_	_
1095	=	=	JJ	_	_	_
1096	>	>	JJR	_	_	_
1097	PEACH	peach	NN	_	_	_
1098	:	:	:	_	_	_
1099	666.7	666.7	CD	_	_	_
1100	,	,	,	_	_	_
1101	OAT	oat	NN	_	_	_
1102	:	:	:	_	_	_
1103	222.2	222.2	CD	_	_	_
1104	,	,	,	_	_	_
1105	SWEET	SWEET	NNP	_	_	_
1106	_	_	NNP	_	_	_
1107	POTATO	POTATO	NNP	_	_	_
1108	:	:	:	_	_	_
1109	55.6	55.6	CD	_	_	_
1110	,	,	,	_	_	_
1111	CHICK	CHICK	NNP	_	_	_
1112	:	:	:	_	_	_
1113	55.6	55.6	CD	_	_	_
1114	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1115	diet	diet	NN	_	_	_
1116	:	:	:	_	_	_
1117	Mouse	mouse	NN	_	_	_
1118	was	be	VBD	_	_	_
1119	fed	feed	VBN	_	_	_
1120	a	a	DT	_	_	_
1121	meal	meal	NN	_	_	_
1122	of	of	IN	_	_	_
1123	human	human	JJ	_	_	_
1124	pureed	pureed	NN	_	_	_
1125	food	food	NN	_	_	_
1126	in	in	IN	_	_	_
1127	the	the	DT	_	_	_
1128	following	follow	VBG	_	_	_
1129	concentrations	concentration	NNS	_	_	_
1130	-LRB-	-lrb-	-LRB-	_	_	_
1131	g/kg	g/kg	NN	_	_	_
1132	-RRB-	-rrb-	-RRB-	_	_	_
1133	=	=	JJ	_	_	_
1134	>	>	JJR	_	_	_
1135	PEACH	peach	NN	_	_	_
1136	:	:	:	_	_	_
1137	666.7	666.7	CD	_	_	_
1138	,	,	,	_	_	_
1139	PEA	PEA	NNP	_	_	_
1140	:	:	:	_	_	_
1141	222.2	222.2	CD	_	_	_
1142	,	,	,	_	_	_
1143	APPLE	APPLE	NNP	_	_	_
1144	:	:	:	_	_	_
1145	55.6	55.6	CD	_	_	_
1146	,	,	,	_	_	_
1147	CHICK	CHICK	NNP	_	_	_
1148	:	:	:	_	_	_
1149	55.6	55.6	CD	_	_	_
1150	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1151	diet	diet	NN	_	_	_
1152	:	:	:	_	_	_
1153	Mouse	mouse	NN	_	_	_
1154	was	be	VBD	_	_	_
1155	fed	feed	VBN	_	_	_
1156	a	a	DT	_	_	_
1157	meal	meal	NN	_	_	_
1158	of	of	IN	_	_	_
1159	human	human	JJ	_	_	_
1160	pureed	pureed	NN	_	_	_
1161	food	food	NN	_	_	_
1162	in	in	IN	_	_	_
1163	the	the	DT	_	_	_
1164	following	follow	VBG	_	_	_
1165	concentrations	concentration	NNS	_	_	_
1166	-LRB-	-lrb-	-LRB-	_	_	_
1167	g/kg	g/kg	NN	_	_	_
1168	-RRB-	-rrb-	-RRB-	_	_	_
1169	=	=	JJ	_	_	_
1170	>	>	JJR	_	_	_
1171	PEACH	peach	NN	_	_	_
1172	:	:	:	_	_	_
1173	666.7	666.7	CD	_	_	_
1174	,	,	,	_	_	_
1175	PEA	PEA	NNP	_	_	_
1176	:	:	:	_	_	_
1177	222.2	222.2	CD	_	_	_
1178	,	,	,	_	_	_
1179	OAT	oat	NN	_	_	_
1180	:	:	:	_	_	_
1181	55.6	55.6	CD	_	_	_
1182	,	,	,	_	_	_
1183	RICE	RICE	NNP	_	_	_
1184	:	:	:	_	_	_
1185	55.6	55.6	CD	_	_	_
1186	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1187	diet	diet	NN	_	_	_
1188	:	:	:	_	_	_
1189	Mouse	mouse	NN	_	_	_
1190	was	be	VBD	_	_	_
1191	fed	feed	VBN	_	_	_
1192	a	a	DT	_	_	_
1193	meal	meal	NN	_	_	_
1194	of	of	IN	_	_	_
1195	human	human	JJ	_	_	_
1196	pureed	pureed	NN	_	_	_
1197	food	food	NN	_	_	_
1198	in	in	IN	_	_	_
1199	the	the	DT	_	_	_
1200	following	follow	VBG	_	_	_
1201	concentrations	concentration	NNS	_	_	_
1202	-LRB-	-lrb-	-LRB-	_	_	_
1203	g/kg	g/kg	NN	_	_	_
1204	-RRB-	-rrb-	-RRB-	_	_	_
1205	=	=	JJ	_	_	_
1206	>	>	JJR	_	_	_
1207	PEACH	peach	NN	_	_	_
1208	:	:	:	_	_	_
1209	666.7	666.7	CD	_	_	_
1210	,	,	,	_	_	_
1211	PEA	PEA	NNP	_	_	_
1212	:	:	:	_	_	_
1213	222.2	222.2	CD	_	_	_
1214	,	,	,	_	_	_
1215	RICE	RICE	NNP	_	_	_
1216	:	:	:	_	_	_
1217	55.6	55.6	CD	_	_	_
1218	,	,	,	_	_	_
1219	BEEF	beef	NN	_	_	_
1220	:	:	:	_	_	_
1221	55.6	55.6	CD	_	_	_
1222	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1223	diet	diet	NN	_	_	_
1224	:	:	:	_	_	_
1225	Mouse	mouse	NN	_	_	_
1226	was	be	VBD	_	_	_
1227	fed	feed	VBN	_	_	_
1228	a	a	DT	_	_	_
1229	meal	meal	NN	_	_	_
1230	of	of	IN	_	_	_
1231	human	human	JJ	_	_	_
1232	pureed	pureed	NN	_	_	_
1233	food	food	NN	_	_	_
1234	in	in	IN	_	_	_
1235	the	the	DT	_	_	_
1236	following	follow	VBG	_	_	_
1237	concentrations	concentration	NNS	_	_	_
1238	-LRB-	-lrb-	-LRB-	_	_	_
1239	g/kg	g/kg	NN	_	_	_
1240	-RRB-	-rrb-	-RRB-	_	_	_
1241	=	=	JJ	_	_	_
1242	>	>	JJR	_	_	_
1243	RICE	rice	NN	_	_	_
1244	:	:	:	_	_	_
1245	666.7	666.7	CD	_	_	_
1246	,	,	,	_	_	_
1247	APPLE	APPLE	NNP	_	_	_
1248	:	:	:	_	_	_
1249	222.2	222.2	CD	_	_	_
1250	,	,	,	_	_	_
1251	SWEET	SWEET	NNP	_	_	_
1252	_	_	NNP	_	_	_
1253	POTATO	POTATO	NNP	_	_	_
1254	:	:	:	_	_	_
1255	55.6	55.6	CD	_	_	_
1256	,	,	,	_	_	_
1257	BEEF	beef	NN	_	_	_
1258	:	:	:	_	_	_
1259	55.6	55.6	CD	_	_	_
1260	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1261	diet	diet	NN	_	_	_
1262	:	:	:	_	_	_
1263	Mouse	mouse	NN	_	_	_
1264	was	be	VBD	_	_	_
1265	fed	feed	VBN	_	_	_
1266	a	a	DT	_	_	_
1267	meal	meal	NN	_	_	_
1268	of	of	IN	_	_	_
1269	human	human	JJ	_	_	_
1270	pureed	pureed	NN	_	_	_
1271	food	food	NN	_	_	_
1272	in	in	IN	_	_	_
1273	the	the	DT	_	_	_
1274	following	follow	VBG	_	_	_
1275	concentrations	concentration	NNS	_	_	_
1276	-LRB-	-lrb-	-LRB-	_	_	_
1277	g/kg	g/kg	NN	_	_	_
1278	-RRB-	-rrb-	-RRB-	_	_	_
1279	=	=	JJ	_	_	_
1280	>	>	JJR	_	_	_
1281	SWEET	sweet	JJ	_	_	_
1282	_	_	NN	_	_	_
1283	POTATO	potato	NN	_	_	_
1284	:	:	:	_	_	_
1285	250	250	CD	_	_	_
1286	,	,	,	_	_	_
1287	APPLE	APPLE	NNP	_	_	_
1288	:	:	:	_	_	_
1289	250	250	CD	_	_	_
1290	,	,	,	_	_	_
1291	PEACH	PEACH	NNP	_	_	_
1292	:	:	:	_	_	_
1293	250	250	CD	_	_	_
1294	,	,	,	_	_	_
1295	BEEF	beef	NN	_	_	_
1296	:	:	:	_	_	_
1297	250	250	CD	_	_	_
1298	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1299	diet	diet	NN	_	_	_
1300	:	:	:	_	_	_
1301	Mouse	mouse	NN	_	_	_
1302	was	be	VBD	_	_	_
1303	fed	feed	VBN	_	_	_
1304	a	a	DT	_	_	_
1305	meal	meal	NN	_	_	_
1306	of	of	IN	_	_	_
1307	human	human	JJ	_	_	_
1308	pureed	pureed	NN	_	_	_
1309	food	food	NN	_	_	_
1310	in	in	IN	_	_	_
1311	the	the	DT	_	_	_
1312	following	follow	VBG	_	_	_
1313	concentrations	concentration	NNS	_	_	_
1314	-LRB-	-lrb-	-LRB-	_	_	_
1315	g/kg	g/kg	NN	_	_	_
1316	-RRB-	-rrb-	-RRB-	_	_	_
1317	=	=	JJ	_	_	_
1318	>	>	JJR	_	_	_
1319	SWEET	sweet	JJ	_	_	_
1320	_	_	NN	_	_	_
1321	POTATO	potato	NN	_	_	_
1322	:	:	:	_	_	_
1323	250	250	CD	_	_	_
1324	,	,	,	_	_	_
1325	BEEF	beef	NN	_	_	_
1326	:	:	:	_	_	_
1327	250	250	CD	_	_	_
1328	,	,	,	_	_	_
1329	PEACH	PEACH	NNP	_	_	_
1330	:	:	:	_	_	_
1331	250	250	CD	_	_	_
1332	,	,	,	_	_	_
1333	RICE	RICE	NNP	_	_	_
1334	:	:	:	_	_	_
1335	250	250	CD	_	_	_
1336	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1337	diet	diet	NN	_	_	_
1338	:	:	:	_	_	_
1339	Mouse	mouse	NN	_	_	_
1340	was	be	VBD	_	_	_
1341	fed	feed	VBN	_	_	_
1342	a	a	DT	_	_	_
1343	meal	meal	NN	_	_	_
1344	of	of	IN	_	_	_
1345	human	human	JJ	_	_	_
1346	pureed	pureed	NN	_	_	_
1347	food	food	NN	_	_	_
1348	in	in	IN	_	_	_
1349	the	the	DT	_	_	_
1350	following	follow	VBG	_	_	_
1351	concentrations	concentration	NNS	_	_	_
1352	-LRB-	-lrb-	-LRB-	_	_	_
1353	g/kg	g/kg	NN	_	_	_
1354	-RRB-	-rrb-	-RRB-	_	_	_
1355	=	=	JJ	_	_	_
1356	>	>	JJR	_	_	_
1357	SWEET	sweet	JJ	_	_	_
1358	_	_	NN	_	_	_
1359	POTATO	potato	NN	_	_	_
1360	:	:	:	_	_	_
1361	421.1	421.1	CD	_	_	_
1362	,	,	,	_	_	_
1363	OAT	oat	NN	_	_	_
1364	:	:	:	_	_	_
1365	421.1	421.1	CD	_	_	_
1366	,	,	,	_	_	_
1367	CHICK	CHICK	NNP	_	_	_
1368	:	:	:	_	_	_
1369	105.3	105.3	CD	_	_	_
1370	,	,	,	_	_	_
1371	RICE	RICE	NNP	_	_	_
1372	:	:	:	_	_	_
1373	52.6	52.6	CD	_	_	_
1374	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1375	diet	diet	NN	_	_	_
1376	:	:	:	_	_	_
1377	Mouse	mouse	NN	_	_	_
1378	was	be	VBD	_	_	_
1379	fed	feed	VBN	_	_	_
1380	a	a	DT	_	_	_
1381	meal	meal	NN	_	_	_
1382	of	of	IN	_	_	_
1383	human	human	JJ	_	_	_
1384	pureed	pureed	NN	_	_	_
1385	food	food	NN	_	_	_
1386	in	in	IN	_	_	_
1387	the	the	DT	_	_	_
1388	following	follow	VBG	_	_	_
1389	concentrations	concentration	NNS	_	_	_
1390	-LRB-	-lrb-	-LRB-	_	_	_
1391	g/kg	g/kg	NN	_	_	_
1392	-RRB-	-rrb-	-RRB-	_	_	_
1393	=	=	JJ	_	_	_
1394	>	>	JJR	_	_	_
1395	SWEET	sweet	JJ	_	_	_
1396	_	_	NN	_	_	_
1397	POTATO	potato	NN	_	_	_
1398	:	:	:	_	_	_
1399	421.1	421.1	CD	_	_	_
1400	,	,	,	_	_	_
1401	RICE	RICE	NNP	_	_	_
1402	:	:	:	_	_	_
1403	421.1	421.1	CD	_	_	_
1404	,	,	,	_	_	_
1405	CHICK	CHICK	NNP	_	_	_
1406	:	:	:	_	_	_
1407	105.3	105.3	CD	_	_	_
1408	,	,	,	_	_	_
1409	PEA	PEA	NNP	_	_	_
1410	:	:	:	_	_	_
1411	52.6	52.6	CD	_	_	_
1412	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1413	diet	diet	NN	_	_	_
1414	:	:	:	_	_	_
1415	Mouse	mouse	NN	_	_	_
1416	was	be	VBD	_	_	_
1417	fed	feed	VBN	_	_	_
1418	a	a	DT	_	_	_
1419	meal	meal	NN	_	_	_
1420	of	of	IN	_	_	_
1421	human	human	JJ	_	_	_
1422	pureed	pureed	NN	_	_	_
1423	food	food	NN	_	_	_
1424	in	in	IN	_	_	_
1425	the	the	DT	_	_	_
1426	following	follow	VBG	_	_	_
1427	concentrations	concentration	NNS	_	_	_
1428	-LRB-	-lrb-	-LRB-	_	_	_
1429	g/kg	g/kg	NN	_	_	_
1430	-RRB-	-rrb-	-RRB-	_	_	_
1431	=	=	JJ	_	_	_
1432	>	>	JJR	_	_	_
1433	SWEET	sweet	JJ	_	_	_
1434	_	_	NN	_	_	_
1435	POTATO	potato	NN	_	_	_
1436	:	:	:	_	_	_
1437	666.7	666.7	CD	_	_	_
1438	,	,	,	_	_	_
1439	APPLE	APPLE	NNP	_	_	_
1440	:	:	:	_	_	_
1441	222.2	222.2	CD	_	_	_
1442	,	,	,	_	_	_
1443	BEEF	beef	NN	_	_	_
1444	:	:	:	_	_	_
1445	55.6	55.6	CD	_	_	_
1446	,	,	,	_	_	_
1447	PEACH	PEACH	NNP	_	_	_
1448	:	:	:	_	_	_
1449	55.6	55.6	CD	_	_	_
1450	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1451	diet	diet	NN	_	_	_
1452	:	:	:	_	_	_
1453	Mouse	mouse	NN	_	_	_
1454	was	be	VBD	_	_	_
1455	fed	feed	VBN	_	_	_
1456	a	a	DT	_	_	_
1457	meal	meal	NN	_	_	_
1458	of	of	IN	_	_	_
1459	human	human	JJ	_	_	_
1460	pureed	pureed	NN	_	_	_
1461	food	food	NN	_	_	_
1462	in	in	IN	_	_	_
1463	the	the	DT	_	_	_
1464	following	follow	VBG	_	_	_
1465	concentrations	concentration	NNS	_	_	_
1466	-LRB-	-lrb-	-LRB-	_	_	_
1467	g/kg	g/kg	NN	_	_	_
1468	-RRB-	-rrb-	-RRB-	_	_	_
1469	=	=	JJ	_	_	_
1470	>	>	JJR	_	_	_
1471	SWEET	sweet	JJ	_	_	_
1472	_	_	NN	_	_	_
1473	POTATO	potato	NN	_	_	_
1474	:	:	:	_	_	_
1475	666.7	666.7	CD	_	_	_
1476	,	,	,	_	_	_
1477	CHICK	CHICK	NNP	_	_	_
1478	:	:	:	_	_	_
1479	222.2	222.2	CD	_	_	_
1480	,	,	,	_	_	_
1481	BEEF	beef	NN	_	_	_
1482	:	:	:	_	_	_
1483	55.6	55.6	CD	_	_	_
1484	,	,	,	_	_	_
1485	PEA	PEA	NNP	_	_	_
1486	:	:	:	_	_	_
1487	55.6	55.6	CD	_	_	_
1488	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1489	diet	diet	NN	_	_	_
1490	:	:	:	_	_	_
1491	Mouse	mouse	NN	_	_	_
1492	was	be	VBD	_	_	_
1493	fed	feed	VBN	_	_	_
1494	a	a	DT	_	_	_
1495	meal	meal	NN	_	_	_
1496	of	of	IN	_	_	_
1497	human	human	JJ	_	_	_
1498	pureed	pureed	NN	_	_	_
1499	food	food	NN	_	_	_
1500	in	in	IN	_	_	_
1501	the	the	DT	_	_	_
1502	following	follow	VBG	_	_	_
1503	concentrations	concentration	NNS	_	_	_
1504	-LRB-	-lrb-	-LRB-	_	_	_
1505	g/kg	g/kg	NN	_	_	_
1506	-RRB-	-rrb-	-RRB-	_	_	_
1507	=	=	JJ	_	_	_
1508	>	>	JJR	_	_	_
1509	SWEET	sweet	JJ	_	_	_
1510	_	_	NN	_	_	_
1511	POTATO	potato	NN	_	_	_
1512	:	:	:	_	_	_
1513	666.7	666.7	CD	_	_	_
1514	,	,	,	_	_	_
1515	OAT	oat	NN	_	_	_
1516	:	:	:	_	_	_
1517	222.2	222.2	CD	_	_	_
1518	,	,	,	_	_	_
1519	PEACH	PEACH	NNP	_	_	_
1520	:	:	:	_	_	_
1521	55.6	55.6	CD	_	_	_
1522	,	,	,	_	_	_
1523	PEA	PEA	NNP	_	_	_
1524	:	:	:	_	_	_
1525	55.6	55.6	CD	_	_	_
1526	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1527	diet	diet	NN	_	_	_
1528	:	:	:	_	_	_
1529	Mouse	mouse	NN	_	_	_
1530	was	be	VBD	_	_	_
1531	fed	feed	VBN	_	_	_
1532	a	a	DT	_	_	_
1533	meal	meal	NN	_	_	_
1534	of	of	IN	_	_	_
1535	human	human	JJ	_	_	_
1536	pureed	pureed	NN	_	_	_
1537	food	food	NN	_	_	_
1538	in	in	IN	_	_	_
1539	the	the	DT	_	_	_
1540	following	follow	VBG	_	_	_
1541	concentrations	concentration	NNS	_	_	_
1542	-LRB-	-lrb-	-LRB-	_	_	_
1543	g/kg	g/kg	NN	_	_	_
1544	-RRB-	-rrb-	-RRB-	_	_	_
1545	=	=	JJ	_	_	_
1546	>	>	JJR	_	_	_
1547	SWEET	sweet	JJ	_	_	_
1548	_	_	NN	_	_	_
1549	POTATO	potato	NN	_	_	_
1550	:	:	:	_	_	_
1551	666.7	666.7	CD	_	_	_
1552	,	,	,	_	_	_
1553	RICE	RICE	NNP	_	_	_
1554	:	:	:	_	_	_
1555	222.2	222.2	CD	_	_	_
1556	,	,	,	_	_	_
1557	PEACH	PEACH	NNP	_	_	_
1558	:	:	:	_	_	_
1559	55.6	55.6	CD	_	_	_
1560	,	,	,	_	_	_
1561	BEEF	beef	NN	_	_	_
1562	:	:	:	_	_	_
1563	55.6	55.6	CD	_	_	_
1564	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1565	diet	diet	NN	_	_	_
1566	:	:	:	_	_	_
1567	Mouse	mouse	NN	_	_	_
1568	was	be	VBD	_	_	_
1569	fed	feed	VBN	_	_	_
1570	Harlan	Harlan	NNP	_	_	_
1571	Teklad	Teklad	NNP	_	_	_
1572	Diet	Diet	NNP	_	_	_
1573	TD	TD	NNP	_	_	_
1574	.09049	.09049	CD	_	_	_
1575	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1576	diet	diet	NN	_	_	_
1577	:	:	:	_	_	_
1578	Mouse	mouse	NN	_	_	_
1579	was	be	VBD	_	_	_
1580	fed	feed	VBN	_	_	_
1581	Harlan	Harlan	NNP	_	_	_
1582	Teklad	Teklad	NNP	_	_	_
1583	Diet	Diet	NNP	_	_	_
1584	TD	TD	NNP	_	_	_
1585	.09050	.09050	CD	_	_	_
1586	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1587	diet	diet	NN	_	_	_
1588	:	:	:	_	_	_
1589	Mouse	mouse	NN	_	_	_
1590	was	be	VBD	_	_	_
1591	fed	feed	VBN	_	_	_
1592	Harlan	Harlan	NNP	_	_	_
1593	Teklad	Teklad	NNP	_	_	_
1594	Diet	Diet	NNP	_	_	_
1595	TD	TD	NNP	_	_	_
1596	.09051	.09051	CD	_	_	_
1597	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1598	diet	diet	NN	_	_	_
1599	:	:	:	_	_	_
1600	Mouse	mouse	NN	_	_	_
1601	was	be	VBD	_	_	_
1602	fed	feed	VBN	_	_	_
1603	Harlan	Harlan	NNP	_	_	_
1604	Teklad	Teklad	NNP	_	_	_
1605	Diet	Diet	NNP	_	_	_
1606	TD	TD	NNP	_	_	_
1607	.09052	.09052	CD	_	_	_
1608	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1609	diet	diet	NN	_	_	_
1610	:	:	:	_	_	_
1611	Mouse	mouse	NN	_	_	_
1612	was	be	VBD	_	_	_
1613	fed	feed	VBN	_	_	_
1614	Harlan	Harlan	NNP	_	_	_
1615	Teklad	Teklad	NNP	_	_	_
1616	Diet	Diet	NNP	_	_	_
1617	TD	TD	NNP	_	_	_
1618	.09053	.09053	CD	_	_	_
1619	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1620	diet	diet	NN	_	_	_
1621	:	:	:	_	_	_
1622	Mouse	mouse	NN	_	_	_
1623	was	be	VBD	_	_	_
1624	fed	feed	VBN	_	_	_
1625	Harlan	Harlan	NNP	_	_	_
1626	Teklad	Teklad	NNP	_	_	_
1627	Diet	Diet	NNP	_	_	_
1628	TD	TD	NNP	_	_	_
1629	.09054	.09054	CD	_	_	_
1630	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1631	diet	diet	NN	_	_	_
1632	:	:	:	_	_	_
1633	Mouse	mouse	NN	_	_	_
1634	was	be	VBD	_	_	_
1635	fed	feed	VBN	_	_	_
1636	Harlan	Harlan	NNP	_	_	_
1637	Teklad	Teklad	NNP	_	_	_
1638	Diet	Diet	NNP	_	_	_
1639	TD	TD	NNP	_	_	_
1640	.09055	.09055	CD	_	_	_
1641	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1642	diet	diet	NN	_	_	_
1643	:	:	:	_	_	_
1644	Mouse	mouse	NN	_	_	_
1645	was	be	VBD	_	_	_
1646	fed	feed	VBN	_	_	_
1647	Harlan	Harlan	NNP	_	_	_
1648	Teklad	Teklad	NNP	_	_	_
1649	Diet	Diet	NNP	_	_	_
1650	TD	TD	NNP	_	_	_
1651	.09055	.09055	CD	_	_	_
1652	.	.	.	_	_	_

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	Differential	differential	JJ	_	_	_
91	expression	expression	NN	_	_	_
92	analysis	analysis	NN	_	_	_
93	was	be	VBD	_	_	_
94	carried	carry	VBN	_	_	_
95	out	out	RP	_	_	_
96	using	use	VBG	_	_	_
97	cuffdiff	cuffdiff	JJ	_	_	_
98	v.	v.	CC	_	_	_
99	2.0.2	2.0.2	CD	_	_	_
100	with	with	IN	_	_	_
101	upper-quartile	upper-quartile	JJ	_	_	_
102	normalization	normalization	NN	_	_	_
103	and	and	CC	_	_	_
104	fr-firststrand	fr-firststrand	NN	_	_	_
105	for	for	IN	_	_	_
106	library	library	NN	_	_	_
107	type	type	NN	_	_	_
108	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
109	Differential	differential	JJ	_	_	_
110	expression	expression	NN	_	_	_
111	analysis	analysis	NN	_	_	_
112	was	be	VBD	_	_	_
113	performed	perform	VBN	_	_	_
114	with	with	IN	_	_	_
115	R	r	NN	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	version	version	NN	_	_	_
118	3.1.1	3.1.1	CD	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	and	and	CC	_	_	_
121	edgeR	edger	NN	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	version	version	NN	_	_	_
124	3.8.5	3.8.5	CD	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	Bioconductor	bioconductor	NN	_	_	_
128	-RRB-	-rrb-	-RRB-	_	_	_
129	.	.	.	_	_	_

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	Differential	differential	JJ	_	_	_
19	expression	expression	NN	_	_	_
20	between	between	IN	_	_	_
21	aerobic	aerobic	JJ	_	_	_
22	and	and	CC	_	_	_
23	anaerobic	anaerobic	JJ	_	_	_
24	environments	environment	NNS	_	_	_
25	was	be	VBD	_	_	_
26	identified	identify	VBN	_	_	_
27	by	by	IN	_	_	_
28	using	use	VBG	_	_	_
29	DESeq2	deseq2	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Love	love	NN	_	_	_
32	M	m	NN	_	_	_
33	,	,	,	_	_	_
34	Huber	Huber	NNP	_	_	_
35	W	W	NNP	_	_	_
36	and	and	CC	_	_	_
37	Anders	Anders	NNP	_	_	_
38	S	s	NN	_	_	_
39	,	,	,	_	_	_
40	2014	2014	CD	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	differential	differential	JJ	_	_	_
44	expression	expression	NN	_	_	_
45	:	:	:	_	_	_
46	Bioconductor	Bioconductor	NNP	_	_	_
47	package	package	NN	_	_	_
48	edgeR	edger	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	version	version	NN	_	_	_
51	3.2.3	3.2.3	CD	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	;	;	:	_	_	_
54	default	default	NN	_	_	_
55	parameters	parameter	NNS	_	_	_
56	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
57	Differential	differential	JJ	_	_	_
58	expression	expression	NN	_	_	_
59	testing	testing	NN	_	_	_
60	between	between	IN	_	_	_
61	sample	sample	NN	_	_	_
62	groups	group	NNS	_	_	_
63	was	be	VBD	_	_	_
64	performed	perform	VBN	_	_	_
65	in	in	IN	_	_	_
66	Rstudio	Rstudio	NNP	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	v.	v.	CC	_	_	_
69	1.0.36	1.0.36	CD	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	using	use	VBG	_	_	_
72	DESeq2	deseq2	NN	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	v.	v.	CC	_	_	_
75	1.14.1	1.14.1	CD	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	Differential	differential	JJ	_	_	_
79	gene	gene	NN	_	_	_
80	expression	expression	NN	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	DGE	dge	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	was	be	VBD	_	_	_
85	then	then	RB	_	_	_
86	performed	perform	VBN	_	_	_
87	on	on	IN	_	_	_
88	fragments	fragment	NNS	_	_	_
89	per	per	IN	_	_	_
90	kilobase	kilobase	NN	_	_	_
91	mapped	map	VBN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	FPKM	fpkm	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	values	value	NNS	_	_	_
96	in	in	IN	_	_	_
97	Cufflinks	Cufflinks	NNP	_	_	_
98	'	'	POS	_	_	_
99	Cuffdiff	cuffdiff	JJ	_	_	_
100	package	package	NN	_	_	_
101	-LRB-	-lrb-	-LRB-	_	_	_
102	version	version	NN	_	_	_
103	0.0.7	0.0.7	CD	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Differentially	differentially	RB	_	_	_
3	expressed	express	VBD	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	DE	de	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	genes	gene	NNS	_	_	_
8	in	in	IN	_	_	_
9	all	all	DT	_	_	_
10	stress	stress	NN	_	_	_
11	evolved	evolve	VBD	_	_	_
12	strains	strain	NNS	_	_	_
13	were	be	VBD	_	_	_
14	found	find	VBN	_	_	_
15	relative	relative	JJ	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	expression	expression	NN	_	_	_
19	levels	level	NNS	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	reference	reference	NN	_	_	_
23	G500	g500	NN	_	_	_
24	strain	strain	NN	_	_	_
25	using	use	VBG	_	_	_
26	the	the	DT	_	_	_
27	edgeR	edger	NN	_	_	_
28	R	r	NN	_	_	_
29	package	package	NN	_	_	_
30	.	.	.	_	_	_

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	Dilution	Dilution	NNP	_	_	_
3	rate	rate	NN	_	_	_
4	=	=	JJ	_	_	_
5	0.14	0.14	CD	_	_	_
6	/	/	:	_	_	_
7	h	h	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	dinI	dini	NN	GEN	_	_
10	___	___	CD	_	_	_
11	U	U	NNP	_	_	_
12	_	_	NNP	_	_	_
13	N0025	N0025	NNP	_	_	_
14	_	_	NNP	_	_	_
15	r1	r1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	dinI	dini	NN	GEN	_	_
18	___	___	CD	_	_	_
19	U	U	NNP	_	_	_
20	_	_	NNP	_	_	_
21	N0025	N0025	NNP	_	_	_
22	_	_	SYM	_	_	_
23	r2	r2	FW	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
25	dinI	dini	NN	GEN	_	_
26	___	___	CD	_	_	_
27	U	U	NNP	_	_	_
28	_	_	NNP	_	_	_
29	N0025	N0025	NNP	_	_	_
30	_	_	SYM	_	_	_
31	r3	r3	FW	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
33	dinI	dini	NN	GEN	_	_
34	upregulation	upregulation	NN	_	_	_
35	,	,	,	_	_	_
36	amp	amp	NN	_	_	_
37	50ug/ml	50ug/ml	NN	_	_	_
38	,	,	,	_	_	_
39	0.0125	0.0125	CD	_	_	_
40	%	%	NN	_	_	_
41	arabinose	arabinose	NN	_	_	_
42	,	,	,	_	_	_
43	0.025	0.025	CD	_	_	_
44	ug/ml	ug/ml	NN	_	_	_
45	norfloxacin	norfloxacin	NN	_	_	_
46	OD	od	NN	_	_	_
47	~	~	NN	_	_	_
48	0.3	0.3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	dinP	dinp	NN	_	_	_
51	___	___	CD	_	_	_
52	U	U	NNP	_	_	_
53	_	_	NNP	_	_	_
54	N0025	N0025	NNP	_	_	_
55	_	_	SYM	_	_	_
56	r1	r1	FW	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
58	dinP	dinp	NN	_	_	_
59	___	___	CD	_	_	_
60	U	U	NNP	_	_	_
61	_	_	NNP	_	_	_
62	N0025	N0025	NNP	_	_	_
63	_	_	SYM	_	_	_
64	r2	r2	FW	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
66	dinP	dinp	NN	_	_	_
67	___	___	CD	_	_	_
68	U	U	NNP	_	_	_
69	_	_	NNP	_	_	_
70	N0025	N0025	NNP	_	_	_
71	_	_	SYM	_	_	_
72	r3	r3	FW	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
74	dinP	dinp	NN	_	_	_
75	upregulation	upregulation	NN	_	_	_
76	,	,	,	_	_	_
77	amp	amp	NN	_	_	_
78	50ug/ml	50ug/ml	NN	_	_	_
79	,	,	,	_	_	_
80	0.0125	0.0125	CD	_	_	_
81	%	%	NN	_	_	_
82	arabinose	arabinose	NN	_	_	_
83	,	,	,	_	_	_
84	0.025	0.025	CD	_	_	_
85	ug/ml	ug/ml	NN	_	_	_
86	norfloxacin	norfloxacin	NN	_	_	_
87	OD	od	NN	_	_	_
88	~	~	NN	_	_	_
89	0.3	0.3	CD	_	_	_
90	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
91	Direct	Direct	NNP	_	_	_
92	testing	testing	NN	_	_	_
93	of	of	IN	_	_	_
94	culture	culture	NN	_	_	_
95	broth	broth	NN	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	Standard	standard	JJ	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	or	or	CC	_	_	_
100	after	after	IN	_	_	_
101	centrifugation	centrifugation	NN	_	_	_
102	of	of	IN	_	_	_
103	culture	culture	NN	_	_	_
104	broth	broth	NN	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	Supernatant	supernatant	NN	_	_	_
107	-RRB-	-rrb-	-RRB-	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	disease	disease	NN	_	_	_
110	state	state	NN	_	_	_
111	:	:	:	_	_	_
112	control	control	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	disease	disease	NN	_	_	_
115	state	state	NN	_	_	_
116	:	:	:	_	_	_
117	cystic	cystic	JJ	_	_	_
118	fibrosis	fibrosis	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Dividing	divide	VBG	_	_	_
121	t	t	NN	_	_	_
122	=	=	JJ	_	_	_
123	2	2	CD	_	_	_
124	hours	hour	NNS	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	DksA	dksa	NN	_	_	_
127	ChIP	chip	NN	_	_	_
128	DNA	dna	NN	_	_	_
129	from	from	IN	_	_	_
130	DdksA	ddksa	NN	_	_	_
131	cells	cell	NNS	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
133	DksA	dksa	NN	_	_	_
134	ChIP	chip	NN	_	_	_
135	DNA	dna	NN	_	_	_
136	from	from	IN	_	_	_
137	wt	wt	JJ	_	_	_
138	cells	cell	NNS	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	DksA	dksa	NN	_	_	_
141	_	_	CD	_	_	_
142	DdksA	ddksa	NN	_	_	_
143	_	_	NN	_	_	_
144	untreated	untreated	JJ	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	DksA	dksa	NN	_	_	_
147	_	_	CD	_	_	_
148	wt	wt	JJ	_	_	_
149	_	_	NN	_	_	_
150	untreated	untreated	JJ	_	_	_
151	_	_	NN	_	_	_
152	rep1	rep1	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	DksA	dksa	NN	_	_	_
155	_	_	CD	_	_	_
156	wt	wt	JJ	_	_	_
157	_	_	NN	_	_	_
158	untreated	untreated	JJ	_	_	_
159	_	_	NN	_	_	_
160	rep2	rep2	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	DL4184	dl4184	NN	_	_	_
163	biological	biological	JJ	_	_	_
164	repeat	repeat	NN	_	_	_
165	1	1	CD	_	_	_
166	RecA	reca	NN	_	_	_
167	ChIP	chip	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	DL4184	dl4184	NN	_	_	_
170	biological	biological	JJ	_	_	_
171	repeat	repeat	NN	_	_	_
172	2	2	CD	_	_	_
173	RecA	reca	NN	_	_	_
174	ChIP	chip	NN	_	_	_
175	_	_	NN	_	_	_
176	reanalyzed	reanalyze	VBN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	DL4184C	dl4184c	NN	_	_	_
179	_	_	CD	_	_	_
180	ChIP-seq	ChIP-seq	NNP	_	_	_
181	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
182	DL4201	dl4201	NN	_	_	_
183	biological	biological	JJ	_	_	_
184	repeat	repeat	NN	_	_	_
185	1	1	CD	_	_	_
186	RecA	reca	NN	_	_	_
187	ChIP	chip	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	DL4201	dl4201	NN	_	_	_
190	biological	biological	JJ	_	_	_
191	repeat	repeat	NN	_	_	_
192	2	2	CD	_	_	_
193	RecA	reca	NN	_	_	_
194	ChIP	chip	NN	_	_	_
195	_	_	NN	_	_	_
196	reanalyzed	reanalyze	VBN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	DL4201C	dl4201c	NN	_	_	_
199	_	_	CD	_	_	_
200	ChIP-seq	ChIP-seq	NNP	_	_	_
201	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
202	DL4311C	DL4311C	NNP	_	_	_
203	_	_	SYM	_	_	_
204	ChIP-seq	ChIP-seq	NNP	_	_	_
205	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
206	DL4312C	DL4312C	NNP	_	_	_
207	_	_	SYM	_	_	_
208	ChIP-seq	ChIP-seq	NNP	_	_	_
209	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
210	DL4899	dl4899	NN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	DL4900	dl4900	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	DL4900	dl4900	NN	_	_	_
215	_	_	NN	_	_	_
216	input	input	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	DL5215	dl5215	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	DL5322	dl5322	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	DL5324	dl5324	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	DL5326	dl5326	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	DL5328	dl5328	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	DL5330	dl5330	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	DL5699	dl5699	NN	_	_	_
231	biological	biological	JJ	_	_	_
232	repeat	repeat	NN	_	_	_
233	1	1	CD	_	_	_
234	RecA	reca	NN	_	_	_
235	ChIP	chip	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	DL5699	dl5699	NN	_	_	_
238	biological	biological	JJ	_	_	_
239	repeat	repeat	NN	_	_	_
240	2	2	CD	_	_	_
241	RecA	reca	NN	_	_	_
242	ChIP	chip	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	DL6204	dl6204	NN	_	_	_
245	biological	biological	JJ	_	_	_
246	repeat	repeat	NN	_	_	_
247	1	1	CD	_	_	_
248	RecA	reca	NN	_	_	_
249	ChIP	chip	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	DL6204	dl6204	NN	_	_	_
252	biological	biological	JJ	_	_	_
253	repeat	repeat	NN	_	_	_
254	2	2	CD	_	_	_
255	RecA	reca	NN	_	_	_
256	ChIP	chip	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	DMS-MaPSeq	dms-mapseq	NN	_	_	_
259	of	of	IN	_	_	_
260	purified	purify	VBN	_	_	_
261	cspA	cspa	NN	GEN	_	_
262	mRNA	mrna	NN	_	_	_
263	at	at	IN	_	_	_
264	10	10	CD	_	_	_
265	°C	°c	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	DMS-MaPSeq	dms-mapseq	NN	_	_	_
268	of	of	IN	_	_	_
269	purified	purify	VBN	_	_	_
270	cspA	cspa	NN	GEN	_	_
271	mRNA	mrna	NN	_	_	_
272	at	at	IN	_	_	_
273	10	10	CD	_	_	_
274	°C	°c	NN	_	_	_
275	,	,	,	_	_	_
276	rep1	rep1	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	DMS-MaPSeq	dms-mapseq	NN	_	_	_
279	of	of	IN	_	_	_
280	purified	purify	VBN	_	_	_
281	cspA	cspa	NN	GEN	_	_
282	mRNA	mrna	NN	_	_	_
283	at	at	IN	_	_	_
284	10	10	CD	_	_	_
285	°C	°c	NN	_	_	_
286	,	,	,	_	_	_
287	rep2	rep2	NN	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	DMS-MaPSeq	dms-mapseq	NN	_	_	_
290	of	of	IN	_	_	_
291	purified	purify	VBN	_	_	_
292	cspA	cspa	NN	GEN	_	_
293	mRNA	mrna	NN	_	_	_
294	at	at	IN	_	_	_
295	10	10	CD	_	_	_
296	°C	°c	NN	_	_	_
297	,	,	,	_	_	_
298	rep	rep	NN	GEN	_	_
299	3	3	CD	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	DMS-MaPSeq	dms-mapseq	NN	_	_	_
302	of	of	IN	_	_	_
303	purified	purify	VBN	_	_	_
304	cspA	cspa	NN	GEN	_	_
305	mRNA	mrna	NN	_	_	_
306	at	at	IN	_	_	_
307	10	10	CD	_	_	_
308	°C	°c	NN	_	_	_
309	,	,	,	_	_	_
310	rep	rep	NN	GEN	_	_
311	4	4	CD	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	DMS-MaPSeq	dms-mapseq	NN	_	_	_
314	of	of	IN	_	_	_
315	purified	purify	VBN	_	_	_
316	cspA	cspa	NN	GEN	_	_
317	mRNA	mrna	NN	_	_	_
318	at	at	IN	_	_	_
319	10	10	CD	_	_	_
320	°C	°c	NN	_	_	_
321	with	with	IN	_	_	_
322	0.025	0.025	CD	_	_	_
323	mM	mm	NN	KWSUPP	_	_
324	CspA	cspa	NN	TF	_	_
325	protein	protein	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	DMS-MaPSeq	dms-mapseq	NN	_	_	_
328	of	of	IN	_	_	_
329	purified	purify	VBN	_	_	_
330	cspA	cspa	NN	GEN	_	_
331	mRNA	mrna	NN	_	_	_
332	at	at	IN	_	_	_
333	10	10	CD	_	_	_
334	°C	°c	NN	_	_	_
335	with	with	IN	_	_	_
336	0.05	0.05	CD	_	_	_
337	mM	mm	NN	KWSUPP	_	_
338	CspA	cspa	NN	TF	_	_
339	protein	protein	NN	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	DMS-MaPSeq	dms-mapseq	NN	_	_	_
342	of	of	IN	_	_	_
343	purified	purify	VBN	_	_	_
344	cspA	cspa	NN	GEN	_	_
345	mRNA	mrna	NN	_	_	_
346	at	at	IN	_	_	_
347	10	10	CD	_	_	_
348	°C	°c	NN	_	_	_
349	with	with	IN	_	_	_
350	0.1	0.1	CD	_	_	_
351	mM	mm	NN	KWSUPP	_	_
352	CspA	cspa	NN	TF	_	_
353	protein	protein	NN	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	DMS-MaPSeq	dms-mapseq	NN	_	_	_
356	of	of	IN	_	_	_
357	purified	purify	VBN	_	_	_
358	cspA	cspa	NN	GEN	_	_
359	mRNA	mrna	NN	_	_	_
360	at	at	IN	_	_	_
361	10	10	CD	_	_	_
362	°C	°c	NN	_	_	_
363	with	with	IN	_	_	_
364	0.1	0.1	CD	_	_	_
365	mM	mm	NN	KWSUPP	_	_
366	CspA	cspa	NN	TF	_	_
367	protein	protein	NN	_	_	_
368	,	,	,	_	_	_
369	rep1	rep1	NN	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	DMS-MaPSeq	dms-mapseq	NN	_	_	_
372	of	of	IN	_	_	_
373	purified	purify	VBN	_	_	_
374	cspA	cspa	NN	GEN	_	_
375	mRNA	mrna	NN	_	_	_
376	at	at	IN	_	_	_
377	10	10	CD	_	_	_
378	°C	°c	NN	_	_	_
379	with	with	IN	_	_	_
380	0.1	0.1	CD	_	_	_
381	mM	mm	NN	KWSUPP	_	_
382	CspA	cspa	NN	TF	_	_
383	protein	protein	NN	_	_	_
384	,	,	,	_	_	_
385	rep	rep	NN	GEN	_	_
386	2	2	CD	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	DMS-MaPSeq	dms-mapseq	NN	_	_	_
389	of	of	IN	_	_	_
390	purified	purify	VBN	_	_	_
391	cspA	cspa	NN	GEN	_	_
392	mRNA	mrna	NN	_	_	_
393	at	at	IN	_	_	_
394	10	10	CD	_	_	_
395	°C	°c	NN	_	_	_
396	with	with	IN	_	_	_
397	0.1	0.1	CD	_	_	_
398	mM	mm	NN	KWSUPP	_	_
399	CspA	cspa	NN	TF	_	_
400	protein	protein	NN	_	_	_
401	,	,	,	_	_	_
402	rep	rep	NN	GEN	_	_
403	3	3	CD	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
405	DMS-MaPSeq	dms-mapseq	NN	_	_	_
406	of	of	IN	_	_	_
407	purified	purify	VBN	_	_	_
408	cspA	cspa	NN	GEN	_	_
409	mRNA	mrna	NN	_	_	_
410	at	at	IN	_	_	_
411	10	10	CD	_	_	_
412	°C	°c	NN	_	_	_
413	with	with	IN	_	_	_
414	0.1	0.1	CD	_	_	_
415	mM	mm	NN	KWSUPP	_	_
416	CspA	cspa	NN	TF	_	_
417	protein	protein	NN	_	_	_
418	,	,	,	_	_	_
419	rep	rep	NN	GEN	_	_
420	4	4	CD	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	DMS-MaPSeq	dms-mapseq	NN	_	_	_
423	of	of	IN	_	_	_
424	purified	purify	VBN	_	_	_
425	cspA	cspa	NN	GEN	_	_
426	mRNA	mrna	NN	_	_	_
427	at	at	IN	_	_	_
428	37	37	CD	_	_	_
429	°C	°c	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	DMS-MaPSeq	dms-mapseq	NN	_	_	_
432	of	of	IN	_	_	_
433	purified	purify	VBN	_	_	_
434	cspA	cspa	NN	GEN	_	_
435	mRNA	mrna	NN	_	_	_
436	at	at	IN	_	_	_
437	37	37	CD	_	_	_
438	°C	°c	NN	_	_	_
439	,	,	,	_	_	_
440	rep1	rep1	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	DMS-MaPSeq	dms-mapseq	NN	_	_	_
443	of	of	IN	_	_	_
444	purified	purify	VBN	_	_	_
445	cspA	cspa	NN	GEN	_	_
446	mRNA	mrna	NN	_	_	_
447	at	at	IN	_	_	_
448	37	37	CD	_	_	_
449	°C	°c	NN	_	_	_
450	,	,	,	_	_	_
451	rep	rep	NN	GEN	_	_
452	2	2	CD	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
454	DMSO	dmso	NN	_	_	_
455	_	_	VBD	_	_	_
456	0	0	CD	_	_	_
457	min	min	NN	_	_	_
458	_	_	CD	_	_	_
459	rep1	rep1	NN	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
461	DMSO	dmso	NN	_	_	_
462	_	_	VBD	_	_	_
463	0	0	CD	_	_	_
464	min	min	NN	_	_	_
465	_	_	CD	_	_	_
466	rep2	rep2	NN	_	_	_
467	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
468	DMSO	dmso	NN	_	_	_
469	_	_	VBD	_	_	_
470	0	0	CD	_	_	_
471	min	min	NN	_	_	_
472	_	_	CD	_	_	_
473	rep3	rep3	NN	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
475	DMSO	dmso	NN	_	_	_
476	_	_	SYM	_	_	_
477	60	60	CD	_	_	_
478	min	min	NN	_	_	_
479	_	_	CD	_	_	_
480	rep1	rep1	NN	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
482	DMSO	dmso	NN	_	_	_
483	_	_	SYM	_	_	_
484	60	60	CD	_	_	_
485	min	min	NN	_	_	_
486	_	_	CD	_	_	_
487	rep2	rep2	NN	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
489	DMSO	dmso	NN	_	_	_
490	_	_	SYM	_	_	_
491	60	60	CD	_	_	_
492	min	min	NN	_	_	_
493	_	_	CD	_	_	_
494	rep3	rep3	NN	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
496	DMSO	dmso	NN	_	_	_
497	_	_	SYM	_	_	_
498	60	60	CD	_	_	_
499	min	min	NN	_	_	_
500	_	_	CD	_	_	_
501	rep4	rep4	NN	_	_	_
502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
503	DMSO-Only	dmso-only	JJ	_	_	_
504	Treatment	treatment	NN	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
506	DMSO	dmso	NN	_	_	_
507	treatment	treatment	NN	_	_	_
508	,	,	,	_	_	_
509	0	0	CD	_	_	_
510	min	min	NN	_	_	_
511	,	,	,	_	_	_
512	replicate	replicate	VB	_	_	_
513	1	1	CD	_	_	_
514	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
515	DMSO	dmso	NN	_	_	_
516	treatment	treatment	NN	_	_	_
517	,	,	,	_	_	_
518	0	0	CD	_	_	_
519	min	min	NN	_	_	_
520	,	,	,	_	_	_
521	replicate	replicate	VB	_	_	_
522	2	2	CD	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
524	DMSO	dmso	NN	_	_	_
525	treatment	treatment	NN	_	_	_
526	,	,	,	_	_	_
527	0	0	CD	_	_	_
528	min	min	NN	_	_	_
529	,	,	,	_	_	_
530	replicate	replicate	VB	_	_	_
531	3	3	CD	_	_	_
532	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
533	DMSO	dmso	NN	_	_	_
534	treatment	treatment	NN	_	_	_
535	,	,	,	_	_	_
536	60	60	CD	_	_	_
537	min	min	NN	_	_	_
538	,	,	,	_	_	_
539	replicate	replicate	VB	_	_	_
540	1	1	CD	_	_	_
541	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
542	DMSO	dmso	NN	_	_	_
543	treatment	treatment	NN	_	_	_
544	,	,	,	_	_	_
545	60	60	CD	_	_	_
546	min	min	NN	_	_	_
547	,	,	,	_	_	_
548	replicate	replicate	VB	_	_	_
549	2	2	CD	_	_	_
550	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
551	DMSO	dmso	NN	_	_	_
552	treatment	treatment	NN	_	_	_
553	,	,	,	_	_	_
554	60	60	CD	_	_	_
555	min	min	NN	_	_	_
556	,	,	,	_	_	_
557	replicate	replicate	VB	_	_	_
558	3	3	CD	_	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
560	DMSO	dmso	NN	_	_	_
561	treatment	treatment	NN	_	_	_
562	,	,	,	_	_	_
563	60	60	CD	_	_	_
564	min	min	NN	_	_	_
565	,	,	,	_	_	_
566	replicate	replicate	VB	_	_	_
567	4	4	CD	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
569	DMS-seq	dms-seq	JJ	_	_	_
570	30	30	CD	_	_	_
571	min	min	NN	_	_	_
572	after	after	IN	_	_	_
573	shift	shift	NN	_	_	_
574	to	to	TO	_	_	_
575	10	10	CD	_	_	_
576	°C	°c	NN	_	_	_
577	in	in	IN	_	_	_
578	WT	wt	JJ	_	_	_
579	cells	cell	NNS	_	_	_
580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
581	DMS-seq	dms-seq	NN	_	_	_
582	6	6	CD	_	_	_
583	hr	hr	NN	_	_	_
584	after	after	IN	_	_	_
585	shift	shift	NN	_	_	_
586	to	to	TO	_	_	_
587	10	10	CD	_	_	_
588	°C	°c	NN	_	_	_
589	in	in	IN	_	_	_
590	WT	wt	JJ	_	_	_
591	cells	cell	NNS	_	_	_
592	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
593	DMS-seq	dms-seq	NN	_	_	_
594	8	8	CD	_	_	_
595	hr	hr	NN	_	_	_
596	after	after	IN	_	_	_
597	shift	shift	NN	_	_	_
598	to	to	TO	_	_	_
599	10	10	CD	_	_	_
600	°C	°c	NN	_	_	_
601	in	in	IN	_	_	_
602	∆	∆	CD	_	_	_
603	cspABEG	cspabeg	NN	_	_	_
604	cells	cell	NNS	_	_	_
605	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
606	DMS-seq	dms-seq	NN	_	_	_
607	8	8	CD	_	_	_
608	hr	hr	NN	_	_	_
609	after	after	IN	_	_	_
610	shift	shift	NN	_	_	_
611	to	to	TO	_	_	_
612	10	10	CD	_	_	_
613	°C	°c	NN	_	_	_
614	in	in	IN	_	_	_
615	∆	∆	CD	_	_	_
616	cspBG	cspbg	NN	_	_	_
617	cells	cell	NNS	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	DMS-seq	dms-seq	NN	_	_	_
620	8	8	CD	_	_	_
621	hr	hr	NN	_	_	_
622	after	after	IN	_	_	_
623	shift	shift	NN	_	_	_
624	to	to	TO	_	_	_
625	10	10	CD	_	_	_
626	°C	°c	NN	_	_	_
627	in	in	IN	_	_	_
628	WT	wt	JJ	_	_	_
629	cells	cell	NNS	_	_	_
630	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
631	DMS-seq	dms-seq	NN	_	_	_
632	of	of	IN	_	_	_
633	purified	purify	VBN	_	_	_
634	mRNA	mrna	NN	_	_	_
635	in	in	FW	_	_	_
636	vitro	vitro	FW	_	_	_
637	at	at	IN	_	_	_
638	10	10	CD	_	_	_
639	°C	°c	NN	_	_	_
640	,	,	,	_	_	_
641	rep1	rep1	NN	_	_	_
642	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
643	DMS-seq	dms-seq	NN	_	_	_
644	of	of	IN	_	_	_
645	purified	purify	VBN	_	_	_
646	mRNA	mrna	NN	_	_	_
647	in	in	FW	_	_	_
648	vitro	vitro	FW	_	_	_
649	at	at	IN	_	_	_
650	10	10	CD	_	_	_
651	°C	°c	NN	_	_	_
652	,	,	,	_	_	_
653	rep2	rep2	NN	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
655	DMS-seq	dms-seq	NN	_	_	_
656	of	of	IN	_	_	_
657	WT	wt	JJ	_	_	_
658	cells	cell	NNS	_	_	_
659	after	after	IN	_	_	_
660	kasugamycin	kasugamycin	NN	_	_	_
661	treatment	treatment	NN	_	_	_
662	at	at	IN	_	_	_
663	10	10	CD	_	_	_
664	°C	°c	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	DMS-seq	dms-seq	NN	_	_	_
667	-LRB-	-lrb-	-LRB-	_	_	_
668	Ribo	Ribo	NNP	_	_	_
669	-	-	:	_	_	_
670	RNA	rna	NN	_	_	_
671	-RRB-	-rrb-	-RRB-	_	_	_
672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
673	DMS-seq	dms-seq	NN	_	_	_
674	-LRB-	-lrb-	-LRB-	_	_	_
675	Total	total	JJ	_	_	_
676	RNA	rna	NN	_	_	_
677	-RRB-	-rrb-	-RRB-	_	_	_
678	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
679	dnaA	dnaa	NN	GEN	_	_
680	__	__	CD	_	_	_
681	U	U	NNP	_	_	_
682	_	_	NNP	_	_	_
683	N0075	N0075	NNP	_	_	_
684	_	_	VBD	_	_	_
685	r1	r1	NN	_	_	_
686	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
687	dnaA	dnaa	NN	GEN	_	_
688	__	__	CD	_	_	_
689	U	U	NNP	_	_	_
690	_	_	NNP	_	_	_
691	N0075	N0075	NNP	_	_	_
692	_	_	VBD	_	_	_
693	r2	r2	NN	_	_	_
694	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
695	dnaA	dnaa	NN	GEN	_	_
696	__	__	CD	_	_	_
697	U	U	NNP	_	_	_
698	_	_	NNP	_	_	_
699	N0075	N0075	NNP	_	_	_
700	_	_	VBD	_	_	_
701	r3	r3	NN	_	_	_
702	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
703	dnaA	dnaa	NN	GEN	_	_
704	upregulation	upregulation	NN	_	_	_
705	,	,	,	_	_	_
706	0.075	0.075	CD	_	_	_
707	ug/ml	ug/ml	NN	_	_	_
708	norfloxacin	norfloxacin	NN	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	dnaB-Ts	dnab-t	NNS	_	_	_
711	_	_	VBP	_	_	_
712	30	30	CD	_	_	_
713	°C	°c	NN	_	_	_
714	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
715	dnaB-Ts	dnab-t	NNS	_	_	_
716	_	_	VBP	_	_	_
717	42	42	CD	_	_	_
718	°C	°c	NN	_	_	_
719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
720	dnaB-Ts	dnab-t	NNS	_	_	_
721	Î	î	NN	_	_	_
722	''	''	''	_	_	_
723	ahpC	ahpc	NN	GEN	_	_
724	_	_	CD	_	_	_
725	30	30	CD	_	_	_
726	°C	°c	NN	_	_	_
727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
728	dnaB-Ts	dnab-t	NNS	_	_	_
729	Î	î	NN	_	_	_
730	''	''	''	_	_	_
731	ahpC	ahpc	NN	GEN	_	_
732	_	_	CD	_	_	_
733	42	42	CD	_	_	_
734	°C	°c	NN	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
736	dnaC2	dnac2	NN	_	_	_
737	30	30	CD	_	_	_
738	'	'	''	_	_	_
739	at	at	IN	_	_	_
740	30	30	CD	_	_	_
741	deg	deg	NN	_	_	_
742	,	,	,	_	_	_
743	2	2	CD	_	_	_
744	ug	ug	NN	_	_	_
745	gen	gen	NN	_	_	_
746	DNA	dna	NN	_	_	_
747	,	,	,	_	_	_
748	pdN6	pdn6	NN	_	_	_
749	RT	rt	NN	_	_	_
750	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
751	dnaC2	dnac2	NN	_	_	_
752	90	90	CD	_	_	_
753	'	'	''	_	_	_
754	at	at	IN	_	_	_
755	42	42	CD	_	_	_
756	deg	deg	NN	_	_	_
757	,	,	,	_	_	_
758	2	2	CD	_	_	_
759	ug	ug	NN	_	_	_
760	gen	gen	NN	_	_	_
761	DNA	dna	NN	_	_	_
762	,	,	,	_	_	_
763	pdN6	pdn6	NN	_	_	_
764	RT	rt	NN	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
766	dnaC2	dnac2	NN	_	_	_
767	synchrony	synchrony	NN	_	_	_
768	30	30	CD	_	_	_
769	'	'	''	_	_	_
770	after	after	IN	_	_	_
771	shift	shift	NN	_	_	_
772	,	,	,	_	_	_
773	print	print	NN	_	_	_
774	7	7	CD	_	_	_
775	array	array	NN	_	_	_
776	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
777	dnaC	dnac	NN	GEN	_	_
778	fully	fully	RB	_	_	_
779	replicated	replicate	VBN	_	_	_
780	,	,	,	_	_	_
781	2	2	CD	_	_	_
782	ug	ug	NN	_	_	_
783	Sau3AI	sau3ai	NN	_	_	_
784	,	,	,	_	_	_
785	pdN6	pdn6	NN	_	_	_
786	RT	rt	NN	_	_	_
787	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
788	dnaC	dnac	NN	GEN	_	_
789	fully	fully	RB	_	_	_
790	replicated	replicate	VBN	_	_	_
791	,	,	,	_	_	_
792	2	2	CD	_	_	_
793	ug	ug	NN	_	_	_
794	Say3AI	say3ai	NN	_	_	_
795	,	,	,	_	_	_
796	pdN6	pdn6	NN	_	_	_
797	RT	rt	NN	_	_	_
798	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
799	dnaC	dnac	NN	GEN	_	_
800	genomic	genomic	JJ	_	_	_
801	DNA	dna	NN	_	_	_
802	,	,	,	_	_	_
803	Sau3A	sau3a	NN	_	_	_
804	,	,	,	_	_	_
805	2	2	CD	_	_	_
806	ug	ug	NN	_	_	_
807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
808	DNA	dna	NN	_	_	_
809	detected	detect	VBN	_	_	_
810	with	with	IN	_	_	_
811	GyrA	gyra	NN	_	_	_
812	immunoglobulin	immunoglobulin	NN	_	_	_
813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
814	DNA	dna	NN	_	_	_
815	extraction	extraction	NN	_	_	_
816	:	:	:	_	_	_
817	Genomic	genomic	JJ	_	_	_
818	DNA	dna	NN	_	_	_
819	was	be	VBD	_	_	_
820	isolated	isolate	VBN	_	_	_
821	and	and	CC	_	_	_
822	purified	purify	VBN	_	_	_
823	according	accord	VBG	_	_	_
824	to	to	TO	_	_	_
825	standard	standard	JJ	_	_	_
826	procedures	procedure	NNS	_	_	_
827	-LRB-	-lrb-	-LRB-	_	_	_
828	Ausubel	Ausubel	NNP	_	_	_
829	et	et	FW	_	_	_
830	al.	al.	FW	_	_	_
831	1994	1994	CD	_	_	_
832	-RRB-	-rrb-	-RRB-	_	_	_
833	.	.	.	_	_	_

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/chloroform	phenol/chloroform	NN	_	_	_
16	extraction	extraction	NN	_	_	_
17	and	and	CC	_	_	_
18	ethanol	ethanol	NN	_	_	_
19	precipitated	precipitate	VBD	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	fragments	fragment	NNS	_	_	_
4	were	be	VBD	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	Epicentre	Epicentre	NNP	_	_	_
8	End-It	end-it	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	End	end	NN	_	_	_
11	Repair	Repair	NNP	_	_	_
12	Kit	kit	NN	_	_	_
13	and	and	CC	_	_	_
14	3	3	CD	_	_	_
15	'	'	''	_	_	_
16	A	a	DT	_	_	_
17	overhangs	overhang	NNS	_	_	_
18	were	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	with	with	IN	_	_	_
21	DNA	dna	NN	_	_	_
22	polymerase	polymerase	NN	_	_	_
23	I	i	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Klenow	klenow	NN	_	_	_
26	fragment	fragment	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

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	NN	_	_	_
2	dnaJ-ala-1	dnaj-ala-1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	dnaJ-ala-2	dnaj-ala-2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	dnaJ-gln-1	dnaj-gln-1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	dnaJ-gln-2	dnaj-gln-2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	dnaJ	dnaj	NN	GEN	_	_
11	mutant	mutant	NN	_	_	_
12	in	in	IN	_	_	_
13	Ala	Ala	NNP	_	_	_
14	media	media	NNS	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	dnaJ	dnaj	NN	GEN	_	_
17	mutant	mutant	NN	_	_	_
18	in	in	IN	_	_	_
19	Gln	gln	NN	_	_	_
20	media	media	NNS	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	DnaK	dnak	NN	_	_	_
23	deletant	deletant	JJ	_	_	_
24	_	_	NN	_	_	_
25	37C	37c	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	DNA	dna	NN	_	_	_
28	libraries	library	NNS	_	_	_
29	were	be	VBD	_	_	_
30	prepared	prepare	VBN	_	_	_
31	for	for	IN	_	_	_
32	sequencing	sequencing	NN	_	_	_
33	using	use	VBG	_	_	_
34	standard	standard	JJ	_	_	_
35	Illumina	Illumina	NNP	_	_	_
36	protocols	protocol	NNS	_	_	_
37	by	by	IN	_	_	_
38	FASTERIS	FASTERIS	NNP	_	_	_
39	SA	SA	NNP	_	_	_
40	,	,	,	_	_	_
41	Switzerland	Switzerland	NNP	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	dnaN	dnaN	NNP	GEN	_	_
44	__	__	VBD	_	_	_
45	U	U	NNP	_	_	_
46	_	_	NNP	_	_	_
47	N0075	N0075	NNP	_	_	_
48	_	_	VBD	_	_	_
49	r1	r1	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	dnaN	dnan	NN	GEN	_	_
52	__	__	CD	_	_	_
53	U	U	NNP	_	_	_
54	_	_	NNP	_	_	_
55	N0075	N0075	NNP	_	_	_
56	_	_	VBD	_	_	_
57	r2	r2	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	dnaN	dnan	NN	GEN	_	_
60	__	__	CD	_	_	_
61	U	U	NNP	_	_	_
62	_	_	NNP	_	_	_
63	N0075	N0075	NNP	_	_	_
64	_	_	VBD	_	_	_
65	r3	r3	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	dnaN	dnan	NN	GEN	_	_
68	upregulation	upregulation	NN	_	_	_
69	,	,	,	_	_	_
70	0.075	0.075	CD	_	_	_
71	ug/ml	ug/ml	NN	_	_	_
72	norfloxacin	norfloxacin	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	DNA	dna	NN	_	_	_
75	samples	sample	NNS	_	_	_
76	were	be	VBD	_	_	_
77	submitted	submit	VBN	_	_	_
78	to	to	TO	_	_	_
79	the	the	DT	_	_	_
80	University	University	NNP	_	_	_
81	of	of	IN	_	_	_
82	Wisconsin-Madison	Wisconsin-Madison	NNP	_	_	_
83	DNA	DNA	NNP	_	_	_
84	Sequencing	sequencing	NN	_	_	_
85	Facility	facility	NN	_	_	_
86	for	for	IN	_	_	_
87	ChIP-seq	ChIP-seq	NNP	_	_	_
88	library	library	NN	_	_	_
89	preparation	preparation	NN	_	_	_
90	.	.	.	_	_	_

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	NN	_	_	_
2	dnaT	dnat	NN	GEN	_	_
3	__	__	CD	_	_	_
4	U	U	NNP	_	_	_
5	_	_	NNP	_	_	_
6	N0075	N0075	NNP	_	_	_
7	_	_	VBD	_	_	_
8	r1	r1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	dnaT	dnat	NN	GEN	_	_
11	__	__	CD	_	_	_
12	U	U	NNP	_	_	_
13	_	_	NNP	_	_	_
14	N0075	N0075	NNP	_	_	_
15	_	_	VBD	_	_	_
16	r2	r2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	dnaT	dnat	NN	GEN	_	_
19	__	__	CD	_	_	_
20	U	U	NNP	_	_	_
21	_	_	NNP	_	_	_
22	N0075	N0075	NNP	_	_	_
23	_	_	VBD	_	_	_
24	r3	r3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	dnaT	dnat	NN	GEN	_	_
27	upregulation	upregulation	NN	_	_	_
28	,	,	,	_	_	_
29	0.075	0.075	CD	_	_	_
30	ug/ml	ug/ml	NN	_	_	_
31	norfloxacin	norfloxacin	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	DNA	dna	NN	_	_	_
34	was	be	VBD	_	_	_
35	extracted	extract	VBN	_	_	_
36	from	from	IN	_	_	_
37	resulting	result	VBG	_	_	_
38	supernatant	supernatant	JJ	_	_	_
39	with	with	IN	_	_	_
40	phenol/chlorophorm	phenol/chlorophorm	NN	_	_	_
41	method	method	NN	_	_	_
42	followed	follow	VBN	_	_	_
43	by	by	IN	_	_	_
44	ethanol	ethanol	NN	_	_	_
45	precipitation	precipitation	NN	_	_	_
46	.	.	.	_	_	_

1	Mock	mock	JJ	_	_	_
2	controls	control	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	-	-	:	_	_	_
5	IP	IP	NNP	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	were	be	VBD	_	_	_
8	made	make	VBN	_	_	_
9	both	both	DT	_	_	_
10	for	for	IN	_	_	_
11	+	+	CC	_	_	_
12	A	a	DT	_	_	_
13	and	and	CC	_	_	_
14	for	for	IN	_	_	_
15	-	-	:	_	_	_
16	A	a	NN	_	_	_
17	:	:	:	_	_	_
18	100	100	CD	_	_	_
19	μl	μl	NN	_	_	_
20	aliquots	aliquot	NNS	_	_	_
21	of	of	IN	_	_	_
22	lysates	lysate	NNS	_	_	_
23	obtained	obtain	VBN	_	_	_
24	after	after	IN	_	_	_
25	sonication	sonication	NN	_	_	_
26	were	be	VBD	_	_	_
27	deproteinized	deproteinize	VBN	_	_	_
28	and	and	CC	_	_	_
29	DNA	dna	NN	_	_	_
30	was	be	VBD	_	_	_
31	purified	purify	VBN	_	_	_
32	as	as	IN	_	_	_
33	described	describe	VBN	_	_	_
34	earlier	earlier	RBR	_	_	_
35	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	procedure	procedure	NN	_	_	_
3	described	describe	VBD	_	_	_
4	gives	give	VBZ	_	_	_
5	a	a	DT	_	_	_
6	quartet	quartet	NN	_	_	_
7	of	of	IN	_	_	_
8	samples	sample	NNS	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	+	+	CC	_	_	_
11	A+IP	a+ip	NN	_	_	_
12	,	,	,	_	_	_
13	+	+	CC	_	_	_
14	A-IP	a-ip	NN	_	_	_
15	,	,	,	_	_	_
16	-	-	:	_	_	_
17	A+IP	a+ip	NN	_	_	_
18	,	,	,	_	_	_
19	-	-	:	_	_	_
20	A-IP	a-ip	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	where	where	WRB	_	_	_
24	+	+	CC	_	_	_
25	A-IP	a-ip	NN	_	_	_
26	,	,	,	_	_	_
27	-	-	:	_	_	_
28	A+IP	a+ip	NN	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	-	-	:	_	_	_
32	A-IP	a-ip	NN	_	_	_
33	serves	serve	VBZ	_	_	_
34	as	as	IN	_	_	_
35	controls	control	NNS	_	_	_
36	for	for	IN	_	_	_
37	gyrase	gyrase	NN	_	_	_
38	poison	poison	NN	_	_	_
39	action	action	NN	_	_	_
40	and	and	CC	_	_	_
41	immunoprecipitation	immunoprecipitation	NN	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	same	same	JJ	_	_	_
8	manner	manner	NN	_	_	_
9	as	as	IN	_	_	_
10	described	describe	VBN	_	_	_
11	by	by	IN	_	_	_
12	McNulty	McNulty	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	PMID	pmid	NN	_	_	_
17	:	:	:	_	_	_
18	22030749	22030749	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	Cell	cell	NN	_	_	_
9	Lysis	lysis	NN	_	_	_
10	and	and	CC	_	_	_
11	Protein	protein	NN	_	_	_
12	Precipitation	precipitation	NN	_	_	_
13	solutions	solution	NNS	_	_	_
14	.	.	.	_	_	_

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	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	removed	remove	VBN	_	_	_
13	with	with	IN	_	_	_
14	Dnase	Dnase	NNP	_	_	_
15	I.	I.	NNP	_	_	_
16	rRNA	rrna	NN	_	_	_
17	was	be	VBD	_	_	_
18	removed	remove	VBN	_	_	_
19	with	with	IN	_	_	_
20	the	the	DT	_	_	_
21	gram-negative	gram-negative	JJ	_	_	_
22	RiboZero	RiboZero	NNP	_	_	_
23	kit	kit	NN	_	_	_
24	.	.	.	_	_	_

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/barcode	signal-peptide-coding/barcode	JJ	_	_	_
15	region	region	NN	_	_	_
16	of	of	IN	_	_	_
17	the	the	DT	_	_	_
18	fusion	fusion	NN	_	_	_
19	RNAs	rna	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	were	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	and	and	CC	_	_	_
6	purified	purify	VBN	_	_	_
7	as	as	IN	_	_	_
8	described	describe	VBN	_	_	_
9	by	by	IN	_	_	_
10	Muniesa	Muniesa	NNP	_	_	_
11	et	et	FW	_	_	_
12	al.	al.	FW	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	2003	2003	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

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	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	were	be	VBD	_	_	_
4	submitted	submit	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	Joint	Joint	NNP	_	_	_
8	Genome	Genome	NNP	_	_	_
9	Institute	Institute	NNP	_	_	_
10	for	for	IN	_	_	_
11	ChIP-seq	ChIP-seq	NNP	_	_	_
12	library	library	NN	_	_	_
13	preparation	preparation	NN	_	_	_
14	.	.	.	_	_	_

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	NN	_	_	_
2	DNeasy	dneasy	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	Qiagen	qiagen	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Donor	donor	NN	_	_	_
8	was	be	VBD	_	_	_
9	transformed	transform	VBN	_	_	_
10	with	with	IN	_	_	_
11	a	a	DT	_	_	_
12	random	random	JJ	_	_	_
13	genomic	genomic	JJ	_	_	_
14	library	library	NN	_	_	_
15	made	make	VBN	_	_	_
16	from	from	IN	_	_	_
17	E.	e.	FW	_	_	_
18	coli	coli	FW	_	_	_
19	and	and	CC	_	_	_
20	stored	store	VBN	_	_	_
21	as	as	IN	_	_	_
22	glycerol	glycerol	NN	SUPP	_	_
23	stocks	stock	NNS	_	_	_
24	.	.	.	_	_	_

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	NN	_	_	_
2	double	double	JJ	_	_	_
3	mutant	mutant	JJ	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	PPK1	ppk1	NN	_	_	_
6	and	and	CC	_	_	_
7	PPX	ppx	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Double	double	JJ	_	_	_
11	stranded	strand	VBN	_	_	_
12	cDNA	cdna	NN	_	_	_
13	was	be	VBD	_	_	_
14	generated	generate	VBN	_	_	_
15	using	use	VBG	_	_	_
16	Superscript	Superscript	NNP	_	_	_
17	II	II	NNP	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Invitrogen	Invitrogen	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	to	to	TO	_	_	_
22	generate	generate	VB	_	_	_
23	the	the	DT	_	_	_
24	first	first	JJ	_	_	_
25	strand	strand	NN	_	_	_
26	followed	follow	VBN	_	_	_
27	by	by	IN	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	DNA	dna	NN	_	_	_
31	polymerase	polymerase	NN	_	_	_
32	,	,	,	_	_	_
33	RNaseH	rnaseh	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	E.coli	e.coli	NN	_	_	_
37	DNA	dna	NN	_	_	_
38	ligase	ligase	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	NEB	neb	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	to	to	TO	_	_	_
43	generate	generate	VB	_	_	_
44	the	the	DT	_	_	_
45	second	second	JJ	_	_	_
46	strand	strand	NN	_	_	_
47	.	.	.	_	_	_

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	dpiA	dpia	NN	GEN	_	_
3	2x	2x	NN	_	_	_
4	Overexpression	overexpression	NN	_	_	_
5	pHI1429	phi1429	NN	_	_	_
6	in	in	IN	_	_	_
7	LB	lb	NN	_	_	_
8	at	at	IN	_	_	_
9	37	37	CD	_	_	_
10	Mid	Mid	NNP	_	_	_
11	Log	Log	NNP	_	_	_
12	Phase	phase	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	dpiAoverexpressor	dpiaoverexpressor	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	d	d	NN	_	_	_
17	_	_	CD	_	_	_
18	rnr	rnr	NN	GEN	_	_
19	NO3	no3	NN	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	d	d	NN	_	_	_
23	_	_	CD	_	_	_
24	rnr	rnr	NN	GEN	_	_
25	NO3	no3	NN	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	d	d	NN	_	_	_
29	_	_	CD	_	_	_
30	rnr	rnr	NN	GEN	_	_
31	NO3	no3	NN	_	_	_
32	w/propionate	w/propionate	NN	_	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	d	d	NN	_	_	_
36	_	_	CD	_	_	_
37	rnr	rnr	NN	GEN	_	_
38	NO3	no3	NN	_	_	_
39	w/propionate	w/propionate	NN	_	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	d	d	NN	_	_	_
43	_	_	CD	_	_	_
44	rnr	rnr	NN	GEN	_	_
45	O2	o2	CD	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	d	d	NN	_	_	_
49	_	_	CD	_	_	_
50	rnr	rnr	NN	GEN	_	_
51	O2	o2	CD	_	_	_
52	2	2	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	d	d	NN	_	_	_
55	_	_	CD	_	_	_
56	rnr	rnr	NN	GEN	_	_
57	O2	o2	CD	_	_	_
58	w/propionate	w/propionate	NN	_	_	_
59	1	1	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	d	d	NN	_	_	_
62	_	_	CD	_	_	_
63	rnr	rnr	NN	GEN	_	_
64	O2	o2	CD	_	_	_
65	w/propionate	w/propionate	NN	_	_	_
66	2	2	CD	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Drug	Drug	NNP	_	_	_
69	:	:	:	_	_	_
70	bicyclomycin	bicyclomycin	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Drug	drug	NN	_	_	_
73	:	:	:	_	_	_
74	none	none	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	DSP1	dsp1	NN	_	_	_
77	_	_	CD	_	_	_
78	AP	ap	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	DSP1	dsp1	NN	_	_	_
81	_	_	CD	_	_	_
82	Total	total	JJ	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	DSP2	dsp2	NN	_	_	_
85	_	_	CD	_	_	_
86	AP	ap	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	DSP2	dsp2	NN	_	_	_
89	_	_	CD	_	_	_
90	Total	total	JJ	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	DSP3	dsp3	NN	_	_	_
93	_	_	CD	_	_	_
94	AP	ap	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	DSP3	dsp3	NN	_	_	_
97	_	_	CD	_	_	_
98	Total	total	JJ	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
100	Duplicate	duplicate	VB	_	_	_
101	O/N	o/n	NN	_	_	_
102	cultures	culture	NNS	_	_	_
103	in	in	IN	_	_	_
104	LB	lb	NN	_	_	_
105	with	with	IN	_	_	_
106	15	15	CD	_	_	_
107	mg/L	mg/l	NN	_	_	_
108	chloramphenicol	chloramphenicol	NN	_	_	_
109	each	each	DT	_	_	_
110	of	of	IN	_	_	_
111	strains	strain	NNS	_	_	_
112	pCA24N,-gfp	pca24n,-gfp	NN	_	_	_
113	/	/	:	_	_	_
114	DA4201	da4201	NN	_	_	_
115	,	,	,	_	_	_
116	Svi3-3	svi3-3	NN	_	_	_
117	comp	comp	NN	_	_	_
118	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	recoded	recode	VBN	_	_	_
3	Svi3-3	svi3-3	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	/	/	:	_	_	_
6	DA4201	da4201	NN	_	_	_
7	and	and	CC	_	_	_
8	pORF1/DA4201	porf1/da4201	NN	_	_	_
9	were	be	VBD	_	_	_
10	diluted	dilute	VBN	_	_	_
11	1:100	1:100	CD	_	_	_
12	into	into	IN	_	_	_
13	two	two	CD	_	_	_
14	,	,	,	_	_	_
15	four	four	CD	_	_	_
16	and	and	CC	_	_	_
17	four	four	CD	_	_	_
18	cultures	culture	NNS	_	_	_
19	of	of	IN	_	_	_
20	20	20	CD	_	_	_
21	mL	ml	NN	_	_	_
22	M9	m9	NN	_	_	_
23	+	+	CC	_	_	_
24	0.2	0.2	CD	_	_	_
25	%	%	NN	_	_	_
26	glucose	glucose	NN	SUPP	_	_
27	with	with	IN	_	_	_
28	5	5	CD	_	_	_
29	μg/mL	μg/ml	NN	_	_	_
30	chloramphenicol	chloramphenicol	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pCA24N,-gfp	pca24n,-gfp	NN	_	_	_
3	/	/	:	_	_	_
4	DA4201	da4201	NN	_	_	_
5	cultures	culture	NNS	_	_	_
6	and	and	CC	_	_	_
7	two	two	CD	_	_	_
8	cultures	culture	NNS	_	_	_
9	each	each	DT	_	_	_
10	of	of	IN	_	_	_
11	Svi3-3	svi3-3	NN	_	_	_
12	comp	comp	NN	_	_	_
13	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	recoded	recode	VBN	_	_	_
3	Svi3-3	svi3-3	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	/	/	:	_	_	_
6	DA4201	da4201	NN	_	_	_
7	and	and	CC	_	_	_
8	pORF1/DA4201	porf1/da4201	NN	_	_	_
9	were	be	VBD	_	_	_
10	supplemented	supplement	VBN	_	_	_
11	by	by	IN	_	_	_
12	50	50	CD	_	_	_
13	μM	μm	NN	_	_	_
14	IPTG	iptg	NN	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	OD	od	NN	_	_	_
7	0.15-0.2	0.15-0.2	CD	_	_	_
8	and	and	CC	_	_	_
9	cells	cell	NNS	_	_	_
10	were	be	VBD	_	_	_
11	withdrawn	withdraw	VBN	_	_	_
12	for	for	IN	_	_	_
13	RNA	rna	NN	_	_	_
14	extraction	extraction	NN	_	_	_
15	and	and	CC	_	_	_
16	whole	whole	JJ	_	_	_
17	cell	cell	NN	_	_	_
18	proteomics	proteomic	NNS	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E058	e058	NN	_	_	_
3	in	in	FW	_	_	_
4	vitro	vitro	FW	_	_	_
5	,	,	,	_	_	_
6	biological	biological	JJ	_	_	_
7	rep1	rep1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	E058	e058	NN	_	_	_
10	in	in	FW	_	_	_
11	vitro	vitro	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	rep1	rep1	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	E058	e058	NN	_	_	_
24	in	in	FW	_	_	_
25	vivo	vivo	FW	_	_	_
26	,	,	,	_	_	_
27	biological	biological	JJ	_	_	_
28	rep2	rep2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	E058	e058	NN	_	_	_
31	in	in	FW	_	_	_
32	vivo	vivo	FW	_	_	_
33	,	,	,	_	_	_
34	biological	biological	JJ	_	_	_
35	rep3	rep3	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	E058ΔrstAB	e058δrstab	NN	_	_	_
38	in	in	FW	_	_	_
39	vivo	vivo	FW	_	_	_
40	,	,	,	_	_	_
41	biological	biological	JJ	_	_	_
42	rep1	rep1	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	E058ΔrstAB	e058δrstab	NN	_	_	_
45	in	in	FW	_	_	_
46	vivo	vivo	FW	_	_	_
47	,	,	,	_	_	_
48	biological	biological	JJ	_	_	_
49	rep2	rep2	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	E058ΔrstAB	e058δrstab	NN	_	_	_
52	in	in	FW	_	_	_
53	vivo	vivo	FW	_	_	_
54	,	,	,	_	_	_
55	biological	biological	JJ	_	_	_
56	rep3	rep3	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	E0-E1	e0-e1	NN	_	_	_
59	_	_	CD	_	_	_
60	rep1	rep1	NN	_	_	_
61	_	_	VBD	_	_	_
62	a	a	DT	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	E0-E1	e0-e1	NN	_	_	_
65	_	_	CD	_	_	_
66	rep1	rep1	NN	_	_	_
67	_	_	NN	_	_	_
68	b	b	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	E0-E1	e0-e1	NN	_	_	_
71	_	_	CD	_	_	_
72	rep2	rep2	NN	_	_	_
73	_	_	VBD	_	_	_
74	a	a	DT	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	E0-E1	e0-e1	NN	_	_	_
77	_	_	CD	_	_	_
78	rep2	rep2	NN	_	_	_
79	_	_	NN	_	_	_
80	b	b	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	E0-E1	e0-e1	NN	_	_	_
83	_	_	CD	_	_	_
84	rep3	rep3	NN	_	_	_
85	_	_	VBD	_	_	_
86	a	a	DT	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	E0-E1	e0-e1	NN	_	_	_
89	_	_	CD	_	_	_
90	rep3	rep3	NN	_	_	_
91	_	_	NN	_	_	_
92	b	b	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	E11	e11	NN	_	_	_
95	_	_	NN	_	_	_
96	1	1	CD	_	_	_
97	_	_	SYM	_	_	_
98	m1	m1	NN	_	_	_
99	-LSB-	-lsb-	-LRB-	_	_	_
100	COPRO-Seq	copro-seq	NN	_	_	_
101	-RSB-	-rsb-	-RRB-	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	E11	e11	NN	_	_	_
104	_	_	NN	_	_	_
105	1	1	CD	_	_	_
106	_	_	CD	_	_	_
107	m3	m3	NN	_	_	_
108	-LSB-	-lsb-	-LRB-	_	_	_
109	COPRO-Seq	copro-seq	NN	_	_	_
110	-RSB-	-rsb-	-RRB-	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	E11	e11	NN	_	_	_
113	_	_	NN	_	_	_
114	1	1	CD	_	_	_
115	_	_	CD	_	_	_
116	m4	m4	NN	_	_	_
117	-LSB-	-lsb-	-LRB-	_	_	_
118	COPRO-Seq	copro-seq	NN	_	_	_
119	-RSB-	-rsb-	-RRB-	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	E11	e11	NN	_	_	_
122	_	_	NN	_	_	_
123	1	1	CD	_	_	_
124	_	_	CD	_	_	_
125	m5	m5	NN	_	_	_
126	-LSB-	-lsb-	-LRB-	_	_	_
127	COPRO-Seq	copro-seq	NN	_	_	_
128	-RSB-	-rsb-	-RRB-	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	E11	e11	NN	_	_	_
131	_	_	NN	_	_	_
132	1	1	CD	_	_	_
133	_	_	CD	_	_	_
134	m6	m6	NN	_	_	_
135	-LSB-	-lsb-	-LRB-	_	_	_
136	COPRO-Seq	copro-seq	NN	_	_	_
137	-RSB-	-rsb-	-RRB-	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	E11	e11	NN	_	_	_
140	_	_	NN	_	_	_
141	1	1	CD	_	_	_
142	_	_	CD	_	_	_
143	m7	m7	NN	_	_	_
144	-LSB-	-lsb-	-LRB-	_	_	_
145	COPRO-Seq	copro-seq	NN	_	_	_
146	-RSB-	-rsb-	-RRB-	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	E11	e11	NN	_	_	_
149	_	_	NN	_	_	_
150	1	1	CD	_	_	_
151	_	_	CD	_	_	_
152	m8	m8	NN	_	_	_
153	-LSB-	-lsb-	-LRB-	_	_	_
154	COPRO-Seq	copro-seq	NN	_	_	_
155	-RSB-	-rsb-	-RRB-	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	E1	e1	NN	_	_	_
158	_	_	VBD	_	_	_
159	14	14	CD	_	_	_
160	_	_	SYM	_	_	_
161	m1	m1	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	E1	e1	NN	_	_	_
164	_	_	VBD	_	_	_
165	14	14	CD	_	_	_
166	_	_	SYM	_	_	_
167	m1	m1	NN	_	_	_
168	-LSB-	-lsb-	-LRB-	_	_	_
169	COPRO-Seq	copro-seq	NN	_	_	_
170	-RSB-	-rsb-	-RRB-	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	E11	e11	NN	_	_	_
173	_	_	CD	_	_	_
174	4	4	CD	_	_	_
175	_	_	SYM	_	_	_
176	m1	m1	NN	_	_	_
177	-LSB-	-lsb-	-LRB-	_	_	_
178	COPRO-Seq	copro-seq	NN	_	_	_
179	-RSB-	-rsb-	-RRB-	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	E1	e1	NN	_	_	_
182	_	_	VBD	_	_	_
183	14	14	CD	_	_	_
184	_	_	CD	_	_	_
185	m2	m2	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	E1	e1	NN	_	_	_
188	_	_	VBD	_	_	_
189	14	14	CD	_	_	_
190	_	_	CD	_	_	_
191	m2	m2	NN	_	_	_
192	-LSB-	-lsb-	-LRB-	_	_	_
193	COPRO-Seq	copro-seq	NN	_	_	_
194	-RSB-	-rsb-	-RRB-	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	E1	e1	NN	_	_	_
197	_	_	VBD	_	_	_
198	14	14	CD	_	_	_
199	_	_	CD	_	_	_
200	m3	m3	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	E1	e1	NN	_	_	_
203	_	_	VBD	_	_	_
204	14	14	CD	_	_	_
205	_	_	CD	_	_	_
206	m3	m3	NN	_	_	_
207	-LSB-	-lsb-	-LRB-	_	_	_
208	COPRO-Seq	copro-seq	NN	_	_	_
209	-RSB-	-rsb-	-RRB-	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	E1	e1	NN	_	_	_
212	_	_	VBD	_	_	_
213	14	14	CD	_	_	_
214	_	_	CD	_	_	_
215	m4	m4	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	E1	e1	NN	_	_	_
218	_	_	VBD	_	_	_
219	14	14	CD	_	_	_
220	_	_	CD	_	_	_
221	m4	m4	NN	_	_	_
222	-LSB-	-lsb-	-LRB-	_	_	_
223	COPRO-Seq	copro-seq	NN	_	_	_
224	-RSB-	-rsb-	-RRB-	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	E11	e11	NN	_	_	_
227	_	_	CD	_	_	_
228	4	4	CD	_	_	_
229	_	_	NN	_	_	_
230	m4	m4	NN	_	_	_
231	-LSB-	-lsb-	-LRB-	_	_	_
232	COPRO-Seq	copro-seq	NN	_	_	_
233	-RSB-	-rsb-	-RRB-	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	E1	e1	NN	_	_	_
236	_	_	VBD	_	_	_
237	14	14	CD	_	_	_
238	_	_	CD	_	_	_
239	m5	m5	NN	_	_	_
240	-LSB-	-lsb-	-LRB-	_	_	_
241	COPRO-Seq	copro-seq	NN	_	_	_
242	-RSB-	-rsb-	-RRB-	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	E11	e11	NN	_	_	_
245	_	_	CD	_	_	_
246	4	4	CD	_	_	_
247	_	_	NN	_	_	_
248	m5	m5	NN	_	_	_
249	-LSB-	-lsb-	-LRB-	_	_	_
250	COPRO-Seq	copro-seq	NN	_	_	_
251	-RSB-	-rsb-	-RRB-	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	E1	e1	NN	_	_	_
254	_	_	VBD	_	_	_
255	14	14	CD	_	_	_
256	_	_	CD	_	_	_
257	m6	m6	NN	_	_	_
258	-LSB-	-lsb-	-LRB-	_	_	_
259	COPRO-Seq	copro-seq	NN	_	_	_
260	-RSB-	-rsb-	-RRB-	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	E1	e1	NN	_	_	_
263	_	_	VBD	_	_	_
264	14	14	CD	_	_	_
265	_	_	CD	_	_	_
266	m7	m7	NN	_	_	_
267	-LSB-	-lsb-	-LRB-	_	_	_
268	COPRO-Seq	copro-seq	NN	_	_	_
269	-RSB-	-rsb-	-RRB-	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	E11	e11	NN	_	_	_
272	_	_	CD	_	_	_
273	4	4	CD	_	_	_
274	_	_	NN	_	_	_
275	m7	m7	NN	_	_	_
276	-LSB-	-lsb-	-LRB-	_	_	_
277	COPRO-Seq	copro-seq	NN	_	_	_
278	-RSB-	-rsb-	-RRB-	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	E1	e1	NN	_	_	_
281	_	_	VBD	_	_	_
282	14	14	CD	_	_	_
283	_	_	CD	_	_	_
284	m8	m8	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	E1	e1	NN	_	_	_
287	_	_	VBD	_	_	_
288	14	14	CD	_	_	_
289	_	_	CD	_	_	_
290	m8	m8	NN	_	_	_
291	-LSB-	-lsb-	-LRB-	_	_	_
292	COPRO-Seq	copro-seq	NN	_	_	_
293	-RSB-	-rsb-	-RRB-	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	E11	e11	NN	_	_	_
296	_	_	CD	_	_	_
297	4	4	CD	_	_	_
298	_	_	NN	_	_	_
299	m8	m8	NN	_	_	_
300	-LSB-	-lsb-	-LRB-	_	_	_
301	COPRO-Seq	copro-seq	NN	_	_	_
302	-RSB-	-rsb-	-RRB-	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	E11	e11	NN	_	_	_
305	_	_	CD	_	_	_
306	6	6	CD	_	_	_
307	_	_	NN	_	_	_
308	m2	m2	NN	_	_	_
309	-LSB-	-lsb-	-LRB-	_	_	_
310	COPRO-Seq	copro-seq	NN	_	_	_
311	-RSB-	-rsb-	-RRB-	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	E11	e11	NN	_	_	_
314	_	_	CD	_	_	_
315	6	6	CD	_	_	_
316	_	_	NN	_	_	_
317	m3	m3	NN	_	_	_
318	-LSB-	-lsb-	-LRB-	_	_	_
319	COPRO-Seq	copro-seq	NN	_	_	_
320	-RSB-	-rsb-	-RRB-	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	E11	e11	NN	_	_	_
323	_	_	CD	_	_	_
324	6	6	CD	_	_	_
325	_	_	NN	_	_	_
326	m4	m4	NN	_	_	_
327	-LSB-	-lsb-	-LRB-	_	_	_
328	COPRO-Seq	copro-seq	NN	_	_	_
329	-RSB-	-rsb-	-RRB-	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	E11	e11	NN	_	_	_
332	_	_	CD	_	_	_
333	6	6	CD	_	_	_
334	_	_	NN	_	_	_
335	m5	m5	NN	_	_	_
336	-LSB-	-lsb-	-LRB-	_	_	_
337	COPRO-Seq	copro-seq	NN	_	_	_
338	-RSB-	-rsb-	-RRB-	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	E11	e11	NN	_	_	_
341	_	_	NN	_	_	_
342	7	7	CD	_	_	_
343	_	_	SYM	_	_	_
344	m1	m1	NN	_	_	_
345	-LSB-	-lsb-	-LRB-	_	_	_
346	COPRO-Seq	copro-seq	NN	_	_	_
347	-RSB-	-rsb-	-RRB-	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	E11	e11	NN	_	_	_
350	_	_	NN	_	_	_
351	7	7	CD	_	_	_
352	_	_	NN	_	_	_
353	m2	m2	NN	_	_	_
354	-LSB-	-lsb-	-LRB-	_	_	_
355	COPRO-Seq	copro-seq	NN	_	_	_
356	-RSB-	-rsb-	-RRB-	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	E11	e11	NN	_	_	_
359	_	_	NN	_	_	_
360	7	7	CD	_	_	_
361	_	_	NN	_	_	_
362	m3	m3	NN	_	_	_
363	-LSB-	-lsb-	-LRB-	_	_	_
364	COPRO-Seq	copro-seq	NN	_	_	_
365	-RSB-	-rsb-	-RRB-	_	_	_
366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
367	E11	e11	NN	_	_	_
368	_	_	NN	_	_	_
369	7	7	CD	_	_	_
370	_	_	NN	_	_	_
371	m4	m4	NN	_	_	_
372	-LSB-	-lsb-	-LRB-	_	_	_
373	COPRO-Seq	copro-seq	NN	_	_	_
374	-RSB-	-rsb-	-RRB-	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	E11	e11	NN	_	_	_
377	_	_	NN	_	_	_
378	7	7	CD	_	_	_
379	_	_	NN	_	_	_
380	m6	m6	NN	_	_	_
381	-LSB-	-lsb-	-LRB-	_	_	_
382	COPRO-Seq	copro-seq	NN	_	_	_
383	-RSB-	-rsb-	-RRB-	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	E11	e11	NN	_	_	_
386	_	_	NN	_	_	_
387	7	7	CD	_	_	_
388	_	_	NN	_	_	_
389	m7	m7	NN	_	_	_
390	-LSB-	-lsb-	-LRB-	_	_	_
391	COPRO-Seq	copro-seq	NN	_	_	_
392	-RSB-	-rsb-	-RRB-	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	E11	e11	NN	_	_	_
395	_	_	NN	_	_	_
396	7	7	CD	_	_	_
397	_	_	NN	_	_	_
398	m8	m8	NN	_	_	_
399	-LSB-	-lsb-	-LRB-	_	_	_
400	COPRO-Seq	copro-seq	NN	_	_	_
401	-RSB-	-rsb-	-RRB-	_	_	_
402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
403	E1	e1	NN	_	_	_
404	_	_	VBD	_	_	_
405	1	1	CD	_	_	_
406	_	_	SYM	_	_	_
407	m1	m1	NN	_	_	_
408	-LSB-	-lsb-	-LRB-	_	_	_
409	COPRO-Seq	copro-seq	NN	_	_	_
410	-RSB-	-rsb-	-RRB-	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	E1	e1	NN	_	_	_
413	_	_	VBD	_	_	_
414	1	1	CD	_	_	_
415	_	_	CD	_	_	_
416	m2	m2	NN	_	_	_
417	-LSB-	-lsb-	-LRB-	_	_	_
418	COPRO-Seq	copro-seq	NN	_	_	_
419	-RSB-	-rsb-	-RRB-	_	_	_
420	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
421	E1	e1	NN	_	_	_
422	_	_	VBD	_	_	_
423	1	1	CD	_	_	_
424	_	_	CD	_	_	_
425	m4	m4	NN	_	_	_
426	-LSB-	-lsb-	-LRB-	_	_	_
427	COPRO-Seq	copro-seq	NN	_	_	_
428	-RSB-	-rsb-	-RRB-	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	E1	e1	NN	_	_	_
431	_	_	VBD	_	_	_
432	1	1	CD	_	_	_
433	_	_	CD	_	_	_
434	m5	m5	NN	_	_	_
435	-LSB-	-lsb-	-LRB-	_	_	_
436	COPRO-Seq	copro-seq	NN	_	_	_
437	-RSB-	-rsb-	-RRB-	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	E1	e1	NN	_	_	_
440	_	_	VBD	_	_	_
441	1	1	CD	_	_	_
442	_	_	CD	_	_	_
443	m7	m7	NN	_	_	_
444	-LSB-	-lsb-	-LRB-	_	_	_
445	COPRO-Seq	copro-seq	NN	_	_	_
446	-RSB-	-rsb-	-RRB-	_	_	_
447	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
448	E1	e1	NN	_	_	_
449	_	_	VBD	_	_	_
450	1	1	CD	_	_	_
451	_	_	CD	_	_	_
452	m8	m8	NN	_	_	_
453	-LSB-	-lsb-	-LRB-	_	_	_
454	COPRO-Seq	copro-seq	NN	_	_	_
455	-RSB-	-rsb-	-RRB-	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	E1	e1	NN	_	_	_
458	_	_	NN	_	_	_
459	2	2	CD	_	_	_
460	_	_	SYM	_	_	_
461	m1	m1	NN	_	_	_
462	-LSB-	-lsb-	-LRB-	_	_	_
463	COPRO-Seq	copro-seq	NN	_	_	_
464	-RSB-	-rsb-	-RRB-	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	E1	e1	NN	_	_	_
467	_	_	NN	_	_	_
468	2	2	CD	_	_	_
469	_	_	CD	_	_	_
470	m2	m2	NN	_	_	_
471	-LSB-	-lsb-	-LRB-	_	_	_
472	COPRO-Seq	copro-seq	NN	_	_	_
473	-RSB-	-rsb-	-RRB-	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	E1	e1	NN	_	_	_
476	_	_	NN	_	_	_
477	2	2	CD	_	_	_
478	_	_	CD	_	_	_
479	m3	m3	NN	_	_	_
480	-LSB-	-lsb-	-LRB-	_	_	_
481	COPRO-Seq	copro-seq	NN	_	_	_
482	-RSB-	-rsb-	-RRB-	_	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
484	E1	e1	NN	_	_	_
485	_	_	NN	_	_	_
486	2	2	CD	_	_	_
487	_	_	CD	_	_	_
488	m4	m4	NN	_	_	_
489	-LSB-	-lsb-	-LRB-	_	_	_
490	COPRO-Seq	copro-seq	NN	_	_	_
491	-RSB-	-rsb-	-RRB-	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
493	E1	e1	NN	_	_	_
494	_	_	NN	_	_	_
495	2	2	CD	_	_	_
496	_	_	CD	_	_	_
497	m5	m5	NN	_	_	_
498	-LSB-	-lsb-	-LRB-	_	_	_
499	COPRO-Seq	copro-seq	NN	_	_	_
500	-RSB-	-rsb-	-RRB-	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	E1	e1	NN	_	_	_
503	_	_	NN	_	_	_
504	2	2	CD	_	_	_
505	_	_	CD	_	_	_
506	m6	m6	NN	_	_	_
507	-LSB-	-lsb-	-LRB-	_	_	_
508	COPRO-Seq	copro-seq	NN	_	_	_
509	-RSB-	-rsb-	-RRB-	_	_	_
510	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
511	E1	e1	NN	_	_	_
512	_	_	NN	_	_	_
513	2	2	CD	_	_	_
514	_	_	CD	_	_	_
515	m7	m7	NN	_	_	_
516	-LSB-	-lsb-	-LRB-	_	_	_
517	COPRO-Seq	copro-seq	NN	_	_	_
518	-RSB-	-rsb-	-RRB-	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	E1	e1	NN	_	_	_
521	_	_	NN	_	_	_
522	2	2	CD	_	_	_
523	_	_	CD	_	_	_
524	m8	m8	NN	_	_	_
525	-LSB-	-lsb-	-LRB-	_	_	_
526	COPRO-Seq	copro-seq	NN	_	_	_
527	-RSB-	-rsb-	-RRB-	_	_	_
528	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
529	E13	e13	NN	_	_	_
530	_	_	NN	_	_	_
531	1	1	CD	_	_	_
532	_	_	SYM	_	_	_
533	m1	m1	NN	_	_	_
534	-LSB-	-lsb-	-LRB-	_	_	_
535	COPRO-Seq	copro-seq	NN	_	_	_
536	-RSB-	-rsb-	-RRB-	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	E13	e13	NN	_	_	_
539	_	_	NN	_	_	_
540	1	1	CD	_	_	_
541	_	_	CD	_	_	_
542	m2	m2	NN	_	_	_
543	-LSB-	-lsb-	-LRB-	_	_	_
544	COPRO-Seq	copro-seq	NN	_	_	_
545	-RSB-	-rsb-	-RRB-	_	_	_
546	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
547	E13	e13	NN	_	_	_
548	_	_	NN	_	_	_
549	1	1	CD	_	_	_
550	_	_	CD	_	_	_
551	m3	m3	NN	_	_	_
552	-LSB-	-lsb-	-LRB-	_	_	_
553	COPRO-Seq	copro-seq	NN	_	_	_
554	-RSB-	-rsb-	-RRB-	_	_	_
555	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
556	E13	e13	NN	_	_	_
557	_	_	NN	_	_	_
558	1	1	CD	_	_	_
559	_	_	CD	_	_	_
560	m4	m4	NN	_	_	_
561	-LSB-	-lsb-	-LRB-	_	_	_
562	COPRO-Seq	copro-seq	NN	_	_	_
563	-RSB-	-rsb-	-RRB-	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	E13	e13	NN	_	_	_
566	_	_	NN	_	_	_
567	1	1	CD	_	_	_
568	_	_	CD	_	_	_
569	m5	m5	NN	_	_	_
570	-LSB-	-lsb-	-LRB-	_	_	_
571	COPRO-Seq	copro-seq	NN	_	_	_
572	-RSB-	-rsb-	-RRB-	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	E13	e13	NN	_	_	_
575	_	_	NN	_	_	_
576	1	1	CD	_	_	_
577	_	_	CD	_	_	_
578	m6	m6	NN	_	_	_
579	-LSB-	-lsb-	-LRB-	_	_	_
580	COPRO-Seq	copro-seq	NN	_	_	_
581	-RSB-	-rsb-	-RRB-	_	_	_
582	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
583	E13	e13	NN	_	_	_
584	_	_	NN	_	_	_
585	1	1	CD	_	_	_
586	_	_	CD	_	_	_
587	m7	m7	NN	_	_	_
588	-LSB-	-lsb-	-LRB-	_	_	_
589	COPRO-Seq	copro-seq	NN	_	_	_
590	-RSB-	-rsb-	-RRB-	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	E13	e13	NN	_	_	_
593	_	_	NN	_	_	_
594	1	1	CD	_	_	_
595	_	_	CD	_	_	_
596	m8	m8	NN	_	_	_
597	-LSB-	-lsb-	-LRB-	_	_	_
598	COPRO-Seq	copro-seq	NN	_	_	_
599	-RSB-	-rsb-	-RRB-	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
601	E13	e13	NN	_	_	_
602	_	_	CD	_	_	_
603	4	4	CD	_	_	_
604	_	_	SYM	_	_	_
605	m1	m1	NN	_	_	_
606	-LSB-	-lsb-	-LRB-	_	_	_
607	COPRO-Seq	copro-seq	NN	_	_	_
608	-RSB-	-rsb-	-RRB-	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	E13	e13	NN	_	_	_
611	_	_	CD	_	_	_
612	4	4	CD	_	_	_
613	_	_	NN	_	_	_
614	m3	m3	NN	_	_	_
615	-LSB-	-lsb-	-LRB-	_	_	_
616	COPRO-Seq	copro-seq	NN	_	_	_
617	-RSB-	-rsb-	-RRB-	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	E13	e13	NN	_	_	_
620	_	_	CD	_	_	_
621	4	4	CD	_	_	_
622	_	_	NN	_	_	_
623	m4	m4	NN	_	_	_
624	-LSB-	-lsb-	-LRB-	_	_	_
625	COPRO-Seq	copro-seq	NN	_	_	_
626	-RSB-	-rsb-	-RRB-	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	E13	e13	NN	_	_	_
629	_	_	CD	_	_	_
630	4	4	CD	_	_	_
631	_	_	NN	_	_	_
632	m5	m5	NN	_	_	_
633	-LSB-	-lsb-	-LRB-	_	_	_
634	COPRO-Seq	copro-seq	NN	_	_	_
635	-RSB-	-rsb-	-RRB-	_	_	_
636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
637	E13	e13	NN	_	_	_
638	_	_	CD	_	_	_
639	4	4	CD	_	_	_
640	_	_	NN	_	_	_
641	m6	m6	NN	_	_	_
642	-LSB-	-lsb-	-LRB-	_	_	_
643	COPRO-Seq	copro-seq	NN	_	_	_
644	-RSB-	-rsb-	-RRB-	_	_	_
645	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
646	E13	e13	NN	_	_	_
647	_	_	CD	_	_	_
648	4	4	CD	_	_	_
649	_	_	NN	_	_	_
650	m7	m7	NN	_	_	_
651	-LSB-	-lsb-	-LRB-	_	_	_
652	COPRO-Seq	copro-seq	NN	_	_	_
653	-RSB-	-rsb-	-RRB-	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
655	E13	e13	NN	_	_	_
656	_	_	CD	_	_	_
657	4	4	CD	_	_	_
658	_	_	NN	_	_	_
659	m8	m8	NN	_	_	_
660	-LSB-	-lsb-	-LRB-	_	_	_
661	COPRO-Seq	copro-seq	NN	_	_	_
662	-RSB-	-rsb-	-RRB-	_	_	_
663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
664	E13	e13	NN	_	_	_
665	_	_	CD	_	_	_
666	6	6	CD	_	_	_
667	_	_	NN	_	_	_
668	m1	m1	NN	_	_	_
669	-LSB-	-lsb-	-LRB-	_	_	_
670	COPRO-Seq	copro-seq	NN	_	_	_
671	-RSB-	-rsb-	-RRB-	_	_	_
672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
673	E13	e13	NN	_	_	_
674	_	_	CD	_	_	_
675	6	6	CD	_	_	_
676	_	_	NN	_	_	_
677	m4	m4	NN	_	_	_
678	-LSB-	-lsb-	-LRB-	_	_	_
679	COPRO-Seq	copro-seq	NN	_	_	_
680	-RSB-	-rsb-	-RRB-	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	E13	e13	NN	_	_	_
683	_	_	CD	_	_	_
684	6	6	CD	_	_	_
685	_	_	NN	_	_	_
686	m5	m5	NN	_	_	_
687	-LSB-	-lsb-	-LRB-	_	_	_
688	COPRO-Seq	copro-seq	NN	_	_	_
689	-RSB-	-rsb-	-RRB-	_	_	_
690	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
691	E13	e13	NN	_	_	_
692	_	_	NN	_	_	_
693	7	7	CD	_	_	_
694	_	_	SYM	_	_	_
695	m1	m1	NN	_	_	_
696	-LSB-	-lsb-	-LRB-	_	_	_
697	COPRO-Seq	copro-seq	NN	_	_	_
698	-RSB-	-rsb-	-RRB-	_	_	_
699	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
700	E13	e13	NN	_	_	_
701	_	_	NN	_	_	_
702	7	7	CD	_	_	_
703	_	_	NN	_	_	_
704	m2	m2	NN	_	_	_
705	-LSB-	-lsb-	-LRB-	_	_	_
706	COPRO-Seq	copro-seq	NN	_	_	_
707	-RSB-	-rsb-	-RRB-	_	_	_
708	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
709	E13	e13	NN	_	_	_
710	_	_	NN	_	_	_
711	7	7	CD	_	_	_
712	_	_	NN	_	_	_
713	m4	m4	NN	_	_	_
714	-LSB-	-lsb-	-LRB-	_	_	_
715	COPRO-Seq	copro-seq	NN	_	_	_
716	-RSB-	-rsb-	-RRB-	_	_	_
717	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
718	E13	e13	NN	_	_	_
719	_	_	NN	_	_	_
720	7	7	CD	_	_	_
721	_	_	NN	_	_	_
722	m5	m5	NN	_	_	_
723	-LSB-	-lsb-	-LRB-	_	_	_
724	COPRO-Seq	copro-seq	NN	_	_	_
725	-RSB-	-rsb-	-RRB-	_	_	_
726	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
727	E13	e13	NN	_	_	_
728	_	_	NN	_	_	_
729	7	7	CD	_	_	_
730	_	_	NN	_	_	_
731	m6	m6	NN	_	_	_
732	-LSB-	-lsb-	-LRB-	_	_	_
733	COPRO-Seq	copro-seq	NN	_	_	_
734	-RSB-	-rsb-	-RRB-	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
736	E13	e13	NN	_	_	_
737	_	_	NN	_	_	_
738	7	7	CD	_	_	_
739	_	_	NN	_	_	_
740	m7	m7	NN	_	_	_
741	-LSB-	-lsb-	-LRB-	_	_	_
742	COPRO-Seq	copro-seq	NN	_	_	_
743	-RSB-	-rsb-	-RRB-	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	E13	e13	NN	_	_	_
746	_	_	NN	_	_	_
747	7	7	CD	_	_	_
748	_	_	NN	_	_	_
749	m8	m8	NN	_	_	_
750	-LSB-	-lsb-	-LRB-	_	_	_
751	COPRO-Seq	copro-seq	NN	_	_	_
752	-RSB-	-rsb-	-RRB-	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	E1	e1	NN	_	_	_
755	_	_	VBD	_	_	_
756	4	4	CD	_	_	_
757	_	_	SYM	_	_	_
758	m1	m1	NN	_	_	_
759	-LSB-	-lsb-	-LRB-	_	_	_
760	COPRO-Seq	copro-seq	NN	_	_	_
761	-RSB-	-rsb-	-RRB-	_	_	_
762	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
763	E1	e1	NN	_	_	_
764	_	_	VBD	_	_	_
765	4	4	CD	_	_	_
766	_	_	CD	_	_	_
767	m2	m2	NN	_	_	_
768	-LSB-	-lsb-	-LRB-	_	_	_
769	COPRO-Seq	copro-seq	NN	_	_	_
770	-RSB-	-rsb-	-RRB-	_	_	_
771	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
772	E1	e1	NN	_	_	_
773	_	_	VBD	_	_	_
774	4	4	CD	_	_	_
775	_	_	CD	_	_	_
776	m3	m3	NN	_	_	_
777	-LSB-	-lsb-	-LRB-	_	_	_
778	COPRO-Seq	copro-seq	NN	_	_	_
779	-RSB-	-rsb-	-RRB-	_	_	_
780	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
781	E1	e1	NN	_	_	_
782	_	_	VBD	_	_	_
783	4	4	CD	_	_	_
784	_	_	CD	_	_	_
785	m4	m4	NN	_	_	_
786	-LSB-	-lsb-	-LRB-	_	_	_
787	COPRO-Seq	copro-seq	NN	_	_	_
788	-RSB-	-rsb-	-RRB-	_	_	_
789	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
790	E1	e1	NN	_	_	_
791	_	_	VBD	_	_	_
792	4	4	CD	_	_	_
793	_	_	CD	_	_	_
794	m5	m5	NN	_	_	_
795	-LSB-	-lsb-	-LRB-	_	_	_
796	COPRO-Seq	copro-seq	NN	_	_	_
797	-RSB-	-rsb-	-RRB-	_	_	_
798	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
799	E1	e1	NN	_	_	_
800	_	_	VBD	_	_	_
801	4	4	CD	_	_	_
802	_	_	CD	_	_	_
803	m6	m6	NN	_	_	_
804	-LSB-	-lsb-	-LRB-	_	_	_
805	COPRO-Seq	copro-seq	NN	_	_	_
806	-RSB-	-rsb-	-RRB-	_	_	_
807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
808	E1	e1	NN	_	_	_
809	_	_	VBD	_	_	_
810	4	4	CD	_	_	_
811	_	_	CD	_	_	_
812	m7	m7	NN	_	_	_
813	-LSB-	-lsb-	-LRB-	_	_	_
814	COPRO-Seq	copro-seq	NN	_	_	_
815	-RSB-	-rsb-	-RRB-	_	_	_
816	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
817	E1	e1	NN	_	_	_
818	_	_	VBD	_	_	_
819	4	4	CD	_	_	_
820	_	_	CD	_	_	_
821	m8	m8	NN	_	_	_
822	-LSB-	-lsb-	-LRB-	_	_	_
823	COPRO-Seq	copro-seq	NN	_	_	_
824	-RSB-	-rsb-	-RRB-	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	E15	e15	CD	_	_	_
827	_	_	NN	_	_	_
828	1	1	CD	_	_	_
829	_	_	SYM	_	_	_
830	m1	m1	NN	_	_	_
831	-LSB-	-lsb-	-LRB-	_	_	_
832	COPRO-Seq	copro-seq	NN	_	_	_
833	-RSB-	-rsb-	-RRB-	_	_	_
834	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
835	E15	e15	CD	_	_	_
836	_	_	NN	_	_	_
837	1	1	CD	_	_	_
838	_	_	CD	_	_	_
839	m2	m2	NN	_	_	_
840	-LSB-	-lsb-	-LRB-	_	_	_
841	COPRO-Seq	copro-seq	NN	_	_	_
842	-RSB-	-rsb-	-RRB-	_	_	_
843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
844	E15	e15	CD	_	_	_
845	_	_	NN	_	_	_
846	1	1	CD	_	_	_
847	_	_	CD	_	_	_
848	m3	m3	NN	_	_	_
849	-LSB-	-lsb-	-LRB-	_	_	_
850	COPRO-Seq	copro-seq	NN	_	_	_
851	-RSB-	-rsb-	-RRB-	_	_	_
852	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
853	E15	e15	CD	_	_	_
854	_	_	NN	_	_	_
855	1	1	CD	_	_	_
856	_	_	CD	_	_	_
857	m4	m4	NN	_	_	_
858	-LSB-	-lsb-	-LRB-	_	_	_
859	COPRO-Seq	copro-seq	NN	_	_	_
860	-RSB-	-rsb-	-RRB-	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
862	E15	e15	CD	_	_	_
863	_	_	NN	_	_	_
864	1	1	CD	_	_	_
865	_	_	CD	_	_	_
866	m5	m5	NN	_	_	_
867	-LSB-	-lsb-	-LRB-	_	_	_
868	COPRO-Seq	copro-seq	NN	_	_	_
869	-RSB-	-rsb-	-RRB-	_	_	_
870	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
871	E15	e15	CD	_	_	_
872	_	_	NN	_	_	_
873	1	1	CD	_	_	_
874	_	_	CD	_	_	_
875	m7	m7	NN	_	_	_
876	-LSB-	-lsb-	-LRB-	_	_	_
877	COPRO-Seq	copro-seq	NN	_	_	_
878	-RSB-	-rsb-	-RRB-	_	_	_
879	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
880	E15	e15	CD	_	_	_
881	_	_	NN	_	_	_
882	1	1	CD	_	_	_
883	_	_	CD	_	_	_
884	m8	m8	NN	_	_	_
885	-LSB-	-lsb-	-LRB-	_	_	_
886	COPRO-Seq	copro-seq	NN	_	_	_
887	-RSB-	-rsb-	-RRB-	_	_	_
888	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
889	E15	e15	CD	_	_	_
890	_	_	NN	_	_	_
891	4	4	CD	_	_	_
892	_	_	SYM	_	_	_
893	m1	m1	NN	_	_	_
894	-LSB-	-lsb-	-LRB-	_	_	_
895	COPRO-Seq	copro-seq	NN	_	_	_
896	-RSB-	-rsb-	-RRB-	_	_	_
897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
898	E15	e15	CD	_	_	_
899	_	_	NN	_	_	_
900	4	4	CD	_	_	_
901	_	_	NN	_	_	_
902	m2	m2	NN	_	_	_
903	-LSB-	-lsb-	-LRB-	_	_	_
904	COPRO-Seq	copro-seq	NN	_	_	_
905	-RSB-	-rsb-	-RRB-	_	_	_
906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
907	E15	e15	CD	_	_	_
908	_	_	NN	_	_	_
909	4	4	CD	_	_	_
910	_	_	NN	_	_	_
911	m3	m3	NN	_	_	_
912	-LSB-	-lsb-	-LRB-	_	_	_
913	COPRO-Seq	copro-seq	NN	_	_	_
914	-RSB-	-rsb-	-RRB-	_	_	_
915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
916	E15	e15	CD	_	_	_
917	_	_	NN	_	_	_
918	4	4	CD	_	_	_
919	_	_	NN	_	_	_
920	m4	m4	NN	_	_	_
921	-LSB-	-lsb-	-LRB-	_	_	_
922	COPRO-Seq	copro-seq	NN	_	_	_
923	-RSB-	-rsb-	-RRB-	_	_	_
924	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
925	E15	e15	CD	_	_	_
926	_	_	NN	_	_	_
927	4	4	CD	_	_	_
928	_	_	NN	_	_	_
929	m6	m6	NN	_	_	_
930	-LSB-	-lsb-	-LRB-	_	_	_
931	COPRO-Seq	copro-seq	NN	_	_	_
932	-RSB-	-rsb-	-RRB-	_	_	_
933	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
934	E15	e15	CD	_	_	_
935	_	_	NN	_	_	_
936	4	4	CD	_	_	_
937	_	_	NN	_	_	_
938	m7	m7	NN	_	_	_
939	-LSB-	-lsb-	-LRB-	_	_	_
940	COPRO-Seq	copro-seq	NN	_	_	_
941	-RSB-	-rsb-	-RRB-	_	_	_
942	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
943	E15	e15	CD	_	_	_
944	_	_	NN	_	_	_
945	4	4	CD	_	_	_
946	_	_	NN	_	_	_
947	m8	m8	NN	_	_	_
948	-LSB-	-lsb-	-LRB-	_	_	_
949	COPRO-Seq	copro-seq	NN	_	_	_
950	-RSB-	-rsb-	-RRB-	_	_	_
951	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
952	E15	e15	CD	_	_	_
953	_	_	SYM	_	_	_
954	6	6	CD	_	_	_
955	_	_	SYM	_	_	_
956	m1	m1	NN	_	_	_
957	-LSB-	-lsb-	-LRB-	_	_	_
958	COPRO-Seq	copro-seq	NN	_	_	_
959	-RSB-	-rsb-	-RRB-	_	_	_
960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
961	E15	e15	CD	_	_	_
962	_	_	NN	_	_	_
963	6	6	CD	_	_	_
964	_	_	NN	_	_	_
965	m3	m3	NN	_	_	_
966	-LSB-	-lsb-	-LRB-	_	_	_
967	COPRO-Seq	copro-seq	NN	_	_	_
968	-RSB-	-rsb-	-RRB-	_	_	_
969	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
970	E15	e15	CD	_	_	_
971	_	_	NN	_	_	_
972	6	6	CD	_	_	_
973	_	_	NN	_	_	_
974	m5	m5	NN	_	_	_
975	-LSB-	-lsb-	-LRB-	_	_	_
976	COPRO-Seq	copro-seq	NN	_	_	_
977	-RSB-	-rsb-	-RRB-	_	_	_
978	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
979	E15	e15	CD	_	_	_
980	_	_	NN	_	_	_
981	6	6	CD	_	_	_
982	_	_	NN	_	_	_
983	m6	m6	NN	_	_	_
984	-LSB-	-lsb-	-LRB-	_	_	_
985	COPRO-Seq	copro-seq	NN	_	_	_
986	-RSB-	-rsb-	-RRB-	_	_	_
987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
988	E15	e15	CD	_	_	_
989	_	_	NN	_	_	_
990	6	6	CD	_	_	_
991	_	_	NN	_	_	_
992	m7	m7	NN	_	_	_
993	-LSB-	-lsb-	-LRB-	_	_	_
994	COPRO-Seq	copro-seq	NN	_	_	_
995	-RSB-	-rsb-	-RRB-	_	_	_
996	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
997	E15	e15	CD	_	_	_
998	_	_	NN	_	_	_
999	6	6	CD	_	_	_
1000	_	_	NN	_	_	_
1001	m8	m8	NN	_	_	_
1002	-LSB-	-lsb-	-LRB-	_	_	_
1003	COPRO-Seq	copro-seq	NN	_	_	_
1004	-RSB-	-rsb-	-RRB-	_	_	_
1005	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1006	E15	e15	CD	_	_	_
1007	_	_	NN	_	_	_
1008	7	7	CD	_	_	_
1009	_	_	SYM	_	_	_
1010	m1	m1	NN	_	_	_
1011	-LSB-	-lsb-	-LRB-	_	_	_
1012	COPRO-Seq	copro-seq	NN	_	_	_
1013	-RSB-	-rsb-	-RRB-	_	_	_
1014	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1015	E15	e15	CD	_	_	_
1016	_	_	NN	_	_	_
1017	7	7	CD	_	_	_
1018	_	_	NN	_	_	_
1019	m3	m3	NN	_	_	_
1020	-LSB-	-lsb-	-LRB-	_	_	_
1021	COPRO-Seq	copro-seq	NN	_	_	_
1022	-RSB-	-rsb-	-RRB-	_	_	_
1023	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1024	E15	e15	CD	_	_	_
1025	_	_	NN	_	_	_
1026	7	7	CD	_	_	_
1027	_	_	NN	_	_	_
1028	m4	m4	NN	_	_	_
1029	-LSB-	-lsb-	-LRB-	_	_	_
1030	COPRO-Seq	copro-seq	NN	_	_	_
1031	-RSB-	-rsb-	-RRB-	_	_	_
1032	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1033	E15	e15	CD	_	_	_
1034	_	_	NN	_	_	_
1035	7	7	CD	_	_	_
1036	_	_	NN	_	_	_
1037	m5	m5	NN	_	_	_
1038	-LSB-	-lsb-	-LRB-	_	_	_
1039	COPRO-Seq	copro-seq	NN	_	_	_
1040	-RSB-	-rsb-	-RRB-	_	_	_
1041	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1042	E15	e15	CD	_	_	_
1043	_	_	NN	_	_	_
1044	7	7	CD	_	_	_
1045	_	_	NN	_	_	_
1046	m7	m7	NN	_	_	_
1047	-LSB-	-lsb-	-LRB-	_	_	_
1048	COPRO-Seq	copro-seq	NN	_	_	_
1049	-RSB-	-rsb-	-RRB-	_	_	_
1050	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1051	E15	e15	CD	_	_	_
1052	_	_	NN	_	_	_
1053	7	7	CD	_	_	_
1054	_	_	NN	_	_	_
1055	m8	m8	NN	_	_	_
1056	-LSB-	-lsb-	-LRB-	_	_	_
1057	COPRO-Seq	copro-seq	NN	_	_	_
1058	-RSB-	-rsb-	-RRB-	_	_	_
1059	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1060	E17	e17	NN	_	_	_
1061	_	_	NN	_	_	_
1062	1	1	CD	_	_	_
1063	_	_	SYM	_	_	_
1064	m1	m1	NN	_	_	_
1065	-LSB-	-lsb-	-LRB-	_	_	_
1066	COPRO-Seq	copro-seq	NN	_	_	_
1067	-RSB-	-rsb-	-RRB-	_	_	_
1068	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1069	E17	e17	NN	_	_	_
1070	_	_	NN	_	_	_
1071	1	1	CD	_	_	_
1072	_	_	CD	_	_	_
1073	m2	m2	NN	_	_	_
1074	-LSB-	-lsb-	-LRB-	_	_	_
1075	COPRO-Seq	copro-seq	NN	_	_	_
1076	-RSB-	-rsb-	-RRB-	_	_	_
1077	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1078	E17	e17	NN	_	_	_
1079	_	_	NN	_	_	_
1080	1	1	CD	_	_	_
1081	_	_	CD	_	_	_
1082	m3	m3	NN	_	_	_
1083	-LSB-	-lsb-	-LRB-	_	_	_
1084	COPRO-Seq	copro-seq	NN	_	_	_
1085	-RSB-	-rsb-	-RRB-	_	_	_
1086	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1087	E17	e17	NN	_	_	_
1088	_	_	NN	_	_	_
1089	1	1	CD	_	_	_
1090	_	_	CD	_	_	_
1091	m4	m4	NN	_	_	_
1092	-LSB-	-lsb-	-LRB-	_	_	_
1093	COPRO-Seq	copro-seq	NN	_	_	_
1094	-RSB-	-rsb-	-RRB-	_	_	_
1095	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1096	E17	e17	NN	_	_	_
1097	_	_	NN	_	_	_
1098	1	1	CD	_	_	_
1099	_	_	CD	_	_	_
1100	m5	m5	NN	_	_	_
1101	-LSB-	-lsb-	-LRB-	_	_	_
1102	COPRO-Seq	copro-seq	NN	_	_	_
1103	-RSB-	-rsb-	-RRB-	_	_	_
1104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1105	E17	e17	NN	_	_	_
1106	_	_	NN	_	_	_
1107	1	1	CD	_	_	_
1108	_	_	CD	_	_	_
1109	m6	m6	NN	_	_	_
1110	-LSB-	-lsb-	-LRB-	_	_	_
1111	COPRO-Seq	copro-seq	NN	_	_	_
1112	-RSB-	-rsb-	-RRB-	_	_	_
1113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1114	E17	e17	NN	_	_	_
1115	_	_	NN	_	_	_
1116	1	1	CD	_	_	_
1117	_	_	CD	_	_	_
1118	m7	m7	NN	_	_	_
1119	-LSB-	-lsb-	-LRB-	_	_	_
1120	COPRO-Seq	copro-seq	NN	_	_	_
1121	-RSB-	-rsb-	-RRB-	_	_	_
1122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1123	E17	e17	NN	_	_	_
1124	_	_	NN	_	_	_
1125	1	1	CD	_	_	_
1126	_	_	CD	_	_	_
1127	m8	m8	NN	_	_	_
1128	-LSB-	-lsb-	-LRB-	_	_	_
1129	COPRO-Seq	copro-seq	NN	_	_	_
1130	-RSB-	-rsb-	-RRB-	_	_	_
1131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1132	E17	e17	NN	_	_	_
1133	_	_	CD	_	_	_
1134	4	4	CD	_	_	_
1135	_	_	SYM	_	_	_
1136	m1	m1	NN	_	_	_
1137	-LSB-	-lsb-	-LRB-	_	_	_
1138	COPRO-Seq	copro-seq	NN	_	_	_
1139	-RSB-	-rsb-	-RRB-	_	_	_
1140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1141	E17	e17	NN	_	_	_
1142	_	_	CD	_	_	_
1143	4	4	CD	_	_	_
1144	_	_	NN	_	_	_
1145	m2	m2	NN	_	_	_
1146	-LSB-	-lsb-	-LRB-	_	_	_
1147	COPRO-Seq	copro-seq	NN	_	_	_
1148	-RSB-	-rsb-	-RRB-	_	_	_
1149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1150	E17	e17	NN	_	_	_
1151	_	_	CD	_	_	_
1152	4	4	CD	_	_	_
1153	_	_	NN	_	_	_
1154	m3	m3	NN	_	_	_
1155	-LSB-	-lsb-	-LRB-	_	_	_
1156	COPRO-Seq	copro-seq	NN	_	_	_
1157	-RSB-	-rsb-	-RRB-	_	_	_
1158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1159	E17	e17	NN	_	_	_
1160	_	_	CD	_	_	_
1161	4	4	CD	_	_	_
1162	_	_	NN	_	_	_
1163	m4	m4	NN	_	_	_
1164	-LSB-	-lsb-	-LRB-	_	_	_
1165	COPRO-Seq	copro-seq	NN	_	_	_
1166	-RSB-	-rsb-	-RRB-	_	_	_
1167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1168	E17	e17	NN	_	_	_
1169	_	_	CD	_	_	_
1170	4	4	CD	_	_	_
1171	_	_	NN	_	_	_
1172	m5	m5	NN	_	_	_
1173	-LSB-	-lsb-	-LRB-	_	_	_
1174	COPRO-Seq	copro-seq	NN	_	_	_
1175	-RSB-	-rsb-	-RRB-	_	_	_
1176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1177	E17	e17	NN	_	_	_
1178	_	_	CD	_	_	_
1179	4	4	CD	_	_	_
1180	_	_	NN	_	_	_
1181	m6	m6	NN	_	_	_
1182	-LSB-	-lsb-	-LRB-	_	_	_
1183	COPRO-Seq	copro-seq	NN	_	_	_
1184	-RSB-	-rsb-	-RRB-	_	_	_
1185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1186	E17	e17	NN	_	_	_
1187	_	_	CD	_	_	_
1188	4	4	CD	_	_	_
1189	_	_	NN	_	_	_
1190	m7	m7	NN	_	_	_
1191	-LSB-	-lsb-	-LRB-	_	_	_
1192	COPRO-Seq	copro-seq	NN	_	_	_
1193	-RSB-	-rsb-	-RRB-	_	_	_
1194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1195	E17	e17	NN	_	_	_
1196	_	_	CD	_	_	_
1197	4	4	CD	_	_	_
1198	_	_	NN	_	_	_
1199	m8	m8	NN	_	_	_
1200	-LSB-	-lsb-	-LRB-	_	_	_
1201	COPRO-Seq	copro-seq	NN	_	_	_
1202	-RSB-	-rsb-	-RRB-	_	_	_
1203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1204	E17	e17	NN	_	_	_
1205	_	_	CD	_	_	_
1206	6	6	CD	_	_	_
1207	_	_	NN	_	_	_
1208	m1	m1	NN	_	_	_
1209	-LSB-	-lsb-	-LRB-	_	_	_
1210	COPRO-Seq	copro-seq	NN	_	_	_
1211	-RSB-	-rsb-	-RRB-	_	_	_
1212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1213	E17	e17	NN	_	_	_
1214	_	_	CD	_	_	_
1215	6	6	CD	_	_	_
1216	_	_	NN	_	_	_
1217	m3	m3	NN	_	_	_
1218	-LSB-	-lsb-	-LRB-	_	_	_
1219	COPRO-Seq	copro-seq	NN	_	_	_
1220	-RSB-	-rsb-	-RRB-	_	_	_
1221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1222	E17	e17	NN	_	_	_
1223	_	_	CD	_	_	_
1224	6	6	CD	_	_	_
1225	_	_	NN	_	_	_
1226	m4	m4	NN	_	_	_
1227	-LSB-	-lsb-	-LRB-	_	_	_
1228	COPRO-Seq	copro-seq	NN	_	_	_
1229	-RSB-	-rsb-	-RRB-	_	_	_
1230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1231	E17	e17	NN	_	_	_
1232	_	_	CD	_	_	_
1233	6	6	CD	_	_	_
1234	_	_	NN	_	_	_
1235	m5	m5	NN	_	_	_
1236	-LSB-	-lsb-	-LRB-	_	_	_
1237	COPRO-Seq	copro-seq	NN	_	_	_
1238	-RSB-	-rsb-	-RRB-	_	_	_
1239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1240	E17	e17	NN	_	_	_
1241	_	_	CD	_	_	_
1242	6	6	CD	_	_	_
1243	_	_	NN	_	_	_
1244	m6	m6	NN	_	_	_
1245	-LSB-	-lsb-	-LRB-	_	_	_
1246	COPRO-Seq	copro-seq	NN	_	_	_
1247	-RSB-	-rsb-	-RRB-	_	_	_
1248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1249	E17	e17	NN	_	_	_
1250	_	_	CD	_	_	_
1251	6	6	CD	_	_	_
1252	_	_	NN	_	_	_
1253	m7	m7	NN	_	_	_
1254	-LSB-	-lsb-	-LRB-	_	_	_
1255	COPRO-Seq	copro-seq	NN	_	_	_
1256	-RSB-	-rsb-	-RRB-	_	_	_
1257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1258	E17	e17	NN	_	_	_
1259	_	_	CD	_	_	_
1260	6	6	CD	_	_	_
1261	_	_	NN	_	_	_
1262	m8	m8	NN	_	_	_
1263	-LSB-	-lsb-	-LRB-	_	_	_
1264	COPRO-Seq	copro-seq	NN	_	_	_
1265	-RSB-	-rsb-	-RRB-	_	_	_
1266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1267	E17	e17	NN	_	_	_
1268	_	_	NN	_	_	_
1269	7	7	CD	_	_	_
1270	_	_	SYM	_	_	_
1271	m1	m1	NN	_	_	_
1272	-LSB-	-lsb-	-LRB-	_	_	_
1273	COPRO-Seq	copro-seq	NN	_	_	_
1274	-RSB-	-rsb-	-RRB-	_	_	_
1275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1276	E17	e17	NN	_	_	_
1277	_	_	NN	_	_	_
1278	7	7	CD	_	_	_
1279	_	_	NN	_	_	_
1280	m2	m2	NN	_	_	_
1281	-LSB-	-lsb-	-LRB-	_	_	_
1282	COPRO-Seq	copro-seq	NN	_	_	_
1283	-RSB-	-rsb-	-RRB-	_	_	_
1284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1285	E17	e17	NN	_	_	_
1286	_	_	NN	_	_	_
1287	7	7	CD	_	_	_
1288	_	_	NN	_	_	_
1289	m3	m3	NN	_	_	_
1290	-LSB-	-lsb-	-LRB-	_	_	_
1291	COPRO-Seq	copro-seq	NN	_	_	_
1292	-RSB-	-rsb-	-RRB-	_	_	_
1293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1294	E17	e17	NN	_	_	_
1295	_	_	NN	_	_	_
1296	7	7	CD	_	_	_
1297	_	_	NN	_	_	_
1298	m4	m4	NN	_	_	_
1299	-LSB-	-lsb-	-LRB-	_	_	_
1300	COPRO-Seq	copro-seq	NN	_	_	_
1301	-RSB-	-rsb-	-RRB-	_	_	_
1302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1303	E17	e17	NN	_	_	_
1304	_	_	NN	_	_	_
1305	7	7	CD	_	_	_
1306	_	_	NN	_	_	_
1307	m6	m6	NN	_	_	_
1308	-LSB-	-lsb-	-LRB-	_	_	_
1309	COPRO-Seq	copro-seq	NN	_	_	_
1310	-RSB-	-rsb-	-RRB-	_	_	_
1311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1312	E17	e17	NN	_	_	_
1313	_	_	NN	_	_	_
1314	7	7	CD	_	_	_
1315	_	_	NN	_	_	_
1316	m7	m7	NN	_	_	_
1317	-LSB-	-lsb-	-LRB-	_	_	_
1318	COPRO-Seq	copro-seq	NN	_	_	_
1319	-RSB-	-rsb-	-RRB-	_	_	_
1320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1321	E1	e1	NN	_	_	_
1322	_	_	NN	_	_	_
1323	7	7	CD	_	_	_
1324	_	_	SYM	_	_	_
1325	m1	m1	NN	_	_	_
1326	-LSB-	-lsb-	-LRB-	_	_	_
1327	COPRO-Seq	copro-seq	NN	_	_	_
1328	-RSB-	-rsb-	-RRB-	_	_	_
1329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1330	E1	e1	NN	_	_	_
1331	_	_	NN	_	_	_
1332	7	7	CD	_	_	_
1333	_	_	NN	_	_	_
1334	m2	m2	NN	_	_	_
1335	-LSB-	-lsb-	-LRB-	_	_	_
1336	COPRO-Seq	copro-seq	NN	_	_	_
1337	-RSB-	-rsb-	-RRB-	_	_	_
1338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1339	E1	e1	NN	_	_	_
1340	_	_	NN	_	_	_
1341	7	7	CD	_	_	_
1342	_	_	NN	_	_	_
1343	m3	m3	NN	_	_	_
1344	-LSB-	-lsb-	-LRB-	_	_	_
1345	COPRO-Seq	copro-seq	NN	_	_	_
1346	-RSB-	-rsb-	-RRB-	_	_	_
1347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1348	E1	e1	NN	_	_	_
1349	_	_	NN	_	_	_
1350	7	7	CD	_	_	_
1351	_	_	NN	_	_	_
1352	m4	m4	NN	_	_	_
1353	-LSB-	-lsb-	-LRB-	_	_	_
1354	COPRO-Seq	copro-seq	NN	_	_	_
1355	-RSB-	-rsb-	-RRB-	_	_	_
1356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1357	E1	e1	NN	_	_	_
1358	_	_	NN	_	_	_
1359	7	7	CD	_	_	_
1360	_	_	NN	_	_	_
1361	m5	m5	NN	_	_	_
1362	-LSB-	-lsb-	-LRB-	_	_	_
1363	COPRO-Seq	copro-seq	NN	_	_	_
1364	-RSB-	-rsb-	-RRB-	_	_	_
1365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1366	E1	e1	NN	_	_	_
1367	_	_	NN	_	_	_
1368	7	7	CD	_	_	_
1369	_	_	NN	_	_	_
1370	m6	m6	NN	_	_	_
1371	-LSB-	-lsb-	-LRB-	_	_	_
1372	COPRO-Seq	copro-seq	NN	_	_	_
1373	-RSB-	-rsb-	-RRB-	_	_	_
1374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1375	E1	e1	NN	_	_	_
1376	_	_	NN	_	_	_
1377	7	7	CD	_	_	_
1378	_	_	NN	_	_	_
1379	m7	m7	NN	_	_	_
1380	-LSB-	-lsb-	-LRB-	_	_	_
1381	COPRO-Seq	copro-seq	NN	_	_	_
1382	-RSB-	-rsb-	-RRB-	_	_	_
1383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1384	E1	e1	NN	_	_	_
1385	_	_	NN	_	_	_
1386	7	7	CD	_	_	_
1387	_	_	NN	_	_	_
1388	m8	m8	NN	_	_	_
1389	-LSB-	-lsb-	-LRB-	_	_	_
1390	COPRO-Seq	copro-seq	NN	_	_	_
1391	-RSB-	-rsb-	-RRB-	_	_	_
1392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1393	E19	e19	NN	_	_	_
1394	_	_	NN	_	_	_
1395	1	1	CD	_	_	_
1396	_	_	SYM	_	_	_
1397	m1	m1	NN	_	_	_
1398	-LSB-	-lsb-	-LRB-	_	_	_
1399	COPRO-Seq	copro-seq	NN	_	_	_
1400	-RSB-	-rsb-	-RRB-	_	_	_
1401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1402	E19	e19	NN	_	_	_
1403	_	_	NN	_	_	_
1404	1	1	CD	_	_	_
1405	_	_	CD	_	_	_
1406	m2	m2	NN	_	_	_
1407	-LSB-	-lsb-	-LRB-	_	_	_
1408	COPRO-Seq	copro-seq	NN	_	_	_
1409	-RSB-	-rsb-	-RRB-	_	_	_
1410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1411	E19	e19	NN	_	_	_
1412	_	_	NN	_	_	_
1413	1	1	CD	_	_	_
1414	_	_	CD	_	_	_
1415	m3	m3	NN	_	_	_
1416	-LSB-	-lsb-	-LRB-	_	_	_
1417	COPRO-Seq	copro-seq	NN	_	_	_
1418	-RSB-	-rsb-	-RRB-	_	_	_
1419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1420	E19	e19	NN	_	_	_
1421	_	_	NN	_	_	_
1422	1	1	CD	_	_	_
1423	_	_	CD	_	_	_
1424	m4	m4	NN	_	_	_
1425	-LSB-	-lsb-	-LRB-	_	_	_
1426	COPRO-Seq	copro-seq	NN	_	_	_
1427	-RSB-	-rsb-	-RRB-	_	_	_
1428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1429	E19	e19	NN	_	_	_
1430	_	_	NN	_	_	_
1431	1	1	CD	_	_	_
1432	_	_	CD	_	_	_
1433	m5	m5	NN	_	_	_
1434	-LSB-	-lsb-	-LRB-	_	_	_
1435	COPRO-Seq	copro-seq	NN	_	_	_
1436	-RSB-	-rsb-	-RRB-	_	_	_
1437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1438	E19	e19	NN	_	_	_
1439	_	_	NN	_	_	_
1440	1	1	CD	_	_	_
1441	_	_	CD	_	_	_
1442	m6	m6	NN	_	_	_
1443	-LSB-	-lsb-	-LRB-	_	_	_
1444	COPRO-Seq	copro-seq	NN	_	_	_
1445	-RSB-	-rsb-	-RRB-	_	_	_
1446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1447	E19	e19	NN	_	_	_
1448	_	_	NN	_	_	_
1449	1	1	CD	_	_	_
1450	_	_	CD	_	_	_
1451	m7	m7	NN	_	_	_
1452	-LSB-	-lsb-	-LRB-	_	_	_
1453	COPRO-Seq	copro-seq	NN	_	_	_
1454	-RSB-	-rsb-	-RRB-	_	_	_
1455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1456	E19	e19	NN	_	_	_
1457	_	_	NN	_	_	_
1458	1	1	CD	_	_	_
1459	_	_	CD	_	_	_
1460	m8	m8	NN	_	_	_
1461	-LSB-	-lsb-	-LRB-	_	_	_
1462	COPRO-Seq	copro-seq	NN	_	_	_
1463	-RSB-	-rsb-	-RRB-	_	_	_
1464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1465	E19	e19	NN	_	_	_
1466	_	_	CD	_	_	_
1467	4	4	CD	_	_	_
1468	_	_	NN	_	_	_
1469	m2	m2	NN	_	_	_
1470	-LSB-	-lsb-	-LRB-	_	_	_
1471	COPRO-Seq	copro-seq	NN	_	_	_
1472	-RSB-	-rsb-	-RRB-	_	_	_
1473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1474	E19	e19	NN	_	_	_
1475	_	_	CD	_	_	_
1476	4	4	CD	_	_	_
1477	_	_	NN	_	_	_
1478	m3	m3	NN	_	_	_
1479	-LSB-	-lsb-	-LRB-	_	_	_
1480	COPRO-Seq	copro-seq	NN	_	_	_
1481	-RSB-	-rsb-	-RRB-	_	_	_
1482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1483	E19	e19	NN	_	_	_
1484	_	_	CD	_	_	_
1485	4	4	CD	_	_	_
1486	_	_	NN	_	_	_
1487	m4	m4	NN	_	_	_
1488	-LSB-	-lsb-	-LRB-	_	_	_
1489	COPRO-Seq	copro-seq	NN	_	_	_
1490	-RSB-	-rsb-	-RRB-	_	_	_
1491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1492	E19	e19	NN	_	_	_
1493	_	_	CD	_	_	_
1494	4	4	CD	_	_	_
1495	_	_	NN	_	_	_
1496	m5	m5	NN	_	_	_
1497	-LSB-	-lsb-	-LRB-	_	_	_
1498	COPRO-Seq	copro-seq	NN	_	_	_
1499	-RSB-	-rsb-	-RRB-	_	_	_
1500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1501	E19	e19	NN	_	_	_
1502	_	_	CD	_	_	_
1503	4	4	CD	_	_	_
1504	_	_	NN	_	_	_
1505	m6	m6	NN	_	_	_
1506	-LSB-	-lsb-	-LRB-	_	_	_
1507	COPRO-Seq	copro-seq	NN	_	_	_
1508	-RSB-	-rsb-	-RRB-	_	_	_
1509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1510	E19	e19	NN	_	_	_
1511	_	_	CD	_	_	_
1512	4	4	CD	_	_	_
1513	_	_	NN	_	_	_
1514	m7	m7	NN	_	_	_
1515	-LSB-	-lsb-	-LRB-	_	_	_
1516	COPRO-Seq	copro-seq	NN	_	_	_
1517	-RSB-	-rsb-	-RRB-	_	_	_
1518	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1519	E19	e19	NN	_	_	_
1520	_	_	CD	_	_	_
1521	4	4	CD	_	_	_
1522	_	_	NN	_	_	_
1523	m8	m8	NN	_	_	_
1524	-LSB-	-lsb-	-LRB-	_	_	_
1525	COPRO-Seq	copro-seq	NN	_	_	_
1526	-RSB-	-rsb-	-RRB-	_	_	_
1527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1528	E19	e19	NN	_	_	_
1529	_	_	CD	_	_	_
1530	6	6	CD	_	_	_
1531	_	_	NN	_	_	_
1532	m1	m1	NN	_	_	_
1533	-LSB-	-lsb-	-LRB-	_	_	_
1534	COPRO-Seq	copro-seq	NN	_	_	_
1535	-RSB-	-rsb-	-RRB-	_	_	_
1536	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1537	E19	e19	NN	_	_	_
1538	_	_	CD	_	_	_
1539	6	6	CD	_	_	_
1540	_	_	NN	_	_	_
1541	m2	m2	NN	_	_	_
1542	-LSB-	-lsb-	-LRB-	_	_	_
1543	COPRO-Seq	copro-seq	NN	_	_	_
1544	-RSB-	-rsb-	-RRB-	_	_	_
1545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1546	E19	e19	NN	_	_	_
1547	_	_	CD	_	_	_
1548	6	6	CD	_	_	_
1549	_	_	NN	_	_	_
1550	m3	m3	NN	_	_	_
1551	-LSB-	-lsb-	-LRB-	_	_	_
1552	COPRO-Seq	copro-seq	NN	_	_	_
1553	-RSB-	-rsb-	-RRB-	_	_	_
1554	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1555	E19	e19	NN	_	_	_
1556	_	_	CD	_	_	_
1557	6	6	CD	_	_	_
1558	_	_	NN	_	_	_
1559	m4	m4	NN	_	_	_
1560	-LSB-	-lsb-	-LRB-	_	_	_
1561	COPRO-Seq	copro-seq	NN	_	_	_
1562	-RSB-	-rsb-	-RRB-	_	_	_
1563	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1564	E19	e19	NN	_	_	_
1565	_	_	CD	_	_	_
1566	6	6	CD	_	_	_
1567	_	_	NN	_	_	_
1568	m5	m5	NN	_	_	_
1569	-LSB-	-lsb-	-LRB-	_	_	_
1570	COPRO-Seq	copro-seq	NN	_	_	_
1571	-RSB-	-rsb-	-RRB-	_	_	_
1572	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1573	E19	e19	NN	_	_	_
1574	_	_	CD	_	_	_
1575	6	6	CD	_	_	_
1576	_	_	NN	_	_	_
1577	m6	m6	NN	_	_	_
1578	-LSB-	-lsb-	-LRB-	_	_	_
1579	COPRO-Seq	copro-seq	NN	_	_	_
1580	-RSB-	-rsb-	-RRB-	_	_	_
1581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1582	E19	e19	NN	_	_	_
1583	_	_	CD	_	_	_
1584	6	6	CD	_	_	_
1585	_	_	NN	_	_	_
1586	m7	m7	NN	_	_	_
1587	-LSB-	-lsb-	-LRB-	_	_	_
1588	COPRO-Seq	copro-seq	NN	_	_	_
1589	-RSB-	-rsb-	-RRB-	_	_	_
1590	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1591	E19	e19	NN	_	_	_
1592	_	_	CD	_	_	_
1593	6	6	CD	_	_	_
1594	_	_	NN	_	_	_
1595	m8	m8	NN	_	_	_
1596	-LSB-	-lsb-	-LRB-	_	_	_
1597	COPRO-Seq	copro-seq	NN	_	_	_
1598	-RSB-	-rsb-	-RRB-	_	_	_
1599	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1600	E19	e19	NN	_	_	_
1601	_	_	NN	_	_	_
1602	7	7	CD	_	_	_
1603	_	_	SYM	_	_	_
1604	m1	m1	NN	_	_	_
1605	-LSB-	-lsb-	-LRB-	_	_	_
1606	COPRO-Seq	copro-seq	NN	_	_	_
1607	-RSB-	-rsb-	-RRB-	_	_	_
1608	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1609	E19	e19	NN	_	_	_
1610	_	_	NN	_	_	_
1611	7	7	CD	_	_	_
1612	_	_	NN	_	_	_
1613	m2	m2	NN	_	_	_
1614	-LSB-	-lsb-	-LRB-	_	_	_
1615	COPRO-Seq	copro-seq	NN	_	_	_
1616	-RSB-	-rsb-	-RRB-	_	_	_
1617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1618	E19	e19	NN	_	_	_
1619	_	_	NN	_	_	_
1620	7	7	CD	_	_	_
1621	_	_	NN	_	_	_
1622	m3	m3	NN	_	_	_
1623	-LSB-	-lsb-	-LRB-	_	_	_
1624	COPRO-Seq	copro-seq	NN	_	_	_
1625	-RSB-	-rsb-	-RRB-	_	_	_
1626	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1627	E19	e19	NN	_	_	_
1628	_	_	NN	_	_	_
1629	7	7	CD	_	_	_
1630	_	_	NN	_	_	_
1631	m4	m4	NN	_	_	_
1632	-LSB-	-lsb-	-LRB-	_	_	_
1633	COPRO-Seq	copro-seq	NN	_	_	_
1634	-RSB-	-rsb-	-RRB-	_	_	_
1635	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1636	E19	e19	NN	_	_	_
1637	_	_	NN	_	_	_
1638	7	7	CD	_	_	_
1639	_	_	NN	_	_	_
1640	m5	m5	NN	_	_	_
1641	-LSB-	-lsb-	-LRB-	_	_	_
1642	COPRO-Seq	copro-seq	NN	_	_	_
1643	-RSB-	-rsb-	-RRB-	_	_	_
1644	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1645	E19	e19	NN	_	_	_
1646	_	_	NN	_	_	_
1647	7	7	CD	_	_	_
1648	_	_	NN	_	_	_
1649	m6	m6	NN	_	_	_
1650	-LSB-	-lsb-	-LRB-	_	_	_
1651	COPRO-Seq	copro-seq	NN	_	_	_
1652	-RSB-	-rsb-	-RRB-	_	_	_
1653	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1654	E19	e19	NN	_	_	_
1655	_	_	NN	_	_	_
1656	7	7	CD	_	_	_
1657	_	_	NN	_	_	_
1658	m7	m7	NN	_	_	_
1659	-LSB-	-lsb-	-LRB-	_	_	_
1660	COPRO-Seq	copro-seq	NN	_	_	_
1661	-RSB-	-rsb-	-RRB-	_	_	_
1662	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1663	E19	e19	NN	_	_	_
1664	_	_	NN	_	_	_
1665	7	7	CD	_	_	_
1666	_	_	NN	_	_	_
1667	m8	m8	NN	_	_	_
1668	-LSB-	-lsb-	-LRB-	_	_	_
1669	COPRO-Seq	copro-seq	NN	_	_	_
1670	-RSB-	-rsb-	-RRB-	_	_	_
1671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1672	E2	e2	NN	_	_	_
1673	_	_	CD	_	_	_
1674	14	14	CD	_	_	_
1675	_	_	SYM	_	_	_
1676	m1	m1	NN	_	_	_
1677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1678	E2	e2	NN	_	_	_
1679	_	_	CD	_	_	_
1680	14	14	CD	_	_	_
1681	_	_	SYM	_	_	_
1682	m1	m1	NN	_	_	_
1683	-LSB-	-lsb-	-LRB-	_	_	_
1684	COPRO-Seq	copro-seq	NN	_	_	_
1685	-RSB-	-rsb-	-RRB-	_	_	_
1686	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1687	E2	e2	NN	_	_	_
1688	_	_	CD	_	_	_
1689	14	14	CD	_	_	_
1690	_	_	NN	_	_	_
1691	m2	m2	NN	_	_	_
1692	-LSB-	-lsb-	-LRB-	_	_	_
1693	COPRO-Seq	copro-seq	NN	_	_	_
1694	-RSB-	-rsb-	-RRB-	_	_	_
1695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1696	E2	e2	NN	_	_	_
1697	_	_	CD	_	_	_
1698	14	14	CD	_	_	_
1699	_	_	NN	_	_	_
1700	m3	m3	NN	_	_	_
1701	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1702	E2	e2	NN	_	_	_
1703	_	_	CD	_	_	_
1704	14	14	CD	_	_	_
1705	_	_	NN	_	_	_
1706	m3	m3	NN	_	_	_
1707	-LSB-	-lsb-	-LRB-	_	_	_
1708	COPRO-Seq	copro-seq	NN	_	_	_
1709	-RSB-	-rsb-	-RRB-	_	_	_
1710	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1711	E2	e2	NN	_	_	_
1712	_	_	CD	_	_	_
1713	14	14	CD	_	_	_
1714	_	_	NN	_	_	_
1715	m4	m4	NN	_	_	_
1716	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1717	E2	e2	NN	_	_	_
1718	_	_	CD	_	_	_
1719	14	14	CD	_	_	_
1720	_	_	NN	_	_	_
1721	m4	m4	NN	_	_	_
1722	-LSB-	-lsb-	-LRB-	_	_	_
1723	COPRO-Seq	copro-seq	NN	_	_	_
1724	-RSB-	-rsb-	-RRB-	_	_	_
1725	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1726	E2	e2	NN	_	_	_
1727	_	_	CD	_	_	_
1728	14	14	CD	_	_	_
1729	_	_	NN	_	_	_
1730	m5	m5	NN	_	_	_
1731	-LSB-	-lsb-	-LRB-	_	_	_
1732	COPRO-Seq	copro-seq	NN	_	_	_
1733	-RSB-	-rsb-	-RRB-	_	_	_
1734	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1735	E2	e2	NN	_	_	_
1736	_	_	CD	_	_	_
1737	14	14	CD	_	_	_
1738	_	_	NN	_	_	_
1739	m6	m6	NN	_	_	_
1740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1741	E2	e2	NN	_	_	_
1742	_	_	CD	_	_	_
1743	14	14	CD	_	_	_
1744	_	_	NN	_	_	_
1745	m6	m6	NN	_	_	_
1746	-LSB-	-lsb-	-LRB-	_	_	_
1747	COPRO-Seq	copro-seq	NN	_	_	_
1748	-RSB-	-rsb-	-RRB-	_	_	_
1749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1750	E2	e2	NN	_	_	_
1751	_	_	CD	_	_	_
1752	14	14	CD	_	_	_
1753	_	_	NN	_	_	_
1754	m7	m7	NN	_	_	_
1755	-LSB-	-lsb-	-LRB-	_	_	_
1756	COPRO-Seq	copro-seq	NN	_	_	_
1757	-RSB-	-rsb-	-RRB-	_	_	_
1758	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1759	E2	e2	NN	_	_	_
1760	_	_	CD	_	_	_
1761	14	14	CD	_	_	_
1762	_	_	NN	_	_	_
1763	m8	m8	NN	_	_	_
1764	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1765	E2	e2	NN	_	_	_
1766	_	_	NN	_	_	_
1767	1	1	CD	_	_	_
1768	_	_	SYM	_	_	_
1769	m1	m1	NN	_	_	_
1770	-LSB-	-lsb-	-LRB-	_	_	_
1771	COPRO-Seq	copro-seq	NN	_	_	_
1772	-RSB-	-rsb-	-RRB-	_	_	_
1773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1774	E2	e2	NN	_	_	_
1775	_	_	NN	_	_	_
1776	1	1	CD	_	_	_
1777	_	_	CD	_	_	_
1778	m2	m2	NN	_	_	_
1779	-LSB-	-lsb-	-LRB-	_	_	_
1780	COPRO-Seq	copro-seq	NN	_	_	_
1781	-RSB-	-rsb-	-RRB-	_	_	_
1782	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1783	E2	e2	NN	_	_	_
1784	_	_	NN	_	_	_
1785	1	1	CD	_	_	_
1786	_	_	CD	_	_	_
1787	m3	m3	NN	_	_	_
1788	-LSB-	-lsb-	-LRB-	_	_	_
1789	COPRO-Seq	copro-seq	NN	_	_	_
1790	-RSB-	-rsb-	-RRB-	_	_	_
1791	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1792	E2	e2	NN	_	_	_
1793	_	_	NN	_	_	_
1794	1	1	CD	_	_	_
1795	_	_	CD	_	_	_
1796	m4	m4	NN	_	_	_
1797	-LSB-	-lsb-	-LRB-	_	_	_
1798	COPRO-Seq	copro-seq	NN	_	_	_
1799	-RSB-	-rsb-	-RRB-	_	_	_
1800	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1801	E2	e2	NN	_	_	_
1802	_	_	NN	_	_	_
1803	1	1	CD	_	_	_
1804	_	_	CD	_	_	_
1805	m5	m5	NN	_	_	_
1806	-LSB-	-lsb-	-LRB-	_	_	_
1807	COPRO-Seq	copro-seq	NN	_	_	_
1808	-RSB-	-rsb-	-RRB-	_	_	_
1809	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1810	E2	e2	NN	_	_	_
1811	_	_	NN	_	_	_
1812	1	1	CD	_	_	_
1813	_	_	CD	_	_	_
1814	m6	m6	NN	_	_	_
1815	-LSB-	-lsb-	-LRB-	_	_	_
1816	COPRO-Seq	copro-seq	NN	_	_	_
1817	-RSB-	-rsb-	-RRB-	_	_	_
1818	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1819	E2	e2	NN	_	_	_
1820	_	_	NN	_	_	_
1821	1	1	CD	_	_	_
1822	_	_	CD	_	_	_
1823	m7	m7	NN	_	_	_
1824	-LSB-	-lsb-	-LRB-	_	_	_
1825	COPRO-Seq	copro-seq	NN	_	_	_
1826	-RSB-	-rsb-	-RRB-	_	_	_
1827	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1828	E2	e2	NN	_	_	_
1829	_	_	NN	_	_	_
1830	1	1	CD	_	_	_
1831	_	_	CD	_	_	_
1832	m8	m8	NN	_	_	_
1833	-LSB-	-lsb-	-LRB-	_	_	_
1834	COPRO-Seq	copro-seq	NN	_	_	_
1835	-RSB-	-rsb-	-RRB-	_	_	_
1836	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1837	E22	e22	NN	_	_	_
1838	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1839	E2	e2	NN	_	_	_
1840	_	_	NN	_	_	_
1841	2	2	CD	_	_	_
1842	_	_	SYM	_	_	_
1843	m1	m1	NN	_	_	_
1844	-LSB-	-lsb-	-LRB-	_	_	_
1845	COPRO-Seq	copro-seq	NN	_	_	_
1846	-RSB-	-rsb-	-RRB-	_	_	_
1847	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1848	E2	e2	NN	_	_	_
1849	_	_	NN	_	_	_
1850	2	2	CD	_	_	_
1851	_	_	CD	_	_	_
1852	m2	m2	NN	_	_	_
1853	-LSB-	-lsb-	-LRB-	_	_	_
1854	COPRO-Seq	copro-seq	NN	_	_	_
1855	-RSB-	-rsb-	-RRB-	_	_	_
1856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1857	E2	e2	NN	_	_	_
1858	_	_	NN	_	_	_
1859	2	2	CD	_	_	_
1860	_	_	CD	_	_	_
1861	m3	m3	NN	_	_	_
1862	-LSB-	-lsb-	-LRB-	_	_	_
1863	COPRO-Seq	copro-seq	NN	_	_	_
1864	-RSB-	-rsb-	-RRB-	_	_	_
1865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1866	E2	e2	NN	_	_	_
1867	_	_	NN	_	_	_
1868	2	2	CD	_	_	_
1869	_	_	CD	_	_	_
1870	m4	m4	NN	_	_	_
1871	-LSB-	-lsb-	-LRB-	_	_	_
1872	COPRO-Seq	copro-seq	NN	_	_	_
1873	-RSB-	-rsb-	-RRB-	_	_	_
1874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1875	E2	e2	NN	_	_	_
1876	_	_	NN	_	_	_
1877	2	2	CD	_	_	_
1878	_	_	CD	_	_	_
1879	m5	m5	NN	_	_	_
1880	-LSB-	-lsb-	-LRB-	_	_	_
1881	COPRO-Seq	copro-seq	NN	_	_	_
1882	-RSB-	-rsb-	-RRB-	_	_	_
1883	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1884	E2	e2	NN	_	_	_
1885	_	_	NN	_	_	_
1886	2	2	CD	_	_	_
1887	_	_	CD	_	_	_
1888	m6	m6	NN	_	_	_
1889	-LSB-	-lsb-	-LRB-	_	_	_
1890	COPRO-Seq	copro-seq	NN	_	_	_
1891	-RSB-	-rsb-	-RRB-	_	_	_
1892	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1893	E2	e2	NN	_	_	_
1894	_	_	NN	_	_	_
1895	2	2	CD	_	_	_
1896	_	_	CD	_	_	_
1897	m7	m7	NN	_	_	_
1898	-LSB-	-lsb-	-LRB-	_	_	_
1899	COPRO-Seq	copro-seq	NN	_	_	_
1900	-RSB-	-rsb-	-RRB-	_	_	_
1901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1902	E2	e2	NN	_	_	_
1903	_	_	NN	_	_	_
1904	2	2	CD	_	_	_
1905	_	_	CD	_	_	_
1906	m8	m8	NN	_	_	_
1907	-LSB-	-lsb-	-LRB-	_	_	_
1908	COPRO-Seq	copro-seq	NN	_	_	_
1909	-RSB-	-rsb-	-RRB-	_	_	_
1910	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1911	E2	e2	NN	_	_	_
1912	_	_	CD	_	_	_
1913	4	4	CD	_	_	_
1914	_	_	SYM	_	_	_
1915	m1	m1	NN	_	_	_
1916	-LSB-	-lsb-	-LRB-	_	_	_
1917	COPRO-Seq	copro-seq	NN	_	_	_
1918	-RSB-	-rsb-	-RRB-	_	_	_
1919	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1920	E2	e2	NN	_	_	_
1921	_	_	CD	_	_	_
1922	4	4	CD	_	_	_
1923	_	_	NN	_	_	_
1924	m2	m2	NN	_	_	_
1925	-LSB-	-lsb-	-LRB-	_	_	_
1926	COPRO-Seq	copro-seq	NN	_	_	_
1927	-RSB-	-rsb-	-RRB-	_	_	_
1928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1929	E2	e2	NN	_	_	_
1930	_	_	CD	_	_	_
1931	4	4	CD	_	_	_
1932	_	_	NN	_	_	_
1933	m3	m3	NN	_	_	_
1934	-LSB-	-lsb-	-LRB-	_	_	_
1935	COPRO-Seq	copro-seq	NN	_	_	_
1936	-RSB-	-rsb-	-RRB-	_	_	_
1937	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1938	E2	e2	NN	_	_	_
1939	_	_	CD	_	_	_
1940	4	4	CD	_	_	_
1941	_	_	NN	_	_	_
1942	m4	m4	NN	_	_	_
1943	-LSB-	-lsb-	-LRB-	_	_	_
1944	COPRO-Seq	copro-seq	NN	_	_	_
1945	-RSB-	-rsb-	-RRB-	_	_	_
1946	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1947	E2	e2	NN	_	_	_
1948	_	_	CD	_	_	_
1949	4	4	CD	_	_	_
1950	_	_	NN	_	_	_
1951	m5	m5	NN	_	_	_
1952	-LSB-	-lsb-	-LRB-	_	_	_
1953	COPRO-Seq	copro-seq	NN	_	_	_
1954	-RSB-	-rsb-	-RRB-	_	_	_
1955	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1956	E2	e2	NN	_	_	_
1957	_	_	CD	_	_	_
1958	4	4	CD	_	_	_
1959	_	_	NN	_	_	_
1960	m6	m6	NN	_	_	_
1961	-LSB-	-lsb-	-LRB-	_	_	_
1962	COPRO-Seq	copro-seq	NN	_	_	_
1963	-RSB-	-rsb-	-RRB-	_	_	_
1964	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1965	E2	e2	NN	_	_	_
1966	_	_	CD	_	_	_
1967	4	4	CD	_	_	_
1968	_	_	NN	_	_	_
1969	m7	m7	NN	_	_	_
1970	-LSB-	-lsb-	-LRB-	_	_	_
1971	COPRO-Seq	copro-seq	NN	_	_	_
1972	-RSB-	-rsb-	-RRB-	_	_	_
1973	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1974	E2	e2	NN	_	_	_
1975	_	_	CD	_	_	_
1976	4	4	CD	_	_	_
1977	_	_	NN	_	_	_
1978	m8	m8	NN	_	_	_
1979	-LSB-	-lsb-	-LRB-	_	_	_
1980	COPRO-Seq	copro-seq	NN	_	_	_
1981	-RSB-	-rsb-	-RRB-	_	_	_
1982	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1983	E2	e2	NN	_	_	_
1984	_	_	NN	_	_	_
1985	7	7	CD	_	_	_
1986	_	_	SYM	_	_	_
1987	m1	m1	NN	_	_	_
1988	-LSB-	-lsb-	-LRB-	_	_	_
1989	COPRO-Seq	copro-seq	NN	_	_	_
1990	-RSB-	-rsb-	-RRB-	_	_	_
1991	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1992	E2	e2	NN	_	_	_
1993	_	_	NN	_	_	_
1994	7	7	CD	_	_	_
1995	_	_	NN	_	_	_
1996	m2	m2	NN	_	_	_
1997	-LSB-	-lsb-	-LRB-	_	_	_
1998	COPRO-Seq	copro-seq	NN	_	_	_
1999	-RSB-	-rsb-	-RRB-	_	_	_
2000	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2001	E2	e2	NN	_	_	_
2002	_	_	NN	_	_	_
2003	7	7	CD	_	_	_
2004	_	_	NN	_	_	_
2005	m3	m3	NN	_	_	_
2006	-LSB-	-lsb-	-LRB-	_	_	_
2007	COPRO-Seq	copro-seq	NN	_	_	_
2008	-RSB-	-rsb-	-RRB-	_	_	_
2009	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2010	E2	e2	NN	_	_	_
2011	_	_	NN	_	_	_
2012	7	7	CD	_	_	_
2013	_	_	NN	_	_	_
2014	m4	m4	NN	_	_	_
2015	-LSB-	-lsb-	-LRB-	_	_	_
2016	COPRO-Seq	copro-seq	NN	_	_	_
2017	-RSB-	-rsb-	-RRB-	_	_	_
2018	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2019	E2	e2	NN	_	_	_
2020	_	_	NN	_	_	_
2021	7	7	CD	_	_	_
2022	_	_	NN	_	_	_
2023	m5	m5	NN	_	_	_
2024	-LSB-	-lsb-	-LRB-	_	_	_
2025	COPRO-Seq	copro-seq	NN	_	_	_
2026	-RSB-	-rsb-	-RRB-	_	_	_
2027	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2028	E2	e2	NN	_	_	_
2029	_	_	NN	_	_	_
2030	7	7	CD	_	_	_
2031	_	_	NN	_	_	_
2032	m6	m6	NN	_	_	_
2033	-LSB-	-lsb-	-LRB-	_	_	_
2034	COPRO-Seq	copro-seq	NN	_	_	_
2035	-RSB-	-rsb-	-RRB-	_	_	_
2036	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2037	E2	e2	NN	_	_	_
2038	_	_	NN	_	_	_
2039	7	7	CD	_	_	_
2040	_	_	NN	_	_	_
2041	m7	m7	NN	_	_	_
2042	-LSB-	-lsb-	-LRB-	_	_	_
2043	COPRO-Seq	copro-seq	NN	_	_	_
2044	-RSB-	-rsb-	-RRB-	_	_	_
2045	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2046	E2	e2	NN	_	_	_
2047	_	_	NN	_	_	_
2048	7	7	CD	_	_	_
2049	_	_	NN	_	_	_
2050	m8	m8	NN	_	_	_
2051	-LSB-	-lsb-	-LRB-	_	_	_
2052	COPRO-Seq	copro-seq	NN	_	_	_
2053	-RSB-	-rsb-	-RRB-	_	_	_
2054	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2055	E3	e3	NN	_	_	_
2056	_	_	CD	_	_	_
2057	14	14	CD	_	_	_
2058	_	_	SYM	_	_	_
2059	m1	m1	NN	_	_	_
2060	-LSB-	-lsb-	-LRB-	_	_	_
2061	COPRO-Seq	copro-seq	NN	_	_	_
2062	-RSB-	-rsb-	-RRB-	_	_	_
2063	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2064	E3	e3	NN	_	_	_
2065	_	_	CD	_	_	_
2066	14	14	CD	_	_	_
2067	_	_	NN	_	_	_
2068	m2	m2	NN	_	_	_
2069	-LSB-	-lsb-	-LRB-	_	_	_
2070	COPRO-Seq	copro-seq	NN	_	_	_
2071	-RSB-	-rsb-	-RRB-	_	_	_
2072	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2073	E3	e3	NN	_	_	_
2074	_	_	CD	_	_	_
2075	14	14	CD	_	_	_
2076	_	_	NN	_	_	_
2077	m3	m3	NN	_	_	_
2078	-LSB-	-lsb-	-LRB-	_	_	_
2079	COPRO-Seq	copro-seq	NN	_	_	_
2080	-RSB-	-rsb-	-RRB-	_	_	_
2081	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2082	E3	e3	NN	_	_	_
2083	_	_	CD	_	_	_
2084	14	14	CD	_	_	_
2085	_	_	NN	_	_	_
2086	m4	m4	NN	_	_	_
2087	-LSB-	-lsb-	-LRB-	_	_	_
2088	COPRO-Seq	copro-seq	NN	_	_	_
2089	-RSB-	-rsb-	-RRB-	_	_	_
2090	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2091	E3	e3	NN	_	_	_
2092	_	_	CD	_	_	_
2093	14	14	CD	_	_	_
2094	_	_	NN	_	_	_
2095	m6	m6	NN	_	_	_
2096	-LSB-	-lsb-	-LRB-	_	_	_
2097	COPRO-Seq	copro-seq	NN	_	_	_
2098	-RSB-	-rsb-	-RRB-	_	_	_
2099	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2100	E3	e3	NN	_	_	_
2101	_	_	CD	_	_	_
2102	14	14	CD	_	_	_
2103	_	_	NN	_	_	_
2104	m7	m7	NN	_	_	_
2105	-LSB-	-lsb-	-LRB-	_	_	_
2106	COPRO-Seq	copro-seq	NN	_	_	_
2107	-RSB-	-rsb-	-RRB-	_	_	_
2108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2109	E3	e3	NN	_	_	_
2110	_	_	CD	_	_	_
2111	14	14	CD	_	_	_
2112	_	_	NN	_	_	_
2113	m8	m8	NN	_	_	_
2114	-LSB-	-lsb-	-LRB-	_	_	_
2115	COPRO-Seq	copro-seq	NN	_	_	_
2116	-RSB-	-rsb-	-RRB-	_	_	_
2117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2118	E3	e3	NN	_	_	_
2119	_	_	NN	_	_	_
2120	1	1	CD	_	_	_
2121	_	_	SYM	_	_	_
2122	m1	m1	NN	_	_	_
2123	-LSB-	-lsb-	-LRB-	_	_	_
2124	COPRO-Seq	copro-seq	NN	_	_	_
2125	-RSB-	-rsb-	-RRB-	_	_	_
2126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2127	E3	e3	NN	_	_	_
2128	_	_	NN	_	_	_
2129	1	1	CD	_	_	_
2130	_	_	CD	_	_	_
2131	m2	m2	NN	_	_	_
2132	-LSB-	-lsb-	-LRB-	_	_	_
2133	COPRO-Seq	copro-seq	NN	_	_	_
2134	-RSB-	-rsb-	-RRB-	_	_	_
2135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2136	E3	e3	NN	_	_	_
2137	_	_	NN	_	_	_
2138	1	1	CD	_	_	_
2139	_	_	CD	_	_	_
2140	m3	m3	NN	_	_	_
2141	-LSB-	-lsb-	-LRB-	_	_	_
2142	COPRO-Seq	copro-seq	NN	_	_	_
2143	-RSB-	-rsb-	-RRB-	_	_	_
2144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2145	E3	e3	NN	_	_	_
2146	_	_	NN	_	_	_
2147	1	1	CD	_	_	_
2148	_	_	CD	_	_	_
2149	m4	m4	NN	_	_	_
2150	-LSB-	-lsb-	-LRB-	_	_	_
2151	COPRO-Seq	copro-seq	NN	_	_	_
2152	-RSB-	-rsb-	-RRB-	_	_	_
2153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2154	E3	e3	NN	_	_	_
2155	_	_	NN	_	_	_
2156	1	1	CD	_	_	_
2157	_	_	CD	_	_	_
2158	m5	m5	NN	_	_	_
2159	-LSB-	-lsb-	-LRB-	_	_	_
2160	COPRO-Seq	copro-seq	NN	_	_	_
2161	-RSB-	-rsb-	-RRB-	_	_	_
2162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2163	E3	e3	NN	_	_	_
2164	_	_	NN	_	_	_
2165	1	1	CD	_	_	_
2166	_	_	CD	_	_	_
2167	m6	m6	NN	_	_	_
2168	-LSB-	-lsb-	-LRB-	_	_	_
2169	COPRO-Seq	copro-seq	NN	_	_	_
2170	-RSB-	-rsb-	-RRB-	_	_	_
2171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2172	E3	e3	NN	_	_	_
2173	_	_	NN	_	_	_
2174	1	1	CD	_	_	_
2175	_	_	CD	_	_	_
2176	m7	m7	NN	_	_	_
2177	-LSB-	-lsb-	-LRB-	_	_	_
2178	COPRO-Seq	copro-seq	NN	_	_	_
2179	-RSB-	-rsb-	-RRB-	_	_	_
2180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2181	E3	e3	NN	_	_	_
2182	_	_	NN	_	_	_
2183	1	1	CD	_	_	_
2184	_	_	CD	_	_	_
2185	m8	m8	NN	_	_	_
2186	-LSB-	-lsb-	-LRB-	_	_	_
2187	COPRO-Seq	copro-seq	NN	_	_	_
2188	-RSB-	-rsb-	-RRB-	_	_	_
2189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2190	E3	e3	NN	_	_	_
2191	_	_	NN	_	_	_
2192	2	2	CD	_	_	_
2193	_	_	SYM	_	_	_
2194	m1	m1	NN	_	_	_
2195	-LSB-	-lsb-	-LRB-	_	_	_
2196	COPRO-Seq	copro-seq	NN	_	_	_
2197	-RSB-	-rsb-	-RRB-	_	_	_
2198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2199	E3	e3	NN	_	_	_
2200	_	_	NN	_	_	_
2201	2	2	CD	_	_	_
2202	_	_	CD	_	_	_
2203	m2	m2	NN	_	_	_
2204	-LSB-	-lsb-	-LRB-	_	_	_
2205	COPRO-Seq	copro-seq	NN	_	_	_
2206	-RSB-	-rsb-	-RRB-	_	_	_
2207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2208	E3	e3	NN	_	_	_
2209	_	_	NN	_	_	_
2210	2	2	CD	_	_	_
2211	_	_	CD	_	_	_
2212	m3	m3	NN	_	_	_
2213	-LSB-	-lsb-	-LRB-	_	_	_
2214	COPRO-Seq	copro-seq	NN	_	_	_
2215	-RSB-	-rsb-	-RRB-	_	_	_
2216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2217	E3	e3	NN	_	_	_
2218	_	_	NN	_	_	_
2219	2	2	CD	_	_	_
2220	_	_	CD	_	_	_
2221	m4	m4	NN	_	_	_
2222	-LSB-	-lsb-	-LRB-	_	_	_
2223	COPRO-Seq	copro-seq	NN	_	_	_
2224	-RSB-	-rsb-	-RRB-	_	_	_
2225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2226	E3	e3	NN	_	_	_
2227	_	_	NN	_	_	_
2228	2	2	CD	_	_	_
2229	_	_	CD	_	_	_
2230	m5	m5	NN	_	_	_
2231	-LSB-	-lsb-	-LRB-	_	_	_
2232	COPRO-Seq	copro-seq	NN	_	_	_
2233	-RSB-	-rsb-	-RRB-	_	_	_
2234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2235	E3	e3	NN	_	_	_
2236	_	_	NN	_	_	_
2237	2	2	CD	_	_	_
2238	_	_	CD	_	_	_
2239	m6	m6	NN	_	_	_
2240	-LSB-	-lsb-	-LRB-	_	_	_
2241	COPRO-Seq	copro-seq	NN	_	_	_
2242	-RSB-	-rsb-	-RRB-	_	_	_
2243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2244	E3	e3	NN	_	_	_
2245	_	_	NN	_	_	_
2246	2	2	CD	_	_	_
2247	_	_	CD	_	_	_
2248	m7	m7	NN	_	_	_
2249	-LSB-	-lsb-	-LRB-	_	_	_
2250	COPRO-Seq	copro-seq	NN	_	_	_
2251	-RSB-	-rsb-	-RRB-	_	_	_
2252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2253	E3	e3	NN	_	_	_
2254	_	_	NN	_	_	_
2255	2	2	CD	_	_	_
2256	_	_	CD	_	_	_
2257	m8	m8	NN	_	_	_
2258	-LSB-	-lsb-	-LRB-	_	_	_
2259	COPRO-Seq	copro-seq	NN	_	_	_
2260	-RSB-	-rsb-	-RRB-	_	_	_
2261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2262	E3	e3	NN	_	_	_
2263	_	_	CD	_	_	_
2264	4	4	CD	_	_	_
2265	_	_	NN	_	_	_
2266	m2	m2	NN	_	_	_
2267	-LSB-	-lsb-	-LRB-	_	_	_
2268	COPRO-Seq	copro-seq	NN	_	_	_
2269	-RSB-	-rsb-	-RRB-	_	_	_
2270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2271	E3	e3	NN	_	_	_
2272	_	_	CD	_	_	_
2273	4	4	CD	_	_	_
2274	_	_	NN	_	_	_
2275	m3	m3	NN	_	_	_
2276	-LSB-	-lsb-	-LRB-	_	_	_
2277	COPRO-Seq	copro-seq	NN	_	_	_
2278	-RSB-	-rsb-	-RRB-	_	_	_
2279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2280	E3	e3	NN	_	_	_
2281	_	_	CD	_	_	_
2282	4	4	CD	_	_	_
2283	_	_	NN	_	_	_
2284	m4	m4	NN	_	_	_
2285	-LSB-	-lsb-	-LRB-	_	_	_
2286	COPRO-Seq	copro-seq	NN	_	_	_
2287	-RSB-	-rsb-	-RRB-	_	_	_
2288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2289	E3	e3	NN	_	_	_
2290	_	_	CD	_	_	_
2291	4	4	CD	_	_	_
2292	_	_	NN	_	_	_
2293	m5	m5	NN	_	_	_
2294	-LSB-	-lsb-	-LRB-	_	_	_
2295	COPRO-Seq	copro-seq	NN	_	_	_
2296	-RSB-	-rsb-	-RRB-	_	_	_
2297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2298	E3	e3	NN	_	_	_
2299	_	_	CD	_	_	_
2300	4	4	CD	_	_	_
2301	_	_	NN	_	_	_
2302	m6	m6	NN	_	_	_
2303	-LSB-	-lsb-	-LRB-	_	_	_
2304	COPRO-Seq	copro-seq	NN	_	_	_
2305	-RSB-	-rsb-	-RRB-	_	_	_
2306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2307	E3	e3	NN	_	_	_
2308	_	_	CD	_	_	_
2309	4	4	CD	_	_	_
2310	_	_	NN	_	_	_
2311	m7	m7	NN	_	_	_
2312	-LSB-	-lsb-	-LRB-	_	_	_
2313	COPRO-Seq	copro-seq	NN	_	_	_
2314	-RSB-	-rsb-	-RRB-	_	_	_
2315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2316	E3	e3	NN	_	_	_
2317	_	_	CD	_	_	_
2318	4	4	CD	_	_	_
2319	_	_	NN	_	_	_
2320	m8	m8	NN	_	_	_
2321	-LSB-	-lsb-	-LRB-	_	_	_
2322	COPRO-Seq	copro-seq	NN	_	_	_
2323	-RSB-	-rsb-	-RRB-	_	_	_
2324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2325	E3	e3	NN	_	_	_
2326	_	_	NN	_	_	_
2327	7	7	CD	_	_	_
2328	_	_	SYM	_	_	_
2329	m1	m1	NN	_	_	_
2330	-LSB-	-lsb-	-LRB-	_	_	_
2331	COPRO-Seq	copro-seq	NN	_	_	_
2332	-RSB-	-rsb-	-RRB-	_	_	_
2333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2334	E3	e3	NN	_	_	_
2335	_	_	NN	_	_	_
2336	7	7	CD	_	_	_
2337	_	_	NN	_	_	_
2338	m2	m2	NN	_	_	_
2339	-LSB-	-lsb-	-LRB-	_	_	_
2340	COPRO-Seq	copro-seq	NN	_	_	_
2341	-RSB-	-rsb-	-RRB-	_	_	_
2342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2343	E3	e3	NN	_	_	_
2344	_	_	NN	_	_	_
2345	7	7	CD	_	_	_
2346	_	_	NN	_	_	_
2347	m3	m3	NN	_	_	_
2348	-LSB-	-lsb-	-LRB-	_	_	_
2349	COPRO-Seq	copro-seq	NN	_	_	_
2350	-RSB-	-rsb-	-RRB-	_	_	_
2351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2352	E3	e3	NN	_	_	_
2353	_	_	NN	_	_	_
2354	7	7	CD	_	_	_
2355	_	_	NN	_	_	_
2356	m4	m4	NN	_	_	_
2357	-LSB-	-lsb-	-LRB-	_	_	_
2358	COPRO-Seq	copro-seq	NN	_	_	_
2359	-RSB-	-rsb-	-RRB-	_	_	_
2360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2361	E3	e3	NN	_	_	_
2362	_	_	NN	_	_	_
2363	7	7	CD	_	_	_
2364	_	_	NN	_	_	_
2365	m5	m5	NN	_	_	_
2366	-LSB-	-lsb-	-LRB-	_	_	_
2367	COPRO-Seq	copro-seq	NN	_	_	_
2368	-RSB-	-rsb-	-RRB-	_	_	_
2369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2370	E3	e3	NN	_	_	_
2371	_	_	NN	_	_	_
2372	7	7	CD	_	_	_
2373	_	_	NN	_	_	_
2374	m6	m6	NN	_	_	_
2375	-LSB-	-lsb-	-LRB-	_	_	_
2376	COPRO-Seq	copro-seq	NN	_	_	_
2377	-RSB-	-rsb-	-RRB-	_	_	_
2378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2379	E3	e3	NN	_	_	_
2380	_	_	NN	_	_	_
2381	7	7	CD	_	_	_
2382	_	_	NN	_	_	_
2383	m7	m7	NN	_	_	_
2384	-LSB-	-lsb-	-LRB-	_	_	_
2385	COPRO-Seq	copro-seq	NN	_	_	_
2386	-RSB-	-rsb-	-RRB-	_	_	_
2387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2388	E3	e3	NN	_	_	_
2389	_	_	NN	_	_	_
2390	7	7	CD	_	_	_
2391	_	_	NN	_	_	_
2392	m8	m8	NN	_	_	_
2393	-LSB-	-lsb-	-LRB-	_	_	_
2394	COPRO-Seq	copro-seq	NN	_	_	_
2395	-RSB-	-rsb-	-RRB-	_	_	_
2396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2397	E4	e4	NN	_	_	_
2398	-	-	:	_	_	_
2399	O2	o2	CD	_	_	_
2400	1	1	CD	_	_	_
2401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2402	E4	e4	NN	_	_	_
2403	+	+	CC	_	_	_
2404	O2	o2	CD	_	_	_
2405	1	1	CD	_	_	_
2406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2407	E4	e4	NN	_	_	_
2408	-	-	:	_	_	_
2409	O2	o2	CD	_	_	_
2410	2	2	CD	_	_	_
2411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2412	E4	e4	NN	_	_	_
2413	+	+	CC	_	_	_
2414	O2	o2	CD	_	_	_
2415	2	2	CD	_	_	_
2416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2417	E4	e4	NN	_	_	_
2418	-	-	:	_	_	_
2419	O2	o2	CD	_	_	_
2420	3	3	CD	_	_	_
2421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2422	E4	e4	NN	_	_	_
2423	+	+	CC	_	_	_
2424	O2	o2	CD	_	_	_
2425	3	3	CD	_	_	_
2426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2427	E9	e9	NN	_	_	_
2428	_	_	NN	_	_	_
2429	1	1	CD	_	_	_
2430	_	_	SYM	_	_	_
2431	m1	m1	NN	_	_	_
2432	-LSB-	-lsb-	-LRB-	_	_	_
2433	COPRO-Seq	copro-seq	NN	_	_	_
2434	-RSB-	-rsb-	-RRB-	_	_	_
2435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2436	E9	e9	NN	_	_	_
2437	_	_	NN	_	_	_
2438	1	1	CD	_	_	_
2439	_	_	CD	_	_	_
2440	m2	m2	NN	_	_	_
2441	-LSB-	-lsb-	-LRB-	_	_	_
2442	COPRO-Seq	copro-seq	NN	_	_	_
2443	-RSB-	-rsb-	-RRB-	_	_	_
2444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2445	E9	e9	NN	_	_	_
2446	_	_	NN	_	_	_
2447	1	1	CD	_	_	_
2448	_	_	CD	_	_	_
2449	m3	m3	NN	_	_	_
2450	-LSB-	-lsb-	-LRB-	_	_	_
2451	COPRO-Seq	copro-seq	NN	_	_	_
2452	-RSB-	-rsb-	-RRB-	_	_	_
2453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2454	E9	e9	NN	_	_	_
2455	_	_	NN	_	_	_
2456	1	1	CD	_	_	_
2457	_	_	CD	_	_	_
2458	m4	m4	NN	_	_	_
2459	-LSB-	-lsb-	-LRB-	_	_	_
2460	COPRO-Seq	copro-seq	NN	_	_	_
2461	-RSB-	-rsb-	-RRB-	_	_	_
2462	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2463	E9	e9	NN	_	_	_
2464	_	_	NN	_	_	_
2465	1	1	CD	_	_	_
2466	_	_	CD	_	_	_
2467	m5	m5	NN	_	_	_
2468	-LSB-	-lsb-	-LRB-	_	_	_
2469	COPRO-Seq	copro-seq	NN	_	_	_
2470	-RSB-	-rsb-	-RRB-	_	_	_
2471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2472	E9	e9	NN	_	_	_
2473	_	_	NN	_	_	_
2474	1	1	CD	_	_	_
2475	_	_	CD	_	_	_
2476	m6	m6	NN	_	_	_
2477	-LSB-	-lsb-	-LRB-	_	_	_
2478	COPRO-Seq	copro-seq	NN	_	_	_
2479	-RSB-	-rsb-	-RRB-	_	_	_
2480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2481	E9	e9	NN	_	_	_
2482	_	_	NN	_	_	_
2483	1	1	CD	_	_	_
2484	_	_	CD	_	_	_
2485	m7	m7	NN	_	_	_
2486	-LSB-	-lsb-	-LRB-	_	_	_
2487	COPRO-Seq	copro-seq	NN	_	_	_
2488	-RSB-	-rsb-	-RRB-	_	_	_
2489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2490	E9	e9	NN	_	_	_
2491	_	_	NN	_	_	_
2492	1	1	CD	_	_	_
2493	_	_	CD	_	_	_
2494	m8	m8	NN	_	_	_
2495	-LSB-	-lsb-	-LRB-	_	_	_
2496	COPRO-Seq	copro-seq	NN	_	_	_
2497	-RSB-	-rsb-	-RRB-	_	_	_
2498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2499	E9	e9	NN	_	_	_
2500	_	_	CD	_	_	_
2501	4	4	CD	_	_	_
2502	_	_	SYM	_	_	_
2503	m1	m1	NN	_	_	_
2504	-LSB-	-lsb-	-LRB-	_	_	_
2505	COPRO-Seq	copro-seq	NN	_	_	_
2506	-RSB-	-rsb-	-RRB-	_	_	_
2507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2508	E9	e9	NN	_	_	_
2509	_	_	CD	_	_	_
2510	4	4	CD	_	_	_
2511	_	_	NN	_	_	_
2512	m2	m2	NN	_	_	_
2513	-LSB-	-lsb-	-LRB-	_	_	_
2514	COPRO-Seq	copro-seq	NN	_	_	_
2515	-RSB-	-rsb-	-RRB-	_	_	_
2516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2517	E9	e9	NN	_	_	_
2518	_	_	CD	_	_	_
2519	4	4	CD	_	_	_
2520	_	_	NN	_	_	_
2521	m3	m3	NN	_	_	_
2522	-LSB-	-lsb-	-LRB-	_	_	_
2523	COPRO-Seq	copro-seq	NN	_	_	_
2524	-RSB-	-rsb-	-RRB-	_	_	_
2525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2526	E9	e9	NN	_	_	_
2527	_	_	CD	_	_	_
2528	4	4	CD	_	_	_
2529	_	_	NN	_	_	_
2530	m4	m4	NN	_	_	_
2531	-LSB-	-lsb-	-LRB-	_	_	_
2532	COPRO-Seq	copro-seq	NN	_	_	_
2533	-RSB-	-rsb-	-RRB-	_	_	_
2534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2535	E9	e9	NN	_	_	_
2536	_	_	CD	_	_	_
2537	4	4	CD	_	_	_
2538	_	_	NN	_	_	_
2539	m5	m5	NN	_	_	_
2540	-LSB-	-lsb-	-LRB-	_	_	_
2541	COPRO-Seq	copro-seq	NN	_	_	_
2542	-RSB-	-rsb-	-RRB-	_	_	_
2543	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2544	E9	e9	NN	_	_	_
2545	_	_	CD	_	_	_
2546	4	4	CD	_	_	_
2547	_	_	NN	_	_	_
2548	m6	m6	NN	_	_	_
2549	-LSB-	-lsb-	-LRB-	_	_	_
2550	COPRO-Seq	copro-seq	NN	_	_	_
2551	-RSB-	-rsb-	-RRB-	_	_	_
2552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2553	E9	e9	NN	_	_	_
2554	_	_	CD	_	_	_
2555	4	4	CD	_	_	_
2556	_	_	NN	_	_	_
2557	m7	m7	NN	_	_	_
2558	-LSB-	-lsb-	-LRB-	_	_	_
2559	COPRO-Seq	copro-seq	NN	_	_	_
2560	-RSB-	-rsb-	-RRB-	_	_	_
2561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2562	E9	e9	NN	_	_	_
2563	_	_	CD	_	_	_
2564	4	4	CD	_	_	_
2565	_	_	NN	_	_	_
2566	m8	m8	NN	_	_	_
2567	-LSB-	-lsb-	-LRB-	_	_	_
2568	COPRO-Seq	copro-seq	NN	_	_	_
2569	-RSB-	-rsb-	-RRB-	_	_	_
2570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2571	E9	e9	NN	_	_	_
2572	_	_	CD	_	_	_
2573	6	6	CD	_	_	_
2574	_	_	NN	_	_	_
2575	m2	m2	NN	_	_	_
2576	-LSB-	-lsb-	-LRB-	_	_	_
2577	COPRO-Seq	copro-seq	NN	_	_	_
2578	-RSB-	-rsb-	-RRB-	_	_	_
2579	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2580	E9	e9	NN	_	_	_
2581	_	_	CD	_	_	_
2582	6	6	CD	_	_	_
2583	_	_	NN	_	_	_
2584	m3	m3	NN	_	_	_
2585	-LSB-	-lsb-	-LRB-	_	_	_
2586	COPRO-Seq	copro-seq	NN	_	_	_
2587	-RSB-	-rsb-	-RRB-	_	_	_
2588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2589	E9	e9	NN	_	_	_
2590	_	_	CD	_	_	_
2591	6	6	CD	_	_	_
2592	_	_	NN	_	_	_
2593	m4	m4	NN	_	_	_
2594	-LSB-	-lsb-	-LRB-	_	_	_
2595	COPRO-Seq	copro-seq	NN	_	_	_
2596	-RSB-	-rsb-	-RRB-	_	_	_
2597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2598	E9	e9	NN	_	_	_
2599	_	_	CD	_	_	_
2600	6	6	CD	_	_	_
2601	_	_	NN	_	_	_
2602	m5	m5	NN	_	_	_
2603	-LSB-	-lsb-	-LRB-	_	_	_
2604	COPRO-Seq	copro-seq	NN	_	_	_
2605	-RSB-	-rsb-	-RRB-	_	_	_
2606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2607	E9	e9	NN	_	_	_
2608	_	_	CD	_	_	_
2609	6	6	CD	_	_	_
2610	_	_	NN	_	_	_
2611	m7	m7	NN	_	_	_
2612	-LSB-	-lsb-	-LRB-	_	_	_
2613	COPRO-Seq	copro-seq	NN	_	_	_
2614	-RSB-	-rsb-	-RRB-	_	_	_
2615	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2616	E9	e9	NN	_	_	_
2617	_	_	NN	_	_	_
2618	7	7	CD	_	_	_
2619	_	_	NN	_	_	_
2620	m2	m2	NN	_	_	_
2621	-LSB-	-lsb-	-LRB-	_	_	_
2622	COPRO-Seq	copro-seq	NN	_	_	_
2623	-RSB-	-rsb-	-RRB-	_	_	_
2624	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2625	E9	e9	NN	_	_	_
2626	_	_	NN	_	_	_
2627	7	7	CD	_	_	_
2628	_	_	NN	_	_	_
2629	m3	m3	NN	_	_	_
2630	-LSB-	-lsb-	-LRB-	_	_	_
2631	COPRO-Seq	copro-seq	NN	_	_	_
2632	-RSB-	-rsb-	-RRB-	_	_	_
2633	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2634	E9	e9	NN	_	_	_
2635	_	_	NN	_	_	_
2636	7	7	CD	_	_	_
2637	_	_	NN	_	_	_
2638	m4	m4	NN	_	_	_
2639	-LSB-	-lsb-	-LRB-	_	_	_
2640	COPRO-Seq	copro-seq	NN	_	_	_
2641	-RSB-	-rsb-	-RRB-	_	_	_
2642	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2643	E9	e9	NN	_	_	_
2644	_	_	NN	_	_	_
2645	7	7	CD	_	_	_
2646	_	_	NN	_	_	_
2647	m5	m5	NN	_	_	_
2648	-LSB-	-lsb-	-LRB-	_	_	_
2649	COPRO-Seq	copro-seq	NN	_	_	_
2650	-RSB-	-rsb-	-RRB-	_	_	_
2651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2652	E9	e9	NN	_	_	_
2653	_	_	NN	_	_	_
2654	7	7	CD	_	_	_
2655	_	_	NN	_	_	_
2656	m6	m6	NN	_	_	_
2657	-LSB-	-lsb-	-LRB-	_	_	_
2658	COPRO-Seq	copro-seq	NN	_	_	_
2659	-RSB-	-rsb-	-RRB-	_	_	_
2660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2661	E9	e9	NN	_	_	_
2662	_	_	NN	_	_	_
2663	7	7	CD	_	_	_
2664	_	_	NN	_	_	_
2665	m7	m7	NN	_	_	_
2666	-LSB-	-lsb-	-LRB-	_	_	_
2667	COPRO-Seq	copro-seq	NN	_	_	_
2668	-RSB-	-rsb-	-RRB-	_	_	_
2669	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2670	E9	e9	NN	_	_	_
2671	_	_	NN	_	_	_
2672	7	7	CD	_	_	_
2673	_	_	NN	_	_	_
2674	m8	m8	NN	_	_	_
2675	-LSB-	-lsb-	-LRB-	_	_	_
2676	COPRO-Seq	copro-seq	NN	_	_	_
2677	-RSB-	-rsb-	-RRB-	_	_	_
2678	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2679	Each	each	DT	_	_	_
2680	bacteria	bacterium	NNS	_	_	_
2681	pellet	pellet	NN	_	_	_
2682	from	from	IN	_	_	_
2683	a	a	DT	_	_	_
2684	25	25	CD	_	_	_
2685	ml	ml	NN	_	_	_
2686	culture	culture	NN	_	_	_
2687	-LRB-	-lrb-	-LRB-	_	_	_
2688	OD600	od600	NN	_	_	_
2689	~	~	NN	_	_	_
2690	0.3	0.3	CD	_	_	_
2691	-RRB-	-rrb-	-RRB-	_	_	_
2692	was	be	VBD	_	_	_
2693	homogeneously	homogeneously	RB	_	_	_
2694	resuspended	resuspend	VBN	_	_	_
2695	in	in	IN	_	_	_
2696	200	200	CD	_	_	_
2697	µl	µl	NN	_	_	_
2698	of	of	IN	_	_	_
2699	Buffer	Buffer	NNP	_	_	_
2700	A	A	NNP	_	_	_
2701	-LSB-	-lsb-	-LRB-	_	_	_
2702	10	10	CD	_	_	_
2703	mM	mm	NN	KWSUPP	_	_
2704	Tris	Tris	NNP	_	_	_
2705	pH	ph	NN	_	_	_
2706	8.0	8.0	CD	_	_	_
2707	;	;	:	_	_	_
2708	20	20	CD	_	_	_
2709	%	%	NN	_	_	_
2710	Sucrose	sucrose	NN	_	_	_
2711	;	;	:	_	_	_
2712	100	100	CD	_	_	_
2713	mM	mm	NN	KWSUPP	_	_
2714	NaCl	nacl	NN	_	_	_
2715	-RSB-	-rsb-	-RRB-	_	_	_
2716	supplemented	supplement	VBN	_	_	_
2717	with	with	IN	_	_	_
2718	200	200	CD	_	_	_
2719	U	U	NNP	_	_	_
2720	SUPERase	SUPERase	NNP	_	_	_
2721	•	•	SYM	_	_	_
2722	In	in	IN	_	_	_
2723	™	™	CD	_	_	_
2724	RNase	rnase	NN	_	_	_
2725	Inhibitor	inhibitor	NN	_	_	_
2726	,	,	,	_	_	_
2727	by	by	IN	_	_	_
2728	pipetting	pipetting	NN	_	_	_
2729	.	.	.	_	_	_

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/v	w/v	NN	_	_	_
22	sucrose	sucrose	NN	_	_	_
23	gradient	gradient	NN	_	_	_
24	-LSB-	-lsb-	-LRB-	_	_	_
25	10	10	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	Tris	Tris	NNP	_	_	_
28	pH	ph	NN	_	_	_
29	8.0	8.0	CD	_	_	_
30	;	;	:	_	_	_
31	1	1	CD	_	_	_
32	M	m	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	;	;	:	_	_	_
35	1	1	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	EDTA	edta	NN	_	_	_
38	;	;	:	_	_	_
39	1	1	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	DTT	dtt	NN	_	_	_
42	-RSB-	-rsb-	-RRB-	_	_	_
43	,	,	,	_	_	_
44	and	and	CC	_	_	_
45	centrifuged	centrifuge	VBD	_	_	_
46	at	at	IN	_	_	_
47	17,000	17,000	CD	_	_	_
48	RPM	rpm	NN	_	_	_
49	in	in	IN	_	_	_
50	a	a	DT	_	_	_
51	SW55Ti	sw55ti	NN	_	_	_
52	rotor	rotor	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	Beckman	Beckman	NNP	_	_	_
55	Coulter	Coulter	NNP	_	_	_
56	,	,	,	_	_	_
57	cat	cat	NN	_	_	_
58	.	.	.	_	_	_

1	342194	342194	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	for	for	IN	_	_	_
4	9	9	CD	_	_	_
5	minutes	minute	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	4	4	CD	_	_	_
8	°C	°c	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	nucleoid	nucleoid	JJ	_	_	_
6	fraction	fraction	NN	_	_	_
7	was	be	VBD	_	_	_
8	collected	collect	VBN	_	_	_
9	using	use	VBG	_	_	_
10	a	a	DT	_	_	_
11	syringe	syringe	NN	_	_	_
12	with	with	IN	_	_	_
13	a	a	DT	_	_	_
14	18G	18g	NN	_	_	_
15	blunt	blunt	JJ	_	_	_
16	fill	fill	NN	_	_	_
17	needle	needle	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	transferred	transfer	VBN	_	_	_
21	to	to	TO	_	_	_
22	a	a	DT	_	_	_
23	new	new	JJ	_	_	_
24	centrifuge	centrifuge	NN	_	_	_
25	tube	tube	NN	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	remaining	remain	VBG	_	_	_
3	gradient	gradient	NN	_	_	_
4	was	be	VBD	_	_	_
5	assumed	assume	VBN	_	_	_
6	to	to	TO	_	_	_
7	represent	represent	VB	_	_	_
8	the	the	DT	_	_	_
9	cytosolic	cytosolic	JJ	_	_	_
10	fraction	fraction	NN	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	nucleoid	nucleoid	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	resuspended	resuspend	VBN	_	_	_
6	in	in	IN	_	_	_
7	2.5	2.5	CD	_	_	_
8	ml	ml	NN	_	_	_
9	Wash	Wash	NNP	_	_	_
10	&	&	CC	_	_	_
11	Resuspension	Resuspension	NNP	_	_	_
12	buffer	buffer	NN	_	_	_
13	-LSB-	-lsb-	-LRB-	_	_	_
14	40	40	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	Tris	Tris	NNP	_	_	_
17	pH	ph	NN	_	_	_
18	7.5	7.5	CD	_	_	_
19	;	;	:	_	_	_
20	150	150	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	KCl	kcl	NN	_	_	_
23	;	;	:	_	_	_
24	10	10	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	MgCl2	mgcl2	NN	_	_	_
27	;	;	:	_	_	_
28	1	1	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	DTT	dtt	NN	_	_	_
31	;	;	:	_	_	_
32	0.01	0.01	CD	_	_	_
33	%	%	NN	_	_	_
34	Triton	Triton	NNP	_	_	_
35	X-100	x-100	NN	_	_	_
36	-RSB-	-rsb-	-RRB-	_	_	_
37	supplemented	supplement	VBN	_	_	_
38	with	with	IN	_	_	_
39	200	200	CD	_	_	_
40	U	U	NNP	_	_	_
41	SUPERase	SUPERase	NNP	_	_	_
42	•	•	SYM	_	_	_
43	In	in	IN	_	_	_
44	™	™	CD	_	_	_
45	RNase	rnase	NN	_	_	_
46	Inhibitor	inhibitor	NN	_	_	_
47	,	,	,	_	_	_
48	pulse	pulse	NN	_	_	_
49	vortexed	vortex	VBD	_	_	_
50	for	for	IN	_	_	_
51	5	5	CD	_	_	_
52	seconds	seconds	NNS	_	_	_
53	,	,	,	_	_	_
54	and	and	CC	_	_	_
55	then	then	RB	_	_	_
56	centrifuged	centrifuge	VBD	_	_	_
57	at	at	IN	_	_	_
58	28,000	28,000	CD	_	_	_
59	RPM	rpm	NN	_	_	_
60	in	in	IN	_	_	_
61	a	a	DT	_	_	_
62	SW55Ti	sw55ti	NN	_	_	_
63	rotor	rotor	NN	_	_	_
64	for	for	IN	_	_	_
65	30	30	CD	_	_	_
66	minutes	minute	NNS	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	0	0	CD	_	_	_
69	°C	°c	NN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	the	the	DT	_	_	_
4	supernatant	supernatant	NN	_	_	_
5	was	be	VBD	_	_	_
6	decanted	decant	VBN	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	the	the	DT	_	_	_
10	nucleoid	nucleoid	JJ	_	_	_
11	pellet	pellet	NN	_	_	_
12	was	be	VBD	_	_	_
13	washed	wash	VBN	_	_	_
14	twice	twice	RB	_	_	_
15	with	with	IN	_	_	_
16	2	2	CD	_	_	_
17	ml	ml	NN	_	_	_
18	of	of	IN	_	_	_
19	Wash	Wash	NNP	_	_	_
20	&	&	CC	_	_	_
21	Resuspension	Resuspension	NNP	_	_	_
22	buffer	buffer	NN	_	_	_
23	,	,	,	_	_	_
24	taking	take	VBG	_	_	_
25	care	care	NN	_	_	_
26	not	not	RB	_	_	_
27	to	to	TO	_	_	_
28	disturb	disturb	VB	_	_	_
29	it	it	PRP	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	nucleoid	nucleoid	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	resuspended	resuspend	VBN	_	_	_
6	in	in	IN	_	_	_
7	500	500	CD	_	_	_
8	µl	µl	NN	_	_	_
9	Wash	Wash	NNP	_	_	_
10	&	&	CC	_	_	_
11	Resuspension	Resuspension	NNP	_	_	_
12	buffer	buffer	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	solubilized	solubilize	VBN	_	_	_
16	by	by	IN	_	_	_
17	addition	addition	NN	_	_	_
18	of	of	IN	_	_	_
19	0.1	0.1	CD	_	_	_
20	gr	gr	NN	_	_	_
21	acid-washed	acid-washed	JJ	_	_	_
22	glass	glass	NN	_	_	_
23	beads	bead	NNS	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Sigma	Sigma	NNP	_	_	_
26	,	,	,	_	_	_
27	cat	cat	NN	_	_	_
28	.	.	.	_	_	_

1	G1145	g1145	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	,	,	,	_	_	_
4	and	and	CC	_	_	_
5	shaking	shake	VBG	_	_	_
6	for	for	IN	_	_	_
7	5	5	CD	_	_	_
8	minutes	minute	NNS	_	_	_
9	in	in	IN	_	_	_
10	a	a	DT	_	_	_
11	TissueLyser	TissueLyser	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	QIAGEN	QIAGEN	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	100	100	CD	_	_	_
4	µl	µl	NN	_	_	_
5	of	of	IN	_	_	_
6	purified	purify	VBN	_	_	_
7	nucleoids	nucleoid	NNS	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	or	or	CC	_	_	_
10	cytosolic	cytosolic	JJ	_	_	_
11	fraction	fraction	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	1	1	CD	_	_	_
15	ml	ml	NN	_	_	_
16	of	of	IN	_	_	_
17	TRIzol	trizol	NN	_	_	_
18	®	®	CD	_	_	_
19	Reagent	Reagent	NNP	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Invitrogen	Invitrogen	NNP	_	_	_
22	,	,	,	_	_	_
23	cat	cat	NN	_	_	_
24	.	.	.	_	_	_

1	15596-018	15596-018	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	extracted	extract	VBN	_	_	_
10	following	follow	VBG	_	_	_
11	manufacturer	manufacturer	NN	_	_	_
12	's	's	POS	_	_	_
13	instructions	instruction	NNS	_	_	_
14	.	.	.	_	_	_

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

1	In	in	IN	_	_	_
2	all	all	DT	_	_	_
3	experiments	experiment	NNS	_	_	_
4	,	,	,	_	_	_
5	RNA	rna	NN	_	_	_
6	from	from	IN	_	_	_
7	cytosolic	cytosolic	JJ	_	_	_
8	fraction	fraction	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	corresponding	correspond	VBG	_	_	_
11	to	to	TO	_	_	_
12	mature	mature	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	species	species	NNS	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	had	have	VBD	_	_	_
17	RIN	RIN	NNP	_	_	_
18	>	>	JJR	_	_	_
19	9.5	9.5	CD	_	_	_
20	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	yield	yield	NN	_	_	_
4	from	from	IN	_	_	_
5	nucleoid	nucleoid	JJ	_	_	_
6	fraction	fraction	NN	_	_	_
7	was	be	VBD	_	_	_
8	~	~	CD	_	_	_
9	6	6	CD	_	_	_
10	%	%	NN	_	_	_
11	of	of	IN	_	_	_
12	the	the	DT	_	_	_
13	total	total	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	content	content	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Each	each	DT	_	_	_
3	dataset	dataset	NN	_	_	_
4	was	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	to	to	TO	_	_	_
7	reads	read	VBZ	_	_	_
8	per	per	IN	_	_	_
9	million	million	CD	_	_	_
10	per	per	IN	_	_	_
11	position	position	NN	_	_	_
12	prior	prior	RB	_	_	_
13	to	to	TO	_	_	_
14	further	further	JJ	_	_	_
15	analysis	analysis	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Each	each	DT	_	_	_
3	strain	strain	NN	_	_	_
4	was	be	VBD	_	_	_
5	inoculated	inoculate	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	frozen	frozen	JJ	_	_	_
9	stock	stock	NN	_	_	_
10	into	into	IN	_	_	_
11	10	10	CD	_	_	_
12	mL	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	M9	m9	NN	_	_	_
15	medium	medium	NN	_	_	_
16	for	for	IN	_	_	_
17	preculture	preculture	NN	_	_	_
18	.	.	.	_	_	_

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	v/v	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	ethanol	ethanol	NN	_	_	_
23	in	in	IN	_	_	_
24	10	10	CD	_	_	_
25	mL	ml	NN	_	_	_
26	test	test	NN	_	_	_
27	tube	tube	NN	_	_	_
28	with	with	IN	_	_	_
29	screw	screw	NN	_	_	_
30	cap	cap	NN	_	_	_
31	and	and	CC	_	_	_
32	cultured	culture	VBN	_	_	_
33	for	for	IN	_	_	_
34	10	10	CD	_	_	_
35	generations	generation	NNS	_	_	_
36	.	.	.	_	_	_

1	When	when	WRB	_	_	_
2	OD600nm	od600nm	NN	_	_	_
3	reached	reach	VBD	_	_	_
4	0.05	0.05	CD	_	_	_
5	within	within	IN	_	_	_
6	the	the	DT	_	_	_
7	exponential	exponential	JJ	_	_	_
8	growth	growth	NN	_	_	_
9	phase	phase	NN	_	_	_
10	,	,	,	_	_	_
11	cell	cell	NN	_	_	_
12	were	be	VBD	_	_	_
13	collected	collect	VBN	_	_	_
14	.	.	.	_	_	_

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/ml	µg/ml	JJ	_	_	_
15	heparin	heparin	NN	_	_	_
16	at	at	IN	_	_	_
17	the	the	DT	_	_	_
18	final	final	JJ	_	_	_
19	concentrations	concentration	NNS	_	_	_
20	as	as	RB	_	_	_
21	well	well	RB	_	_	_
22	as	as	IN	_	_	_
23	74	74	CD	_	_	_
24	ml	ml	NN	_	_	_
25	DNaseI	dnasei	NN	_	_	_
26	buffer	buffer	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	10	10	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	MnCl2	mncl2	NN	SUPP	_	_
31	10	10	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	Tris-HCl	tris-hcl	NN	_	_	_
34	,	,	,	_	_	_
35	pH	ph	NN	_	_	_
36	7.5	7.5	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	were	be	VBD	_	_	_
39	added	add	VBN	_	_	_
40	to	to	TO	_	_	_
41	the	the	DT	_	_	_
42	mixture	mixture	NN	_	_	_
43	and	and	CC	_	_	_
44	incubated	incubate	VBN	_	_	_
45	for	for	IN	_	_	_
46	10	10	CD	_	_	_
47	min	min	NN	_	_	_
48	at	at	IN	_	_	_
49	RT.	RT.	NNP	_	_	_
50	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	remove	remove	VB	_	_	_
3	cell	cell	NN	_	_	_
4	debris	debris	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	mixture	mixture	NN	_	_	_
8	was	be	VBD	_	_	_
9	centrifuged	centrifuge	VBN	_	_	_
10	at	at	IN	_	_	_
11	20,000	20,000	CD	_	_	_
12	x	x	CC	_	_	_
13	g	g	NN	_	_	_
14	for	for	IN	_	_	_
15	3	3	CD	_	_	_
16	min	min	NN	_	_	_
17	at	at	IN	_	_	_
18	4	4	CD	_	_	_
19	˚C	˚c	NN	_	_	_
20	and	and	CC	_	_	_
21	the	the	DT	_	_	_
22	supernatant	supernatant	NN	_	_	_
23	was	be	VBD	_	_	_
24	collected	collect	VBN	_	_	_
25	into	into	IN	_	_	_
26	a	a	DT	_	_	_
27	new	new	JJ	_	_	_
28	1.5	1.5	CD	_	_	_
29	ml	ml	NN	_	_	_
30	tube	tube	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	JJ	_	_	_
3	including	include	VBG	_	_	_
4	RNAPs	rnap	NNS	_	_	_
5	that	that	WDT	_	_	_
6	form	form	VBP	_	_	_
7	ternary	ternary	JJ	_	_	_
8	complexes	complex	NNS	_	_	_
9	with	with	IN	_	_	_
10	RNA/DNA	rna/dna	NN	_	_	_
11	were	be	VBD	_	_	_
12	immobilized	immobilize	VBN	_	_	_
13	on	on	IN	_	_	_
14	~	~	NN	_	_	_
15	155	155	CD	_	_	_
16	µl	µl	NN	_	_	_
17	Ni-NTA	ni-nta	NN	_	_	_
18	agarose	agarose	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Qiagen	qiagen	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	pre-equilibrated	pre-equilibrated	JJ	_	_	_
23	with	with	IN	_	_	_
24	the	the	DT	_	_	_
25	binding	binding	NN	_	_	_
26	buffer	buffer	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	0.5	0.5	CD	_	_	_
29	M	m	NN	_	_	_
30	NaCl	nacl	NN	_	_	_
31	,	,	,	_	_	_
32	5	5	CD	_	_	_
33	mM	mm	NN	KWSUPP	_	_
34	imidazole	imidazole	NN	_	_	_
35	,	,	,	_	_	_
36	5	5	CD	_	_	_
37	%	%	NN	_	_	_
38	glycerol	glycerol	NN	SUPP	_	_
39	,	,	,	_	_	_
40	20	20	CD	_	_	_
41	mM	mm	NN	KWSUPP	_	_
42	Tris-HCl	tris-hcl	NN	_	_	_
43	,	,	,	_	_	_
44	pH7	ph7	NN	_	_	_
45	.9	.9	NN	_	_	_
46	,	,	,	_	_	_
47	1	1	CD	_	_	_
48	mM	mm	NN	KWSUPP	_	_
49	2-mercaptoethanol	2-mercaptoethanol	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	with	with	IN	_	_	_
52	shaking	shake	VBG	_	_	_
53	for	for	IN	_	_	_
54	10	10	CD	_	_	_
55	min	min	NN	_	_	_
56	at	at	IN	_	_	_
57	4	4	CD	_	_	_
58	˚C	˚c	NN	_	_	_
59	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	immobilized	immobilize	VBN	_	_	_
3	ternary	ternary	JJ	_	_	_
4	complexes	complex	NNS	_	_	_
5	were	be	VBD	_	_	_
6	washed	wash	VBN	_	_	_
7	five	five	CD	_	_	_
8	times	time	NNS	_	_	_
9	with	with	IN	_	_	_
10	the	the	DT	_	_	_
11	wash	wash	NN	_	_	_
12	buffer	buffer	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	1M	1m	NN	_	_	_
15	NaCl	nacl	NN	_	_	_
16	,	,	,	_	_	_
17	15	15	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	imidazole	imidazole	NN	_	_	_
20	,	,	,	_	_	_
21	5	5	CD	_	_	_
22	%	%	NN	_	_	_
23	glycerol	glycerol	NN	SUPP	_	_
24	,	,	,	_	_	_
25	pH7	ph7	NN	_	_	_
26	.9	.9	NN	_	_	_
27	,	,	,	_	_	_
28	1	1	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	2-mercaptoethanol	2-mercaptoethanol	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	at	at	IN	_	_	_
33	4	4	CD	_	_	_
34	˚C	˚c	NN	_	_	_
35	,	,	,	_	_	_
36	washed	wash	VBN	_	_	_
37	twice	twice	RB	_	_	_
38	with	with	IN	_	_	_
39	the	the	DT	_	_	_
40	nuclease	nuclease	NN	_	_	_
41	buffer	buffer	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	40	40	CD	_	_	_
44	mM	mm	NN	KWSUPP	_	_
45	KCl	kcl	NN	_	_	_
46	,	,	,	_	_	_
47	15	15	CD	_	_	_
48	mM	mm	NN	KWSUPP	_	_
49	imidazole	imidazole	NN	_	_	_
50	,	,	,	_	_	_
51	20	20	CD	_	_	_
52	mM	mm	NN	KWSUPP	_	_
53	Tris-HCl	tris-hcl	NN	_	_	_
54	,	,	,	_	_	_
55	pH	ph	NN	_	_	_
56	7.9	7.9	CD	_	_	_
57	,	,	,	_	_	_
58	0.3	0.3	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	MgCl2	mgcl2	NN	_	_	_
61	5	5	CD	_	_	_
62	%	%	NN	_	_	_
63	glycerol	glycerol	NN	SUPP	_	_
64	,	,	,	_	_	_
65	1	1	CD	_	_	_
66	mM	mm	NN	KWSUPP	_	_
67	2-mercaptoethanol	2-mercaptoethanol	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	at	at	IN	_	_	_
70	4	4	CD	_	_	_
71	˚C	˚c	NN	_	_	_
72	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	transcript	transcript	NN	_	_	_
4	and	and	CC	_	_	_
5	DNA	dna	NN	_	_	_
6	unprotected	unprotected	JJ	_	_	_
7	by	by	IN	_	_	_
8	RNAP	rnap	NN	_	_	_
9	were	be	VBD	_	_	_
10	cleaved	cleave	VBN	_	_	_
11	by	by	IN	_	_	_
12	the	the	DT	_	_	_
13	additions	addition	NNS	_	_	_
14	of	of	IN	_	_	_
15	0.4	0.4	CD	_	_	_
16	U	U	NNP	_	_	_
17	RNase	rnase	NN	_	_	_
18	V1	v1	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Invitrogen	invitrogen	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	0.7	0.7	CD	_	_	_
24	U	U	NNP	_	_	_
25	RNase	rnase	NN	_	_	_
26	T1	t1	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Sigma	Sigma	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	and	and	CC	_	_	_
32	5	5	CD	_	_	_
33	U	U	NNP	_	_	_
34	DNase	dnase	NN	_	_	_
35	I	i	CD	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Takara	Takara	NNP	_	_	_
38	Bio	Bio	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	to	to	TO	_	_	_
41	the	the	DT	_	_	_
42	immobilized	immobilize	VBN	_	_	_
43	complexes	complex	NNS	_	_	_
44	and	and	CC	_	_	_
45	incubation	incubation	NN	_	_	_
46	for	for	IN	_	_	_
47	7	7	CD	_	_	_
48	min	min	NN	_	_	_
49	at	at	IN	_	_	_
50	RT.	RT.	NNP	_	_	_
51	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	nuclease-treated	nuclease-treated	JJ	_	_	_
3	complexes	complex	NNS	_	_	_
4	were	be	VBD	_	_	_
5	washed	wash	VBN	_	_	_
6	twice	twice	RB	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	wash	wash	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	,	,	,	_	_	_
12	twice	twice	RB	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	MnCl2-free	mncl2-free	NN	_	_	_
16	nuclease	nuclease	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	at	at	IN	_	_	_
19	4	4	CD	_	_	_
20	˚C	˚c	NN	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	eluted	elute	VBN	_	_	_
24	by	by	IN	_	_	_
25	increasing	increase	VBG	_	_	_
26	the	the	DT	_	_	_
27	concentration	concentration	NN	_	_	_
28	of	of	IN	_	_	_
29	imidazole	imidazole	NN	_	_	_
30	to	to	TO	_	_	_
31	100	100	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	followed	follow	VBN	_	_	_
34	by	by	IN	_	_	_
35	shaking	shake	VBG	_	_	_
36	for	for	IN	_	_	_
37	10	10	CD	_	_	_
38	min	min	NN	_	_	_
39	at	at	IN	_	_	_
40	4	4	CD	_	_	_
41	˚C	˚c	NN	_	_	_
42	in	in	IN	_	_	_
43	the	the	DT	_	_	_
44	presence	presence	NN	_	_	_
45	of	of	IN	_	_	_
46	30	30	CD	_	_	_
47	U	U	NNP	_	_	_
48	SUPERase	SUPERase	NNP	_	_	_
49	RNase	rnase	NN	_	_	_
50	inhibitor	inhibitor	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Ambion	ambion	NN	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Each	each	DT	_	_	_
3	type	type	NN	_	_	_
4	of	of	IN	_	_	_
5	error	error	NN	_	_	_
6	rates	rate	NNS	_	_	_
7	per	per	IN	_	_	_
8	position	position	NN	_	_	_
9	was	be	VBD	_	_	_
10	determined	determine	VBN	_	_	_
11	as	as	IN	_	_	_
12	the	the	DT	_	_	_
13	number	number	NN	_	_	_
14	of	of	IN	_	_	_
15	sequence	sequence	NN	_	_	_
16	reads	read	VBZ	_	_	_
17	with	with	IN	_	_	_
18	a	a	DT	_	_	_
19	particular	particular	JJ	_	_	_
20	type	type	NN	_	_	_
21	of	of	IN	_	_	_
22	base-substitution	base-substitution	NN	_	_	_
23	divided	divide	VBN	_	_	_
24	by	by	IN	_	_	_
25	the	the	DT	_	_	_
26	number	number	NN	_	_	_
27	of	of	IN	_	_	_
28	the	the	DT	_	_	_
29	reads	read	VBZ	_	_	_
30	with	with	IN	_	_	_
31	the	the	DT	_	_	_
32	reference	reference	NN	_	_	_
33	base	base	NN	_	_	_
34	in	in	IN	_	_	_
35	each	each	DT	_	_	_
36	DNA	dna	NN	_	_	_
37	position	position	NN	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	early	early	JJ	GrowthPhase	_	_
3	stationary	stationary	JJ	GrowthPhase	_	_
4	phase	phase	NN	GrowthPhase	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	early	early	JJ	GrowthPhase	_	_
8	stationary	stationary	JJ	GrowthPhase	_	_
9	phase	phase	NN	GrowthPhase	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	early	early	JJ	GrowthPhase	_	_
13	stationary	stationary	JJ	GrowthPhase	_	_
14	phase	phase	NN	GrowthPhase	_	_
15	3	3	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	early	early	JJ	GrowthPhase	_	_
18	stationary	stationary	JJ	GrowthPhase	_	_
19	phase	phase	NN	GrowthPhase	_	_
20	4	4	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	early	early	JJ	GrowthPhase	_	_
23	stationary	stationary	JJ	GrowthPhase	_	_
24	phase	phase	NN	GrowthPhase	_	_
25	5	5	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	EC12n090	ec12n090	NN	_	_	_
28	RpoE	rpoe	NN	_	_	_
29	2.5	2.5	CD	_	_	_
30	min	min	NN	_	_	_
31	Time	Time	NNP	_	_	_
32	course	course	NN	_	_	_
33	4	4	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	EC12n091	ec12n091	NN	_	_	_
36	RpoE	rpoe	NN	_	_	_
37	5	5	CD	_	_	_
38	min	min	NN	_	_	_
39	Time	Time	NNP	_	_	_
40	course	course	NN	_	_	_
41	4	4	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	EC12n092a	ec12n092a	NN	_	_	_
44	RpoE	rpoe	NN	_	_	_
45	10	10	CD	_	_	_
46	min	min	NN	_	_	_
47	Time	Time	NNP	_	_	_
48	course	course	NN	_	_	_
49	4	4	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	EC12n093	ec12n093	NN	_	_	_
52	RpoE	rpoe	NN	_	_	_
53	20	20	CD	_	_	_
54	min	min	NN	_	_	_
55	Time	Time	NNP	_	_	_
56	course	course	NN	_	_	_
57	4	4	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	EC12n094	ec12n094	NN	_	_	_
60	RpoE	rpoe	NN	_	_	_
61	30	30	CD	_	_	_
62	min	min	NN	_	_	_
63	Time	Time	NNP	_	_	_
64	course	course	NN	_	_	_
65	4	4	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	EC12n095	ec12n095	NN	_	_	_
68	RpoE	rpoe	NN	_	_	_
69	60	60	CD	_	_	_
70	min	min	NN	_	_	_
71	Time	Time	NNP	_	_	_
72	course	course	NN	_	_	_
73	4	4	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	EC12n096	ec12n096	NN	_	_	_
76	RpoE	rpoe	NN	_	_	_
77	0	0	CD	_	_	_
78	min	min	NN	_	_	_
79	Time	Time	NNP	_	_	_
80	course	course	NN	_	_	_
81	4	4	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	EC12n097	ec12n097	NN	_	_	_
84	delta	delta	NN	_	_	_
85	rseA	rsea	NN	GEN	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	EC12n098	ec12n098	NN	_	_	_
88	delta	delta	NN	_	_	_
89	rseA	rsea	NN	GEN	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	EC12n099	ec12n099	NN	_	_	_
92	delta	delta	NN	_	_	_
93	rseA	rsea	NN	GEN	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	EC12n101	ec12n101	NN	_	_	_
96	RpoE	rpoe	NN	_	_	_
97	0	0	CD	_	_	_
98	min	min	NN	_	_	_
99	Time	Time	NNP	_	_	_
100	course	course	NN	_	_	_
101	3	3	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	EC18n018	ec18n018	NN	_	_	_
104	hfq	hfq	NN	GEN	_	_
105	+	+	CC	_	_	_
106	rpoE	rpoe	NN	GEN	_	_
107	overexpression	overexpression	NN	_	_	_
108	20	20	CD	_	_	_
109	min	min	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	EC18n019	ec18n019	NN	_	_	_
112	hfq	hfq	NN	GEN	_	_
113	-	-	:	_	_	_
114	rpoE	rpoe	NN	GEN	_	_
115	overexpression	overexpression	NN	_	_	_
116	20	20	CD	_	_	_
117	min	min	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	EC18n035	ec18n035	NN	_	_	_
120	delta	delta	NN	_	_	_
121	rseA	rsea	NN	GEN	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	EC18n036	ec18n036	NN	_	_	_
124	delta	delta	NN	_	_	_
125	rseA	rsea	NN	GEN	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	EC18n037	ec18n037	NN	_	_	_
128	delta	delta	NN	_	_	_
129	hfq	hfq	NN	GEN	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	EC18n038	ec18n038	NN	_	_	_
132	delta	delta	NN	_	_	_
133	hfq	hfq	NN	GEN	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	EC18n039	ec18n039	NN	_	_	_
136	delta	delta	NN	_	_	_
137	hfq	hfq	NN	GEN	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	EC18n040	ec18n040	NN	_	_	_
140	delta	delta	NN	_	_	_
141	hfq	hfq	NN	GEN	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	EC18n122	ec18n122	NN	_	_	_
144	RpoH	rpoh	NN	_	_	_
145	10	10	CD	_	_	_
146	min	min	NN	_	_	_
147	Time	Time	NNP	_	_	_
148	course	course	NN	_	_	_
149	4	4	CD	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	EC18n136	ec18n136	NN	_	_	_
152	hfq	hfq	NN	GEN	_	_
153	+	+	CC	_	_	_
154	rpoE	rpoe	NN	GEN	_	_
155	overexpression	overexpression	NN	_	_	_
156	20	20	CD	_	_	_
157	min	min	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	Ec18n137	ec18n137	NN	_	_	_
160	hfq	hfq	NN	GEN	_	_
161	-	-	:	_	_	_
162	rpoE	rpoe	NN	GEN	_	_
163	overexpression	overexpression	NN	_	_	_
164	20	20	CD	_	_	_
165	min	min	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	EC18n139	ec18n139	NN	_	_	_
168	hfq	hfq	NN	GEN	_	_
169	+	+	CC	_	_	_
170	rpoE	rpoe	NN	GEN	_	_
171	overexpression	overexpression	NN	_	_	_
172	20	20	CD	_	_	_
173	min	min	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	EC18n140	ec18n140	NN	_	_	_
176	hfq	hfq	NN	GEN	_	_
177	-	-	:	_	_	_
178	rpoE	rpoe	NN	GEN	_	_
179	overexpression	overexpression	NN	_	_	_
180	20	20	CD	_	_	_
181	min	min	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	EC18n167	ec18n167	NN	_	_	_
184	RpoH	rpoh	NN	_	_	_
185	0	0	CD	_	_	_
186	min	min	NN	_	_	_
187	Time	Time	NNP	_	_	_
188	course	course	NN	_	_	_
189	2	2	CD	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	EC18n168	ec18n168	NN	_	_	_
192	RpoH	rpoh	NN	_	_	_
193	2.5	2.5	CD	_	_	_
194	min	min	NN	_	_	_
195	Time	Time	NNP	_	_	_
196	course	course	NN	_	_	_
197	2	2	CD	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	EC18n169	ec18n169	NN	_	_	_
200	RpoH	rpoh	NN	_	_	_
201	5	5	CD	_	_	_
202	min	min	NN	_	_	_
203	Time	Time	NNP	_	_	_
204	course	course	NN	_	_	_
205	2	2	CD	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	EC18n170	ec18n170	NN	_	_	_
208	RpoH	rpoh	NN	_	_	_
209	10	10	CD	_	_	_
210	min	min	NN	_	_	_
211	Time	Time	NNP	_	_	_
212	course	course	NN	_	_	_
213	2	2	CD	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	EC18n171	ec18n171	NN	_	_	_
216	RpoH	rpoh	NN	_	_	_
217	20	20	CD	_	_	_
218	min	min	NN	_	_	_
219	Time	Time	NNP	_	_	_
220	course	course	NN	_	_	_
221	2	2	CD	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	EC18n177	ec18n177	NN	_	_	_
224	RpoH	rpoh	NN	_	_	_
225	0	0	CD	_	_	_
226	min	min	NN	_	_	_
227	Time	Time	NNP	_	_	_
228	course	course	NN	_	_	_
229	1	1	CD	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	EC18n178	ec18n178	NN	_	_	_
232	RpoH	rpoh	NN	_	_	_
233	2.5	2.5	CD	_	_	_
234	min	min	NN	_	_	_
235	Time	Time	NNP	_	_	_
236	course	course	NN	_	_	_
237	1	1	CD	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	EC18n179	ec18n179	NN	_	_	_
240	RpoH	rpoh	NN	_	_	_
241	5	5	CD	_	_	_
242	min	min	NN	_	_	_
243	Time	Time	NNP	_	_	_
244	course	course	NN	_	_	_
245	1	1	CD	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	EC18n180	ec18n180	NN	_	_	_
248	RpoH	rpoh	NN	_	_	_
249	10	10	CD	_	_	_
250	min	min	NN	_	_	_
251	Time	Time	NNP	_	_	_
252	course	course	NN	_	_	_
253	1	1	CD	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	EC18n181	ec18n181	NN	_	_	_
256	RpoH	rpoh	NN	_	_	_
257	20	20	CD	_	_	_
258	min	min	NN	_	_	_
259	Time	Time	NNP	_	_	_
260	course	course	NN	_	_	_
261	1	1	CD	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	EC18n182	ec18n182	NN	_	_	_
264	RpoH	rpoh	NN	_	_	_
265	0	0	CD	_	_	_
266	min	min	NN	_	_	_
267	Time	Time	NNP	_	_	_
268	course	course	NN	_	_	_
269	3	3	CD	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	EC18n183	ec18n183	NN	_	_	_
272	RpoH	rpoh	NN	_	_	_
273	2.5	2.5	CD	_	_	_
274	min	min	NN	_	_	_
275	Time	Time	NNP	_	_	_
276	course	course	NN	_	_	_
277	3	3	CD	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	EC18n184	ec18n184	NN	_	_	_
280	RpoH	rpoh	NN	_	_	_
281	5	5	CD	_	_	_
282	min	min	NN	_	_	_
283	Time	Time	NNP	_	_	_
284	course	course	NN	_	_	_
285	3	3	CD	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	EC18n185	ec18n185	NN	_	_	_
288	RpoH	rpoh	NN	_	_	_
289	10	10	CD	_	_	_
290	min	min	NN	_	_	_
291	Time	Time	NNP	_	_	_
292	course	course	NN	_	_	_
293	3	3	CD	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	EC18n186	ec18n186	NN	_	_	_
296	RpoH	rpoh	NN	_	_	_
297	20	20	CD	_	_	_
298	min	min	NN	_	_	_
299	Time	Time	NNP	_	_	_
300	course	course	NN	_	_	_
301	3	3	CD	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	EC19n075	ec19n075	NN	_	_	_
304	delta	delta	NN	_	_	_
305	hfq	hfq	NN	GEN	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	EC19n076	ec19n076	NN	_	_	_
308	delta	delta	NN	_	_	_
309	hfq	hfq	NN	GEN	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	EC19n098	ec19n098	NN	_	_	_
312	delta	delta	NN	_	_	_
313	hfq	hfq	NN	GEN	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	EC19n099	ec19n099	NN	_	_	_
316	delta	delta	NN	_	_	_
317	hfq	hfq	NN	GEN	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	EC19n100	ec19n100	NN	_	_	_
320	delta	delta	NN	_	_	_
321	rseA	rsea	NN	GEN	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	EC19n101	ec19n101	NN	_	_	_
324	delta	delta	NN	_	_	_
325	rseA	rsea	NN	GEN	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	EC7n018	ec7n018	NN	_	_	_
328	RpoE	rpoe	NN	_	_	_
329	5	5	CD	_	_	_
330	min	min	NN	_	_	_
331	Time	Time	NNP	_	_	_
332	course	course	NN	_	_	_
333	1	1	CD	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	EC7n019	ec7n019	NN	_	_	_
336	RpoE	rpoe	NN	_	_	_
337	15	15	CD	_	_	_
338	min	min	NN	_	_	_
339	Time	Time	NNP	_	_	_
340	course	course	NN	_	_	_
341	1	1	CD	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	EC7n065	ec7n065	NN	_	_	_
344	RpoE	rpoe	NN	_	_	_
345	5	5	CD	_	_	_
346	min	min	NN	_	_	_
347	Time	Time	NNP	_	_	_
348	course	course	NN	_	_	_
349	2	2	CD	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	EC7n066	ec7n066	NN	_	_	_
352	RpoE	rpoe	NN	_	_	_
353	15	15	CD	_	_	_
354	min	min	NN	_	_	_
355	Time	Time	NNP	_	_	_
356	course	course	NN	_	_	_
357	2	2	CD	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	EC7n067	ec7n067	NN	_	_	_
360	RpoE	rpoe	NN	_	_	_
361	30	30	CD	_	_	_
362	min	min	NN	_	_	_
363	Time	Time	NNP	_	_	_
364	course	course	NN	_	_	_
365	2	2	CD	_	_	_
366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
367	EC7n068	ec7n068	NN	_	_	_
368	RpoE	rpoe	NN	_	_	_
369	60	60	CD	_	_	_
370	min	min	NN	_	_	_
371	Time	Time	NNP	_	_	_
372	course	course	NN	_	_	_
373	2	2	CD	_	_	_
374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
375	EC7n071	ec7n071	NN	_	_	_
376	RpoE	rpoe	NN	_	_	_
377	60	60	CD	_	_	_
378	min	min	NN	_	_	_
379	Time	Time	NNP	_	_	_
380	course	course	NN	_	_	_
381	1	1	CD	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	EC8n021	ec8n021	NN	_	_	_
384	RpoE	rpoe	NN	_	_	_
385	2.5	2.5	CD	_	_	_
386	min	min	NN	_	_	_
387	Time	Time	NNP	_	_	_
388	course	course	NN	_	_	_
389	3	3	CD	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	EC8n022	ec8n022	NN	_	_	_
392	RpoE	rpoe	NN	_	_	_
393	5	5	CD	_	_	_
394	min	min	NN	_	_	_
395	Time	Time	NNP	_	_	_
396	course	course	NN	_	_	_
397	3	3	CD	_	_	_
398	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
399	EC8n050	ec8n050	NN	_	_	_
400	RpoE	rpoe	NN	_	_	_
401	10	10	CD	_	_	_
402	min	min	NN	_	_	_
403	Time	Time	NNP	_	_	_
404	course	course	NN	_	_	_
405	3	3	CD	_	_	_
406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
407	EC8n051	ec8n051	NN	_	_	_
408	RpoE	rpoe	NN	_	_	_
409	20	20	CD	_	_	_
410	min	min	NN	_	_	_
411	Time	Time	NNP	_	_	_
412	course	course	NN	_	_	_
413	3	3	CD	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	EC8n052	ec8n052	NN	_	_	_
416	RpoE	rpoe	NN	_	_	_
417	30	30	CD	_	_	_
418	min	min	NN	_	_	_
419	Time	Time	NNP	_	_	_
420	course	course	NN	_	_	_
421	3	3	CD	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	EC8n053	ec8n053	NN	_	_	_
424	RpoE	rpoe	NN	_	_	_
425	60	60	CD	_	_	_
426	min	min	NN	_	_	_
427	Time	Time	NNP	_	_	_
428	course	course	NN	_	_	_
429	3	3	CD	_	_	_
430	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
431	EC	EC	NNP	_	_	_
432	_	_	VBD	_	_	_
433	Cont1	cont1	NN	_	_	_
434	_	_	NN	_	_	_
435	DNA	dna	NN	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	EC	ec	NN	_	_	_
438	_	_	CD	_	_	_
439	Cont1	cont1	NN	_	_	_
440	_	_	NN	_	_	_
441	RNA	rna	NN	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	EC	ec	NN	_	_	_
444	_	_	CD	_	_	_
445	Cont2	cont2	NN	_	_	_
446	_	_	NN	_	_	_
447	DNA	dna	NN	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	EC	ec	NN	_	_	_
450	_	_	CD	_	_	_
451	Cont2	cont2	NN	_	_	_
452	_	_	NN	_	_	_
453	RNA	rna	NN	_	_	_
454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
455	ecd3-c-0081429	ecd3-c-0081429	NN	_	_	_
456	wt	wt	JJ	_	_	_
457	vs	vs	CC	_	_	_
458	dpiAoverexpressor	dpiaoverexpressor	JJ	_	_	_
459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
460	ecd3-c-0101429	ecd3-c-0101429	NN	_	_	_
461	wt	wt	JJ	_	_	_
462	vs	vs	CC	_	_	_
463	dpiAoverexpressor	dpiaoverexpressor	JJ	_	_	_
464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
465	ECDH5	ecdh5	NN	_	_	_
466	_	_	CD	_	_	_
467	GD	gd	NN	_	_	_
468	_	_	CD	_	_	_
469	RP1	rp1	NN	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	EcJR-8	ecjr-8	NN	_	_	_
472	grown	grow	VBN	_	_	_
473	to	to	TO	_	_	_
474	OD600	od600	NN	_	_	_
475	=	=	JJ	_	_	_
476	0.5	0.5	CD	_	_	_
477	in	in	IN	_	_	_
478	DMEM-MOPS	dmem-mops	NN	_	_	_
479	0.4	0.4	CD	_	_	_
480	%	%	NN	_	_	_
481	glucose	glucose	NN	SUPP	_	_
482	at	at	IN	_	_	_
483	a	a	DT	_	_	_
484	10:1	10:1	CD	_	_	_
485	flask-to-media	flask-to-media	NN	_	_	_
486	volume	volume	NN	_	_	_
487	in	in	IN	_	_	_
488	a	a	DT	_	_	_
489	rotary	rotary	JJ	_	_	_
490	shaker	shaker	NN	_	_	_
491	-LRB-	-lrb-	-LRB-	_	_	_
492	180	180	CD	_	_	_
493	RPM	rpm	NN	_	_	_
494	-RRB-	-rrb-	-RRB-	_	_	_
495	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	eco	eco	VBP	GEN	_	_
3	_	_	SYM	_	_	_
4	0.21	0.21	CD	_	_	_
5	_	_	SYM	_	_	_
6	0.11	0.11	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	eco	eco	NN	GEN	_	_
9	_	_	CD	_	_	_
10	0.26	0.26	CD	_	_	_
11	_	_	SYM	_	_	_
12	0.11	0.11	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	eco	eco	NN	GEN	_	_
15	_	_	CD	_	_	_
16	0.31	0.31	CD	_	_	_
17	_	_	SYM	_	_	_
18	0.11	0.11	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	eco	eco	NN	GEN	_	_
21	_	_	CD	_	_	_
22	0.36	0.36	CD	_	_	_
23	_	_	SYM	_	_	_
24	0.11	0.11	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	eco	eco	NN	GEN	_	_
27	_	_	CD	_	_	_
28	0.40	0.40	CD	_	_	_
29	_	_	SYM	_	_	_
30	0.11	0.11	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	eco	eco	NN	GEN	_	_
33	_	_	CD	_	_	_
34	0.48	0.48	CD	_	_	_
35	_	_	SYM	_	_	_
36	0.11	0.11	CD	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Eco	Eco	NNP	_	_	_
39	50ng	50ng	SYM	_	_	_
40	-	-	:	_	_	_
41	0	0	CD	_	_	_
42	%	%	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Eco	eco	NN	_	_	_
45	50ng	50ng	SYM	_	_	_
46	-	-	:	_	_	_
47	10	10	CD	_	_	_
48	%	%	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Eco	eco	NN	_	_	_
51	50ng	50ng	SYM	_	_	_
52	-	-	:	_	_	_
53	15	15	CD	_	_	_
54	%	%	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Eco	eco	NN	_	_	_
57	50ng	50ng	SYM	_	_	_
58	-	-	:	_	_	_
59	20	20	CD	_	_	_
60	%	%	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Eco	eco	NN	_	_	_
63	50ng	50ng	SYM	_	_	_
64	-	-	:	_	_	_
65	25	25	CD	_	_	_
66	%	%	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Eco	eco	NN	_	_	_
69	50ng	50ng	SYM	_	_	_
70	-	-	:	_	_	_
71	32.5	32.5	CD	_	_	_
72	%	%	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Eco	eco	NN	_	_	_
75	50ng	50ng	SYM	_	_	_
76	-	-	:	_	_	_
77	45	45	CD	_	_	_
78	%	%	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Eco	eco	NN	_	_	_
81	50ng	50ng	SYM	_	_	_
82	-	-	:	_	_	_
83	5	5	CD	_	_	_
84	%	%	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Eco	eco	NN	_	_	_
87	5ng	5ng	SYM	_	_	_
88	-	-	:	_	_	_
89	0	0	CD	_	_	_
90	%	%	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Eco	eco	NN	_	_	_
93	5ng	5ng	SYM	_	_	_
94	-	-	:	_	_	_
95	10	10	CD	_	_	_
96	%	%	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Eco	eco	NN	_	_	_
99	5ng	5ng	SYM	_	_	_
100	-	-	:	_	_	_
101	15	15	CD	_	_	_
102	%	%	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Eco	eco	NN	_	_	_
105	5ng	5ng	SYM	_	_	_
106	-	-	:	_	_	_
107	20	20	CD	_	_	_
108	%	%	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	Eco	eco	NN	_	_	_
111	5ng	5ng	SYM	_	_	_
112	-	-	:	_	_	_
113	25	25	CD	_	_	_
114	%	%	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Eco	eco	NN	_	_	_
117	5ng	5ng	SYM	_	_	_
118	-	-	:	_	_	_
119	32.5	32.5	CD	_	_	_
120	%	%	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	Eco	eco	NN	_	_	_
123	5ng	5ng	SYM	_	_	_
124	-	-	:	_	_	_
125	45	45	CD	_	_	_
126	%	%	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Eco	eco	NN	_	_	_
129	5ng	5ng	SYM	_	_	_
130	-	-	:	_	_	_
131	5	5	CD	_	_	_
132	%	%	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	E.	e.	FW	_	_	_
135	coli	coli	FW	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	E.	e.	FW	_	_	_
138	coli	coli	FW	_	_	_
139	042	042	CD	_	_	_
140	WT	wt	JJ	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	E	e	NN	_	_	_
143	coli	coli	NN	_	_	_
144	,	,	,	_	_	_
145	0	0	CD	_	_	_
146	min	min	NN	_	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	E.	E.	NNP	_	_	_
149	coli	coli	NN	_	_	_
150	-	-	:	_	_	_
151	0	0	CD	_	_	_
152	min	min	NN	_	_	_
153	before	before	IN	_	_	_
154	nutrient	nutrient	NN	_	_	_
155	shift	shift	NN	_	_	_
156	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
157	E.	E.	NNP	_	_	_
158	coli	coli	NN	_	_	_
159	0	0	CD	_	_	_
160	mins	min	NNS	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	E.coli	e.coli	NN	_	_	_
163	0	0	CD	_	_	_
164	minutes	minute	NNS	_	_	_
165	after	after	IN	_	_	_
166	BRP	brp	NN	_	_	_
167	induction	induction	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	E.coli	e.coli	NNS	_	_	_
170	_	_	VBP	_	_	_
171	0	0	CD	_	_	_
172	%	%	NN	_	_	_
173	tannin	tannin	NN	_	_	_
174	_	_	NN	_	_	_
175	#	#	#	_	_	_
176	2	2	CD	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	E.coli	e.coli	NNS	_	_	_
179	_	_	VBP	_	_	_
180	0	0	CD	_	_	_
181	%	%	NN	_	_	_
182	tannin	tannin	NN	_	_	_
183	_	_	NN	_	_	_
184	#	#	#	_	_	_
185	8	8	CD	_	_	_
186	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
187	E.	E.	NNP	_	_	_
188	coli	coli	NN	_	_	_
189	10	10	CD	_	_	_
190	mins	min	NNS	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	E.coli	e.coli	NN	_	_	_
193	-10	-10	CD	_	_	_
194	minutes	minute	NNS	_	_	_
195	after	after	IN	_	_	_
196	BRP	brp	NN	_	_	_
197	induction	induction	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	E.coli	e.coli	NN	_	_	_
200	10	10	CD	_	_	_
201	minutes	minute	NNS	_	_	_
202	after	after	IN	_	_	_
203	BRP	BRP	NNP	_	_	_
204	induction	induction	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	E	e	NN	_	_	_
207	coli	coli	NN	_	_	_
208	,	,	,	_	_	_
209	15	15	CD	_	_	_
210	min	min	NN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	E.coli	e.coli	NNS	_	_	_
213	_	_	VBP	_	_	_
214	15	15	CD	_	_	_
215	min	min	NN	_	_	_
216	_	_	CD	_	_	_
217	AE	ae	NN	_	_	_
218	_	_	NN	_	_	_
219	1	1	CD	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	E.coli	e.coli	NNS	_	_	_
222	_	_	VBP	_	_	_
223	15	15	CD	_	_	_
224	min	min	NN	_	_	_
225	_	_	CD	_	_	_
226	AE	ae	NN	_	_	_
227	_	_	NN	_	_	_
228	2	2	CD	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	E.coli	e.coli	NNS	_	_	_
231	_	_	VBP	_	_	_
232	15	15	CD	_	_	_
233	min	min	NN	_	_	_
234	_	_	CD	_	_	_
235	aerobic	aerobic	JJ	_	_	_
236	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
237	E.	E.	NNP	_	_	_
238	coli	coli	NN	_	_	_
239	-	-	:	_	_	_
240	15	15	CD	_	_	_
241	min	min	NN	_	_	_
242	after	after	IN	_	_	_
243	shift	shift	NN	_	_	_
244	to	to	TO	_	_	_
245	limiting	limit	VBG	_	_	_
246	medium	medium	NN	_	_	_
247	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
248	E.	E.	NNP	_	_	_
249	coli	coli	NN	_	_	_
250	-	-	:	_	_	_
251	15	15	CD	_	_	_
252	min	min	NN	_	_	_
253	after	after	IN	_	_	_
254	shift	shift	NN	_	_	_
255	to	to	TO	_	_	_
256	thymineless	thymineless	JJ	_	_	_
257	medium	medium	NN	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	E.coli	e.coli	NNS	_	_	_
260	_	_	VBP	_	_	_
261	15	15	CD	_	_	_
262	min	min	NN	_	_	_
263	_	_	CD	_	_	_
264	ANA	ANA	NNP	_	_	_
265	_	_	SYM	_	_	_
266	1	1	CD	_	_	_
267	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
268	E.	e.	FW	_	_	_
269	coli	coli	FW	_	_	_
270	_	_	SYM	_	_	_
271	15	15	CD	_	_	_
272	min	min	NN	_	_	_
273	_	_	CD	_	_	_
274	ANA	ANA	NNP	_	_	_
275	_	_	NN	_	_	_
276	2	2	CD	_	_	_
277	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
278	E.	e.	FW	_	_	_
279	coli	coli	FW	_	_	_
280	_	_	SYM	_	_	_
281	15	15	CD	_	_	_
282	min	min	NN	_	_	_
283	_	_	NN	_	_	_
284	anaerobic	anaerobic	JJ	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	E.coli	e.coli	NNS	_	_	_
287	_	_	VBP	_	_	_
288	15	15	CD	_	_	_
289	min	min	NN	_	_	_
290	_	_	NN	_	_	_
291	anaerobic	anaerobic	JJ	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	E.coli	e.coli	NNS	_	_	_
294	_	_	VBP	_	_	_
295	15	15	CD	_	_	_
296	min	min	NN	_	_	_
297	_	_	CD	_	_	_
298	CORM-2	corm-2	NN	_	_	_
299	treated	treat	VBN	_	_	_
300	_	_	SYM	_	_	_
301	aerobic	aerobic	JJ	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	E.coli	e.coli	NNS	_	_	_
304	_	_	VBP	_	_	_
305	15	15	CD	_	_	_
306	min	min	NN	_	_	_
307	_	_	CD	_	_	_
308	CORM-2	corm-2	NN	_	_	_
309	treated	treat	VBN	_	_	_
310	_	_	SYM	_	_	_
311	anaerobic	anaerobic	JJ	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	E.coli	e.coli	NNS	_	_	_
314	_	_	VBP	_	_	_
315	15	15	CD	_	_	_
316	min	min	NN	_	_	_
317	_	_	CD	_	_	_
318	CORM	CORM	NNP	_	_	_
319	_	_	CD	_	_	_
320	AE	AE	NNP	_	_	_
321	_	_	SYM	_	_	_
322	1	1	CD	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	E.coli	e.coli	NNS	_	_	_
325	_	_	VBP	_	_	_
326	15	15	CD	_	_	_
327	min	min	NN	_	_	_
328	_	_	CD	_	_	_
329	CORM	CORM	NNP	_	_	_
330	_	_	CD	_	_	_
331	AE	AE	NNP	_	_	_
332	_	_	NN	_	_	_
333	2	2	CD	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	E.coli	e.coli	NNS	_	_	_
336	_	_	VBP	_	_	_
337	15	15	CD	_	_	_
338	min	min	NN	_	_	_
339	_	_	CD	_	_	_
340	CORM	CORM	NNP	_	_	_
341	_	_	NNP	_	_	_
342	ANA	ANA	NNP	_	_	_
343	_	_	SYM	_	_	_
344	1	1	CD	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	E.coli	e.coli	NNS	_	_	_
347	_	_	VBP	_	_	_
348	15	15	CD	_	_	_
349	min	min	NN	_	_	_
350	_	_	CD	_	_	_
351	CORM	CORM	NNP	_	_	_
352	_	_	NNP	_	_	_
353	ANA	ANA	NNP	_	_	_
354	_	_	NN	_	_	_
355	2	2	CD	_	_	_
356	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
357	E.	E.	NNP	_	_	_
358	coli	coli	NN	_	_	_
359	15	15	CD	_	_	_
360	minute	minute	NN	_	_	_
361	5	5	CD	_	_	_
362	µM	µm	NN	_	_	_
363	cadmium	cadmium	NN	_	_	_
364	dye	dye	VB	_	_	_
365	swap	swap	NN	_	_	_
366	treatment	treatment	NN	_	_	_
367	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
368	E.	E.	NNP	_	_	_
369	coli	coli	NN	_	_	_
370	15	15	CD	_	_	_
371	minute	minute	NN	_	_	_
372	5	5	CD	_	_	_
373	µM	µm	NN	_	_	_
374	cadmium	cadmium	NN	_	_	_
375	treatment	treatment	NN	_	_	_
376	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
377	E.	E.	NNP	_	_	_
378	coli	coli	NN	_	_	_
379	15	15	CD	_	_	_
380	minute	minute	NN	_	_	_
381	pH	ph	NN	_	_	_
382	only	only	RB	_	_	_
383	dye	dye	VB	_	_	_
384	swap	swap	NN	_	_	_
385	treatment	treatment	NN	_	_	_
386	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
387	E.	E.	NNP	_	_	_
388	coli	coli	NN	_	_	_
389	15	15	CD	_	_	_
390	minute	minute	NN	_	_	_
391	pH	ph	NN	_	_	_
392	only	only	RB	_	_	_
393	treatment	treatment	NN	_	_	_
394	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
395	E.	E.	NNP	_	_	_
396	coli	coli	NN	_	_	_
397	,	,	,	_	_	_
398	15	15	CD	_	_	_
399	minutes	minute	NNS	_	_	_
400	,	,	,	_	_	_
401	5	5	CD	_	_	_
402	µM	µm	NN	_	_	_
403	cadmium	cadmium	NN	_	_	_
404	,	,	,	_	_	_
405	pH	ph	NN	_	_	_
406	5	5	CD	_	_	_
407	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
408	E.	E.	NNP	_	_	_
409	coli	coli	NN	_	_	_
410	,	,	,	_	_	_
411	15	15	CD	_	_	_
412	minutes	minute	NNS	_	_	_
413	,	,	,	_	_	_
414	5	5	CD	_	_	_
415	µM	µm	NN	_	_	_
416	cadmium	cadmium	NN	_	_	_
417	,	,	,	_	_	_
418	pH	ph	NN	_	_	_
419	7	7	CD	_	_	_
420	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
421	E.	E.	NNP	_	_	_
422	coli	coli	NN	_	_	_
423	,	,	,	_	_	_
424	15	15	CD	_	_	_
425	minutes	minute	NNS	_	_	_
426	,	,	,	_	_	_
427	no	no	DT	_	_	_
428	cadmium	cadmium	NN	_	_	_
429	,	,	,	_	_	_
430	pH	ph	NN	_	_	_
431	5	5	CD	_	_	_
432	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
433	E.	E.	NNP	_	_	_
434	coli	coli	NN	_	_	_
435	,	,	,	_	_	_
436	15	15	CD	_	_	_
437	minutes	minute	NNS	_	_	_
438	,	,	,	_	_	_
439	no	no	DT	_	_	_
440	cadmium	cadmium	NN	_	_	_
441	,	,	,	_	_	_
442	pH	ph	NN	_	_	_
443	7	7	CD	_	_	_
444	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
445	E.	E.	NNP	_	_	_
446	coli	coli	NN	_	_	_
447	,	,	,	_	_	_
448	1-h	1-h	NN	_	_	_
449	,	,	,	_	_	_
450	serine	serine	NN	_	_	_
451	hydroxamate	hydroxamate	NN	_	_	_
452	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
453	E.coli	e.coli	NNS	_	_	_
454	_	_	VBP	_	_	_
455	1	1	CD	_	_	_
456	%	%	NN	_	_	_
457	tannin	tannin	NN	_	_	_
458	_	_	NN	_	_	_
459	#	#	#	_	_	_
460	3	3	CD	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	e.coli	e.coli	NNS	_	_	_
463	_	_	VBP	_	_	_
464	1	1	CD	_	_	_
465	%	%	NN	_	_	_
466	tannin	tannin	NN	_	_	_
467	_	_	NN	_	_	_
468	#	#	#	_	_	_
469	5	5	CD	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	E.coli-1x	e.coli-1x	NN	_	_	_
472	CORM2-rep1	corm2-rep1	NN	_	_	_
473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
474	E.coli-1x	e.coli-1x	NN	_	_	_
475	CORM2-rep2	corm2-rep2	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	E.coli-1x	e.coli-1x	NN	_	_	_
478	CORM2-rep3	corm2-rep3	NN	_	_	_
479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
480	E.coli-1x	e.coli-1x	NN	_	_	_
481	CORM2-rep4	corm2-rep4	NN	_	_	_
482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
483	E.coli-1x	e.coli-1x	NN	_	_	_
484	vehicle-rep1	vehicle-rep1	NN	_	_	_
485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
486	E.coli-1x	e.coli-1x	NN	_	_	_
487	vehicle-rep2	vehicle-rep2	NN	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
489	E.coli-1x	e.coli-1x	NN	_	_	_
490	vehicle-rep3	vehicle-rep3	NN	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	E.coli-1x	e.coli-1x	NN	_	_	_
493	vehicle-rep4	vehicle-rep4	NN	_	_	_
494	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
495	E.coli	e.coli	NN	_	_	_
496	20	20	CD	_	_	_
497	minutes	minute	NNS	_	_	_
498	after	after	IN	_	_	_
499	BRP	brp	NN	_	_	_
500	induction	induction	NN	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	E.coli-20x	e.coli-20x	NN	_	_	_
503	CORM2-rep1	corm2-rep1	NN	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	E.coli-20x	e.coli-20x	NN	_	_	_
506	CORM2-rep2	corm2-rep2	NN	_	_	_
507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
508	E.coli-20x	e.coli-20x	NN	_	_	_
509	CORM2-rep3	corm2-rep3	NN	_	_	_
510	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
511	E.coli-20x	e.coli-20x	NN	_	_	_
512	CORM2-rep4	corm2-rep4	NN	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	E.coli-20x	e.coli-20x	NN	_	_	_
515	vehicle-rep1	vehicle-rep1	NN	_	_	_
516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
517	E.coli-20x	e.coli-20x	NN	_	_	_
518	vehicle-rep2	vehicle-rep2	NN	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	E.coli-20x	e.coli-20x	NN	_	_	_
521	vehicle-rep3	vehicle-rep3	NN	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
523	E.coli-20x	e.coli-20x	NN	_	_	_
524	vehicle-rep4	vehicle-rep4	NN	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	E	e	NN	_	_	_
527	coli	coli	NN	_	_	_
528	,	,	,	_	_	_
529	25	25	CD	_	_	_
530	min	min	NN	_	_	_
531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
532	E	e	NN	_	_	_
533	coli	coli	NN	_	_	_
534	,	,	,	_	_	_
535	25	25	CD	_	_	_
536	min	min	NN	_	_	_
537	after	after	IN	_	_	_
538	turning	turn	VBG	_	_	_
539	off	off	RP	_	_	_
540	oxygen	oxygen	NN	_	_	_
541	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
542	E.	e.	FW	_	_	_
543	coli	coli	FW	_	_	_
544	2.5	2.5	CD	_	_	_
545	mins	min	NNS	_	_	_
546	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
547	Ecoli	Ecoli	NNP	_	_	_
548	,	,	,	_	_	_
549	2	2	CD	_	_	_
550	min	min	NN	_	_	_
551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
552	E	e	NN	_	_	_
553	coli	coli	NN	_	_	_
554	,	,	,	_	_	_
555	2	2	CD	_	_	_
556	min	min	NN	_	_	_
557	after	after	IN	_	_	_
558	turning	turn	VBG	_	_	_
559	off	off	RP	_	_	_
560	oxygen	oxygen	NN	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	E.coli	e.coli	NN	_	_	_
563	2	2	CD	_	_	_
564	minutes	minute	NNS	_	_	_
565	after	after	IN	_	_	_
566	BRP	BRP	NNP	_	_	_
567	induction	induction	NN	_	_	_
568	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
569	E.	E.	NNP	_	_	_
570	coli	coli	NN	_	_	_
571	2	2	CD	_	_	_
572	%	%	NN	_	_	_
573	NaCl	nacl	NN	_	_	_
574	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
575	E.	E.	NNP	_	_	_
576	coli	coli	NN	_	_	_
577	-	-	:	_	_	_
578	30	30	CD	_	_	_
579	min	min	NN	_	_	_
580	after	after	IN	_	_	_
581	shift	shift	NN	_	_	_
582	to	to	TO	_	_	_
583	limiting	limit	VBG	_	_	_
584	medium	medium	NN	_	_	_
585	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
586	E.	E.	NNP	_	_	_
587	coli	coli	NN	_	_	_
588	-	-	:	_	_	_
589	30	30	CD	_	_	_
590	min	min	NN	_	_	_
591	after	after	IN	_	_	_
592	shift	shift	NN	_	_	_
593	to	to	TO	_	_	_
594	thymineless	thymineless	JJ	_	_	_
595	medium	medium	NN	_	_	_
596	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
597	E.	E.	NNP	_	_	_
598	coli	coli	NN	_	_	_
599	30	30	CD	_	_	_
600	mins	min	NNS	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	E.coli	e.coli	NN	_	_	_
603	30	30	CD	_	_	_
604	minutes	minute	NNS	_	_	_
605	after	after	IN	_	_	_
606	BRP	BRP	NNP	_	_	_
607	induction	induction	NN	_	_	_
608	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
609	E.	E.	NNP	_	_	_
610	coli	coli	NN	_	_	_
611	3538	3538	CD	_	_	_
612	#	#	#	_	_	_
613	1	1	CD	_	_	_
614	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
615	E.	E.	NNP	_	_	_
616	coli	coli	NN	_	_	_
617	3538	3538	CD	_	_	_
618	#	#	#	_	_	_
619	2	2	CD	_	_	_
620	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
621	ecoli	ecolus	NNS	_	_	_
622	_	_	VBP	_	_	_
623	3538	3538	CD	_	_	_
624	_	_	SYM	_	_	_
625	2x	2x	FW	_	_	_
626	_	_	FW	_	_	_
627	v2	v2	FW	_	_	_
628	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
629	E.	e.	FW	_	_	_
630	coli	coli	FW	_	_	_
631	3538	3538	CD	_	_	_
632	#	#	#	_	_	_
633	3	3	CD	_	_	_
634	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
635	ecoli	ecolus	NNS	_	_	_
636	_	_	VBP	_	_	_
637	3538	3538	CD	_	_	_
638	_	_	SYM	_	_	_
639	3x	3x	FW	_	_	_
640	_	_	FW	_	_	_
641	v2	v2	FW	_	_	_
642	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
643	ecoli	ecolus	NNS	_	_	_
644	_	_	VBP	_	_	_
645	3538	3538	CD	_	_	_
646	_	_	SYM	_	_	_
647	4x	4x	FW	_	_	_
648	_	_	FW	_	_	_
649	v2	v2	FW	_	_	_
650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
651	E	e	NN	_	_	_
652	coli	coli	NN	_	_	_
653	,	,	,	_	_	_
654	35	35	CD	_	_	_
655	min	min	NN	_	_	_
656	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
657	E	e	NN	_	_	_
658	coli	coli	NN	_	_	_
659	,	,	,	_	_	_
660	35	35	CD	_	_	_
661	min	min	NN	_	_	_
662	after	after	IN	_	_	_
663	turning	turn	VBG	_	_	_
664	off	off	RP	_	_	_
665	oxygen	oxygen	NN	_	_	_
666	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
667	E.	e.	FW	_	_	_
668	coli	coli	FW	_	_	_
669	3.5	3.5	CD	_	_	_
670	%	%	NN	_	_	_
671	NaCl	nacl	NN	_	_	_
672	,	,	,	_	_	_
673	replicate	replicate	VB	_	_	_
674	1	1	CD	_	_	_
675	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
676	E.	E.	NNP	_	_	_
677	coli	coli	NN	_	_	_
678	3.5	3.5	CD	_	_	_
679	%	%	NN	_	_	_
680	NaCl	nacl	NN	_	_	_
681	,	,	,	_	_	_
682	replicate	replicate	VB	_	_	_
683	2	2	CD	_	_	_
684	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
685	e.coli	e.coli	NNS	_	_	_
686	,	,	,	_	_	_
687	37	37	CD	_	_	_
688	°C	°c	NN	_	_	_
689	,	,	,	_	_	_
690	60	60	CD	_	_	_
691	min	min	NN	_	_	_
692	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
693	E.coli	e.coli	NNS	_	_	_
694	,	,	,	_	_	_
695	37	37	CD	_	_	_
696	°C	°c	NN	_	_	_
697	,	,	,	_	_	_
698	60	60	CD	_	_	_
699	min	min	NN	_	_	_
700	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
701	E.coli	e.coli	NN	_	_	_
702	,37	,37	CD	_	_	_
703	°C	°c	NN	_	_	_
704	,	,	,	_	_	_
705	60	60	CD	_	_	_
706	min	min	NN	_	_	_
707	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
708	E.coli	e.coli	NN	_	_	_
709	，	，	NN	_	_	_
710	37	37	CD	_	_	_
711	°C	°c	NN	_	_	_
712	，	，	CD	_	_	_
713	60	60	CD	_	_	_
714	min	min	NN	_	_	_
715	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
716	E.	E.	NNP	_	_	_
717	coli	coli	NN	_	_	_
718	37L	37l	NN	_	_	_
719	evolved	evolve	VBD	_	_	_
720	strain	strain	NN	_	_	_
721	,	,	,	_	_	_
722	under	under	IN	_	_	_
723	37ºC	37ºc	NN	_	_	_
724	,	,	,	_	_	_
725	rep	rep	NN	GEN	_	_
726	1	1	CD	_	_	_
727	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
728	E.	E.	NNP	_	_	_
729	coli	coli	NN	_	_	_
730	37L	37l	NN	_	_	_
731	evolved	evolve	VBD	_	_	_
732	strain	strain	NN	_	_	_
733	,	,	,	_	_	_
734	under	under	IN	_	_	_
735	37ºC	37ºc	NN	_	_	_
736	,	,	,	_	_	_
737	rep	rep	NN	GEN	_	_
738	2	2	CD	_	_	_
739	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
740	E.	E.	NNP	_	_	_
741	coli	coli	NN	_	_	_
742	37L	37l	NN	_	_	_
743	evolved	evolve	VBD	_	_	_
744	strain	strain	NN	_	_	_
745	,	,	,	_	_	_
746	under	under	IN	_	_	_
747	37ºC	37ºc	NN	_	_	_
748	,	,	,	_	_	_
749	rep	rep	NN	GEN	_	_
750	3	3	CD	_	_	_
751	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
752	E.	E.	NNP	_	_	_
753	coli	coli	NN	_	_	_
754	3	3	CD	_	_	_
755	'	'	''	_	_	_
756	RACE	race	NN	_	_	_
757	Rep1	rep1	JJ	_	_	_
758	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
759	E.	e.	FW	_	_	_
760	coli	coli	FW	_	_	_
761	3	3	CD	_	_	_
762	'	'	''	_	_	_
763	RACE	race	NN	_	_	_
764	Rep2	rep2	JJ	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
766	E.	e.	FW	_	_	_
767	coli	coli	FW	_	_	_
768	41B	41b	NN	_	_	_
769	evolved	evolve	VBD	_	_	_
770	strain	strain	NN	_	_	_
771	,	,	,	_	_	_
772	evolutionary	evolutionary	JJ	_	_	_
773	temperature	temperature	NN	_	_	_
774	,	,	,	_	_	_
775	rep	rep	NN	GEN	_	_
776	1	1	CD	_	_	_
777	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
778	E.	E.	NNP	_	_	_
779	coli	coli	NN	_	_	_
780	41B	41b	NN	_	_	_
781	evolved	evolve	VBD	_	_	_
782	strain	strain	NN	_	_	_
783	,	,	,	_	_	_
784	evolutionary	evolutionary	JJ	_	_	_
785	temperature	temperature	NN	_	_	_
786	,	,	,	_	_	_
787	rep	rep	NN	GEN	_	_
788	2	2	CD	_	_	_
789	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
790	E.	E.	NNP	_	_	_
791	coli	coli	NN	_	_	_
792	41B	41b	NN	_	_	_
793	evolved	evolve	VBD	_	_	_
794	strain	strain	NN	_	_	_
795	,	,	,	_	_	_
796	evolutionary	evolutionary	JJ	_	_	_
797	temperature	temperature	NN	_	_	_
798	,	,	,	_	_	_
799	rep	rep	NN	GEN	_	_
800	3	3	CD	_	_	_
801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
802	E.	e.	FW	_	_	_
803	coli	coli	FW	_	_	_
804	41B	41b	NN	_	_	_
805	evolved	evolve	VBD	_	_	_
806	strain	strain	NN	_	_	_
807	,	,	,	_	_	_
808	regular	regular	JJ	_	_	_
809	temperature	temperature	NN	_	_	_
810	,	,	,	_	_	_
811	rep	rep	NN	GEN	_	_
812	1	1	CD	_	_	_
813	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
814	E.	E.	NNP	_	_	_
815	coli	coli	NN	_	_	_
816	41B	41b	NN	_	_	_
817	evolved	evolve	VBD	_	_	_
818	strain	strain	NN	_	_	_
819	,	,	,	_	_	_
820	regular	regular	JJ	_	_	_
821	temperature	temperature	NN	_	_	_
822	,	,	,	_	_	_
823	rep	rep	NN	GEN	_	_
824	2	2	CD	_	_	_
825	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
826	E.	E.	NNP	_	_	_
827	coli	coli	NN	_	_	_
828	41B	41b	NN	_	_	_
829	evolved	evolve	VBD	_	_	_
830	strain	strain	NN	_	_	_
831	,	,	,	_	_	_
832	regular	regular	JJ	_	_	_
833	temperature	temperature	NN	_	_	_
834	,	,	,	_	_	_
835	rep	rep	NN	GEN	_	_
836	3	3	CD	_	_	_
837	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
838	E.	e.	FW	_	_	_
839	coli	coli	FW	_	_	_
840	41B	41b	NN	_	_	_
841	evolved	evolve	VBD	_	_	_
842	strain	strain	NN	_	_	_
843	,	,	,	_	_	_
844	under	under	IN	_	_	_
845	37ºC	37ºc	NN	_	_	_
846	,	,	,	_	_	_
847	rep	rep	NN	GEN	_	_
848	1	1	CD	_	_	_
849	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
850	E.	E.	NNP	_	_	_
851	coli	coli	NN	_	_	_
852	41B	41b	NN	_	_	_
853	evolved	evolve	VBD	_	_	_
854	strain	strain	NN	_	_	_
855	,	,	,	_	_	_
856	under	under	IN	_	_	_
857	37ºC	37ºc	NN	_	_	_
858	,	,	,	_	_	_
859	rep	rep	NN	GEN	_	_
860	2	2	CD	_	_	_
861	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
862	E.	E.	NNP	_	_	_
863	coli	coli	NN	_	_	_
864	41B	41b	NN	_	_	_
865	evolved	evolve	VBD	_	_	_
866	strain	strain	NN	_	_	_
867	,	,	,	_	_	_
868	under	under	IN	_	_	_
869	37ºC	37ºc	NN	_	_	_
870	,	,	,	_	_	_
871	rep	rep	NN	GEN	_	_
872	3	3	CD	_	_	_
873	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
874	E.	e.	FW	_	_	_
875	coli	coli	FW	_	_	_
876	41B	41b	NN	_	_	_
877	evolved	evolve	VBD	_	_	_
878	strain	strain	NN	_	_	_
879	,	,	,	_	_	_
880	under	under	IN	_	_	_
881	41ºC	41ºc	NN	_	_	_
882	,	,	,	_	_	_
883	rep	rep	NN	GEN	_	_
884	1	1	CD	_	_	_
885	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
886	E.	E.	NNP	_	_	_
887	coli	coli	NN	_	_	_
888	41B	41b	NN	_	_	_
889	evolved	evolve	VBD	_	_	_
890	strain	strain	NN	_	_	_
891	,	,	,	_	_	_
892	under	under	IN	_	_	_
893	41ºC	41ºc	NN	_	_	_
894	,	,	,	_	_	_
895	rep	rep	NN	GEN	_	_
896	2	2	CD	_	_	_
897	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
898	E.	E.	NNP	_	_	_
899	coli	coli	NN	_	_	_
900	41B	41b	NN	_	_	_
901	evolved	evolve	VBD	_	_	_
902	strain	strain	NN	_	_	_
903	,	,	,	_	_	_
904	under	under	IN	_	_	_
905	41ºC	41ºc	NN	_	_	_
906	,	,	,	_	_	_
907	rep	rep	NN	GEN	_	_
908	3	3	CD	_	_	_
909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
910	E.	e.	FW	_	_	_
911	coli	coli	FW	_	_	_
912	41B	41b	NN	_	_	_
913	strain	strain	NN	_	_	_
914	,	,	,	_	_	_
915	30	30	CD	_	_	_
916	min	min	NN	_	_	_
917	heat	heat	NN	_	_	_
918	shock	shock	NN	_	_	_
919	at	at	IN	_	_	_
920	45ºC	45ºc	NN	_	_	_
921	,	,	,	_	_	_
922	rep	rep	NN	GEN	_	_
923	1	1	CD	_	_	_
924	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
925	E.	E.	NNP	_	_	_
926	coli	coli	NN	_	_	_
927	41B	41b	NN	_	_	_
928	strain	strain	NN	_	_	_
929	,	,	,	_	_	_
930	30	30	CD	_	_	_
931	min	min	NN	_	_	_
932	heat	heat	NN	_	_	_
933	shock	shock	NN	_	_	_
934	at	at	IN	_	_	_
935	45ºC	45ºc	NN	_	_	_
936	,	,	,	_	_	_
937	rep	rep	NN	GEN	_	_
938	2	2	CD	_	_	_
939	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
940	E.	E.	NNP	_	_	_
941	coli	coli	NN	_	_	_
942	41B	41b	NN	_	_	_
943	strain	strain	NN	_	_	_
944	,	,	,	_	_	_
945	5	5	CD	_	_	_
946	min	min	NN	_	_	_
947	heat	heat	NN	_	_	_
948	shock	shock	NN	_	_	_
949	at	at	IN	_	_	_
950	45ºC	45ºc	NN	_	_	_
951	,	,	,	_	_	_
952	rep	rep	NN	GEN	_	_
953	1	1	CD	_	_	_
954	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
955	E.	E.	NNP	_	_	_
956	coli	coli	NN	_	_	_
957	41B	41b	NN	_	_	_
958	strain	strain	NN	_	_	_
959	,	,	,	_	_	_
960	5	5	CD	_	_	_
961	min	min	NN	_	_	_
962	heat	heat	NN	_	_	_
963	shock	shock	NN	_	_	_
964	at	at	IN	_	_	_
965	45ºC	45ºc	NN	_	_	_
966	,	,	,	_	_	_
967	rep	rep	NN	GEN	_	_
968	2	2	CD	_	_	_
969	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
970	E.	E.	NNP	_	_	_
971	coli	coli	NN	_	_	_
972	41B	41b	NN	_	_	_
973	strain	strain	NN	_	_	_
974	,	,	,	_	_	_
975	heat	heat	NN	_	_	_
976	shock	shock	NN	_	_	_
977	,	,	,	_	_	_
978	long	long	RB	_	_	_
979	,	,	,	_	_	_
980	rep	rep	NN	GEN	_	_
981	1	1	CD	_	_	_
982	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
983	E.	E.	NNP	_	_	_
984	coli	coli	NN	_	_	_
985	41B	41b	NN	_	_	_
986	strain	strain	NN	_	_	_
987	,	,	,	_	_	_
988	heat	heat	NN	_	_	_
989	shock	shock	NN	_	_	_
990	,	,	,	_	_	_
991	long	long	RB	_	_	_
992	,	,	,	_	_	_
993	rep	rep	NN	GEN	_	_
994	2	2	CD	_	_	_
995	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
996	E.	E.	NNP	_	_	_
997	coli	coli	NN	_	_	_
998	41B	41b	NN	_	_	_
999	strain	strain	NN	_	_	_
1000	,	,	,	_	_	_
1001	heat	heat	NN	_	_	_
1002	shock	shock	NN	_	_	_
1003	,	,	,	_	_	_
1004	rep	rep	NN	GEN	_	_
1005	1	1	CD	_	_	_
1006	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1007	E.	E.	NNP	_	_	_
1008	coli	coli	NN	_	_	_
1009	41B	41b	NN	_	_	_
1010	strain	strain	NN	_	_	_
1011	,	,	,	_	_	_
1012	heat	heat	NN	_	_	_
1013	shock	shock	NN	_	_	_
1014	,	,	,	_	_	_
1015	rep	rep	NN	GEN	_	_
1016	2	2	CD	_	_	_
1017	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1018	E.	E.	NNP	_	_	_
1019	coli	coli	NN	_	_	_
1020	43B	43b	NN	_	_	_
1021	evolved	evolve	VBD	_	_	_
1022	strain	strain	NN	_	_	_
1023	,	,	,	_	_	_
1024	evolutionary	evolutionary	JJ	_	_	_
1025	temperature	temperature	NN	_	_	_
1026	,	,	,	_	_	_
1027	rep	rep	NN	GEN	_	_
1028	1	1	CD	_	_	_
1029	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1030	E.	E.	NNP	_	_	_
1031	coli	coli	NN	_	_	_
1032	43B	43b	NN	_	_	_
1033	evolved	evolve	VBD	_	_	_
1034	strain	strain	NN	_	_	_
1035	,	,	,	_	_	_
1036	evolutionary	evolutionary	JJ	_	_	_
1037	temperature	temperature	NN	_	_	_
1038	,	,	,	_	_	_
1039	rep	rep	NN	GEN	_	_
1040	2	2	CD	_	_	_
1041	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1042	E.	E.	NNP	_	_	_
1043	coli	coli	NN	_	_	_
1044	43B	43b	NN	_	_	_
1045	evolved	evolve	VBD	_	_	_
1046	strain	strain	NN	_	_	_
1047	,	,	,	_	_	_
1048	evolutionary	evolutionary	JJ	_	_	_
1049	temperature	temperature	NN	_	_	_
1050	,	,	,	_	_	_
1051	rep	rep	NN	GEN	_	_
1052	3	3	CD	_	_	_
1053	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1054	E.	e.	FW	_	_	_
1055	coli	coli	FW	_	_	_
1056	43B	43b	NN	_	_	_
1057	evolved	evolve	VBD	_	_	_
1058	strain	strain	NN	_	_	_
1059	,	,	,	_	_	_
1060	regular	regular	JJ	_	_	_
1061	temperature	temperature	NN	_	_	_
1062	,	,	,	_	_	_
1063	rep	rep	NN	GEN	_	_
1064	1	1	CD	_	_	_
1065	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1066	E.	E.	NNP	_	_	_
1067	coli	coli	NN	_	_	_
1068	43B	43b	NN	_	_	_
1069	evolved	evolve	VBD	_	_	_
1070	strain	strain	NN	_	_	_
1071	,	,	,	_	_	_
1072	regular	regular	JJ	_	_	_
1073	temperature	temperature	NN	_	_	_
1074	,	,	,	_	_	_
1075	rep	rep	NN	GEN	_	_
1076	2	2	CD	_	_	_
1077	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1078	E.	E.	NNP	_	_	_
1079	coli	coli	NN	_	_	_
1080	43B	43b	NN	_	_	_
1081	evolved	evolve	VBD	_	_	_
1082	strain	strain	NN	_	_	_
1083	,	,	,	_	_	_
1084	regular	regular	JJ	_	_	_
1085	temperature	temperature	NN	_	_	_
1086	,	,	,	_	_	_
1087	rep	rep	NN	GEN	_	_
1088	3	3	CD	_	_	_
1089	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1090	E.	e.	FW	_	_	_
1091	coli	coli	FW	_	_	_
1092	43B	43b	NN	_	_	_
1093	evolved	evolve	VBD	_	_	_
1094	strain	strain	NN	_	_	_
1095	,	,	,	_	_	_
1096	under	under	IN	_	_	_
1097	37ºC	37ºc	NN	_	_	_
1098	,	,	,	_	_	_
1099	rep	rep	NN	GEN	_	_
1100	1	1	CD	_	_	_
1101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1102	E.	E.	NNP	_	_	_
1103	coli	coli	NN	_	_	_
1104	43B	43b	NN	_	_	_
1105	evolved	evolve	VBD	_	_	_
1106	strain	strain	NN	_	_	_
1107	,	,	,	_	_	_
1108	under	under	IN	_	_	_
1109	37ºC	37ºc	NN	_	_	_
1110	,	,	,	_	_	_
1111	rep	rep	NN	GEN	_	_
1112	2	2	CD	_	_	_
1113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1114	E.	E.	NNP	_	_	_
1115	coli	coli	NN	_	_	_
1116	43B	43b	NN	_	_	_
1117	evolved	evolve	VBD	_	_	_
1118	strain	strain	NN	_	_	_
1119	,	,	,	_	_	_
1120	under	under	IN	_	_	_
1121	37ºC	37ºc	NN	_	_	_
1122	,	,	,	_	_	_
1123	rep	rep	NN	GEN	_	_
1124	3	3	CD	_	_	_
1125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1126	E.	e.	FW	_	_	_
1127	coli	coli	FW	_	_	_
1128	43B	43b	NN	_	_	_
1129	evolved	evolve	VBD	_	_	_
1130	strain	strain	NN	_	_	_
1131	,	,	,	_	_	_
1132	under	under	IN	_	_	_
1133	43ºC	43ºc	NN	_	_	_
1134	,	,	,	_	_	_
1135	rep	rep	NN	GEN	_	_
1136	1	1	CD	_	_	_
1137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1138	E.	E.	NNP	_	_	_
1139	coli	coli	NN	_	_	_
1140	43B	43b	NN	_	_	_
1141	evolved	evolve	VBD	_	_	_
1142	strain	strain	NN	_	_	_
1143	,	,	,	_	_	_
1144	under	under	IN	_	_	_
1145	43ºC	43ºc	NN	_	_	_
1146	,	,	,	_	_	_
1147	rep	rep	NN	GEN	_	_
1148	2	2	CD	_	_	_
1149	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1150	E.	E.	NNP	_	_	_
1151	coli	coli	NN	_	_	_
1152	43B	43b	NN	_	_	_
1153	evolved	evolve	VBD	_	_	_
1154	strain	strain	NN	_	_	_
1155	,	,	,	_	_	_
1156	under	under	IN	_	_	_
1157	43ºC	43ºc	NN	_	_	_
1158	,	,	,	_	_	_
1159	rep	rep	NN	GEN	_	_
1160	3	3	CD	_	_	_
1161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1162	E.	e.	FW	_	_	_
1163	coli	coli	FW	_	_	_
1164	43B	43b	NN	_	_	_
1165	strain	strain	NN	_	_	_
1166	,	,	,	_	_	_
1167	30	30	CD	_	_	_
1168	min	min	NN	_	_	_
1169	heat	heat	NN	_	_	_
1170	shock	shock	NN	_	_	_
1171	at	at	IN	_	_	_
1172	45ºC	45ºc	NN	_	_	_
1173	,	,	,	_	_	_
1174	rep	rep	NN	GEN	_	_
1175	1	1	CD	_	_	_
1176	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1177	E.	E.	NNP	_	_	_
1178	coli	coli	NN	_	_	_
1179	43B	43b	NN	_	_	_
1180	strain	strain	NN	_	_	_
1181	,	,	,	_	_	_
1182	30	30	CD	_	_	_
1183	min	min	NN	_	_	_
1184	heat	heat	NN	_	_	_
1185	shock	shock	NN	_	_	_
1186	at	at	IN	_	_	_
1187	45ºC	45ºc	NN	_	_	_
1188	,	,	,	_	_	_
1189	rep	rep	NN	GEN	_	_
1190	2	2	CD	_	_	_
1191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1192	E.	E.	NNP	_	_	_
1193	coli	coli	NN	_	_	_
1194	43B	43b	NN	_	_	_
1195	strain	strain	NN	_	_	_
1196	,	,	,	_	_	_
1197	5	5	CD	_	_	_
1198	min	min	NN	_	_	_
1199	heat	heat	NN	_	_	_
1200	shock	shock	NN	_	_	_
1201	at	at	IN	_	_	_
1202	45ºC	45ºc	NN	_	_	_
1203	,	,	,	_	_	_
1204	rep	rep	NN	GEN	_	_
1205	1	1	CD	_	_	_
1206	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1207	E.	E.	NNP	_	_	_
1208	coli	coli	NN	_	_	_
1209	43B	43b	NN	_	_	_
1210	strain	strain	NN	_	_	_
1211	,	,	,	_	_	_
1212	5	5	CD	_	_	_
1213	min	min	NN	_	_	_
1214	heat	heat	NN	_	_	_
1215	shock	shock	NN	_	_	_
1216	at	at	IN	_	_	_
1217	45ºC	45ºc	NN	_	_	_
1218	,	,	,	_	_	_
1219	rep	rep	NN	GEN	_	_
1220	2	2	CD	_	_	_
1221	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1222	E.	E.	NNP	_	_	_
1223	coli	coli	NN	_	_	_
1224	43B	43b	NN	_	_	_
1225	strain	strain	NN	_	_	_
1226	,	,	,	_	_	_
1227	heat	heat	NN	_	_	_
1228	shock	shock	NN	_	_	_
1229	,	,	,	_	_	_
1230	long	long	RB	_	_	_
1231	,	,	,	_	_	_
1232	rep	rep	NN	GEN	_	_
1233	1	1	CD	_	_	_
1234	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1235	E.	E.	NNP	_	_	_
1236	coli	coli	NN	_	_	_
1237	43B	43b	NN	_	_	_
1238	strain	strain	NN	_	_	_
1239	,	,	,	_	_	_
1240	heat	heat	NN	_	_	_
1241	shock	shock	NN	_	_	_
1242	,	,	,	_	_	_
1243	long	long	RB	_	_	_
1244	,	,	,	_	_	_
1245	rep	rep	NN	GEN	_	_
1246	2	2	CD	_	_	_
1247	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1248	E.	E.	NNP	_	_	_
1249	coli	coli	NN	_	_	_
1250	43B	43b	NN	_	_	_
1251	strain	strain	NN	_	_	_
1252	,	,	,	_	_	_
1253	heat	heat	NN	_	_	_
1254	shock	shock	NN	_	_	_
1255	,	,	,	_	_	_
1256	rep	rep	NN	GEN	_	_
1257	1	1	CD	_	_	_
1258	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1259	E.	E.	NNP	_	_	_
1260	coli	coli	NN	_	_	_
1261	43B	43b	NN	_	_	_
1262	strain	strain	NN	_	_	_
1263	,	,	,	_	_	_
1264	heat	heat	NN	_	_	_
1265	shock	shock	NN	_	_	_
1266	,	,	,	_	_	_
1267	rep	rep	NN	GEN	_	_
1268	2	2	CD	_	_	_
1269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1270	e.coli	e.coli	NNS	_	_	_
1271	,	,	,	_	_	_
1272	43	43	CD	_	_	_
1273	°C	°c	NN	_	_	_
1274	,	,	,	_	_	_
1275	60	60	CD	_	_	_
1276	min	min	NN	_	_	_
1277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1278	E.coli	e.coli	NNS	_	_	_
1279	,	,	,	_	_	_
1280	43	43	CD	_	_	_
1281	°C	°c	NN	_	_	_
1282	,	,	,	_	_	_
1283	60	60	CD	_	_	_
1284	min	min	NN	_	_	_
1285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1286	E.coli	e.coli	NN	_	_	_
1287	,43	,43	CD	_	_	_
1288	°C	°c	NN	_	_	_
1289	,	,	,	_	_	_
1290	60	60	CD	_	_	_
1291	min	min	NN	_	_	_
1292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1293	E.coli	e.coli	NN	_	_	_
1294	，	，	CD	_	_	_
1295	43	43	CD	_	_	_
1296	°C	°c	NN	_	_	_
1297	，	，	CD	_	_	_
1298	60	60	CD	_	_	_
1299	min	min	NN	_	_	_
1300	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1301	E.	E.	NNP	_	_	_
1302	coli	coli	NN	_	_	_
1303	45L	45l	NN	_	_	_
1304	evolved	evolve	VBD	_	_	_
1305	strain	strain	NN	_	_	_
1306	,	,	,	_	_	_
1307	evolutionary	evolutionary	JJ	_	_	_
1308	temperature	temperature	NN	_	_	_
1309	,	,	,	_	_	_
1310	rep	rep	NN	GEN	_	_
1311	1	1	CD	_	_	_
1312	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1313	E.	E.	NNP	_	_	_
1314	coli	coli	NN	_	_	_
1315	45L	45l	NN	_	_	_
1316	evolved	evolve	VBD	_	_	_
1317	strain	strain	NN	_	_	_
1318	,	,	,	_	_	_
1319	evolutionary	evolutionary	JJ	_	_	_
1320	temperature	temperature	NN	_	_	_
1321	,	,	,	_	_	_
1322	rep	rep	NN	GEN	_	_
1323	2	2	CD	_	_	_
1324	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1325	E.	E.	NNP	_	_	_
1326	coli	coli	NN	_	_	_
1327	45L	45l	NN	_	_	_
1328	evolved	evolve	VBD	_	_	_
1329	strain	strain	NN	_	_	_
1330	,	,	,	_	_	_
1331	evolutionary	evolutionary	JJ	_	_	_
1332	temperature	temperature	NN	_	_	_
1333	,	,	,	_	_	_
1334	rep	rep	NN	GEN	_	_
1335	3	3	CD	_	_	_
1336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1337	E.	e.	FW	_	_	_
1338	coli	coli	FW	_	_	_
1339	45L	45l	NN	_	_	_
1340	evolved	evolve	VBD	_	_	_
1341	strain	strain	NN	_	_	_
1342	,	,	,	_	_	_
1343	regular	regular	JJ	_	_	_
1344	temperature	temperature	NN	_	_	_
1345	,	,	,	_	_	_
1346	rep	rep	NN	GEN	_	_
1347	1	1	CD	_	_	_
1348	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1349	E.	E.	NNP	_	_	_
1350	coli	coli	NN	_	_	_
1351	45L	45l	NN	_	_	_
1352	evolved	evolve	VBD	_	_	_
1353	strain	strain	NN	_	_	_
1354	,	,	,	_	_	_
1355	regular	regular	JJ	_	_	_
1356	temperature	temperature	NN	_	_	_
1357	,	,	,	_	_	_
1358	rep	rep	NN	GEN	_	_
1359	2	2	CD	_	_	_
1360	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1361	E.	E.	NNP	_	_	_
1362	coli	coli	NN	_	_	_
1363	45L	45l	NN	_	_	_
1364	evolved	evolve	VBD	_	_	_
1365	strain	strain	NN	_	_	_
1366	,	,	,	_	_	_
1367	regular	regular	JJ	_	_	_
1368	temperature	temperature	NN	_	_	_
1369	,	,	,	_	_	_
1370	rep	rep	NN	GEN	_	_
1371	3	3	CD	_	_	_
1372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1373	E.	e.	FW	_	_	_
1374	coli	coli	FW	_	_	_
1375	45L	45l	NN	_	_	_
1376	evolved	evolve	VBD	_	_	_
1377	strain	strain	NN	_	_	_
1378	,	,	,	_	_	_
1379	under	under	IN	_	_	_
1380	37ºC	37ºc	NN	_	_	_
1381	,	,	,	_	_	_
1382	rep	rep	NN	GEN	_	_
1383	1	1	CD	_	_	_
1384	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1385	E.	E.	NNP	_	_	_
1386	coli	coli	NN	_	_	_
1387	45L	45l	NN	_	_	_
1388	evolved	evolve	VBD	_	_	_
1389	strain	strain	NN	_	_	_
1390	,	,	,	_	_	_
1391	under	under	IN	_	_	_
1392	37ºC	37ºc	NN	_	_	_
1393	,	,	,	_	_	_
1394	rep	rep	NN	GEN	_	_
1395	2	2	CD	_	_	_
1396	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1397	E.	E.	NNP	_	_	_
1398	coli	coli	NN	_	_	_
1399	45L	45l	NN	_	_	_
1400	evolved	evolve	VBD	_	_	_
1401	strain	strain	NN	_	_	_
1402	,	,	,	_	_	_
1403	under	under	IN	_	_	_
1404	37ºC	37ºc	NN	_	_	_
1405	,	,	,	_	_	_
1406	rep	rep	NN	GEN	_	_
1407	3	3	CD	_	_	_
1408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1409	E.	e.	FW	_	_	_
1410	coli	coli	FW	_	_	_
1411	45L	45l	NN	_	_	_
1412	evolved	evolve	VBD	_	_	_
1413	strain	strain	NN	_	_	_
1414	,	,	,	_	_	_
1415	under	under	IN	_	_	_
1416	45ºC	45ºc	NN	_	_	_
1417	,	,	,	_	_	_
1418	rep	rep	NN	GEN	_	_
1419	1	1	CD	_	_	_
1420	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1421	E.	E.	NNP	_	_	_
1422	coli	coli	NN	_	_	_
1423	45L	45l	NN	_	_	_
1424	evolved	evolve	VBD	_	_	_
1425	strain	strain	NN	_	_	_
1426	,	,	,	_	_	_
1427	under	under	IN	_	_	_
1428	45ºC	45ºc	NN	_	_	_
1429	,	,	,	_	_	_
1430	rep	rep	NN	GEN	_	_
1431	2	2	CD	_	_	_
1432	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1433	E.	E.	NNP	_	_	_
1434	coli	coli	NN	_	_	_
1435	45L	45l	NN	_	_	_
1436	evolved	evolve	VBD	_	_	_
1437	strain	strain	NN	_	_	_
1438	,	,	,	_	_	_
1439	under	under	IN	_	_	_
1440	45ºC	45ºc	NN	_	_	_
1441	,	,	,	_	_	_
1442	rep	rep	NN	GEN	_	_
1443	3	3	CD	_	_	_
1444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1445	E.	e.	FW	_	_	_
1446	coli	coli	FW	_	_	_
1447	45L	45l	NN	_	_	_
1448	strain	strain	NN	_	_	_
1449	,	,	,	_	_	_
1450	30	30	CD	_	_	_
1451	min	min	NN	_	_	_
1452	heat	heat	NN	_	_	_
1453	shock	shock	NN	_	_	_
1454	at	at	IN	_	_	_
1455	45ºC	45ºc	NN	_	_	_
1456	,	,	,	_	_	_
1457	rep	rep	NN	GEN	_	_
1458	1	1	CD	_	_	_
1459	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1460	E.	E.	NNP	_	_	_
1461	coli	coli	NN	_	_	_
1462	45L	45l	NN	_	_	_
1463	strain	strain	NN	_	_	_
1464	,	,	,	_	_	_
1465	30	30	CD	_	_	_
1466	min	min	NN	_	_	_
1467	heat	heat	NN	_	_	_
1468	shock	shock	NN	_	_	_
1469	at	at	IN	_	_	_
1470	45ºC	45ºc	NN	_	_	_
1471	,	,	,	_	_	_
1472	rep	rep	NN	GEN	_	_
1473	2	2	CD	_	_	_
1474	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1475	E.	E.	NNP	_	_	_
1476	coli	coli	NN	_	_	_
1477	45L	45l	NN	_	_	_
1478	strain	strain	NN	_	_	_
1479	,	,	,	_	_	_
1480	5	5	CD	_	_	_
1481	min	min	NN	_	_	_
1482	heat	heat	NN	_	_	_
1483	shock	shock	NN	_	_	_
1484	at	at	IN	_	_	_
1485	45ºC	45ºc	NN	_	_	_
1486	,	,	,	_	_	_
1487	rep	rep	NN	GEN	_	_
1488	1	1	CD	_	_	_
1489	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1490	E.	E.	NNP	_	_	_
1491	coli	coli	NN	_	_	_
1492	45L	45l	NN	_	_	_
1493	strain	strain	NN	_	_	_
1494	,	,	,	_	_	_
1495	5	5	CD	_	_	_
1496	min	min	NN	_	_	_
1497	heat	heat	NN	_	_	_
1498	shock	shock	NN	_	_	_
1499	at	at	IN	_	_	_
1500	45ºC	45ºc	NN	_	_	_
1501	,	,	,	_	_	_
1502	rep	rep	NN	GEN	_	_
1503	2	2	CD	_	_	_
1504	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1505	E.	E.	NNP	_	_	_
1506	coli	coli	NN	_	_	_
1507	45L	45l	NN	_	_	_
1508	strain	strain	NN	_	_	_
1509	,	,	,	_	_	_
1510	heat	heat	NN	_	_	_
1511	shock	shock	NN	_	_	_
1512	,	,	,	_	_	_
1513	long	long	RB	_	_	_
1514	,	,	,	_	_	_
1515	rep	rep	NN	GEN	_	_
1516	1	1	CD	_	_	_
1517	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1518	E.	E.	NNP	_	_	_
1519	coli	coli	NN	_	_	_
1520	45L	45l	NN	_	_	_
1521	strain	strain	NN	_	_	_
1522	,	,	,	_	_	_
1523	heat	heat	NN	_	_	_
1524	shock	shock	NN	_	_	_
1525	,	,	,	_	_	_
1526	long	long	RB	_	_	_
1527	,	,	,	_	_	_
1528	rep	rep	NN	GEN	_	_
1529	2	2	CD	_	_	_
1530	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1531	E.	E.	NNP	_	_	_
1532	coli	coli	NN	_	_	_
1533	45L	45l	NN	_	_	_
1534	strain	strain	NN	_	_	_
1535	,	,	,	_	_	_
1536	heat	heat	NN	_	_	_
1537	shock	shock	NN	_	_	_
1538	,	,	,	_	_	_
1539	rep	rep	NN	GEN	_	_
1540	1	1	CD	_	_	_
1541	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1542	E.	E.	NNP	_	_	_
1543	coli	coli	NN	_	_	_
1544	45L	45l	NN	_	_	_
1545	strain	strain	NN	_	_	_
1546	,	,	,	_	_	_
1547	heat	heat	NN	_	_	_
1548	shock	shock	NN	_	_	_
1549	,	,	,	_	_	_
1550	rep	rep	NN	GEN	_	_
1551	2	2	CD	_	_	_
1552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1553	E	e	NN	_	_	_
1554	coli	coli	NN	_	_	_
1555	,	,	,	_	_	_
1556	45	45	CD	_	_	_
1557	min	min	NN	_	_	_
1558	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1559	E.	E.	NNP	_	_	_
1560	coli	coli	NN	_	_	_
1561	-	-	:	_	_	_
1562	45	45	CD	_	_	_
1563	min	min	NN	_	_	_
1564	after	after	IN	_	_	_
1565	shift	shift	NN	_	_	_
1566	to	to	TO	_	_	_
1567	limiting	limit	VBG	_	_	_
1568	medium	medium	NN	_	_	_
1569	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1570	E.	E.	NNP	_	_	_
1571	coli	coli	NN	_	_	_
1572	-	-	:	_	_	_
1573	45	45	CD	_	_	_
1574	min	min	NN	_	_	_
1575	after	after	IN	_	_	_
1576	shift	shift	NN	_	_	_
1577	to	to	TO	_	_	_
1578	thymineless	thymineless	JJ	_	_	_
1579	medium	medium	NN	_	_	_
1580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1581	E	e	NN	_	_	_
1582	coli	coli	NN	_	_	_
1583	,	,	,	_	_	_
1584	45	45	CD	_	_	_
1585	min	min	NN	_	_	_
1586	after	after	IN	_	_	_
1587	turning	turn	VBG	_	_	_
1588	off	off	RP	_	_	_
1589	oxygen	oxygen	NN	_	_	_
1590	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1591	E.coli	e.coli	NN	_	_	_
1592	45	45	CD	_	_	_
1593	minutes	minute	NNS	_	_	_
1594	after	after	IN	_	_	_
1595	BRP	BRP	NNP	_	_	_
1596	induction	induction	NN	_	_	_
1597	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1598	E.	E.	NNP	_	_	_
1599	coli	coli	NN	_	_	_
1600	4.5	4.5	CD	_	_	_
1601	%	%	NN	_	_	_
1602	NaCl	nacl	NN	_	_	_
1603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1604	E	e	NN	_	_	_
1605	coli	coli	NN	_	_	_
1606	,	,	,	_	_	_
1607	55	55	CD	_	_	_
1608	min	min	NN	_	_	_
1609	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1610	E.	E.	NNP	_	_	_
1611	coli	coli	NN	_	_	_
1612	5.5	5.5	CD	_	_	_
1613	%	%	NN	_	_	_
1614	NaCl	nacl	NN	_	_	_
1615	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1616	E	e	NN	_	_	_
1617	coli	coli	NN	_	_	_
1618	,	,	,	_	_	_
1619	5	5	CD	_	_	_
1620	min	min	NN	_	_	_
1621	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1622	Ecoli	Ecoli	NNP	_	_	_
1623	,	,	,	_	_	_
1624	5	5	CD	_	_	_
1625	min	min	NN	_	_	_
1626	after	after	IN	_	_	_
1627	turning	turn	VBG	_	_	_
1628	off	off	RP	_	_	_
1629	oxygen	oxygen	NN	_	_	_
1630	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1631	E	e	NN	_	_	_
1632	coli	coli	NN	_	_	_
1633	,	,	,	_	_	_
1634	5	5	CD	_	_	_
1635	min	min	NN	_	_	_
1636	after	after	IN	_	_	_
1637	turning	turn	VBG	_	_	_
1638	off	off	RP	_	_	_
1639	oxygen	oxygen	NN	_	_	_
1640	first	first	RB	_	_	_
1641	replicate	replicate	VB	_	_	_
1642	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1643	E.	e.	FW	_	_	_
1644	coli	coli	FW	_	_	_
1645	5	5	CD	_	_	_
1646	minute	minute	NN	_	_	_
1647	5	5	CD	_	_	_
1648	µM	µm	NN	_	_	_
1649	cadmium	cadmium	NN	_	_	_
1650	dye	dye	VB	_	_	_
1651	swap	swap	NN	_	_	_
1652	treatment	treatment	NN	_	_	_
1653	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1654	E.	E.	NNP	_	_	_
1655	coli	coli	NN	_	_	_
1656	5	5	CD	_	_	_
1657	minute	minute	NN	_	_	_
1658	5	5	CD	_	_	_
1659	µM	µm	NN	_	_	_
1660	cadmium	cadmium	NN	_	_	_
1661	treatment	treatment	NN	_	_	_
1662	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1663	E.	E.	NNP	_	_	_
1664	coli	coli	NN	_	_	_
1665	5	5	CD	_	_	_
1666	minute	minute	NN	_	_	_
1667	pH	ph	NN	_	_	_
1668	only	only	RB	_	_	_
1669	dye	dye	VB	_	_	_
1670	swap	swap	NN	_	_	_
1671	treatment	treatment	NN	_	_	_
1672	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1673	E.	E.	NNP	_	_	_
1674	coli	coli	NN	_	_	_
1675	5	5	CD	_	_	_
1676	minute	minute	NN	_	_	_
1677	pH	ph	NN	_	_	_
1678	only	only	RB	_	_	_
1679	treatment	treatment	NN	_	_	_
1680	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1681	E.	E.	NNP	_	_	_
1682	coli	coli	NN	_	_	_
1683	,	,	,	_	_	_
1684	5	5	CD	_	_	_
1685	minutes	minute	NNS	_	_	_
1686	,	,	,	_	_	_
1687	5	5	CD	_	_	_
1688	µM	µm	NN	_	_	_
1689	cadmium	cadmium	NN	_	_	_
1690	,	,	,	_	_	_
1691	pH	ph	NN	_	_	_
1692	5	5	CD	_	_	_
1693	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1694	E.	E.	NNP	_	_	_
1695	coli	coli	NN	_	_	_
1696	,	,	,	_	_	_
1697	5	5	CD	_	_	_
1698	minutes	minute	NNS	_	_	_
1699	,	,	,	_	_	_
1700	5	5	CD	_	_	_
1701	µM	µm	NN	_	_	_
1702	cadmium	cadmium	NN	_	_	_
1703	,	,	,	_	_	_
1704	pH	ph	NN	_	_	_
1705	7	7	CD	_	_	_
1706	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1707	E.coli	e.coli	NNS	_	_	_
1708	5	5	CD	_	_	_
1709	minutes	minute	NNS	_	_	_
1710	after	after	IN	_	_	_
1711	BRP	BRP	NNP	_	_	_
1712	induction	induction	NN	_	_	_
1713	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1714	E.	E.	NNP	_	_	_
1715	coli	coli	NN	_	_	_
1716	,	,	,	_	_	_
1717	5	5	CD	_	_	_
1718	minutes	minute	NNS	_	_	_
1719	,	,	,	_	_	_
1720	no	no	DT	_	_	_
1721	cadmium	cadmium	NN	_	_	_
1722	,	,	,	_	_	_
1723	pH	ph	NN	_	_	_
1724	5	5	CD	_	_	_
1725	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1726	E.	E.	NNP	_	_	_
1727	coli	coli	NN	_	_	_
1728	,	,	,	_	_	_
1729	5	5	CD	_	_	_
1730	minutes	minute	NNS	_	_	_
1731	,	,	,	_	_	_
1732	no	no	DT	_	_	_
1733	cadmium	cadmium	NN	_	_	_
1734	,	,	,	_	_	_
1735	pH	ph	NN	_	_	_
1736	7	7	CD	_	_	_
1737	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1738	E.	e.	FW	_	_	_
1739	coli	coli	FW	_	_	_
1740	5	5	CD	_	_	_
1741	%	%	NN	_	_	_
1742	NaCl	nacl	NN	_	_	_
1743	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1744	E.	E.	NNP	_	_	_
1745	coli	coli	NN	_	_	_
1746	-	-	:	_	_	_
1747	60	60	CD	_	_	_
1748	min	min	NN	_	_	_
1749	after	after	IN	_	_	_
1750	shift	shift	NN	_	_	_
1751	to	to	TO	_	_	_
1752	limiting	limit	VBG	_	_	_
1753	medium	medium	NN	_	_	_
1754	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1755	E.	E.	NNP	_	_	_
1756	coli	coli	NN	_	_	_
1757	-	-	:	_	_	_
1758	60	60	CD	_	_	_
1759	min	min	NN	_	_	_
1760	after	after	IN	_	_	_
1761	shift	shift	NN	_	_	_
1762	to	to	TO	_	_	_
1763	thymineless	thymineless	JJ	_	_	_
1764	medium	medium	NN	_	_	_
1765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1766	E.coli	e.coli	NN	_	_	_
1767	60	60	CD	_	_	_
1768	minutes	minute	NNS	_	_	_
1769	after	after	IN	_	_	_
1770	BRP	BRP	NNP	_	_	_
1771	induction	induction	NN	_	_	_
1772	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1773	E.	E.	NNP	_	_	_
1774	coli	coli	NN	_	_	_
1775	7	7	CD	_	_	_
1776	mins	min	NNS	_	_	_
1777	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1778	E.	e.	FW	_	_	_
1779	coli	coli	FW	_	_	_
1780	8624	8624	CD	_	_	_
1781	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1782	E.	E.	NNP	_	_	_
1783	coli	coli	NN	_	_	_
1784	8624	8624	CD	_	_	_
1785	qseF	qsef	NN	_	_	_
1786	deletion	deletion	NN	_	_	_
1787	mutant	mutant	JJ	_	_	_
1788	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1789	E.	e.	FW	_	_	_
1790	coli	coli	FW	_	_	_
1791	8624	8624	CD	_	_	_
1792	WT	WT	NNP	_	_	_
1793	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1794	E.	E.	NNP	_	_	_
1795	coli	coli	NN	_	_	_
1796	-	-	:	_	_	_
1797	90	90	CD	_	_	_
1798	min	min	NN	_	_	_
1799	after	after	IN	_	_	_
1800	shift	shift	NN	_	_	_
1801	to	to	TO	_	_	_
1802	limiting	limit	VBG	_	_	_
1803	medium	medium	NN	_	_	_
1804	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1805	E.	E.	NNP	_	_	_
1806	coli	coli	NN	_	_	_
1807	-	-	:	_	_	_
1808	90	90	CD	_	_	_
1809	min	min	NN	_	_	_
1810	after	after	IN	_	_	_
1811	shift	shift	NN	_	_	_
1812	to	to	TO	_	_	_
1813	thymineless	thymineless	JJ	_	_	_
1814	medium	medium	NN	_	_	_
1815	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1816	E.	E.	NNP	_	_	_
1817	coli	coli	NN	_	_	_
1818	AcrA	AcrA	NNP	_	_	_
1819	Multidrug	Multidrug	NNP	_	_	_
1820	Efflux	Efflux	NNP	_	_	_
1821	Mutant	mutant	JJ	_	_	_
1822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1823	E.	e.	FW	_	_	_
1824	coli	coli	FW	_	_	_
1825	AcrB	acrb	NN	_	_	_
1826	and	and	CC	_	_	_
1827	EmrAB	EmrAB	NNP	_	_	_
1828	Multidrug	Multidrug	NNP	_	_	_
1829	Efflux	Efflux	NNP	_	_	_
1830	Double	double	JJ	_	_	_
1831	Mutant	mutant	JJ	_	_	_
1832	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1833	E.	e.	FW	_	_	_
1834	coli	coli	FW	_	_	_
1835	AcrB	acrb	NN	_	_	_
1836	Multidrug	multidrug	JJ	_	_	_
1837	Efflux	efflux	NN	_	_	_
1838	Mutant	mutant	JJ	_	_	_
1839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1840	ecoli	ecolus	NNS	_	_	_
1841	_	_	VBP	_	_	_
1842	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1843	_	_	NN	_	_	_
1844	0	0	CD	_	_	_
1845	min	min	NN	_	_	_
1846	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1847	ecoli	ecolus	NNS	_	_	_
1848	_	_	VBP	_	_	_
1849	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1850	_	_	NN	_	_	_
1851	15	15	CD	_	_	_
1852	min	min	NN	_	_	_
1853	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1854	ecoli	ecolus	NNS	_	_	_
1855	_	_	VBP	_	_	_
1856	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1857	_	_	NN	_	_	_
1858	25	25	CD	_	_	_
1859	min	min	NN	_	_	_
1860	_	_	CD	_	_	_
1861	rep1	rep1	NN	_	_	_
1862	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1863	ecoli	ecolus	NNS	_	_	_
1864	_	_	VBP	_	_	_
1865	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1866	_	_	NN	_	_	_
1867	25	25	CD	_	_	_
1868	min	min	NN	_	_	_
1869	_	_	CD	_	_	_
1870	rep2	rep2	NN	_	_	_
1871	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1872	ecoli	ecolus	NNS	_	_	_
1873	_	_	VBP	_	_	_
1874	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1875	_	_	NN	_	_	_
1876	2	2	CD	_	_	_
1877	min	min	NN	_	_	_
1878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1879	ecoli	ecolus	NNS	_	_	_
1880	_	_	VBP	_	_	_
1881	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1882	_	_	NN	_	_	_
1883	35	35	CD	_	_	_
1884	min	min	NN	_	_	_
1885	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1886	ecoli	ecolus	NNS	_	_	_
1887	_	_	VBP	_	_	_
1888	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1889	_	_	NN	_	_	_
1890	45	45	CD	_	_	_
1891	min	min	NN	_	_	_
1892	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1893	ecoli	ecolus	NNS	_	_	_
1894	_	_	VBP	_	_	_
1895	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1896	_	_	NN	_	_	_
1897	55	55	CD	_	_	_
1898	min	min	NN	_	_	_
1899	_	_	CD	_	_	_
1900	rep1	rep1	NN	_	_	_
1901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1902	ecoli	ecolus	NNS	_	_	_
1903	_	_	VBP	_	_	_
1904	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1905	_	_	NN	_	_	_
1906	55	55	CD	_	_	_
1907	min	min	NN	_	_	_
1908	_	_	CD	_	_	_
1909	rep2	rep2	NN	_	_	_
1910	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1911	ecoli	ecolus	NNS	_	_	_
1912	_	_	VBP	_	_	_
1913	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1914	_	_	NN	_	_	_
1915	5	5	CD	_	_	_
1916	min	min	NN	_	_	_
1917	_	_	SYM	_	_	_
1918	Rep1	rep1	JJ	_	_	_
1919	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1920	ecoli	ecolus	NNS	_	_	_
1921	_	_	VBP	_	_	_
1922	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
1923	_	_	NN	_	_	_
1924	5	5	CD	_	_	_
1925	min	min	NN	_	_	_
1926	_	_	CD	_	_	_
1927	rep2	rep2	NN	_	_	_
1928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1929	Ecoli	ecolus	NNS	_	_	_
1930	_	_	VBP	_	_	_
1931	Ag0	ag0	NN	_	_	_
1932	.0	.0	CD	_	_	_
1933	_	_	NN	_	_	_
1934	rep1	rep1	NN	_	_	_
1935	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1936	Ecoli	ecolus	NNS	_	_	_
1937	_	_	VBP	_	_	_
1938	Ag0	ag0	NN	_	_	_
1939	.0	.0	CD	_	_	_
1940	_	_	NN	_	_	_
1941	rep2	rep2	NN	_	_	_
1942	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1943	Ecoli	ecolus	NNS	_	_	_
1944	_	_	VBP	_	_	_
1945	Ag0	ag0	NN	_	_	_
1946	.0	.0	CD	_	_	_
1947	_	_	NN	_	_	_
1948	rep3	rep3	NN	_	_	_
1949	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1950	Ecoli	ecolus	NNS	_	_	_
1951	_	_	VBP	_	_	_
1952	Ag5	ag5	NN	_	_	_
1953	.0	.0	CD	_	_	_
1954	_	_	NN	_	_	_
1955	rep1	rep1	NN	_	_	_
1956	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1957	Ecoli	ecolus	NNS	_	_	_
1958	_	_	VBP	_	_	_
1959	Ag5	ag5	NN	_	_	_
1960	.0	.0	CD	_	_	_
1961	_	_	NN	_	_	_
1962	rep2	rep2	NN	_	_	_
1963	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1964	Ecoli	ecolus	NNS	_	_	_
1965	_	_	VBP	_	_	_
1966	Ag5	ag5	NN	_	_	_
1967	.0	.0	CD	_	_	_
1968	_	_	NN	_	_	_
1969	rep3	rep3	NN	_	_	_
1970	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1971	Ecoli	ecolus	NNS	_	_	_
1972	_	_	VBP	_	_	_
1973	Ag6	ag6	NN	_	_	_
1974	.5	.5	CD	_	_	_
1975	_	_	NN	_	_	_
1976	rep1	rep1	NN	_	_	_
1977	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1978	Ecoli	ecolus	NNS	_	_	_
1979	_	_	VBP	_	_	_
1980	Ag6	ag6	NN	_	_	_
1981	.5	.5	CD	_	_	_
1982	_	_	NN	_	_	_
1983	rep2	rep2	NN	_	_	_
1984	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1985	Ecoli	ecolus	NNS	_	_	_
1986	_	_	VBP	_	_	_
1987	Ag6	ag6	NN	_	_	_
1988	.5	.5	CD	_	_	_
1989	_	_	NN	_	_	_
1990	rep3	rep3	NN	_	_	_
1991	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1992	Ecoli	ecolus	NNS	_	_	_
1993	_	_	VBP	_	_	_
1994	Ag8	ag8	NN	_	_	_
1995	.5	.5	CD	_	_	_
1996	_	_	NN	_	_	_
1997	rep1	rep1	NN	_	_	_
1998	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1999	Ecoli	ecolus	NNS	_	_	_
2000	_	_	VBP	_	_	_
2001	Ag8	ag8	NN	_	_	_
2002	.5	.5	CD	_	_	_
2003	_	_	NN	_	_	_
2004	rep2	rep2	NN	_	_	_
2005	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2006	Ecoli	ecolus	NNS	_	_	_
2007	_	_	VBP	_	_	_
2008	Ag8	ag8	NN	_	_	_
2009	.5	.5	CD	_	_	_
2010	_	_	SYM	_	_	_
2011	rep3	rep3	CD	_	_	_
2012	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2013	Ecoli	Ecoli	NNP	_	_	_
2014	_	_	NNP	_	_	_
2015	Ampicillin	Ampicillin	NNP	_	_	_
2016	treatment	treatment	NN	_	_	_
2017	T1	t1	NN	_	_	_
2018	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2019	Ecoli	Ecoli	NNP	_	_	_
2020	_	_	NNP	_	_	_
2021	Ampicillin	Ampicillin	NNP	_	_	_
2022	treatment	treatment	NN	_	_	_
2023	T2	t2	NN	_	_	_
2024	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2025	Ecoli	Ecoli	NNP	_	_	_
2026	_	_	NNP	_	_	_
2027	Ampicillin	Ampicillin	NNP	_	_	_
2028	treatment	treatment	NN	_	_	_
2029	T3	t3	NN	_	_	_
2030	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2031	Ecoli	Ecoli	NNP	_	_	_
2032	_	_	NNP	_	_	_
2033	Ampicillin	Ampicillin	NNP	_	_	_
2034	treatment	treatment	NN	_	_	_
2035	T4	t4	NN	_	_	_
2036	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2037	Ecoli	Ecoli	NNP	_	_	_
2038	_	_	NNP	_	_	_
2039	Ampicillin	Ampicillin	NNP	_	_	_
2040	treatment	treatment	NN	_	_	_
2041	T5	t5	NN	_	_	_
2042	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2043	Ecoli	Ecoli	NNP	_	_	_
2044	_	_	NNP	_	_	_
2045	Ampicillin	Ampicillin	NNP	_	_	_
2046	treatment	treatment	NN	_	_	_
2047	T6	t6	NN	_	_	_
2048	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2049	Ecoli	ecolus	NNS	_	_	_
2050	_	_	VBP	_	_	_
2051	Anaerobic	anaerobic	JJ	_	_	_
2052	growth	growth	NN	_	_	_
2053	in	in	IN	_	_	_
2054	M9	m9	NN	_	_	_
2055	+	+	CC	_	_	_
2056	glucose	glucose	NN	SUPP	_	_
2057	+	+	CC	_	_	_
2058	fumarate	fumarate	NN	SUPP	_	_
2059	,	,	,	_	_	_
2060	reference	reference	NN	_	_	_
2061	Genomic	genomic	JJ	_	_	_
2062	DNA	dna	NN	_	_	_
2063	T1	t1	NN	_	_	_
2064	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2065	Ecoli	ecolus	NNS	_	_	_
2066	_	_	VBP	_	_	_
2067	Anaerobic	anaerobic	JJ	_	_	_
2068	growth	growth	NN	_	_	_
2069	in	in	IN	_	_	_
2070	M9	m9	NN	_	_	_
2071	+	+	CC	_	_	_
2072	glucose	glucose	NN	SUPP	_	_
2073	+	+	CC	_	_	_
2074	fumarate	fumarate	NN	SUPP	_	_
2075	,	,	,	_	_	_
2076	reference	reference	NN	_	_	_
2077	Genomic	genomic	JJ	_	_	_
2078	DNA	dna	NN	_	_	_
2079	T2	t2	NN	_	_	_
2080	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2081	Ecoli	ecolus	NNS	_	_	_
2082	_	_	VBP	_	_	_
2083	Anaerobic	anaerobic	JJ	_	_	_
2084	growth	growth	NN	_	_	_
2085	in	in	IN	_	_	_
2086	M9	m9	NN	_	_	_
2087	+	+	CC	_	_	_
2088	glucose	glucose	NN	SUPP	_	_
2089	+	+	CC	_	_	_
2090	fumarate	fumarate	NN	SUPP	_	_
2091	,	,	,	_	_	_
2092	reference	reference	NN	_	_	_
2093	Genomic	genomic	JJ	_	_	_
2094	DNA	dna	NN	_	_	_
2095	T3	t3	NN	_	_	_
2096	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2097	Ecoli	ecolus	NNS	_	_	_
2098	_	_	VBP	_	_	_
2099	Anaerobic	anaerobic	JJ	_	_	_
2100	growth	growth	NN	_	_	_
2101	in	in	IN	_	_	_
2102	M9	m9	NN	_	_	_
2103	+	+	CC	_	_	_
2104	glucose	glucose	NN	SUPP	_	_
2105	+	+	CC	_	_	_
2106	fumarate	fumarate	NN	SUPP	_	_
2107	,	,	,	_	_	_
2108	reference	reference	NN	_	_	_
2109	Genomic	genomic	JJ	_	_	_
2110	DNA	dna	NN	_	_	_
2111	T4	t4	NN	_	_	_
2112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2113	Ecoli	ecolus	NNS	_	_	_
2114	_	_	VBP	_	_	_
2115	Anaerobic	anaerobic	JJ	_	_	_
2116	growth	growth	NN	_	_	_
2117	in	in	IN	_	_	_
2118	M9	m9	NN	_	_	_
2119	+	+	CC	_	_	_
2120	glucose	glucose	NN	SUPP	_	_
2121	+	+	CC	_	_	_
2122	fumarate	fumarate	NN	SUPP	_	_
2123	,	,	,	_	_	_
2124	reference	reference	NN	_	_	_
2125	Genomic	genomic	JJ	_	_	_
2126	DNA	dna	NN	_	_	_
2127	T5	t5	NN	_	_	_
2128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2129	Ecoli	ecolus	NNS	_	_	_
2130	_	_	VBP	_	_	_
2131	Anaerobic	anaerobic	JJ	_	_	_
2132	growth	growth	NN	_	_	_
2133	in	in	IN	_	_	_
2134	M9	m9	NN	_	_	_
2135	+	+	CC	_	_	_
2136	glucose	glucose	NN	SUPP	_	_
2137	+	+	CC	_	_	_
2138	fumarate	fumarate	NN	SUPP	_	_
2139	,	,	,	_	_	_
2140	reference	reference	NN	_	_	_
2141	Genomic	genomic	JJ	_	_	_
2142	DNA	dna	NN	_	_	_
2143	T6	t6	NN	_	_	_
2144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2145	Ecoli	ecolus	NNS	_	_	_
2146	_	_	VBP	_	_	_
2147	Anaerobic	anaerobic	JJ	_	_	_
2148	growth	growth	NN	_	_	_
2149	in	in	IN	_	_	_
2150	M9	m9	NN	_	_	_
2151	+	+	CC	_	_	_
2152	glucose	glucose	NN	SUPP	_	_
2153	+	+	CC	_	_	_
2154	fumarate	fumarate	NN	SUPP	_	_
2155	vs	vs	CC	_	_	_
2156	Aerobic	aerobic	JJ	_	_	_
2157	OD	od	NN	_	_	_
2158	0.4	0.4	CD	_	_	_
2159	T1	t1	NN	_	_	_
2160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2161	Ecoli	ecolus	NNS	_	_	_
2162	_	_	VBP	_	_	_
2163	Anaerobic	anaerobic	JJ	_	_	_
2164	growth	growth	NN	_	_	_
2165	in	in	IN	_	_	_
2166	M9	m9	NN	_	_	_
2167	+	+	CC	_	_	_
2168	glucose	glucose	NN	SUPP	_	_
2169	+	+	CC	_	_	_
2170	fumarate	fumarate	NN	SUPP	_	_
2171	vs	vs	CC	_	_	_
2172	Aerobic	aerobic	JJ	_	_	_
2173	OD	od	NN	_	_	_
2174	0.4	0.4	CD	_	_	_
2175	T2	t2	NN	_	_	_
2176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2177	Ecoli	ecolus	NNS	_	_	_
2178	_	_	VBP	_	_	_
2179	Anaerobic	anaerobic	JJ	_	_	_
2180	growth	growth	NN	_	_	_
2181	in	in	IN	_	_	_
2182	M9	m9	NN	_	_	_
2183	+	+	CC	_	_	_
2184	glucose	glucose	NN	SUPP	_	_
2185	+	+	CC	_	_	_
2186	fumarate	fumarate	NN	SUPP	_	_
2187	vs	vs	CC	_	_	_
2188	Aerobic	aerobic	JJ	_	_	_
2189	OD	od	NN	_	_	_
2190	0.4	0.4	CD	_	_	_
2191	T3	t3	NN	_	_	_
2192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2193	Ecoli	ecolus	NNS	_	_	_
2194	_	_	VBP	_	_	_
2195	Anaerobic	anaerobic	JJ	_	_	_
2196	growth	growth	NN	_	_	_
2197	in	in	IN	_	_	_
2198	M9	m9	NN	_	_	_
2199	+	+	CC	_	_	_
2200	glucose	glucose	NN	SUPP	_	_
2201	+	+	CC	_	_	_
2202	fumarate	fumarate	NN	SUPP	_	_
2203	vs	vs	CC	_	_	_
2204	Aerobic	aerobic	JJ	_	_	_
2205	OD	od	NN	_	_	_
2206	0.4	0.4	CD	_	_	_
2207	T4	t4	NN	_	_	_
2208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2209	Ecoli	ecolus	NNS	_	_	_
2210	_	_	VBP	_	_	_
2211	Anaerobic	anaerobic	JJ	_	_	_
2212	growth	growth	NN	_	_	_
2213	in	in	IN	_	_	_
2214	M9	m9	NN	_	_	_
2215	+	+	CC	_	_	_
2216	glucose	glucose	NN	SUPP	_	_
2217	+	+	CC	_	_	_
2218	fumarate	fumarate	NN	SUPP	_	_
2219	vs	vs	CC	_	_	_
2220	Aerobic	aerobic	JJ	_	_	_
2221	OD	od	NN	_	_	_
2222	0.4	0.4	CD	_	_	_
2223	T5	t5	NN	_	_	_
2224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2225	Ecoli	ecolus	NNS	_	_	_
2226	_	_	VBP	_	_	_
2227	Anaerobic	anaerobic	JJ	_	_	_
2228	growth	growth	NN	_	_	_
2229	in	in	IN	_	_	_
2230	M9	m9	NN	_	_	_
2231	+	+	CC	_	_	_
2232	glucose	glucose	NN	SUPP	_	_
2233	+	+	CC	_	_	_
2234	fumarate	fumarate	NN	SUPP	_	_
2235	vs	vs	CC	_	_	_
2236	Aerobic	aerobic	JJ	_	_	_
2237	OD	od	NN	_	_	_
2238	0.4	0.4	CD	_	_	_
2239	T6	t6	NN	_	_	_
2240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2241	Ecoli	ecolus	NNS	_	_	_
2242	_	_	VBP	_	_	_
2243	Anaerobic	anaerobic	JJ	_	_	_
2244	growth	growth	NN	_	_	_
2245	in	in	IN	_	_	_
2246	M9	m9	NN	_	_	_
2247	+	+	CC	_	_	_
2248	glucose	glucose	NN	SUPP	_	_
2249	,	,	,	_	_	_
2250	reference	reference	NN	_	_	_
2251	Genomic	genomic	JJ	_	_	_
2252	DNA	dna	NN	_	_	_
2253	T1	t1	NN	_	_	_
2254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2255	Ecoli	ecolus	NNS	_	_	_
2256	_	_	VBP	_	_	_
2257	Anaerobic	anaerobic	JJ	_	_	_
2258	growth	growth	NN	_	_	_
2259	in	in	IN	_	_	_
2260	M9	m9	NN	_	_	_
2261	+	+	CC	_	_	_
2262	glucose	glucose	NN	SUPP	_	_
2263	,	,	,	_	_	_
2264	reference	reference	NN	_	_	_
2265	Genomic	genomic	JJ	_	_	_
2266	DNA	dna	NN	_	_	_
2267	T2	t2	NN	_	_	_
2268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2269	Ecoli	ecolus	NNS	_	_	_
2270	_	_	VBP	_	_	_
2271	Anaerobic	anaerobic	JJ	_	_	_
2272	growth	growth	NN	_	_	_
2273	in	in	IN	_	_	_
2274	M9	m9	NN	_	_	_
2275	+	+	CC	_	_	_
2276	glucose	glucose	NN	SUPP	_	_
2277	,	,	,	_	_	_
2278	reference	reference	NN	_	_	_
2279	Genomic	genomic	JJ	_	_	_
2280	DNA	dna	NN	_	_	_
2281	T3	t3	NN	_	_	_
2282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2283	Ecoli	ecolus	NNS	_	_	_
2284	_	_	VBP	_	_	_
2285	Anaerobic	anaerobic	JJ	_	_	_
2286	growth	growth	NN	_	_	_
2287	in	in	IN	_	_	_
2288	M9	m9	NN	_	_	_
2289	+	+	CC	_	_	_
2290	glucose	glucose	NN	SUPP	_	_
2291	,	,	,	_	_	_
2292	reference	reference	NN	_	_	_
2293	Genomic	genomic	JJ	_	_	_
2294	DNA	dna	NN	_	_	_
2295	T4	t4	NN	_	_	_
2296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2297	Ecoli	ecolus	NNS	_	_	_
2298	_	_	VBP	_	_	_
2299	Anaerobic	anaerobic	JJ	_	_	_
2300	growth	growth	NN	_	_	_
2301	in	in	IN	_	_	_
2302	M9	m9	NN	_	_	_
2303	+	+	CC	_	_	_
2304	glucose	glucose	NN	SUPP	_	_
2305	,	,	,	_	_	_
2306	reference	reference	NN	_	_	_
2307	Genomic	genomic	JJ	_	_	_
2308	DNA	dna	NN	_	_	_
2309	T5	t5	NN	_	_	_
2310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2311	Ecoli	ecolus	NNS	_	_	_
2312	_	_	VBP	_	_	_
2313	Anaerobic	anaerobic	JJ	_	_	_
2314	growth	growth	NN	_	_	_
2315	in	in	IN	_	_	_
2316	M9	m9	NN	_	_	_
2317	+	+	CC	_	_	_
2318	glucose	glucose	NN	SUPP	_	_
2319	,	,	,	_	_	_
2320	reference	reference	NN	_	_	_
2321	Genomic	genomic	JJ	_	_	_
2322	DNA	dna	NN	_	_	_
2323	T6	t6	NN	_	_	_
2324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2325	Ecoli	ecolus	NNS	_	_	_
2326	_	_	VBP	_	_	_
2327	Anaerobic	anaerobic	JJ	_	_	_
2328	growth	growth	NN	_	_	_
2329	in	in	IN	_	_	_
2330	M9	m9	NN	_	_	_
2331	+	+	CC	_	_	_
2332	glucose	glucose	NN	SUPP	_	_
2333	vs	vs	CC	_	_	_
2334	Aerobic	aerobic	JJ	_	_	_
2335	OD	od	NN	_	_	_
2336	0.4	0.4	CD	_	_	_
2337	T1	t1	NN	_	_	_
2338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2339	Ecoli	ecolus	NNS	_	_	_
2340	_	_	VBP	_	_	_
2341	Anaerobic	anaerobic	JJ	_	_	_
2342	growth	growth	NN	_	_	_
2343	in	in	IN	_	_	_
2344	M9	m9	NN	_	_	_
2345	+	+	CC	_	_	_
2346	glucose	glucose	NN	SUPP	_	_
2347	vs	vs	CC	_	_	_
2348	Aerobic	aerobic	JJ	_	_	_
2349	OD	od	NN	_	_	_
2350	0.4	0.4	CD	_	_	_
2351	T2	t2	NN	_	_	_
2352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2353	Ecoli	ecolus	NNS	_	_	_
2354	_	_	VBP	_	_	_
2355	Anaerobic	anaerobic	JJ	_	_	_
2356	growth	growth	NN	_	_	_
2357	in	in	IN	_	_	_
2358	M9	m9	NN	_	_	_
2359	+	+	CC	_	_	_
2360	glucose	glucose	NN	SUPP	_	_
2361	vs	vs	CC	_	_	_
2362	Aerobic	aerobic	JJ	_	_	_
2363	OD	od	NN	_	_	_
2364	0.4	0.4	CD	_	_	_
2365	T3	t3	NN	_	_	_
2366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2367	Ecoli	ecolus	NNS	_	_	_
2368	_	_	VBP	_	_	_
2369	Anaerobic	anaerobic	JJ	_	_	_
2370	growth	growth	NN	_	_	_
2371	in	in	IN	_	_	_
2372	M9	m9	NN	_	_	_
2373	+	+	CC	_	_	_
2374	glucose	glucose	NN	SUPP	_	_
2375	vs	vs	CC	_	_	_
2376	Aerobic	aerobic	JJ	_	_	_
2377	OD	od	NN	_	_	_
2378	0.4	0.4	CD	_	_	_
2379	T4	t4	NN	_	_	_
2380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2381	Ecoli	ecolus	NNS	_	_	_
2382	_	_	VBP	_	_	_
2383	Anaerobic	anaerobic	JJ	_	_	_
2384	growth	growth	NN	_	_	_
2385	in	in	IN	_	_	_
2386	M9	m9	NN	_	_	_
2387	+	+	CC	_	_	_
2388	glucose	glucose	NN	SUPP	_	_
2389	vs	vs	CC	_	_	_
2390	Aerobic	aerobic	JJ	_	_	_
2391	OD	od	NN	_	_	_
2392	0.4	0.4	CD	_	_	_
2393	T5	t5	NN	_	_	_
2394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2395	Ecoli	ecolus	NNS	_	_	_
2396	_	_	VBP	_	_	_
2397	Anaerobic	anaerobic	JJ	_	_	_
2398	growth	growth	NN	_	_	_
2399	in	in	IN	_	_	_
2400	M9	m9	NN	_	_	_
2401	+	+	CC	_	_	_
2402	glucose	glucose	NN	SUPP	_	_
2403	vs	vs	CC	_	_	_
2404	Aerobic	aerobic	JJ	_	_	_
2405	OD	od	NN	_	_	_
2406	0.4	0.4	CD	_	_	_
2407	T6	t6	NN	_	_	_
2408	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2409	E.	E.	NNP	_	_	_
2410	coli	coli	NN	_	_	_
2411	ancestor	ancestor	NN	_	_	_
2412	strain	strain	NN	_	_	_
2413	,	,	,	_	_	_
2414	30	30	CD	_	_	_
2415	min	min	NN	_	_	_
2416	heat	heat	NN	_	_	_
2417	shock	shock	NN	_	_	_
2418	at	at	IN	_	_	_
2419	45ºC	45ºc	NN	_	_	_
2420	,	,	,	_	_	_
2421	rep	rep	NN	GEN	_	_
2422	1	1	CD	_	_	_
2423	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2424	E.	E.	NNP	_	_	_
2425	coli	coli	NN	_	_	_
2426	ancestor	ancestor	NN	_	_	_
2427	strain	strain	NN	_	_	_
2428	,	,	,	_	_	_
2429	30	30	CD	_	_	_
2430	min	min	NN	_	_	_
2431	heat	heat	NN	_	_	_
2432	shock	shock	NN	_	_	_
2433	at	at	IN	_	_	_
2434	45ºC	45ºc	NN	_	_	_
2435	,	,	,	_	_	_
2436	rep	rep	NN	GEN	_	_
2437	2	2	CD	_	_	_
2438	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2439	E.	E.	NNP	_	_	_
2440	coli	coli	NN	_	_	_
2441	ancestor	ancestor	NN	_	_	_
2442	strain	strain	NN	_	_	_
2443	,	,	,	_	_	_
2444	5	5	CD	_	_	_
2445	min	min	NN	_	_	_
2446	heat	heat	NN	_	_	_
2447	shock	shock	NN	_	_	_
2448	at	at	IN	_	_	_
2449	45ºC	45ºc	NN	_	_	_
2450	,	,	,	_	_	_
2451	rep	rep	NN	GEN	_	_
2452	1	1	CD	_	_	_
2453	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2454	E.	E.	NNP	_	_	_
2455	coli	coli	NN	_	_	_
2456	ancestor	ancestor	NN	_	_	_
2457	strain	strain	NN	_	_	_
2458	,	,	,	_	_	_
2459	5	5	CD	_	_	_
2460	min	min	NN	_	_	_
2461	heat	heat	NN	_	_	_
2462	shock	shock	NN	_	_	_
2463	at	at	IN	_	_	_
2464	45ºC	45ºc	NN	_	_	_
2465	,	,	,	_	_	_
2466	rep	rep	NN	GEN	_	_
2467	2	2	CD	_	_	_
2468	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2469	E.	E.	NNP	_	_	_
2470	coli	coli	NN	_	_	_
2471	ancestor	ancestor	NN	_	_	_
2472	strain	strain	NN	_	_	_
2473	,	,	,	_	_	_
2474	under	under	IN	_	_	_
2475	37ºC	37ºc	NN	_	_	_
2476	,	,	,	_	_	_
2477	rep	rep	NN	GEN	_	_
2478	1	1	CD	_	_	_
2479	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2480	E.	E.	NNP	_	_	_
2481	coli	coli	NN	_	_	_
2482	ancestor	ancestor	NN	_	_	_
2483	strain	strain	NN	_	_	_
2484	,	,	,	_	_	_
2485	under	under	IN	_	_	_
2486	37ºC	37ºc	NN	_	_	_
2487	,	,	,	_	_	_
2488	rep	rep	NN	GEN	_	_
2489	2	2	CD	_	_	_
2490	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2491	E.	E.	NNP	_	_	_
2492	coli	coli	NN	_	_	_
2493	ancestor	ancestor	NN	_	_	_
2494	strain	strain	NN	_	_	_
2495	,	,	,	_	_	_
2496	under	under	IN	_	_	_
2497	37ºC	37ºc	NN	_	_	_
2498	,	,	,	_	_	_
2499	rep	rep	NN	GEN	_	_
2500	3	3	CD	_	_	_
2501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2502	E.	e.	FW	_	_	_
2503	coli	coli	FW	_	_	_
2504	Anc	anc	NN	_	_	_
2505	strain	strain	NN	_	_	_
2506	,	,	,	_	_	_
2507	heat	heat	NN	_	_	_
2508	shock	shock	NN	_	_	_
2509	,	,	,	_	_	_
2510	long	long	RB	_	_	_
2511	,	,	,	_	_	_
2512	rep	rep	NN	GEN	_	_
2513	1	1	CD	_	_	_
2514	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2515	E.	e.	FW	_	_	_
2516	coli	coli	FW	_	_	_
2517	Anc	anc	NN	_	_	_
2518	strain	strain	NN	_	_	_
2519	,	,	,	_	_	_
2520	heat	heat	NN	_	_	_
2521	shock	shock	NN	_	_	_
2522	,	,	,	_	_	_
2523	long	long	RB	_	_	_
2524	,	,	,	_	_	_
2525	rep	rep	NN	GEN	_	_
2526	2	2	CD	_	_	_
2527	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2528	E.	e.	FW	_	_	_
2529	coli	coli	FW	_	_	_
2530	Anc	anc	NN	_	_	_
2531	strain	strain	NN	_	_	_
2532	,	,	,	_	_	_
2533	heat	heat	NN	_	_	_
2534	shock	shock	NN	_	_	_
2535	,	,	,	_	_	_
2536	rep	rep	NN	GEN	_	_
2537	1	1	CD	_	_	_
2538	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2539	E.	e.	FW	_	_	_
2540	coli	coli	FW	_	_	_
2541	Anc	anc	NN	_	_	_
2542	strain	strain	NN	_	_	_
2543	,	,	,	_	_	_
2544	heat	heat	NN	_	_	_
2545	shock	shock	NN	_	_	_
2546	,	,	,	_	_	_
2547	rep	rep	NN	GEN	_	_
2548	2	2	CD	_	_	_
2549	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2550	E.	e.	FW	_	_	_
2551	coli	coli	FW	_	_	_
2552	Anc	anc	NN	_	_	_
2553	strain	strain	NN	_	_	_
2554	,	,	,	_	_	_
2555	regular	regular	JJ	_	_	_
2556	temperature	temperature	NN	_	_	_
2557	,	,	,	_	_	_
2558	rep	rep	NN	GEN	_	_
2559	1	1	CD	_	_	_
2560	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2561	E.	e.	FW	_	_	_
2562	coli	coli	FW	_	_	_
2563	Anc	anc	NN	_	_	_
2564	strain	strain	NN	_	_	_
2565	,	,	,	_	_	_
2566	regular	regular	JJ	_	_	_
2567	temperature	temperature	NN	_	_	_
2568	,	,	,	_	_	_
2569	rep	rep	NN	GEN	_	_
2570	2	2	CD	_	_	_
2571	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2572	E.	e.	FW	_	_	_
2573	coli	coli	FW	_	_	_
2574	Anc	anc	NN	_	_	_
2575	strain	strain	NN	_	_	_
2576	,	,	,	_	_	_
2577	regular	regular	JJ	_	_	_
2578	temperature	temperature	NN	_	_	_
2579	,	,	,	_	_	_
2580	rep	rep	NN	GEN	_	_
2581	3	3	CD	_	_	_
2582	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2583	E.	E.	NNP	_	_	_
2584	coli	coli	NN	_	_	_
2585	and	and	CC	_	_	_
2586	S.	S.	NNP	_	_	_
2587	Typhimurium	Typhimurium	NNP	_	_	_
2588	cells	cell	NNS	_	_	_
2589	-LRB-	-lrb-	-LRB-	_	_	_
2590	at	at	IN	_	_	_
2591	mid-exponential	mid-exponential	JJ	_	_	_
2592	growth	growth	NN	_	_	_
2593	phase	phase	NN	_	_	_
2594	-RRB-	-rrb-	-RRB-	_	_	_
2595	were	be	VBD	_	_	_
2596	fixed	fix	VBN	_	_	_
2597	with	with	IN	_	_	_
2598	formaldehyde	formaldehyde	NN	_	_	_
2599	-LRB-	-lrb-	-LRB-	_	_	_
2600	1	1	CD	_	_	_
2601	%	%	NN	_	_	_
2602	final	final	JJ	_	_	_
2603	concentration	concentration	NN	_	_	_
2604	-RRB-	-rrb-	-RRB-	_	_	_
2605	for	for	IN	_	_	_
2606	20	20	CD	_	_	_
2607	min	min	NN	_	_	_
2608	at	at	IN	_	_	_
2609	30	30	CD	_	_	_
2610	°C	°c	NN	_	_	_
2611	with	with	IN	_	_	_
2612	shaking	shake	VBG	_	_	_
2613	.	.	.	_	_	_

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	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	ArgR	argr	NN	TF	_	_
37	ChIP	chip	NN	_	_	_
38	DNA	dna	NN	_	_	_
39	Arginine	arginine	NN	_	_	_
40	1	1	CD	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	E.	E.	NNP	_	_	_
43	Coli	Coli	NNP	_	_	_
44	ArgR	argr	NN	TF	_	_
45	ChIP	chip	NN	_	_	_
46	DNA	dna	NN	_	_	_
47	Arginine	arginine	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	E.	NNP	_	_	_
51	Coli	Coli	NNP	_	_	_
52	ArgR	argr	NN	TF	_	_
53	ChIP	chip	NN	_	_	_
54	DNA	dna	NN	_	_	_
55	NH4Cl	nh4cl	NN	_	_	_
56	1	1	CD	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	E.	E.	NNP	_	_	_
59	Coli	Coli	NNP	_	_	_
60	ArgR	argr	NN	TF	_	_
61	ChIP	chip	NN	_	_	_
62	DNA	dna	NN	_	_	_
63	NH4Cl	nh4cl	NN	_	_	_
64	2	2	CD	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	ATCC	atcc	NN	_	_	_
69	25922	25922	CD	_	_	_
70	marR	marr	NN	GEN	_	_
71	deletion	deletion	NN	_	_	_
72	+	+	CC	_	_	_
73	QnrS	qnrs	NN	_	_	_
74	replicate	replicate	VBP	_	_	_
75	1	1	CD	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	E.	E.	NNP	_	_	_
78	coli	coli	NN	_	_	_
79	ATCC	atcc	NN	_	_	_
80	25922	25922	CD	_	_	_
81	marR	marr	NN	GEN	_	_
82	deletion	deletion	NN	_	_	_
83	+	+	CC	_	_	_
84	QnrS	qnrs	NN	_	_	_
85	replicate	replicate	VBP	_	_	_
86	2	2	CD	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	E.	E.	NNP	_	_	_
89	coli	coli	NN	_	_	_
90	ATCC	atcc	NN	_	_	_
91	25922	25922	CD	_	_	_
92	QnrS	qnrs	NN	_	_	_
93	replicate	replicate	VBP	_	_	_
94	1	1	CD	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	E.	E.	NNP	_	_	_
97	coli	coli	NN	_	_	_
98	ATCC	atcc	NN	_	_	_
99	25922	25922	CD	_	_	_
100	QnrS	qnrs	NN	_	_	_
101	replicate	replicate	VBP	_	_	_
102	2	2	CD	_	_	_
103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
104	E.	E.	NNP	_	_	_
105	coli	coli	NN	_	_	_
106	ATCC	atcc	NN	_	_	_
107	25922	25922	CD	_	_	_
108	Ser83Leu	ser83leu	NN	_	_	_
109	+	+	CC	_	_	_
110	QnrS	qnrs	NN	_	_	_
111	replicate	replicate	VBP	_	_	_
112	1	1	CD	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	E.	E.	NNP	_	_	_
115	coli	coli	NN	_	_	_
116	ATCC	atcc	NN	_	_	_
117	25922	25922	CD	_	_	_
118	Ser83Leu	ser83leu	NN	_	_	_
119	+	+	CC	_	_	_
120	QnrS	qnrs	NN	_	_	_
121	replicate	replicate	VBP	_	_	_
122	2	2	CD	_	_	_
123	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
124	E.	E.	NNP	_	_	_
125	coli	coli	NN	_	_	_
126	ATCC	atcc	NN	_	_	_
127	25922	25922	CD	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	wild-type	wild-type	JJ	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	and	and	CC	_	_	_
132	EC14	ec14	NN	_	_	_
133	,	,	,	_	_	_
134	EC19	ec19	NN	_	_	_
135	,	,	,	_	_	_
136	EC24	ec24	NN	_	_	_
137	-LRB-	-lrb-	-LRB-	_	_	_
138	LLQR	llqr	NN	_	_	_
139	-RRB-	-rrb-	-RRB-	_	_	_
140	isogenic	isogenic	JJ	_	_	_
141	strains	strain	NNS	_	_	_
142	were	be	VBD	_	_	_
143	tested	test	VBN	_	_	_
144	to	to	TO	_	_	_
145	evaluate	evaluate	VB	_	_	_
146	the	the	DT	_	_	_
147	global	global	JJ	_	_	_
148	response	response	NN	_	_	_
149	to	to	TO	_	_	_
150	relevant	relevant	JJ	_	_	_
151	fix	fix	NN	_	_	_
152	concentration	concentration	NN	_	_	_
153	of	of	IN	_	_	_
154	ciprofloxacin	ciprofloxacin	NN	_	_	_
155	-LRB-	-lrb-	-LRB-	_	_	_
156	1	1	CD	_	_	_
157	mg/L	mg/l	NN	_	_	_
158	,	,	,	_	_	_
159	breakpoint	breakpoint	NN	_	_	_
160	for	for	IN	_	_	_
161	reduced	reduce	VBN	_	_	_
162	susceptibility	susceptibility	NN	_	_	_
163	according	accord	VBG	_	_	_
164	to	to	TO	_	_	_
165	CLSI	clsi	NN	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	of	of	IN	_	_	_
3	them	they	PRP	_	_	_
4	were	be	VBD	_	_	_
5	susceptible	susceptible	JJ	_	_	_
6	to	to	TO	_	_	_
7	quinolones	quinolone	NNS	_	_	_
8	according	accord	VBG	_	_	_
9	to	to	TO	_	_	_
10	CLSI	CLSI	NNP	_	_	_
11	breakpoints	breakpoint	NNS	_	_	_
12	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	CLSI	clsi	NN	_	_	_
3	,	,	,	_	_	_
4	n.d.	n.d.	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	Cultures	culture	NNS	_	_	_
7	were	be	VBD	_	_	_
8	started	start	VBN	_	_	_
9	from	from	IN	_	_	_
10	single	single	JJ	_	_	_
11	colonies	colony	NNS	_	_	_
12	and	and	CC	_	_	_
13	grown	grow	VBN	_	_	_
14	overnight	overnight	JJ	_	_	_
15	in	in	IN	_	_	_
16	25	25	CD	_	_	_
17	ml	ml	NN	_	_	_
18	of	of	IN	_	_	_
19	LB	lb	NN	_	_	_
20	.	.	.	_	_	_

1	These	these	DT	_	_	_
2	cell	cell	NN	_	_	_
3	were	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:100	1:100	CD	_	_	_
6	and	and	CC	_	_	_
7	growth	growth	NN	_	_	_
8	to	to	TO	_	_	_
9	cell	cell	NN	_	_	_
10	concentration	concentration	NN	_	_	_
11	of	of	IN	_	_	_
12	4x108	4x108	CD	_	_	_
13	cells/ml	cells/ml	NNS	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	OD600	od600	CD	_	_	_
16	nm	nm	NN	_	_	_
17	=	=	JJ	_	_	_
18	0.4	0.4	CD	_	_	_
19	,	,	,	_	_	_
20	exponential	exponential	JJ	GrowthPhase	_	_
21	phase	phase	NN	GrowthPhase	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	for	for	IN	_	_	_
24	treatment	treatment	NN	_	_	_
25	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	biological	biological	JJ	_	_	_
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/L	mg/l	NN	_	_	_
11	of	of	IN	_	_	_
12	ciprofloxacin	ciprofloxacin	NN	_	_	_
13	during	during	IN	_	_	_
14	60	60	CD	_	_	_
15	minutes	minute	NNS	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	that	that	WDT	_	_	_
18	means	mean	VBZ	_	_	_
19	250xMIC	250xmic	NN	_	_	_
20	for	for	IN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	ATCC	atcc	NN	_	_	_
24	25922	25922	CD	_	_	_
25	,	,	,	_	_	_
26	8xMIC	8xmic	NN	_	_	_
27	for	for	IN	_	_	_
28	EC14	ec14	NN	_	_	_
29	,	,	,	_	_	_
30	2xMIC	2xmic	NN	_	_	_
31	for	for	IN	_	_	_
32	EC19	ec19	NN	_	_	_
33	and	and	CC	_	_	_
34	1xMIC	1xmic	NN	_	_	_
35	for	for	IN	_	_	_
36	EC24	ec24	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	Approximately	approximately	RB	_	_	_
2	109	109	CD	_	_	_
3	cells	cell	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	2	2	CD	_	_	_
6	ml	ml	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	were	be	VBD	_	_	_
9	taken	take	VBN	_	_	_
10	for	for	IN	_	_	_
11	RNA	rna	NN	_	_	_
12	isolation	isolation	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	B178	b178	NN	_	_	_
5	groESL	groesl	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	-	-	:	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	expressing	express	VBG	_	_	_
10	human	human	JJ	_	_	_
11	Hsp60	hsp60	NN	_	_	_
12	and	and	CC	_	_	_
13	Hsp10	hsp10	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	B178	b178	NN	_	_	_
18	groESL	groesl	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	-	-	:	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	expressing	express	VBG	_	_	_
23	human	human	JJ	_	_	_
24	wt	wt	JJ	_	_	_
25	and	and	CC	_	_	_
26	Val98Ile	val98ile	NN	_	_	_
27	Hsp60	hsp60	NN	_	_	_
28	and	and	CC	_	_	_
29	Hsp10	hsp10	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	batch	batch	NN	_	_	_
34	culture	culture	NN	_	_	_
35	without	without	IN	_	_	_
36	TAP	tap	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	batch	batch	NN	_	_	_
41	culture	culture	NN	_	_	_
42	with	with	IN	_	_	_
43	TAP	tap	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	E.	e.	FW	_	_	_
46	coli	coli	FW	_	_	_
47	BL21	bl21	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	DE3	de3	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	cells	cell	NNS	_	_	_
52	expressing	express	VBG	_	_	_
53	catalytically	catalytically	RB	_	_	_
54	inactive	inactive	JJ	_	_	_
55	mutant	mutant	NN	_	_	_
56	of	of	IN	_	_	_
57	M.HpyAVIB	m.hpyavib	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
59	E.	e.	FW	_	_	_
60	coli	coli	FW	_	_	_
61	BL21	bl21	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	DE3	de3	NN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	cells	cell	NNS	_	_	_
66	expressing	express	VBG	_	_	_
67	wild-type	wild-type	JJ	_	_	_
68	M.HpyAVIB	m.hpyavib	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	E.	e.	FW	_	_	_
71	coli	coli	FW	_	_	_
72	BW25113	bw25113	NN	_	_	_
73	were	be	VBD	_	_	_
74	maintained	maintain	VBN	_	_	_
75	in	in	IN	_	_	_
76	Luria-Bertani	luria-bertani	JJ	_	_	_
77	medium	medium	NN	_	_	_
78	at	at	IN	_	_	_
79	37ºC	37ºc	NN	_	_	_
80	for	for	IN	_	_	_
81	about	about	RB	_	_	_
82	14	14	CD	_	_	_
83	h	h	NN	_	_	_
84	until	until	IN	_	_	_
85	they	they	PRP	_	_	_
86	reached	reach	VBD	_	_	_
87	the	the	DT	_	_	_
88	stationary	stationary	JJ	GrowthPhase	_	_
89	phase	phase	NN	GrowthPhase	_	_
90	of	of	IN	_	_	_
91	cell	cell	NN	_	_	_
92	growth	growth	NN	_	_	_
93	before	before	IN	_	_	_
94	treatment	treatment	NN	_	_	_
95	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Ecoli	Ecoli	NNP	_	_	_
3	_	_	SYM	_	_	_
4	CaCl2	cacl2	NN	_	_	_
5	wash	wash	NN	_	_	_
6	T1	t1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Ecoli	ecolus	NNS	_	_	_
9	_	_	VBP	_	_	_
10	CaCl2	cacl2	NN	_	_	_
11	wash	wash	NN	_	_	_
12	T2	t2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Ecoli	ecolus	NNS	_	_	_
15	_	_	VBP	_	_	_
16	CaCl2	cacl2	NN	_	_	_
17	wash	wash	NN	_	_	_
18	T3	t3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Ecoli	ecolus	NNS	_	_	_
21	_	_	VBP	_	_	_
22	CaCl2	cacl2	NN	_	_	_
23	wash	wash	NN	_	_	_
24	T4	t4	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Ecoli	ecolus	NNS	_	_	_
27	_	_	VBP	_	_	_
28	CaCl2	cacl2	NN	_	_	_
29	wash	wash	NN	_	_	_
30	T5	t5	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Ecoli	ecolus	NNS	_	_	_
33	_	_	VBP	_	_	_
34	CaCl2	cacl2	NN	_	_	_
35	wash	wash	NN	_	_	_
36	T6	t6	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	CC72	cc72	NN	_	_	_
41	was	be	VBD	_	_	_
42	grown	grow	VBN	_	_	_
43	in	in	IN	_	_	_
44	water	water	NN	_	_	_
45	bath	bath	NN	_	_	_
46	to	to	TO	_	_	_
47	early-exponential	early-exponential	JJ	_	_	_
48	phase	phase	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	OD600	od600	NN	_	_	_
51	0.2	0.2	CD	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	at	at	IN	_	_	_
54	37	37	CD	_	_	_
55	°C	°c	NN	_	_	_
56	in	in	IN	_	_	_
57	LB	lb	NN	MED	_	_
58	medium	medium	NN	MED	_	_
59	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	_	_	CD	_	_	_
5	CCCP	CCCP	NNP	_	_	_
6	_	_	SYM	_	_	_
7	15	15	CD	_	_	_
8	min	min	NN	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	E.	E.	NNP	_	_	_
11	coli	coli	NN	_	_	_
12	cell	cell	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	E.	E.	NNP	_	_	_
15	coli	coli	NN	_	_	_
16	cell	cell	NN	_	_	_
17	cultures	culture	NNS	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	E	e	NN	_	_	_
20	coli	coli	NN	_	_	_
21	cells	cell	NNS	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	E.coli	e.coli	NN	_	_	_
24	cells	cell	NNS	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	E.	E.	NNP	_	_	_
27	coli	coli	NN	_	_	_
28	cells	cell	NNS	_	_	_
29	0	0	CD	_	_	_
30	min	min	NN	_	_	_
31	before	before	IN	_	_	_
32	perturbation	perturbation	NN	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	E.	E.	NNP	_	_	_
35	coli	coli	NN	_	_	_
36	cells	cell	NNS	_	_	_
37	10	10	CD	_	_	_
38	min	min	NN	_	_	_
39	after	after	IN	_	_	_
40	specific	specific	JJ	_	_	_
41	perturbation	perturbation	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	E.coli	e.coli	NN	_	_	_
44	cells	cell	NNS	_	_	_
45	at	at	IN	_	_	_
46	1.5	1.5	CD	_	_	_
47	hrs	hr	NNS	_	_	_
48	after	after	IN	_	_	_
49	addition	addition	NN	_	_	_
50	of	of	IN	_	_	_
51	high	high	JJ	_	_	_
52	IPTG	iptg	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	1.0	1.0	CD	_	_	_
55	mM	mm	NN	KWSUPP	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	,	,	,	_	_	_
58	biological	biological	JJ	_	_	_
59	rep1	rep1	NN	_	_	_
60	,	,	,	_	_	_
61	technical	technical	JJ	_	_	_
62	rep	rep	NN	GEN	_	_
63	1	1	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	E.coli	e.coli	NN	_	_	_
66	cells	cell	NNS	_	_	_
67	at	at	IN	_	_	_
68	1.5	1.5	CD	_	_	_
69	hrs	hr	NNS	_	_	_
70	after	after	IN	_	_	_
71	addition	addition	NN	_	_	_
72	of	of	IN	_	_	_
73	high	high	JJ	_	_	_
74	IPTG	iptg	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	1.0	1.0	CD	_	_	_
77	mM	mm	NN	KWSUPP	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	,	,	,	_	_	_
80	biological	biological	JJ	_	_	_
81	rep1	rep1	NN	_	_	_
82	,	,	,	_	_	_
83	technical	technical	JJ	_	_	_
84	rep2	rep2	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	E.coli	e.coli	NN	_	_	_
87	cells	cell	NNS	_	_	_
88	at	at	IN	_	_	_
89	1.5	1.5	CD	_	_	_
90	hrs	hr	NNS	_	_	_
91	after	after	IN	_	_	_
92	addition	addition	NN	_	_	_
93	of	of	IN	_	_	_
94	high	high	JJ	_	_	_
95	IPTG	iptg	NN	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	1.0	1.0	CD	_	_	_
98	mM	mm	NN	KWSUPP	_	_
99	-RRB-	-rrb-	-RRB-	_	_	_
100	,	,	,	_	_	_
101	biological	biological	JJ	_	_	_
102	rep2	rep2	NN	_	_	_
103	,	,	,	_	_	_
104	technical	technical	JJ	_	_	_
105	rep	rep	NN	GEN	_	_
106	1	1	CD	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	E.coli	e.coli	NN	_	_	_
109	cells	cell	NNS	_	_	_
110	at	at	IN	_	_	_
111	1.5	1.5	CD	_	_	_
112	hrs	hr	NNS	_	_	_
113	after	after	IN	_	_	_
114	addition	addition	NN	_	_	_
115	of	of	IN	_	_	_
116	high	high	JJ	_	_	_
117	IPTG	iptg	NN	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	1.0	1.0	CD	_	_	_
120	mM	mm	NN	KWSUPP	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	,	,	,	_	_	_
123	biological	biological	JJ	_	_	_
124	rep2	rep2	NN	_	_	_
125	,	,	,	_	_	_
126	technical	technical	JJ	_	_	_
127	rep2	rep2	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	E.coli	e.coli	NN	_	_	_
130	cells	cell	NNS	_	_	_
131	at	at	IN	_	_	_
132	1.5	1.5	CD	_	_	_
133	hrs	hr	NNS	_	_	_
134	after	after	IN	_	_	_
135	addition	addition	NN	_	_	_
136	of	of	IN	_	_	_
137	low	low	JJ	_	_	_
138	IPTG	iptg	NN	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	0.1	0.1	CD	_	_	_
141	mM	mm	NN	KWSUPP	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	,	,	,	_	_	_
144	biological	biological	JJ	_	_	_
145	rep1	rep1	NN	_	_	_
146	,	,	,	_	_	_
147	technical	technical	JJ	_	_	_
148	rep	rep	NN	GEN	_	_
149	1	1	CD	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	E.coli	e.coli	NN	_	_	_
152	cells	cell	NNS	_	_	_
153	at	at	IN	_	_	_
154	1.5	1.5	CD	_	_	_
155	hrs	hr	NNS	_	_	_
156	after	after	IN	_	_	_
157	addition	addition	NN	_	_	_
158	of	of	IN	_	_	_
159	low	low	JJ	_	_	_
160	IPTG	iptg	NN	_	_	_
161	-LRB-	-lrb-	-LRB-	_	_	_
162	0.1	0.1	CD	_	_	_
163	mM	mm	NN	KWSUPP	_	_
164	-RRB-	-rrb-	-RRB-	_	_	_
165	,	,	,	_	_	_
166	biological	biological	JJ	_	_	_
167	rep1	rep1	NN	_	_	_
168	,	,	,	_	_	_
169	technical	technical	JJ	_	_	_
170	rep2	rep2	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	E.coli	e.coli	NN	_	_	_
173	cells	cell	NNS	_	_	_
174	at	at	IN	_	_	_
175	1.5	1.5	CD	_	_	_
176	hrs	hr	NNS	_	_	_
177	after	after	IN	_	_	_
178	addition	addition	NN	_	_	_
179	of	of	IN	_	_	_
180	low	low	JJ	_	_	_
181	IPTG	iptg	NN	_	_	_
182	-LRB-	-lrb-	-LRB-	_	_	_
183	0.1	0.1	CD	_	_	_
184	mM	mm	NN	KWSUPP	_	_
185	-RRB-	-rrb-	-RRB-	_	_	_
186	,	,	,	_	_	_
187	biological	biological	JJ	_	_	_
188	rep2	rep2	NN	_	_	_
189	,	,	,	_	_	_
190	technical	technical	JJ	_	_	_
191	rep	rep	NN	GEN	_	_
192	1	1	CD	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	E.coli	e.coli	NN	_	_	_
195	cells	cell	NNS	_	_	_
196	at	at	IN	_	_	_
197	1.5	1.5	CD	_	_	_
198	hrs	hr	NNS	_	_	_
199	after	after	IN	_	_	_
200	addition	addition	NN	_	_	_
201	of	of	IN	_	_	_
202	low	low	JJ	_	_	_
203	IPTG	iptg	NN	_	_	_
204	-LRB-	-lrb-	-LRB-	_	_	_
205	0.1	0.1	CD	_	_	_
206	mM	mm	NN	KWSUPP	_	_
207	-RRB-	-rrb-	-RRB-	_	_	_
208	,	,	,	_	_	_
209	biological	biological	JJ	_	_	_
210	rep2	rep2	NN	_	_	_
211	,	,	,	_	_	_
212	technical	technical	JJ	_	_	_
213	rep2	rep2	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	E.coli	e.coli	NN	_	_	_
216	cells	cell	NNS	_	_	_
217	at	at	IN	_	_	_
218	1.5	1.5	CD	_	_	_
219	hrs	hr	NNS	_	_	_
220	after	after	IN	_	_	_
221	addition	addition	NN	_	_	_
222	of	of	IN	_	_	_
223	no	no	DT	_	_	_
224	IPTG	iptg	NN	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	0	0	CD	_	_	_
227	mM	mm	NN	KWSUPP	_	_
228	-RRB-	-rrb-	-RRB-	_	_	_
229	,	,	,	_	_	_
230	biological	biological	JJ	_	_	_
231	rep1	rep1	NN	_	_	_
232	,	,	,	_	_	_
233	technical	technical	JJ	_	_	_
234	rep	rep	NN	GEN	_	_
235	1	1	CD	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	E.coli	e.coli	NN	_	_	_
238	cells	cell	NNS	_	_	_
239	at	at	IN	_	_	_
240	1.5	1.5	CD	_	_	_
241	hrs	hr	NNS	_	_	_
242	after	after	IN	_	_	_
243	addition	addition	NN	_	_	_
244	of	of	IN	_	_	_
245	no	no	DT	_	_	_
246	IPTG	iptg	NN	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	0	0	CD	_	_	_
249	mM	mm	NN	KWSUPP	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	,	,	,	_	_	_
252	biological	biological	JJ	_	_	_
253	rep1	rep1	NN	_	_	_
254	,	,	,	_	_	_
255	technical	technical	JJ	_	_	_
256	rep2	rep2	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	E.coli	e.coli	NN	_	_	_
259	cells	cell	NNS	_	_	_
260	at	at	IN	_	_	_
261	1.5	1.5	CD	_	_	_
262	hrs	hr	NNS	_	_	_
263	after	after	IN	_	_	_
264	addition	addition	NN	_	_	_
265	of	of	IN	_	_	_
266	no	no	DT	_	_	_
267	IPTG	iptg	NN	_	_	_
268	-LRB-	-lrb-	-LRB-	_	_	_
269	0	0	CD	_	_	_
270	mM	mm	NN	KWSUPP	_	_
271	-RRB-	-rrb-	-RRB-	_	_	_
272	,	,	,	_	_	_
273	biological	biological	JJ	_	_	_
274	rep2	rep2	NN	_	_	_
275	,	,	,	_	_	_
276	technical	technical	JJ	_	_	_
277	rep	rep	NN	GEN	_	_
278	1	1	CD	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	E.coli	e.coli	NN	_	_	_
281	cells	cell	NNS	_	_	_
282	at	at	IN	_	_	_
283	1.5	1.5	CD	_	_	_
284	hrs	hr	NNS	_	_	_
285	after	after	IN	_	_	_
286	addition	addition	NN	_	_	_
287	of	of	IN	_	_	_
288	no	no	DT	_	_	_
289	IPTG	iptg	NN	_	_	_
290	-LRB-	-lrb-	-LRB-	_	_	_
291	0	0	CD	_	_	_
292	mM	mm	NN	KWSUPP	_	_
293	-RRB-	-rrb-	-RRB-	_	_	_
294	,	,	,	_	_	_
295	biological	biological	JJ	_	_	_
296	rep2	rep2	NN	_	_	_
297	,	,	,	_	_	_
298	technical	technical	JJ	_	_	_
299	rep2	rep2	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	E.coli	e.coli	NN	_	_	_
302	cells	cell	NNS	_	_	_
303	at	at	IN	_	_	_
304	1.5	1.5	CD	_	_	_
305	hrs	hr	NNS	_	_	_
306	after	after	IN	_	_	_
307	induction	induction	NN	_	_	_
308	with	with	IN	_	_	_
309	0.1	0.1	CD	_	_	_
310	mM	mm	NN	KWSUPP	_	_
311	IPTG	iptg	NN	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	E.coli	e.coli	NN	_	_	_
314	cells	cell	NNS	_	_	_
315	at	at	IN	_	_	_
316	1.5	1.5	CD	_	_	_
317	hrs	hr	NNS	_	_	_
318	after	after	IN	_	_	_
319	induction	induction	NN	_	_	_
320	with	with	IN	_	_	_
321	0	0	CD	_	_	_
322	mM	mm	NN	KWSUPP	_	_
323	IPTG	iptg	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	E.coli	e.coli	NN	_	_	_
326	cells	cell	NNS	_	_	_
327	at	at	IN	_	_	_
328	1.5	1.5	CD	_	_	_
329	hrs	hr	NNS	_	_	_
330	after	after	IN	_	_	_
331	induction	induction	NN	_	_	_
332	with	with	IN	_	_	_
333	1.0	1.0	CD	_	_	_
334	mM	mm	NN	KWSUPP	_	_
335	IPTG	iptg	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	E.coli	e.coli	NN	_	_	_
338	cells	cell	NNS	_	_	_
339	at	at	IN	_	_	_
340	3.5	3.5	CD	_	_	_
341	hrs	hr	NNS	_	_	_
342	after	after	IN	_	_	_
343	addition	addition	NN	_	_	_
344	of	of	IN	_	_	_
345	high	high	JJ	_	_	_
346	IPTG	iptg	NN	_	_	_
347	-LRB-	-lrb-	-LRB-	_	_	_
348	1.0	1.0	CD	_	_	_
349	mM	mm	NN	KWSUPP	_	_
350	-RRB-	-rrb-	-RRB-	_	_	_
351	,	,	,	_	_	_
352	biological	biological	JJ	_	_	_
353	rep1	rep1	NN	_	_	_
354	,	,	,	_	_	_
355	technical	technical	JJ	_	_	_
356	rep	rep	NN	GEN	_	_
357	1	1	CD	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	E.coli	e.coli	NN	_	_	_
360	cells	cell	NNS	_	_	_
361	at	at	IN	_	_	_
362	3.5	3.5	CD	_	_	_
363	hrs	hr	NNS	_	_	_
364	after	after	IN	_	_	_
365	addition	addition	NN	_	_	_
366	of	of	IN	_	_	_
367	high	high	JJ	_	_	_
368	IPTG	iptg	NN	_	_	_
369	-LRB-	-lrb-	-LRB-	_	_	_
370	1.0	1.0	CD	_	_	_
371	mM	mm	NN	KWSUPP	_	_
372	-RRB-	-rrb-	-RRB-	_	_	_
373	,	,	,	_	_	_
374	biological	biological	JJ	_	_	_
375	rep1	rep1	NN	_	_	_
376	,	,	,	_	_	_
377	technical	technical	JJ	_	_	_
378	rep2	rep2	NN	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	E.coli	e.coli	NN	_	_	_
381	cells	cell	NNS	_	_	_
382	at	at	IN	_	_	_
383	3.5	3.5	CD	_	_	_
384	hrs	hr	NNS	_	_	_
385	after	after	IN	_	_	_
386	addition	addition	NN	_	_	_
387	of	of	IN	_	_	_
388	high	high	JJ	_	_	_
389	IPTG	iptg	NN	_	_	_
390	-LRB-	-lrb-	-LRB-	_	_	_
391	1.0	1.0	CD	_	_	_
392	mM	mm	NN	KWSUPP	_	_
393	-RRB-	-rrb-	-RRB-	_	_	_
394	,	,	,	_	_	_
395	biological	biological	JJ	_	_	_
396	rep2	rep2	NN	_	_	_
397	,	,	,	_	_	_
398	technical	technical	JJ	_	_	_
399	rep	rep	NN	GEN	_	_
400	1	1	CD	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	E.coli	e.coli	NN	_	_	_
403	cells	cell	NNS	_	_	_
404	at	at	IN	_	_	_
405	3.5	3.5	CD	_	_	_
406	hrs	hr	NNS	_	_	_
407	after	after	IN	_	_	_
408	addition	addition	NN	_	_	_
409	of	of	IN	_	_	_
410	high	high	JJ	_	_	_
411	IPTG	iptg	NN	_	_	_
412	-LRB-	-lrb-	-LRB-	_	_	_
413	1.0	1.0	CD	_	_	_
414	mM	mm	NN	KWSUPP	_	_
415	-RRB-	-rrb-	-RRB-	_	_	_
416	,	,	,	_	_	_
417	biological	biological	JJ	_	_	_
418	rep2	rep2	NN	_	_	_
419	,	,	,	_	_	_
420	technical	technical	JJ	_	_	_
421	rep2	rep2	NN	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	E.coli	e.coli	NN	_	_	_
424	cells	cell	NNS	_	_	_
425	at	at	IN	_	_	_
426	3.5	3.5	CD	_	_	_
427	hrs	hr	NNS	_	_	_
428	after	after	IN	_	_	_
429	addition	addition	NN	_	_	_
430	of	of	IN	_	_	_
431	low	low	JJ	_	_	_
432	IPTG	iptg	NN	_	_	_
433	-LRB-	-lrb-	-LRB-	_	_	_
434	0.1	0.1	CD	_	_	_
435	mM	mm	NN	KWSUPP	_	_
436	-RRB-	-rrb-	-RRB-	_	_	_
437	,	,	,	_	_	_
438	biological	biological	JJ	_	_	_
439	rep1	rep1	NN	_	_	_
440	,	,	,	_	_	_
441	technical	technical	JJ	_	_	_
442	rep	rep	NN	GEN	_	_
443	1	1	CD	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	E.coli	e.coli	NN	_	_	_
446	cells	cell	NNS	_	_	_
447	at	at	IN	_	_	_
448	3.5	3.5	CD	_	_	_
449	hrs	hr	NNS	_	_	_
450	after	after	IN	_	_	_
451	addition	addition	NN	_	_	_
452	of	of	IN	_	_	_
453	low	low	JJ	_	_	_
454	IPTG	iptg	NN	_	_	_
455	-LRB-	-lrb-	-LRB-	_	_	_
456	0.1	0.1	CD	_	_	_
457	mM	mm	NN	KWSUPP	_	_
458	-RRB-	-rrb-	-RRB-	_	_	_
459	,	,	,	_	_	_
460	biological	biological	JJ	_	_	_
461	rep1	rep1	NN	_	_	_
462	,	,	,	_	_	_
463	technical	technical	JJ	_	_	_
464	rep2	rep2	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	E.coli	e.coli	NN	_	_	_
467	cells	cell	NNS	_	_	_
468	at	at	IN	_	_	_
469	3.5	3.5	CD	_	_	_
470	hrs	hr	NNS	_	_	_
471	after	after	IN	_	_	_
472	addition	addition	NN	_	_	_
473	of	of	IN	_	_	_
474	low	low	JJ	_	_	_
475	IPTG	iptg	NN	_	_	_
476	-LRB-	-lrb-	-LRB-	_	_	_
477	0.1	0.1	CD	_	_	_
478	mM	mm	NN	KWSUPP	_	_
479	-RRB-	-rrb-	-RRB-	_	_	_
480	,	,	,	_	_	_
481	biological	biological	JJ	_	_	_
482	rep2	rep2	NN	_	_	_
483	,	,	,	_	_	_
484	technical	technical	JJ	_	_	_
485	rep	rep	NN	GEN	_	_
486	1	1	CD	_	_	_
487	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
488	E.coli	e.coli	NN	_	_	_
489	cells	cell	NNS	_	_	_
490	at	at	IN	_	_	_
491	3.5	3.5	CD	_	_	_
492	hrs	hr	NNS	_	_	_
493	after	after	IN	_	_	_
494	addition	addition	NN	_	_	_
495	of	of	IN	_	_	_
496	low	low	JJ	_	_	_
497	IPTG	iptg	NN	_	_	_
498	-LRB-	-lrb-	-LRB-	_	_	_
499	0.1	0.1	CD	_	_	_
500	mM	mm	NN	KWSUPP	_	_
501	-RRB-	-rrb-	-RRB-	_	_	_
502	,	,	,	_	_	_
503	biological	biological	JJ	_	_	_
504	rep2	rep2	NN	_	_	_
505	,	,	,	_	_	_
506	technical	technical	JJ	_	_	_
507	rep2	rep2	NN	_	_	_
508	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
509	E.coli	e.coli	NN	_	_	_
510	cells	cell	NNS	_	_	_
511	at	at	IN	_	_	_
512	3.5	3.5	CD	_	_	_
513	hrs	hr	NNS	_	_	_
514	after	after	IN	_	_	_
515	addition	addition	NN	_	_	_
516	of	of	IN	_	_	_
517	no	no	DT	_	_	_
518	IPTG	iptg	NN	_	_	_
519	-LRB-	-lrb-	-LRB-	_	_	_
520	0	0	CD	_	_	_
521	mM	mm	NN	KWSUPP	_	_
522	-RRB-	-rrb-	-RRB-	_	_	_
523	,	,	,	_	_	_
524	biological	biological	JJ	_	_	_
525	rep1	rep1	NN	_	_	_
526	,	,	,	_	_	_
527	technical	technical	JJ	_	_	_
528	rep	rep	NN	GEN	_	_
529	1	1	CD	_	_	_
530	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
531	E.coli	e.coli	NN	_	_	_
532	cells	cell	NNS	_	_	_
533	at	at	IN	_	_	_
534	3.5	3.5	CD	_	_	_
535	hrs	hr	NNS	_	_	_
536	after	after	IN	_	_	_
537	addition	addition	NN	_	_	_
538	of	of	IN	_	_	_
539	no	no	DT	_	_	_
540	IPTG	iptg	NN	_	_	_
541	-LRB-	-lrb-	-LRB-	_	_	_
542	0	0	CD	_	_	_
543	mM	mm	NN	KWSUPP	_	_
544	-RRB-	-rrb-	-RRB-	_	_	_
545	,	,	,	_	_	_
546	biological	biological	JJ	_	_	_
547	rep1	rep1	NN	_	_	_
548	,	,	,	_	_	_
549	technical	technical	JJ	_	_	_
550	rep2	rep2	NN	_	_	_
551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
552	E.coli	e.coli	NN	_	_	_
553	cells	cell	NNS	_	_	_
554	at	at	IN	_	_	_
555	3.5	3.5	CD	_	_	_
556	hrs	hr	NNS	_	_	_
557	after	after	IN	_	_	_
558	addition	addition	NN	_	_	_
559	of	of	IN	_	_	_
560	no	no	DT	_	_	_
561	IPTG	iptg	NN	_	_	_
562	-LRB-	-lrb-	-LRB-	_	_	_
563	0	0	CD	_	_	_
564	mM	mm	NN	KWSUPP	_	_
565	-RRB-	-rrb-	-RRB-	_	_	_
566	,	,	,	_	_	_
567	biological	biological	JJ	_	_	_
568	rep2	rep2	NN	_	_	_
569	,	,	,	_	_	_
570	technical	technical	JJ	_	_	_
571	rep	rep	NN	GEN	_	_
572	1	1	CD	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	E.coli	e.coli	NN	_	_	_
575	cells	cell	NNS	_	_	_
576	at	at	IN	_	_	_
577	3.5	3.5	CD	_	_	_
578	hrs	hr	NNS	_	_	_
579	after	after	IN	_	_	_
580	addition	addition	NN	_	_	_
581	of	of	IN	_	_	_
582	no	no	DT	_	_	_
583	IPTG	iptg	NN	_	_	_
584	-LRB-	-lrb-	-LRB-	_	_	_
585	0	0	CD	_	_	_
586	mM	mm	NN	KWSUPP	_	_
587	-RRB-	-rrb-	-RRB-	_	_	_
588	,	,	,	_	_	_
589	biological	biological	JJ	_	_	_
590	rep2	rep2	NN	_	_	_
591	,	,	,	_	_	_
592	technical	technical	JJ	_	_	_
593	rep2	rep2	NN	_	_	_
594	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
595	E.coli	e.coli	NN	_	_	_
596	cells	cell	NNS	_	_	_
597	at	at	IN	_	_	_
598	3.5	3.5	CD	_	_	_
599	hrs	hr	NNS	_	_	_
600	after	after	IN	_	_	_
601	induction	induction	NN	_	_	_
602	with	with	IN	_	_	_
603	0.1	0.1	CD	_	_	_
604	mM	mm	NN	KWSUPP	_	_
605	IPTG	iptg	NN	_	_	_
606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
607	E.coli	e.coli	NN	_	_	_
608	cells	cell	NNS	_	_	_
609	at	at	IN	_	_	_
610	3.5	3.5	CD	_	_	_
611	hrs	hr	NNS	_	_	_
612	after	after	IN	_	_	_
613	induction	induction	NN	_	_	_
614	with	with	IN	_	_	_
615	0	0	CD	_	_	_
616	mM	mm	NN	KWSUPP	_	_
617	IPTG	iptg	NN	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	E.coli	e.coli	NN	_	_	_
620	cells	cell	NNS	_	_	_
621	at	at	IN	_	_	_
622	3.5	3.5	CD	_	_	_
623	hrs	hr	NNS	_	_	_
624	after	after	IN	_	_	_
625	induction	induction	NN	_	_	_
626	with	with	IN	_	_	_
627	1.0	1.0	CD	_	_	_
628	mM	mm	NN	KWSUPP	_	_
629	IPTG	iptg	NN	_	_	_
630	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
631	E.coli	e.coli	NN	_	_	_
632	cells	cell	NNS	_	_	_
633	at	at	IN	_	_	_
634	the	the	DT	_	_	_
635	time	time	NN	_	_	_
636	of	of	IN	_	_	_
637	IPTG	iptg	NN	_	_	_
638	induction	induction	NN	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	E.coli	e.coli	NN	_	_	_
641	cells	cell	NNS	_	_	_
642	at	at	IN	_	_	_
643	the	the	DT	_	_	_
644	time	time	NN	_	_	_
645	of	of	IN	_	_	_
646	IPTG	iptg	NN	_	_	_
647	induction	induction	NN	_	_	_
648	-LRB-	-lrb-	-LRB-	_	_	_
649	T	t	NN	_	_	_
650	=	=	JJ	_	_	_
651	0	0	CD	_	_	_
652	hrs	hr	NNS	_	_	_
653	-RRB-	-rrb-	-RRB-	_	_	_
654	,	,	,	_	_	_
655	biological	biological	JJ	_	_	_
656	rep1	rep1	NN	_	_	_
657	,	,	,	_	_	_
658	technical	technical	JJ	_	_	_
659	rep	rep	NN	GEN	_	_
660	1	1	CD	_	_	_
661	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
662	E.coli	e.coli	NN	_	_	_
663	cells	cell	NNS	_	_	_
664	at	at	IN	_	_	_
665	the	the	DT	_	_	_
666	time	time	NN	_	_	_
667	of	of	IN	_	_	_
668	IPTG	iptg	NN	_	_	_
669	induction	induction	NN	_	_	_
670	-LRB-	-lrb-	-LRB-	_	_	_
671	T	t	NN	_	_	_
672	=	=	JJ	_	_	_
673	0	0	CD	_	_	_
674	hrs	hr	NNS	_	_	_
675	-RRB-	-rrb-	-RRB-	_	_	_
676	,	,	,	_	_	_
677	biological	biological	JJ	_	_	_
678	rep1	rep1	NN	_	_	_
679	,	,	,	_	_	_
680	technical	technical	JJ	_	_	_
681	rep2	rep2	NN	_	_	_
682	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
683	E.coli	e.coli	NN	_	_	_
684	cells	cell	NNS	_	_	_
685	at	at	IN	_	_	_
686	the	the	DT	_	_	_
687	time	time	NN	_	_	_
688	of	of	IN	_	_	_
689	IPTG	iptg	NN	_	_	_
690	induction	induction	NN	_	_	_
691	-LRB-	-lrb-	-LRB-	_	_	_
692	T	t	NN	_	_	_
693	=	=	JJ	_	_	_
694	0	0	CD	_	_	_
695	hrs	hr	NNS	_	_	_
696	-RRB-	-rrb-	-RRB-	_	_	_
697	,	,	,	_	_	_
698	biological	biological	JJ	_	_	_
699	rep2	rep2	NN	_	_	_
700	,	,	,	_	_	_
701	technical	technical	JJ	_	_	_
702	rep	rep	NN	GEN	_	_
703	1	1	CD	_	_	_
704	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
705	E.coli	e.coli	NN	_	_	_
706	cells	cell	NNS	_	_	_
707	at	at	IN	_	_	_
708	the	the	DT	_	_	_
709	time	time	NN	_	_	_
710	of	of	IN	_	_	_
711	IPTG	iptg	NN	_	_	_
712	induction	induction	NN	_	_	_
713	-LRB-	-lrb-	-LRB-	_	_	_
714	T	t	NN	_	_	_
715	=	=	JJ	_	_	_
716	0	0	CD	_	_	_
717	hrs	hr	NNS	_	_	_
718	-RRB-	-rrb-	-RRB-	_	_	_
719	,	,	,	_	_	_
720	biological	biological	JJ	_	_	_
721	rep2	rep2	NN	_	_	_
722	,	,	,	_	_	_
723	technical	technical	JJ	_	_	_
724	rep2	rep2	NN	_	_	_
725	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
726	E.	E.	NNP	_	_	_
727	coli	coli	NN	_	_	_
728	cells	cell	NNS	_	_	_
729	containing	contain	VBG	_	_	_
730	a	a	DT	_	_	_
731	pBAD18	pbad18	NN	_	_	_
732	vector	vector	NN	_	_	_
733	encoding	encode	VBG	_	_	_
734	synthetic	synthetic	JJ	_	_	_
735	protein	protein	NN	_	_	_
736	DX	DX	NNP	_	_	_
737	exposed	expose	VBN	_	_	_
738	to	to	TO	_	_	_
739	arabinose	arabinose	VB	_	_	_
740	inducer	inducer	NN	_	_	_
741	for	for	IN	_	_	_
742	0.5	0.5	CD	_	_	_
743	h.	h.	NN	_	_	_
744	RNA	rna	NN	_	_	_
745	extracted	extract	VBN	_	_	_
746	with	with	IN	_	_	_
747	Invitrogen	Invitrogen	NNP	_	_	_
748	PureLink	PureLink	NNP	_	_	_
749	kit	kit	NN	_	_	_
750	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	from	from	IN	_	_	_
6	biofilm	biofilm	NN	_	_	_
7	1	1	CD	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	E.	E.	NNP	_	_	_
10	coli	coli	NN	_	_	_
11	cells	cell	NNS	_	_	_
12	from	from	IN	_	_	_
13	biofilm	biofilm	NN	_	_	_
14	2	2	CD	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	E.	E.	NNP	_	_	_
17	coli	coli	NN	_	_	_
18	cells	cell	NNS	_	_	_
19	from	from	IN	_	_	_
20	planktonic	planktonic	JJ	_	_	_
21	culture	culture	NN	_	_	_
22	1	1	CD	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	E.	E.	NNP	_	_	_
25	coli	coli	NN	_	_	_
26	cells	cell	NNS	_	_	_
27	from	from	IN	_	_	_
28	planktonic	planktonic	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	E.	E.	NNP	_	_	_
33	coli	coli	NN	_	_	_
34	cells	cell	NNS	_	_	_
35	grown	grow	VBN	_	_	_
36	to	to	TO	_	_	_
37	mid-exponential	mid-exponential	JJ	_	_	_
38	phase	phase	NN	_	_	_
39	after	after	IN	_	_	_
40	6-8	6-8	CD	_	_	_
41	generations	generation	NNS	_	_	_
42	after	after	IN	_	_	_
43	stationary	stationary	JJ	GrowthPhase	_	_
44	phase	phase	NN	GrowthPhase	_	_
45	in	in	IN	_	_	_
46	M9	m9	NN	MED	_	_
47	minimal	minimal	JJ	MED	_	_
48	medium	medium	NN	MED	_	_
49	+	+	CC	_	_	_
50	0.4	0.4	CD	_	_	_
51	%	%	NN	_	_	_
52	glucose	glucose	NN	SUPP	_	_
53	.	.	.	_	_	_

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/without	with/without	NN	_	_	_
24	200	200	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	glyphosate	glyphosate	NN	_	_	_
27	for	for	IN	_	_	_
28	1	1	CD	_	_	_
29	h	h	NN	_	_	_
30	,	,	,	_	_	_
31	after	after	IN	_	_	_
32	that	that	IN	_	_	_
33	the	the	DT	_	_	_
34	cells	cell	NNS	_	_	_
35	were	be	VBD	_	_	_
36	harvested	harvest	VBN	_	_	_
37	to	to	TO	_	_	_
38	extract	extract	NN	_	_	_
39	RNA	rna	NN	_	_	_
40	.	.	.	_	_	_

1	LB	lb	NN	MED	_	_
2	medium	medium	NN	MED	_	_
3	recipe	recipe	NN	_	_	_
4	is	be	VBZ	_	_	_
5	as	as	IN	_	_	_
6	follow	follow	VB	_	_	_
7	:	:	:	_	_	_
8	10g	10g	CD	_	_	_
9	tryptone	tryptone	NN	SUPP	_	_
10	,	,	,	_	_	_
11	5g	5g	NN	_	_	_
12	yeast	yeast	NN	SUPP	_	_
13	extract	extract	NN	SUPP	_	_
14	,	,	,	_	_	_
15	10g	10g	CD	_	_	_
16	NaCl	nacl	NN	_	_	_
17	per	per	IN	_	_	_
18	1	1	CD	_	_	_
19	liter	liter	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	_	_	VBP	_	_	_
6	HS15min	hs15min	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	cells	cell	NNS	_	_	_
11	_	_	VBP	_	_	_
12	HS30min	hs30min	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	cells	cell	NNS	_	_	_
17	_	_	VBP	_	_	_
18	HS60min	hs60min	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	cells	cell	NNS	_	_	_
23	_	_	VBP	_	_	_
24	LB	lb	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	OD	od	NN	_	_	_
27	=	=	JJ	_	_	_
28	0.87	0.87	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	E.	E.	NNP	_	_	_
32	coli	coli	NN	_	_	_
33	cells	cell	NNS	_	_	_
34	_	_	VBP	_	_	_
35	M-P0h	m-p0h	JJ	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	E.	E.	NNP	_	_	_
38	coli	coli	NN	_	_	_
39	cells	cell	NNS	_	_	_
40	_	_	VBP	_	_	_
41	M-P2h	m-p2h	JJ	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	E.	E.	NNP	_	_	_
44	coli	coli	NN	_	_	_
45	cells	cell	NNS	_	_	_
46	_	_	VBP	_	_	_
47	M-P4h	m-p4h	JJ	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
49	E.	e.	FW	_	_	_
50	coli	coli	FW	_	_	_
51	cells	cell	NNS	_	_	_
52	were	be	VBD	_	_	_
53	crosslinked	crosslink	VBN	_	_	_
54	in	in	IN	_	_	_
55	1	1	CD	_	_	_
56	%	%	NN	_	_	_
57	formaldehyde	formaldehyde	NN	_	_	_
58	for	for	IN	_	_	_
59	25	25	CD	_	_	_
60	minutes	minute	NNS	_	_	_
61	at	at	IN	_	_	_
62	RT	rt	NN	_	_	_
63	on	on	IN	_	_	_
64	a	a	DT	_	_	_
65	rocker	rocker	NN	_	_	_
66	,	,	,	_	_	_
67	then	then	RB	_	_	_
68	washed	wash	VBN	_	_	_
69	3	3	CD	_	_	_
70	times	time	NNS	_	_	_
71	with	with	IN	_	_	_
72	50	50	CD	_	_	_
73	ml	ml	NN	_	_	_
74	of	of	IN	_	_	_
75	ice-cold	ice-cold	JJ	_	_	_
76	TBS	tbs	NN	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	Tris	tris	NN	_	_	_
79	buffered	buffer	VBN	_	_	_
80	saline	saline	NN	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	each	each	DT	_	_	_
83	time	time	NN	_	_	_
84	.	.	.	_	_	_

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	at	at	IN	_	_	_
8	22	22	CD	_	_	_
9	°C	°c	NN	_	_	_
10	,	,	,	_	_	_
11	30	30	CD	_	_	_
12	°C	°c	NN	_	_	_
13	and	and	CC	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	in	in	IN	_	_	_
17	either	either	CC	_	_	_
18	Lennox	Lennox	NNP	_	_	_
19	Broth	Broth	NNP	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	LB	LB	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	or	or	CC	_	_	_
24	liquid	liquid	JJ	_	_	_
25	minimal	minimal	JJ	_	_	_
26	medium	medium	NN	_	_	_
27	A	a	DT	_	_	_
28	supplemented	supplement	VBN	_	_	_
29	with	with	IN	_	_	_
30	0.12	0.12	CD	_	_	_
31	%	%	NN	_	_	_
32	casamino	casamino	NN	SUPP	_	_
33	acids	acid	NNS	SUPP	_	_
34	and	and	CC	_	_	_
35	0.4	0.4	CD	_	_	_
36	%	%	NN	_	_	_
37	glucose	glucose	NN	SUPP	_	_
38	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	were	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	in	in	IN	_	_	_
8	annular	annular	JJ	_	_	_
9	reactor	reactor	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	BioSurface	BioSurface	NNP	_	_	_
12	Technologies	Technologies	NNPS	_	_	_
13	,	,	,	_	_	_
14	Bozeman	Bozeman	NNP	_	_	_
15	,	,	,	_	_	_
16	MT	MT	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	inoculated	inoculate	VBN	_	_	_
19	with	with	IN	_	_	_
20	1	1	CD	_	_	_
21	ml	ml	NN	_	_	_
22	overnight	overnight	JJ	_	_	_
23	cultures	culture	NNS	_	_	_
24	and	and	CC	_	_	_
25	supplied	supply	VBN	_	_	_
26	with	with	IN	_	_	_
27	fresh	fresh	JJ	_	_	_
28	10-fold	10-fold	JJ	_	_	_
29	diluted	diluted	JJ	_	_	_
30	Luria	Luria	NNP	MED	_	_
31	broth	broth	NN	MED	_	_
32	at	at	IN	_	_	_
33	100	100	CD	_	_	_
34	ml/h	ml/h	NN	_	_	_
35	at	at	IN	_	_	_
36	room	room	NN	_	_	_
37	temperature	temperature	NN	_	_	_
38	for	for	IN	_	_	_
39	7-days	7-day	NNS	_	_	_
40	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	onto	onto	IN	_	_	_
5	membrane	membrane	NN	_	_	_
6	filters	filter	NNS	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	pore	pore	NN	_	_	_
9	size	size	NN	_	_	_
10	0.45	0.45	CD	_	_	_
11	micrometer	micrometer	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	after	after	IN	_	_	_
14	pre-filtering	pre-filter	VBG	_	_	_
15	out	out	RP	_	_	_
16	aggregates	aggregate	NNS	_	_	_
17	larger	larger	JJR	_	_	_
18	than	than	IN	_	_	_
19	5	5	CD	_	_	_
20	micrometer	micrometer	NN	_	_	_
21	from	from	IN	_	_	_
22	planktonic	planktonic	JJ	_	_	_
23	cultures	culture	NNS	_	_	_
24	in	in	IN	_	_	_
25	the	the	DT	_	_	_
26	reactor	reactor	NN	_	_	_
27	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	re-suspended	re-suspended	JJ	_	_	_
4	in	in	IN	_	_	_
5	RNAlater	rnalater	NN	_	_	_
6	after	after	IN	_	_	_
7	harvest	harvest	NN	_	_	_
8	and	and	CC	_	_	_
9	stored	store	VBD	_	_	_
10	at	at	IN	_	_	_
11	4	4	CD	_	_	_
12	degree	degree	NN	_	_	_
13	C	c	NN	_	_	_
14	overnight	overnight	JJ	_	_	_
15	.	.	.	_	_	_

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/vol	wt/vol	NN	_	_	_
15	-RSB-	-rsb-	-RRB-	_	_	_
16	K2HPO4	k2hpo4	NN	_	_	_
17	,	,	,	_	_	_
18	0.85	0.85	CD	_	_	_
19	%	%	NN	_	_	_
20	-LSB-	-lsb-	-LRB-	_	_	_
21	wt/vol	wt/vol	NN	_	_	_
22	-RSB-	-rsb-	-RRB-	_	_	_
23	KH2PO4	kh2po4	NN	_	_	_
24	,	,	,	_	_	_
25	0.6	0.6	CD	_	_	_
26	%	%	NN	_	_	_
27	-LSB-	-lsb-	-LRB-	_	_	_
28	wt/vol	wt/vol	NN	_	_	_
29	-RSB-	-rsb-	-RRB-	_	_	_
30	yeast	yeast	NN	SUPP	_	_
31	extract	extract	NN	SUPP	_	_
32	containing	contain	VBG	_	_	_
33	0.5	0.5	CD	_	_	_
34	%	%	NN	_	_	_
35	-LSB-	-lsb-	-LRB-	_	_	_
36	wt/vol	wt/vol	NN	_	_	_
37	-RSB-	-rsb-	-RRB-	_	_	_
38	glucose	glucose	NN	SUPP	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	to	to	TO	_	_	_
41	mid-exponential	mid-exponential	JJ	_	_	_
42	phase	phase	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	OD600	od600	NN	_	_	_
45	=	=	JJ	_	_	_
46	~	~	NN	_	_	_
47	0.6	0.6	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	at	at	IN	_	_	_
50	37C	37c	NN	_	_	_
51	and	and	CC	_	_	_
52	shaking	shake	VBG	_	_	_
53	250rpm	250rpm	JJ	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	E.	e.	FW	_	_	_
56	coli	coli	FW	_	_	_
57	cells	cell	NNS	_	_	_
58	were	be	VBD	_	_	_
59	grown	grow	VBN	_	_	_
60	in	in	IN	_	_	_
61	Luria	Luria	NNP	_	_	_
62	Broth	Broth	NNP	_	_	_
63	supplemented	supplement	VBN	_	_	_
64	with	with	IN	_	_	_
65	100ug/ml	100ug/ml	JJ	_	_	_
66	ampicillin	ampicillin	NN	_	_	_
67	to	to	TO	_	_	_
68	retain	retain	VB	_	_	_
69	the	the	DT	_	_	_
70	plasmids	plasmid	NNS	_	_	_
71	.	.	.	_	_	_

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	until	until	IN	_	_	_
8	mid-exponential	mid-exponential	JJ	_	_	_
9	phase	phase	NN	_	_	_
10	and	and	CC	_	_	_
11	treated	treat	VBN	_	_	_
12	with	with	IN	_	_	_
13	0.5	0.5	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	isopropyl-β-d-thiogalactopyranoside	isopropyl-β-d-thiogalactopyranoside	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	IPTG	iptg	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	to	to	TO	_	_	_
20	induce	induce	VB	_	_	_
21	expression	expression	NN	_	_	_
22	of	of	IN	_	_	_
23	the	the	DT	_	_	_
24	empty	empty	JJ	_	_	_
25	vector	vector	NN	_	_	_
26	or	or	CC	_	_	_
27	the	the	DT	_	_	_
28	small	small	JJ	_	_	_
29	RNA	rna	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	construct	construct	NN	_	_	_
7	and	and	CC	_	_	_
8	control	control	NN	_	_	_
9	plasmids	plasmid	NNS	_	_	_
10	were	be	VBD	_	_	_
11	grown	grow	VBN	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	overnight	overnight	JJ	_	_	_
16	with	with	IN	_	_	_
17	aeration	aeration	NN	_	_	_
18	in	in	IN	_	_	_
19	a	a	DT	_	_	_
20	shaking	shake	VBG	_	_	_
21	incubator	incubator	NN	_	_	_
22	in	in	IN	_	_	_
23	5	5	CD	_	_	_
24	ml	ml	NN	_	_	_
25	of	of	IN	_	_	_
26	defined	define	VBN	_	_	_
27	supplemented	supplement	VBN	_	_	_
28	M9	m9	NN	_	_	_
29	medium	medium	NN	_	_	_
30	with	with	IN	_	_	_
31	the	the	DT	_	_	_
32	appropriate	appropriate	JJ	_	_	_
33	antibiotic	antibiotic	JJ	_	_	_
34	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	or	or	CC	_	_	_
7	without	without	IN	_	_	_
8	BnTR1	bntr1	NN	_	_	_
9	were	be	VBD	_	_	_
10	transferred	transfer	VBN	_	_	_
11	and	and	CC	_	_	_
12	incubated	incubate	VBN	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	and	and	CC	_	_	_
17	42	42	CD	_	_	_
18	°C	°c	NN	_	_	_
19	for	for	IN	_	_	_
20	1	1	CD	_	_	_
21	hour	hour	NN	_	_	_
22	,	,	,	_	_	_
23	respectively	respectively	RB	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	E.	E.	NNP	_	_	_
26	coli	coli	NN	_	_	_
27	CFT073	cft073	NN	_	_	_
28	carrying	carry	VBG	_	_	_
29	either	either	CC	_	_	_
30	pBAD	pbad	NN	_	_	_
31	or	or	CC	_	_	_
32	pBAD-tosR-his6	pbad-tosr-his6	NN	_	_	_
33	were	be	VBD	_	_	_
34	cultured	culture	VBN	_	_	_
35	overnight	overnight	JJ	_	_	_
36	in	in	IN	_	_	_
37	biological	biological	JJ	_	_	_
38	triplicates	triplicate	NNS	_	_	_
39	in	in	IN	_	_	_
40	LB	lb	NN	MED	_	_
41	medium	medium	NN	MED	_	_
42	containing	contain	VBG	_	_	_
43	ampicillin	ampicillin	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	100	100	CD	_	_	_
46	µg/ml	µg/ml	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

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	LB	lb	NN	MED	_	_
8	medium	medium	NN	MED	_	_
9	containing	contain	VBG	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	L-arabinose	l-arabinose	NN	_	_	_
13	and	and	CC	_	_	_
14	ampicillin	ampicillin	NN	_	_	_
15	and	and	CC	_	_	_
16	cultured	culture	VBN	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	with	with	IN	_	_	_
21	aeration	aeration	NN	_	_	_
22	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	400	400	CD	_	_	_
3	µL	µl	NN	_	_	_
4	sample	sample	NN	_	_	_
5	was	be	VBD	_	_	_
6	collected	collect	VBN	_	_	_
7	between	between	IN	_	_	_
8	OD600	od600	CD	_	_	_
9	0.46-0.96	0.46-0.96	CD	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	stabilized	stabilize	VBN	_	_	_
13	by	by	IN	_	_	_
14	the	the	DT	_	_	_
15	immediate	immediate	JJ	_	_	_
16	addition	addition	NN	_	_	_
17	of	of	IN	_	_	_
18	800	800	CD	_	_	_
19	µl	µl	NN	_	_	_
20	of	of	IN	_	_	_
21	RNAprotect	rnaprotect	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Qiagen	qiagen	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

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	NNP	_	_	_
19	E.	E.	NNP	_	_	_
20	coli	coli	NN	_	_	_
21	Cholic	Cholic	NNP	_	_	_
22	Acid	Acid	NNP	_	_	_
23	Treatment	treatment	NN	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	E.	E.	NNP	_	_	_
26	coli	coli	NN	_	_	_
27	CMA540	cma540	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	MG1693	mg1693	NN	_	_	_
30	∆	∆	CD	_	_	_
31	hfq	hfq	NN	GEN	_	_
32	:	:	:	_	_	_
33	:	:	:	_	_	_
34	cat	cat	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Ecoli	ecolus	NNS	_	_	_
38	,	,	,	_	_	_
39	completely	completely	RB	_	_	_
40	aerobic	aerobic	JJ	_	_	_
41	conditions	condition	NNS	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	E.	e.	FW	_	_	_
44	coli	coli	FW	_	_	_
45	_	_	FW	_	_	_
46	control	control	NN	_	_	_
47	_	_	SYM	_	_	_
48	30	30	CD	_	_	_
49	min	min	NN	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Ecoli	Ecoli	NNP	_	_	_
52	_	_	NN	_	_	_
53	control	control	NN	_	_	_
54	_	_	CD	_	_	_
55	5h	5h	NN	_	_	_
56	_	_	CD	_	_	_
57	rep1	rep1	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
59	Ecoli	ecoli	JJ	_	_	_
60	_	_	NN	_	_	_
61	control	control	NN	_	_	_
62	_	_	CD	_	_	_
63	5h	5h	NN	_	_	_
64	_	_	CD	_	_	_
65	rep2	rep2	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	Ecoli	ecoli	JJ	_	_	_
68	_	_	NN	_	_	_
69	control	control	NN	_	_	_
70	_	_	CD	_	_	_
71	5h	5h	NN	_	_	_
72	_	_	CD	_	_	_
73	rep3	rep3	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
75	Ecoli	ecoli	JJ	_	_	_
76	_	_	NN	_	_	_
77	control	control	NN	_	_	_
78	_	_	CD	_	_	_
79	5h	5h	JJ	_	_	_
80	_	_	NN	_	_	_
81	rep4	rep4	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	E.	e.	FW	_	_	_
84	coli	coli	FW	_	_	_
85	control	control	NN	_	_	_
86	,	,	,	_	_	_
87	biological	biological	JJ	_	_	_
88	replicate	replicate	VB	_	_	_
89	1	1	CD	_	_	_
90	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
91	E.	E.	NNP	_	_	_
92	coli	coli	NN	_	_	_
93	control	control	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	biological	biological	JJ	_	_	_
96	replicate	replicate	VBP	_	_	_
97	2	2	LS	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	E.coli	e.coli	NNS	_	_	_
101	,	,	,	_	_	_
102	control	control	JJ	_	_	_
103	culture	culture	NN	_	_	_
104	,	,	,	_	_	_
105	20	20	CD	_	_	_
106	minutes	minute	NNS	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	t2	t2	NN	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	after	after	IN	_	_	_
111	treatment	treatment	NN	_	_	_
112	,	,	,	_	_	_
113	replicate	replicate	VB	_	_	_
114	A	a	DT	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	E.coli	e.coli	NNS	_	_	_
117	,	,	,	_	_	_
118	control	control	JJ	_	_	_
119	culture	culture	NN	_	_	_
120	,	,	,	_	_	_
121	20	20	CD	_	_	_
122	minutes	minute	NNS	_	_	_
123	-LRB-	-lrb-	-LRB-	_	_	_
124	t2	t2	NN	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	after	after	IN	_	_	_
127	treatment	treatment	NN	_	_	_
128	,	,	,	_	_	_
129	replicate	replicate	VB	_	_	_
130	B	b	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	E.coli	e.coli	NNS	_	_	_
133	,	,	,	_	_	_
134	control	control	JJ	_	_	_
135	culture	culture	NN	_	_	_
136	,	,	,	_	_	_
137	20	20	CD	_	_	_
138	minutes	minute	NNS	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	t2	t2	NN	_	_	_
141	-RRB-	-rrb-	-RRB-	_	_	_
142	after	after	IN	_	_	_
143	treatment	treatment	NN	_	_	_
144	,	,	,	_	_	_
145	replicate	replicate	VB	_	_	_
146	C	c	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	E.coli	e.coli	NNS	_	_	_
149	,	,	,	_	_	_
150	control	control	JJ	_	_	_
151	culture	culture	NN	_	_	_
152	,	,	,	_	_	_
153	40	40	CD	_	_	_
154	minutes	minute	NNS	_	_	_
155	-LRB-	-lrb-	-LRB-	_	_	_
156	t3	t3	NN	_	_	_
157	-RRB-	-rrb-	-RRB-	_	_	_
158	after	after	IN	_	_	_
159	treatment	treatment	NN	_	_	_
160	,	,	,	_	_	_
161	replicate	replicate	VB	_	_	_
162	A	a	DT	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	E.coli	e.coli	NNS	_	_	_
165	,	,	,	_	_	_
166	control	control	JJ	_	_	_
167	culture	culture	NN	_	_	_
168	,	,	,	_	_	_
169	40	40	CD	_	_	_
170	minutes	minute	NNS	_	_	_
171	-LRB-	-lrb-	-LRB-	_	_	_
172	t3	t3	NN	_	_	_
173	-RRB-	-rrb-	-RRB-	_	_	_
174	after	after	IN	_	_	_
175	treatment	treatment	NN	_	_	_
176	,	,	,	_	_	_
177	replicate	replicate	VB	_	_	_
178	B	b	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	E.coli	e.coli	NNS	_	_	_
181	,	,	,	_	_	_
182	control	control	JJ	_	_	_
183	culture	culture	NN	_	_	_
184	,	,	,	_	_	_
185	40	40	CD	_	_	_
186	minutes	minute	NNS	_	_	_
187	-LRB-	-lrb-	-LRB-	_	_	_
188	t3	t3	NN	_	_	_
189	-RRB-	-rrb-	-RRB-	_	_	_
190	after	after	IN	_	_	_
191	treatment	treatment	NN	_	_	_
192	,	,	,	_	_	_
193	replicate	replicate	VB	_	_	_
194	C	c	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	E.coli	e.coli	NNS	_	_	_
197	,	,	,	_	_	_
198	control	control	JJ	_	_	_
199	culture	culture	NN	_	_	_
200	,	,	,	_	_	_
201	5h	5h	NN	_	_	_
202	in	in	IN	_	_	_
203	10	10	CD	_	_	_
204	mM	mm	NN	KWSUPP	_	_
205	NaCl	nacl	NN	_	_	_
206	,	,	,	_	_	_
207	replicate	replicate	VB	_	_	_
208	1	1	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	E.coli	e.coli	NNS	_	_	_
211	,	,	,	_	_	_
212	control	control	JJ	_	_	_
213	culture	culture	NN	_	_	_
214	,	,	,	_	_	_
215	5h	5h	NN	_	_	_
216	in	in	IN	_	_	_
217	10	10	CD	_	_	_
218	mM	mm	NN	KWSUPP	_	_
219	NaCl	nacl	NN	_	_	_
220	,	,	,	_	_	_
221	replicate	replicate	VB	_	_	_
222	2	2	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
224	E.coli	e.coli	NNS	_	_	_
225	,	,	,	_	_	_
226	control	control	JJ	_	_	_
227	culture	culture	NN	_	_	_
228	,	,	,	_	_	_
229	5h	5h	NN	_	_	_
230	in	in	IN	_	_	_
231	10	10	CD	_	_	_
232	mM	mm	NN	KWSUPP	_	_
233	NaCl	nacl	NN	_	_	_
234	,	,	,	_	_	_
235	replicate	replicate	VB	_	_	_
236	3	3	CD	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	E.coli	e.coli	NNS	_	_	_
239	,	,	,	_	_	_
240	control	control	JJ	_	_	_
241	culture	culture	NN	_	_	_
242	,	,	,	_	_	_
243	5h	5h	NN	_	_	_
244	in	in	IN	_	_	_
245	10	10	CD	_	_	_
246	mM	mm	NN	KWSUPP	_	_
247	NaCl	nacl	NN	_	_	_
248	,	,	,	_	_	_
249	replicate	replicate	VB	_	_	_
250	4	4	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
252	E.coli	e.coli	NNS	_	_	_
253	,	,	,	_	_	_
254	control	control	JJ	_	_	_
255	culture	culture	NN	_	_	_
256	,	,	,	_	_	_
257	at	at	IN	_	_	_
258	the	the	DT	_	_	_
259	time	time	NN	_	_	_
260	of	of	IN	_	_	_
261	treatment	treatment	NN	_	_	_
262	-LRB-	-lrb-	-LRB-	_	_	_
263	t1	t1	NN	_	_	_
264	-RRB-	-rrb-	-RRB-	_	_	_
265	,	,	,	_	_	_
266	replicate	replicate	VB	_	_	_
267	A	a	DT	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	E.coli	e.coli	NNS	_	_	_
270	,	,	,	_	_	_
271	control	control	JJ	_	_	_
272	culture	culture	NN	_	_	_
273	,	,	,	_	_	_
274	at	at	IN	_	_	_
275	the	the	DT	_	_	_
276	time	time	NN	_	_	_
277	of	of	IN	_	_	_
278	treatment	treatment	NN	_	_	_
279	-LRB-	-lrb-	-LRB-	_	_	_
280	t1	t1	NN	_	_	_
281	-RRB-	-rrb-	-RRB-	_	_	_
282	,	,	,	_	_	_
283	replicate	replicate	VB	_	_	_
284	B	b	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	E.coli	e.coli	NNS	_	_	_
287	,	,	,	_	_	_
288	control	control	JJ	_	_	_
289	culture	culture	NN	_	_	_
290	,	,	,	_	_	_
291	at	at	IN	_	_	_
292	the	the	DT	_	_	_
293	time	time	NN	_	_	_
294	of	of	IN	_	_	_
295	treatment	treatment	NN	_	_	_
296	-LRB-	-lrb-	-LRB-	_	_	_
297	t1	t1	NN	_	_	_
298	-RRB-	-rrb-	-RRB-	_	_	_
299	,	,	,	_	_	_
300	replicate	replicate	VB	_	_	_
301	C	c	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
303	E.coli	e.coli	JJ	_	_	_
304	_	_	NN	_	_	_
305	control	control	NN	_	_	_
306	_	_	CD	_	_	_
307	repA	repa	NN	_	_	_
308	_	_	CD	_	_	_
309	t1	t1	NN	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	E.coli	e.coli	NNS	_	_	_
312	_	_	VBP	_	_	_
313	control	control	NN	_	_	_
314	_	_	CD	_	_	_
315	repA	repa	NN	_	_	_
316	_	_	CD	_	_	_
317	t2	t2	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	E.coli	e.coli	NNS	_	_	_
320	_	_	VBP	_	_	_
321	control	control	NN	_	_	_
322	_	_	CD	_	_	_
323	repA	repa	NN	_	_	_
324	_	_	CD	_	_	_
325	t3	t3	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	E.coli	e.coli	NNS	_	_	_
328	_	_	VBP	_	_	_
329	control	control	NN	_	_	_
330	_	_	CD	_	_	_
331	repB	repb	NN	_	_	_
332	_	_	CD	_	_	_
333	t1	t1	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	E.coli	e.coli	NNS	_	_	_
336	_	_	VBP	_	_	_
337	control	control	NN	_	_	_
338	_	_	CD	_	_	_
339	repB	repb	NN	_	_	_
340	_	_	CD	_	_	_
341	t2	t2	NN	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	E.coli	e.coli	NNS	_	_	_
344	_	_	VBP	_	_	_
345	control	control	NN	_	_	_
346	_	_	CD	_	_	_
347	repB	repb	NN	_	_	_
348	_	_	CD	_	_	_
349	t3	t3	NN	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	E.coli	e.coli	NNS	_	_	_
352	_	_	VBP	_	_	_
353	control	control	NN	_	_	_
354	_	_	CD	_	_	_
355	repC	repc	NN	_	_	_
356	_	_	CD	_	_	_
357	t1	t1	NN	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	E.coli	e.coli	NNS	_	_	_
360	_	_	VBP	_	_	_
361	control	control	NN	_	_	_
362	_	_	CD	_	_	_
363	repC	repc	NN	_	_	_
364	_	_	CD	_	_	_
365	t2	t2	NN	_	_	_
366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
367	E.coli	e.coli	NNS	_	_	_
368	_	_	VBP	_	_	_
369	control	control	NN	_	_	_
370	_	_	CD	_	_	_
371	repC	repc	NN	_	_	_
372	_	_	CD	_	_	_
373	t3	t3	NN	_	_	_
374	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
375	E.	e.	FW	_	_	_
376	coli	coli	FW	_	_	_
377	CRP	crp	NN	TF	_	_
378	N	n	NN	_	_	_
379	strain	strain	NN	_	_	_
380	_	_	NN	_	_	_
381	acetate	acetate	NN	SUPP	_	_
382	_	_	NN	_	_	_
383	exponential	exponential	JJ	GrowthPhase	_	_
384	phase	phase	NN	GrowthPhase	_	_
385	_	_	NN	_	_	_
386	repl1	repl1	NN	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	E.	e.	FW	_	_	_
389	coli	coli	FW	_	_	_
390	CRP	crp	NN	TF	_	_
391	N	n	NN	_	_	_
392	strain	strain	NN	_	_	_
393	_	_	NN	_	_	_
394	acetate	acetate	NN	SUPP	_	_
395	_	_	NN	_	_	_
396	exponential	exponential	JJ	GrowthPhase	_	_
397	phase	phase	NN	GrowthPhase	_	_
398	_	_	NN	_	_	_
399	repl2	repl2	NN	_	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	E.	e.	FW	_	_	_
402	coli	coli	FW	_	_	_
403	CRP	crp	NN	TF	_	_
404	N	n	NN	_	_	_
405	strain	strain	NN	_	_	_
406	_	_	NN	_	_	_
407	acetate	acetate	NN	SUPP	_	_
408	_	_	NN	_	_	_
409	stationary	stationary	JJ	GrowthPhase	_	_
410	phase	phase	NN	GrowthPhase	_	_
411	_	_	NN	_	_	_
412	repl1	repl1	NN	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	E.	e.	FW	_	_	_
415	coli	coli	FW	_	_	_
416	CRP	crp	NN	TF	_	_
417	N	n	NN	_	_	_
418	strain	strain	NN	_	_	_
419	_	_	NN	_	_	_
420	acetate	acetate	NN	SUPP	_	_
421	_	_	NN	_	_	_
422	stationary	stationary	JJ	GrowthPhase	_	_
423	phase	phase	NN	GrowthPhase	_	_
424	_	_	NN	_	_	_
425	repl2	repl2	NN	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	E.	e.	FW	_	_	_
428	coli	coli	FW	_	_	_
429	CRP	crp	NN	TF	_	_
430	N	n	NN	_	_	_
431	strain	strain	NN	_	_	_
432	_	_	NN	_	_	_
433	glucose	glucose	NN	SUPP	_	_
434	_	_	NN	_	_	_
435	exponential	exponential	JJ	GrowthPhase	_	_
436	phase	phase	NN	GrowthPhase	_	_
437	_	_	NN	_	_	_
438	repl1	repl1	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	E.	e.	FW	_	_	_
441	coli	coli	FW	_	_	_
442	CRP	crp	NN	TF	_	_
443	N	n	NN	_	_	_
444	strain	strain	NN	_	_	_
445	_	_	NN	_	_	_
446	glucose	glucose	NN	SUPP	_	_
447	_	_	NN	_	_	_
448	exponential	exponential	JJ	GrowthPhase	_	_
449	phase	phase	NN	GrowthPhase	_	_
450	_	_	NN	_	_	_
451	repl2	repl2	NN	_	_	_
452	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
453	E.	e.	FW	_	_	_
454	coli	coli	FW	_	_	_
455	CRP	crp	NN	TF	_	_
456	N	n	NN	_	_	_
457	strain	strain	NN	_	_	_
458	_	_	NN	_	_	_
459	glucose	glucose	NN	SUPP	_	_
460	_	_	NN	_	_	_
461	stationary	stationary	JJ	GrowthPhase	_	_
462	phase	phase	NN	GrowthPhase	_	_
463	_	_	NN	_	_	_
464	repl1	repl1	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	E.	e.	FW	_	_	_
467	coli	coli	FW	_	_	_
468	CRP	crp	NN	TF	_	_
469	N	n	NN	_	_	_
470	strain	strain	NN	_	_	_
471	_	_	NN	_	_	_
472	glucose	glucose	NN	SUPP	_	_
473	_	_	NN	_	_	_
474	stationary	stationary	JJ	GrowthPhase	_	_
475	phase	phase	NN	GrowthPhase	_	_
476	_	_	NN	_	_	_
477	repl2	repl2	NN	_	_	_
478	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
479	E.	e.	FW	_	_	_
480	coli	coli	FW	_	_	_
481	CRP	crp	NN	TF	_	_
482	N	n	NN	_	_	_
483	strain	strain	NN	_	_	_
484	grown	grow	VBN	_	_	_
485	in	in	IN	_	_	_
486	acetate	acetate	NN	SUPP	_	_
487	batch	batch	NN	_	_	_
488	minimal	minimal	JJ	_	_	_
489	media	media	NNS	_	_	_
490	,	,	,	_	_	_
491	cells	cell	NNS	_	_	_
492	were	be	VBD	_	_	_
493	harvested	harvest	VBN	_	_	_
494	at	at	IN	_	_	_
495	exponential	exponential	JJ	GrowthPhase	_	_
496	phase	phase	NN	GrowthPhase	_	_
497	,	,	,	_	_	_
498	biological	biological	JJ	_	_	_
499	rep1	rep1	NN	_	_	_
500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
501	E.	e.	FW	_	_	_
502	coli	coli	FW	_	_	_
503	CRP	crp	NN	TF	_	_
504	N	n	NN	_	_	_
505	strain	strain	NN	_	_	_
506	grown	grow	VBN	_	_	_
507	in	in	IN	_	_	_
508	acetate	acetate	NN	SUPP	_	_
509	batch	batch	NN	_	_	_
510	minimal	minimal	JJ	_	_	_
511	media	media	NNS	_	_	_
512	,	,	,	_	_	_
513	cells	cell	NNS	_	_	_
514	were	be	VBD	_	_	_
515	harvested	harvest	VBN	_	_	_
516	at	at	IN	_	_	_
517	exponential	exponential	JJ	GrowthPhase	_	_
518	phase	phase	NN	GrowthPhase	_	_
519	,	,	,	_	_	_
520	biological	biological	JJ	_	_	_
521	rep2	rep2	NN	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
523	E.	e.	FW	_	_	_
524	coli	coli	FW	_	_	_
525	CRP	crp	NN	TF	_	_
526	N	n	NN	_	_	_
527	strain	strain	NN	_	_	_
528	grown	grow	VBN	_	_	_
529	in	in	IN	_	_	_
530	acetate	acetate	NN	SUPP	_	_
531	batch	batch	NN	_	_	_
532	minimal	minimal	JJ	_	_	_
533	media	media	NNS	_	_	_
534	,	,	,	_	_	_
535	cells	cell	NNS	_	_	_
536	were	be	VBD	_	_	_
537	harvested	harvest	VBN	_	_	_
538	at	at	IN	_	_	_
539	stationary	stationary	JJ	GrowthPhase	_	_
540	phase	phase	NN	GrowthPhase	_	_
541	,	,	,	_	_	_
542	biological	biological	JJ	_	_	_
543	rep1	rep1	NN	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	E.	e.	FW	_	_	_
546	coli	coli	FW	_	_	_
547	CRP	crp	NN	TF	_	_
548	N	n	NN	_	_	_
549	strain	strain	NN	_	_	_
550	grown	grow	VBN	_	_	_
551	in	in	IN	_	_	_
552	acetate	acetate	NN	SUPP	_	_
553	batch	batch	NN	_	_	_
554	minimal	minimal	JJ	_	_	_
555	media	media	NNS	_	_	_
556	,	,	,	_	_	_
557	cells	cell	NNS	_	_	_
558	were	be	VBD	_	_	_
559	harvested	harvest	VBN	_	_	_
560	at	at	IN	_	_	_
561	stationary	stationary	JJ	GrowthPhase	_	_
562	phase	phase	NN	GrowthPhase	_	_
563	,	,	,	_	_	_
564	biological	biological	JJ	_	_	_
565	rep2	rep2	NN	_	_	_
566	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
567	E.	e.	FW	_	_	_
568	coli	coli	FW	_	_	_
569	CRP	crp	NN	TF	_	_
570	N	n	NN	_	_	_
571	strain	strain	NN	_	_	_
572	grown	grow	VBN	_	_	_
573	in	in	IN	_	_	_
574	glucose	glucose	NN	SUPP	_	_
575	batch	batch	NN	_	_	_
576	minimal	minimal	JJ	_	_	_
577	media	media	NNS	_	_	_
578	,	,	,	_	_	_
579	cells	cell	NNS	_	_	_
580	were	be	VBD	_	_	_
581	harvested	harvest	VBN	_	_	_
582	at	at	IN	_	_	_
583	exponential	exponential	JJ	GrowthPhase	_	_
584	phase	phase	NN	GrowthPhase	_	_
585	,	,	,	_	_	_
586	biological	biological	JJ	_	_	_
587	rep1	rep1	NN	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
589	E.	e.	FW	_	_	_
590	coli	coli	FW	_	_	_
591	CRP	crp	NN	TF	_	_
592	N	n	NN	_	_	_
593	strain	strain	NN	_	_	_
594	grown	grow	VBN	_	_	_
595	in	in	IN	_	_	_
596	glucose	glucose	NN	SUPP	_	_
597	batch	batch	NN	_	_	_
598	minimal	minimal	JJ	_	_	_
599	media	media	NNS	_	_	_
600	,	,	,	_	_	_
601	cells	cell	NNS	_	_	_
602	were	be	VBD	_	_	_
603	harvested	harvest	VBN	_	_	_
604	at	at	IN	_	_	_
605	exponential	exponential	JJ	GrowthPhase	_	_
606	phase	phase	NN	GrowthPhase	_	_
607	,	,	,	_	_	_
608	biological	biological	JJ	_	_	_
609	rep2	rep2	NN	_	_	_
610	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
611	E.	e.	FW	_	_	_
612	coli	coli	FW	_	_	_
613	CRP	crp	NN	TF	_	_
614	N	n	NN	_	_	_
615	strain	strain	NN	_	_	_
616	grown	grow	VBN	_	_	_
617	in	in	IN	_	_	_
618	glucose	glucose	NN	SUPP	_	_
619	batch	batch	NN	_	_	_
620	minimal	minimal	JJ	_	_	_
621	media	media	NNS	_	_	_
622	,	,	,	_	_	_
623	cells	cell	NNS	_	_	_
624	were	be	VBD	_	_	_
625	harvested	harvest	VBN	_	_	_
626	at	at	IN	_	_	_
627	stationary	stationary	JJ	GrowthPhase	_	_
628	phase	phase	NN	GrowthPhase	_	_
629	,	,	,	_	_	_
630	biological	biological	JJ	_	_	_
631	rep1	rep1	NN	_	_	_
632	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
633	E.	e.	FW	_	_	_
634	coli	coli	FW	_	_	_
635	CRP	crp	NN	TF	_	_
636	N	n	NN	_	_	_
637	strain	strain	NN	_	_	_
638	grown	grow	VBN	_	_	_
639	in	in	IN	_	_	_
640	glucose	glucose	NN	SUPP	_	_
641	batch	batch	NN	_	_	_
642	minimal	minimal	JJ	_	_	_
643	media	media	NNS	_	_	_
644	,	,	,	_	_	_
645	cells	cell	NNS	_	_	_
646	were	be	VBD	_	_	_
647	harvested	harvest	VBN	_	_	_
648	at	at	IN	_	_	_
649	stationary	stationary	JJ	GrowthPhase	_	_
650	phase	phase	NN	GrowthPhase	_	_
651	,	,	,	_	_	_
652	biological	biological	JJ	_	_	_
653	rep2	rep2	NN	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
655	E.	e.	FW	_	_	_
656	coli	coli	FW	_	_	_
657	CRP	crp	NN	TF	_	_
658	Q	Q	NNP	_	_	_
659	strain	strain	NN	_	_	_
660	_	_	NN	_	_	_
661	acetate	acetate	NN	SUPP	_	_
662	_	_	NN	_	_	_
663	exponential	exponential	JJ	GrowthPhase	_	_
664	phase	phase	NN	GrowthPhase	_	_
665	_	_	NN	_	_	_
666	repl1	repl1	NN	_	_	_
667	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
668	E.	e.	FW	_	_	_
669	coli	coli	FW	_	_	_
670	CRP	crp	NN	TF	_	_
671	Q	Q	NNP	_	_	_
672	strain	strain	NN	_	_	_
673	_	_	NN	_	_	_
674	acetate	acetate	NN	SUPP	_	_
675	_	_	NN	_	_	_
676	exponential	exponential	JJ	GrowthPhase	_	_
677	phase	phase	NN	GrowthPhase	_	_
678	_	_	NN	_	_	_
679	repl2	repl2	NN	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	E.	e.	FW	_	_	_
682	coli	coli	FW	_	_	_
683	CRP	crp	NN	TF	_	_
684	Q	Q	NNP	_	_	_
685	strain	strain	NN	_	_	_
686	_	_	NN	_	_	_
687	acetate	acetate	NN	SUPP	_	_
688	_	_	NN	_	_	_
689	stationary	stationary	JJ	GrowthPhase	_	_
690	phase	phase	NN	GrowthPhase	_	_
691	_	_	NN	_	_	_
692	repl1	repl1	NN	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	E.	e.	FW	_	_	_
695	coli	coli	FW	_	_	_
696	CRP	crp	NN	TF	_	_
697	Q	Q	NNP	_	_	_
698	strain	strain	NN	_	_	_
699	_	_	NN	_	_	_
700	acetate	acetate	NN	SUPP	_	_
701	_	_	NN	_	_	_
702	stationary	stationary	JJ	GrowthPhase	_	_
703	phase	phase	NN	GrowthPhase	_	_
704	_	_	NN	_	_	_
705	repl2	repl2	NN	_	_	_
706	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
707	E.	e.	FW	_	_	_
708	coli	coli	FW	_	_	_
709	CRP	crp	NN	TF	_	_
710	Q	Q	NNP	_	_	_
711	strain	strain	NN	_	_	_
712	_	_	NN	_	_	_
713	glucose	glucose	NN	SUPP	_	_
714	_	_	NN	_	_	_
715	exponential	exponential	JJ	GrowthPhase	_	_
716	phase	phase	NN	GrowthPhase	_	_
717	_	_	NN	_	_	_
718	repl1	repl1	NN	_	_	_
719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
720	E.	e.	FW	_	_	_
721	coli	coli	FW	_	_	_
722	CRP	crp	NN	TF	_	_
723	Q	Q	NNP	_	_	_
724	strain	strain	NN	_	_	_
725	_	_	NN	_	_	_
726	glucose	glucose	NN	SUPP	_	_
727	_	_	NN	_	_	_
728	exponential	exponential	JJ	GrowthPhase	_	_
729	phase	phase	NN	GrowthPhase	_	_
730	_	_	NN	_	_	_
731	repl2	repl2	NN	_	_	_
732	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
733	E.	e.	FW	_	_	_
734	coli	coli	FW	_	_	_
735	CRP	crp	NN	TF	_	_
736	Q	Q	NNP	_	_	_
737	strain	strain	NN	_	_	_
738	_	_	NN	_	_	_
739	glucose	glucose	NN	SUPP	_	_
740	_	_	NN	_	_	_
741	stationary	stationary	JJ	GrowthPhase	_	_
742	phase	phase	NN	GrowthPhase	_	_
743	_	_	NN	_	_	_
744	repl1	repl1	NN	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
746	E.	e.	FW	_	_	_
747	coli	coli	FW	_	_	_
748	CRP	crp	NN	TF	_	_
749	Q	Q	NNP	_	_	_
750	strain	strain	NN	_	_	_
751	_	_	NN	_	_	_
752	glucose	glucose	NN	SUPP	_	_
753	_	_	NN	_	_	_
754	stationary	stationary	JJ	GrowthPhase	_	_
755	phase	phase	NN	GrowthPhase	_	_
756	_	_	NN	_	_	_
757	repl2	repl2	NN	_	_	_
758	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
759	E.	e.	FW	_	_	_
760	coli	coli	FW	_	_	_
761	CRP	crp	NN	TF	_	_
762	Q	Q	NNP	_	_	_
763	strain	strain	NN	_	_	_
764	grown	grow	VBN	_	_	_
765	in	in	IN	_	_	_
766	acetate	acetate	NN	SUPP	_	_
767	batch	batch	NN	_	_	_
768	minimal	minimal	JJ	_	_	_
769	media	media	NNS	_	_	_
770	,	,	,	_	_	_
771	cells	cell	NNS	_	_	_
772	were	be	VBD	_	_	_
773	harvested	harvest	VBN	_	_	_
774	at	at	IN	_	_	_
775	exponential	exponential	JJ	GrowthPhase	_	_
776	phase	phase	NN	GrowthPhase	_	_
777	,	,	,	_	_	_
778	biological	biological	JJ	_	_	_
779	rep1	rep1	NN	_	_	_
780	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
781	E.	e.	FW	_	_	_
782	coli	coli	FW	_	_	_
783	CRP	crp	NN	TF	_	_
784	Q	Q	NNP	_	_	_
785	strain	strain	NN	_	_	_
786	grown	grow	VBN	_	_	_
787	in	in	IN	_	_	_
788	acetate	acetate	NN	SUPP	_	_
789	batch	batch	NN	_	_	_
790	minimal	minimal	JJ	_	_	_
791	media	media	NNS	_	_	_
792	,	,	,	_	_	_
793	cells	cell	NNS	_	_	_
794	were	be	VBD	_	_	_
795	harvested	harvest	VBN	_	_	_
796	at	at	IN	_	_	_
797	exponential	exponential	JJ	GrowthPhase	_	_
798	phase	phase	NN	GrowthPhase	_	_
799	,	,	,	_	_	_
800	biological	biological	JJ	_	_	_
801	rep2	rep2	NN	_	_	_
802	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
803	E.	e.	FW	_	_	_
804	coli	coli	FW	_	_	_
805	CRP	crp	NN	TF	_	_
806	Q	Q	NNP	_	_	_
807	strain	strain	NN	_	_	_
808	grown	grow	VBN	_	_	_
809	in	in	IN	_	_	_
810	acetate	acetate	NN	SUPP	_	_
811	batch	batch	NN	_	_	_
812	minimal	minimal	JJ	_	_	_
813	media	media	NNS	_	_	_
814	,	,	,	_	_	_
815	cells	cell	NNS	_	_	_
816	were	be	VBD	_	_	_
817	harvested	harvest	VBN	_	_	_
818	at	at	IN	_	_	_
819	stationary	stationary	JJ	GrowthPhase	_	_
820	phase	phase	NN	GrowthPhase	_	_
821	,	,	,	_	_	_
822	biological	biological	JJ	_	_	_
823	rep1	rep1	NN	_	_	_
824	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
825	E.	e.	FW	_	_	_
826	coli	coli	FW	_	_	_
827	CRP	crp	NN	TF	_	_
828	Q	Q	NNP	_	_	_
829	strain	strain	NN	_	_	_
830	grown	grow	VBN	_	_	_
831	in	in	IN	_	_	_
832	acetate	acetate	NN	SUPP	_	_
833	batch	batch	NN	_	_	_
834	minimal	minimal	JJ	_	_	_
835	media	media	NNS	_	_	_
836	,	,	,	_	_	_
837	cells	cell	NNS	_	_	_
838	were	be	VBD	_	_	_
839	harvested	harvest	VBN	_	_	_
840	at	at	IN	_	_	_
841	stationary	stationary	JJ	GrowthPhase	_	_
842	phase	phase	NN	GrowthPhase	_	_
843	,	,	,	_	_	_
844	biological	biological	JJ	_	_	_
845	rep2	rep2	NN	_	_	_
846	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
847	E.	e.	FW	_	_	_
848	coli	coli	FW	_	_	_
849	CRP	crp	NN	TF	_	_
850	Q	Q	NNP	_	_	_
851	strain	strain	NN	_	_	_
852	grown	grow	VBN	_	_	_
853	in	in	IN	_	_	_
854	glucose	glucose	NN	SUPP	_	_
855	batch	batch	NN	_	_	_
856	minimal	minimal	JJ	_	_	_
857	media	media	NNS	_	_	_
858	,	,	,	_	_	_
859	cells	cell	NNS	_	_	_
860	were	be	VBD	_	_	_
861	harvested	harvest	VBN	_	_	_
862	at	at	IN	_	_	_
863	exponential	exponential	JJ	GrowthPhase	_	_
864	phase	phase	NN	GrowthPhase	_	_
865	,	,	,	_	_	_
866	biological	biological	JJ	_	_	_
867	rep1	rep1	NN	_	_	_
868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
869	E.	e.	FW	_	_	_
870	coli	coli	FW	_	_	_
871	CRP	crp	NN	TF	_	_
872	Q	Q	NNP	_	_	_
873	strain	strain	NN	_	_	_
874	grown	grow	VBN	_	_	_
875	in	in	IN	_	_	_
876	glucose	glucose	NN	SUPP	_	_
877	batch	batch	NN	_	_	_
878	minimal	minimal	JJ	_	_	_
879	media	media	NNS	_	_	_
880	,	,	,	_	_	_
881	cells	cell	NNS	_	_	_
882	were	be	VBD	_	_	_
883	harvested	harvest	VBN	_	_	_
884	at	at	IN	_	_	_
885	exponential	exponential	JJ	GrowthPhase	_	_
886	phase	phase	NN	GrowthPhase	_	_
887	,	,	,	_	_	_
888	biological	biological	JJ	_	_	_
889	rep2	rep2	NN	_	_	_
890	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
891	E.	e.	FW	_	_	_
892	coli	coli	FW	_	_	_
893	CRP	crp	NN	TF	_	_
894	Q	Q	NNP	_	_	_
895	strain	strain	NN	_	_	_
896	grown	grow	VBN	_	_	_
897	in	in	IN	_	_	_
898	glucose	glucose	NN	SUPP	_	_
899	batch	batch	NN	_	_	_
900	minimal	minimal	JJ	_	_	_
901	media	media	NNS	_	_	_
902	,	,	,	_	_	_
903	cells	cell	NNS	_	_	_
904	were	be	VBD	_	_	_
905	harvested	harvest	VBN	_	_	_
906	at	at	IN	_	_	_
907	stationary	stationary	JJ	GrowthPhase	_	_
908	phase	phase	NN	GrowthPhase	_	_
909	,	,	,	_	_	_
910	biological	biological	JJ	_	_	_
911	rep1	rep1	NN	_	_	_
912	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
913	E.	e.	FW	_	_	_
914	coli	coli	FW	_	_	_
915	CRP	crp	NN	TF	_	_
916	Q	Q	NNP	_	_	_
917	strain	strain	NN	_	_	_
918	grown	grow	VBN	_	_	_
919	in	in	IN	_	_	_
920	glucose	glucose	NN	SUPP	_	_
921	batch	batch	NN	_	_	_
922	minimal	minimal	JJ	_	_	_
923	media	media	NNS	_	_	_
924	,	,	,	_	_	_
925	cells	cell	NNS	_	_	_
926	were	be	VBD	_	_	_
927	harvested	harvest	VBN	_	_	_
928	at	at	IN	_	_	_
929	stationary	stationary	JJ	GrowthPhase	_	_
930	phase	phase	NN	GrowthPhase	_	_
931	,	,	,	_	_	_
932	biological	biological	JJ	_	_	_
933	rep2	rep2	NN	_	_	_
934	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
935	E.	e.	FW	_	_	_
936	coli	coli	FW	_	_	_
937	CRP	crp	NN	TF	_	_
938	R	r	NN	_	_	_
939	strain	strain	NN	_	_	_
940	_	_	NN	_	_	_
941	acetate	acetate	NN	SUPP	_	_
942	_	_	NN	_	_	_
943	exponential	exponential	JJ	GrowthPhase	_	_
944	phase	phase	NN	GrowthPhase	_	_
945	_	_	NN	_	_	_
946	repl1	repl1	NN	_	_	_
947	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
948	E.	e.	FW	_	_	_
949	coli	coli	FW	_	_	_
950	CRP	crp	NN	TF	_	_
951	R	r	NN	_	_	_
952	strain	strain	NN	_	_	_
953	_	_	NN	_	_	_
954	acetate	acetate	NN	SUPP	_	_
955	_	_	NN	_	_	_
956	exponential	exponential	JJ	GrowthPhase	_	_
957	phase	phase	NN	GrowthPhase	_	_
958	_	_	NN	_	_	_
959	repl2	repl2	NN	_	_	_
960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
961	E.	e.	FW	_	_	_
962	coli	coli	FW	_	_	_
963	CRP	crp	NN	TF	_	_
964	R	r	NN	_	_	_
965	strain	strain	NN	_	_	_
966	_	_	NN	_	_	_
967	acetate	acetate	NN	SUPP	_	_
968	_	_	NN	_	_	_
969	stationary	stationary	JJ	GrowthPhase	_	_
970	phase	phase	NN	GrowthPhase	_	_
971	_	_	NN	_	_	_
972	repl1	repl1	NN	_	_	_
973	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
974	E.	e.	FW	_	_	_
975	coli	coli	FW	_	_	_
976	CRP	crp	NN	TF	_	_
977	R	r	NN	_	_	_
978	strain	strain	NN	_	_	_
979	_	_	NN	_	_	_
980	acetate	acetate	NN	SUPP	_	_
981	_	_	NN	_	_	_
982	stationary	stationary	JJ	GrowthPhase	_	_
983	phase	phase	NN	GrowthPhase	_	_
984	_	_	NN	_	_	_
985	repl2	repl2	NN	_	_	_
986	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
987	E.	e.	FW	_	_	_
988	coli	coli	FW	_	_	_
989	CRP	crp	NN	TF	_	_
990	R	r	NN	_	_	_
991	strain	strain	NN	_	_	_
992	_	_	NN	_	_	_
993	glucose	glucose	NN	SUPP	_	_
994	_	_	NN	_	_	_
995	exponential	exponential	JJ	GrowthPhase	_	_
996	phase	phase	NN	GrowthPhase	_	_
997	_	_	NN	_	_	_
998	repl1	repl1	NN	_	_	_
999	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1000	E.	e.	FW	_	_	_
1001	coli	coli	FW	_	_	_
1002	CRP	crp	NN	TF	_	_
1003	R	r	NN	_	_	_
1004	strain	strain	NN	_	_	_
1005	_	_	NN	_	_	_
1006	glucose	glucose	NN	SUPP	_	_
1007	_	_	NN	_	_	_
1008	exponential	exponential	JJ	GrowthPhase	_	_
1009	phase	phase	NN	GrowthPhase	_	_
1010	_	_	NN	_	_	_
1011	repl2	repl2	NN	_	_	_
1012	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1013	E.	e.	FW	_	_	_
1014	coli	coli	FW	_	_	_
1015	CRP	crp	NN	TF	_	_
1016	R	r	NN	_	_	_
1017	strain	strain	NN	_	_	_
1018	_	_	NN	_	_	_
1019	glucose	glucose	NN	SUPP	_	_
1020	_	_	NN	_	_	_
1021	stationary	stationary	JJ	GrowthPhase	_	_
1022	phase	phase	NN	GrowthPhase	_	_
1023	_	_	NN	_	_	_
1024	repl1	repl1	NN	_	_	_
1025	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1026	E.	e.	FW	_	_	_
1027	coli	coli	FW	_	_	_
1028	CRP	crp	NN	TF	_	_
1029	R	r	NN	_	_	_
1030	strain	strain	NN	_	_	_
1031	_	_	NN	_	_	_
1032	glucose	glucose	NN	SUPP	_	_
1033	_	_	NN	_	_	_
1034	stationary	stationary	JJ	GrowthPhase	_	_
1035	phase	phase	NN	GrowthPhase	_	_
1036	_	_	NN	_	_	_
1037	repl2	repl2	NN	_	_	_
1038	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1039	E.	e.	FW	_	_	_
1040	coli	coli	FW	_	_	_
1041	CRP	crp	NN	TF	_	_
1042	R	r	NN	_	_	_
1043	strain	strain	NN	_	_	_
1044	grown	grow	VBN	_	_	_
1045	in	in	IN	_	_	_
1046	acetate	acetate	NN	SUPP	_	_
1047	batch	batch	NN	_	_	_
1048	minimal	minimal	JJ	_	_	_
1049	media	media	NNS	_	_	_
1050	,	,	,	_	_	_
1051	cells	cell	NNS	_	_	_
1052	were	be	VBD	_	_	_
1053	harvested	harvest	VBN	_	_	_
1054	at	at	IN	_	_	_
1055	exponential	exponential	JJ	GrowthPhase	_	_
1056	phase	phase	NN	GrowthPhase	_	_
1057	,	,	,	_	_	_
1058	biological	biological	JJ	_	_	_
1059	rep1	rep1	NN	_	_	_
1060	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1061	E.	e.	FW	_	_	_
1062	coli	coli	FW	_	_	_
1063	CRP	crp	NN	TF	_	_
1064	R	r	NN	_	_	_
1065	strain	strain	NN	_	_	_
1066	grown	grow	VBN	_	_	_
1067	in	in	IN	_	_	_
1068	acetate	acetate	NN	SUPP	_	_
1069	batch	batch	NN	_	_	_
1070	minimal	minimal	JJ	_	_	_
1071	media	media	NNS	_	_	_
1072	,	,	,	_	_	_
1073	cells	cell	NNS	_	_	_
1074	were	be	VBD	_	_	_
1075	harvested	harvest	VBN	_	_	_
1076	at	at	IN	_	_	_
1077	exponential	exponential	JJ	GrowthPhase	_	_
1078	phase	phase	NN	GrowthPhase	_	_
1079	,	,	,	_	_	_
1080	biological	biological	JJ	_	_	_
1081	rep2	rep2	NN	_	_	_
1082	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1083	E.	e.	FW	_	_	_
1084	coli	coli	FW	_	_	_
1085	CRP	crp	NN	TF	_	_
1086	R	r	NN	_	_	_
1087	strain	strain	NN	_	_	_
1088	grown	grow	VBN	_	_	_
1089	in	in	IN	_	_	_
1090	acetate	acetate	NN	SUPP	_	_
1091	batch	batch	NN	_	_	_
1092	minimal	minimal	JJ	_	_	_
1093	media	media	NNS	_	_	_
1094	,	,	,	_	_	_
1095	cells	cell	NNS	_	_	_
1096	were	be	VBD	_	_	_
1097	harvested	harvest	VBN	_	_	_
1098	at	at	IN	_	_	_
1099	stationary	stationary	JJ	GrowthPhase	_	_
1100	phase	phase	NN	GrowthPhase	_	_
1101	,	,	,	_	_	_
1102	biological	biological	JJ	_	_	_
1103	rep1	rep1	NN	_	_	_
1104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1105	E.	e.	FW	_	_	_
1106	coli	coli	FW	_	_	_
1107	CRP	crp	NN	TF	_	_
1108	R	r	NN	_	_	_
1109	strain	strain	NN	_	_	_
1110	grown	grow	VBN	_	_	_
1111	in	in	IN	_	_	_
1112	acetate	acetate	NN	SUPP	_	_
1113	batch	batch	NN	_	_	_
1114	minimal	minimal	JJ	_	_	_
1115	media	media	NNS	_	_	_
1116	,	,	,	_	_	_
1117	cells	cell	NNS	_	_	_
1118	were	be	VBD	_	_	_
1119	harvested	harvest	VBN	_	_	_
1120	at	at	IN	_	_	_
1121	stationary	stationary	JJ	GrowthPhase	_	_
1122	phase	phase	NN	GrowthPhase	_	_
1123	,	,	,	_	_	_
1124	biological	biological	JJ	_	_	_
1125	rep2	rep2	NN	_	_	_
1126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1127	E.	e.	FW	_	_	_
1128	coli	coli	FW	_	_	_
1129	CRP	crp	NN	TF	_	_
1130	R	r	NN	_	_	_
1131	strain	strain	NN	_	_	_
1132	grown	grow	VBN	_	_	_
1133	in	in	IN	_	_	_
1134	glucose	glucose	NN	SUPP	_	_
1135	batch	batch	NN	_	_	_
1136	minimal	minimal	JJ	_	_	_
1137	media	media	NNS	_	_	_
1138	,	,	,	_	_	_
1139	cells	cell	NNS	_	_	_
1140	were	be	VBD	_	_	_
1141	harvested	harvest	VBN	_	_	_
1142	at	at	IN	_	_	_
1143	exponential	exponential	JJ	GrowthPhase	_	_
1144	phase	phase	NN	GrowthPhase	_	_
1145	,	,	,	_	_	_
1146	biological	biological	JJ	_	_	_
1147	rep1	rep1	NN	_	_	_
1148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1149	E.	e.	FW	_	_	_
1150	coli	coli	FW	_	_	_
1151	CRP	crp	NN	TF	_	_
1152	R	r	NN	_	_	_
1153	strain	strain	NN	_	_	_
1154	grown	grow	VBN	_	_	_
1155	in	in	IN	_	_	_
1156	glucose	glucose	NN	SUPP	_	_
1157	batch	batch	NN	_	_	_
1158	minimal	minimal	JJ	_	_	_
1159	media	media	NNS	_	_	_
1160	,	,	,	_	_	_
1161	cells	cell	NNS	_	_	_
1162	were	be	VBD	_	_	_
1163	harvested	harvest	VBN	_	_	_
1164	at	at	IN	_	_	_
1165	exponential	exponential	JJ	GrowthPhase	_	_
1166	phase	phase	NN	GrowthPhase	_	_
1167	,	,	,	_	_	_
1168	biological	biological	JJ	_	_	_
1169	rep2	rep2	NN	_	_	_
1170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1171	E.	e.	FW	_	_	_
1172	coli	coli	FW	_	_	_
1173	CRP	crp	NN	TF	_	_
1174	R	r	NN	_	_	_
1175	strain	strain	NN	_	_	_
1176	grown	grow	VBN	_	_	_
1177	in	in	IN	_	_	_
1178	glucose	glucose	NN	SUPP	_	_
1179	batch	batch	NN	_	_	_
1180	minimal	minimal	JJ	_	_	_
1181	media	media	NNS	_	_	_
1182	,	,	,	_	_	_
1183	cells	cell	NNS	_	_	_
1184	were	be	VBD	_	_	_
1185	harvested	harvest	VBN	_	_	_
1186	at	at	IN	_	_	_
1187	stationary	stationary	JJ	GrowthPhase	_	_
1188	phase	phase	NN	GrowthPhase	_	_
1189	,	,	,	_	_	_
1190	biological	biological	JJ	_	_	_
1191	rep1	rep1	NN	_	_	_
1192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1193	E.	e.	FW	_	_	_
1194	coli	coli	FW	_	_	_
1195	CRP	crp	NN	TF	_	_
1196	R	r	NN	_	_	_
1197	strain	strain	NN	_	_	_
1198	grown	grow	VBN	_	_	_
1199	in	in	IN	_	_	_
1200	glucose	glucose	NN	SUPP	_	_
1201	batch	batch	NN	_	_	_
1202	minimal	minimal	JJ	_	_	_
1203	media	media	NNS	_	_	_
1204	,	,	,	_	_	_
1205	cells	cell	NNS	_	_	_
1206	were	be	VBD	_	_	_
1207	harvested	harvest	VBN	_	_	_
1208	at	at	IN	_	_	_
1209	stationary	stationary	JJ	GrowthPhase	_	_
1210	phase	phase	NN	GrowthPhase	_	_
1211	,	,	,	_	_	_
1212	biological	biological	JJ	_	_	_
1213	rep2	rep2	NN	_	_	_
1214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1215	E.	e.	FW	_	_	_
1216	coli	coli	FW	_	_	_
1217	culture	culture	NN	_	_	_
1218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1219	e.coli	e.coli	JJ	_	_	_
1220	culture	culture	NN	_	_	_
1221	protocol	protocol	NN	_	_	_
1222	:	:	:	_	_	_
1223	conditioned	condition	VBN	_	_	_
1224	Caco-2	caco-2	NN	_	_	_
1225	cell	cell	NN	_	_	_
1226	medium	medium	NN	_	_	_
1227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1228	e.coli	e.coli	JJ	_	_	_
1229	culture	culture	NN	_	_	_
1230	protocol	protocol	NN	_	_	_
1231	:	:	:	_	_	_
1232	fresh	fresh	JJ	_	_	_
1233	medium	medium	NN	_	_	_
1234	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1235	E.	E.	NNP	_	_	_
1236	coli	coli	NN	_	_	_
1237	cultures	culture	NNS	_	_	_
1238	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1239	E.	e.	FW	_	_	_
1240	coli	coli	FW	_	_	_
1241	cultures	culture	NNS	_	_	_
1242	were	be	VBD	_	_	_
1243	grown	grow	VBN	_	_	_
1244	at	at	IN	_	_	_
1245	37	37	CD	_	_	_
1246	°C	°c	NN	_	_	_
1247	in	in	IN	_	_	_
1248	M9	m9	NN	MED	_	_
1249	minimal	minimal	JJ	MED	_	_
1250	media	media	NNS	MED	_	_
1251	with	with	IN	_	_	_
1252	glucose	glucose	NN	SUPP	_	_
1253	as	as	IN	_	_	_
1254	the	the	DT	_	_	_
1255	primary	primary	JJ	_	_	_
1256	carbon	carbon	NN	_	_	_
1257	source	source	NN	_	_	_
1258	and	and	CC	_	_	_
1259	harvested	harvest	VBN	_	_	_
1260	at	at	IN	_	_	_
1261	mid	mid	JJ	_	_	_
1262	exponetial	exponetial	JJ	_	_	_
1263	phase	phase	NN	_	_	_
1264	.	.	.	_	_	_

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	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	,	,	,	_	_	_
4	culture	culture	NN	_	_	_
5	with	with	IN	_	_	_
6	ethanol	ethanol	NN	_	_	_
7	20	20	CD	_	_	_
8	%	%	NN	_	_	_
9	,	,	,	_	_	_
10	20	20	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	t2	t2	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	after	after	IN	_	_	_
16	treatment	treatment	NN	_	_	_
17	,	,	,	_	_	_
18	replicate	replicate	VB	_	_	_
19	A	a	DT	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	E.coli	e.coli	NNS	_	_	_
22	,	,	,	_	_	_
23	culture	culture	NN	_	_	_
24	with	with	IN	_	_	_
25	ethanol	ethanol	NN	_	_	_
26	20	20	CD	_	_	_
27	%	%	NN	_	_	_
28	,	,	,	_	_	_
29	20	20	CD	_	_	_
30	minutes	minute	NNS	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	t2	t2	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	after	after	IN	_	_	_
35	treatment	treatment	NN	_	_	_
36	,	,	,	_	_	_
37	replicate	replicate	VB	_	_	_
38	B	b	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	E.coli	e.coli	NNS	_	_	_
41	,	,	,	_	_	_
42	culture	culture	NN	_	_	_
43	with	with	IN	_	_	_
44	ethanol	ethanol	NN	_	_	_
45	20	20	CD	_	_	_
46	%	%	NN	_	_	_
47	,	,	,	_	_	_
48	20	20	CD	_	_	_
49	minutes	minute	NNS	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	t2	t2	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	after	after	IN	_	_	_
54	treatment	treatment	NN	_	_	_
55	,	,	,	_	_	_
56	replicate	replicate	VB	_	_	_
57	C	c	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	E.coli	e.coli	NNS	_	_	_
60	,	,	,	_	_	_
61	culture	culture	NN	_	_	_
62	with	with	IN	_	_	_
63	ethanol	ethanol	NN	_	_	_
64	20	20	CD	_	_	_
65	%	%	NN	_	_	_
66	,	,	,	_	_	_
67	40	40	CD	_	_	_
68	minutes	minute	NNS	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	t3	t3	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	after	after	IN	_	_	_
73	treatment	treatment	NN	_	_	_
74	,	,	,	_	_	_
75	replicate	replicate	VB	_	_	_
76	A	a	DT	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	E.coli	e.coli	NNS	_	_	_
79	,	,	,	_	_	_
80	culture	culture	NN	_	_	_
81	with	with	IN	_	_	_
82	ethanol	ethanol	NN	_	_	_
83	20	20	CD	_	_	_
84	%	%	NN	_	_	_
85	,	,	,	_	_	_
86	40	40	CD	_	_	_
87	minutes	minute	NNS	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	t3	t3	NN	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	after	after	IN	_	_	_
92	treatment	treatment	NN	_	_	_
93	,	,	,	_	_	_
94	replicate	replicate	VB	_	_	_
95	B	b	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	E.coli	e.coli	NNS	_	_	_
98	,	,	,	_	_	_
99	culture	culture	NN	_	_	_
100	with	with	IN	_	_	_
101	ethanol	ethanol	NN	_	_	_
102	20	20	CD	_	_	_
103	%	%	NN	_	_	_
104	,	,	,	_	_	_
105	40	40	CD	_	_	_
106	minutes	minute	NNS	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	t3	t3	NN	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	after	after	IN	_	_	_
111	treatment	treatment	NN	_	_	_
112	,	,	,	_	_	_
113	replicate	replicate	VB	_	_	_
114	C	c	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	E.coli	e.coli	NNS	_	_	_
117	,	,	,	_	_	_
118	culture	culture	NN	_	_	_
119	with	with	IN	_	_	_
120	ethanol	ethanol	NN	_	_	_
121	20	20	CD	_	_	_
122	%	%	NN	_	_	_
123	,	,	,	_	_	_
124	at	at	IN	_	_	_
125	the	the	DT	_	_	_
126	time	time	NN	_	_	_
127	of	of	IN	_	_	_
128	treatment	treatment	NN	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	t1	t1	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	,	,	,	_	_	_
133	replicate	replicate	VB	_	_	_
134	A	a	DT	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	E.coli	e.coli	NNS	_	_	_
137	,	,	,	_	_	_
138	culture	culture	NN	_	_	_
139	with	with	IN	_	_	_
140	ethanol	ethanol	NN	_	_	_
141	20	20	CD	_	_	_
142	%	%	NN	_	_	_
143	,	,	,	_	_	_
144	at	at	IN	_	_	_
145	the	the	DT	_	_	_
146	time	time	NN	_	_	_
147	of	of	IN	_	_	_
148	treatment	treatment	NN	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	t1	t1	NN	_	_	_
151	-RRB-	-rrb-	-RRB-	_	_	_
152	,	,	,	_	_	_
153	replicate	replicate	VB	_	_	_
154	B	b	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	E.coli	e.coli	NNS	_	_	_
157	,	,	,	_	_	_
158	culture	culture	NN	_	_	_
159	with	with	IN	_	_	_
160	ethanol	ethanol	NN	_	_	_
161	20	20	CD	_	_	_
162	%	%	NN	_	_	_
163	,	,	,	_	_	_
164	at	at	IN	_	_	_
165	the	the	DT	_	_	_
166	time	time	NN	_	_	_
167	of	of	IN	_	_	_
168	treatment	treatment	NN	_	_	_
169	-LRB-	-lrb-	-LRB-	_	_	_
170	t1	t1	NN	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	,	,	,	_	_	_
173	replicate	replicate	VB	_	_	_
174	C	c	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	E.coli	e.coli	NNS	_	_	_
177	,	,	,	_	_	_
178	culture	culture	NN	_	_	_
179	with	with	IN	_	_	_
180	VWPE	vwpe	NN	_	_	_
181	extract	extract	NN	_	_	_
182	diluted	dilute	VBN	_	_	_
183	in	in	IN	_	_	_
184	ethanol	ethanol	NN	_	_	_
185	20	20	CD	_	_	_
186	%	%	NN	_	_	_
187	,	,	,	_	_	_
188	20	20	CD	_	_	_
189	minutes	minute	NNS	_	_	_
190	-LRB-	-lrb-	-LRB-	_	_	_
191	t2	t2	NN	_	_	_
192	-RRB-	-rrb-	-RRB-	_	_	_
193	after	after	IN	_	_	_
194	treatment	treatment	NN	_	_	_
195	,	,	,	_	_	_
196	replicate	replicate	VB	_	_	_
197	A	a	DT	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	E.coli	e.coli	NNS	_	_	_
200	,	,	,	_	_	_
201	culture	culture	NN	_	_	_
202	with	with	IN	_	_	_
203	VWPE	vwpe	NN	_	_	_
204	extract	extract	NN	_	_	_
205	diluted	dilute	VBN	_	_	_
206	in	in	IN	_	_	_
207	ethanol	ethanol	NN	_	_	_
208	20	20	CD	_	_	_
209	%	%	NN	_	_	_
210	,	,	,	_	_	_
211	20	20	CD	_	_	_
212	minutes	minute	NNS	_	_	_
213	-LRB-	-lrb-	-LRB-	_	_	_
214	t2	t2	NN	_	_	_
215	-RRB-	-rrb-	-RRB-	_	_	_
216	after	after	IN	_	_	_
217	treatment	treatment	NN	_	_	_
218	,	,	,	_	_	_
219	replicate	replicate	VB	_	_	_
220	B	b	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	E.coli	e.coli	NNS	_	_	_
223	,	,	,	_	_	_
224	culture	culture	NN	_	_	_
225	with	with	IN	_	_	_
226	VWPE	vwpe	NN	_	_	_
227	extract	extract	NN	_	_	_
228	diluted	dilute	VBN	_	_	_
229	in	in	IN	_	_	_
230	ethanol	ethanol	NN	_	_	_
231	20	20	CD	_	_	_
232	%	%	NN	_	_	_
233	,	,	,	_	_	_
234	20	20	CD	_	_	_
235	minutes	minute	NNS	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	t2	t2	NN	_	_	_
238	-RRB-	-rrb-	-RRB-	_	_	_
239	after	after	IN	_	_	_
240	treatment	treatment	NN	_	_	_
241	,	,	,	_	_	_
242	replicate	replicate	VB	_	_	_
243	C	c	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	E.coli	e.coli	NNS	_	_	_
246	,	,	,	_	_	_
247	culture	culture	NN	_	_	_
248	with	with	IN	_	_	_
249	VWPE	vwpe	NN	_	_	_
250	extract	extract	NN	_	_	_
251	diluted	dilute	VBN	_	_	_
252	in	in	IN	_	_	_
253	ethanol	ethanol	NN	_	_	_
254	20	20	CD	_	_	_
255	%	%	NN	_	_	_
256	,	,	,	_	_	_
257	40	40	CD	_	_	_
258	minutes	minute	NNS	_	_	_
259	-LRB-	-lrb-	-LRB-	_	_	_
260	t3	t3	NN	_	_	_
261	-RRB-	-rrb-	-RRB-	_	_	_
262	after	after	IN	_	_	_
263	treatment	treatment	NN	_	_	_
264	,	,	,	_	_	_
265	replicate	replicate	VB	_	_	_
266	A	a	DT	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	E.coli	e.coli	NNS	_	_	_
269	,	,	,	_	_	_
270	culture	culture	NN	_	_	_
271	with	with	IN	_	_	_
272	VWPE	vwpe	NN	_	_	_
273	extract	extract	NN	_	_	_
274	diluted	dilute	VBN	_	_	_
275	in	in	IN	_	_	_
276	ethanol	ethanol	NN	_	_	_
277	20	20	CD	_	_	_
278	%	%	NN	_	_	_
279	,	,	,	_	_	_
280	40	40	CD	_	_	_
281	minutes	minute	NNS	_	_	_
282	-LRB-	-lrb-	-LRB-	_	_	_
283	t3	t3	NN	_	_	_
284	-RRB-	-rrb-	-RRB-	_	_	_
285	after	after	IN	_	_	_
286	treatment	treatment	NN	_	_	_
287	,	,	,	_	_	_
288	replicate	replicate	VB	_	_	_
289	B	b	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	E.coli	e.coli	NNS	_	_	_
292	,	,	,	_	_	_
293	culture	culture	NN	_	_	_
294	with	with	IN	_	_	_
295	VWPE	vwpe	NN	_	_	_
296	extract	extract	NN	_	_	_
297	diluted	dilute	VBN	_	_	_
298	in	in	IN	_	_	_
299	ethanol	ethanol	NN	_	_	_
300	20	20	CD	_	_	_
301	%	%	NN	_	_	_
302	,	,	,	_	_	_
303	40	40	CD	_	_	_
304	minutes	minute	NNS	_	_	_
305	-LRB-	-lrb-	-LRB-	_	_	_
306	t3	t3	NN	_	_	_
307	-RRB-	-rrb-	-RRB-	_	_	_
308	after	after	IN	_	_	_
309	treatment	treatment	NN	_	_	_
310	,	,	,	_	_	_
311	replicate	replicate	VB	_	_	_
312	C	c	NN	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	E.coli	e.coli	NNS	_	_	_
315	,	,	,	_	_	_
316	culture	culture	NN	_	_	_
317	with	with	IN	_	_	_
318	VWPE	vwpe	NN	_	_	_
319	extract	extract	NN	_	_	_
320	diluted	dilute	VBN	_	_	_
321	in	in	IN	_	_	_
322	ethanol	ethanol	NN	_	_	_
323	20	20	CD	_	_	_
324	%	%	NN	_	_	_
325	,	,	,	_	_	_
326	at	at	IN	_	_	_
327	the	the	DT	_	_	_
328	time	time	NN	_	_	_
329	of	of	IN	_	_	_
330	treatment	treatment	NN	_	_	_
331	-LRB-	-lrb-	-LRB-	_	_	_
332	t1	t1	NN	_	_	_
333	-RRB-	-rrb-	-RRB-	_	_	_
334	,	,	,	_	_	_
335	replicate	replicate	VB	_	_	_
336	A	a	DT	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	E.coli	e.coli	NNS	_	_	_
339	,	,	,	_	_	_
340	culture	culture	NN	_	_	_
341	with	with	IN	_	_	_
342	VWPE	vwpe	NN	_	_	_
343	extract	extract	NN	_	_	_
344	diluted	dilute	VBN	_	_	_
345	in	in	IN	_	_	_
346	ethanol	ethanol	NN	_	_	_
347	20	20	CD	_	_	_
348	%	%	NN	_	_	_
349	,	,	,	_	_	_
350	at	at	IN	_	_	_
351	the	the	DT	_	_	_
352	time	time	NN	_	_	_
353	of	of	IN	_	_	_
354	treatment	treatment	NN	_	_	_
355	-LRB-	-lrb-	-LRB-	_	_	_
356	t1	t1	NN	_	_	_
357	-RRB-	-rrb-	-RRB-	_	_	_
358	,	,	,	_	_	_
359	replicate	replicate	VB	_	_	_
360	B	b	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	E.coli	e.coli	NNS	_	_	_
363	,	,	,	_	_	_
364	culture	culture	NN	_	_	_
365	with	with	IN	_	_	_
366	VWPE	vwpe	NN	_	_	_
367	extract	extract	NN	_	_	_
368	diluted	dilute	VBN	_	_	_
369	in	in	IN	_	_	_
370	ethanol	ethanol	NN	_	_	_
371	20	20	CD	_	_	_
372	%	%	NN	_	_	_
373	,	,	,	_	_	_
374	at	at	IN	_	_	_
375	the	the	DT	_	_	_
376	time	time	NN	_	_	_
377	of	of	IN	_	_	_
378	treatment	treatment	NN	_	_	_
379	-LRB-	-lrb-	-LRB-	_	_	_
380	t1	t1	NN	_	_	_
381	-RRB-	-rrb-	-RRB-	_	_	_
382	,	,	,	_	_	_
383	replicate	replicate	VB	_	_	_
384	C	c	NN	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
386	E.	e.	FW	_	_	_
387	coli	coli	FW	_	_	_
388	cultutures	cultuture	NNS	_	_	_
389	were	be	VBD	_	_	_
390	grown	grow	VBN	_	_	_
391	in	in	IN	_	_	_
392	M9	m9	NN	_	_	_
393	media	media	NNS	_	_	_
394	using	use	VBG	_	_	_
395	standard	standard	JJ	_	_	_
396	protocol	protocol	NN	_	_	_
397	,	,	,	_	_	_
398	to	to	TO	_	_	_
399	log	log	VB	_	_	_
400	phase	phase	NN	_	_	_
401	-LRB-	-lrb-	-LRB-	_	_	_
402	OD600	od600	NN	_	_	_
403	of	of	IN	_	_	_
404	0.7-0.8	0.7-0.8	CD	_	_	_
405	-RRB-	-rrb-	-RRB-	_	_	_
406	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
407	E.	e.	FW	_	_	_
408	coli	coli	FW	_	_	_
409	D1	d1	NN	_	_	_
410	#	#	#	_	_	_
411	1	1	CD	_	_	_
412	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
413	E.	E.	NNP	_	_	_
414	coli	coli	NN	_	_	_
415	D1	d1	NN	_	_	_
416	#	#	#	_	_	_
417	2	2	CD	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	ecoli	ecolus	NNS	_	_	_
420	_	_	VBP	_	_	_
421	D1	d1	NN	_	_	_
422	_	_	SYM	_	_	_
423	2x	2x	FW	_	_	_
424	_	_	FW	_	_	_
425	v2	v2	FW	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	E.	e.	FW	_	_	_
428	coli	coli	FW	_	_	_
429	D1	d1	NN	_	_	_
430	#	#	#	_	_	_
431	3	3	CD	_	_	_
432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
433	ecoli	ecolus	NNS	_	_	_
434	_	_	VBP	_	_	_
435	D1	d1	NN	_	_	_
436	_	_	SYM	_	_	_
437	3x	3x	FW	_	_	_
438	_	_	FW	_	_	_
439	v2	v2	FW	_	_	_
440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
441	ecoli	ecolus	NNS	_	_	_
442	_	_	VBP	_	_	_
443	D1	d1	NN	_	_	_
444	_	_	SYM	_	_	_
445	4x	4x	FW	_	_	_
446	_	_	FW	_	_	_
447	v2	v2	FW	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	Ecoli	ecolus	NNS	_	_	_
450	_	_	VBP	_	_	_
451	dFNR	dfnr	NN	_	_	_
452	_	_	CD	_	_	_
453	rep1	rep1	NN	_	_	_
454	_	_	NN	_	_	_
455	anaerobic	anaerobic	JJ	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	Ecoli	ecolus	NNS	_	_	_
458	_	_	VBP	_	_	_
459	dFNR	dfnr	NN	_	_	_
460	_	_	CD	_	_	_
461	rep2	rep2	NN	_	_	_
462	_	_	CD	_	_	_
463	anaerobic	anaerobic	JJ	_	_	_
464	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
465	Ecoli	Ecoli	NNP	_	_	_
466	_	_	NNP	_	_	_
467	Early	Early	NNP	_	_	_
468	Recovery	Recovery	NNP	_	_	_
469	in	in	IN	_	_	_
470	LB	LB	NNP	_	_	_
471	T1	t1	NN	_	_	_
472	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
473	Ecoli	Ecoli	NNP	_	_	_
474	_	_	NNP	_	_	_
475	Early	Early	NNP	_	_	_
476	Recovery	Recovery	NNP	_	_	_
477	in	in	IN	_	_	_
478	LB	LB	NNP	_	_	_
479	T2	t2	NN	_	_	_
480	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
481	Ecoli	Ecoli	NNP	_	_	_
482	_	_	NNP	_	_	_
483	Early	Early	NNP	_	_	_
484	Recovery	Recovery	NNP	_	_	_
485	in	in	IN	_	_	_
486	LB	LB	NNP	_	_	_
487	T3	t3	NN	_	_	_
488	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
489	Ecoli	Ecoli	NNP	_	_	_
490	_	_	NNP	_	_	_
491	Early	Early	NNP	_	_	_
492	Recovery	Recovery	NNP	_	_	_
493	in	in	IN	_	_	_
494	LB	LB	NNP	_	_	_
495	T4	t4	NN	_	_	_
496	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
497	Ecoli	Ecoli	NNP	_	_	_
498	_	_	NNP	_	_	_
499	Early	Early	NNP	_	_	_
500	Recovery	Recovery	NNP	_	_	_
501	in	in	IN	_	_	_
502	LB	LB	NNP	_	_	_
503	T5	T5	NNP	_	_	_
504	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
505	Ecoli	Ecoli	NNP	_	_	_
506	_	_	NNP	_	_	_
507	Early	Early	NNP	_	_	_
508	Recovery	Recovery	NNP	_	_	_
509	in	in	IN	_	_	_
510	LB	LB	NNP	_	_	_
511	T6	T6	NNP	_	_	_
512	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
513	Ecoli	Ecoli	NNP	_	_	_
514	_	_	NNP	_	_	_
515	Early	Early	NNP	_	_	_
516	Recovery	Recovery	NNP	_	_	_
517	in	in	IN	_	_	_
518	LB	LB	NNP	_	_	_
519	T7	T7	NNP	_	_	_
520	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
521	E.	E.	NNP	_	_	_
522	coli	coli	NN	_	_	_
523	EDL933	edl933	NN	_	_	_
524	#	#	#	_	_	_
525	1	1	CD	_	_	_
526	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
527	E.	E.	NNP	_	_	_
528	coli	coli	NN	_	_	_
529	EDL933	edl933	NN	_	_	_
530	#	#	#	_	_	_
531	2	2	CD	_	_	_
532	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
533	ecoli	ecolus	NNS	_	_	_
534	_	_	VBP	_	_	_
535	EDL933	edl933	NN	_	_	_
536	_	_	SYM	_	_	_
537	2x	2x	FW	_	_	_
538	_	_	FW	_	_	_
539	v2	v2	FW	_	_	_
540	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
541	E.	e.	FW	_	_	_
542	coli	coli	FW	_	_	_
543	EDL933	edl933	NN	_	_	_
544	#	#	#	_	_	_
545	3	3	CD	_	_	_
546	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
547	ecoli	ecolus	NNS	_	_	_
548	_	_	VBP	_	_	_
549	EDL933	edl933	NN	_	_	_
550	_	_	SYM	_	_	_
551	3x	3x	FW	_	_	_
552	_	_	FW	_	_	_
553	v2	v2	FW	_	_	_
554	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
555	ecoli	ecolus	NNS	_	_	_
556	_	_	VBP	_	_	_
557	EDL933	edl933	NN	_	_	_
558	_	_	SYM	_	_	_
559	4x	4x	FW	_	_	_
560	_	_	FW	_	_	_
561	v2	v2	FW	_	_	_
562	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
563	E.	e.	FW	_	_	_
564	coli	coli	FW	_	_	_
565	Estradiol	estradiol	NN	_	_	_
566	Treatment	treatment	NN	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	E.coli	e.coli	NN	_	_	_
569	ethanologen	ethanologen	NN	_	_	_
570	strain	strain	NN	_	_	_
571	GLBRCE1	glbrce1	NN	_	_	_
572	or	or	CC	_	_	_
573	GLBRCE1	glbrce1	NN	_	_	_
574	lacking	lack	VBG	_	_	_
575	the	the	DT	_	_	_
576	plasmid-borne	plasmid-borne	JJ	_	_	_
577	PET	pet	NN	_	_	_
578	cassette	cassette	NN	_	_	_
579	-LRB-	-lrb-	-LRB-	_	_	_
580	GLBRCE1	glbrce1	NN	_	_	_
581	_	_	CD	_	_	_
582	pBBR	pbbr	NN	_	_	_
583	-RRB-	-rrb-	-RRB-	_	_	_
584	was	be	VBD	_	_	_
585	grown	grow	VBN	_	_	_
586	in	in	IN	_	_	_
587	AFEX	AFEX	NNP	_	_	_
588	corn	corn	NN	_	_	_
589	stover	stover	NN	_	_	_
590	hydrolysate	hydrolysate	NN	_	_	_
591	-LRB-	-lrb-	-LRB-	_	_	_
592	ACSH	acsh	NN	_	_	_
593	-RRB-	-rrb-	-RRB-	_	_	_
594	.	.	.	_	_	_

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	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	_	_	VBP	_	_	_
4	ethanol	ethanol	NN	_	_	_
5	_	_	NN	_	_	_
6	repA	repa	NN	_	_	_
7	_	_	CD	_	_	_
8	t1	t1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	E.coli	e.coli	NNS	_	_	_
11	_	_	VBP	_	_	_
12	ethanol	ethanol	NN	_	_	_
13	_	_	NN	_	_	_
14	repA	repa	NN	_	_	_
15	_	_	CD	_	_	_
16	t2	t2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	E.coli	e.coli	NNS	_	_	_
19	_	_	VBP	_	_	_
20	ethanol	ethanol	NN	_	_	_
21	_	_	NN	_	_	_
22	repA	repa	NN	_	_	_
23	_	_	CD	_	_	_
24	t3	t3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E.coli	e.coli	NNS	_	_	_
27	_	_	VBP	_	_	_
28	ethanol	ethanol	NN	_	_	_
29	_	_	NN	_	_	_
30	repB	repb	NN	_	_	_
31	_	_	CD	_	_	_
32	t1	t1	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	E.coli	e.coli	NNS	_	_	_
35	_	_	VBP	_	_	_
36	ethanol	ethanol	NN	_	_	_
37	_	_	NN	_	_	_
38	repB	repb	NN	_	_	_
39	_	_	CD	_	_	_
40	t2	t2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	E.coli	e.coli	NNS	_	_	_
43	_	_	VBP	_	_	_
44	ethanol	ethanol	NN	_	_	_
45	_	_	NN	_	_	_
46	repB	repb	NN	_	_	_
47	_	_	CD	_	_	_
48	t3	t3	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	E.coli	e.coli	NNS	_	_	_
51	_	_	VBP	_	_	_
52	ethanol	ethanol	NN	_	_	_
53	_	_	NN	_	_	_
54	repC	repc	NN	_	_	_
55	_	_	CD	_	_	_
56	t1	t1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	E.coli	e.coli	NNS	_	_	_
59	_	_	VBP	_	_	_
60	ethanol	ethanol	NN	_	_	_
61	_	_	NN	_	_	_
62	repC	repc	NN	_	_	_
63	_	_	CD	_	_	_
64	t2	t2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	E.coli	e.coli	NNS	_	_	_
67	_	_	VBP	_	_	_
68	ethanol	ethanol	NN	_	_	_
69	_	_	NN	_	_	_
70	repC	repc	NN	_	_	_
71	_	_	CD	_	_	_
72	t3	t3	NN	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	E.	E.	NNP	_	_	_
75	Coli	Coli	NNP	_	_	_
76	Exponential	Exponential	NNP	_	_	_
77	FecI	FecI	NNP	_	_	_
78	ChIP	ChIP	NNP	_	_	_
79	DNA	dna	NN	_	_	_
80	1	1	CD	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	E.	E.	NNP	_	_	_
83	Coli	Coli	NNP	_	_	_
84	Exponential	Exponential	NNP	_	_	_
85	FecI	FecI	NNP	_	_	_
86	ChIP	ChIP	NNP	_	_	_
87	DNA	dna	NN	_	_	_
88	2	2	CD	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	E.	E.	NNP	_	_	_
91	Coli	Coli	NNP	_	_	_
92	Exponential	Exponential	NNP	_	_	_
93	FecI	FecI	NNP	_	_	_
94	ChIP	ChIP	NNP	_	_	_
95	DNA	DNA	NNP	_	_	_
96	3	3	CD	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	E.	E.	NNP	_	_	_
99	Coli	Coli	NNP	_	_	_
100	Exponential	Exponential	NNP	_	_	_
101	FecI	FecI	NNP	_	_	_
102	ChIP	chip	NN	_	_	_
103	DNA	dna	NN	_	_	_
104	Mock	mock	NN	_	_	_
105	1	1	CD	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	E.	E.	NNP	_	_	_
108	Coli	Coli	NNP	_	_	_
109	Exponential	Exponential	NNP	_	_	_
110	FecI	FecI	NNP	_	_	_
111	ChIP	chip	NN	_	_	_
112	DNA	dna	NN	_	_	_
113	Mock	mock	NN	_	_	_
114	2	2	CD	_	_	_
115	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
116	E.	E.	NNP	_	_	_
117	Coli	Coli	NNP	_	_	_
118	Exponential	Exponential	NNP	_	_	_
119	FecI	FecI	NNP	_	_	_
120	ChIP	chip	NN	_	_	_
121	DNA	dna	NN	_	_	_
122	Mock	mock	NN	_	_	_
123	3	3	CD	_	_	_
124	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
125	E.	E.	NNP	_	_	_
126	Coli	Coli	NNP	_	_	_
127	Exponential	Exponential	NNP	_	_	_
128	RpoB	rpob	NN	_	_	_
129	ChIP	chip	NN	_	_	_
130	DNA	dna	NN	_	_	_
131	1	1	CD	_	_	_
132	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
133	E.	E.	NNP	_	_	_
134	Coli	Coli	NNP	_	_	_
135	Exponential	Exponential	NNP	_	_	_
136	RpoB	rpob	NN	_	_	_
137	ChIP	chip	NN	_	_	_
138	DNA	dna	NN	_	_	_
139	2	2	CD	_	_	_
140	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
141	E.	E.	NNP	_	_	_
142	Coli	Coli	NNP	_	_	_
143	Exponential	Exponential	NNP	_	_	_
144	RpoB	rpob	NN	_	_	_
145	ChIP	chip	NN	_	_	_
146	DNA	dna	NN	_	_	_
147	3	3	CD	_	_	_
148	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
149	E.	E.	NNP	_	_	_
150	Coli	Coli	NNP	_	_	_
151	Exponential	Exponential	NNP	_	_	_
152	RpoB	rpob	NN	_	_	_
153	ChIP	chip	NN	_	_	_
154	DNA	dna	NN	_	_	_
155	Mock	mock	NN	_	_	_
156	1	1	CD	_	_	_
157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
158	E.	E.	NNP	_	_	_
159	Coli	Coli	NNP	_	_	_
160	Exponential	Exponential	NNP	_	_	_
161	RpoB	rpob	NN	_	_	_
162	ChIP	chip	NN	_	_	_
163	DNA	dna	NN	_	_	_
164	Mock	mock	NN	_	_	_
165	2	2	CD	_	_	_
166	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
167	E.	E.	NNP	_	_	_
168	Coli	Coli	NNP	_	_	_
169	Exponential	Exponential	NNP	_	_	_
170	RpoB	rpob	NN	_	_	_
171	ChIP	chip	NN	_	_	_
172	DNA	dna	NN	_	_	_
173	Mock	mock	NN	_	_	_
174	3	3	CD	_	_	_
175	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
176	E.	E.	NNP	_	_	_
177	Coli	Coli	NNP	_	_	_
178	Exponential	Exponential	NNP	_	_	_
179	RpoD	rpod	NN	_	_	_
180	ChIP	chip	NN	_	_	_
181	DNA	dna	NN	_	_	_
182	1	1	CD	_	_	_
183	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
184	E.	E.	NNP	_	_	_
185	Coli	Coli	NNP	_	_	_
186	Exponential	Exponential	NNP	_	_	_
187	RpoD	rpod	NN	_	_	_
188	ChIP	chip	NN	_	_	_
189	DNA	dna	NN	_	_	_
190	2	2	CD	_	_	_
191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
192	E.	E.	NNP	_	_	_
193	Coli	Coli	NNP	_	_	_
194	Exponential	Exponential	NNP	_	_	_
195	RpoD	rpod	NN	_	_	_
196	ChIP	chip	NN	_	_	_
197	DNA	dna	NN	_	_	_
198	3	3	CD	_	_	_
199	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
200	E.	E.	NNP	_	_	_
201	Coli	Coli	NNP	_	_	_
202	Exponential	Exponential	NNP	_	_	_
203	RpoD	rpod	NN	_	_	_
204	ChIP	chip	NN	_	_	_
205	DNA	dna	NN	_	_	_
206	Mock	mock	NN	_	_	_
207	1	1	CD	_	_	_
208	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
209	E.	E.	NNP	_	_	_
210	Coli	Coli	NNP	_	_	_
211	Exponential	Exponential	NNP	_	_	_
212	RpoD	rpod	NN	_	_	_
213	ChIP	chip	NN	_	_	_
214	DNA	dna	NN	_	_	_
215	Mock	mock	NN	_	_	_
216	2	2	CD	_	_	_
217	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
218	E.	E.	NNP	_	_	_
219	Coli	Coli	NNP	_	_	_
220	Exponential	Exponential	NNP	_	_	_
221	RpoD	rpod	NN	_	_	_
222	ChIP	chip	NN	_	_	_
223	DNA	dna	NN	_	_	_
224	Mock	mock	NN	_	_	_
225	3	3	CD	_	_	_
226	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
227	E.	E.	NNP	_	_	_
228	Coli	Coli	NNP	_	_	_
229	Exponential	Exponential	NNP	_	_	_
230	RpoD	rpod	NN	_	_	_
231	DelN	deln	NN	_	_	_
232	ChIP	chip	NN	_	_	_
233	DNA	dna	NN	_	_	_
234	1	1	CD	_	_	_
235	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
236	E.	E.	NNP	_	_	_
237	Coli	Coli	NNP	_	_	_
238	Exponential	Exponential	NNP	_	_	_
239	RpoD	rpod	NN	_	_	_
240	DelN	deln	NN	_	_	_
241	ChIP	chip	NN	_	_	_
242	DNA	dna	NN	_	_	_
243	2	2	CD	_	_	_
244	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
245	E.	E.	NNP	_	_	_
246	Coli	Coli	NNP	_	_	_
247	Exponential	Exponential	NNP	_	_	_
248	RpoD	rpod	NN	_	_	_
249	DelN	deln	NN	_	_	_
250	ChIP	chip	NN	_	_	_
251	DNA	dna	NN	_	_	_
252	Mock	mock	NN	_	_	_
253	1	1	CD	_	_	_
254	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
255	E.	E.	NNP	_	_	_
256	Coli	Coli	NNP	_	_	_
257	Exponential	Exponential	NNP	_	_	_
258	RpoD	rpod	NN	_	_	_
259	DelN	deln	NN	_	_	_
260	ChIP	chip	NN	_	_	_
261	DNA	dna	NN	_	_	_
262	Mock	mock	NN	_	_	_
263	2	2	CD	_	_	_
264	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
265	E.	E.	NNP	_	_	_
266	Coli	Coli	NNP	_	_	_
267	Exponential	Exponential	NNP	_	_	_
268	RpoF	rpof	NN	_	_	_
269	ChIP	chip	NN	_	_	_
270	DNA	dna	NN	_	_	_
271	1	1	CD	_	_	_
272	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
273	E.	E.	NNP	_	_	_
274	Coli	Coli	NNP	_	_	_
275	Exponential	Exponential	NNP	_	_	_
276	RpoF	rpof	NN	_	_	_
277	ChIP	chip	NN	_	_	_
278	DNA	dna	NN	_	_	_
279	2	2	CD	_	_	_
280	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
281	E.	E.	NNP	_	_	_
282	Coli	Coli	NNP	_	_	_
283	Exponential	Exponential	NNP	_	_	_
284	RpoF	rpof	NN	_	_	_
285	ChIP	chip	NN	_	_	_
286	DNA	dna	NN	_	_	_
287	3	3	CD	_	_	_
288	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
289	E.	E.	NNP	_	_	_
290	Coli	Coli	NNP	_	_	_
291	Exponential	Exponential	NNP	_	_	_
292	RpoF	rpof	NN	_	_	_
293	ChIP	chip	NN	_	_	_
294	DNA	dna	NN	_	_	_
295	Mock	mock	NN	_	_	_
296	1	1	CD	_	_	_
297	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
298	E.	E.	NNP	_	_	_
299	Coli	Coli	NNP	_	_	_
300	Exponential	Exponential	NNP	_	_	_
301	RpoF	rpof	NN	_	_	_
302	ChIP	chip	NN	_	_	_
303	DNA	dna	NN	_	_	_
304	Mock	mock	NN	_	_	_
305	2	2	CD	_	_	_
306	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
307	E.	E.	NNP	_	_	_
308	Coli	Coli	NNP	_	_	_
309	Exponential	Exponential	NNP	_	_	_
310	RpoF	rpof	NN	_	_	_
311	ChIP	chip	NN	_	_	_
312	DNA	dna	NN	_	_	_
313	Mock	mock	NN	_	_	_
314	3	3	CD	_	_	_
315	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
316	E.	E.	NNP	_	_	_
317	Coli	Coli	NNP	_	_	_
318	Exponential	Exponential	NNP	_	_	_
319	RpoH	rpoh	NN	_	_	_
320	ChIP	chip	NN	_	_	_
321	DNA	dna	NN	_	_	_
322	1	1	CD	_	_	_
323	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
324	E.	E.	NNP	_	_	_
325	Coli	Coli	NNP	_	_	_
326	Exponential	Exponential	NNP	_	_	_
327	RpoH	rpoh	NN	_	_	_
328	ChIP	chip	NN	_	_	_
329	DNA	dna	NN	_	_	_
330	2	2	CD	_	_	_
331	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
332	E.	E.	NNP	_	_	_
333	Coli	Coli	NNP	_	_	_
334	Exponential	Exponential	NNP	_	_	_
335	RpoH	rpoh	NN	_	_	_
336	ChIP	chip	NN	_	_	_
337	DNA	dna	NN	_	_	_
338	Mock	mock	NN	_	_	_
339	1	1	CD	_	_	_
340	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
341	E.	E.	NNP	_	_	_
342	Coli	Coli	NNP	_	_	_
343	Exponential	Exponential	NNP	_	_	_
344	RpoH	rpoh	NN	_	_	_
345	ChIP	chip	NN	_	_	_
346	DNA	dna	NN	_	_	_
347	Mock	mock	NN	_	_	_
348	2	2	CD	_	_	_
349	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
350	E.	E.	NNP	_	_	_
351	Coli	Coli	NNP	_	_	_
352	Exponential	Exponential	NNP	_	_	_
353	RpoN	rpon	NN	_	_	_
354	ChIP	chip	NN	_	_	_
355	DNA	dna	NN	_	_	_
356	1	1	CD	_	_	_
357	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
358	E.	E.	NNP	_	_	_
359	Coli	Coli	NNP	_	_	_
360	Exponential	Exponential	NNP	_	_	_
361	RpoN	rpon	NN	_	_	_
362	ChIP	chip	NN	_	_	_
363	DNA	dna	NN	_	_	_
364	2	2	CD	_	_	_
365	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
366	E.	E.	NNP	_	_	_
367	Coli	Coli	NNP	_	_	_
368	Exponential	Exponential	NNP	_	_	_
369	RpoN	rpon	NN	_	_	_
370	ChIP	chip	NN	_	_	_
371	DNA	dna	NN	_	_	_
372	3	3	CD	_	_	_
373	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
374	E.	E.	NNP	_	_	_
375	Coli	Coli	NNP	_	_	_
376	Exponential	Exponential	NNP	_	_	_
377	RpoN	rpon	NN	_	_	_
378	ChIP	chip	NN	_	_	_
379	DNA	dna	NN	_	_	_
380	Mock	mock	NN	_	_	_
381	1	1	CD	_	_	_
382	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
383	E.	E.	NNP	_	_	_
384	Coli	Coli	NNP	_	_	_
385	Exponential	Exponential	NNP	_	_	_
386	RpoN	rpon	NN	_	_	_
387	ChIP	chip	NN	_	_	_
388	DNA	dna	NN	_	_	_
389	Mock	mock	NN	_	_	_
390	2	2	CD	_	_	_
391	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
392	E.	E.	NNP	_	_	_
393	Coli	Coli	NNP	_	_	_
394	Exponential	Exponential	NNP	_	_	_
395	RpoN	rpon	NN	_	_	_
396	ChIP	chip	NN	_	_	_
397	DNA	dna	NN	_	_	_
398	Mock	mock	NN	_	_	_
399	3	3	CD	_	_	_
400	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
401	E.	E.	NNP	_	_	_
402	Coli	Coli	NNP	_	_	_
403	Exponential	Exponential	NNP	_	_	_
404	RpoS	rpos	NN	_	_	_
405	ChIP	chip	NN	_	_	_
406	DNA	dna	NN	_	_	_
407	1	1	CD	_	_	_
408	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
409	E.	E.	NNP	_	_	_
410	Coli	Coli	NNP	_	_	_
411	Exponential	Exponential	NNP	_	_	_
412	RpoS	rpos	NN	_	_	_
413	ChIP	chip	NN	_	_	_
414	DNA	dna	NN	_	_	_
415	2	2	CD	_	_	_
416	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
417	E.	E.	NNP	_	_	_
418	Coli	Coli	NNP	_	_	_
419	Exponential	Exponential	NNP	_	_	_
420	RpoS	rpos	NN	_	_	_
421	ChIP	chip	NN	_	_	_
422	DNA	dna	NN	_	_	_
423	Mock	mock	NN	_	_	_
424	1	1	CD	_	_	_
425	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
426	E.	E.	NNP	_	_	_
427	Coli	Coli	NNP	_	_	_
428	Exponential	Exponential	NNP	_	_	_
429	RpoS	rpos	NN	_	_	_
430	ChIP	chip	NN	_	_	_
431	DNA	dna	NN	_	_	_
432	Mock	mock	NN	_	_	_
433	2	2	CD	_	_	_
434	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
435	E.	E.	NNP	_	_	_
436	coli	coli	NN	_	_	_
437	expressing	express	VBG	_	_	_
438	dr1558	dr1558	NN	_	_	_
439	replicate	replicate	VB	_	_	_
440	1	1	CD	_	_	_
441	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
442	E.	E.	NNP	_	_	_
443	coli	coli	NN	_	_	_
444	expressing	express	VBG	_	_	_
445	dr1558	dr1558	NN	_	_	_
446	replicate	replicate	VB	_	_	_
447	2	2	CD	_	_	_
448	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
449	E.	E.	NNP	_	_	_
450	coli	coli	NN	_	_	_
451	expressing	express	VBG	_	_	_
452	dr1558	dr1558	NN	_	_	_
453	replicate	replicate	VB	_	_	_
454	3	3	CD	_	_	_
455	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
456	E.	E.	NNP	_	_	_
457	coli	coli	NN	_	_	_
458	flhD	flhd	NN	GEN	_	_
459	,	,	,	_	_	_
460	A600	a600	NN	_	_	_
461	=	=	JJ	_	_	_
462	0.2	0.2	CD	_	_	_
463	on	on	IN	_	_	_
464	mucus	mucus	NN	_	_	_
465	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
466	E.	E.	NNP	_	_	_
467	coli	coli	NN	_	_	_
468	flhD	flhd	NN	GEN	_	_
469	,	,	,	_	_	_
470	A600	a600	NN	_	_	_
471	=	=	JJ	_	_	_
472	0.4	0.4	CD	_	_	_
473	on	on	IN	_	_	_
474	glucose	glucose	NN	SUPP	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
476	E.	e.	FW	_	_	_
477	coli	coli	FW	_	_	_
478	flhD	flhd	NN	GEN	_	_
479	,	,	,	_	_	_
480	A600	a600	NN	_	_	_
481	=	=	JJ	_	_	_
482	0.4	0.4	CD	_	_	_
483	on	on	IN	_	_	_
484	mannose	mannose	NN	_	_	_
485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
486	E.	e.	FW	_	_	_
487	coli	coli	FW	_	_	_
488	flhD	flhd	NN	GEN	_	_
489	,	,	,	_	_	_
490	A600	a600	NN	_	_	_
491	=	=	JJ	_	_	_
492	0.5	0.5	CD	_	_	_
493	on	on	IN	_	_	_
494	mucus	mucus	NN	_	_	_
495	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
496	E.	E.	NNP	_	_	_
497	Coli	Coli	NNP	_	_	_
498	Fnr-8myc	fnr-8myc	JJ	_	_	_
499	ChIP	chip	NN	_	_	_
500	DNA	dna	NN	_	_	_
501	Mock	mock	NN	_	_	_
502	antibody	antibody	NN	_	_	_
503	anaerobic	anaerobic	JJ	_	_	_
504	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
505	E.	E.	NNP	_	_	_
506	Coli	Coli	NNP	_	_	_
507	Fnr-8myc	fnr-8myc	JJ	_	_	_
508	ChIP	chip	NN	_	_	_
509	DNA	dna	NN	_	_	_
510	Mock	mock	NN	_	_	_
511	antibody	antibody	NN	_	_	_
512	NO3	no3	NN	_	_	_
513	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
514	E.	E.	NNP	_	_	_
515	Coli	Coli	NNP	_	_	_
516	Fnr	Fnr	NNP	_	_	_
517	ChIP	ChIP	NNP	_	_	_
518	DNA	DNA	NNP	_	_	_
519	anaerobic	anaerobic	JJ	_	_	_
520	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
521	E.	E.	NNP	_	_	_
522	Coli	Coli	NNP	_	_	_
523	Fnr	Fnr	NNP	_	_	_
524	ChIP	ChIP	NNP	_	_	_
525	DNA	DNA	NNP	_	_	_
526	NO3	no3	NN	_	_	_
527	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
528	E.	E.	NNP	_	_	_
529	coli	coli	NN	_	_	_
530	Frag1	frag1	NN	_	_	_
531	-LRB-	-lrb-	-LRB-	_	_	_
532	biological	biological	JJ	_	_	_
533	replicate	replicate	VBP	_	_	_
534	2	2	LS	_	_	_
535	-RRB-	-rrb-	-RRB-	_	_	_
536	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
537	E.	e.	FW	_	_	_
538	coli	coli	FW	_	_	_
539	Frag1	frag1	NN	_	_	_
540	-LRB-	-lrb-	-LRB-	_	_	_
541	control	control	NN	_	_	_
542	sample	sample	NN	_	_	_
543	1	1	CD	_	_	_
544	-RRB-	-rrb-	-RRB-	_	_	_
545	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
546	E.	e.	FW	_	_	_
547	coli	coli	FW	_	_	_
548	Frag1	frag1	NN	_	_	_
549	,	,	,	_	_	_
550	hyperosmotic	hyperosmotic	JJ	_	_	_
551	NaCl	nacl	NN	_	_	_
552	treatment	treatment	NN	_	_	_
553	-LRB-	-lrb-	-LRB-	_	_	_
554	biological	biological	JJ	_	_	_
555	replicate	replicate	VBP	_	_	_
556	1	1	LS	_	_	_
557	-RRB-	-rrb-	-RRB-	_	_	_
558	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
559	E.	e.	FW	_	_	_
560	coli	coli	FW	_	_	_
561	Frag1	frag1	NN	_	_	_
562	,	,	,	_	_	_
563	NaCl	nacl	NN	_	_	_
564	hyperosmotic	hyperosmotic	JJ	_	_	_
565	treatment	treatment	NN	_	_	_
566	-LRB-	-lrb-	-LRB-	_	_	_
567	biological	biological	JJ	_	_	_
568	replicate	replicate	VBP	_	_	_
569	2	2	LS	_	_	_
570	-RRB-	-rrb-	-RRB-	_	_	_
571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
572	E.coli	e.coli	NN	_	_	_
573	Frag1	frag1	NN	_	_	_
574	,	,	,	_	_	_
575	sucrose	sucrose	NN	_	_	_
576	hyperosmotic	hyperosmotic	JJ	_	_	_
577	treatment	treatment	NN	_	_	_
578	-LRB-	-lrb-	-LRB-	_	_	_
579	biological	biological	JJ	_	_	_
580	replicate	replicate	VBP	_	_	_
581	1	1	LS	_	_	_
582	-RRB-	-rrb-	-RRB-	_	_	_
583	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
584	E.	e.	FW	_	_	_
585	coli	coli	FW	_	_	_
586	Frag1	frag1	NN	_	_	_
587	,	,	,	_	_	_
588	sucrose	sucrose	NN	_	_	_
589	hyperosmotic	hyperosmotic	JJ	_	_	_
590	treatment	treatment	NN	_	_	_
591	-LRB-	-lrb-	-LRB-	_	_	_
592	biological	biological	JJ	_	_	_
593	replicate	replicate	VBP	_	_	_
594	2	2	LS	_	_	_
595	-RRB-	-rrb-	-RRB-	_	_	_
596	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
597	E.	E.	NNP	_	_	_
598	coli	coli	NN	_	_	_
599	G	g	NN	_	_	_
600	1/2	1/2	CD	_	_	_
601	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
602	E.	E.	NNP	_	_	_
603	coli	coli	NN	_	_	_
604	G4/9	g4/9	NN	_	_	_
605	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
606	E.	e.	FW	_	_	_
607	coli	coli	FW	_	_	_
608	G5	g5	NN	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	E.	e.	FW	_	_	_
611	coli	coli	FW	_	_	_
612	galT	galt	NN	GEN	_	_
613	mutant	mutant	JJ	_	_	_
614	cells	cell	NNS	_	_	_
615	were	be	VBD	_	_	_
616	cultivated	cultivate	VBN	_	_	_
617	in	in	IN	_	_	_
618	125-mL	125-ml	NN	_	_	_
619	corning	corning	NN	_	_	_
620	flasks	flask	NNS	_	_	_
621	containing	contain	VBG	_	_	_
622	30	30	CD	_	_	_
623	mL	ml	NN	_	_	_
624	of	of	IN	_	_	_
625	M63	m63	NN	_	_	_
626	minimal	minimal	JJ	_	_	_
627	medium	medium	NN	_	_	_
628	plus	plus	CC	_	_	_
629	glycerol	glycerol	NN	SUPP	_	_
630	-LRB-	-lrb-	-LRB-	_	_	_
631	final	final	JJ	_	_	_
632	0.3	0.3	CD	_	_	_
633	%	%	NN	_	_	_
634	-RRB-	-rrb-	-RRB-	_	_	_
635	at	at	IN	_	_	_
636	37	37	CD	_	_	_
637	°C	°c	NN	_	_	_
638	.	.	.	_	_	_

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	Ecoli	Ecoli	NNP	_	_	_
17	_	_	NNP	_	_	_
18	Gamma	Gamma	NNP	_	_	_
19	treatment	treatment	NN	_	_	_
20	T1	t1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Ecoli	ecolus	NNS	_	_	_
23	_	_	VBP	_	_	_
24	Gamma	gamma	NN	_	_	_
25	treatment	treatment	NN	_	_	_
26	T2	t2	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Ecoli	ecolus	NNS	_	_	_
29	_	_	VBP	_	_	_
30	Gamma	gamma	NN	_	_	_
31	treatment	treatment	NN	_	_	_
32	T3	t3	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Ecoli	ecolus	NNS	_	_	_
35	_	_	VBP	_	_	_
36	Gamma	gamma	NN	_	_	_
37	treatment	treatment	NN	_	_	_
38	T4	t4	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Ecoli	ecolus	NNS	_	_	_
41	_	_	VBP	_	_	_
42	Gamma	gamma	NN	_	_	_
43	treatment	treatment	NN	_	_	_
44	T5	t5	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	E.coli	e.coli	NN	_	_	_
47	gene	gene	NN	_	_	_
48	expression	expression	NN	_	_	_
49	data	datum	NNS	_	_	_
50	in	in	IN	_	_	_
51	deletion	deletion	NN	_	_	_
52	of	of	IN	_	_	_
53	chaperone	chaperone	NN	_	_	_
54	DnaK	dnak	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	E.	e.	FW	_	_	_
57	coli	coli	FW	_	_	_
58	_	_	FW	_	_	_
59	gentamicin	gentamicin	NN	_	_	_
60	_	_	SYM	_	_	_
61	30	30	CD	_	_	_
62	min	min	NN	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	E.	E.	NNP	_	_	_
65	coli	coli	NN	_	_	_
66	,	,	,	_	_	_
67	glucose	glucose	NN	SUPP	_	_
68	limitation	limitation	NN	_	_	_
69	,	,	,	_	_	_
70	110	110	CD	_	_	_
71	min	min	NN	_	_	_
72	after	after	IN	_	_	_
73	depletion	depletion	NN	_	_	_
74	of	of	IN	_	_	_
75	extracellular	extracellular	JJ	_	_	_
76	acetate	acetate	NN	SUPP	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	E.	E.	NNP	_	_	_
79	coli	coli	NN	_	_	_
80	,	,	,	_	_	_
81	glucose	glucose	NN	SUPP	_	_
82	limitation	limitation	NN	_	_	_
83	,	,	,	_	_	_
84	170	170	CD	_	_	_
85	min	min	NN	_	_	_
86	after	after	IN	_	_	_
87	depletion	depletion	NN	_	_	_
88	of	of	IN	_	_	_
89	extracellular	extracellular	JJ	_	_	_
90	acetate	acetate	NN	SUPP	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	E.	E.	NNP	_	_	_
93	coli	coli	NN	_	_	_
94	,	,	,	_	_	_
95	glucose	glucose	NN	SUPP	_	_
96	limitation	limitation	NN	_	_	_
97	,	,	,	_	_	_
98	230	230	CD	_	_	_
99	min	min	NN	_	_	_
100	after	after	IN	_	_	_
101	depletion	depletion	NN	_	_	_
102	of	of	IN	_	_	_
103	extracellular	extracellular	JJ	_	_	_
104	acetate	acetate	NN	SUPP	_	_
105	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
106	E.	E.	NNP	_	_	_
107	coli	coli	NN	_	_	_
108	,	,	,	_	_	_
109	glucose	glucose	NN	SUPP	_	_
110	limitation	limitation	NN	_	_	_
111	,	,	,	_	_	_
112	30	30	CD	_	_	_
113	min	min	NN	_	_	_
114	after	after	IN	_	_	_
115	depletion	depletion	NN	_	_	_
116	of	of	IN	_	_	_
117	extracellular	extracellular	JJ	_	_	_
118	acetate	acetate	NN	SUPP	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	E.	E.	NNP	_	_	_
121	coli	coli	NN	_	_	_
122	,	,	,	_	_	_
123	glucose	glucose	NN	SUPP	_	_
124	limitation	limitation	NN	_	_	_
125	,	,	,	_	_	_
126	350	350	CD	_	_	_
127	min	min	NN	_	_	_
128	after	after	IN	_	_	_
129	depletion	depletion	NN	_	_	_
130	of	of	IN	_	_	_
131	extracellular	extracellular	JJ	_	_	_
132	acetate	acetate	NN	SUPP	_	_
133	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
134	E.	E.	NNP	_	_	_
135	coli	coli	NN	_	_	_
136	,	,	,	_	_	_
137	glucose	glucose	NN	SUPP	_	_
138	limitation	limitation	NN	_	_	_
139	,	,	,	_	_	_
140	50	50	CD	_	_	_
141	min	min	NN	_	_	_
142	after	after	IN	_	_	_
143	depletion	depletion	NN	_	_	_
144	of	of	IN	_	_	_
145	extracellular	extracellular	JJ	_	_	_
146	acetate	acetate	NN	SUPP	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	E.	E.	NNP	_	_	_
149	coli	coli	NN	_	_	_
150	,	,	,	_	_	_
151	glucose	glucose	NN	SUPP	_	_
152	limitation	limitation	NN	_	_	_
153	,	,	,	_	_	_
154	acetate	acetate	NN	SUPP	_	_
155	concentration	concentration	NN	_	_	_
156	≤	≤	CD	_	_	_
157	0.35	0.35	CD	_	_	_
158	gL-1	gl-1	NN	_	_	_
159	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
160	E.	E.	NNP	_	_	_
161	coli	coli	NN	_	_	_
162	,	,	,	_	_	_
163	glucose	glucose	NN	SUPP	_	_
164	limitation	limitation	NN	_	_	_
165	-LRB-	-lrb-	-LRB-	_	_	_
166	glucose	glucose	NN	SUPP	_	_
167	concentration	concentration	NN	_	_	_
168	<	<	JJR	_	_	_
169	0.05	0.05	CD	_	_	_
170	gL-1	gl-1	NN	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	E.	e.	FW	_	_	_
174	coli	coli	FW	_	_	_
175	,	,	,	_	_	_
176	glucose	glucose	NN	SUPP	_	_
177	limitation	limitation	NN	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	glucose	glucose	NN	SUPP	_	_
180	concentration	concentration	NN	_	_	_
181	<	<	JJR	_	_	_
182	0.05	0.05	CD	_	_	_
183	gL-1	gl-1	NN	_	_	_
184	-RRB-	-rrb-	-RRB-	_	_	_
185	,	,	,	_	_	_
186	fed-batch	fed-batch	JJ	_	_	_
187	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
188	E.	e.	FW	_	_	_
189	coli	coli	FW	_	_	_
190	glutamine	glutamine	NN	_	_	_
191	1	1	CD	_	_	_
192	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
193	E.	E.	NNP	_	_	_
194	coli	coli	NN	_	_	_
195	glutamine	glutamine	NN	_	_	_
196	2	2	CD	_	_	_
197	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
198	E.	E.	NNP	_	_	_
199	Coli	Coli	NNP	_	_	_
200	Glutamine	Glutamine	NNP	_	_	_
201	RpoB	rpob	NN	_	_	_
202	ChIP	chip	NN	_	_	_
203	DNA	dna	NN	_	_	_
204	1	1	CD	_	_	_
205	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
206	E.	E.	NNP	_	_	_
207	Coli	Coli	NNP	_	_	_
208	Glutamine	Glutamine	NNP	_	_	_
209	RpoB	rpob	NN	_	_	_
210	ChIP	chip	NN	_	_	_
211	DNA	dna	NN	_	_	_
212	2	2	CD	_	_	_
213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
214	E.	E.	NNP	_	_	_
215	Coli	Coli	NNP	_	_	_
216	Glutamine	Glutamine	NNP	_	_	_
217	RpoB	rpob	NN	_	_	_
218	ChIP	chip	NN	_	_	_
219	DNA	dna	NN	_	_	_
220	Mock	mock	NN	_	_	_
221	1	1	CD	_	_	_
222	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
223	E.	E.	NNP	_	_	_
224	Coli	Coli	NNP	_	_	_
225	Glutamine	Glutamine	NNP	_	_	_
226	RpoB	rpob	NN	_	_	_
227	ChIP	chip	NN	_	_	_
228	DNA	dna	NN	_	_	_
229	Mock	mock	NN	_	_	_
230	2	2	CD	_	_	_
231	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
232	E.	E.	NNP	_	_	_
233	Coli	Coli	NNP	_	_	_
234	Glutamine	Glutamine	NNP	_	_	_
235	RpoD	rpod	NN	_	_	_
236	ChIP	chip	NN	_	_	_
237	DNA	dna	NN	_	_	_
238	1	1	CD	_	_	_
239	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
240	E.	E.	NNP	_	_	_
241	Coli	Coli	NNP	_	_	_
242	Glutamine	Glutamine	NNP	_	_	_
243	RpoD	rpod	NN	_	_	_
244	ChIP	chip	NN	_	_	_
245	DNA	dna	NN	_	_	_
246	2	2	CD	_	_	_
247	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
248	E.	E.	NNP	_	_	_
249	Coli	Coli	NNP	_	_	_
250	Glutamine	Glutamine	NNP	_	_	_
251	RpoD	rpod	NN	_	_	_
252	ChIP	chip	NN	_	_	_
253	DNA	dna	NN	_	_	_
254	Mock	mock	NN	_	_	_
255	1	1	CD	_	_	_
256	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
257	E.	E.	NNP	_	_	_
258	Coli	Coli	NNP	_	_	_
259	Glutamine	Glutamine	NNP	_	_	_
260	RpoD	rpod	NN	_	_	_
261	ChIP	chip	NN	_	_	_
262	DNA	dna	NN	_	_	_
263	Mock	mock	NN	_	_	_
264	2	2	CD	_	_	_
265	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
266	E.	E.	NNP	_	_	_
267	Coli	Coli	NNP	_	_	_
268	Glutamine	Glutamine	NNP	_	_	_
269	RpoN	rpon	NN	_	_	_
270	ChIP	chip	NN	_	_	_
271	DNA	dna	NN	_	_	_
272	1	1	CD	_	_	_
273	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
274	E.	E.	NNP	_	_	_
275	Coli	Coli	NNP	_	_	_
276	Glutamine	Glutamine	NNP	_	_	_
277	RpoN	rpon	NN	_	_	_
278	ChIP	chip	NN	_	_	_
279	DNA	dna	NN	_	_	_
280	2	2	CD	_	_	_
281	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
282	E.	E.	NNP	_	_	_
283	Coli	Coli	NNP	_	_	_
284	Glutamine	Glutamine	NNP	_	_	_
285	RpoN	rpon	NN	_	_	_
286	ChIP	chip	NN	_	_	_
287	DNA	dna	NN	_	_	_
288	Mock	mock	NN	_	_	_
289	1	1	CD	_	_	_
290	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
291	E.	E.	NNP	_	_	_
292	Coli	Coli	NNP	_	_	_
293	Glutamine	Glutamine	NNP	_	_	_
294	RpoN	rpon	NN	_	_	_
295	ChIP	chip	NN	_	_	_
296	DNA	dna	NN	_	_	_
297	Mock	mock	NN	_	_	_
298	2	2	CD	_	_	_
299	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
300	E.	E.	NNP	_	_	_
301	coli	coli	NN	_	_	_
302	grow	grow	VB	_	_	_
303	in	in	IN	_	_	_
304	LB	lb	NN	_	_	_
305	rich	rich	JJ	MED	_	_
306	medium	medium	NN	MED	_	_
307	to	to	TO	_	_	_
308	OD600	od600	NN	_	_	_
309	=	=	JJ	_	_	_
310	2.4	2.4	CD	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	E.coli	e.coli	NNS	_	_	_
313	,	,	,	_	_	_
314	grown	grow	VBN	_	_	_
315	in	in	IN	_	_	_
316	LB	lb	NN	_	_	_
317	+	+	CC	_	_	_
318	glycerol	glycerol	NN	SUPP	_	_
319	to0	to0	NN	_	_	_
320	.8	.8	CD	_	_	_
321	OD	od	NN	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	E.coli	e.coli	NNS	_	_	_
324	,	,	,	_	_	_
325	grown	grow	VBN	_	_	_
326	in	in	IN	_	_	_
327	LB	lb	NN	_	_	_
328	+	+	CC	_	_	_
329	glycerol	glycerol	NN	SUPP	_	_
330	to	to	TO	_	_	_
331	0.8	0.8	CD	_	_	_
332	OD	od	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	E.coli	e.coli	NNS	_	_	_
335	,	,	,	_	_	_
336	grown	grow	VBN	_	_	_
337	in	in	IN	_	_	_
338	LB	lb	NN	_	_	_
339	to	to	TO	_	_	_
340	0.8	0.8	CD	_	_	_
341	OD	od	NN	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	E.coli	e.coli	NNS	_	_	_
344	,	,	,	_	_	_
345	grown	grow	VBN	_	_	_
346	in	in	IN	_	_	_
347	LB	lb	NN	_	_	_
348	to0	to0	NN	_	_	_
349	.8	.8	CD	_	_	_
350	OD	od	NN	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	Ecoli	ecolus	NNS	_	_	_
353	_	_	VBP	_	_	_
354	gyrArparCr	gyrarparcr	NN	_	_	_
355	_	_	CD	_	_	_
356	Norfloxacin	norfloxacin	NN	_	_	_
357	-LRB-	-lrb-	-LRB-	_	_	_
358	15	15	CD	_	_	_
359	ug/ml	ug/ml	NN	_	_	_
360	-RRB-	-rrb-	-RRB-	_	_	_
361	treatment	treatment	NN	_	_	_
362	T1	t1	NN	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	Ecoli	ecolus	NNS	_	_	_
365	_	_	VBP	_	_	_
366	gyrArparCr	gyrarparcr	NN	_	_	_
367	_	_	CD	_	_	_
368	Norfloxacin	norfloxacin	NN	_	_	_
369	-LRB-	-lrb-	-LRB-	_	_	_
370	15	15	CD	_	_	_
371	ug/ml	ug/ml	NN	_	_	_
372	-RRB-	-rrb-	-RRB-	_	_	_
373	treatment	treatment	NN	_	_	_
374	T2	t2	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	Ecoli	ecolus	NNS	_	_	_
377	_	_	VBP	_	_	_
378	gyrArparCr	gyrarparcr	NN	_	_	_
379	_	_	CD	_	_	_
380	Norfloxacin	norfloxacin	NN	_	_	_
381	-LRB-	-lrb-	-LRB-	_	_	_
382	15	15	CD	_	_	_
383	ug/ml	ug/ml	NN	_	_	_
384	-RRB-	-rrb-	-RRB-	_	_	_
385	treatment	treatment	NN	_	_	_
386	T3	t3	NN	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	Ecoli	ecolus	NNS	_	_	_
389	_	_	VBP	_	_	_
390	gyrArparCr	gyrarparcr	NN	_	_	_
391	_	_	CD	_	_	_
392	Norfloxacin	norfloxacin	NN	_	_	_
393	-LRB-	-lrb-	-LRB-	_	_	_
394	15	15	CD	_	_	_
395	ug/ml	ug/ml	NN	_	_	_
396	-RRB-	-rrb-	-RRB-	_	_	_
397	treatment	treatment	NN	_	_	_
398	T4	t4	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	Ecoli	ecolus	NNS	_	_	_
401	_	_	VBP	_	_	_
402	gyrArparCr	gyrarparcr	NN	_	_	_
403	_	_	CD	_	_	_
404	Norfloxacin	norfloxacin	NN	_	_	_
405	-LRB-	-lrb-	-LRB-	_	_	_
406	15	15	CD	_	_	_
407	ug/ml	ug/ml	NN	_	_	_
408	-RRB-	-rrb-	-RRB-	_	_	_
409	treatment	treatment	NN	_	_	_
410	T5	t5	NN	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	Ecoli	ecolus	NNS	_	_	_
413	_	_	VBP	_	_	_
414	gyrArparCr	gyrarparcr	NN	_	_	_
415	_	_	CD	_	_	_
416	Norfloxacin	norfloxacin	NN	_	_	_
417	-LRB-	-lrb-	-LRB-	_	_	_
418	50	50	CD	_	_	_
419	ug/ml	ug/ml	NN	_	_	_
420	-RRB-	-rrb-	-RRB-	_	_	_
421	treatment	treatment	NN	_	_	_
422	T1	t1	NN	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	Ecoli	ecolus	NNS	_	_	_
425	_	_	VBP	_	_	_
426	gyrArparCr	gyrarparcr	NN	_	_	_
427	_	_	CD	_	_	_
428	Norfloxacin	norfloxacin	NN	_	_	_
429	-LRB-	-lrb-	-LRB-	_	_	_
430	50	50	CD	_	_	_
431	ug/ml	ug/ml	NN	_	_	_
432	-RRB-	-rrb-	-RRB-	_	_	_
433	treatment	treatment	NN	_	_	_
434	T2	t2	NN	_	_	_
435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
436	Ecoli	ecolus	NNS	_	_	_
437	_	_	VBP	_	_	_
438	gyrArparCr	gyrarparcr	NN	_	_	_
439	_	_	CD	_	_	_
440	Norfloxacin	norfloxacin	NN	_	_	_
441	-LRB-	-lrb-	-LRB-	_	_	_
442	50	50	CD	_	_	_
443	ug/ml	ug/ml	NN	_	_	_
444	-RRB-	-rrb-	-RRB-	_	_	_
445	treatment	treatment	NN	_	_	_
446	T3	t3	NN	_	_	_
447	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
448	Ecoli	ecolus	NNS	_	_	_
449	_	_	VBP	_	_	_
450	gyrArparCr	gyrarparcr	NN	_	_	_
451	_	_	CD	_	_	_
452	Norfloxacin	norfloxacin	NN	_	_	_
453	-LRB-	-lrb-	-LRB-	_	_	_
454	50	50	CD	_	_	_
455	ug/ml	ug/ml	NN	_	_	_
456	-RRB-	-rrb-	-RRB-	_	_	_
457	treatment	treatment	NN	_	_	_
458	T4	t4	NN	_	_	_
459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
460	Ecoli	ecolus	NNS	_	_	_
461	_	_	VBP	_	_	_
462	gyrArparCr	gyrarparcr	NN	_	_	_
463	_	_	CD	_	_	_
464	Norfloxacin	norfloxacin	NN	_	_	_
465	-LRB-	-lrb-	-LRB-	_	_	_
466	50	50	CD	_	_	_
467	ug/ml	ug/ml	NN	_	_	_
468	-RRB-	-rrb-	-RRB-	_	_	_
469	treatment	treatment	NN	_	_	_
470	T5	t5	NN	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	E.	e.	FW	_	_	_
473	coli	coli	FW	_	_	_
474	harboring	harboring	NN	_	_	_
475	pRadGro	pradgro	NN	_	_	_
476	replicate	replicate	VBP	_	_	_
477	1	1	CD	_	_	_
478	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
479	E.	E.	NNP	_	_	_
480	coli	coli	NN	_	_	_
481	harboring	harboring	NN	_	_	_
482	pRadGro	pradgro	NN	_	_	_
483	replicate	replicate	VBP	_	_	_
484	2	2	CD	_	_	_
485	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
486	E.	E.	NNP	_	_	_
487	coli	coli	NN	_	_	_
488	harboring	harboring	NN	_	_	_
489	pRadGro	pradgro	NN	_	_	_
490	replicate	replicate	VBP	_	_	_
491	3	3	CD	_	_	_
492	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
493	E.	E.	NNP	_	_	_
494	coli	coli	NN	_	_	_
495	HB101	hb101	NN	_	_	_
496	grown	grow	VBN	_	_	_
497	in	in	IN	_	_	_
498	Terrific	Terrific	NNP	_	_	_
499	broth	broth	NN	_	_	_
500	media	media	NNS	_	_	_
501	for	for	IN	_	_	_
502	12	12	CD	_	_	_
503	hours	hour	NNS	_	_	_
504	were	be	VBD	_	_	_
505	washed	wash	VBN	_	_	_
506	three	three	CD	_	_	_
507	times	time	NNS	_	_	_
508	in	in	IN	_	_	_
509	sdH2O	sdh2o	NN	_	_	_
510	and	and	CC	_	_	_
511	re-suspended	re-suspended	JJ	_	_	_
512	in	in	IN	_	_	_
513	S-Basal	s-basal	JJ	_	_	_
514	complete	complete	JJ	_	_	_
515	medium	medium	NN	_	_	_
516	.	.	.	_	_	_

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	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	coli	coli	NN	_	_	_
20	heatshock	heatshock	NN	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	E.	E.	NNP	_	_	_
24	coli	coli	NN	_	_	_
25	heatshock	heatshock	NN	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	E.	E.	NNP	_	_	_
29	coli	coli	NN	_	_	_
30	heat	heat	NN	_	_	_
31	shock	shock	NN	_	_	_
32	gene	gene	NN	_	_	_
33	expression	expression	NN	_	_	_
34	data	datum	NNS	_	_	_
35	using	use	VBG	_	_	_
36	direct	direct	JJ	_	_	_
37	labeling	labeling	NN	_	_	_
38	method	method	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	replicate-1	replicate-1	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	E.	e.	FW	_	_	_
44	coli	coli	FW	_	_	_
45	heat	heat	NN	_	_	_
46	shock	shock	NN	_	_	_
47	gene	gene	NN	_	_	_
48	expression	expression	NN	_	_	_
49	data	datum	NNS	_	_	_
50	using	use	VBG	_	_	_
51	direct	direct	JJ	_	_	_
52	labeling	labeling	NN	_	_	_
53	method	method	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	replicate-2	replicate-2	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	E.	e.	FW	_	_	_
59	coli	coli	FW	_	_	_
60	heat	heat	NN	_	_	_
61	shock	shock	NN	_	_	_
62	gene	gene	NN	_	_	_
63	expression	expression	NN	_	_	_
64	data	datum	NNS	_	_	_
65	using	use	VBG	_	_	_
66	PAOD	paod	NN	_	_	_
67	method	method	NN	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	replicate-1	replicate-1	NN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	E.	e.	FW	_	_	_
73	coli	coli	FW	_	_	_
74	heat	heat	NN	_	_	_
75	shock	shock	NN	_	_	_
76	gene	gene	NN	_	_	_
77	expression	expression	NN	_	_	_
78	data	datum	NNS	_	_	_
79	using	use	VBG	_	_	_
80	PAOD	paod	NN	_	_	_
81	method	method	NN	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	replicate-2	replicate-2	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	E.	e.	FW	_	_	_
87	coli	coli	FW	_	_	_
88	heat	heat	NN	_	_	_
89	shock	shock	NN	_	_	_
90	gene	gene	NN	_	_	_
91	expression	expression	NN	_	_	_
92	data	datum	NNS	_	_	_
93	using	use	VBG	_	_	_
94	random	random	JJ	_	_	_
95	priming	priming	NN	_	_	_
96	method	method	NN	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	replicate-1	replicate-1	NN	_	_	_
99	-RRB-	-rrb-	-RRB-	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	E.	e.	FW	_	_	_
102	coli	coli	FW	_	_	_
103	heat	heat	NN	_	_	_
104	shock	shock	NN	_	_	_
105	gene	gene	NN	_	_	_
106	expression	expression	NN	_	_	_
107	data	datum	NNS	_	_	_
108	using	use	VBG	_	_	_
109	random	random	JJ	_	_	_
110	priming	priming	NN	_	_	_
111	method	method	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	replicate-2	replicate-2	NN	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
116	E.	E.	NNP	_	_	_
117	Coli	Coli	NNP	_	_	_
118	Heatshock	Heatshock	NNP	_	_	_
119	RpoB	rpob	NN	_	_	_
120	ChIP	chip	NN	_	_	_
121	DNA	dna	NN	_	_	_
122	1	1	CD	_	_	_
123	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
124	E.	E.	NNP	_	_	_
125	Coli	Coli	NNP	_	_	_
126	Heatshock	Heatshock	NNP	_	_	_
127	RpoB	rpob	NN	_	_	_
128	ChIP	chip	NN	_	_	_
129	DNA	dna	NN	_	_	_
130	2	2	CD	_	_	_
131	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
132	E.	E.	NNP	_	_	_
133	Coli	Coli	NNP	_	_	_
134	Heatshock	Heatshock	NNP	_	_	_
135	RpoB	rpob	NN	_	_	_
136	ChIP	chip	NN	_	_	_
137	DNA	dna	NN	_	_	_
138	Mock	mock	NN	_	_	_
139	1	1	CD	_	_	_
140	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
141	E.	E.	NNP	_	_	_
142	Coli	Coli	NNP	_	_	_
143	Heatshock	Heatshock	NNP	_	_	_
144	RpoB	rpob	NN	_	_	_
145	ChIP	chip	NN	_	_	_
146	DNA	dna	NN	_	_	_
147	Mock	mock	NN	_	_	_
148	2	2	CD	_	_	_
149	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
150	E.	E.	NNP	_	_	_
151	Coli	Coli	NNP	_	_	_
152	Heatshock	Heatshock	NNP	_	_	_
153	RpoD	rpod	NN	_	_	_
154	ChIP	chip	NN	_	_	_
155	DNA	dna	NN	_	_	_
156	1	1	CD	_	_	_
157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
158	E.	E.	NNP	_	_	_
159	Coli	Coli	NNP	_	_	_
160	Heatshock	Heatshock	NNP	_	_	_
161	RpoD	rpod	NN	_	_	_
162	ChIP	chip	NN	_	_	_
163	DNA	dna	NN	_	_	_
164	2	2	CD	_	_	_
165	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
166	E.	E.	NNP	_	_	_
167	Coli	Coli	NNP	_	_	_
168	Heatshock	Heatshock	NNP	_	_	_
169	RpoD	rpod	NN	_	_	_
170	ChIP	chip	NN	_	_	_
171	DNA	dna	NN	_	_	_
172	Mock	mock	NN	_	_	_
173	1	1	CD	_	_	_
174	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
175	E.	E.	NNP	_	_	_
176	Coli	Coli	NNP	_	_	_
177	Heatshock	Heatshock	NNP	_	_	_
178	RpoD	rpod	NN	_	_	_
179	ChIP	chip	NN	_	_	_
180	DNA	dna	NN	_	_	_
181	Mock	mock	NN	_	_	_
182	2	2	CD	_	_	_
183	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
184	E.	E.	NNP	_	_	_
185	Coli	Coli	NNP	_	_	_
186	Heatshock	Heatshock	NNP	_	_	_
187	RpoH	rpoh	NN	_	_	_
188	ChIP	chip	NN	_	_	_
189	DNA	dna	NN	_	_	_
190	1	1	CD	_	_	_
191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
192	E.	E.	NNP	_	_	_
193	Coli	Coli	NNP	_	_	_
194	Heatshock	Heatshock	NNP	_	_	_
195	RpoH	rpoh	NN	_	_	_
196	ChIP	chip	NN	_	_	_
197	DNA	dna	NN	_	_	_
198	2	2	CD	_	_	_
199	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
200	E.	E.	NNP	_	_	_
201	Coli	Coli	NNP	_	_	_
202	Heatshock	Heatshock	NNP	_	_	_
203	RpoH	rpoh	NN	_	_	_
204	ChIP	chip	NN	_	_	_
205	DNA	dna	NN	_	_	_
206	3	3	CD	_	_	_
207	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
208	E.	E.	NNP	_	_	_
209	Coli	Coli	NNP	_	_	_
210	Heatshock	Heatshock	NNP	_	_	_
211	RpoH	rpoh	NN	_	_	_
212	ChIP	chip	NN	_	_	_
213	DNA	dna	NN	_	_	_
214	Mock	mock	NN	_	_	_
215	1	1	CD	_	_	_
216	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
217	E.	E.	NNP	_	_	_
218	Coli	Coli	NNP	_	_	_
219	Heatshock	Heatshock	NNP	_	_	_
220	RpoH	rpoh	NN	_	_	_
221	ChIP	chip	NN	_	_	_
222	DNA	dna	NN	_	_	_
223	Mock	mock	NN	_	_	_
224	2	2	CD	_	_	_
225	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
226	E.	E.	NNP	_	_	_
227	Coli	Coli	NNP	_	_	_
228	Heatshock	Heatshock	NNP	_	_	_
229	RpoH	rpoh	NN	_	_	_
230	ChIP	chip	NN	_	_	_
231	DNA	dna	NN	_	_	_
232	Mock	mock	NN	_	_	_
233	3	3	CD	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	E.	e.	FW	_	_	_
236	coli	coli	FW	_	_	_
237	hhahha2	hhahha2	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	E.	e.	FW	_	_	_
240	coli	coli	FW	_	_	_
241	hns	hns	FW	GEN	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	E.	e.	FW	_	_	_
244	coli	coli	FW	_	_	_
245	hns2	hns2	NN	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	E.	e.	FW	_	_	_
248	coli	coli	FW	_	_	_
249	hnshns2	hnshns2	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	E.coli	e.coli	NN	_	_	_
252	/	/	:	_	_	_
253	Hsp60-wt/VAL98Ile	hsp60-wt/val98ile	NN	_	_	_
254	-LRB-	-lrb-	-LRB-	_	_	_
255	-	-	:	_	_	_
256	/	/	:	_	_	_
257	+	+	CC	_	_	_
258	-RRB-	-rrb-	-RRB-	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	E.coli	e.coli	NN	_	_	_
261	/	/	:	_	_	_
262	Hsp60-wt/wt	hsp60-wt/wt	NN	_	_	_
263	-LRB-	-lrb-	-LRB-	_	_	_
264	-	-	:	_	_	_
265	/	/	:	_	_	_
266	+	+	CC	_	_	_
267	-RRB-	-rrb-	-RRB-	_	_	_
268	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
269	E.	e.	FW	_	_	_
270	coli	coli	FW	_	_	_
271	Hydrocortisone	hydrocortisone	NN	_	_	_
272	Treatment	treatment	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	E	e	NN	_	_	_
275	coli	coli	NN	_	_	_
276	,	,	,	_	_	_
277	immediately	immediately	RB	_	_	_
278	after	after	IN	_	_	_
279	turning	turn	VBG	_	_	_
280	off	off	RP	_	_	_
281	oxygen	oxygen	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
283	E.	e.	FW	_	_	_
284	coli	coli	FW	_	_	_
285	imp	imp	FW	_	_	_
286	fabI	fabi	NN	GEN	_	_
287	-LRB-	-lrb-	-LRB-	_	_	_
288	G93V	g93v	NN	_	_	_
289	-RRB-	-rrb-	-RRB-	_	_	_
290	-LSB-	-lsb-	-LRB-	_	_	_
291	control	control	NN	_	_	_
292	-RSB-	-rsb-	-RRB-	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	E.	e.	FW	_	_	_
295	coli	coli	FW	_	_	_
296	imp	imp	FW	_	_	_
297	fabI	fabi	NN	GEN	_	_
298	-LRB-	-lrb-	-LRB-	_	_	_
299	G94V	g94v	NN	_	_	_
300	-RRB-	-rrb-	-RRB-	_	_	_
301	-LSB-	-lsb-	-LRB-	_	_	_
302	control	control	NN	_	_	_
303	-RSB-	-rsb-	-RRB-	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	E.	e.	FW	_	_	_
306	coli	coli	FW	_	_	_
307	incubated	incubate	VBN	_	_	_
308	with	with	IN	_	_	_
309	GST-fused	gst-fused	JJ	_	_	_
310	Drosophila	drosophila	NN	_	_	_
311	immune	immune	JJ	_	_	_
312	proteins	protein	NNS	_	_	_
313	for	for	IN	_	_	_
314	10	10	CD	_	_	_
315	min	min	NN	_	_	_
316	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
317	E.	E.	NNP	_	_	_
318	coli	coli	NN	_	_	_
319	incubated	incubate	VBN	_	_	_
320	with	with	IN	_	_	_
321	GST-fused	gst-fused	JJ	_	_	_
322	Drosophila	drosophila	NN	_	_	_
323	immune	immune	JJ	_	_	_
324	proteins	protein	NNS	_	_	_
325	for	for	IN	_	_	_
326	10	10	CD	_	_	_
327	min	min	NN	_	_	_
328	,	,	,	_	_	_
329	biological	biological	JJ	_	_	_
330	rep1	rep1	NN	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	E.	e.	FW	_	_	_
333	coli	coli	FW	_	_	_
334	incubated	incubate	VBN	_	_	_
335	with	with	IN	_	_	_
336	GST-fused	gst-fused	JJ	_	_	_
337	Drosophila	drosophila	NN	_	_	_
338	immune	immune	JJ	_	_	_
339	proteins	protein	NNS	_	_	_
340	for	for	IN	_	_	_
341	10	10	CD	_	_	_
342	min	min	NN	_	_	_
343	,	,	,	_	_	_
344	biological	biological	JJ	_	_	_
345	rep2	rep2	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	E.	e.	FW	_	_	_
348	coli	coli	FW	_	_	_
349	incubated	incubate	VBN	_	_	_
350	with	with	IN	_	_	_
351	GST-fused	gst-fused	JJ	_	_	_
352	Drosophila	drosophila	NN	_	_	_
353	immune	immune	JJ	_	_	_
354	proteins	protein	NNS	_	_	_
355	for	for	IN	_	_	_
356	10	10	CD	_	_	_
357	min	min	NN	_	_	_
358	,	,	,	_	_	_
359	biological	biological	JJ	_	_	_
360	rep3	rep3	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	E.	e.	FW	_	_	_
363	coli	coli	FW	_	_	_
364	incubated	incubate	VBN	_	_	_
365	with	with	IN	_	_	_
366	GST	gst	NN	_	_	_
367	protein	protein	NN	_	_	_
368	alone	alone	RB	_	_	_
369	for	for	IN	_	_	_
370	10	10	CD	_	_	_
371	min	min	NN	_	_	_
372	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
373	E.	E.	NNP	_	_	_
374	coli	coli	NN	_	_	_
375	incubated	incubate	VBN	_	_	_
376	with	with	IN	_	_	_
377	GST	gst	NN	_	_	_
378	protein	protein	NN	_	_	_
379	for	for	IN	_	_	_
380	10	10	CD	_	_	_
381	min	min	NN	_	_	_
382	,	,	,	_	_	_
383	biological	biological	JJ	_	_	_
384	rep1	rep1	NN	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	E.	e.	FW	_	_	_
387	coli	coli	FW	_	_	_
388	incubated	incubate	VBN	_	_	_
389	with	with	IN	_	_	_
390	GST	gst	NN	_	_	_
391	protein	protein	NN	_	_	_
392	for	for	IN	_	_	_
393	10	10	CD	_	_	_
394	min	min	NN	_	_	_
395	,	,	,	_	_	_
396	biological	biological	JJ	_	_	_
397	rep2	rep2	NN	_	_	_
398	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
399	E.	e.	FW	_	_	_
400	coli	coli	FW	_	_	_
401	incubated	incubate	VBN	_	_	_
402	with	with	IN	_	_	_
403	GST	gst	NN	_	_	_
404	protein	protein	NN	_	_	_
405	for	for	IN	_	_	_
406	10	10	CD	_	_	_
407	min	min	NN	_	_	_
408	,	,	,	_	_	_
409	biological	biological	JJ	_	_	_
410	rep3	rep3	NN	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	Ecoli	ecolus	NNS	_	_	_
413	_	_	VBP	_	_	_
414	Indol-acrylate	indol-acrylate	JJ	_	_	_
415	-LRB-	-lrb-	-LRB-	_	_	_
416	10	10	CD	_	_	_
417	ug/ml	ug/ml	NN	_	_	_
418	-RRB-	-rrb-	-RRB-	_	_	_
419	treatment	treatment	NN	_	_	_
420	T1	t1	NN	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	Ecoli	ecolus	NNS	_	_	_
423	_	_	VBP	_	_	_
424	Indol-acrylate	indol-acrylate	JJ	_	_	_
425	-LRB-	-lrb-	-LRB-	_	_	_
426	10	10	CD	_	_	_
427	ug/ml	ug/ml	NN	_	_	_
428	-RRB-	-rrb-	-RRB-	_	_	_
429	treatment	treatment	NN	_	_	_
430	T2	t2	NN	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	Ecoli	ecolus	NNS	_	_	_
433	_	_	VBP	_	_	_
434	Indol-acrylate	indol-acrylate	JJ	_	_	_
435	-LRB-	-lrb-	-LRB-	_	_	_
436	10	10	CD	_	_	_
437	ug/ml	ug/ml	NN	_	_	_
438	-RRB-	-rrb-	-RRB-	_	_	_
439	treatment	treatment	NN	_	_	_
440	T3	t3	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	Ecoli	ecolus	NNS	_	_	_
443	_	_	VBP	_	_	_
444	Indol-acrylate	indol-acrylate	JJ	_	_	_
445	-LRB-	-lrb-	-LRB-	_	_	_
446	10	10	CD	_	_	_
447	ug/ml	ug/ml	NN	_	_	_
448	-RRB-	-rrb-	-RRB-	_	_	_
449	treatment	treatment	NN	_	_	_
450	T4	t4	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	Ecoli	ecolus	NNS	_	_	_
453	_	_	VBP	_	_	_
454	Indol-acrylate	indol-acrylate	JJ	_	_	_
455	-LRB-	-lrb-	-LRB-	_	_	_
456	15	15	CD	_	_	_
457	ug/ml	ug/ml	NN	_	_	_
458	-RRB-	-rrb-	-RRB-	_	_	_
459	treatment	treatment	NN	_	_	_
460	T1	t1	NN	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	Ecoli	ecolus	NNS	_	_	_
463	_	_	VBP	_	_	_
464	Indol-acrylate	indol-acrylate	JJ	_	_	_
465	-LRB-	-lrb-	-LRB-	_	_	_
466	15	15	CD	_	_	_
467	ug/ml	ug/ml	NN	_	_	_
468	-RRB-	-rrb-	-RRB-	_	_	_
469	treatment	treatment	NN	_	_	_
470	T2	t2	NN	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	Ecoli	ecolus	NNS	_	_	_
473	_	_	VBP	_	_	_
474	Indol-acrylate	indol-acrylate	JJ	_	_	_
475	-LRB-	-lrb-	-LRB-	_	_	_
476	15	15	CD	_	_	_
477	ug/ml	ug/ml	NN	_	_	_
478	-RRB-	-rrb-	-RRB-	_	_	_
479	treatment	treatment	NN	_	_	_
480	T3	t3	NN	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	Ecoli	ecolus	NNS	_	_	_
483	_	_	VBP	_	_	_
484	Indol-acrylate	indol-acrylate	JJ	_	_	_
485	-LRB-	-lrb-	-LRB-	_	_	_
486	15	15	CD	_	_	_
487	ug/ml	ug/ml	NN	_	_	_
488	-RRB-	-rrb-	-RRB-	_	_	_
489	treatment	treatment	NN	_	_	_
490	T4	t4	NN	_	_	_
491	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
492	E.	E.	NNP	_	_	_
493	Coli	Coli	NNP	_	_	_
494	Iron	Iron	NNP	_	_	_
495	RpoD	rpod	NN	_	_	_
496	ChIP	chip	NN	_	_	_
497	DNA	dna	NN	_	_	_
498	1	1	CD	_	_	_
499	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
500	E.	E.	NNP	_	_	_
501	Coli	Coli	NNP	_	_	_
502	Iron	Iron	NNP	_	_	_
503	RpoD	rpod	NN	_	_	_
504	ChIP	chip	NN	_	_	_
505	DNA	dna	NN	_	_	_
506	2	2	CD	_	_	_
507	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
508	E.	E.	NNP	_	_	_
509	Coli	Coli	NNP	_	_	_
510	Iron	Iron	NNP	_	_	_
511	RpoD	rpod	NN	_	_	_
512	ChIP	chip	NN	_	_	_
513	DNA	dna	NN	_	_	_
514	Mock	mock	NN	_	_	_
515	1	1	CD	_	_	_
516	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
517	E.	E.	NNP	_	_	_
518	Coli	Coli	NNP	_	_	_
519	Iron	Iron	NNP	_	_	_
520	RpoD	rpod	NN	_	_	_
521	ChIP	chip	NN	_	_	_
522	DNA	dna	NN	_	_	_
523	Mock	mock	NN	_	_	_
524	2	2	CD	_	_	_
525	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
526	E.	E.	NNP	_	_	_
527	coli	coli	NN	_	_	_
528	isolate	isolate	NN	_	_	_
529	G	g	NN	_	_	_
530	1/2	1/2	CD	_	_	_
531	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
532	E.	E.	NNP	_	_	_
533	coli	coli	NN	_	_	_
534	isolate	isolate	NN	_	_	_
535	G	g	NN	_	_	_
536	3/10	3/10	CD	_	_	_
537	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
538	E.	E.	NNP	_	_	_
539	coli	coli	NN	_	_	_
540	isolate	isolate	NN	_	_	_
541	G3/10	g3/10	NN	_	_	_
542	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
543	E.	E.	NNP	_	_	_
544	coli	coli	NN	_	_	_
545	isolate	isolate	NN	_	_	_
546	G4/9	g4/9	NN	_	_	_
547	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
548	E.	E.	NNP	_	_	_
549	coli	coli	NN	_	_	_
550	isolate	isolate	NN	_	_	_
551	G5	g5	NN	_	_	_
552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
553	E.coli	e.coli	NNS	_	_	_
554	_	_	VBP	_	_	_
555	IVT-RNA	ivt-rna	NN	_	_	_
556	_	_	CD	_	_	_
557	sigma70-1	sigma70-1	NN	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
559	E.coli	e.coli	NNS	_	_	_
560	_	_	VBP	_	_	_
561	IVT-RNA	ivt-rna	NN	_	_	_
562	_	_	CD	_	_	_
563	sigma70-2	sigma70-2	NN	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	E.coli	e.coli	NNS	_	_	_
566	_	_	VBP	_	_	_
567	IVT-RNA	ivt-rna	NN	_	_	_
568	_	_	CD	_	_	_
569	sigmaS	sigmas	NN	_	_	_
570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
571	E.coli	e.coli	NNS	_	_	_
572	_	_	VBP	_	_	_
573	IVT-RNA	ivt-rna	NN	_	_	_
574	_	_	CD	_	_	_
575	sigmaS-2	sigmas-2	NN	_	_	_
576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
577	ecoli	ecolus	NNS	_	_	_
578	_	_	VBP	_	_	_
579	k12	k12	NN	_	_	_
580	_	_	SYM	_	_	_
581	30C	30c	FW	_	_	_
582	_	_	FW	_	_	_
583	f	f	FW	_	_	_
584	_	_	SYM	_	_	_
585	1	1	CD	_	_	_
586	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
587	ecoli	ecolus	NNS	_	_	_
588	_	_	VBP	_	_	_
589	k12	k12	NN	_	_	_
590	_	_	SYM	_	_	_
591	30C	30c	FW	_	_	_
592	_	_	FW	_	_	_
593	f	f	FW	_	_	_
594	_	_	SYM	_	_	_
595	2	2	CD	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
597	ecoli	ecolus	NNS	_	_	_
598	_	_	VBP	_	_	_
599	k12	k12	NN	_	_	_
600	_	_	SYM	_	_	_
601	30C	30c	FW	_	_	_
602	_	_	FW	_	_	_
603	f	f	FW	_	_	_
604	_	_	SYM	_	_	_
605	3	3	CD	_	_	_
606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
607	ecoli	ecolus	NNS	_	_	_
608	_	_	VBP	_	_	_
609	k12	k12	NN	_	_	_
610	_	_	SYM	_	_	_
611	30C	30c	CD	_	_	_
612	_	_	NN	_	_	_
613	m	m	NN	_	_	_
614	_	_	NN	_	_	_
615	1	1	CD	_	_	_
616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
617	ecoli	ecolus	NNS	_	_	_
618	_	_	VBP	_	_	_
619	k12	k12	NN	_	_	_
620	_	_	SYM	_	_	_
621	30C	30c	CD	_	_	_
622	_	_	NN	_	_	_
623	m	m	NN	_	_	_
624	_	_	NN	_	_	_
625	2	2	CD	_	_	_
626	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
627	ecoli	ecolus	NNS	_	_	_
628	_	_	VBP	_	_	_
629	k12	k12	NN	_	_	_
630	_	_	SYM	_	_	_
631	30C	30c	CD	_	_	_
632	_	_	NN	_	_	_
633	m	m	NN	_	_	_
634	_	_	NN	_	_	_
635	3	3	CD	_	_	_
636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
637	ecoli	ecolus	NNS	_	_	_
638	_	_	VBP	_	_	_
639	k12	k12	NN	_	_	_
640	_	_	SYM	_	_	_
641	42C	42c	CD	_	_	_
642	_	_	SYM	_	_	_
643	10	10	CD	_	_	_
644	min	min	NN	_	_	_
645	_	_	NN	_	_	_
646	f	f	FW	_	_	_
647	_	_	FW	_	_	_
648	1	1	CD	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	ecoli	ecolus	NNS	_	_	_
651	_	_	VBP	_	_	_
652	k12	k12	NN	_	_	_
653	_	_	SYM	_	_	_
654	42C	42c	CD	_	_	_
655	_	_	SYM	_	_	_
656	10	10	CD	_	_	_
657	min	min	NN	_	_	_
658	_	_	NN	_	_	_
659	f	f	FW	_	_	_
660	_	_	FW	_	_	_
661	2	2	CD	_	_	_
662	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
663	ecoli	ecolus	NNS	_	_	_
664	_	_	VBP	_	_	_
665	k12	k12	NN	_	_	_
666	_	_	SYM	_	_	_
667	42C	42c	CD	_	_	_
668	_	_	SYM	_	_	_
669	10	10	CD	_	_	_
670	min	min	NN	_	_	_
671	_	_	NN	_	_	_
672	f	f	FW	_	_	_
673	_	_	FW	_	_	_
674	3	3	CD	_	_	_
675	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
676	ecoli	ecolus	NNS	_	_	_
677	_	_	VBP	_	_	_
678	k12	k12	NN	_	_	_
679	_	_	SYM	_	_	_
680	42C	42c	CD	_	_	_
681	_	_	SYM	_	_	_
682	10	10	CD	_	_	_
683	min	min	NN	_	_	_
684	_	_	NN	_	_	_
685	m	m	NN	_	_	_
686	_	_	NN	_	_	_
687	1	1	CD	_	_	_
688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
689	ecoli	ecolus	NNS	_	_	_
690	_	_	VBP	_	_	_
691	k12	k12	NN	_	_	_
692	_	_	SYM	_	_	_
693	42C	42c	CD	_	_	_
694	_	_	SYM	_	_	_
695	10	10	CD	_	_	_
696	min	min	NN	_	_	_
697	_	_	NN	_	_	_
698	m	m	NN	_	_	_
699	_	_	NN	_	_	_
700	2	2	CD	_	_	_
701	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
702	ecoli	ecolus	NNS	_	_	_
703	_	_	VBP	_	_	_
704	k12	k12	NN	_	_	_
705	_	_	SYM	_	_	_
706	42C	42c	CD	_	_	_
707	_	_	SYM	_	_	_
708	10	10	CD	_	_	_
709	min	min	NN	_	_	_
710	_	_	NN	_	_	_
711	m	m	NN	_	_	_
712	_	_	NN	_	_	_
713	3	3	CD	_	_	_
714	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
715	ecoli	ecolus	NNS	_	_	_
716	_	_	VBP	_	_	_
717	k12	k12	NN	_	_	_
718	_	_	SYM	_	_	_
719	42C	42c	CD	_	_	_
720	_	_	SYM	_	_	_
721	20	20	CD	_	_	_
722	min	min	NN	_	_	_
723	_	_	NN	_	_	_
724	f	f	FW	_	_	_
725	_	_	FW	_	_	_
726	1	1	CD	_	_	_
727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
728	ecoli	ecolus	NNS	_	_	_
729	_	_	VBP	_	_	_
730	k12	k12	NN	_	_	_
731	_	_	SYM	_	_	_
732	42C	42c	CD	_	_	_
733	_	_	SYM	_	_	_
734	20	20	CD	_	_	_
735	min	min	NN	_	_	_
736	_	_	NN	_	_	_
737	f	f	FW	_	_	_
738	_	_	FW	_	_	_
739	2	2	CD	_	_	_
740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
741	ecoli	ecolus	NNS	_	_	_
742	_	_	VBP	_	_	_
743	k12	k12	NN	_	_	_
744	_	_	SYM	_	_	_
745	42C	42c	CD	_	_	_
746	_	_	SYM	_	_	_
747	20	20	CD	_	_	_
748	min	min	NN	_	_	_
749	_	_	NN	_	_	_
750	f	f	FW	_	_	_
751	_	_	FW	_	_	_
752	3	3	CD	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	ecoli	ecolus	NNS	_	_	_
755	_	_	VBP	_	_	_
756	k12	k12	NN	_	_	_
757	_	_	SYM	_	_	_
758	42C	42c	CD	_	_	_
759	_	_	SYM	_	_	_
760	20	20	CD	_	_	_
761	min	min	NN	_	_	_
762	_	_	NN	_	_	_
763	m	m	NN	_	_	_
764	_	_	NN	_	_	_
765	1	1	CD	_	_	_
766	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
767	ecoli	ecolus	NNS	_	_	_
768	_	_	VBP	_	_	_
769	k12	k12	NN	_	_	_
770	_	_	SYM	_	_	_
771	42C	42c	CD	_	_	_
772	_	_	SYM	_	_	_
773	20	20	CD	_	_	_
774	min	min	NN	_	_	_
775	_	_	NN	_	_	_
776	m	m	NN	_	_	_
777	_	_	NN	_	_	_
778	2	2	CD	_	_	_
779	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
780	ecoli	ecolus	NNS	_	_	_
781	_	_	VBP	_	_	_
782	k12	k12	NN	_	_	_
783	_	_	SYM	_	_	_
784	42C	42c	CD	_	_	_
785	_	_	SYM	_	_	_
786	20	20	CD	_	_	_
787	min	min	NN	_	_	_
788	_	_	NN	_	_	_
789	m	m	NN	_	_	_
790	_	_	SYM	_	_	_
791	3	3	CD	_	_	_
792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
793	E.	e.	FW	_	_	_
794	coli	coli	FW	_	_	_
795	K-12	k-12	NN	_	_	_
796	BW25113	bw25113	NN	_	_	_
797	mqsR	mqsr	NN	GEN	_	_
798	mutant	mutant	NN	_	_	_
799	at	at	IN	_	_	_
800	OD600	od600	NN	_	_	_
801	=	=	JJ	_	_	_
802	0.5	0.5	CD	_	_	_
803	LB	lb	NN	_	_	_
804	37C	37c	NN	_	_	_
805	suspension	suspension	NN	_	_	_
806	cell	cell	NN	_	_	_
807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
808	E.	e.	FW	_	_	_
809	coli	coli	FW	_	_	_
810	K-12	k-12	NN	_	_	_
811	BW25113/pBAD-Myc-His	bw25113/pbad-myc-his	NN	_	_	_
812	C	c	NN	_	_	_
813	in	in	IN	_	_	_
814	LB	lb	NN	_	_	_
815	for	for	IN	_	_	_
816	24	24	CD	_	_	_
817	h	h	NN	_	_	_
818	37oC	37oc	NN	_	_	_
819	with	with	IN	_	_	_
820	0.5	0.5	CD	_	_	_
821	%	%	NN	_	_	_
822	L-arabinose	l-arabinose	JJ	_	_	_
823	suspension	suspension	NN	_	_	_
824	cell	cell	NN	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	E.	e.	FW	_	_	_
827	coli	coli	FW	_	_	_
828	K-12	k-12	NN	_	_	_
829	BW25113/pBAD-Myc-His	bw25113/pbad-myc-his	NN	_	_	_
830	C-mqsA	c-mqsa	NN	_	_	_
831	in	in	IN	_	_	_
832	LB	lb	NN	_	_	_
833	for	for	IN	_	_	_
834	24	24	CD	_	_	_
835	h	h	NN	_	_	_
836	37oC	37oc	NN	_	_	_
837	with	with	IN	_	_	_
838	0.5	0.5	CD	_	_	_
839	%	%	NN	_	_	_
840	L-arabinose	l-arabinose	JJ	_	_	_
841	suspension	suspension	NN	_	_	_
842	cell	cell	NN	_	_	_
843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
844	E.	e.	FW	_	_	_
845	coli	coli	FW	_	_	_
846	K-12	k-12	NN	_	_	_
847	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
848	at	at	IN	_	_	_
849	OD600	od600	NN	_	_	_
850	=	=	JJ	_	_	_
851	0.5	0.5	CD	_	_	_
852	LB	lb	NN	_	_	_
853	37C	37c	NN	_	_	_
854	2	2	CD	_	_	_
855	mM	mm	NN	KWSUPP	_	_
856	IPTG	iptg	NN	_	_	_
857	suspension	suspension	NN	_	_	_
858	cell	cell	NN	_	_	_
859	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
860	E.	e.	FW	_	_	_
861	coli	coli	FW	_	_	_
862	K-12	k-12	NN	_	_	_
863	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
864	at	at	IN	_	_	_
865	OD600	od600	NN	_	_	_
866	=	=	JJ	_	_	_
867	0.5	0.5	CD	_	_	_
868	LB	lb	NN	_	_	_
869	37C	37c	NN	_	_	_
870	then	then	RB	_	_	_
871	2	2	CD	_	_	_
872	mM	mm	NN	KWSUPP	_	_
873	IPTG	iptg	NN	_	_	_
874	for	for	IN	_	_	_
875	15	15	CD	_	_	_
876	min	min	NN	_	_	_
877	short	short	JJ	_	_	_
878	time	time	NN	_	_	_
879	suspension	suspension	NN	_	_	_
880	cell	cell	NN	_	_	_
881	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
882	E.	e.	FW	_	_	_
883	coli	coli	FW	_	_	_
884	K-12	k-12	NN	_	_	_
885	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
886	in	in	IN	_	_	_
887	LB	lb	NN	_	_	_
888	for	for	IN	_	_	_
889	24	24	CD	_	_	_
890	h	h	NN	_	_	_
891	37oC	37oc	NN	_	_	_
892	with	with	IN	_	_	_
893	2	2	CD	_	_	_
894	mM	mm	NN	KWSUPP	_	_
895	IPTG	iptg	NN	_	_	_
896	biofilm	biofilm	NN	_	_	_
897	cell	cell	NN	_	_	_
898	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
899	E.	e.	FW	_	_	_
900	coli	coli	FW	_	_	_
901	K-12	k-12	NN	_	_	_
902	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
903	at	at	IN	_	_	_
904	OD600	od600	NN	_	_	_
905	=	=	JJ	_	_	_
906	0.5	0.5	CD	_	_	_
907	LB	lb	NN	_	_	_
908	37C	37c	NN	_	_	_
909	2	2	CD	_	_	_
910	mM	mm	NN	KWSUPP	_	_
911	IPTG	iptg	NN	_	_	_
912	suspension	suspension	NN	_	_	_
913	cell	cell	NN	_	_	_
914	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
915	E.	e.	FW	_	_	_
916	coli	coli	FW	_	_	_
917	K-12	k-12	NN	_	_	_
918	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
919	at	at	IN	_	_	_
920	OD600	od600	NN	_	_	_
921	=	=	JJ	_	_	_
922	0.5	0.5	CD	_	_	_
923	LB	lb	NN	_	_	_
924	37C	37c	NN	_	_	_
925	then	then	RB	_	_	_
926	2	2	CD	_	_	_
927	mM	mm	NN	KWSUPP	_	_
928	IPTG	iptg	NN	_	_	_
929	for	for	IN	_	_	_
930	15	15	CD	_	_	_
931	min	min	NN	_	_	_
932	short	short	JJ	_	_	_
933	time	time	NN	_	_	_
934	suspension	suspension	NN	_	_	_
935	cell	cell	NN	_	_	_
936	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
937	E.	e.	FW	_	_	_
938	coli	coli	FW	_	_	_
939	K-12	k-12	NN	_	_	_
940	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
941	in	in	IN	_	_	_
942	LB	lb	NN	_	_	_
943	for	for	IN	_	_	_
944	24	24	CD	_	_	_
945	h	h	NN	_	_	_
946	37oC	37oc	NN	_	_	_
947	with	with	IN	_	_	_
948	2	2	CD	_	_	_
949	mM	mm	NN	KWSUPP	_	_
950	IPTG	iptg	NN	_	_	_
951	biofilm	biofilm	NN	_	_	_
952	cell	cell	NN	_	_	_
953	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
954	E.	e.	FW	_	_	_
955	coli	coli	FW	_	_	_
956	K-12	k-12	NN	_	_	_
957	BW25113	bw25113	NN	_	_	_
958	wt	wt	JJ	_	_	_
959	at	at	IN	_	_	_
960	OD600	od600	NN	_	_	_
961	=	=	JJ	_	_	_
962	0.5	0.5	CD	_	_	_
963	LB	lb	NN	_	_	_
964	37C	37c	NN	_	_	_
965	suspension	suspension	NN	_	_	_
966	cell	cell	NN	_	_	_
967	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
968	E.	e.	FW	_	_	_
969	coli	coli	FW	_	_	_
970	K12	k12	NN	_	_	_
971	cells	cell	NNS	_	_	_
972	,	,	,	_	_	_
973	M9	m9	NN	_	_	_
974	,	,	,	_	_	_
975	8	8	CD	_	_	_
976	h	h	NN	_	_	_
977	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
978	E.	E.	NNP	_	_	_
979	coli	coli	NN	_	_	_
980	K12	k12	NN	_	_	_
981	grown	grow	VBN	_	_	_
982	in	in	IN	_	_	_
983	M63	m63	NN	_	_	_
984	glucose	glucose	NN	SUPP	_	_
985	-LRB-	-lrb-	-LRB-	_	_	_
986	0.2	0.2	CD	_	_	_
987	%	%	NN	_	_	_
988	-RRB-	-rrb-	-RRB-	_	_	_
989	minimal	minimal	JJ	_	_	_
990	media	media	NNS	_	_	_
991	,	,	,	_	_	_
992	sampled	sample	VBN	_	_	_
993	in	in	IN	_	_	_
994	exponential	exponential	JJ	GrowthPhase	_	_
995	phase	phase	NN	GrowthPhase	_	_
996	OD600	od600	NN	_	_	_
997	=	=	JJ	_	_	_
998	0.3	0.3	CD	_	_	_
999	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1000	E.	E.	NNP	_	_	_
1001	coli	coli	NN	_	_	_
1002	K12	k12	NN	_	_	_
1003	grown	grow	VBN	_	_	_
1004	in	in	IN	_	_	_
1005	M63	m63	NN	_	_	_
1006	glucose	glucose	NN	SUPP	_	_
1007	-LRB-	-lrb-	-LRB-	_	_	_
1008	0.2	0.2	CD	_	_	_
1009	%	%	NN	_	_	_
1010	-RRB-	-rrb-	-RRB-	_	_	_
1011	minimal	minimal	JJ	_	_	_
1012	media	media	NNS	_	_	_
1013	,	,	,	_	_	_
1014	sampled	sample	VBN	_	_	_
1015	in	in	IN	_	_	_
1016	stationary	stationary	JJ	GrowthPhase	_	_
1017	phase	phase	NN	GrowthPhase	_	_
1018	OD600	od600	NN	_	_	_
1019	=	=	JJ	_	_	_
1020	1.5	1.5	CD	_	_	_
1021	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1022	E.	E.	NNP	_	_	_
1023	coli	coli	NN	_	_	_
1024	K12	k12	NN	_	_	_
1025	grown	grow	VBN	_	_	_
1026	in	in	IN	_	_	_
1027	minimal	minimal	JJ	_	_	_
1028	medium	medium	NN	_	_	_
1029	with	with	IN	_	_	_
1030	added	add	VBN	_	_	_
1031	5	5	CD	_	_	_
1032	μM	μm	NN	_	_	_
1033	TPEN	tpen	NN	_	_	_
1034	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1035	E.	e.	FW	_	_	_
1036	coli	coli	FW	_	_	_
1037	K12	k12	NN	_	_	_
1038	grown	grow	VBN	_	_	_
1039	in	in	IN	_	_	_
1040	minimal	minimal	JJ	_	_	_
1041	medium	medium	NN	_	_	_
1042	without	without	IN	_	_	_
1043	added	add	VBN	_	_	_
1044	TPEN	tpen	NN	_	_	_
1045	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1046	E.	e.	FW	_	_	_
1047	coli	coli	FW	_	_	_
1048	K12	k12	NN	_	_	_
1049	interacted	interact	VBD	_	_	_
1050	with	with	IN	_	_	_
1051	lettuce	lettuce	NN	_	_	_
1052	rhizosphere	rhizosphere	NN	_	_	_
1053	rep1	rep1	NN	_	_	_
1054	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1055	E.	e.	FW	_	_	_
1056	coli	coli	FW	_	_	_
1057	K12	k12	NN	_	_	_
1058	interacted	interact	VBD	_	_	_
1059	with	with	IN	_	_	_
1060	lettuce	lettuce	NN	_	_	_
1061	rhizosphere	rhizosphere	NN	_	_	_
1062	rep2	rep2	NN	_	_	_
1063	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1064	E.	e.	FW	_	_	_
1065	coli	coli	FW	_	_	_
1066	K12	k12	NN	_	_	_
1067	interacted	interact	VBD	_	_	_
1068	with	with	IN	_	_	_
1069	lettuce	lettuce	NN	_	_	_
1070	rhizosphere	rhizosphere	NN	_	_	_
1071	rep3	rep3	NN	_	_	_
1072	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1073	E.	e.	FW	_	_	_
1074	coli	coli	FW	_	_	_
1075	K12	k12	NN	_	_	_
1076	interacted	interact	VBD	_	_	_
1077	with	with	IN	_	_	_
1078	lettuce	lettuce	NN	_	_	_
1079	rhizosphere	rhizosphere	NN	_	_	_
1080	rep4	rep4	NN	_	_	_
1081	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1082	E.	e.	FW	_	_	_
1083	coli	coli	FW	_	_	_
1084	K12	k12	NN	_	_	_
1085	interacted	interact	VBD	_	_	_
1086	with	with	IN	_	_	_
1087	lettuce	lettuce	NN	_	_	_
1088	rhizosphere	rhizosphere	NN	_	_	_
1089	rep5	rep5	NN	_	_	_
1090	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1091	E.	e.	FW	_	_	_
1092	coli	coli	FW	_	_	_
1093	K12	k12	NN	_	_	_
1094	interacted	interact	VBD	_	_	_
1095	with	with	IN	_	_	_
1096	lettuce	lettuce	NN	_	_	_
1097	rhizosphere	rhizosphere	NN	_	_	_
1098	rep6	rep6	NN	_	_	_
1099	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1100	E.	e.	FW	_	_	_
1101	coli	coli	FW	_	_	_
1102	K-12	k-12	NN	_	_	_
1103	MG1655	mg1655	NN	_	_	_
1104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1105	E.	e.	FW	_	_	_
1106	coli	coli	FW	_	_	_
1107	K12	k12	NN	_	_	_
1108	MG1655	mg1655	NN	_	_	_
1109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1110	E.	e.	FW	_	_	_
1111	coli	coli	FW	_	_	_
1112	K-12	k-12	NN	_	_	_
1113	MG1655	mg1655	NN	_	_	_
1114	cra-8myc	cra-8myc	NN	_	_	_
1115	tagged	tag	VBD	_	_	_
1116	strains	strain	NNS	_	_	_
1117	was	be	VBD	_	_	_
1118	grown	grow	VBN	_	_	_
1119	to	to	TO	_	_	_
1120	mid-log	mid-log	JJ	_	_	_
1121	phase	phase	NN	_	_	_
1122	aerobically	aerobically	RB	_	_	_
1123	at	at	IN	_	_	_
1124	37	37	CD	_	_	_
1125	°C	°c	NN	_	_	_
1126	in	in	IN	_	_	_
1127	M9	m9	NN	MED	_	_
1128	minimal	minimal	JJ	MED	_	_
1129	media	media	NNS	MED	_	_
1130	supplemented	supplement	VBN	_	_	_
1131	with	with	IN	_	_	_
1132	0.2	0.2	CD	_	_	_
1133	%	%	NN	_	_	_
1134	glucose	glucose	NN	SUPP	_	_
1135	,	,	,	_	_	_
1136	fructose	fructose	NN	_	_	_
1137	and	and	CC	_	_	_
1138	acetate	acetate	NN	SUPP	_	_
1139	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	-LSB-	-lsb-	-LRB-	_	_	_
5	K-12	k-12	NN	_	_	_
6	MG1655	mg1655	NN	_	_	_
7	strain	strain	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	U00096	u00096	NN	_	_	_
10	.2	.2	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	was	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	overnight	overnight	RB	_	_	_
16	at	at	IN	_	_	_
17	30	30	CD	_	_	_
18	°C	°c	NN	_	_	_
19	in	in	IN	_	_	_
20	LB	lb	NN	MED	_	_
21	medium	medium	NN	MED	_	_
22	.	.	.	_	_	_

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	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG	mg	NN	_	_	_
6	1655	1655	CD	_	_	_
7	was	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	LB-Miller	lb-miller	NN	_	_	_
11	broth	broth	NN	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	,160	,160	CD	_	_	_
16	rpm	rpm	NN	_	_	_
17	to	to	TO	_	_	_
18	an	a	DT	_	_	_
19	O.D.	o.d.	NN	_	_	_
20	600	600	CD	_	_	_
21	nm	nm	NN	_	_	_
22	of	of	IN	_	_	_
23	0	0	CD	_	_	_
24	.	.	.	_	_	_

1	7	7	CD	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	E.	E.	NNP	_	_	_
4	coli	coli	NN	_	_	_
5	K12	k12	NN	_	_	_
6	MG1655	mg1655	NN	_	_	_
7	was	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	to	to	TO	_	_	_
10	mid-log	mid-log	JJ	_	_	_
11	phase	phase	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	O.D.	o.d.	NN	_	_	_
14	600nm	600nm	CD	_	_	_
15	0.5	0.5	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	or	or	CC	_	_	_
18	to	to	TO	_	_	_
19	stationary	stationary	JJ	GrowthPhase	_	_
20	phase	phase	NN	GrowthPhase	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	O.D.	o.d.	NN	_	_	_
23	600nm	600nm	CD	_	_	_
24	1.5	1.5	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	aerobically	aerobically	RB	_	_	_
27	at	at	IN	_	_	_
28	37	37	CD	_	_	_
29	°C	°c	NN	_	_	_
30	in	in	IN	_	_	_
31	M9	m9	NN	MED	_	_
32	minimal	minimal	JJ	MED	_	_
33	media	media	NNS	MED	_	_
34	supplemented	supplement	VBN	_	_	_
35	with	with	IN	_	_	_
36	0.2	0.2	CD	_	_	_
37	%	%	NN	_	_	_
38	glucose	glucose	NN	SUPP	_	_
39	or	or	CC	_	_	_
40	W2	w2	NN	_	_	_
41	minimal	minimal	JJ	_	_	_
42	media	media	NNS	_	_	_
43	supplemented	supplement	VBN	_	_	_
44	with	with	IN	_	_	_
45	0.2	0.2	CD	_	_	_
46	%	%	NN	_	_	_
47	glucose	glucose	NN	SUPP	_	_
48	and	and	CC	_	_	_
49	0.2	0.2	CD	_	_	_
50	%	%	NN	_	_	_
51	glutamine	glutamine	NN	_	_	_
52	.	.	.	_	_	_

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	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	WT	wt	NN	_	_	_
7	and	and	CC	_	_	_
8	Fur-8-myc	fur-8-myc	NN	_	_	_
9	tagged	tag	VBD	_	_	_
10	strains	strain	NNS	_	_	_
11	were	be	VBD	_	_	_
12	grown	grow	VBN	_	_	_
13	to	to	TO	_	_	_
14	mid-log	mid-log	JJ	_	_	_
15	phase	phase	NN	_	_	_
16	aerobically	aerobically	RB	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	in	in	IN	_	_	_
21	M9	m9	NN	MED	_	_
22	minimal	minimal	JJ	MED	_	_
23	media	media	NNS	MED	_	_
24	supplemented	supplement	VBN	_	_	_
25	with	with	IN	_	_	_
26	0.2	0.2	CD	_	_	_
27	%	%	NN	_	_	_
28	glucose	glucose	NN	SUPP	_	_
29	.	.	.	_	_	_

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/mL	mg/ml	NN	_	_	_
20	at	at	IN	_	_	_
21	mid-log	mid-log	JJ	_	_	_
22	phase	phase	NN	_	_	_
23	and	and	CC	_	_	_
24	stirred	stir	VBD	_	_	_
25	for	for	IN	_	_	_
26	20	20	CD	_	_	_
27	min	min	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	WT	WT	NNP	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	Δcra	Δcra	NNP	_	_	_
10	were	be	VBD	_	_	_
11	grown	grow	VBN	_	_	_
12	to	to	TO	_	_	_
13	mid-log	mid-log	JJ	_	_	_
14	phase	phase	NN	_	_	_
15	aerobically	aerobically	RB	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	in	in	IN	_	_	_
20	M9	m9	NN	MED	_	_
21	minimal	minimal	JJ	MED	_	_
22	media	media	NNS	MED	_	_
23	supplemented	supplement	VBN	_	_	_
24	with	with	IN	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	glucose	glucose	NN	SUPP	_	_
28	,	,	,	_	_	_
29	fructose	fructose	NN	_	_	_
30	and	and	CC	_	_	_
31	acetate	acetate	NN	SUPP	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	WT	wt	NN	_	_	_
7	and	and	CC	_	_	_
8	Δfur	δfur	NN	_	_	_
9	were	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	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	WT	wt	NN	_	_	_
7	and	and	CC	_	_	_
8	ΔompR	δompr	NN	_	_	_
9	were	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	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	WT	WT	NNP	_	_	_
7	,	,	,	_	_	_
8	GadE-8-myc	gade-8-myc	NN	_	_	_
9	,	,	,	_	_	_
10	GadW-8-myc	gadw-8-myc	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	GadX-8-myc	gadx-8-myc	NN	_	_	_
14	tagged	tag	VBD	_	_	_
15	strains	strain	NNS	_	_	_
16	were	be	VBD	_	_	_
17	grown	grow	VBN	_	_	_
18	to	to	TO	_	_	_
19	mid-log	mid-log	JJ	_	_	_
20	phase	phase	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	OD600	od600	NN	_	_	_
23	=	=	JJ	_	_	_
24	0.3	0.3	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	aerobically	aerobically	RB	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	250	250	CD	_	_	_
29	rpm	rpm	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	at	at	IN	_	_	_
32	37	37	CD	_	_	_
33	°C	°c	NN	_	_	_
34	in	in	IN	_	_	_
35	M9	m9	NN	MED	_	_
36	minimal	minimal	JJ	MED	_	_
37	media	media	NNS	MED	_	_
38	supplemented	supplement	VBN	_	_	_
39	with	with	IN	_	_	_
40	0.2	0.2	CD	_	_	_
41	%	%	NN	_	_	_
42	glucose	glucose	NN	SUPP	_	_
43	at	at	IN	_	_	_
44	pH	ph	NN	_	_	_
45	5.5	5.5	CD	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	WT	wt	NN	_	_	_
7	,	,	,	_	_	_
8	gadE	gade	NN	GEN	_	_
9	,	,	,	_	_	_
10	gadW	gadw	NN	GEN	_	_
11	and	and	CC	_	_	_
12	gadX	gadx	NN	GEN	_	_
13	mutant	mutant	JJ	_	_	_
14	cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	grown	grow	VBN	_	_	_
17	to	to	TO	_	_	_
18	mid-log	mid-log	JJ	_	_	_
19	phase	phase	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	OD600	od600	NN	_	_	_
22	=	=	JJ	_	_	_
23	0.3	0.3	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	aerobically	aerobically	RB	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	250	250	CD	_	_	_
28	rpm	rpm	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	at	at	IN	_	_	_
31	37	37	CD	_	_	_
32	°C	°c	NN	_	_	_
33	in	in	IN	_	_	_
34	M9	m9	NN	MED	_	_
35	minimal	minimal	JJ	MED	_	_
36	media	media	NNS	MED	_	_
37	supplemented	supplement	VBN	_	_	_
38	with	with	IN	_	_	_
39	0.2	0.2	CD	_	_	_
40	%	%	NN	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	at	at	IN	_	_	_
43	pH	ph	NN	_	_	_
44	5.5	5.5	CD	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	WT	wt	NN	_	_	_
7	,	,	,	_	_	_
8	ΔoxyR	δoxyr	NN	_	_	_
9	,	,	,	_	_	_
10	ΔsoxR	δsoxr	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	ΔsoxS	δsoxs	NN	_	_	_
14	were	be	VBD	_	_	_
15	grown	grow	VBN	_	_	_
16	to	to	TO	_	_	_
17	mid-log	mid-log	JJ	_	_	_
18	phase	phase	NN	_	_	_
19	aerobically	aerobically	RB	_	_	_
20	at	at	IN	_	_	_
21	37	37	CD	_	_	_
22	°C	°c	NN	_	_	_
23	in	in	IN	_	_	_
24	M9	m9	NN	MED	_	_
25	minimal	minimal	JJ	MED	_	_
26	media	media	NNS	MED	_	_
27	supplemented	supplement	VBN	_	_	_
28	with	with	IN	_	_	_
29	0.2	0.2	CD	_	_	_
30	%	%	NN	_	_	_
31	glucose	glucose	NN	SUPP	_	_
32	.	.	.	_	_	_

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	NN	_	_	_
2	ecoli	ecolus	NNS	_	_	_
3	_	_	VBP	_	_	_
4	k12	k12	NN	_	_	_
5	_	_	SYM	_	_	_
6	pBAD	pbad	FW	_	_	_
7	_	_	FW	_	_	_
8	30C	30c	FW	_	_	_
9	_	_	FW	_	_	_
10	f	f	FW	_	_	_
11	_	_	SYM	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	ecoli	ecolus	NNS	_	_	_
15	_	_	VBP	_	_	_
16	k12	k12	NN	_	_	_
17	_	_	SYM	_	_	_
18	pBad	pbad	FW	_	_	_
19	_	_	FW	_	_	_
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	pBAD	pbad	FW	_	_	_
31	_	_	FW	_	_	_
32	30C	30c	FW	_	_	_
33	_	_	FW	_	_	_
34	f	f	FW	_	_	_
35	_	_	SYM	_	_	_
36	3	3	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	ecoli	ecolus	NNS	_	_	_
39	_	_	VBP	_	_	_
40	k12	k12	NN	_	_	_
41	_	_	SYM	_	_	_
42	pBAD	pbad	FW	_	_	_
43	_	_	FW	_	_	_
44	30C	30c	FW	_	_	_
45	_	_	FW	_	_	_
46	f	f	FW	_	_	_
47	_	_	SYM	_	_	_
48	4	4	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	ecoli	ecolus	NNS	_	_	_
51	_	_	VBP	_	_	_
52	k12	k12	NN	_	_	_
53	_	_	CD	_	_	_
54	pBAD	pbad	NN	_	_	_
55	_	_	SYM	_	_	_
56	30C	30c	CD	_	_	_
57	_	_	NN	_	_	_
58	m	m	NN	_	_	_
59	_	_	NN	_	_	_
60	1	1	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	ecoli	ecolus	NNS	_	_	_
63	_	_	VBP	_	_	_
64	k12	k12	NN	_	_	_
65	_	_	CD	_	_	_
66	pBAD	pbad	NN	_	_	_
67	_	_	SYM	_	_	_
68	30C	30c	CD	_	_	_
69	_	_	NN	_	_	_
70	m	m	NN	_	_	_
71	_	_	NN	_	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	ecoli	ecolus	NNS	_	_	_
75	_	_	VBP	_	_	_
76	k12	k12	NN	_	_	_
77	_	_	CD	_	_	_
78	pBAD	pbad	NN	_	_	_
79	_	_	SYM	_	_	_
80	30C	30c	CD	_	_	_
81	_	_	NN	_	_	_
82	m	m	NN	_	_	_
83	_	_	NN	_	_	_
84	3	3	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	ecoli	ecolus	NNS	_	_	_
87	_	_	VBP	_	_	_
88	k12	k12	NN	_	_	_
89	_	_	CD	_	_	_
90	pBAD	pbad	NN	_	_	_
91	_	_	SYM	_	_	_
92	30C	30c	CD	_	_	_
93	_	_	NN	_	_	_
94	m	m	NN	_	_	_
95	_	_	NN	_	_	_
96	4	4	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	ecoli	ecolus	NNS	_	_	_
99	_	_	VBP	_	_	_
100	k12	k12	NN	_	_	_
101	_	_	CD	_	_	_
102	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
103	_	_	SYM	_	_	_
104	30C	30c	FW	_	_	_
105	_	_	FW	_	_	_
106	f	f	FW	_	_	_
107	_	_	SYM	_	_	_
108	1	1	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	ecoli	ecolus	NNS	_	_	_
111	_	_	VBP	_	_	_
112	k12	k12	NN	_	_	_
113	_	_	CD	_	_	_
114	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
115	_	_	SYM	_	_	_
116	30C	30c	FW	_	_	_
117	_	_	FW	_	_	_
118	f	f	FW	_	_	_
119	_	_	SYM	_	_	_
120	2	2	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	ecoli	ecolus	NNS	_	_	_
123	_	_	VBP	_	_	_
124	k12	k12	NN	_	_	_
125	_	_	CD	_	_	_
126	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
127	_	_	SYM	_	_	_
128	30C	30c	CD	_	_	_
129	_	_	NN	_	_	_
130	m	m	NN	_	_	_
131	_	_	NN	_	_	_
132	1	1	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	ecoli	ecolus	NNS	_	_	_
135	_	_	VBP	_	_	_
136	k12	k12	NN	_	_	_
137	_	_	CD	_	_	_
138	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
139	_	_	SYM	_	_	_
140	30C	30c	CD	_	_	_
141	_	_	NN	_	_	_
142	m	m	NN	_	_	_
143	_	_	NN	_	_	_
144	2	2	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	ecoli	ecolus	NNS	_	_	_
147	_	_	VBP	_	_	_
148	k12	k12	NN	_	_	_
149	_	_	CD	_	_	_
150	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
151	_	_	SYM	_	_	_
152	30C	30c	FW	_	_	_
153	_	_	FW	_	_	_
154	f	f	FW	_	_	_
155	_	_	SYM	_	_	_
156	1	1	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	ecoli	ecolus	NNS	_	_	_
159	_	_	VBP	_	_	_
160	k12	k12	NN	_	_	_
161	_	_	CD	_	_	_
162	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
163	_	_	SYM	_	_	_
164	30C	30c	FW	_	_	_
165	_	_	FW	_	_	_
166	f	f	FW	_	_	_
167	_	_	SYM	_	_	_
168	2	2	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	ecoli	ecolus	NNS	_	_	_
171	_	_	VBP	_	_	_
172	k12	k12	NN	_	_	_
173	_	_	CD	_	_	_
174	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
175	_	_	SYM	_	_	_
176	30C	30c	FW	_	_	_
177	_	_	FW	_	_	_
178	f	f	FW	_	_	_
179	_	_	SYM	_	_	_
180	3	3	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	ecoli	ecolus	NNS	_	_	_
183	_	_	VBP	_	_	_
184	k12	k12	NN	_	_	_
185	_	_	CD	_	_	_
186	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
187	_	_	SYM	_	_	_
188	30C	30c	CD	_	_	_
189	_	_	NN	_	_	_
190	m	m	NN	_	_	_
191	_	_	NN	_	_	_
192	1	1	CD	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	ecoli	ecolus	NNS	_	_	_
195	_	_	VBP	_	_	_
196	k12	k12	NN	_	_	_
197	_	_	CD	_	_	_
198	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
199	_	_	SYM	_	_	_
200	30C	30c	CD	_	_	_
201	_	_	NN	_	_	_
202	m	m	NN	_	_	_
203	_	_	NN	_	_	_
204	2	2	CD	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	ecoli	ecolus	NNS	_	_	_
207	_	_	VBP	_	_	_
208	k12	k12	NN	_	_	_
209	_	_	CD	_	_	_
210	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
211	_	_	SYM	_	_	_
212	30C	30c	CD	_	_	_
213	_	_	NN	_	_	_
214	m	m	NN	_	_	_
215	_	_	SYM	_	_	_
216	3	3	CD	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	E.	e.	FW	_	_	_
219	coli	coli	FW	_	_	_
220	K-12	k-12	NN	_	_	_
221	strain	strain	NN	_	_	_
222	BW25113	bw25113	NN	_	_	_
223	was	be	VBD	_	_	_
224	evolved	evolve	VBN	_	_	_
225	in	in	IN	_	_	_
226	chemostats	chemostat	NNS	_	_	_
227	.	.	.	_	_	_

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/L	g/l	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	with	with	IN	_	_	_
15	increasing	increase	VBG	_	_	_
16	concentrations	concentration	NNS	_	_	_
17	of	of	IN	_	_	_
18	n-butanol	n-butanol	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K12	k12	NN	_	_	_
5	strain	strain	NN	_	_	_
6	JM109	jm109	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	K12	k12	NN	_	_	_
11	substrain	substrain	NN	_	_	_
12	W3110	w3110	NN	_	_	_
13	was	be	VBD	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	this	this	DT	_	_	_
17	study	study	NN	_	_	_
18	.	.	.	_	_	_

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	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	K-12	k-12	NN	_	_	_
44	W3110	w3110	NN	_	_	_
45	#	#	#	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	E.	e.	FW	_	_	_
49	coli	coli	FW	_	_	_
50	K-12	k-12	NN	_	_	_
51	W3110	w3110	NN	_	_	_
52	#	#	#	_	_	_
53	2	2	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	E.	e.	FW	_	_	_
56	coli	coli	FW	_	_	_
57	K-12	k-12	NN	_	_	_
58	W3110	w3110	NN	_	_	_
59	#	#	#	_	_	_
60	3	3	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	E.	e.	FW	_	_	_
63	coli	coli	FW	_	_	_
64	K12	k12	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	W3110	w3110	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	,	,	,	_	_	_
69	fed-batch/linear	fed-batch/linear	JJ	_	_	_
70	feed	feed	NN	_	_	_
71	,	,	,	_	_	_
72	glucose	glucose	NN	SUPP	_	_
73	limitation	limitation	NN	_	_	_
74	,	,	,	_	_	_
75	110	110	CD	_	_	_
76	min	min	NN	_	_	_
77	after	after	IN	_	_	_
78	depletion	depletion	NN	_	_	_
79	of	of	IN	_	_	_
80	extracellular	extracellular	JJ	_	_	_
81	acetate	acetate	NN	SUPP	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	E.	E.	NNP	_	_	_
84	coli	coli	NN	_	_	_
85	K12	k12	NN	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	W3110	w3110	NN	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	,	,	,	_	_	_
90	fed-batch/linear	fed-batch/linear	JJ	_	_	_
91	feed	feed	NN	_	_	_
92	,	,	,	_	_	_
93	glucose	glucose	NN	SUPP	_	_
94	limitation	limitation	NN	_	_	_
95	,	,	,	_	_	_
96	170	170	CD	_	_	_
97	min	min	NN	_	_	_
98	after	after	IN	_	_	_
99	depletion	depletion	NN	_	_	_
100	of	of	IN	_	_	_
101	extracellular	extracellular	JJ	_	_	_
102	acetate	acetate	NN	SUPP	_	_
103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
104	E.	E.	NNP	_	_	_
105	coli	coli	NN	_	_	_
106	K12	k12	NN	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	W3110	w3110	NN	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	,	,	,	_	_	_
111	fed-batch/linear	fed-batch/linear	JJ	_	_	_
112	feed	feed	NN	_	_	_
113	,	,	,	_	_	_
114	glucose	glucose	NN	SUPP	_	_
115	limitation	limitation	NN	_	_	_
116	,	,	,	_	_	_
117	230	230	CD	_	_	_
118	min	min	NN	_	_	_
119	after	after	IN	_	_	_
120	depletion	depletion	NN	_	_	_
121	of	of	IN	_	_	_
122	extracellular	extracellular	JJ	_	_	_
123	acetate	acetate	NN	SUPP	_	_
124	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
125	E.	E.	NNP	_	_	_
126	coli	coli	NN	_	_	_
127	K12	k12	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	W3110	w3110	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	,	,	,	_	_	_
132	fed-batch/linear	fed-batch/linear	JJ	_	_	_
133	feed	feed	NN	_	_	_
134	,	,	,	_	_	_
135	glucose	glucose	NN	SUPP	_	_
136	limitation	limitation	NN	_	_	_
137	,	,	,	_	_	_
138	30	30	CD	_	_	_
139	min	min	NN	_	_	_
140	after	after	IN	_	_	_
141	depletion	depletion	NN	_	_	_
142	of	of	IN	_	_	_
143	extracellular	extracellular	JJ	_	_	_
144	acetate	acetate	NN	SUPP	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	E.	E.	NNP	_	_	_
147	coli	coli	NN	_	_	_
148	K12	k12	NN	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	W3110	w3110	NN	_	_	_
151	-RRB-	-rrb-	-RRB-	_	_	_
152	,	,	,	_	_	_
153	fed-batch/linear	fed-batch/linear	JJ	_	_	_
154	feed	feed	NN	_	_	_
155	,	,	,	_	_	_
156	glucose	glucose	NN	SUPP	_	_
157	limitation	limitation	NN	_	_	_
158	,	,	,	_	_	_
159	350	350	CD	_	_	_
160	min	min	NN	_	_	_
161	after	after	IN	_	_	_
162	depletion	depletion	NN	_	_	_
163	of	of	IN	_	_	_
164	extracellular	extracellular	JJ	_	_	_
165	acetate	acetate	NN	SUPP	_	_
166	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
167	E.	E.	NNP	_	_	_
168	coli	coli	NN	_	_	_
169	K12	k12	NN	_	_	_
170	-LRB-	-lrb-	-LRB-	_	_	_
171	W3110	w3110	NN	_	_	_
172	-RRB-	-rrb-	-RRB-	_	_	_
173	,	,	,	_	_	_
174	fed-batch/linear	fed-batch/linear	JJ	_	_	_
175	feed	feed	NN	_	_	_
176	,	,	,	_	_	_
177	glucose	glucose	NN	SUPP	_	_
178	limitation	limitation	NN	_	_	_
179	,	,	,	_	_	_
180	50	50	CD	_	_	_
181	min	min	NN	_	_	_
182	after	after	IN	_	_	_
183	depletion	depletion	NN	_	_	_
184	of	of	IN	_	_	_
185	extracellular	extracellular	JJ	_	_	_
186	acetate	acetate	NN	SUPP	_	_
187	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
188	E.	E.	NNP	_	_	_
189	coli	coli	NN	_	_	_
190	K12	k12	NN	_	_	_
191	-LRB-	-lrb-	-LRB-	_	_	_
192	W3110	w3110	NN	_	_	_
193	-RRB-	-rrb-	-RRB-	_	_	_
194	,	,	,	_	_	_
195	fed-batch/linear	fed-batch/linear	JJ	_	_	_
196	feed	feed	NN	_	_	_
197	,	,	,	_	_	_
198	glucose	glucose	NN	SUPP	_	_
199	limitation	limitation	NN	_	_	_
200	,	,	,	_	_	_
201	acetate	acetate	NN	SUPP	_	_
202	concentration	concentration	NN	_	_	_
203	≤	≤	CD	_	_	_
204	0.35	0.35	CD	_	_	_
205	gL-1	gl-1	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
207	E.	e.	FW	_	_	_
208	coli	coli	FW	_	_	_
209	K12	k12	NN	_	_	_
210	-LRB-	-lrb-	-LRB-	_	_	_
211	W3110	w3110	NN	_	_	_
212	-RRB-	-rrb-	-RRB-	_	_	_
213	,	,	,	_	_	_
214	fed-batch/linear	fed-batch/linear	JJ	_	_	_
215	feed	feed	NN	_	_	_
216	,	,	,	_	_	_
217	glucose	glucose	NN	SUPP	_	_
218	limitation	limitation	NN	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	glucose	glucose	NN	SUPP	_	_
221	concentration	concentration	NN	_	_	_
222	<	<	JJR	_	_	_
223	0.05	0.05	CD	_	_	_
224	gL-1	gl-1	NN	_	_	_
225	-RRB-	-rrb-	-RRB-	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	E.	e.	FW	_	_	_
228	coli	coli	FW	_	_	_
229	K12	k12	NN	_	_	_
230	-LRB-	-lrb-	-LRB-	_	_	_
231	W3110	w3110	NN	_	_	_
232	-RRB-	-rrb-	-RRB-	_	_	_
233	,	,	,	_	_	_
234	fed-batch/linear	fed-batch/linear	JJ	_	_	_
235	feed	feed	NN	_	_	_
236	,	,	,	_	_	_
237	unlimited	unlimited	JJ	_	_	_
238	growth	growth	NN	_	_	_
239	-LRB-	-lrb-	-LRB-	_	_	_
240	batch	batch	NN	_	_	_
241	-RRB-	-rrb-	-RRB-	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	E.	e.	FW	_	_	_
244	coli	coli	FW	_	_	_
245	K12	k12	NN	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	W3110	w3110	NN	_	_	_
248	-RRB-	-rrb-	-RRB-	_	_	_
249	,	,	,	_	_	_
250	fed-batch/linear	fed-batch/linear	JJ	_	_	_
251	feed	feed	NN	_	_	_
252	,	,	,	_	_	_
253	unlimited	unlimited	JJ	_	_	_
254	growth	growth	NN	_	_	_
255	-LRB-	-lrb-	-LRB-	_	_	_
256	batch	batch	NN	_	_	_
257	-RRB-	-rrb-	-RRB-	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	E.coli	e.coli	NN	_	_	_
260	K12	k12	NN	_	_	_
261	was	be	VBD	_	_	_
262	cultured	culture	VBN	_	_	_
263	in	in	IN	_	_	_
264	LB	lb	NN	_	_	_
265	and	and	CC	_	_	_
266	grown	grow	VBN	_	_	_
267	at	at	IN	_	_	_
268	37	37	CD	_	_	_
269	°C	°c	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
271	E.	e.	FW	_	_	_
272	coli	coli	FW	_	_	_
273	K-12	k-12	NN	_	_	_
274	was	be	VBD	_	_	_
275	incubated	incubate	VBN	_	_	_
276	in	in	IN	_	_	_
277	5	5	CD	_	_	_
278	ml	ml	NN	_	_	_
279	LB	lb	NN	_	_	_
280	liquid	liquid	NN	_	_	_
281	for	for	IN	_	_	_
282	16	16	CD	_	_	_
283	h	h	NN	_	_	_
284	at	at	IN	_	_	_
285	37	37	CD	_	_	_
286	°C	°c	NN	_	_	_
287	with	with	IN	_	_	_
288	constant	constant	JJ	_	_	_
289	shaking	shake	VBG	_	_	_
290	,	,	,	_	_	_
291	and	and	CC	_	_	_
292	then	then	RB	_	_	_
293	100	100	CD	_	_	_
294	µl	µl	NN	_	_	_
295	of	of	IN	_	_	_
296	each	each	DT	_	_	_
297	myxotoxin	myxotoxin	NN	_	_	_
298	dissolved	dissolve	VBN	_	_	_
299	in	in	IN	_	_	_
300	acetonitrile	acetonitrile	NN	_	_	_
301	was	be	VBD	_	_	_
302	added	add	VBN	_	_	_
303	to	to	TO	_	_	_
304	each	each	DT	_	_	_
305	culture	culture	NN	_	_	_
306	to	to	TO	_	_	_
307	a	a	DT	_	_	_
308	final	final	JJ	_	_	_
309	concentration	concentration	NN	_	_	_
310	of	of	IN	_	_	_
311	0.2	0.2	CD	_	_	_
312	,	,	,	_	_	_
313	and	and	CC	_	_	_
314	2	2	CD	_	_	_
315	ppm	ppm	NN	_	_	_
316	.	.	.	_	_	_

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	NN	_	_	_
9	E.coli	e.coli	NN	_	_	_
10	K12	k12	NN	_	_	_
11	with	with	IN	_	_	_
12	ccdB	ccdb	NN	_	_	_
13	upregulation	upregulation	NN	_	_	_
14	0	0	CD	_	_	_
15	minutes	minute	NNS	_	_	_
16	after	after	IN	_	_	_
17	induction	induction	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	E.coli	e.coli	NN	_	_	_
20	K12	k12	NN	_	_	_
21	with	with	IN	_	_	_
22	ccdB	ccdb	NN	_	_	_
23	upregulation	upregulation	NN	_	_	_
24	120	120	CD	_	_	_
25	minutes	minute	NNS	_	_	_
26	after	after	IN	_	_	_
27	induction	induction	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	E.coli	e.coli	NN	_	_	_
30	K12	k12	NN	_	_	_
31	with	with	IN	_	_	_
32	ccdB	ccdb	NN	_	_	_
33	upregulation	upregulation	NN	_	_	_
34	30	30	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	after	after	IN	_	_	_
37	induction	induction	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	E.coli	e.coli	NN	_	_	_
40	K12	k12	NN	_	_	_
41	with	with	IN	_	_	_
42	ccdB	ccdb	NN	_	_	_
43	upregulation	upregulation	NN	_	_	_
44	60	60	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	after	after	IN	_	_	_
47	induction	induction	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	E.coli	e.coli	NN	_	_	_
50	K12	k12	NN	_	_	_
51	with	with	IN	_	_	_
52	ccdB	ccdb	NN	_	_	_
53	upregulation	upregulation	NN	_	_	_
54	90	90	CD	_	_	_
55	minutes	minute	NNS	_	_	_
56	after	after	IN	_	_	_
57	induction	induction	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	E.coli	e.coli	NN	_	_	_
60	K12	k12	NN	_	_	_
61	with	with	IN	_	_	_
62	lacZ	lacz	NN	GEN	_	_
63	upregulation	upregulation	NN	_	_	_
64	0	0	CD	_	_	_
65	minutes	minute	NNS	_	_	_
66	after	after	IN	_	_	_
67	induction	induction	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	E.coli	e.coli	NN	_	_	_
70	K12	k12	NN	_	_	_
71	with	with	IN	_	_	_
72	lacZ	lacz	NN	GEN	_	_
73	upregulation	upregulation	NN	_	_	_
74	120	120	CD	_	_	_
75	minutes	minute	NNS	_	_	_
76	after	after	IN	_	_	_
77	induction	induction	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	E.coli	e.coli	NN	_	_	_
80	K12	k12	NN	_	_	_
81	with	with	IN	_	_	_
82	lacZ	lacz	NN	GEN	_	_
83	upregulation	upregulation	NN	_	_	_
84	30	30	CD	_	_	_
85	minutes	minute	NNS	_	_	_
86	after	after	IN	_	_	_
87	induction	induction	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	E.coli	e.coli	NN	_	_	_
90	K12	k12	NN	_	_	_
91	with	with	IN	_	_	_
92	lacZ	lacz	NN	GEN	_	_
93	upregulation	upregulation	NN	_	_	_
94	60	60	CD	_	_	_
95	minutes	minute	NNS	_	_	_
96	after	after	IN	_	_	_
97	induction	induction	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	E.coli	e.coli	NN	_	_	_
100	K12	k12	NN	_	_	_
101	with	with	IN	_	_	_
102	lacZ	lacz	NN	GEN	_	_
103	upregulation	upregulation	NN	_	_	_
104	90	90	CD	_	_	_
105	minutes	minute	NNS	_	_	_
106	after	after	IN	_	_	_
107	induction	induction	NN	_	_	_
108	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
109	E.	E.	NNP	_	_	_
110	coli	coli	NN	_	_	_
111	K12	k12	NN	_	_	_
112	_	_	CD	_	_	_
113	WT	WT	NNP	_	_	_
114	_	_	NNP	_	_	_
115	M9	M9	NNP	_	_	_
116	_	_	SYM	_	_	_
117	rep1	rep1	CD	_	_	_
118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
119	E.	E.	NNP	_	_	_
120	coli	coli	NN	_	_	_
121	K12	k12	NN	_	_	_
122	_	_	CD	_	_	_
123	WT	WT	NNP	_	_	_
124	_	_	NNP	_	_	_
125	M9	M9	NNP	_	_	_
126	_	_	SYM	_	_	_
127	rep2	rep2	CD	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	E.	E.	NNP	_	_	_
130	coli	coli	NN	_	_	_
131	K12	k12	NN	_	_	_
132	ybjN	ybjn	NN	GEN	_	_
133	mutant	mutant	JJ	_	_	_
134	cells	cell	NNS	_	_	_
135	,	,	,	_	_	_
136	M9	m9	NN	_	_	_
137	,	,	,	_	_	_
138	8	8	CD	_	_	_
139	h	h	NN	_	_	_
140	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
141	E.	E.	NNP	_	_	_
142	coli	coli	NN	_	_	_
143	K12	k12	NN	_	_	_
144	_	_	CD	_	_	_
145	ybjN	ybjn	NN	GEN	_	_
146	_	_	CD	_	_	_
147	MUTANT	mutant	JJ	_	_	_
148	_	_	NN	_	_	_
149	M9	m9	NN	_	_	_
150	_	_	CD	_	_	_
151	rep1	rep1	NN	_	_	_
152	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
153	E.	E.	NNP	_	_	_
154	coli	coli	NN	_	_	_
155	K12	k12	NN	_	_	_
156	_	_	CD	_	_	_
157	ybjN	ybjn	NN	GEN	_	_
158	_	_	CD	_	_	_
159	MUTANT	mutant	JJ	_	_	_
160	_	_	NN	_	_	_
161	M9	m9	NN	_	_	_
162	_	_	CD	_	_	_
163	rep2	rep2	NN	_	_	_
164	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
165	E.	E.	NNP	_	_	_
166	coli	coli	NN	_	_	_
167	K12	k12	NN	_	_	_
168	_	_	CD	_	_	_
169	ybjN	ybjn	NN	GEN	_	_
170	_	_	CD	_	_	_
171	MUTANT	mutant	JJ	_	_	_
172	_	_	NN	_	_	_
173	M9	m9	NN	_	_	_
174	_	_	CD	_	_	_
175	rep3	rep3	NN	_	_	_
176	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
177	E.	E.	NNP	_	_	_
178	coli	coli	NN	_	_	_
179	K12	k12	NN	_	_	_
180	ybjN	ybjn	NN	GEN	_	_
181	over-expression	over-expression	NN	_	_	_
182	cells	cell	NNS	_	_	_
183	,	,	,	_	_	_
184	M9	m9	NN	_	_	_
185	,	,	,	_	_	_
186	8	8	CD	_	_	_
187	h	h	NN	_	_	_
188	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
189	E.	E.	NNP	_	_	_
190	coli	coli	NN	_	_	_
191	K12	k12	NN	_	_	_
192	_	_	CD	_	_	_
193	ybjN	ybjn	NN	GEN	_	_
194	_	_	NN	_	_	_
195	OVER-EXPRESSION	over-expression	NN	_	_	_
196	_	_	CD	_	_	_
197	M9	m9	NN	_	_	_
198	_	_	CD	_	_	_
199	rep1	rep1	NN	_	_	_
200	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
201	E.	E.	NNP	_	_	_
202	coli	coli	NN	_	_	_
203	K12	k12	NN	_	_	_
204	_	_	CD	_	_	_
205	ybjN	ybjn	NN	GEN	_	_
206	_	_	NN	_	_	_
207	OVER-EXPRESSION	over-expression	NN	_	_	_
208	_	_	CD	_	_	_
209	M9	m9	NN	_	_	_
210	_	_	CD	_	_	_
211	rep2	rep2	NN	_	_	_
212	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
213	E.	E.	NNP	_	_	_
214	coli	coli	NN	_	_	_
215	K12	k12	NN	_	_	_
216	_	_	CD	_	_	_
217	ybjN	ybjn	NN	GEN	_	_
218	_	_	NN	_	_	_
219	OVER-EXPRESSION	over-expression	NN	_	_	_
220	_	_	CD	_	_	_
221	M9	m9	NN	_	_	_
222	_	_	CD	_	_	_
223	rep3	rep3	NN	_	_	_
224	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
225	Ecoli	Ecoli	NNP	_	_	_
226	_	_	NNP	_	_	_
227	Kanamycin	Kanamycin	NNP	_	_	_
228	treatment	treatment	NN	_	_	_
229	T1	t1	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	Ecoli	ecolus	NNS	_	_	_
232	_	_	VBP	_	_	_
233	Kanamycin	kanamycin	NN	_	_	_
234	treatment	treatment	NN	_	_	_
235	T2	t2	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	Ecoli	ecolus	NNS	_	_	_
238	_	_	VBP	_	_	_
239	Kanamycin	kanamycin	NN	_	_	_
240	treatment	treatment	NN	_	_	_
241	T3	t3	NN	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	Ecoli	ecolus	NNS	_	_	_
244	_	_	VBP	_	_	_
245	Kanamycin	kanamycin	NN	_	_	_
246	treatment	treatment	NN	_	_	_
247	T4	t4	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	Ecoli	ecolus	NNS	_	_	_
250	_	_	VBP	_	_	_
251	Kanamycin	kanamycin	NN	_	_	_
252	treatment	treatment	NN	_	_	_
253	T5	t5	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	Ecoli	ecolus	NNS	_	_	_
256	_	_	VBP	_	_	_
257	Kanamycin	kanamycin	NN	_	_	_
258	treatment	treatment	NN	_	_	_
259	T6	t6	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	Ecoli	ecolus	NNS	_	_	_
262	_	_	VBP	_	_	_
263	ko	ko	NN	_	_	_
264	_	_	NN	_	_	_
265	arcA	arca	NN	GEN	_	_
266	_	_	NN	_	_	_
267	1	1	CD	_	_	_
268	%	%	NN	_	_	_
269	_	_	CD	_	_	_
270	isobutanol	isobutanol	NN	_	_	_
271	_	_	NN	_	_	_
272	Sample1	sample1	NN	_	_	_
273	_	_	CD	_	_	_
274	TechRep1	techrep1	NN	_	_	_
275	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
276	Ecoli	Ecoli	NNP	_	_	_
277	_	_	SYM	_	_	_
278	ko	ko	FW	_	_	_
279	_	_	FW	_	_	_
280	arcA	arca	NN	GEN	_	_
281	_	_	NN	_	_	_
282	1	1	CD	_	_	_
283	%	%	NN	_	_	_
284	_	_	CD	_	_	_
285	isobutanol	isobutanol	NN	_	_	_
286	_	_	NN	_	_	_
287	Sample1	sample1	NN	_	_	_
288	_	_	CD	_	_	_
289	TechRep2	techrep2	NN	_	_	_
290	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
291	Ecoli	Ecoli	NNP	_	_	_
292	_	_	SYM	_	_	_
293	ko	ko	FW	_	_	_
294	_	_	FW	_	_	_
295	arcA	arca	NN	GEN	_	_
296	_	_	NN	_	_	_
297	1	1	CD	_	_	_
298	%	%	NN	_	_	_
299	_	_	CD	_	_	_
300	isobutanol	isobutanol	NN	_	_	_
301	_	_	NN	_	_	_
302	Sample2	sample2	NN	_	_	_
303	_	_	CD	_	_	_
304	TechRep1	techrep1	NN	_	_	_
305	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
306	Ecoli	Ecoli	NNP	_	_	_
307	_	_	SYM	_	_	_
308	ko	ko	FW	_	_	_
309	_	_	FW	_	_	_
310	arcA	arca	NN	GEN	_	_
311	_	_	NN	_	_	_
312	1	1	CD	_	_	_
313	%	%	NN	_	_	_
314	_	_	CD	_	_	_
315	isobutanol	isobutanol	NN	_	_	_
316	_	_	NN	_	_	_
317	Sample2	sample2	NN	_	_	_
318	_	_	CD	_	_	_
319	TechRep2	techrep2	NN	_	_	_
320	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
321	Ecoli	Ecoli	NNP	_	_	_
322	_	_	SYM	_	_	_
323	ko	ko	FW	_	_	_
324	_	_	FW	_	_	_
325	arcA	arca	NN	GEN	_	_
326	_	_	NN	_	_	_
327	1	1	CD	_	_	_
328	%	%	NN	_	_	_
329	_	_	CD	_	_	_
330	isobutanol	isobutanol	NN	_	_	_
331	_	_	NN	_	_	_
332	Sample3	sample3	NN	_	_	_
333	_	_	CD	_	_	_
334	TechRep1	techrep1	NN	_	_	_
335	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
336	Ecoli	Ecoli	NNP	_	_	_
337	_	_	SYM	_	_	_
338	ko	ko	FW	_	_	_
339	_	_	FW	_	_	_
340	arcA	arca	NN	GEN	_	_
341	_	_	NN	_	_	_
342	1	1	CD	_	_	_
343	%	%	NN	_	_	_
344	_	_	CD	_	_	_
345	isobutanol	isobutanol	NN	_	_	_
346	_	_	NN	_	_	_
347	Sample3	sample3	NN	_	_	_
348	_	_	CD	_	_	_
349	TechRep2	techrep2	NN	_	_	_
350	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
351	Ecoli	Ecoli	NNP	_	_	_
352	_	_	SYM	_	_	_
353	ko	ko	FW	_	_	_
354	_	_	FW	_	_	_
355	arcA	arca	NN	GEN	_	_
356	_	_	NN	_	_	_
357	1	1	CD	_	_	_
358	%	%	NN	_	_	_
359	_	_	CD	_	_	_
360	isobutanol	isobutanol	NN	_	_	_
361	_	_	NN	_	_	_
362	Sample4	sample4	NN	_	_	_
363	_	_	CD	_	_	_
364	TechRep1	techrep1	NN	_	_	_
365	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
366	Ecoli	Ecoli	NNP	_	_	_
367	_	_	SYM	_	_	_
368	ko	ko	FW	_	_	_
369	_	_	FW	_	_	_
370	arcA	arca	NN	GEN	_	_
371	_	_	NN	_	_	_
372	1	1	CD	_	_	_
373	%	%	NN	_	_	_
374	_	_	CD	_	_	_
375	isobutanol	isobutanol	NN	_	_	_
376	_	_	NN	_	_	_
377	Sample4	sample4	NN	_	_	_
378	_	_	CD	_	_	_
379	TechRep2	techrep2	NN	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
381	Ecoli	ecoli	JJ	_	_	_
382	ko-arcA	ko-arca	NN	_	_	_
383	grown	grow	VBN	_	_	_
384	in	in	IN	_	_	_
385	MOPS	MOPS	NNP	MED	_	_
386	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
387	Ecoli	Ecoli	NNP	_	_	_
388	ko-arcA	ko-arcA	NNP	_	_	_
389	grown	grow	VBN	_	_	_
390	in	in	IN	_	_	_
391	MOPS	MOPS	NNP	MED	_	_
392	,	,	,	_	_	_
393	10	10	CD	_	_	_
394	minutes	minute	NNS	_	_	_
395	after	after	IN	_	_	_
396	1	1	CD	_	_	_
397	%	%	NN	_	_	_
398	isobutanol	isobutanol	NN	_	_	_
399	treatment	treatment	NN	_	_	_
400	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
401	Ecoli	Ecoli	NNP	_	_	_
402	_	_	SYM	_	_	_
403	ko	ko	FW	_	_	_
404	_	_	FW	_	_	_
405	fur	fur	NN	GEN	_	_
406	_	_	NN	_	_	_
407	1	1	CD	_	_	_
408	%	%	NN	_	_	_
409	_	_	CD	_	_	_
410	isobutanol	isobutanol	NN	_	_	_
411	_	_	NN	_	_	_
412	Sample1	sample1	NN	_	_	_
413	_	_	CD	_	_	_
414	TechRep1	techrep1	NN	_	_	_
415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
416	Ecoli	ecolus	NNS	_	_	_
417	_	_	VBP	_	_	_
418	ko	ko	NN	_	_	_
419	_	_	NN	_	_	_
420	fur	fur	NN	GEN	_	_
421	_	_	NN	_	_	_
422	1	1	CD	_	_	_
423	%	%	NN	_	_	_
424	_	_	CD	_	_	_
425	isobutanol	isobutanol	NN	_	_	_
426	_	_	NN	_	_	_
427	Sample1	sample1	NN	_	_	_
428	_	_	CD	_	_	_
429	TechRep2	techrep2	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	Ecoli	ecolus	NNS	_	_	_
432	_	_	VBP	_	_	_
433	ko	ko	NN	_	_	_
434	_	_	NN	_	_	_
435	fur	fur	NN	GEN	_	_
436	_	_	NN	_	_	_
437	1	1	CD	_	_	_
438	%	%	NN	_	_	_
439	_	_	CD	_	_	_
440	isobutanol	isobutanol	NN	_	_	_
441	_	_	SYM	_	_	_
442	Sample2	sample2	FW	_	_	_
443	_	_	FW	_	_	_
444	TechRep1	techrep1	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	Ecoli	ecolus	NNS	_	_	_
447	_	_	VBP	_	_	_
448	ko	ko	NN	_	_	_
449	_	_	NN	_	_	_
450	fur	fur	NN	GEN	_	_
451	_	_	NN	_	_	_
452	1	1	CD	_	_	_
453	%	%	NN	_	_	_
454	_	_	CD	_	_	_
455	isobutanol	isobutanol	NN	_	_	_
456	_	_	NN	_	_	_
457	Sample2	sample2	NN	_	_	_
458	_	_	CD	_	_	_
459	TechRep2	techrep2	NN	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	Ecoli	ecolus	NNS	_	_	_
462	_	_	VBP	_	_	_
463	ko	ko	NN	_	_	_
464	_	_	NN	_	_	_
465	fur	fur	NN	GEN	_	_
466	_	_	NN	_	_	_
467	1	1	CD	_	_	_
468	%	%	NN	_	_	_
469	_	_	CD	_	_	_
470	isobutanol	isobutanol	NN	_	_	_
471	_	_	SYM	_	_	_
472	Sample3	sample3	FW	_	_	_
473	_	_	FW	_	_	_
474	TechRep1	techrep1	NN	_	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
476	Ecoli	ecolus	NNS	_	_	_
477	_	_	VBP	_	_	_
478	ko	ko	NN	_	_	_
479	_	_	NN	_	_	_
480	fur	fur	NN	GEN	_	_
481	_	_	NN	_	_	_
482	1	1	CD	_	_	_
483	%	%	NN	_	_	_
484	_	_	CD	_	_	_
485	isobutanol	isobutanol	NN	_	_	_
486	_	_	SYM	_	_	_
487	Sample3	sample3	FW	_	_	_
488	_	_	FW	_	_	_
489	TechRep2	techrep2	NN	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	Ecoli	ecolus	NNS	_	_	_
492	_	_	VBP	_	_	_
493	ko	ko	NN	_	_	_
494	_	_	NN	_	_	_
495	fur	fur	NN	GEN	_	_
496	_	_	NN	_	_	_
497	1	1	CD	_	_	_
498	%	%	NN	_	_	_
499	_	_	CD	_	_	_
500	isobutanol	isobutanol	NN	_	_	_
501	_	_	NN	_	_	_
502	Sample4	sample4	NN	_	_	_
503	_	_	CD	_	_	_
504	TechRep1	techrep1	NN	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	Ecoli	ecolus	NNS	_	_	_
507	_	_	VBP	_	_	_
508	ko	ko	NN	_	_	_
509	_	_	NN	_	_	_
510	fur	fur	NN	GEN	_	_
511	_	_	NN	_	_	_
512	1	1	CD	_	_	_
513	%	%	NN	_	_	_
514	_	_	CD	_	_	_
515	isobutanol	isobutanol	NN	_	_	_
516	_	_	NN	_	_	_
517	Sample4	sample4	NN	_	_	_
518	_	_	CD	_	_	_
519	TechRep2	techrep2	NN	_	_	_
520	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
521	Ecoli	ecoli	JJ	_	_	_
522	ko-fur	ko-fur	JJ	_	_	_
523	grown	grow	VBN	_	_	_
524	in	in	IN	_	_	_
525	MOPS	MOPS	NNP	MED	_	_
526	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
527	Ecoli	Ecoli	NNP	_	_	_
528	ko-fur	ko-fur	JJ	_	_	_
529	grown	grow	VBN	_	_	_
530	in	in	IN	_	_	_
531	MOPS	MOPS	NNP	MED	_	_
532	,	,	,	_	_	_
533	10	10	CD	_	_	_
534	minutes	minute	NNS	_	_	_
535	after	after	IN	_	_	_
536	1	1	CD	_	_	_
537	%	%	NN	_	_	_
538	isobutanol	isobutanol	NN	_	_	_
539	treatment	treatment	NN	_	_	_
540	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
541	Ecoli	Ecoli	NNP	_	_	_
542	ko-furgrown	ko-furgrown	NN	_	_	_
543	in	in	IN	_	_	_
544	MOPS	MOPS	NNP	MED	_	_
545	,	,	,	_	_	_
546	10	10	CD	_	_	_
547	minutes	minute	NNS	_	_	_
548	after	after	IN	_	_	_
549	1	1	CD	_	_	_
550	%	%	NN	_	_	_
551	isobutanol	isobutanol	NN	_	_	_
552	treatment	treatment	NN	_	_	_
553	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
554	Ecoli	Ecoli	NNP	_	_	_
555	_	_	SYM	_	_	_
556	ko	ko	FW	_	_	_
557	_	_	FW	_	_	_
558	ihfA	ihfa	NN	GEN	_	_
559	_	_	NN	_	_	_
560	1	1	CD	_	_	_
561	%	%	NN	_	_	_
562	_	_	CD	_	_	_
563	isobutanol	isobutanol	NN	_	_	_
564	_	_	NN	_	_	_
565	Sample1	sample1	NN	_	_	_
566	_	_	CD	_	_	_
567	TechRep1	techrep1	NN	_	_	_
568	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
569	Ecoli	Ecoli	NNP	_	_	_
570	_	_	SYM	_	_	_
571	ko	ko	FW	_	_	_
572	_	_	FW	_	_	_
573	ihfA	ihfa	NN	GEN	_	_
574	_	_	NN	_	_	_
575	1	1	CD	_	_	_
576	%	%	NN	_	_	_
577	_	_	CD	_	_	_
578	isobutanol	isobutanol	NN	_	_	_
579	_	_	NN	_	_	_
580	Sample1	sample1	NN	_	_	_
581	_	_	CD	_	_	_
582	TechRep2	techrep2	NN	_	_	_
583	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
584	Ecoli	Ecoli	NNP	_	_	_
585	_	_	SYM	_	_	_
586	ko	ko	FW	_	_	_
587	_	_	FW	_	_	_
588	ihfA	ihfa	NN	GEN	_	_
589	_	_	NN	_	_	_
590	1	1	CD	_	_	_
591	%	%	NN	_	_	_
592	_	_	CD	_	_	_
593	isobutanol	isobutanol	NN	_	_	_
594	_	_	NN	_	_	_
595	Sample2	sample2	NN	_	_	_
596	_	_	CD	_	_	_
597	TechRep1	techrep1	NN	_	_	_
598	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
599	Ecoli	Ecoli	NNP	_	_	_
600	_	_	SYM	_	_	_
601	ko	ko	FW	_	_	_
602	_	_	FW	_	_	_
603	ihfA	ihfa	NN	GEN	_	_
604	_	_	NN	_	_	_
605	1	1	CD	_	_	_
606	%	%	NN	_	_	_
607	_	_	CD	_	_	_
608	isobutanol	isobutanol	NN	_	_	_
609	_	_	NN	_	_	_
610	Sample2	sample2	NN	_	_	_
611	_	_	CD	_	_	_
612	TechRep2	techrep2	NN	_	_	_
613	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
614	Ecoli	Ecoli	NNP	_	_	_
615	_	_	SYM	_	_	_
616	ko	ko	FW	_	_	_
617	_	_	FW	_	_	_
618	ihfA	ihfa	NN	GEN	_	_
619	_	_	NN	_	_	_
620	1	1	CD	_	_	_
621	%	%	NN	_	_	_
622	_	_	CD	_	_	_
623	isobutanol	isobutanol	NN	_	_	_
624	_	_	NN	_	_	_
625	Sample3	sample3	NN	_	_	_
626	_	_	CD	_	_	_
627	TechRep1	techrep1	NN	_	_	_
628	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
629	Ecoli	Ecoli	NNP	_	_	_
630	_	_	SYM	_	_	_
631	ko	ko	FW	_	_	_
632	_	_	FW	_	_	_
633	ihfA	ihfa	NN	GEN	_	_
634	_	_	NN	_	_	_
635	1	1	CD	_	_	_
636	%	%	NN	_	_	_
637	_	_	CD	_	_	_
638	isobutanol	isobutanol	NN	_	_	_
639	_	_	NN	_	_	_
640	Sample3	sample3	NN	_	_	_
641	_	_	CD	_	_	_
642	TechRep2	techrep2	NN	_	_	_
643	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
644	Ecoli	Ecoli	NNP	_	_	_
645	_	_	SYM	_	_	_
646	ko	ko	FW	_	_	_
647	_	_	FW	_	_	_
648	ihfA	ihfa	NN	GEN	_	_
649	_	_	NN	_	_	_
650	1	1	CD	_	_	_
651	%	%	NN	_	_	_
652	_	_	CD	_	_	_
653	isobutanol	isobutanol	NN	_	_	_
654	_	_	NN	_	_	_
655	Sample4	sample4	NN	_	_	_
656	_	_	CD	_	_	_
657	TechRep1	techrep1	NN	_	_	_
658	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
659	Ecoli	Ecoli	NNP	_	_	_
660	_	_	SYM	_	_	_
661	ko	ko	FW	_	_	_
662	_	_	FW	_	_	_
663	ihfA	ihfa	NN	GEN	_	_
664	_	_	NN	_	_	_
665	1	1	CD	_	_	_
666	%	%	NN	_	_	_
667	_	_	CD	_	_	_
668	isobutanol	isobutanol	NN	_	_	_
669	_	_	NN	_	_	_
670	Sample4	sample4	NN	_	_	_
671	_	_	CD	_	_	_
672	TechRep2	techrep2	NN	_	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
674	Ecoli	ecoli	JJ	_	_	_
675	ko-ihfA	ko-ihfa	NN	_	_	_
676	grown	grow	VBN	_	_	_
677	in	in	IN	_	_	_
678	MOPS	MOPS	NNP	MED	_	_
679	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
680	Ecoli	Ecoli	NNP	_	_	_
681	ko-ihfA	ko-ihfA	NNP	_	_	_
682	grown	grow	VBN	_	_	_
683	in	in	IN	_	_	_
684	MOPS	MOPS	NNP	MED	_	_
685	,	,	,	_	_	_
686	10	10	CD	_	_	_
687	minutes	minute	NNS	_	_	_
688	after	after	IN	_	_	_
689	1	1	CD	_	_	_
690	%	%	NN	_	_	_
691	isobutanol	isobutanol	NN	_	_	_
692	treatment	treatment	NN	_	_	_
693	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
694	Ecoli	Ecoli	NNP	_	_	_
695	_	_	SYM	_	_	_
696	ko	ko	FW	_	_	_
697	_	_	FW	_	_	_
698	phoB	phob	NN	GEN	_	_
699	_	_	NN	_	_	_
700	1	1	CD	_	_	_
701	%	%	NN	_	_	_
702	_	_	CD	_	_	_
703	isobutanol	isobutanol	NN	_	_	_
704	_	_	NN	_	_	_
705	Sample1	sample1	NN	_	_	_
706	_	_	CD	_	_	_
707	TechRep1	techrep1	NN	_	_	_
708	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
709	Ecoli	Ecoli	NNP	_	_	_
710	_	_	SYM	_	_	_
711	ko	ko	FW	_	_	_
712	_	_	FW	_	_	_
713	phoB	phob	NN	GEN	_	_
714	_	_	NN	_	_	_
715	1	1	CD	_	_	_
716	%	%	NN	_	_	_
717	_	_	CD	_	_	_
718	isobutanol	isobutanol	NN	_	_	_
719	_	_	NN	_	_	_
720	Sample1	sample1	NN	_	_	_
721	_	_	CD	_	_	_
722	TechRep2	techrep2	NN	_	_	_
723	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
724	Ecoli	Ecoli	NNP	_	_	_
725	_	_	SYM	_	_	_
726	ko	ko	FW	_	_	_
727	_	_	FW	_	_	_
728	phoB	phob	NN	GEN	_	_
729	_	_	NN	_	_	_
730	1	1	CD	_	_	_
731	%	%	NN	_	_	_
732	_	_	CD	_	_	_
733	isobutanol	isobutanol	NN	_	_	_
734	_	_	NN	_	_	_
735	Sample2	sample2	NN	_	_	_
736	_	_	CD	_	_	_
737	TechRep1	techrep1	NN	_	_	_
738	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
739	Ecoli	Ecoli	NNP	_	_	_
740	_	_	SYM	_	_	_
741	ko	ko	FW	_	_	_
742	_	_	FW	_	_	_
743	phoB	phob	NN	GEN	_	_
744	_	_	NN	_	_	_
745	1	1	CD	_	_	_
746	%	%	NN	_	_	_
747	_	_	CD	_	_	_
748	isobutanol	isobutanol	NN	_	_	_
749	_	_	NN	_	_	_
750	Sample2	sample2	NN	_	_	_
751	_	_	CD	_	_	_
752	TechRep2	techrep2	NN	_	_	_
753	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
754	Ecoli	Ecoli	NNP	_	_	_
755	_	_	SYM	_	_	_
756	ko	ko	FW	_	_	_
757	_	_	FW	_	_	_
758	phoB	phob	NN	GEN	_	_
759	_	_	NN	_	_	_
760	1	1	CD	_	_	_
761	%	%	NN	_	_	_
762	_	_	CD	_	_	_
763	isobutanol	isobutanol	NN	_	_	_
764	_	_	NN	_	_	_
765	Sample3	sample3	NN	_	_	_
766	_	_	CD	_	_	_
767	TechRep1	techrep1	NN	_	_	_
768	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
769	Ecoli	Ecoli	NNP	_	_	_
770	_	_	SYM	_	_	_
771	ko	ko	FW	_	_	_
772	_	_	FW	_	_	_
773	phoB	phob	NN	GEN	_	_
774	_	_	NN	_	_	_
775	1	1	CD	_	_	_
776	%	%	NN	_	_	_
777	_	_	CD	_	_	_
778	isobutanol	isobutanol	NN	_	_	_
779	_	_	NN	_	_	_
780	Sample3	sample3	NN	_	_	_
781	_	_	CD	_	_	_
782	TechRep2	techrep2	NN	_	_	_
783	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
784	Ecoli	Ecoli	NNP	_	_	_
785	_	_	SYM	_	_	_
786	ko	ko	FW	_	_	_
787	_	_	FW	_	_	_
788	phoB	phob	NN	GEN	_	_
789	_	_	NN	_	_	_
790	1	1	CD	_	_	_
791	%	%	NN	_	_	_
792	_	_	CD	_	_	_
793	isobutanol	isobutanol	NN	_	_	_
794	_	_	NN	_	_	_
795	Sample4	sample4	NN	_	_	_
796	_	_	CD	_	_	_
797	TechRep1	techrep1	NN	_	_	_
798	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
799	Ecoli	Ecoli	NNP	_	_	_
800	_	_	SYM	_	_	_
801	ko	ko	FW	_	_	_
802	_	_	FW	_	_	_
803	phoB	phob	NN	GEN	_	_
804	_	_	NN	_	_	_
805	1	1	CD	_	_	_
806	%	%	NN	_	_	_
807	_	_	CD	_	_	_
808	isobutanol	isobutanol	NN	_	_	_
809	_	_	NN	_	_	_
810	Sample4	sample4	NN	_	_	_
811	_	_	CD	_	_	_
812	TechRep2	techrep2	NN	_	_	_
813	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
814	Ecoli	ecoli	JJ	_	_	_
815	ko-phoB	ko-phob	NN	_	_	_
816	grown	grow	VBN	_	_	_
817	in	in	IN	_	_	_
818	MOPS	MOPS	NNP	MED	_	_
819	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
820	Ecoli	Ecoli	NNP	_	_	_
821	ko-phoB	ko-phob	NN	_	_	_
822	grown	grow	VBN	_	_	_
823	in	in	IN	_	_	_
824	MOPS	MOPS	NNP	MED	_	_
825	,	,	,	_	_	_
826	10	10	CD	_	_	_
827	minutes	minute	NNS	_	_	_
828	after	after	IN	_	_	_
829	1	1	CD	_	_	_
830	%	%	NN	_	_	_
831	isobutanol	isobutanol	NN	_	_	_
832	treatment	treatment	NN	_	_	_
833	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
834	Ecoli	Ecoli	NNP	_	_	_
835	_	_	SYM	_	_	_
836	ko	ko	FW	_	_	_
837	_	_	FW	_	_	_
838	ubiE	ubie	NN	GEN	_	_
839	_	_	NN	_	_	_
840	1	1	CD	_	_	_
841	%	%	NN	_	_	_
842	_	_	CD	_	_	_
843	isobutanol	isobutanol	NN	_	_	_
844	_	_	NN	_	_	_
845	Sample1	sample1	NN	_	_	_
846	_	_	CD	_	_	_
847	TechRep1	techrep1	NN	_	_	_
848	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
849	Ecoli	Ecoli	NNP	_	_	_
850	_	_	SYM	_	_	_
851	ko	ko	FW	_	_	_
852	_	_	FW	_	_	_
853	ubiE	ubie	NN	GEN	_	_
854	_	_	NN	_	_	_
855	1	1	CD	_	_	_
856	%	%	NN	_	_	_
857	_	_	CD	_	_	_
858	isobutanol	isobutanol	NN	_	_	_
859	_	_	NN	_	_	_
860	Sample1	sample1	NN	_	_	_
861	_	_	CD	_	_	_
862	TechRep2	techrep2	NN	_	_	_
863	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
864	Ecoli	Ecoli	NNP	_	_	_
865	_	_	SYM	_	_	_
866	ko	ko	FW	_	_	_
867	_	_	FW	_	_	_
868	ubiE	ubie	NN	GEN	_	_
869	_	_	NN	_	_	_
870	1	1	CD	_	_	_
871	%	%	NN	_	_	_
872	_	_	CD	_	_	_
873	isobutanol	isobutanol	NN	_	_	_
874	_	_	SYM	_	_	_
875	Sample2	sample2	FW	_	_	_
876	_	_	FW	_	_	_
877	TechRep1	techrep1	NN	_	_	_
878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
879	Ecoli	ecolus	NNS	_	_	_
880	_	_	VBP	_	_	_
881	ko	ko	NN	_	_	_
882	_	_	NN	_	_	_
883	ubiE	ubie	NN	GEN	_	_
884	_	_	NN	_	_	_
885	1	1	CD	_	_	_
886	%	%	NN	_	_	_
887	_	_	CD	_	_	_
888	isobutanol	isobutanol	NN	_	_	_
889	_	_	NN	_	_	_
890	Sample2	sample2	NN	_	_	_
891	_	_	CD	_	_	_
892	TechRep2	techrep2	NN	_	_	_
893	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
894	Ecoli	ecoli	JJ	_	_	_
895	ko-ubiE	ko-ubie	NN	_	_	_
896	grown	grow	VBN	_	_	_
897	in	in	IN	_	_	_
898	MOPS	MOPS	NNP	MED	_	_
899	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
900	Ecoli	Ecoli	NNP	_	_	_
901	ko-ubiE	ko-ubiE	NNP	_	_	_
902	grown	grow	VBN	_	_	_
903	in	in	IN	_	_	_
904	MOPS	MOPS	NNP	MED	_	_
905	,	,	,	_	_	_
906	10	10	CD	_	_	_
907	minutes	minute	NNS	_	_	_
908	after	after	IN	_	_	_
909	1	1	CD	_	_	_
910	%	%	NN	_	_	_
911	isobutanol	isobutanol	NN	_	_	_
912	treatment	treatment	NN	_	_	_
913	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
914	Ecoli	Ecoli	NNP	_	_	_
915	_	_	NNP	_	_	_
916	Late	Late	NNP	_	_	_
917	Recovery	Recovery	NNP	_	_	_
918	in	in	IN	_	_	_
919	LB	LB	NNP	_	_	_
920	T1	t1	NN	_	_	_
921	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
922	Ecoli	Ecoli	NNP	_	_	_
923	_	_	NNP	_	_	_
924	Late	Late	NNP	_	_	_
925	Recovery	Recovery	NNP	_	_	_
926	in	in	IN	_	_	_
927	LB	LB	NNP	_	_	_
928	T2	t2	NN	_	_	_
929	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
930	Ecoli	Ecoli	NNP	_	_	_
931	_	_	NNP	_	_	_
932	Late	Late	NNP	_	_	_
933	Recovery	Recovery	NNP	_	_	_
934	in	in	IN	_	_	_
935	LB	LB	NNP	_	_	_
936	T3	t3	NN	_	_	_
937	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
938	Ecoli	Ecoli	NNP	_	_	_
939	_	_	NNP	_	_	_
940	Late	Late	NNP	_	_	_
941	Recovery	Recovery	NNP	_	_	_
942	in	in	IN	_	_	_
943	LB	LB	NNP	_	_	_
944	T4	t4	NN	_	_	_
945	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
946	Ecoli	Ecoli	NNP	_	_	_
947	_	_	NNP	_	_	_
948	Late	Late	NNP	_	_	_
949	Recovery	Recovery	NNP	_	_	_
950	in	in	IN	_	_	_
951	LB	LB	NNP	_	_	_
952	T5	T5	NNP	_	_	_
953	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
954	Ecoli	Ecoli	NNP	_	_	_
955	_	_	NNP	_	_	_
956	Late	Late	NNP	_	_	_
957	Recovery	Recovery	NNP	_	_	_
958	in	in	IN	_	_	_
959	LB	LB	NNP	_	_	_
960	T6	T6	NNP	_	_	_
961	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
962	Ecoli	Ecoli	NNP	_	_	_
963	_	_	NNP	_	_	_
964	Late	Late	NNP	_	_	_
965	Recovery	Recovery	NNP	_	_	_
966	in	in	IN	_	_	_
967	LB	LB	NNP	_	_	_
968	T7	T7	NNP	_	_	_
969	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
970	Ecoli	Ecoli	NNP	_	_	_
971	_	_	NNP	_	_	_
972	LB	LB	NNP	_	_	_
973	growth	growth	NN	_	_	_
974	T1	t1	NN	_	_	_
975	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
976	Ecoli	ecolus	NNS	_	_	_
977	_	_	VBP	_	_	_
978	LB	lb	NN	_	_	_
979	growth	growth	NN	_	_	_
980	T10	t10	NN	_	_	_
981	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
982	Ecoli	ecolus	NNS	_	_	_
983	_	_	VBP	_	_	_
984	LB	lb	NN	_	_	_
985	growth	growth	NN	_	_	_
986	T11	t11	NN	_	_	_
987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
988	Ecoli	ecolus	NNS	_	_	_
989	_	_	VBP	_	_	_
990	LB	lb	NN	_	_	_
991	growth	growth	NN	_	_	_
992	T2	t2	NN	_	_	_
993	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
994	Ecoli	ecolus	NNS	_	_	_
995	_	_	VBP	_	_	_
996	LB	lb	NN	_	_	_
997	growth	growth	NN	_	_	_
998	T3	t3	NN	_	_	_
999	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1000	Ecoli	ecolus	NNS	_	_	_
1001	_	_	VBP	_	_	_
1002	LB	lb	NN	_	_	_
1003	growth	growth	NN	_	_	_
1004	T4	t4	NN	_	_	_
1005	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1006	Ecoli	ecolus	NNS	_	_	_
1007	_	_	VBP	_	_	_
1008	LB	lb	NN	_	_	_
1009	growth	growth	NN	_	_	_
1010	T5	t5	NN	_	_	_
1011	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1012	Ecoli	ecolus	NNS	_	_	_
1013	_	_	VBP	_	_	_
1014	LB	lb	NN	_	_	_
1015	growth	growth	NN	_	_	_
1016	T6	t6	NN	_	_	_
1017	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1018	Ecoli	ecolus	NNS	_	_	_
1019	_	_	VBP	_	_	_
1020	LB	lb	NN	_	_	_
1021	growth	growth	NN	_	_	_
1022	T7	t7	NN	_	_	_
1023	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1024	Ecoli	ecolus	NNS	_	_	_
1025	_	_	VBP	_	_	_
1026	LB	lb	NN	_	_	_
1027	growth	growth	NN	_	_	_
1028	T8	t8	NN	_	_	_
1029	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1030	Ecoli	ecolus	NNS	_	_	_
1031	_	_	VBP	_	_	_
1032	LB	lb	NN	_	_	_
1033	growth	growth	NN	_	_	_
1034	T9	t9	NN	_	_	_
1035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1036	E.coli	e.coli	NNS	_	_	_
1037	_	_	VBP	_	_	_
1038	LB	lb	NN	_	_	_
1039	_	_	CD	_	_	_
1040	rep2	rep2	NN	_	_	_
1041	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1042	E.coli	e.coli	NNS	_	_	_
1043	_	_	VBP	_	_	_
1044	LB	lb	NN	_	_	_
1045	_	_	CD	_	_	_
1046	rep3	rep3	NN	_	_	_
1047	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1048	E.coli	e.coli	NNS	_	_	_
1049	_	_	VBP	_	_	_
1050	log	log	NN	_	_	_
1051	_	_	NN	_	_	_
1052	dynamic	dynamic	JJ	_	_	_
1053	_	_	NN	_	_	_
1054	1	1	CD	_	_	_
1055	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1056	E.coli	e.coli	NNS	_	_	_
1057	_	_	VBP	_	_	_
1058	log	log	NN	_	_	_
1059	_	_	NN	_	_	_
1060	dynamic	dynamic	JJ	_	_	_
1061	_	_	NN	_	_	_
1062	2	2	CD	_	_	_
1063	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1064	E.coli	e.coli	NNS	_	_	_
1065	_	_	VBP	_	_	_
1066	log	log	NN	_	_	_
1067	_	_	NN	_	_	_
1068	dynamic	dynamic	JJ	_	_	_
1069	_	_	NN	_	_	_
1070	3	3	CD	_	_	_
1071	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1072	E.coli	e.coli	NNS	_	_	_
1073	_	_	VBP	_	_	_
1074	log	log	NN	_	_	_
1075	_	_	SYM	_	_	_
1076	rif	rif	FW	_	_	_
1077	_	_	FW	_	_	_
1078	1	1	CD	_	_	_
1079	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1080	E.coli	e.coli	NNS	_	_	_
1081	_	_	VBP	_	_	_
1082	log	log	NN	_	_	_
1083	_	_	CD	_	_	_
1084	rif	rif	NN	_	_	_
1085	_	_	NN	_	_	_
1086	2	2	CD	_	_	_
1087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1088	E.coli	e.coli	NNS	_	_	_
1089	_	_	VBP	_	_	_
1090	log	log	NN	_	_	_
1091	_	_	SYM	_	_	_
1092	rif	rif	FW	_	_	_
1093	_	_	FW	_	_	_
1094	3	3	CD	_	_	_
1095	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1096	E.	E.	NNP	_	_	_
1097	Coli	Coli	NNP	_	_	_
1098	Lrp	Lrp	NNP	TF	_	_
1099	ChIP	chip	NN	_	_	_
1100	DNA	dna	NN	_	_	_
1101	Leucine	leucine	NN	_	_	_
1102	1	1	CD	_	_	_
1103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1104	E.	E.	NNP	_	_	_
1105	Coli	Coli	NNP	_	_	_
1106	Lrp	Lrp	NNP	TF	_	_
1107	ChIP	ChIP	NNP	_	_	_
1108	DNA	DNA	NNP	_	_	_
1109	Leucine	leucine	NN	_	_	_
1110	2	2	CD	_	_	_
1111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1112	E.	E.	NNP	_	_	_
1113	Coli	Coli	NNP	_	_	_
1114	Lrp	Lrp	NNP	TF	_	_
1115	ChIP	chip	NN	_	_	_
1116	DNA	dna	NN	_	_	_
1117	Leucine	leucine	NN	_	_	_
1118	3	3	CD	_	_	_
1119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1120	E.	E.	NNP	_	_	_
1121	Coli	Coli	NNP	_	_	_
1122	Lrp	Lrp	NNP	TF	_	_
1123	ChIP	ChIP	NNP	_	_	_
1124	DNA	DNA	NNP	_	_	_
1125	NH4Cl	nh4cl	NN	_	_	_
1126	1	1	CD	_	_	_
1127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1128	E.	E.	NNP	_	_	_
1129	Coli	Coli	NNP	_	_	_
1130	Lrp	Lrp	NNP	TF	_	_
1131	ChIP	ChIP	NNP	_	_	_
1132	DNA	DNA	NNP	_	_	_
1133	NH4Cl	nh4cl	NN	_	_	_
1134	2	2	CD	_	_	_
1135	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1136	E.	E.	NNP	_	_	_
1137	Coli	Coli	NNP	_	_	_
1138	Lrp	Lrp	NNP	TF	_	_
1139	ChIP	ChIP	NNP	_	_	_
1140	DNA	DNA	NNP	_	_	_
1141	NH4Cl	nh4cl	NN	_	_	_
1142	3	3	CD	_	_	_
1143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1144	E.	e.	FW	_	_	_
1145	coli	coli	FW	_	_	_
1146	MC4100	mc4100	NN	_	_	_
1147	strain	strain	NN	_	_	_
1148	was	be	VBD	_	_	_
1149	cultured	culture	VBN	_	_	_
1150	at	at	IN	_	_	_
1151	37	37	CD	_	_	_
1152	°C	°c	NN	_	_	_
1153	to	to	TO	_	_	_
1154	mid-log	mid-log	JJ	_	_	_
1155	phase	phase	NN	_	_	_
1156	-LRB-	-lrb-	-LRB-	_	_	_
1157	OD600	od600	NN	_	_	_
1158	~	~	NN	_	_	_
1159	0.4	0.4	CD	_	_	_
1160	-RRB-	-rrb-	-RRB-	_	_	_
1161	in	in	IN	_	_	_
1162	LB	lb	NN	MED	_	_
1163	media	media	NNS	MED	_	_
1164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1165	E.	e.	FW	_	_	_
1166	coli	coli	FW	_	_	_
1167	MDS42	mds42	NN	_	_	_
1168	,	,	,	_	_	_
1169	osmotic	osmotic	JJ	_	_	_
1170	pressure	pressure	NN	_	_	_
1171	NaCl	nacl	NN	_	_	_
1172	0.20	0.20	CD	_	_	_
1173	M	m	NN	_	_	_
1174	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1175	E.	e.	FW	_	_	_
1176	coli	coli	FW	_	_	_
1177	MDS42	mds42	NN	_	_	_
1178	,	,	,	_	_	_
1179	osmotic	osmotic	JJ	_	_	_
1180	pressure	pressure	NN	_	_	_
1181	,	,	,	_	_	_
1182	NaCl	nacl	NN	_	_	_
1183	0.20	0.20	CD	_	_	_
1184	M	m	NN	_	_	_
1185	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1186	E.	e.	FW	_	_	_
1187	coli	coli	FW	_	_	_
1188	MDS42	mds42	NN	_	_	_
1189	,	,	,	_	_	_
1190	osmotic	osmotic	JJ	_	_	_
1191	pressure	pressure	NN	_	_	_
1192	NaCl	nacl	NN	_	_	_
1193	0.20	0.20	CD	_	_	_
1194	M	m	NN	_	_	_
1195	,	,	,	_	_	_
1196	rep	rep	NN	GEN	_	_
1197	1	1	CD	_	_	_
1198	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1199	E.	E.	NNP	_	_	_
1200	coli	coli	NN	_	_	_
1201	MDS42	mds42	NN	_	_	_
1202	,	,	,	_	_	_
1203	osmotic	osmotic	JJ	_	_	_
1204	pressure	pressure	NN	_	_	_
1205	,	,	,	_	_	_
1206	NaCl	nacl	NN	_	_	_
1207	0.20	0.20	CD	_	_	_
1208	M	m	NN	_	_	_
1209	,	,	,	_	_	_
1210	rep	rep	NN	GEN	_	_
1211	2	2	CD	_	_	_
1212	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1213	E.	E.	NNP	_	_	_
1214	coli	coli	NN	_	_	_
1215	MDS42	mds42	NN	_	_	_
1216	,	,	,	_	_	_
1217	osmotic	osmotic	JJ	_	_	_
1218	pressure	pressure	NN	_	_	_
1219	,	,	,	_	_	_
1220	NaCl	nacl	NN	_	_	_
1221	0.20	0.20	CD	_	_	_
1222	M	m	NN	_	_	_
1223	,	,	,	_	_	_
1224	rep	rep	NN	GEN	_	_
1225	3	3	CD	_	_	_
1226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1227	E.	e.	FW	_	_	_
1228	coli	coli	FW	_	_	_
1229	MDS42	mds42	NN	_	_	_
1230	,	,	,	_	_	_
1231	osmotic	osmotic	JJ	_	_	_
1232	pressure	pressure	NN	_	_	_
1233	,	,	,	_	_	_
1234	NaCl	nacl	NN	_	_	_
1235	0.45	0.45	CD	_	_	_
1236	M	m	NN	_	_	_
1237	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1238	E.	e.	FW	_	_	_
1239	coli	coli	FW	_	_	_
1240	MDS42	mds42	NN	_	_	_
1241	,	,	,	_	_	_
1242	osmotic	osmotic	JJ	_	_	_
1243	pressure	pressure	NN	_	_	_
1244	,	,	,	_	_	_
1245	NaCl	nacl	NN	_	_	_
1246	0.45	0.45	CD	_	_	_
1247	M	m	NN	_	_	_
1248	,	,	,	_	_	_
1249	rep	rep	NN	GEN	_	_
1250	1	1	CD	_	_	_
1251	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1252	E.	E.	NNP	_	_	_
1253	coli	coli	NN	_	_	_
1254	MDS42	mds42	NN	_	_	_
1255	,	,	,	_	_	_
1256	osmotic	osmotic	JJ	_	_	_
1257	pressure	pressure	NN	_	_	_
1258	,	,	,	_	_	_
1259	NaCl	nacl	NN	_	_	_
1260	0.45	0.45	CD	_	_	_
1261	M	m	NN	_	_	_
1262	,	,	,	_	_	_
1263	rep	rep	NN	GEN	_	_
1264	2	2	CD	_	_	_
1265	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1266	E.	E.	NNP	_	_	_
1267	coli	coli	NN	_	_	_
1268	MDS42	mds42	NN	_	_	_
1269	,	,	,	_	_	_
1270	osmotic	osmotic	JJ	_	_	_
1271	pressure	pressure	NN	_	_	_
1272	,	,	,	_	_	_
1273	NaCl	nacl	NN	_	_	_
1274	0.45	0.45	CD	_	_	_
1275	M	m	NN	_	_	_
1276	,	,	,	_	_	_
1277	rep	rep	NN	GEN	_	_
1278	3	3	CD	_	_	_
1279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1280	E.	e.	FW	_	_	_
1281	coli	coli	FW	_	_	_
1282	MDS42	mds42	NN	_	_	_
1283	,	,	,	_	_	_
1284	osmotic	osmotic	JJ	_	_	_
1285	pressure	pressure	NN	_	_	_
1286	,	,	,	_	_	_
1287	NaCl	nacl	NN	_	_	_
1288	0.55	0.55	CD	_	_	_
1289	M	m	NN	_	_	_
1290	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1291	E.	e.	FW	_	_	_
1292	coli	coli	FW	_	_	_
1293	MDS42	mds42	NN	_	_	_
1294	,	,	,	_	_	_
1295	osmotic	osmotic	JJ	_	_	_
1296	pressure	pressure	NN	_	_	_
1297	,	,	,	_	_	_
1298	NaCl	nacl	NN	_	_	_
1299	0.55	0.55	CD	_	_	_
1300	M	m	NN	_	_	_
1301	,	,	,	_	_	_
1302	rep	rep	NN	GEN	_	_
1303	1	1	CD	_	_	_
1304	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1305	E.	E.	NNP	_	_	_
1306	coli	coli	NN	_	_	_
1307	MDS42	mds42	NN	_	_	_
1308	,	,	,	_	_	_
1309	osmotic	osmotic	JJ	_	_	_
1310	pressure	pressure	NN	_	_	_
1311	,	,	,	_	_	_
1312	NaCl	nacl	NN	_	_	_
1313	0.55	0.55	CD	_	_	_
1314	M	m	NN	_	_	_
1315	,	,	,	_	_	_
1316	rep	rep	NN	GEN	_	_
1317	2	2	CD	_	_	_
1318	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1319	E.	E.	NNP	_	_	_
1320	coli	coli	NN	_	_	_
1321	MDS42	mds42	NN	_	_	_
1322	,	,	,	_	_	_
1323	osmotic	osmotic	JJ	_	_	_
1324	pressure	pressure	NN	_	_	_
1325	,	,	,	_	_	_
1326	NaCl	nacl	NN	_	_	_
1327	0.55	0.55	CD	_	_	_
1328	M	m	NN	_	_	_
1329	,	,	,	_	_	_
1330	rep	rep	NN	GEN	_	_
1331	3	3	CD	_	_	_
1332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1333	E.	e.	FW	_	_	_
1334	coli	coli	FW	_	_	_
1335	MDS42	mds42	NN	_	_	_
1336	,	,	,	_	_	_
1337	regular	regular	JJ	_	_	_
1338	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1339	E.	e.	FW	_	_	_
1340	coli	coli	FW	_	_	_
1341	MDS42	mds42	NN	_	_	_
1342	,	,	,	_	_	_
1343	regular	regular	JJ	_	_	_
1344	,	,	,	_	_	_
1345	rep	rep	NN	GEN	_	_
1346	1	1	CD	_	_	_
1347	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1348	E.	E.	NNP	_	_	_
1349	coli	coli	NN	_	_	_
1350	MDS42	mds42	NN	_	_	_
1351	,	,	,	_	_	_
1352	regular	regular	JJ	_	_	_
1353	,	,	,	_	_	_
1354	rep	rep	NN	GEN	_	_
1355	2	2	CD	_	_	_
1356	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1357	E.	E.	NNP	_	_	_
1358	coli	coli	NN	_	_	_
1359	MDS42	mds42	NN	_	_	_
1360	,	,	,	_	_	_
1361	regular	regular	JJ	_	_	_
1362	,	,	,	_	_	_
1363	rep	rep	NN	GEN	_	_
1364	3	3	CD	_	_	_
1365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1366	E.	e.	FW	_	_	_
1367	coli	coli	FW	_	_	_
1368	MDS42	mds42	NN	_	_	_
1369	,	,	,	_	_	_
1370	starvation	starvation	NN	_	_	_
1371	,	,	,	_	_	_
1372	SHX	shx	NN	_	_	_
1373	100	100	CD	_	_	_
1374	ng/ml	ng/ml	NN	_	_	_
1375	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1376	E.	E.	NNP	_	_	_
1377	coli	coli	NN	_	_	_
1378	MDS42	mds42	NN	_	_	_
1379	,	,	,	_	_	_
1380	starvation	starvation	NN	_	_	_
1381	,	,	,	_	_	_
1382	SHX	shx	NN	_	_	_
1383	100	100	CD	_	_	_
1384	ng/ml	ng/ml	NN	_	_	_
1385	,	,	,	_	_	_
1386	rep	rep	NN	GEN	_	_
1387	1	1	CD	_	_	_
1388	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1389	E.	E.	NNP	_	_	_
1390	coli	coli	NN	_	_	_
1391	MDS42	mds42	NN	_	_	_
1392	,	,	,	_	_	_
1393	starvation	starvation	NN	_	_	_
1394	,	,	,	_	_	_
1395	SHX	shx	NN	_	_	_
1396	100	100	CD	_	_	_
1397	ng/ml	ng/ml	NN	_	_	_
1398	,	,	,	_	_	_
1399	rep	rep	NN	GEN	_	_
1400	2	2	CD	_	_	_
1401	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1402	E.	E.	NNP	_	_	_
1403	coli	coli	NN	_	_	_
1404	MDS42	mds42	NN	_	_	_
1405	,	,	,	_	_	_
1406	starvation	starvation	NN	_	_	_
1407	,	,	,	_	_	_
1408	SHX	shx	NN	_	_	_
1409	100	100	CD	_	_	_
1410	ng/ml	ng/ml	NN	_	_	_
1411	,	,	,	_	_	_
1412	rep	rep	NN	GEN	_	_
1413	3	3	CD	_	_	_
1414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1415	E.	e.	FW	_	_	_
1416	coli	coli	FW	_	_	_
1417	MDS42	mds42	NN	_	_	_
1418	,	,	,	_	_	_
1419	starvation	starvation	NN	_	_	_
1420	,	,	,	_	_	_
1421	SHX	shx	NN	_	_	_
1422	150	150	CD	_	_	_
1423	ng/ml	ng/ml	NN	_	_	_
1424	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1425	E.	E.	NNP	_	_	_
1426	coli	coli	NN	_	_	_
1427	MDS42	mds42	NN	_	_	_
1428	,	,	,	_	_	_
1429	starvation	starvation	NN	_	_	_
1430	,	,	,	_	_	_
1431	SHX	shx	NN	_	_	_
1432	150	150	CD	_	_	_
1433	ng/ml	ng/ml	NN	_	_	_
1434	,	,	,	_	_	_
1435	rep	rep	NN	GEN	_	_
1436	1	1	CD	_	_	_
1437	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1438	E.	E.	NNP	_	_	_
1439	coli	coli	NN	_	_	_
1440	MDS42	mds42	NN	_	_	_
1441	,	,	,	_	_	_
1442	starvation	starvation	NN	_	_	_
1443	,	,	,	_	_	_
1444	SHX	shx	NN	_	_	_
1445	150	150	CD	_	_	_
1446	ng/ml	ng/ml	NN	_	_	_
1447	,	,	,	_	_	_
1448	rep	rep	NN	GEN	_	_
1449	2	2	CD	_	_	_
1450	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1451	E.	E.	NNP	_	_	_
1452	coli	coli	NN	_	_	_
1453	MDS42	mds42	NN	_	_	_
1454	,	,	,	_	_	_
1455	starvation	starvation	NN	_	_	_
1456	,	,	,	_	_	_
1457	SHX	shx	NN	_	_	_
1458	150	150	CD	_	_	_
1459	ng/ml	ng/ml	NN	_	_	_
1460	,	,	,	_	_	_
1461	rep	rep	NN	GEN	_	_
1462	3	3	CD	_	_	_
1463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1464	E.	e.	FW	_	_	_
1465	coli	coli	FW	_	_	_
1466	MDS42	mds42	NN	_	_	_
1467	,	,	,	_	_	_
1468	starvation	starvation	NN	_	_	_
1469	,	,	,	_	_	_
1470	SHX	SHX	NNP	_	_	_
1471	50	50	CD	_	_	_
1472	ng/ml	ng/ml	NN	_	_	_
1473	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1474	E.	E.	NNP	_	_	_
1475	coli	coli	NN	_	_	_
1476	MDS42	mds42	NN	_	_	_
1477	,	,	,	_	_	_
1478	starvation	starvation	NN	_	_	_
1479	,	,	,	_	_	_
1480	SHX	SHX	NNP	_	_	_
1481	50	50	CD	_	_	_
1482	ng/ml	ng/ml	NN	_	_	_
1483	,	,	,	_	_	_
1484	rep	rep	NN	GEN	_	_
1485	1	1	CD	_	_	_
1486	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1487	E.	E.	NNP	_	_	_
1488	coli	coli	NN	_	_	_
1489	MDS42	mds42	NN	_	_	_
1490	,	,	,	_	_	_
1491	starvation	starvation	NN	_	_	_
1492	,	,	,	_	_	_
1493	SHX	SHX	NNP	_	_	_
1494	50	50	CD	_	_	_
1495	ng/ml	ng/ml	NN	_	_	_
1496	,	,	,	_	_	_
1497	rep	rep	NN	GEN	_	_
1498	2	2	CD	_	_	_
1499	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1500	E.	E.	NNP	_	_	_
1501	coli	coli	NN	_	_	_
1502	MDS42	mds42	NN	_	_	_
1503	,	,	,	_	_	_
1504	starvation	starvation	NN	_	_	_
1505	,	,	,	_	_	_
1506	SHX	SHX	NNP	_	_	_
1507	50	50	CD	_	_	_
1508	ng/ml	ng/ml	NN	_	_	_
1509	,	,	,	_	_	_
1510	rep	rep	NN	GEN	_	_
1511	3	3	CD	_	_	_
1512	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1513	E.	e.	FW	_	_	_
1514	coli	coli	FW	_	_	_
1515	MDS42	mds42	NN	_	_	_
1516	,	,	,	_	_	_
1517	temperature	temperature	NN	_	_	_
1518	change	change	NN	_	_	_
1519	,	,	,	_	_	_
1520	40.0	40.0	CD	_	_	_
1521	deg	deg	NN	_	_	_
1522	C	c	NN	_	_	_
1523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1524	E.	e.	FW	_	_	_
1525	coli	coli	FW	_	_	_
1526	MDS42	mds42	NN	_	_	_
1527	,	,	,	_	_	_
1528	temperature	temperature	NN	_	_	_
1529	change	change	NN	_	_	_
1530	,	,	,	_	_	_
1531	40.0	40.0	CD	_	_	_
1532	deg	deg	NN	_	_	_
1533	C	c	NN	_	_	_
1534	,	,	,	_	_	_
1535	rep	rep	NN	GEN	_	_
1536	1	1	CD	_	_	_
1537	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1538	E.	E.	NNP	_	_	_
1539	coli	coli	NN	_	_	_
1540	MDS42	mds42	NN	_	_	_
1541	,	,	,	_	_	_
1542	temperature	temperature	NN	_	_	_
1543	change	change	NN	_	_	_
1544	,	,	,	_	_	_
1545	40.0	40.0	CD	_	_	_
1546	deg	deg	NN	_	_	_
1547	C	c	NN	_	_	_
1548	,	,	,	_	_	_
1549	rep	rep	NN	GEN	_	_
1550	2	2	CD	_	_	_
1551	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1552	E.	E.	NNP	_	_	_
1553	coli	coli	NN	_	_	_
1554	MDS42	mds42	NN	_	_	_
1555	,	,	,	_	_	_
1556	temperature	temperature	NN	_	_	_
1557	change	change	NN	_	_	_
1558	,	,	,	_	_	_
1559	40.0	40.0	CD	_	_	_
1560	deg	deg	NN	_	_	_
1561	C	c	NN	_	_	_
1562	,	,	,	_	_	_
1563	rep	rep	NN	GEN	_	_
1564	3	3	CD	_	_	_
1565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1566	E.	e.	FW	_	_	_
1567	coli	coli	FW	_	_	_
1568	MDS42	mds42	NN	_	_	_
1569	,	,	,	_	_	_
1570	temperature	temperature	NN	_	_	_
1571	change	change	NN	_	_	_
1572	,	,	,	_	_	_
1573	41.5	41.5	CD	_	_	_
1574	deg	deg	NN	_	_	_
1575	C	c	NN	_	_	_
1576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1577	E.	e.	FW	_	_	_
1578	coli	coli	FW	_	_	_
1579	MDS42	mds42	NN	_	_	_
1580	,	,	,	_	_	_
1581	temperature	temperature	NN	_	_	_
1582	change	change	NN	_	_	_
1583	,	,	,	_	_	_
1584	41.5	41.5	CD	_	_	_
1585	deg	deg	NN	_	_	_
1586	C	c	NN	_	_	_
1587	,	,	,	_	_	_
1588	rep	rep	NN	GEN	_	_
1589	1	1	CD	_	_	_
1590	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1591	E.	E.	NNP	_	_	_
1592	coli	coli	NN	_	_	_
1593	MDS42	mds42	NN	_	_	_
1594	,	,	,	_	_	_
1595	temperature	temperature	NN	_	_	_
1596	change	change	NN	_	_	_
1597	,	,	,	_	_	_
1598	41.5	41.5	CD	_	_	_
1599	deg	deg	NN	_	_	_
1600	C	c	NN	_	_	_
1601	,	,	,	_	_	_
1602	rep	rep	NN	GEN	_	_
1603	2	2	CD	_	_	_
1604	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1605	E.	E.	NNP	_	_	_
1606	coli	coli	NN	_	_	_
1607	MDS42	mds42	NN	_	_	_
1608	,	,	,	_	_	_
1609	temperature	temperature	NN	_	_	_
1610	change	change	NN	_	_	_
1611	,	,	,	_	_	_
1612	41.5	41.5	CD	_	_	_
1613	deg	deg	NN	_	_	_
1614	C	c	NN	_	_	_
1615	,	,	,	_	_	_
1616	rep	rep	NN	GEN	_	_
1617	3	3	CD	_	_	_
1618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1619	E.	e.	FW	_	_	_
1620	coli	coli	FW	_	_	_
1621	MDS42	mds42	NN	_	_	_
1622	,	,	,	_	_	_
1623	temperature	temperature	NN	_	_	_
1624	change	change	NN	_	_	_
1625	,	,	,	_	_	_
1626	41.8	41.8	CD	_	_	_
1627	deg	deg	NN	_	_	_
1628	C	c	NN	_	_	_
1629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1630	E.	e.	FW	_	_	_
1631	coli	coli	FW	_	_	_
1632	MDS42	mds42	NN	_	_	_
1633	,	,	,	_	_	_
1634	temperature	temperature	NN	_	_	_
1635	change	change	NN	_	_	_
1636	,	,	,	_	_	_
1637	41.8	41.8	CD	_	_	_
1638	deg	deg	NN	_	_	_
1639	C	c	NN	_	_	_
1640	,	,	,	_	_	_
1641	rep	rep	NN	GEN	_	_
1642	1	1	CD	_	_	_
1643	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1644	E.	E.	NNP	_	_	_
1645	coli	coli	NN	_	_	_
1646	MDS42	mds42	NN	_	_	_
1647	,	,	,	_	_	_
1648	temperature	temperature	NN	_	_	_
1649	change	change	NN	_	_	_
1650	,	,	,	_	_	_
1651	41.8	41.8	CD	_	_	_
1652	deg	deg	NN	_	_	_
1653	C	c	NN	_	_	_
1654	,	,	,	_	_	_
1655	rep	rep	NN	GEN	_	_
1656	2	2	CD	_	_	_
1657	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1658	E.	E.	NNP	_	_	_
1659	coli	coli	NN	_	_	_
1660	MDS42	mds42	NN	_	_	_
1661	,	,	,	_	_	_
1662	temperature	temperature	NN	_	_	_
1663	change	change	NN	_	_	_
1664	,	,	,	_	_	_
1665	41.8	41.8	CD	_	_	_
1666	deg	deg	NN	_	_	_
1667	C	c	NN	_	_	_
1668	,	,	,	_	_	_
1669	rep	rep	NN	GEN	_	_
1670	3	3	CD	_	_	_
1671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1672	E.coli	e.coli	NNS	_	_	_
1673	MG1063	mg1063	NN	_	_	_
1674	-LRB-	-lrb-	-LRB-	_	_	_
1675	recA56	reca56	NN	_	_	_
1676	=	=	JJ	_	_	_
1677	recA	reca	NN	GEN	_	_
1678	-	-	:	_	_	_
1679	-RRB-	-rrb-	-RRB-	_	_	_
1680	with	with	IN	_	_	_
1681	ccdB	ccdb	NN	_	_	_
1682	upregulation	upregulation	NN	_	_	_
1683	0	0	CD	_	_	_
1684	minutes	minute	NNS	_	_	_
1685	after	after	IN	_	_	_
1686	induction	induction	NN	_	_	_
1687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1688	E.coli	e.coli	NN	_	_	_
1689	MG1063	mg1063	NN	_	_	_
1690	-LRB-	-lrb-	-LRB-	_	_	_
1691	recA56	reca56	NN	_	_	_
1692	=	=	JJ	_	_	_
1693	recA	reca	NN	GEN	_	_
1694	-	-	:	_	_	_
1695	-RRB-	-rrb-	-RRB-	_	_	_
1696	with	with	IN	_	_	_
1697	ccdB	ccdb	NN	_	_	_
1698	upregulation	upregulation	NN	_	_	_
1699	120	120	CD	_	_	_
1700	minutes	minute	NNS	_	_	_
1701	after	after	IN	_	_	_
1702	induction	induction	NN	_	_	_
1703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1704	E.coli	e.coli	NN	_	_	_
1705	MG1063	mg1063	NN	_	_	_
1706	-LRB-	-lrb-	-LRB-	_	_	_
1707	recA56	reca56	NN	_	_	_
1708	=	=	JJ	_	_	_
1709	recA	reca	NN	GEN	_	_
1710	-	-	:	_	_	_
1711	-RRB-	-rrb-	-RRB-	_	_	_
1712	with	with	IN	_	_	_
1713	ccdB	ccdb	NN	_	_	_
1714	upregulation	upregulation	NN	_	_	_
1715	30	30	CD	_	_	_
1716	minutes	minute	NNS	_	_	_
1717	after	after	IN	_	_	_
1718	induction	induction	NN	_	_	_
1719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1720	E.coli	e.coli	NN	_	_	_
1721	MG1063	mg1063	NN	_	_	_
1722	-LRB-	-lrb-	-LRB-	_	_	_
1723	recA56	reca56	NN	_	_	_
1724	=	=	JJ	_	_	_
1725	recA	reca	NN	GEN	_	_
1726	-	-	:	_	_	_
1727	-RRB-	-rrb-	-RRB-	_	_	_
1728	with	with	IN	_	_	_
1729	ccdB	ccdb	NN	_	_	_
1730	upregulation	upregulation	NN	_	_	_
1731	60	60	CD	_	_	_
1732	minutes	minute	NNS	_	_	_
1733	after	after	IN	_	_	_
1734	induction	induction	NN	_	_	_
1735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1736	E.coli	e.coli	NN	_	_	_
1737	MG1063	mg1063	NN	_	_	_
1738	-LRB-	-lrb-	-LRB-	_	_	_
1739	recA56	reca56	NN	_	_	_
1740	=	=	JJ	_	_	_
1741	recA	reca	NN	GEN	_	_
1742	-	-	:	_	_	_
1743	-RRB-	-rrb-	-RRB-	_	_	_
1744	with	with	IN	_	_	_
1745	ccdB	ccdb	NN	_	_	_
1746	upregulation	upregulation	NN	_	_	_
1747	90	90	CD	_	_	_
1748	minutes	minute	NNS	_	_	_
1749	after	after	IN	_	_	_
1750	induction	induction	NN	_	_	_
1751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1752	E.coli	e.coli	NN	_	_	_
1753	MG1063	mg1063	NN	_	_	_
1754	-LRB-	-lrb-	-LRB-	_	_	_
1755	recA56	reca56	NN	_	_	_
1756	=	=	JJ	_	_	_
1757	recA	reca	NN	GEN	_	_
1758	-	-	:	_	_	_
1759	-RRB-	-rrb-	-RRB-	_	_	_
1760	with	with	IN	_	_	_
1761	lacZ	lacz	NN	GEN	_	_
1762	upregulation	upregulation	NN	_	_	_
1763	0	0	CD	_	_	_
1764	minutes	minute	NNS	_	_	_
1765	after	after	IN	_	_	_
1766	induction	induction	NN	_	_	_
1767	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1768	E.coli	e.coli	NN	_	_	_
1769	MG1063	mg1063	NN	_	_	_
1770	-LRB-	-lrb-	-LRB-	_	_	_
1771	recA56	reca56	NN	_	_	_
1772	=	=	JJ	_	_	_
1773	recA	reca	NN	GEN	_	_
1774	-	-	:	_	_	_
1775	-RRB-	-rrb-	-RRB-	_	_	_
1776	with	with	IN	_	_	_
1777	lacZ	lacz	NN	GEN	_	_
1778	upregulation	upregulation	NN	_	_	_
1779	120	120	CD	_	_	_
1780	minutes	minute	NNS	_	_	_
1781	after	after	IN	_	_	_
1782	induction	induction	NN	_	_	_
1783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1784	E.coli	e.coli	NN	_	_	_
1785	MG1063	mg1063	NN	_	_	_
1786	-LRB-	-lrb-	-LRB-	_	_	_
1787	recA56	reca56	NN	_	_	_
1788	=	=	JJ	_	_	_
1789	recA	reca	NN	GEN	_	_
1790	-	-	:	_	_	_
1791	-RRB-	-rrb-	-RRB-	_	_	_
1792	with	with	IN	_	_	_
1793	lacZ	lacz	NN	GEN	_	_
1794	upregulation	upregulation	NN	_	_	_
1795	30	30	CD	_	_	_
1796	minutes	minute	NNS	_	_	_
1797	after	after	IN	_	_	_
1798	induction	induction	NN	_	_	_
1799	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1800	E.coli	e.coli	NN	_	_	_
1801	MG1063	mg1063	NN	_	_	_
1802	-LRB-	-lrb-	-LRB-	_	_	_
1803	recA56	reca56	NN	_	_	_
1804	=	=	JJ	_	_	_
1805	recA	reca	NN	GEN	_	_
1806	-	-	:	_	_	_
1807	-RRB-	-rrb-	-RRB-	_	_	_
1808	with	with	IN	_	_	_
1809	lacZ	lacz	NN	GEN	_	_
1810	upregulation	upregulation	NN	_	_	_
1811	60	60	CD	_	_	_
1812	minutes	minute	NNS	_	_	_
1813	after	after	IN	_	_	_
1814	induction	induction	NN	_	_	_
1815	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1816	E.coli	e.coli	NN	_	_	_
1817	MG1063	mg1063	NN	_	_	_
1818	-LRB-	-lrb-	-LRB-	_	_	_
1819	recA56	reca56	NN	_	_	_
1820	=	=	JJ	_	_	_
1821	recA	reca	NN	GEN	_	_
1822	-	-	:	_	_	_
1823	-RRB-	-rrb-	-RRB-	_	_	_
1824	with	with	IN	_	_	_
1825	lacZ	lacz	NN	GEN	_	_
1826	upregulation	upregulation	NN	_	_	_
1827	90	90	CD	_	_	_
1828	minutes	minute	NNS	_	_	_
1829	after	after	IN	_	_	_
1830	induction	induction	NN	_	_	_
1831	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1832	E.	E.	NNP	_	_	_
1833	coli	coli	NN	_	_	_
1834	MG1655	mg1655	NN	_	_	_
1835	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1836	E.	e.	FW	_	_	_
1837	coli	coli	FW	_	_	_
1838	MG1655	mg1655	NN	_	_	_
1839	10	10	CD	_	_	_
1840	min	min	NN	_	_	_
1841	after	after	IN	_	_	_
1842	TMP	tmp	NN	_	_	_
1843	+	+	CC	_	_	_
1844	adenine	adenine	NN	_	_	_
1845	+	+	CC	_	_	_
1846	glycine	glycine	NN	_	_	_
1847	+	+	CC	_	_	_
1848	methionine	methionine	NN	SUPP	_	_
1849	treatment	treatment	NN	_	_	_
1850	in	in	IN	_	_	_
1851	M9	m9	NN	_	_	_
1852	media	media	NNS	_	_	_
1853	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1854	E.	e.	FW	_	_	_
1855	coli	coli	FW	_	_	_
1856	MG1655	mg1655	NN	_	_	_
1857	10	10	CD	_	_	_
1858	min	min	NN	_	_	_
1859	after	after	IN	_	_	_
1860	TMP	tmp	NN	_	_	_
1861	+	+	CC	_	_	_
1862	adenine	adenine	NN	_	_	_
1863	treatment	treatment	NN	_	_	_
1864	in	in	IN	_	_	_
1865	M9	m9	NN	_	_	_
1866	media	media	NNS	_	_	_
1867	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1868	E.	e.	FW	_	_	_
1869	coli	coli	FW	_	_	_
1870	MG1655	mg1655	NN	_	_	_
1871	10	10	CD	_	_	_
1872	min	min	NN	_	_	_
1873	after	after	IN	_	_	_
1874	TMP	tmp	NN	_	_	_
1875	+	+	CC	_	_	_
1876	glycine	glycine	NN	_	_	_
1877	+	+	CC	_	_	_
1878	methionine	methionine	NN	SUPP	_	_
1879	treatment	treatment	NN	_	_	_
1880	in	in	IN	_	_	_
1881	M9	m9	NN	_	_	_
1882	media	media	NNS	_	_	_
1883	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1884	E.	e.	FW	_	_	_
1885	coli	coli	FW	_	_	_
1886	MG1655	mg1655	NN	_	_	_
1887	10	10	CD	_	_	_
1888	min	min	NN	_	_	_
1889	after	after	IN	_	_	_
1890	TMP	tmp	NN	_	_	_
1891	+	+	CC	_	_	_
1892	thymine	thymine	NN	_	_	_
1893	+	+	CC	_	_	_
1894	adenine	adenine	NN	_	_	_
1895	+	+	CC	_	_	_
1896	glycine	glycine	NN	_	_	_
1897	+	+	CC	_	_	_
1898	methionine	methionine	NN	SUPP	_	_
1899	treatment	treatment	NN	_	_	_
1900	in	in	IN	_	_	_
1901	M9	m9	NN	_	_	_
1902	media	media	NNS	_	_	_
1903	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1904	E.	e.	FW	_	_	_
1905	coli	coli	FW	_	_	_
1906	MG1655	mg1655	NN	_	_	_
1907	10	10	CD	_	_	_
1908	min	min	NN	_	_	_
1909	after	after	IN	_	_	_
1910	TMP	tmp	NN	_	_	_
1911	treatment	treatment	NN	_	_	_
1912	in	in	IN	_	_	_
1913	LB	LB	NNP	MED	_	_
1914	media	media	NNS	MED	_	_
1915	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1916	E.	e.	FW	_	_	_
1917	coli	coli	FW	_	_	_
1918	MG1655	mg1655	NN	_	_	_
1919	10	10	CD	_	_	_
1920	min	min	NN	_	_	_
1921	after	after	IN	_	_	_
1922	TMP	tmp	NN	_	_	_
1923	treatment	treatment	NN	_	_	_
1924	in	in	IN	_	_	_
1925	M9	m9	NN	_	_	_
1926	media	media	NNS	_	_	_
1927	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1928	E.	e.	FW	_	_	_
1929	coli	coli	FW	_	_	_
1930	MG1655	mg1655	NN	_	_	_
1931	120	120	CD	_	_	_
1932	min	min	NN	_	_	_
1933	after	after	IN	_	_	_
1934	TMP	tmp	NN	_	_	_
1935	+	+	CC	_	_	_
1936	adenine	adenine	NN	_	_	_
1937	+	+	CC	_	_	_
1938	glycine	glycine	NN	_	_	_
1939	+	+	CC	_	_	_
1940	methionine	methionine	NN	SUPP	_	_
1941	treatment	treatment	NN	_	_	_
1942	in	in	IN	_	_	_
1943	M9	m9	NN	_	_	_
1944	media	media	NNS	_	_	_
1945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1946	E.	e.	FW	_	_	_
1947	coli	coli	FW	_	_	_
1948	MG1655	mg1655	NN	_	_	_
1949	120	120	CD	_	_	_
1950	min	min	NN	_	_	_
1951	after	after	IN	_	_	_
1952	TMP	tmp	NN	_	_	_
1953	+	+	CC	_	_	_
1954	adenine	adenine	NN	_	_	_
1955	treatment	treatment	NN	_	_	_
1956	in	in	IN	_	_	_
1957	M9	m9	NN	_	_	_
1958	media	media	NNS	_	_	_
1959	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1960	E.	e.	FW	_	_	_
1961	coli	coli	FW	_	_	_
1962	MG1655	mg1655	NN	_	_	_
1963	120	120	CD	_	_	_
1964	min	min	NN	_	_	_
1965	after	after	IN	_	_	_
1966	TMP	tmp	NN	_	_	_
1967	+	+	CC	_	_	_
1968	glycine	glycine	NN	_	_	_
1969	+	+	CC	_	_	_
1970	methionine	methionine	NN	SUPP	_	_
1971	treatment	treatment	NN	_	_	_
1972	in	in	IN	_	_	_
1973	M9	m9	NN	_	_	_
1974	media	media	NNS	_	_	_
1975	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1976	E.	e.	FW	_	_	_
1977	coli	coli	FW	_	_	_
1978	MG1655	mg1655	NN	_	_	_
1979	120	120	CD	_	_	_
1980	min	min	NN	_	_	_
1981	after	after	IN	_	_	_
1982	TMP	tmp	NN	_	_	_
1983	+	+	CC	_	_	_
1984	thymine	thymine	NN	_	_	_
1985	+	+	CC	_	_	_
1986	adenine	adenine	NN	_	_	_
1987	+	+	CC	_	_	_
1988	glycine	glycine	NN	_	_	_
1989	+	+	CC	_	_	_
1990	methionine	methionine	NN	SUPP	_	_
1991	treatment	treatment	NN	_	_	_
1992	in	in	IN	_	_	_
1993	M9	m9	NN	_	_	_
1994	media	media	NNS	_	_	_
1995	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1996	E.	e.	FW	_	_	_
1997	coli	coli	FW	_	_	_
1998	MG1655	mg1655	NN	_	_	_
1999	120	120	CD	_	_	_
2000	min	min	NN	_	_	_
2001	after	after	IN	_	_	_
2002	TMP	tmp	NN	_	_	_
2003	treatment	treatment	NN	_	_	_
2004	in	in	IN	_	_	_
2005	LB	LB	NNP	MED	_	_
2006	media	media	NNS	MED	_	_
2007	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2008	E.	e.	FW	_	_	_
2009	coli	coli	FW	_	_	_
2010	MG1655	mg1655	NN	_	_	_
2011	120	120	CD	_	_	_
2012	min	min	NN	_	_	_
2013	after	after	IN	_	_	_
2014	TMP	tmp	NN	_	_	_
2015	treatment	treatment	NN	_	_	_
2016	in	in	IN	_	_	_
2017	M9	m9	NN	_	_	_
2018	media	media	NNS	_	_	_
2019	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2020	E.	e.	FW	_	_	_
2021	coli	coli	FW	_	_	_
2022	MG1655	mg1655	NN	_	_	_
2023	30	30	CD	_	_	_
2024	min	min	NN	_	_	_
2025	after	after	IN	_	_	_
2026	TMP	tmp	NN	_	_	_
2027	+	+	CC	_	_	_
2028	adenine	adenine	NN	_	_	_
2029	+	+	CC	_	_	_
2030	glycine	glycine	NN	_	_	_
2031	+	+	CC	_	_	_
2032	methionine	methionine	NN	SUPP	_	_
2033	treatment	treatment	NN	_	_	_
2034	in	in	IN	_	_	_
2035	M9	m9	NN	_	_	_
2036	media	media	NNS	_	_	_
2037	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2038	E.	e.	FW	_	_	_
2039	coli	coli	FW	_	_	_
2040	MG1655	mg1655	NN	_	_	_
2041	30	30	CD	_	_	_
2042	min	min	NN	_	_	_
2043	after	after	IN	_	_	_
2044	TMP	tmp	NN	_	_	_
2045	+	+	CC	_	_	_
2046	adenine	adenine	NN	_	_	_
2047	treatment	treatment	NN	_	_	_
2048	in	in	IN	_	_	_
2049	M9	m9	NN	_	_	_
2050	media	media	NNS	_	_	_
2051	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2052	E.	e.	FW	_	_	_
2053	coli	coli	FW	_	_	_
2054	MG1655	mg1655	NN	_	_	_
2055	30	30	CD	_	_	_
2056	min	min	NN	_	_	_
2057	after	after	IN	_	_	_
2058	TMP	tmp	NN	_	_	_
2059	+	+	CC	_	_	_
2060	glycine	glycine	NN	_	_	_
2061	+	+	CC	_	_	_
2062	methionine	methionine	NN	SUPP	_	_
2063	treatment	treatment	NN	_	_	_
2064	in	in	IN	_	_	_
2065	M9	m9	NN	_	_	_
2066	media	media	NNS	_	_	_
2067	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2068	E.	e.	FW	_	_	_
2069	coli	coli	FW	_	_	_
2070	MG1655	mg1655	NN	_	_	_
2071	30	30	CD	_	_	_
2072	min	min	NN	_	_	_
2073	after	after	IN	_	_	_
2074	TMP	tmp	NN	_	_	_
2075	+	+	CC	_	_	_
2076	thymine	thymine	NN	_	_	_
2077	+	+	CC	_	_	_
2078	adenine	adenine	NN	_	_	_
2079	+	+	CC	_	_	_
2080	glycine	glycine	NN	_	_	_
2081	+	+	CC	_	_	_
2082	methionine	methionine	NN	SUPP	_	_
2083	treatment	treatment	NN	_	_	_
2084	in	in	IN	_	_	_
2085	M9	m9	NN	_	_	_
2086	media	media	NNS	_	_	_
2087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2088	E.	e.	FW	_	_	_
2089	coli	coli	FW	_	_	_
2090	MG1655	mg1655	NN	_	_	_
2091	30	30	CD	_	_	_
2092	min	min	NN	_	_	_
2093	after	after	IN	_	_	_
2094	TMP	tmp	NN	_	_	_
2095	treatment	treatment	NN	_	_	_
2096	in	in	IN	_	_	_
2097	LB	LB	NNP	MED	_	_
2098	media	media	NNS	MED	_	_
2099	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2100	E.	e.	FW	_	_	_
2101	coli	coli	FW	_	_	_
2102	MG1655	mg1655	NN	_	_	_
2103	30	30	CD	_	_	_
2104	min	min	NN	_	_	_
2105	after	after	IN	_	_	_
2106	TMP	tmp	NN	_	_	_
2107	treatment	treatment	NN	_	_	_
2108	in	in	IN	_	_	_
2109	M9	m9	NN	_	_	_
2110	media	media	NNS	_	_	_
2111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2112	E.	e.	FW	_	_	_
2113	coli	coli	FW	_	_	_
2114	MG1655	mg1655	NN	_	_	_
2115	60	60	CD	_	_	_
2116	min	min	NN	_	_	_
2117	after	after	IN	_	_	_
2118	TMP	tmp	NN	_	_	_
2119	+	+	CC	_	_	_
2120	adenine	adenine	NN	_	_	_
2121	+	+	CC	_	_	_
2122	glycine	glycine	NN	_	_	_
2123	+	+	CC	_	_	_
2124	methionine	methionine	NN	SUPP	_	_
2125	treatment	treatment	NN	_	_	_
2126	in	in	IN	_	_	_
2127	M9	m9	NN	_	_	_
2128	media	media	NNS	_	_	_
2129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2130	E.	e.	FW	_	_	_
2131	coli	coli	FW	_	_	_
2132	MG1655	mg1655	NN	_	_	_
2133	60	60	CD	_	_	_
2134	min	min	NN	_	_	_
2135	after	after	IN	_	_	_
2136	TMP	tmp	NN	_	_	_
2137	+	+	CC	_	_	_
2138	adenine	adenine	NN	_	_	_
2139	treatment	treatment	NN	_	_	_
2140	in	in	IN	_	_	_
2141	M9	m9	NN	_	_	_
2142	media	media	NNS	_	_	_
2143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2144	E.	e.	FW	_	_	_
2145	coli	coli	FW	_	_	_
2146	MG1655	mg1655	NN	_	_	_
2147	60	60	CD	_	_	_
2148	min	min	NN	_	_	_
2149	after	after	IN	_	_	_
2150	TMP	tmp	NN	_	_	_
2151	+	+	CC	_	_	_
2152	glycine	glycine	NN	_	_	_
2153	+	+	CC	_	_	_
2154	methionine	methionine	NN	SUPP	_	_
2155	treatment	treatment	NN	_	_	_
2156	in	in	IN	_	_	_
2157	M9	m9	NN	_	_	_
2158	media	media	NNS	_	_	_
2159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2160	E.	e.	FW	_	_	_
2161	coli	coli	FW	_	_	_
2162	MG1655	mg1655	NN	_	_	_
2163	60	60	CD	_	_	_
2164	min	min	NN	_	_	_
2165	after	after	IN	_	_	_
2166	TMP	tmp	NN	_	_	_
2167	+	+	CC	_	_	_
2168	thymine	thymine	NN	_	_	_
2169	+	+	CC	_	_	_
2170	adenine	adenine	NN	_	_	_
2171	+	+	CC	_	_	_
2172	glycine	glycine	NN	_	_	_
2173	+	+	CC	_	_	_
2174	methionine	methionine	NN	SUPP	_	_
2175	treatment	treatment	NN	_	_	_
2176	in	in	IN	_	_	_
2177	M9	m9	NN	_	_	_
2178	media	media	NNS	_	_	_
2179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2180	E.	e.	FW	_	_	_
2181	coli	coli	FW	_	_	_
2182	MG1655	mg1655	NN	_	_	_
2183	60	60	CD	_	_	_
2184	min	min	NN	_	_	_
2185	after	after	IN	_	_	_
2186	TMP	tmp	NN	_	_	_
2187	treatment	treatment	NN	_	_	_
2188	in	in	IN	_	_	_
2189	LB	LB	NNP	MED	_	_
2190	media	media	NNS	MED	_	_
2191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2192	E.	e.	FW	_	_	_
2193	coli	coli	FW	_	_	_
2194	MG1655	mg1655	NN	_	_	_
2195	60	60	CD	_	_	_
2196	min	min	NN	_	_	_
2197	after	after	IN	_	_	_
2198	TMP	tmp	NN	_	_	_
2199	treatment	treatment	NN	_	_	_
2200	in	in	IN	_	_	_
2201	M9	m9	NN	_	_	_
2202	media	media	NNS	_	_	_
2203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2204	E.	e.	FW	_	_	_
2205	coli	coli	FW	_	_	_
2206	MG1655	mg1655	NN	_	_	_
2207	90	90	CD	_	_	_
2208	min	min	NN	_	_	_
2209	after	after	IN	_	_	_
2210	TMP	tmp	NN	_	_	_
2211	+	+	CC	_	_	_
2212	adenine	adenine	NN	_	_	_
2213	+	+	CC	_	_	_
2214	glycine	glycine	NN	_	_	_
2215	+	+	CC	_	_	_
2216	methionine	methionine	NN	SUPP	_	_
2217	treatment	treatment	NN	_	_	_
2218	in	in	IN	_	_	_
2219	M9	m9	NN	_	_	_
2220	media	media	NNS	_	_	_
2221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2222	E.	e.	FW	_	_	_
2223	coli	coli	FW	_	_	_
2224	MG1655	mg1655	NN	_	_	_
2225	90	90	CD	_	_	_
2226	min	min	NN	_	_	_
2227	after	after	IN	_	_	_
2228	TMP	tmp	NN	_	_	_
2229	treatment	treatment	NN	_	_	_
2230	in	in	IN	_	_	_
2231	M9	m9	NN	_	_	_
2232	media	media	NNS	_	_	_
2233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2234	E.	e.	FW	_	_	_
2235	coli	coli	FW	_	_	_
2236	MG1655	mg1655	NN	_	_	_
2237	,	,	,	_	_	_
2238	BCM	BCM	NNP	_	_	_
2239	treated-Replicate1	treated-replicate1	NN	_	_	_
2240	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2241	E.	E.	NNP	_	_	_
2242	coli	coli	NN	_	_	_
2243	MG1655	mg1655	NN	_	_	_
2244	,	,	,	_	_	_
2245	BCM	BCM	NNP	_	_	_
2246	treated-Replicate2	treated-replicate2	NN	_	_	_
2247	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2248	E.	E.	NNP	_	_	_
2249	coli	coli	NN	_	_	_
2250	MG1655-C8-1	mg1655-c8-1	NN	_	_	_
2251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2252	E.	e.	FW	_	_	_
2253	coli	coli	FW	_	_	_
2254	MG1655-C8-3	mg1655-c8-3	NN	_	_	_
2255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2256	E.	e.	FW	_	_	_
2257	coli	coli	FW	_	_	_
2258	MG1655	mg1655	NN	_	_	_
2259	Cold	Cold	NNP	_	_	_
2260	Shock	shock	NN	_	_	_
2261	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2262	E.	E.	NNP	_	_	_
2263	coli	coli	NN	_	_	_
2264	MG1655	mg1655	NN	_	_	_
2265	Cold	Cold	NNP	_	_	_
2266	Shock	shock	NN	_	_	_
2267	was	be	VBD	_	_	_
2268	grown	grow	VBN	_	_	_
2269	at	at	IN	_	_	_
2270	15	15	CD	_	_	_
2271	°C	°c	NN	_	_	_
2272	for	for	IN	_	_	_
2273	4	4	CD	_	_	_
2274	hour	hour	NN	_	_	_
2275	then	then	RB	_	_	_
2276	grown	grow	VBN	_	_	_
2277	untill	untill	JJ	_	_	_
2278	reach	reach	NN	_	_	_
2279	to	to	TO	_	_	_
2280	half	half	NN	_	_	_
2281	of	of	IN	_	_	_
2282	O.D.	O.D.	NNP	_	_	_
2283	600nm	600nm	NNP	_	_	_
2284	of	of	IN	_	_	_
2285	Standard	Standard	NNP	_	_	_
2286	sample	sample	NN	_	_	_
2287	at	at	IN	_	_	_
2288	37	37	CD	_	_	_
2289	°C	°c	NN	_	_	_
2290	in	in	IN	_	_	_
2291	LB	LB	NNP	MED	_	_
2292	media	media	NNS	MED	_	_
2293	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655-control-1	mg1655-control-1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	MG1655-control-2	mg1655-control-2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	MG1655-control-3	mg1655-control-3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
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	Heat	heat	NN	_	_	_
24	Shock	shock	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E.	e.	FW	_	_	_
27	coli	coli	FW	_	_	_
28	MG1655	mg1655	NN	_	_	_
29	Heat	heat	NN	_	_	_
30	Shock	shock	NN	_	_	_
31	was	be	VBD	_	_	_
32	grown	grow	VBN	_	_	_
33	at	at	IN	_	_	_
34	50	50	CD	_	_	_
35	°C	°c	NN	_	_	_
36	for	for	IN	_	_	_
37	4	4	CD	_	_	_
38	hour	hour	NN	_	_	_
39	then	then	RB	_	_	_
40	grown	grow	VBN	_	_	_
41	untill	untill	JJ	_	_	_
42	reach	reach	NN	_	_	_
43	to	to	TO	_	_	_
44	half	half	NN	_	_	_
45	of	of	IN	_	_	_
46	O.D.	O.D.	NNP	_	_	_
47	600nm	600nm	NNP	_	_	_
48	of	of	IN	_	_	_
49	Standard	Standard	NNP	_	_	_
50	sample	sample	NN	_	_	_
51	at	at	IN	_	_	_
52	37	37	CD	_	_	_
53	°C	°c	NN	_	_	_
54	in	in	IN	_	_	_
55	LB	LB	NNP	MED	_	_
56	media	media	NNS	MED	_	_
57	.	.	.	_	_	_

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	,	,	,	_	_	_
6	M9	m9	NN	_	_	_
7	media	media	NNS	_	_	_
8	with	with	IN	_	_	_
9	4	4	CD	_	_	_
10	g/L	g/l	NN	_	_	_
11	glucose	glucose	NN	SUPP	_	_
12	,	,	,	_	_	_
13	aerobic	aerobic	JJ	_	_	_
14	,	,	,	_	_	_
15	log	log	NN	_	_	_
16	phase	phase	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	coli	coli	NN	_	_	_
20	MG1655	mg1655	NN	_	_	_
21	,	,	,	_	_	_
22	M9	m9	NN	_	_	_
23	media	media	NNS	_	_	_
24	with	with	IN	_	_	_
25	4	4	CD	_	_	_
26	g/L	g/l	NN	_	_	_
27	glucose	glucose	NN	SUPP	_	_
28	,	,	,	_	_	_
29	anaerobic	anaerobic	JJ	_	_	_
30	,	,	,	_	_	_
31	log	log	NN	_	_	_
32	phase	phase	NN	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	E.	E.	NNP	_	_	_
35	coli	coli	NN	_	_	_
36	MG1655	mg1655	NN	_	_	_
37	mid-log	mid-log	JJ	_	_	_
38	phase	phase	NN	_	_	_
39	in	in	IN	_	_	_
40	LB	LB	NNP	MED	_	_
41	media	media	NNS	MED	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	E.	e.	FW	_	_	_
44	coli	coli	FW	_	_	_
45	MG1655	mg1655	NN	_	_	_
46	mid-log	mid-log	JJ	_	_	_
47	phase	phase	NN	_	_	_
48	in	in	IN	_	_	_
49	M9	m9	NN	_	_	_
50	media	media	NNS	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	E.	e.	FW	_	_	_
53	coli	coli	FW	_	_	_
54	MG1655	mg1655	NN	_	_	_
55	minimal	minimal	JJ	_	_	_
56	C	c	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	E.	e.	FW	_	_	_
59	coli	coli	FW	_	_	_
60	MG1655	mg1655	NN	_	_	_
61	minimal	minimal	JJ	_	_	_
62	C&N	c&n	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	E.	e.	FW	_	_	_
65	coli	coli	FW	_	_	_
66	MG1655	mg1655	NN	_	_	_
67	minimal	minimal	JJ	_	_	_
68	C&N	C&N	NNP	_	_	_
69	Source	Source	NNP	_	_	_
70	was	be	VBD	_	_	_
71	grown	grow	VBN	_	_	_
72	untill	untill	JJ	_	_	_
73	reach	reach	NN	_	_	_
74	to	to	TO	_	_	_
75	quater	quater	NN	_	_	_
76	of	of	IN	_	_	_
77	O.D.	O.D.	NNP	_	_	_
78	600nm	600nm	NNP	_	_	_
79	of	of	IN	_	_	_
80	Standard	Standard	NNP	_	_	_
81	sample	sample	NN	_	_	_
82	at	at	IN	_	_	_
83	37	37	CD	_	_	_
84	°C	°c	NN	_	_	_
85	in	in	IN	_	_	_
86	minimal	minimal	JJ	_	_	_
87	C	c	NN	_	_	_
88	and	and	CC	_	_	_
89	N	n	NN	_	_	_
90	source	source	NN	_	_	_
91	MOPS	mop	NNS	MED	_	_
92	media	media	NNS	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	C-N	c-n	NN	_	_	_
95	-	-	:	_	_	_
96	MOPS	mop	NNS	MED	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	.	.	.	_	_	_

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-MOPS	mg1655-mops	NN	_	_	_
5	+2	+2	CD	_	_	_
6	%	%	NN	_	_	_
7	Dextrose	dextrose	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	MG1655-MOPS	mg1655-mops	NN	_	_	_
12	+2	+2	CD	_	_	_
13	%	%	NN	_	_	_
14	Dextrose	dextrose	NN	_	_	_
15	+10	+10	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	C8	c8	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	MG1655	mg1655	NN	_	_	_
22	Osmotic	osmotic	JJ	_	_	_
23	stress	stress	NN	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	E.	E.	NNP	_	_	_
26	coli	coli	NN	_	_	_
27	MG1655	mg1655	NN	_	_	_
28	Osmotic	osmotic	JJ	_	_	_
29	Stress	stress	NN	_	_	_
30	was	be	VBD	_	_	_
31	grown	grow	VBN	_	_	_
32	untill	untill	JJ	_	_	_
33	reach	reach	NN	_	_	_
34	to	to	TO	_	_	_
35	half	half	NN	_	_	_
36	of	of	IN	_	_	_
37	O.D.	O.D.	NNP	_	_	_
38	600nm	600nm	NNP	_	_	_
39	of	of	IN	_	_	_
40	Standard	Standard	NNP	_	_	_
41	sample	sample	NN	_	_	_
42	at	at	IN	_	_	_
43	37	37	CD	_	_	_
44	°C	°c	NN	_	_	_
45	in	in	IN	_	_	_
46	45	45	CD	_	_	_
47	ml	ml	NN	_	_	_
48	MOPS	mop	NNS	MED	_	_
49	media	media	NNS	_	_	_
50	with	with	IN	_	_	_
51	6	6	CD	_	_	_
52	ml	ml	NN	_	_	_
53	4M	4m	NN	_	_	_
54	Sodium	sodium	NN	_	_	_
55	Chloride	chloride	NN	_	_	_
56	.	.	.	_	_	_

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	NN	_	_	_
5	parC	parc	NN	GEN	_	_
6	:	:	:	_	_	_
7	:	:	:	_	_	_
8	flag	flag	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	parE	pare	NN	GEN	_	_
14	:	:	:	_	_	_
15	:	:	:	_	_	_
16	flag	flag	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	coli	coli	NN	_	_	_
20	MG1655	mg1655	NN	_	_	_
21	/	/	:	_	_	_
22	pCA24N	pca24n	NN	_	_	_
23	,	,	,	_	_	_
24	-	-	:	_	_	_
25	gfp	gfp	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	PhoB	phob	NN	TF	_	_
31	knock-out	knock-out	JJ	_	_	_
32	strain	strain	NN	_	_	_
33	grows	grow	VBZ	_	_	_
34	under	under	IN	_	_	_
35	phosphate	phosphate	NN	_	_	_
36	starvation	starvation	NN	_	_	_
37	condition	condition	NN	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	E.	E.	NNP	_	_	_
40	coli	coli	NN	_	_	_
41	MG1655	mg1655	NN	_	_	_
42	/	/	:	_	_	_
43	pORF1	porf1	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	E.	e.	FW	_	_	_
46	coli	coli	FW	_	_	_
47	MG1655	mg1655	NN	_	_	_
48	∆	∆	CD	_	_	_
49	Rac	rac	NN	_	_	_
50	G324D	g324d	NN	_	_	_
51	,	,	,	_	_	_
52	treated-Replicate1-mutant	treated-replicate1-mutant	JJ	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
54	E.	e.	FW	_	_	_
55	coli	coli	FW	_	_	_
56	MG1655	mg1655	NN	_	_	_
57	∆	∆	CD	_	_	_
58	Rac	rac	NN	_	_	_
59	G324D	g324d	NN	_	_	_
60	,	,	,	_	_	_
61	treated-Replicate2-mutant	treated-replicate2-mutant	JJ	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
63	E.	e.	FW	_	_	_
64	coli	coli	FW	_	_	_
65	MG1655	mg1655	NN	_	_	_
66	∆	∆	CD	_	_	_
67	Rac	rac	NN	_	_	_
68	N340S	n340s	NN	_	_	_
69	,	,	,	_	_	_
70	treated-Replicate1-mutant	treated-replicate1-mutant	JJ	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
72	E.	e.	FW	_	_	_
73	coli	coli	FW	_	_	_
74	MG1655	mg1655	NN	_	_	_
75	∆	∆	CD	_	_	_
76	Rac	rac	NN	_	_	_
77	N340S	n340s	NN	_	_	_
78	,	,	,	_	_	_
79	treated-Replicate2-mutant	treated-replicate2-mutant	JJ	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
81	E.	e.	FW	_	_	_
82	coli	coli	FW	_	_	_
83	MG1655	mg1655	NN	_	_	_
84	∆	∆	CD	_	_	_
85	Rac	rac	NN	_	_	_
86	WT	WT	NNP	_	_	_
87	,	,	,	_	_	_
88	control-Replicate1-Wildtype	control-replicate1-wildtype	JJ	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
90	E.	e.	FW	_	_	_
91	coli	coli	FW	_	_	_
92	MG1655	mg1655	NN	_	_	_
93	∆	∆	CD	_	_	_
94	Rac	rac	NN	_	_	_
95	WT	WT	NNP	_	_	_
96	,	,	,	_	_	_
97	control-Replicate2-Wildtype	control-replicate2-wildtype	JJ	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
99	E.	e.	FW	_	_	_
100	coli	coli	FW	_	_	_
101	MG1655	mg1655	NN	_	_	_
102	RNA	rna	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	E.	e.	FW	_	_	_
105	coli	coli	FW	_	_	_
106	MG1655	mg1655	NN	_	_	_
107	Standard	standard	JJ	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	E.	e.	FW	_	_	_
110	coli	coli	FW	_	_	_
111	MG1655	mg1655	NN	_	_	_
112	Standard	Standard	NNP	_	_	_
113	was	be	VBD	_	_	_
114	grown	grow	VBN	_	_	_
115	to	to	TO	_	_	_
116	mid-log	mid-log	JJ	_	_	_
117	phase	phase	NN	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	O.D.	o.d.	NN	_	_	_
120	600nm	600nm	CD	_	_	_
121	0.6	0.6	CD	_	_	_
122	~	~	NN	_	_	_
123	0.8	0.8	CD	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	at	at	IN	_	_	_
126	37	37	CD	_	_	_
127	°C	°c	NN	_	_	_
128	in	in	IN	_	_	_
129	LB	LB	NNP	MED	_	_
130	media	media	NNS	MED	_	_
131	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655star	mg1655star	NN	_	_	_
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	MG1655star	mg1655star	NN	_	_	_
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	MG1655star	mg1655star	NN	_	_	_
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	MG1655star	mg1655star	NN	_	_	_
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	MG1655	mg1655	NN	_	_	_
45	strain	strain	NN	_	_	_
46	was	be	VBD	_	_	_
47	cultured	culture	VBN	_	_	_
48	in	in	IN	_	_	_
49	M9	m9	NN	_	_	_
50	complete	complete	JJ	_	_	_
51	medium	medium	NN	_	_	_
52	at	at	IN	_	_	_
53	37	37	CD	_	_	_
54	°C	°c	NN	_	_	_
55	with	with	IN	_	_	_
56	constant	constant	JJ	_	_	_
57	agitation	agitation	NN	_	_	_
58	and	and	CC	_	_	_
59	harvested	harvest	VBN	_	_	_
60	at	at	IN	_	_	_
61	mid-exponential	mid-exponential	JJ	_	_	_
62	phase	phase	NN	_	_	_
63	.	.	.	_	_	_

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	NNP	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	/	/	:	_	_	_
14	Svi3-3	svi3-3	NN	_	_	_
15	comp	comp	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	thyA	thya	NN	GEN	_	_
6	-	-	:	_	_	_
7	cells	cell	NNS	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	M9	m9	NN	MED	_	_
11	minimal	minimal	JJ	MED	_	_
12	medium	medium	NN	MED	_	_
13	+	+	CC	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	and	and	CC	_	_	_
18	20	20	CD	_	_	_
19	ug/ml	ug/ml	JJ	_	_	_
20	thymine	thymine	NN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	E.	E.	NNP	_	_	_
23	coli	coli	NN	_	_	_
24	MG1655	mg1655	NN	_	_	_
25	UV	uv	NN	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	E.	E.	NNP	_	_	_
28	coli	coli	NN	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	UV	uv	NN	_	_	_
31	was	be	VBD	_	_	_
32	exposed	expose	VBN	_	_	_
33	to	to	TO	_	_	_
34	UV	uv	NN	_	_	_
35	light	light	NN	_	_	_
36	for	for	IN	_	_	_
37	15	15	CD	_	_	_
38	minutes	minute	NNS	_	_	_
39	then	then	RB	_	_	_
40	grown	grow	VBN	_	_	_
41	untill	untill	JJ	_	_	_
42	reach	reach	NN	_	_	_
43	to	to	TO	_	_	_
44	half	half	NN	_	_	_
45	of	of	IN	_	_	_
46	O.D.	O.D.	NNP	_	_	_
47	600nm	600nm	NNP	_	_	_
48	of	of	IN	_	_	_
49	Standard	Standard	NNP	_	_	_
50	sample	sample	NN	_	_	_
51	at	at	IN	_	_	_
52	37	37	CD	_	_	_
53	°C	°c	NN	_	_	_
54	in	in	IN	_	_	_
55	LB	LB	NNP	MED	_	_
56	media	media	NNS	MED	_	_
57	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	,	,	,	_	_	_
6	Vector	Vector	NNP	_	_	_
7	control-Replicate1	control-replicate1	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	E.	E.	NNP	_	_	_
10	coli	coli	NN	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	,	,	,	_	_	_
13	Vector	Vector	NNP	_	_	_
14	control-Replicate2	control-replicate2	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	E.	E.	NNP	_	_	_
17	coli	coli	NN	_	_	_
18	MG1655	mg1655	NN	_	_	_
19	was	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	in	in	IN	_	_	_
22	MOPS	MOPS	NNP	MED	_	_
23	+	+	CC	_	_	_
24	2	2	CD	_	_	_
25	%	%	NN	_	_	_
26	Dextrose	dextrose	NN	_	_	_
27	minimal	minimal	JJ	_	_	_
28	media	media	NNS	_	_	_
29	+	+	CC	_	_	_
30	-	-	:	_	_	_
31	10	10	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	octanoic	octanoic	JJ	_	_	_
34	acid	acid	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	pH	ph	NN	_	_	_
37	=	=	JJ	_	_	_
38	7.0	7.0	CD	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	from	from	IN	_	_	_
41	OD550	od550	NN	_	_	_
42	0.05	0.05	CD	_	_	_
43	to	to	TO	_	_	_
44	~	~	CD	_	_	_
45	0.8	0.8	CD	_	_	_
46	and	and	CC	_	_	_
47	harvested	harvest	VBN	_	_	_
48	at	at	IN	_	_	_
49	Midlog	Midlog	NNP	_	_	_
50	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	wildtype	wildtype	JJ	_	_	_
6	strain	strain	NN	_	_	_
7	grows	grow	VBZ	_	_	_
8	under	under	IN	_	_	_
9	phosphate	phosphate	NN	_	_	_
10	starvation	starvation	NN	_	_	_
11	condition	condition	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	E.	E.	NNP	_	_	_
14	coli	coli	NN	_	_	_
15	MG1655	mg1655	NN	_	_	_
16	,	,	,	_	_	_
17	WT	WT	NNP	_	_	_
18	Rho	rho	NN	_	_	_
19	treated-Replicate1	treated-replicate1	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	,	,	,	_	_	_
25	WT	WT	NNP	_	_	_
26	Rho	rho	NN	_	_	_
27	treated-Replicate2	treated-replicate2	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	MG1693	mg1693	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	E.coli	e.coli	NNS	_	_	_
34	_	_	VBP	_	_	_
35	Na10	na10	NN	_	_	_
36	_	_	CD	_	_	_
37	rep1	rep1	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	E.coli	e.coli	NNS	_	_	_
40	_	_	VBP	_	_	_
41	Na10	na10	NN	_	_	_
42	_	_	CD	_	_	_
43	rep2	rep2	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	E.coli	e.coli	NNS	_	_	_
46	_	_	VBP	_	_	_
47	Na10	na10	NN	_	_	_
48	_	_	CD	_	_	_
49	rep3	rep3	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	E.coli	e.coli	NNS	_	_	_
52	_	_	VBP	_	_	_
53	Na20	na20	NN	_	_	_
54	_	_	CD	_	_	_
55	rep1	rep1	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	E.coli	e.coli	NNS	_	_	_
58	_	_	VBP	_	_	_
59	Na20	na20	NN	_	_	_
60	_	_	CD	_	_	_
61	rep2	rep2	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	E.coli	e.coli	NNS	_	_	_
64	_	_	VBP	_	_	_
65	Na20	na20	NN	_	_	_
66	_	_	CD	_	_	_
67	rep3	rep3	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	E.coli	e.coli	NNS	_	_	_
70	_	_	VBP	_	_	_
71	Na45	na45	NN	_	_	_
72	_	_	CD	_	_	_
73	rep1	rep1	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	E.coli	e.coli	NNS	_	_	_
76	_	_	VBP	_	_	_
77	Na45	na45	NN	_	_	_
78	_	_	CD	_	_	_
79	rep2	rep2	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	E.coli	e.coli	NNS	_	_	_
82	_	_	VBP	_	_	_
83	Na45	na45	NN	_	_	_
84	_	_	CD	_	_	_
85	rep3	rep3	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
87	E.	e.	FW	_	_	_
88	coli	coli	FW	_	_	_
89	NaCl	nacl	NN	_	_	_
90	hyperosmotic	hyperosmotic	JJ	_	_	_
91	treatment	treatment	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	biological	biological	JJ	_	_	_
94	replicate	replicate	VBP	_	_	_
95	1	1	LS	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	E.	e.	FW	_	_	_
99	coli	coli	FW	_	_	_
100	NaCl	nacl	NN	_	_	_
101	hyperosmotic	hyperosmotic	JJ	_	_	_
102	treatment	treatment	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	biological	biological	JJ	_	_	_
105	replicate	replicate	VBP	_	_	_
106	2	2	LS	_	_	_
107	-RRB-	-rrb-	-RRB-	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	ecoli	ecolus	NNS	_	_	_
110	NC	NC	NNP	_	_	_
111	_	_	SYM	_	_	_
112	000913.2	000913.2	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	E	e	NN	_	_	_
115	_	_	CD	_	_	_
116	coli	coli	NN	_	_	_
117	_	_	NN	_	_	_
118	negativ	negativ	NN	_	_	_
119	_	_	NN	_	_	_
120	control	control	NN	_	_	_
121	_	_	CD	_	_	_
122	left	leave	VBD	_	_	_
123	_	_	RB	_	_	_
124	chamber	chamber	NN	_	_	_
125	_	_	CD	_	_	_
126	rep1	rep1	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	E	e	NN	_	_	_
129	_	_	CD	_	_	_
130	coli	coli	NN	_	_	_
131	_	_	NN	_	_	_
132	negativ	negativ	NN	_	_	_
133	_	_	NN	_	_	_
134	control	control	NN	_	_	_
135	_	_	CD	_	_	_
136	left	leave	VBD	_	_	_
137	_	_	RB	_	_	_
138	chamber	chamber	NN	_	_	_
139	_	_	CD	_	_	_
140	rep2	rep2	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	E	e	NN	_	_	_
143	_	_	CD	_	_	_
144	coli	coli	NN	_	_	_
145	_	_	NN	_	_	_
146	negativ	negativ	NN	_	_	_
147	_	_	NN	_	_	_
148	control	control	NN	_	_	_
149	_	_	CD	_	_	_
150	left	leave	VBD	_	_	_
151	_	_	RB	_	_	_
152	chamber	chamber	NN	_	_	_
153	_	_	CD	_	_	_
154	rep3	rep3	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	E	e	NN	_	_	_
157	_	_	CD	_	_	_
158	coli	coli	NN	_	_	_
159	_	_	NN	_	_	_
160	negativ	negativ	NN	_	_	_
161	_	_	NN	_	_	_
162	control	control	NN	_	_	_
163	_	_	RB	_	_	_
164	right	right	JJ	_	_	_
165	_	_	NN	_	_	_
166	chamber	chamber	NN	_	_	_
167	_	_	CD	_	_	_
168	rep1	rep1	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	E	e	NN	_	_	_
171	_	_	CD	_	_	_
172	coli	coli	NN	_	_	_
173	_	_	NN	_	_	_
174	negativ	negativ	NN	_	_	_
175	_	_	NN	_	_	_
176	control	control	NN	_	_	_
177	_	_	RB	_	_	_
178	right	right	JJ	_	_	_
179	_	_	NN	_	_	_
180	chamber	chamber	NN	_	_	_
181	_	_	CD	_	_	_
182	rep2	rep2	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	E	e	NN	_	_	_
185	_	_	CD	_	_	_
186	coli	coli	NN	_	_	_
187	_	_	NN	_	_	_
188	negativ	negativ	NN	_	_	_
189	_	_	NN	_	_	_
190	control	control	NN	_	_	_
191	_	_	RB	_	_	_
192	right	right	JJ	_	_	_
193	_	_	NN	_	_	_
194	chamber	chamber	NN	_	_	_
195	_	_	CD	_	_	_
196	rep3	rep3	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	E.coli	e.coli	NNS	_	_	_
199	_	_	VBP	_	_	_
200	nitrogen	nitrogen	NN	_	_	_
201	_	_	NN	_	_	_
202	dynamic	dynamic	JJ	_	_	_
203	_	_	NN	_	_	_
204	1	1	CD	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	E.coli	e.coli	NNS	_	_	_
207	_	_	VBP	_	_	_
208	nitrogen	nitrogen	NN	_	_	_
209	_	_	NN	_	_	_
210	dynamic	dynamic	JJ	_	_	_
211	_	_	NN	_	_	_
212	2	2	CD	_	_	_
213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
214	Ecoli	Ecoli	NNP	_	_	_
215	_	_	NNP	_	_	_
216	Norfloxacin	Norfloxacin	NNP	_	_	_
217	-LRB-	-lrb-	-LRB-	_	_	_
218	50	50	CD	_	_	_
219	ug/ml	ug/ml	NN	_	_	_
220	-RRB-	-rrb-	-RRB-	_	_	_
221	treatment	treatment	NN	_	_	_
222	T1	t1	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	Ecoli	ecolus	NNS	_	_	_
225	_	_	VBP	_	_	_
226	Norfloxacin	norfloxacin	NN	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	50	50	CD	_	_	_
229	ug/ml	ug/ml	NN	_	_	_
230	-RRB-	-rrb-	-RRB-	_	_	_
231	treatment	treatment	NN	_	_	_
232	T2	t2	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	Ecoli	ecolus	NNS	_	_	_
235	_	_	VBP	_	_	_
236	Norfloxacin	norfloxacin	NN	_	_	_
237	-LRB-	-lrb-	-LRB-	_	_	_
238	50	50	CD	_	_	_
239	ug/ml	ug/ml	NN	_	_	_
240	-RRB-	-rrb-	-RRB-	_	_	_
241	treatment	treatment	NN	_	_	_
242	T3	t3	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	Ecoli	ecolus	NNS	_	_	_
245	_	_	VBP	_	_	_
246	Norfloxacin	norfloxacin	NN	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	50	50	CD	_	_	_
249	ug/ml	ug/ml	NN	_	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	treatment	treatment	NN	_	_	_
252	T4	t4	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	Ecoli	ecolus	NNS	_	_	_
255	_	_	VBP	_	_	_
256	Norfloxacin	norfloxacin	NN	_	_	_
257	-LRB-	-lrb-	-LRB-	_	_	_
258	50	50	CD	_	_	_
259	ug/ml	ug/ml	NN	_	_	_
260	-RRB-	-rrb-	-RRB-	_	_	_
261	treatment	treatment	NN	_	_	_
262	T5	t5	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	Ecoli	ecolus	NNS	_	_	_
265	_	_	VBP	_	_	_
266	Novobiocin	novobiocin	NN	_	_	_
267	treatment	treatment	NN	_	_	_
268	-LRB-	-lrb-	-LRB-	_	_	_
269	200	200	CD	_	_	_
270	ug/ml	ug/ml	NN	_	_	_
271	-RRB-	-rrb-	-RRB-	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	Ecoli	ecolus	NNS	_	_	_
274	_	_	VBP	_	_	_
275	Novobiocin	novobiocin	NN	_	_	_
276	treatment	treatment	NN	_	_	_
277	-LRB-	-lrb-	-LRB-	_	_	_
278	20	20	CD	_	_	_
279	ug/ml	ug/ml	NN	_	_	_
280	-RRB-	-rrb-	-RRB-	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Ecoli	ecolus	NNS	_	_	_
283	_	_	VBP	_	_	_
284	Novobiocin	novobiocin	NN	_	_	_
285	treatment	treatment	NN	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	50	50	CD	_	_	_
288	ug/ml	ug/ml	NN	_	_	_
289	-RRB-	-rrb-	-RRB-	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	Ecoli	ecolus	NNS	_	_	_
292	_	_	VBP	_	_	_
293	Novobiocin	novobiocin	NN	_	_	_
294	treatment	treatment	NN	_	_	_
295	-LRB-	-lrb-	-LRB-	_	_	_
296	5	5	CD	_	_	_
297	ug/ml	ug/ml	NN	_	_	_
298	-RRB-	-rrb-	-RRB-	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	Ecoli	ecolus	NNS	_	_	_
301	_	_	VBP	_	_	_
302	NOX	nox	SYM	_	_	_
303	-	-	:	_	_	_
304	_	_	NN	_	_	_
305	balanced	balanced	JJ	_	_	_
306	groNOX-h	gronox-h	NN	_	_	_
307	at	at	IN	_	_	_
308	OD	OD	NNP	_	_	_
309	0.19	0.19	CD	_	_	_
310	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
311	Ecoli	Ecoli	NNP	_	_	_
312	_	_	NNP	_	_	_
313	NOX	NOX	NNP	_	_	_
314	-	-	:	_	_	_
315	_	_	NN	_	_	_
316	balanced	balanced	JJ	_	_	_
317	groNOX-h	gronox-h	NN	_	_	_
318	at	at	IN	_	_	_
319	OD	od	NN	_	_	_
320	0.3	0.3	CD	_	_	_
321	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
322	Ecoli	Ecoli	NNP	_	_	_
323	_	_	NNP	_	_	_
324	NOX	NOX	NNP	_	_	_
325	-	-	:	_	_	_
326	_	_	NN	_	_	_
327	balanced	balanced	JJ	_	_	_
328	groNOX-h	gronox-h	NN	_	_	_
329	at	at	IN	_	_	_
330	OD	OD	NNP	_	_	_
331	0.41	0.41	CD	_	_	_
332	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
333	Ecoli	Ecoli	NNP	_	_	_
334	_	_	NNP	_	_	_
335	NOX	NOX	NNP	_	_	_
336	-	-	:	_	_	_
337	_	_	NN	_	_	_
338	balanced	balanced	JJ	_	_	_
339	groNOX-h	gronox-h	NN	_	_	_
340	at	at	IN	_	_	_
341	OD	OD	NNP	_	_	_
342	0.49	0.49	CD	_	_	_
343	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
344	Ecoli	Ecoli	NNP	_	_	_
345	_	_	NNP	_	_	_
346	NOX	NOX	NNP	_	_	_
347	-	-	:	_	_	_
348	_	_	NN	_	_	_
349	balanced	balanced	JJ	_	_	_
350	groNOX-h	gronox-h	NN	_	_	_
351	at	at	IN	_	_	_
352	OD	od	NN	_	_	_
353	0.6	0.6	CD	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	Ecoli	ecolus	NNS	_	_	_
356	_	_	VBP	_	_	_
357	NOX	nox	NN	_	_	_
358	+	+	CC	_	_	_
359	_	_	NN	_	_	_
360	balanced	balanced	JJ	_	_	_
361	growth	growth	NN	_	_	_
362	at	at	IN	_	_	_
363	OD	OD	NNP	_	_	_
364	0.13	0.13	CD	_	_	_
365	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
366	Ecoli	Ecoli	NNP	_	_	_
367	_	_	SYM	_	_	_
368	NOX	nox	NN	_	_	_
369	+	+	CC	_	_	_
370	_	_	NN	_	_	_
371	balanced	balanced	JJ	_	_	_
372	growth	growth	NN	_	_	_
373	at	at	IN	_	_	_
374	OD	OD	NNP	_	_	_
375	0.21	0.21	CD	_	_	_
376	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
377	Ecoli	Ecoli	NNP	_	_	_
378	_	_	SYM	_	_	_
379	NOX	nox	NN	_	_	_
380	+	+	CC	_	_	_
381	_	_	NN	_	_	_
382	balanced	balanced	JJ	_	_	_
383	growth	growth	NN	_	_	_
384	at	at	IN	_	_	_
385	OD	OD	NNP	_	_	_
386	0.28	0.28	CD	_	_	_
387	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
388	Ecoli	Ecoli	NNP	_	_	_
389	_	_	SYM	_	_	_
390	NOX	nox	NN	_	_	_
391	+	+	CC	_	_	_
392	_	_	NN	_	_	_
393	balanced	balanced	JJ	_	_	_
394	growth	growth	NN	_	_	_
395	at	at	IN	_	_	_
396	OD	OD	NNP	_	_	_
397	0.34	0.34	CD	_	_	_
398	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
399	Ecoli	Ecoli	NNP	_	_	_
400	_	_	SYM	_	_	_
401	NOX	nox	NN	_	_	_
402	+	+	CC	_	_	_
403	_	_	NN	_	_	_
404	balanced	balanced	JJ	_	_	_
405	growth	growth	NN	_	_	_
406	at	at	IN	_	_	_
407	OD	od	NN	_	_	_
408	0.4	0.4	CD	_	_	_
409	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
410	Ecoli	Ecoli	NNP	_	_	_
411	_	_	SYM	_	_	_
412	NP-TiO2	np-tio2	NN	_	_	_
413	_	_	CD	_	_	_
414	5h	5h	JJ	_	_	_
415	_	_	NN	_	_	_
416	rep1	rep1	NN	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	Ecoli	ecolus	NNS	_	_	_
419	_	_	VBP	_	_	_
420	NP-TiO2	np-tio2	NN	_	_	_
421	_	_	CD	_	_	_
422	5h	5h	JJ	_	_	_
423	_	_	NN	_	_	_
424	rep2	rep2	NN	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	Ecoli	ecolus	NNS	_	_	_
427	_	_	VBP	_	_	_
428	NP-TiO2	np-tio2	NN	_	_	_
429	_	_	CD	_	_	_
430	5h	5h	JJ	_	_	_
431	_	_	NN	_	_	_
432	rep3	rep3	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	Ecoli	ecolus	NNS	_	_	_
435	_	_	VBP	_	_	_
436	NP-TiO2	np-tio2	NN	_	_	_
437	_	_	CD	_	_	_
438	5h	5h	JJ	_	_	_
439	_	_	NN	_	_	_
440	rep4	rep4	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	E.coli	e.coli	NNS	_	_	_
443	,	,	,	_	_	_
444	NP-TiO2	np-tio2	NN	_	_	_
445	exposed	expose	VBN	_	_	_
446	culture	culture	NN	_	_	_
447	,	,	,	_	_	_
448	5h	5h	NN	_	_	_
449	in	in	IN	_	_	_
450	10	10	CD	_	_	_
451	mM	mm	NN	KWSUPP	_	_
452	NaCl	nacl	NN	_	_	_
453	100mg/L	100mg/l	NN	_	_	_
454	NP-TiO2	np-tio2	NN	_	_	_
455	,	,	,	_	_	_
456	replicate	replicate	VB	_	_	_
457	1	1	CD	_	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	E.coli	e.coli	NNS	_	_	_
460	,	,	,	_	_	_
461	NP-TiO2	np-tio2	NN	_	_	_
462	exposed	expose	VBN	_	_	_
463	culture	culture	NN	_	_	_
464	,	,	,	_	_	_
465	5h	5h	NN	_	_	_
466	in	in	IN	_	_	_
467	10	10	CD	_	_	_
468	mM	mm	NN	KWSUPP	_	_
469	NaCl	nacl	NN	_	_	_
470	100mg/L	100mg/l	NN	_	_	_
471	NP-TiO2	np-tio2	NN	_	_	_
472	,	,	,	_	_	_
473	replicate	replicate	VB	_	_	_
474	2	2	CD	_	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
476	E.coli	e.coli	NNS	_	_	_
477	,	,	,	_	_	_
478	NP-TiO2	np-tio2	NN	_	_	_
479	exposed	expose	VBN	_	_	_
480	culture	culture	NN	_	_	_
481	,	,	,	_	_	_
482	5h	5h	NN	_	_	_
483	in	in	IN	_	_	_
484	10	10	CD	_	_	_
485	mM	mm	NN	KWSUPP	_	_
486	NaCl	nacl	NN	_	_	_
487	100mg/L	100mg/l	NN	_	_	_
488	NP-TiO2	np-tio2	NN	_	_	_
489	,	,	,	_	_	_
490	replicate	replicate	VB	_	_	_
491	3	3	CD	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
493	E.coli	e.coli	NNS	_	_	_
494	,	,	,	_	_	_
495	NP-TiO2	np-tio2	NN	_	_	_
496	exposed	expose	VBN	_	_	_
497	culture	culture	NN	_	_	_
498	,	,	,	_	_	_
499	5h	5h	NN	_	_	_
500	in	in	IN	_	_	_
501	10	10	CD	_	_	_
502	mM	mm	NN	KWSUPP	_	_
503	NaCl	nacl	NN	_	_	_
504	100mg/L	100mg/l	NN	_	_	_
505	NP-TiO2	np-tio2	NN	_	_	_
506	,	,	,	_	_	_
507	replicate	replicate	VB	_	_	_
508	4	4	CD	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
510	E.coliO157	e.colio157	NN	_	_	_
511	_	_	CD	_	_	_
512	0.5	0.5	CD	_	_	_
513	%	%	NN	_	_	_
514	-LRB-	-lrb-	-LRB-	_	_	_
515	w/v	w/v	NN	_	_	_
516	-RRB-	-rrb-	-RRB-	_	_	_
517	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
518	_	_	NN	_	_	_
519	0	0	CD	_	_	_
520	min	min	NN	_	_	_
521	_	_	CD	_	_	_
522	rep1	rep1	NN	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	E.coliO157	e.colio157	NN	_	_	_
525	_	_	CD	_	_	_
526	0.5	0.5	CD	_	_	_
527	%	%	NN	_	_	_
528	-LRB-	-lrb-	-LRB-	_	_	_
529	w/v	w/v	NN	_	_	_
530	-RRB-	-rrb-	-RRB-	_	_	_
531	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
532	_	_	NN	_	_	_
533	0	0	CD	_	_	_
534	min	min	NN	_	_	_
535	_	_	CD	_	_	_
536	rep2	rep2	NN	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	E.coliO157	e.colio157	NN	_	_	_
539	_	_	CD	_	_	_
540	0.5	0.5	CD	_	_	_
541	%	%	NN	_	_	_
542	-LRB-	-lrb-	-LRB-	_	_	_
543	w/v	w/v	NN	_	_	_
544	-RRB-	-rrb-	-RRB-	_	_	_
545	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
546	_	_	SYM	_	_	_
547	15	15	CD	_	_	_
548	min	min	NN	_	_	_
549	_	_	CD	_	_	_
550	rep1	rep1	NN	_	_	_
551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
552	E.coliO157	e.colio157	NN	_	_	_
553	_	_	CD	_	_	_
554	0.5	0.5	CD	_	_	_
555	%	%	NN	_	_	_
556	-LRB-	-lrb-	-LRB-	_	_	_
557	w/v	w/v	NN	_	_	_
558	-RRB-	-rrb-	-RRB-	_	_	_
559	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
560	_	_	SYM	_	_	_
561	15	15	CD	_	_	_
562	min	min	NN	_	_	_
563	_	_	CD	_	_	_
564	rep2	rep2	NN	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	E.coliO157	e.colio157	NN	_	_	_
567	_	_	CD	_	_	_
568	0.5	0.5	CD	_	_	_
569	%	%	NN	_	_	_
570	-LRB-	-lrb-	-LRB-	_	_	_
571	w/v	w/v	NN	_	_	_
572	-RRB-	-rrb-	-RRB-	_	_	_
573	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
574	_	_	SYM	_	_	_
575	30	30	CD	_	_	_
576	min	min	NN	_	_	_
577	_	_	CD	_	_	_
578	rep1	rep1	NN	_	_	_
579	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
580	E.coliO157	e.colio157	NN	_	_	_
581	_	_	CD	_	_	_
582	0.5	0.5	CD	_	_	_
583	%	%	NN	_	_	_
584	-LRB-	-lrb-	-LRB-	_	_	_
585	w/v	w/v	NN	_	_	_
586	-RRB-	-rrb-	-RRB-	_	_	_
587	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
588	_	_	SYM	_	_	_
589	30	30	CD	_	_	_
590	min	min	NN	_	_	_
591	_	_	CD	_	_	_
592	rep2	rep2	NN	_	_	_
593	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
594	E.coliO157	e.colio157	NN	_	_	_
595	_	_	CD	_	_	_
596	0.5	0.5	CD	_	_	_
597	%	%	NN	_	_	_
598	-LRB-	-lrb-	-LRB-	_	_	_
599	w/v	w/v	NN	_	_	_
600	-RRB-	-rrb-	-RRB-	_	_	_
601	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
602	_	_	SYM	_	_	_
603	5	5	CD	_	_	_
604	min	min	NN	_	_	_
605	_	_	CD	_	_	_
606	rep1	rep1	NN	_	_	_
607	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
608	E.coliO157	e.colio157	NN	_	_	_
609	_	_	CD	_	_	_
610	0.5	0.5	CD	_	_	_
611	%	%	NN	_	_	_
612	-LRB-	-lrb-	-LRB-	_	_	_
613	w/v	w/v	NN	_	_	_
614	-RRB-	-rrb-	-RRB-	_	_	_
615	sodiumbenzoate	sodiumbenzoate	VBP	_	_	_
616	_	_	SYM	_	_	_
617	5	5	CD	_	_	_
618	min	min	NN	_	_	_
619	_	_	CD	_	_	_
620	rep2	rep2	NN	_	_	_
621	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
622	E.coliO157	e.colio157	NN	_	_	_
623	_	_	CD	_	_	_
624	0.5	0.5	CD	_	_	_
625	%	%	NN	_	_	_
626	-LRB-	-lrb-	-LRB-	_	_	_
627	w/v	w/v	NN	_	_	_
628	-RRB-	-rrb-	-RRB-	_	_	_
629	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
630	_	_	NN	_	_	_
631	60	60	CD	_	_	_
632	min	min	NN	_	_	_
633	_	_	CD	_	_	_
634	rep1	rep1	NN	_	_	_
635	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
636	E.coliO157	e.colio157	NN	_	_	_
637	_	_	CD	_	_	_
638	0.5	0.5	CD	_	_	_
639	%	%	NN	_	_	_
640	-LRB-	-lrb-	-LRB-	_	_	_
641	w/v	w/v	NN	_	_	_
642	-RRB-	-rrb-	-RRB-	_	_	_
643	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
644	_	_	NN	_	_	_
645	60	60	CD	_	_	_
646	min	min	NN	_	_	_
647	_	_	CD	_	_	_
648	rep2	rep2	NN	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	E.coliO157	e.colio157	NN	_	_	_
651	_	_	CD	_	_	_
652	0	0	CD	_	_	_
653	%	%	NN	_	_	_
654	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
655	_	_	NN	_	_	_
656	0	0	CD	_	_	_
657	min	min	NN	_	_	_
658	_	_	CD	_	_	_
659	rep1	rep1	NN	_	_	_
660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
661	E.coliO157	e.colio157	NN	_	_	_
662	_	_	CD	_	_	_
663	0	0	CD	_	_	_
664	%	%	NN	_	_	_
665	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
666	_	_	NN	_	_	_
667	0	0	CD	_	_	_
668	min	min	NN	_	_	_
669	_	_	CD	_	_	_
670	rep2	rep2	NN	_	_	_
671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
672	E.coliO157	e.colio157	NN	_	_	_
673	_	_	CD	_	_	_
674	0	0	CD	_	_	_
675	%	%	NN	_	_	_
676	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
677	_	_	CD	_	_	_
678	15	15	CD	_	_	_
679	min	min	NN	_	_	_
680	_	_	CD	_	_	_
681	rep1	rep1	NN	_	_	_
682	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
683	E.coliO157	e.colio157	NN	_	_	_
684	_	_	CD	_	_	_
685	0	0	CD	_	_	_
686	%	%	NN	_	_	_
687	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
688	_	_	CD	_	_	_
689	15	15	CD	_	_	_
690	min	min	NN	_	_	_
691	_	_	CD	_	_	_
692	rep2	rep2	NN	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	E.coliO157	e.colio157	NN	_	_	_
695	_	_	CD	_	_	_
696	0	0	CD	_	_	_
697	%	%	NN	_	_	_
698	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
699	_	_	CD	_	_	_
700	30	30	CD	_	_	_
701	min	min	NN	_	_	_
702	_	_	CD	_	_	_
703	rep1	rep1	NN	_	_	_
704	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
705	E.coliO157	e.colio157	NN	_	_	_
706	_	_	CD	_	_	_
707	0	0	CD	_	_	_
708	%	%	NN	_	_	_
709	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
710	_	_	CD	_	_	_
711	30	30	CD	_	_	_
712	min	min	NN	_	_	_
713	_	_	CD	_	_	_
714	rep2	rep2	NN	_	_	_
715	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
716	E.coliO157	e.colio157	NN	_	_	_
717	_	_	CD	_	_	_
718	0	0	CD	_	_	_
719	%	%	NN	_	_	_
720	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
721	_	_	CD	_	_	_
722	5	5	CD	_	_	_
723	min	min	NN	_	_	_
724	_	_	CD	_	_	_
725	rep1	rep1	NN	_	_	_
726	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
727	E.coliO157	e.colio157	NN	_	_	_
728	_	_	CD	_	_	_
729	0	0	CD	_	_	_
730	%	%	NN	_	_	_
731	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
732	_	_	CD	_	_	_
733	5	5	CD	_	_	_
734	min	min	NN	_	_	_
735	_	_	CD	_	_	_
736	rep2	rep2	NN	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
738	E.coliO157	e.colio157	NN	_	_	_
739	_	_	CD	_	_	_
740	0	0	CD	_	_	_
741	%	%	NN	_	_	_
742	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
743	_	_	CD	_	_	_
744	60	60	CD	_	_	_
745	min	min	NN	_	_	_
746	_	_	CD	_	_	_
747	rep1	rep1	NN	_	_	_
748	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
749	E.coliO157	e.colio157	NN	_	_	_
750	_	_	CD	_	_	_
751	0	0	CD	_	_	_
752	%	%	NN	_	_	_
753	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
754	_	_	CD	_	_	_
755	60	60	CD	_	_	_
756	min	min	NN	_	_	_
757	_	_	CD	_	_	_
758	rep2	rep2	NN	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
760	E.	e.	FW	_	_	_
761	coli	coli	FW	_	_	_
762	O157	o157	NN	_	_	_
763	:	:	:	_	_	_
764	H7	h7	NN	_	_	_
765	86-24	86-24	CD	_	_	_
766	in	in	IN	_	_	_
767	LB	lb	NN	_	_	_
768	at	at	IN	_	_	_
769	37oC	37oc	NN	_	_	_
770	at	at	IN	_	_	_
771	OD	od	NN	_	_	_
772	4.0	4.0	CD	_	_	_
773	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
774	E.	E.	NNP	_	_	_
775	coli	coli	NN	_	_	_
776	O157	o157	NN	_	_	_
777	:	:	:	_	_	_
778	H7	h7	NN	_	_	_
779	86-24	86-24	CD	_	_	_
780	was	be	VBD	_	_	_
781	inoculated	inoculate	VBN	_	_	_
782	in	in	IN	_	_	_
783	25	25	CD	_	_	_
784	ml	ml	NN	_	_	_
785	of	of	IN	_	_	_
786	LB	lb	NN	_	_	_
787	in	in	IN	_	_	_
788	250	250	CD	_	_	_
789	ml	ml	NN	_	_	_
790	shake	shake	NN	_	_	_
791	flasks	flask	NNS	_	_	_
792	with	with	IN	_	_	_
793	overnight	overnight	JJ	_	_	_
794	cultures	culture	NNS	_	_	_
795	that	that	WDT	_	_	_
796	were	be	VBD	_	_	_
797	diluted	dilute	VBN	_	_	_
798	1:100	1:100	CD	_	_	_
799	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	E.coli	e.coli	NN	_	_	_
10	O157	o157	NN	_	_	_
11	:	:	:	_	_	_
12	H7	h7	NN	_	_	_
13	EDL	edl	NN	_	_	_
14	933	933	CD	_	_	_
15	genomic	genomic	JJ	_	_	_
16	DNA	dna	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	E.coli	e.coli	NN	_	_	_
19	O157	o157	NN	_	_	_
20	:	:	:	_	_	_
21	H7	h7	NN	_	_	_
22	EDL	edl	NN	_	_	_
23	933	933	CD	_	_	_
24	genomic	genomic	JJ	_	_	_
25	DNA	dna	NN	_	_	_
26	hybridization	hybridization	NN	_	_	_
27	to	to	TO	_	_	_
28	LLNL	llnl	NN	_	_	_
29	virulence	virulence	NN	_	_	_
30	mechanism	mechanism	NN	_	_	_
31	array	array	NN	_	_	_
32	v2A	v2a	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	E.	e.	FW	_	_	_
35	coli	coli	FW	_	_	_
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	in	in	IN	_	_	_
73	LB	lb	NN	_	_	_
74	at	at	IN	_	_	_
75	37oC	37oc	NN	_	_	_
76	at	at	IN	_	_	_
77	OD	od	NN	_	_	_
78	4.0	4.0	CD	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	E.	E.	NNP	_	_	_
81	coli	coli	NN	_	_	_
82	O157	o157	NN	_	_	_
83	:	:	:	_	_	_
84	H7	h7	NN	_	_	_
85	EDL933	edl933	NN	_	_	_
86	in	in	IN	_	_	_
87	LB	lb	NN	_	_	_
88	at	at	IN	_	_	_
89	37oC	37oc	NN	_	_	_
90	for	for	IN	_	_	_
91	7	7	CD	_	_	_
92	hrs	hr	NNS	_	_	_
93	incubation	incubation	NN	_	_	_
94	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
95	E.	E.	NNP	_	_	_
96	coli	coli	NN	_	_	_
97	O157	o157	NN	_	_	_
98	:	:	:	_	_	_
99	H7	h7	NN	_	_	_
100	EDL933	edl933	NN	_	_	_
101	in	in	IN	_	_	_
102	LB	lb	NN	_	_	_
103	at	at	IN	_	_	_
104	37oC	37oc	NN	_	_	_
105	for	for	IN	_	_	_
106	7	7	CD	_	_	_
107	hrs	hr	NNS	_	_	_
108	incubation	incubation	NN	_	_	_
109	with	with	IN	_	_	_
110	DMSO	dmso	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
112	E.	e.	FW	_	_	_
113	coli	coli	FW	_	_	_
114	O157	o157	NN	_	_	_
115	:	:	:	_	_	_
116	H7	h7	NN	_	_	_
117	EDL933	edl933	NN	_	_	_
118	in	in	IN	_	_	_
119	LB	lb	NN	_	_	_
120	at	at	IN	_	_	_
121	37oC	37oc	NN	_	_	_
122	for	for	IN	_	_	_
123	7	7	CD	_	_	_
124	hrs	hr	NNS	_	_	_
125	incubation	incubation	NN	_	_	_
126	with	with	IN	_	_	_
127	honey	honey	NN	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	E.	E.	NNP	_	_	_
130	coli	coli	NN	_	_	_
131	O157	o157	NN	_	_	_
132	:	:	:	_	_	_
133	H7	h7	NN	_	_	_
134	EDL933	edl933	NN	_	_	_
135	in	in	IN	_	_	_
136	LB	lb	NN	_	_	_
137	at	at	IN	_	_	_
138	37oC	37oc	NN	_	_	_
139	for	for	IN	_	_	_
140	7	7	CD	_	_	_
141	hrs	hr	NNS	_	_	_
142	incubation	incubation	NN	_	_	_
143	with	with	IN	_	_	_
144	indole-3-acetaldehyde	indole-3-acetaldehyde	JJ	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
146	E.	e.	FW	_	_	_
147	coli	coli	FW	_	_	_
148	O157	o157	NN	_	_	_
149	:	:	:	_	_	_
150	H7	h7	NN	_	_	_
151	EDL933	edl933	NN	_	_	_
152	was	be	VBD	_	_	_
153	inoculated	inoculate	VBN	_	_	_
154	in	in	IN	_	_	_
155	100	100	CD	_	_	_
156	ml	ml	NN	_	_	_
157	of	of	IN	_	_	_
158	LB	lb	NN	_	_	_
159	in	in	IN	_	_	_
160	250	250	CD	_	_	_
161	ml	ml	NN	_	_	_
162	shake	shake	NN	_	_	_
163	flasks	flask	NNS	_	_	_
164	with	with	IN	_	_	_
165	overnight	overnight	JJ	_	_	_
166	cultures	culture	NNS	_	_	_
167	that	that	WDT	_	_	_
168	were	be	VBD	_	_	_
169	diluted	dilute	VBN	_	_	_
170	1:100	1:100	CD	_	_	_
171	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	O157	o157	NN	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	EDL933	edl933	NN	_	_	_
8	was	be	VBD	_	_	_
9	inoculated	inoculate	VBN	_	_	_
10	in	in	IN	_	_	_
11	250	250	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	LB	lb	NN	_	_	_
15	in	in	IN	_	_	_
16	1000	1000	CD	_	_	_
17	ml	ml	NN	_	_	_
18	shake	shake	NN	_	_	_
19	flasks	flask	NNS	_	_	_
20	with	with	IN	_	_	_
21	overnight	overnight	JJ	_	_	_
22	cultures	culture	NNS	_	_	_
23	that	that	WDT	_	_	_
24	were	be	VBD	_	_	_
25	diluted	dilute	VBN	_	_	_
26	1:100	1:100	CD	_	_	_
27	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	O157	o157	NN	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	EDL933	edl933	NN	_	_	_
8	was	be	VBD	_	_	_
9	inoculated	inoculate	VBN	_	_	_
10	in	in	IN	_	_	_
11	25	25	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	LB	lb	NN	_	_	_
15	in	in	IN	_	_	_
16	250	250	CD	_	_	_
17	ml	ml	NN	_	_	_
18	shake	shake	NN	_	_	_
19	flasks	flask	NNS	_	_	_
20	with	with	IN	_	_	_
21	overnight	overnight	JJ	_	_	_
22	cultures	culture	NNS	_	_	_
23	that	that	WDT	_	_	_
24	were	be	VBD	_	_	_
25	diluted	dilute	VBN	_	_	_
26	1:100	1:100	CD	_	_	_
27	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	O157	o157	NN	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	EDL933	edl933	NN	_	_	_
8	was	be	VBD	_	_	_
9	inoculated	inoculate	VBN	_	_	_
10	in	in	IN	_	_	_
11	25	25	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	LB	lb	NN	_	_	_
15	in	in	IN	_	_	_
16	250	250	CD	_	_	_
17	ml	ml	NN	_	_	_
18	shake	shake	NN	_	_	_
19	flasks	flask	NNS	_	_	_
20	with	with	IN	_	_	_
21	overnight	overnight	JJ	_	_	_
22	cultures	culture	NNS	_	_	_
23	that	that	WDT	_	_	_
24	were	be	VBD	_	_	_
25	diluted	dilute	VBN	_	_	_
26	1:100	1:100	CD	_	_	_
27	.	.	.	_	_	_

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	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	O157	o157	NN	_	_	_
4	:	:	:	_	_	_
5	H7	h7	NN	_	_	_
6	in	in	IN	_	_	_
7	LB	lb	NN	_	_	_
8	at	at	IN	_	_	_
9	mid-log	mid-log	JJ	_	_	_
10	phase	phase	NN	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	E.	E.	NNP	_	_	_
13	coli	coli	NN	_	_	_
14	O157	o157	NN	_	_	_
15	:	:	:	_	_	_
16	H7	h7	NN	_	_	_
17	interacted	interact	VBD	_	_	_
18	with	with	IN	_	_	_
19	lettuce	lettuce	NN	_	_	_
20	rhizosphere	rhizosphere	NN	_	_	_
21	biological	biological	JJ	_	_	_
22	rep	rep	NN	GEN	_	_
23	1	1	CD	_	_	_
24	slide	slide	NN	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	E.	E.	NNP	_	_	_
28	coli	coli	NN	_	_	_
29	O157	o157	NN	_	_	_
30	:	:	:	_	_	_
31	H7	h7	NN	_	_	_
32	interacted	interact	VBD	_	_	_
33	with	with	IN	_	_	_
34	lettuce	lettuce	NN	_	_	_
35	rhizosphere	rhizosphere	NN	_	_	_
36	biological	biological	JJ	_	_	_
37	rep	rep	NN	GEN	_	_
38	1	1	CD	_	_	_
39	slide	slide	NN	_	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	E.	E.	NNP	_	_	_
43	coli	coli	NN	_	_	_
44	O157	o157	NN	_	_	_
45	:	:	:	_	_	_
46	H7	h7	NN	_	_	_
47	interacted	interact	VBD	_	_	_
48	with	with	IN	_	_	_
49	lettuce	lettuce	NN	_	_	_
50	rhizosphere	rhizosphere	NN	_	_	_
51	biological	biological	JJ	_	_	_
52	rep	rep	NN	GEN	_	_
53	2	2	CD	_	_	_
54	slide	slide	NN	_	_	_
55	3	3	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	E.	e.	FW	_	_	_
58	coli	coli	FW	_	_	_
59	O157	o157	NN	_	_	_
60	:	:	:	_	_	_
61	H7	h7	NN	_	_	_
62	interacted	interact	VBD	_	_	_
63	with	with	IN	_	_	_
64	lettuce	lettuce	NN	_	_	_
65	rhizosphere	rhizosphere	NN	_	_	_
66	biological	biological	JJ	_	_	_
67	rep	rep	NN	GEN	_	_
68	2	2	CD	_	_	_
69	slide	slide	NN	_	_	_
70	4	4	CD	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	E.	E.	NNP	_	_	_
73	coli	coli	NN	_	_	_
74	O157	o157	NN	_	_	_
75	:	:	:	_	_	_
76	H7	h7	NN	_	_	_
77	interacted	interact	VBD	_	_	_
78	with	with	IN	_	_	_
79	lettuce	lettuce	NN	_	_	_
80	rhizosphere	rhizosphere	NN	_	_	_
81	biological	biological	JJ	_	_	_
82	rep	rep	NN	GEN	_	_
83	3	3	CD	_	_	_
84	slide	slide	NN	_	_	_
85	5	5	CD	_	_	_
86	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
87	E.	E.	NNP	_	_	_
88	coli	coli	NN	_	_	_
89	O157	o157	NN	_	_	_
90	:	:	:	_	_	_
91	H7	h7	NN	_	_	_
92	interacted	interact	VBD	_	_	_
93	with	with	IN	_	_	_
94	lettuce	lettuce	NN	_	_	_
95	rhizosphere	rhizosphere	NN	_	_	_
96	biological	biological	JJ	_	_	_
97	rep	rep	NN	GEN	_	_
98	3	3	CD	_	_	_
99	slide	slide	NN	_	_	_
100	6	6	CD	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	E.	E.	NNP	_	_	_
103	coli	coli	NN	_	_	_
104	O157	o157	NN	_	_	_
105	:	:	:	_	_	_
106	H7	h7	NN	_	_	_
107	was	be	VBD	_	_	_
108	grown	grow	VBN	_	_	_
109	in	in	IN	_	_	_
110	15mL	15ml	NN	_	_	_
111	falcon	falcon	NN	_	_	_
112	tubes	tube	NNS	_	_	_
113	containing	contain	VBG	_	_	_
114	8mL	8ml	NN	_	_	_
115	of	of	IN	_	_	_
116	filtered	filter	VBN	_	_	_
117	rat	rat	NN	_	_	_
118	's	's	POS	_	_	_
119	caecal	caecal	JJ	_	_	_
120	content	content	NN	_	_	_
121	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	O157	o157	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Sakai	Sakai	NNP	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	untreated	untreated	JJ	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	reference	reference	NN	_	_	_
11	sample	sample	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	_	_	SYM	_	_	_
14	rep	rep	NN	GEN	_	_
15	#	#	#	_	_	_
16	1	1	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	coli	coli	NN	_	_	_
20	O157	o157	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Sakai	Sakai	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	untreated	untreated	JJ	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	reference	reference	NN	_	_	_
27	sample	sample	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	_	_	SYM	_	_	_
30	rep	rep	NN	GEN	_	_
31	#	#	#	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	E.	E.	NNP	_	_	_
35	coli	coli	NN	_	_	_
36	O157	o157	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Sakai	Sakai	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	untreated	untreated	JJ	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	reference	reference	NN	_	_	_
43	sample	sample	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	_	_	SYM	_	_	_
46	rep	rep	NN	GEN	_	_
47	#	#	#	_	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	E.	NNP	_	_	_
51	coli	coli	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	OD660	od660	NN	_	_	_
54	nm	nm	NN	_	_	_
55	=	=	JJ	_	_	_
56	0.3	0.3	CD	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	was	be	VBD	_	_	_
59	incubated	incubate	VBN	_	_	_
60	with	with	IN	_	_	_
61	control	control	NN	_	_	_
62	protein	protein	NN	_	_	_
63	or	or	CC	_	_	_
64	antibacterial	antibacterial	JJ	_	_	_
65	preparations	preparation	NNS	_	_	_
66	in	in	IN	_	_	_
67	5	5	CD	_	_	_
68	mM	mm	NN	KWSUPP	_	_
69	TRIS	tris	NN	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	pH	ph	NN	_	_	_
72	7.6	7.6	CD	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	with	with	IN	_	_	_
75	150	150	CD	_	_	_
76	mM	mm	NN	KWSUPP	_	_
77	NaCl	nacl	NN	_	_	_
78	,	,	,	_	_	_
79	10	10	CD	_	_	_
80	µM	µm	NN	_	_	_
81	ZnSO4	znso4	NN	_	_	_
82	,	,	,	_	_	_
83	and	and	CC	_	_	_
84	2	2	CD	_	_	_
85	%	%	NN	_	_	_
86	LB	lb	NN	_	_	_
87	,	,	,	_	_	_
88	at	at	IN	_	_	_
89	37oC	37oc	NN	_	_	_
90	aerobically	aerobically	RB	_	_	_
91	with	with	IN	_	_	_
92	shaking	shake	VBG	_	_	_
93	.	.	.	_	_	_

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	_	_	SYM	_	_	_
51	PGRP	pgrp	SYM	_	_	_
52	_	_	SYM	_	_	_
53	30	30	CD	_	_	_
54	min	min	NN	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	E.	E.	NNP	_	_	_
57	coli	coli	NN	_	_	_
58	phage	phage	NN	_	_	_
59	3538	3538	CD	_	_	_
60	#	#	#	_	_	_
61	1	1	CD	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	E.	E.	NNP	_	_	_
64	coli	coli	NN	_	_	_
65	phage	phage	NN	_	_	_
66	3538	3538	CD	_	_	_
67	#	#	#	_	_	_
68	2	2	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	E.coli	e.coli	JJ	_	_	_
71	_	_	NN	_	_	_
72	polyphenols	polyphenol	NNS	_	_	_
73	_	_	VBP	_	_	_
74	repA	repa	NN	_	_	_
75	_	_	CD	_	_	_
76	t1	t1	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	E.coli	e.coli	NNS	_	_	_
79	_	_	VBP	_	_	_
80	polyphenols	polyphenol	NNS	_	_	_
81	_	_	SYM	_	_	_
82	repA	repA	NNP	_	_	_
83	_	_	SYM	_	_	_
84	t2	t2	FW	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
86	E.coli	e.coli	FW	_	_	_
87	_	_	SYM	_	_	_
88	polyphenols	polyphenol	NNS	_	_	_
89	_	_	VBP	_	_	_
90	repA	repa	NN	_	_	_
91	_	_	CD	_	_	_
92	t3	t3	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	E.coli	e.coli	NNS	_	_	_
95	_	_	VBP	_	_	_
96	polyphenols	polyphenol	NNS	_	_	_
97	_	_	VBP	_	_	_
98	repB	repb	NN	_	_	_
99	_	_	CD	_	_	_
100	t1	t1	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	E.coli	e.coli	NNS	_	_	_
103	_	_	VBP	_	_	_
104	polyphenols	polyphenol	NNS	_	_	_
105	_	_	VBP	_	_	_
106	repB	repb	NN	_	_	_
107	_	_	CD	_	_	_
108	t2	t2	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	E.coli	e.coli	NNS	_	_	_
111	_	_	VBP	_	_	_
112	polyphenols	polyphenol	NNS	_	_	_
113	_	_	VBP	_	_	_
114	repB	repb	NN	_	_	_
115	_	_	CD	_	_	_
116	t3	t3	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	E.coli	e.coli	NNS	_	_	_
119	_	_	VBP	_	_	_
120	polyphenols	polyphenol	NNS	_	_	_
121	_	_	VBP	_	_	_
122	repC	repc	NN	_	_	_
123	_	_	CD	_	_	_
124	t1	t1	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	E.coli	e.coli	NNS	_	_	_
127	_	_	VBP	_	_	_
128	polyphenols	polyphenol	NNS	_	_	_
129	_	_	VBP	_	_	_
130	repC	repc	NN	_	_	_
131	_	_	CD	_	_	_
132	t2	t2	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	E.coli	e.coli	NNS	_	_	_
135	_	_	VBP	_	_	_
136	polyphenols	polyphenol	NNS	_	_	_
137	_	_	VBP	_	_	_
138	repC	repc	NN	_	_	_
139	_	_	CD	_	_	_
140	t3	t3	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
142	E.	e.	FW	_	_	_
143	coli	coli	FW	_	_	_
144	Progesterone	progesterone	NN	_	_	_
145	Treatment	treatment	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	Ecoli	ecolus	NNS	_	_	_
148	_	_	VBP	_	_	_
149	pUC	puc	NN	_	_	_
150	expression	expression	NN	_	_	_
151	OD	od	NN	_	_	_
152	0.2	0.2	CD	_	_	_
153	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
154	Ecoli	Ecoli	NNP	_	_	_
155	_	_	NNP	_	_	_
156	pUC	puc	NN	_	_	_
157	expression	expression	NN	_	_	_
158	OD	od	NN	_	_	_
159	0.5	0.5	CD	_	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
161	Ecoli	Ecoli	NNP	_	_	_
162	_	_	NNP	_	_	_
163	pUC	puc	NN	_	_	_
164	expression	expression	NN	_	_	_
165	OD	od	NN	_	_	_
166	0.9	0.9	CD	_	_	_
167	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
168	E.	E.	NNP	_	_	_
169	Coli	Coli	NNP	_	_	_
170	PurR	purr	NN	TF	_	_
171	ChIP	chip	NN	_	_	_
172	DNA	dna	NN	_	_	_
173	Adenine	adenine	NN	_	_	_
174	1	1	CD	_	_	_
175	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
176	E.	E.	NNP	_	_	_
177	Coli	Coli	NNP	_	_	_
178	PurR	purr	NN	TF	_	_
179	ChIP	chip	NN	_	_	_
180	DNA	dna	NN	_	_	_
181	Adenine	adenine	NN	_	_	_
182	2	2	CD	_	_	_
183	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
184	E.	E.	NNP	_	_	_
185	Coli	Coli	NNP	_	_	_
186	PurR	purr	NN	TF	_	_
187	ChIP	chip	NN	_	_	_
188	DNA	dna	NN	_	_	_
189	glucose	glucose	NN	SUPP	_	_
190	1	1	CD	_	_	_
191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
192	E.	E.	NNP	_	_	_
193	Coli	Coli	NNP	_	_	_
194	PurR	purr	NN	TF	_	_
195	ChIP	chip	NN	_	_	_
196	DNA	dna	NN	_	_	_
197	glucose	glucose	NN	SUPP	_	_
198	2	2	CD	_	_	_
199	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
200	E.	E.	NNP	_	_	_
201	Coli	Coli	NNP	_	_	_
202	PurR	purr	NN	TF	_	_
203	Input	input	NN	_	_	_
204	DNA	dna	NN	_	_	_
205	Adenine	adenine	NN	_	_	_
206	1	1	CD	_	_	_
207	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
208	E.	E.	NNP	_	_	_
209	Coli	Coli	NNP	_	_	_
210	PurR	purr	NN	TF	_	_
211	Input	input	NN	_	_	_
212	DNA	dna	NN	_	_	_
213	Adenine	adenine	NN	_	_	_
214	2	2	CD	_	_	_
215	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
216	E.	E.	NNP	_	_	_
217	Coli	Coli	NNP	_	_	_
218	PurR	PurR	NNP	TF	_	_
219	Input	Input	NNP	_	_	_
220	DNA	DNA	NNP	_	_	_
221	glucose	glucose	NN	SUPP	_	_
222	1	1	CD	_	_	_
223	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
224	E.	E.	NNP	_	_	_
225	Coli	Coli	NNP	_	_	_
226	PurR	PurR	NNP	TF	_	_
227	Input	Input	NNP	_	_	_
228	DNA	DNA	NNP	_	_	_
229	glucose	glucose	NN	SUPP	_	_
230	2	2	CD	_	_	_
231	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
232	E.	E.	NNP	_	_	_
233	coli	coli	NN	_	_	_
234	recoded	recode	VBD	_	_	_
235	ompF	ompf	NN	GEN	_	_
236	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
237	E.	E.	NNP	_	_	_
238	coli	coli	NN	_	_	_
239	recoded	recode	VBD	_	_	_
240	ompF	ompf	NN	GEN	_	_
241	-LRB-	-lrb-	-LRB-	_	_	_
242	recoded	recode	VBN	_	_	_
243	ompF	ompf	NN	GEN	_	_
244	gene	gene	NN	_	_	_
245	-RRB-	-rrb-	-RRB-	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	Ecoli	ecolus	NNS	_	_	_
248	_	_	VBP	_	_	_
249	Recovery	recovery	NN	_	_	_
250	in	in	IN	_	_	_
251	10mM	10mm	NN	_	_	_
252	Na-P	na-p	NN	_	_	_
253	+	+	CC	_	_	_
254	0.2	0.2	CD	_	_	_
255	%	%	NN	_	_	_
256	glucose	glucose	NN	SUPP	_	_
257	T1	t1	NN	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	Ecoli	ecolus	NNS	_	_	_
260	_	_	VBP	_	_	_
261	Recovery	recovery	NN	_	_	_
262	in	in	IN	_	_	_
263	10mM	10mm	NN	_	_	_
264	Na-P	na-p	NN	_	_	_
265	+	+	CC	_	_	_
266	0.2	0.2	CD	_	_	_
267	%	%	NN	_	_	_
268	glucose	glucose	NN	SUPP	_	_
269	T2	t2	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	Ecoli	ecolus	NNS	_	_	_
272	_	_	VBP	_	_	_
273	Recovery	recovery	NN	_	_	_
274	in	in	IN	_	_	_
275	10mM	10mm	NN	_	_	_
276	Na-P	na-p	NN	_	_	_
277	+	+	CC	_	_	_
278	0.2	0.2	CD	_	_	_
279	%	%	NN	_	_	_
280	glucose	glucose	NN	SUPP	_	_
281	T3	t3	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	Ecoli	ecolus	NNS	_	_	_
284	_	_	VBP	_	_	_
285	Recovery	recovery	NN	_	_	_
286	in	in	IN	_	_	_
287	10mM	10mm	NN	_	_	_
288	Na-P	na-p	NN	_	_	_
289	+	+	CC	_	_	_
290	0.2	0.2	CD	_	_	_
291	%	%	NN	_	_	_
292	glucose	glucose	NN	SUPP	_	_
293	T4	t4	NN	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	Ecoli	ecolus	NNS	_	_	_
296	_	_	VBP	_	_	_
297	Recovery	recovery	NN	_	_	_
298	in	in	IN	_	_	_
299	10mM	10mm	NN	_	_	_
300	Na-P	na-p	NN	_	_	_
301	+	+	CC	_	_	_
302	0.2	0.2	CD	_	_	_
303	%	%	NN	_	_	_
304	glucose	glucose	NN	SUPP	_	_
305	T5	t5	NN	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	Ecoli	ecolus	NNS	_	_	_
308	_	_	VBP	_	_	_
309	Recovery	recovery	NN	_	_	_
310	in	in	IN	_	_	_
311	10mM	10mm	NN	_	_	_
312	Na-P	na-p	NN	_	_	_
313	+	+	CC	_	_	_
314	0.2	0.2	CD	_	_	_
315	%	%	NN	_	_	_
316	glucose	glucose	NN	SUPP	_	_
317	T6	t6	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	Ecoli	ecolus	NNS	_	_	_
320	_	_	VBP	_	_	_
321	Recovery	recovery	NN	_	_	_
322	in	in	IN	_	_	_
323	10mM	10mm	NN	_	_	_
324	Na-P	na-p	NN	_	_	_
325	+	+	CC	_	_	_
326	0.2	0.2	CD	_	_	_
327	%	%	NN	_	_	_
328	glucose	glucose	NN	SUPP	_	_
329	T7	t7	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	Ecoli	ecolus	NNS	_	_	_
332	_	_	VBP	_	_	_
333	Recovery	recovery	NN	_	_	_
334	in	in	IN	_	_	_
335	10mM	10mm	NN	_	_	_
336	Na-P	na-p	NN	_	_	_
337	T1	t1	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	Ecoli	ecolus	NNS	_	_	_
340	_	_	VBP	_	_	_
341	Recovery	recovery	NN	_	_	_
342	in	in	IN	_	_	_
343	10mM	10mm	NN	_	_	_
344	Na-P	na-p	NN	_	_	_
345	T2	t2	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	Ecoli	ecolus	NNS	_	_	_
348	_	_	VBP	_	_	_
349	Recovery	recovery	NN	_	_	_
350	in	in	IN	_	_	_
351	10mM	10mm	NN	_	_	_
352	Na-P	na-p	NN	_	_	_
353	T3	t3	NN	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	Ecoli	ecolus	NNS	_	_	_
356	_	_	VBP	_	_	_
357	Recovery	recovery	NN	_	_	_
358	in	in	IN	_	_	_
359	10mM	10mm	NN	_	_	_
360	Na-P	na-p	NN	_	_	_
361	T4	t4	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	Ecoli	ecolus	NNS	_	_	_
364	_	_	VBP	_	_	_
365	Recovery	recovery	NN	_	_	_
366	in	in	IN	_	_	_
367	10mM	10mm	NN	_	_	_
368	Na-P	na-p	NN	_	_	_
369	T5	t5	NN	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	Ecoli	ecolus	NNS	_	_	_
372	_	_	VBP	_	_	_
373	Recovery	recovery	NN	_	_	_
374	in	in	IN	_	_	_
375	10mM	10mm	NN	_	_	_
376	Na-P	na-p	NN	_	_	_
377	T6	t6	NN	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	Ecoli	ecolus	NNS	_	_	_
380	_	_	VBP	_	_	_
381	Recovery	recovery	NN	_	_	_
382	in	in	IN	_	_	_
383	10mM	10mm	NN	_	_	_
384	Na-P	na-p	NN	_	_	_
385	T7	t7	NN	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	E	e	NN	_	_	_
388	_	_	CD	_	_	_
389	coli	coli	NN	_	_	_
390	_	_	NN	_	_	_
391	response	response	NN	_	_	_
392	_	_	NN	_	_	_
393	control	control	NN	_	_	_
394	_	_	CD	_	_	_
395	1mM	1mm	NN	_	_	_
396	_	_	CD	_	_	_
397	H2O2	h2o2	NN	_	_	_
398	_	_	NN	_	_	_
399	added	add	VBD	_	_	_
400	_	_	CD	_	_	_
401	rep1	rep1	NN	_	_	_
402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
403	E	e	NN	_	_	_
404	_	_	CD	_	_	_
405	coli	coli	NN	_	_	_
406	_	_	NN	_	_	_
407	response	response	NN	_	_	_
408	_	_	NN	_	_	_
409	control	control	NN	_	_	_
410	_	_	CD	_	_	_
411	1mM	1mm	NN	_	_	_
412	_	_	CD	_	_	_
413	H2O2	h2o2	NN	_	_	_
414	_	_	NN	_	_	_
415	added	add	VBD	_	_	_
416	_	_	CD	_	_	_
417	rep2	rep2	NN	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	E	e	NN	_	_	_
420	_	_	CD	_	_	_
421	coli	coli	NN	_	_	_
422	_	_	NN	_	_	_
423	response	response	NN	_	_	_
424	_	_	NN	_	_	_
425	control	control	NN	_	_	_
426	_	_	CD	_	_	_
427	1mM	1mm	NN	_	_	_
428	_	_	CD	_	_	_
429	H2O2	h2o2	NN	_	_	_
430	_	_	NN	_	_	_
431	added	add	VBD	_	_	_
432	_	_	CD	_	_	_
433	rep3	rep3	NN	_	_	_
434	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
435	E	e	NN	_	_	_
436	_	_	CD	_	_	_
437	coli	coli	NN	_	_	_
438	_	_	NN	_	_	_
439	response	response	NN	_	_	_
440	_	_	NN	_	_	_
441	control	control	NN	_	_	_
442	_	_	CD	_	_	_
443	water	water	NN	_	_	_
444	_	_	NN	_	_	_
445	added	add	VBD	_	_	_
446	_	_	CD	_	_	_
447	rep1	rep1	NN	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	E	e	NN	_	_	_
450	_	_	CD	_	_	_
451	coli	coli	NN	_	_	_
452	_	_	NN	_	_	_
453	response	response	NN	_	_	_
454	_	_	NN	_	_	_
455	control	control	NN	_	_	_
456	_	_	CD	_	_	_
457	water	water	NN	_	_	_
458	_	_	NN	_	_	_
459	added	add	VBD	_	_	_
460	_	_	CD	_	_	_
461	rep2	rep2	NN	_	_	_
462	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
463	E	e	NN	_	_	_
464	_	_	CD	_	_	_
465	coli	coli	NN	_	_	_
466	_	_	NN	_	_	_
467	response	response	NN	_	_	_
468	_	_	NN	_	_	_
469	control	control	NN	_	_	_
470	_	_	CD	_	_	_
471	water	water	NN	_	_	_
472	_	_	NN	_	_	_
473	added	add	VBD	_	_	_
474	_	_	CD	_	_	_
475	rep3	rep3	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	E.coli	e.coli	NNS	_	_	_
478	RNAP	rnap	NN	_	_	_
479	beta	beta	NN	_	_	_
480	subunit	subunit	NN	_	_	_
481	ChIP	chip	NN	_	_	_
482	DNA	dna	NN	_	_	_
483	from	from	IN	_	_	_
484	heat-shocked	heat-shocked	JJ	_	_	_
485	condition	condition	NN	_	_	_
486	without	without	IN	_	_	_
487	rifampicin	rifampicin	NN	SUPP	_	_
488	treatment	treatment	NN	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	E.coli	e.coli	NNS	_	_	_
491	RNAP	rnap	NN	_	_	_
492	beta	beta	NN	_	_	_
493	subunit	subunit	NN	_	_	_
494	ChIP	chip	NN	_	_	_
495	DNA	dna	NN	_	_	_
496	from	from	IN	_	_	_
497	mid-exponential	mid-exponential	JJ	_	_	_
498	condition	condition	NN	_	_	_
499	without	without	IN	_	_	_
500	rifampicin	rifampicin	NN	SUPP	_	_
501	treatment	treatment	NN	_	_	_
502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
503	E.coli	e.coli	NNS	_	_	_
504	RNAP	rnap	NN	_	_	_
505	beta	beta	NN	_	_	_
506	subunit	subunit	NN	_	_	_
507	ChIP	chip	NN	_	_	_
508	DNA	dna	NN	_	_	_
509	from	from	IN	_	_	_
510	mid-exponential	mid-exponential	JJ	_	_	_
511	condition	condition	NN	_	_	_
512	with	with	IN	_	_	_
513	rifampicin	rifampicin	NN	SUPP	_	_
514	treatment	treatment	NN	_	_	_
515	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
516	E.coli	e.coli	NNS	_	_	_
517	RNAP	rnap	NN	_	_	_
518	beta	beta	NN	_	_	_
519	subunit	subunit	NN	_	_	_
520	ChIP	chip	NN	_	_	_
521	DNA	dna	NN	_	_	_
522	from	from	IN	_	_	_
523	nitrogen-limiting	nitrogen-limiting	JJ	_	_	_
524	condition	condition	NN	_	_	_
525	without	without	IN	_	_	_
526	rifampicin	rifampicin	NN	SUPP	_	_
527	treatment	treatment	NN	_	_	_
528	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
529	E.coli	e.coli	NNS	_	_	_
530	RNAP	rnap	NN	_	_	_
531	beta	beta	NN	_	_	_
532	subunit	subunit	NN	_	_	_
533	ChIP	chip	NN	_	_	_
534	DNA	dna	NN	_	_	_
535	from	from	IN	_	_	_
536	stationary	stationary	JJ	_	_	_
537	condition	condition	NN	_	_	_
538	without	without	IN	_	_	_
539	rifampicin	rifampicin	NN	SUPP	_	_
540	treatment	treatment	NN	_	_	_
541	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
542	E.	E.	NNP	_	_	_
543	coli	coli	NN	_	_	_
544	RNA	rna	NN	_	_	_
545	polymerase	polymerase	NN	_	_	_
546	core	core	NN	_	_	_
547	enzyme	enzyme	NN	_	_	_
548	was	be	VBD	_	_	_
549	purchased	purchase	VBN	_	_	_
550	from	from	IN	_	_	_
551	Epicentre	Epicentre	NNP	_	_	_
552	-LRB-	-lrb-	-LRB-	_	_	_
553	Madison	Madison	NNP	_	_	_
554	,	,	,	_	_	_
555	WI	WI	NNP	_	_	_
556	,	,	,	_	_	_
557	USA	USA	NNP	_	_	_
558	-RRB-	-rrb-	-RRB-	_	_	_
559	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	Rosetta	rosetta	NN	_	_	_
5	cells	cell	NNS	_	_	_
6	transformed	transform	VBN	_	_	_
7	with	with	IN	_	_	_
8	pET-28a	pet-28a	NN	_	_	_
9	or	or	CC	_	_	_
10	pET-28a-BnTR1	pet-28a-bntr1	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	OD600nm	od600nm	NN	_	_	_
13	=	=	JJ	_	_	_
14	0.6	0.6	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	were	be	VBD	_	_	_
17	induced	induce	VBN	_	_	_
18	with	with	IN	_	_	_
19	0.1	0.1	CD	_	_	_
20	mM	mm	NN	KWSUPP	_	_
21	IPTG	iptg	NN	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	for	for	IN	_	_	_
26	1	1	CD	_	_	_
27	hour	hour	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	_	_	VBP	_	_	_
4	RviaT1	rviat1	NN	_	_	_
5	_	_	CD	_	_	_
6	SR1	sr1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	E.coli	e.coli	NNS	_	_	_
9	_	_	VBP	_	_	_
10	RviaT1	rviat1	NN	_	_	_
11	_	_	CD	_	_	_
12	SR2	sr2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	E.coli	e.coli	NNS	_	_	_
15	_	_	VBP	_	_	_
16	RviaT1	rviat1	NN	_	_	_
17	_	_	CD	_	_	_
18	SR3	sr3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	E.coli	e.coli	NNS	_	_	_
21	_	_	VBP	_	_	_
22	RviaT2	rviat2	NN	_	_	_
23	_	_	CD	_	_	_
24	SR1	sr1	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E.coli	e.coli	NNS	_	_	_
27	_	_	VBP	_	_	_
28	RviaT2	rviat2	NN	_	_	_
29	_	_	CD	_	_	_
30	SR2	sr2	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	E.coli	e.coli	NNS	_	_	_
33	_	_	VBP	_	_	_
34	RviaT2	rviat2	NN	_	_	_
35	_	_	CD	_	_	_
36	SR3	sr3	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	E.coli	e.coli	NNS	_	_	_
39	_	_	VBP	_	_	_
40	RviaT3	rviat3	NN	_	_	_
41	_	_	CD	_	_	_
42	SR1	sr1	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	E.coli	e.coli	NNS	_	_	_
45	_	_	VBP	_	_	_
46	RviaT3	rviat3	NN	_	_	_
47	_	_	CD	_	_	_
48	SR2	sr2	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	E.coli	e.coli	NNS	_	_	_
51	_	_	VBP	_	_	_
52	RviaT3	rviat3	NN	_	_	_
53	_	_	CD	_	_	_
54	SR3	sr3	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	E.coli	e.coli	NNS	_	_	_
57	_	_	VBP	_	_	_
58	RviaT4	rviat4	NN	_	_	_
59	_	_	CD	_	_	_
60	SR1	sr1	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	E.coli	e.coli	NNS	_	_	_
63	_	_	VBP	_	_	_
64	RviaT4	rviat4	NN	_	_	_
65	_	_	CD	_	_	_
66	SR2	sr2	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	E.coli	e.coli	NNS	_	_	_
69	_	_	VBP	_	_	_
70	RviaT4	rviat4	NN	_	_	_
71	_	_	CD	_	_	_
72	SR3	sr3	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	E.coli	e.coli	NNS	_	_	_
75	_	_	VBP	_	_	_
76	RviaT5	rviat5	NN	_	_	_
77	_	_	CD	_	_	_
78	SR2	sr2	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	E.coli	e.coli	NNS	_	_	_
81	_	_	VBP	_	_	_
82	RviaT5	rviat5	NN	_	_	_
83	_	_	CD	_	_	_
84	SR3	sr3	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	E.coli	e.coli	NNS	_	_	_
87	_	_	VBP	_	_	_
88	RviaT6	rviat6	NN	_	_	_
89	_	_	CD	_	_	_
90	SR2	sr2	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	E.coli	e.coli	NNS	_	_	_
93	_	_	VBP	_	_	_
94	RviaT6	rviat6	NN	_	_	_
95	_	_	CD	_	_	_
96	SR3	sr3	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	E.coli	e.coli	NNS	_	_	_
99	_	_	VBP	_	_	_
100	RviaT7	rviat7	NN	_	_	_
101	_	_	CD	_	_	_
102	SR2	sr2	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	E.coli	e.coli	NNS	_	_	_
105	_	_	VBP	_	_	_
106	RviaT7	rviat7	NN	_	_	_
107	_	_	CD	_	_	_
108	SR3	sr3	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	E.coli	e.coli	NNS	_	_	_
111	_	_	VBP	_	_	_
112	RviaT8	rviat8	NN	_	_	_
113	_	_	CD	_	_	_
114	SR2	sr2	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	E.coli	e.coli	NNS	_	_	_
117	_	_	VBP	_	_	_
118	RviaT8	rviat8	NN	_	_	_
119	_	_	CD	_	_	_
120	SR3	sr3	NN	_	_	_
121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
122	E.	E.	NNP	_	_	_
123	coli	coli	NN	_	_	_
124	samples	sample	NNS	_	_	_
125	for	for	IN	_	_	_
126	RNA	rna	NN	_	_	_
127	extraction	extraction	NN	_	_	_
128	were	be	VBD	_	_	_
129	taken	take	VBN	_	_	_
130	during	during	IN	_	_	_
131	fermentation	fermentation	NN	_	_	_
132	.	.	.	_	_	_

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	NN	_	_	_
11	E.coli	e.coli	NN	_	_	_
12	SE15	se15	NN	_	_	_
13	is	be	VBZ	_	_	_
14	cultured	culture	VBN	_	_	_
15	in	in	IN	_	_	_
16	LB	lb	NN	MED	_	_
17	broth	broth	NN	MED	_	_
18	and	and	CC	_	_	_
19	LuxS	luxs	NN	_	_	_
20	E.coli	e.coli	NN	_	_	_
21	SE15	se15	NN	_	_	_
22	is	be	VBZ	_	_	_
23	cultured	culture	VBN	_	_	_
24	in	in	IN	_	_	_
25	LB	lb	NN	MED	_	_
26	broth	broth	NN	MED	_	_
27	with	with	IN	_	_	_
28	kanamycine	kanamycine	NN	_	_	_
29	at	at	IN	_	_	_
30	37	37	CD	_	_	_
31	℃	℃	NN	_	_	_
32	and	and	CC	_	_	_
33	in	in	IN	_	_	_
34	150rpm	150rpm	NN	_	_	_
35	shaking	shake	VBG	_	_	_
36	incubator	incubator	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	E.coli	e.coli	NN	_	_	_
39	SE15	se15	NN	_	_	_
40	is	be	VBZ	_	_	_
41	isolated	isolate	VBN	_	_	_
42	from	from	IN	_	_	_
43	indwelling	indwell	VBG	_	_	_
44	catheter	catheter	NN	_	_	_
45	of	of	IN	_	_	_
46	patient	patient	NN	_	_	_
47	and	and	CC	_	_	_
48	deleted	delete	VBN	_	_	_
49	LuxS	luxs	NN	_	_	_
50	gene	gene	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	related	related	JJ	_	_	_
53	to	to	TO	_	_	_
54	quorum	quorum	NN	_	_	_
55	sensing	sense	VBG	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	E.coli	e.coli	NN	_	_	_
59	SE15	se15	NN	_	_	_
60	isolated	isolate	VBN	_	_	_
61	from	from	IN	_	_	_
62	indwelling	indwell	VBG	_	_	_
63	catheter	catheter	NN	_	_	_
64	of	of	IN	_	_	_
65	patient	patient	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	E	e	NN	_	_	_
68	_	_	FW	_	_	_
69	coli	coli	FW	_	_	_
70	_	_	SYM	_	_	_
71	sham	sham	FW	_	_	_
72	_	_	FW	_	_	_
73	powerline	powerline	FW	_	_	_
74	_	_	SYM	_	_	_
75	interm	interm	FW	_	_	_
76	_	_	FW	_	_	_
77	15h	15h	FW	_	_	_
78	_	_	SYM	_	_	_
79	rep1	rep1	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
81	E	e	NN	_	_	_
82	_	_	FW	_	_	_
83	coli	coli	FW	_	_	_
84	_	_	SYM	_	_	_
85	sham	sham	FW	_	_	_
86	_	_	FW	_	_	_
87	powerline	powerline	FW	_	_	_
88	_	_	SYM	_	_	_
89	interm	interm	FW	_	_	_
90	_	_	FW	_	_	_
91	15h	15h	FW	_	_	_
92	_	_	SYM	_	_	_
93	rep2	rep2	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
95	E	e	NN	_	_	_
96	_	_	FW	_	_	_
97	coli	coli	FW	_	_	_
98	_	_	SYM	_	_	_
99	sham	sham	FW	_	_	_
100	_	_	FW	_	_	_
101	powerline	powerline	FW	_	_	_
102	_	_	SYM	_	_	_
103	interm	interm	FW	_	_	_
104	_	_	FW	_	_	_
105	15h	15h	FW	_	_	_
106	_	_	SYM	_	_	_
107	rep3	rep3	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
109	E	e	NN	_	_	_
110	_	_	FW	_	_	_
111	coli	coli	FW	_	_	_
112	_	_	SYM	_	_	_
113	sham	sham	VBP	_	_	_
114	_	_	SYM	_	_	_
115	powerline	powerline	FW	_	_	_
116	_	_	FW	_	_	_
117	interm	interm	FW	_	_	_
118	_	_	SYM	_	_	_
119	2.5	2.5	CD	_	_	_
120	h	h	NN	_	_	_
121	_	_	CD	_	_	_
122	rep1	rep1	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	E	e	NN	_	_	_
125	_	_	FW	_	_	_
126	coli	coli	FW	_	_	_
127	_	_	SYM	_	_	_
128	sham	sham	VBP	_	_	_
129	_	_	SYM	_	_	_
130	powerline	powerline	FW	_	_	_
131	_	_	FW	_	_	_
132	interm	interm	FW	_	_	_
133	_	_	SYM	_	_	_
134	2.5	2.5	CD	_	_	_
135	h	h	NN	_	_	_
136	_	_	CD	_	_	_
137	rep2	rep2	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	E	e	NN	_	_	_
140	_	_	FW	_	_	_
141	coli	coli	FW	_	_	_
142	_	_	SYM	_	_	_
143	sham	sham	VBP	_	_	_
144	_	_	SYM	_	_	_
145	powerline	powerline	FW	_	_	_
146	_	_	FW	_	_	_
147	interm	interm	FW	_	_	_
148	_	_	SYM	_	_	_
149	2.5	2.5	CD	_	_	_
150	h	h	NN	_	_	_
151	_	_	CD	_	_	_
152	rep3	rep3	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	E	e	NN	_	_	_
155	_	_	FW	_	_	_
156	coli	coli	FW	_	_	_
157	_	_	SYM	_	_	_
158	sham	sham	VBP	_	_	_
159	_	_	SYM	_	_	_
160	powerline	powerline	FW	_	_	_
161	_	_	FW	_	_	_
162	interm	interm	FW	_	_	_
163	_	_	SYM	_	_	_
164	8	8	CD	_	_	_
165	min	min	NN	_	_	_
166	_	_	CD	_	_	_
167	rep1	rep1	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	E	e	NN	_	_	_
170	_	_	FW	_	_	_
171	coli	coli	FW	_	_	_
172	_	_	SYM	_	_	_
173	sham	sham	VBP	_	_	_
174	_	_	SYM	_	_	_
175	powerline	powerline	FW	_	_	_
176	_	_	FW	_	_	_
177	interm	interm	FW	_	_	_
178	_	_	SYM	_	_	_
179	8	8	CD	_	_	_
180	min	min	NN	_	_	_
181	_	_	CD	_	_	_
182	rep2	rep2	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	E	e	NN	_	_	_
185	_	_	FW	_	_	_
186	coli	coli	FW	_	_	_
187	_	_	SYM	_	_	_
188	sham	sham	VBP	_	_	_
189	_	_	SYM	_	_	_
190	powerline	powerline	FW	_	_	_
191	_	_	FW	_	_	_
192	interm	interm	FW	_	_	_
193	_	_	SYM	_	_	_
194	8	8	CD	_	_	_
195	min	min	NN	_	_	_
196	_	_	CD	_	_	_
197	rep3	rep3	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	E	e	NN	_	_	_
200	_	_	FW	_	_	_
201	coli	coli	FW	_	_	_
202	_	_	SYM	_	_	_
203	sham	sham	VBP	_	_	_
204	_	_	SYM	_	_	_
205	sinusoidal	sinusoidal	JJ	_	_	_
206	_	_	NN	_	_	_
207	cont	cont	NN	_	_	_
208	_	_	SYM	_	_	_
209	15h	15h	CD	_	_	_
210	_	_	CD	_	_	_
211	rep1	rep1	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	E	e	NN	_	_	_
214	_	_	FW	_	_	_
215	coli	coli	FW	_	_	_
216	_	_	SYM	_	_	_
217	sham	sham	VBP	_	_	_
218	_	_	SYM	_	_	_
219	sinusoidal	sinusoidal	JJ	_	_	_
220	_	_	NN	_	_	_
221	cont	cont	NN	_	_	_
222	_	_	SYM	_	_	_
223	15h	15h	CD	_	_	_
224	_	_	CD	_	_	_
225	rep2	rep2	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	E	e	NN	_	_	_
228	_	_	FW	_	_	_
229	coli	coli	FW	_	_	_
230	_	_	SYM	_	_	_
231	sham	sham	VBP	_	_	_
232	_	_	SYM	_	_	_
233	sinusoidal	sinusoidal	JJ	_	_	_
234	_	_	NN	_	_	_
235	cont	cont	NN	_	_	_
236	_	_	SYM	_	_	_
237	15h	15h	CD	_	_	_
238	_	_	CD	_	_	_
239	rep3	rep3	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	E	e	NN	_	_	_
242	_	_	FW	_	_	_
243	coli	coli	FW	_	_	_
244	_	_	SYM	_	_	_
245	sham	sham	VBP	_	_	_
246	_	_	SYM	_	_	_
247	sinusoidal	sinusoidal	JJ	_	_	_
248	_	_	NN	_	_	_
249	cont	cont	NN	_	_	_
250	_	_	SYM	_	_	_
251	2.5	2.5	CD	_	_	_
252	h	h	NN	_	_	_
253	_	_	CD	_	_	_
254	rep1	rep1	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	E	e	NN	_	_	_
257	_	_	FW	_	_	_
258	coli	coli	FW	_	_	_
259	_	_	SYM	_	_	_
260	sham	sham	VBP	_	_	_
261	_	_	SYM	_	_	_
262	sinusoidal	sinusoidal	JJ	_	_	_
263	_	_	NN	_	_	_
264	cont	cont	NN	_	_	_
265	_	_	SYM	_	_	_
266	2.5	2.5	CD	_	_	_
267	h	h	NN	_	_	_
268	_	_	CD	_	_	_
269	rep2	rep2	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	E	e	NN	_	_	_
272	_	_	FW	_	_	_
273	coli	coli	FW	_	_	_
274	_	_	SYM	_	_	_
275	sham	sham	VBP	_	_	_
276	_	_	SYM	_	_	_
277	sinusoidal	sinusoidal	JJ	_	_	_
278	_	_	NN	_	_	_
279	cont	cont	NN	_	_	_
280	_	_	SYM	_	_	_
281	2.5	2.5	CD	_	_	_
282	h	h	NN	_	_	_
283	_	_	CD	_	_	_
284	rep3	rep3	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	E	e	NN	_	_	_
287	_	_	FW	_	_	_
288	coli	coli	FW	_	_	_
289	_	_	SYM	_	_	_
290	sham	sham	VBP	_	_	_
291	_	_	SYM	_	_	_
292	sinusoidal	sinusoidal	JJ	_	_	_
293	_	_	NN	_	_	_
294	cont	cont	NN	_	_	_
295	_	_	NN	_	_	_
296	8	8	CD	_	_	_
297	min	min	NN	_	_	_
298	_	_	CD	_	_	_
299	rep1	rep1	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	E	e	NN	_	_	_
302	_	_	FW	_	_	_
303	coli	coli	FW	_	_	_
304	_	_	SYM	_	_	_
305	sham	sham	VBP	_	_	_
306	_	_	SYM	_	_	_
307	sinusoidal	sinusoidal	JJ	_	_	_
308	_	_	NN	_	_	_
309	cont	cont	NN	_	_	_
310	_	_	NN	_	_	_
311	8	8	CD	_	_	_
312	min	min	NN	_	_	_
313	_	_	CD	_	_	_
314	rep2	rep2	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	E	e	NN	_	_	_
317	_	_	FW	_	_	_
318	coli	coli	FW	_	_	_
319	_	_	SYM	_	_	_
320	sham	sham	VBP	_	_	_
321	_	_	SYM	_	_	_
322	sinusoidal	sinusoidal	JJ	_	_	_
323	_	_	NN	_	_	_
324	cont	cont	NN	_	_	_
325	_	_	NN	_	_	_
326	8	8	CD	_	_	_
327	min	min	NN	_	_	_
328	_	_	CD	_	_	_
329	rep3	rep3	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	E	e	NN	_	_	_
332	_	_	FW	_	_	_
333	coli	coli	FW	_	_	_
334	_	_	SYM	_	_	_
335	sham	sham	VBP	_	_	_
336	_	_	SYM	_	_	_
337	sinusoidal	sinusoidal	JJ	_	_	_
338	_	_	NN	_	_	_
339	interm	interm	NN	_	_	_
340	_	_	CD	_	_	_
341	15h	15h	JJ	_	_	_
342	_	_	NN	_	_	_
343	rep1	rep1	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	E	e	NN	_	_	_
346	_	_	FW	_	_	_
347	coli	coli	FW	_	_	_
348	_	_	SYM	_	_	_
349	sham	sham	VBP	_	_	_
350	_	_	SYM	_	_	_
351	sinusoidal	sinusoidal	JJ	_	_	_
352	_	_	NN	_	_	_
353	interm	interm	NN	_	_	_
354	_	_	CD	_	_	_
355	15h	15h	JJ	_	_	_
356	_	_	NN	_	_	_
357	rep2	rep2	NN	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	E	e	NN	_	_	_
360	_	_	FW	_	_	_
361	coli	coli	FW	_	_	_
362	_	_	SYM	_	_	_
363	sham	sham	VBP	_	_	_
364	_	_	SYM	_	_	_
365	sinusoidal	sinusoidal	JJ	_	_	_
366	_	_	NN	_	_	_
367	interm	interm	NN	_	_	_
368	_	_	CD	_	_	_
369	15h	15h	JJ	_	_	_
370	_	_	NN	_	_	_
371	rep3	rep3	NN	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	E	e	NN	_	_	_
374	_	_	FW	_	_	_
375	coli	coli	FW	_	_	_
376	_	_	SYM	_	_	_
377	sham	sham	VBP	_	_	_
378	_	_	SYM	_	_	_
379	sinusoidal	sinusoidal	JJ	_	_	_
380	_	_	NN	_	_	_
381	interm	interm	NN	_	_	_
382	_	_	CD	_	_	_
383	2.5	2.5	CD	_	_	_
384	h	h	NN	_	_	_
385	_	_	CD	_	_	_
386	rep1	rep1	NN	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	E	e	NN	_	_	_
389	_	_	FW	_	_	_
390	coli	coli	FW	_	_	_
391	_	_	SYM	_	_	_
392	sham	sham	VBP	_	_	_
393	_	_	SYM	_	_	_
394	sinusoidal	sinusoidal	JJ	_	_	_
395	_	_	NN	_	_	_
396	interm	interm	NN	_	_	_
397	_	_	CD	_	_	_
398	2.5	2.5	CD	_	_	_
399	h	h	NN	_	_	_
400	_	_	CD	_	_	_
401	rep2	rep2	NN	_	_	_
402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
403	E	e	NN	_	_	_
404	_	_	FW	_	_	_
405	coli	coli	FW	_	_	_
406	_	_	SYM	_	_	_
407	sham	sham	VBP	_	_	_
408	_	_	SYM	_	_	_
409	sinusoidal	sinusoidal	JJ	_	_	_
410	_	_	NN	_	_	_
411	interm	interm	NN	_	_	_
412	_	_	CD	_	_	_
413	2.5	2.5	CD	_	_	_
414	h	h	NN	_	_	_
415	_	_	SYM	_	_	_
416	rep3	rep3	CD	_	_	_
417	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
418	Ecoli	Ecoli	NNP	_	_	_
419	_	_	NNP	_	_	_
420	Sodium	sodium	NN	_	_	_
421	Azide	azide	NN	_	_	_
422	treatment	treatment	NN	_	_	_
423	T1	t1	NN	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	Ecoli	ecolus	NNS	_	_	_
426	_	_	VBP	_	_	_
427	Sodium	sodium	NN	_	_	_
428	Azide	azide	NN	_	_	_
429	treatment	treatment	NN	_	_	_
430	T2	t2	NN	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	Ecoli	ecolus	NNS	_	_	_
433	_	_	VBP	_	_	_
434	Sodium	sodium	NN	_	_	_
435	Azide	azide	NN	_	_	_
436	treatment	treatment	NN	_	_	_
437	T3	t3	NN	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	Ecoli	ecolus	NNS	_	_	_
440	_	_	VBP	_	_	_
441	Sodium	sodium	NN	_	_	_
442	Azide	azide	NN	_	_	_
443	treatment	treatment	NN	_	_	_
444	T4	t4	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	E.	e.	FW	_	_	_
447	coli	coli	FW	_	_	_
448	ST131	st131	NN	_	_	_
449	UR40	ur40	NN	_	_	_
450	was	be	VBD	_	_	_
451	treated	treat	VBN	_	_	_
452	with	with	IN	_	_	_
453	ciprofloxacin	ciprofloxacin	NN	_	_	_
454	-LRB-	-lrb-	-LRB-	_	_	_
455	2µg/mL	2µg/ml	NN	_	_	_
456	-RRB-	-rrb-	-RRB-	_	_	_
457	and	and	CC	_	_	_
458	samples	sample	NNS	_	_	_
459	were	be	VBD	_	_	_
460	taken	take	VBN	_	_	_
461	at	at	IN	_	_	_
462	time	time	NN	_	_	_
463	points	point	NNS	_	_	_
464	0	0	CD	_	_	_
465	min	min	NN	_	_	_
466	,	,	,	_	_	_
467	30	30	CD	_	_	_
468	min	min	NN	_	_	_
469	and	and	CC	_	_	_
470	90	90	CD	_	_	_
471	min	min	NN	_	_	_
472	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	_	_	VBP	_	_	_
4	stat	stat	NN	_	_	_
5	_	_	CD	_	_	_
6	dynamic	dynamic	JJ	_	_	_
7	_	_	NN	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	E.coli	e.coli	NNS	_	_	_
11	_	_	VBP	_	_	_
12	stat	stat	NN	_	_	_
13	_	_	CD	_	_	_
14	dynamic	dynamic	JJ	_	_	_
15	_	_	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	coli	coli	NN	_	_	_
20	stationary	stationary	JJ	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	stationary	stationary	JJ	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Ecoli	ecolus	NNS	_	_	_
29	_	_	VBP	_	_	_
30	Stationary	stationary	JJ	_	_	_
31	phase	phase	NN	_	_	_
32	in	in	IN	_	_	_
33	LB	lb	NN	_	_	_
34	T1	t1	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Ecoli	ecolus	NNS	_	_	_
37	_	_	VBP	_	_	_
38	Stationary	stationary	JJ	_	_	_
39	phase	phase	NN	_	_	_
40	in	in	IN	_	_	_
41	LB	lb	NN	_	_	_
42	T2	t2	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Ecoli	ecolus	NNS	_	_	_
45	_	_	VBP	_	_	_
46	Stationary	stationary	JJ	_	_	_
47	phase	phase	NN	_	_	_
48	in	in	IN	_	_	_
49	LB	lb	NN	_	_	_
50	T3	t3	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Ecoli	ecolus	NNS	_	_	_
53	_	_	VBP	_	_	_
54	Stationary	stationary	JJ	_	_	_
55	phase	phase	NN	_	_	_
56	in	in	IN	_	_	_
57	LB	lb	NN	_	_	_
58	T4	t4	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Ecoli	ecolus	NNS	_	_	_
61	_	_	VBP	_	_	_
62	Stationary	stationary	JJ	_	_	_
63	phase	phase	NN	_	_	_
64	in	in	IN	_	_	_
65	LB	LB	NNP	_	_	_
66	T5	T5	NNP	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Ecoli	Ecoli	NNP	_	_	_
69	_	_	NNP	_	_	_
70	Stationary	Stationary	NNP	_	_	_
71	phase	phase	NN	_	_	_
72	in	in	IN	_	_	_
73	LB	LB	NNP	_	_	_
74	T6	T6	NNP	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	E.	E.	NNP	_	_	_
77	Coli	Coli	NNP	_	_	_
78	Stationary	Stationary	NNP	_	_	_
79	RpoB	rpob	NN	_	_	_
80	ChIP	chip	NN	_	_	_
81	DNA	dna	NN	_	_	_
82	1	1	CD	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	E.	E.	NNP	_	_	_
85	Coli	Coli	NNP	_	_	_
86	Stationary	Stationary	NNP	_	_	_
87	RpoB	rpob	NN	_	_	_
88	ChIP	chip	NN	_	_	_
89	DNA	dna	NN	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	E.	E.	NNP	_	_	_
93	Coli	Coli	NNP	_	_	_
94	Stationary	Stationary	NNP	_	_	_
95	RpoB	rpob	NN	_	_	_
96	ChIP	chip	NN	_	_	_
97	DNA	dna	NN	_	_	_
98	Mock	mock	NN	_	_	_
99	1	1	CD	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	E.	E.	NNP	_	_	_
102	Coli	Coli	NNP	_	_	_
103	Stationary	Stationary	NNP	_	_	_
104	RpoB	rpob	NN	_	_	_
105	ChIP	chip	NN	_	_	_
106	DNA	dna	NN	_	_	_
107	Mock	mock	NN	_	_	_
108	2	2	CD	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	E.	E.	NNP	_	_	_
111	Coli	Coli	NNP	_	_	_
112	Stationary	Stationary	NNP	_	_	_
113	RpoD	rpod	NN	_	_	_
114	ChIP	chip	NN	_	_	_
115	DNA	dna	NN	_	_	_
116	1	1	CD	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	E.	E.	NNP	_	_	_
119	Coli	Coli	NNP	_	_	_
120	Stationary	Stationary	NNP	_	_	_
121	RpoD	rpod	NN	_	_	_
122	ChIP	chip	NN	_	_	_
123	DNA	dna	NN	_	_	_
124	2	2	CD	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	E.	E.	NNP	_	_	_
127	Coli	Coli	NNP	_	_	_
128	Stationary	Stationary	NNP	_	_	_
129	RpoD	rpod	NN	_	_	_
130	ChIP	chip	NN	_	_	_
131	DNA	dna	NN	_	_	_
132	Mock	mock	NN	_	_	_
133	1	1	CD	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	E.	E.	NNP	_	_	_
136	Coli	Coli	NNP	_	_	_
137	Stationary	Stationary	NNP	_	_	_
138	RpoD	rpod	NN	_	_	_
139	ChIP	chip	NN	_	_	_
140	DNA	dna	NN	_	_	_
141	Mock	mock	NN	_	_	_
142	2	2	CD	_	_	_
143	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
144	E.	E.	NNP	_	_	_
145	Coli	Coli	NNP	_	_	_
146	Stationary	Stationary	NNP	_	_	_
147	RpoD	rpod	NN	_	_	_
148	DelS	dels	NN	_	_	_
149	ChIP	chip	NN	_	_	_
150	DNA	dna	NN	_	_	_
151	1	1	CD	_	_	_
152	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
153	E.	E.	NNP	_	_	_
154	Coli	Coli	NNP	_	_	_
155	Stationary	Stationary	NNP	_	_	_
156	RpoD	rpod	NN	_	_	_
157	DelS	dels	NN	_	_	_
158	ChIP	chip	NN	_	_	_
159	DNA	dna	NN	_	_	_
160	2	2	CD	_	_	_
161	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
162	E.	E.	NNP	_	_	_
163	Coli	Coli	NNP	_	_	_
164	Stationary	Stationary	NNP	_	_	_
165	RpoD	rpod	NN	_	_	_
166	DelS	dels	NN	_	_	_
167	ChIP	chip	NN	_	_	_
168	DNA	dna	NN	_	_	_
169	Mock	mock	NN	_	_	_
170	1	1	CD	_	_	_
171	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
172	E.	E.	NNP	_	_	_
173	Coli	Coli	NNP	_	_	_
174	Stationary	Stationary	NNP	_	_	_
175	RpoD	rpod	NN	_	_	_
176	DelS	dels	NN	_	_	_
177	ChIP	chip	NN	_	_	_
178	DNA	dna	NN	_	_	_
179	Mock	mock	NN	_	_	_
180	2	2	CD	_	_	_
181	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
182	E.	E.	NNP	_	_	_
183	Coli	Coli	NNP	_	_	_
184	Stationary	Stationary	NNP	_	_	_
185	RpoS	rpos	NN	_	_	_
186	ChIP	chip	NN	_	_	_
187	DNA	dna	NN	_	_	_
188	1	1	CD	_	_	_
189	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
190	E.	E.	NNP	_	_	_
191	Coli	Coli	NNP	_	_	_
192	Stationary	Stationary	NNP	_	_	_
193	RpoS	rpos	NN	_	_	_
194	ChIP	chip	NN	_	_	_
195	DNA	dna	NN	_	_	_
196	2	2	CD	_	_	_
197	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
198	E.	E.	NNP	_	_	_
199	Coli	Coli	NNP	_	_	_
200	Stationary	Stationary	NNP	_	_	_
201	RpoS	rpos	NN	_	_	_
202	ChIP	chip	NN	_	_	_
203	DNA	dna	NN	_	_	_
204	3	3	CD	_	_	_
205	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
206	E.	E.	NNP	_	_	_
207	Coli	Coli	NNP	_	_	_
208	Stationary	Stationary	NNP	_	_	_
209	RpoS	rpos	NN	_	_	_
210	ChIP	chip	NN	_	_	_
211	DNA	dna	NN	_	_	_
212	Mock	mock	NN	_	_	_
213	1	1	CD	_	_	_
214	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
215	E.	E.	NNP	_	_	_
216	Coli	Coli	NNP	_	_	_
217	Stationary	Stationary	NNP	_	_	_
218	RpoS	rpos	NN	_	_	_
219	ChIP	chip	NN	_	_	_
220	DNA	dna	NN	_	_	_
221	Mock	mock	NN	_	_	_
222	2	2	CD	_	_	_
223	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
224	E.	E.	NNP	_	_	_
225	Coli	Coli	NNP	_	_	_
226	Stationary	Stationary	NNP	_	_	_
227	RpoS	rpos	NN	_	_	_
228	ChIP	chip	NN	_	_	_
229	DNA	dna	NN	_	_	_
230	Mock	mock	NN	_	_	_
231	3	3	CD	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	E.	e.	FW	_	_	_
234	coli	coli	FW	_	_	_
235	strain	strain	NN	_	_	_
236	B178	b178	NN	_	_	_
237	-LRB-	-lrb-	-LRB-	_	_	_
238	Georgopoulos	Georgopoulos	NNP	_	_	_
239	et	et	FW	_	_	_
240	al.	al.	FW	_	_	_
241	-LRB-	-lrb-	-LRB-	_	_	_
242	1973	1973	CD	_	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	J	J	NNP	_	_	_
245	Mol	Mol	NNP	_	_	_
246	Biol	Biol	NNP	_	_	_
247	76	76	CD	_	_	_
248	:	:	:	_	_	_
249	45-60	45-60	CD	_	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	in	in	IN	_	_	_
252	which	which	WDT	_	_	_
253	the	the	DT	_	_	_
254	endogenous	endogenous	JJ	_	_	_
255	groES	groes	NN	_	_	_
256	and	and	CC	_	_	_
257	groEL	groel	NN	_	_	_
258	genes	gene	NNS	_	_	_
259	have	have	VBP	_	_	_
260	been	be	VBN	_	_	_
261	deleted	delete	VBN	_	_	_
262	and	and	CC	_	_	_
263	that	that	DT	_	_	_
264	is	be	VBZ	_	_	_
265	maintained	maintain	VBN	_	_	_
266	alive	alive	JJ	_	_	_
267	by	by	IN	_	_	_
268	the	the	DT	_	_	_
269	pOFX-tac1-derived	pofx-tac1-derived	JJ	_	_	_
270	plasmid	plasmid	NN	_	_	_
271	carrying	carry	VBG	_	_	_
272	an	a	DT	_	_	_
273	IPTG-inducible	iptg-inducible	JJ	_	_	_
274	operon	operon	NN	_	_	_
275	with	with	IN	_	_	_
276	cDNA	cdna	NN	_	_	_
277	encoding	encode	VBG	_	_	_
278	human	human	JJ	_	_	_
279	Hsp10	hsp10	NN	_	_	_
280	and	and	CC	_	_	_
281	the	the	DT	_	_	_
282	mature	mature	JJ	_	_	_
283	part	part	NN	_	_	_
284	of	of	IN	_	_	_
285	human	human	JJ	_	_	_
286	wild	wild	JJ	_	_	_
287	type	type	NN	_	_	_
288	Hsp60	hsp60	NN	_	_	_
289	-LRB-	-lrb-	-LRB-	_	_	_
290	Hansen	Hansen	NNP	_	_	_
291	et	et	FW	_	_	_
292	al.	al.	FW	_	_	_
293	,	,	,	_	_	_
294	2002	2002	CD	_	_	_
295	-RRB-	-rrb-	-RRB-	_	_	_
296	.	.	.	_	_	_

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/hisA	pbad/hisa	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Invitrogen	invitrogen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	that	that	WDT	_	_	_
21	contained	contain	VBD	_	_	_
22	an	a	DT	_	_	_
23	operon	operon	NN	_	_	_
24	with	with	IN	_	_	_
25	Hsp10	hsp10	NN	_	_	_
26	and	and	CC	_	_	_
27	the	the	DT	_	_	_
28	Val98Ile	val98ile	NN	_	_	_
29	mutant	mutant	JJ	_	_	_
30	variant	variant	NN	_	_	_
31	of	of	IN	_	_	_
32	Hsp60	hsp60	NN	_	_	_
33	under	under	IN	_	_	_
34	control	control	NN	_	_	_
35	of	of	IN	_	_	_
36	the	the	DT	_	_	_
37	arabinose-inducible	arabinose-inducible	JJ	_	_	_
38	BAD	bad	NN	_	_	_
39	promoter	promoter	NN	_	_	_
40	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pBAD/hisA-derived	pbad/hisa-derived	JJ	_	_	_
3	plasmid	plasmid	NN	_	_	_
4	carries	carry	VBZ	_	_	_
5	a	a	DT	_	_	_
6	pBR322	pbr322	NN	_	_	_
7	origin	origin	NN	_	_	_
8	of	of	IN	_	_	_
9	replication	replication	NN	_	_	_
10	and	and	CC	_	_	_
11	an	a	DT	_	_	_
12	ampicillin	ampicillin	NN	_	_	_
13	resistance	resistance	NN	_	_	_
14	gene	gene	NN	_	_	_
15	and	and	CC	_	_	_
16	can	can	MD	GEN	_	_
17	be	be	VB	_	_	_
18	stably	stably	RB	_	_	_
19	maintained	maintain	VBN	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	same	same	JJ	_	_	_
23	cell	cell	NN	_	_	_
24	with	with	IN	_	_	_
25	the	the	DT	_	_	_
26	p15A-origin/kanamycin	p15a-origin/kanamycin	NN	_	_	_
27	resistance	resistance	NN	_	_	_
28	gene	gene	NN	_	_	_
29	containing	contain	VBG	_	_	_
30	pOFX-tac	pofx-tac	NN	_	_	_
31	derivative	derivative	NN	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strain	strain	NN	_	_	_
5	B178	b178	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Georgopoulos	Georgopoulos	NNP	_	_	_
8	et	et	FW	_	_	_
9	al.	al.	FW	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	1973	1973	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	J	J	NNP	_	_	_
14	Mol	Mol	NNP	_	_	_
15	Biol	Biol	NNP	_	_	_
16	76	76	CD	_	_	_
17	:	:	:	_	_	_
18	45-60	45-60	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	in	in	IN	_	_	_
21	which	which	WDT	_	_	_
22	the	the	DT	_	_	_
23	endogenous	endogenous	JJ	_	_	_
24	groES	groes	NN	_	_	_
25	and	and	CC	_	_	_
26	groEL	groel	NN	_	_	_
27	genes	gene	NNS	_	_	_
28	have	have	VBP	_	_	_
29	been	be	VBN	_	_	_
30	deleted	delete	VBN	_	_	_
31	and	and	CC	_	_	_
32	that	that	DT	_	_	_
33	is	be	VBZ	_	_	_
34	maintained	maintain	VBN	_	_	_
35	alive	alive	JJ	_	_	_
36	by	by	IN	_	_	_
37	the	the	DT	_	_	_
38	pOFX-tac1-derived	pofx-tac1-derived	JJ	_	_	_
39	plasmid	plasmid	NN	_	_	_
40	carrying	carry	VBG	_	_	_
41	an	a	DT	_	_	_
42	IPTG-inducible	iptg-inducible	JJ	_	_	_
43	operon	operon	NN	_	_	_
44	with	with	IN	_	_	_
45	cDNA	cdna	NN	_	_	_
46	encoding	encode	VBG	_	_	_
47	human	human	JJ	_	_	_
48	Hsp10	hsp10	NN	_	_	_
49	and	and	CC	_	_	_
50	the	the	DT	_	_	_
51	mature	mature	JJ	_	_	_
52	part	part	NN	_	_	_
53	of	of	IN	_	_	_
54	human	human	JJ	_	_	_
55	wild	wild	JJ	_	_	_
56	type	type	NN	_	_	_
57	Hsp60	hsp60	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	Hansen	Hansen	NNP	_	_	_
60	et	et	FW	_	_	_
61	al.	al.	FW	_	_	_
62	,	,	,	_	_	_
63	2002	2002	CD	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

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/hisA	pbad/hisa	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Invitrogen	invitrogen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	that	that	WDT	_	_	_
21	contained	contain	VBD	_	_	_
22	an	a	DT	_	_	_
23	operon	operon	NN	_	_	_
24	with	with	IN	_	_	_
25	Hsp10	hsp10	NN	_	_	_
26	and	and	CC	_	_	_
27	wild	wild	JJ	_	_	_
28	type	type	NN	_	_	_
29	Hsp60	hsp60	NN	_	_	_
30	under	under	IN	_	_	_
31	control	control	NN	_	_	_
32	of	of	IN	_	_	_
33	the	the	DT	_	_	_
34	arabinose-inducible	arabinose-inducible	JJ	_	_	_
35	BAD	bad	NN	_	_	_
36	promoter	promoter	NN	_	_	_
37	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pBAD/hisA-derived	pbad/hisa-derived	JJ	_	_	_
3	plasmids	plasmid	NNS	_	_	_
4	carry	carry	VBP	_	_	_
5	a	a	DT	_	_	_
6	pBR322	pbr322	NN	_	_	_
7	origin	origin	NN	_	_	_
8	of	of	IN	_	_	_
9	replication	replication	NN	_	_	_
10	and	and	CC	_	_	_
11	an	a	DT	_	_	_
12	ampicillin	ampicillin	NN	_	_	_
13	resistance	resistance	NN	_	_	_
14	gene	gene	NN	_	_	_
15	and	and	CC	_	_	_
16	can	can	MD	GEN	_	_
17	be	be	VB	_	_	_
18	stably	stably	RB	_	_	_
19	maintained	maintain	VBN	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	same	same	JJ	_	_	_
23	cell	cell	NN	_	_	_
24	with	with	IN	_	_	_
25	the	the	DT	_	_	_
26	p15A-origin/kanamycin	p15a-origin/kanamycin	NN	_	_	_
27	resistance	resistance	NN	_	_	_
28	gene	gene	NN	_	_	_
29	containing	contain	VBG	_	_	_
30	pOFX-tac	pofx-tac	NN	_	_	_
31	derivative	derivative	NN	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strain	strain	NN	_	_	_
5	B-a	b-a	JJ	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	strain	strain	NN	_	_	_
10	B-b	b-b	JJ	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	strain	strain	NN	_	_	_
15	B	b	NN	_	_	_
16	DNA	dna	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	E.	e.	FW	_	_	_
19	coli	coli	FW	_	_	_
20	strain	strain	NN	_	_	_
21	DH5α	dh5α	NN	_	_	_
22	harboring	harbor	VBG	_	_	_
23	pAR060302	par060302	NN	_	_	_
24	was	be	VBD	_	_	_
25	grown	grow	VBN	_	_	_
26	in	in	IN	_	_	_
27	10	10	CD	_	_	_
28	mL	ml	NN	_	_	_
29	DifcoTM	difcotm	NN	_	_	_
30	Luria-Bertani	luria-bertani	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	LB	lb	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	broth	broth	NN	_	_	_
35	aliquots	aliquot	NNS	_	_	_
36	at	at	IN	_	_	_
37	37º	37º	CD	_	_	_
38	C	c	NN	_	_	_
39	with	with	IN	_	_	_
40	shaking	shake	VBG	_	_	_
41	until	until	IN	_	_	_
42	an	a	DT	_	_	_
43	OD600	od600	NN	_	_	_
44	of	of	IN	_	_	_
45	0.5	0.5	CD	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	strain	strain	NN	_	_	_
4	,	,	,	_	_	_
5	DY330	dy330	NN	_	_	_
6	,	,	,	_	_	_
7	was	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	at	at	IN	_	_	_
10	30C	30C	NNP	_	_	_
11	in	in	IN	_	_	_
12	M9	M9	NNP	_	_	_
13	media	media	NNS	_	_	_
14	supplemented	supplement	VBN	_	_	_
15	with	with	IN	_	_	_
16	0.4	0.4	CD	_	_	_
17	%	%	NN	_	_	_
18	glucose	glucose	NN	SUPP	_	_
19	,	,	,	_	_	_
20	vitamins	vitamin	NNS	_	_	_
21	and	and	CC	_	_	_
22	amino	amino	NN	SUPP	_	_
23	acids	acid	NNS	SUPP	_	_
24	.	.	.	_	_	_

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	NNP	_	_	_
87	E.	E.	NNP	_	_	_
88	coli	coli	NN	_	_	_
89	,	,	,	_	_	_
90	strain	strain	NN	_	_	_
91	Frag1	frag1	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	strain	strain	NN	_	_	_
96	isolated	isolate	VBN	_	_	_
97	from	from	IN	_	_	_
98	CF	cf	NN	_	_	_
99	patient	patient	NN	_	_	_
100	stool	stool	VBP	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	E.	e.	FW	_	_	_
103	coli	coli	FW	_	_	_
104	strain	strain	NN	_	_	_
105	isolated	isolate	VBN	_	_	_
106	from	from	IN	_	_	_
107	healthy	healthy	JJ	_	_	_
108	child	child	NN	_	_	_
109	stool	stool	NN	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	E.	E.	NNP	_	_	_
112	coli	coli	NN	_	_	_
113	strain	strain	NN	_	_	_
114	K12	k12	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	E.	e.	FW	_	_	_
117	coli	coli	FW	_	_	_
118	strain	strain	NN	_	_	_
119	K12-a	k12-a	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	E.	e.	FW	_	_	_
122	coli	coli	FW	_	_	_
123	strain	strain	NN	_	_	_
124	K12-b	k12-b	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	E.	e.	FW	_	_	_
127	coli	coli	FW	_	_	_
128	strain	strain	NN	_	_	_
129	K12-c	k12-c	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	E.	e.	FW	_	_	_
132	coli	coli	FW	_	_	_
133	strain	strain	NN	_	_	_
134	K12-d	k12-d	JJ	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
136	E.	e.	FW	_	_	_
137	coli	coli	FW	_	_	_
138	strain	strain	NN	_	_	_
139	K12	k12	NN	_	_	_
140	DNA	dna	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	E.	e.	FW	_	_	_
143	coli	coli	FW	_	_	_
144	strain	strain	NN	_	_	_
145	MC4100relA	mc4100rela	NN	_	_	_
146	+	+	CC	_	_	_
147	in	in	IN	_	_	_
148	mid	mid	JJ	_	_	_
149	log	log	NN	_	_	_
150	phase	phase	NN	_	_	_
151	incubated	incubate	VBN	_	_	_
152	at	at	IN	_	_	_
153	37ºC	37ºc	NN	_	_	_
154	for	for	IN	_	_	_
155	4	4	CD	_	_	_
156	hours	hour	NNS	_	_	_
157	with	with	IN	_	_	_
158	100	100	CD	_	_	_
159	μg/ml	μg/ml	NN	_	_	_
160	NA	na	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	E.	e.	FW	_	_	_
163	coli	coli	FW	_	_	_
164	strain	strain	NN	_	_	_
165	MC4100relA	mc4100rela	NN	_	_	_
166	+	+	CC	_	_	_
167	in	in	IN	_	_	_
168	mid	mid	JJ	_	_	_
169	log	log	NN	_	_	_
170	phase	phase	NN	_	_	_
171	incubated	incubate	VBN	_	_	_
172	at	at	IN	_	_	_
173	37ºC	37ºc	NN	_	_	_
174	for	for	IN	_	_	_
175	4	4	CD	_	_	_
176	hours	hour	NNS	_	_	_
177	with	with	IN	_	_	_
178	10	10	CD	_	_	_
179	μg/ml	μg/ml	NN	_	_	_
180	NA	na	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	E.	e.	FW	_	_	_
183	coli	coli	FW	_	_	_
184	strain	strain	NN	_	_	_
185	MC4100relA	mc4100rela	NN	_	_	_
186	+	+	CC	_	_	_
187	in	in	IN	_	_	_
188	mid	mid	JJ	_	_	_
189	log	log	NN	_	_	_
190	phase	phase	NN	_	_	_
191	incubated	incubate	VBN	_	_	_
192	at	at	IN	_	_	_
193	37ºC	37ºc	NN	_	_	_
194	for	for	IN	_	_	_
195	4	4	CD	_	_	_
196	hours	hour	NNS	_	_	_
197	without	without	IN	_	_	_
198	treatment	treatment	NN	_	_	_
199	.	.	.	_	_	_

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/ml	μg/ml	NN	_	_	_
22	NA	na	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	E.	e.	FW	_	_	_
25	coli	coli	FW	_	_	_
26	strain	strain	NN	_	_	_
27	MC4100relA	mc4100rela	NN	_	_	_
28	+	+	CC	_	_	_
29	∆	∆	SYM	_	_	_
30	mazEF	mazef	NN	_	_	_
31	in	in	IN	_	_	_
32	mid	mid	JJ	_	_	_
33	log	log	NN	_	_	_
34	phase	phase	NN	_	_	_
35	incubated	incubate	VBN	_	_	_
36	at	at	IN	_	_	_
37	37ºC	37ºc	NN	_	_	_
38	for	for	IN	_	_	_
39	4	4	CD	_	_	_
40	hours	hour	NNS	_	_	_
41	with	with	IN	_	_	_
42	10	10	CD	_	_	_
43	μg/ml	μg/ml	NN	_	_	_
44	NA	na	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	strain	strain	NN	_	_	_
49	MC4100relA	mc4100rela	NN	_	_	_
50	+	+	CC	_	_	_
51	∆	∆	SYM	_	_	_
52	mazEF	mazef	NN	_	_	_
53	in	in	IN	_	_	_
54	mid	mid	JJ	_	_	_
55	log	log	NN	_	_	_
56	phase	phase	NN	_	_	_
57	incubated	incubate	VBN	_	_	_
58	at	at	IN	_	_	_
59	37ºC	37ºc	NN	_	_	_
60	for	for	IN	_	_	_
61	4	4	CD	_	_	_
62	hours	hour	NNS	_	_	_
63	without	without	IN	_	_	_
64	treatment	treatment	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	strain	strain	NN	_	_	_
69	MC4100relA	mc4100rela	NN	_	_	_
70	+	+	CC	_	_	_
71	∆	∆	SYM	_	_	_
72	mazEFlexA3	mazeflexa3	NN	_	_	_
73	in	in	IN	_	_	_
74	mid	mid	JJ	_	_	_
75	log	log	NN	_	_	_
76	phase	phase	NN	_	_	_
77	incubated	incubate	VBN	_	_	_
78	at	at	IN	_	_	_
79	37ºC	37ºc	NN	_	_	_
80	for	for	IN	_	_	_
81	4	4	CD	_	_	_
82	hours	hour	NNS	_	_	_
83	with	with	IN	_	_	_
84	100	100	CD	_	_	_
85	μg/ml	μg/ml	NN	_	_	_
86	NA	na	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	E.	e.	FW	_	_	_
89	coli	coli	FW	_	_	_
90	strain	strain	NN	_	_	_
91	MC4100relA	mc4100rela	NN	_	_	_
92	+	+	CC	_	_	_
93	∆	∆	SYM	_	_	_
94	mazEFlexA3	mazeflexa3	NN	_	_	_
95	in	in	IN	_	_	_
96	mid	mid	JJ	_	_	_
97	log	log	NN	_	_	_
98	phase	phase	NN	_	_	_
99	incubated	incubate	VBN	_	_	_
100	at	at	IN	_	_	_
101	37ºC	37ºc	NN	_	_	_
102	for	for	IN	_	_	_
103	4	4	CD	_	_	_
104	hours	hour	NNS	_	_	_
105	with	with	IN	_	_	_
106	10	10	CD	_	_	_
107	μg/ml	μg/ml	NN	_	_	_
108	NA	na	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	E.	e.	FW	_	_	_
111	coli	coli	FW	_	_	_
112	strain	strain	NN	_	_	_
113	MC4100relA	mc4100rela	NN	_	_	_
114	+	+	CC	_	_	_
115	∆	∆	SYM	_	_	_
116	mazEFlexA3	mazeflexa3	NN	_	_	_
117	in	in	IN	_	_	_
118	mid	mid	JJ	_	_	_
119	log	log	NN	_	_	_
120	phase	phase	NN	_	_	_
121	incubated	incubate	VBN	_	_	_
122	at	at	IN	_	_	_
123	37ºC	37ºc	NN	_	_	_
124	for	for	IN	_	_	_
125	4	4	CD	_	_	_
126	hours	hour	NNS	_	_	_
127	without	without	IN	_	_	_
128	treatment	treatment	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	E.coli	e.coli	NN	_	_	_
131	strain	strain	NN	_	_	_
132	MG1655	mg1655	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	E.	e.	FW	_	_	_
135	coli	coli	FW	_	_	_
136	strain	strain	NN	_	_	_
137	NM580	nm580	NN	_	_	_
138	-LRB-	-lrb-	-LRB-	_	_	_
139	genotype	genotype	NN	_	_	_
140	MG1655	mg1655	NN	_	_	_
141	ermBL-ermB	ermbl-ermb	NN	_	_	_
142	'	'	''	_	_	_
143	:	:	:	_	_	_
144	:	:	:	_	_	_
145	LacZ	lacz	NN	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	cells	cell	NNS	_	_	_
148	were	be	VBD	_	_	_
149	grown	grow	VBN	_	_	_
150	in	in	IN	_	_	_
151	LB	lb	NN	MED	_	_
152	broth	broth	NN	MED	_	_
153	-LRB-	-lrb-	-LRB-	_	_	_
154	37	37	CD	_	_	_
155	°C	°c	NN	_	_	_
156	-RRB-	-rrb-	-RRB-	_	_	_
157	until	until	IN	_	_	_
158	OD600	od600	NN	_	_	_
159	of	of	IN	_	_	_
160	~	~	NN	_	_	_
161	0.3	0.3	CD	_	_	_
162	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.Coli	e.coli	NNS	_	_	_
3	,	,	,	_	_	_
4	strain	strain	NN	_	_	_
5	P4XB2	p4xb2	NN	_	_	_
6	mutant	mutant	NN	_	_	_
7	,	,	,	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	presence	presence	NN	_	_	_
11	of	of	IN	_	_	_
12	arginine	arginine	NN	SUPP	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	100	100	CD	_	_	_
15	ug/ml	ug/ml	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	E.Coli	e.coli	NNS	_	_	_
19	,	,	,	_	_	_
20	strain	strain	NN	_	_	_
21	P4X	p4x	NN	_	_	_
22	,	,	,	_	_	_
23	grown	grow	VBN	_	_	_
24	in	in	IN	_	_	_
25	presence	presence	NN	_	_	_
26	of	of	IN	_	_	_
27	arginine	arginine	NN	SUPP	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	100	100	CD	_	_	_
30	ug/ml	ug/ml	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	E.Coli	e.coli	NNS	_	_	_
34	,	,	,	_	_	_
35	strain	strain	NN	_	_	_
36	P4X	p4x	NN	_	_	_
37	,	,	,	_	_	_
38	grown	grow	VBN	_	_	_
39	on	on	IN	_	_	_
40	minimal	minimal	JJ	_	_	_
41	medium	medium	NN	_	_	_
42	,	,	,	_	_	_
43	reference	reference	NN	_	_	_
44	sample	sample	NN	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	E.	E.	NNP	_	_	_
47	coli	coli	NN	_	_	_
48	strains	strain	NNS	_	_	_
49	harboring	harbor	VBG	_	_	_
50	ArgR-8myc	argr-8myc	NN	_	_	_
51	were	be	VBD	_	_	_
52	grown	grow	VBN	_	_	_
53	in	in	IN	_	_	_
54	glucose	glucose	NN	SUPP	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	2	2	CD	_	_	_
57	g/L	g/l	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	minimal	minimal	JJ	_	_	_
60	W2	w2	NN	_	_	_
61	medium	medium	NN	_	_	_
62	supplemented	supplement	VBN	_	_	_
63	with	with	IN	_	_	_
64	1g/L	1g/l	NN	_	_	_
65	arginine	arginine	NN	SUPP	_	_
66	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	harboring	harbor	VBG	_	_	_
6	ArgR-8myc	argr-8myc	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	2	2	CD	_	_	_
13	g/L	g/l	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	minimal	minimal	JJ	_	_	_
16	W2	w2	NN	_	_	_
17	medium	medium	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	2g/L	2g/l	NN	_	_	_
21	glutamine	glutamine	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	harboring	harbor	VBG	_	_	_
6	Lrp-8myc	lrp-8myc	JJ	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	2	2	CD	_	_	_
13	g/L	g/l	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	minimal	minimal	JJ	_	_	_
16	M9	m9	NN	_	_	_
17	medium	medium	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	10	10	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	leucine	leucine	NN	SUPP	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	harboring	harbor	VBG	_	_	_
6	Lrp-8myc	lrp-8myc	JJ	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	2	2	CD	_	_	_
13	g/L	g/l	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	minimal	minimal	JJ	_	_	_
16	M9	m9	NN	_	_	_
17	medium	medium	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	without	without	IN	_	_	_
20	10	10	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	leucine	leucine	NN	SUPP	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	harboring	harbor	VBG	_	_	_
6	PurR-8myc	purr-8myc	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	minimal	minimal	JJ	_	_	_
11	M9	m9	NN	_	_	_
12	medium	medium	NN	_	_	_
13	supplemented	supplement	VBN	_	_	_
14	with	with	IN	_	_	_
15	glucose	glucose	NN	SUPP	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	2	2	CD	_	_	_
18	g/L	g/l	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	then	then	RB	_	_	_
21	inoculated	inoculate	VBN	_	_	_
22	into	into	IN	_	_	_
23	100mL	100ml	NN	_	_	_
24	of	of	IN	_	_	_
25	fresh	fresh	JJ	_	_	_
26	M9	m9	NN	MED	_	_
27	minimal	minimal	JJ	MED	_	_
28	medium	medium	NN	MED	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	harboring	harbor	VBG	_	_	_
6	PurR-8myc	purr-8myc	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	minimal	minimal	JJ	_	_	_
11	M9	m9	NN	_	_	_
12	medium	medium	NN	_	_	_
13	supplemented	supplement	VBN	_	_	_
14	with	with	IN	_	_	_
15	glucose	glucose	NN	SUPP	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	2	2	CD	_	_	_
18	g/L	g/l	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	then	then	RB	_	_	_
21	inoculated	inoculate	VBN	_	_	_
22	into	into	IN	_	_	_
23	100mL	100ml	NN	_	_	_
24	of	of	IN	_	_	_
25	fresh	fresh	JJ	_	_	_
26	M9	m9	NN	MED	_	_
27	minimal	minimal	JJ	MED	_	_
28	medium	medium	NN	MED	_	_
29	supplemented	supplement	VBN	_	_	_
30	with	with	IN	_	_	_
31	100ug/L	100ug/l	NN	_	_	_
32	adenine	adenine	NN	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	harboring	harbor	VBG	_	_	_
6	TrpR-8myc	trpr-8myc	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	2	2	CD	_	_	_
13	g/L	g/l	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	minimal	minimal	JJ	_	_	_
16	M9	m9	NN	_	_	_
17	medium	medium	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	20	20	CD	_	_	_
21	mg/L	mg/l	NN	_	_	_
22	tryptophan	tryptophan	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	harboring	harbor	VBG	_	_	_
6	TrpR-8myc	trpr-8myc	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	2	2	CD	_	_	_
13	g/L	g/l	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	minimal	minimal	JJ	_	_	_
16	M9	m9	NN	_	_	_
17	medium	medium	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	without	without	IN	_	_	_
20	20	20	CD	_	_	_
21	mg/L	mg/l	NN	_	_	_
22	tryptophan	tryptophan	NN	_	_	_
23	.	.	.	_	_	_

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	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	HT874	ht874	NN	_	_	_
6	,	,	,	_	_	_
7	HT873	ht873	NN	_	_	_
8	,	,	,	_	_	_
9	HT875	ht875	NN	_	_	_
10	,	,	,	_	_	_
11	HT873	ht873	NN	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	or	or	CC	_	_	_
15	no	no	DT	_	_	_
16	polyamines	polyamine	NNS	_	_	_
17	by	by	IN	_	_	_
18	Trizol	trizol	NN	_	_	_
19	protocol	protocol	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strain	strain	NN	_	_	_
5	St.	St.	NNP	_	_	_
6	Olav104	Olav104	NNP	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	E.	E.	NNP	_	_	_
9	coli	coli	NN	_	_	_
10	strain	strain	NN	_	_	_
11	St.	St.	NNP	_	_	_
12	Olav157	Olav157	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	E.	E.	NNP	_	_	_
15	coli	coli	NN	_	_	_
16	strain	strain	NN	_	_	_
17	St.	St.	NNP	_	_	_
18	Olav164	Olav164	NNP	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	E.	E.	NNP	_	_	_
21	coli	coli	NN	_	_	_
22	strain	strain	NN	_	_	_
23	St.	St.	NNP	_	_	_
24	Olav17	Olav17	NNP	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	E.	E.	NNP	_	_	_
27	coli	coli	NN	_	_	_
28	strain	strain	NN	_	_	_
29	St.	St.	NNP	_	_	_
30	Olav172	Olav172	NNP	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	E.	E.	NNP	_	_	_
33	coli	coli	NN	_	_	_
34	strain	strain	NN	_	_	_
35	St.	St.	NNP	_	_	_
36	Olav173	Olav173	NNP	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	E.	E.	NNP	_	_	_
39	coli	coli	NN	_	_	_
40	strain	strain	NN	_	_	_
41	St.	St.	NNP	_	_	_
42	Olav174	Olav174	NNP	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	E.	E.	NNP	_	_	_
45	coli	coli	NN	_	_	_
46	strain	strain	NN	_	_	_
47	St.	St.	NNP	_	_	_
48	Olav176	Olav176	NNP	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	E.	NNP	_	_	_
51	coli	coli	NN	_	_	_
52	strain	strain	NN	_	_	_
53	St.	St.	NNP	_	_	_
54	Olav178	Olav178	NNP	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	E.	E.	NNP	_	_	_
57	coli	coli	NN	_	_	_
58	strain	strain	NN	_	_	_
59	St.	St.	NNP	_	_	_
60	Olav179	Olav179	NNP	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	E.	E.	NNP	_	_	_
63	coli	coli	NN	_	_	_
64	strain	strain	NN	_	_	_
65	St.	St.	NNP	_	_	_
66	Olav39	Olav39	NNP	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	E.	E.	NNP	_	_	_
69	coli	coli	NN	_	_	_
70	strain	strain	NN	_	_	_
71	St.	St.	NNP	_	_	_
72	Olav40	Olav40	NNP	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	E.	E.	NNP	_	_	_
75	coli	coli	NN	_	_	_
76	strain	strain	NN	_	_	_
77	St.	St.	NNP	_	_	_
78	Olav63	Olav63	NNP	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	E.	E.	NNP	_	_	_
81	coli	coli	NN	_	_	_
82	strains	strain	NNS	_	_	_
83	was	be	VBD	_	_	_
84	grown	grow	VBN	_	_	_
85	in	in	IN	_	_	_
86	MgM	MgM	NNP	_	_	_
87	media	media	NNS	_	_	_
88	at	at	IN	_	_	_
89	pH	ph	NN	_	_	_
90	5.6	5.6	CD	_	_	_
91	,	,	,	_	_	_
92	7.2	7.2	CD	_	_	_
93	and	and	CC	_	_	_
94	7.2	7.2	CD	_	_	_
95	with	with	IN	_	_	_
96	15	15	CD	_	_	_
97	%	%	NN	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	w/v	w/v	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	sucrose	sucrose	NN	_	_	_
102	to	to	TO	_	_	_
103	O.D	O.D	NNP	_	_	_
104	~	~	NNP	_	_	_
105	0.6	0.6	CD	_	_	_
106	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	were	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	in	in	IN	_	_	_
8	minimal	minimal	JJ	_	_	_
9	M9	m9	NN	_	_	_
10	medium	medium	NN	_	_	_
11	supplemented	supplement	VBN	_	_	_
12	with	with	IN	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	g/L	g/l	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	additional	additional	JJ	_	_	_
20	iron	iron	NN	_	_	_
21	to	to	TO	_	_	_
22	mid-exponential	mid-exponential	JJ	_	_	_
23	phase	phase	NN	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	E.	E.	NNP	_	_	_
26	coli	coli	NN	_	_	_
27	strains	strain	NNS	_	_	_
28	were	be	VBD	_	_	_
29	grown	grow	VBN	_	_	_
30	in	in	IN	_	_	_
31	minimal	minimal	JJ	_	_	_
32	M9	m9	NN	_	_	_
33	medium	medium	NN	_	_	_
34	supplemented	supplement	VBN	_	_	_
35	with	with	IN	_	_	_
36	glucose	glucose	NN	SUPP	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	2	2	CD	_	_	_
39	g/L	g/l	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	to	to	TO	_	_	_
42	mid-exponential	mid-exponential	JJ	_	_	_
43	phase	phase	NN	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	E.	E.	NNP	_	_	_
46	coli	coli	NN	_	_	_
47	strains	strain	NNS	_	_	_
48	were	be	VBD	_	_	_
49	grown	grow	VBN	_	_	_
50	in	in	IN	_	_	_
51	minimal	minimal	JJ	_	_	_
52	M9	m9	NN	_	_	_
53	medium	medium	NN	_	_	_
54	supplemented	supplement	VBN	_	_	_
55	with	with	IN	_	_	_
56	glucose	glucose	NN	SUPP	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	2	2	CD	_	_	_
59	g/L	g/l	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	to	to	TO	_	_	_
62	mid-exponential	mid-exponential	JJ	_	_	_
63	phase	phase	NN	_	_	_
64	and	and	CC	_	_	_
65	treated	treat	VBN	_	_	_
66	with	with	IN	_	_	_
67	heatshock	heatshock	NN	_	_	_
68	for	for	IN	_	_	_
69	10	10	CD	_	_	_
70	min	min	NN	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	E.	E.	NNP	_	_	_
73	coli	coli	NN	_	_	_
74	strains	strain	NNS	_	_	_
75	were	be	VBD	_	_	_
76	grown	grow	VBN	_	_	_
77	in	in	IN	_	_	_
78	minimal	minimal	JJ	_	_	_
79	M9	m9	NN	_	_	_
80	medium	medium	NN	_	_	_
81	supplemented	supplement	VBN	_	_	_
82	with	with	IN	_	_	_
83	glucose	glucose	NN	SUPP	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	2	2	CD	_	_	_
86	g/L	g/l	NN	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	to	to	TO	_	_	_
89	mid-exponential	mid-exponential	JJ	_	_	_
90	phase	phase	NN	_	_	_
91	with	with	IN	_	_	_
92	heatshock	heatshock	NN	_	_	_
93	for	for	IN	_	_	_
94	10	10	CD	_	_	_
95	min	min	NN	_	_	_
96	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
97	E.	E.	NNP	_	_	_
98	coli	coli	NN	_	_	_
99	strains	strain	NNS	_	_	_
100	were	be	VBD	_	_	_
101	grown	grow	VBN	_	_	_
102	in	in	IN	_	_	_
103	minimal	minimal	JJ	_	_	_
104	M9	m9	NN	_	_	_
105	medium	medium	NN	_	_	_
106	supplemented	supplement	VBN	_	_	_
107	with	with	IN	_	_	_
108	glucose	glucose	NN	SUPP	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	2	2	CD	_	_	_
111	g/L	g/l	NN	_	_	_
112	-RRB-	-rrb-	-RRB-	_	_	_
113	to	to	TO	_	_	_
114	stationary	stationary	JJ	GrowthPhase	_	_
115	phase	phase	NN	GrowthPhase	_	_
116	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
117	E.	E.	NNP	_	_	_
118	coli	coli	NN	_	_	_
119	strains	strain	NNS	_	_	_
120	were	be	VBD	_	_	_
121	grown	grow	VBN	_	_	_
122	in	in	IN	_	_	_
123	minimal	minimal	JJ	_	_	_
124	W2	w2	NN	_	_	_
125	medium	medium	NN	_	_	_
126	supplemented	supplement	VBN	_	_	_
127	with	with	IN	_	_	_
128	glucose	glucose	NN	SUPP	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	2	2	CD	_	_	_
131	g/L	g/l	NN	_	_	_
132	-RRB-	-rrb-	-RRB-	_	_	_
133	and	and	CC	_	_	_
134	glutamine	glutamine	NN	_	_	_
135	-LRB-	-lrb-	-LRB-	_	_	_
136	2	2	CD	_	_	_
137	g/L	g/l	NN	_	_	_
138	-RRB-	-rrb-	-RRB-	_	_	_
139	to	to	TO	_	_	_
140	mid-exponential	mid-exponential	JJ	_	_	_
141	phase	phase	NN	_	_	_
142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
143	E.	E.	NNP	_	_	_
144	coli	coli	NN	_	_	_
145	,	,	,	_	_	_
146	stressed	stress	VBN	_	_	_
147	by	by	IN	_	_	_
148	NaCl	nacl	NN	_	_	_
149	,	,	,	_	_	_
150	in	in	IN	_	_	_
151	presence	presence	NN	_	_	_
152	of	of	IN	_	_	_
153	glycine	glycine	NN	_	_	_
154	betaine	betaine	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	e.	e.	FW	_	_	_
157	coli	coli	FW	_	_	_
158	subset	subset	NN	_	_	_
159	:	:	:	_	_	_
160	enterohemorrhagic	enterohemorrhagic	JJ	_	_	_
161	E.coli	e.coli	JJ	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
163	E.	e.	FW	_	_	_
164	coli	coli	FW	_	_	_
165	sucrose	sucrose	NN	_	_	_
166	hyperosmotic	hyperosmotic	JJ	_	_	_
167	treatment	treatment	NN	_	_	_
168	-LRB-	-lrb-	-LRB-	_	_	_
169	biological	biological	JJ	_	_	_
170	replicate	replicate	VBP	_	_	_
171	1	1	LS	_	_	_
172	-RRB-	-rrb-	-RRB-	_	_	_
173	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
174	E.	e.	FW	_	_	_
175	coli	coli	FW	_	_	_
176	sucrose	sucrose	NN	_	_	_
177	hyperosmotic	hyperosmotic	JJ	_	_	_
178	treatment	treatment	NN	_	_	_
179	-LRB-	-lrb-	-LRB-	_	_	_
180	biological	biological	JJ	_	_	_
181	replicate	replicate	VBP	_	_	_
182	2	2	LS	_	_	_
183	-RRB-	-rrb-	-RRB-	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	E.coli	e.coli	NNS	_	_	_
186	_	_	VBP	_	_	_
187	T1viaR	t1viar	NN	_	_	_
188	_	_	CD	_	_	_
189	SR1	sr1	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	E.coli	e.coli	NNS	_	_	_
192	_	_	VBP	_	_	_
193	T1viaR	t1viar	NN	_	_	_
194	_	_	CD	_	_	_
195	SR2	sr2	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	E.coli	e.coli	NNS	_	_	_
198	_	_	VBP	_	_	_
199	T1viaR	t1viar	NN	_	_	_
200	_	_	CD	_	_	_
201	SR3	sr3	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	E.coli	e.coli	NNS	_	_	_
204	_	_	VBP	_	_	_
205	T2viaR	t2viar	NN	_	_	_
206	_	_	CD	_	_	_
207	SR1	sr1	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	E.coli	e.coli	NNS	_	_	_
210	_	_	VBP	_	_	_
211	T2viaR	t2viar	NN	_	_	_
212	_	_	CD	_	_	_
213	SR2	sr2	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	E.coli	e.coli	NNS	_	_	_
216	_	_	VBP	_	_	_
217	T2viaR	t2viar	NN	_	_	_
218	_	_	CD	_	_	_
219	SR3	sr3	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	E.coli	e.coli	NNS	_	_	_
222	_	_	VBP	_	_	_
223	T3viaR	t3viar	NN	_	_	_
224	_	_	CD	_	_	_
225	SR1	sr1	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	E.coli	e.coli	NNS	_	_	_
228	_	_	VBP	_	_	_
229	T3viaR	t3viar	NN	_	_	_
230	_	_	CD	_	_	_
231	SR2	sr2	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	E.coli	e.coli	NNS	_	_	_
234	_	_	VBP	_	_	_
235	T3viaR	t3viar	NN	_	_	_
236	_	_	CD	_	_	_
237	SR3	sr3	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	E.coli	e.coli	NNS	_	_	_
240	_	_	VBP	_	_	_
241	T4viaR	t4viar	NN	_	_	_
242	_	_	CD	_	_	_
243	SR1	sr1	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	E.coli	e.coli	NNS	_	_	_
246	_	_	VBP	_	_	_
247	T4viaR	t4viar	NN	_	_	_
248	_	_	CD	_	_	_
249	SR2	sr2	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	E.coli	e.coli	NNS	_	_	_
252	_	_	VBP	_	_	_
253	T4viaR	t4viar	NN	_	_	_
254	_	_	CD	_	_	_
255	SR3	sr3	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	E.coli	e.coli	NNS	_	_	_
258	_	_	VBP	_	_	_
259	T5viaR	t5viar	NN	_	_	_
260	_	_	CD	_	_	_
261	SR2	sr2	NN	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	E.coli	e.coli	NNS	_	_	_
264	_	_	VBP	_	_	_
265	T5viaR	t5viar	NN	_	_	_
266	_	_	CD	_	_	_
267	SR3	sr3	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	E.coli	e.coli	NNS	_	_	_
270	_	_	VBP	_	_	_
271	T6viaR	t6viar	NN	_	_	_
272	_	_	CD	_	_	_
273	SR2	sr2	NN	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	E.coli	e.coli	NNS	_	_	_
276	_	_	VBP	_	_	_
277	T6viaR	t6viar	NN	_	_	_
278	_	_	CD	_	_	_
279	SR3	sr3	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	E.coli	e.coli	NNS	_	_	_
282	_	_	VBP	_	_	_
283	T7viaR	t7viar	NN	_	_	_
284	_	_	CD	_	_	_
285	SR2	sr2	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	E.coli	e.coli	NNS	_	_	_
288	_	_	VBP	_	_	_
289	T7viaR	t7viar	NN	_	_	_
290	_	_	CD	_	_	_
291	SR3	sr3	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	E.coli	e.coli	NNS	_	_	_
294	_	_	VBP	_	_	_
295	T8viaR	t8viar	NN	_	_	_
296	_	_	CD	_	_	_
297	SR2	sr2	NN	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	E.coli	e.coli	NNS	_	_	_
300	_	_	VBP	_	_	_
301	T8viaR	t8viar	NN	_	_	_
302	_	_	CD	_	_	_
303	SR3	sr3	NN	_	_	_
304	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
305	E.	E.	NNP	_	_	_
306	coli	coli	NN	_	_	_
307	-	-	:	_	_	_
308	TAP	tap	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	E.	e.	FW	_	_	_
311	coli	coli	FW	_	_	_
312	+	+	CC	_	_	_
313	TAP	tap	FW	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
315	Ecoli	ecoli	FW	_	_	_
316	_	_	FW	_	_	_
317	Temperature	temperature	NN	_	_	_
318	upshift	upshift	NN	_	_	_
319	in	in	IN	_	_	_
320	gyrBT	gyrBT	NNP	_	_	_
321	mutant	mutant	JJ	_	_	_
322	T1	t1	NN	_	_	_
323	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
324	Ecoli	Ecoli	NNP	_	_	_
325	_	_	NNP	_	_	_
326	Temperature	Temperature	NNP	_	_	_
327	upshift	upshift	NN	_	_	_
328	in	in	IN	_	_	_
329	gyrBT	gyrBT	NNP	_	_	_
330	mutant	mutant	JJ	_	_	_
331	T2	t2	NN	_	_	_
332	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
333	Ecoli	Ecoli	NNP	_	_	_
334	_	_	NNP	_	_	_
335	Temperature	Temperature	NNP	_	_	_
336	upshift	upshift	NN	_	_	_
337	in	in	IN	_	_	_
338	gyrBT	gyrBT	NNP	_	_	_
339	mutant	mutant	JJ	_	_	_
340	T3	t3	NN	_	_	_
341	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
342	Ecoli	Ecoli	NNP	_	_	_
343	_	_	NNP	_	_	_
344	Temperature	Temperature	NNP	_	_	_
345	upshift	upshift	NN	_	_	_
346	in	in	IN	_	_	_
347	gyrBT	gyrBT	NNP	_	_	_
348	mutant	mutant	JJ	_	_	_
349	T4	t4	NN	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	E.	e.	FW	_	_	_
352	coli	coli	FW	_	_	_
353	TolC	tolc	NN	_	_	_
354	cells	cell	NNS	_	_	_
355	were	be	VBD	_	_	_
356	grown	grow	VBN	_	_	_
357	o/n	o/n	RB	_	_	_
358	in	in	IN	_	_	_
359	LB	lb	NN	MED	_	_
360	medium	medium	NN	MED	_	_
361	at	at	IN	_	_	_
362	37	37	CD	_	_	_
363	°C	°c	NN	_	_	_
364	and	and	CC	_	_	_
365	200	200	CD	_	_	_
366	rpm	rpm	NN	_	_	_
367	.	.	.	_	_	_

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	NN	_	_	_
18	E	e	NN	_	_	_
19	_	_	CD	_	_	_
20	coli	coli	NN	_	_	_
21	_	_	NN	_	_	_
22	treated	treat	VBN	_	_	_
23	_	_	SYM	_	_	_
24	powerline	powerline	FW	_	_	_
25	_	_	FW	_	_	_
26	interm	interm	FW	_	_	_
27	_	_	SYM	_	_	_
28	15h	15h	CD	_	_	_
29	_	_	CD	_	_	_
30	rep1	rep1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	E	e	NN	_	_	_
33	_	_	CD	_	_	_
34	coli	coli	NN	_	_	_
35	_	_	NN	_	_	_
36	treated	treat	VBN	_	_	_
37	_	_	SYM	_	_	_
38	powerline	powerline	FW	_	_	_
39	_	_	FW	_	_	_
40	interm	interm	FW	_	_	_
41	_	_	SYM	_	_	_
42	15h	15h	CD	_	_	_
43	_	_	CD	_	_	_
44	rep2	rep2	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	E	e	NN	_	_	_
47	_	_	CD	_	_	_
48	coli	coli	NN	_	_	_
49	_	_	NN	_	_	_
50	treated	treat	VBN	_	_	_
51	_	_	SYM	_	_	_
52	powerline	powerline	FW	_	_	_
53	_	_	FW	_	_	_
54	interm	interm	FW	_	_	_
55	_	_	SYM	_	_	_
56	15h	15h	CD	_	_	_
57	_	_	CD	_	_	_
58	rep3	rep3	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	E	e	NN	_	_	_
61	_	_	CD	_	_	_
62	coli	coli	NN	_	_	_
63	_	_	NN	_	_	_
64	treated	treat	VBN	_	_	_
65	_	_	SYM	_	_	_
66	powerline	powerline	FW	_	_	_
67	_	_	FW	_	_	_
68	interm	interm	FW	_	_	_
69	_	_	SYM	_	_	_
70	2.5	2.5	CD	_	_	_
71	h	h	NN	_	_	_
72	_	_	CD	_	_	_
73	rep1	rep1	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	E	e	NN	_	_	_
76	_	_	CD	_	_	_
77	coli	coli	NN	_	_	_
78	_	_	NN	_	_	_
79	treated	treat	VBN	_	_	_
80	_	_	SYM	_	_	_
81	powerline	powerline	FW	_	_	_
82	_	_	FW	_	_	_
83	interm	interm	FW	_	_	_
84	_	_	SYM	_	_	_
85	2.5	2.5	CD	_	_	_
86	h	h	NN	_	_	_
87	_	_	CD	_	_	_
88	rep2	rep2	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	E	e	NN	_	_	_
91	_	_	CD	_	_	_
92	coli	coli	NN	_	_	_
93	_	_	NN	_	_	_
94	treated	treat	VBN	_	_	_
95	_	_	SYM	_	_	_
96	powerline	powerline	FW	_	_	_
97	_	_	FW	_	_	_
98	interm	interm	FW	_	_	_
99	_	_	SYM	_	_	_
100	2.5	2.5	CD	_	_	_
101	h	h	NN	_	_	_
102	_	_	CD	_	_	_
103	rep3	rep3	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	E	e	NN	_	_	_
106	_	_	CD	_	_	_
107	coli	coli	NN	_	_	_
108	_	_	NN	_	_	_
109	treated	treat	VBN	_	_	_
110	_	_	SYM	_	_	_
111	powerline	powerline	FW	_	_	_
112	_	_	FW	_	_	_
113	interm	interm	FW	_	_	_
114	_	_	SYM	_	_	_
115	8	8	CD	_	_	_
116	min	min	NN	_	_	_
117	_	_	CD	_	_	_
118	rep1	rep1	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	E	e	NN	_	_	_
121	_	_	CD	_	_	_
122	coli	coli	NN	_	_	_
123	_	_	NN	_	_	_
124	treated	treat	VBN	_	_	_
125	_	_	SYM	_	_	_
126	powerline	powerline	FW	_	_	_
127	_	_	FW	_	_	_
128	interm	interm	FW	_	_	_
129	_	_	SYM	_	_	_
130	8	8	CD	_	_	_
131	min	min	NN	_	_	_
132	_	_	CD	_	_	_
133	rep2	rep2	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	E	e	NN	_	_	_
136	_	_	CD	_	_	_
137	coli	coli	NN	_	_	_
138	_	_	NN	_	_	_
139	treated	treat	VBN	_	_	_
140	_	_	SYM	_	_	_
141	powerline	powerline	FW	_	_	_
142	_	_	FW	_	_	_
143	interm	interm	FW	_	_	_
144	_	_	SYM	_	_	_
145	8	8	CD	_	_	_
146	min	min	NN	_	_	_
147	_	_	CD	_	_	_
148	rep3	rep3	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	E	e	NN	_	_	_
151	_	_	CD	_	_	_
152	coli	coli	NN	_	_	_
153	_	_	NN	_	_	_
154	treated	treat	VBN	_	_	_
155	_	_	SYM	_	_	_
156	sinusoidal	sinusoidal	JJ	_	_	_
157	_	_	NN	_	_	_
158	cont	cont	NN	_	_	_
159	_	_	SYM	_	_	_
160	15h	15h	CD	_	_	_
161	_	_	CD	_	_	_
162	rep1	rep1	NN	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	E	e	NN	_	_	_
165	_	_	CD	_	_	_
166	coli	coli	NN	_	_	_
167	_	_	NN	_	_	_
168	treated	treat	VBN	_	_	_
169	_	_	SYM	_	_	_
170	sinusoidal	sinusoidal	JJ	_	_	_
171	_	_	NN	_	_	_
172	cont	cont	NN	_	_	_
173	_	_	SYM	_	_	_
174	15h	15h	CD	_	_	_
175	_	_	CD	_	_	_
176	rep2	rep2	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	E	e	NN	_	_	_
179	_	_	CD	_	_	_
180	coli	coli	NN	_	_	_
181	_	_	NN	_	_	_
182	treated	treat	VBN	_	_	_
183	_	_	SYM	_	_	_
184	sinusoidal	sinusoidal	JJ	_	_	_
185	_	_	NN	_	_	_
186	cont	cont	NN	_	_	_
187	_	_	SYM	_	_	_
188	15h	15h	CD	_	_	_
189	_	_	CD	_	_	_
190	rep3	rep3	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	E	e	NN	_	_	_
193	_	_	CD	_	_	_
194	coli	coli	NN	_	_	_
195	_	_	NN	_	_	_
196	treated	treat	VBN	_	_	_
197	_	_	SYM	_	_	_
198	sinusoidal	sinusoidal	JJ	_	_	_
199	_	_	NN	_	_	_
200	cont	cont	NN	_	_	_
201	_	_	SYM	_	_	_
202	2.5	2.5	CD	_	_	_
203	h	h	NN	_	_	_
204	_	_	CD	_	_	_
205	rep1	rep1	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	E	e	NN	_	_	_
208	_	_	CD	_	_	_
209	coli	coli	NN	_	_	_
210	_	_	NN	_	_	_
211	treated	treat	VBN	_	_	_
212	_	_	SYM	_	_	_
213	sinusoidal	sinusoidal	JJ	_	_	_
214	_	_	NN	_	_	_
215	cont	cont	NN	_	_	_
216	_	_	SYM	_	_	_
217	2.5	2.5	CD	_	_	_
218	h	h	NN	_	_	_
219	_	_	CD	_	_	_
220	rep2	rep2	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	E	e	NN	_	_	_
223	_	_	CD	_	_	_
224	coli	coli	NN	_	_	_
225	_	_	NN	_	_	_
226	treated	treat	VBN	_	_	_
227	_	_	SYM	_	_	_
228	sinusoidal	sinusoidal	JJ	_	_	_
229	_	_	NN	_	_	_
230	cont	cont	NN	_	_	_
231	_	_	SYM	_	_	_
232	2.5	2.5	CD	_	_	_
233	h	h	NN	_	_	_
234	_	_	CD	_	_	_
235	rep3	rep3	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	E	e	NN	_	_	_
238	_	_	CD	_	_	_
239	coli	coli	NN	_	_	_
240	_	_	NN	_	_	_
241	treated	treat	VBN	_	_	_
242	_	_	SYM	_	_	_
243	sinusoidal	sinusoidal	JJ	_	_	_
244	_	_	NN	_	_	_
245	cont	cont	NN	_	_	_
246	_	_	NN	_	_	_
247	8	8	CD	_	_	_
248	min	min	NN	_	_	_
249	_	_	CD	_	_	_
250	rep1	rep1	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	E	e	NN	_	_	_
253	_	_	CD	_	_	_
254	coli	coli	NN	_	_	_
255	_	_	NN	_	_	_
256	treated	treat	VBN	_	_	_
257	_	_	SYM	_	_	_
258	sinusoidal	sinusoidal	JJ	_	_	_
259	_	_	NN	_	_	_
260	cont	cont	NN	_	_	_
261	_	_	NN	_	_	_
262	8	8	CD	_	_	_
263	min	min	NN	_	_	_
264	_	_	CD	_	_	_
265	rep2	rep2	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	E	e	NN	_	_	_
268	_	_	CD	_	_	_
269	coli	coli	NN	_	_	_
270	_	_	NN	_	_	_
271	treated	treat	VBN	_	_	_
272	_	_	SYM	_	_	_
273	sinusoidal	sinusoidal	JJ	_	_	_
274	_	_	NN	_	_	_
275	cont	cont	NN	_	_	_
276	_	_	NN	_	_	_
277	8	8	CD	_	_	_
278	min	min	NN	_	_	_
279	_	_	CD	_	_	_
280	rep3	rep3	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	E	e	NN	_	_	_
283	_	_	CD	_	_	_
284	coli	coli	NN	_	_	_
285	_	_	NN	_	_	_
286	treated	treat	VBN	_	_	_
287	_	_	SYM	_	_	_
288	sinusoidal	sinusoidal	JJ	_	_	_
289	_	_	NN	_	_	_
290	interm	interm	NN	_	_	_
291	_	_	CD	_	_	_
292	15h	15h	JJ	_	_	_
293	_	_	NN	_	_	_
294	rep1	rep1	NN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	E	e	NN	_	_	_
297	_	_	CD	_	_	_
298	coli	coli	NN	_	_	_
299	_	_	NN	_	_	_
300	treated	treat	VBN	_	_	_
301	_	_	SYM	_	_	_
302	sinusoidal	sinusoidal	JJ	_	_	_
303	_	_	NN	_	_	_
304	interm	interm	NN	_	_	_
305	_	_	CD	_	_	_
306	15h	15h	JJ	_	_	_
307	_	_	NN	_	_	_
308	rep2	rep2	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	E	e	NN	_	_	_
311	_	_	CD	_	_	_
312	coli	coli	NN	_	_	_
313	_	_	NN	_	_	_
314	treated	treat	VBN	_	_	_
315	_	_	SYM	_	_	_
316	sinusoidal	sinusoidal	JJ	_	_	_
317	_	_	NN	_	_	_
318	interm	interm	NN	_	_	_
319	_	_	CD	_	_	_
320	15h	15h	JJ	_	_	_
321	_	_	NN	_	_	_
322	rep3	rep3	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	E	e	NN	_	_	_
325	_	_	CD	_	_	_
326	coli	coli	NN	_	_	_
327	_	_	NN	_	_	_
328	treated	treat	VBN	_	_	_
329	_	_	SYM	_	_	_
330	sinusoidal	sinusoidal	JJ	_	_	_
331	_	_	NN	_	_	_
332	interm	interm	NN	_	_	_
333	_	_	CD	_	_	_
334	2.5	2.5	CD	_	_	_
335	h	h	NN	_	_	_
336	_	_	CD	_	_	_
337	rep1	rep1	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	E	e	NN	_	_	_
340	_	_	CD	_	_	_
341	coli	coli	NN	_	_	_
342	_	_	NN	_	_	_
343	treated	treat	VBN	_	_	_
344	_	_	SYM	_	_	_
345	sinusoidal	sinusoidal	JJ	_	_	_
346	_	_	NN	_	_	_
347	interm	interm	NN	_	_	_
348	_	_	CD	_	_	_
349	2.5	2.5	CD	_	_	_
350	h	h	NN	_	_	_
351	_	_	CD	_	_	_
352	rep2	rep2	NN	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	E	e	NN	_	_	_
355	_	_	CD	_	_	_
356	coli	coli	NN	_	_	_
357	_	_	NN	_	_	_
358	treated	treat	VBN	_	_	_
359	_	_	SYM	_	_	_
360	sinusoidal	sinusoidal	JJ	_	_	_
361	_	_	NN	_	_	_
362	interm	interm	NN	_	_	_
363	_	_	CD	_	_	_
364	2.5	2.5	CD	_	_	_
365	h	h	NN	_	_	_
366	_	_	CD	_	_	_
367	rep3	rep3	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
369	E.	e.	FW	_	_	_
370	coli	coli	FW	_	_	_
371	treated	treat	VBN	_	_	_
372	with	with	IN	_	_	_
373	bicontinious	bicontinious	JJ	_	_	_
374	microemulsion	microemulsion	NN	_	_	_
375	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
376	E.	E.	NNP	_	_	_
377	coli	coli	NNS	_	_	_
378	treated	treat	VBN	_	_	_
379	with	with	IN	_	_	_
380	o/w	o/w	NN	_	_	_
381	microemulsion	microemulsion	NN	_	_	_
382	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
383	E.	E.	NNP	_	_	_
384	coli	coli	NNS	_	_	_
385	treated	treat	VBN	_	_	_
386	with	with	IN	_	_	_
387	w/o	w/o	NN	_	_	_
388	microemulsion	microemulsion	NN	_	_	_
389	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
390	E.	E.	NNP	_	_	_
391	Coli	Coli	NNP	_	_	_
392	TrpR	trpr	NN	TF	_	_
393	ChIP	chip	NN	_	_	_
394	DNA	dna	NN	_	_	_
395	glucose	glucose	NN	SUPP	_	_
396	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
397	E.	E.	NNP	_	_	_
398	Coli	Coli	NNP	_	_	_
399	TrpR	trpr	NN	TF	_	_
400	ChIP	chip	NN	_	_	_
401	DNA	dna	NN	_	_	_
402	Tryptophan	tryptophan	NN	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	E.	e.	FW	_	_	_
405	coli	coli	FW	_	_	_
406	Type	type	NN	_	_	_
407	_	_	CD	_	_	_
408	II	ii	CD	_	_	_
409	genotype	genotype	NN	_	_	_
410	strain	strain	NN	_	_	_
411	,	,	,	_	_	_
412	under	under	IN	_	_	_
413	37ºC	37ºc	NN	_	_	_
414	,	,	,	_	_	_
415	rep	rep	NN	GEN	_	_
416	1	1	CD	_	_	_
417	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
418	E.	E.	NNP	_	_	_
419	coli	coli	NN	_	_	_
420	Type	type	NN	_	_	_
421	_	_	CD	_	_	_
422	II	ii	CD	_	_	_
423	genotype	genotype	NN	_	_	_
424	strain	strain	NN	_	_	_
425	,	,	,	_	_	_
426	under	under	IN	_	_	_
427	37ºC	37ºc	NN	_	_	_
428	,	,	,	_	_	_
429	rep	rep	NN	GEN	_	_
430	2	2	CD	_	_	_
431	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
432	E.	E.	NNP	_	_	_
433	coli	coli	NN	_	_	_
434	Type	type	NN	_	_	_
435	_	_	CD	_	_	_
436	II	ii	CD	_	_	_
437	genotype	genotype	NN	_	_	_
438	strain	strain	NN	_	_	_
439	,	,	,	_	_	_
440	under	under	IN	_	_	_
441	37ºC	37ºc	NN	_	_	_
442	,	,	,	_	_	_
443	rep	rep	NN	GEN	_	_
444	3	3	CD	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	E.	e.	FW	_	_	_
447	coli	coli	FW	_	_	_
448	Type	type	NN	_	_	_
449	_	_	CD	_	_	_
450	II	ii	CD	_	_	_
451	genotype	genotype	NN	_	_	_
452	strain	strain	NN	_	_	_
453	,	,	,	_	_	_
454	under	under	IN	_	_	_
455	45ºC	45ºc	NN	_	_	_
456	,	,	,	_	_	_
457	rep	rep	NN	GEN	_	_
458	1	1	CD	_	_	_
459	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
460	E.	E.	NNP	_	_	_
461	coli	coli	NN	_	_	_
462	Type	type	NN	_	_	_
463	_	_	CD	_	_	_
464	II	ii	CD	_	_	_
465	genotype	genotype	NN	_	_	_
466	strain	strain	NN	_	_	_
467	,	,	,	_	_	_
468	under	under	IN	_	_	_
469	45ºC	45ºc	NN	_	_	_
470	,	,	,	_	_	_
471	rep	rep	NN	GEN	_	_
472	2	2	CD	_	_	_
473	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
474	E.	E.	NNP	_	_	_
475	coli	coli	NN	_	_	_
476	Type	type	NN	_	_	_
477	_	_	CD	_	_	_
478	II	ii	CD	_	_	_
479	genotype	genotype	NN	_	_	_
480	strain	strain	NN	_	_	_
481	,	,	,	_	_	_
482	under	under	IN	_	_	_
483	45ºC	45ºc	NN	_	_	_
484	,	,	,	_	_	_
485	rep	rep	NN	GEN	_	_
486	3	3	CD	_	_	_
487	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
488	E.	e.	FW	_	_	_
489	coli	coli	FW	_	_	_
490	Type	type	NN	_	_	_
491	_	_	CD	_	_	_
492	III	iii	CD	_	_	_
493	genotype	genotype	NN	_	_	_
494	strain	strain	NN	_	_	_
495	,	,	,	_	_	_
496	under	under	IN	_	_	_
497	37ºC	37ºc	NN	_	_	_
498	,	,	,	_	_	_
499	rep	rep	NN	GEN	_	_
500	1	1	CD	_	_	_
501	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
502	E.	E.	NNP	_	_	_
503	coli	coli	NN	_	_	_
504	Type	type	NN	_	_	_
505	_	_	CD	_	_	_
506	III	iii	CD	_	_	_
507	genotype	genotype	NN	_	_	_
508	strain	strain	NN	_	_	_
509	,	,	,	_	_	_
510	under	under	IN	_	_	_
511	37ºC	37ºc	NN	_	_	_
512	,	,	,	_	_	_
513	rep	rep	NN	GEN	_	_
514	2	2	CD	_	_	_
515	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
516	E.	E.	NNP	_	_	_
517	coli	coli	NN	_	_	_
518	Type	type	NN	_	_	_
519	_	_	CD	_	_	_
520	III	iii	CD	_	_	_
521	genotype	genotype	NN	_	_	_
522	strain	strain	NN	_	_	_
523	,	,	,	_	_	_
524	under	under	IN	_	_	_
525	37ºC	37ºc	NN	_	_	_
526	,	,	,	_	_	_
527	rep	rep	NN	GEN	_	_
528	3	3	CD	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	E.	e.	FW	_	_	_
531	coli	coli	FW	_	_	_
532	Type	type	NN	_	_	_
533	_	_	CD	_	_	_
534	III	iii	CD	_	_	_
535	genotype	genotype	NN	_	_	_
536	strain	strain	NN	_	_	_
537	,	,	,	_	_	_
538	under	under	IN	_	_	_
539	45ºC	45ºc	NN	_	_	_
540	,	,	,	_	_	_
541	rep	rep	NN	GEN	_	_
542	1	1	CD	_	_	_
543	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
544	E.	E.	NNP	_	_	_
545	coli	coli	NN	_	_	_
546	Type	type	NN	_	_	_
547	_	_	CD	_	_	_
548	III	iii	CD	_	_	_
549	genotype	genotype	NN	_	_	_
550	strain	strain	NN	_	_	_
551	,	,	,	_	_	_
552	under	under	IN	_	_	_
553	45ºC	45ºc	NN	_	_	_
554	,	,	,	_	_	_
555	rep	rep	NN	GEN	_	_
556	2	2	CD	_	_	_
557	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
558	E.	E.	NNP	_	_	_
559	coli	coli	NN	_	_	_
560	Type	type	NN	_	_	_
561	_	_	CD	_	_	_
562	III	iii	CD	_	_	_
563	genotype	genotype	NN	_	_	_
564	strain	strain	NN	_	_	_
565	,	,	,	_	_	_
566	under	under	IN	_	_	_
567	45ºC	45ºc	NN	_	_	_
568	,	,	,	_	_	_
569	rep	rep	NN	GEN	_	_
570	3	3	CD	_	_	_
571	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
572	E.	E.	NNP	_	_	_
573	coli	coli	NN	_	_	_
574	,	,	,	_	_	_
575	unlimited	unlimited	JJ	_	_	_
576	growth	growth	NN	_	_	_
577	-LRB-	-lrb-	-LRB-	_	_	_
578	batch	batch	NN	_	_	_
579	-RRB-	-rrb-	-RRB-	_	_	_
580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
581	E.	e.	FW	_	_	_
582	coli	coli	FW	_	_	_
583	,	,	,	_	_	_
584	unlimited	unlimited	JJ	_	_	_
585	growth	growth	NN	_	_	_
586	-LRB-	-lrb-	-LRB-	_	_	_
587	batch	batch	NN	_	_	_
588	-RRB-	-rrb-	-RRB-	_	_	_
589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
590	E.coli	e.coli	NN	_	_	_
591	W1863	w1863	NN	_	_	_
592	wt	wt	JJ	_	_	_
593	lambda	lambda	NN	_	_	_
594	-	-	:	_	_	_
595	with	with	IN	_	_	_
596	ccdB	ccdb	NN	_	_	_
597	upregulation	upregulation	NN	_	_	_
598	0	0	CD	_	_	_
599	minutes	minute	NNS	_	_	_
600	after	after	IN	_	_	_
601	induction	induction	NN	_	_	_
602	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
603	E.coli	e.coli	NN	_	_	_
604	W1863	w1863	NN	_	_	_
605	wt	wt	JJ	_	_	_
606	lambda	lambda	NN	_	_	_
607	-	-	:	_	_	_
608	with	with	IN	_	_	_
609	ccdB	ccdb	NN	_	_	_
610	upregulation	upregulation	NN	_	_	_
611	30	30	CD	_	_	_
612	minutes	minute	NNS	_	_	_
613	after	after	IN	_	_	_
614	induction	induction	NN	_	_	_
615	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
616	E.coli	e.coli	NN	_	_	_
617	W1863	w1863	NN	_	_	_
618	wt	wt	JJ	_	_	_
619	lambda	lambda	NN	_	_	_
620	-	-	:	_	_	_
621	with	with	IN	_	_	_
622	ccdB	ccdb	NN	_	_	_
623	upregulation	upregulation	NN	_	_	_
624	60	60	CD	_	_	_
625	minutes	minute	NNS	_	_	_
626	after	after	IN	_	_	_
627	induction	induction	NN	_	_	_
628	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
629	E.coli	e.coli	NN	_	_	_
630	W1863	w1863	NN	_	_	_
631	wt	wt	JJ	_	_	_
632	lambda	lambda	NN	_	_	_
633	-	-	:	_	_	_
634	with	with	IN	_	_	_
635	ccdB	ccdb	NN	_	_	_
636	upregulation	upregulation	NN	_	_	_
637	90	90	CD	_	_	_
638	minutes	minute	NNS	_	_	_
639	after	after	IN	_	_	_
640	induction	induction	NN	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
642	E.coli	e.coli	NN	_	_	_
643	W1863	w1863	NN	_	_	_
644	wt	wt	JJ	_	_	_
645	lambda	lambda	NN	_	_	_
646	-	-	:	_	_	_
647	with	with	IN	_	_	_
648	lacZ	lacz	NN	GEN	_	_
649	upregulation	upregulation	NN	_	_	_
650	0	0	CD	_	_	_
651	minutes	minute	NNS	_	_	_
652	after	after	IN	_	_	_
653	induction	induction	NN	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
655	E.coli	e.coli	NN	_	_	_
656	W1863	w1863	NN	_	_	_
657	wt	wt	JJ	_	_	_
658	lambda	lambda	NN	_	_	_
659	-	-	:	_	_	_
660	with	with	IN	_	_	_
661	lacZ	lacz	NN	GEN	_	_
662	upregulation	upregulation	NN	_	_	_
663	30	30	CD	_	_	_
664	minutes	minute	NNS	_	_	_
665	after	after	IN	_	_	_
666	induction	induction	NN	_	_	_
667	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
668	E.coli	e.coli	NN	_	_	_
669	W1863	w1863	NN	_	_	_
670	wt	wt	JJ	_	_	_
671	lambda	lambda	NN	_	_	_
672	-	-	:	_	_	_
673	with	with	IN	_	_	_
674	lacZ	lacz	NN	GEN	_	_
675	upregulation	upregulation	NN	_	_	_
676	60	60	CD	_	_	_
677	minutes	minute	NNS	_	_	_
678	after	after	IN	_	_	_
679	induction	induction	NN	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	E.coli	e.coli	NN	_	_	_
682	W1863	w1863	NN	_	_	_
683	wt	wt	JJ	_	_	_
684	lambda	lambda	NN	_	_	_
685	-	-	:	_	_	_
686	with	with	IN	_	_	_
687	lacZ	lacz	NN	GEN	_	_
688	upregulation	upregulation	NN	_	_	_
689	90	90	CD	_	_	_
690	minutes	minute	NNS	_	_	_
691	after	after	IN	_	_	_
692	induction	induction	NN	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	E.coli	e.coli	NN	_	_	_
695	W3110	w3110	NN	_	_	_
696	,	,	,	_	_	_
697	15	15	CD	_	_	_
698	minutes	minute	NNS	_	_	_
699	after	after	IN	_	_	_
700	oxygen	oxygen	NN	_	_	_
701	downshift	downshift	NN	_	_	_
702	,	,	,	_	_	_
703	sample	sample	NN	_	_	_
704	S2	s2	NN	_	_	_
705	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
706	E.coli	e.coli	NN	_	_	_
707	W3110	w3110	NN	_	_	_
708	,	,	,	_	_	_
709	15	15	CD	_	_	_
710	minutes	minute	NNS	_	_	_
711	before	before	IN	_	_	_
712	oxygen	oxygen	NN	_	_	_
713	downshift	downshift	NN	_	_	_
714	,	,	,	_	_	_
715	sample	sample	NN	_	_	_
716	S1	s1	NN	_	_	_
717	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
718	ecoli	ecolus	NNS	_	_	_
719	_	_	VBP	_	_	_
720	W3110	w3110	NN	_	_	_
721	_	_	SYM	_	_	_
722	2x	2x	FW	_	_	_
723	_	_	FW	_	_	_
724	v2	v2	FW	_	_	_
725	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
726	ecoli	ecolus	NNS	_	_	_
727	_	_	VBP	_	_	_
728	W3110	w3110	NN	_	_	_
729	_	_	SYM	_	_	_
730	3x	3x	FW	_	_	_
731	_	_	FW	_	_	_
732	v2	v2	FW	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	E.coli	e.coli	NN	_	_	_
735	W3110	w3110	NN	_	_	_
736	,	,	,	_	_	_
737	45	45	CD	_	_	_
738	minutes	minute	NNS	_	_	_
739	after	after	IN	_	_	_
740	oxygen	oxygen	NN	_	_	_
741	downshift	downshift	NN	_	_	_
742	,	,	,	_	_	_
743	sample	sample	NN	_	_	_
744	S3	s3	NN	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
746	ecoli	ecolus	NNS	_	_	_
747	_	_	VBP	_	_	_
748	W3110	w3110	NN	_	_	_
749	_	_	SYM	_	_	_
750	4x	4x	FW	_	_	_
751	_	_	FW	_	_	_
752	v2	v2	FW	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	E.coli	e.coli	NN	_	_	_
755	W3110	w3110	NN	_	_	_
756	,	,	,	_	_	_
757	75	75	CD	_	_	_
758	minutes	minute	NNS	_	_	_
759	after	after	IN	_	_	_
760	oxygen	oxygen	NN	_	_	_
761	downshift	downshift	NN	_	_	_
762	,	,	,	_	_	_
763	sample	sample	NN	_	_	_
764	S4	s4	NN	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
766	E.	e.	FW	_	_	_
767	coli	coli	FW	_	_	_
768	W3110	w3110	NN	_	_	_
769	-LRB-	-lrb-	-LRB-	_	_	_
770	control	control	NN	_	_	_
771	-RRB-	-rrb-	-RRB-	_	_	_
772	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
773	E.	e.	FW	_	_	_
774	coli	coli	FW	_	_	_
775	W3110	w3110	NN	_	_	_
776	expressing	express	VBG	_	_	_
777	PCK	pck	NN	_	_	_
778	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
779	E.	e.	FW	_	_	_
780	coli	coli	FW	_	_	_
781	W3110	w3110	NN	_	_	_
782	expressing	express	VBG	_	_	_
783	ppc	ppc	NN	GEN	_	_
784	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
785	E.	e.	FW	_	_	_
786	coli	coli	FW	_	_	_
787	W3110	w3110	NN	_	_	_
788	expressing	express	VBG	_	_	_
789	ppc	ppc	NN	GEN	_	_
790	at	at	IN	_	_	_
791	LB-GlC	lb-glc	JJ	_	_	_
792	medium	medium	NN	_	_	_
793	,	,	,	_	_	_
794	D	d	NN	_	_	_
795	=	=	JJ	_	_	_
796	0.1	0.1	CD	_	_	_
797	h-1	h-1	NN	_	_	_
798	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
799	E.coli	e.coli	NN	_	_	_
800	W3110	w3110	NN	_	_	_
801	,	,	,	_	_	_
802	fermentation	fermentation	NN	_	_	_
803	sample	sample	NN	_	_	_
804	taken	take	VBN	_	_	_
805	15	15	CD	_	_	_
806	minutes	minute	NNS	_	_	_
807	after	after	IN	_	_	_
808	oxygen	oxygen	NN	_	_	_
809	downshift	downshift	NN	_	_	_
810	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
811	E.coli	e.coli	NN	_	_	_
812	W3110	w3110	NN	_	_	_
813	,	,	,	_	_	_
814	fermentation	fermentation	NN	_	_	_
815	sample	sample	NN	_	_	_
816	taken	take	VBN	_	_	_
817	15	15	CD	_	_	_
818	minutes	minute	NNS	_	_	_
819	before	before	IN	_	_	_
820	oxygen	oxygen	NN	_	_	_
821	downshift	downshift	NN	_	_	_
822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
823	E.coli	e.coli	NN	_	_	_
824	W3110	w3110	NN	_	_	_
825	,	,	,	_	_	_
826	fermentation	fermentation	NN	_	_	_
827	sample	sample	NN	_	_	_
828	taken	take	VBN	_	_	_
829	45	45	CD	_	_	_
830	minutes	minute	NNS	_	_	_
831	after	after	IN	_	_	_
832	oxygen	oxygen	NN	_	_	_
833	downshift	downshift	NN	_	_	_
834	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
835	E.coli	e.coli	NN	_	_	_
836	W3110	w3110	NN	_	_	_
837	,	,	,	_	_	_
838	fermentation	fermentation	NN	_	_	_
839	sample	sample	NN	_	_	_
840	taken	take	VBN	_	_	_
841	75	75	CD	_	_	_
842	minutes	minute	NNS	_	_	_
843	after	after	IN	_	_	_
844	oxygen	oxygen	NN	_	_	_
845	downshift	downshift	NN	_	_	_
846	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
847	E.	E.	NNP	_	_	_
848	coli	coli	NN	_	_	_
849	W3110	w3110	NN	_	_	_
850	grown	grow	VBN	_	_	_
851	at	at	IN	_	_	_
852	glucose-minimal	glucose-minimal	JJ	_	_	_
853	medium	medium	NN	_	_	_
854	-LRB-	-lrb-	-LRB-	_	_	_
855	IPTG	iptg	NN	_	_	_
856	induction	induction	NN	_	_	_
857	-RRB-	-rrb-	-RRB-	_	_	_
858	in	in	IN	_	_	_
859	early	early	JJ	_	_	_
860	log	log	NN	_	_	_
861	phase	phase	NN	_	_	_
862	-LRB-	-lrb-	-LRB-	_	_	_
863	u	u	NN	_	_	_
864	=	=	JJ	_	_	_
865	0.25	0.25	CD	_	_	_
866	h-1	h-1	NN	_	_	_
867	-RRB-	-rrb-	-RRB-	_	_	_
868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
869	E.	e.	FW	_	_	_
870	coli	coli	FW	_	_	_
871	W3110	w3110	NN	_	_	_
872	grown	grow	VBN	_	_	_
873	at	at	IN	_	_	_
874	LB-glucose	lb-glucose	JJ	_	_	_
875	medium	medium	NN	_	_	_
876	-LRB-	-lrb-	-LRB-	_	_	_
877	IPTG	iptg	NN	_	_	_
878	induction	induction	NN	_	_	_
879	-RRB-	-rrb-	-RRB-	_	_	_
880	in	in	IN	_	_	_
881	chemostat	chemostat	NN	_	_	_
882	-LRB-	-lrb-	-LRB-	_	_	_
883	D	d	NN	_	_	_
884	=	=	JJ	_	_	_
885	0.1	0.1	CD	_	_	_
886	h-1	h-1	NN	_	_	_
887	-RRB-	-rrb-	-RRB-	_	_	_
888	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
889	E.	e.	FW	_	_	_
890	coli	coli	FW	_	_	_
891	W3110	w3110	NN	_	_	_
892	-LRB-	-lrb-	-LRB-	_	_	_
893	KCTC	kctc	NN	_	_	_
894	2223	2223	CD	_	_	_
895	-RRB-	-rrb-	-RRB-	_	_	_
896	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
897	E.	e.	FW	_	_	_
898	coli	coli	FW	_	_	_
899	W3110	w3110	NN	_	_	_
900	-LRB-	-lrb-	-LRB-	_	_	_
901	KCTC	kctc	NN	_	_	_
902	2223	2223	CD	_	_	_
903	-RRB-	-rrb-	-RRB-	_	_	_
904	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
905	E.	e.	FW	_	_	_
906	coli	coli	FW	_	_	_
907	W3110	w3110	NN	_	_	_
908	-LRB-	-lrb-	-LRB-	_	_	_
909	KCTC	kctc	NN	_	_	_
910	2223	2223	CD	_	_	_
911	-RRB-	-rrb-	-RRB-	_	_	_
912	at	at	IN	_	_	_
913	LB-GlC	lb-glc	JJ	_	_	_
914	medium	medium	NN	_	_	_
915	,	,	,	_	_	_
916	D	d	NN	_	_	_
917	=	=	JJ	_	_	_
918	0.1	0.1	CD	_	_	_
919	h-1	h-1	NN	_	_	_
920	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
921	E.	E.	NNP	_	_	_
922	coli	coli	NN	_	_	_
923	W3110/pck	w3110/pck	NN	_	_	_
924	grown	grow	VBN	_	_	_
925	at	at	IN	_	_	_
926	LB-glucose	lb-glucose	JJ	_	_	_
927	medium	medium	NN	_	_	_
928	-LRB-	-lrb-	-LRB-	_	_	_
929	IPTG	iptg	NN	_	_	_
930	induction	induction	NN	_	_	_
931	-RRB-	-rrb-	-RRB-	_	_	_
932	in	in	IN	_	_	_
933	chemostat	chemostat	NN	_	_	_
934	-LRB-	-lrb-	-LRB-	_	_	_
935	D	d	NN	_	_	_
936	=	=	JJ	_	_	_
937	0.1	0.1	CD	_	_	_
938	h-1	h-1	NN	_	_	_
939	-RRB-	-rrb-	-RRB-	_	_	_
940	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
941	E.	e.	FW	_	_	_
942	coli	coli	FW	_	_	_
943	W3110/PCK	w3110/pck	NN	_	_	_
944	with	with	IN	_	_	_
945	glucose-minimal	glucose-minimal	JJ	_	_	_
946	medium	medium	NN	_	_	_
947	-LRB-	-lrb-	-LRB-	_	_	_
948	IPTG	iptg	NN	_	_	_
949	induced	induce	VBN	_	_	_
950	-RRB-	-rrb-	-RRB-	_	_	_
951	at	at	IN	_	_	_
952	early	early	JJ	_	_	_
953	log	log	NN	_	_	_
954	phase	phase	NN	_	_	_
955	-LRB-	-lrb-	-LRB-	_	_	_
956	u	u	NN	_	_	_
957	=	=	JJ	_	_	_
958	0.25	0.25	CD	_	_	_
959	-RRB-	-rrb-	-RRB-	_	_	_
960	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
961	E.	e.	FW	_	_	_
962	coli	coli	FW	_	_	_
963	W3110/ppc	w3110/ppc	NN	_	_	_
964	grown	grow	VBN	_	_	_
965	at	at	IN	_	_	_
966	glucose-minimal	glucose-minimal	JJ	_	_	_
967	medium	medium	NN	_	_	_
968	-LRB-	-lrb-	-LRB-	_	_	_
969	IPTG	iptg	NN	_	_	_
970	induction	induction	NN	_	_	_
971	-RRB-	-rrb-	-RRB-	_	_	_
972	in	in	IN	_	_	_
973	early	early	JJ	_	_	_
974	log	log	NN	_	_	_
975	phase	phase	NN	_	_	_
976	-LRB-	-lrb-	-LRB-	_	_	_
977	u	u	NN	_	_	_
978	=	=	JJ	_	_	_
979	0.25	0.25	CD	_	_	_
980	h-1	h-1	NN	_	_	_
981	-RRB-	-rrb-	-RRB-	_	_	_
982	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
983	E.	e.	FW	_	_	_
984	coli	coli	FW	_	_	_
985	W3110/ppc	w3110/ppc	NN	_	_	_
986	grown	grow	VBN	_	_	_
987	at	at	IN	_	_	_
988	LB-glucose	lb-glucose	JJ	_	_	_
989	medium	medium	NN	_	_	_
990	-LRB-	-lrb-	-LRB-	_	_	_
991	IPTG	iptg	NN	_	_	_
992	induction	induction	NN	_	_	_
993	-RRB-	-rrb-	-RRB-	_	_	_
994	in	in	IN	_	_	_
995	chemostat	chemostat	NN	_	_	_
996	-LRB-	-lrb-	-LRB-	_	_	_
997	D	d	NN	_	_	_
998	=	=	JJ	_	_	_
999	0.1	0.1	CD	_	_	_
1000	h-1	h-1	NN	_	_	_
1001	-RRB-	-rrb-	-RRB-	_	_	_
1002	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1003	E.	e.	FW	_	_	_
1004	coli	coli	FW	_	_	_
1005	W3110	w3110	NN	_	_	_
1006	with	with	IN	_	_	_
1007	glucose-minimal	glucose-minimal	JJ	_	_	_
1008	medium	medium	NN	_	_	_
1009	-LRB-	-lrb-	-LRB-	_	_	_
1010	IPTG	iptg	NN	_	_	_
1011	induced	induce	VBN	_	_	_
1012	-RRB-	-rrb-	-RRB-	_	_	_
1013	at	at	IN	_	_	_
1014	early	early	JJ	_	_	_
1015	log	log	NN	_	_	_
1016	phase	phase	NN	_	_	_
1017	-LRB-	-lrb-	-LRB-	_	_	_
1018	u	u	NN	_	_	_
1019	=	=	JJ	_	_	_
1020	0.25	0.25	CD	_	_	_
1021	-RRB-	-rrb-	-RRB-	_	_	_
1022	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1023	E.	E.	NNP	_	_	_
1024	coli	coli	NN	_	_	_
1025	was	be	VBD	_	_	_
1026	grown	grow	VBN	_	_	_
1027	in	in	IN	_	_	_
1028	M9	m9	NN	_	_	_
1029	medium	medium	NN	_	_	_
1030	supplemented	supplement	VBN	_	_	_
1031	with	with	IN	_	_	_
1032	0.4	0.4	CD	_	_	_
1033	%	%	NN	_	_	_
1034	glucose	glucose	NN	SUPP	_	_
1035	.	.	.	_	_	_

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/mL	µg/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	total	total	JJ	_	_	_
31	cadmium	cadmium	NN	_	_	_
32	,	,	,	_	_	_
33	added	add	VBD	_	_	_
34	as	as	IN	_	_	_
35	CdCl2	cdcl2	NN	_	_	_
36	.	.	.	_	_	_

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	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/mL	µg/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	total	total	JJ	_	_	_
31	cadmium	cadmium	NN	_	_	_
32	,	,	,	_	_	_
33	added	add	VBD	_	_	_
34	as	as	IN	_	_	_
35	CdCl2	cdcl2	NN	_	_	_
36	.	.	.	_	_	_

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	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/mL	µg/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	total	total	JJ	_	_	_
31	cadmium	cadmium	NN	_	_	_
32	,	,	,	_	_	_
33	added	add	VBD	_	_	_
34	as	as	IN	_	_	_
35	CdCl2	cdcl2	NN	_	_	_
36	.	.	.	_	_	_

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/mL	µg/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	total	total	JJ	_	_	_
31	cadmium	cadmium	NN	_	_	_
32	,	,	,	_	_	_
33	added	add	VBD	_	_	_
34	as	as	IN	_	_	_
35	CdCl2	cdcl2	NN	_	_	_
36	.	.	.	_	_	_

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	.	.	.	_	_	_

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/mL	µg/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	total	total	JJ	_	_	_
31	cadmium	cadmium	NN	_	_	_
32	,	,	,	_	_	_
33	added	add	VBD	_	_	_
34	as	as	IN	_	_	_
35	CdCl2	cdcl2	NN	_	_	_
36	.	.	.	_	_	_

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/mL	µg/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	total	total	JJ	_	_	_
31	cadmium	cadmium	NN	_	_	_
32	,	,	,	_	_	_
33	added	add	VBD	_	_	_
34	as	as	IN	_	_	_
35	CdCl2	cdcl2	NN	_	_	_
36	.	.	.	_	_	_

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	to	to	TO	_	_	_
7	exponential	exponential	JJ	GrowthPhase	_	_
8	phase	phase	NN	GrowthPhase	_	_
9	in	in	IN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	minimal	minimal	JJ	_	_	_
12	medium	medium	NN	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	presence	presence	NN	_	_	_
16	of	of	IN	_	_	_
17	the	the	DT	_	_	_
18	osmoprotectant	osmoprotectant	JJ	_	_	_
19	glycine	glycine	NN	_	_	_
20	beatine	beatine	NN	_	_	_
21	with	with	IN	_	_	_
22	a	a	DT	_	_	_
23	range	range	NN	_	_	_
24	of	of	IN	_	_	_
25	salt	salt	NN	_	_	_
26	concentrations	concentration	NNS	_	_	_
27	at	at	IN	_	_	_
28	2	2	CD	_	_	_
29	,	,	,	_	_	_
30	3.5	3.5	CD	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	2	2	CD	_	_	_
33	repeats	repeat	NNS	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	4.5	4.5	CD	_	_	_
37	,	,	,	_	_	_
38	5	5	CD	_	_	_
39	and	and	CC	_	_	_
40	5.5	5.5	CD	_	_	_
41	%	%	NN	_	_	_
42	NaCl	nacl	NN	_	_	_
43	.	.	.	_	_	_

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/ml	cfu/ml	NN	_	_	_
8	and	and	CC	_	_	_
9	cultures	culture	NNS	_	_	_
10	incubated	incubate	VBN	_	_	_
11	to	to	TO	_	_	_
12	reach	reach	VB	_	_	_
13	107	107	CD	_	_	_
14	cfu/ml	cfu/ml	NN	_	_	_
15	,	,	,	_	_	_
16	an	a	DT	_	_	_
17	ODs	od	NNS	_	_	_
18	of	of	IN	_	_	_
19	about	about	RB	_	_	_
20	0.03	0.03	CD	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	cultures	culture	NNS	_	_	_
23	entered	enter	VBD	_	_	_
24	stationary	stationary	JJ	GrowthPhase	_	_
25	phase	phase	NN	GrowthPhase	_	_
26	at	at	IN	_	_	_
27	108	108	CD	_	_	_
28	cfu/ml	cfu/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	before	before	IN	_	_	_
31	harvesting	harvest	VBG	_	_	_
32	.	.	.	_	_	_

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	cholic	cholic	JJ	_	_	_
30	acid	acid	NN	_	_	_
31	at	at	IN	_	_	_
32	1	1	CD	_	_	_
33	mM	mm	NN	KWSUPP	_	_
34	final	final	JJ	_	_	_
35	culture	culture	NN	_	_	_
36	concentration	concentration	NN	_	_	_
37	.	.	.	_	_	_

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	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	-LRB-	-lrb-	-LRB-	_	_	_
10	O.D.	o.d.	NN	_	_	_
11	600nm	600nm	CD	_	_	_
12	0.3-0.4	0.3-0.4	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	Lennox	Lennox	NNP	_	_	_
16	LB	LB	NNP	MED	_	_
17	broth	broth	NN	MED	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Becton	Becton	NNP	_	_	_
20	Dickinson	Dickinson	NNP	_	_	_
21	,	,	,	_	_	_
22	Franklin	Franklin	NNP	_	_	_
23	Lakes	Lakes	NNP	_	_	_
24	,	,	,	_	_	_
25	NJ	NJ	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	at	at	IN	_	_	_
28	37	37	CD	_	_	_
29	°C	°c	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	treated	treat	VBN	_	_	_
6	at	at	IN	_	_	_
7	37C	37c	NN	_	_	_
8	aerobically	aerobically	RB	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	with	with	IN	_	_	_
12	BSA	bsa	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	control	control	NN	_	_	_
15	,	,	,	_	_	_
16	100	100	CD	_	_	_
17	µg/ml	µg/ml	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	PGRP	pgrp	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	human	human	JJ	_	_	_
23	recombinant	recombinant	JJ	_	_	_
24	PGLYRP4	pglyrp4	NN	_	_	_
25	,	,	,	_	_	_
26	100	100	CD	_	_	_
27	µg/ml	µg/ml	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	,	,	,	_	_	_
30	or	or	CC	_	_	_
31	gentamicin	gentamicin	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	5	5	CD	_	_	_
34	µg/ml	µg/ml	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	for	for	IN	_	_	_
37	30	30	CD	_	_	_
38	min	min	NN	_	_	_
39	,	,	,	_	_	_
40	or	or	CC	_	_	_
41	with	with	IN	_	_	_
42	CCCP	cccp	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	carbonyl	carbonyl	NN	_	_	_
45	cyanide	cyanide	NN	_	_	_
46	3-chlorophenylhydrazone	3-chlorophenylhydrazone	NN	_	_	_
47	,	,	,	_	_	_
48	800	800	CD	_	_	_
49	µM	µm	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	for	for	IN	_	_	_
52	15	15	CD	_	_	_
53	min	min	NN	_	_	_
54	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	experiment	experiment	NN	_	_	_
3	was	be	VBD	_	_	_
4	repeated	repeat	VBN	_	_	_
5	3	3	CD	_	_	_
6	times	time	NNS	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	defined	define	VBN	_	_	_
8	rich	rich	JJ	MED	_	_
9	media	media	NNS	MED	_	_
10	at	at	IN	_	_	_
11	30C	30C	NNP	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	LB	lb	NN	_	_	_
8	or	or	CC	_	_	_
9	minimal	minimal	JJ	_	_	_
10	medium	medium	NN	_	_	_
11	supplemented	supplement	VBN	_	_	_
12	with	with	IN	_	_	_
13	casaminoacids	casaminoacid	NNS	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	0,1	0,1	CD	_	_	_
16	%	%	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	succinate	succinate	NN	SUPP	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	0,1	0,1	CD	_	_	_
22	%	%	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	until	until	IN	_	_	_
25	OD	od	NN	_	_	_
26	0,2-0,4	0,2-0,4	CD	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	E.	E.	NNP	_	_	_
29	coli	coli	NNS	_	_	_
30	were	be	VBD	_	_	_
31	incubated	incubate	VBN	_	_	_
32	in	in	IN	_	_	_
33	S-Basal	s-basal	JJ	_	_	_
34	complete	complete	JJ	_	_	_
35	medium	medium	NN	_	_	_
36	alone	alone	RB	_	_	_
37	or	or	CC	_	_	_
38	in	in	IN	_	_	_
39	the	the	DT	_	_	_
40	presence	presence	NN	_	_	_
41	of	of	IN	_	_	_
42	C.	C.	NNP	_	_	_
43	elegans	elegan	NNS	_	_	_
44	,	,	,	_	_	_
45	Giardia	Giardia	NNP	_	_	_
46	conditioned	condition	VBD	_	_	_
47	meida	meida	NN	_	_	_
48	,	,	,	_	_	_
49	and	and	CC	_	_	_
50	both	both	DT	_	_	_
51	C.	c.	FW	_	_	_
52	elegans	elegan	NNS	_	_	_
53	and	and	CC	_	_	_
54	Giardia	Giardia	NNP	_	_	_
55	conditioned	condition	VBN	_	_	_
56	media	media	NNS	_	_	_
57	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NNS	_	_	_
4	were	be	VBD	_	_	_
5	sampled	sample	VBN	_	_	_
6	at	at	IN	_	_	_
7	times	time	NNS	_	_	_
8	=	=	JJ	_	_	_
9	0	0	CD	_	_	_
10	,	,	,	_	_	_
11	1	1	CD	_	_	_
12	hour	hour	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	2	2	CD	_	_	_
16	hours	hour	NNS	_	_	_
17	following	follow	VBG	_	_	_
18	release	release	NN	_	_	_
19	from	from	IN	_	_	_
20	stationary	stationary	JJ	GrowthPhase	_	_
21	phase	phase	NN	GrowthPhase	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Ecoli	Ecoli	NNP	_	_	_
3	_	_	SYM	_	_	_
4	wildtype	wildtype	JJ	_	_	_
5	_	_	NN	_	_	_
6	1	1	CD	_	_	_
7	%	%	NN	_	_	_
8	_	_	CD	_	_	_
9	butanol	butanol	NN	_	_	_
10	_	_	SYM	_	_	_
11	Sample1	sample1	FW	_	_	_
12	_	_	FW	_	_	_
13	TechRep1	techrep1	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Ecoli	ecolus	NNS	_	_	_
16	_	_	VBP	_	_	_
17	wildtype	wildtype	JJ	_	_	_
18	_	_	NN	_	_	_
19	1	1	CD	_	_	_
20	%	%	NN	_	_	_
21	_	_	CD	_	_	_
22	butanol	butanol	NN	_	_	_
23	_	_	SYM	_	_	_
24	Sample1	sample1	FW	_	_	_
25	_	_	FW	_	_	_
26	TechRep2	techrep2	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Ecoli	ecolus	NNS	_	_	_
29	_	_	VBP	_	_	_
30	wildtype	wildtype	JJ	_	_	_
31	_	_	NN	_	_	_
32	1	1	CD	_	_	_
33	%	%	NN	_	_	_
34	_	_	CD	_	_	_
35	butanol	butanol	NN	_	_	_
36	_	_	SYM	_	_	_
37	Sample2	sample2	FW	_	_	_
38	_	_	FW	_	_	_
39	TechRep1	techrep1	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Ecoli	ecolus	NNS	_	_	_
42	_	_	VBP	_	_	_
43	wildtype	wildtype	JJ	_	_	_
44	_	_	NN	_	_	_
45	1	1	CD	_	_	_
46	%	%	NN	_	_	_
47	_	_	CD	_	_	_
48	butanol	butanol	NN	_	_	_
49	_	_	SYM	_	_	_
50	Sample2	sample2	FW	_	_	_
51	_	_	FW	_	_	_
52	TechRep2	techrep2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Ecoli	ecolus	NNS	_	_	_
55	_	_	VBP	_	_	_
56	wildtype	wildtype	JJ	_	_	_
57	_	_	NN	_	_	_
58	1	1	CD	_	_	_
59	%	%	NN	_	_	_
60	_	_	CD	_	_	_
61	butanol	butanol	NN	_	_	_
62	_	_	SYM	_	_	_
63	Sample3	sample3	FW	_	_	_
64	_	_	FW	_	_	_
65	TechRep1	techrep1	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Ecoli	ecolus	NNS	_	_	_
68	_	_	VBP	_	_	_
69	wildtype	wildtype	JJ	_	_	_
70	_	_	NN	_	_	_
71	1	1	CD	_	_	_
72	%	%	NN	_	_	_
73	_	_	CD	_	_	_
74	butanol	butanol	NN	_	_	_
75	_	_	SYM	_	_	_
76	Sample3	sample3	FW	_	_	_
77	_	_	FW	_	_	_
78	TechRep2	techrep2	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Ecoli	ecolus	NNS	_	_	_
81	_	_	VBP	_	_	_
82	wildtype	wildtype	JJ	_	_	_
83	_	_	NN	_	_	_
84	1	1	CD	_	_	_
85	%	%	NN	_	_	_
86	_	_	CD	_	_	_
87	butanol	butanol	NN	_	_	_
88	_	_	SYM	_	_	_
89	Sample4	sample4	FW	_	_	_
90	_	_	FW	_	_	_
91	TechRep1	techrep1	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	Ecoli	ecolus	NNS	_	_	_
94	_	_	VBP	_	_	_
95	wildtype	wildtype	JJ	_	_	_
96	_	_	NN	_	_	_
97	1	1	CD	_	_	_
98	%	%	NN	_	_	_
99	_	_	CD	_	_	_
100	butanol	butanol	NN	_	_	_
101	_	_	SYM	_	_	_
102	Sample4	sample4	FW	_	_	_
103	_	_	FW	_	_	_
104	TechRep2	techrep2	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	Ecoli	ecolus	NNS	_	_	_
107	_	_	VBP	_	_	_
108	wildtype	wildtype	JJ	_	_	_
109	_	_	NN	_	_	_
110	1	1	CD	_	_	_
111	%	%	NN	_	_	_
112	_	_	CD	_	_	_
113	isobutanol	isobutanol	NN	_	_	_
114	_	_	NN	_	_	_
115	Sample1	sample1	NN	_	_	_
116	_	_	CD	_	_	_
117	TechRep1	techrep1	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	Ecoli	ecolus	NNS	_	_	_
120	_	_	VBP	_	_	_
121	wildtype	wildtype	JJ	_	_	_
122	_	_	NN	_	_	_
123	1	1	CD	_	_	_
124	%	%	NN	_	_	_
125	_	_	CD	_	_	_
126	isobutanol	isobutanol	NN	_	_	_
127	_	_	NN	_	_	_
128	Sample1	sample1	NN	_	_	_
129	_	_	CD	_	_	_
130	TechRep2	techrep2	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	Ecoli	ecolus	NNS	_	_	_
133	_	_	VBP	_	_	_
134	wildtype	wildtype	JJ	_	_	_
135	_	_	NN	_	_	_
136	1	1	CD	_	_	_
137	%	%	NN	_	_	_
138	_	_	CD	_	_	_
139	isobutanol	isobutanol	NN	_	_	_
140	_	_	SYM	_	_	_
141	Sample2	sample2	FW	_	_	_
142	_	_	FW	_	_	_
143	TechRep1	techrep1	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	Ecoli	ecolus	NNS	_	_	_
146	_	_	VBP	_	_	_
147	wildtype	wildtype	JJ	_	_	_
148	_	_	NN	_	_	_
149	1	1	CD	_	_	_
150	%	%	NN	_	_	_
151	_	_	CD	_	_	_
152	isobutanol	isobutanol	NN	_	_	_
153	_	_	NN	_	_	_
154	Sample2	sample2	NN	_	_	_
155	_	_	CD	_	_	_
156	TechRep2	techrep2	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	Ecoli	ecolus	NNS	_	_	_
159	_	_	VBP	_	_	_
160	wildtype	wildtype	JJ	_	_	_
161	_	_	NN	_	_	_
162	1	1	CD	_	_	_
163	%	%	NN	_	_	_
164	_	_	CD	_	_	_
165	isobutanol	isobutanol	NN	_	_	_
166	_	_	SYM	_	_	_
167	Sample3	sample3	FW	_	_	_
168	_	_	FW	_	_	_
169	TechRep1	techrep1	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	Ecoli	ecolus	NNS	_	_	_
172	_	_	VBP	_	_	_
173	wildtype	wildtype	JJ	_	_	_
174	_	_	NN	_	_	_
175	1	1	CD	_	_	_
176	%	%	NN	_	_	_
177	_	_	CD	_	_	_
178	isobutanol	isobutanol	NN	_	_	_
179	_	_	SYM	_	_	_
180	Sample3	sample3	FW	_	_	_
181	_	_	FW	_	_	_
182	TechRep2	techrep2	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	Ecoli	ecolus	NNS	_	_	_
185	_	_	VBP	_	_	_
186	wildtype	wildtype	JJ	_	_	_
187	_	_	NN	_	_	_
188	1	1	CD	_	_	_
189	%	%	NN	_	_	_
190	_	_	CD	_	_	_
191	isobutanol	isobutanol	NN	_	_	_
192	_	_	NN	_	_	_
193	Sample4	sample4	NN	_	_	_
194	_	_	CD	_	_	_
195	TechRep1	techrep1	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	Ecoli	ecolus	NNS	_	_	_
198	_	_	VBP	_	_	_
199	wildtype	wildtype	JJ	_	_	_
200	_	_	NN	_	_	_
201	1	1	CD	_	_	_
202	%	%	NN	_	_	_
203	_	_	CD	_	_	_
204	isobutanol	isobutanol	NN	_	_	_
205	_	_	NN	_	_	_
206	Sample4	sample4	NN	_	_	_
207	_	_	CD	_	_	_
208	TechRep2	techrep2	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	Ecoli	ecolus	NNS	_	_	_
211	_	_	VBP	_	_	_
212	wildtype	wildtype	JJ	_	_	_
213	_	_	NN	_	_	_
214	1	1	CD	_	_	_
215	%	%	NN	_	_	_
216	_	_	CD	_	_	_
217	isobutanol	isobutanol	NN	_	_	_
218	_	_	SYM	_	_	_
219	Sample5	sample5	FW	_	_	_
220	_	_	FW	_	_	_
221	TechRep1	techrep1	NN	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	Ecoli	ecolus	NNS	_	_	_
224	_	_	VBP	_	_	_
225	wildtype	wildtype	JJ	_	_	_
226	_	_	NN	_	_	_
227	1	1	CD	_	_	_
228	%	%	NN	_	_	_
229	_	_	CD	_	_	_
230	isobutanol	isobutanol	NN	_	_	_
231	_	_	SYM	_	_	_
232	Sample5	sample5	FW	_	_	_
233	_	_	FW	_	_	_
234	TechRep2	techrep2	NN	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	Ecoli	ecolus	NNS	_	_	_
237	_	_	VBP	_	_	_
238	wildtype	wildtype	JJ	_	_	_
239	_	_	NN	_	_	_
240	3	3	CD	_	_	_
241	%	%	NN	_	_	_
242	_	_	CD	_	_	_
243	ethanol	ethanol	NN	_	_	_
244	_	_	SYM	_	_	_
245	Sample1	sample1	FW	_	_	_
246	_	_	FW	_	_	_
247	TechRep1	techrep1	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	Ecoli	ecolus	NNS	_	_	_
250	_	_	VBP	_	_	_
251	wildtype	wildtype	JJ	_	_	_
252	_	_	NN	_	_	_
253	3	3	CD	_	_	_
254	%	%	NN	_	_	_
255	_	_	CD	_	_	_
256	ethanol	ethanol	NN	_	_	_
257	_	_	NN	_	_	_
258	Sample1	sample1	NN	_	_	_
259	_	_	CD	_	_	_
260	TechRep2	techrep2	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	Ecoli	ecolus	NNS	_	_	_
263	_	_	VBP	_	_	_
264	wildtype	wildtype	JJ	_	_	_
265	_	_	NN	_	_	_
266	3	3	CD	_	_	_
267	%	%	NN	_	_	_
268	_	_	CD	_	_	_
269	ethanol	ethanol	NN	_	_	_
270	_	_	SYM	_	_	_
271	Sample2	sample2	FW	_	_	_
272	_	_	FW	_	_	_
273	TechRep1	techrep1	NN	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	Ecoli	ecolus	NNS	_	_	_
276	_	_	VBP	_	_	_
277	wildtype	wildtype	JJ	_	_	_
278	_	_	NN	_	_	_
279	3	3	CD	_	_	_
280	%	%	NN	_	_	_
281	_	_	CD	_	_	_
282	ethanol	ethanol	NN	_	_	_
283	_	_	SYM	_	_	_
284	Sample2	sample2	FW	_	_	_
285	_	_	FW	_	_	_
286	TechRep2	techrep2	NN	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	Ecoli	ecolus	NNS	_	_	_
289	_	_	VBP	_	_	_
290	wildtype	wildtype	JJ	_	_	_
291	_	_	NN	_	_	_
292	3	3	CD	_	_	_
293	%	%	NN	_	_	_
294	_	_	CD	_	_	_
295	ethanol	ethanol	NN	_	_	_
296	_	_	SYM	_	_	_
297	Sample3	sample3	FW	_	_	_
298	_	_	FW	_	_	_
299	TechRep1	techrep1	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	Ecoli	ecolus	NNS	_	_	_
302	_	_	VBP	_	_	_
303	wildtype	wildtype	JJ	_	_	_
304	_	_	NN	_	_	_
305	3	3	CD	_	_	_
306	%	%	NN	_	_	_
307	_	_	CD	_	_	_
308	ethanol	ethanol	NN	_	_	_
309	_	_	SYM	_	_	_
310	Sample3	sample3	FW	_	_	_
311	_	_	FW	_	_	_
312	TechRep2	techrep2	NN	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	Ecoli	ecolus	NNS	_	_	_
315	_	_	VBP	_	_	_
316	wildtype	wildtype	JJ	_	_	_
317	_	_	NN	_	_	_
318	3	3	CD	_	_	_
319	%	%	NN	_	_	_
320	_	_	CD	_	_	_
321	ethanol	ethanol	NN	_	_	_
322	_	_	SYM	_	_	_
323	Sample4	sample4	FW	_	_	_
324	_	_	FW	_	_	_
325	TechRep1	techrep1	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	Ecoli	ecolus	NNS	_	_	_
328	_	_	VBP	_	_	_
329	wildtype	wildtype	JJ	_	_	_
330	_	_	NN	_	_	_
331	3	3	CD	_	_	_
332	%	%	NN	_	_	_
333	_	_	CD	_	_	_
334	ethanol	ethanol	NN	_	_	_
335	_	_	SYM	_	_	_
336	Sample4	sample4	FW	_	_	_
337	_	_	FW	_	_	_
338	TechRep2	techrep2	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	E.	e.	FW	_	_	_
341	coli	coli	FW	_	_	_
342	wild-type	wild-type	JJ	_	_	_
343	,	,	,	_	_	_
344	A600	a600	NN	_	_	_
345	=	=	JJ	_	_	_
346	0.2	0.2	CD	_	_	_
347	on	on	IN	_	_	_
348	mucus	mucus	NN	_	_	_
349	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
350	E.	E.	NNP	_	_	_
351	coli	coli	NN	_	_	_
352	wild-type	wild-type	JJ	_	_	_
353	,	,	,	_	_	_
354	A600	a600	NN	_	_	_
355	=	=	JJ	_	_	_
356	0.4	0.4	CD	_	_	_
357	on	on	IN	_	_	_
358	glucose	glucose	NN	SUPP	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	E.	e.	FW	_	_	_
361	coli	coli	FW	_	_	_
362	wild-type	wild-type	JJ	_	_	_
363	,	,	,	_	_	_
364	A600	a600	NN	_	_	_
365	=	=	JJ	_	_	_
366	0.4	0.4	CD	_	_	_
367	on	on	IN	_	_	_
368	mannose	mannose	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	E.	e.	FW	_	_	_
371	coli	coli	FW	_	_	_
372	wild-type	wild-type	JJ	_	_	_
373	,	,	,	_	_	_
374	A600	a600	NN	_	_	_
375	=	=	JJ	_	_	_
376	0.5	0.5	CD	_	_	_
377	on	on	IN	_	_	_
378	mucus	mucus	NN	_	_	_
379	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
380	E.	E.	NNP	_	_	_
381	coli	coli	NN	_	_	_
382	Wild	Wild	NNP	_	_	_
383	type	type	NN	_	_	_
384	_	_	CD	_	_	_
385	acetate	acetate	NN	SUPP	_	_
386	_	_	NN	_	_	_
387	exponential	exponential	JJ	GrowthPhase	_	_
388	phase	phase	NN	GrowthPhase	_	_
389	_	_	NN	_	_	_
390	repl1	repl1	NN	_	_	_
391	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
392	E.	E.	NNP	_	_	_
393	coli	coli	NN	_	_	_
394	Wild	Wild	NNP	_	_	_
395	type	type	NN	_	_	_
396	_	_	CD	_	_	_
397	acetate	acetate	NN	SUPP	_	_
398	_	_	NN	_	_	_
399	exponential	exponential	JJ	GrowthPhase	_	_
400	phase	phase	NN	GrowthPhase	_	_
401	_	_	NN	_	_	_
402	repl2	repl2	NN	_	_	_
403	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
404	E.	E.	NNP	_	_	_
405	coli	coli	NN	_	_	_
406	Wild	Wild	NNP	_	_	_
407	type	type	NN	_	_	_
408	_	_	CD	_	_	_
409	acetate	acetate	NN	SUPP	_	_
410	_	_	NN	_	_	_
411	stationary	stationary	JJ	GrowthPhase	_	_
412	phase	phase	NN	GrowthPhase	_	_
413	_	_	NN	_	_	_
414	repl1	repl1	NN	_	_	_
415	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
416	E.	E.	NNP	_	_	_
417	coli	coli	NN	_	_	_
418	Wild	Wild	NNP	_	_	_
419	type	type	NN	_	_	_
420	_	_	CD	_	_	_
421	acetate	acetate	NN	SUPP	_	_
422	_	_	NN	_	_	_
423	stationary	stationary	JJ	GrowthPhase	_	_
424	phase	phase	NN	GrowthPhase	_	_
425	_	_	NN	_	_	_
426	repl2	repl2	NN	_	_	_
427	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
428	E.	E.	NNP	_	_	_
429	coli	coli	NN	_	_	_
430	Wild	Wild	NNP	_	_	_
431	type	type	NN	_	_	_
432	and	and	CC	_	_	_
433	its	its	PRP$	_	_	_
434	mutants	mutant	NNS	_	_	_
435	were	be	VBD	_	_	_
436	grown	grow	VBN	_	_	_
437	in	in	IN	_	_	_
438	M9	m9	NN	MED	_	_
439	minimal	minimal	JJ	MED	_	_
440	medium	medium	NN	MED	_	_
441	with	with	IN	_	_	_
442	10mM	10mm	NN	_	_	_
443	glucose	glucose	NN	SUPP	_	_
444	or	or	CC	_	_	_
445	30mM	30mm	NN	_	_	_
446	acetate	acetate	NN	SUPP	_	_
447	as	as	IN	_	_	_
448	sole	sole	JJ	_	_	_
449	carbon	carbon	NN	_	_	_
450	source	source	NN	_	_	_
451	.	.	.	_	_	_

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	Ecoli	Ecoli	NNP	_	_	_
27	_	_	SYM	_	_	_
28	wildtype	wildtype	JJ	_	_	_
29	_	_	NN	_	_	_
30	calibration	calibration	NN	_	_	_
31	_	_	CD	_	_	_
32	Sample1	sample1	NN	_	_	_
33	_	_	CD	_	_	_
34	TechRep1	techrep1	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Ecoli	ecolus	NNS	_	_	_
37	_	_	VBP	_	_	_
38	wildtype	wildtype	JJ	_	_	_
39	_	_	NN	_	_	_
40	calibration	calibration	NN	_	_	_
41	_	_	CD	_	_	_
42	Sample1	sample1	NN	_	_	_
43	_	_	CD	_	_	_
44	TechRep2	techrep2	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Ecoli	ecolus	NNS	_	_	_
47	_	_	VBP	_	_	_
48	wildtype	wildtype	JJ	_	_	_
49	_	_	NN	_	_	_
50	calibration	calibration	NN	_	_	_
51	_	_	SYM	_	_	_
52	Sample2	sample2	FW	_	_	_
53	_	_	FW	_	_	_
54	TechRep1	techrep1	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Ecoli	ecolus	NNS	_	_	_
57	_	_	VBP	_	_	_
58	wildtype	wildtype	JJ	_	_	_
59	_	_	NN	_	_	_
60	calibration	calibration	NN	_	_	_
61	_	_	CD	_	_	_
62	Sample2	sample2	NN	_	_	_
63	_	_	CD	_	_	_
64	TechRep2	techrep2	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	Wild	Wild	NNP	_	_	_
69	type	type	NN	_	_	_
70	_	_	CD	_	_	_
71	glucose	glucose	NN	SUPP	_	_
72	_	_	NN	_	_	_
73	exponential	exponential	JJ	GrowthPhase	_	_
74	phase	phase	NN	GrowthPhase	_	_
75	_	_	NN	_	_	_
76	repl1	repl1	NN	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	E.	E.	NNP	_	_	_
79	coli	coli	NN	_	_	_
80	Wild	Wild	NNP	_	_	_
81	type	type	NN	_	_	_
82	_	_	CD	_	_	_
83	glucose	glucose	NN	SUPP	_	_
84	_	_	NN	_	_	_
85	exponential	exponential	JJ	GrowthPhase	_	_
86	phase	phase	NN	GrowthPhase	_	_
87	_	_	NN	_	_	_
88	repl2	repl2	NN	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	E.	E.	NNP	_	_	_
91	coli	coli	NN	_	_	_
92	Wild	Wild	NNP	_	_	_
93	type	type	NN	_	_	_
94	_	_	CD	_	_	_
95	glucose	glucose	NN	SUPP	_	_
96	_	_	NN	_	_	_
97	stationary	stationary	JJ	GrowthPhase	_	_
98	phase	phase	NN	GrowthPhase	_	_
99	_	_	NN	_	_	_
100	repl1	repl1	NN	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	E.	E.	NNP	_	_	_
103	coli	coli	NN	_	_	_
104	Wild	Wild	NNP	_	_	_
105	type	type	NN	_	_	_
106	_	_	CD	_	_	_
107	glucose	glucose	NN	SUPP	_	_
108	_	_	NN	_	_	_
109	stationary	stationary	JJ	GrowthPhase	_	_
110	phase	phase	NN	GrowthPhase	_	_
111	_	_	SYM	_	_	_
112	repl2	repl2	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
114	Ecoli	ecoli	JJ	_	_	_
115	wildtype	wildtype	JJ	_	_	_
116	grown	grow	VBN	_	_	_
117	in	in	IN	_	_	_
118	MOPS	MOPS	NNP	MED	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	Ecoli	Ecoli	NNP	_	_	_
121	wildtype	wildtype	JJ	_	_	_
122	grown	grow	VBN	_	_	_
123	in	in	IN	_	_	_
124	MOPS	MOPS	NNP	MED	_	_
125	,	,	,	_	_	_
126	10	10	CD	_	_	_
127	minutes	minute	NNS	_	_	_
128	after	after	IN	_	_	_
129	1	1	CD	_	_	_
130	%	%	NN	_	_	_
131	butanol	butanol	NN	_	_	_
132	treatment	treatment	NN	_	_	_
133	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
134	Ecoli	Ecoli	NNP	_	_	_
135	wildtype	wildtype	JJ	_	_	_
136	grown	grow	VBN	_	_	_
137	in	in	IN	_	_	_
138	MOPS	MOPS	NNP	MED	_	_
139	,	,	,	_	_	_
140	10	10	CD	_	_	_
141	minutes	minute	NNS	_	_	_
142	after	after	IN	_	_	_
143	1	1	CD	_	_	_
144	%	%	NN	_	_	_
145	isobutanol	isobutanol	NN	_	_	_
146	treatment	treatment	NN	_	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	Ecoli	Ecoli	NNP	_	_	_
149	wildtype	wildtype	JJ	_	_	_
150	grown	grow	VBN	_	_	_
151	in	in	IN	_	_	_
152	MOPS	MOPS	NNP	MED	_	_
153	,	,	,	_	_	_
154	10	10	CD	_	_	_
155	minutes	minute	NNS	_	_	_
156	after	after	IN	_	_	_
157	3	3	CD	_	_	_
158	%	%	NN	_	_	_
159	ethanol	ethanol	NN	_	_	_
160	treatment	treatment	NN	_	_	_
161	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
162	Ecoli	Ecoli	NNP	_	_	_
163	_	_	NNP	_	_	_
164	wild-type	wild-type	JJ	_	_	_
165	_	_	NN	_	_	_
166	rep1	rep1	NN	_	_	_
167	_	_	NN	_	_	_
168	anaerobic	anaerobic	JJ	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	Ecoli	ecolus	NNS	_	_	_
171	_	_	VBP	_	_	_
172	wild-type	wild-type	JJ	_	_	_
173	_	_	NN	_	_	_
174	rep2	rep2	NN	_	_	_
175	_	_	CD	_	_	_
176	anaerobic	anaerobic	JJ	_	_	_
177	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
178	E.	E.	NNP	_	_	_
179	coli	coli	NN	_	_	_
180	without	without	IN	_	_	_
181	microemulsion	microemulsion	NN	_	_	_
182	treatment	treatment	NN	_	_	_
183	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
184	Ecoli	Ecoli	NNP	_	_	_
185	_	_	NNP	_	_	_
186	WT	WT	NNP	_	_	_
187	_	_	NNP	_	_	_
188	100uM	100uM	NNP	_	_	_
189	_	_	SYM	_	_	_
190	KCN	KCN	NNP	_	_	_
191	_	_	SYM	_	_	_
192	Sample1	sample1	FW	_	_	_
193	_	_	FW	_	_	_
194	TechRep1	techrep1	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	Ecoli	ecolus	NNS	_	_	_
197	_	_	VBP	_	_	_
198	WT	wt	JJ	_	_	_
199	_	_	NN	_	_	_
200	100uM	100um	NN	_	_	_
201	_	_	CD	_	_	_
202	KCN	KCN	NNP	_	_	_
203	_	_	SYM	_	_	_
204	Sample1	sample1	FW	_	_	_
205	_	_	FW	_	_	_
206	TechRep2	techrep2	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	Ecoli	ecolus	NNS	_	_	_
209	_	_	VBP	_	_	_
210	WT	wt	JJ	_	_	_
211	_	_	NN	_	_	_
212	100uM	100um	NN	_	_	_
213	_	_	CD	_	_	_
214	KCN	KCN	NNP	_	_	_
215	_	_	SYM	_	_	_
216	Sample2	sample2	FW	_	_	_
217	_	_	FW	_	_	_
218	TechRep1	techrep1	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	Ecoli	ecolus	NNS	_	_	_
221	_	_	VBP	_	_	_
222	WT	wt	JJ	_	_	_
223	_	_	NN	_	_	_
224	100uM	100um	NN	_	_	_
225	_	_	CD	_	_	_
226	KCN	KCN	NNP	_	_	_
227	_	_	SYM	_	_	_
228	Sample2	sample2	FW	_	_	_
229	_	_	FW	_	_	_
230	TechRep2	techrep2	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	Ecoli	ecolus	NNS	_	_	_
233	_	_	VBP	_	_	_
234	WT	wt	JJ	_	_	_
235	_	_	NN	_	_	_
236	100uM	100um	NN	_	_	_
237	_	_	CD	_	_	_
238	KCN	KCN	NNP	_	_	_
239	_	_	SYM	_	_	_
240	Sample3	sample3	FW	_	_	_
241	_	_	FW	_	_	_
242	TechRep1	techrep1	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	Ecoli	ecolus	NNS	_	_	_
245	_	_	VBP	_	_	_
246	WT	wt	JJ	_	_	_
247	_	_	NN	_	_	_
248	100uM	100um	NN	_	_	_
249	_	_	CD	_	_	_
250	KCN	KCN	NNP	_	_	_
251	_	_	SYM	_	_	_
252	Sample3	sample3	FW	_	_	_
253	_	_	FW	_	_	_
254	TechRep2	techrep2	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	Ecoli	ecolus	NNS	_	_	_
257	_	_	VBP	_	_	_
258	WT	wt	JJ	_	_	_
259	_	_	NN	_	_	_
260	100uM	100um	NN	_	_	_
261	_	_	CD	_	_	_
262	KCN	KCN	NNP	_	_	_
263	_	_	SYM	_	_	_
264	Sample4	sample4	FW	_	_	_
265	_	_	FW	_	_	_
266	TechRep1	techrep1	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	Ecoli	ecolus	NNS	_	_	_
269	_	_	VBP	_	_	_
270	WT	wt	JJ	_	_	_
271	_	_	NN	_	_	_
272	100uM	100um	NN	_	_	_
273	_	_	CD	_	_	_
274	KCN	KCN	NNP	_	_	_
275	_	_	SYM	_	_	_
276	Sample4	sample4	FW	_	_	_
277	_	_	FW	_	_	_
278	TechRep2	techrep2	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	E.	e.	FW	_	_	_
281	coli	coli	FW	_	_	_
282	wt	wt	JJ	_	_	_
283	grown	grow	VBN	_	_	_
284	in	in	IN	_	_	_
285	acetate	acetate	NN	SUPP	_	_
286	batch	batch	NN	_	_	_
287	minimal	minimal	JJ	_	_	_
288	media	media	NNS	_	_	_
289	,	,	,	_	_	_
290	cells	cell	NNS	_	_	_
291	were	be	VBD	_	_	_
292	harvested	harvest	VBN	_	_	_
293	at	at	IN	_	_	_
294	exponential	exponential	JJ	GrowthPhase	_	_
295	phase	phase	NN	GrowthPhase	_	_
296	,	,	,	_	_	_
297	biological	biological	JJ	_	_	_
298	rep1	rep1	NN	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	E.	e.	FW	_	_	_
301	coli	coli	FW	_	_	_
302	wt	wt	JJ	_	_	_
303	grown	grow	VBN	_	_	_
304	in	in	IN	_	_	_
305	acetate	acetate	NN	SUPP	_	_
306	batch	batch	NN	_	_	_
307	minimal	minimal	JJ	_	_	_
308	media	media	NNS	_	_	_
309	,	,	,	_	_	_
310	cells	cell	NNS	_	_	_
311	were	be	VBD	_	_	_
312	harvested	harvest	VBN	_	_	_
313	at	at	IN	_	_	_
314	exponential	exponential	JJ	GrowthPhase	_	_
315	phase	phase	NN	GrowthPhase	_	_
316	,	,	,	_	_	_
317	biological	biological	JJ	_	_	_
318	rep2	rep2	NN	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	E.	e.	FW	_	_	_
321	coli	coli	FW	_	_	_
322	wt	wt	JJ	_	_	_
323	grown	grow	VBN	_	_	_
324	in	in	IN	_	_	_
325	acetate	acetate	NN	SUPP	_	_
326	batch	batch	NN	_	_	_
327	minimal	minimal	JJ	_	_	_
328	media	media	NNS	_	_	_
329	,	,	,	_	_	_
330	cells	cell	NNS	_	_	_
331	were	be	VBD	_	_	_
332	harvested	harvest	VBN	_	_	_
333	at	at	IN	_	_	_
334	stationary	stationary	JJ	GrowthPhase	_	_
335	phase	phase	NN	GrowthPhase	_	_
336	,	,	,	_	_	_
337	biological	biological	JJ	_	_	_
338	rep1	rep1	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	E.	e.	FW	_	_	_
341	coli	coli	FW	_	_	_
342	wt	wt	JJ	_	_	_
343	grown	grow	VBN	_	_	_
344	in	in	IN	_	_	_
345	acetate	acetate	NN	SUPP	_	_
346	batch	batch	NN	_	_	_
347	minimal	minimal	JJ	_	_	_
348	media	media	NNS	_	_	_
349	,	,	,	_	_	_
350	cells	cell	NNS	_	_	_
351	were	be	VBD	_	_	_
352	harvested	harvest	VBN	_	_	_
353	at	at	IN	_	_	_
354	stationary	stationary	JJ	GrowthPhase	_	_
355	phase	phase	NN	GrowthPhase	_	_
356	,	,	,	_	_	_
357	biological	biological	JJ	_	_	_
358	rep2	rep2	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	E.	e.	FW	_	_	_
361	coli	coli	FW	_	_	_
362	wt	wt	JJ	_	_	_
363	grown	grow	VBN	_	_	_
364	in	in	IN	_	_	_
365	glucose	glucose	NN	SUPP	_	_
366	batch	batch	NN	_	_	_
367	minimal	minimal	JJ	_	_	_
368	media	media	NNS	_	_	_
369	,	,	,	_	_	_
370	cells	cell	NNS	_	_	_
371	were	be	VBD	_	_	_
372	harvested	harvest	VBN	_	_	_
373	at	at	IN	_	_	_
374	exponential	exponential	JJ	GrowthPhase	_	_
375	phase	phase	NN	GrowthPhase	_	_
376	,	,	,	_	_	_
377	biological	biological	JJ	_	_	_
378	rep1	rep1	NN	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	E.	e.	FW	_	_	_
381	coli	coli	FW	_	_	_
382	wt	wt	JJ	_	_	_
383	grown	grow	VBN	_	_	_
384	in	in	IN	_	_	_
385	glucose	glucose	NN	SUPP	_	_
386	batch	batch	NN	_	_	_
387	minimal	minimal	JJ	_	_	_
388	media	media	NNS	_	_	_
389	,	,	,	_	_	_
390	cells	cell	NNS	_	_	_
391	were	be	VBD	_	_	_
392	harvested	harvest	VBN	_	_	_
393	at	at	IN	_	_	_
394	exponential	exponential	JJ	GrowthPhase	_	_
395	phase	phase	NN	GrowthPhase	_	_
396	,	,	,	_	_	_
397	biological	biological	JJ	_	_	_
398	rep2	rep2	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	E.	e.	FW	_	_	_
401	coli	coli	FW	_	_	_
402	wt	wt	JJ	_	_	_
403	grown	grow	VBN	_	_	_
404	in	in	IN	_	_	_
405	glucose	glucose	NN	SUPP	_	_
406	batch	batch	NN	_	_	_
407	minimal	minimal	JJ	_	_	_
408	media	media	NNS	_	_	_
409	,	,	,	_	_	_
410	cells	cell	NNS	_	_	_
411	were	be	VBD	_	_	_
412	harvested	harvest	VBN	_	_	_
413	at	at	IN	_	_	_
414	stationary	stationary	JJ	GrowthPhase	_	_
415	phase	phase	NN	GrowthPhase	_	_
416	,	,	,	_	_	_
417	biological	biological	JJ	_	_	_
418	rep1	rep1	NN	_	_	_
419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
420	E.	e.	FW	_	_	_
421	coli	coli	FW	_	_	_
422	wt	wt	JJ	_	_	_
423	grown	grow	VBN	_	_	_
424	in	in	IN	_	_	_
425	glucose	glucose	NN	SUPP	_	_
426	batch	batch	NN	_	_	_
427	minimal	minimal	JJ	_	_	_
428	media	media	NNS	_	_	_
429	,	,	,	_	_	_
430	cells	cell	NNS	_	_	_
431	were	be	VBD	_	_	_
432	harvested	harvest	VBN	_	_	_
433	at	at	IN	_	_	_
434	stationary	stationary	JJ	GrowthPhase	_	_
435	phase	phase	NN	GrowthPhase	_	_
436	,	,	,	_	_	_
437	biological	biological	JJ	_	_	_
438	rep2	rep2	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	E.coli	e.coli	NNS	_	_	_
441	_	_	VBP	_	_	_
442	WT	wt	JJ	_	_	_
443	pH	ph	NN	_	_	_
444	5.6	5.6	CD	_	_	_
445	A	a	DT	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	E.coli	e.coli	NN	_	_	_
448	_	_	CD	_	_	_
449	WT	WT	NNP	_	_	_
450	pH	ph	NN	_	_	_
451	5.6	5.6	CD	_	_	_
452	B	b	NN	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	E.coli	e.coli	NNS	_	_	_
455	_	_	VBP	_	_	_
456	WT	wt	JJ	_	_	_
457	pH	ph	NN	_	_	_
458	5.6	5.6	CD	_	_	_
459	C	c	NN	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	E.coli	e.coli	NNS	_	_	_
462	_	_	VBP	_	_	_
463	WT	wt	JJ	_	_	_
464	pH	ph	NN	_	_	_
465	7.2	7.2	CD	_	_	_
466	+15	+15	CD	_	_	_
467	%	%	NN	_	_	_
468	sucrose	sucrose	NN	_	_	_
469	A	a	NN	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	E.coli	e.coli	NNS	_	_	_
472	_	_	VBP	_	_	_
473	WT	wt	JJ	_	_	_
474	pH	ph	NN	_	_	_
475	7.2	7.2	CD	_	_	_
476	+15	+15	CD	_	_	_
477	%	%	NN	_	_	_
478	sucrose	sucrose	NN	_	_	_
479	B	b	NN	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	E.coli	e.coli	NNS	_	_	_
482	_	_	VBP	_	_	_
483	WT	wt	JJ	_	_	_
484	pH	ph	NN	_	_	_
485	7.2	7.2	CD	_	_	_
486	+15	+15	CD	_	_	_
487	%	%	NN	_	_	_
488	sucrose	sucrose	NN	_	_	_
489	C	c	NN	_	_	_
490	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
491	Ecoli	Ecoli	NNP	_	_	_
492	_	_	NNP	_	_	_
493	WT	WT	NNP	_	_	_
494	_	_	NNP	_	_	_
495	RNAseq	RNAseq	NNP	_	_	_
496	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
497	Eco	Eco	NNP	_	_	_
498	_	_	SYM	_	_	_
499	TolC	tolc	NN	_	_	_
500	_	_	NN	_	_	_
501	0	0	CD	_	_	_
502	min	min	NN	_	_	_
503	_	_	NN	_	_	_
504	A	a	NN	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	Eco	eco	NN	_	_	_
507	_	_	CD	_	_	_
508	TolC	tolc	NN	_	_	_
509	_	_	NN	_	_	_
510	0	0	CD	_	_	_
511	min	min	NN	_	_	_
512	_	_	NN	_	_	_
513	B	b	NN	_	_	_
514	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
515	Eco	Eco	NNP	_	_	_
516	_	_	SYM	_	_	_
517	TolC	tolc	NN	_	_	_
518	_	_	CD	_	_	_
519	15	15	CD	_	_	_
520	min	min	NN	_	_	_
521	_	_	CD	_	_	_
522	Carolacton	Carolacton	NNP	_	_	_
523	_	_	NNP	_	_	_
524	A	A	NNP	_	_	_
525	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
526	Eco	Eco	NNP	_	_	_
527	_	_	SYM	_	_	_
528	TolC	tolc	NN	_	_	_
529	_	_	CD	_	_	_
530	15	15	CD	_	_	_
531	min	min	NN	_	_	_
532	_	_	CD	_	_	_
533	Carolacton	Carolacton	NNP	_	_	_
534	_	_	NN	_	_	_
535	B	b	NN	_	_	_
536	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
537	Eco	Eco	NNP	_	_	_
538	_	_	SYM	_	_	_
539	TolC	tolc	NN	_	_	_
540	_	_	CD	_	_	_
541	15	15	CD	_	_	_
542	min	min	NN	_	_	_
543	_	_	NN	_	_	_
544	control	control	NN	_	_	_
545	_	_	CD	_	_	_
546	A	a	DT	_	_	_
547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
548	Eco	eco	NN	_	_	_
549	_	_	CD	_	_	_
550	TolC	tolc	NN	_	_	_
551	_	_	CD	_	_	_
552	15	15	CD	_	_	_
553	min	min	NN	_	_	_
554	_	_	NN	_	_	_
555	control	control	NN	_	_	_
556	_	_	CD	_	_	_
557	B	b	NN	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
559	Eco	Eco	NNP	_	_	_
560	_	_	SYM	_	_	_
561	TolC	tolc	NN	_	_	_
562	_	_	CD	_	_	_
563	30	30	CD	_	_	_
564	min	min	NN	_	_	_
565	_	_	CD	_	_	_
566	Carolacton	Carolacton	NNP	_	_	_
567	_	_	NNP	_	_	_
568	A	A	NNP	_	_	_
569	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
570	Eco	Eco	NNP	_	_	_
571	_	_	SYM	_	_	_
572	TolC	tolc	NN	_	_	_
573	_	_	CD	_	_	_
574	30	30	CD	_	_	_
575	min	min	NN	_	_	_
576	_	_	CD	_	_	_
577	Carolacton	Carolacton	NNP	_	_	_
578	_	_	NN	_	_	_
579	B	b	NN	_	_	_
580	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
581	Eco	Eco	NNP	_	_	_
582	_	_	SYM	_	_	_
583	TolC	tolc	NN	_	_	_
584	_	_	CD	_	_	_
585	30	30	CD	_	_	_
586	min	min	NN	_	_	_
587	_	_	NN	_	_	_
588	control	control	NN	_	_	_
589	_	_	CD	_	_	_
590	A	a	DT	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	Eco	eco	NN	_	_	_
593	_	_	CD	_	_	_
594	TolC	tolc	NN	_	_	_
595	_	_	CD	_	_	_
596	30	30	CD	_	_	_
597	min	min	NN	_	_	_
598	_	_	NN	_	_	_
599	control	control	NN	_	_	_
600	_	_	CD	_	_	_
601	B	b	NN	_	_	_
602	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
603	Eco	Eco	NNP	_	_	_
604	_	_	SYM	_	_	_
605	TolC	tolc	NN	_	_	_
606	_	_	CD	_	_	_
607	5	5	CD	_	_	_
608	min	min	NN	_	_	_
609	_	_	CD	_	_	_
610	Carolacton	Carolacton	NNP	_	_	_
611	_	_	NNP	_	_	_
612	A	A	NNP	_	_	_
613	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
614	Eco	Eco	NNP	_	_	_
615	_	_	SYM	_	_	_
616	TolC	tolc	NN	_	_	_
617	_	_	CD	_	_	_
618	5	5	CD	_	_	_
619	min	min	NN	_	_	_
620	_	_	CD	_	_	_
621	Carolacton	Carolacton	NNP	_	_	_
622	_	_	NN	_	_	_
623	B	b	NN	_	_	_
624	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
625	Eco	Eco	NNP	_	_	_
626	_	_	SYM	_	_	_
627	TolC	tolc	NN	_	_	_
628	_	_	CD	_	_	_
629	5	5	CD	_	_	_
630	min	min	NN	_	_	_
631	_	_	NN	_	_	_
632	control	control	NN	_	_	_
633	_	_	CD	_	_	_
634	A	a	DT	_	_	_
635	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
636	Eco	eco	NN	_	_	_
637	_	_	CD	_	_	_
638	TolC	tolc	NN	_	_	_
639	_	_	CD	_	_	_
640	5	5	CD	_	_	_
641	min	min	NN	_	_	_
642	_	_	NN	_	_	_
643	control	control	NN	_	_	_
644	_	_	NN	_	_	_
645	B	b	NN	_	_	_
646	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
647	Ec-pR	ec-pr	NN	_	_	_
648	VS	vs	NN	_	_	_
649	Ec-1558	ec-1558	NN	_	_	_
650	rep1	rep1	NN	_	_	_
651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
652	Ec-pR	ec-pr	NN	_	_	_
653	VS	vs	NN	_	_	_
654	Ec-1558	ec-1558	NN	_	_	_
655	rep2	rep2	NN	_	_	_
656	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
657	Ec-pR	ec-pr	NN	_	_	_
658	VS	vs	NN	_	_	_
659	Ec-1558	ec-1558	NN	_	_	_
660	rep3	rep3	NN	_	_	_
661	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
662	EC	EC	NNP	_	_	_
663	_	_	VBD	_	_	_
664	Trim1	trim1	NN	_	_	_
665	_	_	NN	_	_	_
666	DNA	dna	NN	_	_	_
667	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
668	EC	ec	NN	_	_	_
669	_	_	CD	_	_	_
670	Trim1	trim1	NN	_	_	_
671	_	_	NN	_	_	_
672	RNA	rna	NN	_	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
674	EC	ec	NN	_	_	_
675	_	_	CD	_	_	_
676	Trim2	trim2	NN	_	_	_
677	_	_	NN	_	_	_
678	DNA	dna	NN	_	_	_
679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
680	EC	ec	NN	_	_	_
681	_	_	CD	_	_	_
682	Trim2	trim2	NN	_	_	_
683	_	_	NN	_	_	_
684	RNA	rna	NN	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
686	EDC1	edc1	NN	_	_	_
687	_	_	CD	_	_	_
688	AP	ap	NN	_	_	_
689	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
690	EDC1	edc1	NN	_	_	_
691	_	_	CD	_	_	_
692	Total	total	JJ	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	EDL932	edl932	NN	_	_	_
695	exposure	exposure	NN	_	_	_
696	to	to	TO	_	_	_
697	CL	cl	NN	_	_	_
698	MC	MC	NNP	_	_	_
699	fraction	fraction	NN	_	_	_
700	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
701	EDL932	edl932	NN	_	_	_
702	unexposed	unexposed	JJ	_	_	_
703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
704	EDL933	edl933	NN	_	_	_
705	24	24	CD	_	_	_
706	h	h	NN	_	_	_
707	post	post	NN	_	_	_
708	infection	infection	NN	_	_	_
709	in	in	IN	_	_	_
710	THP-1	thp-1	NN	_	_	_
711	humans	human	NNS	_	_	_
712	cells	cell	NNS	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
714	EDL933	edl933	NN	_	_	_
715	8h	8h	NN	_	_	_
716	post-infection	post-infection	NN	_	_	_
717	in	in	IN	_	_	_
718	THP-1	thp-1	NN	_	_	_
719	human	human	JJ	_	_	_
720	cells	cell	NNS	_	_	_
721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
722	EDL933	edl933	NN	_	_	_
723	8h	8h	NN	_	_	_
724	post	post	NN	_	_	_
725	THP-1	thp-1	NN	_	_	_
726	infection	infection	NN	_	_	_
727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
728	EDL	edl	NN	_	_	_
729	933	933	CD	_	_	_
730	at	at	IN	_	_	_
731	37oC	37oc	NN	_	_	_
732	at	at	IN	_	_	_
733	OD	od	NN	_	_	_
734	1.0	1.0	CD	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
736	EDL933	edl933	NN	_	_	_
737	cDNA	cdna	NN	_	_	_
738	24	24	CD	_	_	_
739	h	h	NN	_	_	_
740	post-infcetion	post-infcetion	NN	_	_	_
741	of	of	IN	_	_	_
742	THP-1	thp-1	NN	_	_	_
743	human	human	JJ	_	_	_
744	cells	cell	NNS	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
746	EDL933	edl933	NN	_	_	_
747	cDNA	cdna	NN	_	_	_
748	obtained	obtain	VBN	_	_	_
749	24	24	CD	_	_	_
750	h	h	NN	_	_	_
751	post	post	NN	_	_	_
752	-	-	:	_	_	_
753	infection	infection	NN	_	_	_
754	of	of	IN	_	_	_
755	THP-1	thp-1	NN	_	_	_
756	human	human	JJ	_	_	_
757	cells	cell	NNS	_	_	_
758	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
759	EDL933	edl933	NN	_	_	_
760	cDNA	cdna	NN	_	_	_
761	obtained	obtain	VBN	_	_	_
762	24h	24h	JJ	_	_	_
763	post-infection	post-infection	NN	_	_	_
764	of	of	IN	_	_	_
765	THP-1	thp-1	NN	_	_	_
766	human	human	JJ	_	_	_
767	cells	cell	NNS	_	_	_
768	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
769	EDL933	edl933	NN	_	_	_
770	from	from	IN	_	_	_
771	overnight	overnight	JJ	_	_	_
772	culture	culture	NN	_	_	_
773	in	in	IN	_	_	_
774	LB	lb	NN	MED	_	_
775	broth	broth	NN	MED	_	_
776	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
777	EDL933	edl933	NN	_	_	_
778	genomic	genomic	JJ	_	_	_
779	DNA	dna	NN	_	_	_
780	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
781	EDL933	edl933	NN	_	_	_
782	genomic	genomic	JJ	_	_	_
783	DNA	dna	NN	_	_	_
784	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
785	EDL933	edl933	NN	_	_	_
786	genommic	genommic	JJ	_	_	_
787	DNA	dna	NN	_	_	_
788	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
789	EDL933	edl933	NN	_	_	_
790	infection	infection	NN	_	_	_
791	of	of	IN	_	_	_
792	THP-1	thp-1	NN	_	_	_
793	cells	cell	NNS	_	_	_
794	,	,	,	_	_	_
795	recovered	recover	VBD	_	_	_
796	2	2	CD	_	_	_
797	h	h	NN	_	_	_
798	post-infection	post-infection	JJ	_	_	_
799	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
800	EDL933	edl933	NN	_	_	_
801	infection	infection	NN	_	_	_
802	of	of	IN	_	_	_
803	THP-1	thp-1	NN	_	_	_
804	cells	cell	NNS	_	_	_
805	,	,	,	_	_	_
806	recovered	recover	VBD	_	_	_
807	2h	2h	JJ	_	_	_
808	post-infection	post-infection	JJ	_	_	_
809	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
810	EDL933	edl933	NN	_	_	_
811	in	in	IN	_	_	_
812	humans	human	NNS	_	_	_
813	macrophages	macrophage	NNS	_	_	_
814	8h	8h	VBP	_	_	_
815	post-infection	post-infection	JJ	_	_	_
816	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
817	EDL933	edl933	NN	_	_	_
818	in	in	IN	_	_	_
819	RPMI	rpmi	NN	_	_	_
820	medium	medium	NN	_	_	_
821	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
822	EDL933	edl933	NN	_	_	_
823	in	in	IN	_	_	_
824	THP-1	thp-1	NN	_	_	_
825	cells	cell	NNS	_	_	_
826	8h	8h	VBP	_	_	_
827	post-infection	post-infection	JJ	_	_	_
828	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
829	EDL933	edl933	NN	_	_	_
830	_	_	CD	_	_	_
831	LB	lb	NN	_	_	_
832	_	_	NN	_	_	_
833	I	I	PRP	_	_	_
834	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
835	EDL933	edl933	NN	_	_	_
836	_	_	CD	_	_	_
837	LB	lb	NN	_	_	_
838	_	_	NN	_	_	_
839	II	ii	CD	_	_	_
840	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
841	EDL	edl	NN	_	_	_
842	933	933	CD	_	_	_
843	with	with	IN	_	_	_
844	0.1	0.1	CD	_	_	_
845	mg/ml	mg/ml	NN	_	_	_
846	IAN	IAN	NNP	_	_	_
847	at	at	IN	_	_	_
848	37oC	37oC	NNP	_	_	_
849	at	at	IN	_	_	_
850	OD	OD	NNP	_	_	_
851	1.0	1.0	CD	_	_	_
852	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
853	EDL	edl	NN	_	_	_
854	933	933	CD	_	_	_
855	with	with	IN	_	_	_
856	0.1	0.1	CD	_	_	_
857	mg/ml	mg/ml	NN	_	_	_
858	IAN	ian	NN	_	_	_
859	at	at	IN	_	_	_
860	37oC	37oc	NN	_	_	_
861	at	at	IN	_	_	_
862	OD	od	NN	_	_	_
863	1.0	1.0	CD	_	_	_
864	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
865	EDL	edl	NN	_	_	_
866	-LRB-	-lrb-	-LRB-	_	_	_
867	O157	o157	NN	_	_	_
868	:	:	:	_	_	_
869	H7	h7	NN	_	_	_
870	-RRB-	-rrb-	-RRB-	_	_	_
871	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
872	Efflux	efflux	NN	_	_	_
873	Mutant	mutant	JJ	_	_	_
874	Parent	Parent	NNP	_	_	_
875	Strain	Strain	NNP	_	_	_
876	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
877	EGS084	egs084	NN	_	_	_
878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
879	EGS084	egs084	NN	_	_	_
880	_	_	NN	_	_	_
881	control	control	NN	_	_	_
882	_	_	CD	_	_	_
883	rep	rep	NN	GEN	_	_
884	_	_	NN	_	_	_
885	1	1	CD	_	_	_
886	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
887	EGS084	egs084	NN	_	_	_
888	_	_	NN	_	_	_
889	control	control	NN	_	_	_
890	_	_	CD	_	_	_
891	rep	rep	NN	GEN	_	_
892	_	_	NN	_	_	_
893	2	2	CD	_	_	_
894	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
895	EGS084	egs084	NN	_	_	_
896	_	_	NN	_	_	_
897	control	control	NN	_	_	_
898	_	_	CD	_	_	_
899	rep	rep	NN	GEN	_	_
900	_	_	NN	_	_	_
901	3	3	CD	_	_	_
902	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
903	EGS084	egs084	NN	_	_	_
904	_	_	NN	_	_	_
905	control	control	NN	_	_	_
906	_	_	CD	_	_	_
907	rep	rep	NN	GEN	_	_
908	_	_	NN	_	_	_
909	4	4	CD	_	_	_
910	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
911	EGS084	egs084	NN	_	_	_
912	_	_	NN	_	_	_
913	control	control	NN	_	_	_
914	_	_	CD	_	_	_
915	rep	rep	NN	GEN	_	_
916	_	_	SYM	_	_	_
917	5	5	CD	_	_	_
918	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
919	EGS084	egs084	NN	_	_	_
920	_	_	NN	_	_	_
921	control	control	NN	_	_	_
922	_	_	CD	_	_	_
923	rep	rep	NN	GEN	_	_
924	_	_	NN	_	_	_
925	6	6	CD	_	_	_
926	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
927	EGS212	egs212	NN	_	_	_
928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
929	EGS212	egs212	NN	_	_	_
930	_	_	CD	_	_	_
931	MlfabH	mlfabh	NN	_	_	_
932	_	_	CD	_	_	_
933	rep	rep	NN	GEN	_	_
934	_	_	NN	_	_	_
935	1	1	CD	_	_	_
936	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
937	EGS212	egs212	NN	_	_	_
938	_	_	CD	_	_	_
939	MlfabH	mlfabh	NN	_	_	_
940	_	_	CD	_	_	_
941	rep	rep	NN	GEN	_	_
942	_	_	NN	_	_	_
943	2	2	CD	_	_	_
944	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
945	EGS212	egs212	NN	_	_	_
946	_	_	CD	_	_	_
947	MlfabH	mlfabh	NN	_	_	_
948	_	_	CD	_	_	_
949	rep	rep	NN	GEN	_	_
950	_	_	NN	_	_	_
951	3	3	CD	_	_	_
952	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
953	EGS212	egs212	NN	_	_	_
954	_	_	CD	_	_	_
955	MlfabH	mlfabh	NN	_	_	_
956	_	_	CD	_	_	_
957	rep	rep	NN	GEN	_	_
958	_	_	NN	_	_	_
959	4	4	CD	_	_	_
960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
961	EGS212	egs212	NN	_	_	_
962	_	_	CD	_	_	_
963	MlfabH	mlfabh	NN	_	_	_
964	_	_	NN	_	_	_
965	rep	rep	NN	GEN	_	_
966	_	_	CD	_	_	_
967	5	5	CD	_	_	_
968	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
969	EHEC	ehec	NN	_	_	_
970	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
971	EHEC	ehec	NN	_	_	_
972	either	either	CC	_	_	_
973	grown	grow	VBN	_	_	_
974	on	on	IN	_	_	_
975	plain	plain	JJ	_	_	_
976	LB	lb	NN	_	_	_
977	plates	plate	NNS	_	_	_
978	or	or	CC	_	_	_
979	LB	lb	NN	_	_	_
980	plates	plate	NNS	_	_	_
981	containing	contain	VBG	_	_	_
982	Symbioflor	symbioflor	NN	_	_	_
983	within	within	IN	_	_	_
984	the	the	DT	_	_	_
985	agar	agar	NN	_	_	_
986	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
987	EHEC	ehec	NN	_	_	_
988	in	in	IN	_	_	_
989	LB	LB	NNP	_	_	_
990	Experiment	Experiment	NNP	_	_	_
991	1	1	CD	_	_	_
992	-LSB-	-lsb-	-LRB-	_	_	_
993	RIBO-Seq	ribo-seq	NN	_	_	_
994	-RSB-	-rsb-	-RRB-	_	_	_
995	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
996	EHEC	ehec	NN	_	_	_
997	in	in	IN	_	_	_
998	LB	LB	NNP	_	_	_
999	Experiment	Experiment	NNP	_	_	_
1000	1	1	CD	_	_	_
1001	-LSB-	-lsb-	-LRB-	_	_	_
1002	RNA-Seq	rna-seq	NN	_	_	_
1003	-RSB-	-rsb-	-RRB-	_	_	_
1004	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1005	EHEC	ehec	NN	_	_	_
1006	in	in	IN	_	_	_
1007	LB	LB	NNP	_	_	_
1008	Experiment	Experiment	NNP	_	_	_
1009	2	2	CD	_	_	_
1010	-LSB-	-lsb-	-LRB-	_	_	_
1011	RIBO-Seq	ribo-seq	NN	_	_	_
1012	-RSB-	-rsb-	-RRB-	_	_	_
1013	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1014	EHEC	ehec	NN	_	_	_
1015	in	in	IN	_	_	_
1016	LB	LB	NNP	_	_	_
1017	Experiment	Experiment	NNP	_	_	_
1018	2	2	CD	_	_	_
1019	-LSB-	-lsb-	-LRB-	_	_	_
1020	RNA-Seq	rna-seq	NN	_	_	_
1021	-RSB-	-rsb-	-RRB-	_	_	_
1022	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1023	EHEC	ehec	NN	_	_	_
1024	LB	lb	NN	_	_	_
1025	7	7	CD	_	_	_
1026	h	h	NN	_	_	_
1027	7HI	7HI	NNP	_	_	_
1028	biofilm	biofilm	NN	_	_	_
1029	cells	cell	NNS	_	_	_
1030	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
1031	EHEC	ehec	NN	_	_	_
1032	LB	lb	NN	_	_	_
1033	7	7	CD	_	_	_
1034	h	h	NN	_	_	_
1035	biofilm	biofilm	NN	_	_	_
1036	cells	cell	NNS	_	_	_
1037	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
1038	EHEC	ehec	NN	_	_	_
1039	LB	lb	NN	_	_	_
1040	7	7	CD	_	_	_
1041	h	h	NN	_	_	_
1042	isatin	isatin	NN	_	_	_
1043	biofilm	biofilm	NN	_	_	_
1044	cells	cell	NNS	_	_	_
1045	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
1046	EHEC	ehec	NN	_	_	_
1047	LB	lb	NN	_	_	_
1048	7	7	CD	_	_	_
1049	h	h	NN	_	_	_
1050	suspension	suspension	NN	_	_	_
1051	cells	cell	NNS	_	_	_
1052	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
1053	EHEC	ehec	NN	_	_	_
1054	plus	plus	CC	_	_	_
1055	Symbioflor	symbioflor	JJ	_	_	_
1056	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1057	ehec	ehec	NN	_	_	_
1058	strain	strain	NN	_	_	_
1059	:	:	:	_	_	_
1060	86-24	86-24	CD	_	_	_
1061	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1062	EHEC	ehec	NN	_	_	_
1063	strain	strain	NN	_	_	_
1064	86-24	86-24	CD	_	_	_
1065	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1066	EJW3	ejw3	NN	_	_	_
1067	,	,	,	_	_	_
1068	BW25113	bw25113	NN	_	_	_
1069	rpoC	rpoc	NN	GEN	_	_
1070	K370	k370	NN	_	_	_
1071	_	_	CD	_	_	_
1072	A396dup	a396dup	NN	_	_	_
1073	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1074	EJW3	ejw3	NN	_	_	_
1075	in	in	IN	_	_	_
1076	M9	m9	NN	_	_	_
1077	Replicate	replicate	VB	_	_	_
1078	1	1	CD	_	_	_
1079	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1080	EJW3	ejw3	NN	_	_	_
1081	in	in	IN	_	_	_
1082	M9	m9	NN	_	_	_
1083	Replicate	replicate	VB	_	_	_
1084	2	2	CD	_	_	_
1085	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1086	EJW3	ejw3	NN	_	_	_
1087	in	in	IN	_	_	_
1088	M9	m9	NN	_	_	_
1089	supplemented	supplement	VBN	_	_	_
1090	with	with	IN	_	_	_
1091	0.6	0.6	CD	_	_	_
1092	M	m	NN	_	_	_
1093	NaCl	nacl	NN	_	_	_
1094	Replicate	replicate	VB	_	_	_
1095	1	1	CD	_	_	_
1096	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1097	EJW3	ejw3	NN	_	_	_
1098	in	in	IN	_	_	_
1099	M9	m9	NN	_	_	_
1100	supplemented	supplement	VBN	_	_	_
1101	with	with	IN	_	_	_
1102	0.6	0.6	CD	_	_	_
1103	M	m	NN	_	_	_
1104	NaCl	nacl	NN	_	_	_
1105	Replicate	replicate	VB	_	_	_
1106	2	2	CD	_	_	_
1107	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1108	Elements	element	NNS	_	_	_
1109	with	with	IN	_	_	_
1110	poor	poor	JJ	_	_	_
1111	spot	spot	NN	_	_	_
1112	morphology	morphology	NN	_	_	_
1113	or	or	CC	_	_	_
1114	exhibiting	exhibit	VBG	_	_	_
1115	uneven	uneven	JJ	_	_	_
1116	hybridization	hybridization	NN	_	_	_
1117	caused	cause	VBN	_	_	_
1118	by	by	IN	_	_	_
1119	dust	dust	NN	_	_	_
1120	particles	particle	NNS	_	_	_
1121	or	or	CC	_	_	_
1122	scratches	scratch	NNS	_	_	_
1123	,	,	,	_	_	_
1124	were	be	VBD	_	_	_
1125	flagged	flag	VBN	_	_	_
1126	manually	manually	RB	_	_	_
1127	and	and	CC	_	_	_
1128	excluded	exclude	VBN	_	_	_
1129	from	from	IN	_	_	_
1130	further	further	JJ	_	_	_
1131	analyses	analysis	NNS	_	_	_
1132	.	.	.	_	_	_

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	NN	_	_	_
2	EM1456	em1456	NN	_	_	_
3	wild-type	wild-type	JJ	_	_	_
4	pNM12	pnm12	NN	_	_	_
5	#	#	#	_	_	_
6	1	1	CD	_	_	_
7	+	+	CC	_	_	_
8	arabinose	arabinose	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Emplty	Emplty	NNP	_	_	_
11	Vector	Vector	NNP	_	_	_
12	,	,	,	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	,	,	,	_	_	_
16	replicate	replicate	VB	_	_	_
17	1	1	CD	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Emplty	Emplty	NNP	_	_	_
20	Vector	Vector	NNP	_	_	_
21	,	,	,	_	_	_
22	37	37	CD	_	_	_
23	°C	°c	NN	_	_	_
24	,	,	,	_	_	_
25	replicate	replicate	VB	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Emplty	Emplty	NNP	_	_	_
29	Vector	Vector	NNP	_	_	_
30	,	,	,	_	_	_
31	37	37	CD	_	_	_
32	°C	°c	NN	_	_	_
33	,	,	,	_	_	_
34	replicate	replicate	VB	_	_	_
35	3	3	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Emplty	Emplty	NNP	_	_	_
38	Vector	Vector	NNP	_	_	_
39	,	,	,	_	_	_
40	42	42	CD	_	_	_
41	°C	°c	NN	_	_	_
42	,	,	,	_	_	_
43	replicate	replicate	VB	_	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Emplty	Emplty	NNP	_	_	_
47	Vector	Vector	NNP	_	_	_
48	,	,	,	_	_	_
49	42	42	CD	_	_	_
50	°C	°c	NN	_	_	_
51	,	,	,	_	_	_
52	replicate	replicate	VB	_	_	_
53	2	2	CD	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Emplty	Emplty	NNP	_	_	_
56	Vector	Vector	NNP	_	_	_
57	,	,	,	_	_	_
58	42	42	CD	_	_	_
59	°C	°c	NN	_	_	_
60	,	,	,	_	_	_
61	replicate	replicate	VB	_	_	_
62	3	3	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	emptyvec	emptyvec	NN	_	_	_
65	_	_	NN	_	_	_
66	mRNA	mrna	NN	_	_	_
67	_	_	SYM	_	_	_
68	5m	5m	FW	_	_	_
69	_	_	FW	_	_	_
70	rep1	rep1	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	emptyvec	emptyvec	NN	_	_	_
73	_	_	NN	_	_	_
74	mRNA	mrna	NN	_	_	_
75	_	_	SYM	_	_	_
76	5m	5m	FW	_	_	_
77	_	_	FW	_	_	_
78	rep2	rep2	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	EmptyVector	EmptyVector	NNP	_	_	_
81	_	_	SYM	_	_	_
82	37	37	CD	_	_	_
83	_	_	CD	_	_	_
84	rep1	rep1	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	EmptyVector	EmptyVector	NNP	_	_	_
87	_	_	SYM	_	_	_
88	37	37	CD	_	_	_
89	_	_	CD	_	_	_
90	rep2	rep2	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	EmptyVector	EmptyVector	NNP	_	_	_
93	_	_	SYM	_	_	_
94	37	37	CD	_	_	_
95	_	_	CD	_	_	_
96	rep3	rep3	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	EmptyVector	EmptyVector	NNP	_	_	_
99	_	_	SYM	_	_	_
100	42	42	CD	_	_	_
101	_	_	CD	_	_	_
102	rep1	rep1	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	EmptyVector	EmptyVector	NNP	_	_	_
105	_	_	SYM	_	_	_
106	42	42	CD	_	_	_
107	_	_	CD	_	_	_
108	rep2	rep2	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	EmptyVector	EmptyVector	NNP	_	_	_
111	_	_	SYM	_	_	_
112	42	42	CD	_	_	_
113	_	_	CD	_	_	_
114	rep3	rep3	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	emptyvec	emptyvec	NN	_	_	_
117	_	_	CD	_	_	_
118	totalRNA	totalrna	NN	_	_	_
119	_	_	SYM	_	_	_
120	30m	30m	FW	_	_	_
121	_	_	FW	_	_	_
122	rep1	rep1	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	emptyvec	emptyvec	NN	_	_	_
125	_	_	CD	_	_	_
126	totalRNA	totalrna	NN	_	_	_
127	_	_	SYM	_	_	_
128	30m	30m	FW	_	_	_
129	_	_	FW	_	_	_
130	rep2	rep2	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	emptyvec	emptyvec	NN	_	_	_
133	_	_	CD	_	_	_
134	totalRNA	totalrna	NN	_	_	_
135	_	_	SYM	_	_	_
136	5m	5m	FW	_	_	_
137	_	_	FW	_	_	_
138	rep1	rep1	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	emptyvec	emptyvec	NN	_	_	_
141	_	_	CD	_	_	_
142	totalRNA	totalrna	NN	_	_	_
143	_	_	SYM	_	_	_
144	5m	5m	FW	_	_	_
145	_	_	FW	_	_	_
146	rep2	rep2	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	emrR	emrr	NN	_	_	_
149	__	__	CD	_	_	_
150	U	U	NNP	_	_	_
151	_	_	NNP	_	_	_
152	N0075	N0075	NNP	_	_	_
153	_	_	VBD	_	_	_
154	r1	r1	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	emrR	emrr	NN	_	_	_
157	__	__	CD	_	_	_
158	U	U	NNP	_	_	_
159	_	_	NNP	_	_	_
160	N0075	N0075	NNP	_	_	_
161	_	_	VBD	_	_	_
162	r3	r3	NN	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	emrR	emrr	NN	_	_	_
165	upregulation	upregulation	NN	_	_	_
166	,	,	,	_	_	_
167	0.075	0.075	CD	_	_	_
168	ug/ml	ug/ml	NN	_	_	_
169	norfloxacin	norfloxacin	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	-LSB-	-lsb-	-LRB-	_	_	_
172	E-MTAB-332	e-mtab-332	NN	_	_	_
173	-RSB-	-rsb-	-RRB-	_	_	_
174	fis	fi	VBZ	GEN	_	_
175	early-exponential	early-exponential	JJ	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	-LSB-	-lsb-	-LRB-	_	_	_
178	E-MTAB-332	e-mtab-332	NN	_	_	_
179	-RSB-	-rsb-	-RRB-	_	_	_
180	fis	fi	VBZ	GEN	_	_
181	mid-exponential	mid-exponential	JJ	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	-LSB-	-lsb-	-LRB-	_	_	_
184	E-MTAB-332	e-mtab-332	NN	_	_	_
185	-RSB-	-rsb-	-RRB-	_	_	_
186	H-NS	h-ns	NN	_	_	_
187	early-exponential	early-exponential	JJ	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	-LSB-	-lsb-	-LRB-	_	_	_
190	E-MTAB-332	e-mtab-332	NN	_	_	_
191	-RSB-	-rsb-	-RRB-	_	_	_
192	H-NS	h-ns	NN	_	_	_
193	mid-exponential	mid-exponential	JJ	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	-LSB-	-lsb-	-LRB-	_	_	_
196	E-MTAB-332	e-mtab-332	NN	_	_	_
197	-RSB-	-rsb-	-RRB-	_	_	_
198	H-NS	h-ns	NN	_	_	_
199	stationary	stationary	JJ	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	-LSB-	-lsb-	-LRB-	_	_	_
202	E-MTAB-332	e-mtab-332	NN	_	_	_
203	-RSB-	-rsb-	-RRB-	_	_	_
204	H-NS	h-ns	NN	_	_	_
205	transition-to-stationary	transition-to-stationary	JJ	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	-LSB-	-lsb-	-LRB-	_	_	_
208	E-MTAB-332	e-mtab-332	NN	_	_	_
209	-RSB-	-rsb-	-RRB-	_	_	_
210	rpo	rpo	NN	_	_	_
211	delfis	delfi	VBZ	_	_	_
212	mid-exponential	mid-exponential	JJ	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	-LSB-	-lsb-	-LRB-	_	_	_
215	E-MTAB-332	e-mtab-332	NN	_	_	_
216	-RSB-	-rsb-	-RRB-	_	_	_
217	rpo	rpo	NN	_	_	_
218	delhns	delhn	VBZ	_	_	_
219	mid-exponential	mid-exponential	JJ	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	-LSB-	-lsb-	-LRB-	_	_	_
222	E-MTAB-332	e-mtab-332	NN	_	_	_
223	-RSB-	-rsb-	-RRB-	_	_	_
224	rpo	rpo	NN	_	_	_
225	wt	wt	JJ	_	_	_
226	mid-exponential	mid-exponential	JJ	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
228	Eno	eno	NN	_	_	_
229	-	-	:	_	_	_
230	-LRB-	-lrb-	-LRB-	_	_	_
231	DF261	df261	NN	_	_	_
232	-RRB-	-rrb-	-RRB-	_	_	_
233	in	in	IN	_	_	_
234	M9	m9	NN	_	_	_
235	0.2	0.2	CD	_	_	_
236	%	%	NN	_	_	_
237	Glycerol	glycerol	NN	_	_	_
238	0.2	0.2	CD	_	_	_
239	%	%	NN	_	_	_
240	Tryptone	tryptone	NN	_	_	_
241	40	40	CD	_	_	_
242	mM	mm	NN	KWSUPP	_	_
243	Suc	suc	NN	_	_	_
244	.	.	.	_	_	_

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	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	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	NN	_	_	_
11	∆	∆	CD	_	_	_
12	entC	entc	NN	GEN	_	_
13	parent	parent	NN	_	_	_
14	Sample	sample	NN	_	_	_
15	12	12	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	∆	∆	CD	_	_	_
18	entC	entc	NN	GEN	_	_
19	parent	parent	NN	_	_	_
20	Sample	Sample	NNP	_	_	_
21	31	31	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	∆	∆	CD	_	_	_
24	entC	entc	NN	GEN	_	_
25	parent	parent	NN	_	_	_
26	Sample	sample	NN	_	_	_
27	50	50	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	entC	entc	NN	GEN	_	_
30	suppressor	suppressor	NN	_	_	_
31	1-1	1-1	CD	_	_	_
32	Sample	Sample	NNP	_	_	_
33	13	13	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	entC	entc	NN	GEN	_	_
36	suppressor	suppressor	NN	_	_	_
37	1-1	1-1	CD	_	_	_
38	Sample	sample	NN	_	_	_
39	32	32	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	entC	entc	NN	GEN	_	_
42	suppressor	suppressor	NN	_	_	_
43	1-1	1-1	CD	_	_	_
44	Sample	sample	NN	_	_	_
45	51	51	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	entC	entc	NN	GEN	_	_
48	suppressor	suppressor	NN	_	_	_
49	2-1	2-1	CD	_	_	_
50	Sample	sample	NN	_	_	_
51	14	14	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	entC	entc	NN	GEN	_	_
54	suppressor	suppressor	NN	_	_	_
55	2-1	2-1	CD	_	_	_
56	Sample	sample	NN	_	_	_
57	33	33	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	entC	entc	NN	GEN	_	_
60	suppressor	suppressor	NN	_	_	_
61	2-1	2-1	CD	_	_	_
62	Sample	sample	NN	_	_	_
63	52	52	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	entC	entc	NN	GEN	_	_
66	suppressor	suppressor	NN	_	_	_
67	3-1	3-1	CD	_	_	_
68	Sample	Sample	NNP	_	_	_
69	15	15	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	entC	entc	NN	GEN	_	_
72	suppressor	suppressor	NN	_	_	_
73	3-1	3-1	CD	_	_	_
74	Sample	sample	NN	_	_	_
75	34	34	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	entC	entc	NN	GEN	_	_
78	suppressor	suppressor	NN	_	_	_
79	3-1	3-1	CD	_	_	_
80	Sample	sample	NN	_	_	_
81	53	53	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	Enteroheamorragic	enteroheamorragic	JJ	_	_	_
84	E.	e.	FW	_	_	_
85	coli	coli	FW	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	enterohemorrhagic	enterohemorrhagic	JJ	_	_	_
88	E.	e.	FW	_	_	_
89	coli	coli	FW	_	_	_
90	_	_	SYM	_	_	_
91	172mM	172mm	NN	_	_	_
92	short	short	JJ	_	_	_
93	chain	chain	NN	_	_	_
94	fatty	fatty	JJ	_	_	_
95	acid	acid	NN	_	_	_
96	mix	mix	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	enterohemorrhagic	enterohemorrhagic	JJ	_	_	_
99	E.	e.	FW	_	_	_
100	coli	coli	FW	_	_	_
101	_	_	SYM	_	_	_
102	30mM	30mM	NNP	_	_	_
103	short	short	JJ	_	_	_
104	chain	chain	NN	_	_	_
105	fatty	fatty	JJ	_	_	_
106	acid	acid	NN	_	_	_
107	mix	mix	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Enterohemorrhagic	enterohemorrhagic	JJ	_	_	_
110	Escherichia	escherichia	FW	Organism	_	_
111	coli	coli	FW	Organism	_	_
112	O157	o157	NN	_	_	_
113	:	:	:	_	_	_
114	H7	h7	NN	_	_	_
115	strain	strain	NN	_	_	_
116	EDL933	edl933	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	Enteropathogenic	enteropathogenic	JJ	_	_	_
119	E.	e.	FW	_	_	_
120	coli	coli	FW	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	entF	entf	NN	GEN	_	_
123	KO	ko	NN	_	_	_
124	rep1	rep1	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	entF	entf	NN	GEN	_	_
127	KO	ko	NN	_	_	_
128	rep2	rep2	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	entF	entf	NN	GEN	_	_
131	KO	ko	NN	_	_	_
132	rep3	rep3	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	envz3600	envz3600	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	envz600	envz600	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	envz900	envz900	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	envzM1200	envzm1200	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	envzM2400	envzm2400	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	envzM3600	envzm3600	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	envzM600	envzm600	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	envzM900	envzm900	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	Epicentre	Epicentre	NNP	_	_	_
151	MasterPure	MasterPure	NNP	_	_	_
152	RNA	rna	NN	_	_	_
153	isolation	isolation	NN	_	_	_
154	Kit	kit	NN	_	_	_
155	,	,	,	_	_	_
156	Madison	Madison	NNP	_	_	_
157	,	,	,	_	_	_
158	WI	WI	NNP	_	_	_
159	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
160	era	era	NN	GEN	_	_
161	___	___	CD	_	_	_
162	U	U	NNP	_	_	_
163	_	_	NNP	_	_	_
164	N0075	N0075	NNP	_	_	_
165	_	_	NNP	_	_	_
166	r1	r1	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	era	era	NN	GEN	_	_
169	___	___	CD	_	_	_
170	U	U	NNP	_	_	_
171	_	_	NNP	_	_	_
172	N0075	N0075	NNP	_	_	_
173	_	_	NNP	_	_	_
174	r2	r2	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	era	era	NN	GEN	_	_
177	___	___	CD	_	_	_
178	U	U	NNP	_	_	_
179	_	_	NNP	_	_	_
180	N0075	N0075	NNP	_	_	_
181	_	_	SYM	_	_	_
182	r3	r3	FW	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
184	era	era	NN	GEN	_	_
185	upregulation	upregulation	NN	_	_	_
186	,	,	,	_	_	_
187	0.075	0.075	CD	_	_	_
188	ug/ml	ug/ml	NN	_	_	_
189	norfloxacin	norfloxacin	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	ercc	ercc	NN	_	_	_
192	spike-in	spike-in	NN	_	_	_
193	:	:	:	_	_	_
194	No	no	DT	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	ercc	ercc	NN	_	_	_
197	spike-in	spike-in	NN	_	_	_
198	:	:	:	_	_	_
199	Prior	prior	RB	_	_	_
200	to	to	TO	_	_	_
201	extraction	extraction	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
203	error-prone	error-prone	JJ	_	_	_
204	in	in	FW	_	_	_
205	vitro	vitro	FW	_	_	_
206	-LRB-	-lrb-	-LRB-	_	_	_
207	Mn2	mn2	NN	_	_	_
208	+	+	CC	_	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
211	error-prone	error-prone	JJ	_	_	_
212	in	in	FW	_	_	_
213	vitro	vitro	FW	_	_	_
214	MnCl2	mncl2	NN	SUPP	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
216	error-proof	error-proof	JJ	_	_	_
217	in	in	FW	_	_	_
218	vitro	vitro	FW	_	_	_
219	1	1	CD	_	_	_
220	-LRB-	-lrb-	-LRB-	_	_	_
221	GreAB/Mg2	greab/mg2	NN	_	_	_
222	+	+	CC	_	_	_
223	-RRB-	-rrb-	-RRB-	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
225	error-proof	error-proof	JJ	_	_	_
226	in	in	FW	_	_	_
227	vitro	vitro	FW	_	_	_
228	2	2	CD	_	_	_
229	-LRB-	-lrb-	-LRB-	_	_	_
230	GreAB/Mn2	greab/mn2	NN	_	_	_
231	+	+	CC	_	_	_
232	-RRB-	-rrb-	-RRB-	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
234	error-proof	error-proof	JJ	_	_	_
235	in	in	FW	_	_	_
236	vitro	vitro	FW	_	_	_
237	MgCl2	mgcl2	NN	_	_	_
238	+	+	CC	_	_	_
239	GreAB	greab	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
241	error-proof	error-proof	JJ	_	_	_
242	in	in	FW	_	_	_
243	vitro	vitro	FW	_	_	_
244	MnCl2	mncl2	NN	SUPP	_	_
245	+	+	CC	_	_	_
246	GreAB	greab	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	Erythromycin	erythromycin	NN	_	_	_
249	_	_	NN	_	_	_
250	replicate	replicate	VBP	_	_	_
251	_	_	SYM	_	_	_
252	1	1	CD	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	Erythromycin	erythromycin	NN	_	_	_
255	_	_	NN	_	_	_
256	replicate	replicate	VBP	_	_	_
257	_	_	NN	_	_	_
258	2	2	CD	_	_	_
259	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
260	Erythromycin	Erythromycin	NNP	_	_	_
261	_	_	NNP	_	_	_
262	replicate	replicate	VB	_	_	_
263	_	_	SYM	_	_	_
264	3	3	CD	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	ESBL019	esbl019	NN	_	_	_
267	Coliform	coliform	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	ESBL019	esbl019	NN	_	_	_
270	Filamented	filamented	JJ	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	ESBL019	esbl019	NN	_	_	_
273	Reverted	revert	VBD	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	ESBL019	esbl019	NN	_	_	_
276	Transition	transition	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	Escherchia	escherchia	FW	_	_	_
279	coli	coli	FW	_	_	_
280	HB101	hb101	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Escherchia	escherchia	FW	_	_	_
283	coli	coli	FW	_	_	_
284	HB101	hb101	NN	_	_	_
285	exposed	expose	VBN	_	_	_
286	to	to	TO	_	_	_
287	C.	C.	NNP	_	_	_
288	elegans	elegan	NNS	_	_	_
289	and	and	CC	_	_	_
290	Giardia	Giardia	NNP	_	_	_
291	for	for	IN	_	_	_
292	24	24	CD	_	_	_
293	hours	hour	NNS	_	_	_
294	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
295	Escherchia	Escherchia	NNP	_	_	_
296	coli	coli	NN	_	_	_
297	HB101	hb101	NN	_	_	_
298	exposed	expose	VBN	_	_	_
299	to	to	TO	_	_	_
300	C.	C.	NNP	_	_	_
301	elegans	elegan	NNS	_	_	_
302	for	for	IN	_	_	_
303	24	24	CD	_	_	_
304	hours	hour	NNS	_	_	_
305	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
306	Escherchia	Escherchia	NNP	_	_	_
307	coli	coli	NN	_	_	_
308	HB101	hb101	NN	_	_	_
309	exposed	expose	VBN	_	_	_
310	to	to	TO	_	_	_
311	Giardia	Giardia	NNP	_	_	_
312	for	for	IN	_	_	_
313	24	24	CD	_	_	_
314	hours	hour	NNS	_	_	_
315	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
316	Escherichia	escherichia	FW	Organism	_	_
317	coli	coli	FW	Organism	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	Escherichia	escherichia	FW	Organism	_	_
320	coli	coli	FW	Organism	_	_
321	042	042	CD	_	_	_
322	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
323	Escherichia	escherichia	FW	Organism	_	_
324	coli	coli	FW	Organism	_	_
325	,	,	,	_	_	_
326	0	0	CD	_	_	_
327	µM	µm	NN	_	_	_
328	AgNO3	agno3	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	Escherichia	escherichia	FW	Organism	_	_
331	coli	coli	FW	Organism	_	_
332	,	,	,	_	_	_
333	0	0	CD	_	_	_
334	µM	µm	NN	_	_	_
335	AgNO3	agno3	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	Escherichia	escherichia	FW	Organism	_	_
338	coli	coli	FW	Organism	_	_
339	0	0	CD	_	_	_
340	min	min	NN	_	_	_
341	vs	vs	CC	_	_	_
342	10	10	CD	_	_	_
343	min	min	NN	_	_	_
344	Rep1	rep1	NN	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	Escherichia	escherichia	FW	Organism	_	_
347	coli	coli	FW	Organism	_	_
348	10	10	CD	_	_	_
349	min	min	NN	_	_	_
350	vs	vs	CC	_	_	_
351	0	0	CD	_	_	_
352	min	min	NN	_	_	_
353	Rep2	rep2	JJ	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	Escherichia	escherichia	FW	Organism	_	_
356	coli	coli	FW	Organism	_	_
357	30	30	CD	_	_	_
358	min	min	NN	_	_	_
359	vs	vs	CC	_	_	_
360	60	60	CD	_	_	_
361	min	min	NN	_	_	_
362	Rep1	rep1	NN	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	Escherichia	escherichia	FW	Organism	_	_
365	coli	coli	FW	Organism	_	_
366	,	,	,	_	_	_
367	5	5	CD	_	_	_
368	µM	µm	NN	_	_	_
369	AgNO3	agno3	NN	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	Escherichia	escherichia	FW	Organism	_	_
372	coli	coli	FW	Organism	_	_
373	60	60	CD	_	_	_
374	min	min	NN	_	_	_
375	vs	vs	CC	_	_	_
376	30	30	CD	_	_	_
377	min	min	NN	_	_	_
378	Rep2	rep2	JJ	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	Escherichia	escherichia	FW	Organism	_	_
381	coli	coli	FW	Organism	_	_
382	,	,	,	_	_	_
383	6.5	6.5	CD	_	_	_
384	µM	µm	NN	_	_	_
385	AgNO3	agno3	NN	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	Escherichia	escherichia	FW	Organism	_	_
388	coli	coli	FW	Organism	_	_
389	,	,	,	_	_	_
390	8.5	8.5	CD	_	_	_
391	µM	µm	NN	_	_	_
392	AgNO3	agno3	NN	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	Escherichia	escherichia	FW	Organism	_	_
395	coli	coli	FW	Organism	_	_
396	8624	8624	CD	_	_	_
397	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
398	Escherichia	escherichia	FW	Organism	_	_
399	coli	coli	FW	Organism	_	_
400	8624	8624	CD	_	_	_
401	grown	grow	VBN	_	_	_
402	in	in	IN	_	_	_
403	DMEM	DMEM	NNP	_	_	_
404	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
405	Escherichia	escherichia	FW	Organism	_	_
406	coli	coli	FW	Organism	_	_
407	8624	8624	CD	_	_	_
408	grown	grow	VBN	_	_	_
409	in	in	IN	_	_	_
410	DMEM	dmem	NN	_	_	_
411	with	with	IN	_	_	_
412	AI3	ai3	NN	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	Escherichia	escherichia	FW	Organism	_	_
415	coli	coli	FW	Organism	_	_
416	8624	8624	CD	_	_	_
417	grown	grow	VBN	_	_	_
418	in	in	IN	_	_	_
419	DMEM	dmem	NN	_	_	_
420	with	with	IN	_	_	_
421	Epinephrine	epinephrine	NN	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	Escherichia	escherichia	FW	Organism	_	_
424	coli	coli	FW	Organism	_	_
425	8624	8624	CD	_	_	_
426	grown	grow	VBN	_	_	_
427	in	in	IN	_	_	_
428	LB	LB	NNP	_	_	_
429	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
430	Escherichia	escherichia	FW	Organism	_	_
431	coli	coli	FW	Organism	_	_
432	8624	8624	CD	_	_	_
433	in	in	IN	_	_	_
434	LB	LB	NNP	_	_	_
435	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
436	Escherichia	escherichia	FW	Organism	_	_
437	coli	coli	FW	Organism	_	_
438	8624	8624	CD	_	_	_
439	kdpE	kdpe	NN	GEN	_	_
440	deletion	deletion	NN	_	_	_
441	mutant	mutant	JJ	_	_	_
442	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
443	Escherichia	escherichia	FW	Organism	_	_
444	coli	coli	FW	Organism	_	_
445	8624	8624	CD	_	_	_
446	kdpE	kdpe	NN	GEN	_	_
447	deletion	deletion	NN	_	_	_
448	mutant	mutant	JJ	_	_	_
449	grown	grow	VBN	_	_	_
450	in	in	IN	_	_	_
451	DMEM	DMEM	NNP	_	_	_
452	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
453	Escherichia	escherichia	FW	Organism	_	_
454	coli	coli	FW	Organism	_	_
455	8624	8624	CD	_	_	_
456	qseB	qseb	NN	GEN	_	_
457	deletion	deletion	NN	_	_	_
458	mutant	mutant	JJ	_	_	_
459	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
460	Escherichia	escherichia	FW	Organism	_	_
461	coli	coli	FW	Organism	_	_
462	8624	8624	CD	_	_	_
463	qseB	qseb	NN	GEN	_	_
464	deletion	deletion	NN	_	_	_
465	mutant	mutant	JJ	_	_	_
466	grown	grow	VBN	_	_	_
467	in	in	IN	_	_	_
468	DMEM	DMEM	NNP	_	_	_
469	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
470	Escherichia	escherichia	FW	Organism	_	_
471	coli	coli	FW	Organism	_	_
472	8624	8624	CD	_	_	_
473	qseC	qsec	NN	GEN	_	_
474	deletion	deletion	NN	_	_	_
475	mutant	mutant	JJ	_	_	_
476	grown	grow	VBN	_	_	_
477	in	in	IN	_	_	_
478	DMEM	DMEM	NNP	_	_	_
479	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
480	Escherichia	escherichia	FW	Organism	_	_
481	coli	coli	FW	Organism	_	_
482	8624	8624	CD	_	_	_
483	qseC	qsec	NN	GEN	_	_
484	deletion	deletion	NN	_	_	_
485	mutant	mutant	JJ	_	_	_
486	grown	grow	VBN	_	_	_
487	in	in	IN	_	_	_
488	DMEM	dmem	NN	_	_	_
489	with	with	IN	_	_	_
490	AI3	ai3	NN	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	Escherichia	escherichia	FW	Organism	_	_
493	coli	coli	FW	Organism	_	_
494	8624	8624	CD	_	_	_
495	qseC	qsec	NN	GEN	_	_
496	deletion	deletion	NN	_	_	_
497	mutant	mutant	JJ	_	_	_
498	grown	grow	VBN	_	_	_
499	in	in	IN	_	_	_
500	DMEM	dmem	NN	_	_	_
501	with	with	IN	_	_	_
502	Epinephrine	epinephrine	NN	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	Escherichia	escherichia	FW	Organism	_	_
505	coli	coli	FW	Organism	_	_
506	8624	8624	CD	_	_	_
507	qseC	qsec	NN	GEN	_	_
508	mutant	mutant	JJ	_	_	_
509	grown	grow	VBN	_	_	_
510	in	in	IN	_	_	_
511	LB	LB	NNP	_	_	_
512	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
513	Escherichia	escherichia	FW	Organism	_	_
514	coli	coli	FW	Organism	_	_
515	8624	8624	CD	_	_	_
516	qseC	qsec	NN	GEN	_	_
517	mutant	mutant	NN	_	_	_
518	in	in	IN	_	_	_
519	DMEM	DMEM	NNP	_	_	_
520	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
521	Escherichia	escherichia	FW	Organism	_	_
522	coli	coli	FW	Organism	_	_
523	8624	8624	CD	_	_	_
524	qseC	qsec	NN	GEN	_	_
525	mutant	mutant	NN	_	_	_
526	in	in	IN	_	_	_
527	DMEM	dmem	NN	_	_	_
528	with	with	IN	_	_	_
529	AI3	ai3	NN	_	_	_
530	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
531	Escherichia	escherichia	FW	Organism	_	_
532	coli	coli	FW	Organism	_	_
533	8624	8624	CD	_	_	_
534	qseC	qsec	NN	GEN	_	_
535	mutant	mutant	NN	_	_	_
536	in	in	IN	_	_	_
537	DMEM	dmem	NN	_	_	_
538	with	with	IN	_	_	_
539	epinephrine	epinephrine	NN	_	_	_
540	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
541	Escherichia	escherichia	FW	Organism	_	_
542	coli	coli	FW	Organism	_	_
543	8624	8624	CD	_	_	_
544	qseC	qsec	NN	GEN	_	_
545	mutant	mutant	NN	_	_	_
546	in	in	IN	_	_	_
547	LB	LB	NNP	_	_	_
548	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
549	Escherichia	escherichia	FW	Organism	_	_
550	coli	coli	FW	Organism	_	_
551	8624	8624	CD	_	_	_
552	qseF	qsef	NN	_	_	_
553	deletion	deletion	NN	_	_	_
554	mutant	mutant	JJ	_	_	_
555	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
556	Escherichia	escherichia	FW	Organism	_	_
557	coli	coli	FW	Organism	_	_
558	8624	8624	CD	_	_	_
559	qseF	qsef	NN	_	_	_
560	deletion	deletion	NN	_	_	_
561	mutant	mutant	JJ	_	_	_
562	grown	grow	VBN	_	_	_
563	in	in	IN	_	_	_
564	DMEM	DMEM	NNP	_	_	_
565	media	media	NNS	_	_	_
566	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
567	Escherichia	escherichia	FW	Organism	_	_
568	coli	coli	FW	Organism	_	_
569	AB1157	ab1157	NN	_	_	_
570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
571	Escherichia	escherichia	FW	Organism	_	_
572	coli	coli	FW	Organism	_	_
573	after	after	IN	_	_	_
574	addition	addition	NN	_	_	_
575	of	of	IN	_	_	_
576	CO-RMs	co-rm	NNS	_	_	_
577	to	to	TO	_	_	_
578	aerobically	aerobically	RB	_	_	_
579	growing	grow	VBG	_	_	_
580	cells	cell	NNS	_	_	_
581	-	-	:	_	_	_
582	Sample	sample	NN	_	_	_
583	1a	1a	NN	_	_	_
584	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
585	Escherichia	escherichia	FW	Organism	_	_
586	coli	coli	FW	Organism	_	_
587	after	after	IN	_	_	_
588	addition	addition	NN	_	_	_
589	of	of	IN	_	_	_
590	CO-RMs	co-rm	NNS	_	_	_
591	to	to	TO	_	_	_
592	aerobically	aerobically	RB	_	_	_
593	growing	grow	VBG	_	_	_
594	cells	cell	NNS	_	_	_
595	-	-	:	_	_	_
596	Sample	sample	NN	_	_	_
597	1b	1b	NN	_	_	_
598	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
599	Escherichia	escherichia	FW	Organism	_	_
600	coli	coli	FW	Organism	_	_
601	after	after	IN	_	_	_
602	addition	addition	NN	_	_	_
603	of	of	IN	_	_	_
604	CO-RMs	co-rm	NNS	_	_	_
605	to	to	TO	_	_	_
606	aerobically	aerobically	RB	_	_	_
607	growing	grow	VBG	_	_	_
608	cells	cell	NNS	_	_	_
609	-	-	:	_	_	_
610	Sample	sample	NN	_	_	_
611	2a	2a	NN	_	_	_
612	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
613	Escherichia	escherichia	FW	Organism	_	_
614	coli	coli	FW	Organism	_	_
615	after	after	IN	_	_	_
616	addition	addition	NN	_	_	_
617	of	of	IN	_	_	_
618	CO-RMs	co-rm	NNS	_	_	_
619	to	to	TO	_	_	_
620	aerobically	aerobically	RB	_	_	_
621	growing	grow	VBG	_	_	_
622	cells	cell	NNS	_	_	_
623	-	-	:	_	_	_
624	Sample	sample	NN	_	_	_
625	2b	2b	JJ	_	_	_
626	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
627	Escherichia	escherichia	FW	Organism	_	_
628	coli	coli	FW	Organism	_	_
629	after	after	IN	_	_	_
630	addition	addition	NN	_	_	_
631	of	of	IN	_	_	_
632	CO-RMs	co-rm	NNS	_	_	_
633	to	to	TO	_	_	_
634	aerobically	aerobically	RB	_	_	_
635	growing	grow	VBG	_	_	_
636	cells	cell	NNS	_	_	_
637	-	-	:	_	_	_
638	Sample	sample	NN	_	_	_
639	3a	3a	NN	_	_	_
640	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
641	Escherichia	escherichia	FW	Organism	_	_
642	coli	coli	FW	Organism	_	_
643	after	after	IN	_	_	_
644	addition	addition	NN	_	_	_
645	of	of	IN	_	_	_
646	CO-RMs	co-rm	NNS	_	_	_
647	to	to	TO	_	_	_
648	aerobically	aerobically	RB	_	_	_
649	growing	grow	VBG	_	_	_
650	cells	cell	NNS	_	_	_
651	-	-	:	_	_	_
652	Sample	sample	NN	_	_	_
653	3b	3b	NN	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
655	Escherichia	escherichia	FW	Organism	_	_
656	coli	coli	FW	Organism	_	_
657	after	after	IN	_	_	_
658	addition	addition	NN	_	_	_
659	of	of	IN	_	_	_
660	CO-RMs	co-rm	NNS	_	_	_
661	to	to	TO	_	_	_
662	aerobically	aerobically	RB	_	_	_
663	growing	grow	VBG	_	_	_
664	cells	cell	NNS	_	_	_
665	-	-	:	_	_	_
666	Sample	sample	NN	_	_	_
667	4a	4a	NN	_	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
669	Escherichia	escherichia	FW	Organism	_	_
670	coli	coli	FW	Organism	_	_
671	after	after	IN	_	_	_
672	addition	addition	NN	_	_	_
673	of	of	IN	_	_	_
674	CO-RMs	co-rm	NNS	_	_	_
675	to	to	TO	_	_	_
676	aerobically	aerobically	RB	_	_	_
677	growing	grow	VBG	_	_	_
678	cells	cell	NNS	_	_	_
679	-	-	:	_	_	_
680	Sample	sample	NN	_	_	_
681	4b	4b	NN	_	_	_
682	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
683	Escherichia	escherichia	FW	Organism	_	_
684	coli	coli	FW	Organism	_	_
685	after	after	IN	_	_	_
686	addition	addition	NN	_	_	_
687	of	of	IN	_	_	_
688	CO-RMs	co-rm	NNS	_	_	_
689	to	to	TO	_	_	_
690	anaerobically	anaerobically	RB	_	_	_
691	growing	grow	VBG	_	_	_
692	cells	cell	NNS	_	_	_
693	-	-	:	_	_	_
694	Sample	sample	NN	_	_	_
695	1a	1a	NN	_	_	_
696	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
697	Escherichia	escherichia	FW	Organism	_	_
698	coli	coli	FW	Organism	_	_
699	after	after	IN	_	_	_
700	addition	addition	NN	_	_	_
701	of	of	IN	_	_	_
702	CO-RMs	co-rm	NNS	_	_	_
703	to	to	TO	_	_	_
704	anaerobically	anaerobically	RB	_	_	_
705	growing	grow	VBG	_	_	_
706	cells	cell	NNS	_	_	_
707	-	-	:	_	_	_
708	Sample	sample	NN	_	_	_
709	1b	1b	NN	_	_	_
710	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
711	Escherichia	escherichia	FW	Organism	_	_
712	coli	coli	FW	Organism	_	_
713	after	after	IN	_	_	_
714	addition	addition	NN	_	_	_
715	of	of	IN	_	_	_
716	CO-RMs	co-rm	NNS	_	_	_
717	to	to	TO	_	_	_
718	anaerobically	anaerobically	RB	_	_	_
719	growing	grow	VBG	_	_	_
720	cells	cell	NNS	_	_	_
721	-	-	:	_	_	_
722	Sample	sample	NN	_	_	_
723	2a	2a	NN	_	_	_
724	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
725	Escherichia	escherichia	FW	Organism	_	_
726	coli	coli	FW	Organism	_	_
727	after	after	IN	_	_	_
728	addition	addition	NN	_	_	_
729	of	of	IN	_	_	_
730	CO-RMs	co-rm	NNS	_	_	_
731	to	to	TO	_	_	_
732	anaerobically	anaerobically	RB	_	_	_
733	growing	grow	VBG	_	_	_
734	cells	cell	NNS	_	_	_
735	-	-	:	_	_	_
736	Sample	sample	NN	_	_	_
737	2b	2b	JJ	_	_	_
738	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
739	Escherichia	escherichia	FW	Organism	_	_
740	coli	coli	FW	Organism	_	_
741	after	after	IN	_	_	_
742	addition	addition	NN	_	_	_
743	of	of	IN	_	_	_
744	CO-RMs	co-rm	NNS	_	_	_
745	to	to	TO	_	_	_
746	anaerobically	anaerobically	RB	_	_	_
747	growing	grow	VBG	_	_	_
748	cells	cell	NNS	_	_	_
749	-	-	:	_	_	_
750	Sample	sample	NN	_	_	_
751	3a	3a	NN	_	_	_
752	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
753	Escherichia	escherichia	FW	Organism	_	_
754	coli	coli	FW	Organism	_	_
755	after	after	IN	_	_	_
756	addition	addition	NN	_	_	_
757	of	of	IN	_	_	_
758	CO-RMs	co-rm	NNS	_	_	_
759	to	to	TO	_	_	_
760	anaerobically	anaerobically	RB	_	_	_
761	growing	grow	VBG	_	_	_
762	cells	cell	NNS	_	_	_
763	-	-	:	_	_	_
764	Sample	sample	NN	_	_	_
765	3b	3b	NN	_	_	_
766	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
767	Escherichia	escherichia	FW	Organism	_	_
768	coli	coli	FW	Organism	_	_
769	after	after	IN	_	_	_
770	addition	addition	NN	_	_	_
771	of	of	IN	_	_	_
772	CO-RMs	co-rm	NNS	_	_	_
773	to	to	TO	_	_	_
774	anaerobically	anaerobically	RB	_	_	_
775	growing	grow	VBG	_	_	_
776	cells	cell	NNS	_	_	_
777	-	-	:	_	_	_
778	Sample	sample	NN	_	_	_
779	4a	4a	NN	_	_	_
780	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
781	Escherichia	escherichia	FW	Organism	_	_
782	coli	coli	FW	Organism	_	_
783	after	after	IN	_	_	_
784	addition	addition	NN	_	_	_
785	of	of	IN	_	_	_
786	CO-RMs	co-rm	NNS	_	_	_
787	to	to	TO	_	_	_
788	anaerobically	anaerobically	RB	_	_	_
789	growing	grow	VBG	_	_	_
790	cells	cell	NNS	_	_	_
791	-	-	:	_	_	_
792	Sample	sample	NN	_	_	_
793	4b	4b	NN	_	_	_
794	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
795	Escherichia	escherichia	FW	Organism	_	_
796	coli	coli	FW	Organism	_	_
797	APEC	apec	NN	_	_	_
798	O2	o2	CD	_	_	_
799	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
800	Escherichia	escherichia	FW	Organism	_	_
801	coli	coli	FW	Organism	_	_
802	ATCC	atcc	NN	_	_	_
803	25922	25922	CD	_	_	_
804	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
805	Escherichia	escherichia	FW	Organism	_	_
806	coli	coli	FW	Organism	_	_
807	ATCC	atcc	NN	_	_	_
808	8739	8739	CD	_	_	_
809	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
810	Escherichia	escherichia	FW	Organism	_	_
811	coli	coli	FW	Organism	_	_
812	B	b	NN	_	_	_
813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
814	Escherichia	escherichia	FW	Organism	_	_
815	coli	coli	FW	Organism	_	_
816	_	_	SYM	_	_	_
817	Biofilm	Biofilm	NNP	_	_	_
818	_	_	SYM	_	_	_
819	bioreplicate1	bioreplicate1	CD	_	_	_
820	_	_	NN	_	_	_
821	techreplicate	techreplicate	NN	_	_	_
822	_	_	NN	_	_	_
823	1	1	CD	_	_	_
824	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
825	Escherichia	escherichia	FW	Organism	_	_
826	coli	coli	FW	Organism	_	_
827	_	_	SYM	_	_	_
828	Biofilm	Biofilm	NNP	_	_	_
829	_	_	SYM	_	_	_
830	bioreplicate1	bioreplicate1	CD	_	_	_
831	_	_	NN	_	_	_
832	techreplicate	techreplicate	NN	_	_	_
833	_	_	NN	_	_	_
834	2	2	CD	_	_	_
835	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
836	Escherichia	escherichia	FW	Organism	_	_
837	coli	coli	FW	Organism	_	_
838	_	_	SYM	_	_	_
839	Biofilm	Biofilm	NNP	_	_	_
840	_	_	SYM	_	_	_
841	bioreplicate2	bioreplicate2	CD	_	_	_
842	_	_	NN	_	_	_
843	techreplicate	techreplicate	NN	_	_	_
844	_	_	NN	_	_	_
845	1	1	CD	_	_	_
846	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
847	Escherichia	escherichia	FW	Organism	_	_
848	coli	coli	FW	Organism	_	_
849	_	_	SYM	_	_	_
850	Biofilm	Biofilm	NNP	_	_	_
851	_	_	SYM	_	_	_
852	bioreplicate2	bioreplicate2	CD	_	_	_
853	_	_	NN	_	_	_
854	techreplicate	techreplicate	NN	_	_	_
855	_	_	NN	_	_	_
856	2	2	CD	_	_	_
857	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
858	Escherichia	escherichia	FW	Organism	_	_
859	coli	coli	FW	Organism	_	_
860	BL21	bl21	NN	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
862	Escherichia	escherichia	FW	Organism	_	_
863	coli	coli	FW	Organism	_	_
864	BL21	bl21	NN	_	_	_
865	-LRB-	-lrb-	-LRB-	_	_	_
866	DE3	de3	NN	_	_	_
867	-RRB-	-rrb-	-RRB-	_	_	_
868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
869	Escherichia	escherichia	FW	Organism	_	_
870	coli	coli	FW	Organism	_	_
871	BL21	bl21	NN	_	_	_
872	-LRB-	-lrb-	-LRB-	_	_	_
873	mu	mu	NN	_	_	_
874	=	=	JJ	_	_	_
875	0.20	0.20	CD	_	_	_
876	-RRB-	-rrb-	-RRB-	_	_	_
877	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
878	Escherichia	escherichia	FW	Organism	_	_
879	coli	coli	FW	Organism	_	_
880	BL21	bl21	NN	_	_	_
881	-LRB-	-lrb-	-LRB-	_	_	_
882	mu	mu	NN	_	_	_
883	=	=	JJ	_	_	_
884	0.46	0.46	CD	_	_	_
885	-RRB-	-rrb-	-RRB-	_	_	_
886	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
887	Escherichia	escherichia	FW	Organism	_	_
888	coli	coli	FW	Organism	_	_
889	BL21/pOri1	bl21/pori1	NN	_	_	_
890	-LRB-	-lrb-	-LRB-	_	_	_
891	mu	mu	NN	_	_	_
892	=	=	JJ	_	_	_
893	0.20	0.20	CD	_	_	_
894	-RRB-	-rrb-	-RRB-	_	_	_
895	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
896	Escherichia	escherichia	FW	Organism	_	_
897	coli	coli	FW	Organism	_	_
898	BL21/pOri1	bl21/pori1	NN	_	_	_
899	-LRB-	-lrb-	-LRB-	_	_	_
900	mu	mu	NN	_	_	_
901	=	=	JJ	_	_	_
902	0.39	0.39	CD	_	_	_
903	-RRB-	-rrb-	-RRB-	_	_	_
904	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
905	Escherichia	escherichia	FW	Organism	_	_
906	coli	coli	FW	Organism	_	_
907	BL21/pOri2	bl21/pori2	NN	_	_	_
908	-LRB-	-lrb-	-LRB-	_	_	_
909	mu	mu	NN	_	_	_
910	=	=	JJ	_	_	_
911	0.20	0.20	CD	_	_	_
912	-RRB-	-rrb-	-RRB-	_	_	_
913	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
914	Escherichia	escherichia	FW	Organism	_	_
915	coli	coli	FW	Organism	_	_
916	BL21/pOri2	bl21/pori2	NN	_	_	_
917	-LRB-	-lrb-	-LRB-	_	_	_
918	mu	mu	NN	_	_	_
919	=	=	JJ	_	_	_
920	0.29	0.29	CD	_	_	_
921	-RRB-	-rrb-	-RRB-	_	_	_
922	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
923	Escherichia	escherichia	FW	Organism	_	_
924	coli	coli	FW	Organism	_	_
925	B	b	NN	_	_	_
926	strain	strain	NN	_	_	_
927	REL606	rel606	NN	_	_	_
928	was	be	VBD	_	_	_
929	revived	revive	VBN	_	_	_
930	from	from	IN	_	_	_
931	a	a	DT	_	_	_
932	freezer	freezer	NN	_	_	_
933	stock	stock	NN	_	_	_
934	via	via	IN	_	_	_
935	overnight	overnight	JJ	_	_	_
936	growth	growth	NN	_	_	_
937	in	in	IN	_	_	_
938	10	10	CD	_	_	_
939	ml	ml	NN	_	_	_
940	Davis	Davis	NNP	_	_	_
941	Minimal	minimal	JJ	_	_	_
942	medium	medium	NN	_	_	_
943	supplemented	supplement	VBN	_	_	_
944	with	with	IN	_	_	_
945	limiting	limit	VBG	_	_	_
946	glucose	glucose	NN	SUPP	_	_
947	at	at	IN	_	_	_
948	0.5	0.5	CD	_	_	_
949	g/l	g/l	NN	_	_	_
950	-LRB-	-lrb-	-LRB-	_	_	_
951	DM500	dm500	CD	_	_	_
952	-RRB-	-rrb-	-RRB-	_	_	_
953	in	in	IN	_	_	_
954	a	a	DT	_	_	_
955	50	50	CD	_	_	_
956	ml	ml	NN	_	_	_
957	Erlenmeyer	erlenmeyer	NN	_	_	_
958	flask	flask	NN	_	_	_
959	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	100-fold	100-fold	RB	_	_	_
6	into	into	IN	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	fresh	fresh	JJ	_	_	_
10	DM500	dm500	CD	_	_	_
11	in	in	IN	_	_	_
12	a	a	DT	_	_	_
13	250	250	CD	_	_	_
14	ml	ml	NN	_	_	_
15	Erlenmeyer	erlenmeyer	NN	_	_	_
16	flask	flask	NN	_	_	_
17	and	and	CC	_	_	_
18	incubated	incubate	VBN	_	_	_
19	for	for	IN	_	_	_
20	24	24	CD	_	_	_
21	hours	hour	NNS	_	_	_
22	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	initiate	initiate	VB	_	_	_
3	the	the	DT	_	_	_
4	experiment	experiment	NN	_	_	_
5	,	,	,	_	_	_
6	these	these	DT	_	_	_
7	preconditioned	preconditioned	JJ	_	_	_
8	cultures	culture	NNS	_	_	_
9	were	be	VBD	_	_	_
10	diluted	dilute	VBN	_	_	_
11	100-fold	100-fold	RB	_	_	_
12	into	into	IN	_	_	_
13	50	50	CD	_	_	_
14	ml	ml	NN	_	_	_
15	fresh	fresh	JJ	_	_	_
16	DM500	dm500	CD	_	_	_
17	in	in	IN	_	_	_
18	multiple	multiple	JJ	_	_	_
19	250	250	CD	_	_	_
20	ml	ml	NN	_	_	_
21	Erlenmeyer	erlenmeyer	NN	_	_	_
22	flasks	flask	NNS	_	_	_
23	and	and	CC	_	_	_
24	grown	grow	VBN	_	_	_
25	for	for	IN	_	_	_
26	the	the	DT	_	_	_
27	specified	specify	VBN	_	_	_
28	times	time	NNS	_	_	_
29	until	until	IN	_	_	_
30	harvesting	harvesting	NN	_	_	_
31	cells	cell	NNS	_	_	_
32	for	for	IN	_	_	_
33	total	total	JJ	_	_	_
34	RNA	rna	NN	_	_	_
35	isolation	isolation	NN	_	_	_
36	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	growth	growth	NN	_	_	_
3	steps	step	NNS	_	_	_
4	were	be	VBD	_	_	_
5	conducted	conduct	VBN	_	_	_
6	with	with	IN	_	_	_
7	incubation	incubation	NN	_	_	_
8	at	at	IN	_	_	_
9	37	37	CD	_	_	_
10	°C	°c	NN	_	_	_
11	and	and	CC	_	_	_
12	orbital	orbital	JJ	_	_	_
13	shaking	shake	VBG	_	_	_
14	at	at	IN	_	_	_
15	120	120	CD	_	_	_
16	r.p.m.	r.p.m.	NN	_	_	_
17	over	over	IN	_	_	_
18	a	a	DT	_	_	_
19	one-inch	one-inch	JJ	_	_	_
20	diameter	diameter	NN	_	_	_
21	.	.	.	_	_	_

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

1	REL606	rel606	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	BW13711	bw13711	NN	_	_	_
6	grown	grow	VBN	_	_	_
7	anaerobically	anaerobically	RB	_	_	_
8	in	in	IN	_	_	_
9	continuous	continuous	JJ	_	_	_
10	culture	culture	NN	_	_	_
11	in	in	IN	_	_	_
12	MOPS	MOPS	NNP	MED	_	_
13	medium	medium	NN	_	_	_
14	plus	plus	CC	_	_	_
15	0.4	0.4	CD	_	_	_
16	%	%	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	with	with	IN	_	_	_
19	1	1	CD	_	_	_
20	%	%	NN	_	_	_
21	Acacia	Acacia	NNP	_	_	_
22	mearnsii	mearnsii	NN	_	_	_
23	condensed	condensed	JJ	_	_	_
24	tannins	tannin	NNS	_	_	_
25	.	.	.	_	_	_

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	BW25113	bw25113	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	BW25113	bw25113	NN	_	_	_
9	and	and	CC	_	_	_
10	fur	fur	NN	GEN	_	_
11	mutant	mutant	JJ	_	_	_
12	strains	strain	NNS	_	_	_
13	were	be	VBD	_	_	_
14	cultivated	cultivate	VBN	_	_	_
15	at	at	IN	_	_	_
16	37Co	37co	NN	_	_	_
17	in	in	IN	_	_	_
18	25	25	CD	_	_	_
19	ml	ml	NN	_	_	_
20	of	of	IN	_	_	_
21	LB	lb	NN	MED	_	_
22	medium	medium	NN	MED	_	_
23	using	use	VBG	_	_	_
24	Erlenmeyer	Erlenmeyer	NNP	_	_	_
25	flasks	flask	NNS	_	_	_
26	.	.	.	_	_	_

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/ml	ng/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	BW38028	bw38028	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	C600	c600	NN	_	_	_
9	,	,	,	_	_	_
10	10	10	CD	_	_	_
11	min	min	NN	_	_	_
12	after	after	IN	_	_	_
13	Norfloxacin	Norfloxacin	NNP	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	50	50	CD	_	_	_
16	ug/ml	ug/ml	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	addition	addition	NN	_	_	_
19	in	in	IN	_	_	_
20	LB	LB	NNP	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Escherichia	escherichia	FW	Organism	_	_
23	coli	coli	FW	Organism	_	_
24	C600	c600	NN	_	_	_
25	,	,	,	_	_	_
26	20	20	CD	_	_	_
27	min	min	NN	_	_	_
28	after	after	IN	_	_	_
29	Norfloxacin	Norfloxacin	NNP	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	50	50	CD	_	_	_
32	ug/ml	ug/ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	addition	addition	NN	_	_	_
35	in	in	IN	_	_	_
36	LB	LB	NNP	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Escherichia	escherichia	FW	Organism	_	_
39	coli	coli	FW	Organism	_	_
40	C600	c600	NN	_	_	_
41	,	,	,	_	_	_
42	2	2	CD	_	_	_
43	min	min	NN	_	_	_
44	after	after	IN	_	_	_
45	Norfloxacin	Norfloxacin	NNP	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	50	50	CD	_	_	_
48	ug/ml	ug/ml	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	addition	addition	NN	_	_	_
51	in	in	IN	_	_	_
52	LB	LB	NNP	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	Escherichia	escherichia	FW	Organism	_	_
55	coli	coli	FW	Organism	_	_
56	C600	c600	NN	_	_	_
57	,	,	,	_	_	_
58	30	30	CD	_	_	_
59	min	min	NN	_	_	_
60	after	after	IN	_	_	_
61	Norfloxacin	Norfloxacin	NNP	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	50	50	CD	_	_	_
64	ug/ml	ug/ml	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	addition	addition	NN	_	_	_
67	in	in	IN	_	_	_
68	LB	LB	NNP	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Escherichia	escherichia	FW	Organism	_	_
71	coli	coli	FW	Organism	_	_
72	C600	c600	NN	_	_	_
73	,	,	,	_	_	_
74	5	5	CD	_	_	_
75	min	min	NN	_	_	_
76	after	after	IN	_	_	_
77	Norfloxacin	Norfloxacin	NNP	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	50	50	CD	_	_	_
80	ug/ml	ug/ml	NN	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	addition	addition	NN	_	_	_
83	in	in	IN	_	_	_
84	LB	LB	NNP	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	Escherichia	escherichia	FW	Organism	_	_
87	coli	coli	FW	Organism	_	_
88	C600	c600	NN	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	gyrArparCr	gyrarparcr	NN	_	_	_
91	-RRB-	-rrb-	-RRB-	_	_	_
92	,	,	,	_	_	_
93	10	10	CD	_	_	_
94	min	min	NN	_	_	_
95	after	after	IN	_	_	_
96	Norfloxacin	Norfloxacin	NNP	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	15	15	CD	_	_	_
99	ug/ml	ug/ml	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	addition	addition	NN	_	_	_
102	in	in	IN	_	_	_
103	LB	LB	NNP	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Escherichia	escherichia	FW	Organism	_	_
106	coli	coli	FW	Organism	_	_
107	C600	c600	NN	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	gyrArparCr	gyrarparcr	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	,	,	,	_	_	_
112	10	10	CD	_	_	_
113	min	min	NN	_	_	_
114	after	after	IN	_	_	_
115	Norfloxacin	Norfloxacin	NNP	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	50	50	CD	_	_	_
118	ug/ml	ug/ml	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	addition	addition	NN	_	_	_
121	in	in	IN	_	_	_
122	LB	LB	NNP	_	_	_
123	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
124	Escherichia	escherichia	FW	Organism	_	_
125	coli	coli	FW	Organism	_	_
126	C600	c600	NN	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	gyrArparCr	gyrarparcr	NN	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	,	,	,	_	_	_
131	20	20	CD	_	_	_
132	min	min	NN	_	_	_
133	after	after	IN	_	_	_
134	Norfloxacin	Norfloxacin	NNP	_	_	_
135	-LRB-	-lrb-	-LRB-	_	_	_
136	15	15	CD	_	_	_
137	ug/ml	ug/ml	NN	_	_	_
138	-RRB-	-rrb-	-RRB-	_	_	_
139	addition	addition	NN	_	_	_
140	in	in	IN	_	_	_
141	LB	LB	NNP	_	_	_
142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
143	Escherichia	escherichia	FW	Organism	_	_
144	coli	coli	FW	Organism	_	_
145	C600	c600	NN	_	_	_
146	-LRB-	-lrb-	-LRB-	_	_	_
147	gyrArparCr	gyrarparcr	NN	_	_	_
148	-RRB-	-rrb-	-RRB-	_	_	_
149	,	,	,	_	_	_
150	20	20	CD	_	_	_
151	min	min	NN	_	_	_
152	after	after	IN	_	_	_
153	Norfloxacin	Norfloxacin	NNP	_	_	_
154	-LRB-	-lrb-	-LRB-	_	_	_
155	50	50	CD	_	_	_
156	ug/ml	ug/ml	NN	_	_	_
157	-RRB-	-rrb-	-RRB-	_	_	_
158	addition	addition	NN	_	_	_
159	in	in	IN	_	_	_
160	LB	LB	NNP	_	_	_
161	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
162	Escherichia	escherichia	FW	Organism	_	_
163	coli	coli	FW	Organism	_	_
164	C600	c600	NN	_	_	_
165	-LRB-	-lrb-	-LRB-	_	_	_
166	gyrArparCr	gyrarparcr	NN	_	_	_
167	-RRB-	-rrb-	-RRB-	_	_	_
168	,	,	,	_	_	_
169	2	2	CD	_	_	_
170	min	min	NN	_	_	_
171	after	after	IN	_	_	_
172	Norfloxacin	Norfloxacin	NNP	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	15	15	CD	_	_	_
175	ug/ml	ug/ml	NN	_	_	_
176	-RRB-	-rrb-	-RRB-	_	_	_
177	addition	addition	NN	_	_	_
178	in	in	IN	_	_	_
179	LB	LB	NNP	_	_	_
180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
181	Escherichia	escherichia	FW	Organism	_	_
182	coli	coli	FW	Organism	_	_
183	C600	c600	NN	_	_	_
184	-LRB-	-lrb-	-LRB-	_	_	_
185	gyrArparCr	gyrarparcr	NN	_	_	_
186	-RRB-	-rrb-	-RRB-	_	_	_
187	,	,	,	_	_	_
188	2	2	CD	_	_	_
189	min	min	NN	_	_	_
190	after	after	IN	_	_	_
191	Norfloxacin	Norfloxacin	NNP	_	_	_
192	-LRB-	-lrb-	-LRB-	_	_	_
193	50	50	CD	_	_	_
194	ug/ml	ug/ml	NN	_	_	_
195	-RRB-	-rrb-	-RRB-	_	_	_
196	addition	addition	NN	_	_	_
197	in	in	IN	_	_	_
198	LB	LB	NNP	_	_	_
199	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
200	Escherichia	escherichia	FW	Organism	_	_
201	coli	coli	FW	Organism	_	_
202	C600	c600	NN	_	_	_
203	-LRB-	-lrb-	-LRB-	_	_	_
204	gyrArparCr	gyrarparcr	NN	_	_	_
205	-RRB-	-rrb-	-RRB-	_	_	_
206	,	,	,	_	_	_
207	30	30	CD	_	_	_
208	min	min	NN	_	_	_
209	after	after	IN	_	_	_
210	Norfloxacin	Norfloxacin	NNP	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	15	15	CD	_	_	_
213	ug/ml	ug/ml	NN	_	_	_
214	-RRB-	-rrb-	-RRB-	_	_	_
215	addition	addition	NN	_	_	_
216	in	in	IN	_	_	_
217	LB	LB	NNP	_	_	_
218	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
219	Escherichia	escherichia	FW	Organism	_	_
220	coli	coli	FW	Organism	_	_
221	C600	c600	NN	_	_	_
222	-LRB-	-lrb-	-LRB-	_	_	_
223	gyrArparCr	gyrarparcr	NN	_	_	_
224	-RRB-	-rrb-	-RRB-	_	_	_
225	,	,	,	_	_	_
226	30	30	CD	_	_	_
227	min	min	NN	_	_	_
228	after	after	IN	_	_	_
229	Norfloxacin	Norfloxacin	NNP	_	_	_
230	-LRB-	-lrb-	-LRB-	_	_	_
231	50	50	CD	_	_	_
232	ug/ml	ug/ml	NN	_	_	_
233	-RRB-	-rrb-	-RRB-	_	_	_
234	addition	addition	NN	_	_	_
235	in	in	IN	_	_	_
236	LB	LB	NNP	_	_	_
237	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
238	Escherichia	escherichia	FW	Organism	_	_
239	coli	coli	FW	Organism	_	_
240	C600	c600	NN	_	_	_
241	-LRB-	-lrb-	-LRB-	_	_	_
242	gyrArparCr	gyrarparcr	NN	_	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	,	,	,	_	_	_
245	5	5	CD	_	_	_
246	min	min	NN	_	_	_
247	after	after	IN	_	_	_
248	Norfloxacin	Norfloxacin	NNP	_	_	_
249	-LRB-	-lrb-	-LRB-	_	_	_
250	15	15	CD	_	_	_
251	ug/ml	ug/ml	NN	_	_	_
252	-RRB-	-rrb-	-RRB-	_	_	_
253	addition	addition	NN	_	_	_
254	in	in	IN	_	_	_
255	LB	LB	NNP	_	_	_
256	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
257	Escherichia	escherichia	FW	Organism	_	_
258	coli	coli	FW	Organism	_	_
259	C600	c600	NN	_	_	_
260	-LRB-	-lrb-	-LRB-	_	_	_
261	gyrArparCr	gyrarparcr	NN	_	_	_
262	-RRB-	-rrb-	-RRB-	_	_	_
263	,	,	,	_	_	_
264	5	5	CD	_	_	_
265	min	min	NN	_	_	_
266	after	after	IN	_	_	_
267	Norfloxacin	Norfloxacin	NNP	_	_	_
268	-LRB-	-lrb-	-LRB-	_	_	_
269	50	50	CD	_	_	_
270	ug/ml	ug/ml	NN	_	_	_
271	-RRB-	-rrb-	-RRB-	_	_	_
272	addition	addition	NN	_	_	_
273	in	in	IN	_	_	_
274	LB	LB	NNP	_	_	_
275	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
276	Escherichia	escherichia	FW	Organism	_	_
277	coli	coli	FW	Organism	_	_
278	C600	c600	NN	_	_	_
279	-LRB-	-lrb-	-LRB-	_	_	_
280	gyrArparCr	gyrarparcr	NN	_	_	_
281	-RRB-	-rrb-	-RRB-	_	_	_
282	,	,	,	_	_	_
283	LB	lb	NN	_	_	_
284	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
285	Escherichia	escherichia	FW	Organism	_	_
286	coli	coli	FW	Organism	_	_
287	C600	c600	NN	_	_	_
288	-LRB-	-lrb-	-LRB-	_	_	_
289	gyrArparCr	gyrarparcr	NN	_	_	_
290	-RRB-	-rrb-	-RRB-	_	_	_
291	,	,	,	_	_	_
292	LB	lb	NN	_	_	_
293	,	,	,	_	_	_
294	0	0	CD	_	_	_
295	min	min	NN	_	_	_
296	before	before	IN	_	_	_
297	treatment	treatment	NN	_	_	_
298	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
299	Escherichia	escherichia	FW	Organism	_	_
300	coli	coli	FW	Organism	_	_
301	C600	c600	NN	_	_	_
302	,	,	,	_	_	_
303	LB	lb	NN	_	_	_
304	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
305	Escherichia	escherichia	FW	Organism	_	_
306	coli	coli	FW	Organism	_	_
307	C600	c600	NN	_	_	_
308	,	,	,	_	_	_
309	LB	lb	NN	_	_	_
310	,	,	,	_	_	_
311	0	0	CD	_	_	_
312	min	min	NN	_	_	_
313	before	before	IN	_	_	_
314	treatment	treatment	NN	_	_	_
315	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
316	Escherichia	escherichia	FW	Organism	_	_
317	coli	coli	FW	Organism	_	_
318	cell	cell	NN	_	_	_
319	lysate	lysate	NN	_	_	_
320	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
321	Escherichia	escherichia	FW	Organism	_	_
322	coli	coli	FW	Organism	_	_
323	cells	cell	NNS	_	_	_
324	were	be	VBD	_	_	_
325	grown	grow	VBN	_	_	_
326	in	in	IN	_	_	_
327	LB	lb	NN	_	_	_
328	at	at	IN	_	_	_
329	37oC	37oc	NN	_	_	_
330	with	with	IN	_	_	_
331	shaking	shake	VBG	_	_	_
332	at	at	IN	_	_	_
333	250	250	CD	_	_	_
334	RPM	rpm	NNS	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	Escherichia	escherichia	FW	Organism	_	_
337	coli	coli	FW	Organism	_	_
338	CFT073	cft073	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	Escherichia	escherichia	FW	Organism	_	_
341	coli	coli	FW	Organism	_	_
342	Colony	Colony	NNP	_	_	_
343	Biofilm	Biofilm	NNP	_	_	_
344	Interior	Interior	NNP	_	_	_
345	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
346	Escherichia	escherichia	FW	Organism	_	_
347	coli	coli	FW	Organism	_	_
348	Colony	Colony	NNP	_	_	_
349	Biofilm	Biofilm	NNP	_	_	_
350	Perimeter	Perimeter	NNP	_	_	_
351	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
352	Escherichia	escherichia	FW	Organism	_	_
353	coli	coli	FW	Organism	_	_
354	continous	continous	JJ	_	_	_
355	culture	culture	NN	_	_	_
356	without	without	IN	_	_	_
357	tannins	tannin	NNS	_	_	_
358	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
359	Escherichia	escherichia	FW	Organism	_	_
360	coli	coli	FW	Organism	_	_
361	continuous	continuous	JJ	_	_	_
362	culture	culture	NN	_	_	_
363	with	with	IN	_	_	_
364	1	1	CD	_	_	_
365	%	%	NN	_	_	_
366	tannins	tannin	NNS	_	_	_
367	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
368	Escherichia	escherichia	FW	Organism	_	_
369	coli	coli	FW	Organism	_	_
370	_	_	FW	_	_	_
371	control	control	NN	_	_	_
372	condition	condition	NN	_	_	_
373	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
374	Escherichia	escherichia	FW	Organism	_	_
375	coli	coli	FW	Organism	_	_
376	control	control	NN	_	_	_
377	vs	vs	CC	_	_	_
378	H2O2	h2o2	NN	_	_	_
379	Rep1	rep1	JJ	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
381	Escherichia	escherichia	FW	Organism	_	_
382	coli	coli	FW	Organism	_	_
383	control	control	NN	_	_	_
384	vs	vs	CC	_	_	_
385	H2O2	h2o2	NN	_	_	_
386	Rep2	rep2	JJ	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	Escherichia	escherichia	FW	Organism	_	_
389	coli	coli	FW	Organism	_	_
390	CSH50	csh50	NN	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	Escherichia	escherichia	FW	Organism	_	_
393	coli	coli	FW	Organism	_	_
394	CSH50	csh50	NN	_	_	_
395	Δfis	Δfis	NNP	_	_	_
396	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
397	Escherichia	escherichia	FW	Organism	_	_
398	coli	coli	FW	Organism	_	_
399	CSH50	csh50	NN	_	_	_
400	Δhns	δhns	NNS	_	_	_
401	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
402	Escherichia	escherichia	FW	Organism	_	_
403	coli	coli	FW	Organism	_	_
404	DH1	dh1	NN	_	_	_
405	∆	∆	CD	_	_	_
406	fadE	fade	NN	GEN	_	_
407	control	control	NN	_	_	_
408	and	and	CC	_	_	_
409	test	test	NN	_	_	_
410	strains	strain	NNS	_	_	_
411	were	be	VBD	_	_	_
412	seeded	seed	VBN	_	_	_
413	with	with	IN	_	_	_
414	OD600nm	od600nm	NN	_	_	_
415	0.03	0.03	CD	_	_	_
416	overnight	overnight	JJ	_	_	_
417	cultures	culture	NNS	_	_	_
418	into	into	IN	_	_	_
419	15	15	CD	_	_	_
420	ml	ml	NN	_	_	_
421	tryptic	tryptic	JJ	_	_	_
422	soy	soy	NN	_	_	_
423	broth	broth	NN	_	_	_
424	media	media	NNS	_	_	_
425	and	and	CC	_	_	_
426	grown	grow	VBN	_	_	_
427	at	at	IN	_	_	_
428	37	37	CD	_	_	_
429	°C	°c	NN	_	_	_
430	with	with	IN	_	_	_
431	200rpm	200rpm	JJ	_	_	_
432	agitation	agitation	NN	_	_	_
433	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	DH5	dh5	NN	_	_	_
5	-LSB-	-lsb-	-LRB-	_	_	_
6	alpha	alpha	NN	_	_	_
7	-RSB-	-rsb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	DH5alpha	dh5alpha	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	NEB	neb	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	OD	od	NN	_	_	_
17	0.2	0.2	CD	_	_	_
18	in	in	IN	_	_	_
19	LB	lb	NN	_	_	_
20	+	+	CC	_	_	_
21	Amp	amp	NN	_	_	_
22	,	,	,	_	_	_
23	pUC	puc	NN	_	_	_
24	expression	expression	NN	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Escherichia	escherichia	FW	Organism	_	_
27	coli	coli	FW	Organism	_	_
28	DH5alpha	dh5alpha	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	NEB	neb	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	,	,	,	_	_	_
33	OD	od	NN	_	_	_
34	0.2	0.2	CD	_	_	_
35	in	in	IN	_	_	_
36	LB	LB	NNP	_	_	_
37	,	,	,	_	_	_
38	no	no	DT	_	_	_
39	pUC	puc	NN	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Escherichia	escherichia	FW	Organism	_	_
42	coli	coli	FW	Organism	_	_
43	DH5alpha	dh5alpha	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	NEB	neb	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	,	,	,	_	_	_
48	OD	od	NN	_	_	_
49	0.5	0.5	CD	_	_	_
50	in	in	IN	_	_	_
51	LB	lb	NN	_	_	_
52	+	+	CC	_	_	_
53	Amp	amp	NN	_	_	_
54	,	,	,	_	_	_
55	pUC	puc	NN	_	_	_
56	expression	expression	NN	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Escherichia	escherichia	FW	Organism	_	_
59	coli	coli	FW	Organism	_	_
60	DH5alpha	dh5alpha	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	NEB	neb	NN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	,	,	,	_	_	_
65	OD	od	NN	_	_	_
66	0.5	0.5	CD	_	_	_
67	in	in	IN	_	_	_
68	LB	LB	NNP	_	_	_
69	,	,	,	_	_	_
70	no	no	DT	_	_	_
71	pUC	puc	NN	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Escherichia	escherichia	FW	Organism	_	_
74	coli	coli	FW	Organism	_	_
75	DH5alpha	dh5alpha	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	NEB	neb	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	,	,	,	_	_	_
80	OD	od	NN	_	_	_
81	0.9	0.9	CD	_	_	_
82	in	in	IN	_	_	_
83	LB	lb	NN	_	_	_
84	+	+	CC	_	_	_
85	Amp	amp	NN	_	_	_
86	,	,	,	_	_	_
87	pUC	puc	NN	_	_	_
88	expression	expression	NN	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	Escherichia	escherichia	FW	Organism	_	_
91	coli	coli	FW	Organism	_	_
92	DH5alpha	dh5alpha	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	NEB	neb	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	,	,	,	_	_	_
97	OD	od	NN	_	_	_
98	0.9	0.9	CD	_	_	_
99	in	in	IN	_	_	_
100	LB	LB	NNP	_	_	_
101	,	,	,	_	_	_
102	no	no	DT	_	_	_
103	pUC	puc	NN	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Escherichia	escherichia	FW	Organism	_	_
106	coli	coli	FW	Organism	_	_
107	EDL	edl	NN	_	_	_
108	933	933	CD	_	_	_
109	cells	cell	NNS	_	_	_
110	grown	grow	VBN	_	_	_
111	in	in	IN	_	_	_
112	the	the	DT	_	_	_
113	hydroponic	hydroponic	JJ	_	_	_
114	system	system	NN	_	_	_
115	without	without	IN	_	_	_
116	interacting	interact	VBG	_	_	_
117	with	with	IN	_	_	_
118	the	the	DT	_	_	_
119	lettuce	lettuce	NN	_	_	_
120	rhizosphere	rhizosphere	NN	_	_	_
121	for	for	IN	_	_	_
122	3	3	CD	_	_	_
123	days	day	NNS	_	_	_
124	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
125	Escherichia	escherichia	FW	Organism	_	_
126	coli	coli	FW	Organism	_	_
127	EDL	edl	NN	_	_	_
128	933	933	CD	_	_	_
129	cells	cell	NNS	_	_	_
130	interacted	interact	VBD	_	_	_
131	with	with	IN	_	_	_
132	the	the	DT	_	_	_
133	lettuce	lettuce	NN	_	_	_
134	rhizosphere	rhizosphere	NN	_	_	_
135	for	for	IN	_	_	_
136	3	3	CD	_	_	_
137	days	day	NNS	_	_	_
138	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
139	Escherichia	escherichia	FW	Organism	_	_
140	coli	coli	FW	Organism	_	_
141	EDL	edl	NN	_	_	_
142	933	933	CD	_	_	_
143	were	be	VBD	_	_	_
144	grown	grow	VBN	_	_	_
145	in	in	IN	_	_	_
146	10	10	CD	_	_	_
147	ml	ml	NN	_	_	_
148	of	of	IN	_	_	_
149	LB	lb	NN	MED	_	_
150	medium	medium	NN	MED	_	_
151	until	until	IN	_	_	_
152	stationary	stationary	JJ	GrowthPhase	_	_
153	phase	phase	NN	GrowthPhase	_	_
154	,	,	,	_	_	_
155	collected	collect	VBN	_	_	_
156	by	by	IN	_	_	_
157	centrifugation	centrifugation	NN	_	_	_
158	at	at	IN	_	_	_
159	8,000	8,000	CD	_	_	_
160	×	×	CD	_	_	_
161	g	g	NN	_	_	_
162	for	for	IN	_	_	_
163	10	10	CD	_	_	_
164	min	min	NN	_	_	_
165	,	,	,	_	_	_
166	and	and	CC	_	_	_
167	washed	wash	VBN	_	_	_
168	twice	twice	RB	_	_	_
169	with	with	IN	_	_	_
170	sterilized	sterilize	VBN	_	_	_
171	,	,	,	_	_	_
172	plant	plant	NN	_	_	_
173	growth	growth	NN	_	_	_
174	medium	medium	NN	_	_	_
175	-LRB-	-lrb-	-LRB-	_	_	_
176	Caspersen	Caspersen	NNP	_	_	_
177	et	et	FW	_	_	_
178	al.	al.	FW	_	_	_
179	1999	1999	CD	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	.	.	.	_	_	_

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	CD	_	_	_
22	cells/ml	cells/ml	NNS	_	_	_
23	.	.	.	_	_	_

1	Germinated	germinate	VBN	_	_	_
2	lettuce	lettuce	NN	_	_	_
3	seedlings	seedling	NNS	_	_	_
4	were	be	VBD	_	_	_
5	each	each	DT	_	_	_
6	aseptically	aseptically	RB	_	_	_
7	transferred	transfer	VBN	_	_	_
8	into	into	IN	_	_	_
9	holes	hole	NNS	_	_	_
10	in	in	IN	_	_	_
11	the	the	DT	_	_	_
12	growth	growth	NN	_	_	_
13	boxes	box	NNS	_	_	_
14	filled	fill	VBN	_	_	_
15	with	with	IN	_	_	_
16	300	300	CD	_	_	_
17	ml	ml	NN	_	_	_
18	of	of	IN	_	_	_
19	plant	plant	NN	_	_	_
20	growth	growth	NN	_	_	_
21	medium	medium	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	3	3	CD	_	_	_
25	ml	ml	NN	_	_	_
26	washed	wash	VBN	_	_	_
27	bacterial	bacterial	JJ	_	_	_
28	suspension	suspension	NN	_	_	_
29	was	be	VBD	_	_	_
30	added	add	VBN	_	_	_
31	to	to	TO	_	_	_
32	provide	provide	VB	_	_	_
33	approximately	approximately	RB	_	_	_
34	10E7	10e7	CD	_	_	_
35	cells/ml	cells/ml	NNS	_	_	_
36	of	of	IN	_	_	_
37	growth	growth	NN	_	_	_
38	medium	medium	NN	_	_	_
39	.	.	.	_	_	_

1	Seedling	seedle	VBG	_	_	_
2	boxes	box	NNS	_	_	_
3	were	be	VBD	_	_	_
4	germinated	germinate	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	week	week	NN	_	_	_
8	and	and	CC	_	_	_
9	transferred	transfer	VBN	_	_	_
10	to	to	TO	_	_	_
11	a	a	DT	_	_	_
12	plant	plant	NN	_	_	_
13	growth	growth	NN	_	_	_
14	chamber	chamber	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	aeration	aeration	NN	_	_	_
19	pump	pump	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Luft	luft	NN	_	_	_
22	Pump	pump	NN	_	_	_
23	;	;	:	_	_	_
24	Oceanic	Oceanic	NNP	_	_	_
25	systems	system	NNS	_	_	_
26	Inc.	Inc.	NNP	_	_	_
27	.	.	.	_	_	_

1	Dallas	Dallas	NNP	_	_	_
2	,	,	,	_	_	_
3	TX	TX	NNP	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	was	be	VBD	_	_	_
6	immediately	immediately	RB	_	_	_
7	started	start	VBN	_	_	_
8	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	pump	pump	NN	_	_	_
3	supplied	supply	VBD	_	_	_
4	aeration	aeration	NN	_	_	_
5	of	of	IN	_	_	_
6	three	three	CD	_	_	_
7	growth	growth	NN	_	_	_
8	boxes	box	NNS	_	_	_
9	,	,	,	_	_	_
10	at	at	IN	_	_	_
11	a	a	DT	_	_	_
12	rate	rate	NN	_	_	_
13	of	of	IN	_	_	_
14	1.3	1.3	CD	_	_	_
15	L	l	NN	_	_	_
16	/	/	:	_	_	_
17	min	min	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	seedling	seedling	NN	_	_	_
3	boxes	box	NNS	_	_	_
4	were	be	VBD	_	_	_
5	incubated	incubate	VBN	_	_	_
6	under	under	IN	_	_	_
7	80	80	CD	_	_	_
8	%	%	NN	_	_	_
9	RH	rh	NN	_	_	_
10	at	at	IN	_	_	_
11	25	25	CD	_	_	_
12	°C	°c	NN	_	_	_
13	with	with	IN	_	_	_
14	a	a	DT	_	_	_
15	photoperiod	photoperiod	NN	_	_	_
16	of	of	IN	_	_	_
17	16	16	CD	_	_	_
18	h	h	NN	_	_	_
19	for	for	IN	_	_	_
20	3	3	CD	_	_	_
21	days	day	NNS	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Escherichia	escherichia	FW	Organism	_	_
24	coli	coli	FW	Organism	_	_
25	,	,	,	_	_	_
26	expressing	express	VBG	_	_	_
27	NsrR	nsrr	NN	TF	_	_
28	with	with	IN	_	_	_
29	a	a	DT	_	_	_
30	C-terminal	c-terminal	JJ	_	_	_
31	Flag-tag	flag-tag	NN	_	_	_
32	,	,	,	_	_	_
33	was	be	VBD	_	_	_
34	grown	grow	VBN	_	_	_
35	anaerobically	anaerobically	RB	_	_	_
36	in	in	IN	_	_	_
37	L	l	NN	_	_	_
38	broth	broth	NN	_	_	_
39	supplemented	supplement	VBN	_	_	_
40	with	with	IN	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	.	.	.	_	_	_

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	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	GLBRCE1	glbrce1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	GLBRCE1	glbrce1	NN	_	_	_
9	_	_	CD	_	_	_
10	pBBR	pbbr	NN	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	K-12	k-12	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	K12	k12	NN	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	was	be	VBD	_	_	_
21	cultivated	cultivate	VBN	_	_	_
22	using	use	VBG	_	_	_
23	M9	m9	NN	MED	_	_
24	minimal	minimal	JJ	MED	_	_
25	medium	medium	NN	MED	_	_
26	containing	contain	VBG	_	_	_
27	4.5	4.5	CD	_	_	_
28	g/L	g/l	NN	_	_	_
29	α	α	SYM	_	_	_
30	-	-	:	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	D	d	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	-	-	:	_	_	_
35	glucose	glucose	NN	SUPP	_	_
36	,	,	,	_	_	_
37	pH	ph	NN	_	_	_
38	=	=	JJ	_	_	_
39	7	7	CD	_	_	_
40	,	,	,	_	_	_
41	temperature	temperature	NN	_	_	_
42	37	37	CD	_	_	_
43	ºC	ºc	NN	_	_	_
44	,	,	,	_	_	_
45	aerobic	aerobic	JJ	_	_	_
46	conditions	condition	NNS	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	K12	k12	NN	_	_	_
51	MG1655	mg1655	NN	_	_	_
52	were	be	VBD	_	_	_
53	grown	grow	VBN	_	_	_
54	in	in	IN	_	_	_
55	M9	m9	NN	MED	_	_
56	minimal	minimal	JJ	MED	_	_
57	medium	medium	NN	MED	_	_
58	with	with	IN	_	_	_
59	10	10	CD	_	_	_
60	g/L	g/l	NN	_	_	_
61	glucose	glucose	NN	SUPP	_	_
62	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	cultivated	cultivate	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	chemostat	chemostat	NN	_	_	_
8	at	at	IN	_	_	_
9	specific	specific	JJ	_	_	_
10	growth	growth	NN	_	_	_
11	rate	rate	NN	_	_	_
12	0.3	0.3	CD	_	_	_
13	h-1	h-1	NN	_	_	_
14	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	reaching	reach	VBG	_	_	_
3	steady	steady	JJ	_	_	_
4	state	state	NN	_	_	_
5	,	,	,	_	_	_
6	dilution	dilution	NN	_	_	_
7	rate	rate	NN	_	_	_
8	was	be	VBD	_	_	_
9	increased	increase	VBN	_	_	_
10	with	with	IN	_	_	_
11	constant	constant	JJ	_	_	_
12	rate	rate	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	0.01	0.01	CD	_	_	_
15	h-2	h-2	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	samples	sample	NNS	_	_	_
20	were	be	VBD	_	_	_
21	acquired	acquire	VBN	_	_	_
22	when	when	WRB	_	_	_
23	specific	specific	JJ	_	_	_
24	growth	growth	NN	_	_	_
25	rate	rate	NN	_	_	_
26	reached	reach	VBD	_	_	_
27	0.47	0.47	CD	_	_	_
28	h-1	h-1	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K12	k12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	in	in	IN	_	_	_
9	M9	m9	NN	MED	_	_
10	minimal	minimal	JJ	MED	_	_
11	medium	medium	NN	MED	_	_
12	with	with	IN	_	_	_
13	10	10	CD	_	_	_
14	g/L	g/l	NN	_	_	_
15	glucose	glucose	NN	SUPP	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	cultivated	cultivate	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	chemostat	chemostat	NN	_	_	_
8	at	at	IN	_	_	_
9	specific	specific	JJ	_	_	_
10	growth	growth	NN	_	_	_
11	rate	rate	NN	_	_	_
12	0.3	0.3	CD	_	_	_
13	h-1	h-1	NN	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	acquired	acquire	VBN	_	_	_
19	after	after	IN	_	_	_
20	culture	culture	NN	_	_	_
21	reached	reach	VBD	_	_	_
22	steady	steady	JJ	_	_	_
23	state	state	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K12	k12	NN	_	_	_
5	strain	strain	NN	_	_	_
6	BW25113	bw25113	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Datsenko	Datsenko	NNP	_	_	_
9	&	&	CC	_	_	_
10	Wanner	Wanner	NNP	_	_	_
11	2000	2000	CD	_	_	_
12	.	.	.	_	_	_

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	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	strain	strain	NN	_	_	_
6	MG1655	mg1655	NN	_	_	_
7	was	be	VBD	_	_	_
8	cultivated	cultivate	VBN	_	_	_
9	aerobically	aerobically	RB	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	~	~	SYM	_	_	_
12	0.5	0.5	CD	_	_	_
13	l/min	l/min	JJ	_	_	_
14	air	air	NN	_	_	_
15	supply	supply	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	in	in	IN	_	_	_
18	a	a	DT	_	_	_
19	defined	define	VBN	_	_	_
20	mineral	mineral	NN	_	_	_
21	medium	medium	NN	_	_	_
22	containing	contain	VBG	_	_	_
23	1	1	CD	_	_	_
24	g/l	g/l	NN	_	_	_
25	glucose	glucose	NN	SUPP	_	_
26	in	in	IN	_	_	_
27	continous	continous	JJ	_	_	_
28	cultures	culture	NNS	_	_	_
29	growing	grow	VBG	_	_	_
30	in	in	IN	_	_	_
31	a	a	DT	_	_	_
32	chemostat	chemostat	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	dilution	dilution	NN	_	_	_
35	rate	rate	NN	_	_	_
36	=	=	JJ	_	_	_
37	0.4	0.4	CD	_	_	_
38	h-1	h-1	NN	_	_	_
39	,	,	,	_	_	_
40	working	work	VBG	_	_	_
41	volume	volume	NN	_	_	_
42	=	=	JJ	_	_	_
43	100	100	CD	_	_	_
44	ml	ml	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	menadione	menadione	NN	_	_	_
8	_	_	CD	_	_	_
9	rep	rep	NN	GEN	_	_
10	#	#	#	_	_	_
11	1	1	CD	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	K-12	k-12	NN	_	_	_
16	treated	treat	VBN	_	_	_
17	with	with	IN	_	_	_
18	menadione	menadione	NN	_	_	_
19	_	_	CD	_	_	_
20	rep	rep	NN	GEN	_	_
21	#	#	#	_	_	_
22	2	2	CD	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Escherichia	escherichia	FW	Organism	_	_
25	coli	coli	FW	Organism	_	_
26	K-12	k-12	NN	_	_	_
27	treated	treat	VBN	_	_	_
28	with	with	IN	_	_	_
29	menadione	menadione	NN	_	_	_
30	_	_	CD	_	_	_
31	rep	rep	NN	GEN	_	_
32	#	#	#	_	_	_
33	3	3	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Escherichia	escherichia	FW	Organism	_	_
36	coli	coli	FW	Organism	_	_
37	K-12	k-12	NN	_	_	_
38	tynA	tyna	NN	GEN	_	_
39	-	-	:	_	_	_
40	1h	1h	NN	_	_	_
41	after	after	IN	_	_	_
42	induction	induction	NN	_	_	_
43	of	of	IN	_	_	_
44	tynA	tyna	NN	GEN	_	_
45	expression	expression	NN	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Escherichia	escherichia	FW	Organism	_	_
48	coli	coli	FW	Organism	_	_
49	K-12	k-12	NN	_	_	_
50	tynA	tyna	NN	GEN	_	_
51	-	-	:	_	_	_
52	4h	4h	NN	_	_	_
53	after	after	IN	_	_	_
54	the	the	DT	_	_	_
55	induction	induction	NN	_	_	_
56	of	of	IN	_	_	_
57	tynA	tyna	NN	GEN	_	_
58	expression	expression	NN	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	Escherichia	escherichia	FW	Organism	_	_
61	coli	coli	FW	Organism	_	_
62	K-12	k-12	NN	_	_	_
63	tynA	tyna	NN	GEN	_	_
64	-	-	:	_	_	_
65	at	at	IN	_	_	_
66	time	time	NN	_	_	_
67	of	of	IN	_	_	_
68	induction	induction	NN	_	_	_
69	of	of	IN	_	_	_
70	tynA	tyna	NN	GEN	_	_
71	expression	expression	NN	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Escherichia	escherichia	FW	Organism	_	_
74	coli	coli	FW	Organism	_	_
75	K12	k12	NN	_	_	_
76	wild-type	wild-type	JJ	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	Escherichia	escherichia	FW	Organism	_	_
79	coli	coli	FW	Organism	_	_
80	K-12	k-12	NN	_	_	_
81	wt	wt	JJ	_	_	_
82	1h	1h	NN	_	_	_
83	after	after	IN	_	_	_
84	the	the	DT	_	_	_
85	induction	induction	NN	_	_	_
86	of	of	IN	_	_	_
87	tynA	tyna	NN	GEN	_	_
88	expression	expression	NN	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	Escherichia	escherichia	FW	Organism	_	_
91	coli	coli	FW	Organism	_	_
92	K-12	k-12	NN	_	_	_
93	wt	wt	JJ	_	_	_
94	4h	4h	NN	_	_	_
95	after	after	IN	_	_	_
96	the	the	DT	_	_	_
97	induction	induction	NN	_	_	_
98	of	of	IN	_	_	_
99	tynA	tyna	NN	GEN	_	_
100	expression	expression	NN	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	Escherichia	escherichia	FW	Organism	_	_
103	coli	coli	FW	Organism	_	_
104	K-12	k-12	NN	_	_	_
105	wt	wt	JJ	_	_	_
106	at	at	IN	_	_	_
107	time	time	NN	_	_	_
108	of	of	IN	_	_	_
109	induction	induction	NN	_	_	_
110	of	of	IN	_	_	_
111	tynA	tyna	NN	GEN	_	_
112	expression	expression	NN	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	Escherichia	escherichia	FW	Organism	_	_
115	coli	coli	FW	Organism	_	_
116	LE234	le234	NN	_	_	_
117	acrD	acrd	NN	GEN	_	_
118	-	-	:	_	_	_
119	,	,	,	_	_	_
120	0	0	CD	_	_	_
121	min	min	NN	_	_	_
122	before	before	IN	_	_	_
123	treatment	treatment	NN	_	_	_
124	in	in	IN	_	_	_
125	LB	LB	NNP	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Escherichia	escherichia	FW	Organism	_	_
128	coli	coli	FW	Organism	_	_
129	LE234	le234	NN	_	_	_
130	acrD	acrd	NN	GEN	_	_
131	-	-	:	_	_	_
132	,	,	,	_	_	_
133	5	5	CD	_	_	_
134	min	min	NN	_	_	_
135	after	after	IN	_	_	_
136	Novobiocin	Novobiocin	NNP	_	_	_
137	-LRB-	-lrb-	-LRB-	_	_	_
138	200	200	CD	_	_	_
139	ug/ml	ug/ml	NN	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	addition	addition	NN	_	_	_
142	in	in	IN	_	_	_
143	LB	LB	NNP	_	_	_
144	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
145	Escherichia	escherichia	FW	Organism	_	_
146	coli	coli	FW	Organism	_	_
147	LE234	le234	NN	_	_	_
148	acrD	acrd	NN	GEN	_	_
149	-	-	:	_	_	_
150	,	,	,	_	_	_
151	5	5	CD	_	_	_
152	min	min	NN	_	_	_
153	after	after	IN	_	_	_
154	Novobiocin	Novobiocin	NNP	_	_	_
155	-LRB-	-lrb-	-LRB-	_	_	_
156	20	20	CD	_	_	_
157	ug/ml	ug/ml	NN	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	addition	addition	NN	_	_	_
160	in	in	IN	_	_	_
161	LB	LB	NNP	_	_	_
162	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
163	Escherichia	escherichia	FW	Organism	_	_
164	coli	coli	FW	Organism	_	_
165	LE234	le234	NN	_	_	_
166	acrD	acrd	NN	GEN	_	_
167	-	-	:	_	_	_
168	,	,	,	_	_	_
169	5	5	CD	_	_	_
170	min	min	NN	_	_	_
171	after	after	IN	_	_	_
172	Novobiocin	Novobiocin	NNP	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	50	50	CD	_	_	_
175	ug/ml	ug/ml	NN	_	_	_
176	-RRB-	-rrb-	-RRB-	_	_	_
177	addition	addition	NN	_	_	_
178	in	in	IN	_	_	_
179	LB	LB	NNP	_	_	_
180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
181	Escherichia	escherichia	FW	Organism	_	_
182	coli	coli	FW	Organism	_	_
183	LE234	le234	NN	_	_	_
184	acrD	acrd	NN	GEN	_	_
185	-	-	:	_	_	_
186	,	,	,	_	_	_
187	5	5	CD	_	_	_
188	min	min	NN	_	_	_
189	after	after	IN	_	_	_
190	Novobiocin	Novobiocin	NNP	_	_	_
191	-LRB-	-lrb-	-LRB-	_	_	_
192	5	5	CD	_	_	_
193	ug/ml	ug/ml	NN	_	_	_
194	-RRB-	-rrb-	-RRB-	_	_	_
195	addition	addition	NN	_	_	_
196	in	in	IN	_	_	_
197	LB	LB	NNP	_	_	_
198	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
199	Escherichia	escherichia	FW	Organism	_	_
200	coli	coli	FW	Organism	_	_
201	LE234	le234	NN	_	_	_
202	acrD	acrd	NN	GEN	_	_
203	-	-	:	_	_	_
204	,	,	,	_	_	_
205	LB	LB	NNP	_	_	_
206	,	,	,	_	_	_
207	0	0	CD	_	_	_
208	min	min	NN	_	_	_
209	before	before	IN	_	_	_
210	treatment	treatment	NN	_	_	_
211	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
212	Escherichia	escherichia	FW	Organism	_	_
213	coli	coli	FW	Organism	_	_
214	MG1655	mg1655	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	Escherichia	escherichia	FW	Organism	_	_
217	coli	coli	FW	Organism	_	_
218	MG1655	mg1655	NN	_	_	_
219	,	,	,	_	_	_
220	0	0	CD	_	_	_
221	min	min	NN	_	_	_
222	after	after	IN	_	_	_
223	Ampicillin	Ampicillin	NNP	_	_	_
224	-LRB-	-lrb-	-LRB-	_	_	_
225	100	100	CD	_	_	_
226	ug/ml	ug/ml	NN	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	addition	addition	NN	_	_	_
229	in	in	IN	_	_	_
230	M9	m9	NN	_	_	_
231	+	+	CC	_	_	_
232	glucose	glucose	NN	SUPP	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
234	Escherichia	escherichia	FW	Organism	_	_
235	coli	coli	FW	Organism	_	_
236	MG1655	mg1655	NN	_	_	_
237	,	,	,	_	_	_
238	0	0	CD	_	_	_
239	min	min	NN	_	_	_
240	after	after	IN	_	_	_
241	Kanamycin	Kanamycin	NNP	_	_	_
242	-LRB-	-lrb-	-LRB-	_	_	_
243	100	100	CD	_	_	_
244	ug/ml	ug/ml	NN	_	_	_
245	-RRB-	-rrb-	-RRB-	_	_	_
246	addition	addition	NN	_	_	_
247	in	in	IN	_	_	_
248	M9	m9	NN	_	_	_
249	+	+	CC	_	_	_
250	glucose	glucose	NN	SUPP	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
252	Escherichia	escherichia	FW	Organism	_	_
253	coli	coli	FW	Organism	_	_
254	MG1655	mg1655	NN	_	_	_
255	,	,	,	_	_	_
256	0	0	CD	_	_	_
257	min	min	NN	_	_	_
258	before	before	IN	_	_	_
259	treatment	treatment	NN	_	_	_
260	,	,	,	_	_	_
261	Davis	Davis	NNP	_	_	_
262	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
263	Escherichia	escherichia	FW	Organism	_	_
264	coli	coli	FW	Organism	_	_
265	MG1655	mg1655	NN	_	_	_
266	,	,	,	_	_	_
267	0	0	CD	_	_	_
268	min	min	NN	_	_	_
269	recovery	recovery	NN	_	_	_
270	in	in	IN	_	_	_
271	10mM	10mm	NN	_	_	_
272	Na-P	na-p	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	Escherichia	escherichia	FW	Organism	_	_
275	coli	coli	FW	Organism	_	_
276	MG1655	mg1655	NN	_	_	_
277	,	,	,	_	_	_
278	0	0	CD	_	_	_
279	min	min	NN	_	_	_
280	recovery	recovery	NN	_	_	_
281	in	in	IN	_	_	_
282	10mM	10mm	NN	_	_	_
283	Na-P	na-p	NN	_	_	_
284	+	+	CC	_	_	_
285	0.2	0.2	CD	_	_	_
286	%	%	NN	_	_	_
287	glucose	glucose	NN	SUPP	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	Escherichia	escherichia	FW	Organism	_	_
290	coli	coli	FW	Organism	_	_
291	MG1655	mg1655	NN	_	_	_
292	,	,	,	_	_	_
293	0	0	CD	_	_	_
294	min	min	NN	_	_	_
295	recovery	recovery	NN	_	_	_
296	in	in	IN	_	_	_
297	10	10	CD	_	_	_
298	mM	mm	NN	KWSUPP	_	_
299	Na-P	na-p	NN	_	_	_
300	+	+	CC	_	_	_
301	0.2	0.2	CD	_	_	_
302	%	%	NN	_	_	_
303	glucose	glucose	NN	SUPP	_	_
304	-LRB-	-lrb-	-LRB-	_	_	_
305	pH	ph	NN	_	_	_
306	7.5	7.5	CD	_	_	_
307	-RRB-	-rrb-	-RRB-	_	_	_
308	at	at	IN	_	_	_
309	OD	od	NN	_	_	_
310	0.4	0.4	CD	_	_	_
311	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
312	Escherichia	escherichia	FW	Organism	_	_
313	coli	coli	FW	Organism	_	_
314	MG1655	mg1655	NN	_	_	_
315	,	,	,	_	_	_
316	0	0	CD	_	_	_
317	min	min	NN	_	_	_
318	recovery	recovery	NN	_	_	_
319	in	in	IN	_	_	_
320	10	10	CD	_	_	_
321	mM	mm	NN	KWSUPP	_	_
322	Na-P	na-p	NN	_	_	_
323	-LRB-	-lrb-	-LRB-	_	_	_
324	pH	ph	NN	_	_	_
325	7.5	7.5	CD	_	_	_
326	-RRB-	-rrb-	-RRB-	_	_	_
327	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
328	Escherichia	escherichia	FW	Organism	_	_
329	coli	coli	FW	Organism	_	_
330	MG1655	mg1655	NN	_	_	_
331	,	,	,	_	_	_
332	0	0	CD	_	_	_
333	min	min	NN	_	_	_
334	recovery	recovery	NN	_	_	_
335	in	in	IN	_	_	_
336	LB	lb	NN	_	_	_
337	+0.2	+0.2	CD	_	_	_
338	%	%	NN	_	_	_
339	glc	glc	NN	_	_	_
340	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
341	Escherichia	escherichia	FW	Organism	_	_
342	coli	coli	FW	Organism	_	_
343	MG1655	mg1655	NN	_	_	_
344	,	,	,	_	_	_
345	0	0	CD	_	_	_
346	min	min	NN	_	_	_
347	recovery	recovery	NN	_	_	_
348	in	in	IN	_	_	_
349	LB	lb	NN	_	_	_
350	+	+	CC	_	_	_
351	glucose	glucose	NN	SUPP	_	_
352	at	at	IN	_	_	_
353	OD	od	NN	_	_	_
354	0.4	0.4	CD	_	_	_
355	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
356	Escherichia	escherichia	FW	Organism	_	_
357	coli	coli	FW	Organism	_	_
358	MG1655	mg1655	NN	_	_	_
359	,	,	,	_	_	_
360	0	0	CD	_	_	_
361	min	min	NN	_	_	_
362	recovery	recovery	NN	_	_	_
363	in	in	IN	_	_	_
364	LB	lb	NN	_	_	_
365	+	+	CC	_	_	_
366	glucose	glucose	NN	SUPP	_	_
367	at	at	IN	_	_	_
368	OD	od	NN	_	_	_
369	1.0	1.0	CD	_	_	_
370	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
371	Escherichia	escherichia	FW	Organism	_	_
372	coli	coli	FW	Organism	_	_
373	MG1655	mg1655	NN	_	_	_
374	,	,	,	_	_	_
375	105	105	CD	_	_	_
376	min	min	NN	_	_	_
377	recovery	recovery	NN	_	_	_
378	in	in	IN	_	_	_
379	LB	lb	NN	_	_	_
380	+0.2	+0.2	CD	_	_	_
381	%	%	NN	_	_	_
382	glc	glc	NN	_	_	_
383	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
384	Escherichia	escherichia	FW	Organism	_	_
385	coli	coli	FW	Organism	_	_
386	MG1655	mg1655	NN	_	_	_
387	,	,	,	_	_	_
388	10	10	CD	_	_	_
389	min	min	NN	_	_	_
390	after	after	IN	_	_	_
391	Ampicillin	Ampicillin	NNP	_	_	_
392	-LRB-	-lrb-	-LRB-	_	_	_
393	100	100	CD	_	_	_
394	ug/ml	ug/ml	NN	_	_	_
395	-RRB-	-rrb-	-RRB-	_	_	_
396	addition	addition	NN	_	_	_
397	in	in	IN	_	_	_
398	M9	m9	NN	_	_	_
399	+	+	CC	_	_	_
400	glucose	glucose	NN	SUPP	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
402	Escherichia	escherichia	FW	Organism	_	_
403	coli	coli	FW	Organism	_	_
404	MG1655	mg1655	NN	_	_	_
405	,	,	,	_	_	_
406	10	10	CD	_	_	_
407	min	min	NN	_	_	_
408	after	after	IN	_	_	_
409	Gamma	gamma	NN	_	_	_
410	treatment	treatment	NN	_	_	_
411	in	in	IN	_	_	_
412	Davis	Davis	NNP	_	_	_
413	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
414	Escherichia	escherichia	FW	Organism	_	_
415	coli	coli	FW	Organism	_	_
416	MG1655	mg1655	NN	_	_	_
417	,	,	,	_	_	_
418	10	10	CD	_	_	_
419	min	min	NN	_	_	_
420	after	after	IN	_	_	_
421	Kanamycin	Kanamycin	NNP	_	_	_
422	-LRB-	-lrb-	-LRB-	_	_	_
423	100	100	CD	_	_	_
424	ug/ml	ug/ml	NN	_	_	_
425	-RRB-	-rrb-	-RRB-	_	_	_
426	addition	addition	NN	_	_	_
427	in	in	IN	_	_	_
428	M9	m9	NN	_	_	_
429	+	+	CC	_	_	_
430	glucose	glucose	NN	SUPP	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
432	Escherichia	escherichia	FW	Organism	_	_
433	coli	coli	FW	Organism	_	_
434	MG1655	mg1655	NN	_	_	_
435	10	10	CD	_	_	_
436	minutes	minute	NNS	_	_	_
437	paraquat	paraquat	NN	SUPP	_	_
438	treatment	treatment	NN	_	_	_
439	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
440	Escherichia	escherichia	FW	Organism	_	_
441	coli	coli	FW	Organism	_	_
442	MG1655	mg1655	NN	_	_	_
443	,	,	,	_	_	_
444	133	133	CD	_	_	_
445	min	min	NN	_	_	_
446	recovery	recovery	NN	_	_	_
447	in	in	IN	_	_	_
448	LB	lb	NN	_	_	_
449	+0.2	+0.2	CD	_	_	_
450	%	%	NN	_	_	_
451	glc	glc	NN	_	_	_
452	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
453	Escherichia	escherichia	FW	Organism	_	_
454	coli	coli	FW	Organism	_	_
455	MG1655	mg1655	NN	_	_	_
456	,	,	,	_	_	_
457	1440	1440	CD	_	_	_
458	min	min	NN	_	_	_
459	recovery	recovery	NN	_	_	_
460	in	in	IN	_	_	_
461	LB	lb	NN	_	_	_
462	+0.2	+0.2	CD	_	_	_
463	%	%	NN	_	_	_
464	glc	glc	NN	_	_	_
465	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
466	Escherichia	escherichia	FW	Organism	_	_
467	coli	coli	FW	Organism	_	_
468	MG1655	mg1655	NN	_	_	_
469	,	,	,	_	_	_
470	15	15	CD	_	_	_
471	min	min	NN	_	_	_
472	after	after	IN	_	_	_
473	Ampicillin	Ampicillin	NNP	_	_	_
474	-LRB-	-lrb-	-LRB-	_	_	_
475	100	100	CD	_	_	_
476	ug/ml	ug/ml	NN	_	_	_
477	-RRB-	-rrb-	-RRB-	_	_	_
478	addition	addition	NN	_	_	_
479	in	in	IN	_	_	_
480	M9	m9	NN	_	_	_
481	+	+	CC	_	_	_
482	glucose	glucose	NN	SUPP	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
484	Escherichia	escherichia	FW	Organism	_	_
485	coli	coli	FW	Organism	_	_
486	MG1655	mg1655	NN	_	_	_
487	,	,	,	_	_	_
488	15	15	CD	_	_	_
489	min	min	NN	_	_	_
490	after	after	IN	_	_	_
491	Indol-acrylate	indol-acrylate	JJ	_	_	_
492	-LRB-	-lrb-	-LRB-	_	_	_
493	10	10	CD	_	_	_
494	ug/ml	ug/ml	NN	_	_	_
495	-RRB-	-rrb-	-RRB-	_	_	_
496	addition	addition	NN	_	_	_
497	in	in	IN	_	_	_
498	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
499	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
500	Escherichia	escherichia	FW	Organism	_	_
501	coli	coli	FW	Organism	_	_
502	MG1655	mg1655	NN	_	_	_
503	,	,	,	_	_	_
504	15	15	CD	_	_	_
505	min	min	NN	_	_	_
506	after	after	IN	_	_	_
507	Indol-acrylate	indol-acrylate	JJ	_	_	_
508	-LRB-	-lrb-	-LRB-	_	_	_
509	15	15	CD	_	_	_
510	ug/ml	ug/ml	NN	_	_	_
511	-RRB-	-rrb-	-RRB-	_	_	_
512	addition	addition	NN	_	_	_
513	in	in	IN	_	_	_
514	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
515	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
516	Escherichia	escherichia	FW	Organism	_	_
517	coli	coli	FW	Organism	_	_
518	MG1655	mg1655	NN	_	_	_
519	,	,	,	_	_	_
520	15	15	CD	_	_	_
521	min	min	NN	_	_	_
522	after	after	IN	_	_	_
523	Kanamycin	Kanamycin	NNP	_	_	_
524	-LRB-	-lrb-	-LRB-	_	_	_
525	100	100	CD	_	_	_
526	ug/ml	ug/ml	NN	_	_	_
527	-RRB-	-rrb-	-RRB-	_	_	_
528	addition	addition	NN	_	_	_
529	in	in	IN	_	_	_
530	M9	m9	NN	_	_	_
531	+	+	CC	_	_	_
532	glucose	glucose	NN	SUPP	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
534	Escherichia	escherichia	FW	Organism	_	_
535	coli	coli	FW	Organism	_	_
536	MG1655	mg1655	NN	_	_	_
537	,	,	,	_	_	_
538	15	15	CD	_	_	_
539	min	min	NN	_	_	_
540	recovery	recovery	NN	_	_	_
541	in	in	IN	_	_	_
542	10mM	10mm	NN	_	_	_
543	Na-P	na-p	NN	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	Escherichia	escherichia	FW	Organism	_	_
546	coli	coli	FW	Organism	_	_
547	MG1655	mg1655	NN	_	_	_
548	,	,	,	_	_	_
549	15	15	CD	_	_	_
550	min	min	NN	_	_	_
551	recovery	recovery	NN	_	_	_
552	in	in	IN	_	_	_
553	10mM	10mm	NN	_	_	_
554	Na-P	na-p	NN	_	_	_
555	+	+	CC	_	_	_
556	0.2	0.2	CD	_	_	_
557	%	%	NN	_	_	_
558	glucose	glucose	NN	SUPP	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
560	Escherichia	escherichia	FW	Organism	_	_
561	coli	coli	FW	Organism	_	_
562	MG1655	mg1655	NN	_	_	_
563	,	,	,	_	_	_
564	15	15	CD	_	_	_
565	min	min	NN	_	_	_
566	recovery	recovery	NN	_	_	_
567	in	in	IN	_	_	_
568	10	10	CD	_	_	_
569	mM	mm	NN	KWSUPP	_	_
570	Na-P	na-p	NN	_	_	_
571	+	+	CC	_	_	_
572	0.2	0.2	CD	_	_	_
573	%	%	NN	_	_	_
574	glucose	glucose	NN	SUPP	_	_
575	-LRB-	-lrb-	-LRB-	_	_	_
576	pH	ph	NN	_	_	_
577	7.5	7.5	CD	_	_	_
578	-RRB-	-rrb-	-RRB-	_	_	_
579	at	at	IN	_	_	_
580	OD	od	NN	_	_	_
581	0.4	0.4	CD	_	_	_
582	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
583	Escherichia	escherichia	FW	Organism	_	_
584	coli	coli	FW	Organism	_	_
585	MG1655	mg1655	NN	_	_	_
586	,	,	,	_	_	_
587	15	15	CD	_	_	_
588	min	min	NN	_	_	_
589	recovery	recovery	NN	_	_	_
590	in	in	IN	_	_	_
591	10	10	CD	_	_	_
592	mM	mm	NN	KWSUPP	_	_
593	Na-P	na-p	NN	_	_	_
594	-LRB-	-lrb-	-LRB-	_	_	_
595	pH	ph	NN	_	_	_
596	7.5	7.5	CD	_	_	_
597	-RRB-	-rrb-	-RRB-	_	_	_
598	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
599	Escherichia	escherichia	FW	Organism	_	_
600	coli	coli	FW	Organism	_	_
601	MG1655	mg1655	NN	_	_	_
602	,	,	,	_	_	_
603	15	15	CD	_	_	_
604	min	min	NN	_	_	_
605	recovery	recovery	NN	_	_	_
606	in	in	IN	_	_	_
607	LB	lb	NN	_	_	_
608	+	+	CC	_	_	_
609	glucose	glucose	NN	SUPP	_	_
610	at	at	IN	_	_	_
611	OD	od	NN	_	_	_
612	0.4	0.4	CD	_	_	_
613	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
614	Escherichia	escherichia	FW	Organism	_	_
615	coli	coli	FW	Organism	_	_
616	MG1655	mg1655	NN	_	_	_
617	,	,	,	_	_	_
618	15	15	CD	_	_	_
619	min	min	NN	_	_	_
620	recovery	recovery	NN	_	_	_
621	in	in	IN	_	_	_
622	LB	lb	NN	_	_	_
623	+	+	CC	_	_	_
624	glucose	glucose	NN	SUPP	_	_
625	at	at	IN	_	_	_
626	OD	od	NN	_	_	_
627	1.0	1.0	CD	_	_	_
628	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
629	Escherichia	escherichia	FW	Organism	_	_
630	coli	coli	FW	Organism	_	_
631	MG1655	mg1655	NN	_	_	_
632	,	,	,	_	_	_
633	163	163	CD	_	_	_
634	min	min	NN	_	_	_
635	recovery	recovery	NN	_	_	_
636	in	in	IN	_	_	_
637	LB	lb	NN	_	_	_
638	+0.2	+0.2	CD	_	_	_
639	%	%	NN	_	_	_
640	glc	glc	NN	_	_	_
641	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
642	Escherichia	escherichia	FW	Organism	_	_
643	coli	coli	FW	Organism	_	_
644	MG1655	mg1655	NN	_	_	_
645	,	,	,	_	_	_
646	191	191	CD	_	_	_
647	min	min	NN	_	_	_
648	recovery	recovery	NN	_	_	_
649	in	in	IN	_	_	_
650	LB	lb	NN	_	_	_
651	+0.2	+0.2	CD	_	_	_
652	%	%	NN	_	_	_
653	glc	glc	NN	_	_	_
654	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
655	Escherichia	escherichia	FW	Organism	_	_
656	coli	coli	FW	Organism	_	_
657	MG1655	mg1655	NN	_	_	_
658	,	,	,	_	_	_
659	20	20	CD	_	_	_
660	min	min	NN	_	_	_
661	after	after	IN	_	_	_
662	Ampicillin	Ampicillin	NNP	_	_	_
663	-LRB-	-lrb-	-LRB-	_	_	_
664	100	100	CD	_	_	_
665	ug/ml	ug/ml	NN	_	_	_
666	-RRB-	-rrb-	-RRB-	_	_	_
667	addition	addition	NN	_	_	_
668	in	in	IN	_	_	_
669	M9	m9	NN	_	_	_
670	+	+	CC	_	_	_
671	glucose	glucose	NN	SUPP	_	_
672	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
673	Escherichia	escherichia	FW	Organism	_	_
674	coli	coli	FW	Organism	_	_
675	MG1655	mg1655	NN	_	_	_
676	,	,	,	_	_	_
677	20	20	CD	_	_	_
678	min	min	NN	_	_	_
679	after	after	IN	_	_	_
680	Gamma	gamma	NN	_	_	_
681	treatment	treatment	NN	_	_	_
682	in	in	IN	_	_	_
683	Davis	Davis	NNP	_	_	_
684	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
685	Escherichia	escherichia	FW	Organism	_	_
686	coli	coli	FW	Organism	_	_
687	MG1655	mg1655	NN	_	_	_
688	,	,	,	_	_	_
689	20	20	CD	_	_	_
690	min	min	NN	_	_	_
691	after	after	IN	_	_	_
692	Kanamycin	Kanamycin	NNP	_	_	_
693	-LRB-	-lrb-	-LRB-	_	_	_
694	100	100	CD	_	_	_
695	ug/ml	ug/ml	NN	_	_	_
696	-RRB-	-rrb-	-RRB-	_	_	_
697	addition	addition	NN	_	_	_
698	in	in	IN	_	_	_
699	M9	m9	NN	_	_	_
700	+	+	CC	_	_	_
701	glucose	glucose	NN	SUPP	_	_
702	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
703	Escherichia	escherichia	FW	Organism	_	_
704	coli	coli	FW	Organism	_	_
705	MG1655	mg1655	NN	_	_	_
706	,	,	,	_	_	_
707	218	218	CD	_	_	_
708	min	min	NN	_	_	_
709	recovery	recovery	NN	_	_	_
710	in	in	IN	_	_	_
711	LB	lb	NN	_	_	_
712	+0.2	+0.2	CD	_	_	_
713	%	%	NN	_	_	_
714	glc	glc	NN	_	_	_
715	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
716	Escherichia	escherichia	FW	Organism	_	_
717	coli	coli	FW	Organism	_	_
718	MG1655	mg1655	NN	_	_	_
719	,	,	,	_	_	_
720	261	261	CD	_	_	_
721	min	min	NN	_	_	_
722	recovery	recovery	NN	_	_	_
723	in	in	IN	_	_	_
724	LB	lb	NN	_	_	_
725	+0.2	+0.2	CD	_	_	_
726	%	%	NN	_	_	_
727	glc	glc	NN	_	_	_
728	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
729	Escherichia	escherichia	FW	Organism	_	_
730	coli	coli	FW	Organism	_	_
731	MG1655	mg1655	NN	_	_	_
732	2	2	CD	_	_	_
733	minutes	minute	NNS	_	_	_
734	paraquat	paraquat	NN	SUPP	_	_
735	treatment	treatment	NN	_	_	_
736	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
737	Escherichia	escherichia	FW	Organism	_	_
738	coli	coli	FW	Organism	_	_
739	MG1655	mg1655	NN	_	_	_
740	,	,	,	_	_	_
741	30	30	CD	_	_	_
742	min	min	NN	_	_	_
743	after	after	IN	_	_	_
744	Ampicillin	Ampicillin	NNP	_	_	_
745	-LRB-	-lrb-	-LRB-	_	_	_
746	100	100	CD	_	_	_
747	ug/ml	ug/ml	NN	_	_	_
748	-RRB-	-rrb-	-RRB-	_	_	_
749	addition	addition	NN	_	_	_
750	in	in	IN	_	_	_
751	M9	m9	NN	_	_	_
752	+	+	CC	_	_	_
753	glucose	glucose	NN	SUPP	_	_
754	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
755	Escherichia	escherichia	FW	Organism	_	_
756	coli	coli	FW	Organism	_	_
757	MG1655	mg1655	NN	_	_	_
758	,	,	,	_	_	_
759	30	30	CD	_	_	_
760	min	min	NN	_	_	_
761	after	after	IN	_	_	_
762	Indol-acrylate	indol-acrylate	JJ	_	_	_
763	-LRB-	-lrb-	-LRB-	_	_	_
764	10	10	CD	_	_	_
765	ug/ml	ug/ml	NN	_	_	_
766	-RRB-	-rrb-	-RRB-	_	_	_
767	addition	addition	NN	_	_	_
768	in	in	IN	_	_	_
769	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
770	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
771	Escherichia	escherichia	FW	Organism	_	_
772	coli	coli	FW	Organism	_	_
773	MG1655	mg1655	NN	_	_	_
774	,	,	,	_	_	_
775	30	30	CD	_	_	_
776	min	min	NN	_	_	_
777	after	after	IN	_	_	_
778	Indol-acrylate	indol-acrylate	JJ	_	_	_
779	-LRB-	-lrb-	-LRB-	_	_	_
780	15	15	CD	_	_	_
781	ug/ml	ug/ml	NN	_	_	_
782	-RRB-	-rrb-	-RRB-	_	_	_
783	addition	addition	NN	_	_	_
784	in	in	IN	_	_	_
785	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
786	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
787	Escherichia	escherichia	FW	Organism	_	_
788	coli	coli	FW	Organism	_	_
789	MG1655	mg1655	NN	_	_	_
790	,	,	,	_	_	_
791	30	30	CD	_	_	_
792	min	min	NN	_	_	_
793	after	after	IN	_	_	_
794	Kanamycin	Kanamycin	NNP	_	_	_
795	-LRB-	-lrb-	-LRB-	_	_	_
796	100	100	CD	_	_	_
797	ug/ml	ug/ml	NN	_	_	_
798	-RRB-	-rrb-	-RRB-	_	_	_
799	addition	addition	NN	_	_	_
800	in	in	IN	_	_	_
801	M9	m9	NN	_	_	_
802	+	+	CC	_	_	_
803	glucose	glucose	NN	SUPP	_	_
804	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
805	Escherichia	escherichia	FW	Organism	_	_
806	coli	coli	FW	Organism	_	_
807	MG1655	mg1655	NN	_	_	_
808	,	,	,	_	_	_
809	30	30	CD	_	_	_
810	min	min	NN	_	_	_
811	recovery	recovery	NN	_	_	_
812	in	in	IN	_	_	_
813	10mM	10mm	NN	_	_	_
814	Na-P	na-p	NN	_	_	_
815	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
816	Escherichia	escherichia	FW	Organism	_	_
817	coli	coli	FW	Organism	_	_
818	MG1655	mg1655	NN	_	_	_
819	,	,	,	_	_	_
820	30	30	CD	_	_	_
821	min	min	NN	_	_	_
822	recovery	recovery	NN	_	_	_
823	in	in	IN	_	_	_
824	10mM	10mm	NN	_	_	_
825	Na-P	na-p	NN	_	_	_
826	+	+	CC	_	_	_
827	0.2	0.2	CD	_	_	_
828	%	%	NN	_	_	_
829	glucose	glucose	NN	SUPP	_	_
830	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
831	Escherichia	escherichia	FW	Organism	_	_
832	coli	coli	FW	Organism	_	_
833	MG1655	mg1655	NN	_	_	_
834	,	,	,	_	_	_
835	30	30	CD	_	_	_
836	min	min	NN	_	_	_
837	recovery	recovery	NN	_	_	_
838	in	in	IN	_	_	_
839	10	10	CD	_	_	_
840	mM	mm	NN	KWSUPP	_	_
841	Na-P	na-p	NN	_	_	_
842	+	+	CC	_	_	_
843	0.2	0.2	CD	_	_	_
844	%	%	NN	_	_	_
845	glucose	glucose	NN	SUPP	_	_
846	-LRB-	-lrb-	-LRB-	_	_	_
847	pH	ph	NN	_	_	_
848	7.5	7.5	CD	_	_	_
849	-RRB-	-rrb-	-RRB-	_	_	_
850	at	at	IN	_	_	_
851	OD	od	NN	_	_	_
852	0.4	0.4	CD	_	_	_
853	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
854	Escherichia	escherichia	FW	Organism	_	_
855	coli	coli	FW	Organism	_	_
856	MG1655	mg1655	NN	_	_	_
857	,	,	,	_	_	_
858	30	30	CD	_	_	_
859	min	min	NN	_	_	_
860	recovery	recovery	NN	_	_	_
861	in	in	IN	_	_	_
862	10	10	CD	_	_	_
863	mM	mm	NN	KWSUPP	_	_
864	Na-P	na-p	NN	_	_	_
865	-LRB-	-lrb-	-LRB-	_	_	_
866	pH	ph	NN	_	_	_
867	7.5	7.5	CD	_	_	_
868	-RRB-	-rrb-	-RRB-	_	_	_
869	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
870	Escherichia	escherichia	FW	Organism	_	_
871	coli	coli	FW	Organism	_	_
872	MG1655	mg1655	NN	_	_	_
873	,	,	,	_	_	_
874	30	30	CD	_	_	_
875	min	min	NN	_	_	_
876	recovery	recovery	NN	_	_	_
877	in	in	IN	_	_	_
878	LB	lb	NN	_	_	_
879	+	+	CC	_	_	_
880	glucose	glucose	NN	SUPP	_	_
881	at	at	IN	_	_	_
882	OD	od	NN	_	_	_
883	0.4	0.4	CD	_	_	_
884	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
885	Escherichia	escherichia	FW	Organism	_	_
886	coli	coli	FW	Organism	_	_
887	MG1655	mg1655	NN	_	_	_
888	,	,	,	_	_	_
889	30	30	CD	_	_	_
890	min	min	NN	_	_	_
891	recovery	recovery	NN	_	_	_
892	in	in	IN	_	_	_
893	LB	lb	NN	_	_	_
894	+	+	CC	_	_	_
895	glucose	glucose	NN	SUPP	_	_
896	at	at	IN	_	_	_
897	OD	od	NN	_	_	_
898	1.0	1.0	CD	_	_	_
899	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
900	Escherichia	escherichia	FW	Organism	_	_
901	coli	coli	FW	Organism	_	_
902	MG1655	mg1655	NN	_	_	_
903	,	,	,	_	_	_
904	313	313	CD	_	_	_
905	min	min	NN	_	_	_
906	recovery	recovery	NN	_	_	_
907	in	in	IN	_	_	_
908	LB	lb	NN	_	_	_
909	+0.2	+0.2	CD	_	_	_
910	%	%	NN	_	_	_
911	glc	glc	NN	_	_	_
912	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
913	Escherichia	escherichia	FW	Organism	_	_
914	coli	coli	FW	Organism	_	_
915	MG1655	mg1655	NN	_	_	_
916	,	,	,	_	_	_
917	40	40	CD	_	_	_
918	min	min	NN	_	_	_
919	after	after	IN	_	_	_
920	Ampicillin	Ampicillin	NNP	_	_	_
921	-LRB-	-lrb-	-LRB-	_	_	_
922	100	100	CD	_	_	_
923	ug/ml	ug/ml	NN	_	_	_
924	-RRB-	-rrb-	-RRB-	_	_	_
925	addition	addition	NN	_	_	_
926	in	in	IN	_	_	_
927	M9	m9	NN	_	_	_
928	+	+	CC	_	_	_
929	glucose	glucose	NN	SUPP	_	_
930	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
931	Escherichia	escherichia	FW	Organism	_	_
932	coli	coli	FW	Organism	_	_
933	MG1655	mg1655	NN	_	_	_
934	,	,	,	_	_	_
935	40	40	CD	_	_	_
936	min	min	NN	_	_	_
937	after	after	IN	_	_	_
938	Gamma	gamma	NN	_	_	_
939	treatment	treatment	NN	_	_	_
940	in	in	IN	_	_	_
941	Davis	Davis	NNP	_	_	_
942	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
943	Escherichia	escherichia	FW	Organism	_	_
944	coli	coli	FW	Organism	_	_
945	MG1655	mg1655	NN	_	_	_
946	,	,	,	_	_	_
947	40	40	CD	_	_	_
948	min	min	NN	_	_	_
949	after	after	IN	_	_	_
950	Kanamycin	Kanamycin	NNP	_	_	_
951	-LRB-	-lrb-	-LRB-	_	_	_
952	100	100	CD	_	_	_
953	ug/ml	ug/ml	NN	_	_	_
954	-RRB-	-rrb-	-RRB-	_	_	_
955	addition	addition	NN	_	_	_
956	in	in	IN	_	_	_
957	M9	m9	NN	_	_	_
958	+	+	CC	_	_	_
959	glucose	glucose	NN	SUPP	_	_
960	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
961	Escherichia	escherichia	FW	Organism	_	_
962	coli	coli	FW	Organism	_	_
963	MG1655	mg1655	NN	_	_	_
964	,	,	,	_	_	_
965	443	443	CD	_	_	_
966	min	min	NN	_	_	_
967	recovery	recovery	NN	_	_	_
968	in	in	IN	_	_	_
969	LB	lb	NN	_	_	_
970	+0.2	+0.2	CD	_	_	_
971	%	%	NN	_	_	_
972	glc	glc	NN	_	_	_
973	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
974	Escherichia	escherichia	FW	Organism	_	_
975	coli	coli	FW	Organism	_	_
976	MG1655	mg1655	NN	_	_	_
977	,	,	,	_	_	_
978	45	45	CD	_	_	_
979	min	min	NN	_	_	_
980	after	after	IN	_	_	_
981	Ampicillin	Ampicillin	NNP	_	_	_
982	-LRB-	-lrb-	-LRB-	_	_	_
983	100	100	CD	_	_	_
984	ug/ml	ug/ml	NN	_	_	_
985	-RRB-	-rrb-	-RRB-	_	_	_
986	addition	addition	NN	_	_	_
987	in	in	IN	_	_	_
988	M9	m9	NN	_	_	_
989	+	+	CC	_	_	_
990	glucose	glucose	NN	SUPP	_	_
991	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
992	Escherichia	escherichia	FW	Organism	_	_
993	coli	coli	FW	Organism	_	_
994	MG1655	mg1655	NN	_	_	_
995	,	,	,	_	_	_
996	45	45	CD	_	_	_
997	min	min	NN	_	_	_
998	after	after	IN	_	_	_
999	Kanamycin	Kanamycin	NNP	_	_	_
1000	-LRB-	-lrb-	-LRB-	_	_	_
1001	100	100	CD	_	_	_
1002	ug/ml	ug/ml	NN	_	_	_
1003	-RRB-	-rrb-	-RRB-	_	_	_
1004	addition	addition	NN	_	_	_
1005	in	in	IN	_	_	_
1006	M9	m9	NN	_	_	_
1007	+	+	CC	_	_	_
1008	glucose	glucose	NN	SUPP	_	_
1009	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1010	Escherichia	escherichia	FW	Organism	_	_
1011	coli	coli	FW	Organism	_	_
1012	MG1655	mg1655	NN	_	_	_
1013	,	,	,	_	_	_
1014	45	45	CD	_	_	_
1015	min	min	NN	_	_	_
1016	recovery	recovery	NN	_	_	_
1017	in	in	IN	_	_	_
1018	10mM	10mm	NN	_	_	_
1019	Na-P	na-p	NN	_	_	_
1020	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1021	Escherichia	escherichia	FW	Organism	_	_
1022	coli	coli	FW	Organism	_	_
1023	MG1655	mg1655	NN	_	_	_
1024	,	,	,	_	_	_
1025	45	45	CD	_	_	_
1026	min	min	NN	_	_	_
1027	recovery	recovery	NN	_	_	_
1028	in	in	IN	_	_	_
1029	10mM	10mm	NN	_	_	_
1030	Na-P	na-p	NN	_	_	_
1031	+	+	CC	_	_	_
1032	0.2	0.2	CD	_	_	_
1033	%	%	NN	_	_	_
1034	glucose	glucose	NN	SUPP	_	_
1035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1036	Escherichia	escherichia	FW	Organism	_	_
1037	coli	coli	FW	Organism	_	_
1038	MG1655	mg1655	NN	_	_	_
1039	,	,	,	_	_	_
1040	45	45	CD	_	_	_
1041	min	min	NN	_	_	_
1042	recovery	recovery	NN	_	_	_
1043	in	in	IN	_	_	_
1044	10	10	CD	_	_	_
1045	mM	mm	NN	KWSUPP	_	_
1046	Na-P	na-p	NN	_	_	_
1047	+	+	CC	_	_	_
1048	0.2	0.2	CD	_	_	_
1049	%	%	NN	_	_	_
1050	glucose	glucose	NN	SUPP	_	_
1051	-LRB-	-lrb-	-LRB-	_	_	_
1052	pH	ph	NN	_	_	_
1053	7.5	7.5	CD	_	_	_
1054	-RRB-	-rrb-	-RRB-	_	_	_
1055	at	at	IN	_	_	_
1056	OD	od	NN	_	_	_
1057	0.4	0.4	CD	_	_	_
1058	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1059	Escherichia	escherichia	FW	Organism	_	_
1060	coli	coli	FW	Organism	_	_
1061	MG1655	mg1655	NN	_	_	_
1062	,	,	,	_	_	_
1063	45	45	CD	_	_	_
1064	min	min	NN	_	_	_
1065	recovery	recovery	NN	_	_	_
1066	in	in	IN	_	_	_
1067	10	10	CD	_	_	_
1068	mM	mm	NN	KWSUPP	_	_
1069	Na-P	na-p	NN	_	_	_
1070	-LRB-	-lrb-	-LRB-	_	_	_
1071	pH	ph	NN	_	_	_
1072	7.5	7.5	CD	_	_	_
1073	-RRB-	-rrb-	-RRB-	_	_	_
1074	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1075	Escherichia	escherichia	FW	Organism	_	_
1076	coli	coli	FW	Organism	_	_
1077	MG1655	mg1655	NN	_	_	_
1078	,	,	,	_	_	_
1079	45	45	CD	_	_	_
1080	min	min	NN	_	_	_
1081	recovery	recovery	NN	_	_	_
1082	in	in	IN	_	_	_
1083	LB	lb	NN	_	_	_
1084	+	+	CC	_	_	_
1085	glucose	glucose	NN	SUPP	_	_
1086	at	at	IN	_	_	_
1087	OD	od	NN	_	_	_
1088	0.4	0.4	CD	_	_	_
1089	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1090	Escherichia	escherichia	FW	Organism	_	_
1091	coli	coli	FW	Organism	_	_
1092	MG1655	mg1655	NN	_	_	_
1093	,	,	,	_	_	_
1094	45	45	CD	_	_	_
1095	min	min	NN	_	_	_
1096	recovery	recovery	NN	_	_	_
1097	in	in	IN	_	_	_
1098	LB	lb	NN	_	_	_
1099	+	+	CC	_	_	_
1100	glucose	glucose	NN	SUPP	_	_
1101	at	at	IN	_	_	_
1102	OD	od	NN	_	_	_
1103	1.0	1.0	CD	_	_	_
1104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1105	Escherichia	escherichia	FW	Organism	_	_
1106	coli	coli	FW	Organism	_	_
1107	MG1655	mg1655	NN	_	_	_
1108	4	4	CD	_	_	_
1109	minutes	minute	NNS	_	_	_
1110	paraquat	paraquat	NN	SUPP	_	_
1111	treatment	treatment	NN	_	_	_
1112	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1113	Escherichia	escherichia	FW	Organism	_	_
1114	coli	coli	FW	Organism	_	_
1115	MG1655	mg1655	NN	_	_	_
1116	,	,	,	_	_	_
1117	50	50	CD	_	_	_
1118	min	min	NN	_	_	_
1119	after	after	IN	_	_	_
1120	Ampicillin	Ampicillin	NNP	_	_	_
1121	-LRB-	-lrb-	-LRB-	_	_	_
1122	100	100	CD	_	_	_
1123	ug/ml	ug/ml	NN	_	_	_
1124	-RRB-	-rrb-	-RRB-	_	_	_
1125	addition	addition	NN	_	_	_
1126	in	in	IN	_	_	_
1127	M9	m9	NN	_	_	_
1128	+	+	CC	_	_	_
1129	glucose	glucose	NN	SUPP	_	_
1130	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
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/ml	ug/ml	NN	_	_	_
1142	-RRB-	-rrb-	-RRB-	_	_	_
1143	addition	addition	NN	_	_	_
1144	in	in	IN	_	_	_
1145	M9	m9	NN	_	_	_
1146	+	+	CC	_	_	_
1147	glucose	glucose	NN	SUPP	_	_
1148	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1149	Escherichia	escherichia	FW	Organism	_	_
1150	coli	coli	FW	Organism	_	_
1151	MG1655	mg1655	NN	_	_	_
1152	,	,	,	_	_	_
1153	5	5	CD	_	_	_
1154	min	min	NN	_	_	_
1155	after	after	IN	_	_	_
1156	Ampicillin	Ampicillin	NNP	_	_	_
1157	-LRB-	-lrb-	-LRB-	_	_	_
1158	100	100	CD	_	_	_
1159	ug/ml	ug/ml	NN	_	_	_
1160	-RRB-	-rrb-	-RRB-	_	_	_
1161	addition	addition	NN	_	_	_
1162	in	in	IN	_	_	_
1163	M9	m9	NN	_	_	_
1164	+	+	CC	_	_	_
1165	glucose	glucose	NN	SUPP	_	_
1166	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1167	Escherichia	escherichia	FW	Organism	_	_
1168	coli	coli	FW	Organism	_	_
1169	MG1655	mg1655	NN	_	_	_
1170	,	,	,	_	_	_
1171	5	5	CD	_	_	_
1172	min	min	NN	_	_	_
1173	after	after	IN	_	_	_
1174	Gamma	gamma	NN	_	_	_
1175	treatment	treatment	NN	_	_	_
1176	in	in	IN	_	_	_
1177	Davis	Davis	NNP	_	_	_
1178	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1179	Escherichia	escherichia	FW	Organism	_	_
1180	coli	coli	FW	Organism	_	_
1181	MG1655	mg1655	NN	_	_	_
1182	,	,	,	_	_	_
1183	5	5	CD	_	_	_
1184	min	min	NN	_	_	_
1185	after	after	IN	_	_	_
1186	Indol-acrylate	indol-acrylate	JJ	_	_	_
1187	-LRB-	-lrb-	-LRB-	_	_	_
1188	10	10	CD	_	_	_
1189	ug/ml	ug/ml	NN	_	_	_
1190	-RRB-	-rrb-	-RRB-	_	_	_
1191	addition	addition	NN	_	_	_
1192	in	in	IN	_	_	_
1193	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1194	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1195	Escherichia	escherichia	FW	Organism	_	_
1196	coli	coli	FW	Organism	_	_
1197	MG1655	mg1655	NN	_	_	_
1198	,	,	,	_	_	_
1199	5	5	CD	_	_	_
1200	min	min	NN	_	_	_
1201	after	after	IN	_	_	_
1202	Indol-acrylate	indol-acrylate	JJ	_	_	_
1203	-LRB-	-lrb-	-LRB-	_	_	_
1204	15	15	CD	_	_	_
1205	ug/ml	ug/ml	NN	_	_	_
1206	-RRB-	-rrb-	-RRB-	_	_	_
1207	addition	addition	NN	_	_	_
1208	in	in	IN	_	_	_
1209	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1210	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1211	Escherichia	escherichia	FW	Organism	_	_
1212	coli	coli	FW	Organism	_	_
1213	MG1655	mg1655	NN	_	_	_
1214	,	,	,	_	_	_
1215	5	5	CD	_	_	_
1216	min	min	NN	_	_	_
1217	after	after	IN	_	_	_
1218	Kanamycin	Kanamycin	NNP	_	_	_
1219	-LRB-	-lrb-	-LRB-	_	_	_
1220	100	100	CD	_	_	_
1221	ug/ml	ug/ml	NN	_	_	_
1222	-RRB-	-rrb-	-RRB-	_	_	_
1223	addition	addition	NN	_	_	_
1224	in	in	IN	_	_	_
1225	M9	m9	NN	_	_	_
1226	+	+	CC	_	_	_
1227	glucose	glucose	NN	SUPP	_	_
1228	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1229	Escherichia	escherichia	FW	Organism	_	_
1230	coli	coli	FW	Organism	_	_
1231	MG1655	mg1655	NN	_	_	_
1232	,	,	,	_	_	_
1233	60	60	CD	_	_	_
1234	min	min	NN	_	_	_
1235	after	after	IN	_	_	_
1236	Ampicillin	Ampicillin	NNP	_	_	_
1237	-LRB-	-lrb-	-LRB-	_	_	_
1238	100	100	CD	_	_	_
1239	ug/ml	ug/ml	NN	_	_	_
1240	-RRB-	-rrb-	-RRB-	_	_	_
1241	addition	addition	NN	_	_	_
1242	in	in	IN	_	_	_
1243	M9	m9	NN	_	_	_
1244	+	+	CC	_	_	_
1245	glucose	glucose	NN	SUPP	_	_
1246	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1247	Escherichia	escherichia	FW	Organism	_	_
1248	coli	coli	FW	Organism	_	_
1249	MG1655	mg1655	NN	_	_	_
1250	,	,	,	_	_	_
1251	60	60	CD	_	_	_
1252	min	min	NN	_	_	_
1253	after	after	IN	_	_	_
1254	Gamma	gamma	NN	_	_	_
1255	treatment	treatment	NN	_	_	_
1256	in	in	IN	_	_	_
1257	Davis	Davis	NNP	_	_	_
1258	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1259	Escherichia	escherichia	FW	Organism	_	_
1260	coli	coli	FW	Organism	_	_
1261	MG1655	mg1655	NN	_	_	_
1262	,	,	,	_	_	_
1263	60	60	CD	_	_	_
1264	min	min	NN	_	_	_
1265	after	after	IN	_	_	_
1266	Indol-acrylate	indol-acrylate	JJ	_	_	_
1267	-LRB-	-lrb-	-LRB-	_	_	_
1268	10	10	CD	_	_	_
1269	ug/ml	ug/ml	NN	_	_	_
1270	-RRB-	-rrb-	-RRB-	_	_	_
1271	addition	addition	NN	_	_	_
1272	in	in	IN	_	_	_
1273	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1274	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1275	Escherichia	escherichia	FW	Organism	_	_
1276	coli	coli	FW	Organism	_	_
1277	MG1655	mg1655	NN	_	_	_
1278	,	,	,	_	_	_
1279	60	60	CD	_	_	_
1280	min	min	NN	_	_	_
1281	after	after	IN	_	_	_
1282	Indol-acrylate	indol-acrylate	JJ	_	_	_
1283	-LRB-	-lrb-	-LRB-	_	_	_
1284	15	15	CD	_	_	_
1285	ug/ml	ug/ml	NN	_	_	_
1286	-RRB-	-rrb-	-RRB-	_	_	_
1287	addition	addition	NN	_	_	_
1288	in	in	IN	_	_	_
1289	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1290	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1291	Escherichia	escherichia	FW	Organism	_	_
1292	coli	coli	FW	Organism	_	_
1293	MG1655	mg1655	NN	_	_	_
1294	,	,	,	_	_	_
1295	60	60	CD	_	_	_
1296	min	min	NN	_	_	_
1297	after	after	IN	_	_	_
1298	Kanamycin	Kanamycin	NNP	_	_	_
1299	-LRB-	-lrb-	-LRB-	_	_	_
1300	100	100	CD	_	_	_
1301	ug/ml	ug/ml	NN	_	_	_
1302	-RRB-	-rrb-	-RRB-	_	_	_
1303	addition	addition	NN	_	_	_
1304	in	in	IN	_	_	_
1305	M9	m9	NN	_	_	_
1306	+	+	CC	_	_	_
1307	glucose	glucose	NN	SUPP	_	_
1308	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1309	Escherichia	escherichia	FW	Organism	_	_
1310	coli	coli	FW	Organism	_	_
1311	MG1655	mg1655	NN	_	_	_
1312	,	,	,	_	_	_
1313	60	60	CD	_	_	_
1314	min	min	NN	_	_	_
1315	recovery	recovery	NN	_	_	_
1316	in	in	IN	_	_	_
1317	10mM	10mm	NN	_	_	_
1318	Na-P	na-p	NN	_	_	_
1319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1320	Escherichia	escherichia	FW	Organism	_	_
1321	coli	coli	FW	Organism	_	_
1322	MG1655	mg1655	NN	_	_	_
1323	,	,	,	_	_	_
1324	60	60	CD	_	_	_
1325	min	min	NN	_	_	_
1326	recovery	recovery	NN	_	_	_
1327	in	in	IN	_	_	_
1328	10mM	10mm	NN	_	_	_
1329	Na-P	na-p	NN	_	_	_
1330	+	+	CC	_	_	_
1331	0.2	0.2	CD	_	_	_
1332	%	%	NN	_	_	_
1333	glucose	glucose	NN	SUPP	_	_
1334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1335	Escherichia	escherichia	FW	Organism	_	_
1336	coli	coli	FW	Organism	_	_
1337	MG1655	mg1655	NN	_	_	_
1338	,	,	,	_	_	_
1339	60	60	CD	_	_	_
1340	min	min	NN	_	_	_
1341	recovery	recovery	NN	_	_	_
1342	in	in	IN	_	_	_
1343	10	10	CD	_	_	_
1344	mM	mm	NN	KWSUPP	_	_
1345	Na-P	na-p	NN	_	_	_
1346	+	+	CC	_	_	_
1347	0.2	0.2	CD	_	_	_
1348	%	%	NN	_	_	_
1349	glucose	glucose	NN	SUPP	_	_
1350	-LRB-	-lrb-	-LRB-	_	_	_
1351	pH	ph	NN	_	_	_
1352	7.5	7.5	CD	_	_	_
1353	-RRB-	-rrb-	-RRB-	_	_	_
1354	at	at	IN	_	_	_
1355	OD	od	NN	_	_	_
1356	0.4	0.4	CD	_	_	_
1357	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1358	Escherichia	escherichia	FW	Organism	_	_
1359	coli	coli	FW	Organism	_	_
1360	MG1655	mg1655	NN	_	_	_
1361	,	,	,	_	_	_
1362	60	60	CD	_	_	_
1363	min	min	NN	_	_	_
1364	recovery	recovery	NN	_	_	_
1365	in	in	IN	_	_	_
1366	10	10	CD	_	_	_
1367	mM	mm	NN	KWSUPP	_	_
1368	Na-P	na-p	NN	_	_	_
1369	-LRB-	-lrb-	-LRB-	_	_	_
1370	pH	ph	NN	_	_	_
1371	7.5	7.5	CD	_	_	_
1372	-RRB-	-rrb-	-RRB-	_	_	_
1373	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1374	Escherichia	escherichia	FW	Organism	_	_
1375	coli	coli	FW	Organism	_	_
1376	MG1655	mg1655	NN	_	_	_
1377	,	,	,	_	_	_
1378	60	60	CD	_	_	_
1379	min	min	NN	_	_	_
1380	recovery	recovery	NN	_	_	_
1381	in	in	IN	_	_	_
1382	LB	lb	NN	_	_	_
1383	+	+	CC	_	_	_
1384	glucose	glucose	NN	SUPP	_	_
1385	at	at	IN	_	_	_
1386	OD	od	NN	_	_	_
1387	0.4	0.4	CD	_	_	_
1388	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1389	Escherichia	escherichia	FW	Organism	_	_
1390	coli	coli	FW	Organism	_	_
1391	MG1655	mg1655	NN	_	_	_
1392	,	,	,	_	_	_
1393	60	60	CD	_	_	_
1394	min	min	NN	_	_	_
1395	recovery	recovery	NN	_	_	_
1396	in	in	IN	_	_	_
1397	LB	lb	NN	_	_	_
1398	+	+	CC	_	_	_
1399	glucose	glucose	NN	SUPP	_	_
1400	at	at	IN	_	_	_
1401	OD	od	NN	_	_	_
1402	1.0	1.0	CD	_	_	_
1403	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1404	Escherichia	escherichia	FW	Organism	_	_
1405	coli	coli	FW	Organism	_	_
1406	MG1655	mg1655	NN	_	_	_
1407	6	6	CD	_	_	_
1408	minutes	minute	NNS	_	_	_
1409	paraquat	paraquat	NN	SUPP	_	_
1410	treatment	treatment	NN	_	_	_
1411	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1412	Escherichia	escherichia	FW	Organism	_	_
1413	coli	coli	FW	Organism	_	_
1414	MG1655	mg1655	NN	_	_	_
1415	,	,	,	_	_	_
1416	75	75	CD	_	_	_
1417	min	min	NN	_	_	_
1418	after	after	IN	_	_	_
1419	Ampicillin	Ampicillin	NNP	_	_	_
1420	-LRB-	-lrb-	-LRB-	_	_	_
1421	100	100	CD	_	_	_
1422	ug/ml	ug/ml	NN	_	_	_
1423	-RRB-	-rrb-	-RRB-	_	_	_
1424	addition	addition	NN	_	_	_
1425	in	in	IN	_	_	_
1426	M9	m9	NN	_	_	_
1427	+	+	CC	_	_	_
1428	glucose	glucose	NN	SUPP	_	_
1429	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1430	Escherichia	escherichia	FW	Organism	_	_
1431	coli	coli	FW	Organism	_	_
1432	MG1655	mg1655	NN	_	_	_
1433	,	,	,	_	_	_
1434	75	75	CD	_	_	_
1435	min	min	NN	_	_	_
1436	after	after	IN	_	_	_
1437	Kanamycin	Kanamycin	NNP	_	_	_
1438	-LRB-	-lrb-	-LRB-	_	_	_
1439	100	100	CD	_	_	_
1440	ug/ml	ug/ml	NN	_	_	_
1441	-RRB-	-rrb-	-RRB-	_	_	_
1442	addition	addition	NN	_	_	_
1443	in	in	IN	_	_	_
1444	M9	m9	NN	_	_	_
1445	+	+	CC	_	_	_
1446	glucose	glucose	NN	SUPP	_	_
1447	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1448	Escherichia	escherichia	FW	Organism	_	_
1449	coli	coli	FW	Organism	_	_
1450	MG1655	mg1655	NN	_	_	_
1451	,	,	,	_	_	_
1452	75	75	CD	_	_	_
1453	min	min	NN	_	_	_
1454	recovery	recovery	NN	_	_	_
1455	in	in	IN	_	_	_
1456	10mM	10mm	NN	_	_	_
1457	Na-P	na-p	NN	_	_	_
1458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1459	Escherichia	escherichia	FW	Organism	_	_
1460	coli	coli	FW	Organism	_	_
1461	MG1655	mg1655	NN	_	_	_
1462	,	,	,	_	_	_
1463	75	75	CD	_	_	_
1464	min	min	NN	_	_	_
1465	recovery	recovery	NN	_	_	_
1466	in	in	IN	_	_	_
1467	10mM	10mm	NN	_	_	_
1468	Na-P	na-p	NN	_	_	_
1469	+	+	CC	_	_	_
1470	0.2	0.2	CD	_	_	_
1471	%	%	NN	_	_	_
1472	glucose	glucose	NN	SUPP	_	_
1473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1474	Escherichia	escherichia	FW	Organism	_	_
1475	coli	coli	FW	Organism	_	_
1476	MG1655	mg1655	NN	_	_	_
1477	,	,	,	_	_	_
1478	75	75	CD	_	_	_
1479	min	min	NN	_	_	_
1480	recovery	recovery	NN	_	_	_
1481	in	in	IN	_	_	_
1482	10	10	CD	_	_	_
1483	mM	mm	NN	KWSUPP	_	_
1484	Na-P	na-p	NN	_	_	_
1485	+	+	CC	_	_	_
1486	0.2	0.2	CD	_	_	_
1487	%	%	NN	_	_	_
1488	glucose	glucose	NN	SUPP	_	_
1489	-LRB-	-lrb-	-LRB-	_	_	_
1490	pH	ph	NN	_	_	_
1491	7.5	7.5	CD	_	_	_
1492	-RRB-	-rrb-	-RRB-	_	_	_
1493	at	at	IN	_	_	_
1494	OD	od	NN	_	_	_
1495	0.4	0.4	CD	_	_	_
1496	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1497	Escherichia	escherichia	FW	Organism	_	_
1498	coli	coli	FW	Organism	_	_
1499	MG1655	mg1655	NN	_	_	_
1500	,	,	,	_	_	_
1501	75	75	CD	_	_	_
1502	min	min	NN	_	_	_
1503	recovery	recovery	NN	_	_	_
1504	in	in	IN	_	_	_
1505	10	10	CD	_	_	_
1506	mM	mm	NN	KWSUPP	_	_
1507	Na-P	na-p	NN	_	_	_
1508	-LRB-	-lrb-	-LRB-	_	_	_
1509	pH	ph	NN	_	_	_
1510	7.5	7.5	CD	_	_	_
1511	-RRB-	-rrb-	-RRB-	_	_	_
1512	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1513	Escherichia	escherichia	FW	Organism	_	_
1514	coli	coli	FW	Organism	_	_
1515	MG1655	mg1655	NN	_	_	_
1516	,	,	,	_	_	_
1517	75	75	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	0.4	0.4	CD	_	_	_
1527	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1528	Escherichia	escherichia	FW	Organism	_	_
1529	coli	coli	FW	Organism	_	_
1530	MG1655	mg1655	NN	_	_	_
1531	,	,	,	_	_	_
1532	75	75	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	78	78	CD	_	_	_
1548	min	min	NN	_	_	_
1549	recovery	recovery	NN	_	_	_
1550	in	in	IN	_	_	_
1551	LB	lb	NN	_	_	_
1552	+0.2	+0.2	CD	_	_	_
1553	%	%	NN	_	_	_
1554	glc	glc	NN	_	_	_
1555	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1556	Escherichia	escherichia	FW	Organism	_	_
1557	coli	coli	FW	Organism	_	_
1558	MG1655	mg1655	NN	_	_	_
1559	8	8	CD	_	_	_
1560	minutes	minute	NNS	_	_	_
1561	paraquat	paraquat	NN	SUPP	_	_
1562	treatment	treatment	NN	_	_	_
1563	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1564	Escherichia	escherichia	FW	Organism	_	_
1565	coli	coli	FW	Organism	_	_
1566	MG1655	mg1655	NN	_	_	_
1567	,	,	,	_	_	_
1568	90	90	CD	_	_	_
1569	min	min	NN	_	_	_
1570	recovery	recovery	NN	_	_	_
1571	in	in	IN	_	_	_
1572	10mM	10mm	NN	_	_	_
1573	Na-P	na-p	NN	_	_	_
1574	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1575	Escherichia	escherichia	FW	Organism	_	_
1576	coli	coli	FW	Organism	_	_
1577	MG1655	mg1655	NN	_	_	_
1578	,	,	,	_	_	_
1579	90	90	CD	_	_	_
1580	min	min	NN	_	_	_
1581	recovery	recovery	NN	_	_	_
1582	in	in	IN	_	_	_
1583	10mM	10mm	NN	_	_	_
1584	Na-P	na-p	NN	_	_	_
1585	+	+	CC	_	_	_
1586	0.2	0.2	CD	_	_	_
1587	%	%	NN	_	_	_
1588	glucose	glucose	NN	SUPP	_	_
1589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1590	Escherichia	escherichia	FW	Organism	_	_
1591	coli	coli	FW	Organism	_	_
1592	MG1655	mg1655	NN	_	_	_
1593	,	,	,	_	_	_
1594	90	90	CD	_	_	_
1595	min	min	NN	_	_	_
1596	recovery	recovery	NN	_	_	_
1597	in	in	IN	_	_	_
1598	10	10	CD	_	_	_
1599	mM	mm	NN	KWSUPP	_	_
1600	Na-P	na-p	NN	_	_	_
1601	+	+	CC	_	_	_
1602	0.2	0.2	CD	_	_	_
1603	%	%	NN	_	_	_
1604	glucose	glucose	NN	SUPP	_	_
1605	-LRB-	-lrb-	-LRB-	_	_	_
1606	pH	ph	NN	_	_	_
1607	7.5	7.5	CD	_	_	_
1608	-RRB-	-rrb-	-RRB-	_	_	_
1609	at	at	IN	_	_	_
1610	OD	od	NN	_	_	_
1611	0.4	0.4	CD	_	_	_
1612	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1613	Escherichia	escherichia	FW	Organism	_	_
1614	coli	coli	FW	Organism	_	_
1615	MG1655	mg1655	NN	_	_	_
1616	,	,	,	_	_	_
1617	90	90	CD	_	_	_
1618	min	min	NN	_	_	_
1619	recovery	recovery	NN	_	_	_
1620	in	in	IN	_	_	_
1621	10	10	CD	_	_	_
1622	mM	mm	NN	KWSUPP	_	_
1623	Na-P	na-p	NN	_	_	_
1624	-LRB-	-lrb-	-LRB-	_	_	_
1625	pH	ph	NN	_	_	_
1626	7.5	7.5	CD	_	_	_
1627	-RRB-	-rrb-	-RRB-	_	_	_
1628	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1629	Escherichia	escherichia	FW	Organism	_	_
1630	coli	coli	FW	Organism	_	_
1631	MG1655	mg1655	NN	_	_	_
1632	,	,	,	_	_	_
1633	90	90	CD	_	_	_
1634	min	min	NN	_	_	_
1635	recovery	recovery	NN	_	_	_
1636	in	in	IN	_	_	_
1637	LB	lb	NN	_	_	_
1638	+	+	CC	_	_	_
1639	glucose	glucose	NN	SUPP	_	_
1640	at	at	IN	_	_	_
1641	OD	od	NN	_	_	_
1642	0.4	0.4	CD	_	_	_
1643	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1644	Escherichia	escherichia	FW	Organism	_	_
1645	coli	coli	FW	Organism	_	_
1646	MG1655	mg1655	NN	_	_	_
1647	,	,	,	_	_	_
1648	90	90	CD	_	_	_
1649	min	min	NN	_	_	_
1650	recovery	recovery	NN	_	_	_
1651	in	in	IN	_	_	_
1652	LB	lb	NN	_	_	_
1653	+	+	CC	_	_	_
1654	glucose	glucose	NN	SUPP	_	_
1655	at	at	IN	_	_	_
1656	OD	od	NN	_	_	_
1657	1.0	1.0	CD	_	_	_
1658	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1659	Escherichia	escherichia	FW	Organism	_	_
1660	coli	coli	FW	Organism	_	_
1661	MG1655	mg1655	NN	_	_	_
1662	Aerobic	aerobic	JJ	_	_	_
1663	growth	growth	NN	_	_	_
1664	OD	od	NN	_	_	_
1665	0.4	0.4	CD	_	_	_
1666	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1667	Escherichia	escherichia	FW	Organism	_	_
1668	coli	coli	FW	Organism	_	_
1669	MG1655	mg1655	NN	_	_	_
1670	Aerobic	aerobic	JJ	_	_	_
1671	growth	growth	NN	_	_	_
1672	on	on	IN	_	_	_
1673	M9	m9	NN	_	_	_
1674	+	+	CC	_	_	_
1675	glucose	glucose	NN	SUPP	_	_
1676	+	+	CC	_	_	_
1677	fumarate	fumarate	NN	SUPP	_	_
1678	,	,	,	_	_	_
1679	OD	od	NN	_	_	_
1680	0.4	0.4	CD	_	_	_
1681	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1682	Escherichia	escherichia	FW	Organism	_	_
1683	coli	coli	FW	Organism	_	_
1684	MG1655	mg1655	NN	_	_	_
1685	Aerobic	aerobic	JJ	_	_	_
1686	growth	growth	NN	_	_	_
1687	on	on	IN	_	_	_
1688	M9	m9	NN	_	_	_
1689	+	+	CC	_	_	_
1690	glucose	glucose	NN	SUPP	_	_
1691	,	,	,	_	_	_
1692	OD	od	NN	_	_	_
1693	0.4	0.4	CD	_	_	_
1694	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1695	Escherichia	escherichia	FW	Organism	_	_
1696	coli	coli	FW	Organism	_	_
1697	MG1655	mg1655	NN	_	_	_
1698	after	after	IN	_	_	_
1699	30	30	CD	_	_	_
1700	min	min	NN	_	_	_
1701	incubation	incubation	NN	_	_	_
1702	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1703	Escherichia	escherichia	FW	Organism	_	_
1704	coli	coli	FW	Organism	_	_
1705	MG1655	mg1655	NN	_	_	_
1706	after	after	IN	_	_	_
1707	30	30	CD	_	_	_
1708	min	min	NN	_	_	_
1709	incubation	incubation	NN	_	_	_
1710	following	follow	VBG	_	_	_
1711	colicin	colicin	NN	_	_	_
1712	M	m	NN	_	_	_
1713	treatment	treatment	NN	_	_	_
1714	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1715	Escherichia	escherichia	FW	Organism	_	_
1716	coli	coli	FW	Organism	_	_
1717	MG1655	mg1655	NN	_	_	_
1718	after	after	IN	_	_	_
1719	60	60	CD	_	_	_
1720	min	min	NN	_	_	_
1721	incubation	incubation	NN	_	_	_
1722	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1723	Escherichia	escherichia	FW	Organism	_	_
1724	coli	coli	FW	Organism	_	_
1725	MG1655	mg1655	NN	_	_	_
1726	after	after	IN	_	_	_
1727	60	60	CD	_	_	_
1728	min	min	NN	_	_	_
1729	incubation	incubation	NN	_	_	_
1730	following	follow	VBG	_	_	_
1731	colicin	colicin	NN	_	_	_
1732	M	m	NN	_	_	_
1733	treatment	treatment	NN	_	_	_
1734	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1735	Escherichia	escherichia	FW	Organism	_	_
1736	coli	coli	FW	Organism	_	_
1737	MG1655	mg1655	NN	_	_	_
1738	before	before	IN	_	_	_
1739	paraquat	paraquat	NN	SUPP	_	_
1740	treatment	treatment	NN	_	_	_
1741	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1742	Escherichia	escherichia	FW	Organism	_	_
1743	coli	coli	FW	Organism	_	_
1744	MG1655	mg1655	NN	_	_	_
1745	,	,	,	_	_	_
1746	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1747	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1748	Escherichia	escherichia	FW	Organism	_	_
1749	coli	coli	FW	Organism	_	_
1750	MG1655	mg1655	NN	_	_	_
1751	,	,	,	_	_	_
1752	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1753	,	,	,	_	_	_
1754	0	0	CD	_	_	_
1755	min	min	NN	_	_	_
1756	before	before	IN	_	_	_
1757	treatment	treatment	NN	_	_	_
1758	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1759	Escherichia	escherichia	FW	Organism	_	_
1760	coli	coli	FW	Organism	_	_
1761	MG1655	mg1655	NN	_	_	_
1762	,	,	,	_	_	_
1763	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1764	OD	OD	NNP	_	_	_
1765	~	~	NNP	_	_	_
1766	0.5	0.5	CD	_	_	_
1767	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1768	Escherichia	escherichia	FW	Organism	_	_
1769	coli	coli	FW	Organism	_	_
1770	MG1655	mg1655	NN	_	_	_
1771	cells	cell	NNS	_	_	_
1772	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1773	Escherichia	escherichia	FW	Organism	_	_
1774	coli	coli	FW	Organism	_	_
1775	MG1655	mg1655	NN	_	_	_
1776	cells	cell	NNS	_	_	_
1777	grown	grow	VBN	_	_	_
1778	in	in	IN	_	_	_
1779	the	the	DT	_	_	_
1780	hydroponic	hydroponic	JJ	_	_	_
1781	system	system	NN	_	_	_
1782	without	without	IN	_	_	_
1783	interacting	interact	VBG	_	_	_
1784	with	with	IN	_	_	_
1785	the	the	DT	_	_	_
1786	lettuce	lettuce	NN	_	_	_
1787	rhizosphere	rhizosphere	NN	_	_	_
1788	for	for	IN	_	_	_
1789	3	3	CD	_	_	_
1790	days	day	NNS	_	_	_
1791	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1792	Escherichia	escherichia	FW	Organism	_	_
1793	coli	coli	FW	Organism	_	_
1794	MG1655	mg1655	NN	_	_	_
1795	cells	cell	NNS	_	_	_
1796	interacted	interact	VBD	_	_	_
1797	with	with	IN	_	_	_
1798	the	the	DT	_	_	_
1799	lettuce	lettuce	NN	_	_	_
1800	rhizosphere	rhizosphere	NN	_	_	_
1801	for	for	IN	_	_	_
1802	3	3	CD	_	_	_
1803	days	day	NNS	_	_	_
1804	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1805	Escherichia	escherichia	FW	Organism	_	_
1806	coli	coli	FW	Organism	_	_
1807	MG1655	mg1655	NN	_	_	_
1808	,	,	,	_	_	_
1809	Davis	Davis	NNP	_	_	_
1810	,	,	,	_	_	_
1811	0	0	CD	_	_	_
1812	min	min	NN	_	_	_
1813	before	before	IN	_	_	_
1814	treatment	treatment	NN	_	_	_
1815	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1816	Escherichia	escherichia	FW	Organism	_	_
1817	coli	coli	FW	Organism	_	_
1818	MG1655	mg1655	NN	_	_	_
1819	fis	fis	NN	GEN	_	_
1820	:	:	:	_	_	_
1821	:	:	:	_	_	_
1822	kan	kan	NN	_	_	_
1823	grown	grow	VBN	_	_	_
1824	150	150	CD	_	_	_
1825	minutes	minute	NNS	_	_	_
1826	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1827	Escherichia	escherichia	FW	Organism	_	_
1828	coli	coli	FW	Organism	_	_
1829	MG1655	mg1655	NN	_	_	_
1830	fis	fis	NN	GEN	_	_
1831	:	:	:	_	_	_
1832	:	:	:	_	_	_
1833	kan	kan	NN	_	_	_
1834	grown	grow	VBN	_	_	_
1835	240	240	CD	_	_	_
1836	minutes	minute	NNS	_	_	_
1837	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1838	Escherichia	escherichia	FW	Organism	_	_
1839	coli	coli	FW	Organism	_	_
1840	MG1655	mg1655	NN	_	_	_
1841	fis	fis	NN	GEN	_	_
1842	:	:	:	_	_	_
1843	:	:	:	_	_	_
1844	kan	kan	NN	_	_	_
1845	grown	grow	VBN	_	_	_
1846	360	360	CD	_	_	_
1847	minutes	minute	NNS	_	_	_
1848	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1849	Escherichia	escherichia	FW	Organism	_	_
1850	coli	coli	FW	Organism	_	_
1851	MG1655	mg1655	NN	_	_	_
1852	fis	fis	NN	GEN	_	_
1853	:	:	:	_	_	_
1854	:	:	:	_	_	_
1855	kan	kan	NN	_	_	_
1856	grown	grow	VBN	_	_	_
1857	90	90	CD	_	_	_
1858	minutes	minute	NNS	_	_	_
1859	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1860	Escherichia	escherichia	FW	Organism	_	_
1861	coli	coli	FW	Organism	_	_
1862	MG1655	mg1655	NN	_	_	_
1863	genomic	genomic	JJ	_	_	_
1864	DNA	dna	NN	_	_	_
1865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1866	Escherichia	escherichia	FW	Organism	_	_
1867	coli	coli	FW	Organism	_	_
1868	MG1655	mg1655	NN	_	_	_
1869	K-12	k-12	NN	_	_	_
1870	dFNR	dfnr	NN	_	_	_
1871	-LRB-	-lrb-	-LRB-	_	_	_
1872	PK4854	pk4854	NN	_	_	_
1873	-RRB-	-rrb-	-RRB-	_	_	_
1874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1875	Escherichia	escherichia	FW	Organism	_	_
1876	coli	coli	FW	Organism	_	_
1877	MG1655	mg1655	NN	_	_	_
1878	K-12	k-12	NN	_	_	_
1879	WT	WT	NNP	_	_	_
1880	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1881	Escherichia	escherichia	FW	Organism	_	_
1882	coli	coli	FW	Organism	_	_
1883	MG1655	mg1655	NN	_	_	_
1884	K-12	k-12	NN	_	_	_
1885	WT	wt	NN	_	_	_
1886	and	and	CC	_	_	_
1887	∆	∆	NN	_	_	_
1888	fnr	fnr	NN	GEN	_	_
1889	were	be	VBD	_	_	_
1890	grown	grow	VBN	_	_	_
1891	to	to	TO	_	_	_
1892	mid-log	mid-log	JJ	_	_	_
1893	phase	phase	NN	_	_	_
1894	-LRB-	-lrb-	-LRB-	_	_	_
1895	O.D.	o.d.	NN	_	_	_
1896	600nm	600nm	CD	_	_	_
1897	0.3	0.3	CD	_	_	_
1898	-RRB-	-rrb-	-RRB-	_	_	_
1899	anerobically	anerobically	RB	_	_	_
1900	-LRB-	-lrb-	-LRB-	_	_	_
1901	95	95	CD	_	_	_
1902	%	%	NN	_	_	_
1903	N2	n2	NN	_	_	_
1904	,	,	,	_	_	_
1905	5	5	CD	_	_	_
1906	%	%	NN	_	_	_
1907	CO2	co2	NN	_	_	_
1908	-RRB-	-rrb-	-RRB-	_	_	_
1909	at	at	IN	_	_	_
1910	37	37	CD	_	_	_
1911	°C	°c	NN	_	_	_
1912	in	in	IN	_	_	_
1913	MOPS	MOPS	NNP	MED	_	_
1914	+0.2	+0.2	CD	_	_	_
1915	%	%	NN	_	_	_
1916	glucose	glucose	NN	SUPP	_	_
1917	media	media	NNS	_	_	_
1918	-LRB-	-lrb-	-LRB-	_	_	_
1919	Ref	ref	NN	_	_	_
1920	-RRB-	-rrb-	-RRB-	_	_	_
1921	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	MG1655	mg1655	NN	_	_	_
5	,	,	,	_	_	_
6	M9	m9	NN	_	_	_
7	+	+	CC	_	_	_
8	glucose	glucose	NN	SUPP	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	MG1655	mg1655	NN	_	_	_
13	,	,	,	_	_	_
14	M9	m9	NN	_	_	_
15	+	+	CC	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	,	,	,	_	_	_
18	0	0	CD	_	_	_
19	min	min	NN	_	_	_
20	before	before	IN	_	_	_
21	treatment	treatment	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Escherichia	escherichia	FW	Organism	_	_
24	coli	coli	FW	Organism	_	_
25	MG1655	mg1655	NN	_	_	_
26	,	,	,	_	_	_
27	OD	od	NN	_	_	_
28	0.03	0.03	CD	_	_	_
29	,	,	,	_	_	_
30	anaerobic	anaerobic	JJ	_	_	_
31	growth	growth	NN	_	_	_
32	in	in	IN	_	_	_
33	M9	m9	NN	_	_	_
34	+	+	CC	_	_	_
35	glucose	glucose	NN	SUPP	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	Escherichia	escherichia	FW	Organism	_	_
38	coli	coli	FW	Organism	_	_
39	MG1655	mg1655	NN	_	_	_
40	,	,	,	_	_	_
41	OD	od	NN	_	_	_
42	0.05	0.05	CD	_	_	_
43	,	,	,	_	_	_
44	anaerobic	anaerobic	JJ	_	_	_
45	growth	growth	NN	_	_	_
46	in	in	IN	_	_	_
47	M9	m9	NN	_	_	_
48	+	+	CC	_	_	_
49	glucose	glucose	NN	SUPP	_	_
50	+	+	CC	_	_	_
51	fumarate	fumarate	NN	SUPP	_	_
52	,	,	,	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	Escherichia	escherichia	FW	Organism	_	_
55	coli	coli	FW	Organism	_	_
56	MG1655	mg1655	NN	_	_	_
57	,	,	,	_	_	_
58	OD	od	NN	_	_	_
59	0.08	0.08	CD	_	_	_
60	,	,	,	_	_	_
61	anaerobic	anaerobic	JJ	_	_	_
62	growth	growth	NN	_	_	_
63	in	in	IN	_	_	_
64	M9	m9	NN	_	_	_
65	+	+	CC	_	_	_
66	glucose	glucose	NN	SUPP	_	_
67	,	,	,	_	_	_
68	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
69	Escherichia	escherichia	FW	Organism	_	_
70	coli	coli	FW	Organism	_	_
71	MG1655	mg1655	NN	_	_	_
72	,	,	,	_	_	_
73	OD	od	NN	_	_	_
74	0.15	0.15	CD	_	_	_
75	,	,	,	_	_	_
76	anaerobic	anaerobic	JJ	_	_	_
77	growth	growth	NN	_	_	_
78	in	in	IN	_	_	_
79	M9	m9	NN	_	_	_
80	+	+	CC	_	_	_
81	glucose	glucose	NN	SUPP	_	_
82	,	,	,	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	Escherichia	escherichia	FW	Organism	_	_
85	coli	coli	FW	Organism	_	_
86	MG1655	mg1655	NN	_	_	_
87	,	,	,	_	_	_
88	OD	od	NN	_	_	_
89	0.15	0.15	CD	_	_	_
90	,	,	,	_	_	_
91	anaerobic	anaerobic	JJ	_	_	_
92	growth	growth	NN	_	_	_
93	in	in	IN	_	_	_
94	M9	m9	NN	_	_	_
95	+	+	CC	_	_	_
96	glucose	glucose	NN	SUPP	_	_
97	+	+	CC	_	_	_
98	fumarate	fumarate	NN	SUPP	_	_
99	,	,	,	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	Escherichia	escherichia	FW	Organism	_	_
102	coli	coli	FW	Organism	_	_
103	MG1655	mg1655	NN	_	_	_
104	,	,	,	_	_	_
105	OD	od	NN	_	_	_
106	0.21	0.21	CD	_	_	_
107	,	,	,	_	_	_
108	anaerobic	anaerobic	JJ	_	_	_
109	growth	growth	NN	_	_	_
110	in	in	IN	_	_	_
111	M9	m9	NN	_	_	_
112	+	+	CC	_	_	_
113	glucose	glucose	NN	SUPP	_	_
114	+	+	CC	_	_	_
115	fumarate	fumarate	NN	SUPP	_	_
116	,	,	,	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	Escherichia	escherichia	FW	Organism	_	_
119	coli	coli	FW	Organism	_	_
120	MG1655	mg1655	NN	_	_	_
121	,	,	,	_	_	_
122	OD	od	NN	_	_	_
123	0.2	0.2	CD	_	_	_
124	,	,	,	_	_	_
125	anaerobic	anaerobic	JJ	_	_	_
126	growth	growth	NN	_	_	_
127	in	in	IN	_	_	_
128	M9	m9	NN	_	_	_
129	+	+	CC	_	_	_
130	glucose	glucose	NN	SUPP	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
132	Escherichia	escherichia	FW	Organism	_	_
133	coli	coli	FW	Organism	_	_
134	MG1655	mg1655	NN	_	_	_
135	,	,	,	_	_	_
136	OD	od	NN	_	_	_
137	0.30	0.30	CD	_	_	_
138	,	,	,	_	_	_
139	anaerobic	anaerobic	JJ	_	_	_
140	growth	growth	NN	_	_	_
141	in	in	IN	_	_	_
142	M9	m9	NN	_	_	_
143	+	+	CC	_	_	_
144	glucose	glucose	NN	SUPP	_	_
145	+	+	CC	_	_	_
146	fumarate	fumarate	NN	SUPP	_	_
147	,	,	,	_	_	_
148	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
149	Escherichia	escherichia	FW	Organism	_	_
150	coli	coli	FW	Organism	_	_
151	MG1655	mg1655	NN	_	_	_
152	,	,	,	_	_	_
153	OD	od	NN	_	_	_
154	0.34	0.34	CD	_	_	_
155	,	,	,	_	_	_
156	anaerobic	anaerobic	JJ	_	_	_
157	growth	growth	NN	_	_	_
158	in	in	IN	_	_	_
159	M9	m9	NN	_	_	_
160	+	+	CC	_	_	_
161	glucose	glucose	NN	SUPP	_	_
162	,	,	,	_	_	_
163	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
164	Escherichia	escherichia	FW	Organism	_	_
165	coli	coli	FW	Organism	_	_
166	MG1655	mg1655	NN	_	_	_
167	,	,	,	_	_	_
168	OD	od	NN	_	_	_
169	0.35	0.35	CD	_	_	_
170	,	,	,	_	_	_
171	anaerobic	anaerobic	JJ	_	_	_
172	growth	growth	NN	_	_	_
173	in	in	IN	_	_	_
174	M9	m9	NN	_	_	_
175	+	+	CC	_	_	_
176	glucose	glucose	NN	SUPP	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
178	Escherichia	escherichia	FW	Organism	_	_
179	coli	coli	FW	Organism	_	_
180	MG1655	mg1655	NN	_	_	_
181	,	,	,	_	_	_
182	OD	od	NN	_	_	_
183	0.43	0.43	CD	_	_	_
184	,	,	,	_	_	_
185	anaerobic	anaerobic	JJ	_	_	_
186	growth	growth	NN	_	_	_
187	in	in	IN	_	_	_
188	M9	m9	NN	_	_	_
189	+	+	CC	_	_	_
190	glucose	glucose	NN	SUPP	_	_
191	+	+	CC	_	_	_
192	fumarate	fumarate	NN	SUPP	_	_
193	,	,	,	_	_	_
194	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
195	Escherichia	escherichia	FW	Organism	_	_
196	coli	coli	FW	Organism	_	_
197	MG1655	mg1655	NN	_	_	_
198	,	,	,	_	_	_
199	OD	od	NN	_	_	_
200	0.43	0.43	CD	_	_	_
201	LB	lb	NN	_	_	_
202	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
203	Escherichia	escherichia	FW	Organism	_	_
204	coli	coli	FW	Organism	_	_
205	MG1655	mg1655	NN	_	_	_
206	,	,	,	_	_	_
207	OD	od	NN	_	_	_
208	0.63	0.63	CD	_	_	_
209	,	,	,	_	_	_
210	anaerobic	anaerobic	JJ	_	_	_
211	growth	growth	NN	_	_	_
212	in	in	IN	_	_	_
213	M9	m9	NN	_	_	_
214	+	+	CC	_	_	_
215	glucose	glucose	NN	SUPP	_	_
216	+	+	CC	_	_	_
217	fumarate	fumarate	NN	SUPP	_	_
218	,	,	,	_	_	_
219	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
220	Escherichia	escherichia	FW	Organism	_	_
221	coli	coli	FW	Organism	_	_
222	MG1655	mg1655	NN	_	_	_
223	,	,	,	_	_	_
224	OD	od	NN	_	_	_
225	0.6	0.6	CD	_	_	_
226	,	,	,	_	_	_
227	anaerobic	anaerobic	JJ	_	_	_
228	growth	growth	NN	_	_	_
229	in	in	IN	_	_	_
230	M9	m9	NN	_	_	_
231	+	+	CC	_	_	_
232	glucose	glucose	NN	SUPP	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
234	Escherichia	escherichia	FW	Organism	_	_
235	coli	coli	FW	Organism	_	_
236	MG1655	mg1655	NN	_	_	_
237	,	,	,	_	_	_
238	OD	od	NN	_	_	_
239	0.73	0.73	CD	_	_	_
240	,	,	,	_	_	_
241	anaerobic	anaerobic	JJ	_	_	_
242	growth	growth	NN	_	_	_
243	in	in	IN	_	_	_
244	M9	m9	NN	_	_	_
245	+	+	CC	_	_	_
246	glucose	glucose	NN	SUPP	_	_
247	,	,	,	_	_	_
248	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
249	Escherichia	escherichia	FW	Organism	_	_
250	coli	coli	FW	Organism	_	_
251	MG1655	mg1655	NN	_	_	_
252	,	,	,	_	_	_
253	OD	od	NN	_	_	_
254	0.7	0.7	CD	_	_	_
255	,	,	,	_	_	_
256	anaerobic	anaerobic	JJ	_	_	_
257	growth	growth	NN	_	_	_
258	in	in	IN	_	_	_
259	M9	m9	NN	_	_	_
260	+	+	CC	_	_	_
261	glucose	glucose	NN	SUPP	_	_
262	+	+	CC	_	_	_
263	fumarate	fumarate	NN	SUPP	_	_
264	,	,	,	_	_	_
265	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
266	Escherichia	escherichia	FW	Organism	_	_
267	coli	coli	FW	Organism	_	_
268	MG1655	mg1655	NN	_	_	_
269	,	,	,	_	_	_
270	OD	od	NN	_	_	_
271	0.85	0.85	CD	_	_	_
272	,	,	,	_	_	_
273	anaerobic	anaerobic	JJ	_	_	_
274	growth	growth	NN	_	_	_
275	in	in	IN	_	_	_
276	M9	m9	NN	_	_	_
277	+	+	CC	_	_	_
278	glucose	glucose	NN	SUPP	_	_
279	+	+	CC	_	_	_
280	fumarate	fumarate	NN	SUPP	_	_
281	,	,	,	_	_	_
282	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
283	Escherichia	escherichia	FW	Organism	_	_
284	coli	coli	FW	Organism	_	_
285	MG1655	mg1655	NN	_	_	_
286	,	,	,	_	_	_
287	OD	od	NN	_	_	_
288	0.9	0.9	CD	_	_	_
289	,	,	,	_	_	_
290	anaerobic	anaerobic	JJ	_	_	_
291	growth	growth	NN	_	_	_
292	in	in	IN	_	_	_
293	M9	m9	NN	_	_	_
294	+	+	CC	_	_	_
295	glucose	glucose	NN	SUPP	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
297	Escherichia	escherichia	FW	Organism	_	_
298	coli	coli	FW	Organism	_	_
299	MG1655	mg1655	NN	_	_	_
300	,	,	,	_	_	_
301	OD	od	NN	_	_	_
302	1.02	1.02	CD	_	_	_
303	,	,	,	_	_	_
304	anaerobic	anaerobic	JJ	_	_	_
305	growth	growth	NN	_	_	_
306	in	in	IN	_	_	_
307	M9	m9	NN	_	_	_
308	+	+	CC	_	_	_
309	glucose	glucose	NN	SUPP	_	_
310	,	,	,	_	_	_
311	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
312	Escherichia	escherichia	FW	Organism	_	_
313	coli	coli	FW	Organism	_	_
314	MG1655	mg1655	NN	_	_	_
315	,	,	,	_	_	_
316	OD	od	NN	_	_	_
317	1.07	1.07	CD	_	_	_
318	,	,	,	_	_	_
319	anaerobic	anaerobic	JJ	_	_	_
320	growth	growth	NN	_	_	_
321	in	in	IN	_	_	_
322	M9	m9	NN	_	_	_
323	+	+	CC	_	_	_
324	glucose	glucose	NN	SUPP	_	_
325	+	+	CC	_	_	_
326	fumarate	fumarate	NN	SUPP	_	_
327	,	,	,	_	_	_
328	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
329	Escherichia	escherichia	FW	Organism	_	_
330	coli	coli	FW	Organism	_	_
331	MG1655	mg1655	NN	_	_	_
332	,	,	,	_	_	_
333	OD	od	NN	_	_	_
334	1.27	1.27	CD	_	_	_
335	anaerobic	anaerobic	JJ	_	_	_
336	growth	growth	NN	_	_	_
337	in	in	IN	_	_	_
338	M9	m9	NN	_	_	_
339	+	+	CC	_	_	_
340	glucose	glucose	NN	SUPP	_	_
341	,	,	,	_	_	_
342	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
343	Escherichia	escherichia	FW	Organism	_	_
344	coli	coli	FW	Organism	_	_
345	MG1655	mg1655	NN	_	_	_
346	,	,	,	_	_	_
347	OD	od	NN	_	_	_
348	1.29	1.29	CD	_	_	_
349	anaerobic	anaerobic	JJ	_	_	_
350	growth	growth	NN	_	_	_
351	in	in	IN	_	_	_
352	M9	m9	NN	_	_	_
353	+	+	CC	_	_	_
354	glucose	glucose	NN	SUPP	_	_
355	+	+	CC	_	_	_
356	fumarate	fumarate	NN	SUPP	_	_
357	,	,	,	_	_	_
358	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
359	Escherichia	escherichia	FW	Organism	_	_
360	coli	coli	FW	Organism	_	_
361	MG1655	mg1655	NN	_	_	_
362	,	,	,	_	_	_
363	OD	od	NN	_	_	_
364	1.2	1.2	CD	_	_	_
365	,	,	,	_	_	_
366	anaerobic	anaerobic	JJ	_	_	_
367	growth	growth	NN	_	_	_
368	in	in	IN	_	_	_
369	M9	m9	NN	_	_	_
370	+	+	CC	_	_	_
371	glucose	glucose	NN	SUPP	_	_
372	+	+	CC	_	_	_
373	fumarate	fumarate	NN	SUPP	_	_
374	,	,	,	_	_	_
375	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
376	Escherichia	escherichia	FW	Organism	_	_
377	coli	coli	FW	Organism	_	_
378	MG1655/pTrc99a	mg1655/ptrc99a	NN	_	_	_
379	-LRB-	-lrb-	-LRB-	_	_	_
380	NOX	nox	NN	_	_	_
381	+	+	CC	_	_	_
382	-RRB-	-rrb-	-RRB-	_	_	_
383	,	,	,	_	_	_
384	Balanced	balanced	JJ	_	_	_
385	growth	growth	NN	_	_	_
386	OD	od	NN	_	_	_
387	0.06	0.06	CD	_	_	_
388	in	in	IN	_	_	_
389	M9	m9	NN	_	_	_
390	+	+	CC	_	_	_
391	salts	salt	NNS	_	_	_
392	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
393	Escherichia	escherichia	FW	Organism	_	_
394	coli	coli	FW	Organism	_	_
395	MG1655/pTrc99a	mg1655/ptrc99a	NN	_	_	_
396	-LRB-	-lrb-	-LRB-	_	_	_
397	NOX	nox	NN	_	_	_
398	+	+	CC	_	_	_
399	-RRB-	-rrb-	-RRB-	_	_	_
400	,	,	,	_	_	_
401	Balanced	balanced	JJ	_	_	_
402	growth	growth	NN	_	_	_
403	OD	od	NN	_	_	_
404	0.13	0.13	CD	_	_	_
405	in	in	IN	_	_	_
406	M9	m9	NN	_	_	_
407	+	+	CC	_	_	_
408	salts	salt	NNS	_	_	_
409	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
410	Escherichia	escherichia	FW	Organism	_	_
411	coli	coli	FW	Organism	_	_
412	MG1655/pTrc99a	mg1655/ptrc99a	NN	_	_	_
413	-LRB-	-lrb-	-LRB-	_	_	_
414	NOX	nox	NN	_	_	_
415	-	-	:	_	_	_
416	-RRB-	-rrb-	-RRB-	_	_	_
417	,	,	,	_	_	_
418	Balanced	balanced	JJ	_	_	_
419	growth	growth	NN	_	_	_
420	OD	od	NN	_	_	_
421	0.19	0.19	CD	_	_	_
422	in	in	IN	_	_	_
423	M9	m9	NN	_	_	_
424	+	+	CC	_	_	_
425	salts	salt	NNS	_	_	_
426	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
427	Escherichia	escherichia	FW	Organism	_	_
428	coli	coli	FW	Organism	_	_
429	MG1655/pTrc99a	mg1655/ptrc99a	NN	_	_	_
430	-LRB-	-lrb-	-LRB-	_	_	_
431	NOX	nox	NN	_	_	_
432	-	-	:	_	_	_
433	-RRB-	-rrb-	-RRB-	_	_	_
434	,	,	,	_	_	_
435	Balanced	balanced	JJ	_	_	_
436	growth	growth	NN	_	_	_
437	OD	od	NN	_	_	_
438	0.1	0.1	CD	_	_	_
439	in	in	IN	_	_	_
440	M9	m9	NN	_	_	_
441	+	+	CC	_	_	_
442	salts	salt	NNS	_	_	_
443	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
444	Escherichia	escherichia	FW	Organism	_	_
445	coli	coli	FW	Organism	_	_
446	MG1655/pTrc99a	mg1655/ptrc99a	NN	_	_	_
447	-LRB-	-lrb-	-LRB-	_	_	_
448	NOX	nox	NN	_	_	_
449	+	+	CC	_	_	_
450	-RRB-	-rrb-	-RRB-	_	_	_
451	,	,	,	_	_	_
452	Balanced	balanced	JJ	_	_	_
453	growth	growth	NN	_	_	_
454	OD	od	NN	_	_	_
455	0.21	0.21	CD	_	_	_
456	in	in	IN	_	_	_
457	M9	m9	NN	_	_	_
458	+	+	CC	_	_	_
459	salts	salt	NNS	_	_	_
460	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
461	Escherichia	escherichia	FW	Organism	_	_
462	coli	coli	FW	Organism	_	_
463	MG1655/pTrc99a	mg1655/ptrc99a	NN	_	_	_
464	-LRB-	-lrb-	-LRB-	_	_	_
465	NOX	nox	NN	_	_	_
466	+	+	CC	_	_	_
467	-RRB-	-rrb-	-RRB-	_	_	_
468	,	,	,	_	_	_
469	Balanced	balanced	JJ	_	_	_
470	growth	growth	NN	_	_	_
471	OD	od	NN	_	_	_
472	0.28	0.28	CD	_	_	_
473	in	in	IN	_	_	_
474	M9	m9	NN	_	_	_
475	+	+	CC	_	_	_
476	salts	salt	NNS	_	_	_
477	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
478	Escherichia	escherichia	FW	Organism	_	_
479	coli	coli	FW	Organism	_	_
480	MG1655/pTrc99a	mg1655/ptrc99a	NN	_	_	_
481	-LRB-	-lrb-	-LRB-	_	_	_
482	NOX	nox	NN	_	_	_
483	+	+	CC	_	_	_
484	-RRB-	-rrb-	-RRB-	_	_	_
485	,	,	,	_	_	_
486	Balanced	balanced	JJ	_	_	_
487	growth	growth	NN	_	_	_
488	OD	od	NN	_	_	_
489	0.34	0.34	CD	_	_	_
490	in	in	IN	_	_	_
491	M9	m9	NN	_	_	_
492	+	+	CC	_	_	_
493	salts	salt	NNS	_	_	_
494	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
495	Escherichia	escherichia	FW	Organism	_	_
496	coli	coli	FW	Organism	_	_
497	MG1655/pTrc99a	mg1655/ptrc99a	NN	_	_	_
498	-LRB-	-lrb-	-LRB-	_	_	_
499	NOX	nox	NN	_	_	_
500	+	+	CC	_	_	_
501	-RRB-	-rrb-	-RRB-	_	_	_
502	,	,	,	_	_	_
503	Balanced	balanced	JJ	_	_	_
504	growth	growth	NN	_	_	_
505	OD	od	NN	_	_	_
506	0.4	0.4	CD	_	_	_
507	in	in	IN	_	_	_
508	M9	m9	NN	_	_	_
509	+	+	CC	_	_	_
510	salts	salt	NNS	_	_	_
511	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
512	Escherichia	escherichia	FW	Organism	_	_
513	coli	coli	FW	Organism	_	_
514	MG1655	mg1655	NN	_	_	_
515	,	,	,	_	_	_
516	Sample	sample	NN	_	_	_
517	washed	wash	VBN	_	_	_
518	in	in	IN	_	_	_
519	0.1	0.1	CD	_	_	_
520	M	m	NN	_	_	_
521	CaCl2	cacl2	NN	_	_	_
522	+	+	CC	_	_	_
523	15	15	CD	_	_	_
524	%	%	NN	_	_	_
525	glycerol	glycerol	NN	SUPP	_	_
526	vs	vs	CC	_	_	_
527	before	before	IN	_	_	_
528	washing	wash	VBG	_	_	_
529	OD	od	NN	_	_	_
530	0.43	0.43	CD	_	_	_
531	in	in	IN	_	_	_
532	LB	LB	NNP	_	_	_
533	,	,	,	_	_	_
534	10	10	CD	_	_	_
535	min	min	NN	_	_	_
536	timepoint	timepoint	NN	_	_	_
537	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
538	Escherichia	escherichia	FW	Organism	_	_
539	coli	coli	FW	Organism	_	_
540	MG1655	mg1655	NN	_	_	_
541	,	,	,	_	_	_
542	Sample	sample	NN	_	_	_
543	washed	wash	VBN	_	_	_
544	in	in	IN	_	_	_
545	0.1	0.1	CD	_	_	_
546	M	m	NN	_	_	_
547	CaCl2	cacl2	NN	_	_	_
548	+	+	CC	_	_	_
549	15	15	CD	_	_	_
550	%	%	NN	_	_	_
551	glycerol	glycerol	NN	SUPP	_	_
552	vs	vs	CC	_	_	_
553	before	before	IN	_	_	_
554	washing	wash	VBG	_	_	_
555	OD	od	NN	_	_	_
556	0.43	0.43	CD	_	_	_
557	in	in	IN	_	_	_
558	LB	LB	NNP	_	_	_
559	,	,	,	_	_	_
560	20	20	CD	_	_	_
561	min	min	NN	_	_	_
562	timepoint	timepoint	NN	_	_	_
563	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
564	Escherichia	escherichia	FW	Organism	_	_
565	coli	coli	FW	Organism	_	_
566	MG1655	mg1655	NN	_	_	_
567	,	,	,	_	_	_
568	Sample	sample	NN	_	_	_
569	washed	wash	VBN	_	_	_
570	in	in	IN	_	_	_
571	0.1	0.1	CD	_	_	_
572	M	m	NN	_	_	_
573	CaCl2	cacl2	NN	_	_	_
574	+	+	CC	_	_	_
575	15	15	CD	_	_	_
576	%	%	NN	_	_	_
577	glycerol	glycerol	NN	SUPP	_	_
578	vs	vs	CC	_	_	_
579	before	before	IN	_	_	_
580	washing	wash	VBG	_	_	_
581	OD	od	NN	_	_	_
582	0.43	0.43	CD	_	_	_
583	in	in	IN	_	_	_
584	LB	LB	NNP	_	_	_
585	,	,	,	_	_	_
586	2	2	CD	_	_	_
587	min	min	NN	_	_	_
588	timepoint	timepoint	NN	_	_	_
589	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
590	Escherichia	escherichia	FW	Organism	_	_
591	coli	coli	FW	Organism	_	_
592	MG1655	mg1655	NN	_	_	_
593	,	,	,	_	_	_
594	Sample	sample	NN	_	_	_
595	washed	wash	VBN	_	_	_
596	in	in	IN	_	_	_
597	0.1	0.1	CD	_	_	_
598	M	m	NN	_	_	_
599	CaCl2	cacl2	NN	_	_	_
600	+	+	CC	_	_	_
601	15	15	CD	_	_	_
602	%	%	NN	_	_	_
603	glycerol	glycerol	NN	SUPP	_	_
604	vs	vs	CC	_	_	_
605	before	before	IN	_	_	_
606	washing	wash	VBG	_	_	_
607	OD	od	NN	_	_	_
608	0.43	0.43	CD	_	_	_
609	in	in	IN	_	_	_
610	LB	LB	NNP	_	_	_
611	,	,	,	_	_	_
612	40	40	CD	_	_	_
613	min	min	NN	_	_	_
614	timepoint	timepoint	NN	_	_	_
615	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
616	Escherichia	escherichia	FW	Organism	_	_
617	coli	coli	FW	Organism	_	_
618	MG1655	mg1655	NN	_	_	_
619	,	,	,	_	_	_
620	Sample	sample	NN	_	_	_
621	washed	wash	VBN	_	_	_
622	in	in	IN	_	_	_
623	0.1	0.1	CD	_	_	_
624	M	m	NN	_	_	_
625	CaCl2	cacl2	NN	_	_	_
626	+	+	CC	_	_	_
627	15	15	CD	_	_	_
628	%	%	NN	_	_	_
629	glycerol	glycerol	NN	SUPP	_	_
630	vs	vs	CC	_	_	_
631	before	before	IN	_	_	_
632	washing	wash	VBG	_	_	_
633	OD	od	NN	_	_	_
634	0.43	0.43	CD	_	_	_
635	in	in	IN	_	_	_
636	LB	LB	NNP	_	_	_
637	,	,	,	_	_	_
638	5	5	CD	_	_	_
639	min	min	NN	_	_	_
640	timepoint	timepoint	NN	_	_	_
641	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
642	Escherichia	escherichia	FW	Organism	_	_
643	coli	coli	FW	Organism	_	_
644	MG1655	mg1655	NN	_	_	_
645	,	,	,	_	_	_
646	Sample	sample	NN	_	_	_
647	washed	wash	VBN	_	_	_
648	in	in	IN	_	_	_
649	0.1	0.1	CD	_	_	_
650	M	m	NN	_	_	_
651	CaCl2	cacl2	NN	_	_	_
652	+	+	CC	_	_	_
653	15	15	CD	_	_	_
654	%	%	NN	_	_	_
655	glycerol	glycerol	NN	SUPP	_	_
656	vs	vs	CC	_	_	_
657	before	before	IN	_	_	_
658	washing	wash	VBG	_	_	_
659	OD	od	NN	_	_	_
660	0.43	0.43	CD	_	_	_
661	in	in	IN	_	_	_
662	LB	LB	NNP	_	_	_
663	,	,	,	_	_	_
664	60	60	CD	_	_	_
665	min	min	NN	_	_	_
666	timepoint	timepoint	NN	_	_	_
667	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
668	Escherichia	escherichia	FW	Organism	_	_
669	coli	coli	FW	Organism	_	_
670	MG1655	mg1655	NN	_	_	_
671	,	,	,	_	_	_
672	stationary	stationary	JJ	GrowthPhase	_	_
673	phase	phase	NN	GrowthPhase	_	_
674	anaerobic	anaerobic	JJ	_	_	_
675	growth	growth	NN	_	_	_
676	in	in	IN	_	_	_
677	M9	m9	NN	_	_	_
678	+	+	CC	_	_	_
679	glucose	glucose	NN	SUPP	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
681	Escherichia	escherichia	FW	Organism	_	_
682	coli	coli	FW	Organism	_	_
683	MG1655	mg1655	NN	_	_	_
684	,	,	,	_	_	_
685	stationary	stationary	JJ	GrowthPhase	_	_
686	phase	phase	NN	GrowthPhase	_	_
687	anaerobic	anaerobic	JJ	_	_	_
688	growth	growth	NN	_	_	_
689	in	in	IN	_	_	_
690	M9	m9	NN	_	_	_
691	+	+	CC	_	_	_
692	glucose	glucose	NN	SUPP	_	_
693	+	+	CC	_	_	_
694	fumarate	fumarate	NN	SUPP	_	_
695	,	,	,	_	_	_
696	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
697	Escherichia	escherichia	FW	Organism	_	_
698	coli	coli	FW	Organism	_	_
699	MG1655	mg1655	NN	_	_	_
700	,	,	,	_	_	_
701	Stationary	stationary	JJ	_	_	_
702	phase	phase	NN	_	_	_
703	in	in	IN	_	_	_
704	LB	lb	NN	_	_	_
705	OD	od	NN	_	_	_
706	2.4	2.4	CD	_	_	_
707	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
708	Escherichia	escherichia	FW	Organism	_	_
709	coli	coli	FW	Organism	_	_
710	MG1655	mg1655	NN	_	_	_
711	,	,	,	_	_	_
712	Stationary	stationary	JJ	_	_	_
713	phase	phase	NN	_	_	_
714	in	in	IN	_	_	_
715	LB	lb	NN	_	_	_
716	OD	od	NN	_	_	_
717	2.8	2.8	CD	_	_	_
718	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
719	Escherichia	escherichia	FW	Organism	_	_
720	coli	coli	FW	Organism	_	_
721	MG1655	mg1655	NN	_	_	_
722	,	,	,	_	_	_
723	Stationary	stationary	JJ	_	_	_
724	phase	phase	NN	_	_	_
725	in	in	IN	_	_	_
726	LB	lb	NN	_	_	_
727	OD	od	NN	_	_	_
728	3.1	3.1	CD	_	_	_
729	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
730	Escherichia	escherichia	FW	Organism	_	_
731	coli	coli	FW	Organism	_	_
732	MG1655	mg1655	NN	_	_	_
733	,	,	,	_	_	_
734	Stationary	stationary	JJ	_	_	_
735	phase	phase	NN	_	_	_
736	in	in	IN	_	_	_
737	LB	lb	NN	_	_	_
738	OD	od	NN	_	_	_
739	3.1	3.1	CD	_	_	_
740	for	for	IN	_	_	_
741	20	20	CD	_	_	_
742	min	min	NN	_	_	_
743	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
744	Escherichia	escherichia	FW	Organism	_	_
745	coli	coli	FW	Organism	_	_
746	MG1655	mg1655	NN	_	_	_
747	,	,	,	_	_	_
748	Stationary	stationary	JJ	_	_	_
749	phase	phase	NN	_	_	_
750	in	in	IN	_	_	_
751	LB	lb	NN	_	_	_
752	OD	od	NN	_	_	_
753	3.1	3.1	CD	_	_	_
754	for	for	IN	_	_	_
755	40	40	CD	_	_	_
756	min	min	NN	_	_	_
757	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
758	Escherichia	escherichia	FW	Organism	_	_
759	coli	coli	FW	Organism	_	_
760	MG1655	mg1655	NN	_	_	_
761	,	,	,	_	_	_
762	stationary	stationary	JJ	GrowthPhase	_	_
763	phase	phase	NN	GrowthPhase	_	_
764	in	in	IN	_	_	_
765	LB	lb	NN	_	_	_
766	,	,	,	_	_	_
767	OD	od	NN	_	_	_
768	3.1	3.1	CD	_	_	_
769	for	for	IN	_	_	_
770	60	60	CD	_	_	_
771	min	min	NN	_	_	_
772	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
773	Escherichia	escherichia	FW	Organism	_	_
774	coli	coli	FW	Organism	_	_
775	MG1655	mg1655	NN	_	_	_
776	were	be	VBD	_	_	_
777	grown	grow	VBN	_	_	_
778	in	in	IN	_	_	_
779	10	10	CD	_	_	_
780	ml	ml	NN	_	_	_
781	of	of	IN	_	_	_
782	LB	lb	NN	MED	_	_
783	medium	medium	NN	MED	_	_
784	until	until	IN	_	_	_
785	stationary	stationary	JJ	GrowthPhase	_	_
786	phase	phase	NN	GrowthPhase	_	_
787	,	,	,	_	_	_
788	collected	collect	VBN	_	_	_
789	by	by	IN	_	_	_
790	centrifugation	centrifugation	NN	_	_	_
791	at	at	IN	_	_	_
792	8,000	8,000	CD	_	_	_
793	×	×	CD	_	_	_
794	g	g	NN	_	_	_
795	for	for	IN	_	_	_
796	10	10	CD	_	_	_
797	min	min	NN	_	_	_
798	,	,	,	_	_	_
799	and	and	CC	_	_	_
800	washed	wash	VBN	_	_	_
801	twice	twice	RB	_	_	_
802	with	with	IN	_	_	_
803	sterilized	sterilize	VBN	_	_	_
804	,	,	,	_	_	_
805	plant	plant	NN	_	_	_
806	growth	growth	NN	_	_	_
807	medium	medium	NN	_	_	_
808	-LRB-	-lrb-	-LRB-	_	_	_
809	Caspersen	Caspersen	NNP	_	_	_
810	et	et	FW	_	_	_
811	al.	al.	FW	_	_	_
812	1999	1999	CD	_	_	_
813	-RRB-	-rrb-	-RRB-	_	_	_
814	.	.	.	_	_	_

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	CD	_	_	_
22	cells/ml	cells/ml	NNS	_	_	_
23	.	.	.	_	_	_

1	Germinated	germinate	VBN	_	_	_
2	lettuce	lettuce	NN	_	_	_
3	seedlings	seedling	NNS	_	_	_
4	were	be	VBD	_	_	_
5	each	each	DT	_	_	_
6	aseptically	aseptically	RB	_	_	_
7	transferred	transfer	VBN	_	_	_
8	into	into	IN	_	_	_
9	holes	hole	NNS	_	_	_
10	in	in	IN	_	_	_
11	the	the	DT	_	_	_
12	growth	growth	NN	_	_	_
13	boxes	box	NNS	_	_	_
14	filled	fill	VBN	_	_	_
15	with	with	IN	_	_	_
16	300	300	CD	_	_	_
17	ml	ml	NN	_	_	_
18	of	of	IN	_	_	_
19	plant	plant	NN	_	_	_
20	growth	growth	NN	_	_	_
21	medium	medium	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	3	3	CD	_	_	_
25	ml	ml	NN	_	_	_
26	washed	wash	VBN	_	_	_
27	bacterial	bacterial	JJ	_	_	_
28	suspension	suspension	NN	_	_	_
29	was	be	VBD	_	_	_
30	added	add	VBN	_	_	_
31	to	to	TO	_	_	_
32	provide	provide	VB	_	_	_
33	approximately	approximately	RB	_	_	_
34	10E7	10e7	CD	_	_	_
35	cells/ml	cells/ml	NNS	_	_	_
36	of	of	IN	_	_	_
37	growth	growth	NN	_	_	_
38	medium	medium	NN	_	_	_
39	.	.	.	_	_	_

1	Seedling	seedle	VBG	_	_	_
2	boxes	box	NNS	_	_	_
3	were	be	VBD	_	_	_
4	germinated	germinate	VBN	_	_	_
5	for	for	IN	_	_	_
6	a	a	DT	_	_	_
7	week	week	NN	_	_	_
8	and	and	CC	_	_	_
9	transferred	transfer	VBN	_	_	_
10	to	to	TO	_	_	_
11	a	a	DT	_	_	_
12	plant	plant	NN	_	_	_
13	growth	growth	NN	_	_	_
14	chamber	chamber	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	aeration	aeration	NN	_	_	_
19	pump	pump	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Luft	luft	NN	_	_	_
22	Pump	pump	NN	_	_	_
23	;	;	:	_	_	_
24	Oceanic	Oceanic	NNP	_	_	_
25	systems	system	NNS	_	_	_
26	Inc.	Inc.	NNP	_	_	_
27	.	.	.	_	_	_

1	Dallas	Dallas	NNP	_	_	_
2	,	,	,	_	_	_
3	TX	TX	NNP	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	was	be	VBD	_	_	_
6	immediately	immediately	RB	_	_	_
7	started	start	VBN	_	_	_
8	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	pump	pump	NN	_	_	_
3	supplied	supply	VBD	_	_	_
4	aeration	aeration	NN	_	_	_
5	of	of	IN	_	_	_
6	three	three	CD	_	_	_
7	growth	growth	NN	_	_	_
8	boxes	box	NNS	_	_	_
9	,	,	,	_	_	_
10	at	at	IN	_	_	_
11	a	a	DT	_	_	_
12	rate	rate	NN	_	_	_
13	of	of	IN	_	_	_
14	1.3	1.3	CD	_	_	_
15	L	l	NN	_	_	_
16	/	/	:	_	_	_
17	min	min	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	seedling	seedling	NN	_	_	_
3	boxes	box	NNS	_	_	_
4	were	be	VBD	_	_	_
5	incubated	incubate	VBN	_	_	_
6	under	under	IN	_	_	_
7	80	80	CD	_	_	_
8	%	%	NN	_	_	_
9	RH	rh	NN	_	_	_
10	at	at	IN	_	_	_
11	25	25	CD	_	_	_
12	°C	°c	NN	_	_	_
13	with	with	IN	_	_	_
14	a	a	DT	_	_	_
15	photoperiod	photoperiod	NN	_	_	_
16	of	of	IN	_	_	_
17	16	16	CD	_	_	_
18	h	h	NN	_	_	_
19	for	for	IN	_	_	_
20	3	3	CD	_	_	_
21	days	day	NNS	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Escherichia	escherichia	FW	Organism	_	_
24	coli	coli	FW	Organism	_	_
25	MG1655	mg1655	NN	_	_	_
26	with	with	IN	_	_	_
27	a	a	DT	_	_	_
28	precise	precise	JJ	_	_	_
29	deletion	deletion	NN	_	_	_
30	in	in	IN	_	_	_
31	soxR	soxr	NN	GEN	_	_
32	and	and	CC	_	_	_
33	10	10	CD	_	_	_
34	minutes	minute	NNS	_	_	_
35	paraquat	paraquat	NN	SUPP	_	_
36	treatment	treatment	NN	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Escherichia	escherichia	FW	Organism	_	_
39	coli	coli	FW	Organism	_	_
40	MG1655	mg1655	NN	_	_	_
41	with	with	IN	_	_	_
42	a	a	DT	_	_	_
43	precise	precise	JJ	_	_	_
44	deletion	deletion	NN	_	_	_
45	in	in	IN	_	_	_
46	soxR	soxr	NN	GEN	_	_
47	and	and	CC	_	_	_
48	2	2	CD	_	_	_
49	minutes	minute	NNS	_	_	_
50	paraquat	paraquat	NN	SUPP	_	_
51	treatment	treatment	NN	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	Escherichia	escherichia	FW	Organism	_	_
54	coli	coli	FW	Organism	_	_
55	MG1655	mg1655	NN	_	_	_
56	with	with	IN	_	_	_
57	a	a	DT	_	_	_
58	precise	precise	JJ	_	_	_
59	deletion	deletion	NN	_	_	_
60	in	in	IN	_	_	_
61	soxR	soxr	NN	GEN	_	_
62	and	and	CC	_	_	_
63	4	4	CD	_	_	_
64	minutes	minute	NNS	_	_	_
65	paraquat	paraquat	NN	SUPP	_	_
66	treatment	treatment	NN	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Escherichia	escherichia	FW	Organism	_	_
69	coli	coli	FW	Organism	_	_
70	MG1655	mg1655	NN	_	_	_
71	with	with	IN	_	_	_
72	a	a	DT	_	_	_
73	precise	precise	JJ	_	_	_
74	deletion	deletion	NN	_	_	_
75	in	in	IN	_	_	_
76	soxR	soxr	NN	GEN	_	_
77	and	and	CC	_	_	_
78	6	6	CD	_	_	_
79	minutes	minute	NNS	_	_	_
80	paraquat	paraquat	NN	SUPP	_	_
81	treatment	treatment	NN	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Escherichia	escherichia	FW	Organism	_	_
84	coli	coli	FW	Organism	_	_
85	MG1655	mg1655	NN	_	_	_
86	with	with	IN	_	_	_
87	a	a	DT	_	_	_
88	precise	precise	JJ	_	_	_
89	deletion	deletion	NN	_	_	_
90	in	in	IN	_	_	_
91	soxR	soxr	NN	GEN	_	_
92	and	and	CC	_	_	_
93	8	8	CD	_	_	_
94	minutes	minute	NNS	_	_	_
95	paraquat	paraquat	NN	SUPP	_	_
96	treatment	treatment	NN	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	Escherichia	escherichia	FW	Organism	_	_
99	coli	coli	FW	Organism	_	_
100	MG1655	mg1655	NN	_	_	_
101	with	with	IN	_	_	_
102	a	a	DT	_	_	_
103	precise	precise	JJ	_	_	_
104	deletion	deletion	NN	_	_	_
105	in	in	IN	_	_	_
106	soxR	soxr	NN	GEN	_	_
107	before	before	IN	_	_	_
108	paraquat	paraquat	NN	SUPP	_	_
109	treatment	treatment	NN	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	Escherichia	escherichia	FW	Organism	_	_
112	coli	coli	FW	Organism	_	_
113	MG1655	mg1655	NN	_	_	_
114	wt	wt	JJ	_	_	_
115	grown	grown	JJ	_	_	_
116	150	150	CD	_	_	_
117	minutes	minute	NNS	_	_	_
118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
119	Escherichia	escherichia	FW	Organism	_	_
120	coli	coli	FW	Organism	_	_
121	MG1655	mg1655	NN	_	_	_
122	wt	wt	JJ	_	_	_
123	grown	grown	JJ	_	_	_
124	240	240	CD	_	_	_
125	minutes	minute	NNS	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Escherichia	escherichia	FW	Organism	_	_
128	coli	coli	FW	Organism	_	_
129	MG1655	mg1655	NN	_	_	_
130	wt	wt	JJ	_	_	_
131	grown	grown	JJ	_	_	_
132	360	360	CD	_	_	_
133	minutes	minute	NNS	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	Escherichia	escherichia	FW	Organism	_	_
136	coli	coli	FW	Organism	_	_
137	MG1655	mg1655	NN	_	_	_
138	wt	wt	JJ	_	_	_
139	grown	grown	JJ	_	_	_
140	90	90	CD	_	_	_
141	minutes	minute	NNS	_	_	_
142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
143	Escherichia	escherichia	FW	Organism	_	_
144	coli	coli	FW	Organism	_	_
145	_	_	SYM	_	_	_
146	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
147	_	_	CD	_	_	_
148	bioreplicate1	bioreplicate1	NN	_	_	_
149	_	_	NN	_	_	_
150	techreplicate	techreplicate	NN	_	_	_
151	_	_	NN	_	_	_
152	1	1	CD	_	_	_
153	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
154	Escherichia	escherichia	FW	Organism	_	_
155	coli	coli	FW	Organism	_	_
156	_	_	SYM	_	_	_
157	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
158	_	_	CD	_	_	_
159	bioreplicate1	bioreplicate1	NN	_	_	_
160	_	_	NN	_	_	_
161	techreplicate	techreplicate	NN	_	_	_
162	_	_	NN	_	_	_
163	2	2	CD	_	_	_
164	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
165	Escherichia	escherichia	FW	Organism	_	_
166	coli	coli	FW	Organism	_	_
167	_	_	SYM	_	_	_
168	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
169	_	_	CD	_	_	_
170	bioreplicate1	bioreplicate1	NN	_	_	_
171	_	_	NN	_	_	_
172	techreplicate	techreplicate	NN	_	_	_
173	_	_	NN	_	_	_
174	3	3	CD	_	_	_
175	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
176	Escherichia	escherichia	FW	Organism	_	_
177	coli	coli	FW	Organism	_	_
178	_	_	SYM	_	_	_
179	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
180	_	_	CD	_	_	_
181	bioreplicate2	bioreplicate2	NN	_	_	_
182	_	_	NN	_	_	_
183	techreplicate	techreplicate	NN	_	_	_
184	_	_	NN	_	_	_
185	1	1	CD	_	_	_
186	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
187	Escherichia	escherichia	FW	Organism	_	_
188	coli	coli	FW	Organism	_	_
189	_	_	SYM	_	_	_
190	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
191	_	_	CD	_	_	_
192	bioreplicate2	bioreplicate2	NN	_	_	_
193	_	_	NN	_	_	_
194	techreplicate	techreplicate	NN	_	_	_
195	_	_	NN	_	_	_
196	2	2	CD	_	_	_
197	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
198	Escherichia	escherichia	FW	Organism	_	_
199	coli	coli	FW	Organism	_	_
200	_	_	SYM	_	_	_
201	MixedSpeciesPlanktonic	MixedSpeciesPlanktonic	NNP	_	_	_
202	_	_	CD	_	_	_
203	bioreplicate1	bioreplicate1	NN	_	_	_
204	_	_	NN	_	_	_
205	techreplicate	techreplicate	NN	_	_	_
206	_	_	NN	_	_	_
207	1	1	CD	_	_	_
208	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
209	Escherichia	escherichia	FW	Organism	_	_
210	coli	coli	FW	Organism	_	_
211	_	_	SYM	_	_	_
212	MixedSpeciesPlanktonic	MixedSpeciesPlanktonic	NNP	_	_	_
213	_	_	CD	_	_	_
214	bioreplicate1	bioreplicate1	NN	_	_	_
215	_	_	NN	_	_	_
216	techreplicate	techreplicate	NN	_	_	_
217	_	_	NN	_	_	_
218	2	2	CD	_	_	_
219	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
220	Escherichia	escherichia	FW	Organism	_	_
221	coli	coli	FW	Organism	_	_
222	_	_	SYM	_	_	_
223	MixedSpeciesPlanktonic	MixedSpeciesPlanktonic	NNP	_	_	_
224	_	_	CD	_	_	_
225	bioreplicate2	bioreplicate2	NN	_	_	_
226	_	_	NN	_	_	_
227	techreplicate	techreplicate	NN	_	_	_
228	_	_	NN	_	_	_
229	1	1	CD	_	_	_
230	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
231	Escherichia	escherichia	FW	Organism	_	_
232	coli	coli	FW	Organism	_	_
233	_	_	SYM	_	_	_
234	MixedSpeciesPlanktonic	MixedSpeciesPlanktonic	NNP	_	_	_
235	_	_	CD	_	_	_
236	bioreplicate2	bioreplicate2	NN	_	_	_
237	_	_	NN	_	_	_
238	techreplicate	techreplicate	NN	_	_	_
239	_	_	NN	_	_	_
240	2	2	CD	_	_	_
241	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
242	Escherichia	escherichia	FW	Organism	_	_
243	coli	coli	FW	Organism	_	_
244	_	_	FW	_	_	_
245	nickel	nickel	NN	_	_	_
246	condition	condition	NN	_	_	_
247	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
248	Escherichia	escherichia	FW	Organism	_	_
249	coli	coli	FW	Organism	_	_
250	O08	o08	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	Escherichia	escherichia	FW	Organism	_	_
253	coli	coli	FW	Organism	_	_
254	O104	o104	NN	_	_	_
255	:	:	:	_	_	_
256	H4	h4	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	Escherichia	escherichia	FW	Organism	_	_
259	coli	coli	FW	Organism	_	_
260	O157	o157	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	Escherichia	escherichia	FW	Organism	_	_
263	coli	coli	FW	Organism	_	_
264	O157	o157	NN	_	_	_
265	:	:	:	_	_	_
266	H7	h7	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	Escherichia	escherichia	FW	Organism	_	_
269	coli	coli	FW	Organism	_	_
270	O157	o157	NN	_	_	_
271	:	:	:	_	_	_
272	H7	h7	NN	_	_	_
273	cultivated	cultivate	VBN	_	_	_
274	for	for	IN	_	_	_
275	6	6	CD	_	_	_
276	hours	hour	NNS	_	_	_
277	in	in	IN	_	_	_
278	the	the	DT	_	_	_
279	caecal	caecal	JJ	_	_	_
280	content	content	NN	_	_	_
281	of	of	IN	_	_	_
282	rats	rat	NNS	_	_	_
283	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
284	Escherichia	escherichia	FW	Organism	_	_
285	coli	coli	FW	Organism	_	_
286	O157	o157	NN	_	_	_
287	:	:	:	_	_	_
288	H7	h7	NN	_	_	_
289	EDL933	edl933	NN	_	_	_
290	Inside	inside	IN	_	_	_
291	Acanthamoeba	acanthamoeba	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	Escherichia	escherichia	FW	Organism	_	_
294	coli	coli	FW	Organism	_	_
295	O157	o157	NN	_	_	_
296	:	:	:	_	_	_
297	H7	h7	NN	_	_	_
298	EDL933	edl933	NN	_	_	_
299	Inside	inside	IN	_	_	_
300	Acanthamoeba	acanthamoeba	NN	_	_	_
301	vs.	vs.	CC	_	_	_
302	Control	control	NN	_	_	_
303	Slide	slide	NN	_	_	_
304	1	1	CD	_	_	_
305	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
306	Escherichia	escherichia	FW	Organism	_	_
307	coli	coli	FW	Organism	_	_
308	O157	o157	NN	_	_	_
309	:	:	:	_	_	_
310	H7	h7	NN	_	_	_
311	EDL933	edl933	NN	_	_	_
312	Inside	inside	IN	_	_	_
313	Acanthamoeba	acanthamoeba	NN	_	_	_
314	vs.	vs.	CC	_	_	_
315	Control	control	NN	_	_	_
316	Slide	slide	NN	_	_	_
317	2	2	CD	_	_	_
318	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
319	Escherichia	escherichia	FW	Organism	_	_
320	coli	coli	FW	Organism	_	_
321	O157	o157	NN	_	_	_
322	:	:	:	_	_	_
323	H7	h7	NN	_	_	_
324	EDL933	edl933	NN	_	_	_
325	Inside	inside	IN	_	_	_
326	Acanthamoeba	acanthamoeba	NN	_	_	_
327	vs.	vs.	CC	_	_	_
328	Control	control	NN	_	_	_
329	Slide	slide	NN	_	_	_
330	3	3	CD	_	_	_
331	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
332	Escherichia	escherichia	FW	Organism	_	_
333	coli	coli	FW	Organism	_	_
334	O157	o157	NN	_	_	_
335	:	:	:	_	_	_
336	H7	h7	NN	_	_	_
337	EDL933	edl933	NN	_	_	_
338	Inside	inside	IN	_	_	_
339	Acanthamoeba	acanthamoeba	NN	_	_	_
340	vs.	vs.	CC	_	_	_
341	Control	control	NN	_	_	_
342	Slide	slide	NN	_	_	_
343	4	4	CD	_	_	_
344	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
345	Escherichia	escherichia	FW	Organism	_	_
346	coli	coli	FW	Organism	_	_
347	O157	o157	NN	_	_	_
348	:	:	:	_	_	_
349	H7	h7	NN	_	_	_
350	EDL933	edl933	NN	_	_	_
351	Inside	inside	IN	_	_	_
352	Acanthamoeba	acanthamoeba	NN	_	_	_
353	vs.	vs.	CC	_	_	_
354	Control	control	NN	_	_	_
355	Slide	slide	NN	_	_	_
356	5	5	CD	_	_	_
357	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
358	Escherichia	escherichia	FW	Organism	_	_
359	coli	coli	FW	Organism	_	_
360	O157	o157	NN	_	_	_
361	:	:	:	_	_	_
362	H7	h7	NN	_	_	_
363	EDL933	edl933	NN	_	_	_
364	Inside	inside	IN	_	_	_
365	Acanthamoeba	acanthamoeba	NN	_	_	_
366	vs.	vs.	CC	_	_	_
367	Control	control	NN	_	_	_
368	Slide	slide	NN	_	_	_
369	6	6	CD	_	_	_
370	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
371	Escherichia	escherichia	FW	Organism	_	_
372	coli	coli	FW	Organism	_	_
373	O157	o157	NN	_	_	_
374	:	:	:	_	_	_
375	H7	h7	NN	_	_	_
376	EDL933	edl933	NN	_	_	_
377	Inside	inside	IN	_	_	_
378	Acanthamoeba	acanthamoeba	NN	_	_	_
379	vs.	vs.	CC	_	_	_
380	Control	control	NN	_	_	_
381	Slide	slide	NN	_	_	_
382	7	7	CD	_	_	_
383	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
384	Escherichia	escherichia	FW	Organism	_	_
385	coli	coli	FW	Organism	_	_
386	O157	o157	NN	_	_	_
387	:	:	:	_	_	_
388	H7	h7	NN	_	_	_
389	EDL933	edl933	NN	_	_	_
390	Inside	inside	IN	_	_	_
391	Acanthamoeba	acanthamoeba	NN	_	_	_
392	vs.	vs.	CC	_	_	_
393	Control	control	NN	_	_	_
394	Slide	slide	NN	_	_	_
395	8	8	CD	_	_	_
396	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
397	Escherichia	escherichia	FW	Organism	_	_
398	coli	coli	FW	Organism	_	_
399	O157	o157	NN	_	_	_
400	:	:	:	_	_	_
401	H7	h7	NN	_	_	_
402	EDL933	edl933	NN	_	_	_
403	Inside	inside	IN	_	_	_
404	Acanthamoeba	acanthamoeba	NN	_	_	_
405	vs.	vs.	CC	_	_	_
406	Control	control	NN	_	_	_
407	Slide	slide	NN	_	_	_
408	9	9	CD	_	_	_
409	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
410	Escherichia	escherichia	FW	Organism	_	_
411	coli	coli	FW	Organism	_	_
412	O157	o157	NN	_	_	_
413	:	:	:	_	_	_
414	H7	h7	NN	_	_	_
415	EDL933	edl933	NN	_	_	_
416	Outside	outside	JJ	_	_	_
417	Control	control	NN	_	_	_
418	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
419	Escherichia	escherichia	FW	Organism	_	_
420	coli	coli	FW	Organism	_	_
421	O157	o157	NN	_	_	_
422	:	:	:	_	_	_
423	H7	h7	NN	_	_	_
424	str	str	NN	_	_	_
425	.	.	.	_	_	_

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	O157	o157	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Sakai	Sakai	NNP	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	treated	treat	VBN	_	_	_
10	with	with	IN	_	_	_
11	menadione	menadione	NN	_	_	_
12	_	_	CD	_	_	_
13	rep	rep	NN	GEN	_	_
14	#	#	#	_	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Escherichia	escherichia	FW	Organism	_	_
18	coli	coli	FW	Organism	_	_
19	O157	o157	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Sakai	Sakai	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	treated	treat	VBN	_	_	_
24	with	with	IN	_	_	_
25	menadione	menadione	NN	_	_	_
26	_	_	CD	_	_	_
27	rep	rep	NN	GEN	_	_
28	#	#	#	_	_	_
29	2	2	CD	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Escherichia	escherichia	FW	Organism	_	_
32	coli	coli	FW	Organism	_	_
33	O157	o157	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Sakai	Sakai	NNP	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	treated	treat	VBN	_	_	_
38	with	with	IN	_	_	_
39	menadione	menadione	NN	_	_	_
40	_	_	CD	_	_	_
41	rep	rep	NN	GEN	_	_
42	#	#	#	_	_	_
43	3	3	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Escherichia	escherichia	FW	Organism	_	_
46	coli	coli	FW	Organism	_	_
47	O157	o157	NN	_	_	_
48	TUV93-0	tuv93-0	NN	_	_	_
49	MEM-HEPES	mem-hepes	NN	_	_	_
50	+	+	CC	_	_	_
51	20uM	20um	NN	_	_	_
52	ME0052	me0052	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	in	in	IN	_	_	_
55	DMSO	dmso	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Escherichia	escherichia	FW	Organism	_	_
59	coli	coli	FW	Organism	_	_
60	O157	o157	NN	_	_	_
61	TUV93-0	tuv93-0	NN	_	_	_
62	MEM-HEPES	mem-hepes	NN	_	_	_
63	+	+	CC	_	_	_
64	20uM	20um	NN	_	_	_
65	ME0053	me0053	NN	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	in	in	IN	_	_	_
68	DMSO	dmso	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Escherichia	escherichia	FW	Organism	_	_
72	coli	coli	FW	Organism	_	_
73	O157	o157	NN	_	_	_
74	TUV93-0	tuv93-0	NN	_	_	_
75	MEM-HEPES	mem-hepes	NN	_	_	_
76	+	+	CC	_	_	_
77	20uM	20um	NN	_	_	_
78	ME0054	me0054	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	in	in	IN	_	_	_
81	DMSO	dmso	NN	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Escherichia	escherichia	FW	Organism	_	_
85	coli	coli	FW	Organism	_	_
86	O157	o157	NN	_	_	_
87	TUV93-0	tuv93-0	NN	_	_	_
88	MEM-HEPES	mem-hepes	NN	_	_	_
89	+	+	CC	_	_	_
90	20uM	20um	NN	_	_	_
91	ME0055	me0055	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	in	in	IN	_	_	_
94	DMSO	dmso	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Escherichia	escherichia	FW	Organism	_	_
98	coli	coli	FW	Organism	_	_
99	O157	o157	NN	_	_	_
100	TUV93-0	tuv93-0	NN	_	_	_
101	MEM-HEPES	mem-hepes	NN	_	_	_
102	+	+	CC	_	_	_
103	DMSO	dmso	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	Escherichia	escherichia	FW	Organism	_	_
106	coli	coli	FW	Organism	_	_
107	O157	o157	NN	_	_	_
108	TUV93-0	tuv93-0	NN	_	_	_
109	was	be	VBD	_	_	_
110	grown	grow	VBN	_	_	_
111	at	at	IN	_	_	_
112	37	37	CD	_	_	_
113	degrees	degree	NNS	_	_	_
114	C	c	NN	_	_	_
115	to	to	TO	_	_	_
116	OD	od	NN	_	_	_
117	0.7	0.7	CD	_	_	_
118	in	in	IN	_	_	_
119	MEM-HEPES	mem-hepes	NN	_	_	_
120	supplemented	supplement	VBN	_	_	_
121	with	with	IN	_	_	_
122	0.1	0.1	CD	_	_	_
123	%	%	NN	_	_	_
124	Glucose	glucose	NN	_	_	_
125	and	and	CC	_	_	_
126	250nM	250nm	NN	_	_	_
127	Fe	Fe	NNP	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	NO3	no3	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	2	2	CD	_	_	_
132	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
66	Escherichia	escherichia	FW	Organism	_	_
67	coli	coli	FW	Organism	_	_
68	O25b	o25b	NN	_	_	_
69	:	:	:	_	_	_
70	H4-ST131	h4-st131	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Escherichia	escherichia	FW	Organism	_	_
73	coli	coli	FW	Organism	_	_
74	ptsN	ptsn	NN	GEN	_	_
75	mutant	mutant	JJ	_	_	_
76	strain	strain	NN	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	Escherichia	escherichia	FW	Organism	_	_
79	coli	coli	FW	Organism	_	_
80	SCI-07	sci-07	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Escherichia	escherichia	FW	Organism	_	_
83	coli	coli	FW	Organism	_	_
84	SE15	se15	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Escherichia	escherichia	FW	Organism	_	_
87	coli	coli	FW	Organism	_	_
88	strains	strain	NNS	_	_	_
89	E.coli	e.coli	JJ	_	_	_
90	C	c	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	DSMZ	dsmz	NN	_	_	_
93	4860	4860	CD	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	,	,	,	_	_	_
96	E.	e.	FW	_	_	_
97	coli	coli	FW	_	_	_
98	Crooks	crook	NNS	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	DSMZ	dsmz	NN	_	_	_
101	1576	1576	CD	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	,	,	,	_	_	_
104	E.	e.	FW	_	_	_
105	coli	coli	FW	_	_	_
106	DH5α	dh5α	NN	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	DSMZ	dsmz	NN	_	_	_
109	6897	6897	CD	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	E.	e.	FW	_	_	_
112	coli	coli	FW	_	_	_
113	W	w	NN	_	_	_
114	-LRB-	-lrb-	-LRB-	_	_	_
115	DSMZ	dsmz	NN	_	_	_
116	1116	1116	CD	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	,	,	,	_	_	_
119	E.	e.	FW	_	_	_
120	coli	coli	FW	_	_	_
121	W3110	w3110	NN	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	DSMZ	dsmz	NN	_	_	_
124	5911	5911	CD	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	were	be	VBD	_	_	_
127	obtained	obtain	VBN	_	_	_
128	from	from	IN	_	_	_
129	DSMZ-German	DSMZ-German	NNP	_	_	_
130	Collection	Collection	NNP	_	_	_
131	of	of	IN	_	_	_
132	Microorganism	Microorganism	NNP	_	_	_
133	and	and	CC	_	_	_
134	Cell	cell	NN	_	_	_
135	Cultures	culture	NNS	_	_	_
136	;	;	:	_	_	_
137	E.	e.	FW	_	_	_
138	coli	coli	FW	_	_	_
139	BL21	bl21	NN	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	DE3	de3	NN	_	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	was	be	VBD	_	_	_
144	purchased	purchase	VBN	_	_	_
145	as	as	IN	_	_	_
146	competent	competent	JJ	_	_	_
147	cells	cell	NNS	_	_	_
148	from	from	IN	_	_	_
149	Agilent	Agilent	NNP	_	_	_
150	-LRB-	-lrb-	-LRB-	_	_	_
151	Agilent	Agilent	NNP	_	_	_
152	Technologies	Technologies	NNPS	_	_	_
153	Inc.	Inc.	NNP	_	_	_
154	,	,	,	_	_	_
155	USA	USA	NNP	_	_	_
156	-RRB-	-rrb-	-RRB-	_	_	_
157	,	,	,	_	_	_
158	E.	e.	FW	_	_	_
159	coli	coli	FW	_	_	_
160	K-12	k-12	NN	_	_	_
161	MG1655	mg1655	NN	_	_	_
162	-LRB-	-lrb-	-LRB-	_	_	_
163	ATCC	atcc	NN	_	_	_
164	700926	700926	CD	_	_	_
165	-RRB-	-rrb-	-RRB-	_	_	_
166	.	.	.	_	_	_

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	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	_	_	FW	_	_	_
5	stress	stress	NN	_	_	_
6	experiment	experiment	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	str	str	FW	_	_	_
6	.	.	.	_	_	_

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

1	MG1655star	mg1655star	JJ	_	_	_
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	W3110	w3110	CD	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	0.5	0.5	CD	_	_	_
8	MIC	mic	NN	_	_	_
9	of	of	IN	_	_	_
10	cyadox	cyadox	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	treated	treat	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	%	%	NN	_	_	_
18	DMSO	dmso	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	Escherichia	escherichia	FW	Organism	_	_
21	coli	coli	FW	Organism	_	_
22	treated	treat	VBN	_	_	_
23	with	with	IN	_	_	_
24	MBC	mbc	NN	_	_	_
25	of	of	IN	_	_	_
26	cyadox	cyadox	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Escherichia	escherichia	FW	Organism	_	_
29	coli	coli	FW	Organism	_	_
30	treated	treat	VBN	_	_	_
31	with	with	IN	_	_	_
32	MBC	mbc	NN	_	_	_
33	of	of	IN	_	_	_
34	olaquindox	olaquindox	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Escherichia	escherichia	FW	Organism	_	_
37	coli	coli	FW	Organism	_	_
38	treated	treat	VBN	_	_	_
39	with	with	IN	_	_	_
40	MIC	mic	NN	_	_	_
41	of	of	IN	_	_	_
42	olaquindox	olaquindox	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Escherichia	escherichia	FW	Organism	_	_
45	coli	coli	FW	Organism	_	_
46	W3110	w3110	NN	_	_	_
47	,	,	,	_	_	_
48	0	0	CD	_	_	_
49	min	min	NN	_	_	_
50	before	before	IN	_	_	_
51	treatment	treatment	NN	_	_	_
52	,	,	,	_	_	_
53	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
54	+	+	CC	_	_	_
55	50	50	CD	_	_	_
56	ug/ml	ug/ml	NN	_	_	_
57	Tryptophan	tryptophan	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Escherichia	escherichia	FW	Organism	_	_
60	coli	coli	FW	Organism	_	_
61	W3110	w3110	NN	_	_	_
62	,	,	,	_	_	_
63	0	0	CD	_	_	_
64	min	min	NN	_	_	_
65	before	before	IN	_	_	_
66	treatment	treatment	NN	_	_	_
67	in	in	IN	_	_	_
68	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
69	+	+	CC	_	_	_
70	50	50	CD	_	_	_
71	ug/ml	ug/ml	NN	_	_	_
72	Tryptophan	tryptophan	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Escherichia	escherichia	FW	Organism	_	_
75	coli	coli	FW	Organism	_	_
76	W3110	w3110	NN	_	_	_
77	,5	,5	CD	_	_	_
78	min	min	NN	_	_	_
79	0.01	0.01	CD	_	_	_
80	M	m	NN	_	_	_
81	Sodium	sodium	NN	_	_	_
82	Azide	azide	NN	_	_	_
83	treatment	treatment	NN	_	_	_
84	vs	vs	CC	_	_	_
85	0	0	CD	_	_	_
86	min	min	NN	_	_	_
87	before	before	IN	_	_	_
88	treatment	treatment	NN	_	_	_
89	in	in	IN	_	_	_
90	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
91	+	+	CC	_	_	_
92	50	50	CD	_	_	_
93	ug/ml	ug/ml	NN	_	_	_
94	Tryptophan	tryptophan	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Escherichia	escherichia	FW	Organism	_	_
97	coli	coli	FW	Organism	_	_
98	W3110gyrb234	w3110gyrb234	NN	_	_	_
99	,	,	,	_	_	_
100	LB	lb	NN	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	Escherichia	escherichia	FW	Organism	_	_
103	coli	coli	FW	Organism	_	_
104	W3110gyrb234	w3110gyrb234	NN	_	_	_
105	,	,	,	_	_	_
106	LB	lb	NN	_	_	_
107	,	,	,	_	_	_
108	10	10	CD	_	_	_
109	min	min	NN	_	_	_
110	after	after	IN	_	_	_
111	upshift	upshift	NN	_	_	_
112	to	to	TO	_	_	_
113	42	42	CD	_	_	_
114	C	c	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Escherichia	escherichia	FW	Organism	_	_
117	coli	coli	FW	Organism	_	_
118	W3110gyrb234	w3110gyrb234	NN	_	_	_
119	,	,	,	_	_	_
120	LB	lb	NN	_	_	_
121	,	,	,	_	_	_
122	20	20	CD	_	_	_
123	min	min	NN	_	_	_
124	after	after	IN	_	_	_
125	upshift	upshift	NN	_	_	_
126	to	to	TO	_	_	_
127	42	42	CD	_	_	_
128	C	c	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	Escherichia	escherichia	FW	Organism	_	_
131	coli	coli	FW	Organism	_	_
132	W3110gyrb234	w3110gyrb234	NN	_	_	_
133	,	,	,	_	_	_
134	LB	lb	NN	_	_	_
135	,	,	,	_	_	_
136	2	2	CD	_	_	_
137	min	min	NN	_	_	_
138	after	after	IN	_	_	_
139	upshift	upshift	NN	_	_	_
140	to	to	TO	_	_	_
141	42	42	CD	_	_	_
142	C	c	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	Escherichia	escherichia	FW	Organism	_	_
145	coli	coli	FW	Organism	_	_
146	W3110gyrb234	w3110gyrb234	NN	_	_	_
147	,	,	,	_	_	_
148	LB	lb	NN	_	_	_
149	,	,	,	_	_	_
150	5	5	CD	_	_	_
151	min	min	NN	_	_	_
152	after	after	IN	_	_	_
153	upshift	upshift	NN	_	_	_
154	to	to	TO	_	_	_
155	42	42	CD	_	_	_
156	C	c	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	Escherichia	escherichia	FW	Organism	_	_
159	coli	coli	FW	Organism	_	_
160	was	be	VBD	_	_	_
161	grown	grow	VBN	_	_	_
162	aerobically	aerobically	RB	_	_	_
163	in	in	IN	_	_	_
164	Luria-Bertani	Luria-Bertani	NNP	_	_	_
165	-LRB-	-lrb-	-LRB-	_	_	_
166	LB	LB	NNP	_	_	_
167	-RRB-	-rrb-	-RRB-	_	_	_
168	broth	broth	NN	_	_	_
169	and	and	CC	_	_	_
170	LB	lb	NN	_	_	_
171	+	+	CC	_	_	_
172	glycerol	glycerol	NN	SUPP	_	_
173	at	at	IN	_	_	_
174	30	30	CD	_	_	_
175	°C	°c	NN	_	_	_
176	in	in	IN	_	_	_
177	an	a	DT	_	_	_
178	incubator	incubator	NN	_	_	_
179	shaker	shaker	NN	_	_	_
180	at	at	IN	_	_	_
181	150	150	CD	_	_	_
182	r.p.m.	r.p.m.	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	Escherichia	escherichia	FW	Organism	_	_
185	coli	coli	FW	Organism	_	_
186	was	be	VBD	_	_	_
187	grown	grow	VBN	_	_	_
188	aerobically	aerobically	RB	_	_	_
189	in	in	IN	_	_	_
190	Luria-Bertani	Luria-Bertani	NNP	_	_	_
191	-LRB-	-lrb-	-LRB-	_	_	_
192	LB	LB	NNP	_	_	_
193	-RRB-	-rrb-	-RRB-	_	_	_
194	broth	broth	NN	_	_	_
195	at	at	IN	_	_	_
196	30	30	CD	_	_	_
197	°C	°c	NN	_	_	_
198	in	in	IN	_	_	_
199	an	a	DT	_	_	_
200	incubator	incubator	NN	_	_	_
201	shaker	shaker	NN	_	_	_
202	at	at	IN	_	_	_
203	150	150	CD	_	_	_
204	r.p.m.	r.p.m.	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	Escherichia	escherichia	FW	Organism	_	_
207	coli	coli	FW	Organism	_	_
208	wild	wild	JJ	_	_	_
209	type	type	NN	_	_	_
210	strain	strain	NN	_	_	_
211	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
212	Escherichia	escherichia	FW	Organism	_	_
213	coli	coli	FW	Organism	_	_
214	wild	wild	JJ	_	_	_
215	type	type	NN	_	_	_
216	vs	vs	CC	_	_	_
217	luxS	luxs	NN	GEN	_	_
218	mutants	mutant	NNS	_	_	_
219	with	with	IN	_	_	_
220	10	10	CD	_	_	_
221	%	%	NN	_	_	_
222	H2O2	h2o2	NN	_	_	_
223	Rep1	rep1	JJ	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	Escherichia	escherichia	FW	Organism	_	_
226	coli	coli	FW	Organism	_	_
227	wild	wild	JJ	_	_	_
228	type	type	NN	_	_	_
229	vs	vs	CC	_	_	_
230	luxS	luxs	NN	GEN	_	_
231	mutants	mutant	NNS	_	_	_
232	with	with	IN	_	_	_
233	10	10	CD	_	_	_
234	%	%	NN	_	_	_
235	H2O2	h2o2	NN	_	_	_
236	Rep2	rep2	JJ	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	Escherichia	escherichia	FW	Organism	_	_
239	coli	coli	FW	Organism	_	_
240	wild	wild	JJ	_	_	_
241	type	type	NN	_	_	_
242	vs	vs	CC	_	_	_
243	luxS	luxs	NN	GEN	_	_
244	mutants	mutant	NNS	_	_	_
245	with	with	IN	_	_	_
246	30	30	CD	_	_	_
247	%	%	NN	_	_	_
248	H2O2	h2o2	NN	_	_	_
249	Rep1	rep1	JJ	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	Escherichia	escherichia	FW	Organism	_	_
252	coli	coli	FW	Organism	_	_
253	wild	wild	JJ	_	_	_
254	type	type	NN	_	_	_
255	vs	vs	CC	_	_	_
256	luxS	luxs	NN	GEN	_	_
257	mutants	mutant	NNS	_	_	_
258	with	with	IN	_	_	_
259	30	30	CD	_	_	_
260	%	%	NN	_	_	_
261	H2O2	h2o2	NN	_	_	_
262	Rep2	rep2	JJ	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	Escherichia	escherichia	FW	Organism	_	_
265	coli	coli	FW	Organism	_	_
266	wild	wild	JJ	_	_	_
267	type	type	NN	_	_	_
268	vs	vs	CC	_	_	_
269	luxS	luxs	NN	GEN	_	_
270	mutants	mutant	NNS	_	_	_
271	without	without	IN	_	_	_
272	H2O2	h2o2	NN	_	_	_
273	Rep1	rep1	JJ	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	Escherichia	escherichia	FW	Organism	_	_
276	coli	coli	FW	Organism	_	_
277	wild	wild	JJ	_	_	_
278	type	type	NN	_	_	_
279	vs	vs	CC	_	_	_
280	luxS	luxs	NN	GEN	_	_
281	mutants	mutant	NNS	_	_	_
282	without	without	IN	_	_	_
283	H2O2	h2o2	NN	_	_	_
284	Rep2	rep2	JJ	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	Escherichia	escherichia	FW	Organism	_	_
287	coli	coli	FW	Organism	_	_
288	with	with	IN	_	_	_
289	1	1	CD	_	_	_
290	%	%	NN	_	_	_
291	tannins	tannin	NNS	_	_	_
292	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
293	Escherichia	escherichia	FW	_	_	_
294	ProQ	ProQ	NNP	_	_	_
295	coIP	coIP	NNP	_	_	_
296	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
297	Escherichia	escherichia	FW	_	_	_
298	ProQ	ProQ	NNP	_	_	_
299	Lysate	Lysate	NNP	_	_	_
300	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
301	Escherichia	escherichia	FW	_	_	_
302	WT	WT	NNP	_	_	_
303	coIP	coIP	NNP	_	_	_
304	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
305	Escherichia	escherichia	FW	_	_	_
306	WT	WT	NNP	_	_	_
307	Lysate	Lysate	NNP	_	_	_
308	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
309	Estradiol	Estradiol	NNP	_	_	_
310	Treatment	treatment	NN	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	EtBr	etbr	NN	_	_	_
313	replicate	replicate	VBP	_	_	_
314	1	1	CD	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	EtBr	etbr	NN	_	_	_
317	replicate	replicate	VBP	_	_	_
318	2	2	CD	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	EtBr	etbr	NN	_	_	_
321	replicate	replicate	VBP	_	_	_
322	3	3	CD	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	ethanol	ethanol	NN	_	_	_
325	treatment	treatment	NN	_	_	_
326	:	:	:	_	_	_
327	40	40	CD	_	_	_
328	g	g	NN	_	_	_
329	EtOH/L	etoh/l	NN	_	_	_
330	,	,	,	_	_	_
331	10	10	CD	_	_	_
332	min	min	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	ethanol	ethanol	NN	_	_	_
335	treatment	treatment	NN	_	_	_
336	:	:	:	_	_	_
337	40	40	CD	_	_	_
338	g	g	NN	_	_	_
339	EtOH/L	etoh/l	NN	_	_	_
340	,	,	,	_	_	_
341	70	70	CD	_	_	_
342	min	min	NN	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	ethanol	ethanol	NN	_	_	_
345	treatment	treatment	NN	_	_	_
346	:	:	:	_	_	_
347	no	no	DT	_	_	_
348	ethanol	ethanol	NN	_	_	_
349	exposure	exposure	NN	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	Ethanol	ethanol	NN	_	_	_
352	was	be	VBD	_	_	_
353	added	add	VBN	_	_	_
354	to	to	TO	_	_	_
355	40	40	CD	_	_	_
356	g/L	g/l	NN	_	_	_
357	once	once	RB	_	_	_
358	A600	a600	NN	_	_	_
359	of	of	IN	_	_	_
360	cultures	culture	NNS	_	_	_
361	reached	reach	VBD	_	_	_
362	0.3	0.3	CD	_	_	_
363	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	taken	take	VBN	_	_	_
4	prior	prior	RB	_	_	_
5	to	to	TO	_	_	_
6	ethanol	ethanol	NN	_	_	_
7	addition	addition	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	T0	t0	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	10	10	CD	_	_	_
13	min	min	NN	_	_	_
14	after	after	IN	_	_	_
15	addition	addition	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	T1	t1	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	70	70	CD	_	_	_
22	min	min	NN	_	_	_
23	after	after	IN	_	_	_
24	addition	addition	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	T2	t2	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	rapidly	rapidly	RB	_	_	_
5	onto	onto	IN	_	_	_
6	0.2	0.2	CD	_	_	_
7	µm	µm	NN	_	_	_
8	filters	filter	NNS	_	_	_
9	by	by	IN	_	_	_
10	vacuum	vacuum	NN	_	_	_
11	then	then	RB	_	_	_
12	flash-frozen	flash-frozen	JJ	_	_	_
13	in	in	IN	_	_	_
14	liquid	liquid	JJ	_	_	_
15	nitrogen	nitrogen	NN	_	_	_
16	to	to	TO	_	_	_
17	arrest	arrest	VB	_	_	_
18	ribosomes	ribosome	NNS	_	_	_
19	.	.	.	_	_	_

1	Ribosome	ribosome	NN	_	_	_
2	footprinting	footprinting	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	micrococcal	micrococcal	JJ	_	_	_
8	nuclease	nuclease	NN	_	_	_
9	digestion	digestion	NN	_	_	_
10	followed	follow	VBN	_	_	_
11	by	by	IN	_	_	_
12	monosome	monosome	JJ	_	_	_
13	isolation	isolation	NN	_	_	_
14	by	by	IN	_	_	_
15	sucrose	sucrose	NN	_	_	_
16	gradient	gradient	NN	_	_	_
17	centrifugation	centrifugation	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	EtOH	etoh	NN	_	_	_
3	replicate	replicate	VB	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	EtOH	etoh	NN	_	_	_
7	replicate	replicate	VB	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	EtOH	etoh	NN	_	_	_
11	replicate	replicate	VBP	_	_	_
12	3	3	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	-LSB-	-lsb-	-LRB-	_	_	_
15	Eubacterium	eubacterium	NN	_	_	_
16	-RSB-	-rsb-	-RRB-	_	_	_
17	rectale	rectale	JJ	_	_	_
18	ATCC	atcc	NN	_	_	_
19	33656	33656	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
21	Eureka	eureka	FW	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
23	EvgSc	evgsc	NN	_	_	_
24	_	_	NN	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	EvgSc	evgsc	NN	_	_	_
28	_	_	NN	_	_	_
29	2	2	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	EvgSc	evgsc	NN	_	_	_
32	mutant	mutant	JJ	_	_	_
33	rep	rep	NN	GEN	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	EvgSc	evgsc	NN	_	_	_
37	mutant	mutant	JJ	_	_	_
38	rep	rep	NN	GEN	_	_
39	2	2	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	EvgSc	evgsc	NN	_	_	_
42	_	_	CD	_	_	_
43	ompR	ompr	NN	GEN	_	_
44	_	_	NN	_	_	_
45	1	1	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	EvgSc	evgsc	NN	_	_	_
48	_	_	CD	_	_	_
49	ompR	ompr	NN	GEN	_	_
50	_	_	NN	_	_	_
51	2	2	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	EvgSc	evgsc	NN	_	_	_
54	ompR	ompr	NN	GEN	_	_
55	double	double	JJ	_	_	_
56	mutant	mutant	JJ	_	_	_
57	rep	rep	NN	GEN	_	_
58	1	1	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	EvgSc	evgsc	NN	_	_	_
61	ompR	ompr	NN	GEN	_	_
62	double	double	JJ	_	_	_
63	mutant	mutant	JJ	_	_	_
64	rep	rep	NN	GEN	_	_
65	2	2	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	evolved	evolve	VBD	_	_	_
68	1	1	CD	_	_	_
69	min	min	NN	_	_	_
70	rep6	rep6	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	evolved	evolve	VBD	_	_	_
73	1	1	CD	_	_	_
74	min	min	NN	_	_	_
75	rep8	rep8	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	evolved	evolve	VBD	_	_	_
78	5	5	CD	_	_	_
79	min	min	NN	_	_	_
80	rep6	rep6	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	evolved	evolve	VBD	_	_	_
83	5	5	CD	_	_	_
84	min	min	NN	_	_	_
85	rep8	rep8	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	evolved	evolve	VBD	_	_	_
88	9	9	CD	_	_	_
89	min	min	NN	_	_	_
90	rep6	rep6	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	evolved	evolve	VBD	_	_	_
93	9	9	CD	_	_	_
94	min	min	NN	_	_	_
95	rep7	rep7	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Evolved	evolve	VBD	_	_	_
98	I	I	PRP	_	_	_
99	-	-	:	_	_	_
100	cells	cell	NNS	_	_	_
101	at	at	IN	_	_	_
102	amino	amino	NN	_	_	_
103	acid	acid	NN	_	_	_
104	starvation	starvation	NN	_	_	_
105	in	in	IN	_	_	_
106	monoculture	monoculture	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	Evolved	evolve	VBD	_	_	_
109	I	I	PRP	_	_	_
110	-	-	:	_	_	_
111	cells	cell	NNS	_	_	_
112	at	at	IN	_	_	_
113	log	log	NN	_	_	_
114	phase	phase	NN	_	_	_
115	in	in	IN	_	_	_
116	monoculture	monoculture	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	Evolved	evolve	VBD	_	_	_
119	I	I	PRP	_	_	_
120	-	-	:	_	_	_
121	cells	cell	NNS	_	_	_
122	in	in	IN	_	_	_
123	coculture	coculture	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Evolved	evolve	VBD	_	_	_
126	I	I	PRP	_	_	_
127	-	-	:	_	_	_
128	cells	cell	NNS	_	_	_
129	in	in	IN	_	_	_
130	coculture	coculture	NN	_	_	_
131	,	,	,	_	_	_
132	a	a	DT	_	_	_
133	biological	biological	JJ	_	_	_
134	replicate	replicate	VBP	_	_	_
135	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
136	Evolved	evolve	VBD	_	_	_
137	L	l	NN	_	_	_
138	-	-	:	_	_	_
139	cells	cell	NNS	_	_	_
140	at	at	IN	_	_	_
141	amino	amino	NN	_	_	_
142	acid	acid	NN	_	_	_
143	starvation	starvation	NN	_	_	_
144	in	in	IN	_	_	_
145	monoculture	monoculture	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	Evolved	evolve	VBD	_	_	_
148	L	l	NN	_	_	_
149	-	-	:	_	_	_
150	cells	cell	NNS	_	_	_
151	at	at	IN	_	_	_
152	log	log	NN	_	_	_
153	phase	phase	NN	_	_	_
154	in	in	IN	_	_	_
155	monoculture	monoculture	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	Evolved	evolve	VBD	_	_	_
158	L	l	NN	_	_	_
159	-	-	:	_	_	_
160	cells	cell	NNS	_	_	_
161	at	at	IN	_	_	_
162	log	log	NN	_	_	_
163	phase	phase	NN	_	_	_
164	in	in	IN	_	_	_
165	monoculture	monoculture	NN	_	_	_
166	,	,	,	_	_	_
167	a	a	DT	_	_	_
168	technical	technical	JJ	_	_	_
169	replicate	replicate	VBP	_	_	_
170	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
171	Evolved	evolve	VBD	_	_	_
172	L	l	NN	_	_	_
173	-	-	:	_	_	_
174	cells	cell	NNS	_	_	_
175	in	in	IN	_	_	_
176	coculture	coculture	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	Evolved	evolve	VBD	_	_	_
179	L	l	NN	_	_	_
180	-	-	:	_	_	_
181	cells	cell	NNS	_	_	_
182	in	in	IN	_	_	_
183	coculture	coculture	NN	_	_	_
184	,	,	,	_	_	_
185	a	a	DT	_	_	_
186	biological	biological	JJ	_	_	_
187	replicate	replicate	VBP	_	_	_
188	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
189	Evolved	evolve	VBD	_	_	_
190	strain	strain	NN	_	_	_
191	A	a	NN	_	_	_
192	,	,	,	_	_	_
193	time	time	NN	_	_	_
194	point	point	NN	_	_	_
195	1	1	CD	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	Evolved	evolve	VBN	_	_	_
198	strain	strain	NN	_	_	_
199	A	a	NN	_	_	_
200	,	,	,	_	_	_
201	time	time	NN	_	_	_
202	point	point	NN	_	_	_
203	2	2	CD	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
205	Evolved	evolve	VBN	_	_	_
206	strain	strain	NN	_	_	_
207	A	a	NN	_	_	_
208	,	,	,	_	_	_
209	time	time	NN	_	_	_
210	point	point	NN	_	_	_
211	3	3	CD	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	Evolved	evolve	VBN	_	_	_
214	strain	strain	NN	_	_	_
215	A	a	NN	_	_	_
216	,	,	,	_	_	_
217	time	time	NN	_	_	_
218	point	point	NN	_	_	_
219	4	4	CD	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
221	Evolved	evolve	VBN	_	_	_
222	strain	strain	NN	_	_	_
223	A	a	NN	_	_	_
224	,	,	,	_	_	_
225	time	time	NN	_	_	_
226	point	point	NN	_	_	_
227	5	5	CD	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
229	Evolved	evolve	VBN	_	_	_
230	strain	strain	NN	_	_	_
231	B	b	NN	_	_	_
232	,	,	,	_	_	_
233	time	time	NN	_	_	_
234	point	point	NN	_	_	_
235	1	1	CD	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	Evolved	evolve	VBN	_	_	_
238	strain	strain	NN	_	_	_
239	B	b	NN	_	_	_
240	,	,	,	_	_	_
241	time	time	NN	_	_	_
242	point	point	NN	_	_	_
243	2	2	CD	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
245	Evolved	evolve	VBN	_	_	_
246	strain	strain	NN	_	_	_
247	B	b	NN	_	_	_
248	,	,	,	_	_	_
249	time	time	NN	_	_	_
250	point	point	NN	_	_	_
251	3	3	CD	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	Evolved	evolve	VBN	_	_	_
254	strain	strain	NN	_	_	_
255	B	b	NN	_	_	_
256	,	,	,	_	_	_
257	time	time	NN	_	_	_
258	point	point	NN	_	_	_
259	4	4	CD	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
261	Evolved	evolve	VBN	_	_	_
262	strain	strain	NN	_	_	_
263	B	b	NN	_	_	_
264	,	,	,	_	_	_
265	time	time	NN	_	_	_
266	point	point	NN	_	_	_
267	5	5	CD	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
269	Evolved	evolve	VBN	_	_	_
270	strain	strain	NN	_	_	_
271	C	c	NN	_	_	_
272	,	,	,	_	_	_
273	time	time	NN	_	_	_
274	point	point	NN	_	_	_
275	1	1	CD	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	Evolved	evolve	VBN	_	_	_
278	strain	strain	NN	_	_	_
279	C	c	NN	_	_	_
280	,	,	,	_	_	_
281	time	time	NN	_	_	_
282	point	point	NN	_	_	_
283	2	2	CD	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
285	Evolved	evolve	VBN	_	_	_
286	strain	strain	NN	_	_	_
287	C	c	NN	_	_	_
288	,	,	,	_	_	_
289	time	time	NN	_	_	_
290	point	point	NN	_	_	_
291	3	3	CD	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	Evolved	evolve	VBN	_	_	_
294	strain	strain	NN	_	_	_
295	C	c	NN	_	_	_
296	,	,	,	_	_	_
297	time	time	NN	_	_	_
298	point	point	NN	_	_	_
299	4	4	CD	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
301	Evolved	evolve	VBN	_	_	_
302	strain	strain	NN	_	_	_
303	C	c	NN	_	_	_
304	,	,	,	_	_	_
305	time	time	NN	_	_	_
306	point	point	NN	_	_	_
307	5	5	CD	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
309	Evolved	evolve	VBN	_	_	_
310	strain	strain	NN	_	_	_
311	D	d	NN	_	_	_
312	,	,	,	_	_	_
313	time	time	NN	_	_	_
314	point	point	NN	_	_	_
315	1	1	CD	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	Evolved	evolve	VBN	_	_	_
318	strain	strain	NN	_	_	_
319	D	d	NN	_	_	_
320	,	,	,	_	_	_
321	time	time	NN	_	_	_
322	point	point	NN	_	_	_
323	2	2	CD	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
325	Evolved	evolve	VBN	_	_	_
326	strain	strain	NN	_	_	_
327	D	d	NN	_	_	_
328	,	,	,	_	_	_
329	time	time	NN	_	_	_
330	point	point	NN	_	_	_
331	3	3	CD	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	Evolved	evolve	VBN	_	_	_
334	strain	strain	NN	_	_	_
335	D	d	NN	_	_	_
336	,	,	,	_	_	_
337	time	time	NN	_	_	_
338	point	point	NN	_	_	_
339	4	4	CD	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
341	Evolved	evolve	VBN	_	_	_
342	strain	strain	NN	_	_	_
343	D	d	NN	_	_	_
344	,	,	,	_	_	_
345	time	time	NN	_	_	_
346	point	point	NN	_	_	_
347	5	5	CD	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
349	Evolved	evolve	VBN	_	_	_
350	strain	strain	NN	_	_	_
351	E	e	NN	_	_	_
352	,	,	,	_	_	_
353	time	time	NN	_	_	_
354	point	point	NN	_	_	_
355	1	1	CD	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	Evolved	evolve	VBN	_	_	_
358	strain	strain	NN	_	_	_
359	E	e	NN	_	_	_
360	,	,	,	_	_	_
361	time	time	NN	_	_	_
362	point	point	NN	_	_	_
363	2	2	CD	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
365	Evolved	evolve	VBN	_	_	_
366	strain	strain	NN	_	_	_
367	E	e	NN	_	_	_
368	,	,	,	_	_	_
369	time	time	NN	_	_	_
370	point	point	NN	_	_	_
371	3	3	CD	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	Evolved	evolve	VBN	_	_	_
374	strain	strain	NN	_	_	_
375	E	e	NN	_	_	_
376	,	,	,	_	_	_
377	time	time	NN	_	_	_
378	point	point	NN	_	_	_
379	4	4	CD	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
381	Evolved	evolve	VBN	_	_	_
382	strain	strain	NN	_	_	_
383	E	e	NN	_	_	_
384	,	,	,	_	_	_
385	time	time	NN	_	_	_
386	point	point	NN	_	_	_
387	5	5	CD	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
389	Evolved	evolve	VBN	_	_	_
390	strain	strain	NN	_	_	_
391	F	f	NN	_	_	_
392	,	,	,	_	_	_
393	time	time	NN	_	_	_
394	point	point	NN	_	_	_
395	1	1	CD	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
397	Evolved	evolve	VBN	_	_	_
398	strain	strain	NN	_	_	_
399	F	f	NN	_	_	_
400	,	,	,	_	_	_
401	time	time	NN	_	_	_
402	point	point	NN	_	_	_
403	2	2	CD	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
405	Evolved	evolve	VBN	_	_	_
406	strain	strain	NN	_	_	_
407	F	f	NN	_	_	_
408	,	,	,	_	_	_
409	time	time	NN	_	_	_
410	point	point	NN	_	_	_
411	3	3	CD	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	Evolved	evolve	VBN	_	_	_
414	strain	strain	NN	_	_	_
415	F	f	NN	_	_	_
416	,	,	,	_	_	_
417	time	time	NN	_	_	_
418	point	point	NN	_	_	_
419	4	4	CD	_	_	_
420	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
421	Evolved	evolve	VBN	_	_	_
422	strain	strain	NN	_	_	_
423	F	f	NN	_	_	_
424	,	,	,	_	_	_
425	time	time	NN	_	_	_
426	point	point	NN	_	_	_
427	5	5	CD	_	_	_
428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
429	evolved	evolve	VBD	_	_	_
430	_	_	CD	_	_	_
431	temperature	temperature	NN	_	_	_
432	_	_	CD	_	_	_
433	Up	up	IN	_	_	_
434	_	_	CD	_	_	_
435	0	0	CD	_	_	_
436	min	min	NN	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	evolved	evolve	VBD	_	_	_
439	_	_	CD	_	_	_
440	temperature	temperature	NN	_	_	_
441	_	_	VBD	_	_	_
442	Up	up	RP	_	_	_
443	_	_	SYM	_	_	_
444	16	16	CD	_	_	_
445	min	min	NN	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	evolved	evolve	VBD	_	_	_
448	_	_	CD	_	_	_
449	temperature	temperature	NN	_	_	_
450	_	_	VBD	_	_	_
451	Up	up	RP	_	_	_
452	_	_	SYM	_	_	_
453	44	44	CD	_	_	_
454	min	min	NN	_	_	_
455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
456	evolved	evolve	VBD	_	_	_
457	temperature	temperature	NN	_	_	_
458	up	up	IN	_	_	_
459	shift	shift	NN	_	_	_
460	0	0	CD	_	_	_
461	min	min	NN	_	_	_
462	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
463	evolved	evolve	VBD	_	_	_
464	temperature	temperature	NN	_	_	_
465	up	up	IN	_	_	_
466	shift	shift	NN	_	_	_
467	16	16	CD	_	_	_
468	min	min	NN	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
470	evolved	evolve	VBD	_	_	_
471	temperature	temperature	NN	_	_	_
472	up	up	IN	_	_	_
473	shift	shift	NN	_	_	_
474	44	44	CD	_	_	_
475	min	min	NN	_	_	_
476	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
477	Exact	exact	JJ	_	_	_
478	details	detail	NNS	_	_	_
479	for	for	IN	_	_	_
480	the	the	DT	_	_	_
481	full	full	JJ	_	_	_
482	computational	computational	JJ	_	_	_
483	pipeline	pipeline	NN	_	_	_
484	are	be	VBP	_	_	_
485	available	available	JJ	_	_	_
486	at	at	IN	_	_	_
487	https://github.com/wilkelab/AG3C_starvation_tc_RNAseq	https://github.com/wilkelab/ag3c_starvation_tc_rnaseq	NN	_	_	_
488	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	exopolyphosphatase	exopolyphosphatase	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	PPX	ppx	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	mutant	mutant	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Exp	exp	NN	_	_	_
9	1	1	CD	_	_	_
10	_	_	NN	_	_	_
11	control	control	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Exp	Exp	NNP	_	_	_
14	1	1	CD	_	_	_
15	_	_	CD	_	_	_
16	IP	IP	NNP	_	_	_
17	sample	sample	NN	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Exp	exp	NN	_	_	_
20	2	2	CD	_	_	_
21	_	_	NN	_	_	_
22	control	control	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	Exp	exp	NN	_	_	_
25	2	2	CD	_	_	_
26	_	_	CD	_	_	_
27	IP	IP	NNP	_	_	_
28	sample	sample	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	experiment	experiment	NN	_	_	_
31	#	#	#	_	_	_
32	115	115	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	experiment	experiment	NN	_	_	_
35	#	#	#	_	_	_
36	116	116	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	experiment	experiment	NN	_	_	_
39	#	#	#	_	_	_
40	203	203	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	experiment	experiment	NN	_	_	_
43	#	#	#	_	_	_
44	204	204	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	experiment	experiment	NN	_	_	_
47	#	#	#	_	_	_
48	205	205	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	experiment	experiment	NN	_	_	_
51	#	#	#	_	_	_
52	206	206	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	experiment	experiment	NN	_	_	_
55	#	#	#	_	_	_
56	303	303	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	experiment	experiment	NN	_	_	_
59	#	#	#	_	_	_
60	305	305	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	experiment	experiment	NN	_	_	_
63	#	#	#	_	_	_
64	306	306	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
66	Experimental	experimental	JJ	_	_	_
67	,	,	,	_	_	_
68	biological	biological	JJ	_	_	_
69	rep1	rep1	NN	_	_	_
70	G1	g1	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Experimental	experimental	JJ	_	_	_
73	,	,	,	_	_	_
74	biological	biological	JJ	_	_	_
75	rep1	rep1	NN	_	_	_
76	G2	g2	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	Experimental	experimental	JJ	_	_	_
79	,	,	,	_	_	_
80	biological	biological	JJ	_	_	_
81	rep1	rep1	NN	_	_	_
82	G3	g3	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Experimental	experimental	JJ	_	_	_
85	,	,	,	_	_	_
86	biological	biological	JJ	_	_	_
87	rep2	rep2	NN	_	_	_
88	G4	g4	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Experimental	experimental	JJ	_	_	_
91	,	,	,	_	_	_
92	biological	biological	JJ	_	_	_
93	rep2	rep2	NN	_	_	_
94	G5	g5	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Experimental	experimental	JJ	_	_	_
97	,	,	,	_	_	_
98	biological	biological	JJ	_	_	_
99	rep2	rep2	NN	_	_	_
100	G6	g6	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	Experiments	experiment	NNS	_	_	_
103	were	be	VBD	_	_	_
104	performed	perform	VBN	_	_	_
105	at	at	IN	_	_	_
106	37	37	CD	_	_	_
107	°C	°c	NN	_	_	_
108	and	and	CC	_	_	_
109	followed	follow	VBD	_	_	_
110	three	three	CD	_	_	_
111	steps	step	NNS	_	_	_
112	:	:	:	_	_	_
113	seed	seed	NN	_	_	_
114	culture	culture	NN	_	_	_
115	,	,	,	_	_	_
116	pre-culture	pre-culture	JJ	_	_	_
117	and	and	CC	_	_	_
118	experimental	experimental	JJ	_	_	_
119	culture	culture	NN	_	_	_
120	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Exponential	exponential	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	DO600	do600	NN	_	_	_
6	=	=	JJ	_	_	_
7	0,4	0,4	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	exponential	exponential	JJ	_	_	_
11	culture	culture	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Exponential	Exponential	NNP	_	_	_
14	cultures	culture	NNS	_	_	_
15	of	of	IN	_	_	_
16	transformants	transformant	NNS	_	_	_
17	were	be	VBD	_	_	_
18	inoculated	inoculate	VBN	_	_	_
19	from	from	IN	_	_	_
20	fresh	fresh	JJ	_	_	_
21	overnight	overnight	JJ	_	_	_
22	cultures	culture	NNS	_	_	_
23	in	in	IN	_	_	_
24	LB	lb	NN	MED	_	_
25	medium	medium	NN	MED	_	_
26	supplemented	supplement	VBN	_	_	_
27	with	with	IN	_	_	_
28	25	25	CD	_	_	_
29	µg/ml	µg/ml	NN	_	_	_
30	of	of	IN	_	_	_
31	kanamycin	kanamycin	NN	_	_	_
32	to	to	TO	_	_	_
33	an	a	DT	_	_	_
34	optical	optical	JJ	_	_	_
35	density	density	NN	_	_	_
36	at	at	IN	_	_	_
37	600	600	CD	_	_	_
38	nm	nm	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	OD	od	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	of	of	IN	_	_	_
43	0.1	0.1	CD	_	_	_
44	and	and	CC	_	_	_
45	grown	grow	VBN	_	_	_
46	for	for	IN	_	_	_
47	30	30	CD	_	_	_
48	min	min	NN	_	_	_
49	at	at	IN	_	_	_
50	37	37	CD	_	_	_
51	°C	°c	NN	_	_	_
52	to	to	TO	_	_	_
53	an	a	DT	_	_	_
54	OD	od	NN	_	_	_
55	of	of	IN	_	_	_
56	0.15	0.15	CD	_	_	_
57	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	IPTG	iptg	NN	_	_	_
4	was	be	VBD	_	_	_
5	added	add	VBN	_	_	_
6	to	to	TO	_	_	_
7	a	a	DT	_	_	_
8	final	final	JJ	_	_	_
9	concentration	concentration	NN	_	_	_
10	of	of	IN	_	_	_
11	1	1	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	for	for	IN	_	_	_
14	induction	induction	NN	_	_	_
15	of	of	IN	_	_	_
16	expression	expression	NN	_	_	_
17	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	60	60	CD	_	_	_
3	min	min	NN	_	_	_
4	of	of	IN	_	_	_
5	additional	additional	JJ	_	_	_
6	growth	growth	NN	_	_	_
7	cells	cell	NNS	_	_	_
8	were	be	VBD	_	_	_
9	harvested	harvest	VBN	_	_	_
10	for	for	IN	_	_	_
11	RNA	rna	NN	_	_	_
12	isolation	isolation	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	exponentially	exponentially	RB	_	_	_
3	growing	grow	VBG	_	_	_
4	cells	cell	NNS	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	exponential	exponential	JJ	GrowthPhase	_	_
7	phase	phase	NN	GrowthPhase	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Exponential	Exponential	NNP	_	_	_
10	phase	phase	NN	_	_	_
11	culture	culture	NN	_	_	_
12	of	of	IN	_	_	_
13	EDL933	edl933	NN	_	_	_
14	rpoS	rpos	NN	GEN	_	_
15	mutants	mutant	NNS	_	_	_
16	in	in	IN	_	_	_
17	LB	lb	NN	_	_	_
18	at	at	IN	_	_	_
19	OD600	od600	NN	_	_	_
20	of	of	IN	_	_	_
21	0.3	0.3	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Exponential	exponential	JJ	_	_	_
24	phase	phase	NN	_	_	_
25	culture	culture	NN	_	_	_
26	of	of	IN	_	_	_
27	EDL933	edl933	NN	_	_	_
28	wild	wild	JJ	_	_	_
29	type	type	NN	_	_	_
30	in	in	IN	_	_	_
31	LB	lb	NN	_	_	_
32	at	at	IN	_	_	_
33	OD600	od600	NN	_	_	_
34	of	of	IN	_	_	_
35	0.3	0.3	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	expose	expose	VBP	_	_	_
38	Bacillus	bacillus	NN	_	_	_
39	VOC	voc	NN	_	_	_
40	12h	12h	VBP	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	Expose	expose	VB	_	_	_
43	Bacillus	bacillus	NN	_	_	_
44	VOC-12h	voc-12h	JJ	_	_	_
45	rep1	rep1	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	Expose	expose	VB	_	_	_
48	Bacillus	bacillus	NN	_	_	_
49	VOC-12h	voc-12h	JJ	_	_	_
50	rep2	rep2	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	Expose	expose	VB	_	_	_
53	Bacillus	bacillus	NN	_	_	_
54	VOC-12h	voc-12h	JJ	_	_	_
55	rep3	rep3	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	Expose	expose	VB	_	_	_
58	Bacillus	bacillus	NN	_	_	_
59	VOC-12h	voc-12h	JJ	_	_	_
60	rep4	rep4	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	expose	expose	VBP	_	_	_
63	Bacillus	bacillus	NN	_	_	_
64	VOC24h	voc24h	JJ	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
66	Expose	expose	VB	_	_	_
67	Bacillus	bacillus	NN	_	_	_
68	VOC-24h	voc-24h	JJ	_	_	_
69	rep1	rep1	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
71	Expose	expose	VB	_	_	_
72	Bacillus	bacillus	NN	_	_	_
73	VOC-24h	voc-24h	JJ	_	_	_
74	rep2	rep2	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
76	Expose	expose	VB	_	_	_
77	Bacillus	bacillus	NN	_	_	_
78	VOC-24h	voc-24h	JJ	_	_	_
79	rep3	rep3	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
81	Expose	expose	VB	_	_	_
82	Bacillus	bacillus	NN	_	_	_
83	VOC-24h	voc-24h	JJ	_	_	_
84	rep4	rep4	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
86	expose	expose	VBP	_	_	_
87	Bacillus	bacillus	NN	_	_	_
88	VOC	voc	NN	_	_	_
89	6h	6h	VBP	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
91	Expose	expose	VB	_	_	_
92	Bacillus	bacillus	NN	_	_	_
93	VOC-6h	voc-6h	JJ	_	_	_
94	rep1	rep1	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
96	Expose	expose	VB	_	_	_
97	Bacillus	bacillus	NN	_	_	_
98	VOC-6h	voc-6h	JJ	_	_	_
99	rep2	rep2	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
101	Expose	expose	VB	_	_	_
102	Bacillus	bacillus	NN	_	_	_
103	VOC-6h	voc-6h	JJ	_	_	_
104	rep3	rep3	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
106	Expose	expose	VB	_	_	_
107	Bacillus	bacillus	NN	_	_	_
108	VOC-6h	voc-6h	JJ	_	_	_
109	rep4	rep4	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	Expression	expression	NN	_	_	_
112	data	datum	NNS	_	_	_
113	were	be	VBD	_	_	_
114	analyzed	analyze	VBN	_	_	_
115	with	with	IN	_	_	_
116	the	the	DT	_	_	_
117	Microarray	Microarray	NNP	_	_	_
118	Analysis	analysis	NN	_	_	_
119	Suite	suite	NN	_	_	_
120	,	,	,	_	_	_
121	version	version	NN	_	_	_
122	5.0	5.0	CD	_	_	_
123	-LRB-	-lrb-	-LRB-	_	_	_
124	Affymetrix	Affymetrix	NNP	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	.	.	.	_	_	_

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	NN	_	_	_
2	Expression	expression	NN	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Affymetrix	Affymetrix	NNP	_	_	_
9	microarray	microarray	NN	_	_	_
10	suite	suite	NN	_	_	_
11	5	5	CD	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	MAS5	mas5	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	algorithm	algorithm	NN	_	_	_
16	implemented	implement	VBD	_	_	_
17	in	in	IN	_	_	_
18	Affymetrix	Affymetrix	NNP	_	_	_
19	expression	expression	NN	_	_	_
20	console	console	NN	_	_	_
21	software	software	NN	_	_	_
22	.	.	.	_	_	_

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	Expression	expression	NN	_	_	_
3	of	of	IN	_	_	_
4	introduced	introduce	VBN	_	_	_
5	enzymes	enzyme	NNS	_	_	_
6	for	for	IN	_	_	_
7	3-HP	3-hp	NN	_	_	_
8	productionm	productionm	NN	_	_	_
9	was	be	VBD	_	_	_
10	induced	induce	VBN	_	_	_
11	by	by	IN	_	_	_
12	0.05	0.05	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	IPTG	iptg	NN	_	_	_
15	and	and	CC	_	_	_
16	50	50	CD	_	_	_
17	µM	µm	NN	_	_	_
18	vitamin	vitamin	NN	_	_	_
19	B12	b12	NN	_	_	_
20	when	when	WRB	_	_	_
21	the	the	DT	_	_	_
22	cell	cell	NN	_	_	_
23	reached	reach	VBN	_	_	_
24	at	at	IN	_	_	_
25	the	the	DT	_	_	_
26	early-exponential	early-exponential	JJ	_	_	_
27	growth	growth	NN	_	_	_
28	phase	phase	NN	_	_	_
29	.	.	.	_	_	_

1	T	t	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Expression	expression	NN	_	_	_
4	values	value	NNS	_	_	_
5	were	be	VBD	_	_	_
6	calculated	calculate	VBN	_	_	_
7	by	by	IN	_	_	_
8	the	the	DT	_	_	_
9	software	software	NN	_	_	_
10	package	package	NN	_	_	_
11	Feature	Feature	NNP	_	_	_
12	Extraction	Extraction	NNP	_	_	_
13	10.5.1.1	10.5.1.1	CD	_	_	_
14	using	use	VBG	_	_	_
15	protocol	protocol	NN	_	_	_
16	GE1	ge1	NN	_	_	_
17	_	_	NN	_	_	_
18	105	105	CD	_	_	_
19	_	_	SYM	_	_	_
20	Dec08	dec08	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Agilent	Agilent	NNP	_	_	_
23	Technologies	Technologies	NNPS	_	_	_
24	;	;	:	_	_	_
25	Waldbronn	Waldbronn	NNP	_	_	_
26	,	,	,	_	_	_
27	Germany	Germany	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Exp-rpoS-rep1	exp-rpos-rep1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Exp-rpoS-Rep1	exp-rpos-rep1	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Exp-rpoS-rep2	exp-rpos-rep2	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Exp-rpoS-Rep2	exp-rpos-rep2	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Exp-rpoS-rep3	exp-rpos-rep3	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Exp-rpoS-Rep3	exp-rpos-rep3	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Exp-WT-rep1	exp-wt-rep1	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Exp-WT-Rep1	exp-wt-rep1	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Exp-WT-rep2	exp-wt-rep2	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Exp-WT-Rep2	exp-wt-rep2	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Exp-WT-rep3	exp-wt-rep3	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Exp-WT-Rep3	exp-wt-rep3	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	extracted	extract	VBN	_	_	_
55	molecule	molecule	NN	_	_	_
56	:	:	:	_	_	_
57	plasmid	plasmid	NN	_	_	_
58	DNA	dna	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Extraction	extraction	NN	_	_	_
61	followed	follow	VBN	_	_	_
62	by	by	IN	_	_	_
63	DNase	dnase	NN	_	_	_
64	treatment	treatment	NN	_	_	_
65	with	with	IN	_	_	_
66	TURBO	TURBO	NNP	_	_	_
67	DNA-free	dna-free	JJ	_	_	_
68	kit	kit	NN	_	_	_
69	from	from	IN	_	_	_
70	Ambion	Ambion	NNP	_	_	_
71	.	.	.	_	_	_

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

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

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	Extraction	extraction	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	as	as	IN	_	_	_
6	described	describe	VBN	_	_	_
7	previously	previously	RB	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Li	Li	NNP	_	_	_
10	et	et	FW	_	_	_
11	al.	al.	FW	_	_	_
12	,	,	,	_	_	_
13	2012	2012	CD	_	_	_
14	;	;	:	_	_	_
15	Oh	oh	UH	_	_	_
16	et	et	FW	_	_	_
17	al.	al.	FW	_	_	_
18	,	,	,	_	_	_
19	2011	2011	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

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/mL	u/ml	NN	_	_	_
57	DNase	dnase	NN	_	_	_
58	I	i	CD	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	Roche	Roche	NNP	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	,	,	,	_	_	_
63	1mM	1mm	NN	_	_	_
64	chloramphenicol	chloramphenicol	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	pulverized	pulverize	VBN	_	_	_
4	in	in	IN	_	_	_
5	10mL	10ml	NN	_	_	_
6	canisters	canister	NNS	_	_	_
7	pre-chilled	pre-chill	VBN	_	_	_
8	in	in	IN	_	_	_
9	liquid	liquid	JJ	_	_	_
10	nitrogen	nitrogen	NN	_	_	_
11	.	.	.	_	_	_

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	For	for	IN	_	_	_
2	mRNA-seq	mrna-seq	NN	_	_	_
3	and	and	CC	_	_	_
4	DMS-seq	dms-seq	NN	_	_	_
5	,	,	,	_	_	_
6	cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	pelleted	pellete	VBN	_	_	_
9	by	by	IN	_	_	_
10	centrifuging	centrifuge	VBG	_	_	_
11	for	for	IN	_	_	_
12	2	2	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	8000rpm	8000rpm	CD	_	_	_
16	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	hot	hot	JJ	_	_	_
6	acid	acid	NN	_	_	_
7	phenol	phenol	NN	_	_	_
8	extracted	extract	VBN	_	_	_
9	.	.	.	_	_	_

1	Ribosomal	ribosomal	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	and	and	CC	_	_	_
4	small	small	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	were	be	VBD	_	_	_
7	removed	remove	VBN	_	_	_
8	with	with	IN	_	_	_
9	MICROBExpress	microbexpress	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	ambion	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	or	or	CC	_	_	_
14	Ribozero	ribozero	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Epicenter	epicenter	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	MEGAclear	megaclear	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Ambion	ambion	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	respectively	respectively	RB	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	EYG1	eyg1	NN	_	_	_
3	in	in	IN	_	_	_
4	M9	m9	NN	_	_	_
5	Replicate	replicate	VB	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	EYG1	eyg1	NN	_	_	_
9	in	in	IN	_	_	_
10	M9	m9	NN	_	_	_
11	Replicate	replicate	VB	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	EYG1	eyg1	NN	_	_	_
15	,	,	,	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	rpoC	rpoc	NN	GEN	_	_
18	K370	k370	NN	_	_	_
19	_	_	CD	_	_	_
20	A396dup	a396dup	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	EYG	eyg	NN	_	_	_
23	in	in	IN	_	_	_
24	M9	m9	NN	_	_	_
25	supplemented	supplement	VBN	_	_	_
26	with	with	IN	_	_	_
27	0.6	0.6	CD	_	_	_
28	M	m	NN	_	_	_
29	NaCl	nacl	NN	_	_	_
30	Replicate	replicate	VB	_	_	_
31	1	1	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	EYG	eyg	NN	_	_	_
34	in	in	IN	_	_	_
35	M9	m9	NN	_	_	_
36	supplemented	supplement	VBN	_	_	_
37	with	with	IN	_	_	_
38	0.6	0.6	CD	_	_	_
39	M	m	NN	_	_	_
40	NaCl	nacl	NN	_	_	_
41	Replicate	replicate	VB	_	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	F1	f1	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	F2	f2	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	fadr	fadr	NN	_	_	_
49	KO	ko	NN	_	_	_
50	LB	lb	NN	_	_	_
51	rep1	rep1	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	fadr	fadr	NN	_	_	_
54	KO	ko	NN	_	_	_
55	LB	lb	NN	_	_	_
56	rep2	rep2	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	fadr	fadr	NN	_	_	_
59	KO	ko	NN	_	_	_
60	M9	m9	NN	_	_	_
61	rep1	rep1	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	fadr	fadr	NN	_	_	_
64	KO	ko	NN	_	_	_
65	M9	m9	NN	_	_	_
66	rep2	rep2	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	Faecal	faecal	JJ	_	_	_
69	samples	sample	NNS	_	_	_
70	were	be	VBD	_	_	_
71	collected	collect	VBN	_	_	_
72	by	by	IN	_	_	_
73	the	the	DT	_	_	_
74	Department	Department	NNP	_	_	_
75	of	of	IN	_	_	_
76	Microbiology	Microbiology	NNP	_	_	_
77	and	and	CC	_	_	_
78	Alimentary	Alimentary	NNP	_	_	_
79	Pharmabiotic	Pharmabiotic	NNP	_	_	_
80	Centre	Centre	NNP	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	Cork	Cork	NNP	_	_	_
83	,	,	,	_	_	_
84	Ireland	Ireland	NNP	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	from	from	IN	_	_	_
87	three	three	CD	_	_	_
88	elderly	elderly	JJ	_	_	_
89	patients	patient	NNS	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	176	176	CD	_	_	_
92	,	,	,	_	_	_
93	204	204	CD	_	_	_
94	and	and	CC	_	_	_
95	205	205	CD	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	.	.	.	_	_	_

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	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	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/decile	intermediate/decile	NN	_	_	_
17	in	in	IN	_	_	_
18	the	the	DT	_	_	_
19	case	case	NN	_	_	_
20	of	of	IN	_	_	_
21	SPET-seq	spet-seq	JJ	_	_	_
22	data	datum	NNS	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	XML	xml	NN	_	_	_
2	files	file	NNS	_	_	_
3	for	for	IN	_	_	_
4	mature	mature	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	were	be	VBD	_	_	_
7	passed	pass	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	rf-fold	rf-fold	JJ	_	_	_
11	tool	tool	NN	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	RNA	rna	NN	_	_	_
15	Framework	framework	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	using	use	VBG	_	_	_
18	ViennaRNA	viennarna	NN	_	_	_
19	Package	package	NN	_	_	_
20	2.2	2.2	CD	_	_	_
21	with	with	IN	_	_	_
22	soft	soft	JJ	_	_	_
23	constraints14	constraints14	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	to	to	TO	_	_	_
26	infer	infer	VB	_	_	_
27	mature	mature	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	structures	structure	NNS	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	parameters	parameter	NNS	_	_	_
32	:	:	:	_	_	_
33	-	-	:	_	_	_
34	md	md	NN	_	_	_
35	600	600	CD	_	_	_
36	-	-	:	_	_	_
37	nlp	nlp	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

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	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	NN	_	_	_
2	FASTQ	fastq	NN	_	_	_
3	formatted	format	VBD	_	_	_
4	sequence	sequence	NN	_	_	_
5	files	file	NNS	_	_	_
6	from	from	IN	_	_	_
7	strand-specific	strand-specific	JJ	_	_	_
8	Illumina	Illumina	NNP	_	_	_
9	RNA-Seq	rna-seq	NN	_	_	_
10	reads	read	VBZ	_	_	_
11	were	be	VBD	_	_	_
12	aligned	align	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	GLBRCE1	glbrce1	NN	_	_	_
16	reference	reference	NN	_	_	_
17	genome	genome	NN	_	_	_
18	NC	nc	NN	_	_	_
19	_	_	CD	_	_	_
20	000913	000913	CD	_	_	_
21	using	use	VBG	_	_	_
22	Bowtie	Bowtie	NNP	_	_	_
23	version	version	NN	_	_	_
24	0.12.7	0.12.7	CD	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Langmead	Langmead	NNP	_	_	_
27	et	et	FW	_	_	_
28	al.	al.	FW	_	_	_
29	,	,	,	_	_	_
30	2009	2009	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	with	with	IN	_	_	_
33	'	'	''	_	_	_
34	--	--	:	_	_	_
35	nofw	nofw	NN	_	_	_
36	'	'	''	_	_	_
37	strand-specific	strand-specific	JJ	_	_	_
38	parameter	parameter	NN	_	_	_
39	and	and	CC	_	_	_
40	maximal	maximal	JJ	_	_	_
41	distance	distance	NN	_	_	_
42	between	between	IN	_	_	_
43	the	the	DT	_	_	_
44	paired	paired	JJ	_	_	_
45	reads	read	VBZ	_	_	_
46	of	of	IN	_	_	_
47	1000	1000	CD	_	_	_
48	bp	bp	NN	_	_	_
49	.	.	.	_	_	_

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	NN	_	_	_
2	Fastq	fastq	JJ	_	_	_
3	quality	quality	NN	_	_	_
4	trimming	trim	VBG	_	_	_
5	using	use	VBG	_	_	_
6	FastX	fastx	NN	_	_	_
7	and	and	CC	_	_	_
8	a	a	DT	_	_	_
9	cut-off	cut-off	JJ	_	_	_
10	value	value	NN	_	_	_
11	of	of	IN	_	_	_
12	20	20	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	FastQ	fastq	NN	_	_	_
15	quality	quality	NN	_	_	_
16	trimming	trim	VBG	_	_	_
17	using	use	VBG	_	_	_
18	FastX	fastx	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	version	version	NN	_	_	_
21	0.0.13	0.0.13	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	a	a	DT	_	_	_
25	cut-off	cut-off	JJ	_	_	_
26	value	value	NN	_	_	_
27	of	of	IN	_	_	_
28	20	20	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Fastq	fastq	NN	_	_	_
31	to	to	TO	_	_	_
32	fasta	fasta	NN	_	_	_
33	conversion	conversion	NN	_	_	_
34	using	use	VBG	_	_	_
35	FastX	fastx	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Fastq	fastq	NN	_	_	_
38	to	to	TO	_	_	_
39	fasta	fasta	NN	_	_	_
40	conversion	conversion	NN	_	_	_
41	using	use	VBG	_	_	_
42	FastX	fastx	NN	_	_	_
43	FastX	fastx	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	version	version	NN	_	_	_
46	0.0.13	0.0.13	CD	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	Feature	Feature	NNP	_	_	_
50	fluorescence	fluorescence	NN	_	_	_
51	intensities	intensity	NNS	_	_	_
52	-LSB-	-lsb-	-LRB-	_	_	_
53	F532	f532	NN	_	_	_
54	media-B532	media-b532	NN	_	_	_
55	and	and	CC	_	_	_
56	F635media-B635	f635media-b635	NN	_	_	_
57	-RSB-	-rsb-	-RRB-	_	_	_
58	were	be	VBD	_	_	_
59	extracted	extract	VBN	_	_	_
60	using	use	VBG	_	_	_
61	GenePix	GenePix	NNP	_	_	_
62	Pro	pro	FW	_	_	_
63	6.0	6.0	CD	_	_	_
64	.	.	.	_	_	_

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://pevsnerlab.kennedykrieger.org/snomadinput.html	http://pevsnerlab.kennedykrieger.org/snomadinput.html	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	three	three	CD	_	_	_
3	replicate	replicate	VBP	_	_	_
4	spots	spot	NNS	_	_	_
5	for	for	IN	_	_	_
6	each	each	DT	_	_	_
7	gene	gene	NN	_	_	_
8	were	be	VBD	_	_	_
9	averaged	average	VBN	_	_	_
10	and	and	CC	_	_	_
11	variance	variance	NN	_	_	_
12	was	be	VBD	_	_	_
13	calculated	calculate	VBN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Feature	Feature	NNP	_	_	_
3	intensity	intensity	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	by	by	IN	_	_	_
7	GeneChip	GeneChip	NNP	_	_	_
8	Operating	Operating	NNP	_	_	_
9	System	System	NNP	_	_	_
10	as	as	IN	_	_	_
11	CEL	CEL	NNP	_	_	_
12	files	file	NNS	_	_	_
13	.	.	.	_	_	_

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	Feature	Feature	NNP	_	_	_
3	pixel	pixel	NN	_	_	_
4	median	median	NN	_	_	_
5	minus	minus	CC	_	_	_
6	background	background	NN	_	_	_
7	pixel	pixel	NN	_	_	_
8	mean	mean	NN	_	_	_
9	;	;	:	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Fecal	fecal	JJ	_	_	_
12	samples	sample	NNS	_	_	_
13	obtained	obtain	VBN	_	_	_
14	from	from	IN	_	_	_
15	mice	mouse	NNS	_	_	_
16	were	be	VBD	_	_	_
17	immediately	immediately	RB	_	_	_
18	frozen	freeze	VBN	_	_	_
19	in	in	IN	_	_	_
20	liquid	liquid	JJ	_	_	_
21	nitrogen	nitrogen	NN	_	_	_
22	and	and	CC	_	_	_
23	stored	store	VBD	_	_	_
24	at	at	IN	_	_	_
25	-80	-80	CD	_	_	_
26	°C	°c	NN	_	_	_
27	until	until	IN	_	_	_
28	processing	processing	NN	_	_	_
29	.	.	.	_	_	_

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	Fed	Fed	NNP	_	_	_
3	batch	batch	NN	_	_	_
4	high	high	JJ	_	_	_
5	cell	cell	NN	_	_	_
6	density	density	NN	_	_	_
7	cultivation	cultivation	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	fepA	fepa	NN	GEN	_	_
10	KO	ko	NN	_	_	_
11	LB	lb	NN	_	_	_
12	rep1	rep1	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	fepA	fepa	NN	GEN	_	_
15	KO	ko	NN	_	_	_
16	LB	lb	NN	_	_	_
17	rep2	rep2	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	fepA	fepa	NN	GEN	_	_
20	KO	ko	NN	_	_	_
21	M9	m9	NN	_	_	_
22	rep1	rep1	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	fepA	fepa	NN	GEN	_	_
25	KO	ko	NN	_	_	_
26	M9	m9	NN	_	_	_
27	rep2	rep2	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Fermentations	fermentation	NNS	_	_	_
30	were	be	VBD	_	_	_
31	carried	carry	VBN	_	_	_
32	out	out	RP	_	_	_
33	in	in	IN	_	_	_
34	3	3	CD	_	_	_
35	L	l	NN	_	_	_
36	bioreactors	bioreactor	NNS	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Applikon	Applikon	NNP	_	_	_
39	Biotechnology	Biotechnology	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	containing	contain	VBG	_	_	_
42	2.45	2.45	CD	_	_	_
43	L	l	NN	_	_	_
44	of	of	IN	_	_	_
45	ACSH	acsh	NN	_	_	_
46	or	or	CC	_	_	_
47	SynH	synh	NN	_	_	_
48	media	media	NNS	_	_	_
49	,	,	,	_	_	_
50	and	and	CC	_	_	_
51	cultures	culture	NNS	_	_	_
52	were	be	VBD	_	_	_
53	diluted	dilute	VBN	_	_	_
54	into	into	IN	_	_	_
55	ACSH	acsh	NN	_	_	_
56	or	or	CC	_	_	_
57	SynH	synh	NN	_	_	_
58	with	with	IN	_	_	_
59	initial	initial	JJ	_	_	_
60	OD	od	NN	_	_	_
61	at	at	IN	_	_	_
62	0.2	0.2	CD	_	_	_
63	,	,	,	_	_	_
64	grown	grow	VBN	_	_	_
65	anaerobically	anaerobically	RB	_	_	_
66	overnight	overnight	RB	_	_	_
67	,	,	,	_	_	_
68	and	and	CC	_	_	_
69	then	then	RB	_	_	_
70	inoculated	inoculate	VBN	_	_	_
71	into	into	IN	_	_	_
72	bioreactors	bioreactor	NNS	_	_	_
73	to	to	TO	_	_	_
74	a	a	DT	_	_	_
75	starting	start	VBG	_	_	_
76	OD600	od600	NN	_	_	_
77	of	of	IN	_	_	_
78	0.2	0.2	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Fermentations	fermentation	NNS	_	_	_
81	were	be	VBD	_	_	_
82	carried	carry	VBN	_	_	_
83	out	out	RP	_	_	_
84	in	in	IN	_	_	_
85	3L	3l	NN	_	_	_
86	bioreactors	bioreactor	NNS	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	Applikon	Applikon	NNP	_	_	_
89	Biotechnology	Biotechnology	NNP	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	containing	contain	VBG	_	_	_
92	2.45	2.45	CD	_	_	_
93	L	l	NN	_	_	_
94	of	of	IN	_	_	_
95	ACSH	ACSH	NNP	_	_	_
96	,	,	,	_	_	_
97	SynH	synh	NN	_	_	_
98	,	,	,	_	_	_
99	SynH	synh	NN	_	_	_
100	+	+	CC	_	_	_
101	LT	lt	NN	_	_	_
102	,	,	,	_	_	_
103	or	or	CC	_	_	_
104	SynH	synh	NN	_	_	_
105	+	+	CC	_	_	_
106	Acid/Amide	Acid/Amide	NNP	_	_	_
107	LTs	LTs	NNP	_	_	_
108	,	,	,	_	_	_
109	and	and	CC	_	_	_
110	cultures	culture	NNS	_	_	_
111	were	be	VBD	_	_	_
112	diluted	dilute	VBN	_	_	_
113	into	into	IN	_	_	_
114	ACSH	acsh	NN	_	_	_
115	or	or	CC	_	_	_
116	SynH	synh	NN	_	_	_
117	with	with	IN	_	_	_
118	initial	initial	JJ	_	_	_
119	OD	od	NN	_	_	_
120	at	at	IN	_	_	_
121	0.2	0.2	CD	_	_	_
122	,	,	,	_	_	_
123	grown	grow	VBN	_	_	_
124	anaerobically	anaerobically	RB	_	_	_
125	overnight	overnight	RB	_	_	_
126	,	,	,	_	_	_
127	and	and	CC	_	_	_
128	then	then	RB	_	_	_
129	inoculated	inoculate	VBN	_	_	_
130	into	into	IN	_	_	_
131	bioreactors	bioreactor	NNS	_	_	_
132	to	to	TO	_	_	_
133	a	a	DT	_	_	_
134	starting	start	VBG	_	_	_
135	OD600	od600	NN	_	_	_
136	of	of	IN	_	_	_
137	0.2	0.2	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	fermentation	fermentation	NN	_	_	_
140	time	time	NN	_	_	_
141	:	:	:	_	_	_
142	20h	20h	JJ	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	fermentation	fermentation	NN	_	_	_
145	time	time	NN	_	_	_
146	:	:	:	_	_	_
147	30h	30h	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	fermentation	fermentation	NN	_	_	_
150	time	time	NN	_	_	_
151	:	:	:	_	_	_
152	40h	40h	JJ	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	Fifteen	fifteen	CD	_	_	_
155	mL	ml	NN	_	_	_
156	fermentation	fermentation	NN	_	_	_
157	broth	broth	NN	_	_	_
158	was	be	VBD	_	_	_
159	used	use	VBN	_	_	_
160	for	for	IN	_	_	_
161	each	each	DT	_	_	_
162	RNA	rna	NN	_	_	_
163	extraction	extraction	NN	_	_	_
164	.	.	.	_	_	_

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/mL	mg/ml	NN	_	_	_
31	lysozyme	lysozyme	NN	_	_	_
32	,	,	,	_	_	_
33	and	and	CC	_	_	_
34	incubated	incubate	VBN	_	_	_
35	for	for	IN	_	_	_
36	15	15	CD	_	_	_
37	minutes	minute	NNS	_	_	_
38	at	at	IN	_	_	_
39	room	room	NN	_	_	_
40	temperature	temperature	NN	_	_	_
41	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNAqueousTM-Midi	RNAqueousTM-Midi	NNP	_	_	_
7	Kit	kit	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Ambion	ambion	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	concentration	concentration	NN	_	_	_
3	of	of	IN	_	_	_
4	purified	purify	VBN	_	_	_
5	total	total	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	was	be	VBD	_	_	_
8	determined	determine	VBN	_	_	_
9	spectrophotometrically	spectrophotometrically	RB	_	_	_
10	by	by	IN	_	_	_
11	measuring	measure	VBG	_	_	_
12	absorbance	absorbance	NN	_	_	_
13	at	at	IN	_	_	_
14	260	260	CD	_	_	_
15	nm	nm	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	quality	quality	NN	_	_	_
3	and	and	CC	_	_	_
4	integrity	integrity	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	isolated	isolate	VBN	_	_	_
8	RNA	rna	NN	_	_	_
9	was	be	VBD	_	_	_
10	confirmed	confirm	VBN	_	_	_
11	by	by	IN	_	_	_
12	agarose	agarose	NN	_	_	_
13	gels	gel	NNS	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	clear	clear	JJ	_	_	_
16	23S	23s	NN	_	_	_
17	and	and	CC	_	_	_
18	16S	16s	NN	_	_	_
19	rRNA	rrna	NN	_	_	_
20	bands	band	NNS	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Files	Files	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	coverted	covert	VBN	_	_	_
5	to	to	TO	_	_	_
6	.	.	.	_	_	_

1	bam	bam	NN	_	_	_
2	format	format	NN	_	_	_
3	using	use	VBG	_	_	_
4	samtools	samtool	NNS	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	Filter	Filter	NNP	_	_	_
7	for	for	IN	_	_	_
8	map	map	NN	GEN	_	_
9	quality	quality	NN	_	_	_
10	>	>	JJR	_	_	_
11	=	=	JJ	_	_	_
12	20	20	CD	_	_	_
13	using	use	VBG	_	_	_
14	Samtools	Samtools	NNP	_	_	_
15	0.1.18	0.1.18	CD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Filtering	Filtering	NNP	_	_	_
18	,	,	,	_	_	_
19	Mapping	mapping	NN	_	_	_
20	quality	quality	NN	_	_	_
21	=	=	JJ	_	_	_
22	30	30	CD	_	_	_
23	,	,	,	_	_	_
24	no	no	DT	_	_	_
25	ambiguous	ambiguous	JJ	_	_	_
26	reads	read	VBZ	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Filter	Filter	NNP	_	_	_
29	out	out	IN	_	_	_
30	rRNA	rrna	NN	_	_	_
31	reads	read	VBZ	_	_	_
32	,	,	,	_	_	_
33	multi-mapped	multi-mapped	JJ	_	_	_
34	reads	read	VBZ	_	_	_
35	,	,	,	_	_	_
36	>	>	JJR	_	_	_
37	3	3	CD	_	_	_
38	mismatches	mismatch	NNS	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	gapped	gap	VBD	_	_	_
42	mappings	mapping	NNS	_	_	_
43	using	use	VBG	_	_	_
44	custom	custom	NN	_	_	_
45	Python	Python	NNP	_	_	_
46	script	script	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	FilterBAM2BAM	filterbam2bam	NN	_	_	_
49	from	from	IN	_	_	_
50	http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz	http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
53	First	First	NNP	_	_	_
54	and	and	CC	_	_	_
55	second	second	JJ	_	_	_
56	strand	strand	NN	_	_	_
57	cDNA	cdna	NN	_	_	_
58	synthesis	synthesis	NN	_	_	_
59	was	be	VBD	_	_	_
60	carried	carry	VBN	_	_	_
61	out	out	RP	_	_	_
62	using	use	VBG	_	_	_
63	the	the	DT	_	_	_
64	Ovation	Ovation	NNP	_	_	_
65	®	®	NNP	_	_	_
66	Prokaryotic	Prokaryotic	NNP	_	_	_
67	RNA-Seq	RNA-Seq	NNP	_	_	_
68	System	System	NNP	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	NuGEN	NuGEN	NNP	_	_	_
71	Technologies	Technologies	NNPS	_	_	_
72	Inc.	Inc.	NNP	_	_	_
73	,	,	,	_	_	_
74	San	San	NNP	_	_	_
75	Carlos	Carlos	NNP	_	_	_
76	,	,	,	_	_	_
77	CA	CA	NNP	_	_	_
78	,	,	,	_	_	_
79	USA	USA	NNP	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	,	,	,	_	_	_
82	and	and	CC	_	_	_
83	NuGEN	nugen	NN	_	_	_
84	's	's	POS	_	_	_
85	Encore	encore	NN	_	_	_
86	NGS	ngs	NN	_	_	_
87	Library	Library	NNP	_	_	_
88	System	System	NNP	_	_	_
89	was	be	VBD	_	_	_
90	applied	apply	VBN	_	_	_
91	to	to	TO	_	_	_
92	construct	construct	VB	_	_	_
93	the	the	DT	_	_	_
94	cDNA	cdna	NN	_	_	_
95	library	library	NN	_	_	_
96	for	for	IN	_	_	_
97	the	the	DT	_	_	_
98	IlluminaHiSeq	IlluminaHiSeq	NNP	_	_	_
99	platform	platform	NN	_	_	_
100	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	First	First	NNP	_	_	_
3	biological	biological	JJ	_	_	_
4	repeat	repeat	NN	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	First	First	NNP	_	_	_
9	biological	biological	JJ	_	_	_
10	repeat	repeat	NN	_	_	_
11	50	50	CD	_	_	_
12	°C	°c	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	First	First	NNP	_	_	_
15	,	,	,	_	_	_
16	ribosomal	ribosomal	JJ	_	_	_
17	RNA	rna	NN	_	_	_
18	was	be	VBD	_	_	_
19	depleted	deplete	VBN	_	_	_
20	from	from	IN	_	_	_
21	1	1	CD	_	_	_
22	μg	μg	NN	_	_	_
23	of	of	IN	_	_	_
24	total	total	JJ	_	_	_
25	RNA	rna	NN	_	_	_
26	using	use	VBG	_	_	_
27	the	the	DT	_	_	_
28	Ribo-ZeroTM	Ribo-ZeroTM	NNP	_	_	_
29	Magnetic	magnetic	JJ	_	_	_
30	Kit	kit	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Bacteria	bacterium	NNS	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Epicentre	Epicentre	NNP	_	_	_
36	,	,	,	_	_	_
37	Madison	Madison	NNP	_	_	_
38	,	,	,	_	_	_
39	WI	WI	NNP	_	_	_
40	,	,	,	_	_	_
41	USA	USA	NNP	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	.	.	.	_	_	_

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	NN	_	_	_
2	first	first	JJ	_	_	_
3	strand	strand	NN	_	_	_
4	cDNA	cdna	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	by	by	IN	_	_	_
8	the	the	DT	_	_	_
9	use	use	NN	_	_	_
10	of	of	IN	_	_	_
11	SuperScriptII	superscriptii	NN	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	second	second	JJ	_	_	_
15	strand	strand	NN	_	_	_
16	cDNA	cdna	NN	_	_	_
17	synthesis	synthesis	NN	_	_	_
18	was	be	VBD	_	_	_
19	done	do	VBN	_	_	_
20	before	before	IN	_	_	_
21	end-pair	end-pair	JJ	_	_	_
22	and	and	CC	_	_	_
23	dA-tailing	da-tailing	JJ	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	Fis	fis	NN	TF	_	_
26	--	--	:	_	_	_
27	120	120	CD	_	_	_
28	min	min	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	fis	fis	NN	GEN	_	_
31	150	150	CD	_	_	_
32	minutes	minute	NNS	_	_	_
33	growth	growth	NN	_	_	_
34	rep1	rep1	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	fis	fi	VBZ	GEN	_	_
37	150	150	CD	_	_	_
38	minutes	minute	NNS	_	_	_
39	growth	growth	NN	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	fis	fi	VBZ	GEN	_	_
43	150	150	CD	_	_	_
44	minutes	minute	NNS	_	_	_
45	growth	growth	NN	_	_	_
46	rep3	rep3	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	Fis	fi	VBZ	TF	_	_
49	--	--	:	_	_	_
50	180	180	CD	_	_	_
51	min	min	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	fis	fis	NN	GEN	_	_
54	240	240	CD	_	_	_
55	minutes	minute	NNS	_	_	_
56	growth	growth	NN	_	_	_
57	rep1	rep1	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
59	fis	fi	VBZ	GEN	_	_
60	240	240	CD	_	_	_
61	minutes	minute	NNS	_	_	_
62	growth	growth	NN	_	_	_
63	rep2	rep2	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	fis	fi	VBZ	GEN	_	_
66	240	240	CD	_	_	_
67	minutes	minute	NNS	_	_	_
68	growth	growth	NN	_	_	_
69	rep3	rep3	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
71	fis	fi	VBZ	GEN	_	_
72	360	360	CD	_	_	_
73	minutes	minute	NNS	_	_	_
74	growth	growth	NN	_	_	_
75	rep1	rep1	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
77	fis	fi	VBZ	GEN	_	_
78	360	360	CD	_	_	_
79	minutes	minute	NNS	_	_	_
80	growth	growth	NN	_	_	_
81	rep2	rep2	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
83	fis	fi	VBZ	GEN	_	_
84	360	360	CD	_	_	_
85	minutes	minute	NNS	_	_	_
86	growth	growth	NN	_	_	_
87	rep3	rep3	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
89	Fis	fi	VBZ	TF	_	_
90	--	--	:	_	_	_
91	420	420	CD	_	_	_
92	min	min	NN	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	Fis	Fis	NNP	TF	_	_
95	--	--	:	_	_	_
96	60	60	CD	_	_	_
97	min	min	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	fis	fi	VBZ	GEN	_	_
100	90	90	CD	_	_	_
101	minutes	minute	NNS	_	_	_
102	growth	growth	NN	_	_	_
103	rep1	rep1	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	fis	fi	VBZ	GEN	_	_
106	90	90	CD	_	_	_
107	minutes	minute	NNS	_	_	_
108	growth	growth	NN	_	_	_
109	rep2	rep2	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
111	fis	fi	VBZ	GEN	_	_
112	90	90	CD	_	_	_
113	minutes	minute	NNS	_	_	_
114	growth	growth	NN	_	_	_
115	rep3	rep3	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
117	Fis	fis	NN	TF	_	_
118	,	,	,	_	_	_
119	EE	ee	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	fis.ee.chipseq	fis.ee.chipseq	JJ	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	fis.ee.input	fis.ee.input	JJ	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
125	fis	fi	VBZ	GEN	_	_
126	Escherichia	escherichia	FW	Organism	_	_
127	coli	coli	FW	Organism	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Fis	fis	NN	TF	_	_
130	,	,	,	_	_	_
131	ME	me	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	fis.me.chipseq	fis.me.chipseq	JJ	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	fis.me.input	fis.me.input	JJ	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	fismutant.crp.ee.chipseq	fismutant.crp.ee.chipseq	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	fismutant.crp.ee.input	fismutant.crp.ee.input	JJ	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	fismutant.crp.me.chipseq	fismutant.crp.me.chipseq	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	fismutant.crp.me.input	fismutant.crp.me.input	JJ	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	fis.rep1.ee	fis.rep1.ee	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	fis.rep1.me	fis.rep1.me	JJ	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	fis.rep2.ee	fis.rep2.ee	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	fis.rep2.me	fis.rep2.me	JJ	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
153	fis	fi	VBZ	GEN	_	_
154	___	___	CD	_	_	_
155	U	U	NNP	_	_	_
156	_	_	NNP	_	_	_
157	N0075	N0075	NNP	_	_	_
158	_	_	VBD	_	_	_
159	r1	r1	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
161	fis	fi	VBZ	GEN	_	_
162	___	___	CD	_	_	_
163	U	U	NNP	_	_	_
164	_	_	NNP	_	_	_
165	N0075	N0075	NNP	_	_	_
166	_	_	VBD	_	_	_
167	r2	r2	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
169	fis	fi	VBZ	GEN	_	_
170	___	___	CD	_	_	_
171	U	U	NNP	_	_	_
172	_	_	NNP	_	_	_
173	N0075	N0075	NNP	_	_	_
174	_	_	SYM	_	_	_
175	r3	r3	FW	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
177	fis	fis	FW	GEN	_	_
178	upregulation	upregulation	NN	_	_	_
179	,	,	,	_	_	_
180	0.075	0.075	CD	_	_	_
181	ug/ml	ug/ml	NN	_	_	_
182	norfloxacin	norfloxacin	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	fklB	fklb	NN	GEN	_	_
185	__	__	CD	_	_	_
186	U	U	NNP	_	_	_
187	_	_	NNP	_	_	_
188	N0075	N0075	NNP	_	_	_
189	_	_	VBD	_	_	_
190	r1	r1	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	fklB	fklb	NN	GEN	_	_
193	__	__	CD	_	_	_
194	U	U	NNP	_	_	_
195	_	_	NNP	_	_	_
196	N0075	N0075	NNP	_	_	_
197	_	_	VBD	_	_	_
198	r2	r2	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	fklB	fklb	NN	GEN	_	_
201	__	__	CD	_	_	_
202	U	U	NNP	_	_	_
203	_	_	NNP	_	_	_
204	N0075	N0075	NNP	_	_	_
205	_	_	SYM	_	_	_
206	r3	r3	FW	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
208	fklB	fklb	NN	GEN	_	_
209	upregulation	upregulation	NN	_	_	_
210	,	,	,	_	_	_
211	0.075	0.075	CD	_	_	_
212	ug/ml	ug/ml	NN	_	_	_
213	norfloxacin	norfloxacin	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	Flask	flask	NN	_	_	_
216	state	state	NN	_	_	_
217	1	1	CD	_	_	_
218	-LRB-	-lrb-	-LRB-	_	_	_
219	IPTG	iptg	SYM	_	_	_
220	-	-	:	_	_	_
221	/	/	:	_	_	_
222	aTc	atc	SYM	_	_	_
223	-	-	:	_	_	_
224	/	/	:	_	_	_
225	Ara	Ara	NNP	_	_	_
226	-	-	:	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	Flask	flask	NN	_	_	_
230	state	state	NN	_	_	_
231	2	2	CD	_	_	_
232	-LRB-	-lrb-	-LRB-	_	_	_
233	IPTG	iptg	NN	_	_	_
234	+	+	CC	_	_	_
235	/	/	:	_	_	_
236	aTc	atc	SYM	_	_	_
237	-	-	:	_	_	_
238	/	/	:	_	_	_
239	Ara	Ara	NNP	_	_	_
240	-	-	:	_	_	_
241	-RRB-	-rrb-	-RRB-	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	Flask	flask	NN	_	_	_
244	state	state	NN	_	_	_
245	3	3	CD	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	IPTG	iptg	SYM	_	_	_
248	-	-	:	_	_	_
249	/	/	:	_	_	_
250	aTc	atc	NN	_	_	_
251	+	+	CC	_	_	_
252	/	/	:	_	_	_
253	Ara	Ara	NNP	_	_	_
254	-	-	:	_	_	_
255	-RRB-	-rrb-	-RRB-	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	Flask	flask	NN	_	_	_
258	state	state	NN	_	_	_
259	4	4	CD	_	_	_
260	-LRB-	-lrb-	-LRB-	_	_	_
261	IPTG	iptg	NN	_	_	_
262	+	+	CC	_	_	_
263	/	/	:	_	_	_
264	aTc	atc	NN	_	_	_
265	+	+	CC	_	_	_
266	/	/	:	_	_	_
267	Ara	Ara	NNP	_	_	_
268	-	-	:	_	_	_
269	-RRB-	-rrb-	-RRB-	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	Flask	flask	NN	_	_	_
272	state	state	NN	_	_	_
273	5	5	CD	_	_	_
274	-LRB-	-lrb-	-LRB-	_	_	_
275	IPTG	iptg	SYM	_	_	_
276	-	-	:	_	_	_
277	/	/	:	_	_	_
278	aTc	atc	SYM	_	_	_
279	-	-	:	_	_	_
280	/	/	:	_	_	_
281	Ara	Ara	NNP	_	_	_
282	+	+	CC	_	_	_
283	-RRB-	-rrb-	-RRB-	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	Flask	flask	NN	_	_	_
286	state	state	NN	_	_	_
287	6	6	CD	_	_	_
288	-LRB-	-lrb-	-LRB-	_	_	_
289	IPTG	iptg	NN	_	_	_
290	+	+	CC	_	_	_
291	/	/	:	_	_	_
292	aTc	atc	SYM	_	_	_
293	-	-	:	_	_	_
294	/	/	:	_	_	_
295	Ara	Ara	NNP	_	_	_
296	+	+	CC	_	_	_
297	-RRB-	-rrb-	-RRB-	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	Flask	flask	NN	_	_	_
300	state	state	NN	_	_	_
301	7	7	CD	_	_	_
302	-LRB-	-lrb-	-LRB-	_	_	_
303	IPTG	iptg	SYM	_	_	_
304	-	-	:	_	_	_
305	/	/	:	_	_	_
306	aTc	atc	NN	_	_	_
307	+	+	CC	_	_	_
308	/	/	:	_	_	_
309	Ara	Ara	NNP	_	_	_
310	+	+	CC	_	_	_
311	-RRB-	-rrb-	-RRB-	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	Flask	flask	NN	_	_	_
314	state	state	NN	_	_	_
315	8	8	CD	_	_	_
316	-LRB-	-lrb-	-LRB-	_	_	_
317	IPTG	iptg	NN	_	_	_
318	+	+	CC	_	_	_
319	/	/	:	_	_	_
320	aTc	atc	NN	_	_	_
321	+	+	CC	_	_	_
322	/	/	:	_	_	_
323	Ara	Ara	NNP	_	_	_
324	+	+	CC	_	_	_
325	-RRB-	-rrb-	-RRB-	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	flhD-glucose	flhd-glucose	JJ	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	flhD-mannose	flhd-mannose	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	flhD-mucus-P1	flhd-mucus-p1	NN	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	flhD-mucus-P2	flhd-mucus-p2	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	fliY	fliy	NN	_	_	_
336	KO	ko	NN	_	_	_
337	rep1	rep1	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	fliY	fliy	NN	_	_	_
340	KO	ko	NN	_	_	_
341	rep2	rep2	NN	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	fliY	fliy	NN	_	_	_
344	KO	ko	NN	_	_	_
345	rep3	rep3	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	florfenicol	florfenicol	NN	_	_	_
348	treatment	treatment	NN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	Florfenicol	florfenicol	NN	_	_	_
351	_	_	NN	_	_	_
352	treatment	treatment	NN	_	_	_
353	_	_	NN	_	_	_
354	plasmidmappedreads	plasmidmappedread	NNS	_	_	_
355	_	_	VBP	_	_	_
356	statistical	statistical	JJ	_	_	_
357	_	_	NN	_	_	_
358	output.txt	output.txt	NN	_	_	_
359	:	:	:	_	_	_
360	NC	NC	NNP	_	_	_
361	_	_	NNP	_	_	_
362	012692.1	012692.1	CD	_	_	_
363	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
364	Flor	Flor	NNP	_	_	_
365	_	_	JJ	_	_	_
366	treatment	treatment	NN	_	_	_
367	_	_	NN	_	_	_
368	genomemappedreads	genomemappedread	NNS	_	_	_
369	_	_	VBP	_	_	_
370	statistical	statistical	JJ	_	_	_
371	_	_	NN	_	_	_
372	output.txt	output.txt	NN	_	_	_
373	:	:	:	_	_	_
374	NC	NC	NNP	_	_	_
375	_	_	NNP	_	_	_
376	000913.2	000913.2	CD	_	_	_
377	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
378	Fluorescence	fluorescence	NN	_	_	_
379	intensities	intensity	NNS	_	_	_
380	of	of	IN	_	_	_
381	oligonucleotide	oligonucleotide	NN	_	_	_
382	spots	spot	NNS	_	_	_
383	were	be	VBD	_	_	_
384	extracted	extract	VBN	_	_	_
385	from	from	IN	_	_	_
386	the	the	DT	_	_	_
387	scanned	scan	VBN	_	_	_
388	images	image	NNS	_	_	_
389	using	use	VBG	_	_	_
390	the	the	DT	_	_	_
391	Feature	Feature	NNP	_	_	_
392	Extraction	extraction	NN	_	_	_
393	software	software	NN	_	_	_
394	-LRB-	-lrb-	-LRB-	_	_	_
395	V11	v11	NN	_	_	_
396	.0	.0	CD	_	_	_
397	,	,	,	_	_	_
398	Agilent	Agilent	NNP	_	_	_
399	Technologies	Technologies	NNPS	_	_	_
400	-RRB-	-rrb-	-RRB-	_	_	_
401	.	.	.	_	_	_

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	fluorescent	fluorescent	JJ	_	_	_
3	labeling	labeling	NN	_	_	_
4	and	and	CC	_	_	_
5	hybridization	hybridization	NN	_	_	_
6	and	and	CC	_	_	_
7	scanning	scanning	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	microarray	microarray	NN	_	_	_
11	images	image	NNS	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Balazsi	balazsus	NNS	_	_	_
14	et	et	FW	_	_	_
15	al.	al.	FW	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	fnr	fnr	SYM	GEN	_	_
3	-	-	:	_	_	_
4	aerobic	aerobic	JJ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	fnr	fnr	SYM	GEN	_	_
7	-	-	:	_	_	_
8	aerobic	aerobic	JJ	_	_	_
9	AN	a	DT	_	_	_
10	rep	rep	NN	GEN	_	_
11	1	1	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	fnr	fnr	SYM	GEN	_	_
14	-	-	:	_	_	_
15	aerobic	aerobic	JJ	_	_	_
16	AN	a	DT	_	_	_
17	rep	rep	NN	GEN	_	_
18	2	2	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	fnr	fnr	SYM	GEN	_	_
21	-	-	:	_	_	_
22	aerobic	aerobic	JJ	_	_	_
23	AN	a	DT	_	_	_
24	rep	rep	NN	GEN	_	_
25	3	3	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	fnr	fnr	SYM	GEN	_	_
28	-	-	:	_	_	_
29	aerobic	aerobic	JJ	_	_	_
30	rep	rep	NN	GEN	_	_
31	1	1	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	fnr	fnr	SYM	GEN	_	_
34	-	-	:	_	_	_
35	aerobic	aerobic	JJ	_	_	_
36	rep	rep	NN	GEN	_	_
37	2	2	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
39	fnr	fnr	SYM	GEN	_	_
40	-	-	:	_	_	_
41	aerobic	aerobic	JJ	_	_	_
42	rep	rep	NN	GEN	_	_
43	3	3	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	fnr	fnr	SYM	GEN	_	_
46	-	-	:	_	_	_
47	anaerobic	anaerobic	JJ	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
49	FNR	fnr	SYM	TF	_	_
50	-	-	:	_	_	_
51	Anaerobic	anaerobic	JJ	_	_	_
52	-	-	:	_	_	_
53	A	a	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	FNR	fnr	SYM	TF	_	_
56	-	-	:	_	_	_
57	Anaerobic	anaerobic	JJ	_	_	_
58	-	-	:	_	_	_
59	Affinity	affinity	NN	_	_	_
60	Purified	purify	VBN	_	_	_
61	-	-	:	_	_	_
62	A	a	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	FNR	fnr	SYM	TF	_	_
65	-	-	:	_	_	_
66	Anaerobic	anaerobic	JJ	_	_	_
67	-	-	:	_	_	_
68	Affinity	affinity	NN	_	_	_
69	Purified	purify	VBN	_	_	_
70	-	-	:	_	_	_
71	B	b	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	fnr	fnr	SYM	GEN	_	_
74	-	-	:	_	_	_
75	anaerobic	anaerobic	JJ	_	_	_
76	AN	a	DT	_	_	_
77	rep	rep	NN	GEN	_	_
78	1	1	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	fnr	fnr	SYM	GEN	_	_
81	-	-	:	_	_	_
82	anaerobic	anaerobic	JJ	_	_	_
83	AN	a	DT	_	_	_
84	rep	rep	NN	GEN	_	_
85	2	2	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
87	fnr	fnr	SYM	GEN	_	_
88	-	-	:	_	_	_
89	anaerobic	anaerobic	JJ	_	_	_
90	AN	a	DT	_	_	_
91	rep	rep	NN	GEN	_	_
92	3	3	CD	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	FNR	fnr	SYM	TF	_	_
95	-	-	:	_	_	_
96	Anaerobic	anaerobic	JJ	_	_	_
97	-	-	:	_	_	_
98	B	b	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	FNR	fnr	SYM	TF	_	_
101	-	-	:	_	_	_
102	Anaerobic	anaerobic	JJ	_	_	_
103	-	-	:	_	_	_
104	C	c	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	fnr	fnr	SYM	GEN	_	_
107	-	-	:	_	_	_
108	anaerobic	anaerobic	NN	_	_	_
109	plus	plus	CC	_	_	_
110	NO2	no2	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
112	fnr	fnr	SYM	GEN	_	_
113	-	-	:	_	_	_
114	anaerobic	anaerobic	NN	_	_	_
115	plus	plus	CC	_	_	_
116	NO2	no2	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
118	fnr	fnr	SYM	GEN	_	_
119	-	-	:	_	_	_
120	anaerobic	anaerobic	NN	_	_	_
121	plus	plus	CC	_	_	_
122	NO2	no2	NN	_	_	_
123	AN	a	DT	_	_	_
124	rep	rep	NN	GEN	_	_
125	1	1	CD	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	fnr	fnr	SYM	GEN	_	_
128	-	-	:	_	_	_
129	anaerobic	anaerobic	NN	_	_	_
130	plus	plus	CC	_	_	_
131	NO2	no2	NN	_	_	_
132	AN	a	DT	_	_	_
133	rep	rep	NN	GEN	_	_
134	2	2	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
136	fnr	fnr	SYM	GEN	_	_
137	-	-	:	_	_	_
138	anaerobic	anaerobic	NN	_	_	_
139	plus	plus	CC	_	_	_
140	NO2	no2	NN	_	_	_
141	AN	a	DT	_	_	_
142	rep	rep	NN	GEN	_	_
143	3	3	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	fnr	fnr	SYM	GEN	_	_
146	-	-	:	_	_	_
147	anaerobic	anaerobic	NN	_	_	_
148	plus	plus	CC	_	_	_
149	NO2	no2	NN	_	_	_
150	rep	rep	NN	GEN	_	_
151	1	1	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	fnr	fnr	SYM	GEN	_	_
154	-	-	:	_	_	_
155	anaerobic	anaerobic	NN	_	_	_
156	plus	plus	CC	_	_	_
157	NO2	no2	NN	_	_	_
158	rep	rep	NN	GEN	_	_
159	2	2	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
161	fnr	fnr	SYM	GEN	_	_
162	-	-	:	_	_	_
163	anaerobic	anaerobic	NN	_	_	_
164	plus	plus	CC	_	_	_
165	NO2	no2	NN	_	_	_
166	rep	rep	NN	GEN	_	_
167	3	3	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	fnr	fnr	SYM	GEN	_	_
170	-	-	:	_	_	_
171	anaerobic	anaerobic	NN	_	_	_
172	plus	plus	CC	_	_	_
173	NO3	no3	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
175	fnr	fnr	SYM	GEN	_	_
176	-	-	:	_	_	_
177	anaerobic	anaerobic	NN	_	_	_
178	plus	plus	CC	_	_	_
179	NO3	no3	NN	_	_	_
180	AN	a	DT	_	_	_
181	rep	rep	NN	GEN	_	_
182	1	1	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	fnr	fnr	SYM	GEN	_	_
185	-	-	:	_	_	_
186	anaerobic	anaerobic	NN	_	_	_
187	plus	plus	CC	_	_	_
188	NO3	no3	NN	_	_	_
189	AN	a	DT	_	_	_
190	rep	rep	NN	GEN	_	_
191	2	2	CD	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
193	fnr	fnr	SYM	GEN	_	_
194	-	-	:	_	_	_
195	anaerobic	anaerobic	NN	_	_	_
196	plus	plus	CC	_	_	_
197	NO3	no3	NN	_	_	_
198	AN	a	DT	_	_	_
199	rep	rep	NN	GEN	_	_
200	3	3	CD	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	fnr	fnr	SYM	GEN	_	_
203	-	-	:	_	_	_
204	anaerobic	anaerobic	NN	_	_	_
205	plus	plus	CC	_	_	_
206	NO3	no3	NN	_	_	_
207	rep	rep	NN	GEN	_	_
208	1	1	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	fnr	fnr	SYM	GEN	_	_
211	-	-	:	_	_	_
212	anaerobic	anaerobic	NN	_	_	_
213	plus	plus	CC	_	_	_
214	NO3	no3	NN	_	_	_
215	rep	rep	NN	GEN	_	_
216	2	2	CD	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
218	fnr	fnr	SYM	GEN	_	_
219	-	-	:	_	_	_
220	anaerobic	anaerobic	NN	_	_	_
221	plus	plus	CC	_	_	_
222	NO3	no3	NN	_	_	_
223	rep	rep	NN	GEN	_	_
224	3	3	CD	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	fnr	fnr	SYM	GEN	_	_
227	-	-	:	_	_	_
228	anaerobic	anaerobic	JJ	_	_	_
229	rep	rep	NN	GEN	_	_
230	1	1	CD	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	fnr	fnr	SYM	GEN	_	_
233	-	-	:	_	_	_
234	anaerobic	anaerobic	JJ	_	_	_
235	rep	rep	NN	GEN	_	_
236	2	2	CD	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
238	fnr	fnr	SYM	GEN	_	_
239	-	-	:	_	_	_
240	anaerobic	anaerobic	JJ	_	_	_
241	rep	rep	NN	GEN	_	_
242	3	3	CD	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	FNR	fnr	SYM	TF	_	_
245	-	-	:	_	_	_
246	_	_	SYM	_	_	_
247	Anaerobic	anaerobic	JJ	_	_	_
248	_	_	NN	_	_	_
249	RNAseq	rnaseq	NN	_	_	_
250	_	_	CD	_	_	_
251	A	a	DT	_	_	_
252	_	_	NN	_	_	_
253	Tag	tag	NN	_	_	_
254	_	_	CD	_	_	_
255	Count.txt	count.txt	NN	_	_	_
256	:	:	:	_	_	_
257	U00096	u00096	NN	_	_	_
258	.2	.2	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	FNR	fnr	SYM	TF	_	_
261	-	-	:	_	_	_
262	_	_	SYM	_	_	_
263	Anaerobic	anaerobic	JJ	_	_	_
264	_	_	NN	_	_	_
265	RNAseq	rnaseq	NN	_	_	_
266	_	_	CD	_	_	_
267	A	a	DT	_	_	_
268	_	_	NN	_	_	_
269	WIG.wig	wig.wig	NN	_	_	_
270	:	:	:	_	_	_
271	U00096	u00096	NN	_	_	_
272	.2	.2	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	FNR	fnr	SYM	TF	_	_
275	-	-	:	_	_	_
276	_	_	SYM	_	_	_
277	Anaerobic	anaerobic	JJ	_	_	_
278	_	_	NN	_	_	_
279	RNAseq	rnaseq	NN	_	_	_
280	_	_	NN	_	_	_
281	B	b	NN	_	_	_
282	_	_	CD	_	_	_
283	Tag	tag	NN	_	_	_
284	_	_	CD	_	_	_
285	Count.txt	count.txt	NN	_	_	_
286	:	:	:	_	_	_
287	U00096	u00096	NN	_	_	_
288	.2	.2	NN	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	FNR	fnr	SYM	TF	_	_
291	-	-	:	_	_	_
292	_	_	SYM	_	_	_
293	Anaerobic	anaerobic	JJ	_	_	_
294	_	_	NN	_	_	_
295	RNAseq	rnaseq	NN	_	_	_
296	_	_	NN	_	_	_
297	B	b	NN	_	_	_
298	_	_	CD	_	_	_
299	WIG.wig	wig.wig	NN	_	_	_
300	:	:	:	_	_	_
301	U00096	u00096	NN	_	_	_
302	.2	.2	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	∆	∆	CD	_	_	_
305	fnr	fnr	SYM	GEN	_	_
306	-	-	:	_	_	_
307	Anaeroibc	Anaeroibc	NNP	_	_	_
308	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
309	FNR	FNR	NNP	TF	_	_
310	ChIP	chip	NN	_	_	_
311	DNA	dna	NN	_	_	_
312	from	from	IN	_	_	_
313	∆	∆	CD	_	_	_
314	hns	hn	NNS	GEN	_	_
315	/	/	:	_	_	_
316	∆	∆	SYM	_	_	_
317	stpA	stpA	NNP	GEN	_	_
318	E.	e.	FW	_	_	_
319	coli	coli	FW	_	_	_
320	MG1655	mg1655	NN	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	∆	∆	CD	_	_	_
323	fnr	fnr	NN	GEN	_	_
324	ChIP	chip	NN	_	_	_
325	DNA	dna	NN	_	_	_
326	from	from	IN	_	_	_
327	PK4854	pk4854	NN	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	FNR	fnr	NN	TF	_	_
330	ChIP	chip	NN	_	_	_
331	DNA	dna	NN	_	_	_
332	from	from	IN	_	_	_
333	WT	WT	NNP	_	_	_
334	Escherchia	Escherchia	NNP	_	_	_
335	coli	coli	NN	_	_	_
336	MG1655	mg1655	NN	_	_	_
337	K-12	k-12	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	FNR	fnr	SYM	TF	_	_
340	-	-	:	_	_	_
341	∆	∆	SYM	_	_	_
342	hns	hn	VBZ	GEN	_	_
343	∆	∆	SYM	_	_	_
344	stpA	stpa	NN	GEN	_	_
345	A	a	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	FNR	fnr	SYM	TF	_	_
348	-	-	:	_	_	_
349	∆	∆	SYM	_	_	_
350	hns	hn	VBZ	GEN	_	_
351	∆	∆	SYM	_	_	_
352	stpA	stpa	NN	GEN	_	_
353	B	b	NN	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	FNR	fnr	NN	TF	_	_
356	INPUT	input	NN	_	_	_
357	from	from	IN	_	_	_
358	PK8263	pk8263	NN	_	_	_
359	with	with	IN	_	_	_
360	16	16	CD	_	_	_
361	µM	µm	NN	_	_	_
362	INPUTTG	inputtg	NN	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	FNR	fnr	NN	TF	_	_
365	INPUT	input	NN	_	_	_
366	from	from	IN	_	_	_
367	PK8263	pk8263	NN	_	_	_
368	with	with	IN	_	_	_
369	4	4	CD	_	_	_
370	µM	µm	NN	_	_	_
371	INPUTTG	inputtg	NN	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	FNR	fnr	NN	TF	_	_
374	INPUT	input	NN	_	_	_
375	from	from	IN	_	_	_
376	PK8263	pk8263	NN	_	_	_
377	with	with	IN	_	_	_
378	8	8	CD	_	_	_
379	µM	µm	NN	_	_	_
380	INPUTTG	inputtg	NN	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	FNR	fnr	NN	TF	_	_
383	INPUT	input	NN	_	_	_
384	from	from	IN	_	_	_
385	WT	WT	NNP	_	_	_
386	Escherichia	escherichia	FW	Organism	_	_
387	coli	coli	FW	Organism	_	_
388	MG1655	mg1655	NN	_	_	_
389	K-12	k-12	NN	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	FNR	fnr	NN	TF	_	_
392	IP	IP	NNP	_	_	_
393	ChIP-seq	ChIP-seq	NNP	_	_	_
394	Anaerobic	Anaerobic	NNP	_	_	_
395	A	A	NNP	_	_	_
396	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
397	FNR	FNR	NNP	TF	_	_
398	_	_	SYM	_	_	_
399	IP	IP	NNP	_	_	_
400	_	_	SYM	_	_	_
401	ChIP-seq	ChIP-seq	NNP	_	_	_
402	_	_	SYM	_	_	_
403	Anaerobic	anaerobic	JJ	_	_	_
404	_	_	NN	_	_	_
405	A	a	DT	_	_	_
406	_	_	NN	_	_	_
407	WIG.wig	wig.wig	NN	_	_	_
408	:	:	:	_	_	_
409	U00096	u00096	NN	_	_	_
410	.2	.2	NN	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	FNR	fnr	NN	TF	_	_
413	IP	IP	NNP	_	_	_
414	ChIP-seq	ChIP-seq	NNP	_	_	_
415	Anaerobic	anaerobic	JJ	_	_	_
416	B	b	NN	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	FNR	fnr	NN	TF	_	_
419	_	_	CD	_	_	_
420	IP	IP	NNP	_	_	_
421	_	_	SYM	_	_	_
422	ChIP-seq	ChIP-seq	NNP	_	_	_
423	_	_	SYM	_	_	_
424	Anaerobic	anaerobic	JJ	_	_	_
425	_	_	NN	_	_	_
426	B	b	NN	_	_	_
427	_	_	CD	_	_	_
428	WIG.wig	wig.wig	NN	_	_	_
429	:	:	:	_	_	_
430	U00096	u00096	NN	_	_	_
431	.2	.2	NN	_	_	_
432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
433	FNR	fnr	NN	TF	_	_
434	IP	IP	NNP	_	_	_
435	from	from	IN	_	_	_
436	PK8263	pk8263	NN	_	_	_
437	with	with	IN	_	_	_
438	16	16	CD	_	_	_
439	µM	µm	NN	_	_	_
440	IPTG	iptg	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	FNR	fnr	NN	TF	_	_
443	IP	IP	NNP	_	_	_
444	from	from	IN	_	_	_
445	PK8263	pk8263	NN	_	_	_
446	with	with	IN	_	_	_
447	4	4	CD	_	_	_
448	µM	µm	NN	_	_	_
449	IPTG	iptg	NN	_	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
451	FNR	fnr	NN	TF	_	_
452	IP	IP	NNP	_	_	_
453	from	from	IN	_	_	_
454	PK8263	pk8263	NN	_	_	_
455	with	with	IN	_	_	_
456	8	8	CD	_	_	_
457	µM	µm	NN	_	_	_
458	IPTG	iptg	NN	_	_	_
459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
460	FNR	fnr	NN	TF	_	_
461	IP	IP	NNP	_	_	_
462	from	from	IN	_	_	_
463	WT	WT	NNP	_	_	_
464	Escherichia	escherichia	FW	Organism	_	_
465	coli	coli	FW	Organism	_	_
466	MG1655	mg1655	NN	_	_	_
467	K-12	k-12	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	folA	fola	NN	GEN	_	_
470	__	__	CD	_	_	_
471	U	U	NNP	_	_	_
472	_	_	NNP	_	_	_
473	N0075	N0075	NNP	_	_	_
474	_	_	NNP	_	_	_
475	r1	r1	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	folA	fola	NN	GEN	_	_
478	__	__	CD	_	_	_
479	U	U	NNP	_	_	_
480	_	_	NNP	_	_	_
481	N0075	N0075	NNP	_	_	_
482	_	_	SYM	_	_	_
483	r2	r2	FW	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
485	folA	fola	NN	GEN	_	_
486	__	__	CD	_	_	_
487	U	U	NNP	_	_	_
488	_	_	NNP	_	_	_
489	N0075	N0075	NNP	_	_	_
490	_	_	SYM	_	_	_
491	r3	r3	FW	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
493	folA	fola	NN	GEN	_	_
494	upregulation	upregulation	NN	_	_	_
495	,	,	,	_	_	_
496	0.075	0.075	CD	_	_	_
497	ug/ml	ug/ml	NN	_	_	_
498	norfloxacin	norfloxacin	NN	_	_	_
499	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
500	Following	follow	VBG	_	_	_
501	\	\	SYM	_	_	_
502	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
503	Following	follow	VBG	_	_	_
504	background	background	NN	_	_	_
505	subtraction	subtraction	NN	_	_	_
506	,	,	,	_	_	_
507	spot	spot	NN	_	_	_
508	signal	signal	NN	_	_	_
509	intensities	intensity	NNS	_	_	_
510	were	be	VBD	_	_	_
511	calculated	calculate	VBN	_	_	_
512	as	as	IN	_	_	_
513	percentages	percentage	NNS	_	_	_
514	of	of	IN	_	_	_
515	total	total	JJ	_	_	_
516	signal	signal	NN	_	_	_
517	intensities	intensity	NNS	_	_	_
518	of	of	IN	_	_	_
519	Cy-3	cy-3	NN	_	_	_
520	or	or	CC	_	_	_
521	Cy-5	cy-5	NN	_	_	_
522	signals	signal	NNS	_	_	_
523	on	on	IN	_	_	_
524	each	each	DT	_	_	_
525	microarray	microarray	NN	_	_	_
526	,	,	,	_	_	_
527	as	as	IN	_	_	_
528	a	a	DT	_	_	_
529	means	means	NN	_	_	_
530	of	of	IN	_	_	_
531	normalization	normalization	NN	_	_	_
532	.	.	.	_	_	_

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	NNP	_	_	_
2	Following	follow	VBG	_	_	_
3	incubation	incubation	NN	_	_	_
4	,	,	,	_	_	_
5	roots	root	NNS	_	_	_
6	had	have	VBD	_	_	_
7	been	be	VBN	_	_	_
8	gently	gently	RB	_	_	_
9	rinsed	rinse	VBN	_	_	_
10	to	to	TO	_	_	_
11	remove	remove	VB	_	_	_
12	loosely	loosely	RB	_	_	_
13	attached	attach	VBN	_	_	_
14	bacteria	bacterium	NNS	_	_	_
15	and	and	CC	_	_	_
16	roots	root	NNS	_	_	_
17	were	be	VBD	_	_	_
18	cut	cut	VBN	_	_	_
19	directly	directly	RB	_	_	_
20	into	into	IN	_	_	_
21	100	100	CD	_	_	_
22	ml	ml	NN	_	_	_
23	ice	ice	NN	_	_	_
24	cold	cold	JJ	_	_	_
25	stop	stop	NN	_	_	_
26	solution	solution	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	5	5	CD	_	_	_
29	%	%	NN	_	_	_
30	H2O-saturated	h2o-saturated	JJ	_	_	_
31	phenol	phenol	NN	_	_	_
32	,	,	,	_	_	_
33	pH	ph	NN	_	_	_
34	4.3	4.3	CD	_	_	_
35	,	,	,	_	_	_
36	in	in	IN	_	_	_
37	95	95	CD	_	_	_
38	%	%	NN	_	_	_
39	ethanol	ethanol	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

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	For	for	IN	_	_	_
3	3C-seq	3c-seq	NN	_	_	_
4	:	:	:	_	_	_
5	≈	≈	SYM	_	_	_
6	1-2	1-2	CD	_	_	_
7	x	x	CC	_	_	_
8	109	109	CD	_	_	_
9	crosslinked	crosslink	VBN	_	_	_
10	cells	cell	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	7	7	CD	_	_	_
13	%	%	NN	_	_	_
14	formaldehyde	formaldehyde	NN	_	_	_
15	,	,	,	_	_	_
16	unless	unless	IN	_	_	_
17	otherwise	otherwise	RB	_	_	_
18	stated	state	VBN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	are	be	VBP	_	_	_
21	suspended	suspend	VBN	_	_	_
22	in	in	IN	_	_	_
23	600	600	CD	_	_	_
24	μl	μl	NN	_	_	_
25	Tris	Tris	NNP	_	_	_
26	10	10	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	EDTA	edta	NN	_	_	_
29	0.5	0.5	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	TE	te	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	pH	ph	NN	_	_	_
36	8	8	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	with	with	IN	_	_	_
39	4	4	CD	_	_	_
40	μl	μl	NN	_	_	_
41	of	of	IN	_	_	_
42	lysozyme	lysozyme	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	35	35	CD	_	_	_
45	U/μl	u/μl	NN	_	_	_
46	;	;	:	_	_	_
47	Tebu	Tebu	NNP	_	_	_
48	Bio	Bio	NNP	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	,	,	,	_	_	_
51	and	and	CC	_	_	_
52	incubated	incubate	VBN	_	_	_
53	at	at	IN	_	_	_
54	RT	rt	NN	_	_	_
55	for	for	IN	_	_	_
56	20	20	CD	_	_	_
57	minutes	minute	NNS	_	_	_
58	.	.	.	_	_	_

1	SDS	sds	NN	_	_	_
2	is	be	VBZ	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	mix	mix	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	final	final	JJ	_	_	_
9	concentration	concentration	NN	_	_	_
10	0.5	0.5	CD	_	_	_
11	%	%	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	cells	cell	NNS	_	_	_
16	are	be	VBP	_	_	_
17	incubated	incubate	VBN	_	_	_
18	for	for	IN	_	_	_
19	10	10	CD	_	_	_
20	minutes	minute	NNS	_	_	_
21	at	at	IN	_	_	_
22	RT.	RT.	NNP	_	_	_
23	50μl	50μl	CD	_	_	_
24	of	of	IN	_	_	_
25	lysed	lysed	JJ	_	_	_
26	cells	cell	NNS	_	_	_
27	are	be	VBP	_	_	_
28	then	then	RB	_	_	_
29	transferred	transfer	VBN	_	_	_
30	in	in	IN	_	_	_
31	8	8	CD	_	_	_
32	tubes	tube	NNS	_	_	_
33	containing	contain	VBG	_	_	_
34	450μL	450μl	NN	_	_	_
35	of	of	IN	_	_	_
36	digestion	digestion	NN	_	_	_
37	mix	mix	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	1X	1x	NN	_	_	_
40	NEB	neb	NN	_	_	_
41	1	1	CD	_	_	_
42	buffer	buffer	NN	_	_	_
43	,	,	,	_	_	_
44	1	1	CD	_	_	_
45	%	%	NN	_	_	_
46	triton	triton	NN	_	_	_
47	X-100	x-100	NN	_	_	_
48	,	,	,	_	_	_
49	and	and	CC	_	_	_
50	100U	100u	NN	_	_	_
51	HpaII	hpaii	NN	_	_	_
52	enzyme	enzyme	NN	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	is	be	VBZ	_	_	_
3	digested	digest	VBN	_	_	_
4	for	for	IN	_	_	_
5	3	3	CD	_	_	_
6	hours	hour	NNS	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	,	,	,	_	_	_
11	split	split	NN	_	_	_
12	in	in	IN	_	_	_
13	4	4	CD	_	_	_
14	aliquots	aliquot	NNS	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	diluted	dilute	VBN	_	_	_
18	in	in	IN	_	_	_
19	8	8	CD	_	_	_
20	ml	ml	NN	_	_	_
21	ligation	ligation	NN	_	_	_
22	buffer	buffer	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	1X	1x	NN	_	_	_
25	ligation	ligation	NN	_	_	_
26	buffer	buffer	NN	_	_	_
27	NEB	neb	NN	_	_	_
28	without	without	IN	_	_	_
29	ATP	atp	NN	SUPP	_	_
30	,	,	,	_	_	_
31	1	1	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	ATP	atp	NN	SUPP	_	_
34	,	,	,	_	_	_
35	0.1	0.1	CD	_	_	_
36	mg/ml	mg/ml	JJ	_	_	_
37	BSA	bsa	NN	_	_	_
38	,	,	,	_	_	_
39	125	125	CD	_	_	_
40	Units	unit	NNS	_	_	_
41	of	of	IN	_	_	_
42	T4	t4	NN	_	_	_
43	DNA	dna	NN	_	_	_
44	ligase	ligase	NN	_	_	_
45	5	5	CD	_	_	_
46	U/μl	u/μl	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	Ligation	ligation	NN	_	_	_
2	is	be	VBZ	_	_	_
3	then	then	RB	_	_	_
4	performed	perform	VBN	_	_	_
5	at	at	IN	_	_	_
6	16	16	CD	_	_	_
7	°C	°c	NN	_	_	_
8	for	for	IN	_	_	_
9	4	4	CD	_	_	_
10	hours	hour	NNS	_	_	_
11	,	,	,	_	_	_
12	followed	follow	VBN	_	_	_
13	by	by	IN	_	_	_
14	incubation	incubation	NN	_	_	_
15	overnight	overnight	JJ	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	ON	on	IN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	at	at	IN	_	_	_
20	65	65	CD	_	_	_
21	°C	°c	NN	_	_	_
22	in	in	IN	_	_	_
23	presence	presence	NN	_	_	_
24	of	of	IN	_	_	_
25	250	250	CD	_	_	_
26	μg/ml	μg/ml	JJ	_	_	_
27	proteinase	proteinase	NN	_	_	_
28	K	k	NN	_	_	_
29	and	and	CC	_	_	_
30	5	5	CD	_	_	_
31	mM	mm	NN	KWSUPP	_	_
32	EDTA	edta	NN	_	_	_
33	.	.	.	_	_	_

1	Precipitation	precipitation	NN	_	_	_
2	of	of	IN	_	_	_
3	DNA	dna	NN	_	_	_
4	is	be	VBZ	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	equal	equal	JJ	_	_	_
9	volume	volume	NN	_	_	_
10	of	of	IN	_	_	_
11	3	3	CD	_	_	_
12	M	m	NN	_	_	_
13	Na-Acetate	na-acetate	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	pH	ph	NN	_	_	_
16	5.2	5.2	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	two	two	CD	_	_	_
20	volumes	volume	NNS	_	_	_
21	of	of	IN	_	_	_
22	iso-propanol	iso-propanol	NN	_	_	_
23	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	one	one	CD	_	_	_
3	hour	hour	NN	_	_	_
4	at	at	IN	_	_	_
5	-80	-80	CD	_	_	_
6	°C	°c	NN	_	_	_
7	,	,	,	_	_	_
8	DNA	dna	NN	_	_	_
9	is	be	VBZ	_	_	_
10	pelleted	pelleted	JJ	_	_	_
11	,	,	,	_	_	_
12	suspended	suspend	VBN	_	_	_
13	in	in	IN	_	_	_
14	500μl	500μl	JJ	_	_	_
15	1X	1x	NN	_	_	_
16	TE	te	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	incubated	incubate	VBN	_	_	_
21	for	for	IN	_	_	_
22	30	30	CD	_	_	_
23	minutes	minute	NNS	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	in	in	IN	_	_	_
28	presence	presence	NN	_	_	_
29	of	of	IN	_	_	_
30	RNAse	rnase	NN	_	_	_
31	A	a	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	0.03	0.03	CD	_	_	_
34	mg/ml	mg/ml	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	is	be	VBZ	_	_	_
3	then	then	RB	_	_	_
4	transferred	transfer	VBN	_	_	_
5	into	into	IN	_	_	_
6	2	2	CD	_	_	_
7	ml	ml	NN	_	_	_
8	centrifuge	centrifuge	NN	_	_	_
9	tubes	tube	NNS	_	_	_
10	,	,	,	_	_	_
11	extracted	extract	VBN	_	_	_
12	twice	twice	RB	_	_	_
13	with	with	IN	_	_	_
14	500	500	CD	_	_	_
15	μl	μl	NN	_	_	_
16	phenol-chloroform	phenol-chloroform	NN	_	_	_
17	pH	ph	NN	_	_	_
18	8.0	8.0	CD	_	_	_
19	,	,	,	_	_	_
20	precipitated	precipitated	JJ	_	_	_
21	,	,	,	_	_	_
22	washed	wash	VBN	_	_	_
23	with	with	IN	_	_	_
24	1	1	CD	_	_	_
25	ml	ml	NN	_	_	_
26	cold	cold	JJ	_	_	_
27	ethanol	ethanol	NN	_	_	_
28	70	70	CD	_	_	_
29	%	%	NN	_	_	_
30	and	and	CC	_	_	_
31	diluted	dilute	VBN	_	_	_
32	in	in	IN	_	_	_
33	30	30	CD	_	_	_
34	μl	μl	NN	_	_	_
35	1X	1x	NN	_	_	_
36	TE	te	NN	_	_	_
37	buffer	buffer	NN	_	_	_
38	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	tubes	tube	NNS	_	_	_
3	are	be	VBP	_	_	_
4	pooled	pool	VBN	_	_	_
5	and	and	CC	_	_	_
6	the	the	DT	_	_	_
7	resulting	result	VBG	_	_	_
8	3C	3c	NN	_	_	_
9	library	library	NN	_	_	_
10	is	be	VBZ	_	_	_
11	quantified	quantify	VBN	_	_	_
12	on	on	IN	_	_	_
13	gel	gel	NN	_	_	_
14	using	use	VBG	_	_	_
15	Quantity	Quantity	NNP	_	_	_
16	One	one	CD	_	_	_
17	software	software	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	BioRad	biorad	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	alignment	alignment	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	reads	read	VBZ	_	_	_
7	contained	contain	VBN	_	_	_
8	within	within	IN	_	_	_
9	the	the	DT	_	_	_
10	fastq	fastq	NN	_	_	_
11	files	file	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	_	_	CD	_	_	_
23	U00096	u00096	NN	_	_	_
24	.3	.3	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	the	the	DT	_	_	_
28	short	short	JJ	_	_	_
29	read	read	NN	_	_	_
30	alignment	alignment	NN	_	_	_
31	tool	tool	NN	_	_	_
32	Bowtie2	bowtie2	NN	_	_	_
33	was	be	VBD	_	_	_
34	utilized	utilize	VBN	_	_	_
35	under	under	IN	_	_	_
36	default	default	NN	_	_	_
37	settings	setting	NNS	_	_	_
38	.	.	.	_	_	_

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	NN	_	_	_
2	For	for	IN	_	_	_
3	alignment	alignment	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	SAET	SAET	NNP	_	_	_
7	reads	read	VBZ	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	reference	reference	NN	_	_	_
14	genome	genome	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	RefSeq	refseq	NN	_	_	_
17	NC	nc	NN	_	_	_
18	_	_	SYM	_	_	_
19	000913	000913	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	the	the	DT	_	_	_
23	short	short	JJ	_	_	_
24	read	read	NN	_	_	_
25	alignment	alignment	NN	_	_	_
26	tool	tool	NN	_	_	_
27	Bowtie	Bowtie	NNP	_	_	_
28	ver	ver	NN	_	_	_
29	.	.	.	_	_	_

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	NN	_	_	_
2	For	for	IN	_	_	_
3	all	all	PDT	_	_	_
4	the	the	DT	_	_	_
5	samples	sample	NNS	_	_	_
6	;	;	:	_	_	_
7	when	when	WRB	_	_	_
8	1/3	1/3	CD	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	maximum	maximum	NN	_	_	_
12	OD600	od600	NN	_	_	_
13	was	be	VBD	_	_	_
14	reached	reach	VBN	_	_	_
15	,	,	,	_	_	_
16	cells	cell	NNS	_	_	_
17	were	be	VBD	_	_	_
18	harvested	harvest	VBN	_	_	_
19	by	by	IN	_	_	_
20	centrifugation	centrifugation	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	7,500	7,500	CD	_	_	_
23	rcf	rcf	NN	_	_	_
24	for	for	IN	_	_	_
25	5	5	CD	_	_	_
26	min	min	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	frozen	freeze	VBN	_	_	_
30	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	Wizard	Wizard	NNP	_	_	_
7	Genomic	genomic	JJ	_	_	_
8	DNA	dna	NN	_	_	_
9	Purification	purification	NN	_	_	_
10	Kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Promega	promega	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	all	all	PDT	_	_	_
4	the	the	DT	_	_	_
5	samples	sample	NNS	_	_	_
6	;	;	:	_	_	_
7	when	when	WRB	_	_	_
8	1/3	1/3	CD	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	maximum	maximum	NN	_	_	_
12	OD600	od600	NN	_	_	_
13	was	be	VBD	_	_	_
14	reached	reach	VBN	_	_	_
15	,	,	,	_	_	_
16	cells	cell	NNS	_	_	_
17	were	be	VBD	_	_	_
18	harvested	harvest	VBN	_	_	_
19	by	by	IN	_	_	_
20	centrifugation	centrifugation	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	7,500	7,500	CD	_	_	_
23	rcf	rcf	NN	_	_	_
24	for	for	IN	_	_	_
25	5	5	CD	_	_	_
26	min	min	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	frozen	freeze	VBN	_	_	_
30	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	RNA	rna	NN	_	_	_
3	isolation	isolation	NN	_	_	_
4	,	,	,	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	lysed	lyse	VBN	_	_	_
8	by	by	IN	_	_	_
9	bead	bead	NN	_	_	_
10	beating	beating	NN	_	_	_
11	and	and	CC	_	_	_
12	RNA	rna	NN	_	_	_
13	was	be	VBD	_	_	_
14	purified	purify	VBN	_	_	_
15	using	use	VBG	_	_	_
16	phenol-chloroform	phenol-chloroform	JJ	_	_	_
17	extractions	extraction	NNS	_	_	_
18	and	and	CC	_	_	_
19	ethanol	ethanol	NN	_	_	_
20	precipitations	precipitation	NNS	_	_	_
21	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	from	from	IN	_	_	_
5	the	the	DT	_	_	_
6	sample	sample	NN	_	_	_
7	with	with	IN	_	_	_
8	RNase-free	rnase-free	JJ	_	_	_
9	DNase	dnase	NN	_	_	_
10	I	i	CD	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Fermentas	fermentas	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	treatment	treatment	NN	_	_	_
15	for	for	IN	_	_	_
16	45	45	CD	_	_	_
17	min	min	NN	_	_	_
18	.	.	.	_	_	_

1	Ribolock	ribolock	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	Fermentas	fermentas	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	avoid	avoid	VB	_	_	_
9	RNA	rna	NN	_	_	_
10	degradation	degradation	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	analysis	analysis	NN	_	_	_
4	of	of	IN	_	_	_
5	ChIP-seq	ChIP-seq	NNP	_	_	_
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	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	NN	_	_	_
2	For	for	IN	_	_	_
3	ChIP-seq	chip-seq	JJ	_	_	_
4	experiments	experiment	NNS	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	culture	culture	NN	_	_	_
8	were	be	VBD	_	_	_
9	fixed	fix	VBN	_	_	_
10	with	with	IN	_	_	_
11	formaldehyde	formaldehyde	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	1	1	CD	_	_	_
14	%	%	NN	_	_	_
15	final	final	JJ	_	_	_
16	concentration	concentration	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	;	;	:	_	_	_
19	for	for	IN	_	_	_
20	NorfliP	norflip	NN	_	_	_
21	experiments	experiment	NNS	_	_	_
22	TopoIV	topoiv	NN	_	_	_
23	was	be	VBD	_	_	_
24	crosslinked	crosslink	VBN	_	_	_
25	with	with	IN	_	_	_
26	Norfloxacin	norfloxacin	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	2µM	2µm	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	For	for	IN	_	_	_
32	chromatin	chromatin	NN	_	_	_
33	immunoprecipitation	immunoprecipitation	NN	_	_	_
34	,	,	,	_	_	_
35	cells	cell	NNS	_	_	_
36	were	be	VBD	_	_	_
37	fixed	fix	VBN	_	_	_
38	with	with	IN	_	_	_
39	formaldehyde	formaldehyde	NN	_	_	_
40	and	and	CC	_	_	_
41	glycine	glycine	NN	_	_	_
42	and	and	CC	_	_	_
43	sheared	shear	VBD	_	_	_
44	via	via	IN	_	_	_
45	sonication	sonication	NN	_	_	_
46	.	.	.	_	_	_

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	control	control	NN	_	_	_
4	and	and	CC	_	_	_
5	test	test	NN	_	_	_
6	RNAs	rna	NNS	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	synthesis	synthesis	NN	_	_	_
10	of	of	IN	_	_	_
11	target	target	NN	_	_	_
12	cRNA	crna	NN	_	_	_
13	probes	probe	NNS	_	_	_
14	and	and	CC	_	_	_
15	hybridization	hybridization	NN	_	_	_
16	were	be	VBD	_	_	_
17	performed	perform	VBN	_	_	_
18	using	use	VBG	_	_	_
19	Agilent	Agilent	NNP	_	_	_
20	's	's	POS	_	_	_
21	Low	low	JJ	_	_	_
22	Input	Input	NNP	_	_	_
23	Quick	Quick	NNP	_	_	_
24	Amp	Amp	NNP	_	_	_
25	WT	WT	NNP	_	_	_
26	Labeling	label	VBG	_	_	_
27	Kit	kit	NN	_	_	_
28	,	,	,	_	_	_
29	one	one	CD	_	_	_
30	color	color	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Agilent	Agilent	NNP	_	_	_
33	Technology	Technology	NNP	_	_	_
34	,	,	,	_	_	_
35	USA	USA	NNP	_	_	_
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	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	For	for	IN	_	_	_
3	cross-linking	cross-linking	NN	_	_	_
4	,	,	,	_	_	_
5	30	30	CD	_	_	_
6	mL	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	mixed	mix	VBN	_	_	_
11	with	with	IN	_	_	_
12	300	300	CD	_	_	_
13	uL	ul	NN	_	_	_
14	1M	1m	NN	_	_	_
15	sodium	sodium	NN	_	_	_
16	phosphates	phosphate	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	pH	ph	NN	_	_	_
19	7.6	7.6	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	810	810	CD	_	_	_
23	uL	ul	NN	_	_	_
24	37	37	CD	_	_	_
25	%	%	NN	_	_	_
26	formaldehyde	formaldehyde	NN	_	_	_
27	.	.	.	_	_	_

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/ml	cfu/ml	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	or	or	CC	_	_	_
19	late	late	JJ	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	2.4	2.4	CD	_	_	_
22	x	x	CC	_	_	_
23	10	10	CD	_	_	_
24	^	^	SYM	_	_	_
25	8	8	CD	_	_	_
26	CFU/ml	cfu/ml	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	exponential	exponential	JJ	GrowthPhase	_	_
29	phase	phase	NN	GrowthPhase	_	_
30	.	.	.	_	_	_

1	Batch	batch	NN	_	_	_
2	cultures	culture	NNS	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	MDS42	mds42	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	to	to	TO	_	_	_
10	early	early	JJ	GrowthPhase	_	_
11	exponential	exponential	JJ	GrowthPhase	_	_
12	phase	phase	NN	GrowthPhase	_	_
13	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	obtain	obtain	VB	_	_	_
3	tiling-resolution	tiling-resolution	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	measures	measure	NNS	_	_	_
6	across	across	IN	_	_	_
7	the	the	DT	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	genome	genome	NN	_	_	_
11	,	,	,	_	_	_
12	wild-type	wild-type	JJ	_	_	_
13	cells	cell	NNS	_	_	_
14	were	be	VBD	_	_	_
15	grown	grow	VBN	_	_	_
16	in	in	IN	_	_	_
17	biological	biological	JJ	_	_	_
18	duplicate	duplicate	VBP	_	_	_
19	in	in	IN	_	_	_
20	LB	lb	NN	_	_	_
21	to	to	TO	_	_	_
22	early	early	JJ	GrowthPhase	_	_
23	exponential	exponential	JJ	GrowthPhase	_	_
24	phase	phase	NN	GrowthPhase	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	moved	move	VBN	_	_	_
5	to	to	TO	_	_	_
6	ice	ice	NN	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	the	the	DT	_	_	_
10	Qiagen	Qiagen	NNP	_	_	_
11	RNeasy	RNeasy	NNP	_	_	_
12	kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	P/N	p/n	NN	_	_	_
15	74104	74104	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	was	be	VBD	_	_	_
18	used	use	VBN	_	_	_
19	to	to	TO	_	_	_
20	isolate	isolate	VB	_	_	_
21	total	total	JJ	_	_	_
22	cellular	cellular	JJ	_	_	_
23	RNA	rna	NN	_	_	_
24	.	.	.	_	_	_

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	each	each	DT	_	_	_
4	biological	biological	JJ	_	_	_
5	replicate	replicate	VB	_	_	_
6	,	,	,	_	_	_
7	frozen	frozen	JJ	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	500μl	500μl	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	of	of	IN	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	K12	k12	NN	_	_	_
16	stock	stock	NN	_	_	_
17	cultures	culture	NNS	_	_	_
18	were	be	VBD	_	_	_
19	subcultured	subculture	VBN	_	_	_
20	in	in	IN	_	_	_
21	10	10	CD	_	_	_
22	ml	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	Brain	brain	NN	_	_	_
25	Heart	Heart	NNP	_	_	_
26	Infusion	Infusion	NNP	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	BHI	BHI	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	incubated	incubate	VBN	_	_	_
32	overnight	overnight	JJ	_	_	_
33	at	at	IN	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	.	.	.	_	_	_

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	v/v	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	into	into	IN	_	_	_
11	50	50	CD	_	_	_
12	ml	ml	NN	_	_	_
13	BHI	BHI	NNP	_	_	_
14	broth	broth	NN	_	_	_
15	and	and	CC	_	_	_
16	incubated	incubate	VBN	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	for	for	IN	_	_	_
21	24h	24h	NN	_	_	_
22	under	under	IN	_	_	_
23	constant	constant	JJ	_	_	_
24	agitation	agitation	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	150	150	CD	_	_	_
27	rpm	rpm	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bacterial	bacterial	JJ	_	_	_
3	suspensions	suspension	NNS	_	_	_
4	were	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	inoculated	inoculate	VBN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	1	1	CD	_	_	_
9	%	%	NN	_	_	_
10	v/v	v/v	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	in	in	IN	_	_	_
13	200	200	CD	_	_	_
14	ml	ml	NN	_	_	_
15	BHI	BHI	NNP	_	_	_
16	broth	broth	NN	_	_	_
17	and	and	CC	_	_	_
18	grown	grow	VBN	_	_	_
19	in	in	IN	_	_	_
20	the	the	DT	_	_	_
21	same	same	JJ	_	_	_
22	conditions	condition	NNS	_	_	_
23	to	to	TO	_	_	_
24	stationary	stationary	JJ	GrowthPhase	_	_
25	phase	phase	NN	GrowthPhase	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600nm	od600nm	NN	_	_	_
28	of	of	IN	_	_	_
29	0.9	0.9	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	each	each	DT	_	_	_
4	biological	biological	JJ	_	_	_
5	RNA-Seq	rna-seq	NN	_	_	_
6	replicate	replicate	VB	_	_	_
7	E	e	NN	_	_	_
8	coli	coli	NN	_	_	_
9	K-12	k-12	NN	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	was	be	VBD	_	_	_
12	subcultured	subculture	VBN	_	_	_
13	from	from	IN	_	_	_
14	cyrostorage	cyrostorage	NN	_	_	_
15	on	on	IN	_	_	_
16	Luria-Bertani	Luria-Bertani	NNP	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	LB	LB	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	agar	agar	NN	_	_	_
21	overnight	overnight	JJ	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	.	.	.	_	_	_

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/L	mg/l	NN	_	_	_
43	uracil	uracil	NN	SUPP	_	_
44	and	and	CC	_	_	_
45	500	500	CD	_	_	_
46	µg/L	µg/l	NN	_	_	_
47	thiamine	thiamine	NN	SUPP	_	_
48	,	,	,	_	_	_
49	which	which	WDT	_	_	_
50	was	be	VBD	_	_	_
51	incubated	incubate	VBN	_	_	_
52	at	at	IN	_	_	_
53	37	37	CD	_	_	_
54	°C	°c	NN	_	_	_
55	with	with	IN	_	_	_
56	shaking	shake	VBG	_	_	_
57	at	at	IN	_	_	_
58	250	250	CD	_	_	_
59	rpm	rpm	NN	_	_	_
60	overnight	overnight	JJ	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	~	~	SYM	_	_	_
63	18	18	CD	_	_	_
64	hr	hr	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	overnight	overnight	JJ	_	_	_
3	starter	starter	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	diluted	dilute	VBN	_	_	_
7	1:30	1:30	CD	_	_	_
8	to	to	TO	_	_	_
9	initiate	initiate	VB	_	_	_
10	the	the	DT	_	_	_
11	experimental	experimental	JJ	_	_	_
12	culture	culture	NN	_	_	_
13	and	and	CC	_	_	_
14	divided	divide	VBN	_	_	_
15	into	into	IN	_	_	_
16	three	three	CD	_	_	_
17	500	500	CD	_	_	_
18	ml	ml	NN	_	_	_
19	flasks	flask	NNS	_	_	_
20	with	with	IN	_	_	_
21	100	100	CD	_	_	_
22	ml	ml	NN	_	_	_
23	NM3	nm3	NN	_	_	_
24	in	in	IN	_	_	_
25	each	each	DT	_	_	_
26	,	,	,	_	_	_
27	which	which	WDT	_	_	_
28	were	be	VBD	_	_	_
29	incubated	incubate	VBN	_	_	_
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	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	each	each	DT	_	_	_
4	co-ordinate	co-ordinate	JJ	_	_	_
5	coverage	coverage	NN	_	_	_
6	was	be	VBD	_	_	_
7	calculated	calculate	VBN	_	_	_
8	as	as	IN	_	_	_
9	the	the	DT	_	_	_
10	number	number	NN	_	_	_
11	of	of	IN	_	_	_
12	reads	read	VBZ	_	_	_
13	which	which	WDT	_	_	_
14	was	be	VBD	_	_	_
15	aligned	align	VBN	_	_	_
16	againist	againist	IN	_	_	_
17	the	the	DT	_	_	_
18	position	position	NN	_	_	_
19	.	.	.	_	_	_

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	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	NN	_	_	_
2	For	for	IN	_	_	_
3	each	each	DT	_	_	_
4	peak	peak	NN	_	_	_
5	detected	detect	VBN	_	_	_
6	with	with	IN	_	_	_
7	MACE	MACE	NNP	_	_	_
8	,	,	,	_	_	_
9	binding	bind	VBG	_	_	_
10	intensity	intensity	NN	_	_	_
11	was	be	VBD	_	_	_
12	calculated	calculate	VBN	_	_	_
13	by	by	IN	_	_	_
14	averaging	average	VBG	_	_	_
15	read	read	VBN	_	_	_
16	counts	count	NNS	_	_	_
17	from	from	IN	_	_	_
18	two	two	CD	_	_	_
19	biological	biological	JJ	_	_	_
20	replicates	replicate	VBZ	_	_	_
21	and	and	CC	_	_	_
22	dividing	divide	VBG	_	_	_
23	by	by	IN	_	_	_
24	background	background	NN	_	_	_
25	intensity	intensity	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	each	each	DT	_	_	_
4	sample	sample	NN	_	_	_
5	,	,	,	_	_	_
6	500	500	CD	_	_	_
7	mL	ml	NN	_	_	_
8	liquid	liquid	JJ	_	_	_
9	cultures	culture	NNS	_	_	_
10	were	be	VBD	_	_	_
11	grown	grow	VBN	_	_	_
12	in	in	IN	_	_	_
13	2.8	2.8	CD	_	_	_
14	L	l	NN	_	_	_
15	flasks	flask	NNS	_	_	_
16	with	with	IN	_	_	_
17	shaking	shake	VBG	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	180	180	CD	_	_	_
20	rpm	rpm	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	from	from	IN	_	_	_
26	an	a	DT	_	_	_
27	OD	od	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	600	600	CD	_	_	_
30	nm	nm	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	0.05	0.05	CD	_	_	_
33	to	to	TO	_	_	_
34	OD	od	CD	_	_	_
35	0.45	0.45	CD	_	_	_
36	±	±	SYM	_	_	_
37	0.05	0.05	CD	_	_	_
38	.	.	.	_	_	_

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	NN	_	_	_
2	For	for	IN	_	_	_
3	each	each	DT	_	_	_
4	uniquely	uniquely	RB	_	_	_
5	mapped	map	VBN	_	_	_
6	fragment	fragment	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	ribozero	ribozero	NN	_	_	_
9	treated	treat	VBN	_	_	_
10	samples	sample	NNS	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	or	or	CC	_	_	_
13	all	all	DT	_	_	_
14	mapped	map	VBN	_	_	_
15	fragments	fragment	NNS	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	total	total	JJ	_	_	_
18	RNA	rna	NN	_	_	_
19	samples	sample	NNS	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	at	at	IN	_	_	_
23	all	all	DT	_	_	_
24	aligned	align	VBN	_	_	_
25	positions	position	NNS	_	_	_
26	a	a	DT	_	_	_
27	count	count	NN	_	_	_
28	was	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	.	.	.	_	_	_

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	For	for	IN	_	_	_
12	further	further	JJ	_	_	_
13	analyses	analysis	NNS	_	_	_
14	the	the	DT	_	_	_
15	processed	process	VBN	_	_	_
16	signal	signal	NN	_	_	_
17	intensities	intensity	NNS	_	_	_
18	of	of	IN	_	_	_
19	all	all	DT	_	_	_
20	coding	code	VBG	_	_	_
21	regions	region	NNS	_	_	_
22	and	and	CC	_	_	_
23	RNA	rna	NN	_	_	_
24	genes	gene	NNS	_	_	_
25	were	be	VBD	_	_	_
26	extracted	extract	VBN	_	_	_
27	and	and	CC	_	_	_
28	used	use	VBN	_	_	_
29	.	.	.	_	_	_

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	NN	_	_	_
2	For	for	IN	_	_	_
3	immunoprecipitation	immunoprecipitation	NN	_	_	_
4	,	,	,	_	_	_
5	800	800	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	collected	collect	VBN	_	_	_
9	chromatin	chromatin	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	~	~	CD	_	_	_
12	1000	1000	CD	_	_	_
13	μg	μg	NN	_	_	_
14	of	of	IN	_	_	_
15	protein	protein	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	were	be	VBD	_	_	_
18	incubated	incubate	VBN	_	_	_
19	on	on	IN	_	_	_
20	a	a	DT	_	_	_
21	rotating	rotate	VBG	_	_	_
22	wheel	wheel	NN	_	_	_
23	over	over	IN	_	_	_
24	night	night	NN	_	_	_
25	at	at	IN	_	_	_
26	4	4	CD	_	_	_
27	°C	°c	NN	_	_	_
28	with	with	IN	_	_	_
29	10	10	CD	_	_	_
30	μg	μg	NN	_	_	_
31	of	of	IN	_	_	_
32	either	either	CC	_	_	_
33	rabbit	rabbit	NN	_	_	_
34	anti-Dps	anti-dps	JJ	_	_	_
35	antibodies	antibody	NNS	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	experimental	experimental	JJ	_	_	_
38	sample	sample	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	or	or	CC	_	_	_
41	rabbit	rabbit	NN	_	_	_
42	pre-immune	pre-immune	JJ	_	_	_
43	IgG	igg	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	negative	negative	JJ	_	_	_
46	control	control	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

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/G	a/g	NN	_	_	_
10	beads	bead	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Thermo	Thermo	NNP	_	_	_
13	Scientific	Scientific	NNP	_	_	_
14	,	,	,	_	_	_
15	USA	USA	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	were	be	VBD	_	_	_
18	added	add	VBN	_	_	_
19	to	to	TO	_	_	_
20	the	the	DT	_	_	_
21	samples	sample	NNS	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	incubation	incubation	NN	_	_	_
25	was	be	VBD	_	_	_
26	allowed	allow	VBN	_	_	_
27	for	for	IN	_	_	_
28	a	a	DT	_	_	_
29	further	further	RBR	_	_	_
30	2	2	CD	_	_	_
31	hours	hour	NNS	_	_	_
32	at	at	IN	_	_	_
33	4	4	CD	_	_	_
34	°C	°c	NN	_	_	_
35	on	on	IN	_	_	_
36	a	a	DT	_	_	_
37	rotating	rotate	VBG	_	_	_
38	wheel	wheel	NN	_	_	_
39	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	3	3	CD	_	_	_
6	times	time	NNS	_	_	_
7	with	with	IN	_	_	_
8	1	1	CD	_	_	_
9	ml	ml	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	low-salt	low-salt	JJ	_	_	_
13	buffer	buffer	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	50	50	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	HEPES	hepes	NN	_	_	_
18	pH	ph	NN	_	_	_
19	7.5	7.5	CD	_	_	_
20	,	,	,	_	_	_
21	140	140	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	NaCl	nacl	NN	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	%	%	NN	_	_	_
27	Triton	Triton	NNP	_	_	_
28	X-100	x-100	NN	_	_	_
29	,	,	,	_	_	_
30	1xPIC	1xpic	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	and	and	CC	_	_	_
33	then	then	RB	_	_	_
34	with	with	IN	_	_	_
35	1	1	CD	_	_	_
36	ml	ml	NN	_	_	_
37	of	of	IN	_	_	_
38	the	the	DT	_	_	_
39	high-salt	high-salt	JJ	_	_	_
40	buffer	buffer	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	500	500	CD	_	_	_
43	mM	mm	NN	KWSUPP	_	_
44	NaCl	nacl	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	Immunoprecipitated	immunoprecipitate	VBN	_	_	_
2	DNA-protein	dna-protein	JJ	_	_	_
3	complexes	complex	NNS	_	_	_
4	were	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	beads	bead	NNS	_	_	_
9	by	by	IN	_	_	_
10	3	3	CD	_	_	_
11	h	h	NN	_	_	_
12	shaking	shake	VBG	_	_	_
13	at	at	IN	_	_	_
14	65	65	CD	_	_	_
15	°C	°c	NN	_	_	_
16	and	and	CC	_	_	_
17	1000	1000	CD	_	_	_
18	rpm	rpm	NN	_	_	_
19	in	in	IN	_	_	_
20	110	110	CD	_	_	_
21	μl	μl	NN	_	_	_
22	of	of	IN	_	_	_
23	freshly	freshly	RB	_	_	_
24	prepared	prepared	JJ	_	_	_
25	elution	elution	NN	_	_	_
26	buffer	buffer	NN	_	_	_
27	,	,	,	_	_	_
28	containing	contain	VBG	_	_	_
29	100	100	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	NaHCO3	nahco3	NN	_	_	_
32	and	and	CC	_	_	_
33	1	1	CD	_	_	_
34	%	%	NN	_	_	_
35	SDS	sds	NN	_	_	_
36	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	at	at	IN	_	_	_
4	3000	3000	CD	_	_	_
5	rpm	rpm	NN	_	_	_
6	for	for	IN	_	_	_
7	5	5	CD	_	_	_
8	minutes	minute	NNS	_	_	_
9	,	,	,	_	_	_
10	100	100	CD	_	_	_
11	μl	μl	NN	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	supernatant	supernatant	NN	_	_	_
15	was	be	VBD	_	_	_
16	transferred	transfer	VBN	_	_	_
17	to	to	TO	_	_	_
18	a	a	DT	_	_	_
19	new	new	JJ	_	_	_
20	tube	tube	NN	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	the	the	DT	_	_	_
24	DNA	dna	NN	_	_	_
25	was	be	VBD	_	_	_
26	purified	purify	VBN	_	_	_
27	with	with	IN	_	_	_
28	a	a	DT	_	_	_
29	PCR	pcr	NN	_	_	_
30	Purification	purification	NN	_	_	_
31	Kit	kit	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Qiagen	Qiagen	NNP	_	_	_
34	,	,	,	_	_	_
35	Germany	Germany	NNP	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	DNA	dna	NN	_	_	_
3	concentration	concentration	NN	_	_	_
4	was	be	VBD	_	_	_
5	measured	measure	VBN	_	_	_
6	on	on	IN	_	_	_
7	Qubit	Qubit	NNP	_	_	_
8	2.0	2.0	CD	_	_	_
9	using	use	VBG	_	_	_
10	Qubit	Qubit	NNP	_	_	_
11	dsDNA	dsDNA	NNP	_	_	_
12	HS	hs	NN	_	_	_
13	Assay	assay	NN	_	_	_
14	kit	kit	NN	_	_	_
15	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	total	total	NN	_	_	_
3	of	of	IN	_	_	_
4	8-10	8-10	CD	_	_	_
5	identical	identical	JJ	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	combined	combine	VBN	_	_	_
9	and	and	CC	_	_	_
10	concentrated	concentrate	VBN	_	_	_
11	to	to	TO	_	_	_
12	a	a	DT	_	_	_
13	volume	volume	NN	_	_	_
14	of	of	IN	_	_	_
15	30-50	30-50	CD	_	_	_
16	μl	μl	NN	_	_	_
17	containing	contain	VBG	_	_	_
18	5-10	5-10	CD	_	_	_
19	ng	ng	NN	_	_	_
20	of	of	IN	_	_	_
21	the	the	DT	_	_	_
22	DNA	dna	NN	_	_	_
23	.	.	.	_	_	_

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	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	exponentially	exponentially	RB	_	_	_
12	growing	grow	VBG	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	were	be	VBD	_	_	_
16	incubated	incubate	VBN	_	_	_
17	with	with	IN	_	_	_
18	750	750	CD	_	_	_
19	µL	µl	NN	_	_	_
20	DMS	dms	NN	_	_	_
21	for	for	IN	_	_	_
22	2	2	CD	_	_	_
23	min	min	NN	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	.	.	.	_	_	_

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/mL	mg/ml	NN	_	_	_
18	to	to	TO	_	_	_
19	ΔgcvB	δgcvb	NN	_	_	_
20	cells	cell	NNS	_	_	_
21	for	for	IN	_	_	_
22	2	2	CD	_	_	_
23	min	min	NN	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	prior	prior	RB	_	_	_
28	to	to	TO	_	_	_
29	DMS	DMS	NNP	_	_	_
30	modification	modification	NN	_	_	_
31	.	.	.	_	_	_

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	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	in	in	FW	_	_	_
3	vitro	vitro	FW	_	_	_
4	DMS	dms	NN	_	_	_
5	modifications	modification	NNS	_	_	_
6	,	,	,	_	_	_
7	mRNA	mrna	NN	_	_	_
8	was	be	VBD	_	_	_
9	denatured	denature	VBN	_	_	_
10	at	at	IN	_	_	_
11	95	95	CD	_	_	_
12	°C	°c	NN	_	_	_
13	for	for	IN	_	_	_
14	2	2	CD	_	_	_
15	min	min	NN	_	_	_
16	,	,	,	_	_	_
17	cooled	cool	VBN	_	_	_
18	on	on	IN	_	_	_
19	ice	ice	NN	_	_	_
20	and	and	CC	_	_	_
21	refolded	refold	VBN	_	_	_
22	in	in	IN	_	_	_
23	90	90	CD	_	_	_
24	µL	µl	NN	_	_	_
25	RNA	rna	NN	_	_	_
26	folding	folding	JJ	_	_	_
27	buffer	buffer	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	10	10	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	Tris	Tris	NNP	_	_	_
32	pH	ph	NN	_	_	_
33	8.0	8.0	CD	_	_	_
34	,	,	,	_	_	_
35	100	100	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	NaCl	nacl	NN	_	_	_
38	,	,	,	_	_	_
39	6	6	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	MgCl2	mgcl2	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	at	at	IN	_	_	_
44	37	37	CD	_	_	_
45	°C	°c	NN	_	_	_
46	for	for	IN	_	_	_
47	30	30	CD	_	_	_
48	min	min	NN	_	_	_
49	then	then	RB	_	_	_
50	incubated	incubate	VBN	_	_	_
51	in	in	IN	_	_	_
52	either	either	CC	_	_	_
53	.2	.2	NN	_	_	_
54	%	%	NN	_	_	_
55	DMS	dms	NN	_	_	_
56	for	for	IN	_	_	_
57	1	1	CD	_	_	_
58	min	min	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	95	95	CD	_	_	_
61	°C	°c	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	or	or	CC	_	_	_
64	4	4	CD	_	_	_
65	%	%	NN	_	_	_
66	DMS	dms	NN	_	_	_
67	for	for	IN	_	_	_
68	5	5	CD	_	_	_
69	min	min	NN	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	37	37	CD	_	_	_
72	°C	°c	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Formaldehyde	Formaldehyde	NNP	_	_	_
3	was	be	VBD	_	_	_
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	%	%	NN	_	_	_
12	.	.	.	_	_	_

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	NN	_	_	_
2	For	for	IN	_	_	_
3	metagene	metagene	NN	_	_	_
4	analyses	analysis	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	gene-segment	gene-segment	NN	_	_	_
7	analyses	analysis	NNS	_	_	_
8	and	and	CC	_	_	_
9	codon-type	codon-type	JJ	_	_	_
10	analyses	analysis	NNS	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	,	,	,	_	_	_
13	pseudogenes	pseudogene	NNS	_	_	_
14	and	and	CC	_	_	_
15	genes	gene	NNS	_	_	_
16	not	not	RB	_	_	_
17	represented	represent	VBN	_	_	_
18	in	in	IN	_	_	_
19	one	one	CD	_	_	_
20	or	or	CC	_	_	_
21	more	more	JJR	_	_	_
22	datasets	dataset	NNS	_	_	_
23	were	be	VBD	_	_	_
24	excluded	exclude	VBN	_	_	_
25	,	,	,	_	_	_
26	leaving	leave	VBG	_	_	_
27	3048	3048	CD	_	_	_
28	genes	gene	NNS	_	_	_
29	in	in	IN	_	_	_
30	the	the	DT	_	_	_
31	\	\	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	For	for	IN	_	_	_
34	proteolysis	proteolysis	NN	_	_	_
35	,	,	,	_	_	_
36	affinity	affinity	NN	_	_	_
37	gel	gel	NN	_	_	_
38	obtained	obtain	VBN	_	_	_
39	after	after	IN	_	_	_
40	the	the	DT	_	_	_
41	last	last	JJ	_	_	_
42	centrifugation	centrifugation	NN	_	_	_
43	step	step	NN	_	_	_
44	was	be	VBD	_	_	_
45	diluted	dilute	VBN	_	_	_
46	with	with	IN	_	_	_
47	TES	tes	NN	_	_	_
48	buffer	buffer	NN	_	_	_
49	up	up	IN	_	_	_
50	to	to	TO	_	_	_
51	final	final	JJ	_	_	_
52	volume	volume	NN	_	_	_
53	200	200	CD	_	_	_
54	μl	μl	NN	_	_	_
55	,	,	,	_	_	_
56	proteinase	proteinase	NN	_	_	_
57	K	k	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	Sigma-Aldrich	sigma-aldrich	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	was	be	VBD	_	_	_
62	added	add	VBN	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	0.5	0.5	CD	_	_	_
65	mg/ml	mg/ml	NN	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	and	and	CC	_	_	_
68	samples	sample	NNS	_	_	_
69	were	be	VBD	_	_	_
70	incubated	incubate	VBN	_	_	_
71	at	at	IN	_	_	_
72	55	55	CD	_	_	_
73	°C	°c	NN	_	_	_
74	for	for	IN	_	_	_
75	at	at	IN	_	_	_
76	least	least	JJS	_	_	_
77	3	3	CD	_	_	_
78	hours	hour	NNS	_	_	_
79	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	this	this	DT	_	_	_
3	step	step	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	centrifuged	centrifuge	VBN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	2	2	CD	_	_	_
9	minutes	minute	NNS	_	_	_
10	,	,	,	_	_	_
11	2000xg	2000xg	NN	_	_	_
12	at	at	IN	_	_	_
13	room	room	NN	_	_	_
14	temperature	temperature	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	supernatants	supernatant	NNS	_	_	_
18	were	be	VBD	_	_	_
19	collected	collect	VBN	_	_	_
20	for	for	IN	_	_	_
21	DNA	dna	NN	_	_	_
22	extraction	extraction	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	quantification	quantification	NN	_	_	_
4	of	of	IN	_	_	_
5	gene	gene	NN	_	_	_
6	expression	expression	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	read	read	NN	_	_	_
9	counting	counting	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	the	the	DT	_	_	_
13	alignments	alignment	NNS	_	_	_
14	generated	generate	VBN	_	_	_
15	with	with	IN	_	_	_
16	the	the	DT	_	_	_
17	Genomics	Genomics	NNP	_	_	_
18	Workbench	Workbench	NNP	_	_	_
19	were	be	VBD	_	_	_
20	exported	export	VBN	_	_	_
21	in	in	IN	_	_	_
22	BAM	BAM	NNP	_	_	_
23	format	format	NN	_	_	_
24	.	.	.	_	_	_

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	For	for	IN	_	_	_
7	REC-Seq	rec-seq	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	restriction	restriction	NN	_	_	_
10	enzyme	enzyme	NN	_	_	_
11	cleavage	cleavage	NN	_	_	_
12	--	--	:	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	1	1	CD	_	_	_
16	ug	ug	NN	_	_	_
17	of	of	IN	_	_	_
18	genomic	genomic	JJ	_	_	_
19	DNA	dna	NN	_	_	_
20	from	from	IN	_	_	_
21	C.	c.	FW	_	_	_
22	crescentus	crescentus	FW	_	_	_
23	NA1000	na1000	NN	_	_	_
24	and	and	CC	_	_	_
25	S.	S.	NNP	_	_	_
26	meliloti	melilotus	NNS	_	_	_
27	Rm2011	rm2011	NN	_	_	_
28	was	be	VBD	_	_	_
29	cleaved	cleave	VBN	_	_	_
30	with	with	IN	_	_	_
31	HinfI	hinfi	NN	_	_	_
32	,	,	,	_	_	_
33	a	a	DT	_	_	_
34	blocked	block	VBN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	5	5	CD	_	_	_
37	'	'	''	_	_	_
38	biotinylated	biotinylate	VBN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	specific	specific	JJ	_	_	_
41	adaptor	adaptor	NN	_	_	_
42	was	be	VBD	_	_	_
43	ligated	ligate	VBN	_	_	_
44	to	to	TO	_	_	_
45	the	the	DT	_	_	_
46	ends	end	NNS	_	_	_
47	and	and	CC	_	_	_
48	the	the	DT	_	_	_
49	ligated	ligate	VBN	_	_	_
50	fragments	fragment	NNS	_	_	_
51	were	be	VBD	_	_	_
52	then	then	RB	_	_	_
53	sheared	shear	VBN	_	_	_
54	to	to	TO	_	_	_
55	an	a	DT	_	_	_
56	average	average	JJ	_	_	_
57	size	size	NN	_	_	_
58	of	of	IN	_	_	_
59	150-400	150-400	CD	_	_	_
60	bp	bp	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Fasteris	fasteris	NN	_	_	_
63	SA	SA	NNP	_	_	_
64	,	,	,	_	_	_
65	Geneva	Geneva	NNP	_	_	_
66	,	,	,	_	_	_
67	CH	ch	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	.	.	.	_	_	_

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://www.bioinformatics.babraham.ac.uk/projects/fastqc/	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

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	NN	_	_	_
2	For	for	IN	_	_	_
3	RNA	rna	NN	_	_	_
4	isolation	isolation	NN	_	_	_
5	,	,	,	_	_	_
6	0.5	0.5	CD	_	_	_
7	mL	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	cultures	culture	NNS	_	_	_
11	were	be	VBD	_	_	_
12	mixed	mix	VBN	_	_	_
13	with	with	IN	_	_	_
14	1	1	CD	_	_	_
15	mL	ml	NN	_	_	_
16	RNA	rna	NN	_	_	_
17	protect	protect	VBP	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	,	,	,	_	_	_
21	Ontario	Ontario	NNP	_	_	_
22	,	,	,	_	_	_
23	Canada	Canada	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	RNA	rna	NN	_	_	_
27	was	be	VBD	_	_	_
28	isolated	isolate	VBN	_	_	_
29	using	use	VBG	_	_	_
30	the	the	DT	_	_	_
31	RNeasy	RNeasy	NNP	_	_	_
32	Mini	Mini	NNP	_	_	_
33	kit	kit	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Qiagen	qiagen	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

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	For	for	IN	_	_	_
3	RNA-Seq	rna-seq	NN	_	_	_
4	analysis	analysis	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	fastq	fastq	NN	_	_	_
8	file	file	NN	_	_	_
9	produced	produce	VBN	_	_	_
10	from	from	IN	_	_	_
11	the	the	DT	_	_	_
12	machine	machine	NN	_	_	_
13	was	be	VBD	_	_	_
14	demultiplexed	demultiplex	VBN	_	_	_
15	into	into	IN	_	_	_
16	a	a	DT	_	_	_
17	separate	separate	JJ	_	_	_
18	file	file	NN	_	_	_
19	for	for	IN	_	_	_
20	each	each	DT	_	_	_
21	sample	sample	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	RNA-seq	rna-seq	NN	_	_	_
4	:	:	:	_	_	_
5	total	total	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	was	be	VBD	_	_	_
8	extracted	extract	VBN	_	_	_
9	using	use	VBG	_	_	_
10	RNeasy	RNeasy	NNP	_	_	_
11	Protect	protect	VB	_	_	_
12	Bacteria	bacterium	NNS	_	_	_
13	according	accord	VBG	_	_	_
14	to	to	TO	_	_	_
15	manufacturer	manufacturer	NN	_	_	_
16	instructions	instruction	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	QIAGEN	QIAGEN	NNP	_	_	_
19	-	-	:	_	_	_
20	#	#	#	_	_	_
21	74524	74524	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	For	for	IN	_	_	_
25	the	the	DT	_	_	_
26	first	first	JJ	_	_	_
27	batch	batch	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	from	from	IN	_	_	_
30	WT	WT	NNP	_	_	_
31	_	_	NNP	_	_	_
32	LB	LB	NNP	_	_	_
33	_	_	SYM	_	_	_
34	1	1	CD	_	_	_
35	to	to	TO	_	_	_
36	lacA	lacA	NNP	GEN	_	_
37	_	_	NNP	_	_	_
38	M9	M9	NNP	_	_	_
39	_	_	SYM	_	_	_
40	2	2	LS	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	,	,	,	_	_	_
43	fresh	fresh	JJ	_	_	_
44	colonies	colony	NNS	_	_	_
45	of	of	IN	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	cells	cell	NNS	_	_	_
49	were	be	VBD	_	_	_
50	taken	take	VBN	_	_	_
51	and	and	CC	_	_	_
52	inoculated	inoculate	VBN	_	_	_
53	in	in	IN	_	_	_
54	1	1	CD	_	_	_
55	ml	ml	NN	_	_	_
56	LB	lb	NN	_	_	_
57	and	and	CC	_	_	_
58	grown	grow	VBN	_	_	_
59	for	for	IN	_	_	_
60	8	8	CD	_	_	_
61	h	h	NN	_	_	_
62	at	at	IN	_	_	_
63	37	37	CD	_	_	_
64	°C	°c	NN	_	_	_
65	.	.	.	_	_	_

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/M9	lb/m9	NN	_	_	_
14	medium	medium	NN	_	_	_
15	supplemented	supplement	VBN	_	_	_
16	with	with	IN	_	_	_
17	0.3	0.3	CD	_	_	_
18	%	%	NN	_	_	_
19	glucose	glucose	NN	SUPP	_	_
20	and	and	CC	_	_	_
21	grown	grow	VBN	_	_	_
22	for	for	IN	_	_	_
23	12	12	CD	_	_	_
24	h	h	NN	_	_	_
25	at	at	IN	_	_	_
26	37	37	CD	_	_	_
27	°C	°c	NN	_	_	_
28	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	12	12	CD	_	_	_
3	h	h	NN	_	_	_
4	,	,	,	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	harvested	harvest	VBN	_	_	_
8	for	for	IN	_	_	_
9	the	the	DT	_	_	_
10	RNA-seq	rna-seq	NN	_	_	_
11	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	second	second	JJ	_	_	_
4	batch	batch	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	from	from	IN	_	_	_
7	WT	WT	NNP	_	_	_
8	_	_	SYM	_	_	_
9	1	1	CD	_	_	_
10	to	to	TO	_	_	_
11	aspC	aspC	NNP	GEN	_	_
12	_	_	SYM	_	_	_
13	3	3	LS	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	a	a	DT	_	_	_
17	1:100	1:100	CD	_	_	_
18	dilution	dilution	NN	_	_	_
19	from	from	IN	_	_	_
20	an	a	DT	_	_	_
21	overnight	overnight	JJ	_	_	_
22	culture	culture	NN	_	_	_
23	in	in	IN	_	_	_
24	M9	m9	NN	_	_	_
25	0.4	0.4	CD	_	_	_
26	%	%	NN	_	_	_
27	glucose	glucose	NN	SUPP	_	_
28	was	be	VBD	_	_	_
29	done	do	VBN	_	_	_
30	.	.	.	_	_	_

1	When	when	WRB	_	_	_
2	the	the	DT	_	_	_
3	late	late	JJ	_	_	_
4	stationary	stationary	JJ	GrowthPhase	_	_
5	phase	phase	NN	GrowthPhase	_	_
6	was	be	VBD	_	_	_
7	reached	reach	VBN	_	_	_
8	,	,	,	_	_	_
9	the	the	DT	_	_	_
10	samples	sample	NNS	_	_	_
11	were	be	VBD	_	_	_
12	harvested	harvest	VBN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	the	the	DT	_	_	_
4	Illumina	Illumina	NNP	_	_	_
5	GAII	GAII	NNP	_	_	_
6	platform	platform	NN	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	directional	directional	JJ	_	_	_
10	RNA-seq	rna-seq	NN	_	_	_
11	libraries	library	NNS	_	_	_
12	were	be	VBD	_	_	_
13	constructed	construct	VBN	_	_	_
14	by	by	IN	_	_	_
15	following	follow	VBG	_	_	_
16	an	a	DT	_	_	_
17	Illumina	Illumina	NNP	_	_	_
18	's	's	POS	_	_	_
19	instruction	instruction	NN	_	_	_
20	using	use	VBG	_	_	_
21	their	they	PRP$	_	_	_
22	Small	small	JJ	_	_	_
23	RNA	rna	NN	_	_	_
24	Sample	sample	NN	_	_	_
25	Prep	Prep	NNP	_	_	_
26	Kit	kit	NN	_	_	_
27	with	with	IN	_	_	_
28	some	some	DT	_	_	_
29	modifications	modification	NNS	_	_	_
30	.	.	.	_	_	_

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	NN	_	_	_
2	For	for	IN	_	_	_
3	the	the	DT	_	_	_
4	whole-transcriptome	whole-transcriptome	JJ	_	_	_
5	analysis	analysis	NN	_	_	_
6	,	,	,	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	was	be	VBD	_	_	_
9	verified	verify	VBN	_	_	_
10	using	use	VBG	_	_	_
11	FASTQC	fastqc	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	version	version	NN	_	_	_
14	0.11.2	0.11.2	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	to	to	TO	_	_	_
17	confirm	confirm	VB	_	_	_
18	base-call	base-call	JJ	_	_	_
19	quality	quality	NN	_	_	_
20	in	in	IN	_	_	_
21	each	each	DT	_	_	_
22	indexed	index	VBN	_	_	_
23	file	file	NN	_	_	_
24	.	.	.	_	_	_

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	NN	_	_	_
2	For	for	IN	_	_	_
3	total	total	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	isolation	isolation	NN	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	bacteria	bacterium	NNS	_	_	_
9	were	be	VBD	_	_	_
10	inoculated	inoculate	VBN	_	_	_
11	in	in	IN	_	_	_
12	5	5	CD	_	_	_
13	ml	ml	NN	_	_	_
14	LB	lb	NN	MED	_	_
15	broth	broth	NN	MED	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	℃	℃	NN	_	_	_
19	with	with	IN	_	_	_
20	shaking	shake	VBG	_	_	_
21	for	for	IN	_	_	_
22	16	16	CD	_	_	_
23	h.	h.	NN	_	_	_
24	50	50	CD	_	_	_
25	µl	µl	NN	_	_	_
26	of	of	IN	_	_	_
27	the	the	DT	_	_	_
28	above	above	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	was	be	VBD	_	_	_
31	inoculated	inoculate	VBN	_	_	_
32	in	in	IN	_	_	_
33	5	5	CD	_	_	_
34	ml	ml	NN	_	_	_
35	fresh	fresh	JJ	_	_	_
36	LB	lb	NN	MED	_	_
37	broth	broth	NN	MED	_	_
38	and	and	CC	_	_	_
39	the	the	DT	_	_	_
40	culture	culture	NN	_	_	_
41	was	be	VBD	_	_	_
42	shaken	shake	VBN	_	_	_
43	at	at	IN	_	_	_
44	37	37	CD	_	_	_
45	°C	°c	NN	_	_	_
46	for	for	IN	_	_	_
47	about	about	IN	_	_	_
48	2.5	2.5	CD	_	_	_
49	h	h	NN	_	_	_
50	until	until	IN	_	_	_
51	the	the	DT	_	_	_
52	OD600	od600	NN	_	_	_
53	reached	reach	VBD	_	_	_
54	0.6	0.6	CD	_	_	_
55	.	.	.	_	_	_

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	Forward	forward	RB	_	_	_
3	-	-	:	_	_	_
4	and	and	CC	_	_	_
5	reverse-read	reverse-read	JJ	_	_	_
6	mate-pairs	mate-pair	NNS	_	_	_
7	were	be	VBD	_	_	_
8	assembled	assemble	VBN	_	_	_
9	and	and	CC	_	_	_
10	aligned	align	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	MG1655	mg1655	NN	_	_	_
16	K-12	k-12	NN	_	_	_
17	genome	genome	NN	_	_	_
18	using	use	VBG	_	_	_
19	Bowtie2	bowtie2	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Langmead	langmead	NN	_	_	_
22	and	and	CC	_	_	_
23	Salzberg	Salzberg	NNP	_	_	_
24	,	,	,	_	_	_
25	2012	2012	CD	_	_	_
26	,	,	,	_	_	_
27	Nat	Nat	NNP	_	_	_
28	Methods	method	NNS	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

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	NN	_	_	_
2	Four	four	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	bacterial	bacterial	JJ	_	_	_
7	suspension	suspension	NN	_	_	_
8	in	in	IN	_	_	_
9	RNALater	rnalater	NN	_	_	_
10	II	ii	CD	_	_	_
11	and	and	CC	_	_	_
12	Medium	medium	NN	_	_	_
13	E	e	NN	_	_	_
14	growth	growth	NN	_	_	_
15	medium	medium	NN	_	_	_
16	were	be	VBD	_	_	_
17	spun	spin	VBN	_	_	_
18	down	down	RP	_	_	_
19	at	at	IN	_	_	_
20	200g	200g	NN	_	_	_
21	for	for	IN	_	_	_
22	5	5	CD	_	_	_
23	min	min	NN	_	_	_
24	.	.	.	_	_	_

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	NN	_	_	_
2	Four	four	CD	_	_	_
3	morphologic	morphologic	JJ	_	_	_
4	states	state	NNS	_	_	_
5	of	of	IN	_	_	_
6	ESBL019	esbl019	NN	_	_	_
7	were	be	VBD	_	_	_
8	used	use	VBN	_	_	_
9	during	during	IN	_	_	_
10	the	the	DT	_	_	_
11	experiments	experiment	NNS	_	_	_
12	.	.	.	_	_	_

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/mL	480ng/ml	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	designated	designate	VBN	_	_	_
27	;	;	:	_	_	_
28	ESBL019	esbl019	NN	_	_	_
29	Transition	transition	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	transition	transition	NN	_	_	_
3	from	from	IN	_	_	_
4	coliform	coliform	NN	_	_	_
5	into	into	IN	_	_	_
6	filamented	filamented	JJ	_	_	_
7	occurs	occur	VBZ	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	presence	presence	NN	_	_	_
11	of	of	IN	_	_	_
12	HBEP	hbep	NN	_	_	_
13	cells	cell	NNS	_	_	_
14	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	third	third	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	and	and	CC	_	_	_
11	pre-incubation	pre-incubation	NN	_	_	_
12	for	for	IN	_	_	_
13	3	3	CD	_	_	_
14	hours	hour	NNS	_	_	_
15	in	in	IN	_	_	_
16	CCM	ccm	NN	_	_	_
17	with	with	IN	_	_	_
18	ceftibuten	ceftibuten	NN	_	_	_
19	in	in	IN	_	_	_
20	a	a	DT	_	_	_
21	tube	tube	NN	_	_	_
22	,	,	,	_	_	_
23	in	in	IN	_	_	_
24	order	order	NN	_	_	_
25	to	to	TO	_	_	_
26	induce	induce	VB	_	_	_
27	complete	complete	JJ	_	_	_
28	filamentation	filamentation	NN	_	_	_
29	of	of	IN	_	_	_
30	all	all	DT	_	_	_
31	bacteria	bacterium	NNS	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	third	third	JJ	_	_	_
3	pre-filamented	pre-filamented	JJ	_	_	_
4	ESBL019	esbl019	NN	_	_	_
5	fraction	fraction	NN	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	to	to	TO	_	_	_
9	inoculate	inoculate	VB	_	_	_
10	HBEP	hbep	NN	_	_	_
11	cells	cell	NNS	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	presence	presence	NN	_	_	_
15	of	of	IN	_	_	_
16	ceftibuten	ceftibuten	NN	_	_	_
17	to	to	TO	_	_	_
18	keep	keep	VB	_	_	_
19	the	the	DT	_	_	_
20	bacteria	bacterium	NNS	_	_	_
21	filamented	filament	VBN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	designated	designate	VBN	_	_	_
24	;	;	:	_	_	_
25	ESBL019	esbl019	NN	_	_	_
26	Filamented	filamented	JJ	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	CCM	CCM	NNP	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	pre-filamented	pre-filamented	JJ	_	_	_
6	ESBL019	esbl019	NN	_	_	_
7	fraction	fraction	NN	_	_	_
8	was	be	VBD	_	_	_
9	replaced	replace	VBN	_	_	_
10	with	with	IN	_	_	_
11	CCM	ccm	NN	_	_	_
12	without	without	IN	_	_	_
13	ceftibuten	ceftibuten	NN	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	filamented	filamented	JJ	_	_	_
17	ESBL019	esbl019	NN	_	_	_
18	were	be	VBD	_	_	_
19	allowed	allow	VBN	_	_	_
20	to	to	TO	_	_	_
21	revert	revert	VB	_	_	_
22	completely	completely	RB	_	_	_
23	back	back	RB	_	_	_
24	to	to	TO	_	_	_
25	its	its	PRP$	_	_	_
26	coliform	coliform	NN	_	_	_
27	during	during	IN	_	_	_
28	1	1	CD	_	_	_
29	hour	hour	NN	_	_	_
30	in	in	IN	_	_	_
31	a	a	DT	_	_	_
32	tube	tube	NN	_	_	_
33	prior	prior	RB	_	_	_
34	to	to	TO	_	_	_
35	the	the	DT	_	_	_
36	inoculation	inoculation	NN	_	_	_
37	of	of	IN	_	_	_
38	HBEP	hbep	NN	_	_	_
39	cells	cell	NNS	_	_	_
40	without	without	IN	_	_	_
41	ceftibuten	ceftibuten	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	designated	designate	VBN	_	_	_
44	;	;	:	_	_	_
45	ESBL019	esbl019	NN	_	_	_
46	Reverted	revert	VBD	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	inoculation	inoculation	NN	_	_	_
4	the	the	DT	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	concentrations	concentration	NNS	_	_	_
7	of	of	IN	_	_	_
8	all	all	DT	_	_	_
9	fractions	fraction	NNS	_	_	_
10	were	be	VBD	_	_	_
11	adjusted	adjust	VBN	_	_	_
12	in	in	IN	_	_	_
13	order	order	NN	_	_	_
14	to	to	TO	_	_	_
15	inoculate	inoculate	VB	_	_	_
16	HBEP	hbep	NN	_	_	_
17	cells	cell	NNS	_	_	_
18	with	with	IN	_	_	_
19	a	a	DT	_	_	_
20	multiplicity	multiplicity	NN	_	_	_
21	of	of	IN	_	_	_
22	infection	infection	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	MOI	moi	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	of	of	IN	_	_	_
27	10	10	CD	_	_	_
28	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	inoculated	inoculate	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	incubated	incubate	VBN	_	_	_
6	for	for	IN	_	_	_
7	4	4	CD	_	_	_
8	hours	hour	NNS	_	_	_
9	in	in	IN	_	_	_
10	5	5	CD	_	_	_
11	%	%	NN	_	_	_
12	CO2	co2	NN	_	_	_
13	at	at	IN	_	_	_
14	37oC	37oc	NN	_	_	_
15	after	after	IN	_	_	_
16	which	which	WDT	_	_	_
17	supernatants	supernatant	NNS	_	_	_
18	were	be	VBD	_	_	_
19	collected	collect	VBN	_	_	_
20	and	and	CC	_	_	_
21	centrifuged	centrifuge	VBN	_	_	_
22	5	5	CD	_	_	_
23	min	min	NN	_	_	_
24	at	at	IN	_	_	_
25	5000	5000	CD	_	_	_
26	x	x	CC	_	_	_
27	g	g	NN	_	_	_
28	to	to	TO	_	_	_
29	collect	collect	VB	_	_	_
30	the	the	DT	_	_	_
31	bacteria	bacterium	NNS	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	FPKM	fpkm	NNS	_	_	_
3	were	be	VBD	_	_	_
4	calculated	calculate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Cufflinks	Cufflinks	NNP	_	_	_
7	v.	v.	CC	_	_	_
8	2.0.2	2.0.2	CD	_	_	_
9	with	with	IN	_	_	_
10	upper-quartile	upper-quartile	JJ	_	_	_
11	normalization	normalization	NN	_	_	_
12	and	and	CC	_	_	_
13	fr-firststrand	fr-firststrand	NN	_	_	_
14	for	for	IN	_	_	_
15	library	library	NN	_	_	_
16	type	type	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	fraction	fraction	NN	_	_	_
19	:	:	:	_	_	_
20	input	input	NN	_	_	_
21	DNA	dna	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	fraction	fraction	NN	_	_	_
24	:	:	:	_	_	_
25	input	input	NN	_	_	_
26	DNA	dna	NN	_	_	_
27	,	,	,	_	_	_
28	SeqA	seqa	NN	_	_	_
29	ChIP	chip	NN	_	_	_
30	supernatant	supernatant	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	fraction	fraction	NN	_	_	_
33	:	:	:	_	_	_
34	input	input	NN	_	_	_
35	DNA	dna	NN	_	_	_
36	,	,	,	_	_	_
37	σ32	σ32	NN	_	_	_
38	ChIP	chip	NN	_	_	_
39	supernatant	supernatant	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Fragmentation	fragmentation	NN	_	_	_
42	and	and	CC	_	_	_
43	reverse	reverse	JJ	_	_	_
44	transcription	transcription	NN	_	_	_
45	of	of	IN	_	_	_
46	RNA	rna	NN	_	_	_
47	with	with	IN	_	_	_
48	random	random	JJ	_	_	_
49	primers	primer	NNS	_	_	_
50	was	be	VBD	_	_	_
51	carried	carry	VBN	_	_	_
52	out	out	RP	_	_	_
53	using	use	VBG	_	_	_
54	the	the	DT	_	_	_
55	NEB	NEB	NNP	_	_	_
56	First	First	NNP	_	_	_
57	Strand	Strand	NNP	_	_	_
58	Synthesis	synthesis	NN	_	_	_
59	Module	module	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	New	New	NNP	_	_	_
62	England	England	NNP	_	_	_
63	Biolabs	Biolabs	NNP	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

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	NN	_	_	_
2	Fragments	fragment	NNS	_	_	_
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	FPKM	fpkm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	were	be	VBD	_	_	_
16	calculated	calculate	VBN	_	_	_
17	using	use	VBG	_	_	_
18	cufflinks	cufflink	NNS	_	_	_
19	v.	v.	CC	_	_	_
20	1.3.0	1.3.0	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	FRIK2000	frik2000	NN	_	_	_
23	Cy3	cy3	NN	_	_	_
24	rep1	rep1	NN	_	_	_
25	vs	vs	CC	_	_	_
26	EDL933	edl933	NN	_	_	_
27	pool	pool	NN	_	_	_
28	Cy5	cy5	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	FRIK2000	frik2000	CD	_	_	_
31	Cy3	cy3	NN	_	_	_
32	rep3	rep3	NN	_	_	_
33	vs	vs	CC	_	_	_
34	EDL933	edl933	NN	_	_	_
35	pool	pool	NN	_	_	_
36	Cy5	cy5	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	FRIK2000	frik2000	CD	_	_	_
39	Cy5	cy5	NN	_	_	_
40	rep2	rep2	NN	_	_	_
41	vs	vs	CC	_	_	_
42	EDL933	edl933	NN	_	_	_
43	pool	pool	NN	_	_	_
44	Cy3	cy3	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	FRIK2000	frik2000	CD	_	_	_
47	Cy5	cy5	NN	_	_	_
48	rep4	rep4	NN	_	_	_
49	vs	vs	CC	_	_	_
50	EDL933	edl933	NN	_	_	_
51	pool	pool	NN	_	_	_
52	Cy3	cy3	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	FRIK966	frik966	NN	_	_	_
55	Cy3	cy3	NN	_	_	_
56	rep1	rep1	NN	_	_	_
57	vs	vs	CC	_	_	_
58	EDL933	edl933	NN	_	_	_
59	pool	pool	NN	_	_	_
60	Cy5	cy5	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	FRIK966	frik966	NN	_	_	_
63	Cy3	cy3	NN	_	_	_
64	rep3	rep3	NN	_	_	_
65	vs	vs	CC	_	_	_
66	EDL933	edl933	NN	_	_	_
67	pool	pool	NN	_	_	_
68	Cy5	cy5	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	FRIK966	frik966	NN	_	_	_
71	Cy5	cy5	NN	_	_	_
72	rep2	rep2	NN	_	_	_
73	vs	vs	CC	_	_	_
74	EDL933	edl933	NN	_	_	_
75	pool	pool	NN	_	_	_
76	Cy3	cy3	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	FRIK966	frik966	NN	_	_	_
79	Cy5	cy5	NN	_	_	_
80	rep4	rep4	NN	_	_	_
81	vs	vs	CC	_	_	_
82	EDL933	edl933	NN	_	_	_
83	pool	pool	NN	_	_	_
84	Cy3	cy3	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	From	from	IN	_	_	_
87	the	the	DT	_	_	_
88	cells	cell	NNS	_	_	_
89	cultured	culture	VBN	_	_	_
90	in	in	IN	_	_	_
91	LB	LB	NNP	MED	_	_
92	media	media	NNS	MED	_	_
93	at	at	IN	_	_	_
94	37	37	CD	_	_	_
95	℃	℃	CD	_	_	_
96	,	,	,	_	_	_
97	total	total	JJ	_	_	_
98	RNA	rna	NN	_	_	_
99	was	be	VBD	_	_	_
100	extracted	extract	VBN	_	_	_
101	using	use	VBG	_	_	_
102	RNAsnapTM	rnasnaptm	NN	_	_	_
103	method	method	NN	_	_	_
104	,	,	,	_	_	_
105	followed	follow	VBN	_	_	_
106	by	by	IN	_	_	_
107	the	the	DT	_	_	_
108	ethanol	ethanol	NN	_	_	_
109	precipitation	precipitation	NN	_	_	_
110	.	.	.	_	_	_

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

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	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	12	12	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	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	pgcgrowthcondition	NNS	_	_	_
2	Frozen	frozen	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	pellets	pellet	NNS	_	_	_
5	were	be	VBD	_	_	_
6	lyzed	lyze	VBN	_	_	_
7	with	with	IN	_	_	_
8	lysozyme	lysozyme	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Sigma	Sigma	NNP	_	_	_
11	Aldrich	Aldrich	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	proteinase	proteinase	NN	_	_	_
15	K	k	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	Inc.	Inc.	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	at	at	IN	_	_	_
21	room	room	NN	_	_	_
22	temperature	temperature	NN	_	_	_
23	.	.	.	_	_	_

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/chloroform	phenol/chloroform	NN	_	_	_
19	purification	purification	NN	_	_	_
20	and	and	CC	_	_	_
21	an	a	DT	_	_	_
22	overnight	overnight	JJ	_	_	_
23	precipitation	precipitation	NN	_	_	_
24	at	at	IN	_	_	_
25	-20	-20	CD	_	_	_
26	°C	°c	NN	_	_	_
27	in	in	IN	_	_	_
28	absolute	absolute	JJ	_	_	_
29	ethanol	ethanol	NN	_	_	_
30	containing	contain	VBG	_	_	_
31	LiCl	licl	NN	_	_	_
32	8M	8m	NN	_	_	_
33	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	,	,	,	_	_	_
4	RNA	rna	NN	_	_	_
5	pellets	pellet	NNS	_	_	_
6	were	be	VBD	_	_	_
7	air-dried	air-dried	JJ	_	_	_
8	in	in	IN	_	_	_
9	a	a	DT	_	_	_
10	vacuum	vacuum	NN	_	_	_
11	concentrator	concentrator	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	vacufuge	vacufuge	NN	_	_	_
14	plus	plus	CC	_	_	_
15	;	;	:	_	_	_
16	Eppendorf	eppendorf	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Functional	functional	JJ	_	_	_
3	annotation	annotation	NN	_	_	_
4	was	be	VBD	_	_	_
5	done	do	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Database	database	NN	_	_	_
9	for	for	IN	_	_	_
10	Annotation	Annotation	NNP	_	_	_
11	,	,	,	_	_	_
12	Visualization	visualization	NN	_	_	_
13	and	and	CC	_	_	_
14	Integrated	Integrated	NNP	_	_	_
15	Discovery	Discovery	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	DAVID	DAVID	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	Bioinformatics	Bioinformatics	NNP	_	_	_
20	Resources	Resources	NNP	_	_	_
21	6.7	6.7	CD	_	_	_
22	,	,	,	_	_	_
23	NIAID	NIAID	NNP	_	_	_
24	,	,	,	_	_	_
25	NIH	NIH	NNP	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	http://david.abcc.ncifcrf.gov	http://david.abcc.ncifcrf.gov	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	∆	∆	SYM	_	_	_
3	fur	fur	NN	GEN	_	_
4	Aerobic	aerobic	JJ	_	_	_
5	A	a	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	∆	∆	CD	_	_	_
8	fur	fur	NN	GEN	_	_
9	Aerobic	aerobic	JJ	_	_	_
10	B	b	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	∆	∆	CD	_	_	_
13	fur	fur	NN	GEN	_	_
14	Anaerobic	anaerobic	JJ	_	_	_
15	A	a	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	∆	∆	CD	_	_	_
18	fur	fur	NN	GEN	_	_
19	Anaerobic	anaerobic	JJ	_	_	_
20	B	b	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	∆	∆	CD	_	_	_
23	fur	fur	NN	GEN	_	_
24	Anaerobic	anaerobic	JJ	_	_	_
25	-LSB-	-lsb-	-LRB-	_	_	_
26	IP	IP	NNP	_	_	_
27	vs	vs	CC	_	_	_
28	nput	nput	NN	_	_	_
29	-RSB-	-rsb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	furanone-free	furanone-free	JJ	_	_	_
32	control	control	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
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	_	_	NN	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Furfural-tolerant	furfural-tolerant	JJ	_	_	_
47	IrrE	irre	NN	_	_	_
48	mutant	mutant	JJ	_	_	_
49	F1-37	f1-37	NN	_	_	_
50	,	,	,	_	_	_
51	biological	biological	JJ	_	_	_
52	rep1	rep1	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Furfural-tolerant	furfural-tolerant	JJ	_	_	_
55	IrrE	irre	NN	_	_	_
56	mutant	mutant	JJ	_	_	_
57	F1-37	f1-37	NN	_	_	_
58	,	,	,	_	_	_
59	biological	biological	JJ	_	_	_
60	rep2	rep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Furfural-tolerant	furfural-tolerant	JJ	_	_	_
63	IrrE	irre	NN	_	_	_
64	mutant	mutant	JJ	_	_	_
65	F1-37	f1-37	NN	_	_	_
66	,	,	,	_	_	_
67	biological	biological	JJ	_	_	_
68	rep3	rep3	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	Fur	Fur	NNP	TF	_	_
71	IP	IP	NNP	_	_	_
72	ChIP-Seq	ChIP-Seq	NNP	_	_	_
73	Aerobic	Aerobic	NNP	_	_	_
74	A	A	NNP	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Fur	Fur	NNP	TF	_	_
77	IP	IP	NNP	_	_	_
78	ChIP-Seq	ChIP-Seq	NNP	_	_	_
79	Aerobic	Aerobic	NNP	_	_	_
80	B	B	NNP	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	Fur	Fur	NNP	TF	_	_
83	IP	IP	NNP	_	_	_
84	ChIP-Seq	ChIP-Seq	NNP	_	_	_
85	Aerobic	Aerobic	NNP	_	_	_
86	C	C	NNP	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Fur	Fur	NNP	TF	_	_
89	IP	IP	NNP	_	_	_
90	ChIP-Seq	ChIP-Seq	NNP	_	_	_
91	Anaerobic	Anaerobic	NNP	_	_	_
92	A	A	NNP	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	Fur	Fur	NNP	TF	_	_
95	IP	IP	NNP	_	_	_
96	ChIP-Seq	ChIP-Seq	NNP	_	_	_
97	Anaerobic	anaerobic	JJ	_	_	_
98	B	b	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
100	Fur	Fur	NNP	TF	_	_
101	IP	IP	NNP	_	_	_
102	ChIP-Seq	ChIP-Seq	NNP	_	_	_
103	Anaerobic	Anaerobic	NNP	_	_	_
104	C	C	NNP	_	_	_
105	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
106	Fur	Fur	NNP	TF	_	_
107	IP	IP	NNP	_	_	_
108	ChIP-Seq	ChIP-Seq	NNP	_	_	_
109	Anaerobic	Anaerobic	NNP	_	_	_
110	,	,	,	_	_	_
111	Iron	Iron	NNP	_	_	_
112	Deficient	Deficient	NNP	_	_	_
113	A	A	NNP	_	_	_
114	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
115	Fur	Fur	NNP	TF	_	_
116	IP	IP	NNP	_	_	_
117	ChIP-Seq	ChIP-Seq	NNP	_	_	_
118	Anaerobic	Anaerobic	NNP	_	_	_
119	,	,	,	_	_	_
120	Iron	Iron	NNP	_	_	_
121	Deficient	deficient	JJ	_	_	_
122	B	b	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	Fur-minus	fur-minus	NN	_	_	_
125	_	_	CD	_	_	_
126	cDNA	cdna	NN	_	_	_
127	_	_	CD	_	_	_
128	Aerobic	aerobic	JJ	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	Fur-minus	fur-minus	NN	_	_	_
131	_	_	CD	_	_	_
132	cDNA	cdna	NN	_	_	_
133	_	_	CD	_	_	_
134	Anaerobic	anaerobic	JJ	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	Fur-minus	fur-minus	NN	_	_	_
137	_	_	CD	_	_	_
138	RyhB-minus	RyhB-minus	NNP	_	_	_
139	_	_	NNP	_	_	_
140	cDNA	cdna	NN	_	_	_
141	_	_	CD	_	_	_
142	Aerobic	aerobic	JJ	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	Fur-minus	fur-minus	NN	_	_	_
145	_	_	CD	_	_	_
146	RyhB-minus	RyhB-minus	NNP	_	_	_
147	_	_	NNP	_	_	_
148	cDNA	cdna	NN	_	_	_
149	_	_	CD	_	_	_
150	Anaerobic	anaerobic	JJ	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	fur	fur	NN	GEN	_	_
153	mutant	mutant	JJ	_	_	_
154	pBAD-ryhB	pbad-ryhb	NN	_	_	_
155	#	#	#	_	_	_
156	1	1	CD	_	_	_
157	+	+	CC	_	_	_
158	arabinose	arabinose	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	fur	fur	NN	GEN	_	_
161	mutant	mutant	JJ	_	_	_
162	pBAD-ryhB	pbad-ryhb	NN	_	_	_
163	#	#	#	_	_	_
164	2	2	CD	_	_	_
165	+	+	CC	_	_	_
166	arabinose	arabinose	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	fur	fur	NN	GEN	_	_
169	mutant	mutant	JJ	_	_	_
170	pNM12	pnm12	NN	_	_	_
171	#	#	#	_	_	_
172	1	1	CD	_	_	_
173	+	+	CC	_	_	_
174	arabinose	arabinose	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	fur	fur	NN	GEN	_	_
177	mutant	mutant	JJ	_	_	_
178	pNM12	pnm12	NN	_	_	_
179	#	#	#	_	_	_
180	2	2	CD	_	_	_
181	+	+	CC	_	_	_
182	arabinose	arabinose	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	FUR	fur	NN	_	_	_
185	_	_	CD	_	_	_
186	noCPR	nocpr	NN	_	_	_
187	_	_	NN	_	_	_
188	1	1	CD	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	FUR	fur	NN	_	_	_
191	_	_	CD	_	_	_
192	noCPR	nocpr	NN	_	_	_
193	_	_	NN	_	_	_
194	2	2	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	∆	∆	CD	_	_	_
197	fur	fur	NN	GEN	_	_
198	∆	∆	CD	_	_	_
199	ryhB	ryhb	NN	GEN	_	_
200	Aerobic	aerobic	JJ	_	_	_
201	A	a	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	∆	∆	CD	_	_	_
204	fur	fur	NN	GEN	_	_
205	∆	∆	CD	_	_	_
206	ryhB	ryhb	NN	GEN	_	_
207	Aerobic	aerobic	JJ	_	_	_
208	B	b	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	∆	∆	CD	_	_	_
211	fur	fur	NN	GEN	_	_
212	∆	∆	CD	_	_	_
213	ryhB	ryhb	NN	GEN	_	_
214	Anaerobic	anaerobic	JJ	_	_	_
215	A	a	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	∆	∆	CD	_	_	_
218	fur	fur	NN	GEN	_	_
219	∆	∆	CD	_	_	_
220	ryhB	ryhb	NN	GEN	_	_
221	Anaerobic	anaerobic	JJ	_	_	_
222	B	b	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	further	further	JJ	_	_	_
225	analysis	analysis	NN	_	_	_
226	if	if	IN	_	_	_
227	the	the	DT	_	_	_
228	foreground	foreground	NN	_	_	_
229	intensity	intensity	NN	_	_	_
230	of	of	IN	_	_	_
231	less	less	JJR	_	_	_
232	than	than	IN	_	_	_
233	50	50	CD	_	_	_
234	%	%	NN	_	_	_
235	of	of	IN	_	_	_
236	the	the	DT	_	_	_
237	pixels	pixel	NNS	_	_	_
238	within	within	IN	_	_	_
239	the	the	DT	_	_	_
240	spot	spot	NN	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	further	further	RB	_	_	_
243	processing	process	VBG	_	_	_
244	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
245	Fur	Fur	NNP	TF	_	_
246	with	with	IN	_	_	_
247	DPD	dpd	NN	_	_	_
248	1	1	CD	_	_	_
249	-LRB-	-lrb-	-LRB-	_	_	_
250	ChIP-exo	chip-exo	NN	_	_	_
251	-RRB-	-rrb-	-RRB-	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	Fur	Fur	NNP	TF	_	_
254	with	with	IN	_	_	_
255	DPD	dpd	NN	_	_	_
256	2	2	CD	_	_	_
257	-LRB-	-lrb-	-LRB-	_	_	_
258	ChIP-exo	chip-exo	NN	_	_	_
259	-RRB-	-rrb-	-RRB-	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	Fur	Fur	NNP	TF	_	_
262	with	with	IN	_	_	_
263	Fe	Fe	NNP	_	_	_
264	1	1	CD	_	_	_
265	-LRB-	-lrb-	-LRB-	_	_	_
266	ChIP-exo	chip-exo	NN	_	_	_
267	-RRB-	-rrb-	-RRB-	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	Fur	Fur	NNP	TF	_	_
270	with	with	IN	_	_	_
271	Fe	Fe	NNP	_	_	_
272	2	2	CD	_	_	_
273	-LRB-	-lrb-	-LRB-	_	_	_
274	ChIP-exo	chip-exo	NN	_	_	_
275	-RRB-	-rrb-	-RRB-	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	G21	g21	NN	_	_	_
278	MG1655GFP	mg1655gfp	NN	_	_	_
279	_	_	CD	_	_	_
280	pD864	pd864	NN	_	_	_
281	_	_	NN	_	_	_
282	3	3	CD	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	G23	g23	NN	_	_	_
285	MG1655GFP	mg1655gfp	NN	_	_	_
286	_	_	CD	_	_	_
287	pLys	ply	VBZ	_	_	_
288	_	_	SYM	_	_	_
289	M1	m1	NN	_	_	_
290	_	_	NN	_	_	_
291	3	3	CD	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	G28	g28	NN	_	_	_
294	MG1655GFP	mg1655gfp	NN	_	_	_
295	_	_	CD	_	_	_
296	pD864	pd864	NN	_	_	_
297	_	_	NN	_	_	_
298	3	3	CD	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	G29	g29	NN	_	_	_
301	DH10BGFP	dh10bgfp	NN	_	_	_
302	_	_	CD	_	_	_
303	None	none	NN	_	_	_
304	_	_	NN	_	_	_
305	3	3	CD	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	G2	g2	NN	_	_	_
308	,	,	,	_	_	_
309	osmotolerant	osmotolerant	JJ	_	_	_
310	mutant	mutant	JJ	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	G2	g2	NN	_	_	_
313	Replicate	replicate	VB	_	_	_
314	1	1	CD	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	G2	g2	NN	_	_	_
317	Replicate	replicate	VB	_	_	_
318	2	2	CD	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
320	G3	g3	NN	_	_	_
321	,	,	,	_	_	_
322	osmotolerant	osmotolerant	JJ	_	_	_
323	mutant	mutant	JJ	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	G3	g3	NN	_	_	_
326	Replicate	replicate	VB	_	_	_
327	1	1	CD	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	G3	g3	NN	_	_	_
330	Replicate	replicate	VB	_	_	_
331	2	2	CD	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
333	G4H14	g4h14	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	G4H14	g4h14	NN	_	_	_
336	strain	strain	NN	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	G500	g500	CD	_	_	_
339	_	_	NN	_	_	_
340	1	1	CD	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	G5	g5	NN	_	_	_
343	DH10BGFP	dh10bgfp	NN	_	_	_
344	_	_	CD	_	_	_
345	Lux	lux	FW	_	_	_
346	_	_	FW	_	_	_
347	3	3	CD	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	G5	g5	NN	_	_	_
350	,	,	,	_	_	_
351	osmotolerant	osmotolerant	JJ	_	_	_
352	mutant	mutant	JJ	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	G5	g5	NN	_	_	_
355	Replicate	replicate	VB	_	_	_
356	1	1	CD	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	G5	g5	NN	_	_	_
359	Replicate	replicate	VB	_	_	_
360	2	2	CD	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
362	G6	g6	NN	_	_	_
363	DH10BGFP	dh10bgfp	NN	_	_	_
364	_	_	CD	_	_	_
365	pD864	pd864	NN	_	_	_
366	_	_	CD	_	_	_
367	LacZ	lacz	NN	_	_	_
368	_	_	NN	_	_	_
369	3	3	CD	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	G6	g6	NN	_	_	_
372	,	,	,	_	_	_
373	osmotolerant	osmotolerant	JJ	_	_	_
374	mutant	mutant	JJ	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	G6	g6	NN	_	_	_
377	Replicate	replicate	VB	_	_	_
378	1	1	CD	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	G6	g6	NN	_	_	_
381	Replicate	replicate	VB	_	_	_
382	2	2	CD	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
384	gabT	gabt	NN	GEN	_	_
385	KO	ko	NN	_	_	_
386	rep1	rep1	NN	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	gabT	gabt	NN	GEN	_	_
389	KO	ko	NN	_	_	_
390	rep2	rep2	NN	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	gabT	gabt	NN	GEN	_	_
393	KO	ko	NN	_	_	_
394	rep3	rep3	NN	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	Galaxy1	galaxy1	NN	_	_	_
397	-	-	:	_	_	_
398	-LSB-	-lsb-	-LRB-	_	_	_
399	CV104	cv104	NN	_	_	_
400	_	_	CD	_	_	_
401	pHDB3	phdb3	NN	_	_	_
402	_	_	CD	_	_	_
403	5	5	CD	_	_	_
404	.	.	.	_	_	_

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	galE	gale	NN	GEN	_	_
5	KO	ko	NN	_	_	_
6	rep1	rep1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	galE	gale	NN	GEN	_	_
9	KO	ko	NN	_	_	_
10	rep2	rep2	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	galE	gale	NN	GEN	_	_
13	KO	ko	NN	_	_	_
14	rep3	rep3	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	galF	galf	NN	GEN	_	_
17	__	__	CD	_	_	_
18	U	U	NNP	_	_	_
19	_	_	NNP	_	_	_
20	N0075	N0075	NNP	_	_	_
21	_	_	VBD	_	_	_
22	r1	r1	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	galF	galf	NN	GEN	_	_
25	__	__	CD	_	_	_
26	U	U	NNP	_	_	_
27	_	_	NNP	_	_	_
28	N0075	N0075	NNP	_	_	_
29	_	_	VBD	_	_	_
30	r2	r2	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	galF	galf	NN	GEN	_	_
33	__	__	CD	_	_	_
34	U	U	NNP	_	_	_
35	_	_	NNP	_	_	_
36	N0075	N0075	NNP	_	_	_
37	_	_	SYM	_	_	_
38	r3	r3	FW	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
40	galF	galf	NN	GEN	_	_
41	upregulation	upregulation	NN	_	_	_
42	,	,	,	_	_	_
43	0.075	0.075	CD	_	_	_
44	ug/ml	ug/ml	NN	_	_	_
45	norfloxacin	norfloxacin	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	GATC	gatc	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	GATC	gatc	NN	_	_	_
50	software	software	NN	_	_	_
51	for	for	IN	_	_	_
52	read	read	NN	_	_	_
53	mapping	mapping	NN	_	_	_
54	on	on	IN	_	_	_
55	MG1655	mg1655	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Gave	give	VBD	_	_	_
58	a	a	DT	_	_	_
59	pseudocount	pseudocount	NN	_	_	_
60	of	of	IN	_	_	_
61	0.01	0.01	CD	_	_	_
62	to	to	TO	_	_	_
63	all	all	DT	_	_	_
64	values	value	NNS	_	_	_
65	of	of	IN	_	_	_
66	0	0	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	GCOS	gcos	NN	_	_	_
69	1.0	1.0	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
71	GCOS	gcos	NN	_	_	_
72	was	be	VBD	_	_	_
73	used	use	VBN	_	_	_
74	to	to	TO	_	_	_
75	obtain	obtain	VB	_	_	_
76	detection	detection	NN	_	_	_
77	calls	call	NNS	_	_	_
78	for	for	IN	_	_	_
79	each	each	DT	_	_	_
80	microarray	microarray	NN	_	_	_
81	.	.	.	_	_	_

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	GCRMA	gcrma	NN	_	_	_
3	method	method	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	GCRMA	gcrma	NN	_	_	_
6	normalized	normalize	VBD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	gcvR	gcvr	NN	GEN	_	_
9	__	__	CD	_	_	_
10	U	U	NNP	_	_	_
11	_	_	NNP	_	_	_
12	N0075	N0075	NNP	_	_	_
13	_	_	VBD	_	_	_
14	r1	r1	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	gcvR	gcvr	NN	GEN	_	_
17	__	__	CD	_	_	_
18	U	U	NNP	_	_	_
19	_	_	NNP	_	_	_
20	N0075	N0075	NNP	_	_	_
21	_	_	VBD	_	_	_
22	r2	r2	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	gcvR	gcvr	NN	GEN	_	_
25	__	__	CD	_	_	_
26	U	U	NNP	_	_	_
27	_	_	NNP	_	_	_
28	N0075	N0075	NNP	_	_	_
29	_	_	SYM	_	_	_
30	r3	r3	FW	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
32	gcvR	gcvr	NN	GEN	_	_
33	upregulation	upregulation	NN	_	_	_
34	,	,	,	_	_	_
35	0.075	0.075	CD	_	_	_
36	mg/mL	mg/ml	NN	_	_	_
37	norfloxacin	norfloxacin	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	gcvT-ala-1	gcvt-ala-1	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	gcvT-ala-2	gcvt-ala-2	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	gcvT	gcvt	NN	GEN	_	_
44	mutant	mutant	NN	_	_	_
45	in	in	IN	_	_	_
46	Ala	Ala	NNP	_	_	_
47	media	media	NNS	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	gcvT	gcvt	NN	GEN	_	_
50	mutant	mutant	NN	_	_	_
51	in	in	IN	_	_	_
52	Gln	gln	NN	_	_	_
53	media	media	NNS	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	gDNA	gdna	NN	_	_	_
56	520	520	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	gDNA	gdna	NN	_	_	_
59	521	521	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	gDNA	gdna	NN	_	_	_
62	_	_	CD	_	_	_
63	A	a	DT	_	_	_
64	_	_	NN	_	_	_
65	cy5	cy5	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	gDNA	gdna	NN	_	_	_
68	B02	b02	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	gDNA	gdna	NN	_	_	_
71	B05	b05	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	gDNA	gdna	NN	_	_	_
74	_	_	NN	_	_	_
75	B	b	NN	_	_	_
76	_	_	CD	_	_	_
77	cy3	cy3	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	gDNA	gdna	NN	_	_	_
80	C01	c01	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	gDNA	gdna	NN	_	_	_
83	C02	c02	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	gDNA	gdna	NN	_	_	_
86	_	_	CD	_	_	_
87	EColi	ecolus	NNS	_	_	_
88	_	_	SYM	_	_	_
89	520	520	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	gDNA	gdna	NN	_	_	_
92	_	_	CD	_	_	_
93	EColi	ecolus	NNS	_	_	_
94	_	_	SYM	_	_	_
95	521	521	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	gDNA	gdna	NN	_	_	_
98	_	_	CD	_	_	_
99	EColi	ecolus	NNS	_	_	_
100	_	_	VBP	_	_	_
101	B02	b02	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	gDNA	gdna	NN	_	_	_
104	_	_	CD	_	_	_
105	EColi	ecolus	NNS	_	_	_
106	_	_	VBP	_	_	_
107	B05	b05	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	gDNA	gdna	NN	_	_	_
110	_	_	CD	_	_	_
111	EColi	ecolus	NNS	_	_	_
112	_	_	VBP	_	_	_
113	C01	c01	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	gDNA	gdna	NN	_	_	_
116	_	_	CD	_	_	_
117	EColi	ecolus	NNS	_	_	_
118	_	_	VBP	_	_	_
119	C02	c02	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	gDNA	gdna	NN	_	_	_
122	_	_	CD	_	_	_
123	EColi	ecolus	NNS	_	_	_
124	_	_	VBP	_	_	_
125	F01	f01	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	gDNA	gdna	NN	_	_	_
128	_	_	CD	_	_	_
129	EColi	ecolus	NNS	_	_	_
130	_	_	VBP	_	_	_
131	F02	f02	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	gDNA	gdna	NN	_	_	_
134	_	_	CD	_	_	_
135	EColi	ecolus	NNS	_	_	_
136	_	_	VBP	_	_	_
137	H01	h01	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	gDNA	gdna	NN	_	_	_
140	_	_	CD	_	_	_
141	EColi	ecolus	NNS	_	_	_
142	_	_	VBP	_	_	_
143	H02	h02	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	gDNA	gdna	NN	_	_	_
146	_	_	CD	_	_	_
147	EColi	ecolus	NNS	_	_	_
148	_	_	VBP	_	_	_
149	H03	h03	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	gDNA	gdna	NN	_	_	_
152	_	_	CD	_	_	_
153	EColi	ecolus	NNS	_	_	_
154	_	_	VBP	_	_	_
155	H04	h04	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	gDNA	gdna	NN	_	_	_
158	_	_	CD	_	_	_
159	EColi	ecolus	NNS	_	_	_
160	_	_	VBP	_	_	_
161	H05	h05	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	gDNA	gdna	NN	_	_	_
164	_	_	CD	_	_	_
165	EColi	ecolus	NNS	_	_	_
166	_	_	VBP	_	_	_
167	H12	h12	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	gDNA	gdna	NN	_	_	_
170	_	_	CD	_	_	_
171	EColi	ecolus	NNS	_	_	_
172	_	_	VBP	_	_	_
173	H23	h23	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	gDNA	gdna	NN	_	_	_
176	_	_	CD	_	_	_
177	EColi	ecolus	NNS	_	_	_
178	_	_	VBP	_	_	_
179	H27	h27	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	gDNA	gdna	NN	_	_	_
182	_	_	CD	_	_	_
183	Ecoli	Ecoli	NNP	_	_	_
184	_	_	SYM	_	_	_
185	K12	k12	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	gDNA	gdna	NN	_	_	_
188	_	_	CD	_	_	_
189	EColi	ecolus	NNS	_	_	_
190	_	_	VBP	_	_	_
191	S04	s04	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	gDNA	gdna	NN	_	_	_
194	_	_	CD	_	_	_
195	EColi	ecolus	NNS	_	_	_
196	_	_	VBP	_	_	_
197	S05	s05	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	gDNA	gdna	NN	_	_	_
200	_	_	CD	_	_	_
201	EColi	ecolus	NNS	_	_	_
202	_	_	VBP	_	_	_
203	S13	s13	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	gDNA	gdna	NN	_	_	_
206	F01	f01	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	gDNA	gdna	NN	_	_	_
209	F02	f02	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	gDNA	gdna	NN	_	_	_
212	from	from	IN	_	_	_
213	E.coli	e.coli	JJ	_	_	_
214	K12	k12	NN	_	_	_
215	cyanine	cyanine	NN	_	_	_
216	3	3	CD	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	gDNA	gdna	NN	_	_	_
219	H01	h01	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	gDNA	gdna	NN	_	_	_
222	H02	h02	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	gDNA	gdna	NN	_	_	_
225	H03	h03	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	gDNA	gdna	NN	_	_	_
228	H04	h04	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	gDNA	gdna	NN	_	_	_
231	H05	h05	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	gDNA	gdna	NN	_	_	_
234	H12	h12	NN	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	gDNA	gdna	NN	_	_	_
237	H23	h23	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	gDNA	gdna	NN	_	_	_
240	H27	h27	NN	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	gDNA	gdna	NN	_	_	_
243	K12	k12	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	gDNA	gdna	NN	_	_	_
246	S04	s04	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	gDNA	gdna	NN	_	_	_
249	S05	s05	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	gDNA	gdna	NN	_	_	_
252	S13	s13	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	Gene	gene	NN	_	_	_
255	annotation	annotation	NN	_	_	_
256	was	be	VBD	_	_	_
257	obtained	obtain	VBN	_	_	_
258	from	from	IN	_	_	_
259	the	the	DT	_	_	_
260	EcoCyc	EcoCyc	NNP	_	_	_
261	E.	E.	NNP	_	_	_
262	coli	coli	NN	_	_	_
263	Database	database	NN	_	_	_
264	-LRB-	-lrb-	-LRB-	_	_	_
265	https://ecocyc.org/	https://ecocyc.org/	NN	_	_	_
266	-RRB-	-rrb-	-RRB-	_	_	_
267	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	GeneChip	GeneChip	NNP	_	_	_
3	Operating	Operating	NNP	_	_	_
4	Software	Software	NNP	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	MAS	MAS	NNP	_	_	_
7	5.0	5.0	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	using	use	VBG	_	_	_
10	Affymetrix	Affymetrix	NNP	_	_	_
11	default	default	NN	_	_	_
12	analysis	analysis	NN	_	_	_
13	settings	setting	NNS	_	_	_
14	and	and	CC	_	_	_
15	global	global	JJ	_	_	_
16	scaling	scaling	NN	_	_	_
17	as	as	IN	_	_	_
18	normalization	normalization	NN	_	_	_
19	method	method	NN	_	_	_
20	,	,	,	_	_	_
21	genes	gene	NNS	_	_	_
22	with	with	IN	_	_	_
23	a	a	DT	_	_	_
24	p-value	p-value	NN	_	_	_
25	of	of	IN	_	_	_
26	less	less	JJR	_	_	_
27	than	than	IN	_	_	_
28	0.0025	0.0025	CD	_	_	_
29	or	or	CC	_	_	_
30	greater	greater	JJR	_	_	_
31	than	than	IN	_	_	_
32	0.9975	0.9975	CD	_	_	_
33	were	be	VBD	_	_	_
34	considered	consider	VBN	_	_	_
35	statistically	statistically	RB	_	_	_
36	significant	significant	JJ	_	_	_
37	based	base	VBN	_	_	_
38	on	on	IN	_	_	_
39	Wilcoxon	Wilcoxon	NNP	_	_	_
40	signed	sign	VBD	_	_	_
41	rank	rank	JJ	_	_	_
42	test	test	NN	_	_	_
43	and	and	CC	_	_	_
44	Tukey	tukey	NN	_	_	_
45	Byweight	byweight	NN	_	_	_
46	,	,	,	_	_	_
47	labeled	label	VBN	_	_	_
48	as	as	IN	_	_	_
49	I	I	PRP	_	_	_
50	and	and	CC	_	_	_
51	D	d	NN	_	_	_
52	in	in	IN	_	_	_
53	the	the	DT	_	_	_
54	attached	attach	VBN	_	_	_
55	txt	txt	NN	_	_	_
56	file	file	NN	_	_	_
57	.	.	.	_	_	_

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	GeneChips	genechip	NNS	_	_	_
3	were	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	and	and	CC	_	_	_
6	stained	stain	VBN	_	_	_
7	with	with	IN	_	_	_
8	an	a	DT	_	_	_
9	FS450	fs450	NN	_	_	_
10	fluidics	fluidic	NNS	_	_	_
11	machine	machine	NN	_	_	_
12	and	and	CC	_	_	_
13	scanned	scan	VBN	_	_	_
14	using	use	VBG	_	_	_
15	a	a	DT	_	_	_
16	GeneChip	GeneChip	NNP	_	_	_
17	Scanner	Scanner	NNP	_	_	_
18	3000	3000	CD	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	gene	gene	NN	_	_	_
21	counting	counting	NN	_	_	_
22	:	:	:	_	_	_
23	HTSeq-Count	htseq-count	JJ	_	_	_
24	0.6.0	0.6.0	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Gene	gene	NN	_	_	_
27	expression	expression	NN	_	_	_
28	analysis	analysis	NN	_	_	_
29	was	be	VBD	_	_	_
30	performed	perform	VBN	_	_	_
31	using	use	VBG	_	_	_
32	a	a	DT	_	_	_
33	strand-specific	strand-specific	JJ	_	_	_
34	,	,	,	_	_	_
35	paired-end	paired-end	JJ	_	_	_
36	RNA-seq	rna-seq	NN	_	_	_
37	protocol	protocol	NN	_	_	_
38	using	use	VBG	_	_	_
39	the	the	DT	_	_	_
40	dUTP	dutp	NN	_	_	_
41	method	method	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	Levin	Levin	NNP	_	_	_
44	et	et	FW	_	_	_
45	al.	al.	FW	_	_	_
46	,	,	,	_	_	_
47	2010	2010	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	.	.	.	_	_	_

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	Gene	Gene	NNP	_	_	_
3	expression	expression	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	based	base	VBN	_	_	_
6	on	on	IN	_	_	_
7	known	known	JJ	_	_	_
8	genes	gene	NNS	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	determined	determine	VBN	_	_	_
12	using	use	VBG	_	_	_
13	Cufflinks	Cufflinks	NNP	_	_	_
14	2.0.2	2.0.2	CD	_	_	_
15	,	,	,	_	_	_
16	only	only	RB	_	_	_
17	PF	pf	NN	_	_	_
18	reads	read	VBZ	_	_	_
19	were	be	VBD	_	_	_
20	retained	retain	VBN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Gene	Gene	NNP	_	_	_
23	expression	expression	NN	_	_	_
24	data	datum	NNS	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	3	3	CD	_	_	_
27	biological	biological	JJ	_	_	_
28	replicates	replicate	VBZ	_	_	_
29	per	per	IN	_	_	_
30	strain	strain	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	were	be	VBD	_	_	_
33	analyzed	analyze	VBN	_	_	_
34	in	in	IN	_	_	_
35	the	the	DT	_	_	_
36	statistical	statistical	JJ	_	_	_
37	software	software	NN	_	_	_
38	program	program	NN	_	_	_
39	R	r	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	www.r-project.org	www.r-project.org	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	using	use	VBG	_	_	_
44	the	the	DT	_	_	_
45	EdgeR	edger	NN	_	_	_
46	package	package	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	3	3	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	.	.	.	_	_	_

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	gene	gene	NN	_	_	_
3	expression	expression	NN	_	_	_
4	sum	sum	NN	_	_	_
5	normalized	normalize	VBD	_	_	_
6	to	to	TO	_	_	_
7	1	1	CD	_	_	_
8	at	at	IN	_	_	_
9	each	each	DT	_	_	_
10	time	time	NN	_	_	_
11	point	point	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Gene	gene	NN	_	_	_
14	expression	expression	NN	_	_	_
15	was	be	VBD	_	_	_
16	calculated	calculate	VBN	_	_	_
17	as	as	IN	_	_	_
18	reads	read	VBZ	_	_	_
19	per	per	IN	_	_	_
20	gene	gene	NN	_	_	_
21	by	by	IN	_	_	_
22	determining	determine	VBG	_	_	_
23	the	the	DT	_	_	_
24	number	number	NN	_	_	_
25	of	of	IN	_	_	_
26	reads	read	VBZ	_	_	_
27	that	that	IN	_	_	_
28	overlapped	overlap	VBD	_	_	_
29	with	with	IN	_	_	_
30	the	the	DT	_	_	_
31	annotated	annotated	JJ	_	_	_
32	gene	gene	NN	_	_	_
33	loci	locus	NNS	_	_	_
34	using	use	VBG	_	_	_
35	HTSeq	htseq	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Anders	Anders	NNP	_	_	_
38	et	et	FW	_	_	_
39	al.	al.	FW	_	_	_
40	,	,	,	_	_	_
41	2015	2015	CD	_	_	_
42	,	,	,	_	_	_
43	doi	doi	FW	_	_	_
44	:	:	:	_	_	_
45	10.1093	10.1093	CD	_	_	_
46	/	/	:	_	_	_
47	bioinformatics/btu638	bioinformatics/btu638	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	with	with	IN	_	_	_
50	the	the	DT	_	_	_
51	option	option	NN	_	_	_
52	`	`	``	_	_	_
53	intersection-nonempty	intersection-nonempty	NN	_	_	_
54	'	'	''	_	_	_
55	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	GenePix	GenePix	NNP	_	_	_
3	Pro	pro	FW	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	v	v	LS	_	_	_
6	6.1	6.1	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	background	background	NN	_	_	_
12	subtraction	subtraction	NN	_	_	_
13	and	and	CC	_	_	_
14	normalization	normalization	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	GenePix	genepix	NN	_	_	_
3	software	software	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	Axon	Axon	NNP	_	_	_
6	Instruments	Instruments	NNP	_	_	_
7	,	,	,	_	_	_
8	Union	Union	NNP	_	_	_
9	City	City	NNP	_	_	_
10	,	,	,	_	_	_
11	CA	CA	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	version	version	NN	_	_	_
14	5.1	5.1	CD	_	_	_
15	was	be	VBD	_	_	_
16	used	use	VBN	_	_	_
17	to	to	TO	_	_	_
18	process	process	VB	_	_	_
19	the	the	DT	_	_	_
20	scanned	scan	VBN	_	_	_
21	data	datum	NNS	_	_	_
22	and	and	CC	_	_	_
23	generate	generate	VB	_	_	_
24	the	the	DT	_	_	_
25	gpr	gpr	NN	GEN	_	_
26	files	file	NNS	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	generation	generation	NN	_	_	_
3	of	of	IN	_	_	_
4	coverage	coverage	NN	_	_	_
5	graphs	graph	NNS	_	_	_
6	representing	represent	VBG	_	_	_
7	the	the	DT	_	_	_
8	number	number	NN	_	_	_
9	of	of	IN	_	_	_
10	pAA	paa	NN	_	_	_
11	plasmid-associated	plasmid-associated	JJ	_	_	_
12	mapped	map	VBN	_	_	_
13	reads	read	VBZ	_	_	_
14	per	per	IN	_	_	_
15	nucleotide	nucleotide	NN	_	_	_
16	using	use	VBG	_	_	_
17	READemption	reademption	NN	_	_	_
18	0.3.7	0.3.7	CD	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Gene	Gene	NNP	_	_	_
21	selection	selection	NN	_	_	_
22	was	be	VBD	_	_	_
23	done	do	VBN	_	_	_
24	using	use	VBG	_	_	_
25	the	the	DT	_	_	_
26	False	False	NNP	_	_	_
27	Discovery	Discovery	NNP	_	_	_
28	Rate	Rate	NNP	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	FDR	FDR	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	correction	correction	NN	_	_	_
33	procedure	procedure	NN	_	_	_
34	for	for	IN	_	_	_
35	adjusting	adjust	VBG	_	_	_
36	genes	gene	NNS	_	_	_
37	with	with	IN	_	_	_
38	p-value	p-value	JJ	_	_	_
39	smaller	smaller	JJR	_	_	_
40	than	than	IN	_	_	_
41	0.05	0.05	CD	_	_	_
42	and	and	CC	_	_	_
43	Fold	Fold	NNP	_	_	_
44	Change	Change	NNP	_	_	_
45	greater	greater	JJR	_	_	_
46	than	than	IN	_	_	_
47	2	2	CD	_	_	_
48	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Genes	gene	NNS	_	_	_
3	from	from	IN	_	_	_
4	the	the	DT	_	_	_
5	amplified	amplify	VBN	_	_	_
6	regions	region	NNS	_	_	_
7	in	in	IN	_	_	_
8	O500	o500	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	12-fold	12-fold	JJ	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	P500	p500	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	two-fold	two-fold	JJ	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	strains	strain	NNS	_	_	_
18	are	be	VBP	_	_	_
19	significantly	significantly	RB	_	_	_
20	over-expressed	over-expressed	JJ	_	_	_
21	relative	relative	JJ	_	_	_
22	to	to	TO	_	_	_
23	the	the	DT	_	_	_
24	reference	reference	NN	_	_	_
25	:	:	:	_	_	_
26	average	average	JJ	_	_	_
27	log	log	NN	_	_	_
28	Fold	Fold	NNP	_	_	_
29	Change	Change	NNP	_	_	_
30	for	for	IN	_	_	_
31	concentrations	concentration	NNS	_	_	_
32	is	be	VBZ	_	_	_
33	+3.6	+3.6	CD	_	_	_
34	and	and	CC	_	_	_
35	+0.8	+0.8	CD	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	both	both	CC	_	_	_
38	with	with	IN	_	_	_
39	p-values	p-values	NN	_	_	_
40	<	<	JJR	_	_	_
41	10-20	10-20	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	,	,	,	_	_	_
44	respectively	respectively	RB	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	GeneSpring	genespring	NN	_	_	_
3	GX	GX	NNP	_	_	_
4	v.	v.	CC	_	_	_
5	13.1	13.1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	Genes	gene	NNS	_	_	_
8	with	with	IN	_	_	_
9	BH	bh	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Benjamini	Benjamini	NNP	_	_	_
12	and	and	CC	_	_	_
13	Hochberg	Hochberg	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	adjusted	adjust	VBN	_	_	_
16	p-values	p-value	NNS	_	_	_
17	below	below	IN	_	_	_
18	0.05	0.05	CD	_	_	_
19	threshold	threshold	NN	_	_	_
20	were	be	VBD	_	_	_
21	selected	select	VBN	_	_	_
22	as	as	IN	_	_	_
23	DE	de	NN	_	_	_
24	genes	gene	NNS	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genetic	Genetic	NNP	_	_	_
3	background	background	NN	_	_	_
4	:	:	:	_	_	_
5	fnr	fnr	SYM	GEN	_	_
6	-	-	:	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	genetic	genetic	JJ	_	_	_
9	background	background	NN	_	_	_
10	:	:	:	_	_	_
11	O157	o157	NN	_	_	_
12	H19	h19	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Genetic	Genetic	NNP	_	_	_
15	background	background	NN	_	_	_
16	:	:	:	_	_	_
17	wt	wt	JJ	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Genetic	Genetic	NNP	_	_	_
20	background	background	NN	_	_	_
21	:	:	:	_	_	_
22	wt	wt	JJ	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Genetic	Genetic	NNP	_	_	_
25	background	background	NN	_	_	_
26	:	:	:	_	_	_
27	wtGrowth	wtgrowth	NN	_	_	_
28	conditions	condition	NNS	_	_	_
29	:	:	:	_	_	_
30	aerobic	aerobic	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	genetic	genetic	JJ	_	_	_
33	modification	modification	NN	_	_	_
34	:	:	:	_	_	_
35	empty	empty	JJ	_	_	_
36	plasmid	plasmid	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	LJ110/pTM30	lj110/ptm30	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
41	genetic	genetic	JJ	_	_	_
42	modification	modification	NN	_	_	_
43	:	:	:	_	_	_
44	PdhR	pdhr	NN	TF	_	_
45	knockout	knockout	NN	_	_	_
46	mutant	mutant	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	LJ110deltapdhR	lj110deltapdhr	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
51	genetic	genetic	JJ	_	_	_
52	modification	modification	NN	_	_	_
53	:	:	:	_	_	_
54	PdhR	pdhr	NN	TF	_	_
55	overexpression	overexpression	NN	_	_	_
56	strain	strain	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	LJ110/pTM30PdhRhis	lj110/ptm30pdhrhis	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
61	genetic	genetic	JJ	_	_	_
62	modification	modification	NN	_	_	_
63	:	:	:	_	_	_
64	wild	wild	JJ	_	_	_
65	type	type	NN	_	_	_
66	LJ110	lj110	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Gene	gene	NN	_	_	_
69	wise	wise	JJ	_	_	_
70	natural	natural	JJ	_	_	_
71	spline	spline	NN	_	_	_
72	interpolation	interpolation	NN	_	_	_
73	of	of	IN	_	_	_
74	temporal	temporal	JJ	_	_	_
75	data	datum	NNS	_	_	_
76	from	from	IN	_	_	_
77	initial	initial	JJ	_	_	_
78	time	time	NN	_	_	_
79	points	point	NNS	_	_	_
80	to	to	TO	_	_	_
81	a	a	DT	_	_	_
82	dataset	dataset	NN	_	_	_
83	of	of	IN	_	_	_
84	10	10	CD	_	_	_
85	minutes	minute	NNS	_	_	_
86	steps	step	NNS	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	see	see	VB	_	_	_
89	processed	process	VBN	_	_	_
90	data	datum	NNS	_	_	_
91	files	file	NNS	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	.	.	.	_	_	_

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	genome	genome	NN	_	_	_
3	accession	accession	NN	_	_	_
4	:	:	:	_	_	_
5	GCA	gca	NN	_	_	_
6	_	_	SYM	_	_	_
7	000752975	000752975	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	genome	genome	NN	_	_	_
10	accession	accession	NN	_	_	_
11	:	:	:	_	_	_
12	GCA	gca	NN	_	_	_
13	_	_	SYM	_	_	_
14	000753215	000753215	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	genome	genome	NN	_	_	_
17	accession	accession	NN	_	_	_
18	:	:	:	_	_	_
19	GCA	gca	NN	_	_	_
20	_	_	SYM	_	_	_
21	000753275	000753275	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	genome	genome	NN	_	_	_
24	accession	accession	NN	_	_	_
25	:	:	:	_	_	_
26	GCA	gca	NN	_	_	_
27	_	_	SYM	_	_	_
28	000936225	000936225	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	genome	genome	NN	_	_	_
31	accession	accession	NN	_	_	_
32	:	:	:	_	_	_
33	GCA	gca	NN	_	_	_
34	_	_	SYM	_	_	_
35	000936245	000936245	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	genome	genome	NN	_	_	_
38	accession	accession	NN	_	_	_
39	:	:	:	_	_	_
40	GCA	gca	NN	_	_	_
41	_	_	SYM	_	_	_
42	000936475	000936475	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	genome	genome	NN	_	_	_
45	accession	accession	NN	_	_	_
46	:	:	:	_	_	_
47	GCA	gca	NN	_	_	_
48	_	_	SYM	_	_	_
49	000937275	000937275	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	genome	genome	NN	_	_	_
52	accession	accession	NN	_	_	_
53	:	:	:	_	_	_
54	GCA	gca	NN	_	_	_
55	_	_	SYM	_	_	_
56	000938695	000938695	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	genome	genome	NN	_	_	_
59	accession	accession	NN	_	_	_
60	:	:	:	_	_	_
61	GCA	gca	NN	_	_	_
62	_	_	SYM	_	_	_
63	000938995	000938995	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	genome	genome	NN	_	_	_
66	accession	accession	NN	_	_	_
67	:	:	:	_	_	_
68	GCA	gca	NN	_	_	_
69	_	_	SYM	_	_	_
70	000939195	000939195	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	genome	genome	NN	_	_	_
73	accession	accession	NN	_	_	_
74	:	:	:	_	_	_
75	GCA	gca	NN	_	_	_
76	_	_	SYM	_	_	_
77	000939755	000939755	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	genome	genome	NN	_	_	_
80	accession	accession	NN	_	_	_
81	:	:	:	_	_	_
82	GCA	gca	NN	_	_	_
83	_	_	SYM	_	_	_
84	000939955	000939955	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	genome	genome	NN	_	_	_
87	accession	accession	NN	_	_	_
88	:	:	:	_	_	_
89	GCA	gca	NN	_	_	_
90	_	_	SYM	_	_	_
91	000941395	000941395	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	genome	genome	NN	_	_	_
94	accession	accession	NN	_	_	_
95	:	:	:	_	_	_
96	GCA	gca	NN	_	_	_
97	_	_	SYM	_	_	_
98	000941895	000941895	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	genome	genome	NN	_	_	_
101	accession	accession	NN	_	_	_
102	:	:	:	_	_	_
103	GCA	gca	NN	_	_	_
104	_	_	SYM	_	_	_
105	000946755	000946755	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	genome	genome	NN	_	_	_
108	accession	accession	NN	_	_	_
109	:	:	:	_	_	_
110	GCA	gca	NN	_	_	_
111	_	_	SYM	_	_	_
112	000947315	000947315	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	genome	genome	NN	_	_	_
115	accession	accession	NN	_	_	_
116	:	:	:	_	_	_
117	GCA	gca	NN	_	_	_
118	_	_	SYM	_	_	_
119	000951835	000951835	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	genome	genome	NN	_	_	_
122	accession	accession	NN	_	_	_
123	:	:	:	_	_	_
124	GCA	gca	NN	_	_	_
125	_	_	SYM	_	_	_
126	000951875	000951875	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	genome	genome	NN	_	_	_
129	accession	accession	NN	_	_	_
130	:	:	:	_	_	_
131	GCA	gca	NN	_	_	_
132	_	_	SYM	_	_	_
133	000951915	000951915	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	genome	genome	NN	_	_	_
136	accession	accession	NN	_	_	_
137	:	:	:	_	_	_
138	GCA	gca	NN	_	_	_
139	_	_	SYM	_	_	_
140	000965545	000965545	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	genome	genome	NN	_	_	_
143	accession	accession	NN	_	_	_
144	:	:	:	_	_	_
145	GCA	gca	NN	_	_	_
146	_	_	SYM	_	_	_
147	000965555	000965555	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	genome	genome	NN	_	_	_
150	accession	accession	NN	_	_	_
151	:	:	:	_	_	_
152	GCA	gca	NN	_	_	_
153	_	_	SYM	_	_	_
154	000965575	000965575	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	genome	genome	NN	_	_	_
157	accession	accession	NN	_	_	_
158	:	:	:	_	_	_
159	GCA	gca	NN	_	_	_
160	_	_	SYM	_	_	_
161	000965625	000965625	CD	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	genome	genome	NN	_	_	_
164	accession	accession	NN	_	_	_
165	:	:	:	_	_	_
166	GCA	gca	NN	_	_	_
167	_	_	SYM	_	_	_
168	000965635	000965635	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	genome	genome	NN	_	_	_
171	accession	accession	NN	_	_	_
172	:	:	:	_	_	_
173	GCA	gca	NN	_	_	_
174	_	_	SYM	_	_	_
175	000965655	000965655	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	genome	genome	NN	_	_	_
178	accession	accession	NN	_	_	_
179	:	:	:	_	_	_
180	GCA	gca	NN	_	_	_
181	_	_	SYM	_	_	_
182	000965665	000965665	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	genome	genome	NN	_	_	_
185	accession	accession	NN	_	_	_
186	:	:	:	_	_	_
187	GCA	gca	NN	_	_	_
188	_	_	SYM	_	_	_
189	000965705	000965705	CD	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	genome	genome	NN	_	_	_
192	accession	accession	NN	_	_	_
193	:	:	:	_	_	_
194	GCA	gca	NN	_	_	_
195	_	_	SYM	_	_	_
196	000965715	000965715	CD	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	genome	genome	NN	_	_	_
199	accession	accession	NN	_	_	_
200	:	:	:	_	_	_
201	GCA	gca	NN	_	_	_
202	_	_	SYM	_	_	_
203	000966935	000966935	CD	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	genome	genome	NN	_	_	_
206	accession	accession	NN	_	_	_
207	:	:	:	_	_	_
208	PVRW00000000	pvrw00000000	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	Genome	Genome	NNP	_	_	_
211	Build	Build	NNP	_	_	_
212	:	:	:	_	_	_
213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
214	Genome	Genome	NNP	_	_	_
215	_	_	NNP	_	_	_
216	build	build	VB	_	_	_
217	:	:	:	_	_	_
218	ASM1024v1	asm1024v1	NN	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	NCBI	NCBI	NNP	_	_	_
221	E.	E.	NNP	_	_	_
222	coli	coli	NN	_	_	_
223	K12	k12	NN	_	_	_
224	subst	subst	NN	_	_	_
225	.	.	.	_	_	_

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	Genome	Genome	NNP	_	_	_
12	_	_	NNP	_	_	_
13	build	build	VB	_	_	_
14	:	:	:	_	_	_
15	ASM1938v1	asm1938v1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	genome	genome	NN	_	_	_
18	build	build	VB	_	_	_
19	:	:	:	_	_	_
20	ASM584v1	asm584v1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Genome	Genome	NNP	_	_	_
23	_	_	NNP	_	_	_
24	build	build	VB	_	_	_
25	:	:	:	_	_	_
26	ASM584v1	asm584v1	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Genome	Genome	NNP	_	_	_
29	_	_	NNP	_	_	_
30	build	build	VB	_	_	_
31	:	:	:	_	_	_
32	ASM584v1	asm584v1	NN	_	_	_
33	;	;	:	_	_	_
34	Reference	Reference	NNP	_	_	_
35	genome	genome	NN	_	_	_
36	for	for	IN	_	_	_
37	E.	e.	FW	_	_	_
38	coli	coli	FW	_	_	_
39	MG1655	mg1655	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	RefSeq	refseq	NN	_	_	_
42	NC	nc	NN	_	_	_
43	_	_	SYM	_	_	_
44	000913	000913	CD	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Genome	Genome	NNP	_	_	_
17	_	_	NNP	_	_	_
18	build	build	VB	_	_	_
19	:	:	:	_	_	_
20	ASM584v1	asm584v1	NN	_	_	_
21	,	,	,	_	_	_
22	U00096	u00096	NN	_	_	_
23	.2	.2	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Genome	Genome	NNP	_	_	_
26	_	_	NNP	_	_	_
27	build	build	VB	_	_	_
28	:	:	:	_	_	_
29	ASM584v2	asm584v2	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Genome	Genome	NNP	_	_	_
32	_	_	NNP	_	_	_
33	build	build	VB	_	_	_
34	:	:	:	_	_	_
35	ASM584v2	asm584v2	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Escherichia	escherichia	FW	_	_	_
38	_	_	FW	_	_	_
39	coli	coli	FW	_	_	_
40	_	_	SYM	_	_	_
41	str	str	FW	_	_	_
42	_	_	FW	_	_	_
43	k	k	NN	_	_	_
44	_	_	SYM	_	_	_
45	12	12	CD	_	_	_
46	_	_	SYM	_	_	_
47	substr	substr	FW	_	_	_
48	_	_	FW	_	_	_
49	mg1655.GCA	mg1655.gca	NN	_	_	_
50	_	_	SYM	_	_	_
51	000005845.2.24	000005845.2.24	CD	_	_	_
52	.	.	.	_	_	_

1	gtf	gtf	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Genome	Genome	NNP	_	_	_
5	_	_	NNP	_	_	_
6	build	build	VB	_	_	_
7	:	:	:	_	_	_
8	ASM666v1	asm666v1	NN	_	_	_
9	;	;	:	_	_	_
10	NC	NC	NNP	_	_	_
11	_	_	NNP	_	_	_
12	002655.2	002655.2	CD	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Genome	Genome	NNP	_	_	_
15	_	_	NNP	_	_	_
16	build	build	VB	_	_	_
17	:	:	:	_	_	_
18	ATCC8739	atcc8739	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Genome	Genome	NNP	_	_	_
21	_	_	NNP	_	_	_
22	build	build	VB	_	_	_
23	:	:	:	_	_	_
24	CFT073	cft073	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	AE014075	ae014075	NN	_	_	_
27	.1	.1	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Genome	Genome	NNP	_	_	_
31	_	_	NNP	_	_	_
32	build	build	VB	_	_	_
33	:	:	:	_	_	_
34	CFT073	CFT073	NNP	_	_	_
35	E.	E.	NNP	_	_	_
36	coli	coli	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Genome	Genome	NNP	_	_	_
39	_	_	NNP	_	_	_
40	build	build	VB	_	_	_
41	:	:	:	_	_	_
42	CP009273	cp009273	NN	_	_	_
43	.1	.1	CD	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	Genome	Genome	NNP	_	_	_
46	_	_	NNP	_	_	_
47	build	build	VB	_	_	_
48	:	:	:	_	_	_
49	CP018801	cp018801	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	https://www.ncbi.nlm.nih.gov/nuccore/CP018801	https://www.ncbi.nlm.nih.gov/nuccore/cp018801	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Genome	Genome	NNP	_	_	_
55	_	_	NNP	_	_	_
56	build	build	VB	_	_	_
57	:	:	:	_	_	_
58	DL4201	dl4201	NN	_	_	_
59	_	_	NN	_	_	_
60	in	in	IN	_	_	_
61	_	_	NN	_	_	_
62	lab	lab	NN	_	_	_
63	_	_	CD	_	_	_
64	reference	reference	NN	_	_	_
65	_	_	NN	_	_	_
66	genome	genome	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	available	available	JJ	_	_	_
69	on	on	IN	_	_	_
70	series	series	NN	_	_	_
71	record	record	NN	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Genome	Genome	NNP	_	_	_
75	_	_	NNP	_	_	_
76	build	build	VB	_	_	_
77	:	:	:	_	_	_
78	E.coli	e.coli	NN	_	_	_
79	K12	k12	NN	_	_	_
80	BW25113	bw25113	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Genome	Genome	NNP	_	_	_
83	build	build	VB	_	_	_
84	:	:	:	_	_	_
85	E.	e.	FW	_	_	_
86	coli	coli	FW	_	_	_
87	-LSB-	-lsb-	-LRB-	_	_	_
88	K-12	k-12	NN	_	_	_
89	MG1655	mg1655	NN	_	_	_
90	strain	strain	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	U00096	u00096	NN	_	_	_
93	.2	.2	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Genome	Genome	NNP	_	_	_
97	_	_	NNP	_	_	_
98	build	build	VB	_	_	_
99	:	:	:	_	_	_
100	E.	e.	FW	_	_	_
101	coli	coli	FW	_	_	_
102	K-12	k-12	NN	_	_	_
103	MG1655	mg1655	NN	_	_	_
104	-LRB-	-lrb-	-LRB-	_	_	_
105	U00096	u00096	NN	_	_	_
106	.3	.3	NN	_	_	_
107	-RRB-	-rrb-	-RRB-	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Genome	Genome	NNP	_	_	_
110	_	_	NNP	_	_	_
111	build	build	VB	_	_	_
112	:	:	:	_	_	_
113	E.	e.	FW	_	_	_
114	coli	coli	FW	_	_	_
115	MG1655	mg1655	NN	_	_	_
116	GenBank	genbank	NN	_	_	_
117	:	:	:	_	_	_
118	U00096	u00096	NN	_	_	_
119	.2	.2	NN	_	_	_
120	,	,	,	_	_	_
121	total	total	JJ	_	_	_
122	length	length	NN	_	_	_
123	:	:	:	_	_	_
124	4639675	4639675	CD	_	_	_
125	bp	bp	NN	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Genome	Genome	NNP	_	_	_
128	_	_	NNP	_	_	_
129	build	build	VB	_	_	_
130	:	:	:	_	_	_
131	E.	e.	FW	_	_	_
132	coli	coli	FW	_	_	_
133	:	:	:	_	_	_
134	NC	NC	NNP	_	_	_
135	_	_	NNP	_	_	_
136	000913	000913	CD	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	Genome	Genome	NNP	_	_	_
139	_	_	NNP	_	_	_
140	build	build	VB	_	_	_
141	:	:	:	_	_	_
142	E.	e.	FW	_	_	_
143	coli	coli	FW	_	_	_
144	strain	strain	NN	_	_	_
145	BW25113	bw25113	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	Genome	Genome	NNP	_	_	_
148	_	_	NNP	_	_	_
149	build	build	VB	_	_	_
150	:	:	:	_	_	_
151	Escherichia	escherichia	FW	Organism	_	_
152	coli	coli	FW	Organism	_	_
153	B	b	NN	_	_	_
154	str	str	NN	_	_	_
155	.	.	.	_	_	_

1	REL606	rel606	NN	_	_	_
2	;	;	:	_	_	_
3	NC	NC	NNP	_	_	_
4	_	_	NNP	_	_	_
5	012967.1	012967.1	CD	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Genome	Genome	NNP	_	_	_
8	_	_	NNP	_	_	_
9	build	build	VB	_	_	_
10	:	:	:	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	DH10B	dh10b	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Genome	Genome	NNP	_	_	_
18	_	_	NNP	_	_	_
19	build	build	VB	_	_	_
20	:	:	:	_	_	_
21	Escherichia	escherichia	FW	Organism	_	_
22	coli	coli	FW	Organism	_	_
23	K12	k12	NN	_	_	_
24	MG1655	mg1655	NN	_	_	_
25	NC000913	nc000913	NN	_	_	_
26	.3	.3	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Genome	Genome	NNP	_	_	_
29	_	_	NNP	_	_	_
30	build	build	VB	_	_	_
31	:	:	:	_	_	_
32	Escherichia	escherichia	FW	Organism	_	_
33	coli	coli	FW	Organism	_	_
34	K12	k12	NN	_	_	_
35	str	str	NN	_	_	_
36	MG1655	mg1655	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Genome	Genome	NNP	_	_	_
39	_	_	NNP	_	_	_
40	build	build	VB	_	_	_
41	:	:	:	_	_	_
42	Escherichia	escherichia	FW	Organism	_	_
43	coli	coli	FW	Organism	_	_
44	K-12	k-12	NN	_	_	_
45	substr	substr	NN	_	_	_
46	.	.	.	_	_	_

1	DH10B	dh10b	NN	_	_	_
2	ASM1942v1	asm1942v1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Genome	Genome	NNP	_	_	_
5	_	_	NNP	_	_	_
6	build	build	VB	_	_	_
7	:	:	:	_	_	_
8	Escherichia	escherichia	FW	Organism	_	_
9	coli	coli	FW	Organism	_	_
10	K-12	k-12	NN	_	_	_
11	,	,	,	_	_	_
12	substr	substr	NN	_	_	_
13	.	.	.	_	_	_

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	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	MG1655	mg1655	NN	_	_	_
14	K-12	k-12	NN	_	_	_
15	genome	genome	NN	_	_	_
16	version	version	NN	_	_	_
17	U00096	u00096	NN	_	_	_
18	.2	.2	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Genome	Genome	NNP	_	_	_
21	_	_	NNP	_	_	_
22	build	build	VB	_	_	_
23	:	:	:	_	_	_
24	Escherichia	escherichia	FW	Organism	_	_
25	coli	coli	FW	Organism	_	_
26	MG1655	mg1655	NN	_	_	_
27	reference	reference	NN	_	_	_
28	genome	genome	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	NC	nc	NN	_	_	_
31	_	_	CD	_	_	_
32	00091313-Feb-2011	00091313-feb-2011	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Genome	Genome	NNP	_	_	_
35	_	_	NNP	_	_	_
36	build	build	VB	_	_	_
37	:	:	:	_	_	_
38	Escherichia	escherichia	FW	Organism	_	_
39	coli	coli	FW	Organism	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	NC000913	nc000913	NN	_	_	_
42	.2	.2	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Genome	Genome	NNP	_	_	_
46	_	_	NNP	_	_	_
47	build	build	VB	_	_	_
48	:	:	:	_	_	_
49	Escherichia	escherichia	FW	Organism	_	_
50	coli	coli	FW	Organism	_	_
51	strain	strain	NN	_	_	_
52	K12	k12	NN	_	_	_
53	sub-strain	sub-strain	JJ	_	_	_
54	MG1655	mg1655	NN	_	_	_
55	genome	genome	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	GenBank	genbank	NN	_	_	_
58	accession	accession	NN	_	_	_
59	no	no	DT	_	_	_
60	.	.	.	_	_	_

1	U00096	u00096	NN	_	_	_
2	.2	.2	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
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	str	str	FW	_	_	_
12	.	.	.	_	_	_

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	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	,	,	,	_	_	_
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	Genome	Genome	NNP	_	_	_
12	_	_	NNP	_	_	_
13	build	build	VB	_	_	_
14	:	:	:	_	_	_
15	Escherichia	escherichia	FW	Organism	_	_
16	coli	coli	FW	Organism	_	_
17	str	str	FW	_	_	_
18	.	.	.	_	_	_

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	Genome	Genome	NNP	_	_	_
8	_	_	NNP	_	_	_
9	build	build	VB	_	_	_
10	:	:	:	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	W3110	w3110	NN	_	_	_
14	MuSGS	musgs	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	basis	basis	NN	_	_	_
19	of	of	IN	_	_	_
20	NC	NC	NNP	_	_	_
21	_	_	SYM	_	_	_
22	007779.1	007779.1	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

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	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	Genome	Genome	NNP	_	_	_
21	_	_	NNP	_	_	_
22	build	build	VB	_	_	_
23	:	:	:	_	_	_
24	gi	gi	NN	_	_	_
25	|	|	SYM	_	_	_
26	387825439	387825439	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Genome	Genome	NNP	_	_	_
29	_	_	NNP	_	_	_
30	build	build	VB	_	_	_
31	:	:	:	_	_	_
32	http://www.ncbi.nih.gov/nuccore/AP009048.1	http://www.ncbi.nih.gov/nuccore/ap009048.1	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Genome	Genome	NNP	_	_	_
35	_	_	NNP	_	_	_
36	build	build	VB	_	_	_
37	:	:	:	_	_	_
38	K12	k12	SYM	_	_	_
39	-	-	:	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Genome	Genome	NNP	_	_	_
43	_	_	NNP	_	_	_
44	build	build	VB	_	_	_
45	:	:	:	_	_	_
46	K-12	k-12	NN	_	_	_
47	subst	subst	NN	_	_	_
48	.	.	.	_	_	_

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	/	/	:	_	_	_
9	ASM584v1	asm584v1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Genome	Genome	NNP	_	_	_
12	_	_	NNP	_	_	_
13	build	build	VB	_	_	_
14	:	:	:	_	_	_
15	K-12	k-12	NN	_	_	_
16	substr	substr	NN	_	_	_
17	.	.	.	_	_	_

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	/	/	:	_	_	_
9	ASM584v1	asm584v1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Genome	Genome	NNP	_	_	_
12	_	_	NNP	_	_	_
13	build	build	VB	_	_	_
14	:	:	:	_	_	_
15	NC	NC	NNP	_	_	_
16	_	_	NNP	_	_	_
17	000913	000913	CD	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
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	Genome	Genome	NNP	_	_	_
28	_	_	NNP	_	_	_
29	build	build	VB	_	_	_
30	:	:	:	_	_	_
31	NC000913	nc000913	NN	_	_	_
32	.2	.2	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Genome	Genome	NNP	_	_	_
35	_	_	NNP	_	_	_
36	build	build	VB	_	_	_
37	:	:	:	_	_	_
38	NC000913	nc000913	NN	_	_	_
39	.2	.2	NN	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	genome	genome	NN	_	_	_
43	build	build	VB	_	_	_
44	:	:	:	_	_	_
45	NC	NC	NNP	_	_	_
46	_	_	NNP	_	_	_
47	000913.3	000913.3	CD	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	Genome	Genome	NNP	_	_	_
50	_	_	NNP	_	_	_
51	build	build	VB	_	_	_
52	:	:	:	_	_	_
53	NC	NC	NNP	_	_	_
54	_	_	NNP	_	_	_
55	000913.3	000913.3	CD	_	_	_
56	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
57	Genome	Genome	NNP	_	_	_
58	_	_	NNP	_	_	_
59	build	build	VB	_	_	_
60	:	:	:	_	_	_
61	NC	NC	NNP	_	_	_
62	_	_	SYM	_	_	_
63	000913.3	000913.3	CD	_	_	_
64	E.	e.	FW	_	_	_
65	coli	coli	FW	_	_	_
66	K12	k12	NN	_	_	_
67	substr	substr	NN	_	_	_
68	.	.	.	_	_	_

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/ASM584v1	000913/asm584v1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Genome	Genome	NNP	_	_	_
12	_	_	NNP	_	_	_
13	build	build	VB	_	_	_
14	:	:	:	_	_	_
15	NC	NC	NNP	_	_	_
16	_	_	NNP	_	_	_
17	002655	002655	CD	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Genome	Genome	NNP	_	_	_
20	_	_	NNP	_	_	_
21	build	build	VB	_	_	_
22	:	:	:	_	_	_
23	NC	NC	NNP	_	_	_
24	_	_	NNP	_	_	_
25	002655.2	002655.2	CD	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Genome	Genome	NNP	_	_	_
28	_	_	NNP	_	_	_
29	build	build	VB	_	_	_
30	:	:	:	_	_	_
31	NC	NC	NNP	_	_	_
32	_	_	NNP	_	_	_
33	007779.1	007779.1	CD	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	Genome	Genome	NNP	_	_	_
36	_	_	NNP	_	_	_
37	build	build	VB	_	_	_
38	:	:	:	_	_	_
39	NC007779	nc007779	NN	_	_	_
40	.1	.1	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	UCSC	ucsc	NN	_	_	_
43	Archaeal	archaeal	NN	_	_	_
44	Genome	Genome	NNP	_	_	_
45	Browser	Browser	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Genome	Genome	NNP	_	_	_
49	_	_	NNP	_	_	_
50	build	build	VB	_	_	_
51	:	:	:	_	_	_
52	NC	NC	NNP	_	_	_
53	_	_	NNP	_	_	_
54	010473.1	010473.1	CD	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Genome	Genome	NNP	_	_	_
57	_	_	NNP	_	_	_
58	build	build	VB	_	_	_
59	:	:	:	_	_	_
60	NC	NC	NNP	_	_	_
61	_	_	NNP	_	_	_
62	011741	011741	CD	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	E.coli	e.coli	NN	_	_	_
65	strain	strain	NN	_	_	_
66	IAI1	iai1	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	,	,	,	_	_	_
69	NC	nc	NN	_	_	_
70	_	_	SYM	_	_	_
71	000913.2	000913.2	CD	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	E.coli	e.coli	NN	_	_	_
74	strain	strain	NN	_	_	_
75	MG1655	mg1655	NN	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	,	,	,	_	_	_
78	TW09308	tw09308	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	E.coli	e.coli	NN	_	_	_
81	strain	strain	NN	_	_	_
82	TW09308	tw09308	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	,	,	,	_	_	_
85	and	and	CC	_	_	_
86	TW11588	tw11588	NN	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	E.coli	e.coli	NN	_	_	_
89	strain	strain	NN	_	_	_
90	TW11588	tw11588	NN	_	_	_
91	-RRB-	-rrb-	-RRB-	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	Genome	Genome	NNP	_	_	_
94	_	_	NNP	_	_	_
95	build	build	VB	_	_	_
96	:	:	:	_	_	_
97	NC	NC	NNP	_	_	_
98	_	_	NNP	_	_	_
99	011916.1	011916.1	CD	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	Genome	Genome	NNP	_	_	_
102	_	_	NNP	_	_	_
103	build	build	VB	_	_	_
104	:	:	:	_	_	_
105	NC	NC	NNP	_	_	_
106	_	_	NNP	_	_	_
107	012967.1	012967.1	CD	_	_	_
108	plus	plus	CC	_	_	_
109	small	small	JJ	_	_	_
110	RNAs	rna	NNS	_	_	_
111	as	as	IN	_	_	_
112	annotated	annotated	JJ	_	_	_
113	in	in	IN	_	_	_
114	Rfam	Rfam	NNP	_	_	_
115	11.0	11.0	CD	_	_	_
116	database	database	NN	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	Genome	Genome	NNP	_	_	_
119	_	_	NNP	_	_	_
120	build	build	VB	_	_	_
121	:	:	:	_	_	_
122	NC	NC	NNP	_	_	_
123	_	_	NNP	_	_	_
124	016856.1	016856.1	CD	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	Genome	Genome	NNP	_	_	_
127	_	_	NNP	_	_	_
128	build	build	VB	_	_	_
129	:	:	:	_	_	_
130	NC	NC	NNP	_	_	_
131	_	_	NNP	_	_	_
132	017644.1	017644.1	CD	_	_	_
133	-LRB-	-lrb-	-LRB-	_	_	_
134	Escherichia	escherichia	FW	Organism	_	_
135	coli	coli	FW	Organism	_	_
136	NA114	na114	NN	_	_	_
137	-RRB-	-rrb-	-RRB-	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	Genome	Genome	NNP	_	_	_
140	_	_	NNP	_	_	_
141	build	build	VB	_	_	_
142	:	:	:	_	_	_
143	NC	NC	NNP	_	_	_
144	_	_	NNP	_	_	_
145	018220	018220	CD	_	_	_
146	and	and	CC	_	_	_
147	NC	NC	NNP	_	_	_
148	_	_	NNP	_	_	_
149	000913	000913	CD	_	_	_
150	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
151	Genome	Genome	NNP	_	_	_
152	_	_	NNP	_	_	_
153	build	build	VB	_	_	_
154	:	:	:	_	_	_
155	NC	NC	NNP	_	_	_
156	_	_	NNP	_	_	_
157	018658.1	018658.1	CD	_	_	_
158	,	,	,	_	_	_
159	NC	NC	NNP	_	_	_
160	_	_	NNP	_	_	_
161	018659.1	018659.1	CD	_	_	_
162	,	,	,	_	_	_
163	NC	NC	NNP	_	_	_
164	_	_	NNP	_	_	_
165	018660.1	018660.1	CD	_	_	_
166	,	,	,	_	_	_
167	NC	NC	NNP	_	_	_
168	_	_	NNP	_	_	_
169	018666.1	018666.1	CD	_	_	_
170	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
171	Genome	Genome	NNP	_	_	_
172	_	_	NNP	_	_	_
173	build	build	VB	_	_	_
174	:	:	:	_	_	_
175	NCBI	ncbi	NN	_	_	_
176	reference	reference	NN	_	_	_
177	sequence	sequence	NN	_	_	_
178	:	:	:	_	_	_
179	NC	NC	NNP	_	_	_
180	_	_	NNP	_	_	_
181	000913.2	000913.2	CD	_	_	_
182	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
183	Genome	Genome	NNP	_	_	_
184	_	_	NNP	_	_	_
185	build	build	VB	_	_	_
186	:	:	:	_	_	_
187	NCBI	ncbi	NN	_	_	_
188	reference	reference	NN	_	_	_
189	sequence	sequence	NN	_	_	_
190	-LRB-	-lrb-	-LRB-	_	_	_
191	NC	nc	NN	_	_	_
192	_	_	CD	_	_	_
193	017626.1	017626.1	CD	_	_	_
194	-RRB-	-rrb-	-RRB-	_	_	_
195	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
196	Genome	Genome	NNP	_	_	_
197	_	_	NNP	_	_	_
198	build	build	VB	_	_	_
199	:	:	:	_	_	_
200	pPR9	ppr9	NN	_	_	_
201	plasmid	plasmid	NN	_	_	_
202	-LRB-	-lrb-	-LRB-	_	_	_
203	ref	ref	NN	_	_	_
204	is	be	VBZ	_	_	_
205	Kashlec	Kashlec	NNP	_	_	_
206	et	et	FW	_	_	_
207	al.	al.	FW	_	_	_
208	,	,	,	_	_	_
209	1989	1989	CD	_	_	_
210	,	,	,	_	_	_
211	PMID	PMID	NNP	_	_	_
212	:	:	:	_	_	_
213	2547695	2547695	CD	_	_	_
214	-RRB-	-rrb-	-RRB-	_	_	_
215	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
216	Genome	Genome	NNP	_	_	_
217	_	_	NNP	_	_	_
218	build	build	VB	_	_	_
219	:	:	:	_	_	_
220	Reference	Reference	NNP	_	_	_
221	genome	genome	NN	_	_	_
222	for	for	IN	_	_	_
223	E.	e.	FW	_	_	_
224	coli	coli	FW	_	_	_
225	MG1655	mg1655	NN	_	_	_
226	-LRB-	-lrb-	-LRB-	_	_	_
227	RefSeq	refseq	NN	_	_	_
228	NC	nc	NN	_	_	_
229	_	_	CD	_	_	_
230	000913.3	000913.3	CD	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	Reference	Reference	NNP	_	_	_
7	genome	genome	NN	_	_	_
8	used	use	VBN	_	_	_
9	:	:	:	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	K12	k12	NN	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	,	,	,	_	_	_
15	version	version	NN	_	_	_
16	:	:	:	_	_	_
17	iGenome	iGenome	NNP	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Genome	Genome	NNP	_	_	_
20	_	_	NNP	_	_	_
21	build	build	VB	_	_	_
22	:	:	:	_	_	_
23	reference	reference	NN	_	_	_
24	sequence	sequence	NN	_	_	_
25	is	be	VBZ	_	_	_
26	REL606	REL606	NNP	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Genome	Genome	NNP	_	_	_
29	_	_	NNP	_	_	_
30	build	build	VB	_	_	_
31	:	:	:	_	_	_
32	RefSeq	RefSeq	NNP	_	_	_
33	NC	NC	NNP	_	_	_
34	_	_	NNP	_	_	_
35	000913.3	000913.3	CD	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	Genome	Genome	NNP	_	_	_
38	_	_	NNP	_	_	_
39	build	build	VB	_	_	_
40	:	:	:	_	_	_
41	Samples	sample	NNS	_	_	_
42	from	from	IN	_	_	_
43	strain	strain	NN	_	_	_
44	DH10BGFP	dh10bgfp	NN	_	_	_
45	were	be	VBD	_	_	_
46	mapped	map	VBN	_	_	_
47	to	to	TO	_	_	_
48	the	the	DT	_	_	_
49	reference	reference	NN	_	_	_
50	geneome	geneome	NN	_	_	_
51	Escherichia	escherichia	FW	Organism	_	_
52	coli	coli	FW	Organism	_	_
53	str	str	FW	_	_	_
54	.	.	.	_	_	_

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	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	strain	strain	NN	_	_	_
7	MG1655	mg1655	NN	_	_	_
8	,	,	,	_	_	_
9	version	version	NN	_	_	_
10	U00096	u00096	NN	_	_	_
11	.2	.2	NN	_	_	_
12	,	,	,	_	_	_
13	downloaded	download	VBN	_	_	_
14	from	from	IN	_	_	_
15	NCBI	NCBI	NNP	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Genome	Genome	NNP	_	_	_
18	_	_	NNP	_	_	_
19	build	build	VB	_	_	_
20	:	:	:	_	_	_
21	Streptococcus	streptococcus	NN	_	_	_
22	pneumoniae	pneumoniae	FW	_	_	_
23	D39	d39	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	assembly	assembly	NN	_	_	_
26	ASM1436v1	asm1436v1	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Genome	Genome	NNP	_	_	_
30	_	_	NNP	_	_	_
31	build	build	VB	_	_	_
32	:	:	:	_	_	_
33	The	the	DT	_	_	_
34	reference	reference	NN	_	_	_
35	genomes	genome	NNS	_	_	_
36	used	use	VBN	_	_	_
37	for	for	IN	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	K12	k12	NN	_	_	_
41	strain	strain	NN	_	_	_
42	BW25113	bw25113	NN	_	_	_
43	and	and	CC	_	_	_
44	S.	S.	NNP	_	_	_
45	coelicolor	coelicolor	VBP	_	_	_
46	A3	a3	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	2	2	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	strain	strain	NN	_	_	_
51	M145	m145	NN	_	_	_
52	were	be	VBD	_	_	_
53	U00096	u00096	NN	_	_	_
54	.2	.2	NN	_	_	_
55	and	and	CC	_	_	_
56	AL645882	al645882	NN	_	_	_
57	,	,	,	_	_	_
58	respectively	respectively	RB	_	_	_
59	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genome	genome	NN	_	_	_
3	build	build	VB	_	_	_
4	:	:	:	_	_	_
5	U00096	u00096	NN	_	_	_
6	.2	.2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Genome	Genome	NNP	_	_	_
9	_	_	NNP	_	_	_
10	build	build	VB	_	_	_
11	:	:	:	_	_	_
12	U00096	u00096	NN	_	_	_
13	.2	.2	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	-LRB-	-lrb-	-LRB-	_	_	_
22	GenBank	genbank	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Genome	Genome	NNP	_	_	_
26	_	_	NNP	_	_	_
27	build	build	VB	_	_	_
28	:	:	:	_	_	_
29	U00096	u00096	NN	_	_	_
30	.3	.3	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Genome	Genome	NNP	_	_	_
33	_	_	NNP	_	_	_
34	build	build	VB	_	_	_
35	:	:	:	_	_	_
36	U00096	u00096	NN	_	_	_
37	.3	.3	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	E.	e.	FW	_	_	_
40	coli	coli	FW	_	_	_
41	K12	k12	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	and	and	CC	_	_	_
44	NC	nc	NN	_	_	_
45	_	_	VBP	_	_	_
46	001604.1	001604.1	CD	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	T7	t7	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	,	,	,	_	_	_
51	excluding	exclude	VBG	_	_	_
52	ribosomal	ribosomal	JJ	_	_	_
53	genes	gene	NNS	_	_	_
54	,	,	,	_	_	_
55	and	and	CC	_	_	_
56	with	with	IN	_	_	_
57	recoded	recode	VBN	_	_	_
58	gene	gene	NN	_	_	_
59	10	10	CD	_	_	_
60	sequence	sequence	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Bull	bull	NN	_	_	_
63	,	,	,	_	_	_
64	2012	2012	CD	_	_	_
65	,	,	,	_	_	_
66	PMCID	pmcid	NN	_	_	_
67	:	:	:	_	_	_
68	PMC3457771	pmc3457771	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	in	in	IN	_	_	_
71	place	place	NN	_	_	_
72	of	of	IN	_	_	_
73	wild-type	wild-type	JJ	_	_	_
74	sequence	sequence	NN	_	_	_
75	for	for	IN	_	_	_
76	analysis	analysis	NN	_	_	_
77	of	of	IN	_	_	_
78	recoded	recode	VBN	_	_	_
79	and	and	CC	_	_	_
80	evolved	evolve	VBD	_	_	_
81	strains	strain	NNS	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Genome	Genome	NNP	_	_	_
84	_	_	NNP	_	_	_
85	build	build	VB	_	_	_
86	:	:	:	_	_	_
87	UCSC	UCSC	NNP	_	_	_
88	mm10	mm10	CD	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	Genome	Genome	NNP	_	_	_
91	_	_	NNP	_	_	_
92	build	build	VB	_	_	_
93	:	:	:	_	_	_
94	W3110	w3110	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	NC	nc	NN	_	_	_
97	_	_	CD	_	_	_
98	007779	007779	CD	_	_	_
99	-RRB-	-rrb-	-RRB-	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	Genome	Genome	NNP	_	_	_
102	_	_	NNP	_	_	_
103	build	build	VB	_	_	_
104	:	:	:	_	_	_
105	NC	NC	NNP	_	_	_
106	_	_	NNP	_	_	_
107	000913	000913	CD	_	_	_
108	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
109	Genome	Genome	NNP	_	_	_
110	mapping	mapping	NN	_	_	_
111	using	use	VBG	_	_	_
112	Bowtie	Bowtie	NNP	_	_	_
113	,	,	,	_	_	_
114	version	version	NN	_	_	_
115	0.12.9	0.12.9	CD	_	_	_
116	,	,	,	_	_	_
117	parameters	parameter	NNS	_	_	_
118	for	for	IN	_	_	_
119	samples	sample	NNS	_	_	_
120	1-5	1-5	CD	_	_	_
121	:	:	:	_	_	_
122	-	-	:	_	_	_
123	v	v	LS	_	_	_
124	2	2	CD	_	_	_
125	--	--	:	_	_	_
126	best	best	JJS	_	_	_
127	--	--	:	_	_	_
128	strata	strata	SYM	_	_	_
129	-	-	:	_	_	_
130	m	m	NN	_	_	_
131	1	1	CD	_	_	_
132	,	,	,	_	_	_
133	parameters	parameter	NNS	_	_	_
134	for	for	IN	_	_	_
135	samples	sample	NNS	_	_	_
136	6-9	6-9	CD	_	_	_
137	:	:	:	_	_	_
138	-	-	:	_	_	_
139	v	v	LS	_	_	_
140	3	3	CD	_	_	_
141	--	--	:	_	_	_
142	best	best	JJS	_	_	_
143	--	--	:	_	_	_
144	strata	strata	SYM	_	_	_
145	-	-	:	_	_	_
146	m	m	NN	_	_	_
147	1	1	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	Genome	Genome	NNP	_	_	_
150	mapping	mapping	NN	_	_	_
151	using	use	VBG	_	_	_
152	Bowtie	Bowtie	NNP	_	_	_
153	,	,	,	_	_	_
154	version	version	NN	_	_	_
155	1.1.2	1.1.2	CD	_	_	_
156	,	,	,	_	_	_
157	parameters	parameter	NNS	_	_	_
158	for	for	IN	_	_	_
159	samples	sample	NNS	_	_	_
160	1-2	1-2	CD	_	_	_
161	:	:	:	_	_	_
162	-	-	:	_	_	_
163	v	v	LS	_	_	_
164	2	2	CD	_	_	_
165	--	--	:	_	_	_
166	best	best	JJS	_	_	_
167	--	--	:	_	_	_
168	strata	strata	SYM	_	_	_
169	-	-	:	_	_	_
170	m	m	NN	_	_	_
171	1	1	CD	_	_	_
172	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
173	Genomic	genomic	JJ	_	_	_
174	bacterial	bacterial	JJ	_	_	_
175	DNA	dna	NN	_	_	_
176	was	be	VBD	_	_	_
177	extracted	extract	VBN	_	_	_
178	following	follow	VBG	_	_	_
179	the	the	DT	_	_	_
180	protocol	protocol	NN	_	_	_
181	described	describe	VBN	_	_	_
182	in	in	IN	_	_	_
183	Maniatis	Maniatis	NNP	_	_	_
184	Sambrook	Sambrook	NNP	_	_	_
185	-LRB-	-lrb-	-LRB-	_	_	_
186	Sambrook	Sambrook	NNP	_	_	_
187	et	et	FW	_	_	_
188	al.	al.	FW	_	_	_
189	,	,	,	_	_	_
190	1989	1989	CD	_	_	_
191	-RRB-	-rrb-	-RRB-	_	_	_
192	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	genomic	genomic	JJ	_	_	_
3	dna	dna	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	genomic	genomic	JJ	_	_	_
6	DNA	dna	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
8	Genomic	genomic	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	control	control	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
12	Genomic	genomic	JJ	_	_	_
13	DNA	dna	NN	_	_	_
14	control	control	NN	_	_	_
15	from	from	IN	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	K-12	k-12	NN	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	cells	cell	NNS	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
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	treated	treat	VBN	_	_	_
32	with	with	IN	_	_	_
33	100ug/ml	100ug/ml	JJ	_	_	_
34	rifampicin	rifampicin	NN	SUPP	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
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/ml	20ug/ml	JJ	_	_	_
48	bicyclomycin	bicyclomycin	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
50	Genomic	genomic	JJ	_	_	_
51	DNA	dna	NN	_	_	_
52	control	control	NN	_	_	_
53	from	from	IN	_	_	_
54	E.	e.	FW	_	_	_
55	coli	coli	FW	_	_	_
56	K-12	k-12	NN	_	_	_
57	MG1655	mg1655	NN	_	_	_
58	cells	cell	NNS	_	_	_
59	,	,	,	_	_	_
60	untreated	untreated	JJ	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Genomic	genomic	JJ	_	_	_
63	DNA	dna	NN	_	_	_
64	control	control	NN	_	_	_
65	from	from	IN	_	_	_
66	E.	e.	FW	_	_	_
67	coli	coli	FW	_	_	_
68	K-12	k-12	NN	_	_	_
69	MG1655	mg1655	NN	_	_	_
70	HA3	ha3	NN	_	_	_
71	:	:	:	_	_	_
72	:	:	:	_	_	_
73	nusG	nusg	NN	GEN	_	_
74	cells	cell	NNS	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
76	Genomic	genomic	JJ	_	_	_
77	DNA	dna	NN	_	_	_
78	E.	e.	FW	_	_	_
79	coli	coli	FW	_	_	_
80	EDL933	edl933	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
82	Genomic	genomic	JJ	_	_	_
83	DNA	dna	NN	_	_	_
84	Extraction	extraction	NN	_	_	_
85	:	:	:	_	_	_
86	Genomic	genomic	JJ	_	_	_
87	DNA	dna	NN	_	_	_
88	was	be	VBD	_	_	_
89	extracted	extract	VBN	_	_	_
90	according	accord	VBG	_	_	_
91	to	to	TO	_	_	_
92	Current	current	JJ	_	_	_
93	Protocols	protocol	NNS	_	_	_
94	in	in	IN	_	_	_
95	Molecular	molecular	JJ	_	_	_
96	Biology	biology	NN	_	_	_
97	.	.	.	_	_	_

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/organic	aqueous/organic	JJ	_	_	_
10	interface	interface	NN	_	_	_
11	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	purify	purify	VB	_	_	_
3	this	this	DT	_	_	_
4	interface	interface	NN	_	_	_
5	,	,	,	_	_	_
6	all	all	DT	_	_	_
7	aqueous	aqueous	JJ	_	_	_
8	and	and	CC	_	_	_
9	organic	organic	JJ	_	_	_
10	liquid	liquid	NN	_	_	_
11	was	be	VBD	_	_	_
12	removed	remove	VBN	_	_	_
13	by	by	IN	_	_	_
14	pipetting	pipetting	NN	_	_	_
15	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	second	second	JJ	_	_	_
3	extraction	extraction	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	by	by	IN	_	_	_
7	adding	add	VBG	_	_	_
8	500	500	CD	_	_	_
9	μL	μl	NN	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	Tris	Tris	NNP	_	_	_
13	and	and	CC	_	_	_
14	450	450	CD	_	_	_
15	μL	μl	NN	_	_	_
16	24:1	24:1	CD	_	_	_
17	chloroform	chloroform	NN	_	_	_
18	:	:	:	_	_	_
19	isoamyl	isoamyl	NN	_	_	_
20	alcohol	alcohol	NN	_	_	_
21	,	,	,	_	_	_
22	vortexing	vortexing	NN	_	_	_
23	and	and	CC	_	_	_
24	centrifuging	centrifuging	NN	_	_	_
25	.	.	.	_	_	_

1	Again	again	RB	_	_	_
2	,	,	,	_	_	_
3	all	all	DT	_	_	_
4	liquid	liquid	NN	_	_	_
5	was	be	VBD	_	_	_
6	removed	remove	VBN	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	interface	interface	NN	_	_	_
10	by	by	IN	_	_	_
11	pipetting	pipetting	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	residual	residual	JJ	_	_	_
15	liquid	liquid	NN	_	_	_
16	was	be	VBD	_	_	_
17	removed	remove	VBN	_	_	_
18	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	cross-link	cross-link	NN	_	_	_
3	reversal	reversal	NN	_	_	_
4	:	:	:	_	_	_
5	the	the	DT	_	_	_
6	interface	interface	NN	_	_	_
7	was	be	VBD	_	_	_
8	suspended	suspend	VBN	_	_	_
9	in	in	IN	_	_	_
10	500	500	CD	_	_	_
11	μL	μl	NN	_	_	_
12	10	10	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	Tris	Tris	NNP	_	_	_
15	and	and	CC	_	_	_
16	50	50	CD	_	_	_
17	μL	μl	NN	_	_	_
18	10	10	CD	_	_	_
19	%	%	NN	_	_	_
20	SDS	sds	NN	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	placed	place	VBN	_	_	_
24	at	at	IN	_	_	_
25	~	~	NN	_	_	_
26	100	100	CD	_	_	_
27	˚C	˚c	NN	_	_	_
28	for	for	IN	_	_	_
29	30	30	CD	_	_	_
30	minutes	minute	NNS	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	tubes	tube	NNS	_	_	_
3	were	be	VBD	_	_	_
4	placed	place	VBN	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	,	,	,	_	_	_
8	then	then	RB	_	_	_
9	moved	move	VBD	_	_	_
10	to	to	TO	_	_	_
11	65	65	CD	_	_	_
12	˚C	˚c	NN	_	_	_
13	for	for	IN	_	_	_
14	3	3	CD	_	_	_
15	hours	hour	NNS	_	_	_
16	following	follow	VBG	_	_	_
17	addition	addition	NN	_	_	_
18	of	of	IN	_	_	_
19	5	5	CD	_	_	_
20	μL	μl	NN	_	_	_
21	proteinase	proteinase	NN	_	_	_
22	K	k	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	20	20	CD	_	_	_
25	mg/mL	mg/ml	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	heat	heat	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	solutions	solution	NNS	_	_	_
7	were	be	VBD	_	_	_
8	phenol/chloroform	phenol/chloroform	NN	_	_	_
9	extracted	extract	VBN	_	_	_
10	and	and	CC	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	precipitated	precipitate	VBD	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	presence	presence	NN	_	_	_
16	of	of	IN	_	_	_
17	glycogen	glycogen	NN	_	_	_
18	to	to	TO	_	_	_
19	purify	purify	VB	_	_	_
20	the	the	DT	_	_	_
21	DNA	dna	NN	_	_	_
22	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	extraction	extraction	NN	_	_	_
3	:	:	:	_	_	_
4	the	the	DT	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	kit	kit	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	P/N	p/n	NN	_	_	_
10	74104	74104	CD	_	_	_
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	cellular	cellular	JJ	_	_	_
18	RNA	rna	NN	_	_	_
19	.	.	.	_	_	_

1	Immediately	immediately	RB	_	_	_
2	following	follow	VBG	_	_	_
3	elution	elution	NN	_	_	_
4	in	in	IN	_	_	_
5	RNase-free	rnase-free	JJ	_	_	_
6	water	water	NN	_	_	_
7	,	,	,	_	_	_
8	residual	residual	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	was	be	VBD	_	_	_
11	removed	remove	VBN	_	_	_
12	by	by	IN	_	_	_
13	treatment	treatment	NN	_	_	_
14	with	with	IN	_	_	_
15	DNaseI	dnasei	NN	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	for	for	IN	_	_	_
20	15	15	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	again	again	RB	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	kit	kit	NN	_	_	_
10	,	,	,	_	_	_
11	resuspended	resuspend	VBN	_	_	_
12	in	in	IN	_	_	_
13	40	40	CD	_	_	_
14	μl	μl	NN	_	_	_
15	RNase-free	rnase-free	NN	_	_	_
16	water	water	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBD	_	_	_
20	at	at	IN	_	_	_
21	-20	-20	CD	_	_	_
22	°C	°c	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	from	from	IN	_	_	_
5	EDL933	edl933	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	Genomic	genomic	JJ	_	_	_
8	DNA	dna	NN	_	_	_
9	from	from	IN	_	_	_
10	O111	o111	NN	_	_	_
11	strain	strain	NN	_	_	_
12	10828	10828	CD	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Genomic	genomic	JJ	_	_	_
15	DNA	dna	NN	_	_	_
16	from	from	IN	_	_	_
17	O111	o111	NN	_	_	_
18	strain	strain	NN	_	_	_
19	11109	11109	CD	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Genomic	genomic	JJ	_	_	_
22	DNA	dna	NN	_	_	_
23	from	from	IN	_	_	_
24	O111	o111	NN	_	_	_
25	strain	strain	NN	_	_	_
26	11117	11117	CD	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Genomic	genomic	JJ	_	_	_
29	DNA	dna	NN	_	_	_
30	from	from	IN	_	_	_
31	O111	o111	NN	_	_	_
32	strain	strain	NN	_	_	_
33	11128	11128	CD	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	Genomic	genomic	JJ	_	_	_
36	DNA	dna	NN	_	_	_
37	from	from	IN	_	_	_
38	O111	o111	NN	_	_	_
39	strain	strain	NN	_	_	_
40	11619	11619	CD	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Genomic	genomic	JJ	_	_	_
43	DNA	dna	NN	_	_	_
44	from	from	IN	_	_	_
45	O111	o111	NN	_	_	_
46	strain	strain	NN	_	_	_
47	11711	11711	CD	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	Genomic	genomic	JJ	_	_	_
50	DNA	dna	NN	_	_	_
51	from	from	IN	_	_	_
52	O111	o111	NN	_	_	_
53	strain	strain	NN	_	_	_
54	11788	11788	CD	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Genomic	genomic	JJ	_	_	_
57	DNA	dna	NN	_	_	_
58	from	from	IN	_	_	_
59	O111	o111	NN	_	_	_
60	strain	strain	NN	_	_	_
61	11845	11845	CD	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Genomic	genomic	JJ	_	_	_
64	DNA	dna	NN	_	_	_
65	from	from	IN	_	_	_
66	O111	o111	NN	_	_	_
67	strain	strain	NN	_	_	_
68	12009	12009	CD	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Genomic	genomic	JJ	_	_	_
71	DNA	dna	NN	_	_	_
72	from	from	IN	_	_	_
73	O111	o111	NN	_	_	_
74	strain	strain	NN	_	_	_
75	13369	13369	CD	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Genomic	genomic	JJ	_	_	_
78	DNA	dna	NN	_	_	_
79	from	from	IN	_	_	_
80	O111	o111	NN	_	_	_
81	strain	strain	NN	_	_	_
82	ED71	ed71	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
84	Genomic	genomic	JJ	_	_	_
85	DNA	dna	NN	_	_	_
86	from	from	IN	_	_	_
87	O111	o111	NN	_	_	_
88	strain	strain	NN	_	_	_
89	PMK5	pmk5	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
91	Genomic	genomic	JJ	_	_	_
92	DNA	dna	NN	_	_	_
93	from	from	IN	_	_	_
94	O157	o157	NN	_	_	_
95	strain	strain	NN	_	_	_
96	980551	980551	CD	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	Genomic	genomic	JJ	_	_	_
99	DNA	dna	NN	_	_	_
100	from	from	IN	_	_	_
101	O157	o157	NN	_	_	_
102	strain	strain	NN	_	_	_
103	980706	980706	CD	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Genomic	genomic	JJ	_	_	_
106	DNA	dna	NN	_	_	_
107	from	from	IN	_	_	_
108	O157	o157	NN	_	_	_
109	strain	strain	NN	_	_	_
110	980938	980938	CD	_	_	_
111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
112	Genomic	genomic	JJ	_	_	_
113	DNA	dna	NN	_	_	_
114	from	from	IN	_	_	_
115	O157	o157	NN	_	_	_
116	strain	strain	NN	_	_	_
117	981456	981456	CD	_	_	_
118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
119	Genomic	genomic	JJ	_	_	_
120	DNA	dna	NN	_	_	_
121	from	from	IN	_	_	_
122	O157	o157	NN	_	_	_
123	strain	strain	NN	_	_	_
124	981795	981795	CD	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	Genomic	genomic	JJ	_	_	_
127	DNA	dna	NN	_	_	_
128	from	from	IN	_	_	_
129	O157	o157	NN	_	_	_
130	strain	strain	NN	_	_	_
131	982243	982243	CD	_	_	_
132	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
133	Genomic	genomic	JJ	_	_	_
134	DNA	dna	NN	_	_	_
135	from	from	IN	_	_	_
136	O157	o157	NN	_	_	_
137	strain	strain	NN	_	_	_
138	990281	990281	CD	_	_	_
139	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
140	Genomic	genomic	JJ	_	_	_
141	DNA	dna	NN	_	_	_
142	from	from	IN	_	_	_
143	O157	o157	NN	_	_	_
144	strain	strain	NN	_	_	_
145	990570	990570	CD	_	_	_
146	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
147	Genomic	genomic	JJ	_	_	_
148	DNA	dna	NN	_	_	_
149	from	from	IN	_	_	_
150	O26	o26	NN	_	_	_
151	strain	strain	NN	_	_	_
152	11044	11044	CD	_	_	_
153	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
154	Genomic	genomic	JJ	_	_	_
155	DNA	dna	NN	_	_	_
156	from	from	IN	_	_	_
157	O26	o26	NN	_	_	_
158	strain	strain	NN	_	_	_
159	11368	11368	CD	_	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
161	Genomic	genomic	JJ	_	_	_
162	DNA	dna	NN	_	_	_
163	from	from	IN	_	_	_
164	O26	o26	NN	_	_	_
165	strain	strain	NN	_	_	_
166	11656	11656	CD	_	_	_
167	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
168	Genomic	genomic	JJ	_	_	_
169	DNA	dna	NN	_	_	_
170	from	from	IN	_	_	_
171	O26	o26	NN	_	_	_
172	strain	strain	NN	_	_	_
173	12719	12719	CD	_	_	_
174	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
175	Genomic	genomic	JJ	_	_	_
176	DNA	dna	NN	_	_	_
177	from	from	IN	_	_	_
178	O26	o26	NN	_	_	_
179	strain	strain	NN	_	_	_
180	12929	12929	CD	_	_	_
181	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
182	Genomic	genomic	JJ	_	_	_
183	DNA	dna	NN	_	_	_
184	from	from	IN	_	_	_
185	O26	o26	NN	_	_	_
186	strain	strain	NN	_	_	_
187	13065	13065	CD	_	_	_
188	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
189	Genomic	genomic	JJ	_	_	_
190	DNA	dna	NN	_	_	_
191	from	from	IN	_	_	_
192	O26	o26	NN	_	_	_
193	strain	strain	NN	_	_	_
194	13247	13247	CD	_	_	_
195	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
196	Genomic	genomic	JJ	_	_	_
197	DNA	dna	NN	_	_	_
198	from	from	IN	_	_	_
199	O26	o26	NN	_	_	_
200	strain	strain	NN	_	_	_
201	ED411	ed411	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
203	Genomic	genomic	JJ	_	_	_
204	DNA	dna	NN	_	_	_
205	from	from	IN	_	_	_
206	O55	o55	NN	_	_	_
207	:	:	:	_	_	_
208	H6	h6	NN	_	_	_
209	strain	strain	NN	_	_	_
210	ICC219	icc219	NN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
212	Genomic	genomic	JJ	_	_	_
213	DNA	dna	NN	_	_	_
214	from	from	IN	_	_	_
215	O55	o55	NN	_	_	_
216	:	:	:	_	_	_
217	H6	h6	NN	_	_	_
218	strain	strain	NN	_	_	_
219	ICC221	icc221	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
221	Genomic	genomic	JJ	_	_	_
222	DNA	dna	NN	_	_	_
223	from	from	IN	_	_	_
224	O55	o55	NN	_	_	_
225	:	:	:	_	_	_
226	H6	h6	NN	_	_	_
227	strain	strain	NN	_	_	_
228	ICC222	icc222	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
230	Genomic	genomic	JJ	_	_	_
231	DNA	dna	NN	_	_	_
232	from	from	IN	_	_	_
233	O55	o55	NN	_	_	_
234	:	:	:	_	_	_
235	H7	h7	NN	_	_	_
236	strain	strain	NN	_	_	_
237	st58	st58	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
239	Genomic	genomic	JJ	_	_	_
240	DNA	dna	NN	_	_	_
241	from	from	IN	_	_	_
242	O55	o55	NN	_	_	_
243	:	:	:	_	_	_
244	H7	h7	NN	_	_	_
245	strain	strain	NN	_	_	_
246	st957	st957	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
248	Genomic	genomic	JJ	_	_	_
249	DNA	dna	NN	_	_	_
250	from	from	IN	_	_	_
251	O55	o55	NN	_	_	_
252	:	:	:	_	_	_
253	H7	h7	NN	_	_	_
254	strain	strain	NN	_	_	_
255	TB182A	tb182a	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
257	Genomic	genomic	JJ	_	_	_
258	DNA	dna	NN	_	_	_
259	from	from	IN	_	_	_
260	O55	o55	NN	_	_	_
261	:	:	:	_	_	_
262	H7	h7	NN	_	_	_
263	strain	strain	NN	_	_	_
264	WC211	wc211	NN	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
266	Genomic	genomic	JJ	_	_	_
267	DNA	dna	NN	_	_	_
268	from	from	IN	_	_	_
269	O55	o55	NN	_	_	_
270	:	:	:	_	_	_
271	H7	h7	NN	_	_	_
272	strain	strain	NN	_	_	_
273	WC416	wc416	NN	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
275	Genomic	genomic	JJ	_	_	_
276	DNA	dna	NN	_	_	_
277	isolation	isolation	NN	_	_	_
278	according	accord	VBG	_	_	_
279	to	to	TO	_	_	_
280	Grimberg	Grimberg	NNP	_	_	_
281	et	et	FW	_	_	_
282	al.	al.	FW	_	_	_
283	.	.	.	_	_	_

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	Genomic	genomic	JJ	_	_	_
14	DNA	dna	NN	_	_	_
15	of	of	IN	_	_	_
16	all	all	DT	_	_	_
17	strains	strain	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	degraders	degrader	NNS	_	_	_
20	and	and	CC	_	_	_
21	non-degraders	non-degrader	NNS	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	isolated	isolate	VBN	_	_	_
24	individually	individually	RB	_	_	_
25	and	and	CC	_	_	_
26	mixed	mix	VBN	_	_	_
27	in	in	IN	_	_	_
28	equal	equal	JJ	_	_	_
29	ratio	ratio	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	500ng	500ng	CD	_	_	_
32	each	each	DT	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
35	Genomic	genomic	JJ	_	_	_
36	DNA	dna	NN	_	_	_
37	of	of	IN	_	_	_
38	EDL933	edl933	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	Genomic	genomic	JJ	_	_	_
41	DNA	dna	NN	_	_	_
42	of	of	IN	_	_	_
43	Escherichia	escherichia	FW	Organism	_	_
44	coli	coli	FW	Organism	_	_
45	DH5α	dh5α	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
47	Genomic	genomic	JJ	_	_	_
48	DNA	dna	NN	_	_	_
49	of	of	IN	_	_	_
50	mixed	mixed	JJ	_	_	_
51	culture	culture	NN	_	_	_
52	containing	contain	VBG	_	_	_
53	only	only	RB	_	_	_
54	non-degraders	non-degraders	JJ	_	_	_
55	in	in	IN	_	_	_
56	equal	equal	JJ	_	_	_
57	ratio	ratio	NN	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	Genomic	genomic	JJ	_	_	_
60	DNA	dna	NN	_	_	_
61	of	of	IN	_	_	_
62	mixed	mixed	JJ	_	_	_
63	culture	culture	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	Degraders	degrader	NNS	_	_	_
66	and	and	CC	_	_	_
67	non-degraders	non-degrader	NNS	_	_	_
68	in	in	IN	_	_	_
69	2:1	2:1	CD	_	_	_
70	ratio	ratio	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
73	Genomic	genomic	JJ	_	_	_
74	DNA	dna	NN	_	_	_
75	of	of	IN	_	_	_
76	mixed	mixed	JJ	_	_	_
77	culture	culture	NN	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	Degraders	degrader	NNS	_	_	_
80	:	:	:	_	_	_
81	NM-05	nm-05	NN	_	_	_
82	,	,	,	_	_	_
83	IITR-02	iitr-02	NN	_	_	_
84	,	,	,	_	_	_
85	RHA1	rha1	NN	_	_	_
86	;	;	:	_	_	_
87	Non-degraders	non-degrader	NNS	_	_	_
88	:	:	:	_	_	_
89	DH5α	dh5α	NN	_	_	_
90	,	,	,	_	_	_
91	BL21	bl21	NN	_	_	_
92	and	and	CC	_	_	_
93	K12	k12	NN	_	_	_
94	in	in	IN	_	_	_
95	equal	equal	JJ	_	_	_
96	ratio	ratio	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
99	Genomic	genomic	JJ	_	_	_
100	DNA	dna	NN	_	_	_
101	purified	purify	VBN	_	_	_
102	from	from	IN	_	_	_
103	wild	wild	JJ	_	_	_
104	type	type	NN	_	_	_
105	bacteri	bacteri	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
107	Genomic	genomic	JJ	_	_	_
108	DNA	dna	NN	_	_	_
109	purified	purify	VBN	_	_	_
110	from	from	IN	_	_	_
111	wild	wild	JJ	_	_	_
112	type	type	NN	_	_	_
113	bacteria	bacterium	NNS	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
115	Genomic	genomic	JJ	_	_	_
116	DNA	dna	NN	_	_	_
117	served	serve	VBD	_	_	_
118	as	as	IN	_	_	_
119	a	a	DT	_	_	_
120	universal	universal	JJ	_	_	_
121	reference	reference	NN	_	_	_
122	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
123	Genomic	genomic	JJ	_	_	_
124	DNA	dna	NN	_	_	_
125	was	be	VBD	_	_	_
126	extracted	extract	VBN	_	_	_
127	by	by	IN	_	_	_
128	standard	standard	JJ	_	_	_
129	phenol-chloroform	phenol-chloroform	NN	_	_	_
130	method	method	NN	_	_	_
131	-LRB-	-lrb-	-LRB-	_	_	_
132	Sambrook	Sambrook	NNP	_	_	_
133	,	,	,	_	_	_
134	J	J	NNP	_	_	_
135	,	,	,	_	_	_
136	Molecular	molecular	JJ	_	_	_
137	Cloning	cloning	NN	_	_	_
138	,	,	,	_	_	_
139	3rd	3rd	JJ	_	_	_
140	Edition	edition	NN	_	_	_
141	-RRB-	-rrb-	-RRB-	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
143	Genomic	genomic	JJ	_	_	_
144	DNA	dna	NN	_	_	_
145	was	be	VBD	_	_	_
146	extracted	extract	VBN	_	_	_
147	from	from	IN	_	_	_
148	4	4	CD	_	_	_
149	bacteria	bacterium	NNS	_	_	_
150	strains	strain	NNS	_	_	_
151	.	.	.	_	_	_

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	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/phenol/chloroform	lysis/phenol/chloroform	NN	_	_	_
11	method	method	NN	_	_	_
12	described	describe	VBN	_	_	_
13	by	by	IN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Syn	syn	NN	_	_	_
16	CK	ck	NN	_	_	_
17	,	,	,	_	_	_
18	Swarup	Swarup	NNP	_	_	_
19	S	s	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	2000	2000	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	A	a	DT	_	_	_
24	scalable	scalable	JJ	_	_	_
25	protocol	protocol	NN	_	_	_
26	for	for	IN	_	_	_
27	the	the	DT	_	_	_
28	isolation	isolation	NN	_	_	_
29	of	of	IN	_	_	_
30	large-sized	large-sized	JJ	_	_	_
31	genomic	genomic	JJ	_	_	_
32	DNA	dna	NN	_	_	_
33	within	within	IN	_	_	_
34	an	a	DT	_	_	_
35	hour	hour	NN	_	_	_
36	from	from	IN	_	_	_
37	several	several	JJ	_	_	_
38	bacteria	bacterium	NNS	_	_	_
39	.	.	.	_	_	_

1	Anal	Anal	NNP	_	_	_
2	Biochem	Biochem	NNP	_	_	_
3	278	278	CD	_	_	_
4	:	:	:	_	_	_
5	86-90	86-90	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	with	with	IN	_	_	_
8	slight	slight	JJ	_	_	_
9	modifications	modification	NNS	_	_	_
10	as	as	IN	_	_	_
11	follows	follow	VBZ	_	_	_
12	:	:	:	_	_	_
13	subsequent	subsequent	JJ	_	_	_
14	to	to	TO	_	_	_
15	DNA	dna	NN	_	_	_
16	precipitation	precipitation	NN	_	_	_
17	,	,	,	_	_	_
18	spun	spin	VBD	_	_	_
19	pellets	pellet	NNS	_	_	_
20	were	be	VBD	_	_	_
21	treated	treat	VBN	_	_	_
22	with	with	IN	_	_	_
23	50μg	50μg	JJ	_	_	_
24	mL-1	ml-1	NN	_	_	_
25	DNAse-free	dnase-free	JJ	_	_	_
26	RNAse	rnase	NN	_	_	_
27	A	a	NN	_	_	_
28	and	and	CC	_	_	_
29	incubated	incubate	VBN	_	_	_
30	at	at	IN	_	_	_
31	37	37	CD	_	_	_
32	°C	°c	NN	_	_	_
33	for	for	IN	_	_	_
34	30	30	CD	_	_	_
35	min	min	NN	_	_	_
36	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	re-extracted	re-extracted	JJ	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	phenol	phenol	NN	_	_	_
8	:	:	:	_	_	_
9	chloroform	chloroform	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	3:1	3:1	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	once	once	RB	_	_	_
15	with	with	IN	_	_	_
16	phenol	phenol	NN	_	_	_
17	:	:	:	_	_	_
18	chloroform	chloroform	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	1:1	1:1	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	twice	twice	RB	_	_	_
24	with	with	IN	_	_	_
25	chloroform	chloroform	NN	_	_	_
26	,	,	,	_	_	_
27	reprecipitated	reprecipitate	VBN	_	_	_
28	and	and	CC	_	_	_
29	then	then	RB	_	_	_
30	resuspended	resuspend	VBD	_	_	_
31	in	in	IN	_	_	_
32	TE	TE	NNP	_	_	_
33	,	,	,	_	_	_
34	pH	ph	NN	_	_	_
35	8.0	8.0	CD	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Epicentre	Epicentre	NNP	_	_	_
9	DNA	dna	NN	_	_	_
10	extraction	extraction	NN	_	_	_
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	protocols	protocol	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Ultra	Ultra	NNP	_	_	_
8	Clean	Clean	NNP	_	_	_
9	Soil	Soil	NNP	_	_	_
10	DNA	dna	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	MoBio	mobio	NN	_	_	_
13	Laboratories	Laboratories	NNPS	_	_	_
14	,	,	,	_	_	_
15	Solana	Solana	NNP	_	_	_
16	Beach	Beach	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	from	from	IN	_	_	_
7	exponentially	exponentially	RB	_	_	_
8	growing	grow	VBG	_	_	_
9	cells	cell	NNS	_	_	_
10	by	by	IN	_	_	_
11	lysis	lysis	NN	_	_	_
12	in	in	IN	_	_	_
13	lysozyme/mutanolysin	lysozyme/mutanolysin	NN	_	_	_
14	,	,	,	_	_	_
15	incubation	incubation	NN	_	_	_
16	in	in	IN	_	_	_
17	proteinase	proteinase	NN	_	_	_
18	K/SDS	k/sds	NN	_	_	_
19	,	,	,	_	_	_
20	followed	follow	VBN	_	_	_
21	by	by	IN	_	_	_
22	a	a	DT	_	_	_
23	standard	standard	JJ	_	_	_
24	phenol/chloroform	phenol/chloroform	NN	_	_	_
25	extraction	extraction	NN	_	_	_
26	procedure	procedure	NN	_	_	_
27	.	.	.	_	_	_

1	Final	final	JJ	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	dissolved	dissolve	VBN	_	_	_
5	in	in	IN	_	_	_
6	TE	TE	NNP	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	10	10	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	at	at	IN	_	_	_
12	pH	ph	NN	_	_	_
13	8.0	8.0	CD	_	_	_
14	,	,	,	_	_	_
15	1	1	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	EDTA	edta	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Genomic	genomic	JJ	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	digested	digest	VBN	_	_	_
5	to	to	TO	_	_	_
6	completion	completion	NN	_	_	_
7	with	with	IN	_	_	_
8	Sau3A1	sau3a1	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Promega	promega	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	purified	purify	VBN	_	_	_
14	by	by	IN	_	_	_
15	phenol/chloroform	phenol/chloroform	NN	_	_	_
16	extraction	extraction	NN	_	_	_
17	.	.	.	_	_	_

1	Synthesis	synthesis	NN	_	_	_
2	and	and	CC	_	_	_
3	degradation	degradation	NN	_	_	_
4	of	of	IN	_	_	_
5	RNA	rna	NN	_	_	_
6	were	be	VBD	_	_	_
7	stopped	stop	VBN	_	_	_
8	by	by	IN	_	_	_
9	adding	add	VBG	_	_	_
10	1/4	1/4	CD	_	_	_
11	volume	volume	NN	_	_	_
12	of	of	IN	_	_	_
13	stop-solution	stop-solution	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	95	95	CD	_	_	_
16	%	%	NN	_	_	_
17	ethanol/5	ethanol/5	CD	_	_	_
18	%	%	NN	_	_	_
19	phenol	phenol	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	4,000	4,000	CD	_	_	_
8	rpm	rpm	NN	_	_	_
9	,	,	,	_	_	_
10	20	20	CD	_	_	_
11	min	min	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	4	4	CD	_	_	_
15	°C	°c	NN	_	_	_
16	and	and	CC	_	_	_
17	resuspended	resuspend	VBN	_	_	_
18	in	in	IN	_	_	_
19	0.5	0.5	CD	_	_	_
20	mL	ml	NN	_	_	_
21	of	of	IN	_	_	_
22	lysis	lysis	NN	_	_	_
23	buffer	buffer	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	0.5	0.5	CD	_	_	_
26	mg/mL	mg/ml	NN	_	_	_
27	lysozyme	lysozyme	NN	_	_	_
28	,	,	,	_	_	_
29	10	10	CD	_	_	_
30	%	%	NN	_	_	_
31	SDS	sds	NN	_	_	_
32	,	,	,	_	_	_
33	Tris-EDTA	tris-edta	JJ	_	_	_
34	buffer	buffer	NN	_	_	_
35	,	,	,	_	_	_
36	3	3	CD	_	_	_
37	M	m	NN	_	_	_
38	sodium	sodium	NN	SUPP	_	_
39	acetate	acetate	NN	SUPP	_	_
40	,	,	,	_	_	_
41	pH	ph	NN	_	_	_
42	5.2	5.2	CD	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	.	.	.	_	_	_

1	Phenol	phenol	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	0.5	0.5	CD	_	_	_
4	ml	ml	NN	_	_	_
5	,	,	,	_	_	_
6	pH	ph	NN	_	_	_
7	4.5	4.5	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	were	be	VBD	_	_	_
16	vortexed	vortex	VBN	_	_	_
17	vigorously	vigorously	RB	_	_	_
18	before	before	IN	_	_	_
19	incubation	incubation	NN	_	_	_
20	at	at	IN	_	_	_
21	64	64	CD	_	_	_
22	°C	°c	NN	_	_	_
23	for	for	IN	_	_	_
24	6	6	CD	_	_	_
25	min	min	NN	_	_	_
26	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	placing	place	VBG	_	_	_
3	the	the	DT	_	_	_
4	samples	sample	NNS	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	aqueous	aqueous	JJ	_	_	_
10	layer	layer	NN	_	_	_
11	was	be	VBD	_	_	_
12	extracted	extract	VBN	_	_	_
13	with	with	IN	_	_	_
14	1:1	1:1	CD	_	_	_
15	phenol	phenol	NN	_	_	_
16	:	:	:	_	_	_
17	chloroform	chloroform	NN	_	_	_
18	and	and	CC	_	_	_
19	with	with	IN	_	_	_
20	chloroform	chloroform	NN	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	the	the	DT	_	_	_
24	RNA	rna	NN	_	_	_
25	was	be	VBD	_	_	_
26	precipitated	precipitate	VBN	_	_	_
27	with	with	IN	_	_	_
28	ethanol	ethanol	NN	_	_	_
29	at	at	IN	_	_	_
30	-80	-80	CD	_	_	_
31	°C	°c	NN	_	_	_
32	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	resuspension	resuspension	NN	_	_	_
3	,	,	,	_	_	_
4	RNA	rna	NN	_	_	_
5	concentration	concentration	NN	_	_	_
6	and	and	CC	_	_	_
7	purity	purity	NN	_	_	_
8	was	be	VBD	_	_	_
9	assessed	assess	VBN	_	_	_
10	by	by	IN	_	_	_
11	NanoDrop	NanoDrop	NNP	_	_	_
12	ND-1000	ND-1000	NNP	_	_	_
13	UV	uv	NN	_	_	_
14	spectrophotometer	spectrophotometer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Nanodrop	Nanodrop	NNP	_	_	_
17	Technologies	Technologies	NNPS	_	_	_
18	,	,	,	_	_	_
19	Wilmingon	Wilmingon	NNP	_	_	_
20	,	,	,	_	_	_
21	DE	de	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	Agilent	Agilent	NNP	_	_	_
25	2100	2100	CD	_	_	_
26	Bioanalyzer	Bioanalyzer	NNP	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Agilent	Agilent	NNP	_	_	_
29	Technologies	Technologies	NNPS	_	_	_
30	,	,	,	_	_	_
31	Santa	Santa	NNP	_	_	_
32	Clara	Clara	NNP	_	_	_
33	,	,	,	_	_	_
34	CA	CA	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	respectively	respectively	RB	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	20/G	20/g	NN	_	_	_
9	genomic-tip	genomic-tip	JJ	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	according	accord	VBG	_	_	_
15	to	to	TO	_	_	_
16	manufacturer	manufacturer	NN	_	_	_
17	's	's	POS	_	_	_
18	instructions	instruction	NNS	_	_	_
19	and	and	CC	_	_	_
20	was	be	VBD	_	_	_
21	sonicated	sonicate	VBN	_	_	_
22	to	to	TO	_	_	_
23	an	a	DT	_	_	_
24	average	average	JJ	_	_	_
25	size	size	NN	_	_	_
26	of	of	IN	_	_	_
27	~	~	NN	_	_	_
28	500	500	CD	_	_	_
29	bp	bp	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Genomic-tip	genomic-tip	JJ	_	_	_
9	100/G	100/g	NN	_	_	_
10	and	and	CC	_	_	_
11	Genomic	genomic	JJ	_	_	_
12	DNA	dna	NN	_	_	_
13	buffer	buffer	NN	_	_	_
14	set	set	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Qiagen	qiagen	NN	_	_	_
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	instruction	instruction	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genomic	genomic	JJ	_	_	_
3	Library	Library	NNP	_	_	_
4	of	of	IN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	was	be	VBD	_	_	_
8	enriched	enriched	JJ	_	_	_
9	via	via	IN	_	_	_
10	serial	serial	NN	_	_	_
11	transfers	transfer	NNS	_	_	_
12	.	.	.	_	_	_

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/L	g/l	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	in	in	IN	_	_	_
17	increasing	increase	VBG	_	_	_
18	concentration	concentration	NN	_	_	_
19	of	of	IN	_	_	_
20	n-butanol	n-butanol	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	0.5	0.5	CD	_	_	_
23	,	,	,	_	_	_
24	0.9	0.9	CD	_	_	_
25	,	,	,	_	_	_
26	1.3	1.3	CD	_	_	_
27	and	and	CC	_	_	_
28	1.7	1.7	CD	_	_	_
29	%	%	NN	_	_	_
30	v/v	v/v	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	genomic	genomic	JJ	_	_	_
3	_	_	NN	_	_	_
4	ref1	ref1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genomic	genomic	JJ	_	_	_
7	_	_	NN	_	_	_
8	ref2	ref2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	genomic	genomic	JJ	_	_	_
11	_	_	NN	_	_	_
12	ref3	ref3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	genomic	genomic	JJ	_	_	_
15	_	_	NN	_	_	_
16	ref4	ref4	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	genomic	genomic	JJ	_	_	_
19	_	_	NN	_	_	_
20	ref5	ref5	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	genomic	genomic	JJ	_	_	_
23	_	_	NN	_	_	_
24	ref6	ref6	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
26	Genomic	genomic	JJ	_	_	_
27	response	response	NN	_	_	_
28	analysis	analysis	NN	_	_	_
29	of	of	IN	_	_	_
30	E.coli	e.coli	NN	_	_	_
31	during	during	IN	_	_	_
32	coexpression	coexpression	NN	_	_	_
33	of	of	IN	_	_	_
34	a	a	DT	_	_	_
35	bacteriocin	bacteriocin	NN	_	_	_
36	release	release	NN	_	_	_
37	protein	protein	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	genotype	genotype	NN	_	_	_
40	:	:	:	_	_	_
41	285c	285c	JJ	_	_	_
42	rpoD	rpod	NN	GEN	_	_
43	mutation	mutation	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	genotype	genotype	NN	_	_	_
46	:	:	:	_	_	_
47	AB1157	ab1157	NN	_	_	_
48	ybbD	ybbd	NN	GEN	_	_
49	:	:	:	_	_	_
50	:	:	:	_	_	_
51	parS	pars	NN	_	_	_
52	scrambled	scramble	VBD	_	_	_
53	site	site	NN	_	_	_
54	3	3	CD	_	_	_
55	pUTC18	putc18	NN	_	_	_
56	:	:	:	_	_	_
57	:	:	:	_	_	_
58	parB	parb	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	G101S	g101s	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	genotype	genotype	NN	_	_	_
64	:	:	:	_	_	_
65	AB1157	ab1157	NN	_	_	_
66	ybbD	ybbd	NN	GEN	_	_
67	:	:	:	_	_	_
68	:	:	:	_	_	_
69	parS	pars	NN	_	_	_
70	scrambled	scramble	VBD	_	_	_
71	site	site	NN	_	_	_
72	3	3	CD	_	_	_
73	pUTC18	putc18	NN	_	_	_
74	:	:	:	_	_	_
75	:	:	:	_	_	_
76	parB	parb	NN	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	WT	wt	NN	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	genotype	genotype	NN	_	_	_
82	:	:	:	_	_	_
83	AB1157	ab1157	NN	_	_	_
84	ybbD	ybbd	NN	GEN	_	_
85	:	:	:	_	_	_
86	:	:	:	_	_	_
87	parS	pars	NN	_	_	_
88	site	site	NN	_	_	_
89	1	1	CD	_	_	_
90	pUTC18	putc18	NN	_	_	_
91	:	:	:	_	_	_
92	:	:	:	_	_	_
93	parB	parb	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	WT	wt	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	genotype	genotype	NN	_	_	_
99	:	:	:	_	_	_
100	AB1157	ab1157	NN	_	_	_
101	ybbD	ybbd	NN	GEN	_	_
102	:	:	:	_	_	_
103	:	:	:	_	_	_
104	parS	pars	NN	_	_	_
105	site	site	NN	_	_	_
106	2	2	CD	_	_	_
107	pUTC18	putc18	NN	_	_	_
108	:	:	:	_	_	_
109	:	:	:	_	_	_
110	parB	parb	NN	_	_	_
111	-LRB-	-lrb-	-LRB-	_	_	_
112	G101S	g101s	NN	_	_	_
113	-RRB-	-rrb-	-RRB-	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	genotype	genotype	NN	_	_	_
116	:	:	:	_	_	_
117	AB1157	ab1157	NN	_	_	_
118	ybbD	ybbd	NN	GEN	_	_
119	:	:	:	_	_	_
120	:	:	:	_	_	_
121	parS	pars	NN	_	_	_
122	site	site	NN	_	_	_
123	2	2	CD	_	_	_
124	pUTC18	putc18	NN	_	_	_
125	:	:	:	_	_	_
126	:	:	:	_	_	_
127	parB	parb	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	WT	wt	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	genotype	genotype	NN	_	_	_
133	:	:	:	_	_	_
134	AB1157	ab1157	NN	_	_	_
135	ybbD	ybbd	NN	GEN	_	_
136	:	:	:	_	_	_
137	:	:	:	_	_	_
138	parS	pars	NN	_	_	_
139	site	site	NN	_	_	_
140	3	3	CD	_	_	_
141	pUTC18	putc18	NN	_	_	_
142	:	:	:	_	_	_
143	:	:	:	_	_	_
144	parB	parb	NN	_	_	_
145	-LRB-	-lrb-	-LRB-	_	_	_
146	G101S	g101s	NN	_	_	_
147	-RRB-	-rrb-	-RRB-	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	genotype	genotype	NN	_	_	_
150	:	:	:	_	_	_
151	AB1157	ab1157	NN	_	_	_
152	ybbD	ybbd	NN	GEN	_	_
153	:	:	:	_	_	_
154	:	:	:	_	_	_
155	parS	pars	NN	_	_	_
156	site	site	NN	_	_	_
157	3	3	CD	_	_	_
158	pUTC18	putc18	NN	_	_	_
159	:	:	:	_	_	_
160	:	:	:	_	_	_
161	parB	parb	NN	_	_	_
162	-LRB-	-lrb-	-LRB-	_	_	_
163	WT	wt	NN	_	_	_
164	-RRB-	-rrb-	-RRB-	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	genotype	genotype	NN	_	_	_
167	:	:	:	_	_	_
168	AB1157	ab1157	NN	_	_	_
169	ybbD	ybbd	NN	GEN	_	_
170	:	:	:	_	_	_
171	:	:	:	_	_	_
172	parS	pars	NN	_	_	_
173	site	site	NN	_	_	_
174	4	4	CD	_	_	_
175	pUTC18	putc18	NN	_	_	_
176	:	:	:	_	_	_
177	:	:	:	_	_	_
178	parB	parb	NN	_	_	_
179	-LRB-	-lrb-	-LRB-	_	_	_
180	G101S	g101s	NN	_	_	_
181	-RRB-	-rrb-	-RRB-	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	genotype	genotype	NN	_	_	_
184	:	:	:	_	_	_
185	AB1157	ab1157	NN	_	_	_
186	ybbD	ybbd	NN	GEN	_	_
187	:	:	:	_	_	_
188	:	:	:	_	_	_
189	parS	pars	NN	_	_	_
190	site	site	NN	_	_	_
191	4	4	CD	_	_	_
192	pUTC18	putc18	NN	_	_	_
193	:	:	:	_	_	_
194	:	:	:	_	_	_
195	parB	parb	NN	_	_	_
196	-LRB-	-lrb-	-LRB-	_	_	_
197	WT	wt	NN	_	_	_
198	-RRB-	-rrb-	-RRB-	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	genotype	genotype	NN	_	_	_
201	:	:	:	_	_	_
202	AB1157	ab1157	NN	_	_	_
203	ybbD	ybbd	NN	GEN	_	_
204	:	:	:	_	_	_
205	:	:	:	_	_	_
206	parS	pars	NN	_	_	_
207	site	site	NN	_	_	_
208	5	5	CD	_	_	_
209	pUTC18	putc18	NN	_	_	_
210	:	:	:	_	_	_
211	:	:	:	_	_	_
212	parB	parb	NN	_	_	_
213	-LRB-	-lrb-	-LRB-	_	_	_
214	G101S	g101s	NN	_	_	_
215	-RRB-	-rrb-	-RRB-	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	genotype	genotype	NN	_	_	_
218	:	:	:	_	_	_
219	AB1157	ab1157	NN	_	_	_
220	ybbD	ybbd	NN	GEN	_	_
221	:	:	:	_	_	_
222	:	:	:	_	_	_
223	parS	pars	NN	_	_	_
224	site	site	NN	_	_	_
225	5	5	CD	_	_	_
226	pUTC18	putc18	NN	_	_	_
227	:	:	:	_	_	_
228	:	:	:	_	_	_
229	parB	parb	NN	_	_	_
230	-LRB-	-lrb-	-LRB-	_	_	_
231	WT	wt	NN	_	_	_
232	-RRB-	-rrb-	-RRB-	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	genotype	genotype	NN	_	_	_
235	:	:	:	_	_	_
236	AB1157	ab1157	NN	_	_	_
237	ybbD	ybbd	NN	GEN	_	_
238	:	:	:	_	_	_
239	:	:	:	_	_	_
240	parS	pars	NN	_	_	_
241	site	site	NN	_	_	_
242	6	6	CD	_	_	_
243	pUTC18	putc18	NN	_	_	_
244	:	:	:	_	_	_
245	:	:	:	_	_	_
246	parB	parb	NN	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	WT	wt	NN	_	_	_
249	-RRB-	-rrb-	-RRB-	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	genotype	genotype	NN	_	_	_
252	:	:	:	_	_	_
253	AB1157	ab1157	NN	_	_	_
254	ybbD	ybbd	NN	GEN	_	_
255	:	:	:	_	_	_
256	:	:	:	_	_	_
257	parS	pars	NN	_	_	_
258	site	site	NN	_	_	_
259	7	7	CD	_	_	_
260	pUTC18	putc18	NN	_	_	_
261	:	:	:	_	_	_
262	:	:	:	_	_	_
263	parB	parb	NN	_	_	_
264	-LRB-	-lrb-	-LRB-	_	_	_
265	G101S	g101s	NN	_	_	_
266	-RRB-	-rrb-	-RRB-	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	genotype	genotype	NN	_	_	_
269	:	:	:	_	_	_
270	AB1157	ab1157	NN	_	_	_
271	ybbD	ybbd	NN	GEN	_	_
272	:	:	:	_	_	_
273	:	:	:	_	_	_
274	parS	pars	NN	_	_	_
275	site	site	NN	_	_	_
276	7	7	CD	_	_	_
277	pUTC18	putc18	NN	_	_	_
278	:	:	:	_	_	_
279	:	:	:	_	_	_
280	parB	parb	NN	_	_	_
281	-LRB-	-lrb-	-LRB-	_	_	_
282	WT	wt	NN	_	_	_
283	-RRB-	-rrb-	-RRB-	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	genotype	genotype	NN	_	_	_
286	:	:	:	_	_	_
287	ArgR-8myc	argr-8myc	NN	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	genotype	genotype	NN	_	_	_
290	:	:	:	_	_	_
291	BW27784	bw27784	NN	_	_	_
292	delta	delta	NN	_	_	_
293	_	_	CD	_	_	_
294	recD	recd	NN	GEN	_	_
295	lacZ	lacz	NN	GEN	_	_
296	:	:	:	_	_	_
297	:	:	:	_	_	_
298	XXX	xxx	NN	_	_	_
299	mhpR	mhpr	NN	GEN	_	_
300	:	:	:	_	_	_
301	:	:	:	_	_	_
302	XXX	XXX	NNP	_	_	_
303	proA	proA	NNP	GEN	_	_
304	:	:	:	_	_	_
305	:	:	:	_	_	_
306	ISceIcs	isceic	NNS	_	_	_
307	tsx	tsx	NN	GEN	_	_
308	:	:	:	_	_	_
309	:	:	:	_	_	_
310	ISceIcs	isceic	NNS	_	_	_
311	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
312	lacZ	lacz	NN	GEN	_	_
313	+	+	CC	_	_	_
314	cynX	cynx	NN	GEN	_	_
315	:	:	:	_	_	_
316	:	:	:	_	_	_
317	GmR	gmr	NN	_	_	_
318	lacIq	laciq	NN	_	_	_
319	lacZX	laczx	NN	_	_	_
320	-	-	:	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	genotype	genotype	NN	_	_	_
323	:	:	:	_	_	_
324	BW27784	bw27784	NN	_	_	_
325	delta	delta	NN	_	_	_
326	_	_	CD	_	_	_
327	recD	recd	NN	GEN	_	_
328	lacZ	lacz	NN	GEN	_	_
329	:	:	:	_	_	_
330	:	:	:	_	_	_
331	XXX	xxx	NN	_	_	_
332	mhpR	mhpr	NN	GEN	_	_
333	:	:	:	_	_	_
334	:	:	:	_	_	_
335	XXX	XXX	NNP	_	_	_
336	proA	proA	NNP	GEN	_	_
337	:	:	:	_	_	_
338	:	:	:	_	_	_
339	ISceIcs	isceic	NNS	_	_	_
340	tsx	tsx	NN	GEN	_	_
341	:	:	:	_	_	_
342	:	:	:	_	_	_
343	ISceIcs	isceic	NNS	_	_	_
344	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
345	lacZ	lacz	NN	GEN	_	_
346	:	:	:	_	_	_
347	:	:	:	_	_	_
348	pal246	pal246	NN	_	_	_
349	cynX	cynx	NN	GEN	_	_
350	:	:	:	_	_	_
351	:	:	:	_	_	_
352	GmR	gmr	NN	_	_	_
353	lacIq	laciq	NN	_	_	_
354	lacZX	laczx	NN	_	_	_
355	-	-	:	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	genotype	genotype	NN	_	_	_
358	:	:	:	_	_	_
359	BW27784	bw27784	NN	_	_	_
360	lacZ	lacz	NN	GEN	_	_
361	:	:	:	_	_	_
362	:	:	:	_	_	_
363	XXX	xxx	NN	_	_	_
364	mhpR	mhpr	NN	GEN	_	_
365	:	:	:	_	_	_
366	:	:	:	_	_	_
367	XXX	XXX	NNP	_	_	_
368	proA	proA	NNP	GEN	_	_
369	:	:	:	_	_	_
370	:	:	:	_	_	_
371	ISceIcs	isceic	NNS	_	_	_
372	tsx	tsx	NN	GEN	_	_
373	:	:	:	_	_	_
374	:	:	:	_	_	_
375	ISceIcs	isceic	NNS	_	_	_
376	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
377	lacZ	lacz	NN	GEN	_	_
378	+	+	CC	_	_	_
379	cynX	cynx	NN	GEN	_	_
380	:	:	:	_	_	_
381	:	:	:	_	_	_
382	GmR	gmr	NN	_	_	_
383	lacIq	laciq	NN	_	_	_
384	lacZX	laczx	NN	_	_	_
385	-	-	:	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	genotype	genotype	NN	_	_	_
388	:	:	:	_	_	_
389	BW27784	bw27784	NN	_	_	_
390	lacZ	lacz	NN	GEN	_	_
391	:	:	:	_	_	_
392	:	:	:	_	_	_
393	XXX	xxx	NN	_	_	_
394	mhpR	mhpr	NN	GEN	_	_
395	:	:	:	_	_	_
396	:	:	:	_	_	_
397	XXX	XXX	NNP	_	_	_
398	proA	proA	NNP	GEN	_	_
399	:	:	:	_	_	_
400	:	:	:	_	_	_
401	ISceIcs	isceic	NNS	_	_	_
402	tsx	tsx	NN	GEN	_	_
403	:	:	:	_	_	_
404	:	:	:	_	_	_
405	ISceIcs	isceic	NNS	_	_	_
406	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
407	lacZ	lacz	NN	GEN	_	_
408	:	:	:	_	_	_
409	:	:	:	_	_	_
410	pal246	pal246	NN	_	_	_
411	cynX	cynx	NN	GEN	_	_
412	:	:	:	_	_	_
413	:	:	:	_	_	_
414	GmR	gmr	NN	_	_	_
415	lacIq	laciq	NN	_	_	_
416	lacZX	laczx	NN	_	_	_
417	-	-	:	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	genotype	genotype	NN	_	_	_
420	:	:	:	_	_	_
421	crpfis	crpfis	NN	_	_	_
422	mutant	mutant	JJ	_	_	_
423	background	background	NN	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	genotype	genotype	NN	_	_	_
426	:	:	:	_	_	_
427	crp	crp	NN	GEN	_	_
428	mutant	mutant	JJ	_	_	_
429	background	background	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	genotype	genotype	NN	_	_	_
432	:	:	:	_	_	_
433	CV108	cv108	NN	_	_	_
434	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
435	genotype	genotype	NN	_	_	_
436	:	:	:	_	_	_
437	cya	cya	NN	_	_	_
438	mutant	mutant	JJ	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	genotype	genotype	NN	_	_	_
441	:	:	:	_	_	_
442	cya	cya	NN	_	_	_
443	mutant	mutant	JJ	_	_	_
444	background	background	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	genotype	genotype	NN	_	_	_
447	:	:	:	_	_	_
448	del-fis	del-fis	JJ	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	genotype	genotype	NN	_	_	_
451	:	:	:	_	_	_
452	del-hns	del-hns	JJ	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	genotype	genotype	NN	_	_	_
455	:	:	:	_	_	_
456	del	del	DT	_	_	_
457	rpoS	rpos	NN	GEN	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	genotype	genotype	NN	_	_	_
460	:	:	:	_	_	_
461	del	del	DT	_	_	_
462	rsd	rsd	NN	GEN	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	genotype	genotype	NN	_	_	_
465	:	:	:	_	_	_
466	del	del	DT	_	_	_
467	rsd	rsd	NN	GEN	_	_
468	;	;	:	_	_	_
469	del	del	DT	_	_	_
470	ssrS	ssrs	NN	GEN	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	genotype	genotype	NN	_	_	_
473	:	:	:	_	_	_
474	del	del	DT	_	_	_
475	ssrS	ssrs	NN	GEN	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	genotype	genotype	NN	_	_	_
478	:	:	:	_	_	_
479	delta-cra	delta-cra	NN	_	_	_
480	Knock-out	knock-out	JJ	_	_	_
481	strain	strain	NN	_	_	_
482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
483	genotype	genotype	NN	_	_	_
484	:	:	:	_	_	_
485	delta-crp	delta-crp	JJ	_	_	_
486	Knock-out	knock-out	JJ	_	_	_
487	strain	strain	NN	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
489	genotype	genotype	NN	_	_	_
490	:	:	:	_	_	_
491	delta	delta	NN	_	_	_
492	dicF	dicf	NN	GEN	_	_
493	,	,	,	_	_	_
494	lacIq	laciq	NN	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
496	genotype	genotype	NN	_	_	_
497	:	:	:	_	_	_
498	delta-fis	delta-fis	JJ	_	_	_
499	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
500	genotype	genotype	NN	_	_	_
501	:	:	:	_	_	_
502	deltahmp	deltahmp	JJ	_	_	_
503	deltanrfA	deltanrfa	NN	_	_	_
504	deltanorVW	deltanorvw	NN	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	genotype	genotype	NN	_	_	_
507	:	:	:	_	_	_
508	-LCB-	-lcb-	-LRB-	_	_	_
509	delta	delta	NN	_	_	_
510	-RCB-	-rcb-	-RRB-	_	_	_
511	hns	hn	VBZ	GEN	_	_
512	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
513	genotype	genotype	NN	_	_	_
514	:	:	:	_	_	_
515	delta-hns	delta-hn	NNS	_	_	_
516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
517	genotype	genotype	NN	_	_	_
518	:	:	:	_	_	_
519	-LCB-	-lcb-	-LRB-	_	_	_
520	delta	delta	NN	_	_	_
521	-RCB-	-rcb-	-RRB-	_	_	_
522	nusG	nusg	NN	GEN	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	genotype	genotype	NN	_	_	_
525	:	:	:	_	_	_
526	delta	delta	NN	_	_	_
527	_	_	CD	_	_	_
528	ompR	ompr	NN	GEN	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	genotype	genotype	NN	_	_	_
531	:	:	:	_	_	_
532	delta-rac	delta-rac	JJ	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	genotype	genotype	NN	_	_	_
535	:	:	:	_	_	_
536	delta	delta	NN	_	_	_
537	_	_	SYM	_	_	_
538	recG263	recg263	NN	_	_	_
539	:	:	:	_	_	_
540	:	:	:	_	_	_
541	KanR	kanr	NN	_	_	_
542	lacZ	lacz	NN	GEN	_	_
543	:	:	:	_	_	_
544	:	:	:	_	_	_
545	χχχ	χχχ	NN	_	_	_
546	mhpR	mhpr	NN	GEN	_	_
547	:	:	:	_	_	_
548	:	:	:	_	_	_
549	χχχ	χχχ	NN	_	_	_
550	proA	proa	NN	GEN	_	_
551	:	:	:	_	_	_
552	:	:	:	_	_	_
553	ISceIcs	isceic	NNS	_	_	_
554	tsx	tsx	NN	GEN	_	_
555	:	:	:	_	_	_
556	:	:	:	_	_	_
557	ISceIcs	isceic	NNS	_	_	_
558	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
559	lacZ	lacz	NN	GEN	_	_
560	+	+	CC	_	_	_
561	cynX	cynx	NN	GEN	_	_
562	:	:	:	_	_	_
563	:	:	:	_	_	_
564	GmR	gmr	NN	_	_	_
565	lacIq	laciq	NN	_	_	_
566	lacZχ	laczχ	NN	_	_	_
567	-	-	:	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	genotype	genotype	NN	_	_	_
570	:	:	:	_	_	_
571	delta	delta	NN	_	_	_
572	_	_	SYM	_	_	_
573	recG263	recg263	NN	_	_	_
574	:	:	:	_	_	_
575	:	:	:	_	_	_
576	KanR	kanr	NN	_	_	_
577	lacZ	lacz	NN	GEN	_	_
578	:	:	:	_	_	_
579	:	:	:	_	_	_
580	χχχ	χχχ	NN	_	_	_
581	mhpR	mhpr	NN	GEN	_	_
582	:	:	:	_	_	_
583	:	:	:	_	_	_
584	χχχ	χχχ	NN	_	_	_
585	proA	proa	NN	GEN	_	_
586	:	:	:	_	_	_
587	:	:	:	_	_	_
588	ISceIcs	isceic	NNS	_	_	_
589	tsx	tsx	NN	GEN	_	_
590	:	:	:	_	_	_
591	:	:	:	_	_	_
592	ISceIcs	isceic	NNS	_	_	_
593	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
594	lacZ	lacz	NN	GEN	_	_
595	:	:	:	_	_	_
596	:	:	:	_	_	_
597	pal246	pal246	NN	_	_	_
598	cynX	cynx	NN	GEN	_	_
599	:	:	:	_	_	_
600	:	:	:	_	_	_
601	GmR	gmr	NN	_	_	_
602	lacIq	laciq	NN	_	_	_
603	lacZχ	laczχ	NN	_	_	_
604	-	-	:	_	_	_
605	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
606	genotype	genotype	NN	_	_	_
607	:	:	:	_	_	_
608	-LCB-	-lcb-	-LRB-	_	_	_
609	delta	delta	NN	_	_	_
610	-RCB-	-rcb-	-RRB-	_	_	_
611	rho	rho	NN	GEN	_	_
612	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
613	genotype	genotype	NN	_	_	_
614	:	:	:	_	_	_
615	DH1	dh1	NN	_	_	_
616	ΔhisC	δhisc	NN	_	_	_
617	:	:	:	_	_	_
618	:	:	:	_	_	_
619	cat	cat	NN	_	_	_
620	ΔintC	δintc	NN	_	_	_
621	:	:	:	_	_	_
622	:	:	:	_	_	_
623	Ptrc-rfp-tetR-zeocinr	Ptrc-rfp-tetR-zeocinr	NNP	_	_	_
624	ΔgalK	ΔgalK	NNP	_	_	_
625	:	:	:	_	_	_
626	:	:	:	_	_	_
627	PtetA-gfp-hisC-kanr	PtetA-gfp-hisC-kanr	NNP	_	_	_
628	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
629	genotype	genotype	NN	_	_	_
630	:	:	:	_	_	_
631	DH1	dh1	NN	_	_	_
632	ΔhisC	δhisc	NN	_	_	_
633	:	:	:	_	_	_
634	:	:	:	_	_	_
635	cat	cat	NN	_	_	_
636	ΔintC	δintc	NN	_	_	_
637	:	:	:	_	_	_
638	:	:	:	_	_	_
639	Ptrc-rfp-tetR-zeocinr	Ptrc-rfp-tetR-zeocinr	NNP	_	_	_
640	ΔgalK	ΔgalK	NNP	_	_	_
641	:	:	:	_	_	_
642	:	:	:	_	_	_
643	PtetA-gfp-kanr	PtetA-gfp-kanr	NNP	_	_	_
644	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
645	genotype	genotype	NN	_	_	_
646	:	:	:	_	_	_
647	dnaC2	dnac2	NN	_	_	_
648	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
649	genotype	genotype	NN	_	_	_
650	:	:	:	_	_	_
651	dnaC2	dnac2	NN	_	_	_
652	,	,	,	_	_	_
653	pMQ430	pmq430	NN	_	_	_
654	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
655	Genotype	Genotype	NNP	_	_	_
656	:	:	:	_	_	_
657	E.	e.	FW	_	_	_
658	coli	coli	FW	_	_	_
659	K12	k12	NN	_	_	_
660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
661	genotype	genotype	NN	_	_	_
662	:	:	:	_	_	_
663	E.	e.	FW	_	_	_
664	coli	coli	FW	_	_	_
665	-LSB-	-lsb-	-LRB-	_	_	_
666	supE44	supe44	NN	_	_	_
667	hsdS20	hsds20	NN	_	_	_
668	-LRB-	-lrb-	-LRB-	_	_	_
669	rB-mB	rb-mb	NN	_	_	_
670	-	-	:	_	_	_
671	-RRB-	-rrb-	-RRB-	_	_	_
672	recA13	reca13	NN	_	_	_
673	ara-14	ara-14	NN	_	_	_
674	proA2	proa2	NN	_	_	_
675	lacY1	lacy1	NN	_	_	_
676	galK2	galk2	NN	_	_	_
677	rpsL20	rpsl20	NN	_	_	_
678	xyl-5	xyl-5	NN	_	_	_
679	mtl-1	mtl-1	NN	_	_	_
680	-RSB-	-rsb-	-RRB-	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	genotype	genotype	NN	_	_	_
683	:	:	:	_	_	_
684	ethanol-tolerant	ethanol-tolerant	JJ	_	_	_
685	mutant	mutant	JJ	_	_	_
686	E1	e1	NN	_	_	_
687	of	of	IN	_	_	_
688	IrrE	irre	NN	_	_	_
689	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
690	genotype	genotype	NN	_	_	_
691	:	:	:	_	_	_
692	EvgSc	evgsc	NN	_	_	_
693	KO	ko	NN	_	_	_
694	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
695	genotype	genotype	NN	_	_	_
696	:	:	:	_	_	_
697	EvgSc	evgsc	NN	_	_	_
698	ompR	ompr	NN	GEN	_	_
699	KO	ko	NN	_	_	_
700	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
701	genotype	genotype	NN	_	_	_
702	:	:	:	_	_	_
703	∆	∆	CD	_	_	_
704	fadE	fade	NN	GEN	_	_
705	with	with	IN	_	_	_
706	overexpression	overexpression	NN	_	_	_
707	of	of	IN	_	_	_
708	`	`	``	_	_	_
709	tesA	tesa	NN	GEN	_	_
710	and	and	CC	_	_	_
711	MlfabH	mlfabh	NN	_	_	_
712	via	via	IN	_	_	_
713	an	a	DT	_	_	_
714	IPTG-inudcible	iptg-inudcible	JJ	_	_	_
715	promoter	promoter	NN	_	_	_
716	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
717	genotype	genotype	NN	_	_	_
718	:	:	:	_	_	_
719	∆	∆	CD	_	_	_
720	fadE	fade	NN	GEN	_	_
721	with	with	IN	_	_	_
722	overexpression	overexpression	NN	_	_	_
723	of	of	IN	_	_	_
724	`	`	``	_	_	_
725	tesA	tesa	NN	GEN	_	_
726	via	via	IN	_	_	_
727	an	a	DT	_	_	_
728	IPTG-inudcible	iptg-inudcible	JJ	_	_	_
729	promoter	promoter	NN	_	_	_
730	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
731	genotype	genotype	NN	_	_	_
732	:	:	:	_	_	_
733	fis	fi	NNS	GEN	_	_
734	:	:	:	_	_	_
735	:	:	:	_	_	_
736	3xFLAG	3xflag	NN	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
738	genotype	genotype	NN	_	_	_
739	:	:	:	_	_	_
740	fis	fis	NN	GEN	_	_
741	mutant	mutant	JJ	_	_	_
742	background	background	NN	_	_	_
743	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
744	genotype	genotype	NN	_	_	_
745	:	:	:	_	_	_
746	F	f	NN	_	_	_
747	-	-	:	_	_	_
748	lambda	lambda	NN	_	_	_
749	-	-	:	_	_	_
750	ilvG	ilvg	NN	_	_	_
751	-	-	:	_	_	_
752	rfb-50	rfb-50	NN	_	_	_
753	rph-1	rph-1	NN	_	_	_
754	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
755	genotype	genotype	NN	_	_	_
756	:	:	:	_	_	_
757	F	f	NN	_	_	_
758	-	-	:	_	_	_
759	lambda	lambda	NN	_	_	_
760	-	-	:	_	_	_
761	ilvG	ilvg	NN	_	_	_
762	-	-	:	_	_	_
763	rfb-50	rfb-50	NN	_	_	_
764	rph-1	rph-1	NN	_	_	_
765	-LSB-	-lsb-	-LRB-	_	_	_
766	delta	delta	NN	_	_	_
767	-RSB-	-rsb-	-RRB-	_	_	_
768	fis	fi	VBZ	GEN	_	_
769	:	:	:	_	_	_
770	:	:	:	_	_	_
771	frt-kan-frt	frt-kan-frt	JJ	_	_	_
772	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
773	genotype	genotype	NN	_	_	_
774	:	:	:	_	_	_
775	F	f	NN	_	_	_
776	-	-	:	_	_	_
777	lambda	lambda	NN	_	_	_
778	-	-	:	_	_	_
779	ilvG	ilvg	NN	_	_	_
780	-	-	:	_	_	_
781	rfb-50	rfb-50	NN	_	_	_
782	rph-1	rph-1	NN	_	_	_
783	-LSB-	-lsb-	-LRB-	_	_	_
784	delta	delta	NN	_	_	_
785	-RSB-	-rsb-	-RRB-	_	_	_
786	hns	hn	NNS	GEN	_	_
787	:	:	:	_	_	_
788	:	:	:	_	_	_
789	frt	frt	SYM	_	_	_
790	-	-	:	_	_	_
791	kan	kan	SYM	_	_	_
792	-	-	:	_	_	_
793	frt	frt	NN	_	_	_
794	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
795	genotype	genotype	NN	_	_	_
796	:	:	:	_	_	_
797	F	f	NN	_	_	_
798	-	-	:	_	_	_
799	lambda	lambda	NN	_	_	_
800	-	-	:	_	_	_
801	ilvG	ilvg	NN	_	_	_
802	-	-	:	_	_	_
803	rfb-50	rfb-50	NN	_	_	_
804	rph-1	rph-1	NN	_	_	_
805	-LSB-	-lsb-	-LRB-	_	_	_
806	delta	delta	NN	_	_	_
807	-RSB-	-rsb-	-RRB-	_	_	_
808	matP	matp	NN	GEN	_	_
809	:	:	:	_	_	_
810	:	:	:	_	_	_
811	frt-cam-frt	frt-cam-frt	JJ	_	_	_
812	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
813	genotype	genotype	NN	_	_	_
814	:	:	:	_	_	_
815	F	f	NN	_	_	_
816	-	-	:	_	_	_
817	lambda	lambda	NN	_	_	_
818	-	-	:	_	_	_
819	ilvG	ilvg	NN	_	_	_
820	-	-	:	_	_	_
821	rfb-50	rfb-50	NN	_	_	_
822	rph-1	rph-1	NN	_	_	_
823	-LSB-	-lsb-	-LRB-	_	_	_
824	delta	delta	NN	_	_	_
825	-RSB-	-rsb-	-RRB-	_	_	_
826	mukB	mukb	NN	GEN	_	_
827	:	:	:	_	_	_
828	:	:	:	_	_	_
829	frt	frt	SYM	_	_	_
830	-	-	:	_	_	_
831	kan	kan	NN	_	_	_
832	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
833	genotype	genotype	NN	_	_	_
834	:	:	:	_	_	_
835	F	f	NN	_	_	_
836	-	-	:	_	_	_
837	lambda	lambda	NN	_	_	_
838	-	-	:	_	_	_
839	ilvG	ilvg	NN	_	_	_
840	-	-	:	_	_	_
841	rfb-50	rfb-50	NN	_	_	_
842	rph-1	rph-1	NN	_	_	_
843	-LSB-	-lsb-	-LRB-	_	_	_
844	delta	delta	NN	_	_	_
845	-RSB-	-rsb-	-RRB-	_	_	_
846	zapB	zapb	NN	GEN	_	_
847	:	:	:	_	_	_
848	:	:	:	_	_	_
849	frt-kan-frt	frt-kan-frt	JJ	_	_	_
850	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
851	genotype	genotype	NN	_	_	_
852	:	:	:	_	_	_
853	F	f	NN	_	_	_
854	-	-	:	_	_	_
855	lambda	lambda	NN	_	_	_
856	-	-	:	_	_	_
857	ilvG	ilvg	NN	_	_	_
858	-	-	:	_	_	_
859	rfb-50	rfb-50	NN	_	_	_
860	rph-1	rph-1	NN	_	_	_
861	matP	matp	NN	GEN	_	_
862	-LSB-	-lsb-	-LRB-	_	_	_
863	delta	delta	NN	_	_	_
864	-RSB-	-rsb-	-RRB-	_	_	_
865	C20	c20	NN	_	_	_
866	:	:	:	_	_	_
867	:	:	:	_	_	_
868	frt-cam-frt	frt-cam-frt	JJ	_	_	_
869	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
870	genotype	genotype	NN	_	_	_
871	:	:	:	_	_	_
872	F	f	NN	_	_	_
873	-	-	:	_	_	_
874	lambda	lambda	NN	_	_	_
875	-	-	:	_	_	_
876	ilvG	ilvg	NN	_	_	_
877	-	-	:	_	_	_
878	rfb-50	rfb-50	NN	_	_	_
879	rph-1	rph-1	NN	_	_	_
880	phi80	phi80	NN	_	_	_
881	+	+	CC	_	_	_
882	-LSB-	-lsb-	-LRB-	_	_	_
883	delta	delta	NN	_	_	_
884	-RSB-	-rsb-	-RRB-	_	_	_
885	hupA	hupa	NN	GEN	_	_
886	:	:	:	_	_	_
887	:	:	:	_	_	_
888	frt	frt	SYM	_	_	_
889	-	-	:	_	_	_
890	kan	kan	SYM	_	_	_
891	-	-	:	_	_	_
892	frt	frt	NN	_	_	_
893	-LSB-	-lsb-	-LRB-	_	_	_
894	delta	delta	NN	_	_	_
895	-RSB-	-rsb-	-RRB-	_	_	_
896	hupB	hupb	NN	GEN	_	_
897	:	:	:	_	_	_
898	:	:	:	_	_	_
899	frt-cam-frt	frt-cam-frt	JJ	_	_	_
900	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
901	genotype	genotype	NN	_	_	_
902	:	:	:	_	_	_
903	F	f	NN	_	_	_
904	-	-	:	_	_	_
905	lambda	lambda	NN	_	_	_
906	-	-	:	_	_	_
907	ilvG	ilvg	NN	_	_	_
908	-	-	:	_	_	_
909	rfb-50	rfb-50	NN	_	_	_
910	rph-1phi80	rph-1phi80	NN	_	_	_
911	+	+	CC	_	_	_
912	-LSB-	-lsb-	-LRB-	_	_	_
913	delta	delta	NN	_	_	_
914	-RSB-	-rsb-	-RRB-	_	_	_
915	mukB	mukb	NN	GEN	_	_
916	:	:	:	_	_	_
917	:	:	:	_	_	_
918	frt	frt	SYM	_	_	_
919	-	-	:	_	_	_
920	apra	apra	NN	_	_	_
921	-LSB-	-lsb-	-LRB-	_	_	_
922	delta	delta	NN	_	_	_
923	-RSB-	-rsb-	-RRB-	_	_	_
924	matP	matp	NN	GEN	_	_
925	:	:	:	_	_	_
926	:	:	:	_	_	_
927	frt-cam-frt	frt-cam-frt	JJ	_	_	_
928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
929	genotype	genotype	NN	_	_	_
930	:	:	:	_	_	_
931	F	f	NN	_	_	_
932	-	-	:	_	_	_
933	,	,	,	_	_	_
934	lambda	lambda	NN	_	_	_
935	-	-	:	_	_	_
936	,	,	,	_	_	_
937	rph-1	rph-1	NN	_	_	_
938	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
939	Genotype	Genotype	NNP	_	_	_
940	:	:	:	_	_	_
941	F	f	NN	_	_	_
942	-	-	:	_	_	_
943	ompT	ompt	NN	GEN	_	_
944	hsdSB	hsdsb	NN	_	_	_
945	-LRB-	-lrb-	-LRB-	_	_	_
946	rB-mB	rb-mb	NN	_	_	_
947	-	-	:	_	_	_
948	-RRB-	-rrb-	-RRB-	_	_	_
949	gal	gal	NN	_	_	_
950	dcm	dcm	NN	GEN	_	_
951	-LRB-	-lrb-	-LRB-	_	_	_
952	DE3	de3	NN	_	_	_
953	-RRB-	-rrb-	-RRB-	_	_	_
954	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
955	genotype	genotype	NN	_	_	_
956	:	:	:	_	_	_
957	furfural-tolerant	furfural-tolerant	JJ	_	_	_
958	mutant	mutant	JJ	_	_	_
959	F1-37	f1-37	NN	_	_	_
960	of	of	IN	_	_	_
961	IrrE	irre	NN	_	_	_
962	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
963	genotype	genotype	NN	_	_	_
964	:	:	:	_	_	_
965	Fusion	fusion	NN	_	_	_
966	of	of	IN	_	_	_
967	venus	venus	NN	_	_	_
968	to	to	TO	_	_	_
969	the	the	DT	_	_	_
970	3	3	CD	_	_	_
971	'	'	''	_	_	_
972	end	end	NN	_	_	_
973	of	of	IN	_	_	_
974	rpoC	rpoc	NN	GEN	_	_
975	in	in	IN	_	_	_
976	E.	e.	FW	_	_	_
977	coli	coli	FW	_	_	_
978	wild-type	wild-type	JJ	_	_	_
979	MG1655	mg1655	NN	_	_	_
980	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
981	genotype	genotype	NN	_	_	_
982	:	:	:	_	_	_
983	gadE-8myc	gade-8myc	NN	_	_	_
984	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
985	genotype	genotype	NN	_	_	_
986	:	:	:	_	_	_
987	gadW-8myc	gadw-8myc	NN	_	_	_
988	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
989	genotype	genotype	NN	_	_	_
990	:	:	:	_	_	_
991	gadX-8myc	gadx-8myc	NN	_	_	_
992	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
993	genotype	genotype	NN	_	_	_
994	:	:	:	_	_	_
995	Galaxy1	galaxy1	NN	_	_	_
996	-	-	:	_	_	_
997	-LSB-	-lsb-	-LRB-	_	_	_
998	CV104	cv104	NN	_	_	_
999	_	_	CD	_	_	_
1000	pHDB3	phdb3	NN	_	_	_
1001	_	_	CD	_	_	_
1002	5	5	CD	_	_	_
1003	-RSB-	-rsb-	-RRB-	_	_	_
1004	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1005	genotype	genotype	NN	_	_	_
1006	:	:	:	_	_	_
1007	Galaxy2	galaxy2	NN	_	_	_
1008	-	-	:	_	_	_
1009	-LSB-	-lsb-	-LRB-	_	_	_
1010	CV104	cv104	NN	_	_	_
1011	_	_	CD	_	_	_
1012	pLCV1	plcv1	NN	_	_	_
1013	_	_	CD	_	_	_
1014	5	5	CD	_	_	_
1015	-RSB-	-rsb-	-RRB-	_	_	_
1016	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1017	genotype	genotype	NN	_	_	_
1018	:	:	:	_	_	_
1019	Galaxy3	galaxy3	NN	_	_	_
1020	-	-	:	_	_	_
1021	-LSB-	-lsb-	-LRB-	_	_	_
1022	CV104	cv104	NN	_	_	_
1023	_	_	CD	_	_	_
1024	pLCV1	plcv1	NN	_	_	_
1025	_	_	NN	_	_	_
1026	10	10	CD	_	_	_
1027	-RSB-	-rsb-	-RRB-	_	_	_
1028	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1029	genotype	genotype	NN	_	_	_
1030	:	:	:	_	_	_
1031	Galaxy4	galaxy4	NN	_	_	_
1032	-	-	:	_	_	_
1033	-LSB-	-lsb-	-LRB-	_	_	_
1034	CV104	cv104	NN	_	_	_
1035	_	_	CD	_	_	_
1036	pHDB3	phdb3	NN	_	_	_
1037	_	_	CD	_	_	_
1038	20	20	CD	_	_	_
1039	-RSB-	-rsb-	-RRB-	_	_	_
1040	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1041	genotype	genotype	NN	_	_	_
1042	:	:	:	_	_	_
1043	Galaxy5	galaxy5	NN	_	_	_
1044	-	-	:	_	_	_
1045	-LSB-	-lsb-	-LRB-	_	_	_
1046	CV104	cv104	NN	_	_	_
1047	_	_	CD	_	_	_
1048	pLCV1	plcv1	NN	_	_	_
1049	_	_	CD	_	_	_
1050	20	20	CD	_	_	_
1051	-RSB-	-rsb-	-RRB-	_	_	_
1052	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1053	genotype	genotype	NN	_	_	_
1054	:	:	:	_	_	_
1055	Galaxy6	galaxy6	NN	_	_	_
1056	-	-	:	_	_	_
1057	-LSB-	-lsb-	-LRB-	_	_	_
1058	CV104	cv104	NN	_	_	_
1059	_	_	CD	_	_	_
1060	pHDB3	phdb3	NN	_	_	_
1061	_	_	NN	_	_	_
1062	10	10	CD	_	_	_
1063	-RSB-	-rsb-	-RRB-	_	_	_
1064	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1065	genotype	genotype	NN	_	_	_
1066	:	:	:	_	_	_
1067	GATC-cluster	gatc-cluster	NN	_	_	_
1068	:	:	:	_	_	_
1069	:	:	:	_	_	_
1070	hisA	hisA	NNP	GEN	_	_
1071	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1072	genotype	genotype	NN	_	_	_
1073	:	:	:	_	_	_
1074	GATC-cluster	gatc-cluster	NN	_	_	_
1075	:	:	:	_	_	_
1076	:	:	:	_	_	_
1077	srlA	srla	NN	GEN	_	_
1078	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1079	genotype	genotype	NN	_	_	_
1080	:	:	:	_	_	_
1081	GATC-cluster	gatc-cluster	NN	_	_	_
1082	:	:	:	_	_	_
1083	:	:	:	_	_	_
1084	ter	ter	NN	_	_	_
1085	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1086	genotype	genotype	NN	_	_	_
1087	:	:	:	_	_	_
1088	GATC-cluster	gatc-cluster	NN	_	_	_
1089	:	:	:	_	_	_
1090	:	:	:	_	_	_
1091	tnaA	tnaa	NN	GEN	_	_
1092	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1093	genotype	genotype	NN	_	_	_
1094	:	:	:	_	_	_
1095	gss	gss	NN	GEN	_	_
1096	mutant	mutant	JJ	_	_	_
1097	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1098	genotype	genotype	NN	_	_	_
1099	:	:	:	_	_	_
1100	hns	hn	NNS	GEN	_	_
1101	:	:	:	_	_	_
1102	:	:	:	_	_	_
1103	3xFLAG	3xflag	NN	_	_	_
1104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1105	genotype	genotype	NN	_	_	_
1106	:	:	:	_	_	_
1107	lacZ	lacz	NN	GEN	_	_
1108	:	:	:	_	_	_
1109	:	:	:	_	_	_
1110	χχχ	χχχ	NN	_	_	_
1111	mhpR	mhpr	NN	GEN	_	_
1112	:	:	:	_	_	_
1113	:	:	:	_	_	_
1114	χχχ	χχχ	NN	_	_	_
1115	proA	proa	NN	GEN	_	_
1116	:	:	:	_	_	_
1117	:	:	:	_	_	_
1118	ISceIcs	isceic	NNS	_	_	_
1119	tsx	tsx	NN	GEN	_	_
1120	:	:	:	_	_	_
1121	:	:	:	_	_	_
1122	ISceIcs	isceic	NNS	_	_	_
1123	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
1124	lacZ	lacz	NN	GEN	_	_
1125	+	+	CC	_	_	_
1126	cynX	cynx	NN	GEN	_	_
1127	:	:	:	_	_	_
1128	:	:	:	_	_	_
1129	GmR	gmr	NN	_	_	_
1130	lacIq	laciq	NN	_	_	_
1131	lacZχ	laczχ	NN	_	_	_
1132	-	-	:	_	_	_
1133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1134	genotype	genotype	NN	_	_	_
1135	:	:	:	_	_	_
1136	lacZ	lacz	NN	GEN	_	_
1137	:	:	:	_	_	_
1138	:	:	:	_	_	_
1139	χχχ	χχχ	NN	_	_	_
1140	mhpR	mhpr	NN	GEN	_	_
1141	:	:	:	_	_	_
1142	:	:	:	_	_	_
1143	χχχ	χχχ	NN	_	_	_
1144	proA	proa	NN	GEN	_	_
1145	:	:	:	_	_	_
1146	:	:	:	_	_	_
1147	ISceIcs	isceic	NNS	_	_	_
1148	tsx	tsx	NN	GEN	_	_
1149	:	:	:	_	_	_
1150	:	:	:	_	_	_
1151	ISceIcs	isceic	NNS	_	_	_
1152	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
1153	lacZ	lacz	NN	GEN	_	_
1154	:	:	:	_	_	_
1155	:	:	:	_	_	_
1156	pal246	pal246	NN	_	_	_
1157	cynX	cynx	NN	GEN	_	_
1158	:	:	:	_	_	_
1159	:	:	:	_	_	_
1160	GmR	gmr	NN	_	_	_
1161	lacIq	laciq	NN	_	_	_
1162	lacZχ	laczχ	NN	_	_	_
1163	-	-	:	_	_	_
1164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1165	genotype	genotype	NN	_	_	_
1166	:	:	:	_	_	_
1167	Lrp-8myc	lrp-8myc	JJ	_	_	_
1168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1169	genotype	genotype	NN	_	_	_
1170	:	:	:	_	_	_
1171	luxS	luxs	NN	GEN	_	_
1172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1173	genotype	genotype	NN	_	_	_
1174	:	:	:	_	_	_
1175	∆	∆	CD	_	_	_
1176	mazEF	mazef	NN	_	_	_
1177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1178	genotype	genotype	NN	_	_	_
1179	:	:	:	_	_	_
1180	∆	∆	SYM	_	_	_
1181	mazEFlexA3	mazeflexa3	NN	_	_	_
1182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1183	genotype	genotype	NN	_	_	_
1184	:	:	:	_	_	_
1185	mfd	mfd	SYM	GEN	_	_
1186	-	-	:	_	_	_
1187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1188	genotype	genotype	NN	_	_	_
1189	:	:	:	_	_	_
1190	Mfd	mfd	NN	_	_	_
1191	+	+	CC	_	_	_
1192	+	+	CC	_	_	_
1193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1194	genotype	genotype	NN	_	_	_
1195	:	:	:	_	_	_
1196	MG1655	mg1655	NN	_	_	_
1197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1198	genotype	genotype	NN	_	_	_
1199	:	:	:	_	_	_
1200	MG1655	mg1655	NN	_	_	_
1201	DdksA	ddksa	NN	_	_	_
1202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1203	genotype	genotype	NN	_	_	_
1204	:	:	:	_	_	_
1205	MG1655	mg1655	NN	_	_	_
1206	del	del	FW	_	_	_
1207	ssrS	ssrs	FW	GEN	_	_
1208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1209	genotype	genotype	NN	_	_	_
1210	:	:	:	_	_	_
1211	MG1655	mg1655	NN	_	_	_
1212	wild-type	wild-type	JJ	_	_	_
1213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1214	genotype	genotype	NN	_	_	_
1215	:	:	:	_	_	_
1216	mutant	mutant	JJ	_	_	_
1217	hhahha2	hhahha2	NN	_	_	_
1218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1219	genotype	genotype	NN	_	_	_
1220	:	:	:	_	_	_
1221	mutant	mutant	JJ	_	_	_
1222	hhs	hh	NNS	_	_	_
1223	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1224	genotype	genotype	NN	_	_	_
1225	:	:	:	_	_	_
1226	mutant	mutant	JJ	_	_	_
1227	hns2	hns2	NN	_	_	_
1228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1229	genotype	genotype	NN	_	_	_
1230	:	:	:	_	_	_
1231	mutant	mutant	JJ	_	_	_
1232	hnshns2	hnshns2	NN	_	_	_
1233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1234	genotype	genotype	NN	_	_	_
1235	:	:	:	_	_	_
1236	n/a	n/a	NN	_	_	_
1237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1238	genotype	genotype	NN	_	_	_
1239	:	:	:	_	_	_
1240	ompR-8myc	ompr-8myc	NN	_	_	_
1241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1242	genotype	genotype	NN	_	_	_
1243	:	:	:	_	_	_
1244	ompR	ompr	NN	GEN	_	_
1245	deletion	deletion	NN	_	_	_
1246	mutant	mutant	JJ	_	_	_
1247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1248	genotype	genotype	NN	_	_	_
1249	:	:	:	_	_	_
1250	ompR	ompr	NN	GEN	_	_
1251	KO	ko	NN	_	_	_
1252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1253	genotype	genotype	NN	_	_	_
1254	:	:	:	_	_	_
1255	Pck	pck	NN	_	_	_
1256	over-expressed	over-expressed	JJ	_	_	_
1257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1258	genotype	genotype	NN	_	_	_
1259	:	:	:	_	_	_
1260	pHDB3	phdb3	NN	_	_	_
1261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1262	genotype	genotype	NN	_	_	_
1263	:	:	:	_	_	_
1264	plasmid	plasmid	NN	_	_	_
1265	cured	cure	VBD	_	_	_
1266	strain	strain	NN	_	_	_
1267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1268	genotype	genotype	NN	_	_	_
1269	:	:	:	_	_	_
1270	pLCV1	plcv1	NN	_	_	_
1271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1272	genotype	genotype	NN	_	_	_
1273	:	:	:	_	_	_
1274	PNPase	pnpase	NN	_	_	_
1275	mutant	mutant	JJ	_	_	_
1276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1277	genotype	genotype	NN	_	_	_
1278	:	:	:	_	_	_
1279	PurR-8myc	purr-8myc	NN	_	_	_
1280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1281	genotype	genotype	NN	_	_	_
1282	:	:	:	_	_	_
1283	RNase	rnase	NN	_	_	_
1284	II	ii	CD	_	_	_
1285	mutant	mutant	JJ	_	_	_
1286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1287	genotype	genotype	NN	_	_	_
1288	:	:	:	_	_	_
1289	RNase	rnase	NN	_	_	_
1290	R	r	NN	_	_	_
1291	mutant	mutant	JJ	_	_	_
1292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1293	genotype	genotype	NN	_	_	_
1294	:	:	:	_	_	_
1295	rne-3071	rne-3071	NN	_	_	_
1296	-LRB-	-lrb-	-LRB-	_	_	_
1297	ts	t	NNS	_	_	_
1298	-RRB-	-rrb-	-RRB-	_	_	_
1299	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1300	genotype	genotype	NN	_	_	_
1301	:	:	:	_	_	_
1302	rne	rne	NN	GEN	_	_
1303	wild-type	wild-type	JJ	_	_	_
1304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1305	genotype	genotype	NN	_	_	_
1306	:	:	:	_	_	_
1307	rng	rng	NN	GEN	_	_
1308	mutant	mutant	JJ	_	_	_
1309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1310	genotype	genotype	NN	_	_	_
1311	:	:	:	_	_	_
1312	rng	rng	NN	GEN	_	_
1313	wild-type	wild-type	JJ	_	_	_
1314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1315	genotype	genotype	NN	_	_	_
1316	:	:	:	_	_	_
1317	rpoC	rpoc	NN	GEN	_	_
1318	K370	k370	NN	_	_	_
1319	_	_	CD	_	_	_
1320	A396dup	a396dup	NN	_	_	_
1321	mutant	mutant	JJ	_	_	_
1322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1323	genotype	genotype	NN	_	_	_
1324	:	:	:	_	_	_
1325	rpoH-8myc	rpoh-8myc	NN	_	_	_
1326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1327	genotype	genotype	NN	_	_	_
1328	:	:	:	_	_	_
1329	rpoN	rpon	NN	GEN	_	_
1330	mutant	mutant	NN	_	_	_
1331	-LRB-	-lrb-	-LRB-	_	_	_
1332	EcJR-8	ecjr-8	NN	_	_	_
1333	-RRB-	-rrb-	-RRB-	_	_	_
1334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1335	genotype	genotype	NN	_	_	_
1336	:	:	:	_	_	_
1337	rpoS	rpos	NN	GEN	_	_
1338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1339	genotype	genotype	NN	_	_	_
1340	:	:	:	_	_	_
1341	rpoS	rpos	NN	GEN	_	_
1342	mutant	mutant	JJ	_	_	_
1343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1344	genotype	genotype	NN	_	_	_
1345	:	:	:	_	_	_
1346	SgrR	sgrr	NN	TF	_	_
1347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1348	genotype	genotype	NN	_	_	_
1349	:	:	:	_	_	_
1350	sgrS	sgrs	NN	GEN	_	_
1351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1352	genotype	genotype	NN	_	_	_
1353	:	:	:	_	_	_
1354	TolC	tolc	NN	_	_	_
1355	defective	defective	JJ	_	_	_
1356	-LRB-	-lrb-	-LRB-	_	_	_
1357	TolC	tolc	NN	_	_	_
1358	-	-	:	_	_	_
1359	-RRB-	-rrb-	-RRB-	_	_	_
1360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1361	genotype	genotype	NN	_	_	_
1362	:	:	:	_	_	_
1363	triclosan	triclosan	NN	_	_	_
1364	tolerant	tolerant	JJ	_	_	_
1365	mutant	mutant	JJ	_	_	_
1366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1367	genotype	genotype	NN	_	_	_
1368	:	:	:	_	_	_
1369	TrpR-8myc	trpr-8myc	NN	_	_	_
1370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1371	genotype	genotype	NN	_	_	_
1372	:	:	:	_	_	_
1373	tynA	tyna	NN	GEN	_	_
1374	-	-	:	_	_	_
1375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1376	genotype/varation	genotype/varation	NN	_	_	_
1377	:	:	:	_	_	_
1378	mutant	mutant	JJ	_	_	_
1379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1380	genotype/varation	genotype/varation	NN	_	_	_
1381	:	:	:	_	_	_
1382	wild-type	wild-type	JJ	_	_	_
1383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1384	genotype/variaion	genotype/variaion	NN	_	_	_
1385	:	:	:	_	_	_
1386	bla	bla	FW	_	_	_
1387	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1388	genotype/variaion	genotype/variaion	NN	_	_	_
1389	:	:	:	_	_	_
1390	lacZ	lacz	NN	GEN	_	_
1391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1392	genotype/variaion	genotype/variaion	NN	_	_	_
1393	:	:	:	_	_	_
1394	mMaple3	mmaple3	NN	_	_	_
1395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1396	genotype/variaion	genotype/variaion	NN	_	_	_
1397	:	:	:	_	_	_
1398	Mut	mut	NN	_	_	_
1399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1400	genotype/variaion	genotype/variaion	NN	_	_	_
1401	:	:	:	_	_	_
1402	neo	neo	NN	_	_	_
1403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1404	genotype/variaion	genotype/variaion	NN	_	_	_
1405	:	:	:	_	_	_
1406	phoA	phoa	NN	GEN	_	_
1407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1408	genotype/variaion	genotype/variaion	NN	_	_	_
1409	:	:	:	_	_	_
1410	WT	WT	NNP	_	_	_
1411	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1412	genotype/variaion	genotype/variaion	NN	_	_	_
1413	:	:	:	_	_	_
1414	WTKas	wtka	NNS	_	_	_
1415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1416	genotype/variation	genotype/variation	NN	_	_	_
1417	:	:	:	_	_	_
1418	42	42	CD	_	_	_
1419	deletions	deletion	NNS	_	_	_
1420	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1421	genotype/variation	genotype/variation	NN	_	_	_
1422	:	:	:	_	_	_
1423	42	42	CD	_	_	_
1424	deletions	deletion	NNS	_	_	_
1425	,	,	,	_	_	_
1426	ΔnusA	δnusa	NN	_	_	_
1427	*	*	SYM	_	_	_
1428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1429	genotype/variation	genotype/variation	NN	_	_	_
1430	:	:	:	_	_	_
1431	42	42	CD	_	_	_
1432	deletions	deletion	NNS	_	_	_
1433	,	,	,	_	_	_
1434	ΔnusG	δnusg	NN	_	_	_
1435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1436	genotype/variation	genotype/variation	NN	_	_	_
1437	:	:	:	_	_	_
1438	43	43	CD	_	_	_
1439	deletions	deletion	NNS	_	_	_
1440	,	,	,	_	_	_
1441	ΔnusA	δnusa	NN	_	_	_
1442	*	*	SYM	_	_	_
1443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1444	genotype/variation	genotype/variation	NN	_	_	_
1445	:	:	:	_	_	_
1446	43	43	CD	_	_	_
1447	deletions	deletion	NNS	_	_	_
1448	,	,	,	_	_	_
1449	ΔnusG	δnusg	NN	_	_	_
1450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1451	genotype/variation	genotype/variation	NN	_	_	_
1452	:	:	:	_	_	_
1453	AB1157	ab1157	NN	_	_	_
1454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1455	genotype/variation	genotype/variation	NN	_	_	_
1456	:	:	:	_	_	_
1457	AB1157	ab1157	NN	_	_	_
1458	deltamatP	deltamatp	NN	_	_	_
1459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1460	genotype/variation	genotype/variation	NN	_	_	_
1461	:	:	:	_	_	_
1462	AB1157	ab1157	NN	_	_	_
1463	matP-3xflag	matp-3xflag	NN	_	_	_
1464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1465	genotype/variation	genotype/variation	NN	_	_	_
1466	:	:	:	_	_	_
1467	AB1157	ab1157	NN	_	_	_
1468	mukB-3xflag	mukb-3xflag	NN	_	_	_
1469	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1470	genotype/variation	genotype/variation	NN	_	_	_
1471	:	:	:	_	_	_
1472	AB1157	ab1157	NN	_	_	_
1473	mukB-3xflag	mukb-3xflag	NN	_	_	_
1474	deltamatP	deltamatp	NN	_	_	_
1475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1476	genotype/variation	genotype/variation	NN	_	_	_
1477	:	:	:	_	_	_
1478	AB1157	ab1157	NN	_	_	_
1479	mukBDA-3xflag	mukbda-3xflag	NN	_	_	_
1480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1481	genotype/variation	genotype/variation	NN	_	_	_
1482	:	:	:	_	_	_
1483	AB1157	ab1157	NN	_	_	_
1484	mukBEQ-3xflag	mukbeq-3xflag	NN	_	_	_
1485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1486	genotype/variation	genotype/variation	NN	_	_	_
1487	:	:	:	_	_	_
1488	AB1157	ab1157	NN	_	_	_
1489	mukBEQ-3xflag	mukbeq-3xflag	NN	_	_	_
1490	deltamatP	deltamatp	NN	_	_	_
1491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1492	genotype/variation	genotype/variation	NN	_	_	_
1493	:	:	:	_	_	_
1494	Adaptive	adaptive	JJ	_	_	_
1495	mutant	mutant	JJ	_	_	_
1496	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1497	genotype/variation	genotype/variation	NN	_	_	_
1498	:	:	:	_	_	_
1499	adhE	adhe	NN	GEN	_	_
1500	mutant	mutant	JJ	_	_	_
1501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1502	genotype/variation	genotype/variation	NN	_	_	_
1503	:	:	:	_	_	_
1504	AR1	ar1	NN	_	_	_
1505	-	-	:	_	_	_
1506	/	/	:	_	_	_
1507	AR2	ar2	SYM	_	_	_
1508	-	-	:	_	_	_
1509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1510	genotype/variation	genotype/variation	NN	_	_	_
1511	:	:	:	_	_	_
1512	aspC	aspc	NN	GEN	_	_
1513	knockout	knockout	NN	_	_	_
1514	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1515	genotype/variation	genotype/variation	NN	_	_	_
1516	:	:	:	_	_	_
1517	coding	code	VBG	_	_	_
1518	for	for	IN	_	_	_
1519	QnrS1	qnrs1	NN	_	_	_
1520	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1521	genotype/variation	genotype/variation	NN	_	_	_
1522	:	:	:	_	_	_
1523	Combined	combine	VBN	_	_	_
1524	input	input	NN	_	_	_
1525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1526	genotype/variation	genotype/variation	NN	_	_	_
1527	:	:	:	_	_	_
1528	cpxA	cpxa	NN	GEN	_	_
1529	mutant	mutant	JJ	_	_	_
1530	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1531	genotype/variation	genotype/variation	NN	_	_	_
1532	:	:	:	_	_	_
1533	cra-8myc-tagged	cra-8myc-tagged	JJ	_	_	_
1534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1535	genotype/variation	genotype/variation	NN	_	_	_
1536	:	:	:	_	_	_
1537	cra	cra	NN	GEN	_	_
1538	KO	ko	NN	_	_	_
1539	;	;	:	_	_	_
1540	BW25113	bw25113	NN	_	_	_
1541	Dcra	dcra	NN	_	_	_
1542	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1543	genotype/variation	genotype/variation	NN	_	_	_
1544	:	:	:	_	_	_
1545	cysA	cysa	NN	GEN	_	_
1546	knockout	knockout	NN	_	_	_
1547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1548	genotype/variation	genotype/variation	NN	_	_	_
1549	:	:	:	_	_	_
1550	cysG	cysg	NN	GEN	_	_
1551	knockout	knockout	NN	_	_	_
1552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1553	genotype/variation	genotype/variation	NN	_	_	_
1554	:	:	:	_	_	_
1555	cysH	cysh	NN	GEN	_	_
1556	knockout	knockout	NN	_	_	_
1557	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1558	genotype/variation	genotype/variation	NN	_	_	_
1559	:	:	:	_	_	_
1560	cysQ	cysq	NN	GEN	_	_
1561	mutant	mutant	JJ	_	_	_
1562	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1563	genotype/variation	genotype/variation	NN	_	_	_
1564	:	:	:	_	_	_
1565	dcd	dcd	NN	GEN	_	_
1566	knockout	knockout	JJ	_	_	_
1567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1568	genotype/variation	genotype/variation	NN	_	_	_
1569	:	:	:	_	_	_
1570	delta	delta	NN	_	_	_
1571	_	_	SYM	_	_	_
1572	cra	cra	FW	GEN	_	_
1573	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1574	genotype/variation	genotype/variation	NN	_	_	_
1575	:	:	:	_	_	_
1576	-LCB-	-lcb-	-LRB-	_	_	_
1577	delta	delta	NN	_	_	_
1578	-RCB-	-rcb-	-RRB-	_	_	_
1579	cspABCEG	cspabceg	NN	_	_	_
1580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1581	genotype/variation	genotype/variation	NN	_	_	_
1582	:	:	:	_	_	_
1583	-LCB-	-lcb-	-LRB-	_	_	_
1584	delta	delta	NN	_	_	_
1585	-RCB-	-rcb-	-RRB-	_	_	_
1586	cspABEG	cspabeg	NN	_	_	_
1587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1588	genotype/variation	genotype/variation	NN	_	_	_
1589	:	:	:	_	_	_
1590	-LCB-	-lcb-	-LRB-	_	_	_
1591	delta	delta	NN	_	_	_
1592	-RCB-	-rcb-	-RRB-	_	_	_
1593	cspBG	cspbg	NN	_	_	_
1594	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1595	genotype/variation	genotype/variation	NN	_	_	_
1596	:	:	:	_	_	_
1597	delta-gadE	delta-gade	NN	_	_	_
1598	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1599	genotype/variation	genotype/variation	NN	_	_	_
1600	:	:	:	_	_	_
1601	delta-gadW	delta-gadw	NN	_	_	_
1602	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1603	genotype/variation	genotype/variation	NN	_	_	_
1604	:	:	:	_	_	_
1605	delta-gadX	delta-gadx	NN	_	_	_
1606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1607	genotype/variation	genotype/variation	NN	_	_	_
1608	:	:	:	_	_	_
1609	-LCB-	-lcb-	-LRB-	_	_	_
1610	delta	delta	NN	_	_	_
1611	-RCB-	-rcb-	-RRB-	_	_	_
1612	lacZ	lacz	NN	GEN	_	_
1613	,	,	,	_	_	_
1614	-LCB-	-lcb-	-LRB-	_	_	_
1615	delta	delta	NN	_	_	_
1616	-RCB-	-rcb-	-RRB-	_	_	_
1617	tonB	tonb	NN	GEN	_	_
1618	,	,	,	_	_	_
1619	-LCB-	-lcb-	-LRB-	_	_	_
1620	delta	delta	NN	_	_	_
1621	-RCB-	-rcb-	-RRB-	_	_	_
1622	feoA	feoa	NN	GEN	_	_
1623	,	,	,	_	_	_
1624	-LCB-	-lcb-	-LRB-	_	_	_
1625	delta	delta	NN	_	_	_
1626	-RCB-	-rcb-	-RRB-	_	_	_
1627	zupT	zupt	NN	GEN	_	_
1628	K12	k12	NN	_	_	_
1629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1630	genotype/variation	genotype/variation	NN	_	_	_
1631	:	:	:	_	_	_
1632	delta-oxyR	delta-oxyr	NN	_	_	_
1633	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1634	genotype/variation	genotype/variation	NN	_	_	_
1635	:	:	:	_	_	_
1636	-LCB-	-lcb-	-LRB-	_	_	_
1637	delta	delta	NN	_	_	_
1638	-RCB-	-rcb-	-RRB-	_	_	_
1639	perC	perc	NN	_	_	_
1640	:	:	:	_	_	_
1641	:	:	:	_	_	_
1642	kanR	kanr	NN	_	_	_
1643	,	,	,	_	_	_
1644	coisogenic	coisogenic	JJ	_	_	_
1645	to	to	TO	_	_	_
1646	WT	wt	JJ	_	_	_
1647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1648	genotype/variation	genotype/variation	NN	_	_	_
1649	:	:	:	_	_	_
1650	delta	delta	NN	_	_	_
1651	ptsN	ptsn	NN	GEN	_	_
1652	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1653	genotype/variation	genotype/variation	NN	_	_	_
1654	:	:	:	_	_	_
1655	-LCB-	-lcb-	-LRB-	_	_	_
1656	delta	delta	NN	_	_	_
1657	-RCB-	-rcb-	-RRB-	_	_	_
1658	rnr	rnr	NN	GEN	_	_
1659	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1660	genotype/variation	genotype/variation	NN	_	_	_
1661	:	:	:	_	_	_
1662	delta-soxR	delta-soxr	NN	_	_	_
1663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1664	genotype/variation	genotype/variation	NN	_	_	_
1665	:	:	:	_	_	_
1666	delta-soxS	delta-soxs	NN	_	_	_
1667	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1668	genotype/variation	genotype/variation	NN	_	_	_
1669	:	:	:	_	_	_
1670	-LCB-	-lcb-	-LRB-	_	_	_
1671	delta	delta	NN	_	_	_
1672	-RCB-	-rcb-	-RRB-	_	_	_
1673	tonB	tonb	NN	GEN	_	_
1674	,	,	,	_	_	_
1675	-LCB-	-lcb-	-LRB-	_	_	_
1676	delta	delta	NN	_	_	_
1677	-RCB-	-rcb-	-RRB-	_	_	_
1678	feoA	feoa	NN	GEN	_	_
1679	,	,	,	_	_	_
1680	-LCB-	-lcb-	-LRB-	_	_	_
1681	delta	delta	NN	_	_	_
1682	-RCB-	-rcb-	-RRB-	_	_	_
1683	zupT	zupt	NN	GEN	_	_
1684	K12	k12	NN	_	_	_
1685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1686	genotype/variation	genotype/variation	NN	_	_	_
1687	:	:	:	_	_	_
1688	DH1DilvE	dh1dilve	NN	_	_	_
1689	:	:	:	_	_	_
1690	:	:	:	_	_	_
1691	-LRB-	-lrb-	-LRB-	_	_	_
1692	dsred.T3-cat	dsred.t3-cat	NN	_	_	_
1693	-RRB-	-rrb-	-RRB-	_	_	_
1694	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1695	genotype/variation	genotype/variation	NN	_	_	_
1696	:	:	:	_	_	_
1697	DH1DleuB	dh1dleub	NN	_	_	_
1698	:	:	:	_	_	_
1699	:	:	:	_	_	_
1700	-LRB-	-lrb-	-LRB-	_	_	_
1701	gfpuv5-Kmr	gfpuv5-kmr	NN	_	_	_
1702	-RRB-	-rrb-	-RRB-	_	_	_
1703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1704	genotype/variation	genotype/variation	NN	_	_	_
1705	:	:	:	_	_	_
1706	DH1	dh1	NN	_	_	_
1707	-LRB-	-lrb-	-LRB-	_	_	_
1708	GB	gb	NN	_	_	_
1709	:	:	:	_	_	_
1710	AP012030	ap012030	NN	_	_	_
1711	-RRB-	-rrb-	-RRB-	_	_	_
1712	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1713	genotype/variation	genotype/variation	NN	_	_	_
1714	:	:	:	_	_	_
1715	dnaJ	dnaj	NN	GEN	_	_
1716	mutant	mutant	JJ	_	_	_
1717	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1718	genotype/variation	genotype/variation	NN	_	_	_
1719	:	:	:	_	_	_
1720	DnaK	dnak	NN	_	_	_
1721	deletant	deletant	JJ	_	_	_
1722	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1723	genotype/variation	genotype/variation	NN	_	_	_
1724	:	:	:	_	_	_
1725	EDL	edl	NN	_	_	_
1726	933	933	CD	_	_	_
1727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1728	genotype/variation	genotype/variation	NN	_	_	_
1729	:	:	:	_	_	_
1730	empty	empty	JJ	_	_	_
1731	vector	vector	NN	_	_	_
1732	-LRB-	-lrb-	-LRB-	_	_	_
1733	pCA24N	pca24n	NN	_	_	_
1734	-RRB-	-rrb-	-RRB-	_	_	_
1735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1736	genotype/variation	genotype/variation	NN	_	_	_
1737	:	:	:	_	_	_
1738	entF	entf	NN	GEN	_	_
1739	knockout	knockout	NN	_	_	_
1740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1741	genotype/variation	genotype/variation	NN	_	_	_
1742	:	:	:	_	_	_
1743	expressing	express	VBG	_	_	_
1744	pFlagRhlBP238L	pflagrhlbp238l	NN	_	_	_
1745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1746	genotype/variation	genotype/variation	NN	_	_	_
1747	:	:	:	_	_	_
1748	expressing	express	VBG	_	_	_
1749	pFlagRhlBwt	pflagrhlbwt	NN	_	_	_
1750	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1751	genotype/variation	genotype/variation	NN	_	_	_
1752	:	:	:	_	_	_
1753	fadR	fadr	NN	GEN	_	_
1754	knockout	knockout	NN	_	_	_
1755	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1756	genotype/variation	genotype/variation	NN	_	_	_
1757	:	:	:	_	_	_
1758	fepA	fepa	NN	GEN	_	_
1759	knockout	knockout	JJ	_	_	_
1760	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1761	genotype/variation	genotype/variation	NN	_	_	_
1762	:	:	:	_	_	_
1763	flhD	flhd	NN	GEN	_	_
1764	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1765	genotype/variation	genotype/variation	NN	_	_	_
1766	:	:	:	_	_	_
1767	fliY	fliy	NN	_	_	_
1768	knockout	knockout	NN	_	_	_
1769	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1770	genotype/variation	genotype/variation	NN	_	_	_
1771	:	:	:	_	_	_
1772	fur-8myc	fur-8myc	JJ	_	_	_
1773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1774	genotype/variation	genotype/variation	NN	_	_	_
1775	:	:	:	_	_	_
1776	fur-knockout	fur-knockout	JJ	_	_	_
1777	mutant	mutant	JJ	_	_	_
1778	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1779	genotype/variation	genotype/variation	NN	_	_	_
1780	:	:	:	_	_	_
1781	gabT	gabt	NN	GEN	_	_
1782	knockout	knockout	NN	_	_	_
1783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1784	genotype/variation	genotype/variation	NN	_	_	_
1785	:	:	:	_	_	_
1786	galE	gale	NN	GEN	_	_
1787	knockout	knockout	JJ	_	_	_
1788	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1789	genotype/variation	genotype/variation	NN	_	_	_
1790	:	:	:	_	_	_
1791	galT	galt	NN	GEN	_	_
1792	mutant	mutant	JJ	_	_	_
1793	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1794	genotype/variation	genotype/variation	NN	_	_	_
1795	:	:	:	_	_	_
1796	gcvT	gcvt	NN	GEN	_	_
1797	mutant	mutant	JJ	_	_	_
1798	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1799	genotype/variation	genotype/variation	NN	_	_	_
1800	:	:	:	_	_	_
1801	harboring	harbor	VBG	_	_	_
1802	ArcA-8myc	arca-8myc	JJ	_	_	_
1803	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1804	genotype/variation	genotype/variation	NN	_	_	_
1805	:	:	:	_	_	_
1806	harboring	harbor	VBG	_	_	_
1807	Fnr-8myc	fnr-8myc	JJ	_	_	_
1808	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1809	genotype/variation	genotype/variation	NN	_	_	_
1810	:	:	:	_	_	_
1811	hfq	hfq	NN	GEN	_	_
1812	mutant	mutant	JJ	_	_	_
1813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1814	genotype/variation	genotype/variation	NN	_	_	_
1815	:	:	:	_	_	_
1816	Irp	irp	NN	_	_	_
1817	mutant	mutant	JJ	_	_	_
1818	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1819	genotype/variation	genotype/variation	NN	_	_	_
1820	:	:	:	_	_	_
1821	K100Q	k100q	NN	_	_	_
1822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1823	genotype/variation	genotype/variation	NN	_	_	_
1824	:	:	:	_	_	_
1825	K100R	k100r	NN	_	_	_
1826	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1827	genotype/variation	genotype/variation	NN	_	_	_
1828	:	:	:	_	_	_
1829	K-12	k-12	NN	_	_	_
1830	delta-rnr	delta-rnr	NN	_	_	_
1831	mutant	mutant	NN	_	_	_
1832	-LRB-	-lrb-	-LRB-	_	_	_
1833	JW5741-1	jw5741-1	NN	_	_	_
1834	-RRB-	-rrb-	-RRB-	_	_	_
1835	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1836	genotype/variation	genotype/variation	NN	_	_	_
1837	:	:	:	_	_	_
1838	K-12	k-12	NN	_	_	_
1839	wild	wild	JJ	_	_	_
1840	type	type	NN	_	_	_
1841	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1842	genotype/variation	genotype/variation	NN	_	_	_
1843	:	:	:	_	_	_
1844	kefB	kefb	NN	GEN	_	_
1845	knockout	knockout	NN	_	_	_
1846	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1847	genotype/variation	genotype/variation	NN	_	_	_
1848	:	:	:	_	_	_
1849	khc	khc	NN	_	_	_
1850	knockout	knockout	NN	_	_	_
1851	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1852	genotype/variation	genotype/variation	NN	_	_	_
1853	:	:	:	_	_	_
1854	lacA	laca	NN	GEN	_	_
1855	knockout	knockout	JJ	_	_	_
1856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1857	genotype/variation	genotype/variation	NN	_	_	_
1858	:	:	:	_	_	_
1859	lacking	lack	VBG	_	_	_
1860	the	the	DT	_	_	_
1861	small	small	JJ	_	_	_
1862	RNA	rna	NN	_	_	_
1863	RyhB	ryhb	NN	_	_	_
1864	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1865	genotype/variation	genotype/variation	NN	_	_	_
1866	:	:	:	_	_	_
1867	lacking	lack	VBG	_	_	_
1868	the	the	DT	_	_	_
1869	transcription	transcription	NN	_	_	_
1870	factor	factor	NN	_	_	_
1871	Fur	Fur	NNP	TF	_	_
1872	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1873	genotype/variation	genotype/variation	NN	_	_	_
1874	:	:	:	_	_	_
1875	lacking	lack	VBG	_	_	_
1876	the	the	DT	_	_	_
1877	transcription	transcription	NN	_	_	_
1878	factor	factor	NN	_	_	_
1879	Fur	Fur	NNP	TF	_	_
1880	and	and	CC	_	_	_
1881	the	the	DT	_	_	_
1882	small	small	JJ	_	_	_
1883	RNA	rna	NN	_	_	_
1884	RyhB	ryhb	NN	_	_	_
1885	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1886	genotype/variation	genotype/variation	NN	_	_	_
1887	:	:	:	_	_	_
1888	lplA	lpla	NN	GEN	_	_
1889	knockout	knockout	NN	_	_	_
1890	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1891	genotype/variation	genotype/variation	NN	_	_	_
1892	:	:	:	_	_	_
1893	LuxS	luxs	NN	_	_	_
1894	mutant	mutant	JJ	_	_	_
1895	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1896	genotype/variation	genotype/variation	NN	_	_	_
1897	:	:	:	_	_	_
1898	marR	marr	NN	GEN	_	_
1899	deletion	deletion	NN	_	_	_
1900	and	and	CC	_	_	_
1901	coding	code	VBG	_	_	_
1902	for	for	IN	_	_	_
1903	QnrS1	qnrs1	NN	_	_	_
1904	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1905	genotype/variation	genotype/variation	NN	_	_	_
1906	:	:	:	_	_	_
1907	MC4100	mc4100	NN	_	_	_
1908	∆	∆	NN	_	_	_
1909	tig	tig	NN	GEN	_	_
1910	:	:	:	_	_	_
1911	:	:	:	_	_	_
1912	kan	kan	FW	_	_	_
1913	pTig-TEV-Avi	ptig-tev-avi	FW	_	_	_
1914	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1915	genotype/variation	genotype/variation	NN	_	_	_
1916	:	:	:	_	_	_
1917	MG1655star	mg1655star	NN	_	_	_
1918	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1919	genotype/variation	genotype/variation	NN	_	_	_
1920	:	:	:	_	_	_
1921	mgtA	mgta	NN	GEN	_	_
1922	knockout	knockout	NN	_	_	_
1923	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1924	genotype/variation	genotype/variation	NN	_	_	_
1925	:	:	:	_	_	_
1926	mhpD	mhpd	NN	GEN	_	_
1927	knockout	knockout	NN	_	_	_
1928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1929	genotype/variation	genotype/variation	NN	_	_	_
1930	:	:	:	_	_	_
1931	mntR	mntr	NN	GEN	_	_
1932	KO	ko	NN	_	_	_
1933	;	;	:	_	_	_
1934	BW25113	bw25113	NN	_	_	_
1935	DmntR	dmntr	NN	_	_	_
1936	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1937	genotype/variation	genotype/variation	NN	_	_	_
1938	:	:	:	_	_	_
1939	mqsR/pBS	mqsr/pbs	NN	_	_	_
1940	-LRB-	-lrb-	-LRB-	_	_	_
1941	Kan	Kan	NNP	_	_	_
1942	-RRB-	-rrb-	-RRB-	_	_	_
1943	-	-	:	_	_	_
1944	mqsR	mqsr	NN	GEN	_	_
1945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1946	genotype/variation	genotype/variation	NN	_	_	_
1947	:	:	:	_	_	_
1948	mqsR/pBS	mqsr/pbs	NN	_	_	_
1949	-LRB-	-lrb-	-LRB-	_	_	_
1950	Kan	Kan	NNP	_	_	_
1951	-RRB-	-rrb-	-RRB-	_	_	_
1952	-	-	:	_	_	_
1953	mqsR	mqsr	NN	GEN	_	_
1954	2-1	2-1	CD	_	_	_
1955	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1956	genotype/variation	genotype/variation	NN	_	_	_
1957	:	:	:	_	_	_
1958	mutant	mutant	JJ	_	_	_
1959	M.HpyAVIB	m.hpyavib	NN	_	_	_
1960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1961	genotype/variation	genotype/variation	NN	_	_	_
1962	:	:	:	_	_	_
1963	nac	nac	NN	GEN	_	_
1964	KO	ko	NN	_	_	_
1965	;	;	:	_	_	_
1966	BW25113	bw25113	NN	_	_	_
1967	Dnac	dnac	NN	_	_	_
1968	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1969	genotype/variation	genotype/variation	NN	_	_	_
1970	:	:	:	_	_	_
1971	null	null	JJ	_	_	_
1972	polyphosphate	polyphosphate	NN	_	_	_
1973	metabolism	metabolism	NN	_	_	_
1974	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1975	genotype/variation	genotype/variation	NN	_	_	_
1976	:	:	:	_	_	_
1977	overexpression	overexpression	NN	_	_	_
1978	of	of	IN	_	_	_
1979	arT	art	NN	_	_	_
1980	-LRB-	-lrb-	-LRB-	_	_	_
1981	pCA24N	pca24n	NN	_	_	_
1982	_	_	CD	_	_	_
1983	arT	art	NN	_	_	_
1984	-RRB-	-rrb-	-RRB-	_	_	_
1985	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1986	genotype/variation	genotype/variation	NN	_	_	_
1987	:	:	:	_	_	_
1988	overexpression	overexpression	NN	_	_	_
1989	of	of	IN	_	_	_
1990	dosP	dosp	NN	GEN	_	_
1991	-LRB-	-lrb-	-LRB-	_	_	_
1992	pCA24N	pca24n	NN	_	_	_
1993	_	_	CD	_	_	_
1994	dosP	dosp	NN	GEN	_	_
1995	-RRB-	-rrb-	-RRB-	_	_	_
1996	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1997	genotype/variation	genotype/variation	NN	_	_	_
1998	:	:	:	_	_	_
1999	overexpression	overexpression	NN	_	_	_
2000	of	of	IN	_	_	_
2001	empty	empty	JJ	_	_	_
2002	vector	vector	NN	_	_	_
2003	-LRB-	-lrb-	-LRB-	_	_	_
2004	pCA24N	pca24n	NN	_	_	_
2005	-RRB-	-rrb-	-RRB-	_	_	_
2006	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2007	genotype/variation	genotype/variation	NN	_	_	_
2008	:	:	:	_	_	_
2009	oxyR-8myc-tagged	oxyr-8myc-tagged	JJ	_	_	_
2010	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2011	genotype/variation	genotype/variation	NN	_	_	_
2012	:	:	:	_	_	_
2013	PEN205	pen205	NN	_	_	_
2014	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2015	genotype/variation	genotype/variation	NN	_	_	_
2016	:	:	:	_	_	_
2017	pFlag-only	pflag-only	NN	_	_	_
2018	control	control	NN	_	_	_
2019	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2020	genotype/variation	genotype/variation	NN	_	_	_
2021	:	:	:	_	_	_
2022	pgi	pgi	NN	GEN	_	_
2023	mutant	mutant	JJ	_	_	_
2024	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2025	genotype/variation	genotype/variation	NN	_	_	_
2026	:	:	:	_	_	_
2027	PhoB	phob	NN	TF	_	_
2028	_	_	CD	_	_	_
2029	FLAG	flag	NN	_	_	_
2030	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2031	genotype/variation	genotype/variation	NN	_	_	_
2032	:	:	:	_	_	_
2033	PhoB	phob	NN	TF	_	_
2034	knock-out	knock-out	JJ	_	_	_
2035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2036	genotype/variation	genotype/variation	NN	_	_	_
2037	:	:	:	_	_	_
2038	polyphosphate	polyphosphate	NN	_	_	_
2039	accumulation	accumulation	NN	_	_	_
2040	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2041	genotype/variation	genotype/variation	NN	_	_	_
2042	:	:	:	_	_	_
2043	polyphosphate	polyphosphate	NN	_	_	_
2044	depleted	deplete	VBN	_	_	_
2045	levels	level	NNS	_	_	_
2046	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
2047	genotype/variation	genotype/variation	NN	_	_	_
2048	:	:	:	_	_	_
2049	ppk	ppk	NN	GEN	_	_
2050	knockout	knockout	JJ	_	_	_
2051	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2052	genotype/variation	genotype/variation	NN	_	_	_
2053	:	:	:	_	_	_
2054	putP	putp	NN	GEN	_	_
2055	knockout	knockout	NN	_	_	_
2056	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2057	genotype/variation	genotype/variation	NN	_	_	_
2058	:	:	:	_	_	_
2059	rfbA	rfba	NN	GEN	_	_
2060	knockout	knockout	NN	_	_	_
2061	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2062	genotype/variation	genotype/variation	NN	_	_	_
2063	:	:	:	_	_	_
2064	rnc	rnc	SYM	GEN	_	_
2065	-	-	:	_	_	_
2066	deletion	deletion	NN	_	_	_
2067	mutant	mutant	JJ	_	_	_
2068	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2069	genotype/variation	genotype/variation	NN	_	_	_
2070	:	:	:	_	_	_
2071	sdhA	sdha	NN	GEN	_	_
2072	deletion	deletion	NN	_	_	_
2073	mutant	mutant	JJ	_	_	_
2074	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2075	genotype/variation	genotype/variation	NN	_	_	_
2076	:	:	:	_	_	_
2077	sdhC	sdhc	NN	GEN	_	_
2078	knockout	knockout	JJ	_	_	_
2079	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2080	genotype/variation	genotype/variation	NN	_	_	_
2081	:	:	:	_	_	_
2082	Ser83Leu	ser83leu	NN	_	_	_
2083	substitution	substitution	NN	_	_	_
2084	in	in	IN	_	_	_
2085	GyrA	gyra	NN	_	_	_
2086	and	and	CC	_	_	_
2087	coding	code	VBG	_	_	_
2088	for	for	IN	_	_	_
2089	QnrS1	qnrs1	NN	_	_	_
2090	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2091	genotype/variation	genotype/variation	NN	_	_	_
2092	:	:	:	_	_	_
2093	soxR-8myc-tagged	soxr-8myc-tagged	JJ	_	_	_
2094	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2095	genotype/variation	genotype/variation	NN	_	_	_
2096	:	:	:	_	_	_
2097	soxS-8myc-tagged	soxs-8myc-tagged	JJ	_	_	_
2098	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2099	genotype/variation	genotype/variation	NN	_	_	_
2100	:	:	:	_	_	_
2101	trpD	trpd	NN	GEN	_	_
2102	knockout	knockout	NN	_	_	_
2103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2104	genotype/variation	genotype/variation	NN	_	_	_
2105	:	:	:	_	_	_
2106	ugpC	ugpc	NN	GEN	_	_
2107	knockout	knockout	NN	_	_	_
2108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2109	genotype/variation	genotype/variation	NN	_	_	_
2110	:	:	:	_	_	_
2111	W3110	w3110	NN	_	_	_
2112	rpoC-6xHis	rpoc-6xhis	NN	_	_	_
2113	:	:	:	_	_	_
2114	:	:	:	_	_	_
2115	kan	kan	FW	_	_	_
2116	gal490	gal490	FW	_	_	_
2117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2118	genotype/variation	genotype/variation	NN	_	_	_
2119	:	:	:	_	_	_
2120	W3110	w3110	NN	_	_	_
2121	rpoC-6xHis	rpoc-6xhis	NN	_	_	_
2122	:	:	:	_	_	_
2123	:	:	:	_	_	_
2124	kan	kan	NN	_	_	_
2125	greA	grea	NN	GEN	_	_
2126	:	:	:	_	_	_
2127	:	:	:	_	_	_
2128	tet	tet	NN	_	_	_
2129	,	,	,	_	_	_
2130	greB	greb	NN	GEN	_	_
2131	:	:	:	_	_	_
2132	:	:	:	_	_	_
2133	amp	amp	NN	_	_	_
2134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2135	genotype/variation	genotype/variation	NN	_	_	_
2136	:	:	:	_	_	_
2137	wild	wild	JJ	_	_	_
2138	type	type	NN	_	_	_
2139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2140	genotype/variation	genotype/variation	NN	_	_	_
2141	:	:	:	_	_	_
2142	wild-type	wild-type	JJ	_	_	_
2143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2144	genotype/variation	genotype/variation	NN	_	_	_
2145	:	:	:	_	_	_
2146	Wild-type	wild-type	JJ	_	_	_
2147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2148	genotype/variation	genotype/variation	NN	_	_	_
2149	:	:	:	_	_	_
2150	wild	wild	JJ	_	_	_
2151	type	type	NN	_	_	_
2152	-LRB-	-lrb-	-LRB-	_	_	_
2153	control	control	NN	_	_	_
2154	-RRB-	-rrb-	-RRB-	_	_	_
2155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2156	genotype/variation	genotype/variation	NN	_	_	_
2157	:	:	:	_	_	_
2158	wild	wild	JJ	_	_	_
2159	type	type	NN	_	_	_
2160	;	;	:	_	_	_
2161	MG1655	mg1655	NN	_	_	_
2162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2163	genotype/variation	genotype/variation	NN	_	_	_
2164	:	:	:	_	_	_
2165	wild	wild	JJ	_	_	_
2166	type	type	NN	_	_	_
2167	M.HpyAVIB	m.hpyavib	NN	_	_	_
2168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2169	genotype/variation	genotype/variation	NN	_	_	_
2170	:	:	:	_	_	_
2171	Wild	Wild	NNP	_	_	_
2172	type	type	NN	_	_	_
2173	strain	strain	NN	_	_	_
2174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2175	genotype/variation	genotype/variation	NN	_	_	_
2176	:	:	:	_	_	_
2177	WT	WT	NNP	_	_	_
2178	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2179	genotype/variation	genotype/variation	NN	_	_	_
2180	:	:	:	_	_	_
2181	wzc	wzc	NN	GEN	_	_
2182	knockout	knockout	NN	_	_	_
2183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2184	genotype/variation	genotype/variation	NN	_	_	_
2185	:	:	:	_	_	_
2186	ydcR	ydcr	NN	GEN	_	_
2187	-LRB-	-lrb-	-LRB-	_	_	_
2188	b1439	b1439	NN	_	_	_
2189	-RRB-	-rrb-	-RRB-	_	_	_
2190	MUTANT	mutant	JJ	_	_	_
2191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2192	genotype/variation	genotype/variation	NN	_	_	_
2193	:	:	:	_	_	_
2194	yghD	yghd	NN	GEN	_	_
2195	knockout	knockout	NN	_	_	_
2196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2197	genotype/variation	genotype/variation	NN	_	_	_
2198	:	:	:	_	_	_
2199	yjiR	yjir	NN	GEN	_	_
2200	-LRB-	-lrb-	-LRB-	_	_	_
2201	b4340	b4340	NN	_	_	_
2202	-RRB-	-rrb-	-RRB-	_	_	_
2203	MUTANT	mutant	JJ	_	_	_
2204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2205	genotype/variation	genotype/variation	NN	_	_	_
2206	:	:	:	_	_	_
2207	ΔarcA	δarca	NN	_	_	_
2208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2209	genotype/variation	genotype/variation	NN	_	_	_
2210	:	:	:	_	_	_
2211	Δfnr	Δfnr	NNP	_	_	_
2212	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2213	genotype/variation	genotype/variation	NN	_	_	_
2214	:	:	:	_	_	_
2215	Δfur	Δfur	NNP	_	_	_
2216	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2217	genotype/variation	genotype/variation	NN	_	_	_
2218	:	:	:	_	_	_
2219	Δhns	δhns	NNS	_	_	_
2220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2221	genotype/variation	genotype/variation	NN	_	_	_
2222	:	:	:	_	_	_
2223	ΔmqsRA	δmqsra	NN	_	_	_
2224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2225	genotype/variation	genotype/variation	NN	_	_	_
2226	:	:	:	_	_	_
2227	Δrac	Δrac	NNP	_	_	_
2228	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2229	genotype/variation	genotype/variation	NN	_	_	_
2230	:	:	:	_	_	_
2231	Δrac	Δrac	NNP	_	_	_
2232	ΔnusG	ΔnusG	NNP	_	_	_
2233	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2234	genotype/variation	genotype/variation	NN	_	_	_
2235	:	:	:	_	_	_
2236	σ70	σ70	NN	_	_	_
2237	mutation	mutation	NN	_	_	_
2238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2239	genotype	genotype	NN	_	_	_
2240	:	:	:	_	_	_
2241	wildtype	wildtype	JJ	_	_	_
2242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2243	genotype	genotype	NN	_	_	_
2244	:	:	:	_	_	_
2245	wild	wild	JJ	_	_	_
2246	type	type	NN	_	_	_
2247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2248	genotype	genotype	NN	_	_	_
2249	:	:	:	_	_	_
2250	wild	wild	JJ	_	_	_
2251	_	_	NN	_	_	_
2252	type	type	NN	_	_	_
2253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2254	genotype	genotype	NN	_	_	_
2255	:	:	:	_	_	_
2256	wild-type	wild-type	JJ	_	_	_
2257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2258	genotype	genotype	NN	_	_	_
2259	:	:	:	_	_	_
2260	Wildtype	wildtype	JJ	_	_	_
2261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2262	genotype	genotype	NN	_	_	_
2263	:	:	:	_	_	_
2264	Wild-type	wild-type	JJ	_	_	_
2265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2266	genotype	genotype	NN	_	_	_
2267	:	:	:	_	_	_
2268	Wild	Wild	NNP	_	_	_
2269	Type	type	NN	_	_	_
2270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2271	genotype	genotype	NN	_	_	_
2272	:	:	:	_	_	_
2273	wild	wild	JJ	_	_	_
2274	type	type	NN	_	_	_
2275	IrrE	irre	NN	_	_	_
2276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2277	genotype	genotype	NN	_	_	_
2278	:	:	:	_	_	_
2279	Wild-type	wild-type	JJ	_	_	_
2280	strain	strain	NN	_	_	_
2281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2282	genotype	genotype	NN	_	_	_
2283	:	:	:	_	_	_
2284	Wildtype	wildtype	NN	_	_	_
2285	with	with	IN	_	_	_
2286	vector	vector	NN	_	_	_
2287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2288	genotype	genotype	NN	_	_	_
2289	:	:	:	_	_	_
2290	wt	wt	JJ	_	_	_
2291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2292	genotype	genotype	NN	_	_	_
2293	:	:	:	_	_	_
2294	WT	WT	NNP	_	_	_
2295	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2296	genotype	genotype	NN	_	_	_
2297	:	:	:	_	_	_
2298	yajL	yajl	NN	GEN	_	_
2299	mutant	mutant	JJ	_	_	_
2300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2301	genotype	genotype	NN	_	_	_
2302	:	:	:	_	_	_
2303	ybjN	ybjn	NN	GEN	_	_
2304	mutant	mutant	JJ	_	_	_
2305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2306	genotype	genotype	NN	_	_	_
2307	:	:	:	_	_	_
2308	ybjN	ybjn	NN	GEN	_	_
2309	over-expression	over-expression	NN	_	_	_
2310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2311	genotype	genotype	NN	_	_	_
2312	:	:	:	_	_	_
2313	ΔbolA	δbola	NN	_	_	_
2314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2315	genotype	genotype	NN	_	_	_
2316	:	:	:	_	_	_
2317	ΔrpoN	δrpon	NN	_	_	_
2318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2319	genotype	genotype	NN	_	_	_
2320	:	:	:	_	_	_
2321	ΔrpoS	δrpos	NN	_	_	_
2322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2323	genotype	genotype	NN	_	_	_
2324	:	:	:	_	_	_
2325	ΔseqA	δseqa	NN	_	_	_
2326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2327	genotype	genotype	NN	_	_	_
2328	:	:	:	_	_	_
2329	Δ	δ	NN	_	_	_
2330	-LRB-	-lrb-	-LRB-	_	_	_
2331	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
2332	-RRB-	-rrb-	-RRB-	_	_	_
2333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2334	genotype	genotype	NN	_	_	_
2335	:	:	:	_	_	_
2336	Δ	δ	NN	_	_	_
2337	-LRB-	-lrb-	-LRB-	_	_	_
2338	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
2339	-RRB-	-rrb-	-RRB-	_	_	_
2340	ΔleuO	δleuo	NN	_	_	_
2341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2342	genotype	genotype	NN	_	_	_
2343	:	:	:	_	_	_
2344	Δ	δ	NN	_	_	_
2345	-LRB-	-lrb-	-LRB-	_	_	_
2346	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
2347	-RRB-	-rrb-	-RRB-	_	_	_
2348	ΔrcsB	δrcsb	NN	_	_	_
2349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2350	genotyp/variation	genotyp/variation	NN	_	_	_
2351	:	:	:	_	_	_
2352	deltacrp	deltacrp	JJ	_	_	_
2353	JW5702-4	jw5702-4	NN	_	_	_
2354	background	background	NN	_	_	_
2355	with	with	IN	_	_	_
2356	a	a	DT	_	_	_
2357	K100Q	k100q	NN	_	_	_
2358	mutant	mutant	NN	_	_	_
2359	of	of	IN	_	_	_
2360	CRP	crp	NN	TF	_	_
2361	-LRB-	-lrb-	-LRB-	_	_	_
2362	CRP	crp	NN	TF	_	_
2363	Q	Q	NNP	_	_	_
2364	-RRB-	-rrb-	-RRB-	_	_	_
2365	inserted	insert	VBN	_	_	_
2366	into	into	IN	_	_	_
2367	paaH	paah	NN	GEN	_	_
2368	gene	gene	NN	_	_	_
2369	locus	locus	NN	_	_	_
2370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2371	genotyp/variation	genotyp/variation	NN	_	_	_
2372	:	:	:	_	_	_
2373	deltacrp	deltacrp	JJ	_	_	_
2374	JW5702-4	jw5702-4	NN	_	_	_
2375	background	background	NN	_	_	_
2376	with	with	IN	_	_	_
2377	a	a	DT	_	_	_
2378	K100R	k100r	NN	_	_	_
2379	mutant	mutant	NN	_	_	_
2380	of	of	IN	_	_	_
2381	CRP	crp	NN	TF	_	_
2382	-LRB-	-lrb-	-LRB-	_	_	_
2383	CRP	crp	NN	TF	_	_
2384	R	r	NN	_	_	_
2385	-RRB-	-rrb-	-RRB-	_	_	_
2386	inserted	insert	VBN	_	_	_
2387	into	into	IN	_	_	_
2388	paaH	paah	NN	GEN	_	_
2389	gene	gene	NN	_	_	_
2390	locus	locus	NN	_	_	_
2391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2392	genotyp/variation	genotyp/variation	NN	_	_	_
2393	:	:	:	_	_	_
2394	deltacrp	deltacrp	JJ	_	_	_
2395	JW5702-4	jw5702-4	NN	_	_	_
2396	background	background	NN	_	_	_
2397	with	with	IN	_	_	_
2398	a	a	DT	_	_	_
2399	wild	wild	JJ	_	_	_
2400	type	type	NN	_	_	_
2401	CRP	crp	NN	TF	_	_
2402	-LRB-	-lrb-	-LRB-	_	_	_
2403	CRP	crp	NN	TF	_	_
2404	N	n	NN	_	_	_
2405	-RRB-	-rrb-	-RRB-	_	_	_
2406	inserted	insert	VBN	_	_	_
2407	into	into	IN	_	_	_
2408	paaH	paah	NN	GEN	_	_
2409	gene	gene	NN	_	_	_
2410	locus	locus	NN	_	_	_
2411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2412	genotyp/variation	genotyp/variation	NN	_	_	_
2413	:	:	:	_	_	_
2414	wild	wild	JJ	_	_	_
2415	type	type	NN	_	_	_
2416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2417	Genowiz	genowiz	NN	_	_	_
2418	4.0.5.6	4.0.5.6	CD	_	_	_
2419	normalized	normalize	VBD	_	_	_
2420	,	,	,	_	_	_
2421	background	background	NN	_	_	_
2422	subtracted	subtract	VBD	_	_	_
2423	data	datum	NNS	_	_	_
2424	obtained	obtain	VBN	_	_	_
2425	from	from	IN	_	_	_
2426	log2	log2	NN	_	_	_
2427	of	of	IN	_	_	_
2428	processed	process	VBN	_	_	_
2429	Red	Red	NNP	_	_	_
2430	signal/processed	signal/processed	VBD	_	_	_
2431	Green	Green	NNP	_	_	_
2432	signal	signal	NN	_	_	_
2433	.	.	.	_	_	_

1	Agilent	Agilent	NNP	_	_	_
2	software	software	NN	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genoype	genoype	NN	_	_	_
3	:	:	:	_	_	_
4	dFNR	dfnr	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genoype	genoype	NN	_	_	_
7	:	:	:	_	_	_
8	Wild-Type	wild-type	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Gentamicin-1	gentamicin-1	NN	_	_	_
11	,	,	,	_	_	_
12	biological	biological	JJ	_	_	_
13	rep1	rep1	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Gentamicin-2	gentamicin-2	NN	_	_	_
16	,	,	,	_	_	_
17	biological	biological	JJ	_	_	_
18	rep2	rep2	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Gentamicin-3	gentamicin-3	NN	_	_	_
21	,	,	,	_	_	_
22	biological	biological	JJ	_	_	_
23	rep3	rep3	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	gentamycin	gentamycin	NN	_	_	_
26	concentration	concentration	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	ug/ml	ug/ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	:	:	:	_	_	_
31	25	25	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	gentamycin	gentamycin	NN	_	_	_
34	concentration	concentration	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	ug/ml	ug/ml	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	:	:	:	_	_	_
39	50	50	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	gentamycin	gentamycin	NN	_	_	_
42	concentration	concentration	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	ug/ml	ug/ml	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	:	:	:	_	_	_
47	75	75	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Germfree	germfree	JJ	_	_	_
50	rat	rat	NN	_	_	_
51	's	's	POS	_	_	_
52	caecum	caecum	NN	_	_	_
53	,	,	,	_	_	_
54	biological	biological	JJ	_	_	_
55	rep1	rep1	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Germfree	germfree	JJ	_	_	_
58	rat	rat	NN	_	_	_
59	's	's	POS	_	_	_
60	caecum	caecum	NN	_	_	_
61	,	,	,	_	_	_
62	biological	biological	JJ	_	_	_
63	rep2	rep2	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Germfree	germfree	JJ	_	_	_
66	rat	rat	NN	_	_	_
67	's	's	POS	_	_	_
68	caecum	caecum	NN	_	_	_
69	,	,	,	_	_	_
70	biological	biological	JJ	_	_	_
71	rep3	rep3	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	get	get	VBP	_	_	_
74	raw	raw	JJ	_	_	_
75	counts	count	NNS	_	_	_
76	for	for	IN	_	_	_
77	reads	read	VBZ	_	_	_
78	mapped	map	VBN	_	_	_
79	with	with	IN	_	_	_
80	htseq-count	htseq-count	JJ	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	GGG10	ggg10	NN	_	_	_
83	,	,	,	_	_	_
84	steady-state	steady-state	JJ	_	_	_
85	continuous	continuous	JJ	_	_	_
86	cultured	culture	VBN	_	_	_
87	experimental	experimental	JJ	_	_	_
88	samples	sample	NNS	_	_	_
89	at	at	IN	_	_	_
90	37	37	CD	_	_	_
91	°C	°c	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	GGG10	ggg10	NN	_	_	_
94	,	,	,	_	_	_
95	steady-state	steady-state	JJ	_	_	_
96	continuous	continuous	JJ	_	_	_
97	cultured	culture	VBN	_	_	_
98	experimental	experimental	JJ	_	_	_
99	samples	sample	NNS	_	_	_
100	at	at	IN	_	_	_
101	37	37	CD	_	_	_
102	°C	°c	NN	_	_	_
103	and	and	CC	_	_	_
104	then	then	RB	_	_	_
105	15	15	CD	_	_	_
106	minutes	minute	NNS	_	_	_
107	heatshock	heatshock	NN	_	_	_
108	at	at	IN	_	_	_
109	50	50	CD	_	_	_
110	°C	°c	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	GHA507	gha507	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	GLBRCE1	glbrce1	NN	_	_	_
115	_	_	CD	_	_	_
116	ACSH	ACSH	NNP	_	_	_
117	_	_	NNP	_	_	_
118	Exp	Exp	NNP	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	GLBRCE1	glbrce1	NN	_	_	_
121	,	,	,	_	_	_
122	ACSH	ACSH	NNP	_	_	_
123	,	,	,	_	_	_
124	Exp	Exp	NNP	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	GLBRCE1	GLBRCE1	NNP	_	_	_
127	_	_	NNP	_	_	_
128	ACSH	ACSH	NNP	_	_	_
129	_	_	VBD	_	_	_
130	Exp	Exp	NNP	_	_	_
131	_	_	SYM	_	_	_
132	rep318	rep318	CD	_	_	_
133	_	_	NN	_	_	_
134	1	1	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	GLBRCE1	glbrce1	NN	_	_	_
137	_	_	CD	_	_	_
138	ACSH	ACSH	NNP	_	_	_
139	_	_	NNP	_	_	_
140	Exp	Exp	NNP	_	_	_
141	_	_	SYM	_	_	_
142	rep320	rep320	CD	_	_	_
143	_	_	NN	_	_	_
144	1	1	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	GLBRCE1	glbrce1	NN	_	_	_
147	_	_	CD	_	_	_
148	ACSH	ACSH	NNP	_	_	_
149	_	_	NNP	_	_	_
150	Exp	Exp	NNP	_	_	_
151	_	_	SYM	_	_	_
152	rep327	rep327	CD	_	_	_
153	_	_	NN	_	_	_
154	1	1	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	GLBRCE1	glbrce1	NN	_	_	_
157	_	_	CD	_	_	_
158	ACSH	ACSH	NNP	_	_	_
159	_	_	NNP	_	_	_
160	Stat	stat	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	GLBRCE1	glbrce1	NN	_	_	_
163	,	,	,	_	_	_
164	ACSH	ACSH	NNP	_	_	_
165	,	,	,	_	_	_
166	Stat1	stat1	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	GLBRCE1	glbrce1	NN	_	_	_
169	_	_	CD	_	_	_
170	ACSH	ACSH	NNP	_	_	_
171	_	_	SYM	_	_	_
172	Stat1	stat1	NN	_	_	_
173	_	_	CD	_	_	_
174	rep318	rep318	NN	_	_	_
175	_	_	NN	_	_	_
176	1	1	CD	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	GLBRCE1	glbrce1	NN	_	_	_
179	_	_	CD	_	_	_
180	ACSH	ACSH	NNP	_	_	_
181	_	_	SYM	_	_	_
182	Stat1	stat1	NN	_	_	_
183	_	_	CD	_	_	_
184	rep320	rep320	NN	_	_	_
185	_	_	NN	_	_	_
186	1	1	CD	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	GLBRCE1	glbrce1	NN	_	_	_
189	_	_	CD	_	_	_
190	ACSH	ACSH	NNP	_	_	_
191	_	_	SYM	_	_	_
192	Stat1	stat1	NN	_	_	_
193	_	_	CD	_	_	_
194	rep327	rep327	NN	_	_	_
195	_	_	NN	_	_	_
196	1	1	CD	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	GLBRCE1	glbrce1	NN	_	_	_
199	,	,	,	_	_	_
200	ACSH	ACSH	NNP	_	_	_
201	,	,	,	_	_	_
202	Stat2	stat2	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	GLBRCE1	glbrce1	NN	_	_	_
205	_	_	CD	_	_	_
206	ACSH	ACSH	NNP	_	_	_
207	_	_	SYM	_	_	_
208	Stat2	stat2	NN	_	_	_
209	_	_	CD	_	_	_
210	rep318	rep318	NN	_	_	_
211	_	_	NN	_	_	_
212	1	1	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	GLBRCE1	glbrce1	NN	_	_	_
215	_	_	CD	_	_	_
216	ACSH	ACSH	NNP	_	_	_
217	_	_	SYM	_	_	_
218	Stat2	stat2	NN	_	_	_
219	_	_	CD	_	_	_
220	rep320	rep320	NN	_	_	_
221	_	_	NN	_	_	_
222	1	1	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	GLBRCE1	glbrce1	NN	_	_	_
225	_	_	CD	_	_	_
226	ACSH	ACSH	NNP	_	_	_
227	_	_	SYM	_	_	_
228	Stat2	stat2	NN	_	_	_
229	_	_	CD	_	_	_
230	rep327	rep327	NN	_	_	_
231	_	_	NN	_	_	_
232	1	1	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	GLBRCE1	glbrce1	NN	_	_	_
235	_	_	CD	_	_	_
236	ACSH	ACSH	NNP	_	_	_
237	_	_	NNP	_	_	_
238	Trans	Trans	NNP	_	_	_
239	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
240	GLBRCE1	glbrce1	NN	_	_	_
241	,	,	,	_	_	_
242	ACSH	ACSH	NNP	_	_	_
243	,	,	,	_	_	_
244	Trans	Trans	NNP	_	_	_
245	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
246	GLBRCE1	GLBRCE1	NNP	_	_	_
247	_	_	NNP	_	_	_
248	ACSH	ACSH	NNP	_	_	_
249	_	_	VBD	_	_	_
250	Trans	Trans	NNP	_	_	_
251	_	_	SYM	_	_	_
252	rep318	rep318	CD	_	_	_
253	_	_	NN	_	_	_
254	1	1	CD	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	GLBRCE1	glbrce1	NN	_	_	_
257	_	_	CD	_	_	_
258	ACSH	ACSH	NNP	_	_	_
259	_	_	CD	_	_	_
260	Trans	Trans	NNP	_	_	_
261	_	_	SYM	_	_	_
262	rep318	rep318	CD	_	_	_
263	_	_	NN	_	_	_
264	2	2	CD	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	GLBRCE1	glbrce1	NN	_	_	_
267	_	_	CD	_	_	_
268	ACSH	ACSH	NNP	_	_	_
269	_	_	CD	_	_	_
270	Trans	Trans	NNP	_	_	_
271	_	_	SYM	_	_	_
272	rep320	rep320	CD	_	_	_
273	_	_	NN	_	_	_
274	1	1	CD	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	GLBRCE1	glbrce1	NN	_	_	_
277	_	_	CD	_	_	_
278	ACSH	ACSH	NNP	_	_	_
279	_	_	CD	_	_	_
280	Trans	Trans	NNP	_	_	_
281	_	_	SYM	_	_	_
282	rep327	rep327	CD	_	_	_
283	_	_	NN	_	_	_
284	1	1	CD	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	GLBRCE1	glbrce1	NN	_	_	_
287	_	_	CD	_	_	_
288	pBBR	pbbr	NN	_	_	_
289	_	_	CD	_	_	_
290	ACSH	ACSH	NNP	_	_	_
291	_	_	NNP	_	_	_
292	Exp	Exp	NNP	_	_	_
293	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
294	GLBRCE1	glbrce1	NN	_	_	_
295	_	_	CD	_	_	_
296	pBBR	pbbr	NN	_	_	_
297	_	_	SYM	_	_	_
298	ACSH	ACSH	NNP	_	_	_
299	_	_	VBD	_	_	_
300	Stat	stat	NN	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	GLBRCE1	glbrce1	NN	_	_	_
303	_	_	CD	_	_	_
304	pBBR	pbbr	NN	_	_	_
305	_	_	CD	_	_	_
306	ACSH	ACSH	NNP	_	_	_
307	_	_	NNP	_	_	_
308	Trans	Trans	NNP	_	_	_
309	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
310	GLBRCE1	glbrce1	NN	_	_	_
311	,	,	,	_	_	_
312	SynH	synh	NN	_	_	_
313	,	,	,	_	_	_
314	Exp	exp	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	GLBRCE1	glbrce1	NN	_	_	_
317	_	_	CD	_	_	_
318	SynH	synh	NN	_	_	_
319	_	_	CD	_	_	_
320	Exp	exp	NN	_	_	_
321	_	_	CD	_	_	_
322	rep318	rep318	NN	_	_	_
323	_	_	NN	_	_	_
324	1	1	CD	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	GLBRCE1	glbrce1	NN	_	_	_
327	_	_	CD	_	_	_
328	SynH	synh	NN	_	_	_
329	_	_	CD	_	_	_
330	Exp	exp	NN	_	_	_
331	_	_	CD	_	_	_
332	rep318	rep318	NN	_	_	_
333	_	_	NN	_	_	_
334	2	2	CD	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	GLBRCE1	glbrce1	NN	_	_	_
337	_	_	CD	_	_	_
338	SynH	synh	NN	_	_	_
339	_	_	CD	_	_	_
340	Exp	exp	NN	_	_	_
341	_	_	CD	_	_	_
342	rep320	rep320	NN	_	_	_
343	_	_	NN	_	_	_
344	1	1	CD	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	GLBRCE1	glbrce1	NN	_	_	_
347	_	_	CD	_	_	_
348	SynH	synh	NN	_	_	_
349	_	_	CD	_	_	_
350	Exp	exp	NN	_	_	_
351	_	_	CD	_	_	_
352	rep327	rep327	NN	_	_	_
353	_	_	NN	_	_	_
354	1	1	CD	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	GLBRCE1	glbrce1	NN	_	_	_
357	,	,	,	_	_	_
358	SynH	synh	NN	_	_	_
359	_	_	CD	_	_	_
360	LT	lt	NN	_	_	_
361	,	,	,	_	_	_
362	Exp	exp	NN	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	GLBRCE1	glbrce1	NN	_	_	_
365	_	_	CD	_	_	_
366	SynH	synh	NN	_	_	_
367	_	_	CD	_	_	_
368	LT	lt	NN	_	_	_
369	_	_	CD	_	_	_
370	Exp	exp	NN	_	_	_
371	_	_	CD	_	_	_
372	rep318	rep318	NN	_	_	_
373	_	_	NN	_	_	_
374	1	1	CD	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	GLBRCE1	glbrce1	NN	_	_	_
377	_	_	CD	_	_	_
378	SynH	synh	NN	_	_	_
379	_	_	CD	_	_	_
380	LT	lt	NN	_	_	_
381	_	_	CD	_	_	_
382	Exp	exp	NN	_	_	_
383	_	_	CD	_	_	_
384	rep320	rep320	NN	_	_	_
385	_	_	NN	_	_	_
386	1	1	CD	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	GLBRCE1	glbrce1	NN	_	_	_
389	_	_	CD	_	_	_
390	SynH	synh	NN	_	_	_
391	_	_	CD	_	_	_
392	LT	lt	NN	_	_	_
393	_	_	CD	_	_	_
394	Exp	exp	NN	_	_	_
395	_	_	CD	_	_	_
396	rep327	rep327	NN	_	_	_
397	_	_	NN	_	_	_
398	1	1	CD	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	GLBRCE1	glbrce1	NN	_	_	_
401	,	,	,	_	_	_
402	SynH	synh	NN	_	_	_
403	_	_	CD	_	_	_
404	LT	lt	NN	_	_	_
405	,	,	,	_	_	_
406	Stat1	stat1	NN	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	GLBRCE1	glbrce1	NN	_	_	_
409	_	_	CD	_	_	_
410	SynH	synh	NN	_	_	_
411	_	_	CD	_	_	_
412	LT	lt	NN	_	_	_
413	_	_	CD	_	_	_
414	Stat1	stat1	NN	_	_	_
415	_	_	CD	_	_	_
416	rep318	rep318	NN	_	_	_
417	_	_	NN	_	_	_
418	1	1	CD	_	_	_
419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
420	GLBRCE1	glbrce1	NN	_	_	_
421	_	_	CD	_	_	_
422	SynH	synh	NN	_	_	_
423	_	_	CD	_	_	_
424	LT	lt	NN	_	_	_
425	_	_	CD	_	_	_
426	Stat1	stat1	NN	_	_	_
427	_	_	CD	_	_	_
428	rep320	rep320	NN	_	_	_
429	_	_	NN	_	_	_
430	1	1	CD	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	GLBRCE1	glbrce1	NN	_	_	_
433	_	_	CD	_	_	_
434	SynH	synh	NN	_	_	_
435	_	_	CD	_	_	_
436	LT	lt	NN	_	_	_
437	_	_	CD	_	_	_
438	Stat1	stat1	NN	_	_	_
439	_	_	CD	_	_	_
440	rep327	rep327	NN	_	_	_
441	_	_	NN	_	_	_
442	1	1	CD	_	_	_
443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
444	GLBRCE1	glbrce1	NN	_	_	_
445	,	,	,	_	_	_
446	SynH	synh	NN	_	_	_
447	_	_	CD	_	_	_
448	LT	lt	NN	_	_	_
449	,	,	,	_	_	_
450	Stat2	stat2	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	GLBRCE1	glbrce1	NN	_	_	_
453	_	_	CD	_	_	_
454	SynH	synh	NN	_	_	_
455	_	_	CD	_	_	_
456	LT	lt	NN	_	_	_
457	_	_	SYM	_	_	_
458	Stat2	stat2	NN	_	_	_
459	_	_	CD	_	_	_
460	rep318	rep318	NN	_	_	_
461	_	_	NN	_	_	_
462	1	1	CD	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	GLBRCE1	glbrce1	NN	_	_	_
465	_	_	CD	_	_	_
466	SynH	synh	NN	_	_	_
467	_	_	CD	_	_	_
468	LT	lt	NN	_	_	_
469	_	_	SYM	_	_	_
470	Stat2	stat2	NN	_	_	_
471	_	_	CD	_	_	_
472	rep320	rep320	NN	_	_	_
473	_	_	NN	_	_	_
474	1	1	CD	_	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
476	GLBRCE1	glbrce1	NN	_	_	_
477	_	_	CD	_	_	_
478	SynH	synh	NN	_	_	_
479	_	_	CD	_	_	_
480	LT	lt	NN	_	_	_
481	_	_	SYM	_	_	_
482	Stat2	stat2	NN	_	_	_
483	_	_	CD	_	_	_
484	rep327	rep327	NN	_	_	_
485	_	_	NN	_	_	_
486	1	1	CD	_	_	_
487	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
488	GLBRCE1	glbrce1	NN	_	_	_
489	,	,	,	_	_	_
490	SynH	synh	NN	_	_	_
491	_	_	CD	_	_	_
492	LT	lt	NN	_	_	_
493	,	,	,	_	_	_
494	Trans	Trans	NNP	_	_	_
495	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
496	GLBRCE1	glbrce1	NN	_	_	_
497	_	_	CD	_	_	_
498	SynH	synh	NN	_	_	_
499	_	_	CD	_	_	_
500	LT	lt	NN	_	_	_
501	_	_	CD	_	_	_
502	Trans	Trans	NNP	_	_	_
503	_	_	SYM	_	_	_
504	rep318	rep318	CD	_	_	_
505	_	_	NN	_	_	_
506	1	1	CD	_	_	_
507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
508	GLBRCE1	glbrce1	NN	_	_	_
509	_	_	CD	_	_	_
510	SynH	synh	NN	_	_	_
511	_	_	CD	_	_	_
512	LT	lt	NN	_	_	_
513	_	_	CD	_	_	_
514	Trans	Trans	NNP	_	_	_
515	_	_	SYM	_	_	_
516	rep320	rep320	CD	_	_	_
517	_	_	NN	_	_	_
518	1	1	CD	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	GLBRCE1	glbrce1	NN	_	_	_
521	_	_	CD	_	_	_
522	SynH	synh	NN	_	_	_
523	_	_	CD	_	_	_
524	LT	lt	NN	_	_	_
525	_	_	CD	_	_	_
526	Trans	Trans	NNP	_	_	_
527	_	_	SYM	_	_	_
528	rep327	rep327	CD	_	_	_
529	_	_	NN	_	_	_
530	1	1	CD	_	_	_
531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
532	GLBRCE1	glbrce1	NN	_	_	_
533	,	,	,	_	_	_
534	SynH	synh	NN	_	_	_
535	,	,	,	_	_	_
536	Stat1	stat1	NN	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	GLBRCE1	glbrce1	NN	_	_	_
539	_	_	CD	_	_	_
540	SynH	synh	NN	_	_	_
541	_	_	CD	_	_	_
542	Stat1	stat1	NN	_	_	_
543	_	_	CD	_	_	_
544	rep318	rep318	NN	_	_	_
545	_	_	NN	_	_	_
546	1	1	CD	_	_	_
547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
548	GLBRCE1	glbrce1	NN	_	_	_
549	_	_	CD	_	_	_
550	SynH	synh	NN	_	_	_
551	_	_	CD	_	_	_
552	Stat1	stat1	NN	_	_	_
553	_	_	CD	_	_	_
554	rep320	rep320	NN	_	_	_
555	_	_	NN	_	_	_
556	1	1	CD	_	_	_
557	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
558	GLBRCE1	glbrce1	NN	_	_	_
559	_	_	CD	_	_	_
560	SynH	synh	NN	_	_	_
561	_	_	CD	_	_	_
562	Stat1	stat1	NN	_	_	_
563	_	_	CD	_	_	_
564	rep327	rep327	NN	_	_	_
565	_	_	NN	_	_	_
566	1	1	CD	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	GLBRCE1	glbrce1	NN	_	_	_
569	,	,	,	_	_	_
570	SynH	synh	NN	_	_	_
571	,	,	,	_	_	_
572	Stat2	stat2	NN	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	GLBRCE1	glbrce1	NN	_	_	_
575	_	_	CD	_	_	_
576	SynH	synh	NN	_	_	_
577	_	_	CD	_	_	_
578	Stat2	stat2	NN	_	_	_
579	_	_	CD	_	_	_
580	rep327	rep327	NN	_	_	_
581	_	_	NN	_	_	_
582	1	1	CD	_	_	_
583	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
584	GLBRCE1	glbrce1	NN	_	_	_
585	,	,	,	_	_	_
586	SynH	synh	NN	_	_	_
587	,	,	,	_	_	_
588	Trans	Trans	NNP	_	_	_
589	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
590	GLBRCE1	glbrce1	NN	_	_	_
591	_	_	CD	_	_	_
592	SynH	synh	NN	_	_	_
593	_	_	CD	_	_	_
594	Trans	Trans	NNP	_	_	_
595	_	_	SYM	_	_	_
596	rep318	rep318	CD	_	_	_
597	_	_	NN	_	_	_
598	1	1	CD	_	_	_
599	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
600	GLBRCE1	glbrce1	NN	_	_	_
601	_	_	CD	_	_	_
602	SynH	synh	NN	_	_	_
603	_	_	CD	_	_	_
604	Trans	Trans	NNP	_	_	_
605	_	_	SYM	_	_	_
606	rep320	rep320	CD	_	_	_
607	_	_	NN	_	_	_
608	1	1	CD	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	GLBRCE1	glbrce1	NN	_	_	_
611	_	_	CD	_	_	_
612	SynH	synh	NN	_	_	_
613	_	_	CD	_	_	_
614	Trans	Trans	NNP	_	_	_
615	_	_	SYM	_	_	_
616	rep327	rep327	CD	_	_	_
617	_	_	NN	_	_	_
618	1	1	CD	_	_	_
619	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
620	gluconate	gluconate	NN	_	_	_
621	_	_	NN	_	_	_
622	growth	growth	NN	_	_	_
623	:	:	:	_	_	_
624	MURI	MURI	NNP	_	_	_
625	_	_	SYM	_	_	_
626	091	091	CD	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	gluconate	gluconate	NN	_	_	_
629	_	_	NN	_	_	_
630	growth	growth	NN	_	_	_
631	:	:	:	_	_	_
632	MURI	MURI	NNP	_	_	_
633	_	_	SYM	_	_	_
634	092	092	CD	_	_	_
635	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
636	gluconate	gluconate	NN	_	_	_
637	_	_	NN	_	_	_
638	growth	growth	NN	_	_	_
639	:	:	:	_	_	_
640	MURI	MURI	NNP	_	_	_
641	_	_	SYM	_	_	_
642	093	093	CD	_	_	_
643	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
644	gluconate	gluconate	NN	_	_	_
645	_	_	NN	_	_	_
646	growth	growth	NN	_	_	_
647	:	:	:	_	_	_
648	MURI	MURI	NNP	_	_	_
649	_	_	SYM	_	_	_
650	094	094	CD	_	_	_
651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
652	gluconate	gluconate	NN	_	_	_
653	_	_	NN	_	_	_
654	growth	growth	NN	_	_	_
655	:	:	:	_	_	_
656	MURI	MURI	NNP	_	_	_
657	_	_	SYM	_	_	_
658	095	095	CD	_	_	_
659	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
660	gluconate	gluconate	NN	_	_	_
661	_	_	NN	_	_	_
662	growth	growth	NN	_	_	_
663	:	:	:	_	_	_
664	MURI	MURI	NNP	_	_	_
665	_	_	SYM	_	_	_
666	096	096	CD	_	_	_
667	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
668	Glucose	glucose	NN	_	_	_
669	time	time	NN	_	_	_
670	course	course	NN	_	_	_
671	,	,	,	_	_	_
672	168	168	CD	_	_	_
673	hour	hour	NN	_	_	_
674	time	time	NN	_	_	_
675	point	point	NN	_	_	_
676	,	,	,	_	_	_
677	biological	biological	JJ	_	_	_
678	replicate	replicate	VBP	_	_	_
679	1	1	CD	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	Glucose	glucose	NN	_	_	_
682	time	time	NN	_	_	_
683	course	course	NN	_	_	_
684	,	,	,	_	_	_
685	168	168	CD	_	_	_
686	hour	hour	NN	_	_	_
687	time	time	NN	_	_	_
688	point	point	NN	_	_	_
689	,	,	,	_	_	_
690	biological	biological	JJ	_	_	_
691	replicate	replicate	VB	_	_	_
692	2	2	CD	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
694	Glucose	glucose	NN	_	_	_
695	time	time	NN	_	_	_
696	course	course	NN	_	_	_
697	,	,	,	_	_	_
698	168	168	CD	_	_	_
699	hour	hour	NN	_	_	_
700	time	time	NN	_	_	_
701	point	point	NN	_	_	_
702	,	,	,	_	_	_
703	biological	biological	JJ	_	_	_
704	replicate	replicate	VBP	_	_	_
705	3	3	CD	_	_	_
706	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
707	Glucose	glucose	NN	_	_	_
708	time	time	NN	_	_	_
709	course	course	NN	_	_	_
710	,	,	,	_	_	_
711	168	168	CD	_	_	_
712	hour	hour	NN	_	_	_
713	time	time	NN	_	_	_
714	point	point	NN	_	_	_
715	,	,	,	_	_	_
716	biological	biological	JJ	_	_	_
717	replicate	replicate	VBP	_	_	_
718	3	3	CD	_	_	_
719	,	,	,	_	_	_
720	rRNA	rrna	NN	_	_	_
721	not	not	RB	_	_	_
722	depleted	deplete	VBN	_	_	_
723	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
724	Glucose	glucose	NN	_	_	_
725	time	time	NN	_	_	_
726	course	course	NN	_	_	_
727	,	,	,	_	_	_
728	24	24	CD	_	_	_
729	hour	hour	NN	_	_	_
730	time	time	NN	_	_	_
731	point	point	NN	_	_	_
732	,	,	,	_	_	_
733	biological	biological	JJ	_	_	_
734	replicate	replicate	VBP	_	_	_
735	1	1	CD	_	_	_
736	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
737	Glucose	glucose	NN	_	_	_
738	time	time	NN	_	_	_
739	course	course	NN	_	_	_
740	,	,	,	_	_	_
741	24	24	CD	_	_	_
742	hour	hour	NN	_	_	_
743	time	time	NN	_	_	_
744	point	point	NN	_	_	_
745	,	,	,	_	_	_
746	biological	biological	JJ	_	_	_
747	replicate	replicate	VB	_	_	_
748	2	2	CD	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
750	Glucose	glucose	NN	_	_	_
751	time	time	NN	_	_	_
752	course	course	NN	_	_	_
753	,	,	,	_	_	_
754	24	24	CD	_	_	_
755	hour	hour	NN	_	_	_
756	time	time	NN	_	_	_
757	point	point	NN	_	_	_
758	,	,	,	_	_	_
759	biological	biological	JJ	_	_	_
760	replicate	replicate	VBP	_	_	_
761	3	3	CD	_	_	_
762	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
763	Glucose	glucose	NN	_	_	_
764	time	time	NN	_	_	_
765	course	course	NN	_	_	_
766	,	,	,	_	_	_
767	24	24	CD	_	_	_
768	hour	hour	NN	_	_	_
769	time	time	NN	_	_	_
770	point	point	NN	_	_	_
771	,	,	,	_	_	_
772	biological	biological	JJ	_	_	_
773	replicate	replicate	VBP	_	_	_
774	3	3	CD	_	_	_
775	,	,	,	_	_	_
776	rRNA	rrna	NN	_	_	_
777	not	not	RB	_	_	_
778	depleted	deplete	VBN	_	_	_
779	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
780	Glucose	glucose	NN	_	_	_
781	time	time	NN	_	_	_
782	course	course	NN	_	_	_
783	,	,	,	_	_	_
784	336	336	CD	_	_	_
785	hour	hour	NN	_	_	_
786	time	time	NN	_	_	_
787	point	point	NN	_	_	_
788	,	,	,	_	_	_
789	biological	biological	JJ	_	_	_
790	replicate	replicate	VBP	_	_	_
791	1	1	CD	_	_	_
792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
793	Glucose	glucose	NN	_	_	_
794	time	time	NN	_	_	_
795	course	course	NN	_	_	_
796	,	,	,	_	_	_
797	336	336	CD	_	_	_
798	hour	hour	NN	_	_	_
799	time	time	NN	_	_	_
800	point	point	NN	_	_	_
801	,	,	,	_	_	_
802	biological	biological	JJ	_	_	_
803	replicate	replicate	VB	_	_	_
804	2	2	CD	_	_	_
805	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
806	Glucose	glucose	NN	_	_	_
807	time	time	NN	_	_	_
808	course	course	NN	_	_	_
809	,	,	,	_	_	_
810	336	336	CD	_	_	_
811	hour	hour	NN	_	_	_
812	time	time	NN	_	_	_
813	point	point	NN	_	_	_
814	,	,	,	_	_	_
815	biological	biological	JJ	_	_	_
816	replicate	replicate	VBP	_	_	_
817	3	3	CD	_	_	_
818	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
819	Glucose	glucose	NN	_	_	_
820	time	time	NN	_	_	_
821	course	course	NN	_	_	_
822	,	,	,	_	_	_
823	336	336	CD	_	_	_
824	hour	hour	NN	_	_	_
825	time	time	NN	_	_	_
826	point	point	NN	_	_	_
827	,	,	,	_	_	_
828	biological	biological	JJ	_	_	_
829	replicate	replicate	VBP	_	_	_
830	3	3	CD	_	_	_
831	,	,	,	_	_	_
832	rRNA	rrna	NN	_	_	_
833	not	not	RB	_	_	_
834	depleted	deplete	VBN	_	_	_
835	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
836	Glucose	glucose	NN	_	_	_
837	time	time	NN	_	_	_
838	course	course	NN	_	_	_
839	,	,	,	_	_	_
840	3	3	CD	_	_	_
841	hour	hour	NN	_	_	_
842	time	time	NN	_	_	_
843	point	point	NN	_	_	_
844	,	,	,	_	_	_
845	biological	biological	JJ	_	_	_
846	replicate	replicate	VBP	_	_	_
847	1	1	CD	_	_	_
848	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
849	Glucose	glucose	NN	_	_	_
850	time	time	NN	_	_	_
851	course	course	NN	_	_	_
852	,	,	,	_	_	_
853	3	3	CD	_	_	_
854	hour	hour	NN	_	_	_
855	time	time	NN	_	_	_
856	point	point	NN	_	_	_
857	,	,	,	_	_	_
858	biological	biological	JJ	_	_	_
859	replicate	replicate	VB	_	_	_
860	2	2	CD	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
862	Glucose	glucose	NN	_	_	_
863	time	time	NN	_	_	_
864	course	course	NN	_	_	_
865	,	,	,	_	_	_
866	3	3	CD	_	_	_
867	hour	hour	NN	_	_	_
868	time	time	NN	_	_	_
869	point	point	NN	_	_	_
870	,	,	,	_	_	_
871	biological	biological	JJ	_	_	_
872	replicate	replicate	VBP	_	_	_
873	3	3	CD	_	_	_
874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
875	Glucose	glucose	NN	_	_	_
876	time	time	NN	_	_	_
877	course	course	NN	_	_	_
878	,	,	,	_	_	_
879	3	3	CD	_	_	_
880	hour	hour	NN	_	_	_
881	time	time	NN	_	_	_
882	point	point	NN	_	_	_
883	,	,	,	_	_	_
884	biological	biological	JJ	_	_	_
885	replicate	replicate	VBP	_	_	_
886	3	3	CD	_	_	_
887	,	,	,	_	_	_
888	rRNA	rrna	NN	_	_	_
889	not	not	RB	_	_	_
890	depleted	deplete	VBN	_	_	_
891	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
892	Glucose	glucose	NN	_	_	_
893	time	time	NN	_	_	_
894	course	course	NN	_	_	_
895	,	,	,	_	_	_
896	48	48	CD	_	_	_
897	hour	hour	NN	_	_	_
898	time	time	NN	_	_	_
899	point	point	NN	_	_	_
900	,	,	,	_	_	_
901	biological	biological	JJ	_	_	_
902	replicate	replicate	VBP	_	_	_
903	1	1	CD	_	_	_
904	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
905	Glucose	glucose	NN	_	_	_
906	time	time	NN	_	_	_
907	course	course	NN	_	_	_
908	,	,	,	_	_	_
909	48	48	CD	_	_	_
910	hour	hour	NN	_	_	_
911	time	time	NN	_	_	_
912	point	point	NN	_	_	_
913	,	,	,	_	_	_
914	biological	biological	JJ	_	_	_
915	replicate	replicate	VB	_	_	_
916	2	2	CD	_	_	_
917	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
918	Glucose	glucose	NN	_	_	_
919	time	time	NN	_	_	_
920	course	course	NN	_	_	_
921	,	,	,	_	_	_
922	48	48	CD	_	_	_
923	hour	hour	NN	_	_	_
924	time	time	NN	_	_	_
925	point	point	NN	_	_	_
926	,	,	,	_	_	_
927	biological	biological	JJ	_	_	_
928	replicate	replicate	VBP	_	_	_
929	3	3	CD	_	_	_
930	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
931	Glucose	glucose	NN	_	_	_
932	time	time	NN	_	_	_
933	course	course	NN	_	_	_
934	,	,	,	_	_	_
935	48	48	CD	_	_	_
936	hour	hour	NN	_	_	_
937	time	time	NN	_	_	_
938	point	point	NN	_	_	_
939	,	,	,	_	_	_
940	biological	biological	JJ	_	_	_
941	replicate	replicate	VBP	_	_	_
942	3	3	CD	_	_	_
943	,	,	,	_	_	_
944	rRNA	rrna	NN	_	_	_
945	not	not	RB	_	_	_
946	depleted	deplete	VBN	_	_	_
947	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
948	Glucose	glucose	NN	_	_	_
949	time	time	NN	_	_	_
950	course	course	NN	_	_	_
951	,	,	,	_	_	_
952	4	4	CD	_	_	_
953	hour	hour	NN	_	_	_
954	time	time	NN	_	_	_
955	point	point	NN	_	_	_
956	,	,	,	_	_	_
957	biological	biological	JJ	_	_	_
958	replicate	replicate	VBP	_	_	_
959	1	1	CD	_	_	_
960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
961	Glucose	glucose	NN	_	_	_
962	time	time	NN	_	_	_
963	course	course	NN	_	_	_
964	,	,	,	_	_	_
965	4	4	CD	_	_	_
966	hour	hour	NN	_	_	_
967	time	time	NN	_	_	_
968	point	point	NN	_	_	_
969	,	,	,	_	_	_
970	biological	biological	JJ	_	_	_
971	replicate	replicate	VB	_	_	_
972	2	2	CD	_	_	_
973	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
974	Glucose	glucose	NN	_	_	_
975	time	time	NN	_	_	_
976	course	course	NN	_	_	_
977	,	,	,	_	_	_
978	4	4	CD	_	_	_
979	hour	hour	NN	_	_	_
980	time	time	NN	_	_	_
981	point	point	NN	_	_	_
982	,	,	,	_	_	_
983	biological	biological	JJ	_	_	_
984	replicate	replicate	VBP	_	_	_
985	3	3	CD	_	_	_
986	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
987	Glucose	glucose	NN	_	_	_
988	time	time	NN	_	_	_
989	course	course	NN	_	_	_
990	,	,	,	_	_	_
991	4	4	CD	_	_	_
992	hour	hour	NN	_	_	_
993	time	time	NN	_	_	_
994	point	point	NN	_	_	_
995	,	,	,	_	_	_
996	biological	biological	JJ	_	_	_
997	replicate	replicate	VBP	_	_	_
998	3	3	CD	_	_	_
999	,	,	,	_	_	_
1000	rRNA	rrna	NN	_	_	_
1001	not	not	RB	_	_	_
1002	depleted	deplete	VBN	_	_	_
1003	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1004	Glucose	glucose	NN	_	_	_
1005	time	time	NN	_	_	_
1006	course	course	NN	_	_	_
1007	,	,	,	_	_	_
1008	5	5	CD	_	_	_
1009	hour	hour	NN	_	_	_
1010	time	time	NN	_	_	_
1011	point	point	NN	_	_	_
1012	,	,	,	_	_	_
1013	biological	biological	JJ	_	_	_
1014	replicate	replicate	VBP	_	_	_
1015	1	1	CD	_	_	_
1016	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1017	Glucose	glucose	NN	_	_	_
1018	time	time	NN	_	_	_
1019	course	course	NN	_	_	_
1020	,	,	,	_	_	_
1021	5	5	CD	_	_	_
1022	hour	hour	NN	_	_	_
1023	time	time	NN	_	_	_
1024	point	point	NN	_	_	_
1025	,	,	,	_	_	_
1026	biological	biological	JJ	_	_	_
1027	replicate	replicate	VB	_	_	_
1028	2	2	CD	_	_	_
1029	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1030	Glucose	glucose	NN	_	_	_
1031	time	time	NN	_	_	_
1032	course	course	NN	_	_	_
1033	,	,	,	_	_	_
1034	5	5	CD	_	_	_
1035	hour	hour	NN	_	_	_
1036	time	time	NN	_	_	_
1037	point	point	NN	_	_	_
1038	,	,	,	_	_	_
1039	biological	biological	JJ	_	_	_
1040	replicate	replicate	VBP	_	_	_
1041	3	3	CD	_	_	_
1042	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1043	Glucose	glucose	NN	_	_	_
1044	time	time	NN	_	_	_
1045	course	course	NN	_	_	_
1046	,	,	,	_	_	_
1047	5	5	CD	_	_	_
1048	hour	hour	NN	_	_	_
1049	time	time	NN	_	_	_
1050	point	point	NN	_	_	_
1051	,	,	,	_	_	_
1052	biological	biological	JJ	_	_	_
1053	replicate	replicate	VBP	_	_	_
1054	3	3	CD	_	_	_
1055	,	,	,	_	_	_
1056	rRNA	rrna	NN	_	_	_
1057	not	not	RB	_	_	_
1058	depleted	deplete	VBN	_	_	_
1059	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1060	Glucose	glucose	NN	_	_	_
1061	time	time	NN	_	_	_
1062	course	course	NN	_	_	_
1063	,	,	,	_	_	_
1064	6	6	CD	_	_	_
1065	hour	hour	NN	_	_	_
1066	time	time	NN	_	_	_
1067	point	point	NN	_	_	_
1068	,	,	,	_	_	_
1069	biological	biological	JJ	_	_	_
1070	replicate	replicate	VBP	_	_	_
1071	1	1	CD	_	_	_
1072	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1073	Glucose	glucose	NN	_	_	_
1074	time	time	NN	_	_	_
1075	course	course	NN	_	_	_
1076	,	,	,	_	_	_
1077	6	6	CD	_	_	_
1078	hour	hour	NN	_	_	_
1079	time	time	NN	_	_	_
1080	point	point	NN	_	_	_
1081	,	,	,	_	_	_
1082	biological	biological	JJ	_	_	_
1083	replicate	replicate	VB	_	_	_
1084	2	2	CD	_	_	_
1085	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1086	Glucose	glucose	NN	_	_	_
1087	time	time	NN	_	_	_
1088	course	course	NN	_	_	_
1089	,	,	,	_	_	_
1090	6	6	CD	_	_	_
1091	hour	hour	NN	_	_	_
1092	time	time	NN	_	_	_
1093	point	point	NN	_	_	_
1094	,	,	,	_	_	_
1095	biological	biological	JJ	_	_	_
1096	replicate	replicate	VBP	_	_	_
1097	3	3	CD	_	_	_
1098	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1099	Glucose	glucose	NN	_	_	_
1100	time	time	NN	_	_	_
1101	course	course	NN	_	_	_
1102	,	,	,	_	_	_
1103	6	6	CD	_	_	_
1104	hour	hour	NN	_	_	_
1105	time	time	NN	_	_	_
1106	point	point	NN	_	_	_
1107	,	,	,	_	_	_
1108	biological	biological	JJ	_	_	_
1109	replicate	replicate	VBP	_	_	_
1110	3	3	CD	_	_	_
1111	,	,	,	_	_	_
1112	rRNA	rrna	NN	_	_	_
1113	not	not	RB	_	_	_
1114	depleted	deplete	VBN	_	_	_
1115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1116	Glucose	glucose	NN	_	_	_
1117	time	time	NN	_	_	_
1118	course	course	NN	_	_	_
1119	,	,	,	_	_	_
1120	8	8	CD	_	_	_
1121	hour	hour	NN	_	_	_
1122	time	time	NN	_	_	_
1123	point	point	NN	_	_	_
1124	,	,	,	_	_	_
1125	biological	biological	JJ	_	_	_
1126	replicate	replicate	VBP	_	_	_
1127	1	1	CD	_	_	_
1128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1129	Glucose	glucose	NN	_	_	_
1130	time	time	NN	_	_	_
1131	course	course	NN	_	_	_
1132	,	,	,	_	_	_
1133	8	8	CD	_	_	_
1134	hour	hour	NN	_	_	_
1135	time	time	NN	_	_	_
1136	point	point	NN	_	_	_
1137	,	,	,	_	_	_
1138	biological	biological	JJ	_	_	_
1139	replicate	replicate	VB	_	_	_
1140	2	2	CD	_	_	_
1141	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1142	Glucose	glucose	NN	_	_	_
1143	time	time	NN	_	_	_
1144	course	course	NN	_	_	_
1145	,	,	,	_	_	_
1146	8	8	CD	_	_	_
1147	hourt	hourt	NN	_	_	_
1148	ime	ime	NN	_	_	_
1149	point	point	NN	_	_	_
1150	,	,	,	_	_	_
1151	biological	biological	JJ	_	_	_
1152	replicate	replicate	VBP	_	_	_
1153	3	3	CD	_	_	_
1154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1155	Glucose	glucose	NN	_	_	_
1156	time	time	NN	_	_	_
1157	course	course	NN	_	_	_
1158	,	,	,	_	_	_
1159	8	8	CD	_	_	_
1160	hourt	hourt	NN	_	_	_
1161	ime	ime	NN	_	_	_
1162	point	point	NN	_	_	_
1163	,	,	,	_	_	_
1164	biological	biological	JJ	_	_	_
1165	replicate	replicate	VBP	_	_	_
1166	3	3	CD	_	_	_
1167	,	,	,	_	_	_
1168	rRNA	rrna	NN	_	_	_
1169	not	not	RB	_	_	_
1170	depleted	deplete	VBN	_	_	_
1171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1172	glucose	glucose	NN	SUPP	_	_
1173	_	_	CD	_	_	_
1174	time	time	NN	_	_	_
1175	_	_	NN	_	_	_
1176	course	course	NN	_	_	_
1177	:	:	:	_	_	_
1178	MURI	MURI	NNP	_	_	_
1179	_	_	SYM	_	_	_
1180	016	016	CD	_	_	_
1181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1182	glucose	glucose	NN	SUPP	_	_
1183	_	_	CD	_	_	_
1184	time	time	NN	_	_	_
1185	_	_	NN	_	_	_
1186	course	course	NN	_	_	_
1187	:	:	:	_	_	_
1188	MURI	MURI	NNP	_	_	_
1189	_	_	SYM	_	_	_
1190	017	017	CD	_	_	_
1191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1192	glucose	glucose	NN	SUPP	_	_
1193	_	_	CD	_	_	_
1194	time	time	NN	_	_	_
1195	_	_	NN	_	_	_
1196	course	course	NN	_	_	_
1197	:	:	:	_	_	_
1198	MURI	MURI	NNP	_	_	_
1199	_	_	SYM	_	_	_
1200	018	018	CD	_	_	_
1201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1202	glucose	glucose	NN	SUPP	_	_
1203	_	_	CD	_	_	_
1204	time	time	NN	_	_	_
1205	_	_	NN	_	_	_
1206	course	course	NN	_	_	_
1207	:	:	:	_	_	_
1208	MURI	MURI	NNP	_	_	_
1209	_	_	SYM	_	_	_
1210	019	019	CD	_	_	_
1211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1212	glucose	glucose	NN	SUPP	_	_
1213	_	_	CD	_	_	_
1214	time	time	NN	_	_	_
1215	_	_	NN	_	_	_
1216	course	course	NN	_	_	_
1217	:	:	:	_	_	_
1218	MURI	MURI	NNP	_	_	_
1219	_	_	SYM	_	_	_
1220	020	020	CD	_	_	_
1221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1222	glucose	glucose	NN	SUPP	_	_
1223	_	_	CD	_	_	_
1224	time	time	NN	_	_	_
1225	_	_	NN	_	_	_
1226	course	course	NN	_	_	_
1227	:	:	:	_	_	_
1228	MURI	MURI	NNP	_	_	_
1229	_	_	SYM	_	_	_
1230	021	021	CD	_	_	_
1231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1232	glucose	glucose	NN	SUPP	_	_
1233	_	_	CD	_	_	_
1234	time	time	NN	_	_	_
1235	_	_	NN	_	_	_
1236	course	course	NN	_	_	_
1237	:	:	:	_	_	_
1238	MURI	MURI	NNP	_	_	_
1239	_	_	SYM	_	_	_
1240	022	022	CD	_	_	_
1241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1242	glucose	glucose	NN	SUPP	_	_
1243	_	_	CD	_	_	_
1244	time	time	NN	_	_	_
1245	_	_	NN	_	_	_
1246	course	course	NN	_	_	_
1247	:	:	:	_	_	_
1248	MURI	MURI	NNP	_	_	_
1249	_	_	SYM	_	_	_
1250	023	023	CD	_	_	_
1251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1252	glucose	glucose	NN	SUPP	_	_
1253	_	_	CD	_	_	_
1254	time	time	NN	_	_	_
1255	_	_	NN	_	_	_
1256	course	course	NN	_	_	_
1257	:	:	:	_	_	_
1258	MURI	MURI	NNP	_	_	_
1259	_	_	SYM	_	_	_
1260	024	024	CD	_	_	_
1261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1262	glucose	glucose	NN	SUPP	_	_
1263	_	_	CD	_	_	_
1264	time	time	NN	_	_	_
1265	_	_	NN	_	_	_
1266	course	course	NN	_	_	_
1267	:	:	:	_	_	_
1268	MURI	MURI	NNP	_	_	_
1269	_	_	SYM	_	_	_
1270	025	025	CD	_	_	_
1271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1272	glucose	glucose	NN	SUPP	_	_
1273	_	_	CD	_	_	_
1274	time	time	NN	_	_	_
1275	_	_	NN	_	_	_
1276	course	course	NN	_	_	_
1277	:	:	:	_	_	_
1278	MURI	MURI	NNP	_	_	_
1279	_	_	SYM	_	_	_
1280	026	026	CD	_	_	_
1281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1282	glucose	glucose	NN	SUPP	_	_
1283	_	_	CD	_	_	_
1284	time	time	NN	_	_	_
1285	_	_	NN	_	_	_
1286	course	course	NN	_	_	_
1287	:	:	:	_	_	_
1288	MURI	MURI	NNP	_	_	_
1289	_	_	SYM	_	_	_
1290	027	027	CD	_	_	_
1291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1292	glucose	glucose	NN	SUPP	_	_
1293	_	_	CD	_	_	_
1294	time	time	NN	_	_	_
1295	_	_	NN	_	_	_
1296	course	course	NN	_	_	_
1297	:	:	:	_	_	_
1298	MURI	MURI	NNP	_	_	_
1299	_	_	SYM	_	_	_
1300	028	028	CD	_	_	_
1301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1302	glucose	glucose	NN	SUPP	_	_
1303	_	_	CD	_	_	_
1304	time	time	NN	_	_	_
1305	_	_	NN	_	_	_
1306	course	course	NN	_	_	_
1307	:	:	:	_	_	_
1308	MURI	MURI	NNP	_	_	_
1309	_	_	SYM	_	_	_
1310	029	029	CD	_	_	_
1311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1312	glucose	glucose	NN	SUPP	_	_
1313	_	_	CD	_	_	_
1314	time	time	NN	_	_	_
1315	_	_	NN	_	_	_
1316	course	course	NN	_	_	_
1317	:	:	:	_	_	_
1318	MURI	MURI	NNP	_	_	_
1319	_	_	SYM	_	_	_
1320	030	030	CD	_	_	_
1321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1322	glucose	glucose	NN	SUPP	_	_
1323	_	_	CD	_	_	_
1324	time	time	NN	_	_	_
1325	_	_	NN	_	_	_
1326	course	course	NN	_	_	_
1327	:	:	:	_	_	_
1328	MURI	MURI	NNP	_	_	_
1329	_	_	SYM	_	_	_
1330	031	031	CD	_	_	_
1331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1332	glucose	glucose	NN	SUPP	_	_
1333	_	_	CD	_	_	_
1334	time	time	NN	_	_	_
1335	_	_	NN	_	_	_
1336	course	course	NN	_	_	_
1337	:	:	:	_	_	_
1338	MURI	MURI	NNP	_	_	_
1339	_	_	SYM	_	_	_
1340	032	032	CD	_	_	_
1341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1342	glucose	glucose	NN	SUPP	_	_
1343	_	_	CD	_	_	_
1344	time	time	NN	_	_	_
1345	_	_	NN	_	_	_
1346	course	course	NN	_	_	_
1347	:	:	:	_	_	_
1348	MURI	MURI	NNP	_	_	_
1349	_	_	SYM	_	_	_
1350	033	033	CD	_	_	_
1351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1352	glucose	glucose	NN	SUPP	_	_
1353	_	_	CD	_	_	_
1354	time	time	NN	_	_	_
1355	_	_	NN	_	_	_
1356	course	course	NN	_	_	_
1357	:	:	:	_	_	_
1358	MURI	MURI	NNP	_	_	_
1359	_	_	SYM	_	_	_
1360	097	097	CD	_	_	_
1361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1362	glucose	glucose	NN	SUPP	_	_
1363	_	_	CD	_	_	_
1364	time	time	NN	_	_	_
1365	_	_	NN	_	_	_
1366	course	course	NN	_	_	_
1367	:	:	:	_	_	_
1368	MURI	MURI	NNP	_	_	_
1369	_	_	SYM	_	_	_
1370	098	098	CD	_	_	_
1371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1372	glucose	glucose	NN	SUPP	_	_
1373	_	_	CD	_	_	_
1374	time	time	NN	_	_	_
1375	_	_	NN	_	_	_
1376	course	course	NN	_	_	_
1377	:	:	:	_	_	_
1378	MURI	MURI	NNP	_	_	_
1379	_	_	SYM	_	_	_
1380	099	099	CD	_	_	_
1381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1382	glucose	glucose	NN	SUPP	_	_
1383	_	_	CD	_	_	_
1384	time	time	NN	_	_	_
1385	_	_	NN	_	_	_
1386	course	course	NN	_	_	_
1387	:	:	:	_	_	_
1388	MURI	MURI	NNP	_	_	_
1389	_	_	SYM	_	_	_
1390	100	100	CD	_	_	_
1391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1392	glucose	glucose	NN	SUPP	_	_
1393	_	_	CD	_	_	_
1394	time	time	NN	_	_	_
1395	_	_	NN	_	_	_
1396	course	course	NN	_	_	_
1397	:	:	:	_	_	_
1398	MURI	MURI	NNP	_	_	_
1399	_	_	SYM	_	_	_
1400	101	101	CD	_	_	_
1401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1402	glucose	glucose	NN	SUPP	_	_
1403	_	_	CD	_	_	_
1404	time	time	NN	_	_	_
1405	_	_	NN	_	_	_
1406	course	course	NN	_	_	_
1407	:	:	:	_	_	_
1408	MURI	MURI	NNP	_	_	_
1409	_	_	SYM	_	_	_
1410	102	102	CD	_	_	_
1411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1412	glucose	glucose	NN	SUPP	_	_
1413	_	_	CD	_	_	_
1414	time	time	NN	_	_	_
1415	_	_	NN	_	_	_
1416	course	course	NN	_	_	_
1417	:	:	:	_	_	_
1418	MURI	MURI	NNP	_	_	_
1419	_	_	NN	_	_	_
1420	103	103	CD	_	_	_
1421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1422	glucose	glucose	NN	SUPP	_	_
1423	_	_	CD	_	_	_
1424	time	time	NN	_	_	_
1425	_	_	NN	_	_	_
1426	course	course	NN	_	_	_
1427	:	:	:	_	_	_
1428	MURI	MURI	NNP	_	_	_
1429	_	_	VBD	_	_	_
1430	104	104	CD	_	_	_
1431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1432	glucose	glucose	NN	SUPP	_	_
1433	_	_	CD	_	_	_
1434	time	time	NN	_	_	_
1435	_	_	NN	_	_	_
1436	course	course	NN	_	_	_
1437	:	:	:	_	_	_
1438	MURI	MURI	NNP	_	_	_
1439	_	_	SYM	_	_	_
1440	105	105	CD	_	_	_
1441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1442	Glutamate	glutamate	JJ	_	_	_
1443	addition	addition	NN	_	_	_
1444	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1445	Glutamine	Glutamine	NNP	_	_	_
1446	addition	addition	NN	_	_	_
1447	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1448	Glycerol	Glycerol	NNP	_	_	_
1449	replicate	replicate	VB	_	_	_
1450	1	1	CD	_	_	_
1451	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1452	Glycerol	Glycerol	NNP	_	_	_
1453	replicate	replicate	VB	_	_	_
1454	2	2	CD	_	_	_
1455	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1456	Glycerol	Glycerol	NNP	_	_	_
1457	replicate	replicate	VB	_	_	_
1458	3	3	CD	_	_	_
1459	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1460	Glycerol	glycerol	NN	_	_	_
1461	stocks	stock	NNS	_	_	_
1462	of	of	IN	_	_	_
1463	E.	e.	FW	_	_	_
1464	coli	coli	FW	_	_	_
1465	K12	k12	NN	_	_	_
1466	strain	strain	NN	_	_	_
1467	MG1655	mg1655	NN	_	_	_
1468	were	be	VBD	_	_	_
1469	inoculated	inoculate	VBN	_	_	_
1470	into	into	IN	_	_	_
1471	LB	lb	NN	MED	_	_
1472	media	media	NNS	MED	_	_
1473	grown	grow	VBN	_	_	_
1474	at	at	IN	_	_	_
1475	37	37	CD	_	_	_
1476	℃	℃	NN	_	_	_
1477	with	with	IN	_	_	_
1478	constant	constant	JJ	_	_	_
1479	agitation	agitation	NN	_	_	_
1480	overnight	overnight	JJ	_	_	_
1481	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	glycerol	glycerol	NN	SUPP	_	_
3	_	_	CD	_	_	_
4	time	time	NN	_	_	_
5	_	_	NN	_	_	_
6	course	course	NN	_	_	_
7	:	:	:	_	_	_
8	MURI	MURI	NNP	_	_	_
9	_	_	SYM	_	_	_
10	034	034	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	glycerol	glycerol	NN	SUPP	_	_
13	_	_	CD	_	_	_
14	time	time	NN	_	_	_
15	_	_	NN	_	_	_
16	course	course	NN	_	_	_
17	:	:	:	_	_	_
18	MURI	MURI	NNP	_	_	_
19	_	_	SYM	_	_	_
20	035	035	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	glycerol	glycerol	NN	SUPP	_	_
23	_	_	CD	_	_	_
24	time	time	NN	_	_	_
25	_	_	NN	_	_	_
26	course	course	NN	_	_	_
27	:	:	:	_	_	_
28	MURI	MURI	NNP	_	_	_
29	_	_	SYM	_	_	_
30	036	036	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	glycerol	glycerol	NN	SUPP	_	_
33	_	_	CD	_	_	_
34	time	time	NN	_	_	_
35	_	_	NN	_	_	_
36	course	course	NN	_	_	_
37	:	:	:	_	_	_
38	MURI	MURI	NNP	_	_	_
39	_	_	SYM	_	_	_
40	037	037	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	glycerol	glycerol	NN	SUPP	_	_
43	_	_	CD	_	_	_
44	time	time	NN	_	_	_
45	_	_	NN	_	_	_
46	course	course	NN	_	_	_
47	:	:	:	_	_	_
48	MURI	MURI	NNP	_	_	_
49	_	_	SYM	_	_	_
50	038	038	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	glycerol	glycerol	NN	SUPP	_	_
53	_	_	CD	_	_	_
54	time	time	NN	_	_	_
55	_	_	NN	_	_	_
56	course	course	NN	_	_	_
57	:	:	:	_	_	_
58	MURI	MURI	NNP	_	_	_
59	_	_	SYM	_	_	_
60	039	039	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	glycerol	glycerol	NN	SUPP	_	_
63	_	_	CD	_	_	_
64	time	time	NN	_	_	_
65	_	_	NN	_	_	_
66	course	course	NN	_	_	_
67	:	:	:	_	_	_
68	MURI	MURI	NNP	_	_	_
69	_	_	SYM	_	_	_
70	040	040	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	glycerol	glycerol	NN	SUPP	_	_
73	_	_	CD	_	_	_
74	time	time	NN	_	_	_
75	_	_	NN	_	_	_
76	course	course	NN	_	_	_
77	:	:	:	_	_	_
78	MURI	MURI	NNP	_	_	_
79	_	_	SYM	_	_	_
80	041	041	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	glycerol	glycerol	NN	SUPP	_	_
83	_	_	CD	_	_	_
84	time	time	NN	_	_	_
85	_	_	NN	_	_	_
86	course	course	NN	_	_	_
87	:	:	:	_	_	_
88	MURI	MURI	NNP	_	_	_
89	_	_	SYM	_	_	_
90	042	042	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	glycerol	glycerol	NN	SUPP	_	_
93	_	_	CD	_	_	_
94	time	time	NN	_	_	_
95	_	_	NN	_	_	_
96	course	course	NN	_	_	_
97	:	:	:	_	_	_
98	MURI	MURI	NNP	_	_	_
99	_	_	SYM	_	_	_
100	043	043	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	glycerol	glycerol	NN	SUPP	_	_
103	_	_	CD	_	_	_
104	time	time	NN	_	_	_
105	_	_	NN	_	_	_
106	course	course	NN	_	_	_
107	:	:	:	_	_	_
108	MURI	MURI	NNP	_	_	_
109	_	_	SYM	_	_	_
110	044	044	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	glycerol	glycerol	NN	SUPP	_	_
113	_	_	CD	_	_	_
114	time	time	NN	_	_	_
115	_	_	NN	_	_	_
116	course	course	NN	_	_	_
117	:	:	:	_	_	_
118	MURI	MURI	NNP	_	_	_
119	_	_	SYM	_	_	_
120	045	045	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	glycerol	glycerol	NN	SUPP	_	_
123	_	_	CD	_	_	_
124	time	time	NN	_	_	_
125	_	_	NN	_	_	_
126	course	course	NN	_	_	_
127	:	:	:	_	_	_
128	MURI	MURI	NNP	_	_	_
129	_	_	SYM	_	_	_
130	046	046	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	glycerol	glycerol	NN	SUPP	_	_
133	_	_	CD	_	_	_
134	time	time	NN	_	_	_
135	_	_	NN	_	_	_
136	course	course	NN	_	_	_
137	:	:	:	_	_	_
138	MURI	MURI	NNP	_	_	_
139	_	_	SYM	_	_	_
140	047	047	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	glycerol	glycerol	NN	SUPP	_	_
143	_	_	CD	_	_	_
144	time	time	NN	_	_	_
145	_	_	NN	_	_	_
146	course	course	NN	_	_	_
147	:	:	:	_	_	_
148	MURI	MURI	NNP	_	_	_
149	_	_	SYM	_	_	_
150	048	048	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	glycerol	glycerol	NN	SUPP	_	_
153	_	_	CD	_	_	_
154	time	time	NN	_	_	_
155	_	_	NN	_	_	_
156	course	course	NN	_	_	_
157	:	:	:	_	_	_
158	MURI	MURI	NNP	_	_	_
159	_	_	SYM	_	_	_
160	049	049	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	glycerol	glycerol	NN	SUPP	_	_
163	_	_	CD	_	_	_
164	time	time	NN	_	_	_
165	_	_	NN	_	_	_
166	course	course	NN	_	_	_
167	:	:	:	_	_	_
168	MURI	MURI	NNP	_	_	_
169	_	_	SYM	_	_	_
170	050	050	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	glycerol	glycerol	NN	SUPP	_	_
173	_	_	CD	_	_	_
174	time	time	NN	_	_	_
175	_	_	NN	_	_	_
176	course	course	NN	_	_	_
177	:	:	:	_	_	_
178	MURI	MURI	NNP	_	_	_
179	_	_	SYM	_	_	_
180	052	052	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	glycerol	glycerol	NN	SUPP	_	_
183	_	_	CD	_	_	_
184	time	time	NN	_	_	_
185	_	_	NN	_	_	_
186	course	course	NN	_	_	_
187	:	:	:	_	_	_
188	MURI	MURI	NNP	_	_	_
189	_	_	SYM	_	_	_
190	053	053	CD	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	glycerol	glycerol	NN	SUPP	_	_
193	_	_	CD	_	_	_
194	time	time	NN	_	_	_
195	_	_	NN	_	_	_
196	course	course	NN	_	_	_
197	:	:	:	_	_	_
198	MURI	MURI	NNP	_	_	_
199	_	_	SYM	_	_	_
200	054	054	CD	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	glycerol	glycerol	NN	SUPP	_	_
203	_	_	CD	_	_	_
204	time	time	NN	_	_	_
205	_	_	NN	_	_	_
206	course	course	NN	_	_	_
207	:	:	:	_	_	_
208	MURI	MURI	NNP	_	_	_
209	_	_	SYM	_	_	_
210	055	055	CD	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	glycerol	glycerol	NN	SUPP	_	_
213	_	_	CD	_	_	_
214	time	time	NN	_	_	_
215	_	_	NN	_	_	_
216	course	course	NN	_	_	_
217	:	:	:	_	_	_
218	MURI	MURI	NNP	_	_	_
219	_	_	SYM	_	_	_
220	056	056	CD	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	glycerol	glycerol	NN	SUPP	_	_
223	_	_	CD	_	_	_
224	time	time	NN	_	_	_
225	_	_	NN	_	_	_
226	course	course	NN	_	_	_
227	:	:	:	_	_	_
228	MURI	MURI	NNP	_	_	_
229	_	_	SYM	_	_	_
230	057	057	CD	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	glycerol	glycerol	NN	SUPP	_	_
233	_	_	CD	_	_	_
234	time	time	NN	_	_	_
235	_	_	NN	_	_	_
236	course	course	NN	_	_	_
237	:	:	:	_	_	_
238	MURI	MURI	NNP	_	_	_
239	_	_	SYM	_	_	_
240	058	058	CD	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	glycerol	glycerol	NN	SUPP	_	_
243	_	_	CD	_	_	_
244	time	time	NN	_	_	_
245	_	_	NN	_	_	_
246	course	course	NN	_	_	_
247	:	:	:	_	_	_
248	MURI	MURI	NNP	_	_	_
249	_	_	SYM	_	_	_
250	059	059	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
252	Glycine	glycine	NN	_	_	_
253	addition	addition	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	go	go	VB	_	_	_
256	to	to	TO	_	_	_
257	the	the	DT	_	_	_
258	directory	directory	NN	_	_	_
259	:	:	:	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	GPR	gpr	NN	_	_	_
262	files	file	NNS	_	_	_
263	were	be	VBD	_	_	_
264	analyzed	analyze	VBN	_	_	_
265	further	further	RB	_	_	_
266	with	with	IN	_	_	_
267	Acuity	acuity	NN	_	_	_
268	4.0	4.0	CD	_	_	_
269	software	software	NN	_	_	_
270	-LRB-	-lrb-	-LRB-	_	_	_
271	Molecular	molecular	JJ	_	_	_
272	Devices	Devices	NNPS	_	_	_
273	,	,	,	_	_	_
274	USA	USA	NNP	_	_	_
275	-RRB-	-rrb-	-RRB-	_	_	_
276	starting	start	VBG	_	_	_
277	with	with	IN	_	_	_
278	lowess	lowess	NN	_	_	_
279	normalization	normalization	NN	_	_	_
280	.	.	.	_	_	_

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	gpt	gpt	NN	GEN	_	_
3	_	_	NN	_	_	_
4	0	0	CD	_	_	_
5	_	_	NN	_	_	_
6	Hx	hx	NN	_	_	_
7	Rep1	rep1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	gpt	gpt	NN	GEN	_	_
10	_	_	NN	_	_	_
11	0	0	CD	_	_	_
12	_	_	SYM	_	_	_
13	Hx	hx	FW	_	_	_
14	Rep2	rep2	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	gpt	gpt	NN	GEN	_	_
17	_	_	NN	_	_	_
18	0	0	CD	_	_	_
19	_	_	SYM	_	_	_
20	Hx	hx	FW	_	_	_
21	Rep3	rep3	JJ	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	gpt	gpt	NN	GEN	_	_
24	_	_	NN	_	_	_
25	120	120	CD	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Low	low	JJ	_	_	_
28	Dilution	dilution	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	Rep1	rep1	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	gpt	gpt	NN	GEN	_	_
33	_	_	NN	_	_	_
34	120	120	CD	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Low	low	JJ	_	_	_
37	Dilution	dilution	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	Rep2	rep2	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	gpt	gpt	NN	GEN	_	_
42	_	_	NN	_	_	_
43	120	120	CD	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Low	low	JJ	_	_	_
46	Dilution	dilution	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	Rep3	rep3	JJ	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	gpt	gpt	NN	GEN	_	_
51	_	_	CD	_	_	_
52	15	15	CD	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	Low	low	JJ	_	_	_
55	Dilution	dilution	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	Rep1	rep1	JJ	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	gpt	gpt	NN	GEN	_	_
60	_	_	CD	_	_	_
61	15	15	CD	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Low	low	JJ	_	_	_
64	Dilution	dilution	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	Rep2	rep2	JJ	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	gpt	gpt	NN	GEN	_	_
69	_	_	CD	_	_	_
70	15	15	CD	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	Low	low	JJ	_	_	_
73	Dilution	dilution	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	Rep3	rep3	JJ	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	gpt	gpt	NN	GEN	_	_
78	_	_	CD	_	_	_
79	30	30	CD	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	Low	low	JJ	_	_	_
82	Dilution	dilution	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	Rep1	rep1	JJ	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	gpt	gpt	NN	GEN	_	_
87	_	_	CD	_	_	_
88	30	30	CD	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	Low	low	JJ	_	_	_
91	Dilution	dilution	NN	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	Rep2	rep2	JJ	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	gpt	gpt	NN	GEN	_	_
96	_	_	CD	_	_	_
97	30	30	CD	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	Low	low	JJ	_	_	_
100	Dilution	dilution	NN	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	Rep3	rep3	JJ	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	gpt	gpt	NN	GEN	_	_
105	_	_	CD	_	_	_
106	45	45	CD	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	Low	low	JJ	_	_	_
109	Dilution	dilution	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	Rep1	rep1	JJ	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	gpt	gpt	NN	GEN	_	_
114	_	_	CD	_	_	_
115	45	45	CD	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	Low	low	JJ	_	_	_
118	Dilution	dilution	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	Rep2	rep2	JJ	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	gpt	gpt	NN	GEN	_	_
123	_	_	CD	_	_	_
124	45	45	CD	_	_	_
125	-LRB-	-lrb-	-LRB-	_	_	_
126	Low	low	JJ	_	_	_
127	Dilution	dilution	NN	_	_	_
128	-RRB-	-rrb-	-RRB-	_	_	_
129	Rep3	rep3	JJ	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	gpt	gpt	NN	GEN	_	_
132	_	_	CD	_	_	_
133	60	60	CD	_	_	_
134	-LRB-	-lrb-	-LRB-	_	_	_
135	Low	low	JJ	_	_	_
136	Dilution	dilution	NN	_	_	_
137	-RRB-	-rrb-	-RRB-	_	_	_
138	Rep1	rep1	JJ	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	gpt	gpt	NN	GEN	_	_
141	_	_	CD	_	_	_
142	60	60	CD	_	_	_
143	-LRB-	-lrb-	-LRB-	_	_	_
144	Low	low	JJ	_	_	_
145	Dilution	dilution	NN	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	Rep2	rep2	JJ	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	gpt	gpt	NN	GEN	_	_
150	_	_	CD	_	_	_
151	60	60	CD	_	_	_
152	-LRB-	-lrb-	-LRB-	_	_	_
153	Low	low	JJ	_	_	_
154	Dilution	dilution	NN	_	_	_
155	-RRB-	-rrb-	-RRB-	_	_	_
156	Rep3	rep3	JJ	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	gpt	gpt	NN	GEN	_	_
159	strain	strain	NN	_	_	_
160	with	with	IN	_	_	_
161	hypoxanthine	hypoxanthine	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	gpt	gpt	NN	GEN	_	_
164	strain	strain	NN	_	_	_
165	w/o	w/o	NN	_	_	_
166	hypoxanthine	hypoxanthine	NN	_	_	_
167	120	120	CD	_	_	_
168	min	min	NN	_	_	_
169	at	at	IN	_	_	_
170	low	low	JJ	_	_	_
171	dilution	dilution	NN	_	_	_
172	protocol	protocol	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	gpt	gpt	NN	GEN	_	_
175	strain	strain	NN	_	_	_
176	w/o	w/o	NN	_	_	_
177	hypoxanthine	hypoxanthine	NN	_	_	_
178	15	15	CD	_	_	_
179	min	min	NN	_	_	_
180	at	at	IN	_	_	_
181	low	low	JJ	_	_	_
182	dilution	dilution	NN	_	_	_
183	protocol	protocol	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	gpt	gpt	NN	GEN	_	_
186	strain	strain	NN	_	_	_
187	w/o	w/o	NN	_	_	_
188	hypoxanthine	hypoxanthine	NN	_	_	_
189	30	30	CD	_	_	_
190	min	min	NN	_	_	_
191	at	at	IN	_	_	_
192	low	low	JJ	_	_	_
193	dilution	dilution	NN	_	_	_
194	protocol	protocol	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	gpt	gpt	NN	GEN	_	_
197	strain	strain	NN	_	_	_
198	w/o	w/o	NN	_	_	_
199	hypoxanthine	hypoxanthine	NN	_	_	_
200	45	45	CD	_	_	_
201	min	min	NN	_	_	_
202	at	at	IN	_	_	_
203	low	low	JJ	_	_	_
204	dilution	dilution	NN	_	_	_
205	protocol	protocol	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	gpt	gpt	NN	GEN	_	_
208	strain	strain	NN	_	_	_
209	w/o	w/o	NN	_	_	_
210	hypoxanthine	hypoxanthine	NN	_	_	_
211	60	60	CD	_	_	_
212	min	min	NN	_	_	_
213	at	at	IN	_	_	_
214	low	low	JJ	_	_	_
215	dilution	dilution	NN	_	_	_
216	protocol	protocol	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	gram	gram	NN	_	_	_
219	status	status	NN	_	_	_
220	:	:	:	_	_	_
221	Gram-negative	gram-negative	JJ	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	graphics.off	graphics.off	NN	_	_	_
224	-LRB-	-lrb-	-LRB-	_	_	_
225	-RRB-	-rrb-	-RRB-	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	group	group	NN	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	hus/non-hus	hus/non-hus	JJ	_	_	_
230	-RRB-	-rrb-	-RRB-	_	_	_
231	:	:	:	_	_	_
232	HUS	hus	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	group	group	NN	_	_	_
235	-LRB-	-lrb-	-LRB-	_	_	_
236	hus/non-hus	hus/non-hus	JJ	_	_	_
237	-RRB-	-rrb-	-RRB-	_	_	_
238	:	:	:	_	_	_
239	Non-HUS	non-hus	JJ	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
241	Grow	grow	VBP	_	_	_
242	bacteria	bacterium	NNS	_	_	_
243	overnight	overnight	JJ	_	_	_
244	in	in	IN	_	_	_
245	LB	lb	NN	MED	_	_
246	medium	medium	NN	MED	_	_
247	,	,	,	_	_	_
248	reinoculate	reinoculate	NN	_	_	_
249	in	in	IN	_	_	_
250	M9	m9	NN	MED	_	_
251	minimal	minimal	JJ	MED	_	_
252	medium	medium	NN	MED	_	_
253	at	at	IN	_	_	_
254	an	a	DT	_	_	_
255	initial	initial	JJ	_	_	_
256	OD600	od600	NN	_	_	_
257	of	of	IN	_	_	_
258	0.005	0.005	CD	_	_	_
259	.	.	.	_	_	_

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	NNP	_	_	_
9	Growing	grow	VBG	_	_	_
10	t	t	NN	_	_	_
11	=	=	JJ	_	_	_
12	1	1	CD	_	_	_
13	hour	hour	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Grown	grow	VBN	_	_	_
16	in	in	IN	_	_	_
17	Davis	Davis	NNP	_	_	_
18	's	's	POS	_	_	_
19	Mineral	Mineral	NNP	_	_	_
20	Salts	salt	NNS	_	_	_
21	medium	medium	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Gibco	Gibco	NNP	_	_	_
24	BRL	brl	NN	_	_	_
25	Life	Life	NNP	_	_	_
26	Technologies	Technologies	NNP	_	_	_
27	Inc.	Inc.	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	with	with	IN	_	_	_
30	0.1	0.1	CD	_	_	_
31	%	%	NN	_	_	_
32	D-glucose	d-glucose	NN	_	_	_
33	at	at	IN	_	_	_
34	25	25	CD	_	_	_
35	C	c	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	100	100	CD	_	_	_
38	r.p.m.	r.p.m.	NN	_	_	_
39	shaking	shake	VBG	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	until	until	IN	_	_	_
42	an	a	DT	_	_	_
43	OD	od	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	550	550	CD	_	_	_
46	nm	nm	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	of	of	IN	_	_	_
49	0.6	0.6	CD	_	_	_
50	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Grown	Grown	NNP	_	_	_
3	in	in	IN	_	_	_
4	glucose	glucose	NN	SUPP	_	_
5	M9	m9	NN	_	_	_
6	media	media	NNS	_	_	_
7	supplemented	supplement	VBN	_	_	_
8	with	with	IN	_	_	_
9	0.55	0.55	CD	_	_	_
10	M	m	NN	_	_	_
11	NaCl	nacl	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Grown	Grown	NNP	_	_	_
14	in	in	IN	_	_	_
15	glucose	glucose	NN	SUPP	_	_
16	M9	m9	NN	_	_	_
17	media	media	NNS	_	_	_
18	with	with	IN	_	_	_
19	or	or	CC	_	_	_
20	without	without	IN	_	_	_
21	supplementation	supplementation	NN	_	_	_
22	of	of	IN	_	_	_
23	0.6	0.6	CD	_	_	_
24	M	m	NN	_	_	_
25	NaCl	nacl	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	grown	grow	VBN	_	_	_
28	to	to	TO	_	_	_
29	OD600	od600	NN	_	_	_
30	=	=	JJ	_	_	_
31	1.0	1.0	CD	_	_	_
32	in	in	IN	_	_	_
33	DMEM	DMEM	NNP	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	grown	grow	VBN	_	_	_
36	to	to	TO	_	_	_
37	OD600	od600	NN	_	_	_
38	=	=	JJ	_	_	_
39	1.0	1.0	CD	_	_	_
40	in	in	IN	_	_	_
41	DMEM	dmem	NN	_	_	_
42	with	with	IN	_	_	_
43	50	50	CD	_	_	_
44	uM	um	NN	_	_	_
45	epinephrine	epinephrine	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	grown	grow	VBN	_	_	_
48	to	to	TO	_	_	_
49	OD600	od600	NN	_	_	_
50	=	=	JJ	_	_	_
51	1.0	1.0	CD	_	_	_
52	in	in	IN	_	_	_
53	DMEM	dmem	NN	_	_	_
54	with	with	IN	_	_	_
55	AI3	ai3	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	grown	grow	VBN	_	_	_
58	to	to	TO	_	_	_
59	OD600	od600	NN	_	_	_
60	=	=	JJ	_	_	_
61	1.0	1.0	CD	_	_	_
62	in	in	IN	_	_	_
63	DMEM	dmem	NN	_	_	_
64	with	with	IN	_	_	_
65	AI3	ai3	NN	_	_	_
66	signaling	signaling	NN	_	_	_
67	molecule	molecule	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	grown	grow	VBN	_	_	_
70	to	to	TO	_	_	_
71	OD600	od600	NN	_	_	_
72	=	=	JJ	_	_	_
73	1.0	1.0	CD	_	_	_
74	in	in	IN	_	_	_
75	DMEM	dmem	NN	_	_	_
76	with	with	IN	_	_	_
77	Epinephrine	epinephrine	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	grown	grow	VBN	_	_	_
80	to	to	TO	_	_	_
81	OD600	od600	NN	_	_	_
82	=	=	JJ	_	_	_
83	1.0	1.0	CD	_	_	_
84	in	in	IN	_	_	_
85	LB	LB	NNP	_	_	_
86	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
87	Growth	growth	NN	_	_	_
88	:	:	:	_	_	_
89	Anaerobic	anaerobic	JJ	_	_	_
90	to	to	TO	_	_	_
91	early	early	JJ	_	_	_
92	exponential	exponential	JJ	_	_	_
93	growth	growth	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	growth	growth	NN	_	_	_
96	condition	condition	NN	_	_	_
97	:	:	:	_	_	_
98	16	16	CD	_	_	_
99	µM	µm	NN	_	_	_
100	IPTG	iptg	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	growth	growth	NN	_	_	_
103	condition	condition	NN	_	_	_
104	:	:	:	_	_	_
105	25	25	CD	_	_	_
106	μl	μl	NN	_	_	_
107	into	into	IN	_	_	_
108	K-medium	k-medium	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	growth	growth	NN	_	_	_
111	condition	condition	NN	_	_	_
112	:	:	:	_	_	_
113	4	4	CD	_	_	_
114	µM	µm	NN	_	_	_
115	IPTG	iptg	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	growth	growth	NN	_	_	_
118	condition	condition	NN	_	_	_
119	:	:	:	_	_	_
120	50	50	CD	_	_	_
121	µl	µl	NN	_	_	_
122	into	into	IN	_	_	_
123	K-medium	k-medium	NN	_	_	_
124	+	+	CC	_	_	_
125	0.3	0.3	CD	_	_	_
126	M	m	NN	_	_	_
127	NaCl	nacl	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	growth	growth	NN	_	_	_
130	condition	condition	NN	_	_	_
131	:	:	:	_	_	_
132	75	75	CD	_	_	_
133	µl	µl	NN	_	_	_
134	into	into	IN	_	_	_
135	K-medium	k-medium	NN	_	_	_
136	+	+	CC	_	_	_
137	0.6	0.6	CD	_	_	_
138	M	m	NN	_	_	_
139	urea	urea	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	growth	growth	NN	_	_	_
142	condition	condition	NN	_	_	_
143	:	:	:	_	_	_
144	8	8	CD	_	_	_
145	µM	µm	NN	_	_	_
146	IPTG	iptg	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	growth	growth	NN	_	_	_
149	condition	condition	NN	_	_	_
150	:	:	:	_	_	_
151	Adenine	Adenine	NNP	_	_	_
152	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
153	growth	growth	NN	_	_	_
154	condition	condition	NN	_	_	_
155	:	:	:	_	_	_
156	Aerobic	aerobic	JJ	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	growth	growth	NN	_	_	_
159	condition	condition	NN	_	_	_
160	:	:	:	_	_	_
161	Aerobic	Aerobic	NNP	_	_	_
162	Cultures	Cultures	NNP	_	_	_
163	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
164	growth	growth	NN	_	_	_
165	condition	condition	NN	_	_	_
166	:	:	:	_	_	_
167	anaerobic	anaerobic	JJ	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	growth	growth	NN	_	_	_
170	condition	condition	NN	_	_	_
171	:	:	:	_	_	_
172	Anaerobic	anaerobic	JJ	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	growth	growth	NN	_	_	_
175	condition	condition	NN	_	_	_
176	:	:	:	_	_	_
177	Anaerobic	anaerobic	JJ	_	_	_
178	Cultures	culture	NNS	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	growth	growth	NN	_	_	_
181	condition	condition	NN	_	_	_
182	:	:	:	_	_	_
183	early-exponential	early-exponential	JJ	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	growth	growth	NN	_	_	_
186	condition	condition	NN	_	_	_
187	:	:	:	_	_	_
188	Exponential	Exponential	NNP	_	_	_
189	+	+	CC	_	_	_
190	O2	o2	CD	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	growth	growth	NN	_	_	_
193	condition	condition	NN	_	_	_
194	:	:	:	_	_	_
195	glucose	glucose	NN	SUPP	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	growth	growth	NN	_	_	_
198	condition	condition	NN	_	_	_
199	:	:	:	_	_	_
200	Inside	inside	IN	_	_	_
201	Acanthamoeba	acanthamoeba	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	growth	growth	NN	_	_	_
204	condition	condition	NN	_	_	_
205	:	:	:	_	_	_
206	LB	lb	NN	_	_	_
207	at	at	IN	_	_	_
208	30	30	CD	_	_	_
209	°C	°c	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	growth	growth	NN	_	_	_
212	condition	condition	NN	_	_	_
213	:	:	:	_	_	_
214	LB	lb	NN	_	_	_
215	at	at	IN	_	_	_
216	37	37	CD	_	_	_
217	°C	°c	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	growth	growth	NN	_	_	_
220	condition	condition	NN	_	_	_
221	:	:	:	_	_	_
222	LB	lb	NN	MED	_	_
223	broth	broth	NN	MED	_	_
224	alone	alone	RB	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	control	control	NN	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	growth	growth	NN	_	_	_
230	condition	condition	NN	_	_	_
231	:	:	:	_	_	_
232	LB	lb	NN	MED	_	_
233	broth	broth	NN	MED	_	_
234	supplemented	supplement	VBN	_	_	_
235	with	with	IN	_	_	_
236	cranberry	cranberry	NN	_	_	_
237	PACs	pac	NNS	_	_	_
238	-LRB-	-lrb-	-LRB-	_	_	_
239	100	100	CD	_	_	_
240	µg/mL	µg/ml	NN	_	_	_
241	-RRB-	-rrb-	-RRB-	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	growth	growth	NN	_	_	_
244	condition	condition	NN	_	_	_
245	:	:	:	_	_	_
246	mid-exponential	mid-exponential	JJ	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	growth	growth	NN	_	_	_
249	condition	condition	NN	_	_	_
250	:	:	:	_	_	_
251	MM	mm	NN	_	_	_
252	+	+	CC	_	_	_
253	0.12	0.12	CD	_	_	_
254	%	%	NN	_	_	_
255	casaminoacids	casaminoacid	NNS	_	_	_
256	+0.4	+0.4	CD	_	_	_
257	%	%	NN	_	_	_
258	glucose	glucose	NN	SUPP	_	_
259	at	at	IN	_	_	_
260	22	22	CD	_	_	_
261	°C	°c	NN	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	growth	growth	NN	_	_	_
264	condition	condition	NN	_	_	_
265	:	:	:	_	_	_
266	MM	mm	NN	_	_	_
267	+	+	CC	_	_	_
268	0.12	0.12	CD	_	_	_
269	%	%	NN	_	_	_
270	casaminoacids	casaminoacid	NNS	_	_	_
271	+0.4	+0.4	CD	_	_	_
272	%	%	NN	_	_	_
273	glucose	glucose	NN	SUPP	_	_
274	at	at	IN	_	_	_
275	30	30	CD	_	_	_
276	°C	°c	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	growth	growth	NN	_	_	_
279	condition	condition	NN	_	_	_
280	:	:	:	_	_	_
281	normal	normal	JJ	_	_	_
282	condtion	condtion	NN	_	_	_
283	-LRB-	-lrb-	-LRB-	_	_	_
284	5	5	CD	_	_	_
285	%	%	NN	_	_	_
286	w/v	w/v	NN	_	_	_
287	glucose	glucose	NN	SUPP	_	_
288	-RRB-	-rrb-	-RRB-	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	growth	growth	NN	_	_	_
291	condition	condition	NN	_	_	_
292	:	:	:	_	_	_
293	osmotic	osmotic	JJ	_	_	_
294	stress	stress	NN	_	_	_
295	condtion	condtion	NN	_	_	_
296	-LRB-	-lrb-	-LRB-	_	_	_
297	12	12	CD	_	_	_
298	%	%	NN	_	_	_
299	w/v	w/v	NN	_	_	_
300	glucose	glucose	NN	SUPP	_	_
301	-RRB-	-rrb-	-RRB-	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	growth	growth	NN	_	_	_
304	condition	condition	NN	_	_	_
305	:	:	:	_	_	_
306	Outside	outside	JJ	_	_	_
307	Control	control	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	Growth	growth	NN	_	_	_
310	conditions	condition	NNS	_	_	_
311	:	:	:	_	_	_
312	aaerobic	aaerobic	JJ	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
314	Growth	growth	NN	_	_	_
315	conditions	condition	NNS	_	_	_
316	:	:	:	_	_	_
317	aerobic	aerobic	JJ	_	_	_
318	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
319	Growth	growth	NN	_	_	_
320	conditions	condition	NNS	_	_	_
321	:	:	:	_	_	_
322	anaerobic	anaerobic	JJ	_	_	_
323	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
324	Growth	growth	NN	_	_	_
325	conditions	condition	NNS	_	_	_
326	:	:	:	_	_	_
327	anaerobic	anaerobic	JJ	_	_	_
328	plus	plus	CC	_	_	_
329	NO2	no2	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
331	Growth	growth	NN	_	_	_
332	conditions	condition	NNS	_	_	_
333	:	:	:	_	_	_
334	anaerobic	anaerobic	JJ	_	_	_
335	plus	plus	CC	_	_	_
336	NO3	no3	NN	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	growth	growth	NN	_	_	_
339	conditions	condition	NNS	_	_	_
340	:	:	:	_	_	_
341	LB	lb	NN	_	_	_
342	growth	growth	NN	_	_	_
343	OD	od	NN	_	_	_
344	0,3	0,3	CD	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	growth	growth	NN	_	_	_
347	conditions	condition	NNS	_	_	_
348	:	:	:	_	_	_
349	LB	lb	NN	_	_	_
350	growth	growth	NN	_	_	_
351	OD	od	NN	_	_	_
352	0,5	0,5	CD	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	growth	growth	NN	_	_	_
355	conditions	condition	NNS	_	_	_
356	:	:	:	_	_	_
357	Minimal	minimal	JJ	_	_	_
358	Medium	medium	NN	_	_	_
359	A	a	DT	_	_	_
360	supplemented	supplement	VBN	_	_	_
361	with	with	IN	_	_	_
362	casaminoacids	casaminoacid	NNS	_	_	_
363	-LRB-	-lrb-	-LRB-	_	_	_
364	0,1	0,1	CD	_	_	_
365	%	%	NN	_	_	_
366	-RRB-	-rrb-	-RRB-	_	_	_
367	and	and	CC	_	_	_
368	succinate	succinate	NN	SUPP	_	_
369	-LRB-	-lrb-	-LRB-	_	_	_
370	0,2	0,2	CD	_	_	_
371	%	%	NN	_	_	_
372	-RRB-	-rrb-	-RRB-	_	_	_
373	,	,	,	_	_	_
374	OD	od	NN	_	_	_
375	0,2	0,2	CD	_	_	_
376	at	at	IN	_	_	_
377	40	40	CD	_	_	_
378	°C	°c	NN	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	growth	growth	NN	_	_	_
381	condition	condition	NN	_	_	_
382	:	:	:	_	_	_
383	Static	static	JJ	_	_	_
384	+	+	CC	_	_	_
385	O2	o2	CD	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	growth	growth	NN	_	_	_
388	condition	condition	NN	_	_	_
389	:	:	:	_	_	_
390	stationary	stationary	JJ	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	growth	growth	NN	_	_	_
393	condition	condition	NN	_	_	_
394	:	:	:	_	_	_
395	steady-state	steady-state	JJ	_	_	_
396	continuous	continuous	JJ	_	_	_
397	cultivation	cultivation	NN	_	_	_
398	-LRB-	-lrb-	-LRB-	_	_	_
399	dilution	dilution	NN	_	_	_
400	rate	rate	NN	_	_	_
401	of	of	IN	_	_	_
402	0.4	0.4	CD	_	_	_
403	h-1	h-1	NN	_	_	_
404	-RRB-	-rrb-	-RRB-	_	_	_
405	,	,	,	_	_	_
406	aerobic	aerobic	JJ	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	growth	growth	NN	_	_	_
409	condition	condition	NN	_	_	_
410	:	:	:	_	_	_
411	transition-to-stationary	transition-to-stationary	JJ	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
413	Growth	growth	NN	_	_	_
414	curves	curve	NNS	_	_	_
415	of	of	IN	_	_	_
416	all	all	DT	_	_	_
417	selected	select	VBN	_	_	_
418	evolved	evolve	VBD	_	_	_
419	colony	colony	NN	_	_	_
420	types	type	NNS	_	_	_
421	and	and	CC	_	_	_
422	the	the	DT	_	_	_
423	ancestor	ancestor	NN	_	_	_
424	were	be	VBD	_	_	_
425	obtained	obtain	VBN	_	_	_
426	by	by	IN	_	_	_
427	growing	grow	VBG	_	_	_
428	them	they	PRP	_	_	_
429	under	under	IN	_	_	_
430	their	they	PRP$	_	_	_
431	evolved	evolve	VBN	_	_	_
432	environmental	environmental	JJ	_	_	_
433	conditions	condition	NNS	_	_	_
434	in	in	IN	_	_	_
435	LB	lb	NN	MED	_	_
436	medium	medium	NN	MED	_	_
437	until	until	IN	_	_	_
438	Log-phase	log-phase	NN	_	_	_
439	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	grow	grow	VBP	_	_	_
3	|	|	SYM	_	_	_
4	The	the	DT	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	K-12	k-12	NN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	bacterial	bacterial	JJ	_	_	_
10	strains	strain	NNS	_	_	_
11	used	use	VBN	_	_	_
12	in	in	IN	_	_	_
13	this	this	DT	_	_	_
14	work	work	NN	_	_	_
15	are	be	VBP	_	_	_
16	the	the	DT	_	_	_
17	following	following	NN	_	_	_
18	:	:	:	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	MG1655	mg1655	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	F	f	NN	_	_	_
24	-	-	:	_	_	_
25	lambda	lambda	NN	_	_	_
26	-	-	:	_	_	_
27	ilvG	ilvg	NN	_	_	_
28	-	-	:	_	_	_
29	rfb-50	rfb-50	NN	_	_	_
30	rph-1	rph-1	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	;	;	:	_	_	_
33	MG1655	mg1655	NN	_	_	_
34	hns	hn	NNS	GEN	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	hns	hn	NNS	GEN	_	_
37	:	:	:	_	_	_
38	:	:	:	_	_	_
39	Kanr	kanr	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	;	;	:	_	_	_
42	MG1655	mg1655	NN	_	_	_
43	fis	fis	NN	GEN	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	fis	fis	NN	GEN	_	_
46	:	:	:	_	_	_
47	:	:	:	_	_	_
48	Kanr	kanr	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	;	;	:	_	_	_
51	MG1655	mg1655	NN	_	_	_
52	hns-FLAG	hns-flag	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	hns	hn	NNS	GEN	_	_
55	:	:	:	_	_	_
56	:	:	:	_	_	_
57	3xFLAG	3xflag	NN	_	_	_
58	:	:	:	_	_	_
59	:	:	:	_	_	_
60	Kanr	kanr	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	;	;	:	_	_	_
63	MG1655	mg1655	NN	_	_	_
64	fis-FLAG	fis-flag	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	fis	fis	NN	GEN	_	_
67	:	:	:	_	_	_
68	:	:	:	_	_	_
69	3xFLAG	3xflag	NN	_	_	_
70	:	:	:	_	_	_
71	:	:	:	_	_	_
72	Kanr	kanr	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	.	.	.	_	_	_

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/liter	g/liter	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	were	be	VBD	_	_	_
15	used	use	VBN	_	_	_
16	for	for	IN	_	_	_
17	routine	routine	JJ	_	_	_
18	growth	growth	NN	_	_	_
19	.	.	.	_	_	_

1	Where	where	WRB	_	_	_
2	needed	need	VBN	_	_	_
3	,	,	,	_	_	_
4	ampicillin	ampicillin	NN	_	_	_
5	,	,	,	_	_	_
6	kanamycin	kanamycin	NN	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	chloramphenicol	chloramphenicol	NN	_	_	_
10	were	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	at	at	IN	_	_	_
13	final	final	JJ	_	_	_
14	concentrations	concentration	NNS	_	_	_
15	of	of	IN	_	_	_
16	100	100	CD	_	_	_
17	,	,	,	_	_	_
18	30	30	CD	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	30	30	CD	_	_	_
22	ug/ml	ug/ml	NN	_	_	_
23	respectively	respectively	RB	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	growth	growth	NN	_	_	_
3	environment	environment	NN	_	_	_
4	:	:	:	_	_	_
5	Aerobic	aerobic	JJ	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	growth	growth	NN	_	_	_
8	environment	environment	NN	_	_	_
9	:	:	:	_	_	_
10	Anaerobic	anaerobic	JJ	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	growth	growth	NN	_	_	_
13	media	media	NNS	_	_	_
14	:	:	:	_	_	_
15	DMEM	dmem	NN	_	_	_
16	growth	growth	NN	_	_	_
17	media	media	NNS	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	growth	growth	NN	_	_	_
20	media	media	NNS	_	_	_
21	:	:	:	_	_	_
22	LB	lb	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	growth	growth	NN	_	_	_
25	media	media	NNS	_	_	_
26	:	:	:	_	_	_
27	LB	lb	NN	_	_	_
28	;	;	:	_	_	_
29	0.8	0.8	CD	_	_	_
30	%	%	NN	_	_	_
31	bile	bile	NN	_	_	_
32	salts	salt	NNS	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	growth	growth	NN	_	_	_
35	media	media	NNS	_	_	_
36	:	:	:	_	_	_
37	LB	lb	NN	MED	_	_
38	medium	medium	NN	MED	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	growth	growth	NN	_	_	_
41	medium	medium	NN	_	_	_
42	:	:	:	_	_	_
43	Combined	combine	VBN	_	_	_
44	input	input	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	growth	growth	NN	_	_	_
47	medium	medium	NN	_	_	_
48	:	:	:	_	_	_
49	LB	lb	NN	_	_	_
50	+	+	CC	_	_	_
51	glycerol	glycerol	NN	SUPP	_	_
52	medium	medium	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	growth	growth	NN	_	_	_
55	medium	medium	NN	_	_	_
56	:	:	:	_	_	_
57	LB	lb	NN	MED	_	_
58	medium	medium	NN	MED	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	growth	growth	NN	_	_	_
61	medium	medium	NN	_	_	_
62	:	:	:	_	_	_
63	liquid	liquid	JJ	_	_	_
64	culture	culture	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	Growth	Growth	NNP	_	_	_
67	medium	medium	NN	_	_	_
68	:	:	:	_	_	_
69	MOPS	mop	NNS	MED	_	_
70	minimal	minimal	JJ	_	_	_
71	,	,	,	_	_	_
72	0.4	0.4	CD	_	_	_
73	%	%	NN	_	_	_
74	glucose	glucose	NN	SUPP	_	_
75	,	,	,	_	_	_
76	0.5	0.5	CD	_	_	_
77	%	%	NN	_	_	_
78	casamino	casamino	NN	SUPP	_	_
79	acids	acid	NNS	SUPP	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	growth	growth	NN	_	_	_
82	medium	medium	NN	_	_	_
83	:	:	:	_	_	_
84	MOPS	mop	NNS	MED	_	_
85	minimal	minimal	JJ	_	_	_
86	glucose	glucose	NN	SUPP	_	_
87	media	media	NNS	_	_	_
88	containing	contain	VBG	_	_	_
89	10	10	CD	_	_	_
90	µM	µm	NN	_	_	_
91	FeSO4	feso4	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	growth	growth	NN	_	_	_
94	medium	medium	NN	_	_	_
95	:	:	:	_	_	_
96	MOPS	mop	NNS	MED	_	_
97	minimal	minimal	JJ	_	_	_
98	glucose	glucose	NN	SUPP	_	_
99	media	media	NNS	_	_	_
100	containing	contain	VBG	_	_	_
101	1	1	CD	_	_	_
102	µM	µm	NN	_	_	_
103	FeSO4	feso4	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	growth	growth	NN	_	_	_
106	mode	mode	NN	_	_	_
107	:	:	:	_	_	_
108	planktonic	planktonic	JJ	_	_	_
109	culture	culture	NN	_	_	_
110	in	in	IN	_	_	_
111	annular	annular	JJ	_	_	_
112	reactor	reactor	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	growth	growth	NN	_	_	_
115	phase	phase	NN	_	_	_
116	:	:	:	_	_	_
117	30	30	CD	_	_	_
118	min	min	NN	_	_	_
119	post	post	NN	_	_	_
120	stationary	stationary	JJ	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	growth	growth	NN	_	_	_
123	phase	phase	NN	_	_	_
124	:	:	:	_	_	_
125	Early	early	JJ	_	_	_
126	exponential	exponential	JJ	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	growth	growth	NN	_	_	_
129	phase	phase	NN	_	_	_
130	:	:	:	_	_	_
131	Early	early	JJ	_	_	_
132	Exponential	exponential	JJ	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	growth	growth	NN	_	_	_
135	phase	phase	NN	_	_	_
136	:	:	:	_	_	_
137	Exp	exp	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	growth	growth	NN	_	_	_
140	phase	phase	NN	_	_	_
141	:	:	:	_	_	_
142	Exp1	exp1	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	growth	growth	NN	_	_	_
145	phase	phase	NN	_	_	_
146	:	:	:	_	_	_
147	Exp2	exp2	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	growth	growth	NN	_	_	_
150	phase	phase	NN	_	_	_
151	:	:	:	_	_	_
152	Exp3	exp3	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	growth	growth	NN	_	_	_
155	phase	phase	NN	_	_	_
156	:	:	:	_	_	_
157	exponential	exponential	JJ	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	growth	growth	NN	_	_	_
160	phase	phase	NN	_	_	_
161	:	:	:	_	_	_
162	Exponential	exponential	JJ	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	Growth	growth	NN	_	_	_
165	phase	phase	NN	_	_	_
166	:	:	:	_	_	_
167	exponential	exponential	JJ	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	growth	growth	NN	_	_	_
170	phase	phase	NN	_	_	_
171	:	:	:	_	_	_
172	exponential	exponential	JJ	_	_	_
173	growth	growth	NN	_	_	_
174	phase	phase	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	growth	growth	NN	_	_	_
177	phase	phase	NN	_	_	_
178	:	:	:	_	_	_
179	Exponential	Exponential	NNP	_	_	_
180	Phase	phase	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	growth	growth	NN	_	_	_
183	phase	phase	NN	_	_	_
184	:	:	:	_	_	_
185	Late	late	JJ	_	_	_
186	exponential/Early	exponential/early	JJ	_	_	_
187	stationary	stationary	JJ	_	_	_
188	-LRB-	-lrb-	-LRB-	_	_	_
189	OD	od	JJ	_	_	_
190	~	~	NN	_	_	_
191	1.8	1.8	CD	_	_	_
192	-RRB-	-rrb-	-RRB-	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	growth	growth	NN	_	_	_
195	phase	phase	NN	_	_	_
196	:	:	:	_	_	_
197	late	late	JJ	_	_	_
198	_	_	NN	_	_	_
199	stationary	stationary	JJ	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	growth	growth	NN	_	_	_
202	phase	phase	NN	_	_	_
203	:	:	:	_	_	_
204	Late	late	JJ	_	_	_
205	Stationary	stationary	JJ	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	growth	growth	NN	_	_	_
208	phase	phase	NN	_	_	_
209	:	:	:	_	_	_
210	logarithmic	logarithmic	JJ	_	_	_
211	growth	growth	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	growth	growth	NN	_	_	_
214	phase	phase	NN	_	_	_
215	:	:	:	_	_	_
216	log	log	NN	_	_	_
217	phase	phase	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	growth	growth	NN	_	_	_
220	phase	phase	NN	_	_	_
221	:	:	:	_	_	_
222	Log	log	VB	_	_	_
223	phase	phase	NN	_	_	_
224	OD	od	NN	_	_	_
225	0.4	0.4	CD	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	growth	growth	NN	_	_	_
228	phase	phase	NN	_	_	_
229	:	:	:	_	_	_
230	Mid	Mid	NNP	_	_	_
231	exponential	exponential	JJ	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	growth	growth	NN	_	_	_
234	phase	phase	NN	_	_	_
235	:	:	:	_	_	_
236	Mid-Exponential	mid-exponential	JJ	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	growth	growth	NN	_	_	_
239	phase	phase	NN	_	_	_
240	:	:	:	_	_	_
241	mid-log	mid-log	JJ	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	growth	growth	NN	_	_	_
244	phase	phase	NN	_	_	_
245	:	:	:	_	_	_
246	mid-log	mid-log	JJ	_	_	_
247	phase	phase	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	growth	growth	NN	_	_	_
250	phase	phase	NN	_	_	_
251	:	:	:	_	_	_
252	mid-log	mid-log	JJ	_	_	_
253	phase	phase	NN	_	_	_
254	-LRB-	-lrb-	-LRB-	_	_	_
255	OD600	od600	NN	_	_	_
256	=	=	JJ	_	_	_
257	0.3	0.3	CD	_	_	_
258	-RRB-	-rrb-	-RRB-	_	_	_
259	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
260	Growth	Growth	NNP	_	_	_
261	phase	phase	NN	_	_	_
262	:	:	:	_	_	_
263	OD600	od600	NN	_	_	_
264	=	=	JJ	_	_	_
265	0.3	0.3	CD	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	growth	growth	NN	_	_	_
268	phase	phase	NN	_	_	_
269	:	:	:	_	_	_
270	Stat	stat	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	growth	growth	NN	_	_	_
273	phase	phase	NN	_	_	_
274	:	:	:	_	_	_
275	stat	stat	NN	_	_	_
276	1	1	CD	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	growth	growth	NN	_	_	_
279	phase	phase	NN	_	_	_
280	:	:	:	_	_	_
281	Stat1	stat1	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	growth	growth	NN	_	_	_
284	phase	phase	NN	_	_	_
285	:	:	:	_	_	_
286	stat	stat	NN	_	_	_
287	2	2	CD	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	growth	growth	NN	_	_	_
290	phase	phase	NN	_	_	_
291	:	:	:	_	_	_
292	Stat2	stat2	NN	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	growth	growth	NN	_	_	_
295	phase	phase	NN	_	_	_
296	:	:	:	_	_	_
297	stationary	stationary	JJ	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	growth	growth	NN	_	_	_
300	phase	phase	NN	_	_	_
301	:	:	:	_	_	_
302	Stationary	stationary	JJ	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	growth	growth	NN	_	_	_
305	phase	phase	NN	_	_	_
306	:	:	:	_	_	_
307	stationary	stationary	JJ	_	_	_
308	growth	growth	NN	_	_	_
309	phase	phase	NN	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	growth	growth	NN	_	_	_
312	phase	phase	NN	_	_	_
313	:	:	:	_	_	_
314	Stationary	stationary	JJ	_	_	_
315	phase	phase	NN	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	growth	growth	NN	_	_	_
318	phase	phase	NN	_	_	_
319	:	:	:	_	_	_
320	stationary	stationary	JJ	GrowthPhase	_	_
321	phase	phase	NN	GrowthPhase	_	_
322	-LRB-	-lrb-	-LRB-	_	_	_
323	grown	grow	VBN	_	_	_
324	to	to	TO	_	_	_
325	an	a	DT	_	_	_
326	OD600nm	od600nm	NN	_	_	_
327	of	of	IN	_	_	_
328	0.9	0.9	CD	_	_	_
329	-RRB-	-rrb-	-RRB-	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	growth	growth	NN	_	_	_
332	phase	phase	NN	_	_	_
333	:	:	:	_	_	_
334	Trans	Trans	NNP	_	_	_
335	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
336	growth	growth	NN	_	_	_
337	phase	phase	NN	_	_	_
338	:	:	:	_	_	_
339	transition	transition	NN	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	growth	growth	NN	_	_	_
342	phase	phase	NN	_	_	_
343	:	:	:	_	_	_
344	transition	transition	NN	_	_	_
345	growth	growth	NN	_	_	_
346	phase	phase	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	growth	growth	NN	_	_	_
349	phase	phase	NN	_	_	_
350	:	:	:	_	_	_
351	Transition	transition	NN	_	_	_
352	to	to	TO	_	_	_
353	Stationary	stationary	JJ	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	growth	growth	NN	_	_	_
356	protocol	protocol	NN	_	_	_
357	:	:	:	_	_	_
358	Bacteria	bacterium	NNS	_	_	_
359	liquid	liquid	JJ	_	_	_
360	culture	culture	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	growth	growth	NN	_	_	_
363	protocol	protocol	NN	_	_	_
364	:	:	:	_	_	_
365	biofilm	biofilm	NN	_	_	_
366	grown	grow	VBN	_	_	_
367	on	on	IN	_	_	_
368	glass	glass	NN	_	_	_
369	wool	wool	NN	_	_	_
370	,	,	,	_	_	_
371	37C	37c	NN	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	growth	growth	NN	_	_	_
374	protocol	protocol	NN	_	_	_
375	:	:	:	_	_	_
376	control	control	NN	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	growth	growth	NN	_	_	_
379	protocol	protocol	NN	_	_	_
380	:	:	:	_	_	_
381	Controls	Controls	NNP	_	_	_
382	grown	grow	VBN	_	_	_
383	to	to	TO	_	_	_
384	an	a	DT	_	_	_
385	optimal	optimal	JJ	_	_	_
386	temperature	temperature	NN	_	_	_
387	of	of	IN	_	_	_
388	37	37	CD	_	_	_
389	°C	°c	NN	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	growth	growth	NN	_	_	_
392	protocol	protocol	NN	_	_	_
393	:	:	:	_	_	_
394	grown	grow	VBN	_	_	_
395	in	in	IN	_	_	_
396	LB	lb	NN	_	_	_
397	+	+	CC	_	_	_
398	glycerol	glycerol	NN	SUPP	_	_
399	to	to	TO	_	_	_
400	0.8	0.8	CD	_	_	_
401	OD	od	NN	_	_	_
402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
403	growth	growth	NN	_	_	_
404	protocol	protocol	NN	_	_	_
405	:	:	:	_	_	_
406	grown	grow	VBN	_	_	_
407	in	in	IN	_	_	_
408	LB	lb	NN	_	_	_
409	to	to	TO	_	_	_
410	0.8	0.8	CD	_	_	_
411	OD	od	NN	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	growth	growth	NN	_	_	_
414	protocol	protocol	NN	_	_	_
415	:	:	:	_	_	_
416	heat	heat	NN	_	_	_
417	shock	shock	NN	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	growth	growth	NN	_	_	_
420	protocol	protocol	NN	_	_	_
421	:	:	:	_	_	_
422	in	in	IN	_	_	_
423	the	the	DT	_	_	_
424	caecal	caecal	JJ	_	_	_
425	content	content	NN	_	_	_
426	of	of	IN	_	_	_
427	rats	rat	NNS	_	_	_
428	associated	associate	VBN	_	_	_
429	with	with	IN	_	_	_
430	the	the	DT	_	_	_
431	human	human	JJ	_	_	_
432	microbiota	microbiota	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	growth	growth	NN	_	_	_
435	protocol	protocol	NN	_	_	_
436	:	:	:	_	_	_
437	logarithmic	logarithmic	JJ	_	_	_
438	phase	phase	NN	_	_	_
439	in	in	IN	_	_	_
440	DMEM-MOPS	dmem-mops	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	growth	growth	NN	_	_	_
443	protocol	protocol	NN	_	_	_
444	:	:	:	_	_	_
445	Log-phase	log-phase	JJ	_	_	_
446	culture	culture	NN	_	_	_
447	-LRB-	-lrb-	-LRB-	_	_	_
448	LB	lb	NN	MED	_	_
449	broth	broth	NN	MED	_	_
450	,	,	,	_	_	_
451	Miller	Miller	NNP	_	_	_
452	formulation	formulation	NN	_	_	_
453	-RRB-	-rrb-	-RRB-	_	_	_
454	inoculated	inoculate	VBN	_	_	_
455	with	with	IN	_	_	_
456	one	one	CD	_	_	_
457	blue	blue	JJ	_	_	_
458	colony	colony	NN	_	_	_
459	and	and	CC	_	_	_
460	grown	grow	VBN	_	_	_
461	for	for	IN	_	_	_
462	5	5	CD	_	_	_
463	hr	hr	NN	_	_	_
464	at	at	IN	_	_	_
465	37	37	CD	_	_	_
466	degrees	degree	NNS	_	_	_
467	celsius	celsius	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	growth	growth	NN	_	_	_
470	protocol	protocol	NN	_	_	_
471	:	:	:	_	_	_
472	Log-phase	log-phase	JJ	_	_	_
473	culture	culture	NN	_	_	_
474	-LRB-	-lrb-	-LRB-	_	_	_
475	LB	lb	NN	MED	_	_
476	broth	broth	NN	MED	_	_
477	,	,	,	_	_	_
478	Miller	Miller	NNP	_	_	_
479	formulation	formulation	NN	_	_	_
480	-RRB-	-rrb-	-RRB-	_	_	_
481	inoculated	inoculate	VBN	_	_	_
482	with	with	IN	_	_	_
483	one	one	CD	_	_	_
484	pale	pale	JJ	_	_	_
485	colony	colony	NN	_	_	_
486	and	and	CC	_	_	_
487	grown	grow	VBN	_	_	_
488	for	for	IN	_	_	_
489	5	5	CD	_	_	_
490	hr	hr	NN	_	_	_
491	at	at	IN	_	_	_
492	37	37	CD	_	_	_
493	degrees	degree	NNS	_	_	_
494	celsius	celsius	NN	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
496	growth	growth	NN	_	_	_
497	protocol	protocol	NN	_	_	_
498	:	:	:	_	_	_
499	steady	steady	JJ	_	_	_
500	growth	growth	NN	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	growth	growth	NN	_	_	_
503	protocol	protocol	NN	_	_	_
504	:	:	:	_	_	_
505	transition	transition	NN	_	_	_
506	phase	phase	NN	_	_	_
507	in	in	IN	_	_	_
508	DMEM-MOPS	dmem-mops	NN	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	growth	growth	NN	_	_	_
511	protocol	protocol	NN	_	_	_
512	:	:	:	_	_	_
513	Treatment	treatment	NN	_	_	_
514	1	1	CD	_	_	_
515	-LRB-	-lrb-	-LRB-	_	_	_
516	58	58	CD	_	_	_
517	°C	°c	NN	_	_	_
518	F	f	NN	_	_	_
519	=	=	JJ	_	_	_
520	2	2	CD	_	_	_
521	-RRB-	-rrb-	-RRB-	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
523	growth	growth	NN	_	_	_
524	protocol	protocol	NN	_	_	_
525	:	:	:	_	_	_
526	Treatment	treatment	NN	_	_	_
527	2	2	CD	_	_	_
528	-LRB-	-lrb-	-LRB-	_	_	_
529	58	58	CD	_	_	_
530	°C	°c	NN	_	_	_
531	F	f	NN	_	_	_
532	=	=	JJ	_	_	_
533	3	3	CD	_	_	_
534	-RRB-	-rrb-	-RRB-	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	growth	growth	NN	_	_	_
537	protocol	protocol	NN	_	_	_
538	:	:	:	_	_	_
539	Treatment	treatment	NN	_	_	_
540	3	3	CD	_	_	_
541	-LRB-	-lrb-	-LRB-	_	_	_
542	60	60	CD	_	_	_
543	°C	°c	NN	_	_	_
544	F	f	NN	_	_	_
545	=	=	JJ	_	_	_
546	3	3	CD	_	_	_
547	-RRB-	-rrb-	-RRB-	_	_	_
548	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
549	growth	growth	NN	_	_	_
550	protocol	protocol	NN	_	_	_
551	:	:	:	_	_	_
552	Treatment	treatment	NN	_	_	_
553	4	4	CD	_	_	_
554	-LRB-	-lrb-	-LRB-	_	_	_
555	core	core	NN	_	_	_
556	temperature	temperature	NN	_	_	_
557	of	of	IN	_	_	_
558	71	71	CD	_	_	_
559	°C	°c	NN	_	_	_
560	-RRB-	-rrb-	-RRB-	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	growth	growth	NN	_	_	_
563	stage	stage	NN	_	_	_
564	:	:	:	_	_	_
565	log	log	NN	_	_	_
566	phase	phase	NN	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	growth	growth	NN	_	_	_
569	stage	stage	NN	_	_	_
570	:	:	:	_	_	_
571	log-phase	log-phase	JJ	_	_	_
572	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
573	growth	growth	NN	_	_	_
574	stage	stage	NN	_	_	_
575	:	:	:	_	_	_
576	mid	mid	JJ	_	_	_
577	exponetial	exponetial	JJ	_	_	_
578	phase	phase	NN	_	_	_
579	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
580	growth	growth	NN	_	_	_
581	stage	stage	NN	_	_	_
582	:	:	:	_	_	_
583	mid-log	mid-log	JJ	_	_	_
584	phase	phase	NN	_	_	_
585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
586	growth	growth	NN	_	_	_
587	temperature	temperature	NN	_	_	_
588	:	:	:	_	_	_
589	22	22	CD	_	_	_
590	°C	°c	NN	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	growth	growth	NN	_	_	_
593	temperature	temperature	NN	_	_	_
594	:	:	:	_	_	_
595	30C	30c	CD	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
597	growth	growth	NN	_	_	_
598	temperature	temperature	NN	_	_	_
599	:	:	:	_	_	_
600	37	37	CD	_	_	_
601	°C	°c	NN	_	_	_
602	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
603	growth	growth	NN	_	_	_
604	time	time	NN	_	_	_
605	:	:	:	_	_	_
606	7-day	7-day	JJ	_	_	_
607	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
608	growth	growth	NN	_	_	_
609	time	time	NN	_	_	_
610	-LRB-	-lrb-	-LRB-	_	_	_
611	hours	hour	NNS	_	_	_
612	-RRB-	-rrb-	-RRB-	_	_	_
613	:	:	:	_	_	_
614	10	10	CD	_	_	_
615	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
616	growth	growth	NN	_	_	_
617	time	time	NN	_	_	_
618	-LRB-	-lrb-	-LRB-	_	_	_
619	hours	hour	NNS	_	_	_
620	-RRB-	-rrb-	-RRB-	_	_	_
621	:	:	:	_	_	_
622	14	14	CD	_	_	_
623	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
624	growth	growth	NN	_	_	_
625	time	time	NN	_	_	_
626	-LRB-	-lrb-	-LRB-	_	_	_
627	hours	hour	NNS	_	_	_
628	-RRB-	-rrb-	-RRB-	_	_	_
629	:	:	:	_	_	_
630	168	168	CD	_	_	_
631	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
632	growth	growth	NN	_	_	_
633	time	time	NN	_	_	_
634	-LRB-	-lrb-	-LRB-	_	_	_
635	hours	hour	NNS	_	_	_
636	-RRB-	-rrb-	-RRB-	_	_	_
637	:	:	:	_	_	_
638	24	24	CD	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	growth	growth	NN	_	_	_
641	time	time	NN	_	_	_
642	-LRB-	-lrb-	-LRB-	_	_	_
643	hours	hour	NNS	_	_	_
644	-RRB-	-rrb-	-RRB-	_	_	_
645	:	:	:	_	_	_
646	26	26	CD	_	_	_
647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
648	growth	growth	NN	_	_	_
649	time	time	NN	_	_	_
650	-LRB-	-lrb-	-LRB-	_	_	_
651	hours	hour	NNS	_	_	_
652	-RRB-	-rrb-	-RRB-	_	_	_
653	:	:	:	_	_	_
654	27	27	CD	_	_	_
655	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
656	growth	growth	NN	_	_	_
657	time	time	NN	_	_	_
658	-LRB-	-lrb-	-LRB-	_	_	_
659	hours	hour	NNS	_	_	_
660	-RRB-	-rrb-	-RRB-	_	_	_
661	:	:	:	_	_	_
662	28	28	CD	_	_	_
663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
664	growth	growth	NN	_	_	_
665	time	time	NN	_	_	_
666	-LRB-	-lrb-	-LRB-	_	_	_
667	hours	hour	NNS	_	_	_
668	-RRB-	-rrb-	-RRB-	_	_	_
669	:	:	:	_	_	_
670	29	29	CD	_	_	_
671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
672	growth	growth	NN	_	_	_
673	time	time	NN	_	_	_
674	-LRB-	-lrb-	-LRB-	_	_	_
675	hours	hour	NNS	_	_	_
676	-RRB-	-rrb-	-RRB-	_	_	_
677	:	:	:	_	_	_
678	3	3	CD	_	_	_
679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
680	growth	growth	NN	_	_	_
681	time	time	NN	_	_	_
682	-LRB-	-lrb-	-LRB-	_	_	_
683	hours	hour	NNS	_	_	_
684	-RRB-	-rrb-	-RRB-	_	_	_
685	:	:	:	_	_	_
686	336	336	CD	_	_	_
687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
688	growth	growth	NN	_	_	_
689	time	time	NN	_	_	_
690	-LRB-	-lrb-	-LRB-	_	_	_
691	hours	hour	NNS	_	_	_
692	-RRB-	-rrb-	-RRB-	_	_	_
693	:	:	:	_	_	_
694	4	4	CD	_	_	_
695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
696	growth	growth	NN	_	_	_
697	time	time	NN	_	_	_
698	-LRB-	-lrb-	-LRB-	_	_	_
699	hours	hour	NNS	_	_	_
700	-RRB-	-rrb-	-RRB-	_	_	_
701	:	:	:	_	_	_
702	48	48	CD	_	_	_
703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
704	growth	growth	NN	_	_	_
705	time	time	NN	_	_	_
706	-LRB-	-lrb-	-LRB-	_	_	_
707	hours	hour	NNS	_	_	_
708	-RRB-	-rrb-	-RRB-	_	_	_
709	:	:	:	_	_	_
710	5	5	CD	_	_	_
711	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
712	growth	growth	NN	_	_	_
713	time	time	NN	_	_	_
714	-LRB-	-lrb-	-LRB-	_	_	_
715	hours	hour	NNS	_	_	_
716	-RRB-	-rrb-	-RRB-	_	_	_
717	:	:	:	_	_	_
718	5.5	5.5	CD	_	_	_
719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
720	growth	growth	NN	_	_	_
721	time	time	NN	_	_	_
722	-LRB-	-lrb-	-LRB-	_	_	_
723	hours	hour	NNS	_	_	_
724	-RRB-	-rrb-	-RRB-	_	_	_
725	:	:	:	_	_	_
726	6	6	CD	_	_	_
727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
728	growth	growth	NN	_	_	_
729	time	time	NN	_	_	_
730	-LRB-	-lrb-	-LRB-	_	_	_
731	hours	hour	NNS	_	_	_
732	-RRB-	-rrb-	-RRB-	_	_	_
733	:	:	:	_	_	_
734	6.5	6.5	CD	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
736	growth	growth	NN	_	_	_
737	time	time	NN	_	_	_
738	-LRB-	-lrb-	-LRB-	_	_	_
739	hours	hour	NNS	_	_	_
740	-RRB-	-rrb-	-RRB-	_	_	_
741	:	:	:	_	_	_
742	7	7	CD	_	_	_
743	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
744	growth	growth	NN	_	_	_
745	time	time	NN	_	_	_
746	-LRB-	-lrb-	-LRB-	_	_	_
747	hours	hour	NNS	_	_	_
748	-RRB-	-rrb-	-RRB-	_	_	_
749	:	:	:	_	_	_
750	8	8	CD	_	_	_
751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
752	growth	growth	NN	_	_	_
753	time	time	NN	_	_	_
754	-LRB-	-lrb-	-LRB-	_	_	_
755	hours	hour	NNS	_	_	_
756	-RRB-	-rrb-	-RRB-	_	_	_
757	:	:	:	_	_	_
758	9	9	CD	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
760	growth	growth	NN	_	_	_
761	type	type	NN	_	_	_
762	:	:	:	_	_	_
763	amino	amino	NN	_	_	_
764	acid	acid	NN	_	_	_
765	starvation	starvation	NN	_	_	_
766	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
767	growth	growth	NN	_	_	_
768	type	type	NN	_	_	_
769	:	:	:	_	_	_
770	log	log	NN	_	_	_
771	phase	phase	NN	_	_	_
772	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
773	GSH-sepharose	gsh-sepharose	NN	_	_	_
774	4b	4b	NN	_	_	_
775	purification	purification	NN	_	_	_
776	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
777	gss-1	gss-1	NN	_	_	_
778	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
779	gss-2	gss-2	NN	_	_	_
780	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
781	gss-3	gss-3	NN	_	_	_
782	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
783	GST	gst	NN	_	_	_
784	control	control	NN	_	_	_
785	Protoarray	Protoarray	NNP	_	_	_
786	replicate	replicate	VB	_	_	_
787	1	1	CD	_	_	_
788	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
789	Guanosine	Guanosine	NNP	_	_	_
790	addition	addition	NN	_	_	_
791	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
792	gut	gut	NN	_	_	_
793	origin	origin	NN	_	_	_
794	:	:	:	_	_	_
795	Human	human	JJ	_	_	_
796	colon	colon	NN	_	_	_
797	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
798	gyrase	gyrase	NN	_	_	_
799	binding	binding	NN	_	_	_
800	-LRB-	-lrb-	-LRB-	_	_	_
801	ChIP-chip	chip-chip	NN	_	_	_
802	-RRB-	-rrb-	-RRB-	_	_	_
803	no.	no.	NN	_	_	_
804	1	1	CD	_	_	_
805	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
806	gyrase	gyrase	NN	_	_	_
807	binding	binding	NN	_	_	_
808	-LRB-	-lrb-	-LRB-	_	_	_
809	ChIP-chip	chip-chip	NN	_	_	_
810	-RRB-	-rrb-	-RRB-	_	_	_
811	no.	no.	NN	_	_	_
812	2	2	CD	_	_	_
813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
814	gyrase	gyrase	NN	_	_	_
815	binding	binding	NN	_	_	_
816	-LRB-	-lrb-	-LRB-	_	_	_
817	ChIP-chip	chip-chip	NN	_	_	_
818	-RRB-	-rrb-	-RRB-	_	_	_
819	no.	no.	RB	_	_	_
820	3	3	CD	_	_	_
821	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
822	gyrase	gyrase	NN	_	_	_
823	binding	binding	NN	_	_	_
824	-LRB-	-lrb-	-LRB-	_	_	_
825	ChIP-chip	chip-chip	NN	_	_	_
826	-RRB-	-rrb-	-RRB-	_	_	_
827	no.	no.	RB	_	_	_
828	4	4	CD	_	_	_
829	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
830	gyrase	gyrase	NN	_	_	_
831	binding	binding	NN	_	_	_
832	-LRB-	-lrb-	-LRB-	_	_	_
833	ChIP-chip	chip-chip	NN	_	_	_
834	-RRB-	-rrb-	-RRB-	_	_	_
835	no.	no.	RB	_	_	_
836	5	5	CD	_	_	_
837	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
838	gyrase	gyrase	NN	_	_	_
839	binding	binding	NN	_	_	_
840	-LRB-	-lrb-	-LRB-	_	_	_
841	ChIP-chip	chip-chip	NN	_	_	_
842	-RRB-	-rrb-	-RRB-	_	_	_
843	no.	no.	RB	_	_	_
844	6	6	CD	_	_	_
845	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
846	gyrase	gyrase	NN	_	_	_
847	binding	binding	NN	_	_	_
848	-LRB-	-lrb-	-LRB-	_	_	_
849	ChIP-chip	chip-chip	NN	_	_	_
850	-RRB-	-rrb-	-RRB-	_	_	_
851	no.	no.	NN	_	_	_
852	7	7	CD	_	_	_
853	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
854	gyrase	gyrase	NN	_	_	_
855	binding	binding	NN	_	_	_
856	-LRB-	-lrb-	-LRB-	_	_	_
857	ChIP-chip	chip-chip	NN	_	_	_
858	-RRB-	-rrb-	-RRB-	_	_	_
859	no.	no.	RB	_	_	_
860	8	8	CD	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
862	Gyrase	gyrase	NN	_	_	_
863	Cleavage	cleavage	NN	_	_	_
864	Sites	site	NNS	_	_	_
865	-LRB-	-lrb-	-LRB-	_	_	_
866	GCSs	gcss	NNS	_	_	_
867	-RRB-	-rrb-	-RRB-	_	_	_
868	were	be	VBD	_	_	_
869	called	call	VBN	_	_	_
870	using	use	VBG	_	_	_
871	custom	custom	NN	_	_	_
872	script	script	NN	_	_	_
873	-LRB-	-lrb-	-LRB-	_	_	_
874	GCSs_calling.py	gcss_calling.py	NN	_	_	_
875	,	,	,	_	_	_
876	github	github	NN	_	_	_
877	:	:	:	_	_	_
878	https://github.com/sutormin94/Gyrase_Topo-seq	https://github.com/sutormin94/gyrase_topo-seq	NN	_	_	_
879	-RRB-	-rrb-	-RRB-	_	_	_
880	that	that	WDT	_	_	_
881	takes	take	VBZ	_	_	_
882	4	4	CD	_	_	_
883	files	file	NNS	_	_	_
884	-LRB-	-lrb-	-LRB-	_	_	_
885	tetrade	tetrade	NN	_	_	_
886	-RRB-	-rrb-	-RRB-	_	_	_
887	as	as	IN	_	_	_
888	input	input	NN	_	_	_
889	:	:	:	_	_	_
890	+	+	CC	_	_	_
891	A+IP	A+IP	NNP	_	_	_
892	,	,	,	_	_	_
893	+	+	CC	_	_	_
894	A-IP	a-ip	NN	_	_	_
895	,	,	,	_	_	_
896	-	-	:	_	_	_
897	A+IP	a+ip	NN	_	_	_
898	,	,	,	_	_	_
899	-	-	:	_	_	_
900	A-IP	a-ip	NN	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	gyrA	gyra	NN	GEN	_	_
903	__	__	CD	_	_	_
904	U	U	NNP	_	_	_
905	_	_	NNP	_	_	_
906	N0075	N0075	NNP	_	_	_
907	_	_	NNP	_	_	_
908	r1	r1	NN	_	_	_
909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
910	gyrA	gyra	NN	GEN	_	_
911	__	__	CD	_	_	_
912	U	U	NNP	_	_	_
913	_	_	NNP	_	_	_
914	N0075	N0075	NNP	_	_	_
915	_	_	SYM	_	_	_
916	r2	r2	FW	_	_	_
917	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
918	gyrA	gyra	NN	GEN	_	_
919	__	__	CD	_	_	_
920	U	U	NNP	_	_	_
921	_	_	NNP	_	_	_
922	N0075	N0075	NNP	_	_	_
923	_	_	SYM	_	_	_
924	r3	r3	FW	_	_	_
925	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
926	gyrA	gyra	NN	GEN	_	_
927	upregulation	upregulation	NN	_	_	_
928	,	,	,	_	_	_
929	0.075	0.075	CD	_	_	_
930	mg/mL	mg/ml	NN	_	_	_
931	norfloxacin	norfloxacin	NN	_	_	_
932	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
933	gyrI	gyri	NN	_	_	_
934	__	__	CD	_	_	_
935	U	U	NNP	_	_	_
936	_	_	NNP	_	_	_
937	N0075	N0075	NNP	_	_	_
938	_	_	VBD	_	_	_
939	r1	r1	NN	_	_	_
940	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
941	gyrI	gyri	NN	_	_	_
942	__	__	CD	_	_	_
943	U	U	NNP	_	_	_
944	_	_	NNP	_	_	_
945	N0075	N0075	NNP	_	_	_
946	_	_	VBD	_	_	_
947	r2	r2	NN	_	_	_
948	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
949	gyrI	gyri	NN	_	_	_
950	__	__	CD	_	_	_
951	U	U	NNP	_	_	_
952	_	_	NNP	_	_	_
953	N0075	N0075	NNP	_	_	_
954	_	_	VBD	_	_	_
955	r3	r3	NN	_	_	_
956	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
957	gyrI	gyri	NN	_	_	_
958	upregulation	upregulation	NN	_	_	_
959	,	,	,	_	_	_
960	0.075	0.075	CD	_	_	_
961	mg/mL	mg/ml	NN	_	_	_
962	norfloxacin	norfloxacin	NN	_	_	_
963	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
964	H2O2	h2o2	NN	_	_	_
965	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
966	H500	h500	CD	_	_	_
967	_	_	NN	_	_	_
968	1	1	CD	_	_	_
969	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
970	Harvested	harvest	VBN	_	_	_
971	by	by	IN	_	_	_
972	chloramphenicol	chloramphenicol	NN	_	_	_
973	pre-treatment	pre-treatment	NN	_	_	_
974	and	and	CC	_	_	_
975	centrifugation	centrifugation	NN	_	_	_
976	;	;	:	_	_	_
977	DSP	DSP	NNP	_	_	_
978	treated	treat	VBN	_	_	_
979	ex	ex	FW	_	_	_
980	vivo	vivo	FW	_	_	_
981	;	;	:	_	_	_
982	Affinity	affinity	NN	_	_	_
983	purified	purify	VBN	_	_	_
984	TF	tf	NN	_	_	_
985	crosslinked	crosslink	VBD	_	_	_
986	RNC	rnc	NN	_	_	_
987	footprints	footprint	NNS	_	_	_
988	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
989	Harvested	harvest	VBN	_	_	_
990	by	by	IN	_	_	_
991	chloramphenicol	chloramphenicol	NN	_	_	_
992	pre-treatment	pre-treatment	NN	_	_	_
993	and	and	CC	_	_	_
994	centrifugation	centrifugation	NN	_	_	_
995	;	;	:	_	_	_
996	DSP	DSP	NNP	_	_	_
997	treated	treat	VBN	_	_	_
998	ex	ex	FW	_	_	_
999	vivo	vivo	FW	_	_	_
1000	;	;	:	_	_	_
1001	Total	total	JJ	_	_	_
1002	footprints	footprint	NNS	_	_	_
1003	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1004	Harvested	harvest	VBN	_	_	_
1005	by	by	IN	_	_	_
1006	rapid	rapid	JJ	_	_	_
1007	filtration	filtration	NN	_	_	_
1008	;	;	:	_	_	_
1009	DSP	DSP	NNP	_	_	_
1010	treated	treat	VBN	_	_	_
1011	ex	ex	FW	_	_	_
1012	vivo	vivo	FW	_	_	_
1013	;	;	:	_	_	_
1014	Affinity	affinity	NN	_	_	_
1015	purified	purify	VBN	_	_	_
1016	TF	tf	NN	_	_	_
1017	crosslinked	crosslink	VBD	_	_	_
1018	RNC	rnc	NN	_	_	_
1019	footprints	footprint	NNS	_	_	_
1020	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1021	Harvested	harvest	VBN	_	_	_
1022	by	by	IN	_	_	_
1023	rapid	rapid	JJ	_	_	_
1024	filtration	filtration	NN	_	_	_
1025	;	;	:	_	_	_
1026	DSP	DSP	NNP	_	_	_
1027	treated	treat	VBN	_	_	_
1028	ex	ex	FW	_	_	_
1029	vivo	vivo	FW	_	_	_
1030	;	;	:	_	_	_
1031	Total	total	JJ	_	_	_
1032	footprints	footprint	NNS	_	_	_
1033	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1034	Harvested	harvest	VBN	_	_	_
1035	by	by	IN	_	_	_
1036	rapid	rapid	JJ	_	_	_
1037	filtration	filtration	NN	_	_	_
1038	;	;	:	_	_	_
1039	EDC	edc	NN	_	_	_
1040	treated	treat	VBN	_	_	_
1041	ex	ex	FW	_	_	_
1042	vivo	vivo	FW	_	_	_
1043	;	;	:	_	_	_
1044	Affinity	affinity	NN	_	_	_
1045	purified	purify	VBN	_	_	_
1046	TF	tf	NN	_	_	_
1047	crosslinked	crosslink	VBD	_	_	_
1048	RNC	rnc	NN	_	_	_
1049	footprints	footprint	NNS	_	_	_
1050	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1051	Harvested	harvest	VBN	_	_	_
1052	by	by	IN	_	_	_
1053	rapid	rapid	JJ	_	_	_
1054	filtration	filtration	NN	_	_	_
1055	;	;	:	_	_	_
1056	EDC	edc	NN	_	_	_
1057	treated	treat	VBN	_	_	_
1058	ex	ex	FW	_	_	_
1059	vivo	vivo	FW	_	_	_
1060	;	;	:	_	_	_
1061	Total	total	JJ	_	_	_
1062	footprints	footprint	NNS	_	_	_
1063	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1064	Harvested	harvest	VBN	_	_	_
1065	cells	cell	NNS	_	_	_
1066	-LRB-	-lrb-	-LRB-	_	_	_
1067	4	4	CD	_	_	_
1068	×	×	NN	_	_	_
1069	6	6	CD	_	_	_
1070	ml	ml	NN	_	_	_
1071	-RRB-	-rrb-	-RRB-	_	_	_
1072	were	be	VBD	_	_	_
1073	immediately	immediately	RB	_	_	_
1074	combined	combine	VBN	_	_	_
1075	with	with	IN	_	_	_
1076	6	6	CD	_	_	_
1077	ml	ml	NN	_	_	_
1078	RNAlater	rnalater	NN	_	_	_
1079	-LRB-	-lrb-	-LRB-	_	_	_
1080	Life	Life	NNP	_	_	_
1081	Technologies	Technologies	NNPS	_	_	_
1082	,	,	,	_	_	_
1083	Grand	Grand	NNP	_	_	_
1084	Island	Island	NNP	_	_	_
1085	,	,	,	_	_	_
1086	NY	NY	NNP	_	_	_
1087	,	,	,	_	_	_
1088	USA	USA	NNP	_	_	_
1089	-RRB-	-rrb-	-RRB-	_	_	_
1090	,	,	,	_	_	_
1091	centrifuged	centrifuge	VBN	_	_	_
1092	for	for	IN	_	_	_
1093	15	15	CD	_	_	_
1094	min	min	NN	_	_	_
1095	at	at	IN	_	_	_
1096	12000	12000	CD	_	_	_
1097	r.p.m.	r.p.m.	NN	_	_	_
1098	,	,	,	_	_	_
1099	washed	wash	VBN	_	_	_
1100	with	with	IN	_	_	_
1101	1	1	CD	_	_	_
1102	ml	ml	NN	_	_	_
1103	RNAlater	rnalater	NN	_	_	_
1104	-LRB-	-lrb-	-LRB-	_	_	_
1105	3	3	CD	_	_	_
1106	min	min	NN	_	_	_
1107	at	at	IN	_	_	_
1108	15000	15000	CD	_	_	_
1109	r.p.m.	r.p.m.	NN	_	_	_
1110	-RRB-	-rrb-	-RRB-	_	_	_
1111	,	,	,	_	_	_
1112	re-suspended	re-suspended	JJ	_	_	_
1113	in	in	IN	_	_	_
1114	0.5	0.5	CD	_	_	_
1115	ml	ml	NN	_	_	_
1116	RNAlater	rnalater	NN	_	_	_
1117	and	and	CC	_	_	_
1118	stored	store	VBD	_	_	_
1119	at	at	IN	_	_	_
1120	−	−	CD	_	_	_
1121	20	20	CD	_	_	_
1122	°C	°c	NN	_	_	_
1123	.	.	.	_	_	_

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	HB101	hb101	NN	_	_	_
3	,	,	,	_	_	_
4	biological	biological	JJ	_	_	_
5	rep2	rep2	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	HB101	hb101	NN	_	_	_
8	,	,	,	_	_	_
9	biological	biological	JJ	_	_	_
10	rep3	rep3	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	HB101	hb101	NN	_	_	_
13	,	,	,	_	_	_
14	exposed	expose	VBN	_	_	_
15	to	to	TO	_	_	_
16	C.	C.	NNP	_	_	_
17	elegans	elegan	NNS	_	_	_
18	and	and	CC	_	_	_
19	Giardia	Giardia	NNP	_	_	_
20	,	,	,	_	_	_
21	biological	biological	JJ	_	_	_
22	rep1	rep1	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	HB101	hb101	NN	_	_	_
25	,	,	,	_	_	_
26	exposed	expose	VBN	_	_	_
27	to	to	TO	_	_	_
28	C.	C.	NNP	_	_	_
29	elegans	elegan	NNS	_	_	_
30	and	and	CC	_	_	_
31	Giardia	Giardia	NNP	_	_	_
32	,	,	,	_	_	_
33	biological	biological	JJ	_	_	_
34	rep2	rep2	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	HB101	hb101	NN	_	_	_
37	,	,	,	_	_	_
38	exposed	expose	VBN	_	_	_
39	to	to	TO	_	_	_
40	C.	C.	NNP	_	_	_
41	elegans	elegan	NNS	_	_	_
42	and	and	CC	_	_	_
43	Giardia	Giardia	NNP	_	_	_
44	,	,	,	_	_	_
45	biological	biological	JJ	_	_	_
46	rep3	rep3	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	HB101	hb101	NN	_	_	_
49	,	,	,	_	_	_
50	exposed	expose	VBN	_	_	_
51	to	to	TO	_	_	_
52	C.	C.	NNP	_	_	_
53	elegans	elegan	NNS	_	_	_
54	,	,	,	_	_	_
55	biological	biological	JJ	_	_	_
56	rep1	rep1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	HB101	hb101	NN	_	_	_
59	,	,	,	_	_	_
60	exposed	expose	VBN	_	_	_
61	to	to	TO	_	_	_
62	C.	C.	NNP	_	_	_
63	elegans	elegan	NNS	_	_	_
64	,	,	,	_	_	_
65	biological	biological	JJ	_	_	_
66	rep2	rep2	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	HB101	hb101	NN	_	_	_
69	,	,	,	_	_	_
70	exposed	expose	VBN	_	_	_
71	to	to	TO	_	_	_
72	C.	C.	NNP	_	_	_
73	elegans	elegan	NNS	_	_	_
74	,	,	,	_	_	_
75	biological	biological	JJ	_	_	_
76	rep3	rep3	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	HB101	hb101	NN	_	_	_
79	,	,	,	_	_	_
80	exposed	expose	VBN	_	_	_
81	to	to	TO	_	_	_
82	Giardia	Giardia	NNP	_	_	_
83	,	,	,	_	_	_
84	biological	biological	JJ	_	_	_
85	rep1	rep1	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	HB101	hb101	NN	_	_	_
88	,	,	,	_	_	_
89	exposed	expose	VBN	_	_	_
90	to	to	TO	_	_	_
91	Giardia	Giardia	NNP	_	_	_
92	,	,	,	_	_	_
93	biological	biological	JJ	_	_	_
94	rep2	rep2	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	HB101	hb101	NN	_	_	_
97	,	,	,	_	_	_
98	exposed	expose	VBN	_	_	_
99	to	to	TO	_	_	_
100	Giardia	Giardia	NNP	_	_	_
101	,	,	,	_	_	_
102	biological	biological	JJ	_	_	_
103	rep3	rep3	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	HCl	hcl	NN	_	_	_
106	replicate	replicate	VBP	_	_	_
107	1	1	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	HCl	hcl	NN	_	_	_
110	replicate	replicate	VBP	_	_	_
111	3	3	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	heat	heat	NN	_	_	_
114	sensitivity	sensitivity	NN	_	_	_
115	:	:	:	_	_	_
116	resistant	resistant	JJ	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	heat	heat	NN	_	_	_
119	sensitivity	sensitivity	NN	_	_	_
120	:	:	:	_	_	_
121	sensitive	sensitive	JJ	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	heat	heat	NN	_	_	_
124	shock	shock	NN	_	_	_
125	response	response	NN	_	_	_
126	in	in	IN	_	_	_
127	the	the	DT	_	_	_
128	minimal	minimal	JJ	_	_	_
129	medium	medium	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	heat	heat	NN	_	_	_
132	shock	shock	NN	_	_	_
133	time	time	NN	_	_	_
134	:	:	:	_	_	_
135	0	0	CD	_	_	_
136	min	min	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	heat	heat	NN	_	_	_
139	shock	shock	NN	_	_	_
140	time	time	NN	_	_	_
141	:	:	:	_	_	_
142	10	10	CD	_	_	_
143	min	min	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	heat	heat	NN	_	_	_
146	shock	shock	NN	_	_	_
147	time	time	NN	_	_	_
148	:	:	:	_	_	_
149	20	20	CD	_	_	_
150	min	min	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	heat	heat	NN	_	_	_
153	shock	shock	NN	_	_	_
154	time	time	NN	_	_	_
155	:	:	:	_	_	_
156	None	none	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	HEK293T/17	hek293t/17	NN	_	_	_
159	cells	cell	NNS	_	_	_
160	-LRB-	-lrb-	-LRB-	_	_	_
161	ATCC	atcc	NN	_	_	_
162	CRL-11268	crl-11268	NN	_	_	_
163	-RRB-	-rrb-	-RRB-	_	_	_
164	were	be	VBD	_	_	_
165	cultured	culture	VBN	_	_	_
166	in	in	IN	_	_	_
167	DMEM	dmem	NN	_	_	_
168	-LRB-	-lrb-	-LRB-	_	_	_
169	Mediatech	mediatech	NN	_	_	_
170	-RRB-	-rrb-	-RRB-	_	_	_
171	supplemented	supplement	VBN	_	_	_
172	with	with	IN	_	_	_
173	10	10	CD	_	_	_
174	%	%	NN	_	_	_
175	FBS	fbs	NN	_	_	_
176	and	and	CC	_	_	_
177	L-glutamine/penicillin/streptomycin	l-glutamine/penicillin/streptomycin	NN	_	_	_
178	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	hfq-gln-1	hfq-gln-1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	hfq-gln-2	hfq-gln-2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	hfq	hfq	NN	GEN	_	_
7	mutant	mutant	NN	_	_	_
8	in	in	IN	_	_	_
9	Ala	Ala	NNP	_	_	_
10	media	media	NNS	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	hfq	hfq	NN	GEN	_	_
13	mutant	mutant	NN	_	_	_
14	in	in	IN	_	_	_
15	Gln	gln	NN	_	_	_
16	media	media	NNS	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Hfq	hfq	NN	_	_	_
19	mut	mut	NN	_	_	_
20	exp	exp	NN	_	_	_
21	mRNA	mrna	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Hfq	hfq	NN	_	_	_
24	mut	mut	NN	_	_	_
25	exp	exp	NN	_	_	_
26	RPF	rpf	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Hfq	hfq	NN	_	_	_
29	-	-	:	_	_	_
30	RpoE	rpoe	NN	_	_	_
31	overexpression	overexpression	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	20	20	CD	_	_	_
34	min	min	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	hfq	hfq	NN	GEN	_	_
38	+	+	CC	_	_	_
39	Wild	Wild	NNP	_	_	_
40	type	type	NN	_	_	_
41	control	control	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	20	20	CD	_	_	_
44	min	min	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Hfr-2xSFX	hfr-2xsfx	NN	_	_	_
48	-	-	:	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	High	High	NNP	_	_	_
51	succinic	succinic	JJ	_	_	_
52	acid	acid	NN	_	_	_
53	tolerance	tolerance	NN	_	_	_
54	E.coli	e.coli	NNS	_	_	_
55	_	_	VBP	_	_	_
56	rep	rep	NN	GEN	_	_
57	Dn	dn	NN	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	High	High	NNP	_	_	_
60	succinic	succinic	JJ	_	_	_
61	acid	acid	NN	_	_	_
62	tolerance	tolerance	NN	_	_	_
63	E.coli	e.coli	NNS	_	_	_
64	_	_	VBP	_	_	_
65	rep	rep	NN	GEN	_	_
66	Up	up	IN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	HisC	hisc	NN	_	_	_
69	rewired	rewire	VBD	_	_	_
70	strain	strain	NN	_	_	_
71	exponentially	exponentially	RB	_	_	_
72	grown	grow	VBN	_	_	_
73	in	in	IN	_	_	_
74	the	the	DT	_	_	_
75	absence	absence	NN	_	_	_
76	of	of	IN	_	_	_
77	histidine	histidine	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	HisC	hisc	NN	_	_	_
80	rewired	rewire	VBD	_	_	_
81	strain	strain	NN	_	_	_
82	exponentially	exponentially	RB	_	_	_
83	grown	grow	VBN	_	_	_
84	in	in	IN	_	_	_
85	the	the	DT	_	_	_
86	presence	presence	NN	_	_	_
87	of	of	IN	_	_	_
88	histidine	histidine	NN	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	1	1	CD	_	_	_
91	mM	mm	NN	KWSUPP	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Hiseq	hiseq	JJ	_	_	_
95	2500	2500	CD	_	_	_
96	Illumina	Illumina	NNP	_	_	_
97	short	short	JJ	_	_	_
98	reads	read	VBZ	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	50	50	CD	_	_	_
101	bp	bp	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	were	be	VBD	_	_	_
104	mapped	map	VBN	_	_	_
105	back	back	RB	_	_	_
106	to	to	TO	_	_	_
107	the	the	DT	_	_	_
108	Caulobacter	Caulobacter	NNP	_	_	_
109	NA1000	na1000	NN	_	_	_
110	reference	reference	NN	_	_	_
111	genome	genome	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	NCBI	ncbi	NN	_	_	_
114	Reference	Reference	NNP	_	_	_
115	Sequence	sequence	NN	_	_	_
116	:	:	:	_	_	_
117	NC-011916.1	nc-011916.1	NN	_	_	_
118	-RRB-	-rrb-	-RRB-	_	_	_
119	using	use	VBG	_	_	_
120	Bowtie	Bowtie	NNP	_	_	_
121	1	1	CD	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	Langmead	Langmead	NNP	_	_	_
124	et	et	FW	_	_	_
125	al.	al.	FW	_	_	_
126	,	,	,	_	_	_
127	2009	2009	CD	_	_	_
128	-RRB-	-rrb-	-RRB-	_	_	_
129	and	and	CC	_	_	_
130	the	the	DT	_	_	_
131	following	follow	VBG	_	_	_
132	command	command	NN	_	_	_
133	:	:	:	_	_	_
134	bowtie	bowtie	NN	_	_	_
135	-	-	:	_	_	_
136	m	m	NN	_	_	_
137	1	1	CD	_	_	_
138	-	-	:	_	_	_
139	n	n	NN	_	_	_
140	1	1	CD	_	_	_
141	--	--	:	_	_	_
142	best	best	JJS	_	_	_
143	--	--	:	_	_	_
144	strata	strata	SYM	_	_	_
145	-	-	:	_	_	_
146	p	p	NN	_	_	_
147	4	4	CD	_	_	_
148	--	--	:	_	_	_
149	chunkmbs	chunkmb	NNS	_	_	_
150	512	512	CD	_	_	_
151	NA1000-bowtie	na1000-bowtie	NN	_	_	_
152	--	--	:	_	_	_
153	sam	sam	NN	_	_	_
154	*	*	NN	_	_	_
155	.	.	.	_	_	_

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	His-tagged	his-tagged	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	biofilm	biofilm	NN	_	_	_
7	cells	cell	NNS	_	_	_
8	of	of	IN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	K-12	k-12	NN	_	_	_
12	wild	wild	JJ	_	_	_
13	type	type	NN	_	_	_
14	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	empty	empty	JJ	_	_	_
17	vector	vector	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	after	after	IN	_	_	_
20	24	24	CD	_	_	_
21	hours	hour	NNS	_	_	_
22	of	of	IN	_	_	_
23	growth	growth	NN	_	_	_
24	in	in	IN	_	_	_
25	LB	lb	NN	_	_	_
26	with	with	IN	_	_	_
27	glasswool	glasswool	NN	_	_	_
28	at	at	IN	_	_	_
29	37oC	37oc	NN	_	_	_
30	under	under	IN	_	_	_
31	2	2	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	IPTG	iptg	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	His-tagged	his-tagged	JJ	_	_	_
36	DNA	dna	NN	_	_	_
37	extracted	extract	VBN	_	_	_
38	from	from	IN	_	_	_
39	biofilm	biofilm	NN	_	_	_
40	cells	cell	NNS	_	_	_
41	of	of	IN	_	_	_
42	E.	e.	FW	_	_	_
43	coli	coli	FW	_	_	_
44	K-12	k-12	NN	_	_	_
45	wild	wild	JJ	_	_	_
46	type	type	NN	_	_	_
47	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
48	after	after	IN	_	_	_
49	24	24	CD	_	_	_
50	hours	hour	NNS	_	_	_
51	of	of	IN	_	_	_
52	growth	growth	NN	_	_	_
53	in	in	IN	_	_	_
54	LB	lb	NN	_	_	_
55	with	with	IN	_	_	_
56	glasswool	glasswool	NN	_	_	_
57	at	at	IN	_	_	_
58	37oC	37oc	NN	_	_	_
59	under	under	IN	_	_	_
60	2	2	CD	_	_	_
61	mM	mm	NN	KWSUPP	_	_
62	IPTG	iptg	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	His-tagged	his-tagged	JJ	_	_	_
65	DNA	dna	NN	_	_	_
66	extracted	extract	VBN	_	_	_
67	from	from	IN	_	_	_
68	planktonic	planktonic	JJ	_	_	_
69	cells	cell	NNS	_	_	_
70	of	of	IN	_	_	_
71	E.	e.	FW	_	_	_
72	coli	coli	FW	_	_	_
73	K-12	k-12	NN	_	_	_
74	wild	wild	JJ	_	_	_
75	type	type	NN	_	_	_
76	BW25113	bw25113	NN	_	_	_
77	/	/	:	_	_	_
78	/	/	:	_	_	_
79	pBAD-Myc-His	pbad-myc-his	NN	_	_	_
80	C	c	NN	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	empty	empty	JJ	_	_	_
83	vector	vector	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	after	after	IN	_	_	_
86	24	24	CD	_	_	_
87	hours	hour	NNS	_	_	_
88	of	of	IN	_	_	_
89	growth	growth	NN	_	_	_
90	in	in	IN	_	_	_
91	LB	lb	NN	_	_	_
92	at	at	IN	_	_	_
93	37oC	37oc	NN	_	_	_
94	with	with	IN	_	_	_
95	induction	induction	NN	_	_	_
96	of	of	IN	_	_	_
97	0.5	0.5	CD	_	_	_
98	%	%	NN	_	_	_
99	L-arabinose	l-arabinose	JJ	_	_	_
100	suspension	suspension	NN	_	_	_
101	cell	cell	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	His-tagged	his-tagged	JJ	_	_	_
104	DNA	dna	NN	_	_	_
105	extracted	extract	VBN	_	_	_
106	from	from	IN	_	_	_
107	planktonic	planktonic	JJ	_	_	_
108	cells	cell	NNS	_	_	_
109	of	of	IN	_	_	_
110	E.	e.	FW	_	_	_
111	coli	coli	FW	_	_	_
112	K-12	k-12	NN	_	_	_
113	wild	wild	JJ	_	_	_
114	type	type	NN	_	_	_
115	BW25113/pBAD-Myc-His	bw25113/pbad-myc-his	NN	_	_	_
116	C-mqsA	c-mqsa	NN	_	_	_
117	after	after	IN	_	_	_
118	24	24	CD	_	_	_
119	hours	hour	NNS	_	_	_
120	of	of	IN	_	_	_
121	growth	growth	NN	_	_	_
122	in	in	IN	_	_	_
123	LB	lb	NN	_	_	_
124	at	at	IN	_	_	_
125	37oC	37oc	NN	_	_	_
126	with	with	IN	_	_	_
127	induction	induction	NN	_	_	_
128	of	of	IN	_	_	_
129	0.5	0.5	CD	_	_	_
130	%	%	NN	_	_	_
131	L-arabinose	l-arabinose	JJ	_	_	_
132	suspension	suspension	NN	_	_	_
133	cell	cell	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	Histidine	histidine	NN	_	_	_
136	addition	addition	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	hlpA	hlpa	NN	_	_	_
139	__	__	CD	_	_	_
140	U	U	NNP	_	_	_
141	_	_	NNP	_	_	_
142	N0075	N0075	NNP	_	_	_
143	_	_	VBD	_	_	_
144	r1	r1	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	hlpA	hlpa	NN	_	_	_
147	__	__	CD	_	_	_
148	U	U	NNP	_	_	_
149	_	_	NNP	_	_	_
150	N0075	N0075	NNP	_	_	_
151	_	_	VBD	_	_	_
152	r2	r2	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	hlpA	hlpa	NN	_	_	_
155	__	__	CD	_	_	_
156	U	U	NNP	_	_	_
157	_	_	NNP	_	_	_
158	N0075	N0075	NNP	_	_	_
159	_	_	SYM	_	_	_
160	r3	r3	FW	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
162	hlpA	hlpa	NN	_	_	_
163	upregulation	upregulation	NN	_	_	_
164	,	,	,	_	_	_
165	0.075	0.075	CD	_	_	_
166	mg/mL	mg/ml	NN	_	_	_
167	norfloxacin	norfloxacin	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	HNCE3	hnce3	NN	_	_	_
170	is	be	VBZ	_	_	_
171	an	a	DT	_	_	_
172	isogenic	isogenic	JJ	_	_	_
173	mutant	mutant	JJ	_	_	_
174	derived	derive	VBN	_	_	_
175	from	from	IN	_	_	_
176	hyper-resistant	hyper-resistant	JJ	_	_	_
177	AG102	ag102	NN	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	marR1	marr1	NN	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	hns	hn	NNS	GEN	_	_
3	_	_	VBP	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Hns	hn	NNS	_	_	_
7	--	--	:	_	_	_
8	120	120	CD	_	_	_
9	min	min	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
11	Hns	hn	VBZ	_	_	_
12	-180	-180	CD	_	_	_
13	min	min	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	hns	hn	NNS	GEN	_	_
16	_	_	VBP	_	_	_
17	2	2	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	Hns	hn	NNS	_	_	_
20	--	--	:	_	_	_
21	420	420	CD	_	_	_
22	min	min	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Hns	hn	NNS	_	_	_
25	--	--	:	_	_	_
26	60	60	CD	_	_	_
27	min	min	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	HNS	hns	SYM	_	_	_
30	-	-	:	_	_	_
31	Aerobic	aerobic	JJ	_	_	_
32	A	a	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	HNS	hns	SYM	_	_	_
35	-	-	:	_	_	_
36	Aerobic	aerobic	JJ	_	_	_
37	B	b	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
39	HNS	hns	SYM	_	_	_
40	-	-	:	_	_	_
41	Anaerobic	anaerobic	JJ	_	_	_
42	A	a	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	HNS	hns	SYM	_	_	_
45	-	-	:	_	_	_
46	Anaerobic	anaerobic	JJ	_	_	_
47	B	b	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	H-NS	h-ns	NN	_	_	_
50	ChIP	chip	NN	_	_	_
51	DNA	dna	NN	_	_	_
52	from	from	IN	_	_	_
53	MG1655	mg1655	NN	_	_	_
54	cells	cell	NNS	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
56	HNS	hns	NN	_	_	_
57	ChIP	chip	NN	_	_	_
58	DNA	dna	NN	_	_	_
59	from	from	IN	_	_	_
60	WT	WT	NNP	_	_	_
61	Escherichia	escherichia	FW	Organism	_	_
62	coli	coli	FW	Organism	_	_
63	MG1655	mg1655	NN	_	_	_
64	K-12	k-12	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	HNS	hn	VBZ	_	_	_
67	ChIP	chip	NN	_	_	_
68	DNA	dna	NN	_	_	_
69	from	from	IN	_	_	_
70	WT	WT	NNP	_	_	_
71	Escherichia	escherichia	FW	Organism	_	_
72	coli	coli	FW	Organism	_	_
73	MG1655	mg1655	NN	_	_	_
74	K-12	k-12	NN	_	_	_
75	Replicate	replicate	VB	_	_	_
76	B	b	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	H-NS	h-ns	NN	_	_	_
79	,	,	,	_	_	_
80	EE	ee	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	H-NS	h-ns	NN	_	_	_
83	flag	flag	NN	_	_	_
84	tagged	tag	VBD	_	_	_
85	cells	cell	NNS	_	_	_
86	with	with	IN	_	_	_
87	bcm	bcm	NN	_	_	_
88	treatment	treatment	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	H-NS	h-ns	NN	_	_	_
91	flag	flag	NN	_	_	_
92	tagged	tag	VBD	_	_	_
93	cells	cell	NNS	_	_	_
94	without	without	IN	_	_	_
95	bcm	bcm	NN	_	_	_
96	treatment	treatment	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	H-NS	h-ns	NN	_	_	_
99	,	,	,	_	_	_
100	ME	me	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	H-NS	h-ns	NN	_	_	_
103	,	,	,	_	_	_
104	S	s	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	H-NS	h-ns	NN	_	_	_
107	,	,	,	_	_	_
108	TS	ts	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
110	holD	hold	VBP	GEN	_	_
111	__	__	CD	_	_	_
112	U	U	NNP	_	_	_
113	_	_	NNP	_	_	_
114	N0075	N0075	NNP	_	_	_
115	_	_	VBD	_	_	_
116	r1	r1	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
118	holD	hold	VBP	GEN	_	_
119	__	__	CD	_	_	_
120	U	U	NNP	_	_	_
121	_	_	NNP	_	_	_
122	N0075	N0075	NNP	_	_	_
123	_	_	VBD	_	_	_
124	r2	r2	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
126	holD	hold	VBP	GEN	_	_
127	__	__	CD	_	_	_
128	U	U	NNP	_	_	_
129	_	_	NNP	_	_	_
130	N0075	N0075	NNP	_	_	_
131	_	_	VBD	_	_	_
132	r3	r3	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
134	holD	hold	VBP	GEN	_	_
135	upregulation	upregulation	NN	_	_	_
136	,	,	,	_	_	_
137	0.075	0.075	CD	_	_	_
138	mg/mL	mg/ml	NN	_	_	_
139	norfloxacin	norfloxacin	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
141	Hot	hot	JJ	_	_	_
142	phenol	phenol	NN	_	_	_
143	extraction	extraction	NN	_	_	_
144	of	of	IN	_	_	_
145	total	total	JJ	_	_	_
146	RNA	rna	NN	_	_	_
147	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Hot	hot	JJ	_	_	_
3	phenol	phenol	NN	_	_	_
4	RNA	rna	NN	_	_	_
5	extraction	extraction	NN	_	_	_
6	as	as	IN	_	_	_
7	described	describe	VBN	_	_	_
8	in	in	IN	_	_	_
9	Aiba	Aiba	NNP	_	_	_
10	,	,	,	_	_	_
11	Adhya	Adhya	NNP	_	_	_
12	and	and	CC	_	_	_
13	Crombrugge	Crombrugge	NNP	_	_	_
14	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
7	Hot	hot	JJ	_	_	_
8	phenol	phenol	NN	_	_	_
9	RNA	rna	NN	_	_	_
10	extraction	extraction	NN	_	_	_
11	as	as	IN	_	_	_
12	described	describe	VBN	_	_	_
13	in	in	IN	_	_	_
14	Aiba	Aiba	NNP	_	_	_
15	.	.	.	_	_	_

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	Hot	hot	JJ	_	_	_
3	phenol	phenol	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	Sharma	sharma	FW	_	_	_
6	et	et	FW	_	_	_
7	al.	al.	FW	_	_	_
8	2010	2010	CD	_	_	_
9	,	,	,	_	_	_
10	Bloomberg	Bloomberg	NNP	_	_	_
11	1990	1990	CD	_	_	_
12	,	,	,	_	_	_
13	EMBO	EMBO	NNP	_	_	_
14	J	J	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	HP1	hp1	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	HP2	hp2	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	HP3	hp3	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	HP4	hp4	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	HS15min	hs15min	NN	_	_	_
26	_	_	CD	_	_	_
27	r1	r1	NN	_	_	_
28	_	_	CD	_	_	_
29	HiSeq	hiseq	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	HS15min	hs15min	NN	_	_	_
32	_	_	CD	_	_	_
33	r2	r2	NN	_	_	_
34	_	_	CD	_	_	_
35	HiSeq	hiseq	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	HS15min	hs15min	NN	_	_	_
38	_	_	CD	_	_	_
39	r3	r3	NN	_	_	_
40	_	_	SYM	_	_	_
41	GAII	gaii	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	HS30min	hs30min	NN	_	_	_
44	_	_	CD	_	_	_
45	r1	r1	NN	_	_	_
46	_	_	CD	_	_	_
47	HiSeq	hiseq	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	HS30min	hs30min	NN	_	_	_
50	_	_	CD	_	_	_
51	r2	r2	NN	_	_	_
52	_	_	CD	_	_	_
53	HiSeq	hiseq	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	HS60min	hs60min	NN	_	_	_
56	_	_	CD	_	_	_
57	r1	r1	NN	_	_	_
58	_	_	CD	_	_	_
59	HiSeq	hiseq	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	HS60min	hs60min	NN	_	_	_
62	_	_	CD	_	_	_
63	r2	r2	NN	_	_	_
64	_	_	CD	_	_	_
65	HiSeq	hiseq	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	hscA	hsca	VBP	GEN	_	_
68	__	__	CD	_	_	_
69	U	U	NNP	_	_	_
70	_	_	NNP	_	_	_
71	N0075	N0075	NNP	_	_	_
72	_	_	SYM	_	_	_
73	r1	r1	FW	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
75	hscA	hsca	NN	GEN	_	_
76	__	__	CD	_	_	_
77	U	U	NNP	_	_	_
78	_	_	NNP	_	_	_
79	N0075	N0075	NNP	_	_	_
80	_	_	SYM	_	_	_
81	r2	r2	FW	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
83	hscA	hsca	NN	GEN	_	_
84	__	__	CD	_	_	_
85	U	U	NNP	_	_	_
86	_	_	NNP	_	_	_
87	N0075	N0075	NNP	_	_	_
88	_	_	SYM	_	_	_
89	r3	r3	FW	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
91	hscA	hsca	NN	GEN	_	_
92	upregulation	upregulation	NN	_	_	_
93	,	,	,	_	_	_
94	0.075	0.075	CD	_	_	_
95	mg/mL	mg/ml	NN	_	_	_
96	norfloxacin	norfloxacin	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	HT873-Con1	ht873-con1	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	HT873-Con2	ht873-con2	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	HT873-Con3	ht873-con3	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	HT873-PA1	ht873-pa1	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	HT873-PA2	ht873-pa2	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	HT873-PA3	ht873-pa3	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	HT875-Con1	ht875-con1	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	HT875-Con2	ht875-con2	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	HT875-Con3	ht875-con3	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	HT875-PA1	ht875-pa1	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	HT875-PA2	ht875-pa2	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	HT875-PA3	ht875-pa3	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	HTseq-derived	htseq-derived	JJ	_	_	_
123	raw	raw	JJ	_	_	_
124	count	count	NN	_	_	_
125	data	datum	NNS	_	_	_
126	were	be	VBD	_	_	_
127	used	use	VBN	_	_	_
128	as	as	IN	_	_	_
129	input	input	NN	_	_	_
130	after	after	IN	_	_	_
131	a	a	DT	_	_	_
132	non-specific	non-specific	JJ	_	_	_
133	filtering	filter	VBG	_	_	_
134	step	step	NN	_	_	_
135	that	that	WDT	_	_	_
136	removed	remove	VBD	_	_	_
137	residual	residual	JJ	_	_	_
138	rRNAs	rrna	NNS	_	_	_
139	and	and	CC	_	_	_
140	tRNAs	trna	NNS	_	_	_
141	and	and	CC	_	_	_
142	low	low	JJ	_	_	_
143	coverage	coverage	NN	_	_	_
144	genes	gene	NNS	_	_	_
145	with	with	IN	_	_	_
146	fewer	fewer	JJR	_	_	_
147	than	than	IN	_	_	_
148	2	2	CD	_	_	_
149	counts	count	NNS	_	_	_
150	per	per	IN	_	_	_
151	million	million	CD	_	_	_
152	-LRB-	-lrb-	-LRB-	_	_	_
153	16-20	16-20	CD	_	_	_
154	reads	read	VBZ	_	_	_
155	-RRB-	-rrb-	-RRB-	_	_	_
156	in	in	IN	_	_	_
157	more	more	JJR	_	_	_
158	than	than	IN	_	_	_
159	25	25	CD	_	_	_
160	%	%	NN	_	_	_
161	of	of	IN	_	_	_
162	the	the	DT	_	_	_
163	dataset	dataset	NN	_	_	_
164	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	HTSeq	htseq	NN	_	_	_
3	is	be	VBZ	_	_	_
4	used	use	VBN	_	_	_
5	to	to	TO	_	_	_
6	generate	generate	VB	_	_	_
7	expression	expression	NN	_	_	_
8	count	count	NN	_	_	_
9	for	for	IN	_	_	_
10	each	each	DT	_	_	_
11	gene	gene	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	http://david.abcc.ncifcrf.gov/home.jsp	http://david.abcc.ncifcrf.gov/home.jsp	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Human	human	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Human	human	JJ	_	_	_
9	III	iii	CD	_	_	_
10	versus	versus	CC	_	_	_
11	MG1655	mg1655	CD	_	_	_
12	technical	technical	JJ	_	_	_
13	replicate	replicate	VB	_	_	_
14	1	1	CD	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Human	Human	NNP	_	_	_
17	III	III	NNP	_	_	_
18	versus	versus	CC	_	_	_
19	MG1655	MG1655	NNP	_	_	_
20	technical	technical	JJ	_	_	_
21	replicate	replicate	VB	_	_	_
22	2	2	CD	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Human	Human	NNP	_	_	_
25	II	II	NNP	_	_	_
26	versus	versus	CC	_	_	_
27	MG1655	MG1655	NNP	_	_	_
28	technical	technical	JJ	_	_	_
29	replicate	replicate	VB	_	_	_
30	1	1	CD	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Human	Human	NNP	_	_	_
33	II	II	NNP	_	_	_
34	versus	versus	CC	_	_	_
35	MG1655	MG1655	NNP	_	_	_
36	technical	technical	JJ	_	_	_
37	replicate	replicate	VBP	_	_	_
38	2	2	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	Human	human	JJ	_	_	_
41	intestinal	intestinal	JJ	_	_	_
42	microbiota	microbiota	NN	_	_	_
43	associated	associate	VBN	_	_	_
44	rat	rat	NN	_	_	_
45	's	's	POS	_	_	_
46	caecum	caecum	NN	_	_	_
47	,	,	,	_	_	_
48	biological	biological	JJ	_	_	_
49	rep1	rep1	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Human	human	JJ	_	_	_
52	intestinal	intestinal	JJ	_	_	_
53	microbiota	microbiota	NN	_	_	_
54	associated	associate	VBN	_	_	_
55	rat	rat	NN	_	_	_
56	's	's	POS	_	_	_
57	caecum	caecum	NN	_	_	_
58	,	,	,	_	_	_
59	biological	biological	JJ	_	_	_
60	rep2	rep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Human	human	JJ	_	_	_
63	intestinal	intestinal	JJ	_	_	_
64	microbiota	microbiota	NN	_	_	_
65	associated	associate	VBN	_	_	_
66	rat	rat	NN	_	_	_
67	's	's	POS	_	_	_
68	caecum	caecum	NN	_	_	_
69	,	,	,	_	_	_
70	biological	biological	JJ	_	_	_
71	rep3	rep3	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	Human	human	JJ	_	_	_
74	I	I	PRP	_	_	_
75	versus	versus	CC	_	_	_
76	MG1655	mg1655	NN	_	_	_
77	technical	technical	JJ	_	_	_
78	replicate	replicate	VB	_	_	_
79	1	1	CD	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Human	Human	NNP	_	_	_
82	I	I	PRP	_	_	_
83	versus	versus	CC	_	_	_
84	MG1655	mg1655	NN	_	_	_
85	technical	technical	JJ	_	_	_
86	replicate	replicate	VBP	_	_	_
87	2	2	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
89	Human	human	JJ	_	_	_
90	sewage	sewage	NN	_	_	_
91	isolate	isolate	NN	_	_	_
92	H1	h1	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Human	human	JJ	_	_	_
95	sewage	sewage	NN	_	_	_
96	isolate	isolate	NN	_	_	_
97	H2	h2	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	Human	human	JJ	_	_	_
100	sewage	sewage	NN	_	_	_
101	isolate	isolate	NN	_	_	_
102	H3	h3	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	hybridization	hybridization	NN	_	_	_
105	buffer	buffer	NN	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	formamide	formamide	NN	_	_	_
108	content	content	NN	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	:	:	:	_	_	_
111	0	0	CD	_	_	_
112	%	%	NN	_	_	_
113	formamide	formamide	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	hybridization	hybridization	NN	_	_	_
116	buffer	buffer	NN	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	formamide	formamide	NN	_	_	_
119	content	content	NN	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	:	:	:	_	_	_
122	10	10	CD	_	_	_
123	%	%	NN	_	_	_
124	formamide	formamide	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	hybridization	hybridization	NN	_	_	_
127	buffer	buffer	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	formamide	formamide	NN	_	_	_
130	content	content	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	:	:	:	_	_	_
133	15	15	CD	_	_	_
134	%	%	NN	_	_	_
135	formamide	formamide	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	hybridization	hybridization	NN	_	_	_
138	buffer	buffer	NN	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	formamide	formamide	NN	_	_	_
141	content	content	NN	_	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	:	:	:	_	_	_
144	20	20	CD	_	_	_
145	%	%	NN	_	_	_
146	formamide	formamide	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	hybridization	hybridization	NN	_	_	_
149	buffer	buffer	NN	_	_	_
150	-LRB-	-lrb-	-LRB-	_	_	_
151	formamide	formamide	NN	_	_	_
152	content	content	NN	_	_	_
153	-RRB-	-rrb-	-RRB-	_	_	_
154	:	:	:	_	_	_
155	25	25	CD	_	_	_
156	%	%	NN	_	_	_
157	formamide	formamide	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	hybridization	hybridization	NN	_	_	_
160	buffer	buffer	NN	_	_	_
161	-LRB-	-lrb-	-LRB-	_	_	_
162	formamide	formamide	NN	_	_	_
163	content	content	NN	_	_	_
164	-RRB-	-rrb-	-RRB-	_	_	_
165	:	:	:	_	_	_
166	32.5	32.5	CD	_	_	_
167	%	%	NN	_	_	_
168	formamide	formamide	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	hybridization	hybridization	NN	_	_	_
171	buffer	buffer	NN	_	_	_
172	-LRB-	-lrb-	-LRB-	_	_	_
173	formamide	formamide	NN	_	_	_
174	content	content	NN	_	_	_
175	-RRB-	-rrb-	-RRB-	_	_	_
176	:	:	:	_	_	_
177	45	45	CD	_	_	_
178	%	%	NN	_	_	_
179	formamide	formamide	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	hybridization	hybridization	NN	_	_	_
182	buffer	buffer	NN	_	_	_
183	-LRB-	-lrb-	-LRB-	_	_	_
184	formamide	formamide	NN	_	_	_
185	content	content	NN	_	_	_
186	-RRB-	-rrb-	-RRB-	_	_	_
187	:	:	:	_	_	_
188	5	5	CD	_	_	_
189	%	%	NN	_	_	_
190	formamide	formamide	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	hybridization	hybridization	NN	_	_	_
193	buffer	buffer	NN	_	_	_
194	-LRB-	-lrb-	-LRB-	_	_	_
195	total	total	JJ	_	_	_
196	rna	rna	NN	GEN	_	_
197	-RRB-	-rrb-	-RRB-	_	_	_
198	:	:	:	_	_	_
199	50	50	CD	_	_	_
200	ng	ng	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	hybridization	hybridization	NN	_	_	_
203	buffer	buffer	NN	_	_	_
204	-LRB-	-lrb-	-LRB-	_	_	_
205	total	total	JJ	_	_	_
206	rna	rna	NN	GEN	_	_
207	-RRB-	-rrb-	-RRB-	_	_	_
208	:	:	:	_	_	_
209	5	5	CD	_	_	_
210	ng	ng	NN	_	_	_
211	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
212	Hydrocortisone	Hydrocortisone	NNP	_	_	_
213	Treatment	treatment	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	IA-co1	ia-co1	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	IA-co2	ia-co2	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	IAI1	iai1	NN	_	_	_
220	batch	batch	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	IAI1	iai1	NN	_	_	_
223	chemostat	chemostat	NN	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	IAI1	iai1	NN	_	_	_
226	starvation	starvation	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	IAI1	iai1	NN	_	_	_
229	transcriptome	transcriptome	NN	_	_	_
230	from	from	IN	_	_	_
231	batch	batch	NN	_	_	_
232	growth	growth	NN	_	_	_
233	_	_	NN	_	_	_
234	1	1	CD	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	IAI1	iai1	NN	_	_	_
237	transcriptome	transcriptome	NN	_	_	_
238	from	from	IN	_	_	_
239	batch	batch	NN	_	_	_
240	growth	growth	NN	_	_	_
241	_	_	NN	_	_	_
242	2	2	CD	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	IAI1	iai1	NN	_	_	_
245	transcriptome	transcriptome	NN	_	_	_
246	from	from	IN	_	_	_
247	chemostat	chemostat	NN	_	_	_
248	growth	growth	NN	_	_	_
249	_	_	NN	_	_	_
250	1	1	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	IAI1	iai1	NN	_	_	_
253	transcriptome	transcriptome	NN	_	_	_
254	from	from	IN	_	_	_
255	chemostat	chemostat	NN	_	_	_
256	growth	growth	NN	_	_	_
257	_	_	NN	_	_	_
258	2	2	CD	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	IAI1	iai1	NN	_	_	_
261	transcriptome	transcriptome	NN	_	_	_
262	from	from	IN	_	_	_
263	starvation	starvation	NN	_	_	_
264	growth	growth	NN	_	_	_
265	_	_	NN	_	_	_
266	1	1	CD	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	IAI1	iai1	NN	_	_	_
269	transcriptome	transcriptome	NN	_	_	_
270	from	from	IN	_	_	_
271	starvation	starvation	NN	_	_	_
272	growth	growth	NN	_	_	_
273	_	_	NN	_	_	_
274	2	2	CD	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
276	IA-log	ia-log	JJ	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	IA-starve	ia-starve	JJ	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	Identical	identical	JJ	_	_	_
281	to	to	TO	_	_	_
282	Channel	Channel	NNP	_	_	_
283	1	1	CD	_	_	_
284	with	with	IN	_	_	_
285	no	no	DT	_	_	_
286	arabinose	arabinose	NN	_	_	_
287	added	add	VBD	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	IE-co1	ie-co1	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	IE-co2	ie-co2	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	IE-log	ie-log	JJ	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	IE-starve	ie-starve	JJ	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	IFNB	ifnb	NN	_	_	_
298	Multi	multi	JJ	_	_	_
299	SeV0	sev0	NN	_	_	_
300	Rep1	rep1	NN	_	_	_
301	Plasmid	plasmid	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	IFNB	ifnb	NN	_	_	_
304	Multi	multi	JJ	_	_	_
305	SeV10	sev10	NN	_	_	_
306	Rep1	rep1	NN	_	_	_
307	Plasmid	plasmid	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	IFNB	ifnb	NN	_	_	_
310	Single	single	JJ	_	_	_
311	SeV10	sev10	NN	_	_	_
312	Rep1	rep1	NN	_	_	_
313	Plasmid	plasmid	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	IHF	ihf	SYM	TF	_	_
316	-	-	:	_	_	_
317	Anaerobic	anaerobic	JJ	_	_	_
318	A	a	NN	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	IHF	ihf	SYM	TF	_	_
321	-	-	:	_	_	_
322	Anaerobic	anaerobic	JJ	_	_	_
323	B	b	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	IHF	ihf	NN	TF	_	_
326	ChIP	chip	NN	_	_	_
327	DNA	dna	NN	_	_	_
328	from	from	IN	_	_	_
329	WT	WT	NNP	_	_	_
330	Escherichia	escherichia	FW	Organism	_	_
331	coli	coli	FW	Organism	_	_
332	MG1655	mg1655	NN	_	_	_
333	K-12	k-12	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
335	IHF	ihf	VBP	TF	_	_
336	ChIP	chip	NN	_	_	_
337	DNA	dna	NN	_	_	_
338	from	from	IN	_	_	_
339	WT	WT	NNP	_	_	_
340	Escherichia	escherichia	FW	Organism	_	_
341	coli	coli	FW	Organism	_	_
342	MG1655	mg1655	NN	_	_	_
343	K-12	k-12	NN	_	_	_
344	Replicate	replicate	VB	_	_	_
345	B	b	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	IHF	ihf	NN	TF	_	_
348	___	___	CD	_	_	_
349	U	U	NNP	_	_	_
350	_	_	NNP	_	_	_
351	N0075	N0075	NNP	_	_	_
352	_	_	SYM	_	_	_
353	r1	r1	FW	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
355	IHF	ihf	NN	TF	_	_
356	___	___	CD	_	_	_
357	U	U	NNP	_	_	_
358	_	_	NNP	_	_	_
359	N0075	N0075	NNP	_	_	_
360	_	_	SYM	_	_	_
361	r3	r3	FW	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
363	IHF	ihf	NN	TF	_	_
364	upregulation	upregulation	NN	_	_	_
365	,	,	,	_	_	_
366	0.075	0.075	CD	_	_	_
367	mg/mL	mg/ml	NN	_	_	_
368	norfloxacin	norfloxacin	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	ik	ik	NN	_	_	_
371	_	_	NN	_	_	_
372	H2	h2	NN	_	_	_
373	_	_	CD	_	_	_
374	T2	t2	NN	_	_	_
375	.5	.5	CD	_	_	_
376	_	_	NN	_	_	_
377	r1	r1	NN	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	ik	ik	NN	_	_	_
380	_	_	NN	_	_	_
381	H2	h2	NN	_	_	_
382	_	_	CD	_	_	_
383	T3	t3	NN	_	_	_
384	.5	.5	CD	_	_	_
385	_	_	NN	_	_	_
386	r1	r1	NN	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	ik	ik	NN	_	_	_
389	_	_	NN	_	_	_
390	H2	h2	NN	_	_	_
391	_	_	CD	_	_	_
392	T3	t3	NN	_	_	_
393	_	_	CD	_	_	_
394	r1	r1	NN	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	ik	ik	NN	_	_	_
397	_	_	NN	_	_	_
398	H2	h2	NN	_	_	_
399	_	_	CD	_	_	_
400	T4	t4	NN	_	_	_
401	.5	.5	CD	_	_	_
402	_	_	NN	_	_	_
403	r1	r1	NN	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
405	ik	ik	NN	_	_	_
406	_	_	NN	_	_	_
407	H2	h2	NN	_	_	_
408	_	_	CD	_	_	_
409	T4	t4	NN	_	_	_
410	_	_	CD	_	_	_
411	r1	r1	NN	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	ik	ik	NN	_	_	_
414	_	_	NN	_	_	_
415	H2	h2	NN	_	_	_
416	_	_	CD	_	_	_
417	T5	t5	NN	_	_	_
418	.5	.5	CD	_	_	_
419	_	_	NN	_	_	_
420	r1	r1	NN	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	ik	ik	NN	_	_	_
423	_	_	NN	_	_	_
424	H2	h2	NN	_	_	_
425	_	_	CD	_	_	_
426	T5	t5	NN	_	_	_
427	_	_	CD	_	_	_
428	r1	r1	NN	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	ik	ik	NN	_	_	_
431	_	_	NN	_	_	_
432	H2	h2	NN	_	_	_
433	_	_	CD	_	_	_
434	T6	t6	NN	_	_	_
435	_	_	CD	_	_	_
436	r1	r1	NN	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	ik	ik	NN	_	_	_
439	_	_	NN	_	_	_
440	H2	h2	NN	_	_	_
441	_	_	CD	_	_	_
442	T8	t8	NN	_	_	_
443	_	_	CD	_	_	_
444	r1	r1	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	ik	ik	NN	_	_	_
447	_	_	NN	_	_	_
448	L2	l2	NN	_	_	_
449	_	_	CD	_	_	_
450	T2	t2	NN	_	_	_
451	.5	.5	CD	_	_	_
452	_	_	NN	_	_	_
453	r1	r1	NN	_	_	_
454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
455	ik	ik	NN	_	_	_
456	_	_	NN	_	_	_
457	L2	l2	NN	_	_	_
458	_	_	CD	_	_	_
459	T3	t3	NN	_	_	_
460	.5	.5	CD	_	_	_
461	_	_	NN	_	_	_
462	r1	r1	NN	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	ik	ik	NN	_	_	_
465	_	_	NN	_	_	_
466	L2	l2	NN	_	_	_
467	_	_	CD	_	_	_
468	T3	t3	NN	_	_	_
469	_	_	CD	_	_	_
470	r1	r1	NN	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	ik	ik	NN	_	_	_
473	_	_	NN	_	_	_
474	L2	l2	NN	_	_	_
475	_	_	CD	_	_	_
476	T4	t4	NN	_	_	_
477	.5	.5	CD	_	_	_
478	_	_	NN	_	_	_
479	r1	r1	NN	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	ik	ik	NN	_	_	_
482	_	_	NN	_	_	_
483	L2	l2	NN	_	_	_
484	_	_	CD	_	_	_
485	T4	t4	NN	_	_	_
486	_	_	CD	_	_	_
487	r1	r1	NN	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
489	ik	ik	NN	_	_	_
490	_	_	NN	_	_	_
491	L2	l2	NN	_	_	_
492	_	_	CD	_	_	_
493	T5	t5	NN	_	_	_
494	.5	.5	CD	_	_	_
495	_	_	NN	_	_	_
496	r1	r1	NN	_	_	_
497	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
498	ik	ik	NN	_	_	_
499	_	_	NN	_	_	_
500	L2	l2	NN	_	_	_
501	_	_	CD	_	_	_
502	T5	t5	NN	_	_	_
503	_	_	CD	_	_	_
504	r1	r1	NN	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	ik	ik	NN	_	_	_
507	_	_	NN	_	_	_
508	L2	l2	NN	_	_	_
509	_	_	CD	_	_	_
510	T6	t6	NN	_	_	_
511	_	_	CD	_	_	_
512	r1	r1	NN	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	ik	ik	NN	_	_	_
515	_	_	NN	_	_	_
516	L2	l2	NN	_	_	_
517	_	_	CD	_	_	_
518	T8	t8	NN	_	_	_
519	_	_	CD	_	_	_
520	r1	r1	NN	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
522	Illumina	Illumina	NNP	_	_	_
523	Casava1	Casava1	NNP	_	_	_
524	.7	.7	CD	_	_	_
525	software	software	NN	_	_	_
526	used	use	VBN	_	_	_
527	for	for	IN	_	_	_
528	basecalling	basecalling	NN	_	_	_
529	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	Casava	Casava	NNP	_	_	_
4	1.8.2	1.8.2	CD	_	_	_
5	software	software	NN	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	basecalling	basecall	VBG	_	_	_
9	with	with	IN	_	_	_
10	default	default	NN	_	_	_
11	parameter	parameter	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	Casava	Casava	NNP	_	_	_
4	1.8	1.8	CD	_	_	_
5	software	software	NN	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	for	for	IN	_	_	_
9	basecalling	basecalling	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	Casava	Casava	NNP	_	_	_
4	software	software	NN	_	_	_
5	used	use	VBN	_	_	_
6	for	for	IN	_	_	_
7	basecalling	basecalling	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	Casava	Casava	NNP	_	_	_
4	v1	v1	NN	_	_	_
5	.8	.8	CD	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	basecalling	basecalling	NN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	fastq	fastq	NN	_	_	_
4	files	file	NNS	_	_	_
5	were	be	VBD	_	_	_
6	submitted	submit	VBN	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	galaxy	galaxy	NN	_	_	_
10	pipeline	pipeline	NN	_	_	_
11	=	=	JJ	_	_	_
12	>	>	JJR	_	_	_
13	grooming	grooming	NN	_	_	_
14	=	=	JJ	_	_	_
15	>	>	JJR	_	_	_
16	mapping	mapping	NN	_	_	_
17	to	to	TO	_	_	_
18	NC	NC	NNP	_	_	_
19	_	_	SYM	_	_	_
20	002655	002655	CD	_	_	_
21	using	use	VBG	_	_	_
22	bowtie2	bowtie2	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	default	default	NN	_	_	_
25	but	but	CC	_	_	_
26	seed	seed	NN	_	_	_
27	19	19	CD	_	_	_
28	nt	nt	NNS	_	_	_
29	&	&	CC	_	_	_
30	zero	zero	CD	_	_	_
31	mismatches	mismatch	NNS	_	_	_
32	within	within	IN	_	_	_
33	seed	seed	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Illumina	Illumina	NNP	_	_	_
37	GAII	GAII	NNP	_	_	_
38	reads	read	VBZ	_	_	_
39	were	be	VBD	_	_	_
40	filtered	filter	VBN	_	_	_
41	by	by	IN	_	_	_
42	SGA	SGA	NNP	_	_	_
43	version	version	NN	_	_	_
44	0.9.9	0.9.9	CD	_	_	_
45	with	with	IN	_	_	_
46	the	the	DT	_	_	_
47	following	follow	VBG	_	_	_
48	options	option	NNS	_	_	_
49	:	:	:	_	_	_
50	sga	sga	NN	_	_	_
51	preprocess	preprocess	NN	_	_	_
52	-	-	:	_	_	_
53	q	q	NN	_	_	_
54	10	10	CD	_	_	_
55	-	-	:	_	_	_
56	f	f	LS	_	_	_
57	10	10	CD	_	_	_
58	-	-	:	_	_	_
59	m	m	NN	_	_	_
60	25	25	CD	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	quality	quality	NN	_	_	_
63	trim	trim	JJ	_	_	_
64	10	10	CD	_	_	_
65	,	,	,	_	_	_
66	quality	quality	NN	_	_	_
67	filter	filter	NN	_	_	_
68	10	10	CD	_	_	_
69	,	,	,	_	_	_
70	minimal	minimal	JJ	_	_	_
71	length	length	NN	_	_	_
72	25	25	CD	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
75	Illumina	Illumina	NNP	_	_	_
76	read	read	VB	_	_	_
77	were	be	VBD	_	_	_
78	aligned	align	VBN	_	_	_
79	to	to	TO	_	_	_
80	NC	NC	NNP	_	_	_
81	_	_	SYM	_	_	_
82	000913	000913	CD	_	_	_
83	using	use	VBG	_	_	_
84	Bowtie	Bowtie	NNP	_	_	_
85	1	1	CD	_	_	_
86	with	with	IN	_	_	_
87	2	2	CD	_	_	_
88	mismatches	mismatch	NNS	_	_	_
89	allowed	allow	VBD	_	_	_
90	per	per	IN	_	_	_
91	read	read	NN	_	_	_
92	alignment	alignment	NN	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	Illumina	Illumina	NNP	_	_	_
95	Ribozero	Ribozero	NNP	_	_	_
96	rRNA	rrna	NN	_	_	_
97	removal	removal	NN	_	_	_
98	followed	follow	VBN	_	_	_
99	by	by	IN	_	_	_
100	NEB	NEB	NNP	_	_	_
101	Next	next	JJ	_	_	_
102	RNA	rna	NN	_	_	_
103	library	library	NN	_	_	_
104	Prep	Prep	NNP	_	_	_
105	set	set	VBD	_	_	_
106	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	instruments	instrument	NNS	_	_	_
5	generate	generate	VBP	_	_	_
6	per-cycle	per-cycle	JJ	_	_	_
7	BCL	BCL	NNP	_	_	_
8	base	base	NN	_	_	_
9	call	call	NN	_	_	_
10	files	file	NNS	_	_	_
11	as	as	IN	_	_	_
12	primary	primary	JJ	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	output	output	NN	_	_	_
15	in	in	IN	_	_	_
16	bcl2	bcl2	NN	_	_	_
17	format	format	NN	_	_	_
18	.	.	.	_	_	_

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	Image	image	NN	_	_	_
3	analysis	analysis	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	GenePix	GenePix	NNP	_	_	_
8	Pro	pro	FW	_	_	_
9	7	7	CD	_	_	_
10	software	software	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Molecular	molecular	JJ	_	_	_
13	Device	device	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	background	background	NN	_	_	_
17	was	be	VBD	_	_	_
18	defined	define	VBN	_	_	_
19	with	with	IN	_	_	_
20	the	the	DT	_	_	_
21	``	``	``	_	_	_
22	Local	local	JJ	_	_	_
23	features	feature	NNS	_	_	_
24	background	background	NN	_	_	_
25	median	median	NN	_	_	_
26	''	''	''	_	_	_
27	method	method	NN	_	_	_
28	.	.	.	_	_	_

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	Images	image	NNS	_	_	_
3	Analysis	analysis	NN	_	_	_
4	using	use	VBG	_	_	_
5	Agilent	Agilent	NNP	_	_	_
6	Feature	Feature	NNP	_	_	_
7	Extraction	Extraction	NNP	_	_	_
8	Software	Software	NNP	_	_	_
9	Version	Version	NNP	_	_	_
10	11.5	11.5	CD	_	_	_
11	to	to	TO	_	_	_
12	obtain	obtain	VB	_	_	_
13	raw	raw	JJ	_	_	_
14	data.Probe	data.probe	NN	_	_	_
15	intensities	intensity	NNS	_	_	_
16	generated	generate	VBN	_	_	_
17	from	from	IN	_	_	_
18	feature	feature	NN	_	_	_
19	extraction	extraction	NN	_	_	_
20	raw	raw	JJ	_	_	_
21	data	datum	NNS	_	_	_
22	were	be	VBD	_	_	_
23	split	split	VBN	_	_	_
24	based	base	VBN	_	_	_
25	on	on	IN	_	_	_
26	channel	channel	NN	_	_	_
27	type	type	NN	_	_	_
28	and	and	CC	_	_	_
29	analysis	analysis	NN	_	_	_
30	was	be	VBD	_	_	_
31	performed	perform	VBN	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Images	image	NNS	_	_	_
3	were	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	combination	combination	NN	_	_	_
8	of	of	IN	_	_	_
9	GenePix	GenePix	NNP	_	_	_
10	Pro	pro	FW	_	_	_
11	6.0	6.0	CD	_	_	_
12	,	,	,	_	_	_
13	the	the	DT	_	_	_
14	freely	freely	RB	_	_	_
15	available	available	JJ	_	_	_
16	TIGR	tigr	NN	_	_	_
17	TM4	tm4	NN	_	_	_
18	software	software	NN	_	_	_
19	suite	suite	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	www.tm4.org	www.tm4.org	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	Microsoft	Microsoft	NNP	_	_	_
25	Excel	Excel	NNP	_	_	_
26	.	.	.	_	_	_

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	Images	image	NNS	_	_	_
3	were	be	VBD	_	_	_
4	quantified	quantify	VBN	_	_	_
5	and	and	CC	_	_	_
6	normalized	normalize	VBN	_	_	_
7	using	use	VBG	_	_	_
8	extraction	extraction	NN	_	_	_
9	protocol	protocol	NN	_	_	_
10	GE2	ge2	NN	_	_	_
11	_	_	NN	_	_	_
12	107	107	CD	_	_	_
13	_	_	SYM	_	_	_
14	Sept09	sept09	NN	_	_	_
15	and	and	CC	_	_	_
16	Agilent	Agilent	NNP	_	_	_
17	Feature	Feature	NNP	_	_	_
18	Extraction	Extraction	NNP	_	_	_
19	Software	Software	NNP	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	version	version	NN	_	_	_
22	10.7.3.1	10.7.3.1	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

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	10.5.1.1	10.5.1.1	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	obtained	obtain	VBN	_	_	_
15	background	background	NN	_	_	_
16	subtracted	subtract	VBN	_	_	_
17	and	and	CC	_	_	_
18	spatially	spatially	RB	_	_	_
19	detrended	detrend	VBD	_	_	_
20	Processed	processed	JJ	_	_	_
21	Signal	signal	NN	_	_	_
22	intensities	intensity	NNS	_	_	_
23	.	.	.	_	_	_

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	Images	image	NNS	_	_	_
3	were	be	VBD	_	_	_
4	quantified	quantify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Feature	Feature	NNP	_	_	_
7	Extraction	Extraction	NNP	_	_	_
8	Software	Software	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Agilent	Agilent	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	.	.	.	_	_	_

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	Images	image	NNS	_	_	_
17	were	be	VBD	_	_	_
18	quantified	quantify	VBN	_	_	_
19	using	use	VBG	_	_	_
20	GenePix	GenePix	NNP	_	_	_
21	Pro	pro	FW	_	_	_
22	software	software	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Image	image	NN	_	_	_
25	was	be	VBD	_	_	_
26	analized	analize	VBN	_	_	_
27	with	with	IN	_	_	_
28	Genepix	Genepix	NNP	_	_	_
29	6	6	CD	_	_	_
30	pro	pro	JJ	_	_	_
31	followed	follow	VBN	_	_	_
32	by	by	IN	_	_	_
33	background	background	NN	_	_	_
34	substration	substration	NN	_	_	_
35	and	and	CC	_	_	_
36	global	global	JJ	_	_	_
37	LOWESS	lowess	NN	_	_	_
38	normalization	normalization	NN	_	_	_
39	in	in	IN	_	_	_
40	R	r	NN	_	_	_
41	environment	environment	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	KTH	kth	NN	_	_	_
44	package	package	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

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/or	and/or	CC	_	_	_
11	relative	relative	JJ	_	_	_
12	standard	standard	JJ	_	_	_
13	deviation	deviation	NN	_	_	_
14	between	between	IN	_	_	_
15	parallel	parallel	JJ	_	_	_
16	spots	spot	NNS	_	_	_
17	greater	greater	JJR	_	_	_
18	than	than	IN	_	_	_
19	20	20	CD	_	_	_
20	%	%	NN	_	_	_
21	were	be	VBD	_	_	_
22	removed	remove	VBN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Immediately	immediately	RB	_	_	_
3	after	after	IN	_	_	_
4	turning	turn	VBG	_	_	_
5	off	off	RP	_	_	_
6	oxygen	oxygen	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	Immunoprecipitated	immunoprecipitate	VBN	_	_	_
9	DNA	dna	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	imp	imp	NN	_	_	_
12	mutation	mutation	NN	_	_	_
13	:	:	:	_	_	_
14	contains	contain	VBZ	_	_	_
15	a	a	DT	_	_	_
16	23	23	CD	_	_	_
17	codon	codon	NN	_	_	_
18	deletion	deletion	NN	_	_	_
19	allele	allele	NN	_	_	_
20	in	in	IN	_	_	_
21	imp	imp	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	increased	increase	VBN	_	_	_
24	membrane	membrane	NN	_	_	_
25	permeability	permeability	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	,	,	,	_	_	_
28	substitution	substitution	NN	_	_	_
29	of	of	IN	_	_	_
30	the	the	DT	_	_	_
31	93th	93th	JJ	_	_	_
32	codon	codon	NN	_	_	_
33	of	of	IN	_	_	_
34	fabI	fabi	NN	GEN	_	_
35	,	,	,	_	_	_
36	NTG	NTG	NNP	_	_	_
37	treatment	treatment	NN	_	_	_
38	;	;	:	_	_	_
39	fabI	fabi	NN	GEN	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	G93V	g93v	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	,	,	,	_	_	_
44	substitution	substitution	NN	_	_	_
45	of	of	IN	_	_	_
46	Gly	gly	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	the	the	DT	_	_	_
49	93th	93th	JJ	_	_	_
50	codon	codon	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	of	of	IN	_	_	_
53	fabI	fabi	NN	GEN	_	_
54	with	with	IN	_	_	_
55	Val	val	NN	_	_	_
56	,	,	,	_	_	_
57	NTG	NTG	NNP	_	_	_
58	treatment	treatment	NN	_	_	_
59	to	to	TO	_	_	_
60	be	be	VB	_	_	_
61	high	high	JJ	_	_	_
62	resistance	resistance	NN	_	_	_
63	to	to	TO	_	_	_
64	triclosan	triclosan	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	imp	imp	NN	_	_	_
67	mutation	mutation	NN	_	_	_
68	:	:	:	_	_	_
69	contains	contain	VBZ	_	_	_
70	a	a	DT	_	_	_
71	23	23	CD	_	_	_
72	codon	codon	NN	_	_	_
73	deletion	deletion	NN	_	_	_
74	allele	allele	NN	_	_	_
75	in	in	IN	_	_	_
76	imp	imp	NN	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	increased	increase	VBN	_	_	_
79	membrane	membrane	NN	_	_	_
80	permeability	permeability	NN	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	,	,	,	_	_	_
83	substitution	substitution	NN	_	_	_
84	of	of	IN	_	_	_
85	the	the	DT	_	_	_
86	94th	94th	JJ	_	_	_
87	codon	codon	NN	_	_	_
88	of	of	IN	_	_	_
89	fabI	fabi	NN	GEN	_	_
90	,	,	,	_	_	_
91	NTG	NTG	NNP	_	_	_
92	treatment	treatment	NN	_	_	_
93	;	;	:	_	_	_
94	fabI	fabi	NN	GEN	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	G93V	g93v	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	,	,	,	_	_	_
99	substitution	substitution	NN	_	_	_
100	of	of	IN	_	_	_
101	Gly	gly	NN	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	the	the	DT	_	_	_
104	94th	94th	JJ	_	_	_
105	codon	codon	NN	_	_	_
106	-RRB-	-rrb-	-RRB-	_	_	_
107	of	of	IN	_	_	_
108	fabI	fabi	NN	GEN	_	_
109	with	with	IN	_	_	_
110	Val	val	NN	_	_	_
111	,	,	,	_	_	_
112	NTG	NTG	NNP	_	_	_
113	treatment	treatment	NN	_	_	_
114	to	to	TO	_	_	_
115	be	be	VB	_	_	_
116	high	high	JJ	_	_	_
117	resistance	resistance	NN	_	_	_
118	to	to	TO	_	_	_
119	triclosan	triclosan	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	imp	imp	NN	_	_	_
122	mutation	mutation	NN	_	_	_
123	:	:	:	_	_	_
124	contains	contain	VBZ	_	_	_
125	a	a	DT	_	_	_
126	23	23	CD	_	_	_
127	codon	codon	NN	_	_	_
128	detion	detion	NN	_	_	_
129	allele	allele	NN	_	_	_
130	in	in	IN	_	_	_
131	imp	imp	NN	_	_	_
132	-LRB-	-lrb-	-LRB-	_	_	_
133	increased	increase	VBN	_	_	_
134	membrane	membrane	NN	_	_	_
135	permeability	permeability	NN	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	,	,	,	_	_	_
138	substitution	substitution	NN	_	_	_
139	of	of	IN	_	_	_
140	the	the	DT	_	_	_
141	93th	93th	JJ	_	_	_
142	codon	codon	NN	_	_	_
143	of	of	IN	_	_	_
144	fabI	fabi	NN	GEN	_	_
145	;	;	:	_	_	_
146	fabI	fabi	NN	GEN	_	_
147	-LRB-	-lrb-	-LRB-	_	_	_
148	G93V	g93v	NN	_	_	_
149	-RRB-	-rrb-	-RRB-	_	_	_
150	,	,	,	_	_	_
151	substitution	substitution	NN	_	_	_
152	of	of	IN	_	_	_
153	Gly	gly	NN	_	_	_
154	-LRB-	-lrb-	-LRB-	_	_	_
155	the	the	DT	_	_	_
156	93th	93th	JJ	_	_	_
157	codon	codon	NN	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	of	of	IN	_	_	_
160	fabI	fabi	NN	GEN	_	_
161	with	with	IN	_	_	_
162	Val	val	NN	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	imp	imp	NN	_	_	_
165	mutation	mutation	NN	_	_	_
166	:	:	:	_	_	_
167	contains	contain	VBZ	_	_	_
168	a	a	DT	_	_	_
169	23	23	CD	_	_	_
170	codon	codon	NN	_	_	_
171	detion	detion	NN	_	_	_
172	allele	allele	NN	_	_	_
173	in	in	IN	_	_	_
174	imp	imp	NN	_	_	_
175	-LRB-	-lrb-	-LRB-	_	_	_
176	increased	increase	VBN	_	_	_
177	membrane	membrane	NN	_	_	_
178	permeability	permeability	NN	_	_	_
179	-RRB-	-rrb-	-RRB-	_	_	_
180	,	,	,	_	_	_
181	substitution	substitution	NN	_	_	_
182	of	of	IN	_	_	_
183	the	the	DT	_	_	_
184	94th	94th	JJ	_	_	_
185	codon	codon	NN	_	_	_
186	of	of	IN	_	_	_
187	fabI	fabi	NN	GEN	_	_
188	;	;	:	_	_	_
189	fabI	fabi	NN	GEN	_	_
190	-LRB-	-lrb-	-LRB-	_	_	_
191	G93V	g93v	NN	_	_	_
192	-RRB-	-rrb-	-RRB-	_	_	_
193	,	,	,	_	_	_
194	substitution	substitution	NN	_	_	_
195	of	of	IN	_	_	_
196	Gly	gly	NN	_	_	_
197	-LRB-	-lrb-	-LRB-	_	_	_
198	the	the	DT	_	_	_
199	94th	94th	JJ	_	_	_
200	codon	codon	NN	_	_	_
201	-RRB-	-rrb-	-RRB-	_	_	_
202	of	of	IN	_	_	_
203	fabI	fabi	NN	GEN	_	_
204	with	with	IN	_	_	_
205	Val	val	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	incubated	incubate	VBN	_	_	_
208	with	with	IN	_	_	_
209	:	:	:	_	_	_
210	Drosophila	drosophila	FW	_	_	_
211	immune	immune	JJ	_	_	_
212	proteins	protein	NNS	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	incubated	incubate	VBN	_	_	_
215	with	with	IN	_	_	_
216	:	:	:	_	_	_
217	GST	gst	NN	_	_	_
218	alone	alone	RB	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	3	3	CD	_	_	_
221	μM	μm	NN	_	_	_
222	;	;	:	_	_	_
223	control	control	NN	_	_	_
224	-RRB-	-rrb-	-RRB-	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	Incubation	incubation	NN	_	_	_
227	and	and	CC	_	_	_
228	RNA	rna	NN	_	_	_
229	harvesting	harvesting	NN	_	_	_
230	were	be	VBD	_	_	_
231	carried	carry	VBN	_	_	_
232	out	out	RP	_	_	_
233	for	for	IN	_	_	_
234	all	all	DT	_	_	_
235	samples	sample	NNS	_	_	_
236	simultaneously	simultaneously	RB	_	_	_
237	and	and	CC	_	_	_
238	under	under	IN	_	_	_
239	RNase-free	rnase-free	JJ	_	_	_
240	conditions	condition	NNS	_	_	_
241	to	to	TO	_	_	_
242	minimize	minimize	VB	_	_	_
243	biological	biological	JJ	_	_	_
244	variability	variability	NN	_	_	_
245	in	in	IN	_	_	_
246	gene	gene	NN	_	_	_
247	expression	expression	NN	_	_	_
248	between	between	IN	_	_	_
249	each	each	DT	_	_	_
250	sample	sample	NN	_	_	_
251	.	.	.	_	_	_

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	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	duration	duration	NN	_	_	_
19	:	:	:	_	_	_
20	10	10	CD	_	_	_
21	min	min	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	incubation	incubation	NN	_	_	_
24	medium	medium	NN	_	_	_
25	:	:	:	_	_	_
26	10	10	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	NaCl	nacl	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	incubation	incubation	NN	_	_	_
31	medium	medium	NN	_	_	_
32	:	:	:	_	_	_
33	10	10	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	+	+	CC	_	_	_
37	100mg/l	100mg/l	CD	_	_	_
38	TiO2	tio2	NN	_	_	_
39	nanoparticles	nanoparticle	NNS	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Incubation	incubation	NN	_	_	_
42	temperature	temperature	NN	_	_	_
43	=	=	JJ	_	_	_
44	37C	37c	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	incubation	incubation	NN	_	_	_
47	time	time	NN	_	_	_
48	:	:	:	_	_	_
49	0	0	CD	_	_	_
50	min	min	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	incubation	incubation	NN	_	_	_
53	time	time	NN	_	_	_
54	:	:	:	_	_	_
55	10	10	CD	_	_	_
56	min	min	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	incubation	incubation	NN	_	_	_
59	time	time	NN	_	_	_
60	:	:	:	_	_	_
61	5	5	CD	_	_	_
62	hr	hr	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	incubation	incubation	NN	_	_	_
65	time	time	NN	_	_	_
66	:	:	:	_	_	_
67	n/a	n/a	NN	_	_	_
68	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
69	Index	Index	NNP	_	_	_
70	and	and	CC	_	_	_
71	sort	sort	NN	_	_	_
72	alignments	alignment	NNS	_	_	_
73	with	with	IN	_	_	_
74	samtools	samtool	NNS	_	_	_
75	version	version	NN	_	_	_
76	1.2	1.2	CD	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	Index	Index	NNP	_	_	_
79	sequences	sequence	NNS	_	_	_
80	accompanying	accompany	VBG	_	_	_
81	with	with	IN	_	_	_
82	reads	read	VBZ	_	_	_
83	were	be	VBD	_	_	_
84	compared	compare	VBN	_	_	_
85	with	with	IN	_	_	_
86	pre-designed	pre-designed	JJ	_	_	_
87	barcodes	barcode	NNS	_	_	_
88	,	,	,	_	_	_
89	allowing	allow	VBG	_	_	_
90	two	two	CD	_	_	_
91	base	base	NN	_	_	_
92	mismatches	mismatch	NNS	_	_	_
93	at	at	IN	_	_	_
94	most	most	JJS	_	_	_
95	.	.	.	_	_	_

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	individual	individual	NN	_	_	_
25	:	:	:	_	_	_
26	CF	cf	NN	_	_	_
27	patient	patient	NN	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Individual	Individual	NNP	_	_	_
30	clones	clone	NNS	_	_	_
31	of	of	IN	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	DH1	dh1	NN	_	_	_
35	were	be	VBD	_	_	_
36	grown	grow	VBN	_	_	_
37	in	in	IN	_	_	_
38	M9	M9	NNP	_	_	_
39	MOPS	MOPS	NNP	MED	_	_
40	media	media	NNS	_	_	_
41	in	in	IN	_	_	_
42	300	300	CD	_	_	_
43	mL	ml	NN	_	_	_
44	media	media	NNS	_	_	_
45	in	in	IN	_	_	_
46	1	1	CD	_	_	_
47	L	l	NN	_	_	_
48	baffled	baffle	VBD	_	_	_
49	flasks	flask	NNS	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Individual	Individual	NNP	_	_	_
52	colonies	colony	NNS	_	_	_
53	were	be	VBD	_	_	_
54	inoculated	inoculate	VBN	_	_	_
55	into	into	IN	_	_	_
56	MOPS	MOPS	NNP	MED	_	_
57	EZ	EZ	NNP	_	_	_
58	Rich	Rich	NNP	_	_	_
59	Defined	Defined	NNP	_	_	_
60	Medium	medium	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Teknova	teknova	NN	_	_	_
63	,	,	,	_	_	_
64	CA	CA	NNP	_	_	_
65	,	,	,	_	_	_
66	M2105	m2105	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	with	with	IN	_	_	_
69	0.2	0.2	CD	_	_	_
70	%	%	NN	_	_	_
71	glycerol	glycerol	NN	SUPP	_	_
72	carbon	carbon	NN	_	_	_
73	source	source	NN	_	_	_
74	and	and	CC	_	_	_
75	50	50	CD	_	_	_
76	μg/mL	μg/ml	NN	_	_	_
77	kanamycin	kanamycin	NN	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	Gold	gold	NN	_	_	_
80	Biotechnology	biotechnology	NN	_	_	_
81	,	,	,	_	_	_
82	MO	MO	NNP	_	_	_
83	,	,	,	_	_	_
84	K-120-5	k-120-5	NN	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	and	and	CC	_	_	_
87	grown	grow	VBN	_	_	_
88	overnight	overnight	JJ	_	_	_
89	for	for	IN	_	_	_
90	16	16	CD	_	_	_
91	hours	hour	NNS	_	_	_
92	at	at	IN	_	_	_
93	37	37	CD	_	_	_
94	°C	°c	NN	_	_	_
95	and	and	CC	_	_	_
96	1000	1000	CD	_	_	_
97	RPM	RPM	NNP	_	_	_
98	in	in	IN	_	_	_
99	V-bottom	V-bottom	NNP	_	_	_
100	96-well	96-well	JJ	_	_	_
101	plates	plate	NNS	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	Nunc	Nunc	NNP	_	_	_
104	,	,	,	_	_	_
105	Roskilde	Roskilde	NNP	_	_	_
106	,	,	,	_	_	_
107	Denmark	Denmark	NNP	_	_	_
108	,	,	,	_	_	_
109	249952	249952	CD	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	in	in	IN	_	_	_
112	an	a	DT	_	_	_
113	ELMI	ELMI	NNP	_	_	_
114	Digital	Digital	NNP	_	_	_
115	Thermos	Thermos	NNP	_	_	_
116	Microplates	Microplates	NNP	_	_	_
117	shaker	shaker	NN	_	_	_
118	incubator	incubator	NN	_	_	_
119	-LRB-	-lrb-	-LRB-	_	_	_
120	Elmi	Elmi	NNP	_	_	_
121	Ltd	Ltd	NNP	_	_	_
122	,	,	,	_	_	_
123	Riga	Riga	NNP	_	_	_
124	,	,	,	_	_	_
125	Latvia	Latvia	NNP	_	_	_
126	-RRB-	-rrb-	-RRB-	_	_	_
127	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	following	follow	VBG	_	_	_
3	day	day	NN	_	_	_
4	,	,	,	_	_	_
5	cultures	culture	NNS	_	_	_
6	were	be	VBD	_	_	_
7	diluted	dilute	VBN	_	_	_
8	178-fold	178-fold	JJ	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	two	two	CD	_	_	_
11	serial	serial	JJ	_	_	_
12	dilutions	dilution	NNS	_	_	_
13	of	of	IN	_	_	_
14	15	15	CD	_	_	_
15	µL	µl	NN	_	_	_
16	into	into	IN	_	_	_
17	185	185	CD	_	_	_
18	µL	µl	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	into	into	IN	_	_	_
21	EZ	ez	NN	_	_	_
22	Rich	rich	JJ	_	_	_
23	glycerol	glycerol	NN	SUPP	_	_
24	with	with	IN	_	_	_
25	kanamycin	kanamycin	NN	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	grown	grow	VBN	_	_	_
29	under	under	IN	_	_	_
30	the	the	DT	_	_	_
31	same	same	JJ	_	_	_
32	ELMI	elmi	NN	_	_	_
33	shaker	shaker	NN	_	_	_
34	incubator	incubator	NN	_	_	_
35	conditions	condition	NNS	_	_	_
36	for	for	IN	_	_	_
37	three	three	CD	_	_	_
38	hours	hour	NNS	_	_	_
39	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	diluted	dilute	VBN	_	_	_
4	658-fold	658-fold	JJ	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	4.56	4.56	CD	_	_	_
7	µL	µl	NN	_	_	_
8	into	into	IN	_	_	_
9	3	3	CD	_	_	_
10	mL	ml	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	into	into	IN	_	_	_
13	culture	culture	NN	_	_	_
14	tubes	tube	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Falcon	Falcon	NNP	_	_	_
17	14	14	CD	_	_	_
18	mL	ml	NN	_	_	_
19	round-bottom	round-bottom	JJ	_	_	_
20	polypropylene	polypropylene	NN	_	_	_
21	tubes	tube	NNS	_	_	_
22	;	;	:	_	_	_
23	Corning	Corning	NNP	_	_	_
24	,	,	,	_	_	_
25	MA	MA	NNP	_	_	_
26	,	,	,	_	_	_
27	352059	352059	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	containing	contain	VBG	_	_	_
30	EZ	ez	NN	_	_	_
31	Rich	rich	JJ	_	_	_
32	glycerol	glycerol	NN	SUPP	_	_
33	with	with	IN	_	_	_
34	kanamycin	kanamycin	NN	_	_	_
35	and	and	CC	_	_	_
36	inducers	inducer	NNS	_	_	_
37	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	Erlenmeyer	Erlenmeyer	NNP	_	_	_
3	flask	flask	NN	_	_	_
4	assays	assay	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Pyrex	pyrex	NN	_	_	_
7	250	250	CD	_	_	_
8	mL	ml	NN	_	_	_
9	;	;	:	_	_	_
10	Cole-Palmer	Cole-Palmer	NNP	_	_	_
11	,	,	,	_	_	_
12	IL	il	NN	_	_	_
13	,	,	,	_	_	_
14	4980-250	4980-250	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	cells	cell	NNS	_	_	_
18	were	be	VBD	_	_	_
19	diluted	dilute	VBN	_	_	_
20	658-fold	658-fold	JJ	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	76	76	CD	_	_	_
23	µL	µl	NN	_	_	_
24	into	into	IN	_	_	_
25	50	50	CD	_	_	_
26	mL	ml	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	into	into	IN	_	_	_
29	EZ	ez	NN	_	_	_
30	Rich	rich	JJ	_	_	_
31	glycerol	glycerol	NN	SUPP	_	_
32	with	with	IN	_	_	_
33	kanamycin	kanamycin	NN	_	_	_
34	and	and	CC	_	_	_
35	inducers	inducer	NNS	_	_	_
36	.	.	.	_	_	_

1	Eight	eight	CD	_	_	_
2	inducer	inducer	NN	_	_	_
3	combinations	combination	NNS	_	_	_
4	were	be	VBD	_	_	_
5	used	use	VBN	_	_	_
6	that	that	IN	_	_	_
7	cover	cover	VBP	_	_	_
8	the	the	DT	_	_	_
9	presence	presence	NN	_	_	_
10	or	or	CC	_	_	_
11	absence	absence	NN	_	_	_
12	of	of	IN	_	_	_
13	0.5	0.5	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	IPTG	iptg	NN	_	_	_
16	,	,	,	_	_	_
17	10	10	CD	_	_	_
18	ng/mL	ng/ml	NN	_	_	_
19	aTc	atc	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	5	5	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	L-arabinose	l-arabinose	NN	_	_	_
25	.	.	.	_	_	_

1	Culture	culture	NN	_	_	_
2	tubes	tube	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	an	a	DT	_	_	_
8	Innova	Innova	NNP	_	_	_
9	44	44	CD	_	_	_
10	shaker	shaker	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Eppendorf	eppendorf	NN	_	_	_
13	,	,	,	_	_	_
14	CT	ct	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	and	and	CC	_	_	_
20	250	250	CD	_	_	_
21	rpm	rpm	NN	_	_	_
22	for	for	IN	_	_	_
23	five	five	CD	_	_	_
24	hours	hour	NNS	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Individual	Individual	NNP	_	_	_
3	colonies	colony	NNS	_	_	_
4	were	be	VBD	_	_	_
5	inoculated	inoculate	VBN	_	_	_
6	into	into	IN	_	_	_
7	MOPS	MOPS	NNP	MED	_	_
8	EZ	EZ	NNP	_	_	_
9	Rich	Rich	NNP	_	_	_
10	Defined	Defined	NNP	_	_	_
11	Medium	medium	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Teknova	teknova	NN	_	_	_
14	,	,	,	_	_	_
15	CA	CA	NNP	_	_	_
16	,	,	,	_	_	_
17	M2105	m2105	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	with	with	IN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	glycerol	glycerol	NN	SUPP	_	_
23	carbon	carbon	NN	_	_	_
24	source	source	NN	_	_	_
25	and	and	CC	_	_	_
26	50	50	CD	_	_	_
27	μg/mL	μg/ml	NN	_	_	_
28	kanamycin	kanamycin	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Gold	gold	NN	_	_	_
31	Biotechnology	biotechnology	NN	_	_	_
32	,	,	,	_	_	_
33	MO	MO	NNP	_	_	_
34	,	,	,	_	_	_
35	K-120-5	k-120-5	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	and	and	CC	_	_	_
38	grown	grow	VBN	_	_	_
39	overnight	overnight	JJ	_	_	_
40	for	for	IN	_	_	_
41	16	16	CD	_	_	_
42	hours	hour	NNS	_	_	_
43	at	at	IN	_	_	_
44	37	37	CD	_	_	_
45	°C	°c	NN	_	_	_
46	and	and	CC	_	_	_
47	1000	1000	CD	_	_	_
48	RPM	RPM	NNP	_	_	_
49	in	in	IN	_	_	_
50	V-bottom	V-bottom	NNP	_	_	_
51	96-well	96-well	JJ	_	_	_
52	plates	plate	NNS	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	Nunc	Nunc	NNP	_	_	_
55	,	,	,	_	_	_
56	Roskilde	Roskilde	NNP	_	_	_
57	,	,	,	_	_	_
58	Denmark	Denmark	NNP	_	_	_
59	,	,	,	_	_	_
60	249952	249952	CD	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	in	in	IN	_	_	_
63	an	a	DT	_	_	_
64	ELMI	ELMI	NNP	_	_	_
65	Digital	Digital	NNP	_	_	_
66	Thermos	Thermos	NNP	_	_	_
67	Microplates	Microplates	NNP	_	_	_
68	shaker	shaker	NN	_	_	_
69	incubator	incubator	NN	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	Elmi	Elmi	NNP	_	_	_
72	Ltd	Ltd	NNP	_	_	_
73	,	,	,	_	_	_
74	Riga	Riga	NNP	_	_	_
75	,	,	,	_	_	_
76	Latvia	Latvia	NNP	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	following	follow	VBG	_	_	_
3	day	day	NN	_	_	_
4	,	,	,	_	_	_
5	cultures	culture	NNS	_	_	_
6	were	be	VBD	_	_	_
7	diluted	dilute	VBN	_	_	_
8	178-fold	178-fold	JJ	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	two	two	CD	_	_	_
11	serial	serial	JJ	_	_	_
12	dilutions	dilution	NNS	_	_	_
13	of	of	IN	_	_	_
14	15	15	CD	_	_	_
15	µL	µl	NN	_	_	_
16	into	into	IN	_	_	_
17	185	185	CD	_	_	_
18	µL	µl	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	into	into	IN	_	_	_
21	EZ	ez	NN	_	_	_
22	Rich	rich	JJ	_	_	_
23	glycerol	glycerol	NN	SUPP	_	_
24	with	with	IN	_	_	_
25	kanamycin	kanamycin	NN	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	grown	grow	VBN	_	_	_
29	under	under	IN	_	_	_
30	the	the	DT	_	_	_
31	same	same	JJ	_	_	_
32	ELMI	elmi	NN	_	_	_
33	shaker	shaker	NN	_	_	_
34	incubator	incubator	NN	_	_	_
35	conditions	condition	NNS	_	_	_
36	for	for	IN	_	_	_
37	three	three	CD	_	_	_
38	hours	hour	NNS	_	_	_
39	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	culture	culture	NN	_	_	_
3	tube	tube	NN	_	_	_
4	assays	assay	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Falcon	Falcon	NNP	_	_	_
7	14	14	CD	_	_	_
8	mL	ml	NN	_	_	_
9	round-bottom	round-bottom	JJ	_	_	_
10	polypropylene	polypropylene	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	;	;	:	_	_	_
13	Corning	Corning	NNP	_	_	_
14	,	,	,	_	_	_
15	MA	MA	NNP	_	_	_
16	,	,	,	_	_	_
17	352059	352059	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	cells	cell	NNS	_	_	_
21	were	be	VBD	_	_	_
22	diluted	dilute	VBN	_	_	_
23	658-fold	658-fold	JJ	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	4.56	4.56	CD	_	_	_
26	µL	µl	NN	_	_	_
27	into	into	IN	_	_	_
28	3	3	CD	_	_	_
29	mL	ml	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	into	into	IN	_	_	_
32	EZ	ez	NN	_	_	_
33	Rich	rich	JJ	_	_	_
34	glycerol	glycerol	NN	SUPP	_	_
35	with	with	IN	_	_	_
36	kanamycin	kanamycin	NN	_	_	_
37	and	and	CC	_	_	_
38	inducers	inducer	NNS	_	_	_
39	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	Erlenmeyer	Erlenmeyer	NNP	_	_	_
3	flask	flask	NN	_	_	_
4	assays	assay	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Pyrex	pyrex	NN	_	_	_
7	250	250	CD	_	_	_
8	mL	ml	NN	_	_	_
9	;	;	:	_	_	_
10	Cole-Palmer	Cole-Palmer	NNP	_	_	_
11	,	,	,	_	_	_
12	IL	il	NN	_	_	_
13	,	,	,	_	_	_
14	4980-250	4980-250	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	cells	cell	NNS	_	_	_
18	were	be	VBD	_	_	_
19	diluted	dilute	VBN	_	_	_
20	658-fold	658-fold	JJ	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	76	76	CD	_	_	_
23	µL	µl	NN	_	_	_
24	into	into	IN	_	_	_
25	50	50	CD	_	_	_
26	mL	ml	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	into	into	IN	_	_	_
29	EZ	ez	NN	_	_	_
30	Rich	rich	JJ	_	_	_
31	glycerol	glycerol	NN	SUPP	_	_
32	with	with	IN	_	_	_
33	kanamycin	kanamycin	NN	_	_	_
34	and	and	CC	_	_	_
35	inducers	inducer	NNS	_	_	_
36	.	.	.	_	_	_

1	Eight	eight	CD	_	_	_
2	inducer	inducer	NN	_	_	_
3	combinations	combination	NNS	_	_	_
4	were	be	VBD	_	_	_
5	used	use	VBN	_	_	_
6	that	that	IN	_	_	_
7	cover	cover	VBP	_	_	_
8	the	the	DT	_	_	_
9	presence	presence	NN	_	_	_
10	or	or	CC	_	_	_
11	absence	absence	NN	_	_	_
12	of	of	IN	_	_	_
13	0.5	0.5	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	IPTG	iptg	NN	_	_	_
16	,	,	,	_	_	_
17	10	10	CD	_	_	_
18	ng/mL	ng/ml	NN	_	_	_
19	aTc	atc	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	5	5	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	L-arabinose	l-arabinose	NN	_	_	_
25	.	.	.	_	_	_

1	Culture	culture	NN	_	_	_
2	tubes	tube	NNS	_	_	_
3	and	and	CC	_	_	_
4	Erlenmeyer	Erlenmeyer	NNP	_	_	_
5	flasks	flask	NNS	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	an	a	DT	_	_	_
11	Innova	Innova	NNP	_	_	_
12	44	44	CD	_	_	_
13	shaker	shaker	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Eppendorf	eppendorf	NN	_	_	_
16	,	,	,	_	_	_
17	CT	ct	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	at	at	IN	_	_	_
20	37	37	CD	_	_	_
21	°C	°c	NN	_	_	_
22	and	and	CC	_	_	_
23	250	250	CD	_	_	_
24	rpm	rpm	NN	_	_	_
25	for	for	IN	_	_	_
26	five	five	CD	_	_	_
27	hours	hour	NNS	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	individual	individual	NN	_	_	_
3	:	:	:	_	_	_
4	healthy	healthy	JJ	_	_	_
5	child	child	NN	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Indole	Indole	NNP	_	_	_
8	treated	treat	VBN	_	_	_
9	at	at	IN	_	_	_
10	specific	specific	JJ	_	_	_
11	growth	growth	NN	_	_	_
12	rate	rate	NN	_	_	_
13	0.5h-1	0.5h-1	JJ	_	_	_
14	0h	0h	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Indole	indole	FW	_	_	_
17	treated	treat	VBN	_	_	_
18	at	at	IN	_	_	_
19	specific	specific	JJ	_	_	_
20	growth	growth	NN	_	_	_
21	rate	rate	NN	_	_	_
22	0.5h-1	0.5h-1	JJ	_	_	_
23	10h	10h	JJ	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Indole	indole	FW	_	_	_
26	treated	treat	VBN	_	_	_
27	at	at	IN	_	_	_
28	specific	specific	JJ	_	_	_
29	growth	growth	NN	_	_	_
30	rate	rate	NN	_	_	_
31	0.5h-1	0.5h-1	JJ	_	_	_
32	16h	16h	JJ	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Indole	indole	FW	_	_	_
35	treated	treat	VBN	_	_	_
36	at	at	IN	_	_	_
37	specific	specific	JJ	_	_	_
38	growth	growth	NN	_	_	_
39	rate	rate	NN	_	_	_
40	0.5h-1	0.5h-1	JJ	_	_	_
41	5h	5h	JJ	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Indole	indole	FW	_	_	_
44	treated	treat	VBN	_	_	_
45	at	at	IN	_	_	_
46	specific	specific	JJ	_	_	_
47	growth	growth	NN	_	_	_
48	rate	rate	NN	_	_	_
49	0.5h-1	0.5h-1	JJ	_	_	_
50	8h	8h	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	Induced	induce	VBN	_	_	_
53	from	from	IN	_	_	_
54	E.	e.	FW	_	_	_
55	coli	coli	FW	_	_	_
56	strain	strain	NN	_	_	_
57	3538	3538	CD	_	_	_
58	with	with	IN	_	_	_
59	mitomycin	mitomycin	NN	_	_	_
60	C	c	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	induced/non-induced	induced/non-induced	JJ	_	_	_
63	:	:	:	_	_	_
64	Induced	induce	VBN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	induced/non-induced	induced/non-induced	JJ	_	_	_
67	:	:	:	_	_	_
68	Non-induced	non-induced	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	induction	induction	NN	_	_	_
71	:	:	:	_	_	_
72	0.2	0.2	CD	_	_	_
73	%	%	NN	_	_	_
74	arabinose	arabinose	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	induction	induction	NN	_	_	_
77	:	:	:	_	_	_
78	induced	induce	VBN	_	_	_
79	50	50	CD	_	_	_
80	µM	µm	NN	_	_	_
81	IPTG	iptg	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	induction	induction	NN	_	_	_
84	:	:	:	_	_	_
85	None	none	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Infected	infected	JJ	_	_	_
88	kidney	kidney	NN	_	_	_
89	solutions	solution	NNS	_	_	_
90	were	be	VBD	_	_	_
91	centrifuged	centrifuge	VBN	_	_	_
92	at	at	IN	_	_	_
93	5000xg	5000xg	CD	_	_	_
94	for	for	IN	_	_	_
95	10	10	CD	_	_	_
96	min	min	NN	_	_	_
97	to	to	TO	_	_	_
98	separate	separate	JJ	_	_	_
99	bacteria	bacterium	NNS	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	pellet	pellet	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	from	from	IN	_	_	_
104	kidney	kidney	NN	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	surface	surface	NN	_	_	_
107	of	of	IN	_	_	_
108	RNA-later	rna-later	NN	_	_	_
109	solution	solution	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	cells	cell	NNS	_	_	_
112	.	.	.	_	_	_

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	1mg/ml	1mg/ml	CD	_	_	_
17	final	final	JJ	_	_	_
18	concentration	concentration	NN	_	_	_
19	for	for	IN	_	_	_
20	5	5	CD	_	_	_
21	min	min	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	samples	sample	NNS	_	_	_
25	of	of	IN	_	_	_
26	3-5	3-5	CD	_	_	_
27	infected	infected	JJ	_	_	_
28	mice	mouse	NNS	_	_	_
29	were	be	VBD	_	_	_
30	pooled	pool	VBN	_	_	_
31	together	together	RB	_	_	_
32	for	for	IN	_	_	_
33	each	each	DT	_	_	_
34	infection	infection	NN	_	_	_
35	group	group	NN	_	_	_
36	.	.	.	_	_	_

1	Nucleic	nucleic	JJ	_	_	_
2	acids	acid	NNS	_	_	_
3	were	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	via	via	IN	_	_	_
6	the	the	DT	_	_	_
7	RNA	rna	NN	_	_	_
8	extraction	extraction	NN	_	_	_
9	protocol	protocol	NN	_	_	_
10	and	and	CC	_	_	_
11	products	product	NNS	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	RNAeasy	RNAeasy	NNP	_	_	_
15	kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	qiagen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	column	column	NN	_	_	_
3	purification	purification	NN	_	_	_
4	,	,	,	_	_	_
5	RNA	rna	NN	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	treated	treat	VBN	_	_	_
9	with	with	IN	_	_	_
10	DNAse	dnase	NN	_	_	_
11	Turbo	Turbo	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Ambion	Ambion	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	for	for	IN	_	_	_
16	30	30	CD	_	_	_
17	min	min	NN	_	_	_
18	at	at	IN	_	_	_
19	37C	37c	NN	_	_	_
20	,	,	,	_	_	_
21	followed	follow	VBN	_	_	_
22	by	by	IN	_	_	_
23	quantification	quantification	NN	_	_	_
24	of	of	IN	_	_	_
25	RNA	rna	NN	_	_	_
26	using	use	VBG	_	_	_
27	a	a	DT	_	_	_
28	spectrophotometer	spectrophotometer	NN	_	_	_
29	.	.	.	_	_	_

1	Remaining	remain	VBG	_	_	_
2	polyadenylated	polyadenylated	JJ	_	_	_
3	eukaryotic	eukaryotic	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	depleted	deplete	VBN	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	samples	sample	NNS	_	_	_
10	following	follow	VBG	_	_	_
11	the	the	DT	_	_	_
12	MicroEnrich	MicroEnrich	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Ambion	Ambion	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	protocol	protocol	NN	_	_	_
17	and	and	CC	_	_	_
18	resuspended	resuspend	VBN	_	_	_
19	in	in	IN	_	_	_
20	20	20	CD	_	_	_
21	l	l	NN	_	_	_
22	of	of	IN	_	_	_
23	TE	TE	NNP	_	_	_
24	buffer	buffer	NN	_	_	_
25	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	spectrophotometrically	spectrophotometrically	RB	_	_	_
5	and	and	CC	_	_	_
6	equal	equal	JJ	_	_	_
7	amounts	amount	NNS	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	~	~	CD	_	_	_
10	300-500ng	300-500ng	JJ	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	of	of	IN	_	_	_
13	KMD	kmd	NN	_	_	_
14	and	and	CC	_	_	_
15	PC1012	pc1012	NN	_	_	_
16	RNA	rna	NN	_	_	_
17	samples	sample	NNS	_	_	_
18	were	be	VBD	_	_	_
19	subjected	subject	VBN	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	MessageAmp	MessageAmp	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Ambion	Ambion	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	RNA	rna	NN	_	_	_
27	amplification	amplification	NN	_	_	_
28	protocol	protocol	NN	_	_	_
29	.	.	.	_	_	_

1	Resultant	resultant	JJ	_	_	_
2	amplified	amplify	VBN	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	quantified	quantify	VBN	_	_	_
6	and	and	CC	_	_	_
7	equal	equal	JJ	_	_	_
8	amounts	amount	NNS	_	_	_
9	were	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	Affymetrix	Affymetrix	NNP	_	_	_
14	protocol	protocol	NN	_	_	_
15	for	for	IN	_	_	_
16	prokaryotic	prokaryotic	JJ	_	_	_
17	cDNA	cdna	NN	_	_	_
18	synthesis	synthesis	NN	_	_	_
19	and	and	CC	_	_	_
20	biotin	biotin	NN	SUPP	_	_
21	labeling	labeling	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	infection	infection	NN	_	_	_
3	:	:	:	_	_	_
4	T7	t7	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	infinity	infinity	NN	_	_	_
7	.	.	.	_	_	_

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	inhibitor	inhibitor	NN	_	_	_
3	:	:	:	_	_	_
4	20uM	20um	NN	_	_	_
5	ME0052	me0052	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	inhibitor	inhibitor	NN	_	_	_
8	:	:	:	_	_	_
9	20uM	20um	NN	_	_	_
10	ME0053	me0053	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	inhibitor	inhibitor	NN	_	_	_
13	:	:	:	_	_	_
14	20uM	20um	NN	_	_	_
15	ME0054	me0054	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	inhibitor	inhibitor	NN	_	_	_
18	:	:	:	_	_	_
19	20uM	20um	NN	_	_	_
20	ME0055	me0055	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Initial	initial	JJ	_	_	_
23	data	data	NN	_	_	_
24	analysis	analysis	NN	_	_	_
25	was	be	VBD	_	_	_
26	performed	perform	VBN	_	_	_
27	using	use	VBG	_	_	_
28	the	the	DT	_	_	_
29	GeneChip	GeneChip	NNP	_	_	_
30	®	®	NNP	_	_	_
31	Operating	Operating	NNP	_	_	_
32	Software	Software	NNP	_	_	_
33	.	.	.	_	_	_

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	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	In	in	IN	_	_	_
20	order	order	NN	_	_	_
21	to	to	TO	_	_	_
22	distinguish	distinguish	VB	_	_	_
23	between	between	IN	_	_	_
24	3	3	CD	_	_	_
25	'	'	''	_	_	_
26	ends	end	NNS	_	_	_
27	of	of	IN	_	_	_
28	transient	transient	JJ	_	_	_
29	products	product	NNS	_	_	_
30	of	of	IN	_	_	_
31	RNA	rna	NN	_	_	_
32	metabolism	metabolism	NN	_	_	_
33	and	and	CC	_	_	_
34	stable	stable	JJ	_	_	_
35	3	3	CD	_	_	_
36	'	'	''	_	_	_
37	ends	end	VBZ	_	_	_
38	,	,	,	_	_	_
39	we	we	PRP	_	_	_
40	developed	develop	VBD	_	_	_
41	an	a	DT	_	_	_
42	algorithm	algorithm	NN	_	_	_
43	to	to	TO	_	_	_
44	call	call	VB	_	_	_
45	coverage	coverage	NN	_	_	_
46	peaks	peak	NNS	_	_	_
47	.	.	.	_	_	_

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	In	in	IN	_	_	_
3	order	order	NN	_	_	_
4	to	to	TO	_	_	_
5	generate	generate	VB	_	_	_
6	the	the	DT	_	_	_
7	VBNC	vbnc	JJ	_	_	_
8	state	state	NN	_	_	_
9	in	in	IN	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	O157	o157	NN	_	_	_
13	:	:	:	_	_	_
14	H7	h7	NN	_	_	_
15	,	,	,	_	_	_
16	20	20	CD	_	_	_
17	mL	ml	NN	_	_	_
18	of	of	IN	_	_	_
19	the	the	DT	_	_	_
20	exponential-phase	exponential-phase	NN	_	_	_
21	cell	cell	NN	_	_	_
22	suspensions	suspension	NNS	_	_	_
23	in	in	IN	_	_	_
24	a	a	DT	_	_	_
25	50	50	CD	_	_	_
26	mL	ml	NN	_	_	_
27	sterile	sterile	JJ	_	_	_
28	glass	glass	NN	_	_	_
29	tube	tube	NN	_	_	_
30	was	be	VBD	_	_	_
31	treated	treat	VBN	_	_	_
32	by	by	IN	_	_	_
33	HPCD	hpcd	NN	_	_	_
34	at	at	IN	_	_	_
35	5	5	CD	_	_	_
36	MPa	mpa	NN	_	_	_
37	and	and	CC	_	_	_
38	25	25	CD	_	_	_
39	℃	℃	NN	_	_	_
40	for	for	IN	_	_	_
41	40	40	CD	_	_	_
42	min	min	NN	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	INPUT	INPUT	NNP	_	_	_
3	ChIP	chip	NN	_	_	_
4	DNA	dna	NN	_	_	_
5	from	from	IN	_	_	_
6	∆	∆	CD	_	_	_
7	hns	hn	NNS	GEN	_	_
8	/	/	:	_	_	_
9	∆	∆	SYM	_	_	_
10	stpA	stpa	NN	GEN	_	_
11	,	,	,	_	_	_
12	no	no	DT	_	_	_
13	antibody	antibody	NN	_	_	_
14	control	control	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	INPUT	INPUT	NNP	_	_	_
17	ChIP	chip	NN	_	_	_
18	DNA	dna	NN	_	_	_
19	from	from	IN	_	_	_
20	PK9416	pk9416	NN	_	_	_
21	,	,	,	_	_	_
22	no	no	DT	_	_	_
23	ArcA	arca	NN	TF	_	_
24	control	control	NN	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	INPUT	INPUT	NNP	_	_	_
27	ChIP	chip	NN	_	_	_
28	DNA	dna	NN	_	_	_
29	from	from	IN	_	_	_
30	WT	WT	NNP	_	_	_
31	Escherchia	Escherchia	NNP	_	_	_
32	coli	coli	NN	_	_	_
33	MG1655	mg1655	NN	_	_	_
34	K-12	k-12	NN	_	_	_
35	,	,	,	_	_	_
36	no	no	DT	_	_	_
37	antibody	antibody	NN	_	_	_
38	control	control	NN	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	INPUT	INPUT	NNP	_	_	_
41	ChIP	chip	NN	_	_	_
42	DNA	dna	NN	_	_	_
43	from	from	IN	_	_	_
44	WT	WT	NNP	_	_	_
45	Escherchia	Escherchia	NNP	_	_	_
46	coli	coli	NN	_	_	_
47	MG1655	mg1655	NN	_	_	_
48	K-12	k-12	NN	_	_	_
49	,	,	,	_	_	_
50	no	no	DT	_	_	_
51	antibody	antibody	NN	_	_	_
52	control	control	NN	_	_	_
53	,	,	,	_	_	_
54	Replicate	replicate	VB	_	_	_
55	B	b	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	INPUT	input	VBP	_	_	_
58	ChIP	chip	NN	_	_	_
59	DNA	dna	NN	_	_	_
60	from	from	IN	_	_	_
61	WTPK4854	wtpk4854	NN	_	_	_
62	,	,	,	_	_	_
63	no	no	DT	_	_	_
64	antibody	antibody	NN	_	_	_
65	control	control	NN	_	_	_
66	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
67	Input	Input	NNP	_	_	_
68	ChIP-Seq	ChIP-Seq	NNP	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	INPUT	INPUT	NNP	_	_	_
71	_	_	SYM	_	_	_
72	ChIP-seq	ChIP-seq	NNP	_	_	_
73	_	_	NNP	_	_	_
74	Aerobic	Aerobic	NNP	_	_	_
75	_	_	SYM	_	_	_
76	WIG.wig	WIG.wig	NNP	_	_	_
77	:	:	:	_	_	_
78	U00096	u00096	NN	_	_	_
79	.2	.2	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
81	INPUT	input	VBP	_	_	_
82	_	_	SYM	_	_	_
83	ChIP-seq	ChIP-seq	NNP	_	_	_
84	_	_	SYM	_	_	_
85	Anaerobic	anaerobic	JJ	_	_	_
86	_	_	NN	_	_	_
87	WIG.wig	wig.wig	NN	_	_	_
88	:	:	:	_	_	_
89	U00096	u00096	NN	_	_	_
90	.2	.2	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	input	input	NN	_	_	_
93	DNA	dna	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	INPUT	input	NN	_	_	_
96	DNA	dna	NN	_	_	_
97	B	b	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	Input	input	NN	_	_	_
100	DNA	dna	NN	_	_	_
101	from	from	IN	_	_	_
102	DdksA	ddksa	NN	_	_	_
103	cells	cell	NNS	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Input	Input	NNP	_	_	_
106	DNA	dna	NN	_	_	_
107	from	from	IN	_	_	_
108	E.	E.	NNP	_	_	_
109	Coli	Coli	NNP	_	_	_
110	MG1655	MG1655	NNP	_	_	_
111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
112	Input	Input	NNP	_	_	_
113	DNA	dna	NN	_	_	_
114	from	from	IN	_	_	_
115	E.	E.	NNP	_	_	_
116	Coli	Coli	NNP	_	_	_
117	MG1655	MG1655	NNP	_	_	_
118	ΔseqA	ΔseqA	NNP	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	Input	Input	NNP	_	_	_
121	DNA	dna	NN	_	_	_
122	from	from	IN	_	_	_
123	heat-shocked	heat-shocked	JJ	_	_	_
124	condition	condition	NN	_	_	_
125	without	without	IN	_	_	_
126	rifampicin	rifampicin	NN	SUPP	_	_
127	treatment	treatment	NN	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	Input	Input	NNP	_	_	_
130	DNA	dna	NN	_	_	_
131	from	from	IN	_	_	_
132	MDS42	mds42	NN	_	_	_
133	cells	cell	NNS	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	Input	Input	NNP	_	_	_
136	DNA	dna	NN	_	_	_
137	from	from	IN	_	_	_
138	MDS42	mds42	NN	_	_	_
139	ΔnusA	δnusa	NN	_	_	_
140	*	*	SYM	_	_	_
141	cells	cell	NNS	_	_	_
142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
143	Input	Input	NNP	_	_	_
144	DNA	dna	NN	_	_	_
145	from	from	IN	_	_	_
146	MDS42	mds42	NN	_	_	_
147	ΔnusG	δnusg	NN	_	_	_
148	cells	cell	NNS	_	_	_
149	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
150	Input	Input	NNP	_	_	_
151	DNA	dna	NN	_	_	_
152	from	from	IN	_	_	_
153	MG1655	mg1655	NN	_	_	_
154	cells	cell	NNS	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	Input	Input	NNP	_	_	_
157	DNA	dna	NN	_	_	_
158	from	from	IN	_	_	_
159	MG1655	mg1655	NN	_	_	_
160	Δhns	δhns	NN	_	_	_
161	cells	cell	NNS	_	_	_
162	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
163	Input	Input	NNP	_	_	_
164	DNA	dna	NN	_	_	_
165	from	from	IN	_	_	_
166	mid-exponential	mid-exponential	JJ	_	_	_
167	condition	condition	NN	_	_	_
168	without	without	IN	_	_	_
169	rifampicin	rifampicin	NN	SUPP	_	_
170	treatment	treatment	NN	_	_	_
171	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
172	Input	Input	NNP	_	_	_
173	DNA	dna	NN	_	_	_
174	from	from	IN	_	_	_
175	mid-exponential	mid-exponential	JJ	_	_	_
176	condition	condition	NN	_	_	_
177	with	with	IN	_	_	_
178	rifampicin	rifampicin	NN	SUPP	_	_
179	treatment	treatment	NN	_	_	_
180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
181	Input	Input	NNP	_	_	_
182	DNA	dna	NN	_	_	_
183	from	from	IN	_	_	_
184	nitrogen-limiting	nitrogen-limiting	JJ	_	_	_
185	condition	condition	NN	_	_	_
186	without	without	IN	_	_	_
187	rifampicin	rifampicin	NN	SUPP	_	_
188	treatment	treatment	NN	_	_	_
189	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
190	Input	Input	NNP	_	_	_
191	DNA	dna	NN	_	_	_
192	from	from	IN	_	_	_
193	SeqA	seqa	NN	_	_	_
194	ChIP	chip	NN	_	_	_
195	supernatant	supernatant	JJ	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	Input	input	NN	_	_	_
198	DNA	dna	NN	_	_	_
199	from	from	IN	_	_	_
200	starved	starve	VBN	_	_	_
201	DdksA	ddksa	NN	_	_	_
202	cells	cell	NNS	_	_	_
203	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
204	Input	Input	NNP	_	_	_
205	DNA	dna	NN	_	_	_
206	from	from	IN	_	_	_
207	starved	starve	VBN	_	_	_
208	wt	wt	JJ	_	_	_
209	cells	cell	NNS	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
211	Input	input	NN	_	_	_
212	DNA	dna	NN	_	_	_
213	from	from	IN	_	_	_
214	stationary	stationary	JJ	_	_	_
215	condition	condition	NN	_	_	_
216	without	without	IN	_	_	_
217	rifampicin	rifampicin	NN	SUPP	_	_
218	treatment	treatment	NN	_	_	_
219	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
220	Input	Input	NNP	_	_	_
221	DNA	dna	NN	_	_	_
222	from	from	IN	_	_	_
223	wt	wt	JJ	_	_	_
224	cells	cell	NNS	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
226	Input	input	NN	_	_	_
227	DNA	dna	NN	_	_	_
228	from	from	IN	_	_	_
229	ΔseqA-SeqA	δseqa-seqa	NN	_	_	_
230	ChIP	chip	NN	_	_	_
231	supernatant	supernatant	JJ	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	Input	input	NN	_	_	_
234	DNA	dna	NN	_	_	_
235	from	from	IN	_	_	_
236	σ32	σ32	NN	_	_	_
237	ChIP	chip	NN	_	_	_
238	supernatant	supernatant	JJ	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	Input	input	NN	_	_	_
241	∆	∆	CD	_	_	_
242	fur	fur	NN	GEN	_	_
243	Anaerobic	anaerobic	JJ	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	Input	input	NN	_	_	_
246	_	_	CD	_	_	_
247	hns-F	hns-f	NN	_	_	_
248	_	_	SYM	_	_	_
249	bcm	bcm	SYM	_	_	_
250	-	-	:	_	_	_
251	#	#	#	_	_	_
252	1	1	CD	_	_	_
253	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
254	Input	Input	NNP	_	_	_
255	_	_	SYM	_	_	_
256	hns-F	hns-f	JJ	_	_	_
257	_	_	NN	_	_	_
258	bcm	bcm	NN	_	_	_
259	+	+	CC	_	_	_
260	#	#	#	_	_	_
261	1	1	CD	_	_	_
262	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
263	Input	Input	NNP	_	_	_
264	_	_	SYM	_	_	_
265	hns-F	hns-f	JJ	_	_	_
266	_	_	NN	_	_	_
267	bcm	bcm	NN	_	_	_
268	-	-	:	_	_	_
269	#	#	#	_	_	_
270	2	2	CD	_	_	_
271	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
272	Input	Input	NNP	_	_	_
273	_	_	SYM	_	_	_
274	hns-F	hns-f	JJ	_	_	_
275	_	_	NN	_	_	_
276	bcm	bcm	NN	_	_	_
277	+	+	CC	_	_	_
278	#	#	#	_	_	_
279	2	2	CD	_	_	_
280	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
281	Input	Input	NNP	_	_	_
282	ParC-flag	ParC-flag	NNP	_	_	_
283	1	1	CD	_	_	_
284	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
285	Input	Input	NNP	_	_	_
286	ParE-flag	ParE-flag	NNP	_	_	_
287	1	1	CD	_	_	_
288	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
289	Input	Input	NNP	_	_	_
290	ParE-flag	ParE-flag	NNP	_	_	_
291	2	2	CD	_	_	_
292	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
293	Input	Input	NNP	_	_	_
294	ParE-flag	ParE-flag	NNP	_	_	_
295	G1	g1	NN	_	_	_
296	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
297	Input	Input	NNP	_	_	_
298	ParE-flag	ParE-flag	NNP	_	_	_
299	G2	g2	NN	_	_	_
300	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
301	Input	Input	NNP	_	_	_
302	ParE-flag	ParE-flag	NNP	_	_	_
303	S20min	S20min	NNP	_	_	_
304	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
305	Input	Input	NNP	_	_	_
306	ParE-flag	ParE-flag	NNP	_	_	_
307	S40min	s40min	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	input	input	NN	_	_	_
310	signal	signal	NN	_	_	_
311	frequency	frequency	NN	_	_	_
312	:	:	:	_	_	_
313	1/1200	1/1200	CD	_	_	_
314	Hz	hz	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	input	input	NN	_	_	_
317	signal	signal	NN	_	_	_
318	frequency	frequency	NN	_	_	_
319	:	:	:	_	_	_
320	1/2400	1/2400	CD	_	_	_
321	Hz	hz	NN	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	input	input	NN	_	_	_
324	signal	signal	NN	_	_	_
325	frequency	frequency	NN	_	_	_
326	:	:	:	_	_	_
327	1/3600	1/3600	CD	_	_	_
328	Hz	hz	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	input	input	NN	_	_	_
331	signal	signal	NN	_	_	_
332	frequency	frequency	NN	_	_	_
333	:	:	:	_	_	_
334	1/600	1/600	CD	_	_	_
335	Hz	hz	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	input	input	NN	_	_	_
338	signal	signal	NN	_	_	_
339	frequency	frequency	NN	_	_	_
340	:	:	:	_	_	_
341	1/900	1/900	CD	_	_	_
342	Hz	hz	NN	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	intensities	intensity	NNS	_	_	_
345	,	,	,	_	_	_
346	respectively	respectively	RB	_	_	_
347	.	.	.	_	_	_

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	NN	_	_	_
14	Intensity	intensity	NN	_	_	_
15	measures	measure	NNS	_	_	_
16	in	in	IN	_	_	_
17	wild	wild	JJ	_	_	_
18	type	type	NN	_	_	_
19	strain	strain	NN	_	_	_
20	,	,	,	_	_	_
21	replicate	replicate	VBP	_	_	_
22	1	1	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Intensity	intensity	NN	_	_	_
25	measures	measure	NNS	_	_	_
26	in	in	IN	_	_	_
27	wild	wild	JJ	_	_	_
28	type	type	NN	_	_	_
29	strain	strain	NN	_	_	_
30	,	,	,	_	_	_
31	replicate	replicate	VB	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	Intensity	intensity	NN	_	_	_
35	measures	measure	NNS	_	_	_
36	in	in	IN	_	_	_
37	yajL	yajl	NN	GEN	_	_
38	mutant	mutant	JJ	_	_	_
39	strain	strain	NN	_	_	_
40	,	,	,	_	_	_
41	replicate	replicate	VBP	_	_	_
42	1	1	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Intensity	intensity	NN	_	_	_
45	measures	measure	NNS	_	_	_
46	in	in	IN	_	_	_
47	yajL	yajl	NN	GEN	_	_
48	mutant	mutant	JJ	_	_	_
49	strain	strain	NN	_	_	_
50	,	,	,	_	_	_
51	replicate	replicate	VB	_	_	_
52	2	2	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
54	In	in	IN	_	_	_
55	the	the	DT	_	_	_
56	15	15	CD	_	_	_
57	ml	ml	NN	_	_	_
58	centrifuge	centrifuge	NN	_	_	_
59	tube	tube	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	Corning	Corning	NNP	_	_	_
62	,	,	,	_	_	_
63	430791	430791	CD	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	,	,	,	_	_	_
66	the	the	DT	_	_	_
67	overnight	overnight	JJ	_	_	_
68	culture	culture	NN	_	_	_
69	was	be	VBD	_	_	_
70	diluted	dilute	VBN	_	_	_
71	to	to	TO	_	_	_
72	2	2	CD	_	_	_
73	ml	ml	NN	_	_	_
74	in	in	IN	_	_	_
75	fresh	fresh	JJ	_	_	_
76	LB	lb	NN	MED	_	_
77	medium	medium	NN	MED	_	_
78	containing	contain	VBG	_	_	_
79	Ampicillin	ampicillin	NN	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	50	50	CD	_	_	_
82	ng/μl	ng/μl	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	,	,	,	_	_	_
85	Chloramphenicol	chloramphenicol	NN	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	170	170	CD	_	_	_
88	ng/μl	ng/μl	NN	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	and	and	CC	_	_	_
91	IPTG	iptg	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	0.5	0.5	CD	_	_	_
94	mM	mm	NN	KWSUPP	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	to	to	TO	_	_	_
97	reach	reach	VB	_	_	_
98	OD600	od600	NN	_	_	_
99	=	=	JJ	_	_	_
100	0.01	0.01	CD	_	_	_
101	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	LED	LED	NNP	_	_	_
3	tube	tube	NN	_	_	_
4	was	be	VBD	_	_	_
5	screwed	screw	VBN	_	_	_
6	into	into	IN	_	_	_
7	the	the	DT	_	_	_
8	centrifuge	centrifuge	NN	_	_	_
9	tube	tube	NN	_	_	_
10	and	and	CC	_	_	_
11	connected	connect	VBN	_	_	_
12	with	with	IN	_	_	_
13	the	the	DT	_	_	_
14	control	control	NN	_	_	_
15	box	box	NN	_	_	_
16	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	the	the	DT	_	_	_
3	power	power	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	control	control	NN	_	_	_
7	box	box	NN	_	_	_
8	was	be	VBD	_	_	_
9	turned	turn	VBN	_	_	_
10	on	on	RB	_	_	_
11	and	and	CC	_	_	_
12	the	the	DT	_	_	_
13	LED	lead	VBN	_	_	_
14	frequency	frequency	NN	_	_	_
15	input	input	NN	_	_	_
16	was	be	VBD	_	_	_
17	generated	generate	VBN	_	_	_
18	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	last	last	JJ	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	15	15	CD	_	_	_
6	ml	ml	NN	_	_	_
7	centrifuge	centrifuge	NN	_	_	_
8	tube	tube	NN	_	_	_
9	with	with	IN	_	_	_
10	LED	lead	VBN	_	_	_
11	tube	tube	NN	_	_	_
12	was	be	VBD	_	_	_
13	put	put	VBN	_	_	_
14	into	into	IN	_	_	_
15	the	the	DT	_	_	_
16	Thermomixer	Thermomixer	NNP	_	_	_
17	comfort	comfort	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Eppendorf	eppendorf	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	shaken	shake	VBN	_	_	_
23	at	at	IN	_	_	_
24	650	650	CD	_	_	_
25	rpm	rpm	NN	_	_	_
26	and	and	CC	_	_	_
27	37	37	CD	_	_	_
28	°C	°c	NN	_	_	_
29	for	for	IN	_	_	_
30	10	10	CD	_	_	_
31	hours	hour	NNS	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	In	in	FW	_	_	_
3	vitro	vitro	FW	_	_	_
4	RNA	rna	NN	_	_	_
5	preparation	preparation	NN	_	_	_
6	:	:	:	_	_	_
7	The	the	DT	_	_	_
8	5.7	5.7	CD	_	_	_
9	kb	kb	NN	_	_	_
10	RNA	rna	NN	_	_	_
11	was	be	VBD	_	_	_
12	purified	purify	VBN	_	_	_
13	from	from	IN	_	_	_
14	the	the	DT	_	_	_
15	digested	digest	VBN	_	_	_
16	DNA	dna	NN	_	_	_
17	,	,	,	_	_	_
18	NTPs	ntp	NNS	_	_	_
19	,	,	,	_	_	_
20	abortive	abortive	JJ	_	_	_
21	oligo-RNA	oligo-rna	JJ	_	_	_
22	products	product	NNS	_	_	_
23	,	,	,	_	_	_
24	and	and	CC	_	_	_
25	proteins	protein	NNS	_	_	_
26	by	by	IN	_	_	_
27	Acidic	acidic	JJ	_	_	_
28	phenol	phenol	NN	_	_	_
29	extraction	extraction	NN	_	_	_
30	,	,	,	_	_	_
31	G50	g50	NN	_	_	_
32	spin	spin	NN	_	_	_
33	column	column	NN	_	_	_
34	,	,	,	_	_	_
35	followed	follow	VBN	_	_	_
36	by	by	IN	_	_	_
37	EtOH	etoh	NN	_	_	_
38	precipitation	precipitation	NN	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	In	in	FW	_	_	_
3	vitro	vitro	FW	_	_	_
4	transcription	transcription	NN	_	_	_
5	reactions	reaction	NNS	_	_	_
6	were	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	50	50	CD	_	_	_
14	µl	µl	NN	_	_	_
15	.	.	.	_	_	_

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/µl	u/µl	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	Actinomycin	actinomycin	NN	_	_	_
17	D	d	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Sigma	Sigma	NNP	_	_	_
20	Aldrich	Aldrich	NNP	_	_	_
21	,	,	,	_	_	_
22	cat	cat	NN	_	_	_
23	.	.	.	_	_	_

1	A1410	a1410	NN	_	_	_
2	,	,	,	_	_	_
3	dissolved	dissolve	VBN	_	_	_
4	in	in	IN	_	_	_
5	DMSO	dmso	NN	_	_	_
6	to	to	TO	_	_	_
7	5	5	CD	_	_	_
8	μg/μl	μg/μl	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	to	to	TO	_	_	_
11	a	a	DT	_	_	_
12	final	final	JJ	_	_	_
13	concentration	concentration	NN	_	_	_
14	of	of	IN	_	_	_
15	25	25	CD	_	_	_
16	ng/μl	ng/μl	NN	_	_	_
17	.	.	.	_	_	_

1	Reactions	reaction	NNS	_	_	_
2	were	be	VBD	_	_	_
3	diluted	dilute	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	50	50	CD	_	_	_
8	μl	μl	NN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	RNA	rna	NN	_	_	_
12	Polymerase	polymerase	NN	_	_	_
13	Buffer	buffer	NN	_	_	_
14	1X	1x	NN	_	_	_
15	.	.	.	_	_	_

1	DMS	dms	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	Sigma	Sigma	NNP	_	_	_
4	Aldrich	Aldrich	NNP	_	_	_
5	,	,	,	_	_	_
6	cat	cat	NN	_	_	_
7	.	.	.	_	_	_

1	D186309	d186309	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	was	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:6	1:6	CD	_	_	_
6	in	in	IN	_	_	_
7	100	100	CD	_	_	_
8	%	%	NN	_	_	_
9	Ethanol	ethanol	NN	_	_	_
10	to	to	TO	_	_	_
11	a	a	DT	_	_	_
12	final	final	JJ	_	_	_
13	concentration	concentration	NN	_	_	_
14	of	of	IN	_	_	_
15	1.76	1.76	CD	_	_	_
16	M.	m.	NN	_	_	_
17	Diluted	Diluted	NNP	_	_	_
18	DMS	DMS	NNP	_	_	_
19	was	be	VBD	_	_	_
20	added	add	VBN	_	_	_
21	to	to	TO	_	_	_
22	reactions	reaction	NNS	_	_	_
23	to	to	TO	_	_	_
24	a	a	DT	_	_	_
25	final	final	JJ	_	_	_
26	concentration	concentration	NN	_	_	_
27	of	of	IN	_	_	_
28	100	100	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	control	control	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	,	,	,	_	_	_
5	an	a	DT	_	_	_
6	equal	equal	JJ	_	_	_
7	volume	volume	NN	_	_	_
8	of	of	IN	_	_	_
9	a	a	DT	_	_	_
10	1:6	1:6	CD	_	_	_
11	dilution	dilution	NN	_	_	_
12	of	of	IN	_	_	_
13	nuclease-free	nuclease-free	JJ	_	_	_
14	water	water	NN	_	_	_
15	in	in	IN	_	_	_
16	100	100	CD	_	_	_
17	%	%	NN	_	_	_
18	Ethanol	ethanol	NN	_	_	_
19	was	be	VBD	_	_	_
20	added	add	VBN	_	_	_
21	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	incubated	incubate	VBN	_	_	_
4	with	with	IN	_	_	_
5	moderate	moderate	JJ	_	_	_
6	shaking	shake	VBG	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	800	800	CD	_	_	_
9	RPM	rpm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	at	at	IN	_	_	_
12	25	25	CD	_	_	_
13	°C	°c	NN	_	_	_
14	for	for	IN	_	_	_
15	2	2	CD	_	_	_
16	minutes	minute	NNS	_	_	_
17	,	,	,	_	_	_
18	after	after	IN	_	_	_
19	which	which	WDT	_	_	_
20	reactions	reaction	NNS	_	_	_
21	were	be	VBD	_	_	_
22	immediately	immediately	RB	_	_	_
23	transferred	transfer	VBN	_	_	_
24	to	to	TO	_	_	_
25	ice	ice	NN	_	_	_
26	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	volumes	volume	NNS	_	_	_
3	of	of	IN	_	_	_
4	ice-cold	ice-cold	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	Binding	binding	NN	_	_	_
7	Buffer	buffer	NN	_	_	_
8	from	from	IN	_	_	_
9	RNA	rna	NN	_	_	_
10	Clean	Clean	NNP	_	_	_
11	&	&	CC	_	_	_
12	Concentrator	Concentrator	NNP	_	_	_
13	™	™	SYM	_	_	_
14	-5	-5	CD	_	_	_
15	kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Zymo	Zymo	NNP	_	_	_
18	Research	Research	NNP	_	_	_
19	,	,	,	_	_	_
20	cat	cat	NN	_	_	_
21	.	.	.	_	_	_

1	R1014	r1014	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	supplemented	supplement	VBN	_	_	_
4	with	with	IN	_	_	_
5	DTT	dtt	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Sigma	Sigma	NNP	_	_	_
8	Aldrich	Aldrich	NNP	_	_	_
9	,	,	,	_	_	_
10	cat	cat	NN	_	_	_
11	.	.	.	_	_	_

1	43815	43815	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	to	to	TO	_	_	_
4	a	a	DT	_	_	_
5	final	final	JJ	_	_	_
6	concentration	concentration	NN	_	_	_
7	of	of	IN	_	_	_
8	0.7	0.7	CD	_	_	_
9	M	m	NN	_	_	_
10	,	,	,	_	_	_
11	were	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	quench	quench	VB	_	_	_
15	DMS	DMS	NNP	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	samples	sample	NNS	_	_	_
19	were	be	VBD	_	_	_
20	vigorously	vigorously	RB	_	_	_
21	vortexed	vortex	VBN	_	_	_
22	for	for	IN	_	_	_
23	10	10	CD	_	_	_
24	seconds	seconds	NNS	_	_	_
25	.	.	.	_	_	_

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	NNP	_	_	_
2	Ionic	Ionic	NNP	_	_	_
3	silver	silver	NN	_	_	_
4	stock	stock	NN	_	_	_
5	solutions	solution	NNS	_	_	_
6	were	be	VBD	_	_	_
7	prepared	prepare	VBN	_	_	_
8	from	from	IN	_	_	_
9	AgNO3	agno3	NN	_	_	_
10	powder	powder	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Fisher	Fisher	NNP	_	_	_
13	Scientific	Scientific	NNP	_	_	_
14	Bioblock	Bioblock	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	as	as	IN	_	_	_
17	previously	previously	RB	_	_	_
18	described	describe	VBN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Saulou	Saulou	NNP	_	_	_
21	,	,	,	_	_	_
22	Jamme	Jamme	NNP	_	_	_
23	et	et	FW	_	_	_
24	al.	al.	FW	_	_	_
25	,	,	,	_	_	_
26	2013	2013	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	stored	store	VBN	_	_	_
30	in	in	IN	_	_	_
31	darkness	darkness	NN	_	_	_
32	.	.	.	_	_	_

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	Ion	Ion	NNP	_	_	_
3	Xpress	Xpress	NNP	_	_	_
4	barcoded	barcode	VBD	_	_	_
5	libraries	library	NNS	_	_	_
6	were	be	VBD	_	_	_
7	constructed	construct	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	Ribo-Zero	Ribo-Zero	NNP	_	_	_
11	Magnatic	Magnatic	NNP	_	_	_
12	Kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Gram-negative	gram-negative	JJ	_	_	_
15	bacteria	bacterium	NNS	_	_	_
16	,	,	,	_	_	_
17	Epicentre	Epicentre	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	IonXpress	ionxpress	NN	_	_	_
21	RNA-seq	rna-seq	NN	_	_	_
22	v2	v2	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Life	Life	NNP	_	_	_
25	Technologies	Technologies	NNPS	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	kits	kit	NNS	_	_	_
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	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ip	ip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	affinity	affinity	NN	_	_	_
6	purified	purify	VBN	_	_	_
7	anti-Fur	anti-fur	JJ	_	_	_
8	antibody	antibody	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	IP	IP	NNP	_	_	_
11	∆	∆	NNP	_	_	_
12	fur	fur	NN	GEN	_	_
13	Anaerobic	anaerobic	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	IPOD	ipod	NN	_	_	_
16	_	_	NN	_	_	_
17	early	early	JJ	_	_	_
18	_	_	CD	_	_	_
19	log	log	NN	_	_	_
20	_	_	NN	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	IPOD	ipod	NN	_	_	_
24	_	_	RB	_	_	_
25	early	early	JJ	_	_	_
26	_	_	NN	_	_	_
27	log	log	NN	_	_	_
28	_	_	NN	_	_	_
29	2	2	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	IPOD	ipod	VBD	_	_	_
32	_	_	RB	_	_	_
33	late	late	JJ	_	_	_
34	_	_	NN	_	_	_
35	log	log	NN	_	_	_
36	_	_	NN	_	_	_
37	1	1	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	IPOD	ipod	NN	_	_	_
40	_	_	CD	_	_	_
41	late	late	JJ	_	_	_
42	_	_	NN	_	_	_
43	log	log	NN	_	_	_
44	_	_	NN	_	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	IPOD	ipod	VBD	_	_	_
48	_	_	SYM	_	_	_
49	MDS42	mds42	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	IP	IP	NNP	_	_	_
52	ParC-flag	ParC-flag	NNP	_	_	_
53	1	1	CD	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	IP	IP	NNP	_	_	_
56	ParE-flag	ParE-flag	NNP	_	_	_
57	1	1	CD	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	IP	IP	NNP	_	_	_
60	ParE-flag	ParE-flag	NNP	_	_	_
61	2	2	CD	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	IP	IP	NNP	_	_	_
64	ParE-flag	ParE-flag	NNP	_	_	_
65	G1	g1	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	IP	IP	NNP	_	_	_
68	ParE-flag	ParE-flag	NNP	_	_	_
69	G2	g2	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	IP	IP	NNP	_	_	_
72	ParE-flag	ParE-flag	NNP	_	_	_
73	S20min	S20min	NNP	_	_	_
74	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
75	IP	IP	NNP	_	_	_
76	ParE-flag	ParE-flag	NNP	_	_	_
77	S40min	S40min	NNP	_	_	_
78	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
79	Irp	Irp	NNP	_	_	_
80	mutant	mutant	NN	_	_	_
81	in	in	IN	_	_	_
82	Ala	Ala	NNP	_	_	_
83	media	media	NNS	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	Irp	irp	NN	_	_	_
86	mutant	mutant	NN	_	_	_
87	in	in	IN	_	_	_
88	Gln	gln	NN	_	_	_
89	media	media	NNS	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	isolate	isolate	NN	_	_	_
92	:	:	:	_	_	_
93	bovine	bovine	JJ	_	_	_
94	isolate	isolate	NN	_	_	_
95	of	of	IN	_	_	_
96	e	e	SYM	_	_	_
97	coli	coli	FW	_	_	_
98	o157	o157	FW	_	_	_
99	:	:	:	_	_	_
100	H7	h7	NN	_	_	_
101	FRIK2000	frik2000	NN	_	_	_
102	lineage	lineage	NN	_	_	_
103	II	ii	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	isolate	isolate	NN	_	_	_
106	:	:	:	_	_	_
107	bovine	bovine	JJ	_	_	_
108	isolate	isolate	NN	_	_	_
109	of	of	IN	_	_	_
110	e	e	SYM	_	_	_
111	coli	coli	FW	_	_	_
112	o157	o157	FW	_	_	_
113	:	:	:	_	_	_
114	H7	h7	NN	_	_	_
115	FRIK966	frik966	NN	_	_	_
116	lineage	lineage	NN	_	_	_
117	II	ii	CD	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	isolate	isolate	NN	_	_	_
120	:	:	:	_	_	_
121	clinical	clinical	JJ	_	_	_
122	isolate	isolate	JJ	_	_	_
123	e	e	SYM	_	_	_
124	coli	coli	FW	_	_	_
125	o157	o157	FW	_	_	_
126	:	:	:	_	_	_
127	H7	h7	NN	_	_	_
128	lineage	lineage	NN	_	_	_
129	I	I	PRP	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBD	_	_	_
131	isolated	isolate	VBN	_	_	_
132	by	by	IN	_	_	_
133	chloroform	chloroform	NN	_	_	_
134	extraction	extraction	NN	_	_	_
135	and	and	CC	_	_	_
136	precipitation	precipitation	NN	_	_	_
137	by	by	IN	_	_	_
138	isopropanol	isopropanol	NN	_	_	_
139	.	.	.	_	_	_

1	Precipitated	precipitate	VBN	_	_	_
2	RNA	rna	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	feces	fece	NNS	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	HUS	hus	NN	_	_	_
10	patient	patient	NN	_	_	_
11	from	from	IN	_	_	_
12	an	a	DT	_	_	_
13	outbreak	outbreak	NN	_	_	_
14	in	in	IN	_	_	_
15	China	China	NNP	_	_	_
16	in	in	IN	_	_	_
17	1999	1999	CD	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Isolate	Isolate	NNP	_	_	_
20	:	:	:	_	_	_
21	EDL933	edl933	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Isolate	isolate	VB	_	_	_
24	G	g	NN	_	_	_
25	1/2	1/2	CD	_	_	_
26	of	of	IN	_	_	_
27	Symbioflor2	symbioflor2	NN	_	_	_
28	probiotic	probiotic	JJ	_	_	_
29	product	product	NN	_	_	_
30	from	from	IN	_	_	_
31	Symbiopharm	Symbiopharm	NNP	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Isolate	isolate	VB	_	_	_
34	G	g	NN	_	_	_
35	3/10	3/10	CD	_	_	_
36	of	of	IN	_	_	_
37	Symbioflor2	symbioflor2	NN	_	_	_
38	probiotic	probiotic	JJ	_	_	_
39	probiotic	probiotic	JJ	_	_	_
40	from	from	IN	_	_	_
41	Symbiopharm	Symbiopharm	NNP	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	Isolate	isolate	VB	_	_	_
44	G	g	NN	_	_	_
45	3/10	3/10	CD	_	_	_
46	of	of	IN	_	_	_
47	Symbioflor2	symbioflor2	NN	_	_	_
48	probiotic	probiotic	JJ	_	_	_
49	product	product	NN	_	_	_
50	from	from	IN	_	_	_
51	Symbiopharm	Symbiopharm	NNP	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	Isolate	isolate	VB	_	_	_
54	G	g	NN	_	_	_
55	4/9	4/9	CD	_	_	_
56	of	of	IN	_	_	_
57	Symbioflor2	symbioflor2	NN	_	_	_
58	probiotic	probiotic	JJ	_	_	_
59	product	product	NN	_	_	_
60	from	from	IN	_	_	_
61	Symbiopham	Symbiopham	NNP	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Isolate	isolate	VB	_	_	_
64	G	g	NN	_	_	_
65	4/9	4/9	CD	_	_	_
66	of	of	IN	_	_	_
67	Symbioflor2	symbioflor2	NN	_	_	_
68	probiotic	probiotic	JJ	_	_	_
69	product	product	NN	_	_	_
70	from	from	IN	_	_	_
71	Symbiopharm	Symbiopharm	NNP	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Isolate	isolate	VB	_	_	_
74	G5	g5	NN	_	_	_
75	of	of	IN	_	_	_
76	Symbioflor2	symbioflor2	NN	_	_	_
77	probiotic	probiotic	JJ	_	_	_
78	product	product	NN	_	_	_
79	from	from	IN	_	_	_
80	Symbiopharm	Symbiopharm	NNP	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	Isolate	isolate	VB	_	_	_
83	:	:	:	_	_	_
84	MDS42	mds42	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Isolate	isolate	VB	_	_	_
87	:	:	:	_	_	_
88	MG1655	mg1655	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	isolate	isolate	NN	_	_	_
91	:	:	:	_	_	_
92	UR40	ur40	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Isolate	isolate	VB	_	_	_
95	W3110	w3110	NN	_	_	_
96	of	of	IN	_	_	_
97	K-12	k-12	NN	_	_	_
98	strain	strain	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	isolation	isolation	NN	_	_	_
101	source	source	NN	_	_	_
102	:	:	:	_	_	_
103	Mixed	mixed	JJ	_	_	_
104	culture	culture	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	isolation	isolation	NN	_	_	_
107	source	source	NN	_	_	_
108	:	:	:	_	_	_
109	Pure	pure	JJ	_	_	_
110	culture	culture	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Isoleucine	isoleucine	NN	_	_	_
113	addition	addition	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	IspG1	ispg1	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	IspG1	ispg1	NN	_	_	_
118	strain	strain	NN	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	Iterative	iterative	JJ	_	_	_
121	alignment	alignment	NN	_	_	_
122	,	,	,	_	_	_
123	Min-leght	min-leght	NN	_	_	_
124	=	=	JJ	_	_	_
125	20	20	CD	_	_	_
126	,	,	,	_	_	_
127	step	step	NN	_	_	_
128	=	=	JJ	_	_	_
129	5	5	CD	_	_	_
130	,	,	,	_	_	_
131	bowtie2	bowtie2	NN	_	_	_
132	--	--	:	_	_	_
133	very-sensitive	very-sensitive	JJ	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	Jaguar	Jaguar	NNP	_	_	_
136	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
137	JCB570	jcb570	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	JM109-1	jm109-1	NN	_	_	_
140	,	,	,	_	_	_
141	biological	biological	JJ	_	_	_
142	rep1	rep1	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	JM109-2	jm109-2	NN	_	_	_
145	,	,	,	_	_	_
146	biological	biological	JJ	_	_	_
147	rep2	rep2	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	JM109-3	jm109-3	NN	_	_	_
150	,	,	,	_	_	_
151	biological	biological	JJ	_	_	_
152	rep3	rep3	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	JM109	jm109	NN	_	_	_
155	GLY-1	gly-1	NN	_	_	_
156	,	,	,	_	_	_
157	biological	biological	JJ	_	_	_
158	rep1	rep1	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	JM109	jm109	NN	_	_	_
161	GLY-2	gly-2	NN	_	_	_
162	,	,	,	_	_	_
163	biological	biological	JJ	_	_	_
164	rep2	rep2	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	JM109	jm109	NN	_	_	_
167	GLY-3	gly-3	NN	_	_	_
168	,	,	,	_	_	_
169	biological	biological	JJ	_	_	_
170	rep3	rep3	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	JO2057	jo2057	NN	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	WT	wt	NN	_	_	_
175	-RRB-	-rrb-	-RRB-	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	JO2057	jo2057	NN	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	WT	wt	NN	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	,	,	,	_	_	_
182	exponential	exponential	JJ	GrowthPhase	_	_
183	phase	phase	NN	GrowthPhase	_	_
184	,	,	,	_	_	_
185	repetition1	repetition1	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	JO2057	jo2057	NN	_	_	_
188	-LRB-	-lrb-	-LRB-	_	_	_
189	WT	wt	NN	_	_	_
190	-RRB-	-rrb-	-RRB-	_	_	_
191	,	,	,	_	_	_
192	exponential	exponential	JJ	GrowthPhase	_	_
193	phase	phase	NN	GrowthPhase	_	_
194	,	,	,	_	_	_
195	repetition2	repetition2	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	JO2057	jo2057	NN	_	_	_
198	WT	WT	NNP	_	_	_
199	,	,	,	_	_	_
200	LB	LB	NNP	_	_	_
201	,	,	,	_	_	_
202	exponential	exponential	JJ	GrowthPhase	_	_
203	phase	phase	NN	GrowthPhase	_	_
204	,	,	,	_	_	_
205	repetition1	repetition1	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	JO2057	jo2057	NN	_	_	_
208	WT	WT	NNP	_	_	_
209	,	,	,	_	_	_
210	LB	LB	NNP	_	_	_
211	,	,	,	_	_	_
212	exponential	exponential	JJ	GrowthPhase	_	_
213	phase	phase	NN	GrowthPhase	_	_
214	,	,	,	_	_	_
215	repetition2	repetition2	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	JO2057	jo2057	NN	_	_	_
218	WT	WT	NNP	_	_	_
219	,	,	,	_	_	_
220	LB	LB	NNP	_	_	_
221	,	,	,	_	_	_
222	stationary	stationary	JJ	GrowthPhase	_	_
223	phase	phase	NN	GrowthPhase	_	_
224	,	,	,	_	_	_
225	repetition1	repetition1	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	JO2057	jo2057	NN	_	_	_
228	WT	WT	NNP	_	_	_
229	,	,	,	_	_	_
230	LB	LB	NNP	_	_	_
231	,	,	,	_	_	_
232	stationary	stationary	JJ	GrowthPhase	_	_
233	phase	phase	NN	GrowthPhase	_	_
234	,	,	,	_	_	_
235	repetition2	repetition2	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	JO2057	jo2057	NN	_	_	_
238	WT	WT	NNP	_	_	_
239	,	,	,	_	_	_
240	LB	LB	NNP	_	_	_
241	,	,	,	_	_	_
242	transition	transition	NN	_	_	_
243	phase	phase	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	JO2057	jo2057	NN	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	WT	wt	NN	_	_	_
248	-RRB-	-rrb-	-RRB-	_	_	_
249	,	,	,	_	_	_
250	Min	min	NN	_	_	_
251	Glucose	glucose	NN	_	_	_
252	,	,	,	_	_	_
253	exponential	exponential	JJ	GrowthPhase	_	_
254	phase	phase	NN	GrowthPhase	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	JO2057	jo2057	NN	_	_	_
257	WT	WT	NNP	_	_	_
258	,	,	,	_	_	_
259	Min	Min	NNP	_	_	_
260	Glucose	Glucose	NNP	_	_	_
261	,	,	,	_	_	_
262	exponential	exponential	JJ	GrowthPhase	_	_
263	phase	phase	NN	GrowthPhase	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	JO2057	jo2057	NN	_	_	_
266	-LRB-	-lrb-	-LRB-	_	_	_
267	WT	wt	NN	_	_	_
268	-RRB-	-rrb-	-RRB-	_	_	_
269	,	,	,	_	_	_
270	Min	min	NN	_	_	_
271	Glucose	glucose	NN	_	_	_
272	,	,	,	_	_	_
273	stationary	stationary	JJ	GrowthPhase	_	_
274	phase	phase	NN	GrowthPhase	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	JO2057	jo2057	NN	_	_	_
277	WT	WT	NNP	_	_	_
278	,	,	,	_	_	_
279	Min	Min	NNP	_	_	_
280	Glucose	Glucose	NNP	_	_	_
281	,	,	,	_	_	_
282	stationary	stationary	JJ	GrowthPhase	_	_
283	phase	phase	NN	GrowthPhase	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	JO2057	jo2057	NN	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	WT	wt	NN	_	_	_
288	-RRB-	-rrb-	-RRB-	_	_	_
289	,	,	,	_	_	_
290	Min	Min	NNP	_	_	_
291	Glycerol	Glycerol	NNP	_	_	_
292	,	,	,	_	_	_
293	exponential	exponential	JJ	GrowthPhase	_	_
294	phase	phase	NN	GrowthPhase	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	JO2057	jo2057	NN	_	_	_
297	WT	WT	NNP	_	_	_
298	,	,	,	_	_	_
299	Min	Min	NNP	_	_	_
300	Glycerol	Glycerol	NNP	_	_	_
301	,	,	,	_	_	_
302	exponential	exponential	JJ	GrowthPhase	_	_
303	phase	phase	NN	GrowthPhase	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	JO2057	jo2057	NN	_	_	_
306	-LRB-	-lrb-	-LRB-	_	_	_
307	WT	wt	NN	_	_	_
308	-RRB-	-rrb-	-RRB-	_	_	_
309	,	,	,	_	_	_
310	Min	Min	NNP	_	_	_
311	Glycerol	Glycerol	NNP	_	_	_
312	,	,	,	_	_	_
313	stationary	stationary	JJ	GrowthPhase	_	_
314	phase	phase	NN	GrowthPhase	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	JO2057	jo2057	NN	_	_	_
317	WT	WT	NNP	_	_	_
318	,	,	,	_	_	_
319	Min	Min	NNP	_	_	_
320	Glycerol	Glycerol	NNP	_	_	_
321	,	,	,	_	_	_
322	stationary	stationary	JJ	GrowthPhase	_	_
323	phase	phase	NN	GrowthPhase	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	JO2057	jo2057	NN	_	_	_
326	-LRB-	-lrb-	-LRB-	_	_	_
327	WT	wt	NN	_	_	_
328	-RRB-	-rrb-	-RRB-	_	_	_
329	,	,	,	_	_	_
330	stationary	stationary	JJ	GrowthPhase	_	_
331	phase	phase	NN	GrowthPhase	_	_
332	,	,	,	_	_	_
333	repetition1	repetition1	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	JO2057	jo2057	NN	_	_	_
336	-LRB-	-lrb-	-LRB-	_	_	_
337	WT	wt	NN	_	_	_
338	-RRB-	-rrb-	-RRB-	_	_	_
339	,	,	,	_	_	_
340	stationary	stationary	JJ	GrowthPhase	_	_
341	phase	phase	NN	GrowthPhase	_	_
342	,	,	,	_	_	_
343	repetition2	repetition2	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	JO2057	jo2057	NN	_	_	_
346	-LRB-	-lrb-	-LRB-	_	_	_
347	WT	wt	NN	_	_	_
348	-RRB-	-rrb-	-RRB-	_	_	_
349	,	,	,	_	_	_
350	transition	transition	NN	_	_	_
351	phase	phase	NN	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
353	JO2081	jo2081	NN	_	_	_
354	-LRB-	-lrb-	-LRB-	_	_	_
355	hupA	hupa	NN	GEN	_	_
356	-RRB-	-rrb-	-RRB-	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	JO2081	jo2081	NN	_	_	_
359	-LRB-	-lrb-	-LRB-	_	_	_
360	hupA	hupa	NN	GEN	_	_
361	-RRB-	-rrb-	-RRB-	_	_	_
362	,	,	,	_	_	_
363	exponential	exponential	JJ	GrowthPhase	_	_
364	phase	phase	NN	GrowthPhase	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
366	JO2081	jo2081	NN	_	_	_
367	hupA	hupa	NN	GEN	_	_
368	,	,	,	_	_	_
369	LB	lb	NN	_	_	_
370	,	,	,	_	_	_
371	exponential	exponential	JJ	GrowthPhase	_	_
372	phase	phase	NN	GrowthPhase	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	JO2081	jo2081	NN	_	_	_
375	hupA	hupa	NN	GEN	_	_
376	,	,	,	_	_	_
377	LB	lb	NN	_	_	_
378	,	,	,	_	_	_
379	stationary	stationary	JJ	GrowthPhase	_	_
380	phase	phase	NN	GrowthPhase	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	JO2081	jo2081	NN	_	_	_
383	hupA	hupa	NN	GEN	_	_
384	,	,	,	_	_	_
385	LB	lb	NN	_	_	_
386	,	,	,	_	_	_
387	transition	transition	NN	_	_	_
388	phase	phase	NN	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	JO2081	jo2081	NN	_	_	_
391	-LRB-	-lrb-	-LRB-	_	_	_
392	hupA	hupa	NN	GEN	_	_
393	-RRB-	-rrb-	-RRB-	_	_	_
394	,	,	,	_	_	_
395	stationary	stationary	JJ	GrowthPhase	_	_
396	phase	phase	NN	GrowthPhase	_	_
397	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
398	JO2081	jo2081	NN	_	_	_
399	-LRB-	-lrb-	-LRB-	_	_	_
400	hupA	hupa	NN	GEN	_	_
401	-RRB-	-rrb-	-RRB-	_	_	_
402	,	,	,	_	_	_
403	transition	transition	NN	_	_	_
404	phase	phase	NN	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	JO2083	jo2083	NN	_	_	_
407	-LRB-	-lrb-	-LRB-	_	_	_
408	hupB	hupb	NN	GEN	_	_
409	-RRB-	-rrb-	-RRB-	_	_	_
410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
411	JO2083	jo2083	NN	_	_	_
412	-LRB-	-lrb-	-LRB-	_	_	_
413	hupB	hupb	NN	GEN	_	_
414	-RRB-	-rrb-	-RRB-	_	_	_
415	,	,	,	_	_	_
416	exponential	exponential	JJ	GrowthPhase	_	_
417	phase	phase	NN	GrowthPhase	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	JO2083	jo2083	NN	_	_	_
420	hupB	hupb	NN	GEN	_	_
421	,	,	,	_	_	_
422	LB	lb	NN	_	_	_
423	,	,	,	_	_	_
424	exponential	exponential	JJ	GrowthPhase	_	_
425	phase	phase	NN	GrowthPhase	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	JO2083	jo2083	NN	_	_	_
428	hupB	hupb	NN	GEN	_	_
429	,	,	,	_	_	_
430	LB	lb	NN	_	_	_
431	,	,	,	_	_	_
432	stationary	stationary	JJ	GrowthPhase	_	_
433	phase	phase	NN	GrowthPhase	_	_
434	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
435	JO2083	jo2083	NN	_	_	_
436	hupB	hupb	NN	GEN	_	_
437	,	,	,	_	_	_
438	LB	lb	NN	_	_	_
439	,	,	,	_	_	_
440	transition	transition	NN	_	_	_
441	phase	phase	NN	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	JO2083	jo2083	NN	_	_	_
444	-LRB-	-lrb-	-LRB-	_	_	_
445	hupB	hupb	NN	GEN	_	_
446	-RRB-	-rrb-	-RRB-	_	_	_
447	,	,	,	_	_	_
448	stationary	stationary	JJ	GrowthPhase	_	_
449	phase	phase	NN	GrowthPhase	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
451	JO2083	jo2083	NN	_	_	_
452	-LRB-	-lrb-	-LRB-	_	_	_
453	hupB	hupb	NN	GEN	_	_
454	-RRB-	-rrb-	-RRB-	_	_	_
455	,	,	,	_	_	_
456	transition	transition	NN	_	_	_
457	phase	phase	NN	_	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	JO3020	jo3020	NN	_	_	_
460	-LRB-	-lrb-	-LRB-	_	_	_
461	hupAB	hupab	NN	_	_	_
462	-RRB-	-rrb-	-RRB-	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	JO3020	jo3020	NN	_	_	_
465	-LRB-	-lrb-	-LRB-	_	_	_
466	hupAB	hupab	NN	_	_	_
467	-RRB-	-rrb-	-RRB-	_	_	_
468	,	,	,	_	_	_
469	exponential	exponential	JJ	GrowthPhase	_	_
470	phase	phase	NN	GrowthPhase	_	_
471	,	,	,	_	_	_
472	repetition1	repetition1	NN	_	_	_
473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
474	JO3020	jo3020	NN	_	_	_
475	-LRB-	-lrb-	-LRB-	_	_	_
476	hupAB	hupab	NN	_	_	_
477	-RRB-	-rrb-	-RRB-	_	_	_
478	,	,	,	_	_	_
479	exponential	exponential	JJ	GrowthPhase	_	_
480	phase	phase	NN	GrowthPhase	_	_
481	,	,	,	_	_	_
482	repetition2	repetition2	NN	_	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
484	JO3020	jo3020	NN	_	_	_
485	hupAB	hupab	NN	_	_	_
486	,	,	,	_	_	_
487	LB	lb	NN	_	_	_
488	,	,	,	_	_	_
489	exponential	exponential	JJ	GrowthPhase	_	_
490	phase	phase	NN	GrowthPhase	_	_
491	,	,	,	_	_	_
492	repetition1	repetition1	NN	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	JO3020	jo3020	NN	_	_	_
495	hupAB	hupab	NN	_	_	_
496	,	,	,	_	_	_
497	LB	lb	NN	_	_	_
498	,	,	,	_	_	_
499	exponential	exponential	JJ	GrowthPhase	_	_
500	phase	phase	NN	GrowthPhase	_	_
501	,	,	,	_	_	_
502	repetition2	repetition2	NN	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	JO3020	jo3020	NN	_	_	_
505	hupAB	hupab	NN	_	_	_
506	,	,	,	_	_	_
507	LB	lb	NN	_	_	_
508	,	,	,	_	_	_
509	stationary	stationary	JJ	GrowthPhase	_	_
510	phase	phase	NN	GrowthPhase	_	_
511	,	,	,	_	_	_
512	repetition1	repetition1	NN	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	JO3020	jo3020	NN	_	_	_
515	hupAB	hupab	NN	_	_	_
516	,	,	,	_	_	_
517	LB	lb	NN	_	_	_
518	,	,	,	_	_	_
519	stationary	stationary	JJ	GrowthPhase	_	_
520	phase	phase	NN	GrowthPhase	_	_
521	,	,	,	_	_	_
522	repetition2	repetition2	NN	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	JO3020	jo3020	NN	_	_	_
525	hupAB	hupab	NN	_	_	_
526	,	,	,	_	_	_
527	LB	lb	NN	_	_	_
528	,	,	,	_	_	_
529	transition	transition	NN	_	_	_
530	phase	phase	NN	_	_	_
531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
532	JO3020	jo3020	NN	_	_	_
533	-LRB-	-lrb-	-LRB-	_	_	_
534	hupAB	hupab	NN	_	_	_
535	-RRB-	-rrb-	-RRB-	_	_	_
536	,	,	,	_	_	_
537	Min	min	NN	_	_	_
538	Glucose	glucose	NN	_	_	_
539	,	,	,	_	_	_
540	exponential	exponential	JJ	GrowthPhase	_	_
541	phase	phase	NN	GrowthPhase	_	_
542	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
543	JO3020	jo3020	NN	_	_	_
544	hupAB	hupab	NN	_	_	_
545	,	,	,	_	_	_
546	Min	min	NN	_	_	_
547	Glucose	glucose	NN	_	_	_
548	,	,	,	_	_	_
549	exponential	exponential	JJ	GrowthPhase	_	_
550	phase	phase	NN	GrowthPhase	_	_
551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
552	JO3020	jo3020	NN	_	_	_
553	-LRB-	-lrb-	-LRB-	_	_	_
554	hupAB	hupab	NN	_	_	_
555	-RRB-	-rrb-	-RRB-	_	_	_
556	,	,	,	_	_	_
557	Min	min	NN	_	_	_
558	Glucose	glucose	NN	_	_	_
559	,	,	,	_	_	_
560	stationary	stationary	JJ	GrowthPhase	_	_
561	phase	phase	NN	GrowthPhase	_	_
562	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
563	JO3020	jo3020	NN	_	_	_
564	hupAB	hupab	NN	_	_	_
565	,	,	,	_	_	_
566	Min	min	NN	_	_	_
567	Glucose	glucose	NN	_	_	_
568	,	,	,	_	_	_
569	stationary	stationary	JJ	GrowthPhase	_	_
570	phase	phase	NN	GrowthPhase	_	_
571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
572	JO3020	jo3020	NN	_	_	_
573	-LRB-	-lrb-	-LRB-	_	_	_
574	hupAB	hupab	NN	_	_	_
575	-RRB-	-rrb-	-RRB-	_	_	_
576	,	,	,	_	_	_
577	Min	Min	NNP	_	_	_
578	Glycerol	Glycerol	NNP	_	_	_
579	exponential	exponential	JJ	GrowthPhase	_	_
580	phase	phase	NN	GrowthPhase	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	JO3020	jo3020	NN	_	_	_
583	hupAB	hupab	NN	_	_	_
584	,	,	,	_	_	_
585	Min	Min	NNP	_	_	_
586	Glycerol	Glycerol	NNP	_	_	_
587	exponential	exponential	JJ	GrowthPhase	_	_
588	phase	phase	NN	GrowthPhase	_	_
589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
590	JO3020	jo3020	NN	_	_	_
591	-LRB-	-lrb-	-LRB-	_	_	_
592	hupAB	hupab	NN	_	_	_
593	-RRB-	-rrb-	-RRB-	_	_	_
594	,	,	,	_	_	_
595	Min	Min	NNP	_	_	_
596	Glycerol	Glycerol	NNP	_	_	_
597	stationary	stationary	JJ	GrowthPhase	_	_
598	phase	phase	NN	GrowthPhase	_	_
599	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
600	JO3020	jo3020	NN	_	_	_
601	hupAB	hupab	NN	_	_	_
602	,	,	,	_	_	_
603	Min	Min	NNP	_	_	_
604	Glycerol	Glycerol	NNP	_	_	_
605	stationary	stationary	JJ	GrowthPhase	_	_
606	phase	phase	NN	GrowthPhase	_	_
607	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
608	JO3020	jo3020	NN	_	_	_
609	-LRB-	-lrb-	-LRB-	_	_	_
610	hupAB	hupab	NN	_	_	_
611	-RRB-	-rrb-	-RRB-	_	_	_
612	,	,	,	_	_	_
613	stationary	stationary	JJ	GrowthPhase	_	_
614	phase	phase	NN	GrowthPhase	_	_
615	,	,	,	_	_	_
616	repetition1	repetition1	NN	_	_	_
617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
618	JO3020	jo3020	NN	_	_	_
619	-LRB-	-lrb-	-LRB-	_	_	_
620	hupAB	hupab	NN	_	_	_
621	-RRB-	-rrb-	-RRB-	_	_	_
622	,	,	,	_	_	_
623	stationary	stationary	JJ	GrowthPhase	_	_
624	phase	phase	NN	GrowthPhase	_	_
625	,	,	,	_	_	_
626	repetition2	repetition2	NN	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	JO3020	jo3020	NN	_	_	_
629	-LRB-	-lrb-	-LRB-	_	_	_
630	hupAB	hupab	NN	_	_	_
631	-RRB-	-rrb-	-RRB-	_	_	_
632	,	,	,	_	_	_
633	transition	transition	NN	_	_	_
634	phase	phase	NN	_	_	_
635	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
636	JQ004	jq004	NN	_	_	_
637	-LRB-	-lrb-	-LRB-	_	_	_
638	rraA	rraa	NN	GEN	_	_
639	-RRB-	-rrb-	-RRB-	_	_	_
640	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
641	K100Q	k100q	NN	_	_	_
642	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
643	K100Q	k100q	NN	_	_	_
644	rep	rep	NN	GEN	_	_
645	1	1	CD	_	_	_
646	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
647	K100Q	k100q	NN	_	_	_
648	rep	rep	NN	GEN	_	_
649	2	2	CD	_	_	_
650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
651	K100Q	k100q	NN	_	_	_
652	rep	rep	NN	GEN	_	_
653	3	3	CD	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
655	K100R	k100r	NN	_	_	_
656	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
657	K100R	k100r	NN	_	_	_
658	rep	rep	NN	GEN	_	_
659	1	1	CD	_	_	_
660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
661	K100R	k100r	NN	_	_	_
662	rep	rep	NN	GEN	_	_
663	2	2	CD	_	_	_
664	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
665	K100R	k100r	NN	_	_	_
666	rep	rep	NN	GEN	_	_
667	3	3	CD	_	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
669	K12	k12	NN	_	_	_
670	EMG2	emg2	NN	_	_	_
671	on	on	IN	_	_	_
672	LB	lb	NN	_	_	_
673	with	with	IN	_	_	_
674	0.2	0.2	CD	_	_	_
675	percent	percent	NN	_	_	_
676	glucose	glucose	NN	SUPP	_	_
677	,	,	,	_	_	_
678	2.5	2.5	CD	_	_	_
679	hours	hour	NNS	_	_	_
680	post-incubation	post-incubation	JJ	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	K12	k12	NN	_	_	_
683	EMG2	emg2	NN	_	_	_
684	on	on	IN	_	_	_
685	LB	lb	NN	_	_	_
686	with	with	IN	_	_	_
687	0.2	0.2	CD	_	_	_
688	percent	percent	NN	_	_	_
689	glucose	glucose	NN	SUPP	_	_
690	,	,	,	_	_	_
691	3.5	3.5	CD	_	_	_
692	hours	hour	NNS	_	_	_
693	post-incubation	post-incubation	JJ	_	_	_
694	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
695	K12	k12	NN	_	_	_
696	EMG2	emg2	NN	_	_	_
697	on	on	IN	_	_	_
698	LB	lb	NN	_	_	_
699	with	with	IN	_	_	_
700	0.2	0.2	CD	_	_	_
701	percent	percent	NN	_	_	_
702	glucose	glucose	NN	SUPP	_	_
703	,	,	,	_	_	_
704	3	3	CD	_	_	_
705	hours	hour	NNS	_	_	_
706	post-incubation	post-incubation	JJ	_	_	_
707	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
708	K12	k12	NN	_	_	_
709	EMG2	emg2	NN	_	_	_
710	on	on	IN	_	_	_
711	LB	lb	NN	_	_	_
712	with	with	IN	_	_	_
713	0.2	0.2	CD	_	_	_
714	percent	percent	NN	_	_	_
715	glucose	glucose	NN	SUPP	_	_
716	,	,	,	_	_	_
717	4.5	4.5	CD	_	_	_
718	hours	hour	NNS	_	_	_
719	post-incubation	post-incubation	JJ	_	_	_
720	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
721	K12	k12	NN	_	_	_
722	EMG2	emg2	NN	_	_	_
723	on	on	IN	_	_	_
724	LB	lb	NN	_	_	_
725	with	with	IN	_	_	_
726	0.2	0.2	CD	_	_	_
727	percent	percent	NN	_	_	_
728	glucose	glucose	NN	SUPP	_	_
729	,	,	,	_	_	_
730	4	4	CD	_	_	_
731	hours	hour	NNS	_	_	_
732	post-incubation	post-incubation	JJ	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	K12	k12	NN	_	_	_
735	EMG2	emg2	NN	_	_	_
736	on	on	IN	_	_	_
737	LB	lb	NN	_	_	_
738	with	with	IN	_	_	_
739	0.2	0.2	CD	_	_	_
740	percent	percent	NN	_	_	_
741	glucose	glucose	NN	SUPP	_	_
742	,	,	,	_	_	_
743	5.5	5.5	CD	_	_	_
744	hours	hour	NNS	_	_	_
745	post-incubation	post-incubation	JJ	_	_	_
746	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
747	K12	k12	NN	_	_	_
748	EMG2	emg2	NN	_	_	_
749	on	on	IN	_	_	_
750	LB	lb	NN	_	_	_
751	with	with	IN	_	_	_
752	0.2	0.2	CD	_	_	_
753	percent	percent	NN	_	_	_
754	glucose	glucose	NN	SUPP	_	_
755	,	,	,	_	_	_
756	5	5	CD	_	_	_
757	hours	hour	NNS	_	_	_
758	post-incubation	post-incubation	JJ	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
760	K12	k12	NN	_	_	_
761	EMG2	emg2	NN	_	_	_
762	on	on	IN	_	_	_
763	LB	lb	NN	_	_	_
764	with	with	IN	_	_	_
765	0.2	0.2	CD	_	_	_
766	percent	percent	NN	_	_	_
767	glucose	glucose	NN	SUPP	_	_
768	,	,	,	_	_	_
769	6	6	CD	_	_	_
770	hours	hour	NNS	_	_	_
771	post-incubation	post-incubation	JJ	_	_	_
772	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
773	K12	k12	NN	_	_	_
774	EMG2	emg2	NN	_	_	_
775	on	on	IN	_	_	_
776	LB	lb	NN	_	_	_
777	with	with	IN	_	_	_
778	0.2	0.2	CD	_	_	_
779	percent	percent	NN	_	_	_
780	glucose	glucose	NN	SUPP	_	_
781	,	,	,	_	_	_
782	8	8	CD	_	_	_
783	hours	hour	NNS	_	_	_
784	post-incubation	post-incubation	JJ	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	K12	k12	NN	_	_	_
787	EMG2	emg2	NN	_	_	_
788	on	on	IN	_	_	_
789	LB	lb	NN	_	_	_
790	with	with	IN	_	_	_
791	0.4	0.4	CD	_	_	_
792	percent	percent	NN	_	_	_
793	glucose	glucose	NN	SUPP	_	_
794	,	,	,	_	_	_
795	2.5	2.5	CD	_	_	_
796	hours	hour	NNS	_	_	_
797	post-incubation	post-incubation	JJ	_	_	_
798	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
799	K12	k12	NN	_	_	_
800	EMG2	emg2	NN	_	_	_
801	on	on	IN	_	_	_
802	LB	lb	NN	_	_	_
803	with	with	IN	_	_	_
804	0.4	0.4	CD	_	_	_
805	percent	percent	NN	_	_	_
806	glucose	glucose	NN	SUPP	_	_
807	,	,	,	_	_	_
808	3.5	3.5	CD	_	_	_
809	hours	hour	NNS	_	_	_
810	post-incubation	post-incubation	JJ	_	_	_
811	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
812	K12	k12	NN	_	_	_
813	EMG2	emg2	NN	_	_	_
814	on	on	IN	_	_	_
815	LB	lb	NN	_	_	_
816	with	with	IN	_	_	_
817	0.4	0.4	CD	_	_	_
818	percent	percent	NN	_	_	_
819	glucose	glucose	NN	SUPP	_	_
820	,	,	,	_	_	_
821	3	3	CD	_	_	_
822	hours	hour	NNS	_	_	_
823	post-incubation	post-incubation	JJ	_	_	_
824	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
825	K12	k12	NN	_	_	_
826	EMG2	emg2	NN	_	_	_
827	on	on	IN	_	_	_
828	LB	lb	NN	_	_	_
829	with	with	IN	_	_	_
830	0.4	0.4	CD	_	_	_
831	percent	percent	NN	_	_	_
832	glucose	glucose	NN	SUPP	_	_
833	,	,	,	_	_	_
834	4.5	4.5	CD	_	_	_
835	hours	hour	NNS	_	_	_
836	post-incubation	post-incubation	JJ	_	_	_
837	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
838	K12	k12	NN	_	_	_
839	EMG2	emg2	NN	_	_	_
840	on	on	IN	_	_	_
841	LB	lb	NN	_	_	_
842	with	with	IN	_	_	_
843	0.4	0.4	CD	_	_	_
844	percent	percent	NN	_	_	_
845	glucose	glucose	NN	SUPP	_	_
846	,	,	,	_	_	_
847	4	4	CD	_	_	_
848	hours	hour	NNS	_	_	_
849	post-incubation	post-incubation	JJ	_	_	_
850	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
851	K12	k12	NN	_	_	_
852	EMG2	emg2	NN	_	_	_
853	on	on	IN	_	_	_
854	LB	lb	NN	_	_	_
855	with	with	IN	_	_	_
856	0.4	0.4	CD	_	_	_
857	percent	percent	NN	_	_	_
858	glucose	glucose	NN	SUPP	_	_
859	,	,	,	_	_	_
860	5.5	5.5	CD	_	_	_
861	hours	hour	NNS	_	_	_
862	post-incubation	post-incubation	JJ	_	_	_
863	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
864	K12	k12	NN	_	_	_
865	EMG2	emg2	NN	_	_	_
866	on	on	IN	_	_	_
867	LB	lb	NN	_	_	_
868	with	with	IN	_	_	_
869	0.4	0.4	CD	_	_	_
870	percent	percent	NN	_	_	_
871	glucose	glucose	NN	SUPP	_	_
872	,	,	,	_	_	_
873	5	5	CD	_	_	_
874	hours	hour	NNS	_	_	_
875	post-incubation	post-incubation	JJ	_	_	_
876	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
877	K12	k12	NN	_	_	_
878	EMG2	emg2	NN	_	_	_
879	on	on	IN	_	_	_
880	LB	lb	NN	_	_	_
881	with	with	IN	_	_	_
882	0.4	0.4	CD	_	_	_
883	percent	percent	NN	_	_	_
884	glucose	glucose	NN	SUPP	_	_
885	,	,	,	_	_	_
886	6	6	CD	_	_	_
887	hours	hour	NNS	_	_	_
888	post-incubation	post-incubation	JJ	_	_	_
889	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
890	K12	k12	NN	_	_	_
891	EMG2	emg2	NN	_	_	_
892	on	on	IN	_	_	_
893	LB	lb	NN	_	_	_
894	with	with	IN	_	_	_
895	0.4	0.4	CD	_	_	_
896	percent	percent	NN	_	_	_
897	glucose	glucose	NN	SUPP	_	_
898	,	,	,	_	_	_
899	8	8	CD	_	_	_
900	hours	hour	NNS	_	_	_
901	post-incubation	post-incubation	JJ	_	_	_
902	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
903	K12	k12	NN	_	_	_
904	MG1655	mg1655	NN	_	_	_
905	with	with	IN	_	_	_
906	10	10	CD	_	_	_
907	mM	mm	NN	KWSUPP	_	_
908	of	of	IN	_	_	_
909	heptanoic	heptanoic	JJ	_	_	_
910	acid	acid	NN	_	_	_
911	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
912	K12	k12	NN	_	_	_
913	MG1655	mg1655	NN	_	_	_
914	without	without	IN	_	_	_
915	heptanoic	heptanoic	JJ	_	_	_
916	acid	acid	NN	_	_	_
917	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
918	K12	k12	NN	_	_	_
919	strain	strain	NN	_	_	_
920	MG1655	mg1655	NN	_	_	_
921	,	,	,	_	_	_
922	100	100	CD	_	_	_
923	mcg/ml	mcg/ml	NN	_	_	_
924	bicyclomycin	bicyclomycin	NN	_	_	_
925	20	20	CD	_	_	_
926	min	min	NN	_	_	_
927	,	,	,	_	_	_
928	exponential	exponential	JJ	GrowthPhase	_	_
929	phase	phase	NN	GrowthPhase	_	_
930	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
931	K12	k12	NN	_	_	_
932	strain	strain	NN	_	_	_
933	MG1655	mg1655	NN	_	_	_
934	,	,	,	_	_	_
935	10	10	CD	_	_	_
936	mcg/ml	mcg/ml	NN	_	_	_
937	bicyclomycin	bicyclomycin	NN	_	_	_
938	20	20	CD	_	_	_
939	min	min	NN	_	_	_
940	,	,	,	_	_	_
941	exponential	exponential	JJ	GrowthPhase	_	_
942	phase	phase	NN	GrowthPhase	_	_
943	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
944	K12	k12	NN	_	_	_
945	strain	strain	NN	_	_	_
946	MG1655	mg1655	NN	_	_	_
947	,	,	,	_	_	_
948	25	25	CD	_	_	_
949	mcg/ml	mcg/ml	NN	_	_	_
950	bicyclomycin	bicyclomycin	NN	_	_	_
951	20	20	CD	_	_	_
952	min	min	NN	_	_	_
953	,	,	,	_	_	_
954	exponential	exponential	JJ	GrowthPhase	_	_
955	phase	phase	NN	GrowthPhase	_	_
956	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
957	K12	k12	NN	_	_	_
958	strain	strain	NN	_	_	_
959	MG1655	mg1655	NN	_	_	_
960	,	,	,	_	_	_
961	control	control	NN	_	_	_
962	sample	sample	NN	_	_	_
963	,	,	,	_	_	_
964	exponential	exponential	JJ	GrowthPhase	_	_
965	phase	phase	NN	GrowthPhase	_	_
966	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
967	K-12	k-12	NN	_	_	_
968	strain	strain	NN	_	_	_
969	_	_	RB	_	_	_
970	wild	wild	JJ	_	_	_
971	type	type	NN	_	_	_
972	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
973	K-12	k-12	NN	_	_	_
974	strain	strain	NN	_	_	_
975	,	,	,	_	_	_
976	wild	wild	JJ	_	_	_
977	type	type	NN	_	_	_
978	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
979	K12	k12	NN	_	_	_
980	WT	wt	JJ	_	_	_
981	3110	3110	CD	_	_	_
982	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
983	K12	k12	NN	_	_	_
984	Δ	δ	NN	_	_	_
985	-LRB-	-lrb-	-LRB-	_	_	_
986	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
987	-RRB-	-rrb-	-RRB-	_	_	_
988	+	+	CC	_	_	_
989	ctrl	ctrl	NN	_	_	_
990	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
991	K12	k12	NN	_	_	_
992	Δ	δ	NN	_	_	_
993	-LRB-	-lrb-	-LRB-	_	_	_
994	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
995	-RRB-	-rrb-	-RRB-	_	_	_
996	+	+	CC	_	_	_
997	ctrl	ctrl	NN	_	_	_
998	,	,	,	_	_	_
999	biological	biological	JJ	_	_	_
1000	replicate	replicate	VB	_	_	_
1001	1	1	CD	_	_	_
1002	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1003	K12	k12	NN	_	_	_
1004	Δ	δ	NN	_	_	_
1005	-LRB-	-lrb-	-LRB-	_	_	_
1006	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1007	-RRB-	-rrb-	-RRB-	_	_	_
1008	+	+	CC	_	_	_
1009	ctrl	ctrl	NN	_	_	_
1010	,	,	,	_	_	_
1011	biological	biological	JJ	_	_	_
1012	replicate	replicate	VB	_	_	_
1013	2	2	CD	_	_	_
1014	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1015	K12	k12	NN	_	_	_
1016	Δ	δ	NN	_	_	_
1017	-LRB-	-lrb-	-LRB-	_	_	_
1018	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1019	-RRB-	-rrb-	-RRB-	_	_	_
1020	+	+	CC	_	_	_
1021	ctrl	ctrl	NN	_	_	_
1022	,	,	,	_	_	_
1023	biological	biological	JJ	_	_	_
1024	replicate	replicate	VB	_	_	_
1025	3	3	CD	_	_	_
1026	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1027	K12	k12	NN	_	_	_
1028	Δ	δ	NN	_	_	_
1029	-LRB-	-lrb-	-LRB-	_	_	_
1030	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1031	-RRB-	-rrb-	-RRB-	_	_	_
1032	+	+	CC	_	_	_
1033	ctrl	ctrl	NN	_	_	_
1034	,	,	,	_	_	_
1035	biological	biological	JJ	_	_	_
1036	replicate	replicate	VB	_	_	_
1037	4	4	CD	_	_	_
1038	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1039	K12	k12	NN	_	_	_
1040	Δ	δ	NN	_	_	_
1041	-LRB-	-lrb-	-LRB-	_	_	_
1042	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1043	-RRB-	-rrb-	-RRB-	_	_	_
1044	+	+	CC	_	_	_
1045	pBglJ	pbglj	NN	_	_	_
1046	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1047	K12Δ	k12δ	NN	_	_	_
1048	-LRB-	-lrb-	-LRB-	_	_	_
1049	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1050	-RRB-	-rrb-	-RRB-	_	_	_
1051	+	+	CC	_	_	_
1052	pBglJ	pbglj	NN	_	_	_
1053	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1054	K12	k12	NN	_	_	_
1055	Δ	δ	NN	_	_	_
1056	-LRB-	-lrb-	-LRB-	_	_	_
1057	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1058	-RRB-	-rrb-	-RRB-	_	_	_
1059	+	+	CC	_	_	_
1060	pBglJ	pbglj	NN	_	_	_
1061	,	,	,	_	_	_
1062	biological	biological	JJ	_	_	_
1063	replicate	replicate	VB	_	_	_
1064	1	1	CD	_	_	_
1065	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1066	K12	k12	NN	_	_	_
1067	Δ	δ	NN	_	_	_
1068	-LRB-	-lrb-	-LRB-	_	_	_
1069	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1070	-RRB-	-rrb-	-RRB-	_	_	_
1071	+	+	CC	_	_	_
1072	pBglJ	pbglj	NN	_	_	_
1073	,	,	,	_	_	_
1074	biological	biological	JJ	_	_	_
1075	replicate	replicate	VB	_	_	_
1076	2	2	CD	_	_	_
1077	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1078	K12Δ	k12δ	NN	_	_	_
1079	-LRB-	-lrb-	-LRB-	_	_	_
1080	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1081	-RRB-	-rrb-	-RRB-	_	_	_
1082	+	+	CC	_	_	_
1083	pBglJ	pbglj	NN	_	_	_
1084	,	,	,	_	_	_
1085	biological	biological	JJ	_	_	_
1086	replicate	replicate	VB	_	_	_
1087	3	3	CD	_	_	_
1088	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1089	K12	k12	NN	_	_	_
1090	Δ	δ	NN	_	_	_
1091	-LRB-	-lrb-	-LRB-	_	_	_
1092	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1093	-RRB-	-rrb-	-RRB-	_	_	_
1094	+	+	CC	_	_	_
1095	pBglJ	pbglj	NN	_	_	_
1096	,	,	,	_	_	_
1097	biological	biological	JJ	_	_	_
1098	replicate	replicate	VB	_	_	_
1099	4	4	CD	_	_	_
1100	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1101	K12	k12	NN	_	_	_
1102	Δ	δ	NN	_	_	_
1103	-LRB-	-lrb-	-LRB-	_	_	_
1104	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1105	-RRB-	-rrb-	-RRB-	_	_	_
1106	+	+	CC	_	_	_
1107	pLeuO	pleuo	NN	_	_	_
1108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1109	K12	k12	NN	_	_	_
1110	Δ	δ	NN	_	_	_
1111	-LRB-	-lrb-	-LRB-	_	_	_
1112	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1113	-RRB-	-rrb-	-RRB-	_	_	_
1114	+	+	CC	_	_	_
1115	pLeuO	pleuo	NN	_	_	_
1116	,	,	,	_	_	_
1117	biological	biological	JJ	_	_	_
1118	replicate	replicate	VB	_	_	_
1119	1	1	CD	_	_	_
1120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1121	K12	k12	NN	_	_	_
1122	Δ	δ	NN	_	_	_
1123	-LRB-	-lrb-	-LRB-	_	_	_
1124	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1125	-RRB-	-rrb-	-RRB-	_	_	_
1126	+	+	CC	_	_	_
1127	pLeuO	pleuo	NN	_	_	_
1128	,	,	,	_	_	_
1129	biological	biological	JJ	_	_	_
1130	replicate	replicate	VB	_	_	_
1131	2	2	CD	_	_	_
1132	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1133	K12	k12	NN	_	_	_
1134	Δ	δ	NN	_	_	_
1135	-LRB-	-lrb-	-LRB-	_	_	_
1136	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1137	-RRB-	-rrb-	-RRB-	_	_	_
1138	+	+	CC	_	_	_
1139	pLeuO	pleuo	NN	_	_	_
1140	,	,	,	_	_	_
1141	biological	biological	JJ	_	_	_
1142	replicate	replicate	VB	_	_	_
1143	3	3	CD	_	_	_
1144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1145	K12	k12	NN	_	_	_
1146	Δ	δ	NN	_	_	_
1147	-LRB-	-lrb-	-LRB-	_	_	_
1148	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1149	-RRB-	-rrb-	-RRB-	_	_	_
1150	+	+	CC	_	_	_
1151	pLeuO	pleuo	NN	_	_	_
1152	,	,	,	_	_	_
1153	biological	biological	JJ	_	_	_
1154	replicate	replicate	VB	_	_	_
1155	4	4	CD	_	_	_
1156	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1157	K12	k12	NN	_	_	_
1158	Δ	δ	NN	_	_	_
1159	-LRB-	-lrb-	-LRB-	_	_	_
1160	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1161	-RRB-	-rrb-	-RRB-	_	_	_
1162	ΔleuO	δleuo	NN	_	_	_
1163	+	+	CC	_	_	_
1164	ctrl	ctrl	NN	_	_	_
1165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1166	K12	k12	NN	_	_	_
1167	Δ	δ	NN	_	_	_
1168	-LRB-	-lrb-	-LRB-	_	_	_
1169	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1170	-RRB-	-rrb-	-RRB-	_	_	_
1171	ΔleuO	δleuo	NN	_	_	_
1172	+	+	CC	_	_	_
1173	ctrl	ctrl	NN	_	_	_
1174	,	,	,	_	_	_
1175	biological	biological	JJ	_	_	_
1176	replicate	replicate	VB	_	_	_
1177	1	1	CD	_	_	_
1178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1179	K12	k12	NN	_	_	_
1180	Δ	δ	NN	_	_	_
1181	-LRB-	-lrb-	-LRB-	_	_	_
1182	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1183	-RRB-	-rrb-	-RRB-	_	_	_
1184	ΔleuO	δleuo	NN	_	_	_
1185	+	+	CC	_	_	_
1186	ctrl	ctrl	NN	_	_	_
1187	,	,	,	_	_	_
1188	biological	biological	JJ	_	_	_
1189	replicate	replicate	VB	_	_	_
1190	2	2	CD	_	_	_
1191	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1192	K12	k12	NN	_	_	_
1193	Δ	δ	NN	_	_	_
1194	-LRB-	-lrb-	-LRB-	_	_	_
1195	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1196	-RRB-	-rrb-	-RRB-	_	_	_
1197	ΔleuO	δleuo	NN	_	_	_
1198	+	+	CC	_	_	_
1199	ctrl	ctrl	NN	_	_	_
1200	,	,	,	_	_	_
1201	biological	biological	JJ	_	_	_
1202	replicate	replicate	VB	_	_	_
1203	3	3	CD	_	_	_
1204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1205	K12	k12	NN	_	_	_
1206	Δ	δ	NN	_	_	_
1207	-LRB-	-lrb-	-LRB-	_	_	_
1208	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1209	-RRB-	-rrb-	-RRB-	_	_	_
1210	ΔleuO	δleuo	NN	_	_	_
1211	+	+	CC	_	_	_
1212	ctrl	ctrl	NN	_	_	_
1213	,	,	,	_	_	_
1214	biological	biological	JJ	_	_	_
1215	replicate	replicate	VB	_	_	_
1216	4	4	CD	_	_	_
1217	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1218	K12	k12	NN	_	_	_
1219	Δ	δ	NN	_	_	_
1220	-LRB-	-lrb-	-LRB-	_	_	_
1221	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1222	-RRB-	-rrb-	-RRB-	_	_	_
1223	ΔleuO	δleuo	NN	_	_	_
1224	+	+	CC	_	_	_
1225	pBglJ	pbglj	NN	_	_	_
1226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1227	K12	k12	NN	_	_	_
1228	Δ	δ	NN	_	_	_
1229	-LRB-	-lrb-	-LRB-	_	_	_
1230	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1231	-RRB-	-rrb-	-RRB-	_	_	_
1232	ΔleuO	δleuo	NN	_	_	_
1233	+	+	CC	_	_	_
1234	pBglJ	pbglj	NN	_	_	_
1235	,	,	,	_	_	_
1236	biological	biological	JJ	_	_	_
1237	replicate	replicate	VB	_	_	_
1238	1	1	CD	_	_	_
1239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1240	K12	k12	NN	_	_	_
1241	Δ	δ	NN	_	_	_
1242	-LRB-	-lrb-	-LRB-	_	_	_
1243	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1244	-RRB-	-rrb-	-RRB-	_	_	_
1245	ΔleuO	δleuo	NN	_	_	_
1246	+	+	CC	_	_	_
1247	pBglJ	pbglj	NN	_	_	_
1248	,	,	,	_	_	_
1249	biological	biological	JJ	_	_	_
1250	replicate	replicate	VB	_	_	_
1251	2	2	CD	_	_	_
1252	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1253	K12	k12	NN	_	_	_
1254	Δ	δ	NN	_	_	_
1255	-LRB-	-lrb-	-LRB-	_	_	_
1256	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1257	-RRB-	-rrb-	-RRB-	_	_	_
1258	ΔleuO	δleuo	NN	_	_	_
1259	+	+	CC	_	_	_
1260	pBglJ	pbglj	NN	_	_	_
1261	,	,	,	_	_	_
1262	biological	biological	JJ	_	_	_
1263	replicate	replicate	VB	_	_	_
1264	3	3	CD	_	_	_
1265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1266	K12	k12	NN	_	_	_
1267	Δ	δ	NN	_	_	_
1268	-LRB-	-lrb-	-LRB-	_	_	_
1269	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1270	-RRB-	-rrb-	-RRB-	_	_	_
1271	ΔleuO	δleuo	NN	_	_	_
1272	+	+	CC	_	_	_
1273	pBglJ	pbglj	NN	_	_	_
1274	,	,	,	_	_	_
1275	biological	biological	JJ	_	_	_
1276	replicate	replicate	VB	_	_	_
1277	4	4	CD	_	_	_
1278	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1279	K12	k12	NN	_	_	_
1280	Δ	δ	NN	_	_	_
1281	-LRB-	-lrb-	-LRB-	_	_	_
1282	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1283	-RRB-	-rrb-	-RRB-	_	_	_
1284	ΔrcsB	δrcsb	NN	_	_	_
1285	+	+	CC	_	_	_
1286	ctrl	ctrl	NN	_	_	_
1287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1288	K12	k12	NN	_	_	_
1289	Δ	δ	NN	_	_	_
1290	-LRB-	-lrb-	-LRB-	_	_	_
1291	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1292	-RRB-	-rrb-	-RRB-	_	_	_
1293	ΔrcsB	δrcsb	NN	_	_	_
1294	+	+	CC	_	_	_
1295	ctrl	ctrl	NN	_	_	_
1296	,	,	,	_	_	_
1297	biological	biological	JJ	_	_	_
1298	replicate	replicate	VB	_	_	_
1299	1	1	CD	_	_	_
1300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1301	K12	k12	NN	_	_	_
1302	Δ	δ	NN	_	_	_
1303	-LRB-	-lrb-	-LRB-	_	_	_
1304	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1305	-RRB-	-rrb-	-RRB-	_	_	_
1306	ΔrcsB	δrcsb	NN	_	_	_
1307	+	+	CC	_	_	_
1308	ctrl	ctrl	NN	_	_	_
1309	,	,	,	_	_	_
1310	biological	biological	JJ	_	_	_
1311	replicate	replicate	VB	_	_	_
1312	2	2	CD	_	_	_
1313	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1314	K12	k12	NN	_	_	_
1315	Δ	δ	NN	_	_	_
1316	-LRB-	-lrb-	-LRB-	_	_	_
1317	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1318	-RRB-	-rrb-	-RRB-	_	_	_
1319	ΔrcsB	δrcsb	NN	_	_	_
1320	+	+	CC	_	_	_
1321	ctrl	ctrl	NN	_	_	_
1322	,	,	,	_	_	_
1323	biological	biological	JJ	_	_	_
1324	replicate	replicate	VB	_	_	_
1325	3	3	CD	_	_	_
1326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1327	K12	k12	NN	_	_	_
1328	Δ	δ	NN	_	_	_
1329	-LRB-	-lrb-	-LRB-	_	_	_
1330	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1331	-RRB-	-rrb-	-RRB-	_	_	_
1332	ΔrcsB	δrcsb	NN	_	_	_
1333	+	+	CC	_	_	_
1334	ctrl	ctrl	NN	_	_	_
1335	,	,	,	_	_	_
1336	biological	biological	JJ	_	_	_
1337	replicate	replicate	VB	_	_	_
1338	4	4	CD	_	_	_
1339	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1340	K12	k12	NN	_	_	_
1341	Δ	δ	NN	_	_	_
1342	-LRB-	-lrb-	-LRB-	_	_	_
1343	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1344	-RRB-	-rrb-	-RRB-	_	_	_
1345	ΔrcsB	δrcsb	NN	_	_	_
1346	+	+	CC	_	_	_
1347	pBglJ	pbglj	NN	_	_	_
1348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1349	K12	k12	NN	_	_	_
1350	Δ	δ	NN	_	_	_
1351	-LRB-	-lrb-	-LRB-	_	_	_
1352	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1353	-RRB-	-rrb-	-RRB-	_	_	_
1354	ΔrcsB	δrcsb	NN	_	_	_
1355	+	+	CC	_	_	_
1356	pBglJ	pbglj	NN	_	_	_
1357	,	,	,	_	_	_
1358	biological	biological	JJ	_	_	_
1359	replicate	replicate	VB	_	_	_
1360	1	1	CD	_	_	_
1361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1362	K12	k12	NN	_	_	_
1363	Δ	δ	NN	_	_	_
1364	-LRB-	-lrb-	-LRB-	_	_	_
1365	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1366	-RRB-	-rrb-	-RRB-	_	_	_
1367	ΔrcsB	δrcsb	NN	_	_	_
1368	+	+	CC	_	_	_
1369	pBglJ	pbglj	NN	_	_	_
1370	,	,	,	_	_	_
1371	biological	biological	JJ	_	_	_
1372	replicate	replicate	VB	_	_	_
1373	2	2	CD	_	_	_
1374	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1375	K12	k12	NN	_	_	_
1376	Δ	δ	NN	_	_	_
1377	-LRB-	-lrb-	-LRB-	_	_	_
1378	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1379	-RRB-	-rrb-	-RRB-	_	_	_
1380	ΔrcsB	δrcsb	NN	_	_	_
1381	+	+	CC	_	_	_
1382	pBglJ	pbglj	NN	_	_	_
1383	,	,	,	_	_	_
1384	biological	biological	JJ	_	_	_
1385	replicate	replicate	VB	_	_	_
1386	3	3	CD	_	_	_
1387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1388	K12	k12	NN	_	_	_
1389	Δ	δ	NN	_	_	_
1390	-LRB-	-lrb-	-LRB-	_	_	_
1391	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
1392	-RRB-	-rrb-	-RRB-	_	_	_
1393	ΔrcsB	δrcsb	NN	_	_	_
1394	+	+	CC	_	_	_
1395	pBglJ	pbglj	NN	_	_	_
1396	,	,	,	_	_	_
1397	biological	biological	JJ	_	_	_
1398	replicate	replicate	VB	_	_	_
1399	4	4	CD	_	_	_
1400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1401	KCN	kcn	NN	_	_	_
1402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1403	kefB	kefb	NN	GEN	_	_
1404	KO	ko	NN	_	_	_
1405	rep1	rep1	NN	_	_	_
1406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1407	kefB	kefb	NN	GEN	_	_
1408	KO	ko	NN	_	_	_
1409	rep2	rep2	NN	_	_	_
1410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1411	kefB	kefb	NN	GEN	_	_
1412	KO	ko	NN	_	_	_
1413	rep3	rep3	NN	_	_	_
1414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1415	khc	khc	NN	_	_	_
1416	KO	ko	NN	_	_	_
1417	rep1	rep1	NN	_	_	_
1418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1419	khc	khc	NN	_	_	_
1420	KO	ko	NN	_	_	_
1421	rep2	rep2	NN	_	_	_
1422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1423	khc	khc	NN	_	_	_
1424	KO	ko	NN	_	_	_
1425	rep3	rep3	NN	_	_	_
1426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1427	KMD	kmd	NN	_	_	_
1428	1	1	CD	_	_	_
1429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1430	KMD	kmd	NN	_	_	_
1431	2	2	CD	_	_	_
1432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1433	KMD	kmd	NN	_	_	_
1434	3	3	CD	_	_	_
1435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1436	KSL2000	ksl2000	NN	_	_	_
1437	,	,	,	_	_	_
1438	0.1	0.1	CD	_	_	_
1439	%	%	NN	_	_	_
1440	arabinose	arabinose	NN	_	_	_
1441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1442	KSL2000	ksl2000	NN	_	_	_
1443	,	,	,	_	_	_
1444	no	no	DT	_	_	_
1445	arabinose	arabinose	NN	_	_	_
1446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1447	KSL2000	ksl2000	NN	_	_	_
1448	plus	plus	CC	_	_	_
1449	pTrc99A	ptrc99a	NN	_	_	_
1450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1451	KSL2000	ksl2000	NN	_	_	_
1452	plus	plus	CC	_	_	_
1453	pTrc99A-RraA	ptrc99a-rraa	NN	_	_	_
1454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1455	KSL2000-Rne	ksl2000-rne	NN	_	_	_
1456	depletion	depletion	NN	_	_	_
1457	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1458	KSL2000-RraA	ksl2000-rraa	NN	_	_	_
1459	overexpression	overexpression	NN	_	_	_
1460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1461	KSL2009	ksl2009	NN	_	_	_
1462	,	,	,	_	_	_
1463	0.1	0.1	CD	_	_	_
1464	%	%	NN	_	_	_
1465	arabinose	arabinose	NN	_	_	_
1466	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1467	KSL2009	ksl2009	NN	_	_	_
1468	,	,	,	_	_	_
1469	no	no	DT	_	_	_
1470	arabinose	arabinose	NN	_	_	_
1471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1472	KSL2009-N-Rne	ksl2009-n-rne	NN	_	_	_
1473	depletion	depletion	NN	_	_	_
1474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1475	KSL2009	ksl2009	NN	_	_	_
1476	plus	plus	CC	_	_	_
1477	pTrc99A	ptrc99a	NN	_	_	_
1478	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1479	KSL2009	ksl2009	NN	_	_	_
1480	plus	plus	CC	_	_	_
1481	pTrc99A-RraA	ptrc99a-rraa	NN	_	_	_
1482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1483	KSL2009-RraA	ksl2009-rraa	NN	_	_	_
1484	overexpression	overexpression	NN	_	_	_
1485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1486	lacA	laca	NN	GEN	_	_
1487	KO	ko	NN	_	_	_
1488	LB	lb	NN	_	_	_
1489	rep1	rep1	NN	_	_	_
1490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1491	lacA	laca	NN	GEN	_	_
1492	KO	ko	NN	_	_	_
1493	LB	lb	NN	_	_	_
1494	rep2	rep2	NN	_	_	_
1495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1496	lacA	laca	NN	GEN	_	_
1497	KO	ko	NN	_	_	_
1498	M9	m9	NN	_	_	_
1499	rep1	rep1	NN	_	_	_
1500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1501	lacA	laca	NN	GEN	_	_
1502	KO	ko	NN	_	_	_
1503	M9	m9	NN	_	_	_
1504	rep2	rep2	NN	_	_	_
1505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1506	LA-co1	la-co1	NN	_	_	_
1507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1508	LA-co2	la-co2	NN	_	_	_
1509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1510	lactate	lactate	NN	_	_	_
1511	_	_	NN	_	_	_
1512	growth	growth	NN	_	_	_
1513	:	:	:	_	_	_
1514	MURI	MURI	NNP	_	_	_
1515	_	_	SYM	_	_	_
1516	085	085	CD	_	_	_
1517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1518	lactate	lactate	NN	_	_	_
1519	_	_	NN	_	_	_
1520	growth	growth	NN	_	_	_
1521	:	:	:	_	_	_
1522	MURI	MURI	NNP	_	_	_
1523	_	_	SYM	_	_	_
1524	086	086	CD	_	_	_
1525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1526	lactate	lactate	NN	_	_	_
1527	_	_	NN	_	_	_
1528	growth	growth	NN	_	_	_
1529	:	:	:	_	_	_
1530	MURI	MURI	NNP	_	_	_
1531	_	_	SYM	_	_	_
1532	087	087	CD	_	_	_
1533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1534	lactate	lactate	NN	_	_	_
1535	_	_	NN	_	_	_
1536	growth	growth	NN	_	_	_
1537	:	:	:	_	_	_
1538	MURI	MURI	NNP	_	_	_
1539	_	_	SYM	_	_	_
1540	088	088	CD	_	_	_
1541	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1542	lactate	lactate	NN	_	_	_
1543	_	_	NN	_	_	_
1544	growth	growth	NN	_	_	_
1545	:	:	:	_	_	_
1546	MURI	MURI	NNP	_	_	_
1547	_	_	SYM	_	_	_
1548	089	089	CD	_	_	_
1549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1550	lactate	lactate	NN	_	_	_
1551	_	_	NN	_	_	_
1552	growth	growth	NN	_	_	_
1553	:	:	:	_	_	_
1554	MURI	MURI	NNP	_	_	_
1555	_	_	SYM	_	_	_
1556	090	090	CD	_	_	_
1557	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1558	Lactobacillus	lactobacillus	NN	_	_	_
1559	acidophilus	acidophilus	NN	_	_	_
1560	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1561	lacZ	lacz	NN	GEN	_	_
1562	_	_	NN	_	_	_
1563	0	0	CD	_	_	_
1564	min	min	NN	_	_	_
1565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1566	lacZ	lacz	NN	GEN	_	_
1567	_	_	CD	_	_	_
1568	10	10	CD	_	_	_
1569	min	min	NN	_	_	_
1570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1571	lacZ	lacz	NN	GEN	_	_
1572	_	_	CD	_	_	_
1573	15	15	CD	_	_	_
1574	min	min	NN	_	_	_
1575	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1576	lacZ	lacz	NN	GEN	_	_
1577	_	_	NN	_	_	_
1578	1	1	CD	_	_	_
1579	min	min	NN	_	_	_
1580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1581	lacZ	lacz	NN	GEN	_	_
1582	_	_	NN	_	_	_
1583	2	2	CD	_	_	_
1584	min	min	NN	_	_	_
1585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1586	lacZ	lacz	NN	GEN	_	_
1587	_	_	CD	_	_	_
1588	4	4	CD	_	_	_
1589	min	min	NN	_	_	_
1590	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1591	lacZ	lacz	NN	GEN	_	_
1592	_	_	CD	_	_	_
1593	6	6	CD	_	_	_
1594	min	min	NN	_	_	_
1595	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1596	lacZ	lacz	NN	GEN	_	_
1597	_	_	CD	_	_	_
1598	8	8	CD	_	_	_
1599	min	min	NN	_	_	_
1600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1601	lacZ	lacz	NN	GEN	_	_
1602	_	_	CD	_	_	_
1603	K12	k12	NN	_	_	_
1604	_	_	NN	_	_	_
1605	0	0	CD	_	_	_
1606	_	_	NN	_	_	_
1607	r1	r1	NN	_	_	_
1608	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1609	lacZ	lacz	NN	GEN	_	_
1610	_	_	CD	_	_	_
1611	K12	k12	NN	_	_	_
1612	_	_	NN	_	_	_
1613	120	120	CD	_	_	_
1614	_	_	NN	_	_	_
1615	r1	r1	NN	_	_	_
1616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1617	lacZ	lacz	NN	GEN	_	_
1618	_	_	CD	_	_	_
1619	K12	k12	NN	_	_	_
1620	_	_	CD	_	_	_
1621	30	30	CD	_	_	_
1622	_	_	NN	_	_	_
1623	r1	r1	NN	_	_	_
1624	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1625	lacZ	lacz	NN	GEN	_	_
1626	_	_	CD	_	_	_
1627	K12	k12	NN	_	_	_
1628	_	_	NN	_	_	_
1629	60	60	CD	_	_	_
1630	_	_	NN	_	_	_
1631	r1	r1	NN	_	_	_
1632	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1633	lacZ	lacz	NN	GEN	_	_
1634	_	_	CD	_	_	_
1635	K12	k12	NN	_	_	_
1636	_	_	NN	_	_	_
1637	90	90	CD	_	_	_
1638	_	_	NN	_	_	_
1639	r1	r1	NN	_	_	_
1640	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1641	lacZ	lacz	NN	GEN	_	_
1642	_	_	CD	_	_	_
1643	MG1063	mg1063	NN	_	_	_
1644	_	_	NN	_	_	_
1645	0	0	CD	_	_	_
1646	_	_	NN	_	_	_
1647	r1	r1	NN	_	_	_
1648	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1649	lacZ	lacz	NN	GEN	_	_
1650	_	_	CD	_	_	_
1651	MG1063	mg1063	NN	_	_	_
1652	_	_	NN	_	_	_
1653	0	0	CD	_	_	_
1654	_	_	NN	_	_	_
1655	r2	r2	NN	_	_	_
1656	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1657	lacZ	lacz	NN	GEN	_	_
1658	_	_	CD	_	_	_
1659	MG1063	mg1063	NN	_	_	_
1660	_	_	NN	_	_	_
1661	120	120	CD	_	_	_
1662	_	_	NN	_	_	_
1663	r1	r1	NN	_	_	_
1664	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1665	lacZ	lacz	NN	GEN	_	_
1666	_	_	CD	_	_	_
1667	MG1063	mg1063	NN	_	_	_
1668	_	_	CD	_	_	_
1669	30	30	CD	_	_	_
1670	_	_	NN	_	_	_
1671	r1	r1	NN	_	_	_
1672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1673	lacZ	lacz	NN	GEN	_	_
1674	_	_	CD	_	_	_
1675	MG1063	mg1063	NN	_	_	_
1676	_	_	CD	_	_	_
1677	30	30	CD	_	_	_
1678	_	_	NN	_	_	_
1679	r2	r2	NN	_	_	_
1680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1681	lacZ	lacz	NN	GEN	_	_
1682	_	_	CD	_	_	_
1683	MG1063	mg1063	NN	_	_	_
1684	_	_	NN	_	_	_
1685	60	60	CD	_	_	_
1686	_	_	NN	_	_	_
1687	r1	r1	NN	_	_	_
1688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1689	lacZ	lacz	NN	GEN	_	_
1690	_	_	CD	_	_	_
1691	MG1063	mg1063	NN	_	_	_
1692	_	_	NN	_	_	_
1693	60	60	CD	_	_	_
1694	_	_	NN	_	_	_
1695	r2	r2	NN	_	_	_
1696	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1697	lacZ	lacz	NN	GEN	_	_
1698	_	_	CD	_	_	_
1699	MG1063	mg1063	NN	_	_	_
1700	_	_	NN	_	_	_
1701	90	90	CD	_	_	_
1702	_	_	NN	_	_	_
1703	r1	r1	NN	_	_	_
1704	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1705	lacZ	lacz	NN	GEN	_	_
1706	_	_	CD	_	_	_
1707	MG1063	mg1063	NN	_	_	_
1708	_	_	NN	_	_	_
1709	90	90	CD	_	_	_
1710	_	_	NN	_	_	_
1711	r2	r2	NN	_	_	_
1712	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1713	lacZ	lacz	NN	GEN	_	_
1714	_	_	CD	_	_	_
1715	W1863	w1863	NN	_	_	_
1716	_	_	NN	_	_	_
1717	0	0	CD	_	_	_
1718	_	_	NN	_	_	_
1719	r1	r1	NN	_	_	_
1720	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1721	lacZ	lacz	NN	GEN	_	_
1722	_	_	CD	_	_	_
1723	W1863	w1863	NN	_	_	_
1724	_	_	CD	_	_	_
1725	30	30	CD	_	_	_
1726	_	_	NN	_	_	_
1727	r1	r1	NN	_	_	_
1728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1729	lacZ	lacz	NN	GEN	_	_
1730	_	_	CD	_	_	_
1731	W1863	w1863	NN	_	_	_
1732	_	_	NN	_	_	_
1733	60	60	CD	_	_	_
1734	_	_	NN	_	_	_
1735	r1	r1	NN	_	_	_
1736	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1737	lacZ	lacz	NN	GEN	_	_
1738	_	_	CD	_	_	_
1739	W1863	w1863	NN	_	_	_
1740	_	_	NN	_	_	_
1741	90	90	CD	_	_	_
1742	_	_	NN	_	_	_
1743	r1	r1	NN	_	_	_
1744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1745	LA-log	la-log	NN	_	_	_
1746	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1747	LA-log-tr	la-log-tr	NN	_	_	_
1748	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1749	Lambda	Lambda	NNP	_	_	_
1750	phage	phage	NN	_	_	_
1751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1752	LA-starve	la-starve	JJ	_	_	_
1753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1754	late	late	JJ	_	_	_
1755	log	log	NN	_	_	_
1756	phase	phase	NN	_	_	_
1757	grown	grow	VBN	_	_	_
1758	e	e	SYM	_	_	_
1759	coli	coli	NNS	_	_	_
1760	966	966	CD	_	_	_
1761	into	into	IN	_	_	_
1762	RNAprotect	rnaprotect	NN	_	_	_
1763	solution	solution	NN	_	_	_
1764	,	,	,	_	_	_
1765	RNA	rna	NN	_	_	_
1766	extracted	extract	VBN	_	_	_
1767	with	with	IN	_	_	_
1768	qiagen	qiagen	NN	_	_	_
1769	RNA	rna	NN	_	_	_
1770	bacteria	bacterium	NNS	_	_	_
1771	kits	kit	NNS	_	_	_
1772	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1773	late	late	JJ	_	_	_
1774	log	log	NN	_	_	_
1775	phase	phase	NN	_	_	_
1776	grown	grow	VBN	_	_	_
1777	e	e	SYM	_	_	_
1778	coli	coli	FW	_	_	_
1779	EDL933	edl933	FW	_	_	_
1780	into	into	IN	_	_	_
1781	RNAprotect	rnaprotect	NN	_	_	_
1782	solution	solution	NN	_	_	_
1783	,	,	,	_	_	_
1784	RNA	rna	NN	_	_	_
1785	extracted	extract	VBN	_	_	_
1786	with	with	IN	_	_	_
1787	qiagen	qiagen	NN	_	_	_
1788	RNA	rna	NN	_	_	_
1789	bacteria	bacterium	NNS	_	_	_
1790	kits	kit	NNS	_	_	_
1791	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1792	late	late	JJ	_	_	_
1793	stationary	stationary	JJ	_	_	_
1794	culture	culture	NN	_	_	_
1795	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1796	LA	LA	NNP	_	_	_
1797	_	_	NNP	_	_	_
1798	TP1	tp1	NN	_	_	_
1799	_	_	CD	_	_	_
1800	repl1	repl1	NN	_	_	_
1801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1802	LA	LA	NNP	_	_	_
1803	_	_	NNP	_	_	_
1804	TP1	tp1	NN	_	_	_
1805	_	_	CD	_	_	_
1806	repl2	repl2	NN	_	_	_
1807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1808	LA	LA	NNP	_	_	_
1809	_	_	NNP	_	_	_
1810	TP1	tp1	NN	_	_	_
1811	_	_	CD	_	_	_
1812	repl3	repl3	NN	_	_	_
1813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1814	LA	LA	NNP	_	_	_
1815	_	_	NNP	_	_	_
1816	TP1	tp1	NN	_	_	_
1817	_	_	CD	_	_	_
1818	repl4	repl4	NN	_	_	_
1819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1820	LA	LA	NNP	_	_	_
1821	_	_	NNP	_	_	_
1822	TP1	tp1	NN	_	_	_
1823	_	_	CD	_	_	_
1824	repl5	repl5	NN	_	_	_
1825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1826	LA	LA	NNP	_	_	_
1827	_	_	SYM	_	_	_
1828	TP2	tp2	NN	_	_	_
1829	_	_	CD	_	_	_
1830	repl1	repl1	NN	_	_	_
1831	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1832	LA	LA	NNP	_	_	_
1833	_	_	SYM	_	_	_
1834	TP2	tp2	NN	_	_	_
1835	_	_	CD	_	_	_
1836	repl2	repl2	NN	_	_	_
1837	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1838	LA	LA	NNP	_	_	_
1839	_	_	SYM	_	_	_
1840	TP2	tp2	NN	_	_	_
1841	_	_	CD	_	_	_
1842	repl3	repl3	NN	_	_	_
1843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1844	LA	LA	NNP	_	_	_
1845	_	_	SYM	_	_	_
1846	TP2	tp2	NN	_	_	_
1847	_	_	CD	_	_	_
1848	repl4	repl4	NN	_	_	_
1849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1850	LA	LA	NNP	_	_	_
1851	_	_	SYM	_	_	_
1852	TP2	tp2	NN	_	_	_
1853	_	_	CD	_	_	_
1854	repl5	repl5	NN	_	_	_
1855	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1856	LA	LA	NNP	_	_	_
1857	_	_	SYM	_	_	_
1858	TP3	tp3	NN	_	_	_
1859	_	_	CD	_	_	_
1860	repl1	repl1	NN	_	_	_
1861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1862	LA	LA	NNP	_	_	_
1863	_	_	SYM	_	_	_
1864	TP3	tp3	NN	_	_	_
1865	_	_	CD	_	_	_
1866	repl2	repl2	NN	_	_	_
1867	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1868	LA	LA	NNP	_	_	_
1869	_	_	SYM	_	_	_
1870	TP3	tp3	NN	_	_	_
1871	_	_	CD	_	_	_
1872	repl3	repl3	NN	_	_	_
1873	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1874	LA	LA	NNP	_	_	_
1875	_	_	SYM	_	_	_
1876	TP3	tp3	NN	_	_	_
1877	_	_	CD	_	_	_
1878	repl4	repl4	NN	_	_	_
1879	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1880	LA	LA	NNP	_	_	_
1881	_	_	SYM	_	_	_
1882	TP3	tp3	NN	_	_	_
1883	_	_	CD	_	_	_
1884	repl5	repl5	NN	_	_	_
1885	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1886	LA	LA	NNP	_	_	_
1887	_	_	SYM	_	_	_
1888	TP4	tp4	NN	_	_	_
1889	_	_	CD	_	_	_
1890	repl1	repl1	NN	_	_	_
1891	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1892	LA	LA	NNP	_	_	_
1893	_	_	SYM	_	_	_
1894	TP4	tp4	NN	_	_	_
1895	_	_	CD	_	_	_
1896	repl2	repl2	NN	_	_	_
1897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1898	LA	LA	NNP	_	_	_
1899	_	_	SYM	_	_	_
1900	TP4	tp4	NN	_	_	_
1901	_	_	CD	_	_	_
1902	repl3	repl3	NN	_	_	_
1903	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1904	LA	LA	NNP	_	_	_
1905	_	_	SYM	_	_	_
1906	TP4	tp4	NN	_	_	_
1907	_	_	CD	_	_	_
1908	repl4	repl4	NN	_	_	_
1909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1910	LA	LA	NNP	_	_	_
1911	_	_	SYM	_	_	_
1912	TP4	tp4	NN	_	_	_
1913	_	_	CD	_	_	_
1914	repl5	repl5	NN	_	_	_
1915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1916	LB	lb	NN	_	_	_
1917	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1918	LB	lb	NN	_	_	_
1919	0.4	0.4	CD	_	_	_
1920	B1	b1	NN	_	_	_
1921	TEX	tex	NN	_	_	_
1922	neg	neg	NN	_	_	_
1923	L1	l1	NN	_	_	_
1924	GA	ga	NN	_	_	_
1925	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1926	LB	lb	NN	_	_	_
1927	0.4	0.4	CD	_	_	_
1928	B1	b1	NN	_	_	_
1929	TEX	TEX	NNP	_	_	_
1930	pos	po	VBZ	_	_	_
1931	L1	l1	NN	_	_	_
1932	GA	ga	NN	_	_	_
1933	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1934	LB	lb	NN	_	_	_
1935	0.4	0.4	CD	_	_	_
1936	B2	b2	NN	_	_	_
1937	TEX	TEX	NNP	_	_	_
1938	neg	neg	NNP	_	_	_
1939	L1	l1	NN	_	_	_
1940	HS1	hs1	NN	_	_	_
1941	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1942	LB	lb	NN	_	_	_
1943	0.4	0.4	CD	_	_	_
1944	B2	b2	NN	_	_	_
1945	TEX	TEX	NNP	_	_	_
1946	neg	neg	NNP	_	_	_
1947	L1	l1	NN	_	_	_
1948	HS2	hs2	NN	_	_	_
1949	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1950	LB	lb	NN	_	_	_
1951	0.4	0.4	CD	_	_	_
1952	B2	b2	NN	_	_	_
1953	TEX	TEX	NNP	_	_	_
1954	pos	po	VBZ	_	_	_
1955	L1	l1	NN	_	_	_
1956	HS1	hs1	NN	_	_	_
1957	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1958	LB	lb	NN	_	_	_
1959	0.4	0.4	CD	_	_	_
1960	B2	b2	NN	_	_	_
1961	TEX	TEX	NNP	_	_	_
1962	pos	po	VBZ	_	_	_
1963	L1	l1	NN	_	_	_
1964	HS2	hs2	NN	_	_	_
1965	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1966	LB	lb	NN	_	_	_
1967	2.0	2.0	CD	_	_	_
1968	B1	b1	NN	_	_	_
1969	TEX	tex	NN	_	_	_
1970	neg	neg	NN	_	_	_
1971	L1	l1	NN	_	_	_
1972	GA	ga	NN	_	_	_
1973	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1974	LB	lb	NN	_	_	_
1975	2.0	2.0	CD	_	_	_
1976	B1	b1	NN	_	_	_
1977	TEX	TEX	NNP	_	_	_
1978	neg	neg	NNP	_	_	_
1979	L2	l2	NN	_	_	_
1980	HS2	hs2	NN	_	_	_
1981	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1982	LB	lb	NN	_	_	_
1983	2.0	2.0	CD	_	_	_
1984	B1	b1	NN	_	_	_
1985	TEX	TEX	NNP	_	_	_
1986	pos	po	VBZ	_	_	_
1987	L1	l1	NN	_	_	_
1988	GA	ga	NN	_	_	_
1989	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1990	LB	lb	NN	_	_	_
1991	2.0	2.0	CD	_	_	_
1992	B1	b1	NN	_	_	_
1993	TEX	TEX	NNP	_	_	_
1994	pos	po	VBZ	_	_	_
1995	L2	l2	NN	_	_	_
1996	HS2	hs2	NN	_	_	_
1997	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1998	LB	lb	NN	_	_	_
1999	2.0	2.0	CD	_	_	_
2000	B2	b2	NN	_	_	_
2001	TEX	TEX	NNP	_	_	_
2002	neg	neg	NNP	_	_	_
2003	L1	l1	NN	_	_	_
2004	HS1	hs1	NN	_	_	_
2005	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2006	LB	lb	NN	_	_	_
2007	2.0	2.0	CD	_	_	_
2008	B2	b2	NN	_	_	_
2009	TEX	TEX	NNP	_	_	_
2010	neg	neg	NNP	_	_	_
2011	L1	l1	NN	_	_	_
2012	HS2	hs2	NN	_	_	_
2013	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2014	LB	lb	NN	_	_	_
2015	2.0	2.0	CD	_	_	_
2016	B2	b2	NN	_	_	_
2017	TEX	TEX	NNP	_	_	_
2018	neg	neg	NNP	_	_	_
2019	L2	l2	NN	_	_	_
2020	HS2	hs2	NN	_	_	_
2021	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2022	LB	lb	NN	_	_	_
2023	2.0	2.0	CD	_	_	_
2024	B2	b2	NN	_	_	_
2025	TEX	TEX	NNP	_	_	_
2026	pos	po	VBZ	_	_	_
2027	L1	l1	NN	_	_	_
2028	HS1	hs1	NN	_	_	_
2029	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2030	LB	lb	NN	_	_	_
2031	2.0	2.0	CD	_	_	_
2032	B2	b2	NN	_	_	_
2033	TEX	TEX	NNP	_	_	_
2034	pos	po	VBZ	_	_	_
2035	L1	l1	NN	_	_	_
2036	HS2	hs2	NN	_	_	_
2037	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2038	LB	lb	NN	_	_	_
2039	2.0	2.0	CD	_	_	_
2040	B2	b2	NN	_	_	_
2041	TEX	TEX	NNP	_	_	_
2042	pos	po	VBZ	_	_	_
2043	L2	l2	NN	_	_	_
2044	HS2	hs2	NN	_	_	_
2045	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2046	LB	lb	NN	_	_	_
2047	,	,	,	_	_	_
2048	37	37	CD	_	_	_
2049	°C	°c	NN	_	_	_
2050	,	,	,	_	_	_
2051	220	220	CD	_	_	_
2052	rpm	rpm	NN	_	_	_
2053	,	,	,	_	_	_
2054	OD600	od600	NN	_	_	_
2055	=	=	JJ	_	_	_
2056	0.5	0.5	CD	_	_	_
2057	,	,	,	_	_	_
2058	2.0	2.0	CD	_	_	_
2059	,	,	,	_	_	_
2060	2.0	2.0	CD	_	_	_
2061	+6	+6	CD	_	_	_
2062	h	h	NN	_	_	_
2063	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2064	LB	lb	NN	_	_	_
2065	-LRB-	-lrb-	-LRB-	_	_	_
2066	5	5	CD	_	_	_
2067	ml	ml	NN	_	_	_
2068	-RRB-	-rrb-	-RRB-	_	_	_
2069	was	be	VBD	_	_	_
2070	inoculated	inoculate	VBN	_	_	_
2071	by	by	IN	_	_	_
2072	a	a	DT	_	_	_
2073	frozen	frozen	JJ	_	_	_
2074	stock	stock	NN	_	_	_
2075	of	of	IN	_	_	_
2076	WT	WT	NNP	_	_	_
2077	or	or	CC	_	_	_
2078	perC-mutant	perc-mutant	JJ	_	_	_
2079	strain	strain	NN	_	_	_
2080	and	and	CC	_	_	_
2081	incubated	incubate	VBN	_	_	_
2082	at	at	IN	_	_	_
2083	37	37	CD	_	_	_
2084	°C	°c	NN	_	_	_
2085	with	with	IN	_	_	_
2086	225	225	CD	_	_	_
2087	rpm	rpm	NN	_	_	_
2088	shaking	shake	VBG	_	_	_
2089	.	.	.	_	_	_

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	LB	LB	NNP	_	_	_
3	agar	agar	NN	_	_	_
4	plates	plate	NNS	_	_	_
5	,	,	,	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	for	for	IN	_	_	_
9	18	18	CD	_	_	_
10	h	h	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	LB	lb	NN	_	_	_
13	,	,	,	_	_	_
14	biological	biological	JJ	_	_	_
15	rep1	rep1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	LB	lb	NN	_	_	_
18	,	,	,	_	_	_
19	biological	biological	JJ	_	_	_
20	rep2	rep2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	LB	lb	NN	_	_	_
23	,	,	,	_	_	_
24	biological	biological	JJ	_	_	_
25	rep3	rep3	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	LB	lb	NN	_	_	_
28	+	+	CC	_	_	_
29	glycerol	glycerol	NN	SUPP	_	_
30	,	,	,	_	_	_
31	biological	biological	JJ	_	_	_
32	rep1	rep1	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	LB	lb	NN	_	_	_
35	+	+	CC	_	_	_
36	glycerol	glycerol	NN	SUPP	_	_
37	,	,	,	_	_	_
38	biological	biological	JJ	_	_	_
39	rep2	rep2	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	LB	lb	NN	_	_	_
42	+	+	CC	_	_	_
43	glycerol	glycerol	NN	SUPP	_	_
44	,	,	,	_	_	_
45	biological	biological	JJ	_	_	_
46	rep3	rep3	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	LB-grown	lb-grown	JJ	_	_	_
49	overnight	overnight	JJ	_	_	_
50	cultures	culture	NNS	_	_	_
51	were	be	VBD	_	_	_
52	pelleted	pellete	VBN	_	_	_
53	by	by	IN	_	_	_
54	centrifugation	centrifugation	NN	_	_	_
55	,	,	,	_	_	_
56	washed	wash	VBN	_	_	_
57	,	,	,	_	_	_
58	and	and	CC	_	_	_
59	resuspended	resuspend	VBN	_	_	_
60	in	in	IN	_	_	_
61	M9-glutamine	m9-glutamine	NN	_	_	_
62	of	of	IN	_	_	_
63	M9-alanine	m9-alanine	NN	_	_	_
64	media	media	NNS	_	_	_
65	.	.	.	_	_	_

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	NNP	_	_	_
2	LB	LB	NNP	MED	_	_
3	media	media	NNS	MED	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	LB	lb	NN	MED	_	_
6	medium	medium	NN	MED	_	_
7	,	,	,	_	_	_
8	180	180	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	shaking	shake	VBG	_	_	_
11	,	,	,	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	,	,	,	_	_	_
16	between	between	IN	_	_	_
17	exponential	exponential	JJ	_	_	_
18	and	and	CC	_	_	_
19	stationary	stationary	JJ	GrowthPhase	_	_
20	phase	phase	NN	GrowthPhase	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	LB	lb	NN	MED	_	_
23	medium	medium	NN	MED	_	_
24	,	,	,	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	,	,	,	_	_	_
28	airated	airate	VBN	_	_	_
29	,	,	,	_	_	_
30	constant	constant	JJ	_	_	_
31	pH	ph	NN	_	_	_
32	7.5	7.5	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	LB	lb	NN	MED	_	_
35	medium	medium	NN	MED	_	_
36	at	at	IN	_	_	_
37	37ºC	37ºc	NN	_	_	_
38	with	with	IN	_	_	_
39	200rpm	200rpm	JJ	_	_	_
40	agitation	agitation	NN	_	_	_
41	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	LB	lb	NN	_	_	_
3	mRNA	mrna	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	LB	lb	NN	_	_	_
6	mRNA	mrna	NN	_	_	_
7	biological	biological	JJ	_	_	_
8	replicate	replicate	VBP	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	LB	lb	NN	_	_	_
11	mRNA	mrna	NN	_	_	_
12	technical	technical	JJ	_	_	_
13	replicate	replicate	VB	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	LBO	LBO	NNP	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	LB	lb	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	OD	od	NN	_	_	_
20	=	=	JJ	_	_	_
21	0.87	0.87	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	LB	LB	NNP	_	_	_
25	RPF	RPF	NNP	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	LB	LB	NNP	_	_	_
28	RPF	RPF	NNP	_	_	_
29	biological	biological	JJ	_	_	_
30	replicate	replicate	VB	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	LBTMP50	lbtmp50	NN	_	_	_
33	_	_	CD	_	_	_
34	10	10	CD	_	_	_
35	min	min	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	LBTMP50	lbtmp50	NN	_	_	_
38	_	_	NN	_	_	_
39	120	120	CD	_	_	_
40	min	min	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	LBTMP50	lbtmp50	NN	_	_	_
43	_	_	CD	_	_	_
44	30	30	CD	_	_	_
45	min	min	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	LBTMP50	lbtmp50	NN	_	_	_
48	_	_	CD	_	_	_
49	60	60	CD	_	_	_
50	min	min	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	LC1	lc1	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	ldrA	ldra	NN	GEN	_	_
55	__	__	CD	_	_	_
56	U	U	NNP	_	_	_
57	_	_	NNP	_	_	_
58	N0075	N0075	NNP	_	_	_
59	_	_	VBD	_	_	_
60	r1	r1	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	ldrA	ldra	NN	GEN	_	_
63	__	__	CD	_	_	_
64	U	U	NNP	_	_	_
65	_	_	NNP	_	_	_
66	N0075	N0075	NNP	_	_	_
67	_	_	VBD	_	_	_
68	r2	r2	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	ldrA	ldra	NN	GEN	_	_
71	__	__	CD	_	_	_
72	U	U	NNP	_	_	_
73	_	_	NNP	_	_	_
74	N0075	N0075	NNP	_	_	_
75	_	_	VBD	_	_	_
76	r3	r3	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	ldrA	ldra	NN	GEN	_	_
79	upregulation	upregulation	NN	_	_	_
80	,	,	,	_	_	_
81	0.075	0.075	CD	_	_	_
82	mg/mL	mg/ml	NN	_	_	_
83	norfloxacin	norfloxacin	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	LE-co1	le-co1	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	LE-co2	le-co2	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	LELab	lelab	NN	_	_	_
90	_	_	CD	_	_	_
91	ChIP	chip	NN	_	_	_
92	_	_	SYM	_	_	_
93	seq	seq	FW	_	_	_
94	_	_	FW	_	_	_
95	TLS1637	tls1637	NN	_	_	_
96	_	_	NN	_	_	_
97	anti	anti	JJ	_	_	_
98	_	_	CD	_	_	_
99	FLAG	flag	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	LELab	lelab	NN	_	_	_
102	_	_	CD	_	_	_
103	ChIP	chip	NN	_	_	_
104	_	_	SYM	_	_	_
105	seq	seq	FW	_	_	_
106	_	_	FW	_	_	_
107	TLS1638	tls1638	NN	_	_	_
108	_	_	NN	_	_	_
109	anti	anti	JJ	_	_	_
110	_	_	CD	_	_	_
111	FLAG	flag	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	LELab	lelab	NN	_	_	_
114	_	_	CD	_	_	_
115	ChIP	chip	NN	_	_	_
116	_	_	SYM	_	_	_
117	seq	seq	FW	_	_	_
118	_	_	FW	_	_	_
119	TLS1639	tls1639	NN	_	_	_
120	_	_	NN	_	_	_
121	anti	anti	JJ	_	_	_
122	_	_	CD	_	_	_
123	FLAG	flag	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	LELab	lelab	NN	_	_	_
126	_	_	CD	_	_	_
127	ChIP	chip	NN	_	_	_
128	_	_	SYM	_	_	_
129	seq	seq	FW	_	_	_
130	_	_	FW	_	_	_
131	TLS1640	tls1640	NN	_	_	_
132	_	_	NN	_	_	_
133	anti	anti	JJ	_	_	_
134	_	_	CD	_	_	_
135	FLAG	flag	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	LELab	lelab	NN	_	_	_
138	_	_	CD	_	_	_
139	ChIP	chip	NN	_	_	_
140	_	_	SYM	_	_	_
141	seq	seq	FW	_	_	_
142	_	_	FW	_	_	_
143	TLS1641	tls1641	NN	_	_	_
144	_	_	NN	_	_	_
145	anti	anti	JJ	_	_	_
146	_	_	CD	_	_	_
147	FLAG	flag	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	LELab	lelab	NN	_	_	_
150	_	_	CD	_	_	_
151	ChIP	chip	NN	_	_	_
152	_	_	SYM	_	_	_
153	seq	seq	FW	_	_	_
154	_	_	FW	_	_	_
155	TLS1642	tls1642	NN	_	_	_
156	_	_	NN	_	_	_
157	anti	anti	JJ	_	_	_
158	_	_	CD	_	_	_
159	FLAG	flag	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	LELAb	lelab	NN	_	_	_
162	_	_	CD	_	_	_
163	ChIP	chip	NN	_	_	_
164	_	_	SYM	_	_	_
165	seq	seq	FW	_	_	_
166	_	_	FW	_	_	_
167	TLS1643	tls1643	NN	_	_	_
168	_	_	NN	_	_	_
169	anti	anti	JJ	_	_	_
170	_	_	CD	_	_	_
171	FLAG	flag	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	LELab	lelab	NN	_	_	_
174	_	_	CD	_	_	_
175	ChIP	chip	NN	_	_	_
176	_	_	SYM	_	_	_
177	seq	seq	FW	_	_	_
178	_	_	FW	_	_	_
179	TLS1644	tls1644	NN	_	_	_
180	_	_	NN	_	_	_
181	anti	anti	JJ	_	_	_
182	_	_	CD	_	_	_
183	FLAG	flag	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	LELab	lelab	NN	_	_	_
186	_	_	CD	_	_	_
187	ChIP	chip	NN	_	_	_
188	_	_	SYM	_	_	_
189	seq	seq	FW	_	_	_
190	_	_	FW	_	_	_
191	TLS1645	tls1645	NN	_	_	_
192	_	_	NN	_	_	_
193	anti	anti	JJ	_	_	_
194	_	_	CD	_	_	_
195	FLAG	flag	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	LELab	lelab	NN	_	_	_
198	_	_	CD	_	_	_
199	ChIP	chip	NN	_	_	_
200	_	_	SYM	_	_	_
201	seq	seq	FW	_	_	_
202	_	_	FW	_	_	_
203	TLS1646	tls1646	NN	_	_	_
204	_	_	NN	_	_	_
205	anti	anti	JJ	_	_	_
206	_	_	CD	_	_	_
207	FLAG	flag	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	LELab	lelab	NN	_	_	_
210	_	_	CD	_	_	_
211	ChIP	chip	NN	_	_	_
212	_	_	SYM	_	_	_
213	seq	seq	FW	_	_	_
214	_	_	FW	_	_	_
215	TLS1647	tls1647	NN	_	_	_
216	_	_	NN	_	_	_
217	anti	anti	JJ	_	_	_
218	_	_	CD	_	_	_
219	FLAG	flag	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	LELab	lelab	NN	_	_	_
222	_	_	CD	_	_	_
223	ChIP	chip	NN	_	_	_
224	_	_	SYM	_	_	_
225	seq	seq	FW	_	_	_
226	_	_	FW	_	_	_
227	TLS1648	tls1648	NN	_	_	_
228	_	_	NN	_	_	_
229	anti	anti	JJ	_	_	_
230	_	_	CD	_	_	_
231	FLAG	flag	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	LELab	lelab	NN	_	_	_
234	_	_	CD	_	_	_
235	ChIP	chip	NN	_	_	_
236	_	_	SYM	_	_	_
237	seq	seq	FW	_	_	_
238	_	_	FW	_	_	_
239	TLS1649	tls1649	NN	_	_	_
240	_	_	NN	_	_	_
241	anti	anti	JJ	_	_	_
242	_	_	CD	_	_	_
243	FLAG	flag	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	LELab	lelab	NN	_	_	_
246	_	_	CD	_	_	_
247	ChIP	chip	NN	_	_	_
248	_	_	SYM	_	_	_
249	seq	seq	FW	_	_	_
250	_	_	FW	_	_	_
251	TLS1650	tls1650	NN	_	_	_
252	_	_	NN	_	_	_
253	anti	anti	JJ	_	_	_
254	_	_	CD	_	_	_
255	FLAG	flag	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	LE-log	le-log	JJ	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	LE-log-tr	le-log-tr	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	LE-starve	le-starve	JJ	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	-	-	:	_	_	_
264	Leu	leu	NN	_	_	_
265	t	t	NN	_	_	_
266	=	=	JJ	_	_	_
267	0	0	CD	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	-	-	:	_	_	_
270	Leu	leu	NN	_	_	_
271	t	t	NN	_	_	_
272	=	=	JJ	_	_	_
273	0	0	CD	_	_	_
274	charged	charge	VBN	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
276	-	-	:	_	_	_
277	Leu	leu	NN	_	_	_
278	t	t	NN	_	_	_
279	=	=	JJ	_	_	_
280	0	0	CD	_	_	_
281	total	total	JJ	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	-	-	:	_	_	_
284	Leu	leu	NN	_	_	_
285	t	t	NN	_	_	_
286	=	=	JJ	_	_	_
287	17	17	CD	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	-	-	:	_	_	_
290	Leu	leu	NN	_	_	_
291	t	t	NN	_	_	_
292	=	=	JJ	_	_	_
293	17	17	CD	_	_	_
294	charged	charge	VBN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
296	-	-	:	_	_	_
297	Leu	leu	NN	_	_	_
298	t	t	NN	_	_	_
299	=	=	JJ	_	_	_
300	17	17	CD	_	_	_
301	total	total	JJ	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	-	-	:	_	_	_
304	Leu	leu	NN	_	_	_
305	t	t	NN	_	_	_
306	=	=	JJ	_	_	_
307	2	2	CD	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	-	-	:	_	_	_
310	Leu	leu	NN	_	_	_
311	t	t	NN	_	_	_
312	=	=	JJ	_	_	_
313	2	2	CD	_	_	_
314	charged	charge	VBN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
316	-	-	:	_	_	_
317	Leu	leu	NN	_	_	_
318	t	t	NN	_	_	_
319	=	=	JJ	_	_	_
320	2	2	CD	_	_	_
321	total	total	JJ	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	-	-	:	_	_	_
324	Leu	leu	NN	_	_	_
325	t	t	NN	_	_	_
326	=	=	JJ	_	_	_
327	32	32	CD	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	-	-	:	_	_	_
330	Leu	leu	NN	_	_	_
331	t	t	NN	_	_	_
332	=	=	JJ	_	_	_
333	32	32	CD	_	_	_
334	charged	charge	VBN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
336	-	-	:	_	_	_
337	Leu	leu	NN	_	_	_
338	t	t	NN	_	_	_
339	=	=	JJ	_	_	_
340	32	32	CD	_	_	_
341	total	total	JJ	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	-	-	:	_	_	_
344	Leu	leu	NN	_	_	_
345	t	t	NN	_	_	_
346	=	=	JJ	_	_	_
347	7	7	CD	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	-	-	:	_	_	_
350	Leu	leu	NN	_	_	_
351	t	t	NN	_	_	_
352	=	=	JJ	_	_	_
353	7	7	CD	_	_	_
354	charged	charge	VBN	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
356	-	-	:	_	_	_
357	Leu	leu	NN	_	_	_
358	t	t	NN	_	_	_
359	=	=	JJ	_	_	_
360	7	7	CD	_	_	_
361	total	total	JJ	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
363	lexA	lexa	NN	GEN	_	_
364	10	10	CD	_	_	_
365	'	'	''	_	_	_
366	after	after	IN	_	_	_
367	UV	uv	NN	_	_	_
368	vs.	vs.	CC	_	_	_
369	0	0	CD	_	_	_
370	'	'	''	_	_	_
371	,	,	,	_	_	_
372	MG1655	mg1655	NN	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	lexA	lexa	NN	GEN	_	_
375	10	10	CD	_	_	_
376	min	min	NN	_	_	_
377	after	after	IN	_	_	_
378	UV	uv	NN	_	_	_
379	treatment	treatment	NN	_	_	_
380	,	,	,	_	_	_
381	25	25	CD	_	_	_
382	ug	ug	NN	_	_	_
383	total	total	JJ	_	_	_
384	RNA	rna	NN	_	_	_
385	,	,	,	_	_	_
386	2	2	CD	_	_	_
387	ug	ug	NN	_	_	_
388	pdN6	pdn6	NN	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	lexA	lexa	NN	GEN	_	_
391	20	20	CD	_	_	_
392	'	'	''	_	_	_
393	after	after	IN	_	_	_
394	NOuv	NOuv	NNP	_	_	_
395	vs.	vs.	CC	_	_	_
396	0	0	CD	_	_	_
397	'	'	''	_	_	_
398	,	,	,	_	_	_
399	MG1655	mg1655	NN	_	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	lexA	lexa	NN	GEN	_	_
402	20	20	CD	_	_	_
403	'	'	''	_	_	_
404	after	after	IN	_	_	_
405	UV	uv	NN	_	_	_
406	vs.	vs.	CC	_	_	_
407	0	0	CD	_	_	_
408	'	'	''	_	_	_
409	,	,	,	_	_	_
410	MG1655	mg1655	NN	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	lexA	lexa	NN	GEN	_	_
413	20	20	CD	_	_	_
414	min	min	NN	_	_	_
415	after	after	IN	_	_	_
416	NOuv	NOuv	NNP	_	_	_
417	,	,	,	_	_	_
418	25	25	CD	_	_	_
419	ug	ug	NN	_	_	_
420	total	total	JJ	_	_	_
421	RNA	rna	NN	_	_	_
422	,	,	,	_	_	_
423	2	2	CD	_	_	_
424	ug	ug	NN	_	_	_
425	pdN6	pdn6	NN	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	lexA	lexa	NN	GEN	_	_
428	20	20	CD	_	_	_
429	min	min	NN	_	_	_
430	after	after	IN	_	_	_
431	UV	uv	NN	_	_	_
432	treatment	treatment	NN	_	_	_
433	,	,	,	_	_	_
434	25	25	CD	_	_	_
435	ug	ug	NN	_	_	_
436	total	total	JJ	_	_	_
437	RNA	rna	NN	_	_	_
438	,	,	,	_	_	_
439	2	2	CD	_	_	_
440	ug	ug	NN	_	_	_
441	pdN6	pdn6	NN	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	lexA	lexa	NN	GEN	_	_
444	40	40	CD	_	_	_
445	'	'	''	_	_	_
446	after	after	IN	_	_	_
447	UV	uv	NN	_	_	_
448	vs.	vs.	CC	_	_	_
449	0	0	CD	_	_	_
450	'	'	''	_	_	_
451	,	,	,	_	_	_
452	MG1655	mg1655	NN	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	lexA	lexa	NN	GEN	_	_
455	40	40	CD	_	_	_
456	min	min	NN	_	_	_
457	after	after	IN	_	_	_
458	UV	uv	NN	_	_	_
459	treatment	treatment	NN	_	_	_
460	,	,	,	_	_	_
461	25	25	CD	_	_	_
462	ug	ug	NN	_	_	_
463	total	total	JJ	_	_	_
464	RNA	rna	NN	_	_	_
465	,	,	,	_	_	_
466	2	2	CD	_	_	_
467	ug	ug	NN	_	_	_
468	pdN6	pdn6	NN	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
470	lexA	lexa	NN	GEN	_	_
471	5	5	CD	_	_	_
472	'	'	''	_	_	_
473	after	after	IN	_	_	_
474	UV	uv	NN	_	_	_
475	vs.	vs.	CC	_	_	_
476	0	0	CD	_	_	_
477	'	'	''	_	_	_
478	,	,	,	_	_	_
479	MG1655	mg1655	NN	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	lexA	lexa	NN	GEN	_	_
482	5	5	CD	_	_	_
483	min	min	NN	_	_	_
484	after	after	IN	_	_	_
485	UV	uv	NN	_	_	_
486	treatment	treatment	NN	_	_	_
487	,	,	,	_	_	_
488	25	25	CD	_	_	_
489	ug	ug	NN	_	_	_
490	total	total	JJ	_	_	_
491	RNA	rna	NN	_	_	_
492	,	,	,	_	_	_
493	2	2	CD	_	_	_
494	ug	ug	NN	_	_	_
495	pdN6	pdn6	NN	_	_	_
496	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
497	lexA	lexa	NN	GEN	_	_
498	60	60	CD	_	_	_
499	'	'	''	_	_	_
500	after	after	IN	_	_	_
501	NOuv	NOuv	NNP	_	_	_
502	vs.	vs.	CC	_	_	_
503	0	0	CD	_	_	_
504	'	'	''	_	_	_
505	,	,	,	_	_	_
506	MG1655	mg1655	NN	_	_	_
507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
508	lexA	lexa	NN	GEN	_	_
509	60	60	CD	_	_	_
510	'	'	''	_	_	_
511	after	after	IN	_	_	_
512	UV	uv	NN	_	_	_
513	vs.	vs.	CC	_	_	_
514	0	0	CD	_	_	_
515	'	'	''	_	_	_
516	,	,	,	_	_	_
517	MG1655	mg1655	NN	_	_	_
518	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
519	lexA	lexa	NN	GEN	_	_
520	60	60	CD	_	_	_
521	min	min	NN	_	_	_
522	after	after	IN	_	_	_
523	NOuv	NOuv	NNP	_	_	_
524	,	,	,	_	_	_
525	25	25	CD	_	_	_
526	ug	ug	NN	_	_	_
527	total	total	JJ	_	_	_
528	RNA	rna	NN	_	_	_
529	,	,	,	_	_	_
530	2	2	CD	_	_	_
531	ug	ug	NN	_	_	_
532	pdN6	pdn6	NN	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	lexA	lexa	NN	GEN	_	_
535	60	60	CD	_	_	_
536	min	min	NN	_	_	_
537	after	after	IN	_	_	_
538	UV	uv	NN	_	_	_
539	treatment	treatment	NN	_	_	_
540	,	,	,	_	_	_
541	25	25	CD	_	_	_
542	ug	ug	NN	_	_	_
543	total	total	JJ	_	_	_
544	RNA	rna	NN	_	_	_
545	,	,	,	_	_	_
546	2	2	CD	_	_	_
547	ug	ug	NN	_	_	_
548	pdN6	pdn6	NN	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	lexA	lexa	NN	GEN	_	_
551	___	___	CD	_	_	_
552	U	U	NNP	_	_	_
553	_	_	NNP	_	_	_
554	N0025	N0025	NNP	_	_	_
555	_	_	SYM	_	_	_
556	r1	r1	FW	_	_	_
557	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
558	lexA	lexa	NN	GEN	_	_
559	___	___	CD	_	_	_
560	U	U	NNP	_	_	_
561	_	_	NNP	_	_	_
562	N0025	N0025	NNP	_	_	_
563	_	_	SYM	_	_	_
564	r2	r2	FW	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
566	lexA	lexa	NN	GEN	_	_
567	___	___	CD	_	_	_
568	U	U	NNP	_	_	_
569	_	_	NNP	_	_	_
570	N0025	N0025	NNP	_	_	_
571	_	_	SYM	_	_	_
572	r3	r3	FW	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
574	lexA	lexa	NN	GEN	_	_
575	upregulation	upregulation	NN	_	_	_
576	,	,	,	_	_	_
577	amp	amp	NN	_	_	_
578	50ug/ml	50ug/ml	NN	_	_	_
579	,	,	,	_	_	_
580	0.0125	0.0125	CD	_	_	_
581	%	%	NN	_	_	_
582	arabinose	arabinose	NN	_	_	_
583	,	,	,	_	_	_
584	0.025	0.025	CD	_	_	_
585	ug/ml	ug/ml	NN	_	_	_
586	norfloxacin	norfloxacin	NN	_	_	_
587	OD	od	NN	_	_	_
588	~	~	NN	_	_	_
589	0.3	0.3	CD	_	_	_
590	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
591	lexA	lexa	NN	GEN	_	_
592	vs.	vs.	CC	_	_	_
593	wt	wt	JJ	_	_	_
594	,	,	,	_	_	_
595	before	before	IN	_	_	_
596	UV	uv	NN	_	_	_
597	treatment	treatment	NN	_	_	_
598	,	,	,	_	_	_
599	MG1655	mg1655	NN	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
601	L-form	l-form	NN	_	_	_
602	,	,	,	_	_	_
603	brain	brain	NN	_	_	_
604	heart	heart	NN	_	_	_
605	infusion	infusion	NN	_	_	_
606	agar	agar	NN	_	_	_
607	+	+	CC	_	_	_
608	Sucrose	sucrose	NN	_	_	_
609	+	+	CC	_	_	_
610	MgSO4	mgso4	NN	_	_	_
611	+	+	CC	_	_	_
612	Pen	pen	NN	_	_	_
613	G	g	NN	_	_	_
614	,	,	,	_	_	_
615	rep	rep	NN	GEN	_	_
616	1	1	CD	_	_	_
617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
618	L-form	l-form	NN	_	_	_
619	,	,	,	_	_	_
620	brain	brain	NN	_	_	_
621	heart	heart	NN	_	_	_
622	infusion	infusion	NN	_	_	_
623	agar	agar	NN	_	_	_
624	+	+	CC	_	_	_
625	Sucrose	sucrose	NN	_	_	_
626	+	+	CC	_	_	_
627	MgSO4	mgso4	NN	_	_	_
628	+	+	CC	_	_	_
629	Pen	pen	NN	_	_	_
630	G	g	NN	_	_	_
631	,	,	,	_	_	_
632	rep	rep	NN	GEN	_	_
633	2	2	CD	_	_	_
634	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
635	L-form	l-form	NN	_	_	_
636	,	,	,	_	_	_
637	brain	brain	NN	_	_	_
638	heart	heart	NN	_	_	_
639	infusion	infusion	NN	_	_	_
640	agar	agar	NN	_	_	_
641	+	+	CC	_	_	_
642	Sucrose	sucrose	NN	_	_	_
643	+	+	CC	_	_	_
644	MgSO4	mgso4	NN	_	_	_
645	+	+	CC	_	_	_
646	Pen	pen	NN	_	_	_
647	G	g	NN	_	_	_
648	,	,	,	_	_	_
649	rep	rep	NN	GEN	_	_
650	3	3	CD	_	_	_
651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
652	L-form	l-form	JJ	_	_	_
653	colony	colony	NN	_	_	_
654	morphology	morphology	NN	_	_	_
655	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
656	Libraries	Libraries	NNPS	_	_	_
657	for	for	IN	_	_	_
658	Illumina	Illumina	NNP	_	_	_
659	HiSeq	HiSeq	NNP	_	_	_
660	1000	1000	CD	_	_	_
661	sequencing	sequencing	NN	_	_	_
662	using	use	VBG	_	_	_
663	the	the	DT	_	_	_
664	Truseq	Truseq	NNP	_	_	_
665	kit	kit	NN	_	_	_
666	were	be	VBD	_	_	_
667	prepared	prepare	VBN	_	_	_
668	using	use	VBG	_	_	_
669	protocols	protocol	NNS	_	_	_
670	recommended	recommend	VBN	_	_	_
671	by	by	IN	_	_	_
672	the	the	DT	_	_	_
673	manufacturer	manufacturer	NN	_	_	_
674	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Libraries	Libraries	NNPS	_	_	_
3	of	of	IN	_	_	_
4	RNA	rna	NN	_	_	_
5	fractions	fraction	NNS	_	_	_
6	were	be	VBD	_	_	_
7	constructed	construct	VBN	_	_	_
8	with	with	IN	_	_	_
9	the	the	DT	_	_	_
10	ScriptSeq	ScriptSeq	NNP	_	_	_
11	V2	v2	NN	_	_	_
12	RNA-Seq	rna-seq	NN	_	_	_
13	Library	Library	NNP	_	_	_
14	Prep	Prep	NNP	_	_	_
15	Kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Illumina	Illumina	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	according	accord	VBG	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	manufacturers	manufacturer	NNS	_	_	_
23	guidelines	guideline	NNS	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Libraries	Libraries	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	constructed	construct	VBN	_	_	_
5	by	by	IN	_	_	_
6	vertis	vertis	NN	_	_	_
7	Biotechnologie	Biotechnologie	NNP	_	_	_
8	AG	AG	NNP	_	_	_
9	,	,	,	_	_	_
10	Germany	Germany	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	www.vertis-biotech.com	www.vertis-biotech.com	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	as	as	IN	_	_	_
15	a	a	DT	_	_	_
16	service	service	NN	_	_	_
17	that	that	WDT	_	_	_
18	included	include	VBD	_	_	_
19	treating	treat	VBG	_	_	_
20	an	a	DT	_	_	_
21	aliquot	aliquot	NN	_	_	_
22	of	of	IN	_	_	_
23	each	each	DT	_	_	_
24	RNA	rna	NN	_	_	_
25	sample	sample	NN	_	_	_
26	with	with	IN	_	_	_
27	TAP	tap	NN	_	_	_
28	.	.	.	_	_	_

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	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	DNA	dna	NN	_	_	_
13	Sample	sample	NN	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	FC-104-5001	fc-104-5001	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

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	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	VBN	_	_	_
12	up/concentrated	up/concentrated	VBN	_	_	_
13	through	through	IN	_	_	_
14	a	a	DT	_	_	_
15	Qiagen	Qiagen	NNP	_	_	_
16	PCR	pcr	NN	_	_	_
17	column	column	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	end-repaired	end-repaired	JJ	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	blunt	blunt	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	Klenow	Klenow	NNP	_	_	_
8	fragment	fragment	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	exo	exo	NN	_	_	_
11	minus	minus	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	to	to	TO	_	_	_
14	add	add	VB	GEN	_	_
15	an	a	DT	_	_	_
16	A-overhang	a-overhang	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	ligated	ligate	VBN	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	relevant	relevant	JJ	_	_	_
23	Illumina	Illumina	NNP	_	_	_
24	adapter	adapter	NN	_	_	_
25	sequence	sequence	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	either	either	CC	_	_	_
28	with	with	IN	_	_	_
29	our	we	PRP$	_	_	_
30	without	without	IN	_	_	_
31	a	a	DT	_	_	_
32	barcode	barcode	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	Adaptered-DNA	adaptered-dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	size-selected	size-selected	JJ	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	agarose	agarose	NN	_	_	_
8	gel	gel	NN	_	_	_
9	and	and	CC	_	_	_
10	PCR	pcr	NN	_	_	_
11	amplified	amplify	VBD	_	_	_
12	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	purified	purify	VBN	_	_	_
3	PCR	pcr	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	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	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	VBN	_	_	_
12	up/concentrated	up/concentrated	VBN	_	_	_
13	through	through	IN	_	_	_
14	a	a	DT	_	_	_
15	Qiagen	Qiagen	NNP	_	_	_
16	PCR	pcr	NN	_	_	_
17	column	column	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	end-repaired	end-repaired	JJ	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	blunt	blunt	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	Klenow	Klenow	NNP	_	_	_
8	fragment	fragment	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	exo	exo	NN	_	_	_
11	minus	minus	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	to	to	TO	_	_	_
14	add	add	VB	GEN	_	_
15	an	a	DT	_	_	_
16	A-overhang	a-overhang	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	ligated	ligate	VBN	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	relevant	relevant	JJ	_	_	_
23	Illumina	Illumina	NNP	_	_	_
24	adapter	adapter	NN	_	_	_
25	sequence	sequence	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	either	either	CC	_	_	_
28	with	with	IN	_	_	_
29	our	we	PRP$	_	_	_
30	without	without	IN	_	_	_
31	a	a	DT	_	_	_
32	barcode	barcode	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	Adaptered-DNA	adaptered-dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	size-selected	size-selected	JJ	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	agarose	agarose	NN	_	_	_
8	gel	gel	NN	_	_	_
9	and	and	CC	_	_	_
10	PCR	pcr	NN	_	_	_
11	amplified	amplify	VBD	_	_	_
12	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	purified	purify	VBN	_	_	_
3	PCR	pcr	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.library	protocols.library	JJ	_	_	_
13	strategy	strategy	NN	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Libraries	Libraries	NNPS	_	_	_
16	were	be	VBD	_	_	_
17	prepared	prepare	VBN	_	_	_
18	for	for	IN	_	_	_
19	sequencing	sequencing	NN	_	_	_
20	using	use	VBG	_	_	_
21	standard	standard	JJ	_	_	_
22	Illumina	Illumina	NNP	_	_	_
23	protocols	protocol	NNS	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Library	Library	NNP	_	_	_
26	constructed	construct	VBN	_	_	_
27	using	use	VBG	_	_	_
28	KAPA	KAPA	NNP	_	_	_
29	Kit	kit	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	library	library	NN	_	_	_
3	construction	construction	NN	_	_	_
4	followed	follow	VBD	_	_	_
5	Illumina	Illumina	NNP	_	_	_
6	manufacturer	manufacturer	NN	_	_	_
7	protocol	protocol	NN	_	_	_
8	for	for	IN	_	_	_
9	bacteria	bacterium	NNS	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	Nextera	Nextera	NNP	_	_	_
13	XT	XT	NNP	_	_	_
14	DNA	DNA	NNP	_	_	_
15	Library	Library	NNP	_	_	_
16	Preparation	Preparation	NNP	_	_	_
17	Kit	kit	NN	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Library	Library	NNP	_	_	_
20	construction	construction	NN	_	_	_
21	was	be	VBD	_	_	_
22	based	base	VBN	_	_	_
23	on	on	IN	_	_	_
24	the	the	DT	_	_	_
25	method	method	NN	_	_	_
26	described	describe	VBN	_	_	_
27	by	by	IN	_	_	_
28	Rhee	Rhee	NNP	_	_	_
29	et	et	FW	_	_	_
30	al.	al.	FW	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	doi	doi	FW	_	_	_
33	:	:	:	_	_	_
34	10.1016	10.1016	CD	_	_	_
35	/	/	:	_	_	_
36	j.cell	j.cell	JJ	_	_	_
37	.2011.11.013	.2011.11.013	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Library	Library	NNP	_	_	_
3	construction	construction	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	as	as	IN	_	_	_
7	described	describe	VBN	_	_	_
8	in	in	IN	_	_	_
9	Oh	oh	UH	_	_	_
10	et	et	FW	_	_	_
11	al.	al.	FW	_	_	_
12	2011	2011	CD	_	_	_
13	,	,	,	_	_	_
14	Cell	cell	NN	_	_	_
15	147	147	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	6	6	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	:	:	:	_	_	_
20	1295-1308	1295-1308	CD	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	PMCID	pmcid	NN	_	_	_
23	:	:	:	_	_	_
24	PMC3277850	pmc3277850	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

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	Library	Library	NNP	_	_	_
3	construction	construction	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	as	as	IN	_	_	_
7	described	describe	VBN	_	_	_
8	in	in	IN	_	_	_
9	Parkhomchuk	Parkhomchuk	NNP	_	_	_
10	et	et	FW	_	_	_
11	al.	al.	FW	_	_	_
12	2009	2009	CD	_	_	_
13	,	,	,	_	_	_
14	Nucleic	Nucleic	NNP	_	_	_
15	Acids	Acids	NNP	_	_	_
16	Res	Res	NNP	_	_	_
17	37	37	CD	_	_	_
18	:	:	:	_	_	_
19	e123	e123	NN	_	_	_
20	.	.	.	_	_	_

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	Library	Library	NNP	_	_	_
3	construction	construction	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	by	by	IN	_	_	_
7	processing	processing	NN	_	_	_
8	in	in	FW	_	_	_
9	vitro	vitro	FW	_	_	_
10	samples	sample	NNS	_	_	_
11	to	to	TO	_	_	_
12	generate	generate	VB	_	_	_
13	a	a	DT	_	_	_
14	library	library	NN	_	_	_
15	of	of	IN	_	_	_
16	short	short	JJ	_	_	_
17	inserts	insert	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	the	the	DT	_	_	_
20	DNA	dna	NN	_	_	_
21	Colonies	colony	NNS	_	_	_
22	Template	Template	NNP	_	_	_
23	Library	Library	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	by	by	IN	_	_	_
26	Fasteris	Fasteris	NNP	_	_	_
27	SA	SA	NNP	_	_	_
28	,	,	,	_	_	_
29	Switzerland	Switzerland	NNP	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Library	Library	NNP	_	_	_
32	minipreps	miniprep	NNS	_	_	_
33	were	be	VBD	_	_	_
34	performed	perform	VBN	_	_	_
35	with	with	IN	_	_	_
36	the	the	DT	_	_	_
37	Zyppy	Zyppy	NNP	_	_	_
38	Miniprep	Miniprep	NNP	_	_	_
39	kit	kit	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Zymo	Zymo	NNP	_	_	_
42	Technologies	Technologies	NNPS	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	and	and	CC	_	_	_
45	quantified	quantify	VBN	_	_	_
46	using	use	VBG	_	_	_
47	the	the	DT	_	_	_
48	Qubit	Qubit	NNP	_	_	_
49	dsDNA	dsDNA	NNP	_	_	_
50	BR	BR	NNP	_	_	_
51	kit	kit	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	Invitrogen	invitrogen	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	and	and	CC	_	_	_
56	the	the	DT	_	_	_
57	Nanodrop	Nanodrop	NNP	_	_	_
58	spectrophotometer	spectrophotometer	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	Thermo	Thermo	NNP	_	_	_
61	Scientific	Scientific	NNP	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	Library	Library	NNP	_	_	_
65	preparation	preparation	NN	_	_	_
66	was	be	VBD	_	_	_
67	performed	perform	VBN	_	_	_
68	by	by	IN	_	_	_
69	vertis	vertis	NN	_	_	_
70	Biotechnologie	Biotechnologie	NNP	_	_	_
71	AG	AG	NNP	_	_	_
72	,	,	,	_	_	_
73	according	accord	VBG	_	_	_
74	to	to	TO	_	_	_
75	the	the	DT	_	_	_
76	following	follow	VBG	_	_	_
77	protocol	protocol	NN	_	_	_
78	:	:	:	_	_	_
79	RNA	rna	NN	_	_	_
80	samples	sample	NNS	_	_	_
81	were	be	VBD	_	_	_
82	first	first	JJ	_	_	_
83	treated	treat	VBN	_	_	_
84	with	with	IN	_	_	_
85	rDNase	rdnase	NN	_	_	_
86	.	.	.	_	_	_

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/μl	ng/μl	NN	_	_	_
11	using	use	VBG	_	_	_
12	a	a	DT	_	_	_
13	high	high	JJ	_	_	_
14	fidelity	fidelity	NN	_	_	_
15	DNA	dna	NN	_	_	_
16	polymerase	polymerase	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	9-11	9-11	CD	_	_	_
19	cycles	cycle	NNS	_	_	_
20	,	,	,	_	_	_
21	depending	depend	VBG	_	_	_
22	on	on	IN	_	_	_
23	the	the	DT	_	_	_
24	sample	sample	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	Aliquots	aliquot	NNS	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	PCR	pcr	NN	_	_	_
5	amplified	amplify	VBD	_	_	_
6	libraries	library	NNS	_	_	_
7	were	be	VBD	_	_	_
8	examined	examine	VBN	_	_	_
9	by	by	IN	_	_	_
10	capillary	capillary	JJ	_	_	_
11	electrophoresis	electrophoresis	NN	_	_	_
12	.	.	.	_	_	_

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	Library	Library	NNP	_	_	_
3	preparation	preparation	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	TruSeq	TruSeq	NNP	_	_	_
8	Stranded	Stranded	NNP	_	_	_
9	Total	Total	NNP	_	_	_
10	RNA	rna	NN	_	_	_
11	HT	ht	NN	_	_	_
12	Sample	Sample	NNP	_	_	_
13	Prep	Prep	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Illumina	Illumina	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

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	Library	Library	NNP	_	_	_
3	preparation	preparation	NN	_	_	_
4	were	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	Epicentre	Epicentre	NNP	_	_	_
8	ScriptseqTM	ScriptseqTM	NNP	_	_	_
9	v2	v2	NN	_	_	_
10	RNA-Seq	rna-seq	NN	_	_	_
11	Library	Library	NNP	_	_	_
12	preparation	preparation	NN	_	_	_
13	kit	kit	NN	_	_	_
14	with	with	IN	_	_	_
15	50	50	CD	_	_	_
16	ng	ng	NN	_	_	_
17	of	of	IN	_	_	_
18	depleted	deplete	VBN	_	_	_
19	RNA	rna	NN	_	_	_
20	;	;	:	_	_	_
21	Strand	Strand	NNP	_	_	_
22	orientated	orientate	VBD	_	_	_
23	RNA-Seq	rna-seq	JJ	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	Library	Library	NNP	_	_	_
26	strategy	strategy	NN	_	_	_
27	:	:	:	_	_	_
28	3C-seq	3c-seq	JJ	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	library	library	NN	_	_	_
31	strategy	strategy	NN	_	_	_
32	:	:	:	_	_	_
33	3	3	CD	_	_	_
34	'	'	''	_	_	_
35	-	-	:	_	_	_
36	end	end	NN	_	_	_
37	RNA-seq	rna-seq	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	library	library	NN	_	_	_
40	strategy	strategy	NN	_	_	_
41	:	:	:	_	_	_
42	ChIP-exo	ChIP-exo	NNP	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	Library	Library	NNP	_	_	_
45	strategy	strategy	NN	_	_	_
46	:	:	:	_	_	_
47	ChIP-exo	ChIP-exo	NNP	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	library	library	NN	_	_	_
50	strategy	strategy	NN	_	_	_
51	:	:	:	_	_	_
52	ChIP-seq	chip-seq	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	ChIP-exo	chip-exo	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	library	library	NN	_	_	_
58	strategy	strategy	NN	_	_	_
59	:	:	:	_	_	_
60	DMS-seq	dms-seq	JJ	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	Library	Library	NNP	_	_	_
63	strategy	strategy	NN	_	_	_
64	:	:	:	_	_	_
65	REC-Seq	rec-seq	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Library	Library	NNP	_	_	_
68	strategy	strategy	NN	_	_	_
69	:	:	:	_	_	_
70	Ribo-Seq	Ribo-Seq	NNP	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	Library	Library	NNP	_	_	_
73	strategy	strategy	NN	_	_	_
74	:	:	:	_	_	_
75	RIBO-seq	ribo-seq	JJ	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	library	library	NN	_	_	_
78	strategy	strategy	NN	_	_	_
79	:	:	:	_	_	_
80	Ribosome	Ribosome	NNP	_	_	_
81	profiling	profile	VBG	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	library	library	NN	_	_	_
84	strategy	strategy	NN	_	_	_
85	:	:	:	_	_	_
86	Selective	selective	JJ	_	_	_
87	ribosome	ribosome	NN	_	_	_
88	profiling	profile	VBG	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	library	library	NN	_	_	_
91	strategy	strategy	NN	_	_	_
92	:	:	:	_	_	_
93	SPET-seq	spet-seq	JJ	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	ligation	ligation	NN	_	_	_
96	,	,	,	_	_	_
97	rt-PCR	rt-pcr	NN	_	_	_
98	,	,	,	_	_	_
99	PCR	pcr	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	LIMS477	lims477	NN	_	_	_
102	_	_	CD	_	_	_
103	S1	s1	NN	_	_	_
104	_	_	CD	_	_	_
105	T10	t10	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	LIMS477	lims477	NN	_	_	_
108	_	_	CD	_	_	_
109	S1	s1	NN	_	_	_
110	_	_	CD	_	_	_
111	T3	t3	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	LIMS477	lims477	NN	_	_	_
114	_	_	CD	_	_	_
115	S1	s1	NN	_	_	_
116	_	_	CD	_	_	_
117	T6	t6	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	LIMS477	lims477	NN	_	_	_
120	_	_	CD	_	_	_
121	S2	s2	NN	_	_	_
122	_	_	CD	_	_	_
123	T4	t4	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	LIMS477	lims477	NN	_	_	_
126	_	_	CD	_	_	_
127	S2	s2	NN	_	_	_
128	_	_	CD	_	_	_
129	T6	t6	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	LIMS477	lims477	NN	_	_	_
132	_	_	CD	_	_	_
133	S2	s2	NN	_	_	_
134	_	_	CD	_	_	_
135	T8	t8	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	LIMS477	lims477	NN	_	_	_
138	_	_	CD	_	_	_
139	S3	s3	NN	_	_	_
140	_	_	CD	_	_	_
141	T11	t11	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	LIMS477	lims477	NN	_	_	_
144	_	_	CD	_	_	_
145	S3	s3	NN	_	_	_
146	_	_	CD	_	_	_
147	T3	t3	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	LIMS477	lims477	NN	_	_	_
150	_	_	CD	_	_	_
151	S3	s3	NN	_	_	_
152	_	_	CD	_	_	_
153	T6	t6	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	LIMS477	lims477	NN	_	_	_
156	_	_	CD	_	_	_
157	S5	s5	NN	_	_	_
158	_	_	CD	_	_	_
159	T4	t4	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	LIMS477	lims477	NN	_	_	_
162	_	_	CD	_	_	_
163	S5	s5	NN	_	_	_
164	_	_	CD	_	_	_
165	T6	t6	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	LIMS477	lims477	NN	_	_	_
168	_	_	CD	_	_	_
169	S5	s5	NN	_	_	_
170	_	_	CD	_	_	_
171	T8	t8	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	LIMS484	lims484	NN	_	_	_
174	_	_	CD	_	_	_
175	S1	s1	NN	_	_	_
176	_	_	CD	_	_	_
177	T3	t3	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	LIMS484	lims484	NN	_	_	_
180	_	_	CD	_	_	_
181	S1	s1	NN	_	_	_
182	_	_	CD	_	_	_
183	T6	t6	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	LIMS484	lims484	NN	_	_	_
186	_	_	CD	_	_	_
187	S1	s1	NN	_	_	_
188	_	_	CD	_	_	_
189	T8	t8	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	LIMS484	lims484	NN	_	_	_
192	_	_	CD	_	_	_
193	S2	s2	NN	_	_	_
194	_	_	CD	_	_	_
195	T2	t2	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	LIMS484	lims484	NN	_	_	_
198	_	_	CD	_	_	_
199	S2	s2	NN	_	_	_
200	_	_	CD	_	_	_
201	T6	t6	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	LIMS484	lims484	NN	_	_	_
204	_	_	CD	_	_	_
205	S2	s2	NN	_	_	_
206	_	_	CD	_	_	_
207	T8	t8	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	LIMS484	lims484	NN	_	_	_
210	_	_	CD	_	_	_
211	S5	s5	NN	_	_	_
212	_	_	CD	_	_	_
213	T2	t2	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	LIMS484	lims484	NN	_	_	_
216	_	_	CD	_	_	_
217	S5	s5	NN	_	_	_
218	_	_	CD	_	_	_
219	T6	t6	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	LIMS484	lims484	NN	_	_	_
222	_	_	CD	_	_	_
223	S5	s5	NN	_	_	_
224	_	_	CD	_	_	_
225	T8	t8	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	LIMS484	lims484	NN	_	_	_
228	_	_	CD	_	_	_
229	S6	s6	NN	_	_	_
230	_	_	CD	_	_	_
231	T4	t4	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	LIMS484	lims484	NN	_	_	_
234	_	_	CD	_	_	_
235	S6	s6	NN	_	_	_
236	_	_	CD	_	_	_
237	T6	t6	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	LIMS484	lims484	NN	_	_	_
240	_	_	CD	_	_	_
241	S6	s6	NN	_	_	_
242	_	_	CD	_	_	_
243	T8	t8	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	Linearly	linearly	RB	_	_	_
246	scaled	scale	VBN	_	_	_
247	so	so	IN	_	_	_
248	that	that	IN	_	_	_
249	intensity	intensity	NN	_	_	_
250	values	value	NNS	_	_	_
251	in	in	IN	_	_	_
252	gDNA	gdna	NN	_	_	_
253	_	_	CD	_	_	_
254	A	a	DT	_	_	_
255	_	_	NN	_	_	_
256	cy5	cy5	NN	_	_	_
257	,	,	,	_	_	_
258	cDNA	cdna	NN	_	_	_
259	_	_	NN	_	_	_
260	A	a	NN	_	_	_
261	_	_	NN	_	_	_
262	cy3	cy3	NN	_	_	_
263	,	,	,	_	_	_
264	gDNA	gdna	NN	_	_	_
265	_	_	NN	_	_	_
266	B	b	NN	_	_	_
267	_	_	CD	_	_	_
268	cy3	cy3	NN	_	_	_
269	,	,	,	_	_	_
270	and	and	CC	_	_	_
271	cDNA	cdna	NN	_	_	_
272	_	_	NN	_	_	_
273	B	b	NN	_	_	_
274	_	_	CD	_	_	_
275	cy5	cy5	NN	_	_	_
276	are	be	VBP	_	_	_
277	comparable	comparable	JJ	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
279	Linearly	linearly	RB	_	_	_
280	scaled	scale	VBN	_	_	_
281	so	so	IN	_	_	_
282	that	that	IN	_	_	_
283	intensity	intensity	NN	_	_	_
284	values	value	NNS	_	_	_
285	in	in	IN	_	_	_
286	Sigma70	sigma70	NN	_	_	_
287	_	_	CD	_	_	_
288	ChIP	chip	NN	_	_	_
289	_	_	NN	_	_	_
290	control	control	NN	_	_	_
291	_	_	CD	_	_	_
292	A	a	DT	_	_	_
293	_	_	NN	_	_	_
294	cy3	cy3	NN	_	_	_
295	,	,	,	_	_	_
296	Sigma70	sigma70	NN	_	_	_
297	_	_	CD	_	_	_
298	ChIP	chip	NN	_	_	_
299	_	_	CD	_	_	_
300	A	a	DT	_	_	_
301	_	_	NN	_	_	_
302	cy5	cy5	NN	_	_	_
303	,	,	,	_	_	_
304	Sigma70	sigma70	NN	_	_	_
305	_	_	CD	_	_	_
306	ChIP	chip	NN	_	_	_
307	_	_	NN	_	_	_
308	control	control	NN	_	_	_
309	_	_	NN	_	_	_
310	B	b	NN	_	_	_
311	_	_	CD	_	_	_
312	cy3	cy3	NN	_	_	_
313	,	,	,	_	_	_
314	Sigma70	sigma70	NN	_	_	_
315	_	_	CD	_	_	_
316	ChIP	chip	NN	_	_	_
317	_	_	NN	_	_	_
318	B	b	NN	_	_	_
319	_	_	CD	_	_	_
320	cy5	cy5	NN	_	_	_
321	,	,	,	_	_	_
322	Beta	beta	NN	_	_	_
323	_	_	CD	_	_	_
324	ChIP	chip	NN	_	_	_
325	_	_	NN	_	_	_
326	control	control	NN	_	_	_
327	_	_	CD	_	_	_
328	A	a	DT	_	_	_
329	_	_	NN	_	_	_
330	cy3	cy3	NN	_	_	_
331	,	,	,	_	_	_
332	Beta	beta	NN	_	_	_
333	_	_	NN	_	_	_
334	ChIP	chip	NN	_	_	_
335	_	_	CD	_	_	_
336	A	a	DT	_	_	_
337	_	_	NN	_	_	_
338	cy5	cy5	NN	_	_	_
339	,	,	,	_	_	_
340	Beta	beta	NN	_	_	_
341	_	_	NN	_	_	_
342	ChIP	chip	NN	_	_	_
343	_	_	CD	_	_	_
344	control	control	NN	_	_	_
345	_	_	NN	_	_	_
346	B	b	NN	_	_	_
347	_	_	CD	_	_	_
348	cy3	cy3	NN	_	_	_
349	,	,	,	_	_	_
350	Beta	beta	NN	_	_	_
351	_	_	NN	_	_	_
352	ChIP	chip	NN	_	_	_
353	_	_	NN	_	_	_
354	B	b	NN	_	_	_
355	_	_	CD	_	_	_
356	cy5	cy5	NN	_	_	_
357	are	be	VBP	_	_	_
358	comparable	comparable	JJ	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
360	LJ110	lj110	NN	_	_	_
361	del	del	FW	_	_	_
362	pdhr	pdhr	FW	_	_	_
363	LBo	lbo	FW	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	LJ110	lj110	NN	_	_	_
366	del	del	FW	_	_	_
367	pdhr	pdhr	FW	_	_	_
368	MMAcetat	mmacetat	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	LJ110	lj110	NN	_	_	_
371	del	del	FW	_	_	_
372	pdhr	pdhr	FW	_	_	_
373	MMPyruvat	mmpyruvat	NN	_	_	_
374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
375	LJ110	lj110	NN	_	_	_
376	LBo	lbo	NN	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	LJ110	lj110	NN	_	_	_
379	MMAcetat	mmacetat	NN	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
381	LJ110	lj110	NN	_	_	_
382	MMPyruvat	mmpyruvat	NN	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	LJ110	lj110	NN	_	_	_
385	pTM30	ptm30	NN	_	_	_
386	LBo	lbo	NN	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	LJ110	lj110	NN	_	_	_
389	pTM30	ptm30	NN	_	_	_
390	MMAcetat	mmacetat	NN	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	LJ110	lj110	NN	_	_	_
393	pTM30	ptm30	NN	_	_	_
394	MMPyruvat	mmpyruvat	NN	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	LJ110	lj110	NN	_	_	_
397	pTM30pdhr	ptm30pdhr	NN	_	_	_
398	LBo	lbo	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	LJ110	lj110	NN	_	_	_
401	pTM30pdhr	ptm30pdhr	NN	_	_	_
402	MMAcetat	mmacetat	NN	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	LJ110	lj110	NN	_	_	_
405	pTM30pdhr	ptm30pdhr	NN	_	_	_
406	MMPyruvat	mmpyruvat	NN	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	Local	local	JJ	_	_	_
409	Background	background	NN	_	_	_
410	Substracted	Substracted	NNP	_	_	_
411	Signal	Signal	NNP	_	_	_
412	Corrected	Corrected	NNP	_	_	_
413	for	for	IN	_	_	_
414	unequal	unequal	JJ	_	_	_
415	Dye	dye	NN	_	_	_
416	incorporation	incorporation	NN	_	_	_
417	or	or	CC	_	_	_
418	unequal	unequal	JJ	_	_	_
419	load	load	NN	_	_	_
420	of	of	IN	_	_	_
421	labelled	label	VBN	_	_	_
422	product	product	NN	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	location	location	NN	_	_	_
425	:	:	:	_	_	_
426	Earth	Earth	NNP	_	_	_
427	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
428	location	location	NN	_	_	_
429	:	:	:	_	_	_
430	Space	Space	NNP	_	_	_
431	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
432	Log10	log10	NN	_	_	_
433	mRNA	mrna	NN	_	_	_
434	concentration	concentration	NN	_	_	_
435	-LRB-	-lrb-	-LRB-	_	_	_
436	pM	pm	NN	_	_	_
437	-RRB-	-rrb-	-RRB-	_	_	_
438	data	datum	NNS	_	_	_
439	are	be	VBP	_	_	_
440	provided	provide	VBN	_	_	_
441	as	as	IN	_	_	_
442	a	a	DT	_	_	_
443	supplementary	supplementary	JJ	_	_	_
444	file	file	NN	_	_	_
445	.	.	.	_	_	_

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	NN	_	_	_
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	log2	log2	NN	_	_	_
3	ratio	ratio	NN	_	_	_
4	of	of	IN	_	_	_
5	isolate/control	isolate/control	JJ	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	Logarithmic	logarithmic	JJ	_	_	_
8	phase	phase	NN	_	_	_
9	sample	sample	NN	_	_	_
10	1	1	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Logarithmic	logarithmic	JJ	_	_	_
13	phase	phase	NN	_	_	_
14	sample	sample	NN	_	_	_
15	2	2	CD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Logarithmic	logarithmic	JJ	_	_	_
18	phase	phase	NN	_	_	_
19	sample	sample	NN	_	_	_
20	3	3	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Logarithmic	logarithmic	JJ	_	_	_
23	phase	phase	NN	_	_	_
24	sample	sample	NN	_	_	_
25	4	4	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	LogData	logdata	NN	_	_	_
28	=	=	JJ	_	_	_
29	createData	createdata	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Data	data	NN	_	_	_
32	,	,	,	_	_	_
33	n.rep	n.rep	NN	_	_	_
34	=	=	JJ	_	_	_
35	1	1	CD	_	_	_
36	,	,	,	_	_	_
37	log.trans	log.trans	VBZ	_	_	_
38	=	=	JJ	_	_	_
39	TRUE	true	JJ	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	log	log	VBP	_	_	_
43	phase	phase	NN	_	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	log	log	NN	_	_	_
47	phase	phase	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	log	log	VBP	_	_	_
51	phase	phase	NN	_	_	_
52	3	3	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	log	log	NN	_	_	_
55	phase	phase	NN	_	_	_
56	4	4	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	log	log	VBP	_	_	_
59	phase	phase	NN	_	_	_
60	5	5	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Log-phase	log-phase	NN	_	_	_
63	cultures	culture	NNS	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	LB	lb	NN	MED	_	_
66	broth	broth	NN	MED	_	_
67	,	,	,	_	_	_
68	Miller	Miller	NNP	_	_	_
69	formulation	formulation	NN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	inoculated	inoculate	VBN	_	_	_
72	with	with	IN	_	_	_
73	either	either	CC	_	_	_
74	blue	blue	JJ	_	_	_
75	or	or	CC	_	_	_
76	pale	pale	JJ	_	_	_
77	colonies	colony	NNS	_	_	_
78	were	be	VBD	_	_	_
79	grown	grow	VBN	_	_	_
80	for	for	IN	_	_	_
81	5	5	CD	_	_	_
82	hr	hr	NN	_	_	_
83	at	at	IN	_	_	_
84	37	37	CD	_	_	_
85	degrees	degree	NNS	_	_	_
86	celsius	celsius	NN	_	_	_
87	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	lon	lon	NN	GEN	_	_
3	___	___	CD	_	_	_
4	U	U	NNP	_	_	_
5	_	_	NNP	_	_	_
6	N0025	N0025	NNP	_	_	_
7	_	_	NNP	_	_	_
8	r1	r1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	lon	lon	NN	GEN	_	_
11	___	___	CD	_	_	_
12	U	U	NNP	_	_	_
13	_	_	NNP	_	_	_
14	N0025	N0025	NNP	_	_	_
15	_	_	NNP	_	_	_
16	r2	r2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	lon	lon	NN	GEN	_	_
19	___	___	CD	_	_	_
20	U	U	NNP	_	_	_
21	_	_	NNP	_	_	_
22	N0025	N0025	NNP	_	_	_
23	_	_	NNP	_	_	_
24	r3	r3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	lon	lon	NN	GEN	_	_
27	upregulation	upregulation	NN	_	_	_
28	,	,	,	_	_	_
29	amp	amp	NN	_	_	_
30	50ug/ml	50ug/ml	NN	_	_	_
31	,	,	,	_	_	_
32	0.0125	0.0125	CD	_	_	_
33	%	%	NN	_	_	_
34	arabinose	arabinose	NN	_	_	_
35	,	,	,	_	_	_
36	0.025	0.025	CD	_	_	_
37	ug/ml	ug/ml	NN	_	_	_
38	norfloxacin	norfloxacin	NN	_	_	_
39	OD	od	NN	_	_	_
40	~	~	NN	_	_	_
41	0.3	0.3	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	LOWESS	lowess	NN	_	_	_
44	normalised	normalised	JJ	_	_	_
45	data	datum	NNS	_	_	_
46	that	that	WDT	_	_	_
47	represents	represent	VBZ	_	_	_
48	the	the	DT	_	_	_
49	average	average	NN	_	_	_
50	of	of	IN	_	_	_
51	the	the	DT	_	_	_
52	three	three	CD	_	_	_
53	replicate	replicate	VBP	_	_	_
54	experiments	experiment	NNS	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
56	LOWESS	lowess	NN	_	_	_
57	normalized	normalize	VBD	_	_	_
58	,	,	,	_	_	_
59	background	background	NN	_	_	_
60	subtracted	subtract	VBD	_	_	_
61	data	datum	NNS	_	_	_
62	obtained	obtain	VBN	_	_	_
63	from	from	IN	_	_	_
64	log2	log2	NN	_	_	_
65	of	of	IN	_	_	_
66	processed	process	VBN	_	_	_
67	Red	Red	NNP	_	_	_
68	signal/processed	signal/processed	VBD	_	_	_
69	Green	Green	NNP	_	_	_
70	signal	signal	NN	_	_	_
71	.	.	.	_	_	_

1	Agilent	Agilent	NNP	_	_	_
2	software	software	NN	_	_	_
3	GX	GX	NNP	_	_	_
4	7.3	7.3	CD	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	LOWESS	lowess	NN	_	_	_
3	normalized	normalize	VBD	_	_	_
4	,	,	,	_	_	_
5	background	background	NN	_	_	_
6	subtracted	subtract	VBD	_	_	_
7	data	datum	NNS	_	_	_
8	obtained	obtain	VBN	_	_	_
9	from	from	IN	_	_	_
10	signals	signal	NNS	_	_	_
11	.	.	.	_	_	_

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	LOWESS	lowess	NN	_	_	_
3	normalized	normalize	VBD	_	_	_
4	data	datum	NNS	_	_	_
5	obtained	obtain	VBN	_	_	_
6	from	from	IN	_	_	_
7	log2	log2	NN	_	_	_
8	of	of	IN	_	_	_
9	processed	process	VBN	_	_	_
10	Red	red	JJ	_	_	_
11	signal	signal	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	treated	treat	VBN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	/	/	:	_	_	_
16	processed	process	VBN	_	_	_
17	Green	Green	NNP	_	_	_
18	signal	signal	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	control	control	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	are	be	VBP	_	_	_
23	given	give	VBN	_	_	_
24	in	in	IN	_	_	_
25	the	the	DT	_	_	_
26	data	datum	NNS	_	_	_
27	table	table	NN	_	_	_
28	below	below	IN	_	_	_
29	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	microarray	microarray	NN	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	analyzed	analyze	VBN	_	_	_
6	using	use	VBG	_	_	_
7	R	r	NN	_	_	_
8	software	software	NN	_	_	_
9	and	and	CC	_	_	_
10	Limma	limma	NN	_	_	_
11	package	package	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	part	part	NN	_	_	_
14	of	of	IN	_	_	_
15	Bioconductor	Bioconductor	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	All	all	PDT	_	_	_
2	the	the	DT	_	_	_
3	probes	probe	NNS	_	_	_
4	encoding	encode	VBG	_	_	_
5	for	for	IN	_	_	_
6	positive	positive	JJ	_	_	_
7	and	and	CC	_	_	_
8	negative	negative	JJ	_	_	_
9	controls	control	NNS	_	_	_
10	were	be	VBD	_	_	_
11	not	not	RB	_	_	_
12	used	use	VBN	_	_	_
13	and	and	CC	_	_	_
14	have	have	VBP	_	_	_
15	been	be	VBN	_	_	_
16	removed	remove	VBN	_	_	_
17	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	raw	raw	JJ	_	_	_
3	data	datum	NNS	_	_	_
4	superior	superior	JJ	_	_	_
5	to	to	TO	_	_	_
6	background	background	NN	_	_	_
7	values	value	NNS	_	_	_
8	and	and	CC	_	_	_
9	with	with	IN	_	_	_
10	homogeneous	homogeneous	JJ	_	_	_
11	fluorescent	fluorescent	JJ	_	_	_
12	signals	signal	NNS	_	_	_
13	were	be	VBD	_	_	_
14	considered	consider	VBN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	H	h	NN	_	_	_
17	<	<	JJR	_	_	_
18	0.2	0.2	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Red	Red	NNP	_	_	_
2	and	and	CC	_	_	_
3	green	green	JJ	_	_	_
4	signal	signal	NN	_	_	_
5	heterogeneity	heterogeneity	NN	_	_	_
6	was	be	VBD	_	_	_
7	estimated	estimate	VBN	_	_	_
8	as	as	IN	_	_	_
9	followed	follow	VBN	_	_	_
10	:	:	:	_	_	_
11	H	h	NN	_	_	_
12	=	=	JJ	_	_	_
13	|	|	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	trimmed	trimmed	RBR	_	_	_
16	mean	mean	VB	_	_	_
17	of	of	IN	_	_	_
18	raw	raw	JJ	_	_	_
19	intensity	intensity	NN	_	_	_
20	-	-	:	_	_	_
21	median	median	NN	_	_	_
22	of	of	IN	_	_	_
23	raw	raw	JJ	_	_	_
24	intensity	intensity	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	|	|	SYM	_	_	_
27	/	/	:	_	_	_
28	|	|	SYM	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	0.5	0.5	CD	_	_	_
31	*	*	SYM	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	trimmed	trimmed	RBR	_	_	_
34	mean	mean	VB	_	_	_
35	of	of	IN	_	_	_
36	raw	raw	JJ	_	_	_
37	intensity	intensity	NN	_	_	_
38	+	+	CC	_	_	_
39	median	median	NN	_	_	_
40	of	of	IN	_	_	_
41	raw	raw	JJ	_	_	_
42	intensity	intensity	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	LOWESS	lowess	NN	_	_	_
3	normalization	normalization	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	differences	difference	NNS	_	_	_
7	between	between	IN	_	_	_
8	the	the	DT	_	_	_
9	four	four	CD	_	_	_
10	heat-treatments	heat-treatment	NNS	_	_	_
11	were	be	VBD	_	_	_
12	tested	test	VBN	_	_	_
13	by	by	IN	_	_	_
14	Analysis	analysis	NN	_	_	_
15	of	of	IN	_	_	_
16	Variance	variance	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	ANOVA	anova	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	followed	follow	VBN	_	_	_
21	by	by	IN	_	_	_
22	a	a	DT	_	_	_
23	priori	priori	FW	_	_	_
24	tests	test	NNS	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	P-value	p-value	JJ	_	_	_
27	<	<	VBG	_	_	_
28	0.0001	0.0001	CD	_	_	_
29	and	and	CC	_	_	_
30	P-value	p-value	JJ	_	_	_
31	FDR	FDR	NNP	_	_	_
32	after	after	IN	_	_	_
33	Benjamini	Benjamini	NNP	_	_	_
34	Yekutieli	Yekutieli	NNP	_	_	_
35	adjustment	adjustment	NN	_	_	_
36	<	<	JJR	_	_	_
37	0.01	0.01	CD	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

1	Six	six	CD	_	_	_
2	contrasts	contrast	VBZ	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	Contrast1	contrast1	NN	_	_	_
5	:	:	:	_	_	_
6	T1	t1	NN	_	_	_
7	vs	vs	CC	_	_	_
8	T2	t2	NN	_	_	_
9	,	,	,	_	_	_
10	Contrast2	contrast2	NN	_	_	_
11	:	:	:	_	_	_
12	T1	t1	NN	_	_	_
13	vs	vs	CC	_	_	_
14	T3	t3	NN	_	_	_
15	,	,	,	_	_	_
16	Contrast3	contrast3	NN	_	_	_
17	:	:	:	_	_	_
18	T1	t1	NN	_	_	_
19	vs	vs	CC	_	_	_
20	T4	t4	NN	_	_	_
21	,	,	,	_	_	_
22	Contrast4	contrast4	NN	_	_	_
23	:	:	:	_	_	_
24	T2	t2	NN	_	_	_
25	vs	vs	CC	_	_	_
26	T3	t3	NN	_	_	_
27	,	,	,	_	_	_
28	Contrast5	contrast5	NN	_	_	_
29	:	:	:	_	_	_
30	T2	t2	NN	_	_	_
31	vs	vs	CC	_	_	_
32	T4	t4	NN	_	_	_
33	,	,	,	_	_	_
34	Contrast6	contrast6	NN	_	_	_
35	:	:	:	_	_	_
36	T3	t3	NN	_	_	_
37	vs	vs	CC	_	_	_
38	T4	t4	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	were	be	VBD	_	_	_
41	performed	perform	VBN	_	_	_
42	.	.	.	_	_	_

1	Normalized	normalize	VBN	_	_	_
2	Log2	log2	NN	_	_	_
3	ratio	ratio	NN	_	_	_
4	between	between	IN	_	_	_
5	treatments	treatment	NNS	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	results	result	NNS	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	statistical	statistical	JJ	_	_	_
12	analysis	analysis	NN	_	_	_
13	have	have	VBP	_	_	_
14	been	be	VBN	_	_	_
15	linked	link	VBN	_	_	_
16	as	as	IN	_	_	_
17	a	a	DT	_	_	_
18	supplementary	supplementary	JJ	_	_	_
19	file	file	NN	_	_	_
20	on	on	IN	_	_	_
21	the	the	DT	_	_	_
22	Series	Series	NNP	_	_	_
23	record	record	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Lowess	lowess	NN	_	_	_
3	normalized	normalize	VBD	_	_	_
4	data	datum	NNS	_	_	_
5	.	.	.	_	_	_

1	Resultant	resultant	JJ	_	_	_
2	data	datum	NNS	_	_	_
3	is	be	VBZ	_	_	_
4	log2	log2	NN	_	_	_
5	normalized	normalize	VBD	_	_	_
6	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Low	low	JJ	_	_	_
3	quality	quality	NN	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	trimmed	trim	VBN	_	_	_
7	with	with	IN	_	_	_
8	CutAdapt	cutadapt	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	LP1	lp1	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	LP2	lp2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	LP3	lp3	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	LP4	lp4	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	lplA	lpla	NN	GEN	_	_
19	KO	ko	NN	_	_	_
20	rep1	rep1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	lplA	lpla	NN	GEN	_	_
23	KO	ko	NN	_	_	_
24	rep2	rep2	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	lplA	lpla	NN	GEN	_	_
27	KO	ko	NN	_	_	_
28	rep3	rep3	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	lrp-gln-1	lrp-gln-1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	lrp-gln-2	lrp-gln-2	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	Lrp	lrp	VBP	TF	_	_
35	_	_	SYM	_	_	_
36	Leu	Leu	NNP	_	_	_
37	_	_	SYM	_	_	_
38	1	1	CD	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	Lrp	Lrp	NNP	TF	_	_
41	_	_	NNP	_	_	_
42	Leu	Leu	NNP	_	_	_
43	_	_	NNP	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Lrp	Lrp	NNP	TF	_	_
47	_	_	NNP	_	_	_
48	Leu	Leu	NNP	_	_	_
49	_	_	SYM	_	_	_
50	3	3	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	lrp	lrp	SYM	GEN	_	_
53	-	-	:	_	_	_
54	+	+	CC	_	_	_
55	Leu	Leu	NNP	_	_	_
56	vs.	vs.	FW	_	_	_
57	lrp	lrp	SYM	GEN	_	_
58	-	-	:	_	_	_
59	-	-	:	_	_	_
60	Leu	leu	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	lrp	lrp	NN	GEN	_	_
63	-	-	:	_	_	_
64	-	-	:	_	_	_
65	Leu	leu	NN	_	_	_
66	vs.	vs.	CC	_	_	_
67	wt	wt	JJ	_	_	_
68	-	-	:	_	_	_
69	Leu	leu	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	lrp	lrp	NN	GEN	_	_
72	-	-	:	_	_	_
73	+	+	CC	_	_	_
74	Leu	Leu	NNP	_	_	_
75	vs.	vs.	FW	_	_	_
76	wt	wt	JJ	_	_	_
77	-	-	:	_	_	_
78	Leu	leu	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Lrp	lrp	NN	TF	_	_
81	_	_	CD	_	_	_
82	NH4Cl	nh4cl	NN	_	_	_
83	_	_	NN	_	_	_
84	1	1	CD	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	Lrp	Lrp	NNP	TF	_	_
87	_	_	SYM	_	_	_
88	NH4Cl	nh4cl	NN	_	_	_
89	_	_	NN	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	Lrp	Lrp	NNP	TF	_	_
93	_	_	SYM	_	_	_
94	NH4Cl	nh4cl	NN	_	_	_
95	_	_	NN	_	_	_
96	3	3	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	L-threonine	l-threonine	NN	_	_	_
99	producing	produce	VBG	_	_	_
100	strain	strain	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	L-threonine	l-threonine	NN	_	_	_
103	producing	produce	VBG	_	_	_
104	strain	strain	NN	_	_	_
105	vs	vs	CC	_	_	_
106	control	control	NN	_	_	_
107	strain	strain	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	L	l	NN	_	_	_
110	,	,	,	_	_	_
111	TP1	tp1	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	L	l	NN	_	_	_
114	,	,	,	_	_	_
115	TP2	tp2	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	L	l	NN	_	_	_
118	,	,	,	_	_	_
119	TP3	tp3	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	L	l	NN	_	_	_
122	,	,	,	_	_	_
123	TP4	tp4	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	luc2	luc2	NN	_	_	_
126	_	_	CD	_	_	_
127	U	U	NNP	_	_	_
128	_	_	NNP	_	_	_
129	N0000	N0000	NNP	_	_	_
130	_	_	VBD	_	_	_
131	r1	r1	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	luc2	luc2	NN	_	_	_
134	_	_	CD	_	_	_
135	U	U	NNP	_	_	_
136	_	_	NNP	_	_	_
137	N0000	N0000	NNP	_	_	_
138	_	_	VBD	_	_	_
139	r2	r2	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	luc2	luc2	NN	_	_	_
142	_	_	CD	_	_	_
143	U	U	NNP	_	_	_
144	_	_	NNP	_	_	_
145	N0025	N0025	NNP	_	_	_
146	_	_	VBD	_	_	_
147	r1	r1	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	luc2	luc2	NN	_	_	_
150	_	_	CD	_	_	_
151	U	U	NNP	_	_	_
152	_	_	NNP	_	_	_
153	N0025	N0025	NNP	_	_	_
154	_	_	VBD	_	_	_
155	r2	r2	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	luciferase	luciferase	NN	_	_	_
158	0.025	0.025	CD	_	_	_
159	ug/ml	ug/ml	NN	_	_	_
160	norfloxacin	norfloxacin	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	luciferase	luciferase	NN	_	_	_
163	no	no	DT	_	_	_
164	drug	drug	NN	_	_	_
165	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
166	luc	luc	NN	_	_	_
167	___	___	CD	_	_	_
168	U	U	NNP	_	_	_
169	_	_	NNP	_	_	_
170	N0000	N0000	NNP	_	_	_
171	_	_	NNP	_	_	_
172	r1	r1	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	luc	luc	NN	_	_	_
175	___	___	CD	_	_	_
176	U	U	NNP	_	_	_
177	_	_	NNP	_	_	_
178	N0000	N0000	NNP	_	_	_
179	_	_	NNP	_	_	_
180	r2	r2	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	luc	luc	NN	_	_	_
183	___	___	CD	_	_	_
184	U	U	NNP	_	_	_
185	_	_	NNP	_	_	_
186	N0000	N0000	NNP	_	_	_
187	_	_	NNP	_	_	_
188	r3	r3	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	luc	luc	NN	_	_	_
191	___	___	CD	_	_	_
192	U	U	NNP	_	_	_
193	_	_	NNP	_	_	_
194	N0025	N0025	NNP	_	_	_
195	_	_	NNP	_	_	_
196	r1	r1	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	luc	luc	NN	_	_	_
199	___	___	CD	_	_	_
200	U	U	NNP	_	_	_
201	_	_	NNP	_	_	_
202	N0025	N0025	NNP	_	_	_
203	_	_	NNP	_	_	_
204	r2	r2	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	luc	luc	NN	_	_	_
207	___	___	CD	_	_	_
208	U	U	NNP	_	_	_
209	_	_	NNP	_	_	_
210	N0025	N0025	NNP	_	_	_
211	_	_	NNP	_	_	_
212	r3	r3	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	luc	luc	NN	_	_	_
215	___	___	CD	_	_	_
216	U	U	NNP	_	_	_
217	_	_	NNP	_	_	_
218	N0075	N0075	NNP	_	_	_
219	_	_	NNP	_	_	_
220	r1	r1	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	luc	luc	NN	_	_	_
223	___	___	CD	_	_	_
224	U	U	NNP	_	_	_
225	_	_	NNP	_	_	_
226	N0075	N0075	NNP	_	_	_
227	_	_	NNP	_	_	_
228	r2	r2	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	luc	luc	NN	_	_	_
231	___	___	CD	_	_	_
232	U	U	NNP	_	_	_
233	_	_	NNP	_	_	_
234	N0075	N0075	NNP	_	_	_
235	_	_	NNP	_	_	_
236	r3	r3	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	luc	luc	NN	_	_	_
239	upregulation	upregulation	NN	_	_	_
240	,	,	,	_	_	_
241	0.000	0.000	CD	_	_	_
242	ug/ml	ug/ml	NN	_	_	_
243	norfloxacin	norfloxacin	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	luc	luc	NN	_	_	_
246	upregulation	upregulation	NN	_	_	_
247	,	,	,	_	_	_
248	0.075	0.075	CD	_	_	_
249	ug/ml	ug/ml	NN	_	_	_
250	norfloxacin	norfloxacin	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	luc	luc	NN	_	_	_
253	upregulation	upregulation	NN	_	_	_
254	,	,	,	_	_	_
255	amp	amp	NN	_	_	_
256	50ug/ml	50ug/ml	NN	_	_	_
257	,	,	,	_	_	_
258	0.0125	0.0125	CD	_	_	_
259	%	%	NN	_	_	_
260	arabinose	arabinose	NN	_	_	_
261	,	,	,	_	_	_
262	0.025	0.025	CD	_	_	_
263	ug/ml	ug/ml	NN	_	_	_
264	norfloxacin	norfloxacin	NN	_	_	_
265	OD	od	NN	_	_	_
266	~	~	NN	_	_	_
267	0.3	0.3	CD	_	_	_
268	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
269	Luria	Luria	NNP	MED	_	_
270	broth	broth	NN	MED	_	_
271	-LRB-	-lrb-	-LRB-	_	_	_
272	LB	lb	NN	_	_	_
273	-RRB-	-rrb-	-RRB-	_	_	_
274	medium	medium	NN	_	_	_
275	under	under	IN	_	_	_
276	aeration	aeration	NN	_	_	_
277	,	,	,	_	_	_
278	exponential	exponential	JJ	GrowthPhase	_	_
279	phase	phase	NN	GrowthPhase	_	_
280	OD600	od600	NN	_	_	_
281	=	=	JJ	_	_	_
282	0.3	0.3	CD	_	_	_
283	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	luxS	luxs	NN	GEN	_	_
3	mutants	mutant	NNS	_	_	_
4	,	,	,	_	_	_
5	10	10	CD	_	_	_
6	%	%	NN	_	_	_
7	H2O2	h2o2	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	luxS	luxs	NN	GEN	_	_
10	mutants	mutant	NNS	_	_	_
11	,	,	,	_	_	_
12	30	30	CD	_	_	_
13	%	%	NN	_	_	_
14	H2O2	h2o2	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	luxS	luxs	NN	GEN	_	_
17	mutants	mutant	NNS	_	_	_
18	,	,	,	_	_	_
19	without	without	IN	_	_	_
20	H2O2	h2o2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Lysates	lysate	NNS	_	_	_
23	were	be	VBD	_	_	_
24	diluted	dilute	VBN	_	_	_
25	with	with	IN	_	_	_
26	1	1	CD	_	_	_
27	ml	ml	NN	_	_	_
28	of	of	IN	_	_	_
29	TES	tes	NN	_	_	_
30	buffer	buffer	NN	_	_	_
31	and	and	CC	_	_	_
32	100	100	CD	_	_	_
33	μl	μl	NN	_	_	_
34	of	of	IN	_	_	_
35	ANTI-FLAG	anti-flag	NN	_	_	_
36	®	®	CD	_	_	_
37	M2	m2	NN	_	_	_
38	affinity	affinity	NN	_	_	_
39	gel	gel	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Sigma-Aldrich	sigma-aldrich	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	was	be	VBD	_	_	_
44	added	add	VBN	_	_	_
45	.	.	.	_	_	_

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	Lysine	Lysine	NNP	_	_	_
3	addition	addition	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	M1655	m1655	NN	_	_	_
6	wild	wild	JJ	_	_	_
7	type	type	NN	_	_	_
8	at	at	IN	_	_	_
9	t0	t0	NN	_	_	_
10	,	,	,	_	_	_
11	rep1	rep1	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	M1655	m1655	NN	_	_	_
14	wild	wild	JJ	_	_	_
15	type	type	NN	_	_	_
16	at	at	IN	_	_	_
17	t0	t0	NN	_	_	_
18	,	,	,	_	_	_
19	rep2	rep2	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	M1655	m1655	NN	_	_	_
22	wild	wild	JJ	_	_	_
23	type	type	NN	_	_	_
24	at	at	IN	_	_	_
25	t10	t10	NN	_	_	_
26	,	,	,	_	_	_
27	rep1	rep1	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	M1655	m1655	NN	_	_	_
30	wild	wild	JJ	_	_	_
31	type	type	NN	_	_	_
32	at	at	IN	_	_	_
33	t10	t10	NN	_	_	_
34	,	,	,	_	_	_
35	rep2	rep2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	M1655	m1655	NN	_	_	_
38	wild	wild	JJ	_	_	_
39	type	type	NN	_	_	_
40	at	at	IN	_	_	_
41	t2	t2	NN	_	_	_
42	,	,	,	_	_	_
43	rep1	rep1	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	M1655	m1655	NN	_	_	_
46	wild	wild	JJ	_	_	_
47	type	type	NN	_	_	_
48	at	at	IN	_	_	_
49	t2	t2	NN	_	_	_
50	,	,	,	_	_	_
51	rep2	rep2	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	M1655	m1655	NN	_	_	_
54	wild	wild	JJ	_	_	_
55	type	type	NN	_	_	_
56	at	at	IN	_	_	_
57	t4	t4	NN	_	_	_
58	,	,	,	_	_	_
59	rep1	rep1	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	M1655	m1655	NN	_	_	_
62	wild	wild	JJ	_	_	_
63	type	type	NN	_	_	_
64	at	at	IN	_	_	_
65	t4	t4	NN	_	_	_
66	,	,	,	_	_	_
67	rep2	rep2	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	M1655	m1655	NN	_	_	_
70	wild	wild	JJ	_	_	_
71	type	type	NN	_	_	_
72	at	at	IN	_	_	_
73	t6	t6	NN	_	_	_
74	,	,	,	_	_	_
75	rep1	rep1	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	M1655	m1655	NN	_	_	_
78	wild	wild	JJ	_	_	_
79	type	type	NN	_	_	_
80	at	at	IN	_	_	_
81	t6	t6	NN	_	_	_
82	,	,	,	_	_	_
83	rep2	rep2	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	M1655	m1655	NN	_	_	_
86	wild	wild	JJ	_	_	_
87	type	type	NN	_	_	_
88	at	at	IN	_	_	_
89	t8	t8	NN	_	_	_
90	,	,	,	_	_	_
91	rep1	rep1	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	M1655	m1655	NN	_	_	_
94	wild	wild	JJ	_	_	_
95	type	type	NN	_	_	_
96	at	at	IN	_	_	_
97	t8	t8	NN	_	_	_
98	,	,	,	_	_	_
99	rep2	rep2	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	M1655	m1655	NN	_	_	_
102	with	with	IN	_	_	_
103	deletion	deletion	NN	_	_	_
104	in	in	IN	_	_	_
105	soxR	soxr	NN	GEN	_	_
106	at	at	IN	_	_	_
107	t0	t0	NN	_	_	_
108	,	,	,	_	_	_
109	rep1	rep1	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	M1655	m1655	NN	_	_	_
112	with	with	IN	_	_	_
113	deletion	deletion	NN	_	_	_
114	in	in	IN	_	_	_
115	soxR	soxr	NN	GEN	_	_
116	at	at	IN	_	_	_
117	t10	t10	NN	_	_	_
118	,	,	,	_	_	_
119	rep1	rep1	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	M1655	m1655	NN	_	_	_
122	with	with	IN	_	_	_
123	deletion	deletion	NN	_	_	_
124	in	in	IN	_	_	_
125	soxR	soxr	NN	GEN	_	_
126	at	at	IN	_	_	_
127	t2	t2	NN	_	_	_
128	,	,	,	_	_	_
129	rep1	rep1	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	M1655	m1655	NN	_	_	_
132	with	with	IN	_	_	_
133	deletion	deletion	NN	_	_	_
134	in	in	IN	_	_	_
135	soxR	soxr	NN	GEN	_	_
136	at	at	IN	_	_	_
137	t4	t4	NN	_	_	_
138	,	,	,	_	_	_
139	rep1	rep1	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	M1655	m1655	NN	_	_	_
142	with	with	IN	_	_	_
143	deletion	deletion	NN	_	_	_
144	in	in	IN	_	_	_
145	soxR	soxr	NN	GEN	_	_
146	at	at	IN	_	_	_
147	t6	t6	NN	_	_	_
148	,	,	,	_	_	_
149	rep1	rep1	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	M1655	m1655	NN	_	_	_
152	with	with	IN	_	_	_
153	deletion	deletion	NN	_	_	_
154	in	in	IN	_	_	_
155	soxR	soxr	NN	GEN	_	_
156	at	at	IN	_	_	_
157	t8	t8	NN	_	_	_
158	,	,	,	_	_	_
159	rep1	rep1	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	M63	m63	NN	_	_	_
162	0.4	0.4	CD	_	_	_
163	B1	b1	NN	_	_	_
164	TEX	tex	NN	_	_	_
165	neg	neg	NN	_	_	_
166	L1	l1	NN	_	_	_
167	GA	ga	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	M63	m63	NN	_	_	_
170	0.4	0.4	CD	_	_	_
171	B1	b1	NN	_	_	_
172	TEX	TEX	NNP	_	_	_
173	pos	po	VBZ	_	_	_
174	L1	l1	NN	_	_	_
175	GA	ga	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	M63	m63	NN	_	_	_
178	0.4	0.4	CD	_	_	_
179	B2	b2	NN	_	_	_
180	TEX	TEX	NNP	_	_	_
181	neg	neg	NNP	_	_	_
182	L1	l1	NN	_	_	_
183	HS1	hs1	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	M63	m63	NN	_	_	_
186	0.4	0.4	CD	_	_	_
187	B2	b2	NN	_	_	_
188	TEX	TEX	NNP	_	_	_
189	neg	neg	NNP	_	_	_
190	L1	l1	NN	_	_	_
191	HS2	hs2	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	M63	m63	NN	_	_	_
194	0.4	0.4	CD	_	_	_
195	B2	b2	NN	_	_	_
196	TEX	TEX	NNP	_	_	_
197	pos	po	VBZ	_	_	_
198	L1	l1	NN	_	_	_
199	HS1	hs1	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	M63	m63	NN	_	_	_
202	0.4	0.4	CD	_	_	_
203	B2	b2	NN	_	_	_
204	TEX	TEX	NNP	_	_	_
205	pos	po	VBZ	_	_	_
206	L1	l1	NN	_	_	_
207	HS2	hs2	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	M9	m9	NN	_	_	_
210	defined	define	VBN	_	_	_
211	medium	medium	NN	_	_	_
212	-LRB-	-lrb-	-LRB-	_	_	_
213	0.6	0.6	CD	_	_	_
214	%	%	NN	_	_	_
215	Na2HPO4	na2hpo4	NN	_	_	_
216	,	,	,	_	_	_
217	0.3	0.3	CD	_	_	_
218	%	%	NN	_	_	_
219	KH2PO4	kh2po4	NN	_	_	_
220	,	,	,	_	_	_
221	0.05	0.05	CD	_	_	_
222	%	%	NN	_	_	_
223	NaCl	nacl	NN	_	_	_
224	,	,	,	_	_	_
225	0.01	0.01	CD	_	_	_
226	%	%	NN	_	_	_
227	NH4Cl	nh4cl	NN	_	_	_
228	,	,	,	_	_	_
229	0.1	0.1	CD	_	_	_
230	mM	mm	NN	KWSUPP	_	_
231	CaCl2	cacl2	NN	_	_	_
232	,	,	,	_	_	_
233	1	1	CD	_	_	_
234	mM	mm	NN	KWSUPP	_	_
235	MgSO4	mgso4	NN	_	_	_
236	,	,	,	_	_	_
237	5	5	CD	_	_	_
238	x	x	CC	_	_	_
239	10	10	CD	_	_	_
240	−	−	NN	_	_	_
241	4	4	CD	_	_	_
242	%	%	NN	_	_	_
243	Thiamin	thiamin	NN	_	_	_
244	-RRB-	-rrb-	-RRB-	_	_	_
245	supplemented	supplement	VBN	_	_	_
246	with	with	IN	_	_	_
247	0.5	0.5	CD	_	_	_
248	%	%	NN	_	_	_
249	glucose	glucose	NN	SUPP	_	_
250	and	and	CC	_	_	_
251	0.1	0.1	CD	_	_	_
252	%	%	NN	_	_	_
253	amino	amino	NN	SUPP	_	_
254	acids	acid	NNS	SUPP	_	_
255	was	be	VBD	_	_	_
256	used	use	VBN	_	_	_
257	for	for	IN	_	_	_
258	RNA-seq	rna-seq	NN	_	_	_
259	experiments	experiment	NNS	_	_	_
260	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	M9	m9	NN	_	_	_
3	mineral	mineral	NN	_	_	_
4	medium	medium	NN	_	_	_
5	containing	contain	VBG	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	D	d	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	-	-	:	_	_	_
10	xylose	xylose	NN	_	_	_
11	as	as	IN	_	_	_
12	the	the	DT	_	_	_
13	only	only	JJ	_	_	_
14	carbon	carbon	NN	_	_	_
15	source	source	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	100	100	CD	_	_	_
18	ml	ml	NN	_	_	_
19	in	in	IN	_	_	_
20	500	500	CD	_	_	_
21	ml	ml	NN	_	_	_
22	shake	shake	NN	_	_	_
23	flasks	flask	NNS	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	was	be	VBD	_	_	_
26	inoculated	inoculate	VBN	_	_	_
27	from	from	IN	_	_	_
28	exponentially	exponentially	RB	_	_	_
29	growing	grow	VBG	_	_	_
30	wild-type	wild-type	JJ	_	_	_
31	cells	cell	NNS	_	_	_
32	or	or	CC	_	_	_
33	synthetic	synthetic	JJ	_	_	_
34	cells	cell	NNS	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	cultivated	cultivate	VBN	_	_	_
37	on	on	IN	_	_	_
38	xylose	xylose	NN	_	_	_
39	M9	m9	NN	_	_	_
40	medium	medium	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	to	to	TO	_	_	_
43	adjust	adjust	VB	_	_	_
44	an	a	DT	_	_	_
45	OD	od	NN	_	_	_
46	of	of	IN	_	_	_
47	~	~	NN	_	_	_
48	0.1	0.1	CD	_	_	_
49	.	.	.	_	_	_

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	M9	m9	NN	_	_	_
3	minimal	minimal	JJ	_	_	_
4	complete	complete	JJ	_	_	_
5	media	media	NNS	_	_	_
6	,	,	,	_	_	_
7	cultures	culture	NNS	_	_	_
8	grown	grow	VBN	_	_	_
9	aerobically	aerobically	RB	_	_	_
10	at	at	IN	_	_	_
11	30	30	CD	_	_	_
12	degrees	degree	NNS	_	_	_
13	C	c	NN	_	_	_
14	in	in	IN	_	_	_
15	a	a	DT	_	_	_
16	gyratory	gyratory	JJ	_	_	_
17	water	water	NN	_	_	_
18	bath	bath	NN	_	_	_
19	shaking	shake	VBG	_	_	_
20	at	at	IN	_	_	_
21	240	240	CD	_	_	_
22	rpm	rpm	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	M9TMP5	m9tmp5	NN	_	_	_
25	_	_	CD	_	_	_
26	10	10	CD	_	_	_
27	min	min	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	M9TMP5	m9tmp5	NN	_	_	_
30	_	_	NN	_	_	_
31	120	120	CD	_	_	_
32	min	min	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	M9TMP5	m9tmp5	NN	_	_	_
35	_	_	CD	_	_	_
36	30	30	CD	_	_	_
37	min	min	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	M9TMP5	m9tmp5	NN	_	_	_
40	_	_	CD	_	_	_
41	60	60	CD	_	_	_
42	min	min	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	M9TMP5	m9tmp5	NN	_	_	_
45	_	_	CD	_	_	_
46	90	90	CD	_	_	_
47	min	min	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	M9TMP5	m9tmp5	NN	_	_	_
50	_	_	CD	_	_	_
51	AdAA	adaa	NN	_	_	_
52	_	_	NN	_	_	_
53	10	10	CD	_	_	_
54	min	min	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	M9TMP5	m9tmp5	NN	_	_	_
57	_	_	CD	_	_	_
58	AdAA	adaa	NN	_	_	_
59	_	_	NN	_	_	_
60	120	120	CD	_	_	_
61	min	min	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	M9TMP5	m9tmp5	NN	_	_	_
64	_	_	CD	_	_	_
65	AdAA	adaa	NN	_	_	_
66	_	_	CD	_	_	_
67	30	30	CD	_	_	_
68	min	min	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	M9TMP5	m9tmp5	NN	_	_	_
71	_	_	CD	_	_	_
72	AdAA	adaa	NN	_	_	_
73	_	_	NN	_	_	_
74	60	60	CD	_	_	_
75	min	min	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	M9TMP5	m9tmp5	NN	_	_	_
78	_	_	CD	_	_	_
79	AdAA	adaa	NN	_	_	_
80	_	_	NN	_	_	_
81	90	90	CD	_	_	_
82	min	min	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	M9	m9	NN	_	_	_
85	_	_	CD	_	_	_
86	TMP5	tmp5	NN	_	_	_
87	_	_	NN	_	_	_
88	THY	thy	NN	_	_	_
89	_	_	CD	_	_	_
90	Ad	ad	NN	_	_	_
91	_	_	SYM	_	_	_
92	AA	aa	SYM	_	_	_
93	_	_	SYM	_	_	_
94	10	10	CD	_	_	_
95	min	min	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	M9	m9	NN	_	_	_
98	_	_	CD	_	_	_
99	TMP5	tmp5	NN	_	_	_
100	_	_	CD	_	_	_
101	THY	THY	NNP	_	_	_
102	_	_	SYM	_	_	_
103	Ad	ad	FW	_	_	_
104	_	_	FW	_	_	_
105	AA	aa	NN	_	_	_
106	_	_	NN	_	_	_
107	120	120	CD	_	_	_
108	min	min	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	M9	m9	NN	_	_	_
111	_	_	CD	_	_	_
112	TMP5	tmp5	NN	_	_	_
113	_	_	CD	_	_	_
114	THY	THY	NNP	_	_	_
115	_	_	SYM	_	_	_
116	Ad	ad	FW	_	_	_
117	_	_	FW	_	_	_
118	AA	aa	NN	_	_	_
119	_	_	SYM	_	_	_
120	30	30	CD	_	_	_
121	min	min	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	M9	m9	NN	_	_	_
124	_	_	CD	_	_	_
125	TMP5	tmp5	NN	_	_	_
126	_	_	CD	_	_	_
127	THY	THY	NNP	_	_	_
128	_	_	SYM	_	_	_
129	Ad	ad	FW	_	_	_
130	_	_	FW	_	_	_
131	AA	aa	NN	_	_	_
132	_	_	NN	_	_	_
133	60	60	CD	_	_	_
134	min	min	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	M9TMP	m9tmp	NN	_	_	_
137	_	_	CD	_	_	_
138	AA	aa	NN	_	_	_
139	_	_	NN	_	_	_
140	10	10	CD	_	_	_
141	min	min	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	M9TMP	m9tmp	NN	_	_	_
144	_	_	CD	_	_	_
145	AA	aa	NN	_	_	_
146	_	_	NN	_	_	_
147	120	120	CD	_	_	_
148	min	min	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	M9TMP	m9tmp	NN	_	_	_
151	_	_	CD	_	_	_
152	AA	aa	NN	_	_	_
153	_	_	SYM	_	_	_
154	30	30	CD	_	_	_
155	min	min	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	M9TMP	m9tmp	NN	_	_	_
158	_	_	CD	_	_	_
159	AA	aa	NN	_	_	_
160	_	_	NN	_	_	_
161	60	60	CD	_	_	_
162	min	min	NN	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	M9TMP	m9tmp	NN	_	_	_
165	_	_	CD	_	_	_
166	Ad	ad	NN	_	_	_
167	_	_	SYM	_	_	_
168	10	10	CD	_	_	_
169	min	min	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	M9TMP	m9tmp	NN	_	_	_
172	_	_	CD	_	_	_
173	Ad	ad	NN	_	_	_
174	_	_	NN	_	_	_
175	120	120	CD	_	_	_
176	min	min	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	M9TMP	m9tmp	NN	_	_	_
179	_	_	CD	_	_	_
180	Ad	ad	NN	_	_	_
181	_	_	SYM	_	_	_
182	30	30	CD	_	_	_
183	min	min	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	M9TMP	m9tmp	NN	_	_	_
186	_	_	CD	_	_	_
187	Ad	ad	NN	_	_	_
188	_	_	SYM	_	_	_
189	60	60	CD	_	_	_
190	min	min	NN	_	_	_
191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
192	MACE	MACE	NNP	_	_	_
193	software	software	NN	_	_	_
194	-LRB-	-lrb-	-LRB-	_	_	_
195	https://code.google.com/p/chip-exo/	https://code.google.com/p/chip-exo/	NN	_	_	_
196	-RRB-	-rrb-	-RRB-	_	_	_
197	was	be	VBD	_	_	_
198	used	use	VBN	_	_	_
199	to	to	TO	_	_	_
200	detect	detect	VB	_	_	_
201	peaks	peak	NNS	_	_	_
202	with	with	IN	_	_	_
203	aligned	align	VBN	_	_	_
204	output	output	NN	_	_	_
205	from	from	IN	_	_	_
206	bowtie	bowtie	NN	_	_	_
207	mapping	mapping	NN	_	_	_
208	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
34	Mapped	map	VBD	_	_	_
35	R1	r1	NN	_	_	_
36	reads	read	VBZ	_	_	_
37	in	in	IN	_	_	_
38	single-end	single-end	JJ	_	_	_
39	mode	mode	NN	_	_	_
40	using	use	VBG	_	_	_
41	Bowtie2	bowtie2	NN	_	_	_
42	2.1.0	2.1.0	CD	_	_	_
43	with	with	IN	_	_	_
44	the	the	DT	_	_	_
45	--	--	:	_	_	_
46	k	k	NN	_	_	_
47	1	1	CD	_	_	_
48	option	option	NN	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Mapped	Mapped	NNP	_	_	_
51	read	read	VBD	_	_	_
52	counts	count	NNS	_	_	_
53	were	be	VBD	_	_	_
54	analyzed	analyze	VBN	_	_	_
55	for	for	IN	_	_	_
56	differential	differential	JJ	_	_	_
57	expression	expression	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	false	false	JJ	_	_	_
60	discovery	discovery	NN	_	_	_
61	rate	rate	NN	_	_	_
62	of	of	IN	_	_	_
63	<	<	JJR	_	_	_
64	0.01	0.01	CD	_	_	_
65	,	,	,	_	_	_
66	fold-change	fold-change	JJ	_	_	_
67	>	>	RBR	_	_	_
68	2	2	LS	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	using	use	VBG	_	_	_
71	the	the	DT	_	_	_
72	baySeq	bayseq	NN	_	_	_
73	package	package	NN	_	_	_
74	in	in	IN	_	_	_
75	R	r	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	Hardcastle	hardcastle	NN	_	_	_
78	and	and	CC	_	_	_
79	Kelly	Kelly	NNP	_	_	_
80	,	,	,	_	_	_
81	2010	2010	CD	_	_	_
82	,	,	,	_	_	_
83	BMC	BMC	NNP	_	_	_
84	Bioinformatics	Bioinformatics	NNPS	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	.	.	.	_	_	_

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	Mapped	map	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	per	per	IN	_	_	_
5	annotated	annotated	JJ	_	_	_
6	gene	gene	NN	_	_	_
7	were	be	VBD	_	_	_
8	counted	count	VBN	_	_	_
9	by	by	IN	_	_	_
10	Bam2readcount	bam2readcount	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Mapped	map	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	counted	count	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Python	Python	NNP	_	_	_
9	package	package	NN	_	_	_
10	HTSeq	htseq	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	v.	v.	CC	_	_	_
13	0.6.1	0.6.1	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	using	use	VBG	_	_	_
16	the	the	DT	_	_	_
17	following	follow	VBG	_	_	_
18	parameters	parameter	NNS	_	_	_
19	;	;	:	_	_	_
20	htseq-count	htseq-count	NN	_	_	_
21	-	-	:	_	_	_
22	m	m	NN	_	_	_
23	union	union	NN	_	_	_
24	-	-	:	_	_	_
25	r	r	NN	_	_	_
26	pos	pos	SYM	_	_	_
27	-	-	:	_	_	_
28	i	i	FW	_	_	_
29	gene	gene	NN	_	_	_
30	_	_	NN	_	_	_
31	name	name	NN	_	_	_
32	-	-	:	_	_	_
33	a	a	DT	_	_	_
34	10	10	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	Mapped	map	VBD	_	_	_
37	reads	read	VBZ	_	_	_
38	were	be	VBD	_	_	_
39	quality	quality	JJ	_	_	_
40	checked	check	VBN	_	_	_
41	with	with	IN	_	_	_
42	SAMstat	samstat	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	version	version	NN	_	_	_
45	1.08	1.08	CD	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	,	,	,	_	_	_
48	and	and	CC	_	_	_
49	transcripts	transcript	NNS	_	_	_
50	were	be	VBD	_	_	_
51	assembled	assemble	VBN	_	_	_
52	in	in	IN	_	_	_
53	Cufflinks	Cufflinks	NNP	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	version	version	NN	_	_	_
56	2.0.2	2.0.2	CD	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	mapping	mapping	NN	_	_	_
60	:	:	:	_	_	_
61	bowtie	bowtie	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Galaxy	galaxy	NN	_	_	_
64	Version	version	NN	_	_	_
65	1.1.2	1.1.2	CD	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	;	;	:	_	_	_
68	28	28	CD	_	_	_
69	nt	nt	NNS	_	_	_
70	seed	seed	NN	_	_	_
71	length	length	NN	_	_	_
72	,	,	,	_	_	_
73	maximal	maximal	JJ	_	_	_
74	two	two	CD	_	_	_
75	mismatches	mismatch	NNS	_	_	_
76	in	in	IN	_	_	_
77	the	the	DT	_	_	_
78	seed	seed	NN	_	_	_
79	,	,	,	_	_	_
80	a	a	DT	_	_	_
81	maximal	maximal	JJ	_	_	_
82	threshold	threshold	NN	_	_	_
83	of	of	IN	_	_	_
84	70	70	CD	_	_	_
85	for	for	IN	_	_	_
86	the	the	DT	_	_	_
87	sum	sum	NN	_	_	_
88	of	of	IN	_	_	_
89	the	the	DT	_	_	_
90	quality	quality	NN	_	_	_
91	values	value	NNS	_	_	_
92	at	at	IN	_	_	_
93	mismatched	mismatched	JJ	_	_	_
94	positions	position	NNS	_	_	_
95	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	mapping	mapping	NN	_	_	_
3	of	of	IN	_	_	_
4	non-rRNA	non-rrna	JJ	_	_	_
5	and	and	CC	_	_	_
6	tRNA	trna	NN	_	_	_
7	reads	read	VBZ	_	_	_
8	to	to	TO	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	O104	o104	NN	_	_	_
12	:	:	:	_	_	_
13	H4	h4	NN	_	_	_
14	chromosome	chromosome	NN	_	_	_
15	and	and	CC	_	_	_
16	plasmids	plasmid	NNS	_	_	_
17	using	use	VBG	_	_	_
18	READemption	reademption	NN	_	_	_
19	0.3.7	0.3.7	CD	_	_	_
20	and	and	CC	_	_	_
21	segemehl	segemehl	NN	_	_	_
22	0.2.0	0.2.0	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	mapping	mapping	NN	_	_	_
25	of	of	IN	_	_	_
26	reads	read	VBZ	_	_	_
27	to	to	TO	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	O104	o104	NN	_	_	_
31	:	:	:	_	_	_
32	H4	h4	NN	_	_	_
33	rRNAs	rrna	NNS	_	_	_
34	and	and	CC	_	_	_
35	tRNAs	trna	NNS	_	_	_
36	using	use	VBG	_	_	_
37	READemption	reademption	NN	_	_	_
38	0.3.7	0.3.7	CD	_	_	_
39	and	and	CC	_	_	_
40	segemehl	segemehl	NN	_	_	_
41	0.2.0	0.2.0	CD	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	Mapping	mapping	NN	_	_	_
44	of	of	IN	_	_	_
45	the	the	DT	_	_	_
46	trimmed	trimmed	RBR	_	_	_
47	reads	read	VBZ	_	_	_
48	to	to	TO	_	_	_
49	the	the	DT	_	_	_
50	reference	reference	NN	_	_	_
51	sequences	sequence	NNS	_	_	_
52	was	be	VBD	_	_	_
53	also	also	RB	_	_	_
54	performed	perform	VBN	_	_	_
55	with	with	IN	_	_	_
56	the	the	DT	_	_	_
57	CLC	clc	NN	_	_	_
58	Genomics	genomic	NNS	_	_	_
59	Workbench	workbench	JJ	_	_	_
60	9.0	9.0	CD	_	_	_
61	using	use	VBG	_	_	_
62	the	the	DT	_	_	_
63	`	`	``	_	_	_
64	Map	map	NN	_	_	_
65	Reads	read	VBZ	_	_	_
66	to	to	TO	_	_	_
67	Reference	Reference	NNP	_	_	_
68	'	'	POS	_	_	_
69	tool	tool	NN	_	_	_
70	with	with	IN	_	_	_
71	standard	standard	JJ	_	_	_
72	parameters	parameter	NNS	_	_	_
73	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Mapping	mapping	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	BWA	BWA	NNP	_	_	_
7	tool	tool	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	version	version	NN	_	_	_
10	0.5.9	0.5.9	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	against	against	IN	_	_	_
13	the	the	DT	_	_	_
14	reference	reference	NN	_	_	_
15	genome	genome	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Map	map	NN	_	_	_
18	reads	read	VBZ	_	_	_
19	to	to	TO	_	_	_
20	theEscherichia	theescherichia	FW	_	_	_
21	coli	coli	FW	_	_	_
22	MG1655	mg1655	NN	_	_	_
23	K-12	k-12	NN	_	_	_
24	genome	genome	NN	_	_	_
25	,	,	,	_	_	_
26	Bowtie	Bowtie	NNP	_	_	_
27	2	2	CD	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Map	map	NN	_	_	_
30	RNA-Seq	rna-seq	NN	_	_	_
31	reads	read	VBZ	_	_	_
32	to	to	TO	_	_	_
33	reference	reference	VB	_	_	_
34	genomes	genome	NNS	_	_	_
35	using	use	VBG	_	_	_
36	Bowtie	Bowtie	NNP	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Langmead	Langmead	NNP	_	_	_
39	et	et	FW	_	_	_
40	al.	al.	FW	_	_	_
41	,	,	,	_	_	_
42	2009	2009	CD	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	with	with	IN	_	_	_
45	alignment	alignment	NN	_	_	_
46	parameters	parameter	NNS	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	-	-	:	_	_	_
49	n	n	NN	_	_	_
50	2-e	2-e	JJ	_	_	_
51	70-l	70-l	JJ	_	_	_
52	28	28	CD	_	_	_
53	--	--	:	_	_	_
54	best	best	JJS	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	Map	map	NN	_	_	_
58	to	to	TO	_	_	_
59	MG1655	mg1655	NN	_	_	_
60	reference	reference	NN	_	_	_
61	using	use	VBG	_	_	_
62	BWA	BWA	NNP	_	_	_
63	0.7.4	0.7.4	CD	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	bwa	bwa	NN	_	_	_
66	mem	mem	NN	_	_	_
67	,	,	,	_	_	_
68	default	default	NN	_	_	_
69	parameters	parameter	NNS	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	map	map	NN	GEN	_	_
73	trimmed	trim	VBD	_	_	_
74	reads	read	VBZ	_	_	_
75	to	to	TO	_	_	_
76	reference	reference	NN	_	_	_
77	sequence	sequence	NN	_	_	_
78	in	in	IN	_	_	_
79	indexes	index	NNS	_	_	_
80	file	file	VBP	_	_	_
81	with	with	IN	_	_	_
82	bowtie2	bowtie2	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Marvinbryantia	marvinbryantia	NN	_	_	_
85	formatexigens	formatexigen	NNS	_	_	_
86	DSM	DSM	NNP	_	_	_
87	14469	14469	CD	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	MAS	MAS	NNP	_	_	_
90	5.0	5.0	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	MAS5	mas5	NN	_	_	_
93	.0	.0	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	MAS	mas	NN	_	_	_
96	5.0	5.0	CD	_	_	_
97	Expression	expression	NN	_	_	_
98	Analysis	analysis	NN	_	_	_
99	Default	Default	NNP	_	_	_
100	Setting	Setting	NNP	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	MAS	MAS	NNP	_	_	_
103	5.0	5.0	CD	_	_	_
104	Expression	expression	NN	_	_	_
105	Analysis	analysis	NN	_	_	_
106	Default	Default	NNP	_	_	_
107	Setting	Setting	NNP	_	_	_
108	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	MasterPure	masterpure	NN	_	_	_
3	RNA	rna	NN	_	_	_
4	purification	purification	NN	_	_	_
5	Kit	kit	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	MasterPure	masterpure	NN	_	_	_
8	RNA	rna	NN	_	_	_
9	purification	purification	NN	_	_	_
10	Kit	kit	NN	_	_	_
11	per	per	IN	_	_	_
12	manufacturers	manufacturer	NNS	_	_	_
13	protocol	protocol	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	material	material	NN	_	_	_
16	type	type	NN	_	_	_
17	:	:	:	_	_	_
18	whole	whole	JJ	_	_	_
19	_	_	JJ	_	_	_
20	organism	organism	NN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	MATLAB	MATLAB	NNP	_	_	_
23	v.	v.	CC	_	_	_
24	R2012b	r2012b	NN	_	_	_
25	program	program	NN	_	_	_
26	using	use	VBG	_	_	_
27	GCRMA	GCRMA	NNP	_	_	_
28	algorithm	algorithm	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	MatP	matp	NN	_	_	_
31	37	37	CD	_	_	_
32	°C	°c	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	∆	∆	CD	_	_	_
35	mazEF	mazef	NN	_	_	_
36	0	0	CD	_	_	_
37	μg/ml	μg/ml	NN	_	_	_
38	NA	na	NN	_	_	_
39	rep1	rep1	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	∆	∆	CD	_	_	_
42	mazEF	mazef	NN	_	_	_
43	0	0	CD	_	_	_
44	μg/ml	μg/ml	NN	_	_	_
45	NA	na	NN	_	_	_
46	rep2	rep2	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	∆	∆	CD	_	_	_
49	mazEF	mazef	NN	_	_	_
50	100	100	CD	_	_	_
51	μg/ml	μg/ml	NN	_	_	_
52	NA	na	NN	_	_	_
53	rep1	rep1	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	∆	∆	CD	_	_	_
56	mazEF	mazef	NN	_	_	_
57	100	100	CD	_	_	_
58	μg/ml	μg/ml	NN	_	_	_
59	NA	na	NN	_	_	_
60	rep2	rep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	∆	∆	CD	_	_	_
63	mazEF	mazef	NN	_	_	_
64	100	100	CD	_	_	_
65	μg/ml	μg/ml	NN	_	_	_
66	NA	na	NN	_	_	_
67	rep3	rep3	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	∆	∆	CD	_	_	_
70	mazEF	mazef	NN	_	_	_
71	10	10	CD	_	_	_
72	μg/ml	μg/ml	NN	_	_	_
73	NA	na	NN	_	_	_
74	rep1	rep1	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	∆	∆	CD	_	_	_
77	mazEF	mazef	NN	_	_	_
78	10	10	CD	_	_	_
79	μg/ml	μg/ml	NN	_	_	_
80	NA	na	NN	_	_	_
81	rep2	rep2	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	∆	∆	CD	_	_	_
84	mazEFlexA3	mazeflexa3	NN	_	_	_
85	0	0	CD	_	_	_
86	μg/ml	μg/ml	NN	_	_	_
87	NA	na	NN	_	_	_
88	rep1	rep1	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	∆	∆	CD	_	_	_
91	mazEFlexA3	mazeflexa3	NN	_	_	_
92	0	0	CD	_	_	_
93	μg/ml	μg/ml	NN	_	_	_
94	NA	na	NN	_	_	_
95	rep2	rep2	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	∆	∆	CD	_	_	_
98	mazEFlexA3	mazeflexa3	NN	_	_	_
99	100	100	CD	_	_	_
100	μg/ml	μg/ml	NN	_	_	_
101	NA	na	NN	_	_	_
102	rep1	rep1	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	∆	∆	CD	_	_	_
105	mazEFlexA3	mazeflexa3	NN	_	_	_
106	100	100	CD	_	_	_
107	μg/ml	μg/ml	NN	_	_	_
108	NA	na	NN	_	_	_
109	rep2	rep2	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	∆	∆	CD	_	_	_
112	mazEFlexA3	mazeflexa3	NN	_	_	_
113	10	10	CD	_	_	_
114	μg/ml	μg/ml	NN	_	_	_
115	NA	na	NN	_	_	_
116	rep1	rep1	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	∆	∆	CD	_	_	_
119	mazEFlexA3	mazeflexa3	NN	_	_	_
120	10	10	CD	_	_	_
121	μg/ml	μg/ml	NN	_	_	_
122	NA	na	NN	_	_	_
123	rep2	rep2	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	mazF	mazf	NN	GEN	_	_
126	_	_	CD	_	_	_
127	chpA	chpa	NN	_	_	_
128	upregulation	upregulation	NN	_	_	_
129	,	,	,	_	_	_
130	amp	amp	NN	_	_	_
131	50ug/ml	50ug/ml	NN	_	_	_
132	,	,	,	_	_	_
133	0.0125	0.0125	CD	_	_	_
134	%	%	NN	_	_	_
135	arabinose	arabinose	NN	_	_	_
136	,	,	,	_	_	_
137	0.025	0.025	CD	_	_	_
138	ug/ml	ug/ml	NN	_	_	_
139	norfloxacin	norfloxacin	NN	_	_	_
140	OD	od	NN	_	_	_
141	~	~	NN	_	_	_
142	0.3	0.3	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	MazF	mazf	NN	_	_	_
145	_	_	NN	_	_	_
146	mRNA	mrna	NN	_	_	_
147	_	_	SYM	_	_	_
148	5m	5m	FW	_	_	_
149	_	_	FW	_	_	_
150	rep1	rep1	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	MazF	mazf	NN	_	_	_
153	_	_	NN	_	_	_
154	mRNA	mrna	NN	_	_	_
155	_	_	SYM	_	_	_
156	5m	5m	FW	_	_	_
157	_	_	FW	_	_	_
158	rep2	rep2	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	MazF	mazf	NN	_	_	_
161	_	_	CD	_	_	_
162	totalRNA	totalrna	NN	_	_	_
163	_	_	SYM	_	_	_
164	30m	30m	FW	_	_	_
165	_	_	FW	_	_	_
166	rep1	rep1	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	MazF	mazf	NN	_	_	_
169	_	_	CD	_	_	_
170	totalRNA	totalrna	NN	_	_	_
171	_	_	SYM	_	_	_
172	30m	30m	FW	_	_	_
173	_	_	FW	_	_	_
174	rep2	rep2	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	MazF	mazf	NN	_	_	_
177	_	_	CD	_	_	_
178	totalRNA	totalrna	NN	_	_	_
179	_	_	SYM	_	_	_
180	5m	5m	FW	_	_	_
181	_	_	FW	_	_	_
182	rep1	rep1	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	MazF	mazf	NN	_	_	_
185	_	_	CD	_	_	_
186	totalRNA	totalrna	NN	_	_	_
187	_	_	SYM	_	_	_
188	5m	5m	FW	_	_	_
189	_	_	FW	_	_	_
190	rep2	rep2	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	MazF	mazf	NN	_	_	_
193	_	_	CD	_	_	_
194	totalRNA	totalrna	NN	_	_	_
195	_	_	SYM	_	_	_
196	60m	60m	FW	_	_	_
197	_	_	FW	_	_	_
198	rep1	rep1	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	MazF	mazf	NN	_	_	_
201	_	_	CD	_	_	_
202	totalRNA	totalrna	NN	_	_	_
203	_	_	SYM	_	_	_
204	60m	60m	FW	_	_	_
205	_	_	FW	_	_	_
206	rep2	rep2	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	mazF	mazf	NN	GEN	_	_
209	___	___	CD	_	_	_
210	U	U	NNP	_	_	_
211	_	_	NNP	_	_	_
212	N0025	N0025	NNP	_	_	_
213	_	_	VBD	_	_	_
214	r1	r1	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	mazF	mazf	NN	GEN	_	_
217	___	___	CD	_	_	_
218	U	U	NNP	_	_	_
219	_	_	NNP	_	_	_
220	N0025	N0025	NNP	_	_	_
221	_	_	VBD	_	_	_
222	r2	r2	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	mazF	mazf	NN	GEN	_	_
225	___	___	CD	_	_	_
226	U	U	NNP	_	_	_
227	_	_	NNP	_	_	_
228	N0025	N0025	NNP	_	_	_
229	_	_	SYM	_	_	_
230	r3	r3	FW	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
232	MBC	mbc	NN	_	_	_
233	of	of	IN	_	_	_
234	CYA	CYA	NNP	_	_	_
235	,	,	,	_	_	_
236	biological	biological	JJ	_	_	_
237	rep1	rep1	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	MBC	mbc	NN	_	_	_
240	of	of	IN	_	_	_
241	CYA	CYA	NNP	_	_	_
242	,	,	,	_	_	_
243	biological	biological	JJ	_	_	_
244	rep2	rep2	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	MBC	mbc	NN	_	_	_
247	of	of	IN	_	_	_
248	CYA	CYA	NNP	_	_	_
249	,	,	,	_	_	_
250	biological	biological	JJ	_	_	_
251	rep3	rep3	NN	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	MBC	mbc	NN	_	_	_
254	of	of	IN	_	_	_
255	OLA	OLA	NNP	_	_	_
256	,	,	,	_	_	_
257	biological	biological	JJ	_	_	_
258	rep1	rep1	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	MBC	mbc	NN	_	_	_
261	of	of	IN	_	_	_
262	OLA	OLA	NNP	_	_	_
263	,	,	,	_	_	_
264	biological	biological	JJ	_	_	_
265	rep2	rep2	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	MBC	mbc	NN	_	_	_
268	of	of	IN	_	_	_
269	OLA	OLA	NNP	_	_	_
270	,	,	,	_	_	_
271	biological	biological	JJ	_	_	_
272	rep3	rep3	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	mcrB	mcrb	NN	GEN	_	_
275	__	__	CD	_	_	_
276	U	U	NNP	_	_	_
277	_	_	NNP	_	_	_
278	N0075	N0075	NNP	_	_	_
279	_	_	VBD	_	_	_
280	r1	r1	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	mcrB	mcrb	NN	GEN	_	_
283	__	__	CD	_	_	_
284	U	U	NNP	_	_	_
285	_	_	NNP	_	_	_
286	N0075	N0075	NNP	_	_	_
287	_	_	VBD	_	_	_
288	r2	r2	NN	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	mcrB	mcrb	NN	GEN	_	_
291	__	__	CD	_	_	_
292	U	U	NNP	_	_	_
293	_	_	NNP	_	_	_
294	N0075	N0075	NNP	_	_	_
295	_	_	VBD	_	_	_
296	r3	r3	NN	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	mcrB	mcrb	NN	GEN	_	_
299	upregulation	upregulation	NN	_	_	_
300	,	,	,	_	_	_
301	0.075	0.075	CD	_	_	_
302	mg/mL	mg/ml	NN	_	_	_
303	norfloxacin	norfloxacin	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	mcrC	mcrc	NN	GEN	_	_
306	__	__	CD	_	_	_
307	U	U	NNP	_	_	_
308	_	_	NNP	_	_	_
309	N0075	N0075	NNP	_	_	_
310	_	_	VBD	_	_	_
311	r1	r1	NN	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	mcrC	mcrc	NN	GEN	_	_
314	__	__	CD	_	_	_
315	U	U	NNP	_	_	_
316	_	_	NNP	_	_	_
317	N0075	N0075	NNP	_	_	_
318	_	_	VBD	_	_	_
319	r2	r2	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	mcrC	mcrc	NN	GEN	_	_
322	__	__	CD	_	_	_
323	U	U	NNP	_	_	_
324	_	_	NNP	_	_	_
325	N0075	N0075	NNP	_	_	_
326	_	_	VBD	_	_	_
327	r3	r3	NN	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	mcrC	mcrc	NN	GEN	_	_
330	upregulation	upregulation	NN	_	_	_
331	,	,	,	_	_	_
332	0.075	0.075	CD	_	_	_
333	mg/mL	mg/ml	NN	_	_	_
334	norfloxacin	norfloxacin	NN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	MC	MC	NNP	_	_	_
337	_	_	NNP	_	_	_
338	Val	val	NN	_	_	_
339	_	_	SYM	_	_	_
340	G1	g1	NN	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	MC	MC	NNP	_	_	_
343	_	_	NNP	_	_	_
344	Val	val	NN	_	_	_
345	_	_	SYM	_	_	_
346	G2	g2	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	MC	MC	NNP	_	_	_
349	_	_	NNP	_	_	_
350	Val	val	NN	_	_	_
351	_	_	SYM	_	_	_
352	G3	g3	NN	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	MC	MC	NNP	_	_	_
355	_	_	NNP	_	_	_
356	Val	val	NN	_	_	_
357	_	_	CD	_	_	_
358	G5	g5	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	MDS42	mds42	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	MDS42	mds42	NN	_	_	_
363	1	1	CD	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	MDS42	mds42	NN	_	_	_
366	2	2	CD	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	MDS42	mds42	NN	_	_	_
369	+	+	CC	_	_	_
370	20	20	CD	_	_	_
371	ug/ml	ug/ml	NN	_	_	_
372	bicyclomycin	bicyclomycin	NN	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	MDS42	mds42	NN	_	_	_
375	+	+	CC	_	_	_
376	20	20	CD	_	_	_
377	ug/ml	ug/ml	NN	_	_	_
378	bicyclomycin	bicyclomycin	NN	_	_	_
379	1	1	CD	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
381	MDS42	mds42	NN	_	_	_
382	+	+	CC	_	_	_
383	20	20	CD	_	_	_
384	ug/ml	ug/ml	NN	_	_	_
385	bicyclomycin	bicyclomycin	NN	_	_	_
386	2	2	CD	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	MDS42	mds42	NN	_	_	_
389	,	,	,	_	_	_
390	biological	biological	JJ	_	_	_
391	rep	rep	NN	GEN	_	_
392	1	1	CD	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	MDS42	mds42	NN	_	_	_
395	,	,	,	_	_	_
396	biological	biological	JJ	_	_	_
397	rep	rep	NN	GEN	_	_
398	2	2	CD	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	MDS42	mds42	NN	_	_	_
401	,	,	,	_	_	_
402	biological	biological	JJ	_	_	_
403	rep	rep	NN	GEN	_	_
404	3	3	CD	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	MDS42	mds42	NN	_	_	_
407	,	,	,	_	_	_
408	biological	biological	JJ	_	_	_
409	rep	rep	NN	GEN	_	_
410	4	4	CD	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	MDS42	mds42	NN	_	_	_
413	,	,	,	_	_	_
414	biological	biological	JJ	_	_	_
415	rep	rep	NN	GEN	_	_
416	5	5	CD	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	MDS42	mds42	NN	_	_	_
419	,	,	,	_	_	_
420	biological	biological	JJ	_	_	_
421	rep	rep	NN	GEN	_	_
422	6	6	CD	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	MDS42	mds42	NN	_	_	_
425	,	,	,	_	_	_
426	biological	biological	JJ	_	_	_
427	rep	rep	NN	GEN	_	_
428	7	7	CD	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	MDS42	mds42	NN	_	_	_
431	DNA	dna	NN	_	_	_
432	isolated	isolate	VBN	_	_	_
433	from	from	IN	_	_	_
434	early-phase	early-phase	JJ	_	_	_
435	DNA-protein	dna-protein	JJ	_	_	_
436	complexes	complex	NNS	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	MDS42	mds42	NN	_	_	_
439	exponentially	exponentially	RB	_	_	_
440	grown	grow	VBN	_	_	_
441	in	in	IN	_	_	_
442	the	the	DT	_	_	_
443	minimal	minimal	JJ	_	_	_
444	medium	medium	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	MDS42	mds42	NN	_	_	_
447	,	,	,	_	_	_
448	heat	heat	NN	_	_	_
449	shock	shock	NN	_	_	_
450	,	,	,	_	_	_
451	biological	biological	JJ	_	_	_
452	rep	rep	NN	GEN	_	_
453	1	1	CD	_	_	_
454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
455	MDS42	mds42	NN	_	_	_
456	,	,	,	_	_	_
457	heat	heat	NN	_	_	_
458	shock	shock	NN	_	_	_
459	,	,	,	_	_	_
460	biological	biological	JJ	_	_	_
461	rep	rep	NN	GEN	_	_
462	2	2	CD	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	MDS42	mds42	NN	_	_	_
465	,	,	,	_	_	_
466	heat	heat	NN	_	_	_
467	shock	shock	NN	_	_	_
468	,	,	,	_	_	_
469	biological	biological	JJ	_	_	_
470	rep	rep	NN	GEN	_	_
471	3	3	CD	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	MDS42	mds42	NN	_	_	_
474	RNAP	rnap	NN	_	_	_
475	1	1	CD	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	MDS42	mds42	NN	_	_	_
478	RNAP	rnap	NN	_	_	_
479	2	2	CD	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	MDS42	mds42	NN	_	_	_
482	ΔnusA	δnusa	NN	_	_	_
483	*	*	SYM	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	MDS42	mds42	NN	_	_	_
486	ΔnusA	δnusa	NN	_	_	_
487	*	*	SYM	_	_	_
488	1	1	CD	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	MDS42	mds42	NN	_	_	_
491	ΔnusA	δnusa	NN	_	_	_
492	*	*	SYM	_	_	_
493	2	2	CD	_	_	_
494	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
495	MDS42	mds42	NN	_	_	_
496	ΔnusA	δnusa	NN	_	_	_
497	*	*	SYM	_	_	_
498	RNAP	rnap	NN	_	_	_
499	1	1	CD	_	_	_
500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
501	MDS42	mds42	NN	_	_	_
502	ΔnusA	δnusa	NN	_	_	_
503	*	*	SYM	_	_	_
504	RNAP	rnap	NN	_	_	_
505	2	2	CD	_	_	_
506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
507	MDS42	mds42	NN	_	_	_
508	ΔnusG	δnusg	NN	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	MDS42	mds42	NN	_	_	_
511	ΔnusG	δnusg	NN	_	_	_
512	1	1	CD	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	MDS42	mds42	NN	_	_	_
515	ΔnusG	δnusg	NN	_	_	_
516	2	2	CD	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	MDS42	mds42	NN	_	_	_
519	ΔnusG	δnusg	NN	_	_	_
520	RNAP	rnap	NN	_	_	_
521	1	1	CD	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
523	MDS42	mds42	NN	_	_	_
524	ΔnusG	δnusg	NN	_	_	_
525	RNAP	rnap	NN	_	_	_
526	2	2	CD	_	_	_
527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
528	ME0052	me0052	NN	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	ME0053	me0053	NN	_	_	_
531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
532	ME0054	me0054	NN	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	ME0055	me0055	NN	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	media	media	NNS	_	_	_
537	:	:	:	_	_	_
538	Defined	define	VBN	_	_	_
539	MOPS	mop	NNS	MED	_	_
540	Minimal	minimal	JJ	_	_	_
541	+	+	CC	_	_	_
542	0.4	0.4	CD	_	_	_
543	%	%	NN	_	_	_
544	Glycerol	glycerol	NN	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	media	media	NNS	_	_	_
547	:	:	:	_	_	_
548	Defined	define	VBN	_	_	_
549	MOPS	mop	NNS	MED	_	_
550	Minimal	minimal	JJ	_	_	_
551	+	+	CC	_	_	_
552	0.4	0.4	CD	_	_	_
553	%	%	NN	_	_	_
554	Glycerol	glycerol	NN	_	_	_
555	+0.5	+0.5	CD	_	_	_
556	%	%	NN	_	_	_
557	2-DG	2-dg	JJ	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
559	media	media	NNS	_	_	_
560	:	:	:	_	_	_
561	Defined	define	VBN	_	_	_
562	MOPS	mop	NNS	MED	_	_
563	Minimal	minimal	JJ	_	_	_
564	+	+	CC	_	_	_
565	0.4	0.4	CD	_	_	_
566	%	%	NN	_	_	_
567	Glycerol	glycerol	NN	_	_	_
568	+0.5	+0.5	CD	_	_	_
569	%	%	NN	_	_	_
570	aMG	amg	NN	_	_	_
571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
572	media	media	NNS	_	_	_
573	:	:	:	_	_	_
574	Defined	define	VBN	_	_	_
575	MOPS	mop	NNS	MED	_	_
576	Rich	rich	JJ	_	_	_
577	+	+	CC	_	_	_
578	0.2	0.2	CD	_	_	_
579	%	%	NN	_	_	_
580	Glucose	glucose	NN	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	media	media	NNS	_	_	_
583	:	:	:	_	_	_
584	Defined	define	VBN	_	_	_
585	MOPS	mop	NNS	MED	_	_
586	Rich	rich	JJ	_	_	_
587	+	+	CC	_	_	_
588	0.4	0.4	CD	_	_	_
589	%	%	NN	_	_	_
590	Glycerol	glycerol	NN	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	media	media	NNS	_	_	_
593	:	:	:	_	_	_
594	Defined	define	VBN	_	_	_
595	MOPS	mop	NNS	MED	_	_
596	Rich	rich	JJ	_	_	_
597	+	+	CC	_	_	_
598	0.4	0.4	CD	_	_	_
599	%	%	NN	_	_	_
600	Glycerol	glycerol	NN	_	_	_
601	+0.5	+0.5	CD	_	_	_
602	%	%	NN	_	_	_
603	aMG	amg	NN	_	_	_
604	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
605	media	media	NNS	_	_	_
606	:	:	:	_	_	_
607	fully	fully	RB	_	_	_
608	supplemented	supplement	VBN	_	_	_
609	MOPS	mop	NNS	MED	_	_
610	glucose	glucose	NN	SUPP	_	_
611	media	media	NNS	_	_	_
612	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
613	media	media	NNS	_	_	_
614	:	:	:	_	_	_
615	LB	lb	NN	_	_	_
616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
617	media	media	NNS	_	_	_
618	:	:	:	_	_	_
619	LB	lb	NN	_	_	_
620	+	+	CC	_	_	_
621	0.5	0.5	CD	_	_	_
622	%	%	NN	_	_	_
623	aMG	amg	NN	_	_	_
624	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
625	media	media	NNS	_	_	_
626	:	:	:	_	_	_
627	LB	lb	NN	MED	_	_
628	broth	broth	NN	MED	_	_
629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
630	media	media	NNS	_	_	_
631	:	:	:	_	_	_
632	M9	m9	NN	_	_	_
633	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
634	media	media	NNS	_	_	_
635	:	:	:	_	_	_
636	MEM-HEPES	mem-hepes	NN	_	_	_
637	supplemented	supplement	VBN	_	_	_
638	with	with	IN	_	_	_
639	0.1	0.1	CD	_	_	_
640	%	%	NN	_	_	_
641	Glucose	glucose	NN	_	_	_
642	and	and	CC	_	_	_
643	250nM	250nm	NN	_	_	_
644	Fe	Fe	NNP	_	_	_
645	-LRB-	-lrb-	-LRB-	_	_	_
646	NO3	no3	NN	_	_	_
647	-RRB-	-rrb-	-RRB-	_	_	_
648	2	2	CD	_	_	_
649	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
650	Media	Media	NNP	_	_	_
651	:	:	:	_	_	_
652	Minimal	minimal	JJ	_	_	_
653	salts	salt	NNS	_	_	_
654	+	+	CC	_	_	_
655	20	20	CD	_	_	_
656	mM	mm	NN	KWSUPP	_	_
657	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
658	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
659	Media	Media	NNP	_	_	_
660	:	:	:	_	_	_
661	Minimal	minimal	JJ	_	_	_
662	salts	salt	NNS	_	_	_
663	+	+	CC	_	_	_
664	20	20	CD	_	_	_
665	mM	mm	NN	KWSUPP	_	_
666	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
667	+2.5	+2.5	CD	_	_	_
668	mM	mm	NN	KWSUPP	_	_
669	sodium	sodium	NN	_	_	_
670	nitrite	nitrite	JJ	_	_	_
671	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
672	media	media	NNS	_	_	_
673	:	:	:	_	_	_
674	MOPS	MOPS	NNP	MED	_	_
675	EZ	EZ	NNP	_	_	_
676	Rich	Rich	NNP	_	_	_
677	Defined	Defined	NNP	_	_	_
678	Media	Media	NNP	_	_	_
679	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
680	Median	median	JJ	_	_	_
681	of	of	IN	_	_	_
682	intensity	intensity	NN	_	_	_
683	data	datum	NNS	_	_	_
684	was	be	VBD	_	_	_
685	extracted	extract	VBN	_	_	_
686	,	,	,	_	_	_
687	LOESS	LOESS	NNP	_	_	_
688	normalized	normalize	VBD	_	_	_
689	and	and	CC	_	_	_
690	an	a	DT	_	_	_
691	ANOVA	ANOVA	NNP	_	_	_
692	model	model	NN	_	_	_
693	was	be	VBD	_	_	_
694	fit	fit	VBN	_	_	_
695	using	use	VBG	_	_	_
696	the	the	DT	_	_	_
697	MAANOVA	MAANOVA	NNP	_	_	_
698	package	package	NN	_	_	_
699	in	in	IN	_	_	_
700	R	r	NN	_	_	_
701	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Log	log	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	Cy5/Cy3	cy5/cy3	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	values	value	NNS	_	_	_
7	were	be	VBD	_	_	_
8	extracted	extract	VBN	_	_	_
9	from	from	IN	_	_	_
10	the	the	DT	_	_	_
11	VG	vg	NN	_	_	_
12	matrix	matrix	NN	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	model	model	NN	_	_	_
16	fit	fit	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	media	media	NNS	_	_	_
3	:	:	:	_	_	_
4	Tryptone	tryptone	NN	_	_	_
5	broth	broth	NN	_	_	_
6	buffered	buffer	VBD	_	_	_
7	to	to	TO	_	_	_
8	pH	ph	NN	_	_	_
9	7	7	CD	_	_	_
10	supplemented	supplement	VBN	_	_	_
11	with	with	IN	_	_	_
12	22	22	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	glucose	glucose	NN	SUPP	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	medium	medium	NN	_	_	_
17	:	:	:	_	_	_
18	ACSH	ACSH	NNP	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	medium	medium	NN	_	_	_
21	:	:	:	_	_	_
22	defined	define	VBN	_	_	_
23	mineral	mineral	JJ	_	_	_
24	medium	medium	NN	_	_	_
25	with	with	IN	_	_	_
26	1	1	CD	_	_	_
27	g/l	g/l	NN	_	_	_
28	glucose	glucose	NN	SUPP	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	medium	medium	NN	_	_	_
31	:	:	:	_	_	_
32	LB	lb	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	medium	medium	NN	_	_	_
35	:	:	:	_	_	_
36	M63	m63	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	medium	medium	NN	_	_	_
39	:	:	:	_	_	_
40	M9	m9	NN	_	_	_
41	medium	medium	NN	_	_	_
42	supplemented	supplement	VBN	_	_	_
43	with	with	IN	_	_	_
44	0.2	0.2	CD	_	_	_
45	%	%	NN	_	_	_
46	glucose	glucose	NN	SUPP	_	_
47	and	and	CC	_	_	_
48	5	5	CD	_	_	_
49	%	%	NN	_	_	_
50	LB	lb	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	medium	medium	NN	_	_	_
53	:	:	:	_	_	_
54	MOPS	mop	NNS	MED	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
56	medium	medium	NN	_	_	_
57	:	:	:	_	_	_
58	Neidhardt	Neidhardt	NNP	_	_	_
59	's	's	POS	_	_	_
60	EZ	EZ	NNP	_	_	_
61	Rich	Rich	NNP	_	_	_
62	Defined	Defined	NNP	_	_	_
63	Medium	medium	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	Teknova	Teknova	NNP	_	_	_
66	,	,	,	_	_	_
67	USA	USA	NNP	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
70	medium	medium	NN	_	_	_
71	:	:	:	_	_	_
72	SB	sb	NN	_	_	_
73	broth	broth	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	medium	medium	NN	_	_	_
76	:	:	:	_	_	_
77	SynH	synh	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	medium	medium	NN	_	_	_
80	:	:	:	_	_	_
81	SynH	synh	NN	_	_	_
82	_	_	NN	_	_	_
83	Acids	acid	NNS	_	_	_
84	_	_	VBP	_	_	_
85	Amides	amide	NNS	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
87	medium	medium	NN	_	_	_
88	:	:	:	_	_	_
89	SynH	synh	NN	_	_	_
90	_	_	CD	_	_	_
91	LT	lt	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	medium	medium	NN	_	_	_
94	:	:	:	_	_	_
95	SynH	synh	NN	_	_	_
96	+	+	CC	_	_	_
97	LTs	lts	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
99	medium	medium	NN	_	_	_
100	:	:	:	_	_	_
101	SynH	synh	NN	_	_	_
102	w/o	w/o	NN	_	_	_
103	osmoprotectants	osmoprotectant	NNS	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
105	medium	medium	NN	_	_	_
106	:	:	:	_	_	_
107	SynH	synh	NN	_	_	_
108	w/o	w/o	NN	_	_	_
109	osmoprotectants	osmoprotectant	NNS	_	_	_
110	+	+	CC	_	_	_
111	LTs	lt	NNS	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
113	menB	menb	NN	GEN	_	_
114	__	__	CD	_	_	_
115	U	U	NNP	_	_	_
116	_	_	NNP	_	_	_
117	N0075	N0075	NNP	_	_	_
118	_	_	VBD	_	_	_
119	r1	r1	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	menB	menb	NN	GEN	_	_
122	__	__	CD	_	_	_
123	U	U	NNP	_	_	_
124	_	_	NNP	_	_	_
125	N0075	N0075	NNP	_	_	_
126	_	_	VBD	_	_	_
127	r2	r2	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	menB	menb	NN	GEN	_	_
130	__	__	CD	_	_	_
131	U	U	NNP	_	_	_
132	_	_	NNP	_	_	_
133	N0075	N0075	NNP	_	_	_
134	_	_	VBD	_	_	_
135	r3	r3	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	menB	menb	NN	GEN	_	_
138	upregulation	upregulation	NN	_	_	_
139	,	,	,	_	_	_
140	0.075	0.075	CD	_	_	_
141	mg/mL	mg/ml	NN	_	_	_
142	norfloxacin	norfloxacin	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	menC	menc	NN	GEN	_	_
145	__	__	CD	_	_	_
146	U	U	NNP	_	_	_
147	_	_	NNP	_	_	_
148	N0075	N0075	NNP	_	_	_
149	_	_	NNP	_	_	_
150	r1	r1	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	menC	menc	NN	GEN	_	_
153	__	__	CD	_	_	_
154	U	U	NNP	_	_	_
155	_	_	NNP	_	_	_
156	N0075	N0075	NNP	_	_	_
157	_	_	SYM	_	_	_
158	r2	r2	FW	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
160	menC	menc	NN	GEN	_	_
161	__	__	CD	_	_	_
162	U	U	NNP	_	_	_
163	_	_	NNP	_	_	_
164	N0075	N0075	NNP	_	_	_
165	_	_	SYM	_	_	_
166	r3	r3	FW	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
168	menC	menc	NN	GEN	_	_
169	upregulation	upregulation	NN	_	_	_
170	,	,	,	_	_	_
171	0.075	0.075	CD	_	_	_
172	mg/mL	mg/ml	NN	_	_	_
173	norfloxacin	norfloxacin	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
175	Merge	merge	VBP	_	_	_
176	the	the	DT	_	_	_
177	replicates	replicate	VBZ	_	_	_
178	for	for	IN	_	_	_
179	each	each	DT	_	_	_
180	sample	sample	NN	_	_	_
181	.	.	.	_	_	_

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	metabolic	metabolic	JJ	_	_	_
20	response	response	NN	_	_	_
21	:	:	:	_	_	_
22	BL21	bl21	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	DE3	de3	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	is	be	VBZ	_	_	_
27	very	very	RB	_	_	_
28	susceptible	susceptible	JJ	_	_	_
29	to	to	TO	_	_	_
30	heptanoic	heptanoic	JJ	_	_	_
31	acid	acid	NN	_	_	_
32	,	,	,	_	_	_
33	because	because	IN	_	_	_
34	several	several	JJ	_	_	_
35	acid	acid	NN	_	_	_
36	resistance	resistance	NN	_	_	_
37	systems	system	NNS	_	_	_
38	stay	stay	VBP	_	_	_
39	inactive	inactive	JJ	_	_	_
40	under	under	IN	_	_	_
41	this	this	DT	_	_	_
42	stress	stress	NN	_	_	_
43	condition	condition	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	metabolic	metabolic	JJ	_	_	_
46	response	response	NN	_	_	_
47	:	:	:	_	_	_
48	K12	k12	NN	_	_	_
49	MG1655	mg1655	NN	_	_	_
50	activates	activate	VBZ	_	_	_
51	various	various	JJ	_	_	_
52	acid	acid	NN	_	_	_
53	resistance	resistance	NN	_	_	_
54	systems	system	NNS	_	_	_
55	under	under	IN	_	_	_
56	heptanoic	heptanoic	JJ	_	_	_
57	acid	acid	NN	_	_	_
58	stress	stress	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Metabolome	metabolome	NN	_	_	_
61	data	datum	NNS	_	_	_
62	for	for	IN	_	_	_
63	these	these	DT	_	_	_
64	cultures	culture	NNS	_	_	_
65	are	be	VBP	_	_	_
66	also	also	RB	_	_	_
67	provided	provide	VBN	_	_	_
68	in	in	IN	_	_	_
69	the	the	DT	_	_	_
70	supplementary	supplementary	JJ	_	_	_
71	file	file	NN	_	_	_
72	\	\	SYM	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
74	Methionine	Methionine	NNP	_	_	_
75	addition	addition	NN	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Methylation	methylation	NN	_	_	_
78	in	in	IN	_	_	_
79	0	0	CD	_	_	_
80	min	min	NN	_	_	_
81	dnaC2	dnac2	NN	_	_	_
82	rep1	rep1	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Methylation	methylation	NN	_	_	_
85	in	in	IN	_	_	_
86	0	0	CD	_	_	_
87	min	min	NN	_	_	_
88	dnaC2	dnac2	NN	_	_	_
89	rep2	rep2	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	Methylation	methylation	NN	_	_	_
92	in	in	IN	_	_	_
93	15	15	CD	_	_	_
94	min	min	NN	_	_	_
95	dnaC2	dnac2	NN	_	_	_
96	rep1	rep1	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Methylation	methylation	NN	_	_	_
99	in	in	IN	_	_	_
100	15	15	CD	_	_	_
101	min	min	NN	_	_	_
102	dnaC2	dnac2	NN	_	_	_
103	rep2	rep2	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	mev	mev	NN	_	_	_
106	data	datum	NNS	_	_	_
107	obtained	obtain	VBN	_	_	_
108	from	from	IN	_	_	_
109	the	the	DT	_	_	_
110	feature	feature	NN	_	_	_
111	extraction	extraction	NN	_	_	_
112	file	file	NN	_	_	_
113	used	use	VBN	_	_	_
114	,	,	,	_	_	_
115	no	no	DT	_	_	_
116	further	further	JJ	_	_	_
117	normalization	normalization	NN	_	_	_
118	needed	need	VBD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	mfd	mfd	NN	GEN	_	_
121	_	_	NN	_	_	_
122	1	1	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	MFD	mfd	NN	_	_	_
125	+	+	CC	_	_	_
126	+	+	CC	_	_	_
127	_	_	SYM	_	_	_
128	1	1	CD	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	mfd	mfd	NN	GEN	_	_
131	_	_	NN	_	_	_
132	2	2	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	MFD	mfd	NN	_	_	_
135	+	+	CC	_	_	_
136	+	+	CC	_	_	_
137	_	_	SYM	_	_	_
138	2	2	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	mfd	mfd	NN	GEN	_	_
141	_	_	NN	_	_	_
142	3	3	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	mg1655	mg1655	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	MG1655	mg1655	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	MG1655	mg1655	NN	_	_	_
149	1	1	CD	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	MG1655	mg1655	NN	_	_	_
152	_	_	NN	_	_	_
153	1	1	CD	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	MG1655	mg1655	NN	_	_	_
156	2	2	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	MG1655	mg1655	NN	_	_	_
159	_	_	NN	_	_	_
160	2	2	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	MG1655	mg1655	NN	_	_	_
163	+	+	CC	_	_	_
164	20	20	CD	_	_	_
165	ug/ml	ug/ml	NN	_	_	_
166	bicyclomycin	bicyclomycin	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	MG1655	mg1655	NN	_	_	_
169	+	+	CC	_	_	_
170	20	20	CD	_	_	_
171	ug/ml	ug/ml	NN	_	_	_
172	bicyclomycin	bicyclomycin	NN	_	_	_
173	1	1	CD	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	MG1655	mg1655	NN	_	_	_
176	+	+	CC	_	_	_
177	20	20	CD	_	_	_
178	ug/ml	ug/ml	NN	_	_	_
179	bicyclomycin	bicyclomycin	NN	_	_	_
180	2	2	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	MG1655	mg1655	NN	_	_	_
183	2	2	CD	_	_	_
184	'	'	''	_	_	_
185	post	post	JJ	_	_	_
186	rif	rif	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	MG1655	mg1655	NN	_	_	_
189	_	_	CD	_	_	_
190	3	3	CD	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	MG1655	mg1655	NN	_	_	_
193	4	4	CD	_	_	_
194	'	'	''	_	_	_
195	post	post	JJ	_	_	_
196	rif	rif	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	MG1655	mg1655	NN	_	_	_
199	6	6	CD	_	_	_
200	'	'	''	_	_	_
201	post	post	JJ	_	_	_
202	rif	rif	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	MG1655	mg1655	NN	_	_	_
205	8	8	CD	_	_	_
206	'	'	''	_	_	_
207	post	post	JJ	_	_	_
208	rif	rif	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	MG1655-aMG	mg1655-amg	NN	_	_	_
211	_	_	NN	_	_	_
212	1	1	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	MG1655	mg1655	NN	_	_	_
215	+	+	CC	_	_	_
216	aMG	amg	NN	_	_	_
217	_	_	NN	_	_	_
218	1	1	CD	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	MG1655-aMG	mg1655-amg	NN	_	_	_
221	_	_	NN	_	_	_
222	2	2	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	MG1655	mg1655	NN	_	_	_
225	+	+	CC	_	_	_
226	aMG	amg	NN	_	_	_
227	_	_	NN	_	_	_
228	2	2	CD	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	MG1655-aMG	mg1655-amg	NN	_	_	_
231	_	_	CD	_	_	_
232	3	3	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	MG1655	mg1655	NN	_	_	_
235	+	+	CC	_	_	_
236	aMG	amg	NN	_	_	_
237	_	_	CD	_	_	_
238	3	3	CD	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	MG1655	mg1655	NN	_	_	_
241	at	at	IN	_	_	_
242	30	30	CD	_	_	_
243	Degrees	degree	NNS	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	MG1655	mg1655	NN	_	_	_
246	batch	batch	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	MG1655	mg1655	NN	_	_	_
249	,	,	,	_	_	_
250	biological	biological	JJ	_	_	_
251	rep	rep	NN	GEN	_	_
252	1	1	CD	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	MG1655	mg1655	NN	_	_	_
255	,	,	,	_	_	_
256	biological	biological	JJ	_	_	_
257	rep	rep	NN	GEN	_	_
258	2	2	CD	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	MG1655	mg1655	NN	_	_	_
261	,	,	,	_	_	_
262	biological	biological	JJ	_	_	_
263	rep	rep	NN	GEN	_	_
264	3	3	CD	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	MG1655	mg1655	NN	_	_	_
267	,	,	,	_	_	_
268	biological	biological	JJ	_	_	_
269	rep	rep	NN	GEN	_	_
270	4	4	CD	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	MG1655	mg1655	NN	_	_	_
273	,	,	,	_	_	_
274	biological	biological	JJ	_	_	_
275	rep	rep	NN	GEN	_	_
276	5	5	CD	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	MG1655	mg1655	NN	_	_	_
279	,	,	,	_	_	_
280	biological	biological	JJ	_	_	_
281	rep	rep	NN	GEN	_	_
282	6	6	CD	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	MG1655	mg1655	NN	_	_	_
285	,	,	,	_	_	_
286	biological	biological	JJ	_	_	_
287	rep	rep	NN	GEN	_	_
288	7	7	CD	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	MG1655	mg1655	NN	_	_	_
291	chemostat	chemostat	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	MG1655	mg1655	NN	_	_	_
294	∆	∆	CD	_	_	_
295	cspABCEG	cspabceg	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	MG1655	mg1655	NN	_	_	_
298	∆	∆	CD	_	_	_
299	cspABEG	cspabeg	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	MG1655	mg1655	NN	_	_	_
302	∆	∆	CD	_	_	_
303	cspBG	cspbg	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	MG1655	mg1655	NN	_	_	_
306	DNA	dna	NN	_	_	_
307	isolated	isolate	VBN	_	_	_
308	from	from	IN	_	_	_
309	early-phase	early-phase	JJ	_	_	_
310	DNA-protein	dna-protein	JJ	_	_	_
311	complexes	complex	NNS	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	MG1655	mg1655	NN	_	_	_
314	DNA	dna	NN	_	_	_
315	isolated	isolate	VBN	_	_	_
316	from	from	IN	_	_	_
317	late-phase	late-phase	JJ	_	_	_
318	DNA-protein	dna-protein	JJ	_	_	_
319	complexes	complex	NNS	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	MG1655	mg1655	NN	_	_	_
322	exponentially	exponentially	RB	_	_	_
323	grown	grow	VBN	_	_	_
324	in	in	IN	_	_	_
325	the	the	DT	_	_	_
326	minimal	minimal	JJ	_	_	_
327	medium	medium	NN	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	MG1655	mg1655	NN	_	_	_
330	,	,	,	_	_	_
331	exponential	exponential	JJ	GrowthPhase	_	_
332	phase	phase	NN	GrowthPhase	_	_
333	,	,	,	_	_	_
334	LB	lb	NN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	MG1655	mg1655	NN	_	_	_
337	G181D	g181d	NN	_	_	_
338	NusA	nusa	NN	_	_	_
339	BR1	br1	NN	_	_	_
340	,	,	,	_	_	_
341	treated	treat	VBN	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	MG1655	mg1655	NN	_	_	_
344	G181D	g181d	NN	_	_	_
345	NusA	nusa	NN	_	_	_
346	BR2	br2	NN	_	_	_
347	,	,	,	_	_	_
348	treated	treat	VBN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	MG1655	mg1655	NN	_	_	_
351	G181D	g181d	NN	_	_	_
352	NusA	nusa	NN	_	_	_
353	BR	br	NN	_	_	_
354	,	,	,	_	_	_
355	treated	treat	VBN	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	MG1655	mg1655	NN	_	_	_
358	G181D	g181d	NN	_	_	_
359	NusA	nusa	NN	_	_	_
360	,	,	,	_	_	_
361	treated	treat	VBN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	MG1655	mg1655	NN	_	_	_
364	genomic	genomic	JJ	_	_	_
365	DNA	dna	NN	_	_	_
366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
367	MG1655	mg1655	NN	_	_	_
368	,	,	,	_	_	_
369	heat	heat	NN	_	_	_
370	shock	shock	NN	_	_	_
371	,	,	,	_	_	_
372	biological	biological	JJ	_	_	_
373	rep	rep	NN	GEN	_	_
374	1	1	CD	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	MG1655	mg1655	NN	_	_	_
377	,	,	,	_	_	_
378	heat	heat	NN	_	_	_
379	shock	shock	NN	_	_	_
380	,	,	,	_	_	_
381	biological	biological	JJ	_	_	_
382	rep	rep	NN	GEN	_	_
383	2	2	CD	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	MG1655	mg1655	NN	_	_	_
386	,	,	,	_	_	_
387	heat	heat	NN	_	_	_
388	shock	shock	NN	_	_	_
389	,	,	,	_	_	_
390	biological	biological	JJ	_	_	_
391	rep	rep	NN	GEN	_	_
392	3	3	CD	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	MG1655	mg1655	NN	_	_	_
395	H-NS	h-ns	NN	_	_	_
396	1	1	CD	_	_	_
397	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
398	MG1655	mg1655	NN	_	_	_
399	H-NS	h-ns	NN	_	_	_
400	2	2	CD	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	MG1655	mg1655	NN	_	_	_
403	hns-FLAG	hns-flag	NN	_	_	_
404	cells	cell	NNS	_	_	_
405	were	be	VBD	_	_	_
406	grown	grow	VBN	_	_	_
407	in	in	IN	_	_	_
408	liquid	liquid	JJ	_	_	_
409	LB	lb	NN	MED	_	_
410	medium	medium	NN	MED	_	_
411	with	with	IN	_	_	_
412	and	and	CC	_	_	_
413	without	without	IN	_	_	_
414	bicyclomycin	bicyclomycin	NN	_	_	_
415	-LRB-	-lrb-	-LRB-	_	_	_
416	BCM	bcm	NN	_	_	_
417	-RRB-	-rrb-	-RRB-	_	_	_
418	at	at	IN	_	_	_
419	37	37	CD	_	_	_
420	degree	degree	NN	_	_	_
421	with	with	IN	_	_	_
422	shaking	shake	VBG	_	_	_
423	at	at	IN	_	_	_
424	200rpm	200rpm	JJ	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	MG1655	mg1655	NN	_	_	_
427	HPA	hpa	NN	_	_	_
428	0mM	0mm	NN	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	MG1655	mg1655	NN	_	_	_
431	HPA	hpa	NN	_	_	_
432	10mM	10mm	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	MG1655	mg1655	NN	_	_	_
435	_	_	CD	_	_	_
436	LB	lb	NN	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	MG1655	mg1655	NN	_	_	_
439	_	_	CD	_	_	_
440	LB1	lb1	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	MG1655	mg1655	NN	_	_	_
443	_	_	CD	_	_	_
444	LB2	lb2	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	MG1655	mg1655	NN	_	_	_
447	_	_	CD	_	_	_
448	minus	minus	CC	_	_	_
449	_	_	SYM	_	_	_
450	aMG	aMG	NNP	_	_	_
451	_	_	SYM	_	_	_
452	1	1	CD	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	MG1655	mg1655	NN	_	_	_
455	_	_	CD	_	_	_
456	minus	minus	CC	_	_	_
457	_	_	SYM	_	_	_
458	aMG	aMG	NNP	_	_	_
459	_	_	SYM	_	_	_
460	2	2	CD	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	MG1655	mg1655	NN	_	_	_
463	_	_	CD	_	_	_
464	minus	minus	CC	_	_	_
465	_	_	SYM	_	_	_
466	aMG	aMG	NNP	_	_	_
467	_	_	SYM	_	_	_
468	3	3	CD	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
470	MG1655	mg1655	NN	_	_	_
471	pCA24N	pca24n	NN	_	_	_
472	and	and	CC	_	_	_
473	MG1655	mg1655	NN	_	_	_
474	pCA24N-Mfd	pca24n-mfd	NN	_	_	_
475	cells	cell	NNS	_	_	_
476	were	be	VBD	_	_	_
477	grown	grow	VBN	_	_	_
478	to	to	TO	_	_	_
479	an	a	DT	_	_	_
480	OD560	od560	NN	_	_	_
481	of	of	IN	_	_	_
482	approximately	approximately	RB	_	_	_
483	0.25	0.25	CD	_	_	_
484	and	and	CC	_	_	_
485	treated	treat	VBN	_	_	_
486	with	with	IN	_	_	_
487	100	100	CD	_	_	_
488	μM	μm	NN	_	_	_
489	IPTG	iptg	NN	_	_	_
490	for	for	IN	_	_	_
491	1	1	CD	_	_	_
492	hour	hour	NN	_	_	_
493	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	MG1655	mg1655	NN	_	_	_
3	PhtpG	phtpg	NN	_	_	_
4	:	:	:	_	_	_
5	:	:	:	_	_	_
6	lacZ	lacz	NN	GEN	_	_
7	delta	delta	NN	_	_	_
8	lacX74/pTG2	lacx74/ptg2	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	vector	vector	NN	_	_	_
11	carrying	carrying	NN	_	_	_
12	inducible	inducible	JJ	_	_	_
13	Ptrc	ptrc	NN	_	_	_
14	:	:	:	_	_	_
15	:	:	:	_	_	_
16	rpoH	rpoh	NN	GEN	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	PhtpG	phtpg	NN	_	_	_
21	:	:	:	_	_	_
22	:	:	:	_	_	_
23	lacZ	lacz	NN	GEN	_	_
24	delta	delta	NN	_	_	_
25	lacX74/ptrc99A	lacx74/ptrc99a	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	control	control	NN	_	_	_
28	vector	vector	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	MG1655	mg1655	NN	_	_	_
32	_	_	NN	_	_	_
33	plus	plus	CC	_	_	_
34	_	_	SYM	_	_	_
35	aMG	aMG	NNP	_	_	_
36	_	_	SYM	_	_	_
37	1	1	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	MG1655	mg1655	NN	_	_	_
40	_	_	NN	_	_	_
41	plus	plus	CC	_	_	_
42	_	_	SYM	_	_	_
43	aMG	aMG	NNP	_	_	_
44	_	_	SYM	_	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	MG1655	mg1655	NN	_	_	_
48	_	_	NN	_	_	_
49	plus	plus	CC	_	_	_
50	_	_	SYM	_	_	_
51	aMG	aMG	NNP	_	_	_
52	_	_	SYM	_	_	_
53	3	3	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	MG1655	mg1655	NN	_	_	_
56	R258C	r258c	NN	_	_	_
57	NusA	nusa	NN	_	_	_
58	BR1	br1	NN	_	_	_
59	,	,	,	_	_	_
60	treated	treat	VBN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	MG1655	mg1655	NN	_	_	_
63	R258C	r258c	NN	_	_	_
64	NusA	nusa	NN	_	_	_
65	BR2	br2	NN	_	_	_
66	,	,	,	_	_	_
67	treated	treat	VBN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	MG1655	mg1655	NN	_	_	_
70	R258C	r258c	NN	_	_	_
71	NusA	nusa	NN	_	_	_
72	BR	br	NN	_	_	_
73	,	,	,	_	_	_
74	treated	treat	VBN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	MG1655	mg1655	NN	_	_	_
77	R258C	r258c	NN	_	_	_
78	NusA	nusa	NN	_	_	_
79	,	,	,	_	_	_
80	treated	treat	VBN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	MG1655	mg1655	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	Repaired	repair	VBN	_	_	_
85	MCM	mcm	NN	_	_	_
86	3416	3416	CD	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	in	in	IN	_	_	_
89	M9	m9	NN	_	_	_
90	+	+	CC	_	_	_
91	0.2	0.2	CD	_	_	_
92	%	%	NN	_	_	_
93	Glucose	glucose	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	MG1655	mg1655	NN	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	Repaired	repair	VBN	_	_	_
98	MCM	mcm	NN	_	_	_
99	3416	3416	CD	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	in	in	IN	_	_	_
102	M9	m9	NN	_	_	_
103	+	+	CC	_	_	_
104	0.2	0.2	CD	_	_	_
105	%	%	NN	_	_	_
106	Glucose	glucose	NN	_	_	_
107	8	8	CD	_	_	_
108	'	'	''	_	_	_
109	post	post	JJ	_	_	_
110	rif	rif	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	MG1655	mg1655	NN	_	_	_
113	-LRB-	-lrb-	-LRB-	_	_	_
114	Repaired	repair	VBN	_	_	_
115	NCM	NCM	NNP	_	_	_
116	3416	3416	CD	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	in	in	IN	_	_	_
119	M9	m9	NN	_	_	_
120	+	+	CC	_	_	_
121	0.2	0.2	CD	_	_	_
122	%	%	NN	_	_	_
123	Glucose	glucose	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	MG1655	mg1655	NN	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	Repaired	repair	VBN	_	_	_
128	NCM	NCM	NNP	_	_	_
129	3416	3416	CD	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	in	in	IN	_	_	_
132	M9	m9	NN	_	_	_
133	+	+	CC	_	_	_
134	0.2	0.2	CD	_	_	_
135	%	%	NN	_	_	_
136	Glucose	glucose	NN	_	_	_
137	2	2	CD	_	_	_
138	'	'	''	_	_	_
139	post	post	JJ	_	_	_
140	rif	rif	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	MG1655	mg1655	NN	_	_	_
143	-LRB-	-lrb-	-LRB-	_	_	_
144	Repaired	repair	VBN	_	_	_
145	NCM	NCM	NNP	_	_	_
146	3416	3416	CD	_	_	_
147	-RRB-	-rrb-	-RRB-	_	_	_
148	in	in	IN	_	_	_
149	M9	m9	NN	_	_	_
150	+	+	CC	_	_	_
151	0.2	0.2	CD	_	_	_
152	%	%	NN	_	_	_
153	Glucose	glucose	NN	_	_	_
154	4	4	CD	_	_	_
155	'	'	''	_	_	_
156	post	post	JJ	_	_	_
157	rif	rif	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	MG1655	mg1655	NN	_	_	_
160	-LRB-	-lrb-	-LRB-	_	_	_
161	Repaired	repair	VBN	_	_	_
162	NCM	NCM	NNP	_	_	_
163	3416	3416	CD	_	_	_
164	-RRB-	-rrb-	-RRB-	_	_	_
165	in	in	IN	_	_	_
166	M9	m9	NN	_	_	_
167	+	+	CC	_	_	_
168	0.2	0.2	CD	_	_	_
169	%	%	NN	_	_	_
170	Glucose	glucose	NN	_	_	_
171	6	6	CD	_	_	_
172	'	'	''	_	_	_
173	post	post	JJ	_	_	_
174	rif	rif	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	MG1655	mg1655	NN	_	_	_
177	-LRB-	-lrb-	-LRB-	_	_	_
178	Repaired	repair	VBN	_	_	_
179	NCM	NCM	NNP	_	_	_
180	3416	3416	CD	_	_	_
181	-RRB-	-rrb-	-RRB-	_	_	_
182	in	in	IN	_	_	_
183	M9	m9	NN	_	_	_
184	+	+	CC	_	_	_
185	0.2	0.2	CD	_	_	_
186	%	%	NN	_	_	_
187	Glucose	glucose	NN	_	_	_
188	8	8	CD	_	_	_
189	'	'	''	_	_	_
190	post	post	JJ	_	_	_
191	rif	rif	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	MG1655	mg1655	NN	_	_	_
194	RNA	rna	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	MG1655	mg1655	NN	_	_	_
197	RNAP	rnap	NN	_	_	_
198	1	1	CD	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	MG1655	mg1655	NN	_	_	_
201	RNAP	rnap	NN	_	_	_
202	2	2	CD	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	MG1655	mg1655	NN	_	_	_
205	∆	∆	CD	_	_	_
206	rnr	rnr	NN	GEN	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	MG1655	mg1655	NN	_	_	_
209	rpoHp3	rpohp3	NN	Pr	_	_
210	:	:	:	_	_	_
211	:	:	:	_	_	_
212	lacZ	lacz	NN	GEN	_	_
213	delta	delta	NN	_	_	_
214	lacX74	lacx74	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	MG1655	mg1655	NN	_	_	_
217	rpoHp3	rpohp3	NN	Pr	_	_
218	:	:	:	_	_	_
219	:	:	:	_	_	_
220	lacZ	lacz	NN	GEN	_	_
221	delta	delta	NN	_	_	_
222	lacX74	lacx74	NN	_	_	_
223	hfq1	hfq1	NN	_	_	_
224	:	:	:	_	_	_
225	:	:	:	_	_	_
226	omega	omega	NN	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	Km	km	NN	_	_	_
229	;	;	:	_	_	_
230	BclI	bcli	NN	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	-LRB-	-lrb-	-LRB-	_	_	_
233	hfq	hfq	SYM	GEN	_	_
234	-	-	:	_	_	_
235	-RRB-	-rrb-	-RRB-	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	MG1655	mg1655	NN	_	_	_
238	rpoHp3	rpohp3	NN	Pr	_	_
239	:	:	:	_	_	_
240	:	:	:	_	_	_
241	lacZ	lacz	NN	GEN	_	_
242	delta	delta	NN	_	_	_
243	lacX74	lacx74	NN	_	_	_
244	hfq1	hfq1	NN	_	_	_
245	:	:	:	_	_	_
246	:	:	:	_	_	_
247	omega	omega	NN	_	_	_
248	-LRB-	-lrb-	-LRB-	_	_	_
249	Km	km	NN	_	_	_
250	;	;	:	_	_	_
251	BclI	bcli	NN	_	_	_
252	-RRB-	-rrb-	-RRB-	_	_	_
253	-LRB-	-lrb-	-LRB-	_	_	_
254	hfq	hfq	SYM	GEN	_	_
255	-	-	:	_	_	_
256	-RRB-	-rrb-	-RRB-	_	_	_
257	/	/	:	_	_	_
258	pLC245	plc245	NN	_	_	_
259	-LRB-	-lrb-	-LRB-	_	_	_
260	vector	vector	NN	_	_	_
261	carrying	carrying	NN	_	_	_
262	inducible	inducible	JJ	_	_	_
263	Ptrc	ptrc	NN	_	_	_
264	:	:	:	_	_	_
265	:	:	:	_	_	_
266	rpoE	rpoe	NN	GEN	_	_
267	-RRB-	-rrb-	-RRB-	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	MG1655	mg1655	NN	_	_	_
270	rpoHp3	rpohp3	NN	Pr	_	_
271	:	:	:	_	_	_
272	:	:	:	_	_	_
273	lacZ	lacz	NN	GEN	_	_
274	delta	delta	NN	_	_	_
275	lacX74	lacx74	NN	_	_	_
276	hfq2	hfq2	NN	_	_	_
277	:	:	:	_	_	_
278	:	:	:	_	_	_
279	omega	omega	NN	_	_	_
280	-LRB-	-lrb-	-LRB-	_	_	_
281	Km	km	NN	_	_	_
282	;	;	:	_	_	_
283	KpnI	kpni	NN	_	_	_
284	-RRB-	-rrb-	-RRB-	_	_	_
285	-LRB-	-lrb-	-LRB-	_	_	_
286	hfq	hfq	NN	GEN	_	_
287	+	+	CC	_	_	_
288	-RRB-	-rrb-	-RRB-	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	MG1655	mg1655	NN	_	_	_
291	rpoHp3	rpohp3	NN	Pr	_	_
292	:	:	:	_	_	_
293	:	:	:	_	_	_
294	lacZ	lacz	NN	GEN	_	_
295	delta	delta	NN	_	_	_
296	lacX74	lacx74	NN	_	_	_
297	hfq2	hfq2	NN	_	_	_
298	:	:	:	_	_	_
299	:	:	:	_	_	_
300	omega	omega	NN	_	_	_
301	-LRB-	-lrb-	-LRB-	_	_	_
302	Km	km	NN	_	_	_
303	;	;	:	_	_	_
304	KpnI	kpni	NN	_	_	_
305	-RRB-	-rrb-	-RRB-	_	_	_
306	-LRB-	-lrb-	-LRB-	_	_	_
307	hfq	hfq	NN	GEN	_	_
308	+	+	CC	_	_	_
309	-RRB-	-rrb-	-RRB-	_	_	_
310	/	/	:	_	_	_
311	pLC245	plc245	NN	_	_	_
312	-LRB-	-lrb-	-LRB-	_	_	_
313	vector	vector	NN	_	_	_
314	carrying	carrying	NN	_	_	_
315	inducible	inducible	JJ	_	_	_
316	Ptrc	ptrc	NN	_	_	_
317	:	:	:	_	_	_
318	:	:	:	_	_	_
319	rpoE	rpoe	NN	GEN	_	_
320	-RRB-	-rrb-	-RRB-	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	MG1655	mg1655	NN	_	_	_
323	rpoHp3	rpohp3	NN	Pr	_	_
324	:	:	:	_	_	_
325	:	:	:	_	_	_
326	lacZ	lacz	NN	GEN	_	_
327	delta	delta	NN	_	_	_
328	lacX74	lacx74	NN	_	_	_
329	hfq2	hfq2	NN	_	_	_
330	:	:	:	_	_	_
331	:	:	:	_	_	_
332	omega	omega	NN	_	_	_
333	-LRB-	-lrb-	-LRB-	_	_	_
334	Km	km	NN	_	_	_
335	;	;	:	_	_	_
336	KpnI	kpni	NN	_	_	_
337	-RRB-	-rrb-	-RRB-	_	_	_
338	-LRB-	-lrb-	-LRB-	_	_	_
339	hfq	hfq	NN	GEN	_	_
340	+	+	CC	_	_	_
341	-RRB-	-rrb-	-RRB-	_	_	_
342	/	/	:	_	_	_
343	ptrc99A	ptrc99a	NN	_	_	_
344	-LRB-	-lrb-	-LRB-	_	_	_
345	control	control	NN	_	_	_
346	vector	vector	NN	_	_	_
347	-RRB-	-rrb-	-RRB-	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	MG1655	mg1655	NN	_	_	_
350	rpoHp3	rpohp3	NN	Pr	_	_
351	:	:	:	_	_	_
352	:	:	:	_	_	_
353	lacZ	lacz	NN	GEN	_	_
354	delta	delta	NN	_	_	_
355	lacX74	lacx74	NN	_	_	_
356	nadB	nadb	NN	GEN	_	_
357	:	:	:	_	_	_
358	:	:	:	_	_	_
359	Tn10	tn10	NN	_	_	_
360	drseA	drsea	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	MG1655	mg1655	NN	_	_	_
363	rpoHp3	rpohp3	NN	Pr	_	_
364	:	:	:	_	_	_
365	:	:	:	_	_	_
366	lacZ	lacz	NN	GEN	_	_
367	delta	delta	NN	_	_	_
368	lacX74/pLC245	lacx74/plc245	NN	_	_	_
369	-LRB-	-lrb-	-LRB-	_	_	_
370	vector	vector	NN	_	_	_
371	carrying	carrying	NN	_	_	_
372	inducible	inducible	JJ	_	_	_
373	Ptrc	ptrc	NN	_	_	_
374	:	:	:	_	_	_
375	:	:	:	_	_	_
376	rpoE	rpoe	NN	GEN	_	_
377	-RRB-	-rrb-	-RRB-	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	MG1655	mg1655	NN	_	_	_
380	rpoHp3	rpohp3	NN	Pr	_	_
381	:	:	:	_	_	_
382	:	:	:	_	_	_
383	lacZ	lacz	NN	GEN	_	_
384	delta	delta	NN	_	_	_
385	lacX74/ptrc99A	lacx74/ptrc99a	NN	_	_	_
386	-LRB-	-lrb-	-LRB-	_	_	_
387	control	control	NN	_	_	_
388	vector	vector	NN	_	_	_
389	-RRB-	-rrb-	-RRB-	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	MG1655	mg1655	NN	_	_	_
392	rpoS	rpos	NN	GEN	_	_
393	mutants	mutant	NNS	_	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
395	MG1655	mg1655	NN	_	_	_
396	,	,	,	_	_	_
397	SD197	sd197	NN	_	_	_
398	,	,	,	_	_	_
399	SB227	sb227	NN	_	_	_
400	,	,	,	_	_	_
401	SF301	sf301	NN	_	_	_
402	and	and	CC	_	_	_
403	SS046	ss046	NN	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
405	MG1655	mg1655	NN	_	_	_
406	,	,	,	_	_	_
407	SD197	sd197	NN	_	_	_
408	,	,	,	_	_	_
409	SB227	sb227	NN	_	_	_
410	,	,	,	_	_	_
411	SF301	sf301	NN	_	_	_
412	and	and	CC	_	_	_
413	SS046	ss046	NN	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	MG1655	mg1655	NN	_	_	_
416	_	_	CD	_	_	_
417	standard	standard	JJ	_	_	_
418	_	_	NN	_	_	_
419	condition	condition	NN	_	_	_
420	_	_	CD	_	_	_
421	rep1	rep1	NN	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	MG1655	mg1655	NN	_	_	_
424	_	_	CD	_	_	_
425	standard	standard	JJ	_	_	_
426	_	_	NN	_	_	_
427	condition	condition	NN	_	_	_
428	_	_	CD	_	_	_
429	rep2	rep2	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	MG1655star-glucose	mg1655star-glucose	JJ	_	_	_
432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
433	MG1655star-mannose	mg1655star-mannose	JJ	_	_	_
434	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
435	MG1655star-mucus-P1	mg1655star-mucus-p1	NN	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	MG1655star-mucus-P2	mg1655star-mucus-p2	NN	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	MG1655	mg1655	NN	_	_	_
440	starvation	starvation	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	MG1655	mg1655	NN	_	_	_
443	,	,	,	_	_	_
444	stationary	stationary	JJ	GrowthPhase	_	_
445	phase	phase	NN	GrowthPhase	_	_
446	,	,	,	_	_	_
447	LB	lb	NN	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	MG1655	mg1655	NN	_	_	_
450	strain	strain	NN	_	_	_
451	of	of	IN	_	_	_
452	E.	e.	FW	_	_	_
453	coli	coli	FW	_	_	_
454	K-12	k-12	NN	_	_	_
455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
456	MG1655	mg1655	NN	_	_	_
457	transcriptome	transcriptome	NN	_	_	_
458	from	from	IN	_	_	_
459	batch	batch	NN	_	_	_
460	growth	growth	NN	_	_	_
461	_	_	NN	_	_	_
462	1	1	CD	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	MG1655	mg1655	NN	_	_	_
465	transcriptome	transcriptome	NN	_	_	_
466	from	from	IN	_	_	_
467	batch	batch	NN	_	_	_
468	growth	growth	NN	_	_	_
469	_	_	NN	_	_	_
470	2	2	CD	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	MG1655	mg1655	NN	_	_	_
473	transcriptome	transcriptome	NN	_	_	_
474	from	from	IN	_	_	_
475	chemostat	chemostat	NN	_	_	_
476	growth	growth	NN	_	_	_
477	_	_	NN	_	_	_
478	1	1	CD	_	_	_
479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
480	MG1655	mg1655	NN	_	_	_
481	transcriptome	transcriptome	NN	_	_	_
482	from	from	IN	_	_	_
483	chemostat	chemostat	NN	_	_	_
484	growth	growth	NN	_	_	_
485	_	_	NN	_	_	_
486	2	2	CD	_	_	_
487	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
488	MG1655	mg1655	NN	_	_	_
489	transcriptome	transcriptome	NN	_	_	_
490	from	from	IN	_	_	_
491	starvation	starvation	NN	_	_	_
492	growth	growth	NN	_	_	_
493	_	_	NN	_	_	_
494	1	1	CD	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
496	MG1655	mg1655	NN	_	_	_
497	transcriptome	transcriptome	NN	_	_	_
498	from	from	IN	_	_	_
499	starvation	starvation	NN	_	_	_
500	growth	growth	NN	_	_	_
501	_	_	NN	_	_	_
502	2	2	CD	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	MG1655	mg1655	NN	_	_	_
505	_	_	NN	_	_	_
506	under	under	IN	_	_	_
507	_	_	CD	_	_	_
508	ColdShock	ColdShock	NNP	_	_	_
509	_	_	CD	_	_	_
510	rep1	rep1	NN	_	_	_
511	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
512	MG1655	mg1655	NN	_	_	_
513	_	_	NN	_	_	_
514	under	under	IN	_	_	_
515	_	_	CD	_	_	_
516	ColdShock	ColdShock	NNP	_	_	_
517	_	_	CD	_	_	_
518	rep2	rep2	NN	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	MG1655	mg1655	NN	_	_	_
521	_	_	NN	_	_	_
522	under	under	IN	_	_	_
523	_	_	NN	_	_	_
524	HeatShock	heatshock	NN	_	_	_
525	_	_	CD	_	_	_
526	rep2	rep2	NN	_	_	_
527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
528	MG1655	mg1655	NN	_	_	_
529	_	_	NN	_	_	_
530	under	under	IN	_	_	_
531	_	_	NNP	_	_	_
532	Low	Low	NNP	_	_	_
533	_	_	NNP	_	_	_
534	pH	ph	NN	_	_	_
535	_	_	CD	_	_	_
536	rep1	rep1	NN	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	MG1655	mg1655	NN	_	_	_
539	_	_	NN	_	_	_
540	under	under	IN	_	_	_
541	_	_	NN	_	_	_
542	minimal	minimal	JJ	_	_	_
543	_	_	NN	_	_	_
544	C&N	c&n	NN	_	_	_
545	_	_	NN	_	_	_
546	source	source	NN	_	_	_
547	_	_	CD	_	_	_
548	rep1	rep1	NN	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	MG1655	mg1655	NN	_	_	_
551	_	_	NN	_	_	_
552	under	under	IN	_	_	_
553	_	_	NN	_	_	_
554	minimal	minimal	JJ	_	_	_
555	_	_	NN	_	_	_
556	C&N	c&n	NN	_	_	_
557	_	_	NN	_	_	_
558	source	source	NN	_	_	_
559	_	_	CD	_	_	_
560	rep2	rep2	NN	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	MG1655	mg1655	NN	_	_	_
563	_	_	NN	_	_	_
564	under	under	IN	_	_	_
565	_	_	NN	_	_	_
566	minimal	minimal	JJ	_	_	_
567	_	_	NN	_	_	_
568	C	c	NN	_	_	_
569	_	_	NN	_	_	_
570	source	source	NN	_	_	_
571	_	_	CD	_	_	_
572	rep1	rep1	NN	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	MG1655	mg1655	NN	_	_	_
575	_	_	NN	_	_	_
576	under	under	IN	_	_	_
577	_	_	NN	_	_	_
578	minimal	minimal	JJ	_	_	_
579	_	_	NN	_	_	_
580	C	c	NN	_	_	_
581	_	_	NN	_	_	_
582	source	source	NN	_	_	_
583	_	_	CD	_	_	_
584	rep2	rep2	NN	_	_	_
585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
586	MG1655	mg1655	NN	_	_	_
587	_	_	NN	_	_	_
588	under	under	IN	_	_	_
589	_	_	NN	_	_	_
590	minimal	minimal	JJ	_	_	_
591	_	_	CD	_	_	_
592	N	n	NN	_	_	_
593	_	_	NN	_	_	_
594	source	source	NN	_	_	_
595	_	_	CD	_	_	_
596	rep1	rep1	NN	_	_	_
597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
598	MG1655	mg1655	NN	_	_	_
599	_	_	NN	_	_	_
600	under	under	IN	_	_	_
601	_	_	NN	_	_	_
602	minimal	minimal	JJ	_	_	_
603	_	_	CD	_	_	_
604	N	n	NN	_	_	_
605	_	_	NN	_	_	_
606	source	source	NN	_	_	_
607	_	_	CD	_	_	_
608	rep2	rep2	NN	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	MG1655	mg1655	NN	_	_	_
611	_	_	NN	_	_	_
612	under	under	IN	_	_	_
613	_	_	NNP	_	_	_
614	Osmotic	Osmotic	NNP	_	_	_
615	_	_	NNP	_	_	_
616	Stress	stress	NN	_	_	_
617	_	_	NN	_	_	_
618	rep1	rep1	NN	_	_	_
619	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
620	MG1655	mg1655	NN	_	_	_
621	_	_	NN	_	_	_
622	under	under	IN	_	_	_
623	_	_	CD	_	_	_
624	Osmotic	osmotic	JJ	_	_	_
625	_	_	NN	_	_	_
626	Stress	stress	NN	_	_	_
627	_	_	CD	_	_	_
628	rep2	rep2	NN	_	_	_
629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
630	MG1655	mg1655	NN	_	_	_
631	_	_	NN	_	_	_
632	under	under	IN	_	_	_
633	_	_	NNP	_	_	_
634	Oxidative	oxidative	JJ	_	_	_
635	_	_	NN	_	_	_
636	Stress	stress	NN	_	_	_
637	_	_	CD	_	_	_
638	rep1	rep1	NN	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	MG1655	mg1655	NN	_	_	_
641	_	_	NN	_	_	_
642	under	under	IN	_	_	_
643	_	_	NNP	_	_	_
644	Oxidative	oxidative	JJ	_	_	_
645	_	_	NN	_	_	_
646	Stress	stress	NN	_	_	_
647	_	_	CD	_	_	_
648	rep2	rep2	NN	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	MG1655	mg1655	NN	_	_	_
651	_	_	CD	_	_	_
652	UV	uv	NN	_	_	_
653	_	_	NN	_	_	_
654	Treatment	treatment	NN	_	_	_
655	_	_	CD	_	_	_
656	rep1	rep1	NN	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
658	MG1655	mg1655	NN	_	_	_
659	_	_	CD	_	_	_
660	UV	uv	NN	_	_	_
661	_	_	NN	_	_	_
662	Treatment	treatment	NN	_	_	_
663	_	_	CD	_	_	_
664	rep2	rep2	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	MG1655	mg1655	NN	_	_	_
667	_	_	NN	_	_	_
668	vector	vector	NN	_	_	_
669	_	_	NN	_	_	_
670	1	1	CD	_	_	_
671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
672	MG1655	mg1655	NN	_	_	_
673	_	_	NN	_	_	_
674	vector	vector	NN	_	_	_
675	_	_	NN	_	_	_
676	2	2	CD	_	_	_
677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
678	MG1655	mg1655	NN	_	_	_
679	wild	wild	JJ	_	_	_
680	type	type	NN	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	MG1655	mg1655	NN	_	_	_
683	WT	WT	NNP	_	_	_
684	NusA	NusA	NNP	_	_	_
685	BR1	br1	NN	_	_	_
686	,	,	,	_	_	_
687	control	control	NN	_	_	_
688	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
689	MG1655	MG1655	NNP	_	_	_
690	WT	WT	NNP	_	_	_
691	NusA	nusa	NN	_	_	_
692	BR2	br2	NN	_	_	_
693	,	,	,	_	_	_
694	control	control	NN	_	_	_
695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
696	MG1655	mg1655	NN	_	_	_
697	WT	WT	NNP	_	_	_
698	NusA	NusA	NNP	_	_	_
699	BR	BR	NNP	_	_	_
700	,	,	,	_	_	_
701	control	control	NN	_	_	_
702	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
703	MG1655	mg1655	NN	_	_	_
704	WT	WT	NNP	_	_	_
705	NusA	NusA	NNP	_	_	_
706	,	,	,	_	_	_
707	control	control	NN	_	_	_
708	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
709	MG1655	mg1655	NN	_	_	_
710	Δhns	δhns	NNS	_	_	_
711	RNAP	rnap	NN	_	_	_
712	1	1	CD	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
714	MG1655	mg1655	NN	_	_	_
715	Δhns	δhns	NNS	_	_	_
716	RNAP	rnap	NN	_	_	_
717	2	2	CD	_	_	_
718	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
719	mg	mg	NN	_	_	_
720	+2	+2	NN	_	_	_
721	-LRB-	-lrb-	-LRB-	_	_	_
722	levels	level	NNS	_	_	_
723	-RRB-	-rrb-	-RRB-	_	_	_
724	:	:	:	_	_	_
725	baseMg	basemg	NN	_	_	_
726	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
727	mg	mg	NN	_	_	_
728	+2	+2	NN	_	_	_
729	-LRB-	-lrb-	-LRB-	_	_	_
730	levels	level	NNS	_	_	_
731	-RRB-	-rrb-	-RRB-	_	_	_
732	:	:	:	_	_	_
733	highMg	highmg	NN	_	_	_
734	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
735	mg	mg	NN	_	_	_
736	+2	+2	NN	_	_	_
737	-LRB-	-lrb-	-LRB-	_	_	_
738	levels	level	NNS	_	_	_
739	-RRB-	-rrb-	-RRB-	_	_	_
740	:	:	:	_	_	_
741	lowMg	lowmg	NN	_	_	_
742	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
743	mg	mg	NN	_	_	_
744	+2	+2	NN	_	_	_
745	-LRB-	-lrb-	-LRB-	_	_	_
746	mm	mm	NN	_	_	_
747	-RRB-	-rrb-	-RRB-	_	_	_
748	:	:	:	_	_	_
749	0.005	0.005	CD	_	_	_
750	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
751	mg	mg	NN	_	_	_
752	+2	+2	NN	_	_	_
753	-LRB-	-lrb-	-LRB-	_	_	_
754	mm	mm	NN	_	_	_
755	-RRB-	-rrb-	-RRB-	_	_	_
756	:	:	:	_	_	_
757	0.01	0.01	CD	_	_	_
758	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
759	mg	mg	NN	_	_	_
760	+2	+2	NN	_	_	_
761	-LRB-	-lrb-	-LRB-	_	_	_
762	mm	mm	NN	_	_	_
763	-RRB-	-rrb-	-RRB-	_	_	_
764	:	:	:	_	_	_
765	0.02	0.02	CD	_	_	_
766	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
767	mg	mg	NN	_	_	_
768	+2	+2	NN	_	_	_
769	-LRB-	-lrb-	-LRB-	_	_	_
770	mm	mm	NN	_	_	_
771	-RRB-	-rrb-	-RRB-	_	_	_
772	:	:	:	_	_	_
773	0.04	0.04	CD	_	_	_
774	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
775	mg	mg	NN	_	_	_
776	+2	+2	NN	_	_	_
777	-LRB-	-lrb-	-LRB-	_	_	_
778	mm	mm	NN	_	_	_
779	-RRB-	-rrb-	-RRB-	_	_	_
780	:	:	:	_	_	_
781	0.08	0.08	CD	_	_	_
782	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
783	mg	mg	NN	_	_	_
784	+2	+2	NN	_	_	_
785	-LRB-	-lrb-	-LRB-	_	_	_
786	mm	mm	NN	_	_	_
787	-RRB-	-rrb-	-RRB-	_	_	_
788	:	:	:	_	_	_
789	0.8	0.8	CD	_	_	_
790	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
791	mg	mg	NN	_	_	_
792	+2	+2	NN	_	_	_
793	-LRB-	-lrb-	-LRB-	_	_	_
794	mm	mm	NN	_	_	_
795	-RRB-	-rrb-	-RRB-	_	_	_
796	:	:	:	_	_	_
797	200	200	CD	_	_	_
798	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
799	mg	mg	NN	_	_	_
800	+2	+2	NN	_	_	_
801	-LRB-	-lrb-	-LRB-	_	_	_
802	mm	mm	NN	_	_	_
803	-RRB-	-rrb-	-RRB-	_	_	_
804	:	:	:	_	_	_
805	400	400	CD	_	_	_
806	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
807	mg	mg	NN	_	_	_
808	+2	+2	NN	_	_	_
809	-LRB-	-lrb-	-LRB-	_	_	_
810	mm	mm	NN	_	_	_
811	-RRB-	-rrb-	-RRB-	_	_	_
812	:	:	:	_	_	_
813	50	50	CD	_	_	_
814	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
815	mg	mg	NN	_	_	_
816	+2	+2	NN	_	_	_
817	-LRB-	-lrb-	-LRB-	_	_	_
818	mm	mm	NN	_	_	_
819	-RRB-	-rrb-	-RRB-	_	_	_
820	:	:	:	_	_	_
821	8	8	CD	_	_	_
822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
823	MG6	mg6	NN	_	_	_
824	_	_	NN	_	_	_
825	replicated	replicate	VBN	_	_	_
826	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
827	MgSO4	mgso4	NN	_	_	_
828	_	_	CD	_	_	_
829	stress	stress	NN	_	_	_
830	_	_	RB	_	_	_
831	high	high	JJ	_	_	_
832	:	:	:	_	_	_
833	MURI	MURI	NNP	_	_	_
834	_	_	SYM	_	_	_
835	106	106	CD	_	_	_
836	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
837	MgSO4	mgso4	NN	_	_	_
838	_	_	CD	_	_	_
839	stress	stress	NN	_	_	_
840	_	_	RB	_	_	_
841	high	high	JJ	_	_	_
842	:	:	:	_	_	_
843	MURI	MURI	NNP	_	_	_
844	_	_	SYM	_	_	_
845	107	107	CD	_	_	_
846	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
847	MgSO4	mgso4	NN	_	_	_
848	_	_	CD	_	_	_
849	stress	stress	NN	_	_	_
850	_	_	RB	_	_	_
851	high	high	JJ	_	_	_
852	:	:	:	_	_	_
853	MURI	MURI	NNP	_	_	_
854	_	_	SYM	_	_	_
855	108	108	CD	_	_	_
856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
857	MgSO4	mgso4	NN	_	_	_
858	_	_	CD	_	_	_
859	stress	stress	NN	_	_	_
860	_	_	RB	_	_	_
861	high	high	JJ	_	_	_
862	:	:	:	_	_	_
863	MURI	MURI	NNP	_	_	_
864	_	_	SYM	_	_	_
865	109	109	CD	_	_	_
866	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
867	MgSO4	mgso4	NN	_	_	_
868	_	_	CD	_	_	_
869	stress	stress	NN	_	_	_
870	_	_	RB	_	_	_
871	high	high	JJ	_	_	_
872	:	:	:	_	_	_
873	MURI	MURI	NNP	_	_	_
874	_	_	SYM	_	_	_
875	110	110	CD	_	_	_
876	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
877	MgSO4	mgso4	NN	_	_	_
878	_	_	CD	_	_	_
879	stress	stress	NN	_	_	_
880	_	_	RB	_	_	_
881	high	high	JJ	_	_	_
882	:	:	:	_	_	_
883	MURI	MURI	NNP	_	_	_
884	_	_	SYM	_	_	_
885	111	111	CD	_	_	_
886	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
887	MgSO4	mgso4	NN	_	_	_
888	_	_	CD	_	_	_
889	stress	stress	NN	_	_	_
890	_	_	RB	_	_	_
891	high	high	JJ	_	_	_
892	:	:	:	_	_	_
893	MURI	MURI	NNP	_	_	_
894	_	_	SYM	_	_	_
895	112	112	CD	_	_	_
896	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
897	MgSO4	mgso4	NN	_	_	_
898	_	_	CD	_	_	_
899	stress	stress	NN	_	_	_
900	_	_	RB	_	_	_
901	high	high	JJ	_	_	_
902	:	:	:	_	_	_
903	MURI	MURI	NNP	_	_	_
904	_	_	SYM	_	_	_
905	113	113	CD	_	_	_
906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
907	MgSO4	mgso4	NN	_	_	_
908	_	_	CD	_	_	_
909	stress	stress	NN	_	_	_
910	_	_	RB	_	_	_
911	high	high	JJ	_	_	_
912	:	:	:	_	_	_
913	MURI	MURI	NNP	_	_	_
914	_	_	VBD	_	_	_
915	114	114	CD	_	_	_
916	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
917	MgSO4	mgso4	NN	_	_	_
918	_	_	CD	_	_	_
919	stress	stress	NN	_	_	_
920	_	_	RB	_	_	_
921	high	high	JJ	_	_	_
922	:	:	:	_	_	_
923	MURI	MURI	NNP	_	_	_
924	_	_	SYM	_	_	_
925	115	115	CD	_	_	_
926	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
927	MgSO4	mgso4	NN	_	_	_
928	_	_	CD	_	_	_
929	stress	stress	NN	_	_	_
930	_	_	RB	_	_	_
931	high	high	JJ	_	_	_
932	:	:	:	_	_	_
933	MURI	MURI	NNP	_	_	_
934	_	_	SYM	_	_	_
935	116	116	CD	_	_	_
936	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
937	MgSO4	mgso4	NN	_	_	_
938	_	_	CD	_	_	_
939	stress	stress	NN	_	_	_
940	_	_	RB	_	_	_
941	high	high	JJ	_	_	_
942	:	:	:	_	_	_
943	MURI	MURI	NNP	_	_	_
944	_	_	SYM	_	_	_
945	117	117	CD	_	_	_
946	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
947	MgSO4	mgso4	NN	_	_	_
948	_	_	CD	_	_	_
949	stress	stress	NN	_	_	_
950	_	_	RB	_	_	_
951	high	high	JJ	_	_	_
952	:	:	:	_	_	_
953	MURI	MURI	NNP	_	_	_
954	_	_	SYM	_	_	_
955	118	118	CD	_	_	_
956	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
957	MgSO4	mgso4	NN	_	_	_
958	_	_	CD	_	_	_
959	stress	stress	NN	_	_	_
960	_	_	RB	_	_	_
961	high	high	JJ	_	_	_
962	:	:	:	_	_	_
963	MURI	MURI	NNP	_	_	_
964	_	_	SYM	_	_	_
965	119	119	CD	_	_	_
966	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
967	MgSO4	mgso4	NN	_	_	_
968	_	_	CD	_	_	_
969	stress	stress	NN	_	_	_
970	_	_	RB	_	_	_
971	high	high	JJ	_	_	_
972	:	:	:	_	_	_
973	MURI	MURI	NNP	_	_	_
974	_	_	SYM	_	_	_
975	120	120	CD	_	_	_
976	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
977	MgSO4	mgso4	NN	_	_	_
978	_	_	CD	_	_	_
979	stress	stress	NN	_	_	_
980	_	_	RB	_	_	_
981	high	high	JJ	_	_	_
982	:	:	:	_	_	_
983	MURI	MURI	NNP	_	_	_
984	_	_	SYM	_	_	_
985	121	121	CD	_	_	_
986	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
987	MgSO4	mgso4	NN	_	_	_
988	_	_	CD	_	_	_
989	stress	stress	NN	_	_	_
990	_	_	RB	_	_	_
991	high	high	JJ	_	_	_
992	:	:	:	_	_	_
993	MURI	MURI	NNP	_	_	_
994	_	_	SYM	_	_	_
995	122	122	CD	_	_	_
996	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
997	MgSO4	mgso4	NN	_	_	_
998	_	_	CD	_	_	_
999	stress	stress	NN	_	_	_
1000	_	_	RB	_	_	_
1001	high	high	JJ	_	_	_
1002	:	:	:	_	_	_
1003	MURI	MURI	NNP	_	_	_
1004	_	_	SYM	_	_	_
1005	123	123	CD	_	_	_
1006	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1007	MgSO4	mgso4	NN	_	_	_
1008	_	_	CD	_	_	_
1009	stress	stress	NN	_	_	_
1010	_	_	RB	_	_	_
1011	high	high	JJ	_	_	_
1012	:	:	:	_	_	_
1013	MURI	MURI	NNP	_	_	_
1014	_	_	VBD	_	_	_
1015	124	124	CD	_	_	_
1016	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1017	MgSO4	mgso4	NN	_	_	_
1018	_	_	CD	_	_	_
1019	stress	stress	NN	_	_	_
1020	_	_	RB	_	_	_
1021	high	high	JJ	_	_	_
1022	:	:	:	_	_	_
1023	MURI	MURI	NNP	_	_	_
1024	_	_	SYM	_	_	_
1025	125	125	CD	_	_	_
1026	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1027	MgSO4	mgso4	NN	_	_	_
1028	_	_	CD	_	_	_
1029	stress	stress	NN	_	_	_
1030	_	_	RB	_	_	_
1031	high	high	JJ	_	_	_
1032	:	:	:	_	_	_
1033	MURI	MURI	NNP	_	_	_
1034	_	_	SYM	_	_	_
1035	126	126	CD	_	_	_
1036	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1037	MgSO4	mgso4	NN	_	_	_
1038	_	_	CD	_	_	_
1039	stress	stress	NN	_	_	_
1040	_	_	RB	_	_	_
1041	high	high	JJ	_	_	_
1042	:	:	:	_	_	_
1043	MURI	MURI	NNP	_	_	_
1044	_	_	SYM	_	_	_
1045	127	127	CD	_	_	_
1046	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1047	MgSO4	mgso4	NN	_	_	_
1048	_	_	CD	_	_	_
1049	stress	stress	NN	_	_	_
1050	_	_	RB	_	_	_
1051	high	high	JJ	_	_	_
1052	:	:	:	_	_	_
1053	MURI	MURI	NNP	_	_	_
1054	_	_	SYM	_	_	_
1055	128	128	CD	_	_	_
1056	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1057	MgSO4	mgso4	NN	_	_	_
1058	_	_	CD	_	_	_
1059	stress	stress	NN	_	_	_
1060	_	_	RB	_	_	_
1061	high	high	JJ	_	_	_
1062	:	:	:	_	_	_
1063	MURI	MURI	NNP	_	_	_
1064	_	_	SYM	_	_	_
1065	129	129	CD	_	_	_
1066	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1067	MgSO4	mgso4	NN	_	_	_
1068	_	_	CD	_	_	_
1069	stress	stress	NN	_	_	_
1070	_	_	RB	_	_	_
1071	high	high	JJ	_	_	_
1072	:	:	:	_	_	_
1073	MURI	MURI	NNP	_	_	_
1074	_	_	SYM	_	_	_
1075	130	130	CD	_	_	_
1076	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1077	MgSO4	mgso4	NN	_	_	_
1078	_	_	CD	_	_	_
1079	stress	stress	NN	_	_	_
1080	_	_	RB	_	_	_
1081	high	high	JJ	_	_	_
1082	:	:	:	_	_	_
1083	MURI	MURI	NNP	_	_	_
1084	_	_	SYM	_	_	_
1085	131	131	CD	_	_	_
1086	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1087	MgSO4	mgso4	NN	_	_	_
1088	_	_	CD	_	_	_
1089	stress	stress	NN	_	_	_
1090	_	_	RB	_	_	_
1091	high	high	JJ	_	_	_
1092	:	:	:	_	_	_
1093	MURI	MURI	NNP	_	_	_
1094	_	_	SYM	_	_	_
1095	132	132	CD	_	_	_
1096	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1097	MgSO4	mgso4	NN	_	_	_
1098	_	_	CD	_	_	_
1099	stress	stress	NN	_	_	_
1100	_	_	RB	_	_	_
1101	high	high	JJ	_	_	_
1102	:	:	:	_	_	_
1103	MURI	MURI	NNP	_	_	_
1104	_	_	SYM	_	_	_
1105	133	133	CD	_	_	_
1106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1107	MgSO4	mgso4	NN	_	_	_
1108	_	_	CD	_	_	_
1109	stress	stress	NN	_	_	_
1110	_	_	RB	_	_	_
1111	high	high	JJ	_	_	_
1112	:	:	:	_	_	_
1113	MURI	MURI	NNP	_	_	_
1114	_	_	SYM	_	_	_
1115	134	134	CD	_	_	_
1116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1117	MgSO4	mgso4	NN	_	_	_
1118	_	_	CD	_	_	_
1119	stress	stress	NN	_	_	_
1120	_	_	RB	_	_	_
1121	high	high	JJ	_	_	_
1122	:	:	:	_	_	_
1123	MURI	MURI	NNP	_	_	_
1124	_	_	SYM	_	_	_
1125	135	135	CD	_	_	_
1126	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1127	MgSO4	mgso4	NN	_	_	_
1128	_	_	CD	_	_	_
1129	stress	stress	NN	_	_	_
1130	_	_	RB	_	_	_
1131	high	high	JJ	_	_	_
1132	:	:	:	_	_	_
1133	MURI	MURI	NNP	_	_	_
1134	_	_	VBD	_	_	_
1135	136	136	CD	_	_	_
1136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1137	MgSO4	mgso4	NN	_	_	_
1138	_	_	CD	_	_	_
1139	stress	stress	NN	_	_	_
1140	_	_	RB	_	_	_
1141	high	high	JJ	_	_	_
1142	:	:	:	_	_	_
1143	MURI	MURI	NNP	_	_	_
1144	_	_	SYM	_	_	_
1145	137	137	CD	_	_	_
1146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1147	MgSO4	mgso4	NN	_	_	_
1148	_	_	CD	_	_	_
1149	stress	stress	NN	_	_	_
1150	_	_	RB	_	_	_
1151	high	high	JJ	_	_	_
1152	:	:	:	_	_	_
1153	MURI	MURI	NNP	_	_	_
1154	_	_	SYM	_	_	_
1155	138	138	CD	_	_	_
1156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1157	MgSO4	mgso4	NN	_	_	_
1158	_	_	CD	_	_	_
1159	stress	stress	NN	_	_	_
1160	_	_	RB	_	_	_
1161	high	high	JJ	_	_	_
1162	:	:	:	_	_	_
1163	MURI	MURI	NNP	_	_	_
1164	_	_	SYM	_	_	_
1165	139	139	CD	_	_	_
1166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1167	MgSO4	mgso4	NN	_	_	_
1168	_	_	CD	_	_	_
1169	stress	stress	NN	_	_	_
1170	_	_	RB	_	_	_
1171	high	high	JJ	_	_	_
1172	:	:	:	_	_	_
1173	MURI	MURI	NNP	_	_	_
1174	_	_	SYM	_	_	_
1175	140	140	CD	_	_	_
1176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1177	MgSO4	mgso4	NN	_	_	_
1178	_	_	CD	_	_	_
1179	stress	stress	NN	_	_	_
1180	_	_	RB	_	_	_
1181	high	high	JJ	_	_	_
1182	:	:	:	_	_	_
1183	MURI	MURI	NNP	_	_	_
1184	_	_	SYM	_	_	_
1185	141	141	CD	_	_	_
1186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1187	MgSO4	mgso4	NN	_	_	_
1188	_	_	CD	_	_	_
1189	stress	stress	NN	_	_	_
1190	_	_	RB	_	_	_
1191	low	low	JJ	_	_	_
1192	:	:	:	_	_	_
1193	MURI	MURI	NNP	_	_	_
1194	_	_	SYM	_	_	_
1195	142	142	CD	_	_	_
1196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1197	MgSO4	mgso4	NN	_	_	_
1198	_	_	CD	_	_	_
1199	stress	stress	NN	_	_	_
1200	_	_	RB	_	_	_
1201	low	low	JJ	_	_	_
1202	:	:	:	_	_	_
1203	MURI	MURI	NNP	_	_	_
1204	_	_	SYM	_	_	_
1205	143	143	CD	_	_	_
1206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1207	MgSO4	mgso4	NN	_	_	_
1208	_	_	CD	_	_	_
1209	stress	stress	NN	_	_	_
1210	_	_	RB	_	_	_
1211	low	low	JJ	_	_	_
1212	:	:	:	_	_	_
1213	MURI	MURI	NNP	_	_	_
1214	_	_	SYM	_	_	_
1215	144	144	CD	_	_	_
1216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1217	MgSO4	mgso4	NN	_	_	_
1218	_	_	CD	_	_	_
1219	stress	stress	NN	_	_	_
1220	_	_	RB	_	_	_
1221	low	low	JJ	_	_	_
1222	:	:	:	_	_	_
1223	MURI	MURI	NNP	_	_	_
1224	_	_	SYM	_	_	_
1225	145	145	CD	_	_	_
1226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1227	MgSO4	mgso4	NN	_	_	_
1228	_	_	CD	_	_	_
1229	stress	stress	NN	_	_	_
1230	_	_	RB	_	_	_
1231	low	low	JJ	_	_	_
1232	:	:	:	_	_	_
1233	MURI	MURI	NNP	_	_	_
1234	_	_	SYM	_	_	_
1235	146	146	CD	_	_	_
1236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1237	MgSO4	mgso4	NN	_	_	_
1238	_	_	CD	_	_	_
1239	stress	stress	NN	_	_	_
1240	_	_	RB	_	_	_
1241	low	low	JJ	_	_	_
1242	:	:	:	_	_	_
1243	MURI	MURI	NNP	_	_	_
1244	_	_	SYM	_	_	_
1245	147	147	CD	_	_	_
1246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1247	MgSO4	mgso4	NN	_	_	_
1248	_	_	CD	_	_	_
1249	stress	stress	NN	_	_	_
1250	_	_	RB	_	_	_
1251	low	low	JJ	_	_	_
1252	:	:	:	_	_	_
1253	MURI	MURI	NNP	_	_	_
1254	_	_	VBD	_	_	_
1255	148	148	CD	_	_	_
1256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1257	MgSO4	mgso4	NN	_	_	_
1258	_	_	CD	_	_	_
1259	stress	stress	NN	_	_	_
1260	_	_	RB	_	_	_
1261	low	low	JJ	_	_	_
1262	:	:	:	_	_	_
1263	MURI	MURI	NNP	_	_	_
1264	_	_	VBD	_	_	_
1265	149	149	CD	_	_	_
1266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1267	MgSO4	mgso4	NN	_	_	_
1268	_	_	CD	_	_	_
1269	stress	stress	NN	_	_	_
1270	_	_	RB	_	_	_
1271	low	low	JJ	_	_	_
1272	:	:	:	_	_	_
1273	MURI	MURI	NNP	_	_	_
1274	_	_	SYM	_	_	_
1275	150	150	CD	_	_	_
1276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1277	MgSO4	mgso4	NN	_	_	_
1278	_	_	CD	_	_	_
1279	stress	stress	NN	_	_	_
1280	_	_	RB	_	_	_
1281	low	low	JJ	_	_	_
1282	:	:	:	_	_	_
1283	MURI	MURI	NNP	_	_	_
1284	_	_	SYM	_	_	_
1285	151	151	CD	_	_	_
1286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1287	MgSO4	mgso4	NN	_	_	_
1288	_	_	CD	_	_	_
1289	stress	stress	NN	_	_	_
1290	_	_	RB	_	_	_
1291	low	low	JJ	_	_	_
1292	:	:	:	_	_	_
1293	MURI	MURI	NNP	_	_	_
1294	_	_	SYM	_	_	_
1295	152	152	CD	_	_	_
1296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1297	MgSO4	mgso4	NN	_	_	_
1298	_	_	CD	_	_	_
1299	stress	stress	NN	_	_	_
1300	_	_	RB	_	_	_
1301	low	low	JJ	_	_	_
1302	:	:	:	_	_	_
1303	MURI	MURI	NNP	_	_	_
1304	_	_	SYM	_	_	_
1305	153	153	CD	_	_	_
1306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1307	MgSO4	mgso4	NN	_	_	_
1308	_	_	CD	_	_	_
1309	stress	stress	NN	_	_	_
1310	_	_	RB	_	_	_
1311	low	low	JJ	_	_	_
1312	:	:	:	_	_	_
1313	MURI	MURI	NNP	_	_	_
1314	_	_	VBD	_	_	_
1315	154	154	CD	_	_	_
1316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1317	MgSO4	mgso4	NN	_	_	_
1318	_	_	CD	_	_	_
1319	stress	stress	NN	_	_	_
1320	_	_	RB	_	_	_
1321	low	low	JJ	_	_	_
1322	:	:	:	_	_	_
1323	MURI	MURI	NNP	_	_	_
1324	_	_	VBD	_	_	_
1325	155	155	CD	_	_	_
1326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1327	MgSO4	mgso4	NN	_	_	_
1328	_	_	CD	_	_	_
1329	stress	stress	NN	_	_	_
1330	_	_	RB	_	_	_
1331	low	low	JJ	_	_	_
1332	:	:	:	_	_	_
1333	MURI	MURI	NNP	_	_	_
1334	_	_	SYM	_	_	_
1335	156	156	CD	_	_	_
1336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1337	MgSO4	mgso4	NN	_	_	_
1338	_	_	CD	_	_	_
1339	stress	stress	NN	_	_	_
1340	_	_	RB	_	_	_
1341	low	low	JJ	_	_	_
1342	:	:	:	_	_	_
1343	MURI	MURI	NNP	_	_	_
1344	_	_	SYM	_	_	_
1345	157	157	CD	_	_	_
1346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1347	MgSO4	mgso4	NN	_	_	_
1348	_	_	CD	_	_	_
1349	stress	stress	NN	_	_	_
1350	_	_	RB	_	_	_
1351	low	low	JJ	_	_	_
1352	:	:	:	_	_	_
1353	MURI	MURI	NNP	_	_	_
1354	_	_	VBD	_	_	_
1355	158	158	CD	_	_	_
1356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1357	MgSO4	mgso4	NN	_	_	_
1358	_	_	CD	_	_	_
1359	stress	stress	NN	_	_	_
1360	_	_	RB	_	_	_
1361	low	low	JJ	_	_	_
1362	:	:	:	_	_	_
1363	MURI	MURI	NNP	_	_	_
1364	_	_	SYM	_	_	_
1365	159	159	CD	_	_	_
1366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1367	MgSO4	mgso4	NN	_	_	_
1368	_	_	CD	_	_	_
1369	stress	stress	NN	_	_	_
1370	_	_	RB	_	_	_
1371	low	low	JJ	_	_	_
1372	:	:	:	_	_	_
1373	MURI	MURI	NNP	_	_	_
1374	_	_	SYM	_	_	_
1375	160	160	CD	_	_	_
1376	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1377	MgSO4	mgso4	NN	_	_	_
1378	_	_	CD	_	_	_
1379	stress	stress	NN	_	_	_
1380	_	_	RB	_	_	_
1381	low	low	JJ	_	_	_
1382	:	:	:	_	_	_
1383	MURI	MURI	NNP	_	_	_
1384	_	_	SYM	_	_	_
1385	161	161	CD	_	_	_
1386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1387	MgSO4	mgso4	NN	_	_	_
1388	_	_	CD	_	_	_
1389	stress	stress	NN	_	_	_
1390	_	_	RB	_	_	_
1391	low	low	JJ	_	_	_
1392	:	:	:	_	_	_
1393	MURI	MURI	NNP	_	_	_
1394	_	_	SYM	_	_	_
1395	162	162	CD	_	_	_
1396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1397	MgSO4	mgso4	NN	_	_	_
1398	_	_	CD	_	_	_
1399	stress	stress	NN	_	_	_
1400	_	_	RB	_	_	_
1401	low	low	JJ	_	_	_
1402	:	:	:	_	_	_
1403	MURI	MURI	NNP	_	_	_
1404	_	_	SYM	_	_	_
1405	163	163	CD	_	_	_
1406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1407	MgSO4	mgso4	NN	_	_	_
1408	_	_	CD	_	_	_
1409	stress	stress	NN	_	_	_
1410	_	_	RB	_	_	_
1411	low	low	JJ	_	_	_
1412	:	:	:	_	_	_
1413	MURI	MURI	NNP	_	_	_
1414	_	_	SYM	_	_	_
1415	164	164	CD	_	_	_
1416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1417	MgSO4	mgso4	NN	_	_	_
1418	_	_	CD	_	_	_
1419	stress	stress	NN	_	_	_
1420	_	_	RB	_	_	_
1421	low	low	JJ	_	_	_
1422	:	:	:	_	_	_
1423	MURI	MURI	NNP	_	_	_
1424	_	_	SYM	_	_	_
1425	165	165	CD	_	_	_
1426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1427	MgSO4	mgso4	NN	_	_	_
1428	_	_	CD	_	_	_
1429	stress	stress	NN	_	_	_
1430	_	_	RB	_	_	_
1431	low	low	JJ	_	_	_
1432	:	:	:	_	_	_
1433	MURI	MURI	NNP	_	_	_
1434	_	_	VBD	_	_	_
1435	166	166	CD	_	_	_
1436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1437	MgSO4	mgso4	NN	_	_	_
1438	_	_	CD	_	_	_
1439	stress	stress	NN	_	_	_
1440	_	_	RB	_	_	_
1441	low	low	JJ	_	_	_
1442	:	:	:	_	_	_
1443	MURI	MURI	NNP	_	_	_
1444	_	_	SYM	_	_	_
1445	167	167	CD	_	_	_
1446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1447	MgSO4	mgso4	NN	_	_	_
1448	_	_	CD	_	_	_
1449	stress	stress	NN	_	_	_
1450	_	_	RB	_	_	_
1451	low	low	JJ	_	_	_
1452	:	:	:	_	_	_
1453	MURI	MURI	NNP	_	_	_
1454	_	_	SYM	_	_	_
1455	168	168	CD	_	_	_
1456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1457	MgSO4	mgso4	NN	_	_	_
1458	_	_	CD	_	_	_
1459	stress	stress	NN	_	_	_
1460	_	_	RB	_	_	_
1461	low	low	JJ	_	_	_
1462	:	:	:	_	_	_
1463	MURI	MURI	NNP	_	_	_
1464	_	_	SYM	_	_	_
1465	169	169	CD	_	_	_
1466	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1467	MgSO4	mgso4	NN	_	_	_
1468	_	_	CD	_	_	_
1469	stress	stress	NN	_	_	_
1470	_	_	RB	_	_	_
1471	low	low	JJ	_	_	_
1472	:	:	:	_	_	_
1473	MURI	MURI	NNP	_	_	_
1474	_	_	SYM	_	_	_
1475	170	170	CD	_	_	_
1476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1477	MgSO4	mgso4	NN	_	_	_
1478	_	_	CD	_	_	_
1479	stress	stress	NN	_	_	_
1480	_	_	RB	_	_	_
1481	low	low	JJ	_	_	_
1482	:	:	:	_	_	_
1483	MURI	MURI	NNP	_	_	_
1484	_	_	SYM	_	_	_
1485	171	171	CD	_	_	_
1486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1487	mgtA	mgta	NN	GEN	_	_
1488	KO	ko	NN	_	_	_
1489	rep1	rep1	NN	_	_	_
1490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1491	mgtA	mgta	NN	GEN	_	_
1492	KO	ko	NN	_	_	_
1493	rep2	rep2	NN	_	_	_
1494	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1495	mgtA	mgta	NN	GEN	_	_
1496	KO	ko	NN	_	_	_
1497	rep3	rep3	NN	_	_	_
1498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1499	mhpD	mhpd	NN	GEN	_	_
1500	KO	ko	NN	_	_	_
1501	rep1	rep1	NN	_	_	_
1502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1503	mhpD	mhpd	NN	GEN	_	_
1504	KO	ko	NN	_	_	_
1505	rep2	rep2	NN	_	_	_
1506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1507	mhpD	mhpd	NN	GEN	_	_
1508	KO	ko	NN	_	_	_
1509	rep3	rep3	NN	_	_	_
1510	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1511	MIC	mic	NN	_	_	_
1512	of	of	IN	_	_	_
1513	OLA	OLA	NNP	_	_	_
1514	,	,	,	_	_	_
1515	biological	biological	JJ	_	_	_
1516	rep1	rep1	NN	_	_	_
1517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1518	MIC	mic	NN	_	_	_
1519	of	of	IN	_	_	_
1520	OLA	OLA	NNP	_	_	_
1521	,	,	,	_	_	_
1522	biological	biological	JJ	_	_	_
1523	rep2	rep2	NN	_	_	_
1524	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1525	MIC	mic	NN	_	_	_
1526	of	of	IN	_	_	_
1527	OLA	OLA	NNP	_	_	_
1528	,	,	,	_	_	_
1529	biological	biological	JJ	_	_	_
1530	rep3	rep3	NN	_	_	_
1531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1532	Microarray	microarray	NN	_	_	_
1533	analysis	analysis	NN	_	_	_
1534	including	include	VBG	_	_	_
1535	pre-processing	pre-processing	JJ	_	_	_
1536	,	,	,	_	_	_
1537	normalisation	normalisation	NN	_	_	_
1538	anmd	anmd	NN	_	_	_
1539	statistical	statistical	JJ	_	_	_
1540	analysis	analysis	NN	_	_	_
1541	were	be	VBD	_	_	_
1542	performed	perform	VBN	_	_	_
1543	using	use	VBG	_	_	_
1544	R	r	NN	_	_	_
1545	-LRB-	-lrb-	-LRB-	_	_	_
1546	R	r	NN	_	_	_
1547	,	,	,	_	_	_
1548	2007	2007	CD	_	_	_
1549	-RRB-	-rrb-	-RRB-	_	_	_
1550	version	version	NN	_	_	_
1551	2.6	2.6	CD	_	_	_
1552	and	and	CC	_	_	_
1553	Bioconductor	Bioconductor	NNP	_	_	_
1554	-LRB-	-lrb-	-LRB-	_	_	_
1555	Gentleman	Gentleman	NNP	_	_	_
1556	et	et	FW	_	_	_
1557	al.	al.	FW	_	_	_
1558	2004	2004	CD	_	_	_
1559	,	,	,	_	_	_
1560	Genome	Genome	NNP	_	_	_
1561	Biol	Biol	NNP	_	_	_
1562	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Microarray	Microarray	NNP	_	_	_
3	data	data	NN	_	_	_
4	analyses	analysis	NNS	_	_	_
5	were	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Acuity	acuity	NN	_	_	_
9	4.0	4.0	CD	_	_	_
10	software	software	NN	_	_	_
11	.	.	.	_	_	_

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	635/532	635/532	CD	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	values	value	NNS	_	_	_
12	.	.	.	_	_	_

1	Genes	gene	NNS	_	_	_
2	were	be	VBD	_	_	_
3	included	include	VBN	_	_	_
4	in	in	IN	_	_	_
5	the	the	DT	_	_	_
6	final	final	JJ	_	_	_
7	dataset	dataset	NN	_	_	_
8	that	that	WDT	_	_	_
9	exhibit	exhibit	VBP	_	_	_
10	significance	significance	NN	_	_	_
11	based	base	VBN	_	_	_
12	upon	upon	IN	_	_	_
13	a	a	DT	_	_	_
14	very	very	RB	_	_	_
15	conservative	conservative	JJ	_	_	_
16	FDR	FDR	NNP	_	_	_
17	less	less	JJR	_	_	_
18	than	than	IN	_	_	_
19	2.5	2.5	CD	_	_	_
20	%	%	NN	_	_	_
21	-LSB-	-lsb-	-LRB-	_	_	_
22	27	27	CD	_	_	_
23	-RSB-	-rsb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	at	at	IN	_	_	_
26	least	least	JJS	_	_	_
27	2.0-fold	2.0-fold	JJ	_	_	_
28	comparative	comparative	JJ	_	_	_
29	regulation	regulation	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Microarray	Microarray	NNP	_	_	_
3	data	data	NN	_	_	_
4	analysis	analysis	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	with	with	IN	_	_	_
8	free	free	JJ	_	_	_
9	software	software	NN	_	_	_
10	genArise	genarise	NN	_	_	_
11	,	,	,	_	_	_
12	developed	develop	VBN	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	Computing	Computing	NNP	_	_	_
16	Unit	unit	NN	_	_	_
17	of	of	IN	_	_	_
18	Cellular	cellular	JJ	_	_	_
19	Physiology	Physiology	NNP	_	_	_
20	Institute	Institute	NNP	_	_	_
21	of	of	IN	_	_	_
22	UNAM	UNAM	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	http://www.ifc.unam.mx/genarise/	http://www.ifc.unam.mx/genarise/	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	GenArise	GenArise	NNP	_	_	_
2	carry	carry	VBP	_	_	_
3	out	out	RP	_	_	_
4	a	a	DT	_	_	_
5	number	number	NN	_	_	_
6	of	of	IN	_	_	_
7	transformations	transformation	NNS	_	_	_
8	:	:	:	_	_	_
9	background	background	NN	_	_	_
10	correction	correction	NN	_	_	_
11	,	,	,	_	_	_
12	normalization	normalization	NN	_	_	_
13	,	,	,	_	_	_
14	intensity	intensity	NN	_	_	_
15	filter	filter	NN	_	_	_
16	,	,	,	_	_	_
17	replicates	replicate	VBZ	_	_	_
18	analysis	analysis	NN	_	_	_
19	and	and	CC	_	_	_
20	selecting	select	VBG	_	_	_
21	differentially	differentially	RB	_	_	_
22	expressed	express	VBN	_	_	_
23	genes	gene	NNS	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	goal	goal	NN	_	_	_
3	of	of	IN	_	_	_
4	genArise	genarise	NN	_	_	_
5	is	be	VBZ	_	_	_
6	to	to	TO	_	_	_
7	identify	identify	VB	_	_	_
8	which	which	WDT	_	_	_
9	genes	gene	NNS	_	_	_
10	show	show	VBP	_	_	_
11	good	good	JJ	_	_	_
12	evidence	evidence	NN	_	_	_
13	of	of	IN	_	_	_
14	being	be	VBG	_	_	_
15	differentially	differentially	RB	_	_	_
16	expressed	express	VBN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	software	software	NN	_	_	_
3	identifies	identify	VBZ	_	_	_
4	differential	differential	JJ	_	_	_
5	expressed	express	VBN	_	_	_
6	genes	gene	NNS	_	_	_
7	by	by	IN	_	_	_
8	calculating	calculate	VBG	_	_	_
9	an	a	DT	_	_	_
10	intensity-dependent	intensity-dependent	JJ	_	_	_
11	z-score	z-score	NN	_	_	_
12	.	.	.	_	_	_

1	Using	use	VBG	_	_	_
2	a	a	DT	_	_	_
3	sliding	slide	VBG	_	_	_
4	window	window	NN	_	_	_
5	algorithm	algorithm	NN	_	_	_
6	to	to	TO	_	_	_
7	calculate	calculate	VB	_	_	_
8	the	the	DT	_	_	_
9	mean	mean	NN	_	_	_
10	and	and	CC	_	_	_
11	standard	standard	JJ	_	_	_
12	deviation	deviation	NN	_	_	_
13	within	within	IN	_	_	_
14	a	a	DT	_	_	_
15	window	window	NN	_	_	_
16	surrounding	surround	VBG	_	_	_
17	each	each	DT	_	_	_
18	data	datum	NNS	_	_	_
19	point	point	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	define	define	VB	_	_	_
23	a	a	DT	_	_	_
24	z-score	z-score	NN	_	_	_
25	where	where	WRB	_	_	_
26	z	z	SYM	_	_	_
27	measures	measure	VBZ	_	_	_
28	the	the	DT	_	_	_
29	number	number	NN	_	_	_
30	of	of	IN	_	_	_
31	standard	standard	JJ	_	_	_
32	deviations	deviation	NNS	_	_	_
33	a	a	DT	_	_	_
34	data	data	NN	_	_	_
35	is	be	VBZ	_	_	_
36	from	from	IN	_	_	_
37	the	the	DT	_	_	_
38	mean	mean	NN	_	_	_
39	.	.	.	_	_	_

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

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	,	,	,	_	_	_
26	2008	2008	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	the	the	DT	_	_	_
30	thermodynamic	thermodynamic	JJ	_	_	_
31	model	model	NN	_	_	_
32	of	of	IN	_	_	_
33	non-specific	non-specific	JJ	_	_	_
34	binding	binding	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	NSB	nsb	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	on	on	IN	_	_	_
39	short	short	JJ	_	_	_
40	nucleotide	nucleotide	NN	_	_	_
41	microarrays	microarray	NNS	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	Furusawa	Furusawa	NNP	_	_	_
44	et	et	FW	_	_	_
45	al	al	FW	_	_	_
46	,	,	,	_	_	_
47	2009	2009	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	.	.	.	_	_	_

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	,	,	,	_	_	_
26	2008	2008	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	the	the	DT	_	_	_
30	thermodynamic	thermodynamic	JJ	_	_	_
31	model	model	NN	_	_	_
32	of	of	IN	_	_	_
33	non-specific	non-specific	JJ	_	_	_
34	binding	binding	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	NSB	nsb	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	on	on	IN	_	_	_
39	short	short	JJ	_	_	_
40	nucleotide	nucleotide	NN	_	_	_
41	microarrays	microarray	NNS	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	Furusawa	Furusawa	NNP	_	_	_
44	et	et	FW	_	_	_
45	al	al	FW	_	_	_
46	,	,	,	_	_	_
47	2009	2009	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Microarray	Microarray	NNP	_	_	_
3	normalization	normalization	NN	_	_	_
4	is	be	VBZ	_	_	_
5	carried	carry	VBN	_	_	_
6	out	out	RP	_	_	_
7	using	use	VBG	_	_	_
8	maanova	maanova	NN	_	_	_
9	function	function	NN	_	_	_
10	in	in	IN	_	_	_
11	R	r	NN	_	_	_
12	program	program	NN	_	_	_
13	version	version	NN	_	_	_
14	2.2.1	2.2.1	CD	_	_	_
15	.	.	.	_	_	_

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	NNP	_	_	_
2	Microarray	Microarray	NNP	_	_	_
3	suit	suit	NN	_	_	_
4	5.0	5.0	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Affymetrix	Affymetrix	NNP	_	_	_
7	Inc.	Inc.	NNP	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	average	average	VB	_	_	_
13	the	the	DT	_	_	_
14	scans	scan	NNS	_	_	_
15	and	and	CC	_	_	_
16	process	process	NN	_	_	_
17	the	the	DT	_	_	_
18	data	datum	NNS	_	_	_
19	,	,	,	_	_	_
20	further	further	RB	_	_	_
21	data	data	NN	_	_	_
22	analysis	analysis	NN	_	_	_
23	was	be	VBD	_	_	_
24	conducted	conduct	VBN	_	_	_
25	using	use	VBG	_	_	_
26	Affymetrix	Affymetrix	NNP	_	_	_
27	®	®	NNP	_	_	_
28	Data	Data	NNP	_	_	_
29	Mining	Mining	NNP	_	_	_
30	Tool	Tool	NNP	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	DMT	DMT	NNP	_	_	_
33	3.0	3.0	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Microarray	Microarray	NNP	_	_	_
3	suite	suite	NN	_	_	_
4	5.0	5.0	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Microcin	microcin	NN	_	_	_
7	B17	b17	NN	_	_	_
8	Rep	Rep	NNP	_	_	_
9	1	1	CD	_	_	_
10	+	+	CC	_	_	_
11	A-IP	a-ip	JJ	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Microcin	microcin	NN	_	_	_
14	B17	b17	NN	_	_	_
15	Rep	Rep	NNP	_	_	_
16	1	1	CD	_	_	_
17	+	+	CC	_	_	_
18	A+IP	A+IP	NNP	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Microcin	Microcin	NNP	_	_	_
21	B17	B17	NNP	_	_	_
22	Rep	Rep	NNP	_	_	_
23	2	2	CD	_	_	_
24	+	+	CC	_	_	_
25	A-IP	a-ip	JJ	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Microcin	microcin	NN	_	_	_
28	B17	b17	NN	_	_	_
29	Rep	Rep	NNP	_	_	_
30	2	2	CD	_	_	_
31	+	+	CC	_	_	_
32	A+IP	A+IP	NNP	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Microcin	Microcin	NNP	_	_	_
35	B17	B17	NNP	_	_	_
36	Rep	Rep	NNP	_	_	_
37	3	3	CD	_	_	_
38	+	+	CC	_	_	_
39	A-IP	a-ip	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Microcin	microcin	NN	_	_	_
42	B17	b17	NN	_	_	_
43	Rep	Rep	NNP	_	_	_
44	3	3	CD	_	_	_
45	+	+	CC	_	_	_
46	A+IP	A+IP	NNP	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Microcin	Microcin	NNP	_	_	_
49	_	_	NNP	_	_	_
50	IN	in	IN	_	_	_
51	_	_	CD	_	_	_
52	50mkM	50mkm	NN	_	_	_
53	_	_	NN	_	_	_
54	3	3	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Microcin	microcin	NN	_	_	_
57	_	_	CD	_	_	_
58	IN	in	IN	_	_	_
59	_	_	CD	_	_	_
60	Mu	mu	NN	_	_	_
61	_	_	CD	_	_	_
62	10mkM	10mkm	NN	_	_	_
63	_	_	NN	_	_	_
64	1	1	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Microcin	microcin	NN	_	_	_
67	_	_	CD	_	_	_
68	IN	in	IN	_	_	_
69	_	_	CD	_	_	_
70	Mu	mu	NN	_	_	_
71	_	_	NN	_	_	_
72	10mkM	10mkm	NN	_	_	_
73	_	_	NN	_	_	_
74	2	2	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	Microcin	microcin	NN	_	_	_
77	_	_	CD	_	_	_
78	IP	IP	NNP	_	_	_
79	_	_	NNP	_	_	_
80	50mkM	50mkM	NNP	_	_	_
81	_	_	SYM	_	_	_
82	3	3	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	MIcrocin	microcin	NN	_	_	_
85	_	_	CD	_	_	_
86	IP	IP	NNP	_	_	_
87	_	_	SYM	_	_	_
88	Mu	mu	FW	_	_	_
89	_	_	FW	_	_	_
90	10mkM	10mkm	NN	_	_	_
91	_	_	NN	_	_	_
92	1	1	CD	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Microcin	microcin	NN	_	_	_
95	_	_	CD	_	_	_
96	IP	IP	NNP	_	_	_
97	_	_	SYM	_	_	_
98	Mu	mu	FW	_	_	_
99	_	_	FW	_	_	_
100	10mkM	10mkm	NN	_	_	_
101	_	_	NN	_	_	_
102	2	2	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Mid	Mid	NNP	_	_	_
105	log	log	NN	_	_	_
106	_	_	SYM	_	_	_
107	cra	cra	FW	GEN	_	_
108	KO	ko	FW	_	_	_
109	_	_	SYM	_	_	_
110	glc	glc	NN	_	_	_
111	minimal	minimal	JJ	_	_	_
112	media	media	NNS	_	_	_
113	_	_	NN	_	_	_
114	aerobic	aerobic	JJ	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Mid	Mid	NNP	_	_	_
117	log	log	NN	_	_	_
118	_	_	SYM	_	_	_
119	cra	cra	FW	GEN	_	_
120	KO	ko	FW	_	_	_
121	_	_	SYM	_	_	_
122	glc	glc	NN	_	_	_
123	minimal	minimal	JJ	_	_	_
124	media	media	NNS	_	_	_
125	+	+	CC	_	_	_
126	L-tryptophan	l-tryptophan	JJ	_	_	_
127	_	_	NN	_	_	_
128	aerobic	aerobic	JJ	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	Mid	Mid	NNP	_	_	_
131	log	log	NN	_	_	_
132	cultures	culture	NNS	_	_	_
133	were	be	VBD	_	_	_
134	treated	treat	VBN	_	_	_
135	with	with	IN	_	_	_
136	Qiagen	Qiagen	NNP	_	_	_
137	RNA	rna	NN	_	_	_
138	Protect	protect	VB	_	_	_
139	reagent	reagent	NN	_	_	_
140	following	follow	VBG	_	_	_
141	the	the	DT	_	_	_
142	vendor	vendor	NN	_	_	_
143	's	's	POS	_	_	_
144	protocol	protocol	NN	_	_	_
145	.	.	.	_	_	_

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	minD	mind	NN	GEN	_	_
151	__	__	CD	_	_	_
152	U	U	NNP	_	_	_
153	_	_	NNP	_	_	_
154	N0075	N0075	NNP	_	_	_
155	_	_	NNP	_	_	_
156	r1	r1	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	minD	mind	NN	GEN	_	_
159	__	__	CD	_	_	_
160	U	U	NNP	_	_	_
161	_	_	NNP	_	_	_
162	N0075	N0075	NNP	_	_	_
163	_	_	SYM	_	_	_
164	r2	r2	FW	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
166	minD	mind	NN	GEN	_	_
167	__	__	CD	_	_	_
168	U	U	NNP	_	_	_
169	_	_	NNP	_	_	_
170	N0075	N0075	NNP	_	_	_
171	_	_	SYM	_	_	_
172	r3	r3	FW	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
174	minD	mind	NN	GEN	_	_
175	upregulation	upregulation	NN	_	_	_
176	,	,	,	_	_	_
177	0.075	0.075	CD	_	_	_
178	mg/mL	mg/ml	NN	_	_	_
179	norfloxacin	norfloxacin	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	minE	mine	NN	GEN	_	_
182	__	__	CD	_	_	_
183	U	U	NNP	_	_	_
184	_	_	NNP	_	_	_
185	N0075	N0075	NNP	_	_	_
186	_	_	NNP	_	_	_
187	r1	r1	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	minE	mine	NN	GEN	_	_
190	__	__	CD	_	_	_
191	U	U	NNP	_	_	_
192	_	_	NNP	_	_	_
193	N0075	N0075	NNP	_	_	_
194	_	_	NNP	_	_	_
195	r2	r2	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	minE	mine	NN	GEN	_	_
198	__	__	CD	_	_	_
199	U	U	NNP	_	_	_
200	_	_	NNP	_	_	_
201	N0075	N0075	NNP	_	_	_
202	_	_	SYM	_	_	_
203	r3	r3	FW	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
205	minE	mine	NN	GEN	_	_
206	upregulation	upregulation	NN	_	_	_
207	,	,	,	_	_	_
208	0.075	0.075	CD	_	_	_
209	mg/mL	mg/ml	NN	_	_	_
210	norfloxacin	norfloxacin	NN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	MiSeq	miseq	NN	_	_	_
213	for	for	IN	_	_	_
214	base	base	NN	_	_	_
215	calling	call	VBG	_	_	_
216	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
217	Mixed	Mixed	NNP	_	_	_
218	model	model	NN	_	_	_
219	analysis	analysis	NN	_	_	_
220	was	be	VBD	_	_	_
221	conducted	conduct	VBN	_	_	_
222	as	as	IN	_	_	_
223	previously	previously	RB	_	_	_
224	described	describe	VBN	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	Madsen	Madsen	NNP	_	_	_
227	,	,	,	_	_	_
228	et	et	FW	_	_	_
229	al.	al.	FW	_	_	_
230	,	,	,	_	_	_
231	2006	2006	CD	_	_	_
232	-RRB-	-rrb-	-RRB-	_	_	_
233	excluding	exclude	VBG	_	_	_
234	slide	slide	NN	_	_	_
235	region	region	NN	_	_	_
236	and	and	CC	_	_	_
237	slide-by-region	slide-by-region	NN	_	_	_
238	interaction	interaction	NN	_	_	_
239	effects	effect	NNS	_	_	_
240	.	.	.	_	_	_

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	MMAcetat	mmacetat	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	mMaple3	mmaple3	NN	_	_	_
16	_	_	NN	_	_	_
17	0	0	CD	_	_	_
18	min	min	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	mMaple3	mmaple3	NN	_	_	_
21	_	_	CD	_	_	_
22	10	10	CD	_	_	_
23	min	min	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	mMaple3	mmaple3	NN	_	_	_
26	_	_	CD	_	_	_
27	15	15	CD	_	_	_
28	min	min	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	mMaple3	mmaple3	NN	_	_	_
31	_	_	NN	_	_	_
32	1	1	CD	_	_	_
33	min	min	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	mMaple3	mmaple3	NN	_	_	_
36	_	_	NN	_	_	_
37	2	2	CD	_	_	_
38	min	min	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	mMaple3	mmaple3	NN	_	_	_
41	_	_	CD	_	_	_
42	4	4	CD	_	_	_
43	min	min	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	mMaple3	mmaple3	NN	_	_	_
46	_	_	CD	_	_	_
47	6	6	CD	_	_	_
48	min	min	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	mMaple3	mmaple3	NN	_	_	_
51	_	_	CD	_	_	_
52	8	8	CD	_	_	_
53	min	min	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	MMPyruvat	mmpyruvat	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	mntR	mntr	NN	GEN	_	_
58	KO	ko	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	mntR	mntr	NN	GEN	_	_
61	KO	ko	SYM	_	_	_
62	-	-	:	_	_	_
63	O2	o2	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	Mock	mock	JJ	_	_	_
66	community	community	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	molecule	molecule	NN	_	_	_
69	subtype	subtype	NN	_	_	_
70	:	:	:	_	_	_
71	DMS-modified	dms-modified	JJ	_	_	_
72	mRNA	mrna	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	molecule	molecule	NN	_	_	_
75	subtype	subtype	NN	_	_	_
76	:	:	:	_	_	_
77	In	in	FW	_	_	_
78	vitro	vitro	FW	_	_	_
79	synthesized	synthesize	VBN	_	_	_
80	RNase	rnase	NN	_	_	_
81	P	p	NN	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	rnpB	rnpb	NN	GEN	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	RNA	rna	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	molecule	molecule	NN	_	_	_
88	subtype	subtype	NN	_	_	_
89	:	:	:	_	_	_
90	mRNA	mrna	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	molecule	molecule	NN	_	_	_
93	subtype	subtype	NN	_	_	_
94	:	:	:	_	_	_
95	nascent	nascent	JJ	_	_	_
96	3	3	CD	_	_	_
97	'	'	''	_	_	_
98	RNA	rna	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	molecule	molecule	NN	_	_	_
101	subtype	subtype	NN	_	_	_
102	:	:	:	_	_	_
103	ribosome-depeleted	ribosome-depeleted	JJ	_	_	_
104	RNA	rna	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	molecule	molecule	NN	_	_	_
107	subtype	subtype	NN	_	_	_
108	:	:	:	_	_	_
109	ribosome	ribosome	NN	_	_	_
110	protected	protect	VBD	_	_	_
111	mRNA	mrna	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	molecule	molecule	NN	_	_	_
114	subtype	subtype	NN	_	_	_
115	:	:	:	_	_	_
116	Ribosome	ribosome	NN	_	_	_
117	protected	protect	VBD	_	_	_
118	mRNA	mrna	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	molecule	molecule	NN	_	_	_
121	subtype	subtype	NN	_	_	_
122	:	:	:	_	_	_
123	rRNA-depleted	rrna-depleted	JJ	_	_	_
124	total	total	JJ	_	_	_
125	RNA	rna	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	molecule	molecule	NN	_	_	_
128	subtype	subtype	NN	_	_	_
129	:	:	:	_	_	_
130	total	total	JJ	_	_	_
131	RNA	rna	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	molecule	molecule	NN	_	_	_
134	subtype	subtype	NN	_	_	_
135	:	:	:	_	_	_
136	Total	total	JJ	_	_	_
137	RNA	rna	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	molecule	molecule	NN	_	_	_
140	subtype	subtype	NN	_	_	_
141	:	:	:	_	_	_
142	Total	total	JJ	_	_	_
143	RNA	rna	NN	_	_	_
144	-LRB-	-lrb-	-LRB-	_	_	_
145	Cytosolic	cytosolic	JJ	_	_	_
146	fraction	fraction	NN	_	_	_
147	-RRB-	-rrb-	-RRB-	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	molecule	molecule	NN	_	_	_
150	subtype	subtype	NN	_	_	_
151	:	:	:	_	_	_
152	Total	total	JJ	_	_	_
153	RNA	rna	NN	_	_	_
154	-LRB-	-lrb-	-LRB-	_	_	_
155	Nucleoid	nucleoid	NN	_	_	_
156	fraction	fraction	NN	_	_	_
157	-RRB-	-rrb-	-RRB-	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	molecule	molecule	NN	_	_	_
160	subtype	subtype	NN	_	_	_
161	:	:	:	_	_	_
162	total	total	JJ	_	_	_
163	RNA	rna	NN	_	_	_
164	-LRB-	-lrb-	-LRB-	_	_	_
165	ribosome-depleted	ribosome-depleted	JJ	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	molecule	molecule	NN	_	_	_
169	subtype	subtype	NN	_	_	_
170	:	:	:	_	_	_
171	total	total	JJ	_	_	_
172	RNA	rna	NN	_	_	_
173	,	,	,	_	_	_
174	rRNA	rrna	NN	_	_	_
175	depleted	deplete	VBD	_	_	_
176	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
177	Monoclonal	monoclonal	JJ	_	_	_
178	antibody	antibody	NN	_	_	_
179	for	for	IN	_	_	_
180	HA	HA	NNP	_	_	_
181	-LRB-	-lrb-	-LRB-	_	_	_
182	12CA5	12ca5	NN	_	_	_
183	-RRB-	-rrb-	-RRB-	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	Monoclonal	monoclonal	JJ	_	_	_
186	antibody	antibody	NN	_	_	_
187	for	for	IN	_	_	_
188	NusA	nusa	NN	_	_	_
189	-LRB-	-lrb-	-LRB-	_	_	_
190	1NA1	1na1	NN	_	_	_
191	-RRB-	-rrb-	-RRB-	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	Monoclonal	monoclonal	JJ	_	_	_
194	antibody	antibody	NN	_	_	_
195	for	for	IN	_	_	_
196	RNA	rna	NN	_	_	_
197	polymerase	polymerase	NN	_	_	_
198	Beta	beta	NN	_	_	_
199	'	'	''	_	_	_
200	subunit	subunit	NN	_	_	_
201	-LRB-	-lrb-	-LRB-	_	_	_
202	NT73	nt73	NN	_	_	_
203	-RRB-	-rrb-	-RRB-	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	Monoclonal	monoclonal	JJ	_	_	_
206	antibody	antibody	NN	_	_	_
207	for	for	IN	_	_	_
208	Sigma70	sigma70	NN	_	_	_
209	-LRB-	-lrb-	-LRB-	_	_	_
210	2G10	2g10	NN	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	morphology	morphology	NN	_	_	_
214	:	:	:	_	_	_
215	a	a	DT	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	morphology	morphology	NN	_	_	_
218	:	:	:	_	_	_
219	b	b	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	morphology	morphology	NN	_	_	_
222	:	:	:	_	_	_
223	c	c	NN	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	morphology	morphology	NN	_	_	_
226	:	:	:	_	_	_
227	Coliform	coliform	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	morphology	morphology	NN	_	_	_
230	:	:	:	_	_	_
231	Filamented	filamented	JJ	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	morphology	morphology	NN	_	_	_
234	:	:	:	_	_	_
235	Reverted	revert	VBN	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	reverted	revert	VBD	_	_	_
238	back	back	RB	_	_	_
239	from	from	IN	_	_	_
240	a	a	DT	_	_	_
241	Filamented	filamented	JJ	_	_	_
242	shape	shape	NN	_	_	_
243	into	into	IN	_	_	_
244	a	a	DT	_	_	_
245	coli	coli	NN	_	_	_
246	shape	shape	NN	_	_	_
247	-RRB-	-rrb-	-RRB-	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	morphology	morphology	NN	_	_	_
250	:	:	:	_	_	_
251	Transition	transition	NN	_	_	_
252	-LRB-	-lrb-	-LRB-	_	_	_
253	from	from	IN	_	_	_
254	Coli	Coli	NNP	_	_	_
255	into	into	IN	_	_	_
256	Filamented	Filamented	NNP	_	_	_
257	-RRB-	-rrb-	-RRB-	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	mouse	mouse	NN	_	_	_
260	feces	fece	VBZ	_	_	_
261	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
262	Mouse	Mouse	NNP	_	_	_
263	kidneys	kidney	NNS	_	_	_
264	were	be	VBD	_	_	_
265	homogonized	homogonize	VBN	_	_	_
266	in	in	IN	_	_	_
267	RNALater	rnalater	NN	_	_	_
268	solution	solution	NN	_	_	_
269	-LRB-	-lrb-	-LRB-	_	_	_
270	Ambion	ambion	NN	_	_	_
271	-RRB-	-rrb-	-RRB-	_	_	_
272	and	and	CC	_	_	_
273	bacterial	bacterial	JJ	_	_	_
274	titers	titer	NNS	_	_	_
275	were	be	VBD	_	_	_
276	taken	take	VBN	_	_	_
277	.	.	.	_	_	_

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	M-P0h	m-p0h	NN	_	_	_
12	_	_	CD	_	_	_
13	r1	r1	NN	_	_	_
14	_	_	CD	_	_	_
15	HiSeq	hiseq	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	M-P0h	m-p0h	NN	_	_	_
18	_	_	CD	_	_	_
19	r2	r2	NN	_	_	_
20	_	_	CD	_	_	_
21	HiSeq	hiseq	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	M-P2h	m-p2h	NN	_	_	_
24	_	_	CD	_	_	_
25	r1	r1	NN	_	_	_
26	_	_	CD	_	_	_
27	HiSeq	hiseq	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	M-P2h	m-p2h	NN	_	_	_
30	_	_	CD	_	_	_
31	r2	r2	NN	_	_	_
32	_	_	CD	_	_	_
33	HiSeq	hiseq	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	M-P4h	m-p4h	NN	_	_	_
36	_	_	CD	_	_	_
37	r1	r1	NN	_	_	_
38	_	_	CD	_	_	_
39	HiSeq	hiseq	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	M-P4h	m-p4h	NN	_	_	_
42	_	_	CD	_	_	_
43	r2	r2	NN	_	_	_
44	_	_	CD	_	_	_
45	HiSeq	hiseq	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	M-P4h	m-p4h	NN	_	_	_
48	_	_	CD	_	_	_
49	r3	r3	NN	_	_	_
50	_	_	CD	_	_	_
51	HiSeq	hiseq	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	mRNA	mrna	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	mRNA	mrna	NN	_	_	_
56	fragments	fragment	NNS	_	_	_
57	were	be	VBD	_	_	_
58	size	size	NN	_	_	_
59	selected	select	VBN	_	_	_
60	via	via	IN	_	_	_
61	gel	gel	NN	_	_	_
62	purification	purification	NN	_	_	_
63	,	,	,	_	_	_
64	and	and	CC	_	_	_
65	ligated	ligate	VBN	_	_	_
66	to	to	TO	_	_	_
67	5	5	CD	_	_	_
68	'	'	''	_	_	_
69	adenylated	adenylate	VBN	_	_	_
70	DNA	dna	NN	_	_	_
71	oligo	oligo	JJ	_	_	_
72	.	.	.	_	_	_

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	37	37	CD	_	_	_
40	°C	°c	NN	_	_	_
41	in	in	IN	_	_	_
42	WT	wt	JJ	_	_	_
43	with	with	IN	_	_	_
44	control	control	NN	_	_	_
45	plasmid	plasmid	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	mRNA-seq	mrna-seq	NN	_	_	_
48	37	37	CD	_	_	_
49	°C	°c	NN	_	_	_
50	in	in	IN	_	_	_
51	WT	wt	JJ	_	_	_
52	with	with	IN	_	_	_
53	plasmid	plasmid	NN	_	_	_
54	expressing	express	VBG	_	_	_
55	mini-ORF	mini-orf	NN	_	_	_
56	CUA	cua	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	mRNA-seq	mrna-seq	NN	_	_	_
59	37	37	CD	_	_	_
60	°C	°c	NN	_	_	_
61	in	in	IN	_	_	_
62	WT	wt	JJ	_	_	_
63	with	with	IN	_	_	_
64	plasmid	plasmid	NN	_	_	_
65	expressing	express	VBG	_	_	_
66	mini-ORF	mini-orf	NN	_	_	_
67	CUG	cug	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	mRNA-seq	mrna-seq	NN	_	_	_
70	3	3	CD	_	_	_
71	hr	hr	NN	_	_	_
72	after	after	IN	_	_	_
73	shift	shift	NN	_	_	_
74	to	to	TO	_	_	_
75	10	10	CD	_	_	_
76	°C	°c	NN	_	_	_
77	in	in	IN	_	_	_
78	WT	wt	JJ	_	_	_
79	cells	cell	NNS	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	mRNA-seq	mrna-seq	NN	_	_	_
82	4	4	CD	_	_	_
83	hr	hr	NN	_	_	_
84	after	after	IN	_	_	_
85	shift	shift	NN	_	_	_
86	to	to	TO	_	_	_
87	10	10	CD	_	_	_
88	°C	°c	NN	_	_	_
89	in	in	IN	_	_	_
90	WT	wt	JJ	_	_	_
91	cells	cell	NNS	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	mRNA-seq	mrna-seq	NN	_	_	_
94	6	6	CD	_	_	_
95	hr	hr	NN	_	_	_
96	after	after	IN	_	_	_
97	shift	shift	NN	_	_	_
98	to	to	TO	_	_	_
99	10	10	CD	_	_	_
100	°C	°c	NN	_	_	_
101	in	in	IN	_	_	_
102	WT	wt	JJ	_	_	_
103	cells	cell	NNS	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	mRNA-seq	mrna-seq	NN	_	_	_
106	8	8	CD	_	_	_
107	hr	hr	NN	_	_	_
108	after	after	IN	_	_	_
109	shift	shift	NN	_	_	_
110	to	to	TO	_	_	_
111	10	10	CD	_	_	_
112	°C	°c	NN	_	_	_
113	in	in	IN	_	_	_
114	∆	∆	CD	_	_	_
115	cspABEG	cspabeg	NN	_	_	_
116	cells	cell	NNS	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
118	mRNA-seq	mrna-seq	NN	_	_	_
119	8	8	CD	_	_	_
120	hr	hr	NN	_	_	_
121	after	after	IN	_	_	_
122	shift	shift	NN	_	_	_
123	to	to	TO	_	_	_
124	10	10	CD	_	_	_
125	°C	°c	NN	_	_	_
126	in	in	IN	_	_	_
127	WT	wt	JJ	_	_	_
128	cells	cell	NNS	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	mRNA-seq	mrna-seq	NN	_	_	_
131	at	at	IN	_	_	_
132	37	37	CD	_	_	_
133	°C	°c	NN	_	_	_
134	in	in	IN	_	_	_
135	∆	∆	CD	_	_	_
136	cspABCEG	cspabceg	NN	_	_	_
137	cells	cell	NNS	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
139	mRNA-seq	mrna-seq	NN	_	_	_
140	at	at	IN	_	_	_
141	37	37	CD	_	_	_
142	°C	°c	NN	_	_	_
143	in	in	IN	_	_	_
144	WT	wt	JJ	_	_	_
145	cells	cell	NNS	_	_	_
146	_	_	VBP	_	_	_
147	1	1	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	mRNA-seq	mrna-seq	NN	_	_	_
150	at	at	IN	_	_	_
151	37	37	CD	_	_	_
152	°C	°c	NN	_	_	_
153	in	in	IN	_	_	_
154	WT	wt	JJ	_	_	_
155	cells	cell	NNS	_	_	_
156	_	_	VBP	_	_	_
157	2	2	CD	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
159	mRNA-seq	mrna-seq	NN	_	_	_
160	in	in	IN	_	_	_
161	rich	rich	JJ	_	_	_
162	defined	define	VBN	_	_	_
163	media	media	NNS	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	mRNA-seq	mrna-seq	NN	_	_	_
166	MicL-S	micl-s	NN	_	_	_
167	t0	t0	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	mRNA-seq	mrna-seq	NN	_	_	_
170	MicL-S	micl-s	NN	_	_	_
171	t10	t10	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	mRNA-seq	mrna-seq	NN	_	_	_
174	MicL-S	micl-s	NN	_	_	_
175	t20	t20	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	mRNA-seq	mrna-seq	NN	_	_	_
178	MicL-S	micl-s	NN	_	_	_
179	t4	t4	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	mRNA-seq	mrna-seq	NN	_	_	_
182	MicL	micl	NN	_	_	_
183	t0	t0	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	mRNA-seq	mrna-seq	NN	_	_	_
186	MicL	micl	NN	_	_	_
187	t10	t10	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	mRNA-seq	mrna-seq	NN	_	_	_
190	MicL	micl	NN	_	_	_
191	t20	t20	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	mRNA-seq	mrna-seq	NN	_	_	_
194	MicL	micl	NN	_	_	_
195	t4	t4	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	mRNA-seq	mrna-seq	NN	_	_	_
198	Vector	Vector	NNP	_	_	_
199	t0	t0	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	mRNA-seq	mrna-seq	NN	_	_	_
202	Vector	Vector	NNP	_	_	_
203	t20	t20	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	mRNA-seq	mrna-seq	NN	_	_	_
206	with	with	IN	_	_	_
207	barcode	barcode	NN	_	_	_
208	-LRB-	-lrb-	-LRB-	_	_	_
209	Illumina	Illumina	NNP	_	_	_
210	TruSeq	TruSeq	NNP	_	_	_
211	Index	Index	NNP	_	_	_
212	1-5	1-5	CD	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	mRNA-seq	mrna-seq	NN	_	_	_
216	WT	wt	JJ	_	_	_
217	t10	t10	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	mRNA-seq	mrna-seq	NN	_	_	_
220	WT	wt	JJ	_	_	_
221	t4	t4	NN	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
223	mrna	mrna	NN	_	_	_
224	synthesis	synthesis	NN	_	_	_
225	:	:	:	_	_	_
226	in	in	FW	_	_	_
227	vitro	vitro	FW	_	_	_
228	MgCl2	mgcl2	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
230	mrna	mrna	NN	_	_	_
231	synthesis	synthesis	NN	_	_	_
232	:	:	:	_	_	_
233	in	in	FW	_	_	_
234	vitro	vitro	FW	_	_	_
235	MgCl2	mgcl2	NN	_	_	_
236	+	+	CC	_	_	_
237	GreAB	greab	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
239	mrna	mrna	NN	_	_	_
240	synthesis	synthesis	NN	_	_	_
241	:	:	:	_	_	_
242	in	in	FW	_	_	_
243	vitro	vitro	FW	_	_	_
244	MnCl2	mncl2	NN	SUPP	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
246	mrna	mrna	NN	_	_	_
247	synthesis	synthesis	NN	_	_	_
248	:	:	:	_	_	_
249	in	in	FW	_	_	_
250	vitro	vitro	FW	_	_	_
251	MnCl2	mncl2	NN	SUPP	_	_
252	+	+	CC	_	_	_
253	GreAB	greab	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
255	mrna	mrna	NN	_	_	_
256	synthesis	synthesis	NN	_	_	_
257	:	:	:	_	_	_
258	in	in	FW	_	_	_
259	vivo	vivo	FW	_	_	_
260	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
261	MT	MT	NNP	_	_	_
262	_	_	SYM	_	_	_
263	12h	12h	CD	_	_	_
264	_	_	CD	_	_	_
265	rep1	rep1	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	MT	mt	NNS	_	_	_
268	_	_	VBP	_	_	_
269	12h	12h	JJ	_	_	_
270	_	_	NN	_	_	_
271	rep2	rep2	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	MT	mt	NNS	_	_	_
274	_	_	VBP	_	_	_
275	24h	24h	JJ	_	_	_
276	_	_	NN	_	_	_
277	rep1	rep1	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	MT	mt	NNS	_	_	_
280	_	_	VBP	_	_	_
281	24h	24h	JJ	_	_	_
282	_	_	NN	_	_	_
283	rep2	rep2	NN	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	MT	mt	NNS	_	_	_
286	_	_	VBP	_	_	_
287	48h	48h	JJ	_	_	_
288	_	_	NN	_	_	_
289	rep1	rep1	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	MT	mt	NNS	_	_	_
292	_	_	VBP	_	_	_
293	48h	48h	JJ	_	_	_
294	_	_	NN	_	_	_
295	rep2	rep2	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	MT	mt	NNS	_	_	_
298	_	_	VBP	_	_	_
299	6h	6h	JJ	_	_	_
300	_	_	NN	_	_	_
301	rep1	rep1	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	MT	mt	NNS	_	_	_
304	_	_	VBP	_	_	_
305	6h	6h	JJ	_	_	_
306	_	_	NN	_	_	_
307	rep2	rep2	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	MukB	mukb	NN	_	_	_
310	22	22	CD	_	_	_
311	°C	°c	NN	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	MukB	mukb	NN	_	_	_
314	37	37	CD	_	_	_
315	°C	°c	NN	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	MukBDA	mukbda	NN	_	_	_
318	22	22	CD	_	_	_
319	°C	°c	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	MukB	mukb	NN	_	_	_
322	deltamatP	deltamatp	NN	_	_	_
323	22	22	CD	_	_	_
324	°C	°c	NN	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	MukBEQ	mukbeq	NN	_	_	_
327	22	22	CD	_	_	_
328	°C	°c	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	MukBEQ	mukbeq	NN	_	_	_
331	deltamatP	deltamatp	NN	_	_	_
332	22	22	CD	_	_	_
333	°C	°c	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	murI	muri	NN	GEN	_	_
336	__	__	CD	_	_	_
337	U	U	NNP	_	_	_
338	_	_	NNP	_	_	_
339	N0075	N0075	NNP	_	_	_
340	_	_	SYM	_	_	_
341	r1	r1	FW	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
343	murI	muri	NN	GEN	_	_
344	__	__	CD	_	_	_
345	U	U	NNP	_	_	_
346	_	_	NNP	_	_	_
347	N0075	N0075	NNP	_	_	_
348	_	_	SYM	_	_	_
349	r2	r2	FW	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
351	murI	muri	NN	GEN	_	_
352	__	__	CD	_	_	_
353	U	U	NNP	_	_	_
354	_	_	NNP	_	_	_
355	N0075	N0075	NNP	_	_	_
356	_	_	SYM	_	_	_
357	r3	r3	FW	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
359	murI	muri	NN	GEN	_	_
360	upregulation	upregulation	NN	_	_	_
361	,	,	,	_	_	_
362	0.075	0.075	CD	_	_	_
363	mg/mL	mg/ml	NN	_	_	_
364	norfloxacin	norfloxacin	NN	_	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
366	musgs	musg	NNS	_	_	_
367	presence	presence	NN	_	_	_
368	:	:	:	_	_	_
369	-	-	:	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	musgs	musg	NNS	_	_	_
372	presence	presence	NN	_	_	_
373	:	:	:	_	_	_
374	MuSGS	musgs	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	mutant	mutant	JJ	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	Mutant	mutant	JJ	_	_	_
379	B8	b8	NN	_	_	_
380	_	_	NN	_	_	_
381	0.8	0.8	CD	_	_	_
382	%	%	NN	_	_	_
383	Bu	bu	NN	_	_	_
384	_	_	CD	_	_	_
385	1.5	1.5	CD	_	_	_
386	h	h	NN	_	_	_
387	_	_	CD	_	_	_
388	rep1	rep1	NN	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
390	Mutant	mutant	JJ	_	_	_
391	B8	b8	NN	_	_	_
392	_	_	NN	_	_	_
393	0.8	0.8	CD	_	_	_
394	%	%	NN	_	_	_
395	Bu	bu	NN	_	_	_
396	_	_	CD	_	_	_
397	1.5	1.5	CD	_	_	_
398	h	h	NN	_	_	_
399	_	_	CD	_	_	_
400	rep2	rep2	NN	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
402	Mutant	mutant	JJ	_	_	_
403	B8	b8	NN	_	_	_
404	_	_	NN	_	_	_
405	0.8	0.8	CD	_	_	_
406	%	%	NN	_	_	_
407	Bu	bu	NN	_	_	_
408	_	_	CD	_	_	_
409	1.5	1.5	CD	_	_	_
410	h	h	NN	_	_	_
411	_	_	CD	_	_	_
412	rep3	rep3	NN	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
414	Mutant	mutant	JJ	_	_	_
415	B8	b8	NN	_	_	_
416	,	,	,	_	_	_
417	0.8	0.8	CD	_	_	_
418	%	%	NN	_	_	_
419	butanol	butanol	NN	_	_	_
420	,1.5	,1.5	CD	_	_	_
421	h	h	NN	_	_	_
422	,	,	,	_	_	_
423	replicate	replicate	VB	_	_	_
424	1	1	CD	_	_	_
425	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
426	Mutant	mutant	JJ	_	_	_
427	B8	b8	NN	_	_	_
428	,	,	,	_	_	_
429	0.8	0.8	CD	_	_	_
430	%	%	NN	_	_	_
431	butanol	butanol	NN	_	_	_
432	,1.5	,1.5	CD	_	_	_
433	h	h	NN	_	_	_
434	,	,	,	_	_	_
435	replicate	replicate	VB	_	_	_
436	2	2	CD	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
438	Mutant	mutant	JJ	_	_	_
439	B8	b8	NN	_	_	_
440	,	,	,	_	_	_
441	0.8	0.8	CD	_	_	_
442	%	%	NN	_	_	_
443	butanol	butanol	NN	_	_	_
444	,1.5	,1.5	CD	_	_	_
445	h	h	NN	_	_	_
446	,	,	,	_	_	_
447	replicate	replicate	VB	_	_	_
448	3	3	CD	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	mutant	mutant	JJ	_	_	_
451	E1	e1	NN	_	_	_
452	,	,	,	_	_	_
453	biological	biological	JJ	_	_	_
454	rep1	rep1	NN	_	_	_
455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
456	mutant	mutant	JJ	_	_	_
457	E1	e1	NN	_	_	_
458	,	,	,	_	_	_
459	biological	biological	JJ	_	_	_
460	rep2	rep2	NN	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	mutant	mutant	JJ	_	_	_
463	E1	e1	NN	_	_	_
464	,	,	,	_	_	_
465	biological	biological	JJ	_	_	_
466	rep3	rep3	NN	_	_	_
467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
468	mutant	mutant	JJ	_	_	_
469	E.	e.	FW	_	_	_
470	coli	coli	FW	_	_	_
471	,	,	,	_	_	_
472	after	after	IN	_	_	_
473	butanol	butanol	NN	_	_	_
474	treatment	treatment	NN	_	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
476	mutant	mutant	JJ	_	_	_
477	E.	e.	FW	_	_	_
478	coli	coli	FW	_	_	_
479	,	,	,	_	_	_
480	before	before	IN	_	_	_
481	butanol	butanol	NN	_	_	_
482	treatment	treatment	NN	_	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
484	Mutant	mutant	JJ	_	_	_
485	E.	e.	FW	_	_	_
486	coli	coli	FW	_	_	_
487	O157	o157	NN	_	_	_
488	treated	treat	VBN	_	_	_
489	with	with	IN	_	_	_
490	6	6	CD	_	_	_
491	ug/ml	ug/ml	NN	_	_	_
492	triclosan	triclosan	NN	_	_	_
493	for	for	IN	_	_	_
494	30	30	CD	_	_	_
495	min	min	NN	_	_	_
496	,	,	,	_	_	_
497	biological	biological	JJ	_	_	_
498	rep	rep	NN	GEN	_	_
499	1	1	CD	_	_	_
500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
501	Mutant	mutant	JJ	_	_	_
502	E.	e.	FW	_	_	_
503	coli	coli	FW	_	_	_
504	O157	o157	NN	_	_	_
505	treated	treat	VBN	_	_	_
506	with	with	IN	_	_	_
507	6	6	CD	_	_	_
508	ug/ml	ug/ml	NN	_	_	_
509	triclosan	triclosan	NN	_	_	_
510	for	for	IN	_	_	_
511	30	30	CD	_	_	_
512	min	min	NN	_	_	_
513	,	,	,	_	_	_
514	biological	biological	JJ	_	_	_
515	rep	rep	NN	GEN	_	_
516	2	2	CD	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
518	Mutant	mutant	JJ	_	_	_
519	E.	e.	FW	_	_	_
520	coli	coli	FW	_	_	_
521	O157	o157	NN	_	_	_
522	treated	treat	VBN	_	_	_
523	with	with	IN	_	_	_
524	6	6	CD	_	_	_
525	ug/ml	ug/ml	NN	_	_	_
526	triclosan	triclosan	NN	_	_	_
527	for	for	IN	_	_	_
528	30	30	CD	_	_	_
529	min	min	NN	_	_	_
530	,	,	,	_	_	_
531	biological	biological	JJ	_	_	_
532	rep	rep	NN	GEN	_	_
533	3	3	CD	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	Mutant	mutant	JJ	_	_	_
536	E.	e.	FW	_	_	_
537	coli	coli	FW	_	_	_
538	O157	o157	NN	_	_	_
539	untreated	untreated	JJ	_	_	_
540	,	,	,	_	_	_
541	biological	biological	JJ	_	_	_
542	rep	rep	NN	GEN	_	_
543	1	1	CD	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	Mutant	mutant	JJ	_	_	_
546	E.	e.	FW	_	_	_
547	coli	coli	FW	_	_	_
548	O157	o157	NN	_	_	_
549	untreated	untreated	JJ	_	_	_
550	,	,	,	_	_	_
551	biological	biological	JJ	_	_	_
552	rep	rep	NN	GEN	_	_
553	2	2	CD	_	_	_
554	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
555	Mutant	mutant	JJ	_	_	_
556	E.	e.	FW	_	_	_
557	coli	coli	FW	_	_	_
558	O157	o157	NN	_	_	_
559	untreated	untreated	JJ	_	_	_
560	,	,	,	_	_	_
561	biological	biological	JJ	_	_	_
562	rep	rep	NN	GEN	_	_
563	3	3	CD	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	Mutant	mutant	JJ	_	_	_
566	-LRB-	-lrb-	-LRB-	_	_	_
567	EP61	ep61	NN	_	_	_
568	-RRB-	-rrb-	-RRB-	_	_	_
569	T0	t0	NN	_	_	_
570	RNA	rna	NN	_	_	_
571	rep	rep	NN	GEN	_	_
572	1	1	CD	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	Mutant	mutant	JJ	_	_	_
575	-LRB-	-lrb-	-LRB-	_	_	_
576	EP61	ep61	NN	_	_	_
577	-RRB-	-rrb-	-RRB-	_	_	_
578	T0	t0	NN	_	_	_
579	RNA	rna	NN	_	_	_
580	rep	rep	NN	GEN	_	_
581	2	2	CD	_	_	_
582	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
583	Mutant	mutant	JJ	_	_	_
584	-LRB-	-lrb-	-LRB-	_	_	_
585	EP61	ep61	NN	_	_	_
586	-RRB-	-rrb-	-RRB-	_	_	_
587	T0	t0	NN	_	_	_
588	RP	rp	NN	_	_	_
589	rep	rep	NN	GEN	_	_
590	1	1	CD	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	Mutant	mutant	JJ	_	_	_
593	-LRB-	-lrb-	-LRB-	_	_	_
594	EP61	ep61	NN	_	_	_
595	-RRB-	-rrb-	-RRB-	_	_	_
596	T0	t0	NN	_	_	_
597	RP	rp	NN	_	_	_
598	rep	rep	NN	GEN	_	_
599	2	2	CD	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
601	Mutant	mutant	JJ	_	_	_
602	-LRB-	-lrb-	-LRB-	_	_	_
603	EP61	ep61	NN	_	_	_
604	-RRB-	-rrb-	-RRB-	_	_	_
605	T1	t1	NN	_	_	_
606	RNA	rna	NN	_	_	_
607	rep	rep	NN	GEN	_	_
608	1	1	CD	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	Mutant	mutant	JJ	_	_	_
611	-LRB-	-lrb-	-LRB-	_	_	_
612	EP61	ep61	NN	_	_	_
613	-RRB-	-rrb-	-RRB-	_	_	_
614	T1	t1	NN	_	_	_
615	RNA	rna	NN	_	_	_
616	rep	rep	NN	GEN	_	_
617	2	2	CD	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
619	Mutant	mutant	JJ	_	_	_
620	-LRB-	-lrb-	-LRB-	_	_	_
621	EP61	ep61	NN	_	_	_
622	-RRB-	-rrb-	-RRB-	_	_	_
623	T1	t1	NN	_	_	_
624	RP	rp	NN	_	_	_
625	rep	rep	NN	GEN	_	_
626	1	1	CD	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	Mutant	mutant	JJ	_	_	_
629	-LRB-	-lrb-	-LRB-	_	_	_
630	EP61	ep61	NN	_	_	_
631	-RRB-	-rrb-	-RRB-	_	_	_
632	T1	t1	NN	_	_	_
633	RP	rp	NN	_	_	_
634	rep	rep	NN	GEN	_	_
635	2	2	CD	_	_	_
636	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
637	Mutant	mutant	JJ	_	_	_
638	-LRB-	-lrb-	-LRB-	_	_	_
639	EP61	ep61	NN	_	_	_
640	-RRB-	-rrb-	-RRB-	_	_	_
641	T2	t2	NN	_	_	_
642	RNA	rna	NN	_	_	_
643	rep	rep	NN	GEN	_	_
644	1	1	CD	_	_	_
645	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
646	Mutant	mutant	JJ	_	_	_
647	-LRB-	-lrb-	-LRB-	_	_	_
648	EP61	ep61	NN	_	_	_
649	-RRB-	-rrb-	-RRB-	_	_	_
650	T2	t2	NN	_	_	_
651	RNA	rna	NN	_	_	_
652	rep	rep	NN	GEN	_	_
653	2	2	CD	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
655	Mutant	mutant	JJ	_	_	_
656	-LRB-	-lrb-	-LRB-	_	_	_
657	EP61	ep61	NN	_	_	_
658	-RRB-	-rrb-	-RRB-	_	_	_
659	T2	t2	NN	_	_	_
660	RP	rp	NN	_	_	_
661	rep	rep	NN	GEN	_	_
662	1	1	CD	_	_	_
663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
664	Mutant	mutant	JJ	_	_	_
665	-LRB-	-lrb-	-LRB-	_	_	_
666	EP61	ep61	NN	_	_	_
667	-RRB-	-rrb-	-RRB-	_	_	_
668	T2	t2	NN	_	_	_
669	RP	rp	NN	_	_	_
670	rep	rep	NN	GEN	_	_
671	2	2	CD	_	_	_
672	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
673	Mutant	mutant	JJ	_	_	_
674	-LRB-	-lrb-	-LRB-	_	_	_
675	RL2325	rl2325	NN	_	_	_
676	-RRB-	-rrb-	-RRB-	_	_	_
677	RNA-seq	rna-seq	NN	_	_	_
678	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
679	mutant	mutant	JJ	_	_	_
680	SdiA1E11	sdia1e11	NN	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	MutRep1	mutrep1	NN	_	_	_
683	_	_	NN	_	_	_
684	0	0	CD	_	_	_
685	min	min	NN	_	_	_
686	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
687	MutRep1	mutrep1	NN	_	_	_
688	_	_	CD	_	_	_
689	10	10	CD	_	_	_
690	min	min	NN	_	_	_
691	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
692	MutRep1	mutrep1	NN	_	_	_
693	_	_	CD	_	_	_
694	15	15	CD	_	_	_
695	min	min	NN	_	_	_
696	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
697	MutRep1	mutrep1	NN	_	_	_
698	_	_	CD	_	_	_
699	20	20	CD	_	_	_
700	min	min	NN	_	_	_
701	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
702	MutRep1	mutrep1	NN	_	_	_
703	_	_	NN	_	_	_
704	2	2	CD	_	_	_
705	min	min	NN	_	_	_
706	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
707	MutRep1	mutrep1	NN	_	_	_
708	_	_	CD	_	_	_
709	4	4	CD	_	_	_
710	min	min	NN	_	_	_
711	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
712	MutRep1	mutrep1	NN	_	_	_
713	_	_	CD	_	_	_
714	6	6	CD	_	_	_
715	min	min	NN	_	_	_
716	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
717	MutRep1	mutrep1	NN	_	_	_
718	_	_	CD	_	_	_
719	8	8	CD	_	_	_
720	min	min	NN	_	_	_
721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
722	MutRep2	mutrep2	NN	_	_	_
723	_	_	NN	_	_	_
724	0	0	CD	_	_	_
725	min	min	NN	_	_	_
726	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
727	MutRep2	mutrep2	NN	_	_	_
728	_	_	CD	_	_	_
729	10	10	CD	_	_	_
730	min	min	NN	_	_	_
731	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
732	MutRep2	mutrep2	NN	_	_	_
733	_	_	CD	_	_	_
734	15	15	CD	_	_	_
735	min	min	NN	_	_	_
736	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
737	MutRep2	mutrep2	NN	_	_	_
738	_	_	CD	_	_	_
739	20	20	CD	_	_	_
740	min	min	NN	_	_	_
741	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
742	MutRep2	mutrep2	NN	_	_	_
743	_	_	NN	_	_	_
744	2	2	CD	_	_	_
745	min	min	NN	_	_	_
746	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
747	MutRep2	mutrep2	NN	_	_	_
748	_	_	CD	_	_	_
749	4	4	CD	_	_	_
750	min	min	NN	_	_	_
751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
752	MutRep2	mutrep2	NN	_	_	_
753	_	_	CD	_	_	_
754	6	6	CD	_	_	_
755	min	min	NN	_	_	_
756	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
757	MutRep2	mutrep2	NN	_	_	_
758	_	_	CD	_	_	_
759	8	8	CD	_	_	_
760	min	min	NN	_	_	_
761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
762	MW30	mw30	NN	_	_	_
763	-LRB-	-lrb-	-LRB-	_	_	_
764	rpoS	rpos	NN	GEN	_	_
765	-RRB-	-rrb-	-RRB-	_	_	_
766	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
767	MW30	mw30	NN	_	_	_
768	-LRB-	-lrb-	-LRB-	_	_	_
769	rpoS	rpos	NN	GEN	_	_
770	-RRB-	-rrb-	-RRB-	_	_	_
771	,	,	,	_	_	_
772	LB	lb	NN	_	_	_
773	,	,	,	_	_	_
774	exponential	exponential	JJ	GrowthPhase	_	_
775	phase	phase	NN	GrowthPhase	_	_
776	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
777	MW30	mw30	NN	_	_	_
778	rpoS	rpos	NN	GEN	_	_
779	,	,	,	_	_	_
780	LB	lb	NN	_	_	_
781	,	,	,	_	_	_
782	exponential	exponential	JJ	GrowthPhase	_	_
783	phase	phase	NN	GrowthPhase	_	_
784	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
785	MW30	mw30	NN	_	_	_
786	-LRB-	-lrb-	-LRB-	_	_	_
787	rpoS	rpos	NN	GEN	_	_
788	-RRB-	-rrb-	-RRB-	_	_	_
789	,	,	,	_	_	_
790	LB	lb	NN	_	_	_
791	,	,	,	_	_	_
792	stationary	stationary	JJ	GrowthPhase	_	_
793	phase	phase	NN	GrowthPhase	_	_
794	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
795	MW30	mw30	NN	_	_	_
796	rpoS	rpos	NN	GEN	_	_
797	,	,	,	_	_	_
798	LB	lb	NN	_	_	_
799	,	,	,	_	_	_
800	stationary	stationary	JJ	GrowthPhase	_	_
801	phase	phase	NN	GrowthPhase	_	_
802	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
803	MY4	my4	NN	_	_	_
804	_	_	NN	_	_	_
805	replicated	replicate	VBN	_	_	_
806	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
807	N172-1	n172-1	NN	_	_	_
808	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
809	N172-2	n172-2	NN	_	_	_
810	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
811	N30-1	n30-1	NN	_	_	_
812	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
813	N30-2	n30-2	NN	_	_	_
814	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
815	N30-3	n30-3	NN	_	_	_
816	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
817	N30-4	n30-4	NN	_	_	_
818	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
819	N3433	n3433	NN	_	_	_
820	-LRB-	-lrb-	-LRB-	_	_	_
821	rne	rne	NN	GEN	_	_
822	deletion	deletion	NN	_	_	_
823	-RRB-	-rrb-	-RRB-	_	_	_
824	pBADRNE	pbadrne	NN	_	_	_
825	in	in	IN	_	_	_
826	LB	lb	NN	_	_	_
827	at	at	IN	_	_	_
828	30	30	CD	_	_	_
829	degrees	degree	NNS	_	_	_
830	C	c	NN	_	_	_
831	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
832	N3433	n3433	NN	_	_	_
833	-LRB-	-lrb-	-LRB-	_	_	_
834	rne	rne	NN	GEN	_	_
835	deletion	deletion	NN	_	_	_
836	-RRB-	-rrb-	-RRB-	_	_	_
837	pBAD-RNE	pbad-rne	NN	_	_	_
838	w/out	w/out	NN	_	_	_
839	Arabinose	arabinose	NN	_	_	_
840	in	in	IN	_	_	_
841	LB	lb	NN	_	_	_
842	at	at	IN	_	_	_
843	30	30	CD	_	_	_
844	degrees	degree	NNS	_	_	_
845	C	c	NN	_	_	_
846	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
847	N3433	n3433	NN	_	_	_
848	-LRB-	-lrb-	-LRB-	_	_	_
849	rne	rne	NN	GEN	_	_
850	deletion	deletion	NN	_	_	_
851	-RRB-	-rrb-	-RRB-	_	_	_
852	pNRNE5	pnrne5	NN	_	_	_
853	at	at	IN	_	_	_
854	30	30	CD	_	_	_
855	degrees	degree	NNS	_	_	_
856	C	c	NN	_	_	_
857	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
858	N3433	n3433	NN	_	_	_
859	-LRB-	-lrb-	-LRB-	_	_	_
860	rne	rne	NN	GEN	_	_
861	deletion	deletion	NN	_	_	_
862	-RRB-	-rrb-	-RRB-	_	_	_
863	pRNG3	prng3	NN	_	_	_
864	at	at	IN	_	_	_
865	30	30	CD	_	_	_
866	degrees	degree	NNS	_	_	_
867	C	c	NN	_	_	_
868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
869	N3433	n3433	NN	_	_	_
870	-LRB-	-lrb-	-LRB-	_	_	_
871	rng	rng	NN	GEN	_	_
872	deletion	deletion	NN	_	_	_
873	-RRB-	-rrb-	-RRB-	_	_	_
874	in	in	IN	_	_	_
875	LB	lb	NN	_	_	_
876	at	at	IN	_	_	_
877	30	30	CD	_	_	_
878	degrees	degree	NNS	_	_	_
879	C	c	NN	_	_	_
880	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
881	N3433	n3433	NN	_	_	_
882	-LRB-	-lrb-	-LRB-	_	_	_
883	rng	rng	NN	GEN	_	_
884	deletion	deletion	NN	_	_	_
885	-RRB-	-rrb-	-RRB-	_	_	_
886	LB	lb	NN	_	_	_
887	at	at	IN	_	_	_
888	30	30	CD	_	_	_
889	C	c	NN	_	_	_
890	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
891	N3433	n3433	NN	_	_	_
892	-LRB-	-lrb-	-LRB-	_	_	_
893	wt	wt	JJ	_	_	_
894	-RRB-	-rrb-	-RRB-	_	_	_
895	in	in	IN	_	_	_
896	LB	lb	NN	_	_	_
897	at	at	IN	_	_	_
898	30	30	CD	_	_	_
899	degrees	degree	NNS	_	_	_
900	C	c	NN	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	N3433	n3433	NN	_	_	_
903	-LRB-	-lrb-	-LRB-	_	_	_
904	wt	wt	JJ	_	_	_
905	-RRB-	-rrb-	-RRB-	_	_	_
906	pPM30	ppm30	NN	_	_	_
907	in	in	IN	_	_	_
908	LB	lb	NN	_	_	_
909	at	at	IN	_	_	_
910	30	30	CD	_	_	_
911	degrees	degree	NNS	_	_	_
912	C	c	NN	_	_	_
913	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
914	N3433	n3433	NN	_	_	_
915	-LRB-	-lrb-	-LRB-	_	_	_
916	wt	wt	JJ	_	_	_
917	-RRB-	-rrb-	-RRB-	_	_	_
918	pRNG3	prng3	NN	_	_	_
919	in	in	IN	_	_	_
920	LB	lb	NN	_	_	_
921	at	at	IN	_	_	_
922	30	30	CD	_	_	_
923	degrees	degree	NNS	_	_	_
924	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
925	N3433	n3433	NN	_	_	_
926	-LRB-	-lrb-	-LRB-	_	_	_
927	wt	wt	JJ	_	_	_
928	-RRB-	-rrb-	-RRB-	_	_	_
929	vs	vs	CC	_	_	_
930	N3433	n3433	NN	_	_	_
931	-LRB-	-lrb-	-LRB-	_	_	_
932	rne	rne	NN	GEN	_	_
933	deletion	deletion	NN	_	_	_
934	-RRB-	-rrb-	-RRB-	_	_	_
935	pBADRNE	pbadrne	NN	_	_	_
936	in	in	IN	_	_	_
937	LB	lb	NN	_	_	_
938	at	at	IN	_	_	_
939	30	30	CD	_	_	_
940	degrees	degree	NNS	_	_	_
941	C	c	NN	_	_	_
942	Trial	trial	NN	_	_	_
943	B	b	NN	_	_	_
944	*	*	SYM	_	_	_
945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
946	N3433	n3433	NN	_	_	_
947	-LRB-	-lrb-	-LRB-	_	_	_
948	wt	wt	JJ	_	_	_
949	-RRB-	-rrb-	-RRB-	_	_	_
950	vs	vs	CC	_	_	_
951	N3433	n3433	NN	_	_	_
952	-LRB-	-lrb-	-LRB-	_	_	_
953	rne	rne	NN	GEN	_	_
954	deletion	deletion	NN	_	_	_
955	-RRB-	-rrb-	-RRB-	_	_	_
956	pBAD-RNE	pbad-rne	NN	_	_	_
957	w/out	w/out	NN	_	_	_
958	Arabinose	arabinose	NN	_	_	_
959	in	in	IN	_	_	_
960	LB	lb	NN	_	_	_
961	at	at	IN	_	_	_
962	30	30	CD	_	_	_
963	degrees	degree	NNS	_	_	_
964	Trial	trial	NN	_	_	_
965	A	a	DT	_	_	_
966	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
967	N3433	n3433	NN	_	_	_
968	-LRB-	-lrb-	-LRB-	_	_	_
969	wt	wt	JJ	_	_	_
970	-RRB-	-rrb-	-RRB-	_	_	_
971	vs	vs	CC	_	_	_
972	N3433	n3433	NN	_	_	_
973	-LRB-	-lrb-	-LRB-	_	_	_
974	rne	rne	NN	GEN	_	_
975	deletion	deletion	NN	_	_	_
976	-RRB-	-rrb-	-RRB-	_	_	_
977	pNRNE5	pnrne5	NN	_	_	_
978	at	at	IN	_	_	_
979	30	30	CD	_	_	_
980	degrees	degree	NNS	_	_	_
981	C	c	NN	_	_	_
982	Trial	trial	NN	_	_	_
983	A	a	NN	_	_	_
984	*	*	SYM	_	_	_
985	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
986	N3433	n3433	NN	_	_	_
987	-LRB-	-lrb-	-LRB-	_	_	_
988	wt	wt	JJ	_	_	_
989	-RRB-	-rrb-	-RRB-	_	_	_
990	vs	vs	CC	_	_	_
991	N3433	n3433	NN	_	_	_
992	-LRB-	-lrb-	-LRB-	_	_	_
993	rne	rne	NN	GEN	_	_
994	deletion	deletion	NN	_	_	_
995	-RRB-	-rrb-	-RRB-	_	_	_
996	pNRNE5	pnrne5	NN	_	_	_
997	at	at	IN	_	_	_
998	30	30	CD	_	_	_
999	degrees	degree	NNS	_	_	_
1000	C	c	NN	_	_	_
1001	Trial	trial	NN	_	_	_
1002	B	b	NN	_	_	_
1003	*	*	SYM	_	_	_
1004	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1005	N3433	n3433	NN	_	_	_
1006	-LRB-	-lrb-	-LRB-	_	_	_
1007	wt	wt	JJ	_	_	_
1008	-RRB-	-rrb-	-RRB-	_	_	_
1009	vs	vs	CC	_	_	_
1010	N3433	n3433	NN	_	_	_
1011	-LRB-	-lrb-	-LRB-	_	_	_
1012	rne	rne	NN	GEN	_	_
1013	deletion	deletion	NN	_	_	_
1014	-RRB-	-rrb-	-RRB-	_	_	_
1015	pRNG3	prng3	NN	_	_	_
1016	at	at	IN	_	_	_
1017	30	30	CD	_	_	_
1018	degrees	degree	NNS	_	_	_
1019	C	c	NN	_	_	_
1020	Trial	trial	NN	_	_	_
1021	A	a	NN	_	_	_
1022	*	*	SYM	_	_	_
1023	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1024	N3433	n3433	NN	_	_	_
1025	-LRB-	-lrb-	-LRB-	_	_	_
1026	wt	wt	JJ	_	_	_
1027	-RRB-	-rrb-	-RRB-	_	_	_
1028	vs	vs	CC	_	_	_
1029	N3433	n3433	NN	_	_	_
1030	-LRB-	-lrb-	-LRB-	_	_	_
1031	rne	rne	NN	GEN	_	_
1032	deletion	deletion	NN	_	_	_
1033	-RRB-	-rrb-	-RRB-	_	_	_
1034	pRNG3	prng3	NN	_	_	_
1035	at	at	IN	_	_	_
1036	30	30	CD	_	_	_
1037	degrees	degree	NNS	_	_	_
1038	C	c	NN	_	_	_
1039	Trial	trial	NN	_	_	_
1040	B	b	NN	_	_	_
1041	*	*	SYM	_	_	_
1042	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1043	N3433	n3433	NN	_	_	_
1044	-LRB-	-lrb-	-LRB-	_	_	_
1045	wt	wt	JJ	_	_	_
1046	-RRB-	-rrb-	-RRB-	_	_	_
1047	vs	vs	CC	_	_	_
1048	N3433	n3433	NN	_	_	_
1049	-LRB-	-lrb-	-LRB-	_	_	_
1050	rng	rng	NN	GEN	_	_
1051	deletion	deletion	NN	_	_	_
1052	-RRB-	-rrb-	-RRB-	_	_	_
1053	in	in	IN	_	_	_
1054	LB	lb	NN	_	_	_
1055	at	at	IN	_	_	_
1056	30	30	CD	_	_	_
1057	degrees	degree	NNS	_	_	_
1058	C	c	NN	_	_	_
1059	Trial	trial	NN	_	_	_
1060	B	b	NN	_	_	_
1061	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1062	N3433	n3433	NN	_	_	_
1063	-LRB-	-lrb-	-LRB-	_	_	_
1064	wt	wt	JJ	_	_	_
1065	-RRB-	-rrb-	-RRB-	_	_	_
1066	vs	vs	CC	_	_	_
1067	N3433	n3433	NN	_	_	_
1068	-LRB-	-lrb-	-LRB-	_	_	_
1069	rng	rng	NN	GEN	_	_
1070	deletion	deletion	NN	_	_	_
1071	-RRB-	-rrb-	-RRB-	_	_	_
1072	LB	lb	NN	_	_	_
1073	at	at	IN	_	_	_
1074	30	30	CD	_	_	_
1075	C	c	NN	_	_	_
1076	Trial	trial	NN	_	_	_
1077	A	a	NN	_	_	_
1078	*	*	SYM	_	_	_
1079	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1080	N3433	n3433	NN	_	_	_
1081	-LRB-	-lrb-	-LRB-	_	_	_
1082	wt	wt	JJ	_	_	_
1083	-RRB-	-rrb-	-RRB-	_	_	_
1084	vs	vs	CC	_	_	_
1085	N3433	n3433	NN	_	_	_
1086	-LRB-	-lrb-	-LRB-	_	_	_
1087	wt	wt	JJ	_	_	_
1088	-RRB-	-rrb-	-RRB-	_	_	_
1089	pRNG3	prng3	NN	_	_	_
1090	in	in	IN	_	_	_
1091	LB	lb	NN	_	_	_
1092	at	at	IN	_	_	_
1093	30	30	CD	_	_	_
1094	degrees	degree	NNS	_	_	_
1095	Trial	trial	NN	_	_	_
1096	A	a	DT	_	_	_
1097	*	*	SYM	_	_	_
1098	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1099	N3433	n3433	NN	_	_	_
1100	-LRB-	-lrb-	-LRB-	_	_	_
1101	wt	wt	JJ	_	_	_
1102	-RRB-	-rrb-	-RRB-	_	_	_
1103	vs	vs	CC	_	_	_
1104	N3433	n3433	NN	_	_	_
1105	-LRB-	-lrb-	-LRB-	_	_	_
1106	wt	wt	JJ	_	_	_
1107	-RRB-	-rrb-	-RRB-	_	_	_
1108	pRNG3	prng3	NN	_	_	_
1109	in	in	IN	_	_	_
1110	LB	lb	NN	_	_	_
1111	at	at	IN	_	_	_
1112	30	30	CD	_	_	_
1113	degrees	degree	NNS	_	_	_
1114	Trial	trial	NN	_	_	_
1115	B	b	NN	_	_	_
1116	*	*	SYM	_	_	_
1117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
1118	NA	NA	NNP	_	_	_
1119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1120	N/A	N/A	NNP	_	_	_
1121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1122	na	na	TO	_	_	_
1123	+1	+1	NN	_	_	_
1124	-LRB-	-lrb-	-LRB-	_	_	_
1125	levels	level	NNS	_	_	_
1126	-RRB-	-rrb-	-RRB-	_	_	_
1127	:	:	:	_	_	_
1128	baseNa	basena	NN	_	_	_
1129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1130	na	na	TO	_	_	_
1131	+1	+1	NN	_	_	_
1132	-LRB-	-lrb-	-LRB-	_	_	_
1133	levels	level	NNS	_	_	_
1134	-RRB-	-rrb-	-RRB-	_	_	_
1135	:	:	:	_	_	_
1136	highNa	highna	NN	_	_	_
1137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1138	na	na	TO	_	_	_
1139	+1	+1	NN	_	_	_
1140	-LRB-	-lrb-	-LRB-	_	_	_
1141	mm	mm	NN	_	_	_
1142	-RRB-	-rrb-	-RRB-	_	_	_
1143	:	:	:	_	_	_
1144	100	100	CD	_	_	_
1145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1146	na	na	TO	_	_	_
1147	+1	+1	NN	_	_	_
1148	-LRB-	-lrb-	-LRB-	_	_	_
1149	mm	mm	NN	_	_	_
1150	-RRB-	-rrb-	-RRB-	_	_	_
1151	:	:	:	_	_	_
1152	200	200	CD	_	_	_
1153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1154	na	na	TO	_	_	_
1155	+1	+1	NN	_	_	_
1156	-LRB-	-lrb-	-LRB-	_	_	_
1157	mm	mm	NN	_	_	_
1158	-RRB-	-rrb-	-RRB-	_	_	_
1159	:	:	:	_	_	_
1160	300	300	CD	_	_	_
1161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1162	na	na	TO	_	_	_
1163	+1	+1	NN	_	_	_
1164	-LRB-	-lrb-	-LRB-	_	_	_
1165	mm	mm	NN	_	_	_
1166	-RRB-	-rrb-	-RRB-	_	_	_
1167	:	:	:	_	_	_
1168	5	5	CD	_	_	_
1169	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1170	Nac	Nac	NNP	TF	_	_
1171	_	_	SYM	_	_	_
1172	ChIPSeq	chipseq	NN	_	_	_
1173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1174	nac	nac	NN	GEN	_	_
1175	KO	ko	NN	_	_	_
1176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1177	nac	nac	NN	GEN	_	_
1178	KO	ko	NN	_	_	_
1179	+	+	CC	_	_	_
1180	ade	ade	NN	_	_	_
1181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1182	NaCl	nacl	NN	_	_	_
1183	replicate	replicate	VBP	_	_	_
1184	1	1	CD	_	_	_
1185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1186	NaCl	nacl	NN	_	_	_
1187	replicate	replicate	VBP	_	_	_
1188	2	2	CD	_	_	_
1189	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1190	NaCl	nacl	NN	_	_	_
1191	replicate	replicate	VBP	_	_	_
1192	3	3	CD	_	_	_
1193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1194	NaCl	nacl	NN	_	_	_
1195	_	_	CD	_	_	_
1196	stress	stress	NN	_	_	_
1197	:	:	:	_	_	_
1198	MURI	MURI	NNP	_	_	_
1199	_	_	SYM	_	_	_
1200	061	061	CD	_	_	_
1201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1202	NaCl	nacl	NN	_	_	_
1203	_	_	CD	_	_	_
1204	stress	stress	NN	_	_	_
1205	:	:	:	_	_	_
1206	MURI	MURI	NNP	_	_	_
1207	_	_	SYM	_	_	_
1208	063	063	CD	_	_	_
1209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1210	NaCl	nacl	NN	_	_	_
1211	_	_	CD	_	_	_
1212	stress	stress	NN	_	_	_
1213	:	:	:	_	_	_
1214	MURI	MURI	NNP	_	_	_
1215	_	_	SYM	_	_	_
1216	064	064	CD	_	_	_
1217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1218	NaCl	nacl	NN	_	_	_
1219	_	_	CD	_	_	_
1220	stress	stress	NN	_	_	_
1221	:	:	:	_	_	_
1222	MURI	MURI	NNP	_	_	_
1223	_	_	SYM	_	_	_
1224	065	065	CD	_	_	_
1225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1226	NaCl	nacl	NN	_	_	_
1227	_	_	CD	_	_	_
1228	stress	stress	NN	_	_	_
1229	:	:	:	_	_	_
1230	MURI	MURI	NNP	_	_	_
1231	_	_	SYM	_	_	_
1232	066	066	CD	_	_	_
1233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1234	NaCl	nacl	NN	_	_	_
1235	_	_	CD	_	_	_
1236	stress	stress	NN	_	_	_
1237	:	:	:	_	_	_
1238	MURI	MURI	NNP	_	_	_
1239	_	_	SYM	_	_	_
1240	067	067	CD	_	_	_
1241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1242	NaCl	nacl	NN	_	_	_
1243	_	_	CD	_	_	_
1244	stress	stress	NN	_	_	_
1245	:	:	:	_	_	_
1246	MURI	MURI	NNP	_	_	_
1247	_	_	SYM	_	_	_
1248	068	068	CD	_	_	_
1249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1250	NaCl	nacl	NN	_	_	_
1251	_	_	CD	_	_	_
1252	stress	stress	NN	_	_	_
1253	:	:	:	_	_	_
1254	MURI	MURI	NNP	_	_	_
1255	_	_	SYM	_	_	_
1256	069	069	CD	_	_	_
1257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1258	NaCl	nacl	NN	_	_	_
1259	_	_	CD	_	_	_
1260	stress	stress	NN	_	_	_
1261	:	:	:	_	_	_
1262	MURI	MURI	NNP	_	_	_
1263	_	_	SYM	_	_	_
1264	070	070	CD	_	_	_
1265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1266	NaCl	nacl	NN	_	_	_
1267	_	_	CD	_	_	_
1268	stress	stress	NN	_	_	_
1269	:	:	:	_	_	_
1270	MURI	MURI	NNP	_	_	_
1271	_	_	SYM	_	_	_
1272	071	071	CD	_	_	_
1273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1274	NaCl	nacl	NN	_	_	_
1275	_	_	CD	_	_	_
1276	stress	stress	NN	_	_	_
1277	:	:	:	_	_	_
1278	MURI	MURI	NNP	_	_	_
1279	_	_	SYM	_	_	_
1280	072	072	CD	_	_	_
1281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1282	NaCl	nacl	NN	_	_	_
1283	_	_	CD	_	_	_
1284	stress	stress	NN	_	_	_
1285	:	:	:	_	_	_
1286	MURI	MURI	NNP	_	_	_
1287	_	_	SYM	_	_	_
1288	073	073	CD	_	_	_
1289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1290	NaCl	nacl	NN	_	_	_
1291	_	_	CD	_	_	_
1292	stress	stress	NN	_	_	_
1293	:	:	:	_	_	_
1294	MURI	MURI	NNP	_	_	_
1295	_	_	SYM	_	_	_
1296	074	074	CD	_	_	_
1297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1298	NaCl	nacl	NN	_	_	_
1299	_	_	CD	_	_	_
1300	stress	stress	NN	_	_	_
1301	:	:	:	_	_	_
1302	MURI	MURI	NNP	_	_	_
1303	_	_	SYM	_	_	_
1304	075	075	CD	_	_	_
1305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1306	NaCl	nacl	NN	_	_	_
1307	_	_	CD	_	_	_
1308	stress	stress	NN	_	_	_
1309	:	:	:	_	_	_
1310	MURI	MURI	NNP	_	_	_
1311	_	_	SYM	_	_	_
1312	076	076	CD	_	_	_
1313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1314	NaCl	nacl	NN	_	_	_
1315	_	_	CD	_	_	_
1316	stress	stress	NN	_	_	_
1317	:	:	:	_	_	_
1318	MURI	MURI	NNP	_	_	_
1319	_	_	SYM	_	_	_
1320	077	077	CD	_	_	_
1321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1322	NaCl	nacl	NN	_	_	_
1323	_	_	CD	_	_	_
1324	stress	stress	NN	_	_	_
1325	:	:	:	_	_	_
1326	MURI	MURI	NNP	_	_	_
1327	_	_	SYM	_	_	_
1328	079	079	CD	_	_	_
1329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1330	NaCl	nacl	NN	_	_	_
1331	_	_	CD	_	_	_
1332	stress	stress	NN	_	_	_
1333	:	:	:	_	_	_
1334	MURI	MURI	NNP	_	_	_
1335	_	_	SYM	_	_	_
1336	080	080	CD	_	_	_
1337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1338	NaCl	nacl	NN	_	_	_
1339	_	_	CD	_	_	_
1340	stress	stress	NN	_	_	_
1341	:	:	:	_	_	_
1342	MURI	MURI	NNP	_	_	_
1343	_	_	SYM	_	_	_
1344	081	081	CD	_	_	_
1345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1346	NaCl	nacl	NN	_	_	_
1347	_	_	CD	_	_	_
1348	stress	stress	NN	_	_	_
1349	:	:	:	_	_	_
1350	MURI	MURI	NNP	_	_	_
1351	_	_	SYM	_	_	_
1352	082	082	CD	_	_	_
1353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1354	NaCl	nacl	NN	_	_	_
1355	_	_	CD	_	_	_
1356	stress	stress	NN	_	_	_
1357	:	:	:	_	_	_
1358	MURI	MURI	NNP	_	_	_
1359	_	_	SYM	_	_	_
1360	083	083	CD	_	_	_
1361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1362	NaCl	nacl	NN	_	_	_
1363	_	_	CD	_	_	_
1364	stress	stress	NN	_	_	_
1365	:	:	:	_	_	_
1366	MURI	MURI	NNP	_	_	_
1367	_	_	SYM	_	_	_
1368	084	084	CD	_	_	_
1369	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1370	Nac	Nac	NNP	TF	_	_
1371	_	_	SYM	_	_	_
1372	RNASeq	rnaseq	NN	_	_	_
1373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1374	NaOH	naoh	NN	_	_	_
1375	replicate	replicate	VBP	_	_	_
1376	1	1	CD	_	_	_
1377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1378	NaOH	naoh	NN	_	_	_
1379	replicate	replicate	VBP	_	_	_
1380	3	3	CD	_	_	_
1381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1382	narXL	narxl	NN	TU	_	_
1383	anaerobic	anaerobic	NN	_	_	_
1384	plus	plus	CC	_	_	_
1385	NO2	no2	NN	_	_	_
1386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1387	narXLP	narxlp	NN	_	_	_
1388	anaerobic	anaerobic	NN	_	_	_
1389	plus	plus	CC	_	_	_
1390	NO2	no2	NN	_	_	_
1391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1392	narXLP	narxlp	NN	_	_	_
1393	rep	rep	NN	GEN	_	_
1394	1	1	CD	_	_	_
1395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1396	narXLP	narxlp	NN	_	_	_
1397	rep	rep	NN	GEN	_	_
1398	2	2	CD	_	_	_
1399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1400	narXLP	narxlp	NN	_	_	_
1401	rep	rep	NN	GEN	_	_
1402	3	3	CD	_	_	_
1403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1404	narXL	narxl	NN	TU	_	_
1405	rep	rep	NN	GEN	_	_
1406	1	1	CD	_	_	_
1407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1408	narXL	narxl	NN	TU	_	_
1409	rep	rep	NN	GEN	_	_
1410	2	2	CD	_	_	_
1411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1412	narXL	narxl	NN	TU	_	_
1413	rep	rep	NN	GEN	_	_
1414	3	3	CD	_	_	_
1415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1416	narXL	narxl	NN	TU	_	_
1417	rep	rep	NN	GEN	_	_
1418	4	4	CD	_	_	_
1419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1420	n-Butanol	n-butanol	NN	_	_	_
1421	-LRB-	-lrb-	-LRB-	_	_	_
1422	0.8	0.8	CD	_	_	_
1423	%	%	NN	_	_	_
1424	,	,	,	_	_	_
1425	v/v	v/v	NN	_	_	_
1426	-RRB-	-rrb-	-RRB-	_	_	_
1427	was	be	VBD	_	_	_
1428	added	add	VBN	_	_	_
1429	at	at	IN	_	_	_
1430	0.8	0.8	CD	_	_	_
1431	OD660	od660	NN	_	_	_
1432	and	and	CC	_	_	_
1433	further	further	JJ	_	_	_
1434	incubated	incubate	VBN	_	_	_
1435	for	for	IN	_	_	_
1436	1.5	1.5	CD	_	_	_
1437	h.	h.	NN	_	_	_
1438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1439	NC	nc	NN	_	_	_
1440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1441	neo	neo	NN	_	_	_
1442	_	_	NN	_	_	_
1443	0	0	CD	_	_	_
1444	min	min	NN	_	_	_
1445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1446	neo	neo	NN	_	_	_
1447	_	_	CD	_	_	_
1448	10	10	CD	_	_	_
1449	min	min	NN	_	_	_
1450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1451	neo	neo	NN	_	_	_
1452	_	_	CD	_	_	_
1453	15	15	CD	_	_	_
1454	min	min	NN	_	_	_
1455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1456	neo	neo	NN	_	_	_
1457	_	_	NN	_	_	_
1458	1	1	CD	_	_	_
1459	min	min	NN	_	_	_
1460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1461	neo	neo	NN	_	_	_
1462	_	_	NN	_	_	_
1463	2	2	CD	_	_	_
1464	min	min	NN	_	_	_
1465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1466	neo	neo	NN	_	_	_
1467	_	_	NN	_	_	_
1468	4	4	CD	_	_	_
1469	min	min	NN	_	_	_
1470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1471	neo	neo	NN	_	_	_
1472	_	_	NN	_	_	_
1473	6	6	CD	_	_	_
1474	min	min	NN	_	_	_
1475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1476	neo	neo	NN	_	_	_
1477	_	_	NN	_	_	_
1478	8	8	CD	_	_	_
1479	min	min	NN	_	_	_
1480	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1481	Next	Next	NNP	_	_	_
1482	,	,	,	_	_	_
1483	a	a	DT	_	_	_
1484	linear	linear	JJ	_	_	_
1485	model	model	NN	_	_	_
1486	was	be	VBD	_	_	_
1487	built	build	VBN	_	_	_
1488	for	for	IN	_	_	_
1489	each	each	DT	_	_	_
1490	comparison	comparison	NN	_	_	_
1491	using	use	VBG	_	_	_
1492	the	the	DT	_	_	_
1493	R	r	NN	_	_	_
1494	LIMMA	limma	NN	_	_	_
1495	package	package	NN	_	_	_
1496	and	and	CC	_	_	_
1497	statistics	statistics	NNS	_	_	_
1498	for	for	IN	_	_	_
1499	differential	differential	JJ	_	_	_
1500	expression	expression	NN	_	_	_
1501	analysis	analysis	NN	_	_	_
1502	were	be	VBD	_	_	_
1503	computed	compute	VBN	_	_	_
1504	.	.	.	_	_	_

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	NNP	_	_	_
2	Next	Next	NNP	_	_	_
3	,	,	,	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	normalized	normalize	VBN	_	_	_
7	,	,	,	_	_	_
8	by	by	IN	_	_	_
9	averaging	average	VBG	_	_	_
10	the	the	DT	_	_	_
11	log	log	NN	_	_	_
12	ratios	ratio	NNS	_	_	_
13	resulting	result	VBG	_	_	_
14	from	from	IN	_	_	_
15	all	all	DT	_	_	_
16	spots	spot	NNS	_	_	_
17	printed	print	VBN	_	_	_
18	by	by	IN	_	_	_
19	a	a	DT	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	NEXTflexRapid	nextflexrapid	NN	_	_	_
22	Directional	directional	JJ	_	_	_
23	RNA-Seq	rna-seq	NN	_	_	_
24	library	library	NN	_	_	_
25	kit	kit	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	NFNT	nfnt	JJ	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	ngs	ng	NNS	_	_	_
30	platform	platform	NN	_	_	_
31	:	:	:	_	_	_
32	Illumina	Illumina	NNP	_	_	_
33	HiSeq	HiSeq	NNP	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	ngs	ng	NNS	_	_	_
36	platform	platform	NN	_	_	_
37	:	:	:	_	_	_
38	Illumina	Illumina	NNP	_	_	_
39	MiSeq	MiSeq	NNP	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	NimbleScan	NimbleScan	NNP	_	_	_
42	software	software	NN	_	_	_
43	package	package	NN	_	_	_
44	,	,	,	_	_	_
45	version	version	NN	_	_	_
46	2.5	2.5	CD	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Roche	Roche	NNP	_	_	_
49	NimbleGen	NimbleGen	NNP	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	was	be	VBD	_	_	_
52	used	use	VBN	_	_	_
53	to	to	TO	_	_	_
54	extract	extract	VB	_	_	_
55	the	the	DT	_	_	_
56	scanned	scan	VBN	_	_	_
57	data	datum	NNS	_	_	_
58	,	,	,	_	_	_
59	which	which	WDT	_	_	_
60	was	be	VBD	_	_	_
61	subsequently	subsequently	RB	_	_	_
62	qunatile	qunatile	JJ	_	_	_
63	normalized	normalize	VBN	_	_	_
64	using	use	VBG	_	_	_
65	the	the	DT	_	_	_
66	statistical	statistical	JJ	_	_	_
67	program	program	NN	_	_	_
68	R	r	NN	_	_	_
69	.	.	.	_	_	_

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/Input	ip/input	NN	_	_	_
12	after	after	IN	_	_	_
13	data	datum	NNS	_	_	_
14	was	be	VBD	_	_	_
15	quantile	quantile	JJ	_	_	_
16	normalized	normalize	VBN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Nineteen	nineteen	CD	_	_	_
3	hours	hour	NNS	_	_	_
4	after	after	IN	_	_	_
5	experiment	experiment	NN	_	_	_
6	start	start	NN	_	_	_
7	,	,	,	_	_	_
8	antibiotic	antibiotic	JJ	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Gentamicin	gentamicin	NN	_	_	_
11	Sulfate	sulfate	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	MP	mp	NN	_	_	_
14	Biomedical	biomedical	NN	_	_	_
15	,	,	,	_	_	_
16	Cat	Cat	NNP	_	_	_
17	No.	No.	NNP	_	_	_
18	1676045	1676045	CD	_	_	_
19	,	,	,	_	_	_
20	Santa	Santa	NNP	_	_	_
21	Ana	Ana	NNP	_	_	_
22	,	,	,	_	_	_
23	CA	CA	NNP	_	_	_
24	,	,	,	_	_	_
25	USA	USA	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	introducing	introduce	VBG	_	_	_
30	into	into	IN	_	_	_
31	the	the	DT	_	_	_
32	cultures	culture	NNS	_	_	_
33	.	.	.	_	_	_

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/mL	ug/ml	NN	_	_	_
15	in	in	IN	_	_	_
16	25	25	CD	_	_	_
17	ug/mL	ug/ml	NN	_	_	_
18	steps	step	NNS	_	_	_
19	.	.	.	_	_	_

1	Thirty	thirty	CD	_	_	_
2	hours	hour	NNS	_	_	_
3	later	later	RB	_	_	_
4	,	,	,	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	fixed	fix	VBN	_	_	_
8	in	in	IN	_	_	_
9	RNA	rna	NN	_	_	_
10	Later	later	RB	_	_	_
11	II	ii	CD	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	ACROS	ACROS	NNP	_	_	_
15	,	,	,	_	_	_
16	Cat	Cat	NNP	_	_	_
17	.	.	.	_	_	_

1	No.	no.	NN	_	_	_
2	41678	41678	CD	_	_	_
3	,	,	,	_	_	_
4	New	New	NNP	_	_	_
5	Jersey	Jersey	NNP	_	_	_
6	,	,	,	_	_	_
7	USA	USA	NNP	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	stored	store	VBN	_	_	_
4	at	at	IN	_	_	_
5	-75	-75	CD	_	_	_
6	C	c	NN	_	_	_
7	until	until	IN	_	_	_
8	return	return	NN	_	_	_
9	to	to	TO	_	_	_
10	Earth	Earth	NNP	_	_	_
11	for	for	IN	_	_	_
12	analyses	analysis	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	NN2	nn2	NN	_	_	_
3	_	_	CD	_	_	_
4	0018	0018	CD	_	_	_
5	_	_	NN	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	NN2	nn2	NN	_	_	_
9	_	_	CD	_	_	_
10	0018	0018	CD	_	_	_
11	_	_	NN	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	-	-	:	_	_	_
16	NO	no	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	+	+	CC	_	_	_
22	NO	no	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	1	1	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	-	-	:	_	_	_
28	NO	no	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	+	+	CC	_	_	_
34	NO	no	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	-	-	:	_	_	_
40	NO	no	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	3	3	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	+	+	CC	_	_	_
46	NO	no	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	No	no	DT	_	_	_
51	further	further	JJ	_	_	_
52	treatment	treatment	NN	_	_	_
53	was	be	VBD	_	_	_
54	applied	apply	VBN	_	_	_
55	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	no	no	DT	_	_	_
3	inhibitor	inhibitor	NN	_	_	_
4	:	:	:	_	_	_
5	equivalent	equivalent	JJ	_	_	_
6	volume	volume	NN	_	_	_
7	of	of	IN	_	_	_
8	DMSO	dmso	NN	_	_	_
9	added	add	VBD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Non-challenged	non-challenged	JJ	_	_	_
12	Library	Library	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Non-crosslinked	non-crosslinked	JJ	_	_	_
15	DNA	dna	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	None	none	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	non-sorted	non-sorted	JJ	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	cells	cell	NNS	_	_	_
23	from	from	IN	_	_	_
24	culture	culture	NN	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	non-sorted	non-sorted	JJ	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	cells	cell	NNS	_	_	_
31	from	from	IN	_	_	_
32	culture	culture	NN	_	_	_
33	2	2	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
35	Non-treated	non-treated	JJ	_	_	_
36	,	,	,	_	_	_
37	fur	fur	NN	GEN	_	_
38	mutant	mutant	JJ	_	_	_
39	sample	sample	NN	_	_	_
40	at	at	IN	_	_	_
41	T0	t0	NN	_	_	_
42	,	,	,	_	_	_
43	biological	biological	JJ	_	_	_
44	rep	rep	NN	GEN	_	_
45	1	1	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Non-treated	non-treated	JJ	_	_	_
48	,	,	,	_	_	_
49	fur	fur	NN	GEN	_	_
50	mutant	mutant	JJ	_	_	_
51	sample	sample	NN	_	_	_
52	at	at	IN	_	_	_
53	T0	t0	NN	_	_	_
54	,	,	,	_	_	_
55	biological	biological	JJ	_	_	_
56	rep	rep	NN	GEN	_	_
57	2	2	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
59	Non-treated	non-treated	JJ	_	_	_
60	,	,	,	_	_	_
61	WT	wt	JJ	_	_	_
62	control	control	NN	_	_	_
63	at	at	IN	_	_	_
64	T0	t0	NN	_	_	_
65	,	,	,	_	_	_
66	biological	biological	JJ	_	_	_
67	rep	rep	NN	GEN	_	_
68	1	1	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Non-treated	non-treated	JJ	_	_	_
71	,	,	,	_	_	_
72	WT	wt	JJ	_	_	_
73	control	control	NN	_	_	_
74	at	at	IN	_	_	_
75	T0	t0	NN	_	_	_
76	,	,	,	_	_	_
77	biological	biological	JJ	_	_	_
78	rep	rep	NN	GEN	_	_
79	2	2	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Non-treatment	non-treatment	JJ	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	NorflIP	norflip	NN	_	_	_
84	Input	input	NN	_	_	_
85	ParC-flag	parc-flag	NN	_	_	_
86	1	1	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	NorflIP	norflip	NN	_	_	_
89	Input	input	NN	_	_	_
90	ParC-flag	parc-flag	NN	_	_	_
91	2	2	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	NorflIP	norflip	NN	_	_	_
94	Input	input	NN	_	_	_
95	ParE-flag	pare-flag	NN	_	_	_
96	1	1	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	NorflIP	norflip	NN	_	_	_
99	IP	IP	NNP	_	_	_
100	ParC-flag	ParC-flag	NNP	_	_	_
101	1	1	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	NorflIP	norflip	NN	_	_	_
104	IP	IP	NNP	_	_	_
105	ParC-flag	ParC-flag	NNP	_	_	_
106	2	2	CD	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	NorflIP	norflip	NN	_	_	_
109	IP	IP	NNP	_	_	_
110	ParE-flag	ParE-flag	NNP	_	_	_
111	1	1	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	NormalData	normaldata	NN	_	_	_
114	=	=	JJ	_	_	_
115	transform.madata	transform.madata	NN	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	LogData	LogData	NNP	_	_	_
118	,	,	,	_	_	_
119	method	method	NN	_	_	_
120	=	=	JJ	_	_	_
121	c	c	NN	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	\	\	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Normalisation	normalisation	NN	_	_	_
126	:	:	:	_	_	_
127	Counts	count	NNS	_	_	_
128	were	be	VBD	_	_	_
129	normalised	normalise	VBN	_	_	_
130	by	by	IN	_	_	_
131	applying	apply	VBG	_	_	_
132	a	a	DT	_	_	_
133	single	single	JJ	_	_	_
134	,	,	,	_	_	_
135	sample-specific	sample-specific	JJ	_	_	_
136	scaling	scaling	NN	_	_	_
137	factor	factor	NN	_	_	_
138	.	.	.	_	_	_

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	Normalization	normalization	NN	_	_	_
12	factors	factor	NNS	_	_	_
13	were	be	VBD	_	_	_
14	calculated	calculate	VBN	_	_	_
15	using	use	VBG	_	_	_
16	a	a	DT	_	_	_
17	non-linear	non-linear	JJ	_	_	_
18	Loess	loess	JJ	_	_	_
19	model	model	NN	_	_	_
20	using	use	VBG	_	_	_
21	csaw	csaw	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Bioconductor	bioconductor	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Normalization	normalization	NN	_	_	_
27	is	be	VBZ	_	_	_
28	performed	perform	VBN	_	_	_
29	by	by	IN	_	_	_
30	TREBAX	trebax	NN	_	_	_
31	,	,	,	_	_	_
32	using	use	VBG	_	_	_
33	MA-plots	ma-plot	NNS	_	_	_
34	.	.	.	_	_	_

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	/	/	:	_	_	_
28	2	2	CD	_	_	_
29	and	and	CC	_	_	_
30	logarithmic	logarithmic	JJ	_	_	_
31	ratio	ratio	NN	_	_	_
32	of	of	IN	_	_	_
33	intensity	intensity	NN	_	_	_
34	Ms	ms	NN	_	_	_
35	=	=	JJ	_	_	_
36	log	log	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Ts/Rs	ts/rs	NNS	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	Here	here	RB	_	_	_
41	,	,	,	_	_	_
42	Ts	t	NNS	_	_	_
43	and	and	CC	_	_	_
44	Rs	rs	NN	_	_	_
45	are	be	VBP	_	_	_
46	the	the	DT	_	_	_
47	intensity	intensity	NN	_	_	_
48	of	of	IN	_	_	_
49	target	target	NN	_	_	_
50	and	and	CC	_	_	_
51	control	control	NN	_	_	_
52	experiments	experiment	NNS	_	_	_
53	for	for	IN	_	_	_
54	sth	sth	NN	_	_	_
55	spot	spot	NN	_	_	_
56	,	,	,	_	_	_
57	respectively.By	respectively.by	NN	_	_	_
58	plotting	plot	VBG	_	_	_
59	values	value	NNS	_	_	_
60	of	of	IN	_	_	_
61	As	as	IN	_	_	_
62	on	on	IN	_	_	_
63	the	the	DT	_	_	_
64	abscissa	abscissa	NN	_	_	_
65	and	and	CC	_	_	_
66	Ms	ms	NN	_	_	_
67	on	on	IN	_	_	_
68	the	the	DT	_	_	_
69	ordinate	ordinate	NN	_	_	_
70	of	of	IN	_	_	_
71	a	a	DT	_	_	_
72	coordinate	coordinate	JJ	_	_	_
73	system	system	NN	_	_	_
74	,	,	,	_	_	_
75	it	it	PRP	_	_	_
76	is	be	VBZ	_	_	_
77	possible	possible	JJ	_	_	_
78	to	to	TO	_	_	_
79	evaluate	evaluate	VB	_	_	_
80	the	the	DT	_	_	_
81	bias	bias	NN	_	_	_
82	error	error	NN	_	_	_
83	with	with	IN	_	_	_
84	respects	respects	NNS	_	_	_
85	to	to	TO	_	_	_
86	the	the	DT	_	_	_
87	average	average	JJ	_	_	_
88	logarithmic	logarithmic	JJ	_	_	_
89	intensities	intensity	NNS	_	_	_
90	.	.	.	_	_	_

1	Normalized	normalize	VBN	_	_	_
2	log	log	NN	_	_	_
3	ratio	ratio	NN	_	_	_
4	M	m	NN	_	_	_
5	''	''	''	_	_	_
6	s	s	NNS	_	_	_
7	is	be	VBZ	_	_	_
8	estimated	estimate	VBN	_	_	_
9	as	as	IN	_	_	_
10	the	the	DT	_	_	_
11	difference	difference	NN	_	_	_
12	between	between	IN	_	_	_
13	Ms	Ms	NNP	_	_	_
14	and	and	CC	_	_	_
15	baseline	baseline	NN	_	_	_
16	M	m	NN	_	_	_
17	's	's	POS	_	_	_
18	.	.	.	_	_	_

1	Here	here	RB	_	_	_
2	,	,	,	_	_	_
3	using	use	VBG	_	_	_
4	a	a	DT	_	_	_
5	relation	relation	NN	_	_	_
6	between	between	IN	_	_	_
7	Ms	Ms	NNP	_	_	_
8	and	and	CC	_	_	_
9	As	as	IN	_	_	_
10	,	,	,	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Ms	ms	NN	_	_	_
13	=	=	JJ	_	_	_
14	f	f	FW	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	As	as	IN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	+	+	CC	_	_	_
19	es	e	NNS	_	_	_
20	,	,	,	_	_	_
21	es	e	NNS	_	_	_
22	is	be	VBZ	_	_	_
23	the	the	DT	_	_	_
24	difference	difference	NN	_	_	_
25	between	between	IN	_	_	_
26	Ms	Ms	NNP	_	_	_
27	and	and	CC	_	_	_
28	f	f	FW	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	As	as	IN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	for	for	IN	_	_	_
33	gene	gene	NN	_	_	_
34	s	s	NNS	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	by	by	IN	_	_	_
37	MA	MA	NNP	_	_	_
38	plot	plot	NN	_	_	_
39	;	;	:	_	_	_
40	the	the	DT	_	_	_
41	baseline	baseline	NN	_	_	_
42	for	for	IN	_	_	_
43	sth	sth	NN	_	_	_
44	spot	spot	NN	_	_	_
45	is	be	VBZ	_	_	_
46	estimated	estimate	VBN	_	_	_
47	by	by	IN	_	_	_
48	M	m	NN	_	_	_
49	'	'	''	_	_	_
50	=	=	JJ	_	_	_
51	f	f	FW	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	A	a	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	genes	gene	NNS	_	_	_
3	whose	whose	WP$	_	_	_
4	signal	signal	NN	_	_	_
5	intensity	intensity	NN	_	_	_
6	is	be	VBZ	_	_	_
7	regarded	regard	VBN	_	_	_
8	as	as	IN	_	_	_
9	zero	zero	CD	_	_	_
10	are	be	VBP	_	_	_
11	eliminated	eliminate	VBN	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	present	present	JJ	_	_	_
15	analysis	analysis	NN	_	_	_
16	.	.	.	_	_	_

1	With	with	IN	_	_	_
2	this	this	DT	_	_	_
3	methodology	methodology	NN	_	_	_
4	,	,	,	_	_	_
5	it	it	PRP	_	_	_
6	is	be	VBZ	_	_	_
7	assumed	assume	VBN	_	_	_
8	that	that	IN	_	_	_
9	there	there	EX	_	_	_
10	is	be	VBZ	_	_	_
11	no	no	DT	_	_	_
12	large	large	JJ	_	_	_
13	error	error	NN	_	_	_
14	due	due	JJ	_	_	_
15	to	to	TO	_	_	_
16	expression	expression	NN	_	_	_
17	intensity	intensity	NN	_	_	_
18	in	in	IN	_	_	_
19	the	the	DT	_	_	_
20	majority	majority	NN	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	spots	spot	NNS	_	_	_
24	and	and	CC	_	_	_
25	that	that	IN	_	_	_
26	expression	expression	NN	_	_	_
27	change	change	NN	_	_	_
28	does	do	VBZ	_	_	_
29	not	not	RB	_	_	_
30	occur	occur	VB	_	_	_
31	on	on	IN	_	_	_
32	the	the	DT	_	_	_
33	majority	majority	NN	_	_	_
34	of	of	IN	_	_	_
35	the	the	DT	_	_	_
36	spots	spot	NNS	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	normalization	normalization	NN	_	_	_
3	of	of	IN	_	_	_
4	graphs	graph	NNS	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	total	total	JJ	_	_	_
8	number	number	NN	_	_	_
9	of	of	IN	_	_	_
10	mapped	map	VBN	_	_	_
11	reads	read	VBZ	_	_	_
12	per	per	IN	_	_	_
13	library	library	NN	_	_	_
14	using	use	VBG	_	_	_
15	READemption	reademption	NN	_	_	_
16	0.3.7	0.3.7	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	normalization	normalization	NN	_	_	_
19	subtracting	subtract	VBG	_	_	_
20	array-median	array-median	JJ	_	_	_
21	log2	log2	NN	_	_	_
22	ratio	ratio	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	normalized	normalize	VBD	_	_	_
3	as	as	IN	_	_	_
4	described	describe	VBN	_	_	_
5	before	before	IN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Tong	Tong	NNP	_	_	_
8	et	et	FW	_	_	_
9	al.	al.	FW	_	_	_
10	2004	2004	CD	_	_	_
11	BBRC	BBRC	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	spots	spot	NNS	_	_	_
4	were	be	VBD	_	_	_
5	excluded	exclude	VBN	_	_	_
6	from	from	IN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Normalized	Normalized	NNP	_	_	_
9	decay	decay	NN	_	_	_
10	values	value	NNS	_	_	_
11	with	with	IN	_	_	_
12	average	average	NN	_	_	_
13	of	of	IN	_	_	_
14	stable	stable	JJ	_	_	_
15	genes	gene	NNS	_	_	_
16	ssrA	ssra	NN	GEN	_	_
17	,	,	,	_	_	_
18	ssrS	ssrs	NN	GEN	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	rnpB	rnpb	NN	GEN	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Normalized	normalize	VBN	_	_	_
24	FPKM	fpkm	NN	_	_	_
25	values	value	NNS	_	_	_
26	were	be	VBD	_	_	_
27	generated	generate	VBN	_	_	_
28	from	from	IN	_	_	_
29	the	the	DT	_	_	_
30	raw	raw	JJ	_	_	_
31	gene	gene	NN	_	_	_
32	counts	count	NNS	_	_	_
33	by	by	IN	_	_	_
34	custom	custom	NN	_	_	_
35	scripts	script	NNS	_	_	_
36	that	that	WDT	_	_	_
37	calculated	calculate	VBD	_	_	_
38	and	and	CC	_	_	_
39	applied	apply	VBD	_	_	_
40	a	a	DT	_	_	_
41	trimmed	trimmed	RBR	_	_	_
42	mean	mean	VB	_	_	_
43	of	of	IN	_	_	_
44	M-values	m-value	NNS	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	TMM	tmm	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	factor	factor	NN	_	_	_
49	using	use	VBG	_	_	_
50	edgeR	edger	NN	_	_	_
51	version	version	NN	_	_	_
52	3.8.6	3.8.6	CD	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Normalized	normalize	VBN	_	_	_
3	log	log	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	2	2	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	ratio	ratio	NN	_	_	_
8	of	of	IN	_	_	_
9	Cy5/Cy3	cy5/cy3	NN	_	_	_
10	,	,	,	_	_	_
11	normalized	normalize	VBD	_	_	_
12	using	use	VBG	_	_	_
13	lowess	lowess	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	normalized	normalize	VBD	_	_	_
16	using	use	VBG	_	_	_
17	lcDNA	lcdna	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	normalizing	normalizing	NN	_	_	_
20	:	:	:	_	_	_
21	convert	convert	VB	_	_	_
22	counts	count	NNS	_	_	_
23	in	in	IN	_	_	_
24	RPKM	rpkm	NN	_	_	_
25	using	use	VBG	_	_	_
26	Excel	Excel	NNP	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	norm.temp	norm.temp	NN	_	_	_
29	<	<	JJR	_	_	_
30	-	-	:	_	_	_
31	cbind	cbind	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	NormalData	NormalData	NNP	_	_	_
34	$	$	$	_	_	_
35	metarow	metarow	JJ	_	_	_
36	,	,	,	_	_	_
37	NormalData	NormalData	NNP	_	_	_
38	$	$	$	_	_	_
39	metacol	metacol	JJ	_	_	_
40	,	,	,	_	_	_
41	NormalData	NormalData	NNP	_	_	_
42	$	$	$	_	_	_
43	row	row	NN	_	_	_
44	,	,	,	_	_	_
45	NormalData	NormalData	NNP	_	_	_
46	$	$	$	_	_	_
47	col	col	CD	_	_	_
48	,	,	,	_	_	_
49	NormalData	NormalData	NNP	_	_	_
50	$	$	$	_	_	_
51	geneID	geneid	JJ	_	_	_
52	,	,	,	_	_	_
53	NormalData	NormalData	NNP	_	_	_
54	$	$	$	_	_	_
55	data	datum	NNS	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	No	no	DT	_	_	_
59	specific	specific	JJ	_	_	_
60	treatment	treatment	NN	_	_	_
61	was	be	VBD	_	_	_
62	done	do	VBN	_	_	_
63	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
13	no	no	DT	_	_	_
14	treatment	treatment	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	No	No	NNP	_	_	_
17	treatment	treatment	NN	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	No	No	NNP	_	_	_
20	treatment	treatment	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	control	control	NN	_	_	_
23	sample	sample	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	No	no	DT	_	_	_
3	treatment	treatment	NN	_	_	_
4	,	,	,	_	_	_
5	just	just	RB	_	_	_
6	comparison	comparison	NN	_	_	_
7	of	of	IN	_	_	_
8	RNAs	rna	NNS	_	_	_
9	from	from	IN	_	_	_
10	wild	wild	JJ	_	_	_
11	type	type	NN	_	_	_
12	and	and	CC	_	_	_
13	mutant	mutant	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	No	no	DT	_	_	_
3	treatment	treatment	NN	_	_	_
4	were	be	VBD	_	_	_
5	studied	study	VBN	_	_	_
6	in	in	IN	_	_	_
7	this	this	DT	_	_	_
8	experience	experience	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	No	no	DT	_	_	_
11	triclosan	triclosan	NN	_	_	_
12	treatment	treatment	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	nrdA	nrda	NN	GEN	_	_
15	__	__	CD	_	_	_
16	U	U	NNP	_	_	_
17	_	_	NNP	_	_	_
18	N0075	N0075	NNP	_	_	_
19	_	_	VBD	_	_	_
20	r1	r1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	nrdA	nrda	NN	GEN	_	_
23	__	__	CD	_	_	_
24	U	U	NNP	_	_	_
25	_	_	NNP	_	_	_
26	N0075	N0075	NNP	_	_	_
27	_	_	VBD	_	_	_
28	r2	r2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	nrdA	nrda	NN	GEN	_	_
31	__	__	CD	_	_	_
32	U	U	NNP	_	_	_
33	_	_	NNP	_	_	_
34	N0075	N0075	NNP	_	_	_
35	_	_	VBD	_	_	_
36	r3	r3	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	nrdA	nrda	NN	GEN	_	_
39	upregulation	upregulation	NN	_	_	_
40	,	,	,	_	_	_
41	0.075	0.075	CD	_	_	_
42	mg/mL	mg/ml	NN	_	_	_
43	norfloxacin	norfloxacin	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	nrdB	nrdb	NN	GEN	_	_
46	__	__	CD	_	_	_
47	U	U	NNP	_	_	_
48	_	_	NNP	_	_	_
49	N0075	N0075	NNP	_	_	_
50	_	_	VBD	_	_	_
51	r1	r1	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	nrdB	nrdb	NN	GEN	_	_
54	__	__	CD	_	_	_
55	U	U	NNP	_	_	_
56	_	_	NNP	_	_	_
57	N0075	N0075	NNP	_	_	_
58	_	_	SYM	_	_	_
59	r3	r3	FW	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
61	nrdB	nrdb	NN	GEN	_	_
62	upregulation	upregulation	NN	_	_	_
63	,	,	,	_	_	_
64	0.075	0.075	CD	_	_	_
65	mg/mL	mg/ml	NN	_	_	_
66	norfloxacin	norfloxacin	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	N-RNaseE	n-rnasee	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	BZ453	bz453	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	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	N-RNaseE	n-rnasee	NN	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	BZ453	bz453	NN	_	_	_
91	-RRB-	-rrb-	-RRB-	_	_	_
92	in	in	IN	_	_	_
93	M9	m9	NN	_	_	_
94	+	+	CC	_	_	_
95	0.2	0.2	CD	_	_	_
96	%	%	NN	_	_	_
97	Glycerol	glycerol	NN	_	_	_
98	,	,	,	_	_	_
99	0.2	0.2	CD	_	_	_
100	%	%	NN	_	_	_
101	Tryptone	tryptone	NN	_	_	_
102	at	at	IN	_	_	_
103	30	30	CD	_	_	_
104	C	c	NN	_	_	_
105	Mid	Mid	NNP	_	_	_
106	Log	Log	NNP	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	N-RNaseE	n-rnasee	NN	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	BZ453	bz453	NN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	in	in	IN	_	_	_
113	M9	m9	NN	_	_	_
114	+	+	CC	_	_	_
115	0.2	0.2	CD	_	_	_
116	%	%	NN	_	_	_
117	Glycerol	glycerol	NN	_	_	_
118	,	,	,	_	_	_
119	0.2	0.2	CD	_	_	_
120	%	%	NN	_	_	_
121	Tryptone	tryptone	NN	_	_	_
122	at	at	IN	_	_	_
123	30	30	CD	_	_	_
124	C	c	NN	_	_	_
125	Mid	Mid	NNP	_	_	_
126	Log	Log	NNP	_	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	N-RNaseE	n-rnasee	NN	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	BZ453	bz453	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	in	in	IN	_	_	_
133	M9	m9	NN	_	_	_
134	+	+	CC	_	_	_
135	0.2	0.2	CD	_	_	_
136	%	%	NN	_	_	_
137	Glycerol	glycerol	NN	_	_	_
138	,	,	,	_	_	_
139	0.2	0.2	CD	_	_	_
140	%	%	NN	_	_	_
141	Tryptone	tryptone	NN	_	_	_
142	at	at	IN	_	_	_
143	30	30	CD	_	_	_
144	C	c	NN	_	_	_
145	Mid	Mid	NNP	_	_	_
146	Log	Log	NNP	_	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	N-RNaseE	n-rnasee	NN	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	BZ453	bz453	NN	_	_	_
151	-RRB-	-rrb-	-RRB-	_	_	_
152	in	in	IN	_	_	_
153	M9	m9	NN	_	_	_
154	+	+	CC	_	_	_
155	0.2	0.2	CD	_	_	_
156	%	%	NN	_	_	_
157	Glycerol	glycerol	NN	_	_	_
158	,	,	,	_	_	_
159	0.2	0.2	CD	_	_	_
160	%	%	NN	_	_	_
161	Tryptone	tryptone	NN	_	_	_
162	at	at	IN	_	_	_
163	30	30	CD	_	_	_
164	C	c	NN	_	_	_
165	Mid	Mid	NNP	_	_	_
166	Log	Log	NNP	_	_	_
167	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
168	N-RNaseE	n-rnasee	NN	_	_	_
169	-LRB-	-lrb-	-LRB-	_	_	_
170	BZ453	bz453	NN	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	in	in	IN	_	_	_
173	M9	m9	NN	_	_	_
174	+	+	CC	_	_	_
175	0.2	0.2	CD	_	_	_
176	%	%	NN	_	_	_
177	Glycerol	glycerol	NN	_	_	_
178	,	,	,	_	_	_
179	0.2	0.2	CD	_	_	_
180	%	%	NN	_	_	_
181	Tryptone	tryptone	NN	_	_	_
182	at	at	IN	_	_	_
183	30	30	CD	_	_	_
184	C	c	NN	_	_	_
185	Mid	Mid	NNP	_	_	_
186	Log	Log	NNP	_	_	_
187	1.5	1.5	CD	_	_	_
188	'	'	''	_	_	_
189	post	post	JJ	_	_	_
190	rif	rif	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	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	3	3	CD	_	_	_
212	'	'	''	_	_	_
213	post	post	JJ	_	_	_
214	rif	rif	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	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	4.5	4.5	CD	_	_	_
236	'	'	''	_	_	_
237	post	post	JJ	_	_	_
238	rif	rif	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	N-RNaseE	n-rnasee	NN	_	_	_
241	-LRB-	-lrb-	-LRB-	_	_	_
242	BZ453	bz453	NN	_	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	in	in	IN	_	_	_
245	M9	m9	NN	_	_	_
246	+	+	CC	_	_	_
247	0.2	0.2	CD	_	_	_
248	%	%	NN	_	_	_
249	Glycerol	glycerol	NN	_	_	_
250	,	,	,	_	_	_
251	0.2	0.2	CD	_	_	_
252	%	%	NN	_	_	_
253	Tryptone	tryptone	NN	_	_	_
254	at	at	IN	_	_	_
255	30	30	CD	_	_	_
256	C	c	NN	_	_	_
257	Mid	Mid	NNP	_	_	_
258	Log	Log	NNP	_	_	_
259	4.5	4.5	CD	_	_	_
260	'	'	''	_	_	_
261	post	post	JJ	_	_	_
262	rif	rif	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	N-RNaseE	n-rnasee	NN	_	_	_
265	-LRB-	-lrb-	-LRB-	_	_	_
266	BZ453	bz453	NN	_	_	_
267	-RRB-	-rrb-	-RRB-	_	_	_
268	in	in	IN	_	_	_
269	M9	m9	NN	_	_	_
270	+	+	CC	_	_	_
271	0.2	0.2	CD	_	_	_
272	%	%	NN	_	_	_
273	Glycerol	glycerol	NN	_	_	_
274	,	,	,	_	_	_
275	0.2	0.2	CD	_	_	_
276	%	%	NN	_	_	_
277	Tryptone	tryptone	NN	_	_	_
278	at	at	IN	_	_	_
279	30	30	CD	_	_	_
280	C	c	NN	_	_	_
281	Mid	Mid	NNP	_	_	_
282	Log	Log	NNP	_	_	_
283	6	6	CD	_	_	_
284	'	'	''	_	_	_
285	post	post	JJ	_	_	_
286	rif	rif	NN	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	NsrR	nsrr	NN	TF	_	_
289	_	_	NN	_	_	_
290	ChIPSeq	chipseq	NN	_	_	_
291	_	_	CD	_	_	_
292	rep1	rep1	NN	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	NsrR	nsrr	NN	TF	_	_
295	_	_	NN	_	_	_
296	ChIPSeq	chipseq	NN	_	_	_
297	_	_	CD	_	_	_
298	rep2	rep2	NN	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	NsrR	nsrr	NN	TF	_	_
301	_	_	NN	_	_	_
302	ChIPSeq	chipseq	NN	_	_	_
303	_	_	CD	_	_	_
304	rep3	rep3	NN	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	NsrR	nsrr	NN	TF	_	_
307	_	_	CD	_	_	_
308	Flagtag	Flagtag	NNP	_	_	_
309	_	_	CD	_	_	_
310	rep1	rep1	NN	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	NsrR	nsrr	NN	TF	_	_
313	_	_	CD	_	_	_
314	Flagtag	Flagtag	NNP	_	_	_
315	_	_	CD	_	_	_
316	rep2	rep2	NN	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	NsrR	nsrr	NN	TF	_	_
319	_	_	CD	_	_	_
320	Flagtag	Flagtag	NNP	_	_	_
321	_	_	CD	_	_	_
322	rep3	rep3	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	NsrR	nsrr	NN	TF	_	_
325	_	_	NN	_	_	_
326	input	input	NN	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	NTG-treated	ntg-treated	JJ	_	_	_
329	E.	e.	FW	_	_	_
330	coli	coli	FW	_	_	_
331	imp	imp	FW	_	_	_
332	fabI	fabi	NN	GEN	_	_
333	-LRB-	-lrb-	-LRB-	_	_	_
334	G93V	g93v	NN	_	_	_
335	-RRB-	-rrb-	-RRB-	_	_	_
336	-LSB-	-lsb-	-LRB-	_	_	_
337	E.	e.	FW	_	_	_
338	coli	coli	FW	_	_	_
339	IFN4	ifn4	NN	_	_	_
340	-RSB-	-rsb-	-RRB-	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	NTG-treated	ntg-treated	JJ	_	_	_
343	E.	e.	FW	_	_	_
344	coli	coli	FW	_	_	_
345	imp	imp	FW	_	_	_
346	fabI	fabi	NN	GEN	_	_
347	-LRB-	-lrb-	-LRB-	_	_	_
348	G93V	g93v	NN	_	_	_
349	-RRB-	-rrb-	-RRB-	_	_	_
350	-LSB-	-lsb-	-LRB-	_	_	_
351	E.	e.	FW	_	_	_
352	coli	coli	FW	_	_	_
353	IFN5	ifn5	NN	_	_	_
354	-RSB-	-rsb-	-RRB-	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	ntg	ntg	NN	_	_	_
357	treatment	treatment	NN	_	_	_
358	:	:	:	_	_	_
359	yes	yes	UH	_	_	_
360	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
361	NtrC	ntrc	NN	TF	_	_
362	_	_	NN	_	_	_
363	ChIPSeq	chipseq	NN	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	nucleic	nucleic	JJ	_	_	_
366	_	_	NN	_	_	_
367	acid	acid	NN	_	_	_
368	_	_	NN	_	_	_
369	extraction	extraction	NN	_	_	_
370	|	|	SYM	_	_	_
371	ChIP	chip	NN	_	_	_
372	was	be	VBD	_	_	_
373	performed	perform	VBN	_	_	_
374	as	as	IN	_	_	_
375	previously	previously	RB	_	_	_
376	described	describe	VBN	_	_	_
377	-LRB-	-lrb-	-LRB-	_	_	_
378	Grainger	Grainger	NNP	_	_	_
379	et	et	FW	_	_	_
380	al	al	FW	_	_	_
381	,	,	,	_	_	_
382	2004	2004	CD	_	_	_
383	-RRB-	-rrb-	-RRB-	_	_	_
384	with	with	IN	_	_	_
385	some	some	DT	_	_	_
386	modifications	modification	NNS	_	_	_
387	to	to	TO	_	_	_
388	the	the	DT	_	_	_
389	protdegree	protdegree	NN	_	_	_
390	Col.	Col.	NNP	_	_	_
391	Cells	cell	NNS	_	_	_
392	were	be	VBD	_	_	_
393	grown	grow	VBN	_	_	_
394	aerobically	aerobically	RB	_	_	_
395	at	at	IN	_	_	_
396	37degree	37degree	CD	_	_	_
397	C	c	NN	_	_	_
398	to	to	TO	_	_	_
399	the	the	DT	_	_	_
400	desired	desire	VBN	_	_	_
401	OD600	od600	NN	_	_	_
402	and	and	CC	_	_	_
403	formaldehyde	formaldehyde	NN	_	_	_
404	was	be	VBD	_	_	_
405	added	add	VBN	_	_	_
406	to	to	TO	_	_	_
407	a	a	DT	_	_	_
408	final	final	JJ	_	_	_
409	concentration	concentration	NN	_	_	_
410	of	of	IN	_	_	_
411	1	1	CD	_	_	_
412	%	%	NN	_	_	_
413	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
33	lysozyme	lysozyme	NN	_	_	_
34	and	and	CC	_	_	_
35	0.1	0.1	CD	_	_	_
36	mg/ml	mg/ml	NN	_	_	_
37	RNase	rnase	NN	_	_	_
38	A	a	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	and	and	CC	_	_	_
41	incubated	incubate	VBN	_	_	_
42	at	at	IN	_	_	_
43	37degree	37degree	CD	_	_	_
44	C	c	NN	_	_	_
45	for	for	IN	_	_	_
46	30	30	CD	_	_	_
47	min	min	NN	_	_	_
48	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	lysis	lysis	NN	_	_	_
3	,	,	,	_	_	_
4	3	3	CD	_	_	_
5	ml	ml	NN	_	_	_
6	immunoprecipitation	immunoprecipitation	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	IP	IP	NNP	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	50	50	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	HEPES-KOH	hepes-koh	NN	_	_	_
15	-LSB-	-lsb-	-LRB-	_	_	_
16	pH	ph	NN	_	_	_
17	7.5	7.5	CD	_	_	_
18	-RSB-	-rsb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	150	150	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	NaCl	nacl	NN	_	_	_
23	,	,	,	_	_	_
24	1	1	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	EDTA	edta	NN	_	_	_
27	,	,	,	_	_	_
28	1	1	CD	_	_	_
29	%	%	NN	_	_	_
30	Triton	Triton	NNP	_	_	_
31	X-100	x-100	NN	_	_	_
32	,	,	,	_	_	_
33	0.1	0.1	CD	_	_	_
34	%	%	NN	_	_	_
35	sodium	sodium	NN	_	_	_
36	deoxycholate	deoxycholate	NN	SUPP	_	_
37	,	,	,	_	_	_
38	0.1	0.1	CD	_	_	_
39	%	%	NN	_	_	_
40	sodium	sodium	NN	_	_	_
41	dodecyl	dodecyl	NN	_	_	_
42	sulfate	sulfate	NN	_	_	_
43	-LSB-	-lsb-	-LRB-	_	_	_
44	SDS	sds	NN	_	_	_
45	-RSB-	-rsb-	-RRB-	_	_	_
46	and	and	CC	_	_	_
47	PMSF	pmsf	NN	_	_	_
48	-LSB-	-lsb-	-LRB-	_	_	_
49	final	final	JJ	_	_	_
50	concentration	concentration	NN	_	_	_
51	1	1	CD	_	_	_
52	mM	mm	NN	KWSUPP	_	_
53	-RSB-	-rsb-	-RRB-	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	was	be	VBD	_	_	_
56	added	add	VBN	_	_	_
57	and	and	CC	_	_	_
58	the	the	DT	_	_	_
59	lysate	lysate	NN	_	_	_
60	passed	pass	VBN	_	_	_
61	through	through	IN	_	_	_
62	a	a	DT	_	_	_
63	French	french	JJ	_	_	_
64	pressure	pressure	NN	_	_	_
65	cell	cell	NN	_	_	_
66	twice	twice	RB	_	_	_
67	.	.	.	_	_	_

1	2	2	CD	_	_	_
2	ml	ml	NN	_	_	_
3	aliquots	aliquot	NNS	_	_	_
4	were	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	DNA	dna	NN	_	_	_
9	sheared	shear	VBD	_	_	_
10	to	to	TO	_	_	_
11	an	a	DT	_	_	_
12	average	average	JJ	_	_	_
13	size	size	NN	_	_	_
14	of	of	IN	_	_	_
15	~	~	NN	_	_	_
16	200	200	CD	_	_	_
17	bp	bp	NN	_	_	_
18	using	use	VBG	_	_	_
19	a	a	DT	_	_	_
20	Bioruptor	bioruptor	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Diagenode	diagenode	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	with	with	IN	_	_	_
25	30	30	CD	_	_	_
26	cycles	cycle	NNS	_	_	_
27	of	of	IN	_	_	_
28	30	30	CD	_	_	_
29	sec	sec	NN	_	_	_
30	on/off	on/off	JJ	_	_	_
31	at	at	IN	_	_	_
32	high	high	JJ	_	_	_
33	setting	setting	NN	_	_	_
34	.	.	.	_	_	_

1	Insoluble	insoluble	JJ	_	_	_
2	cellular	cellular	JJ	_	_	_
3	matter	matter	NN	_	_	_
4	was	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	by	by	IN	_	_	_
7	centrifugation	centrifugation	NN	_	_	_
8	for	for	IN	_	_	_
9	10	10	CD	_	_	_
10	min	min	NN	_	_	_
11	at	at	IN	_	_	_
12	4degree	4degree	CD	_	_	_
13	C	c	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	supernatant	supernatant	NN	_	_	_
18	was	be	VBD	_	_	_
19	split	split	VBN	_	_	_
20	into	into	IN	_	_	_
21	two	two	CD	_	_	_
22	800	800	CD	_	_	_
23	microl	microl	NN	_	_	_
24	aliquots	aliquot	NNS	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	remaining	remain	VBG	_	_	_
3	400	400	CD	_	_	_
4	microl	microl	NN	_	_	_
5	was	be	VBD	_	_	_
6	kept	keep	VBN	_	_	_
7	to	to	TO	_	_	_
8	check	check	VB	_	_	_
9	the	the	DT	_	_	_
10	size	size	NN	_	_	_
11	of	of	IN	_	_	_
12	the	the	DT	_	_	_
13	DNA	dna	NN	_	_	_
14	fragments	fragment	NNS	_	_	_
15	.	.	.	_	_	_

1	<br>	<br>	JJ	_	_	_
2	<br>	<br>	NN	_	_	_
3	Each	each	DT	_	_	_
4	800	800	CD	_	_	_
5	microl	microl	NN	_	_	_
6	aliquot	aliquot	NN	_	_	_
7	was	be	VBD	_	_	_
8	incubated	incubate	VBN	_	_	_
9	with	with	IN	_	_	_
10	20	20	CD	_	_	_
11	microl	microl	NN	_	_	_
12	Protein	protein	NN	_	_	_
13	A/G	a/g	NN	_	_	_
14	UltraLink	UltraLink	NNP	_	_	_
15	Resin	Resin	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Pierce	Pierce	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	on	on	IN	_	_	_
20	a	a	DT	_	_	_
21	rotary	rotary	JJ	_	_	_
22	shaker	shaker	NN	_	_	_
23	for	for	IN	_	_	_
24	45	45	CD	_	_	_
25	min	min	NN	_	_	_
26	at	at	IN	_	_	_
27	room	room	NN	_	_	_
28	temperature	temperature	NN	_	_	_
29	to	to	TO	_	_	_
30	get	get	VB	_	_	_
31	rid	rid	JJ	_	_	_
32	of	of	IN	_	_	_
33	complexes	complex	NNS	_	_	_
34	binding	bind	VBG	_	_	_
35	to	to	TO	_	_	_
36	the	the	DT	_	_	_
37	resin	resin	NN	_	_	_
38	non-specifically	non-specifically	RB	_	_	_
39	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	removed	remove	VBN	_	_	_
6	and	and	CC	_	_	_
7	incubated	incubate	VBN	_	_	_
8	with	with	IN	_	_	_
9	either	either	CC	_	_	_
10	no	no	DT	_	_	_
11	antibody	antibody	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	mdegree	mdegree	NN	_	_	_
14	Ck-IP	ck-ip	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	FLAG	flag	NN	_	_	_
18	mouse	mouse	NN	_	_	_
19	mondegree	mondegree	NN	_	_	_
20	Clonal	clonal	JJ	_	_	_
21	antibody	antibody	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Sigma-Aldrich	sigma-aldrich	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	or	or	CC	_	_	_
26	RNAP	rnap	NN	_	_	_
27	Beta	beta	NN	_	_	_
28	subunit	subunit	NN	_	_	_
29	mouse	mouse	NN	_	_	_
30	mondegree	mondegree	NN	_	_	_
31	Clonal	clonal	JJ	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Nedegree	nedegree	JJ	_	_	_
34	Clone	clone	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	and	and	CC	_	_	_
37	30	30	CD	_	_	_
38	microl	microl	NN	_	_	_
39	Protein	protein	NN	_	_	_
40	A/G	a/g	NN	_	_	_
41	UltraLink	UltraLink	NNP	_	_	_
42	Resin	Resin	NNP	_	_	_
43	,	,	,	_	_	_
44	pre-incubated	pre-incubated	JJ	_	_	_
45	with	with	IN	_	_	_
46	1mg/ml	1mg/ml	JJ	_	_	_
47	bovine	bovine	JJ	_	_	_
48	serum	serum	NN	_	_	_
49	albumin	albumin	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	BSA	bsa	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	in	in	IN	_	_	_
54	TBS	tbs	NN	_	_	_
55	,	,	,	_	_	_
56	on	on	IN	_	_	_
57	a	a	DT	_	_	_
58	rotary	rotary	JJ	_	_	_
59	shaker	shaker	NN	_	_	_
60	at	at	IN	_	_	_
61	4degree	4degree	CD	_	_	_
62	C	c	NN	_	_	_
63	overnight	overnight	JJ	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	FLAG	flag	NN	_	_	_
66	antibody	antibody	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	or	or	CC	_	_	_
69	at	at	IN	_	_	_
70	room	room	NN	_	_	_
71	temperature	temperature	NN	_	_	_
72	for	for	IN	_	_	_
73	90	90	CD	_	_	_
74	min	min	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	RNAP	rnap	NN	_	_	_
77	Beta	beta	NN	_	_	_
78	subunit	subunit	NN	_	_	_
79	antibody	antibody	NN	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	once	once	RB	_	_	_
5	with	with	IN	_	_	_
6	IP	IP	NNP	_	_	_
7	buffer	buffer	NN	_	_	_
8	,	,	,	_	_	_
9	twice	twice	RB	_	_	_
10	with	with	IN	_	_	_
11	IP	IP	NNP	_	_	_
12	buffer	buffer	NN	_	_	_
13	+	+	CC	_	_	_
14	500	500	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	NaCl	nacl	NN	_	_	_
17	,	,	,	_	_	_
18	once	once	RB	_	_	_
19	with	with	IN	_	_	_
20	wash	wash	NN	_	_	_
21	buffer	buffer	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	10	10	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	Tris	tris	NN	_	_	_
26	-LSB-	-lsb-	-LRB-	_	_	_
27	pH	ph	NN	_	_	_
28	8.0	8.0	CD	_	_	_
29	-RSB-	-rsb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	250	250	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	LiCl	licl	NN	_	_	_
34	,	,	,	_	_	_
35	1	1	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	EDTA	edta	NN	_	_	_
38	,	,	,	_	_	_
39	0.5	0.5	CD	_	_	_
40	%	%	NN	_	_	_
41	Nonidet	Nonidet	NNP	_	_	_
42	P-40	P-40	NNP	_	_	_
43	and	and	CC	_	_	_
44	0.5	0.5	CD	_	_	_
45	%	%	NN	_	_	_
46	sodium	sodium	NN	_	_	_
47	deoxycholate	deoxycholate	NN	SUPP	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	and	and	CC	_	_	_
50	once	once	RB	_	_	_
51	with	with	IN	_	_	_
52	TE	te	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	pH	ph	NN	_	_	_
55	7.5	7.5	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	.	.	.	_	_	_

1	Immunoprecipitated	immunoprecipitate	VBN	_	_	_
2	complexes	complex	NNS	_	_	_
3	were	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	in	in	IN	_	_	_
6	100	100	CD	_	_	_
7	microl	microl	NN	_	_	_
8	elution	elution	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	7.5	7.5	CD	_	_	_
17	-RSB-	-rsb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	10	10	CD	_	_	_
20	mM	mm	NN	KWSUPP	_	_
21	EDTA	edta	NN	_	_	_
22	and	and	CC	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	SDS	sds	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	at	at	IN	_	_	_
28	65degree	65degree	CD	_	_	_
29	C	c	NN	_	_	_
30	for	for	IN	_	_	_
31	20	20	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
16	nupC	nupc	NN	GEN	_	_
17	__	__	CD	_	_	_
18	U	U	NNP	_	_	_
19	_	_	NNP	_	_	_
20	N0075	N0075	NNP	_	_	_
21	_	_	VBD	_	_	_
22	r1	r1	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	nupC	nupc	NN	GEN	_	_
25	__	__	CD	_	_	_
26	U	U	NNP	_	_	_
27	_	_	NNP	_	_	_
28	N0075	N0075	NNP	_	_	_
29	_	_	VBD	_	_	_
30	r2	r2	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	nupC	nupc	NN	GEN	_	_
33	__	__	CD	_	_	_
34	U	U	NNP	_	_	_
35	_	_	NNP	_	_	_
36	N0075	N0075	NNP	_	_	_
37	_	_	VBD	_	_	_
38	r3	r3	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	nupC	nupc	NN	GEN	_	_
41	upregulation	upregulation	NN	_	_	_
42	,	,	,	_	_	_
43	0.075	0.075	CD	_	_	_
44	mg/mL	mg/ml	NN	_	_	_
45	norfloxacin	norfloxacin	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	NusA	nusa	NN	_	_	_
48	ChIP-chip	chip-chip	NN	_	_	_
49	in	in	IN	_	_	_
50	E.	e.	FW	_	_	_
51	coli	coli	FW	_	_	_
52	K-12	k-12	NN	_	_	_
53	MG1655	mg1655	NN	_	_	_
54	cells	cell	NNS	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Dataset	Dataset	NNP	_	_	_
57	56226	56226	CD	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	NusA	nusa	NN	_	_	_
61	ChIP-chip	chip-chip	NN	_	_	_
62	in	in	IN	_	_	_
63	E.	e.	FW	_	_	_
64	coli	coli	FW	_	_	_
65	K-12	k-12	NN	_	_	_
66	MG1655	mg1655	NN	_	_	_
67	cells	cell	NNS	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	Dataset	Dataset	NNP	_	_	_
70	61392	61392	CD	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	NusA	nusa	NN	_	_	_
74	ChIP-chip	chip-chip	NN	_	_	_
75	in	in	IN	_	_	_
76	E.	e.	FW	_	_	_
77	coli	coli	FW	_	_	_
78	K-12	k-12	NN	_	_	_
79	MG1655	mg1655	NN	_	_	_
80	cells	cell	NNS	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	Dataset	Dataset	NNP	_	_	_
83	64131	64131	CD	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	NusA	nusa	NN	_	_	_
87	ChIP	chip	NN	_	_	_
88	in	in	IN	_	_	_
89	E.	e.	FW	_	_	_
90	coli	coli	FW	_	_	_
91	K-12	k-12	NN	_	_	_
92	MG1655	mg1655	NN	_	_	_
93	cells	cell	NNS	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
95	NusG	nusg	NN	_	_	_
96	ChIP-chip	chip-chip	NN	_	_	_
97	in	in	IN	_	_	_
98	E.	e.	FW	_	_	_
99	coli	coli	FW	_	_	_
100	K-12	k-12	NN	_	_	_
101	MG1655	mg1655	NN	_	_	_
102	cells	cell	NNS	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	Dataset	Dataset	NNP	_	_	_
105	70568	70568	CD	_	_	_
106	-RRB-	-rrb-	-RRB-	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	NusG	nusg	NN	_	_	_
109	ChIP-chip	chip-chip	NN	_	_	_
110	in	in	IN	_	_	_
111	E.	e.	FW	_	_	_
112	coli	coli	FW	_	_	_
113	K-12	k-12	NN	_	_	_
114	MG1655	mg1655	NN	_	_	_
115	HA3	ha3	NN	_	_	_
116	:	:	:	_	_	_
117	:	:	:	_	_	_
118	nusG	nusg	NN	GEN	_	_
119	cells	cell	NNS	_	_	_
120	-LRB-	-lrb-	-LRB-	_	_	_
121	Dataset	Dataset	NNP	_	_	_
122	62261	62261	CD	_	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	NusG	nusg	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	HA3	ha3	NN	_	_	_
133	:	:	:	_	_	_
134	:	:	:	_	_	_
135	nusG	nusg	NN	GEN	_	_
136	cells	cell	NNS	_	_	_
137	-LRB-	-lrb-	-LRB-	_	_	_
138	Dataset	Dataset	NNP	_	_	_
139	62263	62263	CD	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	NusG	nusg	NN	_	_	_
143	ChIP	chip	NN	_	_	_
144	in	in	IN	_	_	_
145	E.	e.	FW	_	_	_
146	coli	coli	FW	_	_	_
147	K-12	k-12	NN	_	_	_
148	MG1655	mg1655	NN	_	_	_
149	cells	cell	NNS	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
151	NusG	nusg	NN	_	_	_
152	ChIP	chip	NN	_	_	_
153	in	in	IN	_	_	_
154	E.	e.	FW	_	_	_
155	coli	coli	FW	_	_	_
156	K-12	k-12	NN	_	_	_
157	MG1655	mg1655	NN	_	_	_
158	HA3	ha3	NN	_	_	_
159	:	:	:	_	_	_
160	:	:	:	_	_	_
161	nusG	nusg	NN	GEN	_	_
162	cells	cell	NNS	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	∆	∆	CD	_	_	_
165	nusG	nusg	NN	GEN	_	_
166	UvsW	uvsw	NN	_	_	_
167	_	_	CD	_	_	_
168	replicate1	replicate1	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	∆	∆	CD	_	_	_
171	nusG	nusg	NN	GEN	_	_
172	UvsW	uvsw	NN	_	_	_
173	_	_	CD	_	_	_
174	replicate2	replicate2	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	∆	∆	CD	_	_	_
177	nusG	nusg	NN	GEN	_	_
178	UvsW	uvsw	NN	_	_	_
179	_	_	CD	_	_	_
180	replicate3	replicate3	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	NZ502	nz502	NN	_	_	_
183	_	_	CD	_	_	_
184	12	12	CD	_	_	_
185	%	%	NN	_	_	_
186	Glu	glu	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	NZ502	nz502	NN	_	_	_
189	_	_	CD	_	_	_
190	5	5	CD	_	_	_
191	%	%	NN	_	_	_
192	Glu	glu	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	O103	o103	NN	_	_	_
195	no.	no.	NN	_	_	_
196	1	1	CD	_	_	_
197	-LRB-	-lrb-	-LRB-	_	_	_
198	strain	strain	NN	_	_	_
199	10828	10828	CD	_	_	_
200	-RRB-	-rrb-	-RRB-	_	_	_
201	replicate	replicate	VBP	_	_	_
202	1	1	CD	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	O103	o103	NN	_	_	_
205	no.	no.	NN	_	_	_
206	1	1	CD	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	strain	strain	NN	_	_	_
209	10828	10828	CD	_	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	replicate	replicate	VBP	_	_	_
212	2	2	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
214	O103	o103	NN	_	_	_
215	no.	no.	NN	_	_	_
216	2	2	CD	_	_	_
217	-LRB-	-lrb-	-LRB-	_	_	_
218	strain	strain	NN	_	_	_
219	11117	11117	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	2	2	CD	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	strain	strain	NN	_	_	_
229	11117	11117	CD	_	_	_
230	-RRB-	-rrb-	-RRB-	_	_	_
231	replicate	replicate	VBP	_	_	_
232	2	2	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
234	O103	o103	NN	_	_	_
235	no.	no.	NN	_	_	_
236	3	3	CD	_	_	_
237	-LRB-	-lrb-	-LRB-	_	_	_
238	strain	strain	NN	_	_	_
239	11711	11711	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	3	3	CD	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	strain	strain	NN	_	_	_
249	11711	11711	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	4	4	CD	_	_	_
257	-LRB-	-lrb-	-LRB-	_	_	_
258	strain	strain	NN	_	_	_
259	11845	11845	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	4	4	CD	_	_	_
267	-LRB-	-lrb-	-LRB-	_	_	_
268	strain	strain	NN	_	_	_
269	11845	11845	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	5	5	CD	_	_	_
277	-LRB-	-lrb-	-LRB-	_	_	_
278	strain	strain	NN	_	_	_
279	12009	12009	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	5	5	CD	_	_	_
287	-LRB-	-lrb-	-LRB-	_	_	_
288	strain	strain	NN	_	_	_
289	12009	12009	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	6	6	CD	_	_	_
297	-LRB-	-lrb-	-LRB-	_	_	_
298	strain	strain	NN	_	_	_
299	PMK5	pmk5	NN	_	_	_
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	6	6	CD	_	_	_
307	-LRB-	-lrb-	-LRB-	_	_	_
308	strain	strain	NN	_	_	_
309	PMK5	pmk5	NN	_	_	_
310	-RRB-	-rrb-	-RRB-	_	_	_
311	replicate	replicate	VBP	_	_	_
312	2	2	CD	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
314	O111	o111	NN	_	_	_
315	no.	no.	NN	_	_	_
316	1	1	CD	_	_	_
317	-LRB-	-lrb-	-LRB-	_	_	_
318	strain	strain	NN	_	_	_
319	11109	11109	CD	_	_	_
320	-RRB-	-rrb-	-RRB-	_	_	_
321	replicate	replicate	VBP	_	_	_
322	1	1	CD	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	O111	o111	NN	_	_	_
325	no.	no.	NN	_	_	_
326	1	1	CD	_	_	_
327	-LRB-	-lrb-	-LRB-	_	_	_
328	strain	strain	NN	_	_	_
329	11109	11109	CD	_	_	_
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	2	2	CD	_	_	_
337	-LRB-	-lrb-	-LRB-	_	_	_
338	strain	strain	NN	_	_	_
339	11128	11128	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	2	2	CD	_	_	_
347	-LRB-	-lrb-	-LRB-	_	_	_
348	strain	strain	NN	_	_	_
349	11128	11128	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	3	3	CD	_	_	_
357	-LRB-	-lrb-	-LRB-	_	_	_
358	strain	strain	NN	_	_	_
359	11619	11619	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	3	3	CD	_	_	_
367	-LRB-	-lrb-	-LRB-	_	_	_
368	strain	strain	NN	_	_	_
369	11619	11619	CD	_	_	_
370	-RRB-	-rrb-	-RRB-	_	_	_
371	replicate	replicate	VBP	_	_	_
372	2	2	CD	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
374	O111	o111	NN	_	_	_
375	no.	no.	RB	_	_	_
376	4	4	CD	_	_	_
377	-LRB-	-lrb-	-LRB-	_	_	_
378	strain	strain	NN	_	_	_
379	11788	11788	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	4	4	CD	_	_	_
387	-LRB-	-lrb-	-LRB-	_	_	_
388	strain	strain	NN	_	_	_
389	11788	11788	CD	_	_	_
390	-RRB-	-rrb-	-RRB-	_	_	_
391	replicate	replicate	VBP	_	_	_
392	2	2	CD	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
394	O111	o111	NN	_	_	_
395	no.	no.	NN	_	_	_
396	5	5	CD	_	_	_
397	-LRB-	-lrb-	-LRB-	_	_	_
398	strain	strain	NN	_	_	_
399	13369	13369	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	5	5	CD	_	_	_
407	-LRB-	-lrb-	-LRB-	_	_	_
408	strain	strain	NN	_	_	_
409	13369	13369	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	6	6	CD	_	_	_
417	-LRB-	-lrb-	-LRB-	_	_	_
418	strain	strain	NN	_	_	_
419	ED71	ed71	NN	_	_	_
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	6	6	CD	_	_	_
427	-LRB-	-lrb-	-LRB-	_	_	_
428	strain	strain	NN	_	_	_
429	ED71	ed71	NN	_	_	_
430	-RRB-	-rrb-	-RRB-	_	_	_
431	replicate	replicate	VBP	_	_	_
432	2	2	CD	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
434	O157	o157	NN	_	_	_
435	_	_	CD	_	_	_
436	CL	cl	NN	_	_	_
437	MC	MC	NNP	_	_	_
438	fraction	fraction	NN	_	_	_
439	vs	vs	CC	_	_	_
440	control	control	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
442	O157	o157	NN	_	_	_
443	:	:	:	_	_	_
444	H7	h7	NN	_	_	_
445	cells	cell	NNS	_	_	_
446	were	be	VBD	_	_	_
447	grown	grow	VBN	_	_	_
448	to	to	TO	_	_	_
449	mid-log	mid-log	JJ	_	_	_
450	phase	phase	NN	_	_	_
451	in	in	IN	_	_	_
452	Luria	Luria	NNP	MED	_	_
453	broth	broth	NN	MED	_	_
454	with	with	IN	_	_	_
455	or	or	CC	_	_	_
456	without	without	IN	_	_	_
457	0.8	0.8	CD	_	_	_
458	%	%	NN	_	_	_
459	bile	bile	NN	_	_	_
460	salts	salt	NNS	_	_	_
461	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	O157	o157	NN	_	_	_
3	:	:	:	_	_	_
4	H7	h7	NN	_	_	_
5	EDL933	edl933	NN	_	_	_
6	in	in	IN	_	_	_
7	LB	LB	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	O157	o157	NN	_	_	_
10	:	:	:	_	_	_
11	H7	h7	NN	_	_	_
12	EDL933	edl933	NN	_	_	_
13	sdhA	sdha	NN	GEN	_	_
14	in	in	IN	_	_	_
15	LB	LB	NNP	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	O157	o157	NN	_	_	_
18	:	:	:	_	_	_
19	H7	h7	NN	_	_	_
20	EDL933	edl933	NN	_	_	_
21	sdhA	sdha	NN	GEN	_	_
22	in	in	IN	_	_	_
23	LB	lb	NN	_	_	_
24	with	with	IN	_	_	_
25	FA	fa	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	O157	o157	NN	_	_	_
28	:	:	:	_	_	_
29	H7	h7	NN	_	_	_
30	strain	strain	NN	_	_	_
31	EDL933	edl933	NN	_	_	_
32	,	,	,	_	_	_
33	100	100	CD	_	_	_
34	mcg/ml	mcg/ml	NN	_	_	_
35	bicyclomycin	bicyclomycin	NN	_	_	_
36	20	20	CD	_	_	_
37	min	min	NN	_	_	_
38	,	,	,	_	_	_
39	exponential	exponential	JJ	GrowthPhase	_	_
40	phase	phase	NN	GrowthPhase	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	O157	o157	NN	_	_	_
43	:	:	:	_	_	_
44	H7	h7	NN	_	_	_
45	strain	strain	NN	_	_	_
46	EDL933	edl933	NN	_	_	_
47	,	,	,	_	_	_
48	control	control	NN	_	_	_
49	sample	sample	NN	_	_	_
50	,	,	,	_	_	_
51	exponential	exponential	JJ	GrowthPhase	_	_
52	phase	phase	NN	GrowthPhase	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	O157	o157	NN	_	_	_
55	no.	no.	NN	_	_	_
56	2	2	CD	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	strain	strain	NN	_	_	_
59	980938	980938	CD	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	replicate	replicate	VBP	_	_	_
62	1	1	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	O157	o157	NN	_	_	_
65	no.	no.	NN	_	_	_
66	2	2	CD	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	strain	strain	NN	_	_	_
69	980938	980938	CD	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	replicate	replicate	VBP	_	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
74	O157	o157	NN	_	_	_
75	no.	no.	NN	_	_	_
76	3	3	CD	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	strain	strain	NN	_	_	_
79	980706	980706	CD	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	replicate	replicate	VBP	_	_	_
82	1	1	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	O157	o157	NN	_	_	_
85	no.	no.	NN	_	_	_
86	3	3	CD	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	strain	strain	NN	_	_	_
89	980706	980706	CD	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	replicate	replicate	VBP	_	_	_
92	2	2	CD	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
94	O157	o157	NN	_	_	_
95	no.	no.	NN	_	_	_
96	4	4	CD	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	strain	strain	NN	_	_	_
99	990281	990281	CD	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	replicate	replicate	VBP	_	_	_
102	1	1	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	O157	o157	NN	_	_	_
105	no.	no.	NN	_	_	_
106	4	4	CD	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	strain	strain	NN	_	_	_
109	990281	990281	CD	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	replicate	replicate	VBP	_	_	_
112	2	2	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
114	O157	o157	NN	_	_	_
115	no.	no.	NN	_	_	_
116	5	5	CD	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	strain	strain	NN	_	_	_
119	980551	980551	CD	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	replicate	replicate	VBP	_	_	_
122	1	1	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	O157	o157	NN	_	_	_
125	no.	no.	NN	_	_	_
126	5	5	CD	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	strain	strain	NN	_	_	_
129	980551	980551	CD	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	replicate	replicate	VBP	_	_	_
132	2	2	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
134	O157	o157	NN	_	_	_
135	no.	no.	NN	_	_	_
136	6	6	CD	_	_	_
137	-LRB-	-lrb-	-LRB-	_	_	_
138	strain	strain	NN	_	_	_
139	990570	990570	CD	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	replicate	replicate	VBP	_	_	_
142	1	1	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	O157	o157	NN	_	_	_
145	no.	no.	NN	_	_	_
146	6	6	CD	_	_	_
147	-LRB-	-lrb-	-LRB-	_	_	_
148	strain	strain	NN	_	_	_
149	990570	990570	CD	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	replicate	replicate	VBP	_	_	_
152	2	2	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
154	O157	o157	NN	_	_	_
155	no.	no.	NN	_	_	_
156	7	7	CD	_	_	_
157	-LRB-	-lrb-	-LRB-	_	_	_
158	strain	strain	NN	_	_	_
159	981456	981456	CD	_	_	_
160	-RRB-	-rrb-	-RRB-	_	_	_
161	replicate	replicate	VBP	_	_	_
162	1	1	CD	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	O157	o157	NN	_	_	_
165	no.	no.	NN	_	_	_
166	7	7	CD	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	strain	strain	NN	_	_	_
169	981456	981456	CD	_	_	_
170	-RRB-	-rrb-	-RRB-	_	_	_
171	replicate	replicate	VBP	_	_	_
172	2	2	CD	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
174	O157	o157	NN	_	_	_
175	no.	no.	NN	_	_	_
176	8	8	CD	_	_	_
177	-LRB-	-lrb-	-LRB-	_	_	_
178	strain	strain	NN	_	_	_
179	982243	982243	CD	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	replicate	replicate	VBP	_	_	_
182	1	1	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	O157	o157	NN	_	_	_
185	no.	no.	NN	_	_	_
186	8	8	CD	_	_	_
187	-LRB-	-lrb-	-LRB-	_	_	_
188	strain	strain	NN	_	_	_
189	982243	982243	CD	_	_	_
190	-RRB-	-rrb-	-RRB-	_	_	_
191	replicate	replicate	VBP	_	_	_
192	2	2	CD	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
194	O157	o157	NN	_	_	_
195	no.	no.	NN	_	_	_
196	9	9	CD	_	_	_
197	-LRB-	-lrb-	-LRB-	_	_	_
198	strain	strain	NN	_	_	_
199	981795	981795	CD	_	_	_
200	-RRB-	-rrb-	-RRB-	_	_	_
201	replicate	replicate	VBP	_	_	_
202	1	1	CD	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	O157	o157	NN	_	_	_
205	no.	no.	NN	_	_	_
206	9	9	CD	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	strain	strain	NN	_	_	_
209	981795	981795	CD	_	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	replicate	replicate	VBP	_	_	_
212	2	2	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
214	O157	o157	NN	_	_	_
215	strain	strain	NN	_	_	_
216	Sakai	Sakai	NNP	_	_	_
217	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
218	O26	o26	NN	_	_	_
219	no.	no.	NN	_	_	_
220	1	1	CD	_	_	_
221	-LRB-	-lrb-	-LRB-	_	_	_
222	strain	strain	NN	_	_	_
223	11044	11044	CD	_	_	_
224	-RRB-	-rrb-	-RRB-	_	_	_
225	replicate	replicate	VBP	_	_	_
226	1	1	CD	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	O26	o26	NN	_	_	_
229	no.	no.	NN	_	_	_
230	1	1	CD	_	_	_
231	-LRB-	-lrb-	-LRB-	_	_	_
232	strain	strain	NN	_	_	_
233	11044	11044	CD	_	_	_
234	-RRB-	-rrb-	-RRB-	_	_	_
235	replicate	replicate	VBP	_	_	_
236	2	2	CD	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
238	O26	o26	NN	_	_	_
239	no.	no.	NN	_	_	_
240	2	2	CD	_	_	_
241	-LRB-	-lrb-	-LRB-	_	_	_
242	strain	strain	NN	_	_	_
243	11368	11368	CD	_	_	_
244	-RRB-	-rrb-	-RRB-	_	_	_
245	replicate	replicate	VBP	_	_	_
246	1	1	CD	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	O26	o26	NN	_	_	_
249	no.	no.	NN	_	_	_
250	2	2	CD	_	_	_
251	-LRB-	-lrb-	-LRB-	_	_	_
252	strain	strain	NN	_	_	_
253	11368	11368	CD	_	_	_
254	-RRB-	-rrb-	-RRB-	_	_	_
255	replicate	replicate	VBP	_	_	_
256	2	2	CD	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
258	O26	o26	NN	_	_	_
259	no.	no.	NN	_	_	_
260	3	3	CD	_	_	_
261	-LRB-	-lrb-	-LRB-	_	_	_
262	strain	strain	NN	_	_	_
263	11656	11656	CD	_	_	_
264	-RRB-	-rrb-	-RRB-	_	_	_
265	replicate	replicate	VBP	_	_	_
266	1	1	CD	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	O26	o26	NN	_	_	_
269	no.	no.	NN	_	_	_
270	3	3	CD	_	_	_
271	-LRB-	-lrb-	-LRB-	_	_	_
272	strain	strain	NN	_	_	_
273	11656	11656	CD	_	_	_
274	-RRB-	-rrb-	-RRB-	_	_	_
275	replicate	replicate	VBP	_	_	_
276	2	2	CD	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
278	O26	o26	NN	_	_	_
279	no.	no.	NN	_	_	_
280	4	4	CD	_	_	_
281	-LRB-	-lrb-	-LRB-	_	_	_
282	strain	strain	NN	_	_	_
283	12719	12719	CD	_	_	_
284	-RRB-	-rrb-	-RRB-	_	_	_
285	replicate	replicate	VBP	_	_	_
286	1	1	CD	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	O26	o26	NN	_	_	_
289	no.	no.	NN	_	_	_
290	4	4	CD	_	_	_
291	-LRB-	-lrb-	-LRB-	_	_	_
292	strain	strain	NN	_	_	_
293	12719	12719	CD	_	_	_
294	-RRB-	-rrb-	-RRB-	_	_	_
295	replicate	replicate	VBP	_	_	_
296	2	2	CD	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
298	O26	o26	NN	_	_	_
299	no.	no.	NN	_	_	_
300	5	5	CD	_	_	_
301	-LRB-	-lrb-	-LRB-	_	_	_
302	strain	strain	NN	_	_	_
303	12929	12929	CD	_	_	_
304	-RRB-	-rrb-	-RRB-	_	_	_
305	replicate	replicate	VBP	_	_	_
306	1	1	CD	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	O26	o26	NN	_	_	_
309	no.	no.	NN	_	_	_
310	5	5	CD	_	_	_
311	-LRB-	-lrb-	-LRB-	_	_	_
312	strain	strain	NN	_	_	_
313	12929	12929	CD	_	_	_
314	-RRB-	-rrb-	-RRB-	_	_	_
315	replicate	replicate	VBP	_	_	_
316	2	2	CD	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
318	O26	o26	NN	_	_	_
319	no.	no.	NN	_	_	_
320	6	6	CD	_	_	_
321	-LRB-	-lrb-	-LRB-	_	_	_
322	strain	strain	NN	_	_	_
323	13065	13065	CD	_	_	_
324	-RRB-	-rrb-	-RRB-	_	_	_
325	replicate	replicate	VBP	_	_	_
326	1	1	CD	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	O26	o26	NN	_	_	_
329	no.	no.	NN	_	_	_
330	6	6	CD	_	_	_
331	-LRB-	-lrb-	-LRB-	_	_	_
332	strain	strain	NN	_	_	_
333	13065	13065	CD	_	_	_
334	-RRB-	-rrb-	-RRB-	_	_	_
335	replicate	replicate	VBP	_	_	_
336	2	2	CD	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
338	O26	o26	NN	_	_	_
339	no.	no.	NN	_	_	_
340	7	7	CD	_	_	_
341	-LRB-	-lrb-	-LRB-	_	_	_
342	strain	strain	NN	_	_	_
343	13247	13247	CD	_	_	_
344	-RRB-	-rrb-	-RRB-	_	_	_
345	replicate	replicate	VBP	_	_	_
346	1	1	CD	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	O26	o26	NN	_	_	_
349	no.	no.	NN	_	_	_
350	7	7	CD	_	_	_
351	-LRB-	-lrb-	-LRB-	_	_	_
352	strain	strain	NN	_	_	_
353	13247	13247	CD	_	_	_
354	-RRB-	-rrb-	-RRB-	_	_	_
355	replicate	replicate	VBP	_	_	_
356	2	2	CD	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
358	O26	o26	NN	_	_	_
359	no.	no.	NN	_	_	_
360	8	8	CD	_	_	_
361	-LRB-	-lrb-	-LRB-	_	_	_
362	strain	strain	NN	_	_	_
363	ED411	ed411	NN	_	_	_
364	-RRB-	-rrb-	-RRB-	_	_	_
365	replicate	replicate	VBP	_	_	_
366	1	1	CD	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	O26	o26	NN	_	_	_
369	no.	no.	NN	_	_	_
370	8	8	CD	_	_	_
371	-LRB-	-lrb-	-LRB-	_	_	_
372	strain	strain	NN	_	_	_
373	ED411	ed411	NN	_	_	_
374	-RRB-	-rrb-	-RRB-	_	_	_
375	replicate	replicate	VBP	_	_	_
376	2	2	CD	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
378	O500	o500	CD	_	_	_
379	_	_	SYM	_	_	_
380	1	1	CD	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	O500	o500	CD	_	_	_
383	_	_	NN	_	_	_
384	2	2	CD	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	O55	o55	NN	_	_	_
387	:	:	:	_	_	_
388	H6	h6	NN	_	_	_
389	ICC219	icc219	NN	_	_	_
390	replicate	replicate	VBP	_	_	_
391	1	1	CD	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
393	O55	o55	NN	_	_	_
394	:	:	:	_	_	_
395	H6	h6	NN	_	_	_
396	ICC219	icc219	NN	_	_	_
397	replicate	replicate	VBP	_	_	_
398	2	2	CD	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
400	O55	o55	NN	_	_	_
401	:	:	:	_	_	_
402	H6	h6	NN	_	_	_
403	ICC221	icc221	NN	_	_	_
404	replicate	replicate	VBP	_	_	_
405	1	1	CD	_	_	_
406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
407	O55	o55	NN	_	_	_
408	:	:	:	_	_	_
409	H6	h6	NN	_	_	_
410	ICC221	icc221	NN	_	_	_
411	replicate	replicate	VBP	_	_	_
412	2	2	CD	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
414	O55	o55	NN	_	_	_
415	:	:	:	_	_	_
416	H6	h6	NN	_	_	_
417	ICC222	icc222	NN	_	_	_
418	replicate	replicate	VBP	_	_	_
419	1	1	CD	_	_	_
420	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
421	O55	o55	NN	_	_	_
422	:	:	:	_	_	_
423	H6	h6	NN	_	_	_
424	ICC222	icc222	NN	_	_	_
425	replicate	replicate	VBP	_	_	_
426	2	2	CD	_	_	_
427	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
428	O55	o55	NN	_	_	_
429	:	:	:	_	_	_
430	H7	h7	NN	_	_	_
431	st58	st58	NN	_	_	_
432	replicate	replicate	VBP	_	_	_
433	1	1	CD	_	_	_
434	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
435	O55	o55	NN	_	_	_
436	:	:	:	_	_	_
437	H7	h7	NN	_	_	_
438	st58	st58	NN	_	_	_
439	replicate	replicate	VBP	_	_	_
440	2	2	CD	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
442	O55	o55	NN	_	_	_
443	:	:	:	_	_	_
444	H7	h7	NN	_	_	_
445	st957	st957	NN	_	_	_
446	replicate	replicate	VBP	_	_	_
447	1	1	CD	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	O55	o55	NN	_	_	_
450	:	:	:	_	_	_
451	H7	h7	NN	_	_	_
452	st957	st957	NN	_	_	_
453	replicate	replicate	VBP	_	_	_
454	2	2	CD	_	_	_
455	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
456	O55	o55	NN	_	_	_
457	:	:	:	_	_	_
458	H7	h7	NN	_	_	_
459	TB182A	tb182a	NN	_	_	_
460	replicate	replicate	VBP	_	_	_
461	1	1	CD	_	_	_
462	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
463	O55	o55	NN	_	_	_
464	:	:	:	_	_	_
465	H7	h7	NN	_	_	_
466	TB182A	tb182a	NN	_	_	_
467	replicate	replicate	VBP	_	_	_
468	2	2	CD	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
470	O55	o55	NN	_	_	_
471	:	:	:	_	_	_
472	H7	h7	NN	_	_	_
473	WC211	wc211	NN	_	_	_
474	replicate	replicate	VBP	_	_	_
475	1	1	CD	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	O55	o55	NN	_	_	_
478	:	:	:	_	_	_
479	H7	h7	NN	_	_	_
480	WC211	wc211	NN	_	_	_
481	replicate	replicate	VBP	_	_	_
482	2	2	CD	_	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
484	O55	o55	NN	_	_	_
485	:	:	:	_	_	_
486	H7	h7	NN	_	_	_
487	WC416	wc416	NN	_	_	_
488	replicate	replicate	VBP	_	_	_
489	1	1	CD	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	O55	o55	NN	_	_	_
492	:	:	:	_	_	_
493	H7	h7	NN	_	_	_
494	WC416	wc416	NN	_	_	_
495	replicate	replicate	VBP	_	_	_
496	2	2	CD	_	_	_
497	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
498	OD	od	NN	_	_	_
499	:	:	:	_	_	_
500	0.1	0.1	CD	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	OD	od	NN	_	_	_
503	:	:	:	_	_	_
504	0.1	0.1	CD	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	OD	od	NN	_	_	_
507	:	:	:	_	_	_
508	0.3	0.3	CD	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	OD	od	NN	_	_	_
511	:	:	:	_	_	_
512	0.3	0.3	CD	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	OD	od	NN	_	_	_
515	:	:	:	_	_	_
516	0.4	0.4	CD	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	OD	od	NN	_	_	_
519	:	:	:	_	_	_
520	0.4	0.4	CD	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
522	OD	od	NN	_	_	_
523	:	:	:	_	_	_
524	0.5	0.5	CD	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	OD	od	NN	_	_	_
527	:	:	:	_	_	_
528	0.6	0.6	CD	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	OD	od	NN	_	_	_
531	:	:	:	_	_	_
532	0.6	0.6	CD	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	od	od	NN	_	_	_
535	:	:	:	_	_	_
536	0.7	0.7	CD	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	od	od	NN	_	_	_
539	:	:	:	_	_	_
540	0.8	0.8	CD	_	_	_
541	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
542	OD	od	NN	_	_	_
543	:	:	:	_	_	_
544	1.0	1.0	CD	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	OD	od	NN	_	_	_
547	:	:	:	_	_	_
548	1.0	1.0	CD	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	OD	od	NN	_	_	_
551	:	:	:	_	_	_
552	1.3	1.3	CD	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	OD	od	NN	_	_	_
555	:	:	:	_	_	_
556	1.3	1.3	CD	_	_	_
557	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
558	OD	od	NN	_	_	_
559	:	:	:	_	_	_
560	1.7	1.7	CD	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	OD	od	NN	_	_	_
563	:	:	:	_	_	_
564	1.7	1.7	CD	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	OD	od	NN	_	_	_
567	:	:	:	_	_	_
568	2.7	2.7	CD	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	OD	od	NN	_	_	_
571	:	:	:	_	_	_
572	2.7	2.7	CD	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	OD	od	NN	_	_	_
575	:	:	:	_	_	_
576	4.5	4.5	CD	_	_	_
577	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
578	OD	od	NN	_	_	_
579	4.5	4.5	CD	_	_	_
580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
581	OD	od	NN	_	_	_
582	:	:	:	_	_	_
583	4.5	4.5	CD	_	_	_
584	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
585	OD	od	NN	_	_	_
586	:	:	:	_	_	_
587	4.7	4.7	CD	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
589	OD	od	NN	_	_	_
590	:	:	:	_	_	_
591	4.7	4.7	CD	_	_	_
592	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
593	OD	od	NN	_	_	_
594	:	:	:	_	_	_
595	4.8	4.8	CD	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
597	OD	od	NN	_	_	_
598	:	:	:	_	_	_
599	4.8	4.8	CD	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
601	od600	od600	CD	_	_	_
602	:	:	:	_	_	_
603	0.4	0.4	CD	_	_	_
604	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
605	OD600	od600	NN	_	_	_
606	15	15	CD	_	_	_
607	units	unit	NNS	_	_	_
608	of	of	IN	_	_	_
609	cells	cell	NNS	_	_	_
610	were	be	VBD	_	_	_
611	harvested	harvest	VBN	_	_	_
612	for	for	IN	_	_	_
613	each	each	DT	_	_	_
614	ChIP	chip	NN	_	_	_
615	procedure	procedure	NN	_	_	_
616	.	.	.	_	_	_

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/MES	Sanyo/MES	NNP	_	_	_
66	Soniprep	Soniprep	NNP	_	_	_
67	sonicator	sonicator	NN	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	8	8	CD	_	_	_
70	bursts	burst	NNS	_	_	_
71	at	at	IN	_	_	_
72	an	a	DT	_	_	_
73	amplitude	amplitude	NN	_	_	_
74	10	10	CD	_	_	_
75	microns	micron	NNS	_	_	_
76	for	for	IN	_	_	_
77	30	30	CD	_	_	_
78	seconds	seconds	NNS	_	_	_
79	,	,	,	_	_	_
80	with	with	IN	_	_	_
81	1	1	CD	_	_	_
82	minute	minute	NN	_	_	_
83	cooling	cooling	NN	_	_	_
84	between	between	IN	_	_	_
85	bursts	burst	NNS	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	transferred	transfer	VBN	_	_	_
4	to	to	TO	_	_	_
5	a	a	DT	_	_	_
6	2	2	CD	_	_	_
7	ml	ml	NN	_	_	_
8	microfuge	microfuge	NN	_	_	_
9	tube	tube	NN	_	_	_
10	and	and	CC	_	_	_
11	spun	spin	VBD	_	_	_
12	at	at	IN	_	_	_
13	13,200	13,200	CD	_	_	_
14	rpm	rpm	NN	_	_	_
15	for	for	IN	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	at	at	IN	_	_	_
19	4	4	CD	_	_	_
20	°C	°c	NN	_	_	_
21	.	.	.	_	_	_

1	Supernatant	supernatant	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	and	and	CC	_	_	_
5	1	1	CD	_	_	_
6	ml	ml	NN	_	_	_
7	dilution	dilution	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	added.The	added.the	NN	_	_	_
10	chromatin	chromatin	NN	_	_	_
11	material	material	NN	_	_	_
12	was	be	VBD	_	_	_
13	precleared	preclear	VBN	_	_	_
14	by	by	IN	_	_	_
15	adding	add	VBG	_	_	_
16	50	50	CD	_	_	_
17	µl	µl	NN	_	_	_
18	of	of	IN	_	_	_
19	normal	normal	JJ	_	_	_
20	rabbit	rabbit	NN	_	_	_
21	immunoglobulin	immunoglobulin	NN	_	_	_
22	G	g	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	IgG	igg	NN	_	_	_
25	,	,	,	_	_	_
26	1	1	CD	_	_	_
27	mg/ml	mg/ml	NN	_	_	_
28	,	,	,	_	_	_
29	Millipore	Millipore	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	incubated	incubate	VBN	_	_	_
4	for	for	IN	_	_	_
5	1	1	CD	_	_	_
6	h	h	NN	_	_	_
7	at	at	IN	_	_	_
8	4	4	CD	_	_	_
9	°C	°c	NN	_	_	_
10	on	on	IN	_	_	_
11	a	a	DT	_	_	_
12	rotating	rotate	VBG	_	_	_
13	wheel	wheel	NN	_	_	_
14	.	.	.	_	_	_

1	100	100	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	homogenous	homogenous	JJ	_	_	_
5	protein	protein	NN	_	_	_
6	G-agarose	g-agarose	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Roche	Roche	NNP	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	added	add	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	precleared	precleared	JJ	_	_	_
15	chromatin	chromatin	NN	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	samples	sample	NNS	_	_	_
19	were	be	VBD	_	_	_
20	incubated	incubate	VBN	_	_	_
21	for	for	IN	_	_	_
22	3-5	3-5	CD	_	_	_
23	h	h	NN	_	_	_
24	at	at	IN	_	_	_
25	4	4	CD	_	_	_
26	°C	°c	NN	_	_	_
27	on	on	IN	_	_	_
28	a	a	DT	_	_	_
29	rotating	rotate	VBG	_	_	_
30	wheel	wheel	NN	_	_	_
31	.	.	.	_	_	_

1	Samples	sample	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	2	2	CD	_	_	_
9	min	min	NN	_	_	_
10	at	at	IN	_	_	_
11	4	4	CD	_	_	_
12	°C	°c	NN	_	_	_
13	and	and	CC	_	_	_
14	this	this	DT	_	_	_
15	supernatant	supernatant	NN	_	_	_
16	was	be	VBD	_	_	_
17	used	use	VBN	_	_	_
18	to	to	TO	_	_	_
19	set	set	VB	_	_	_
20	up	up	RP	_	_	_
21	immunoprecipitation	immunoprecipitation	NN	_	_	_
22	reactions	reaction	NNS	_	_	_
23	.	.	.	_	_	_

1	200	200	CD	_	_	_
2	µl	µl	NN	_	_	_
3	chromatin	chromatin	NN	_	_	_
4	was	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	and	and	CC	_	_	_
7	used	use	VBN	_	_	_
8	as	as	IN	_	_	_
9	an	a	DT	_	_	_
10	input	input	NN	_	_	_
11	sample	sample	NN	_	_	_
12	.	.	.	_	_	_

1	Experimental	experimental	JJ	_	_	_
2	immunoprecipitation	immunoprecipitation	NN	_	_	_
3	were	be	VBD	_	_	_
4	set	set	VBN	_	_	_
5	up	up	RP	_	_	_
6	using	use	VBG	_	_	_
7	1,350	1,350	CD	_	_	_
8	µl	µl	NN	_	_	_
9	chromatin	chromatin	NN	_	_	_
10	and	and	CC	_	_	_
11	3.3	3.3	CD	_	_	_
12	µg/µl	µg/µl	NN	_	_	_
13	of	of	IN	_	_	_
14	anti-FLAG	anti-flag	JJ	_	_	_
15	antibody	antibody	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Sigma	Sigma	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Mock	mock	JJ	_	_	_
2	immunoprecipitation	immunoprecipitation	NN	_	_	_
3	1,350	1,350	CD	_	_	_
4	µl	µl	NN	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	and	and	CC	_	_	_
7	10	10	CD	_	_	_
8	µg	µg	NN	_	_	_
9	of	of	IN	_	_	_
10	normal	normal	JJ	_	_	_
11	mouse	mouse	NN	_	_	_
12	IgG	igg	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Millipore	millipore	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	incubated	incubate	VBN	_	_	_
4	overnight	overnight	JJ	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotating	rotate	VBG	_	_	_
8	wheel	wheel	NN	_	_	_
9	at	at	IN	_	_	_
10	4	4	CD	_	_	_
11	°C	°c	NN	_	_	_
12	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	centrifuged	centrifuge	VBN	_	_	_
4	at	at	IN	_	_	_
5	13,000	13,000	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	for	for	IN	_	_	_
8	5	5	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	NN	_	_	_
16	was	be	VBD	_	_	_
17	transferred	transfer	VBN	_	_	_
18	to	to	TO	_	_	_
19	2	2	CD	_	_	_
20	ml	ml	NN	_	_	_
21	microfuge	microfuge	NN	_	_	_
22	tubes	tube	NNS	_	_	_
23	.	.	.	_	_	_

1	50	50	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	protein	protein	NN	_	_	_
5	G-agarose	g-agarose	NN	_	_	_
6	was	be	VBD	_	_	_
7	added	add	VBN	_	_	_
8	to	to	TO	_	_	_
9	each	each	DT	_	_	_
10	sample	sample	NN	_	_	_
11	and	and	CC	_	_	_
12	incubated	incubate	VBN	_	_	_
13	at	at	IN	_	_	_
14	4	4	CD	_	_	_
15	°C	°c	NN	_	_	_
16	for	for	IN	_	_	_
17	3	3	CD	_	_	_
18	h	h	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	at	at	IN	_	_	_
6	7,500	7,500	CD	_	_	_
7	rpm	rpm	NN	_	_	_
8	for	for	IN	_	_	_
9	2	2	CD	_	_	_
10	min	min	NN	_	_	_
11	at	at	IN	_	_	_
12	4	4	CD	_	_	_
13	°C	°c	NN	_	_	_
14	to	to	TO	_	_	_
15	pellet	pellet	VB	_	_	_
16	the	the	DT	_	_	_
17	protein	protein	NN	_	_	_
18	G-agarose	g-agarose	NN	_	_	_
19	beads	bead	NNS	_	_	_
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	protein	protein	NN	_	_	_
8	G-agarose	g-agarose	NN	_	_	_
9	beads	bead	NNS	_	_	_
10	were	be	VBD	_	_	_
11	carefully	carefully	RB	_	_	_
12	washed	wash	VBN	_	_	_
13	.	.	.	_	_	_

1	91	91	CD	_	_	_
2	For	for	IN	_	_	_
3	each	each	DT	_	_	_
4	wash	wash	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	wash	wash	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	;	;	:	_	_	_
12	the	the	DT	_	_	_
13	samples	sample	NNS	_	_	_
14	were	be	VBD	_	_	_
15	vortexed	vortex	VBN	_	_	_
16	briefly	briefly	NN	_	_	_
17	and	and	CC	_	_	_
18	were	be	VBD	_	_	_
19	centrifuged	centrifuge	VBN	_	_	_
20	at	at	IN	_	_	_
21	7,500	7,500	CD	_	_	_
22	rpm	rpm	NN	_	_	_
23	for	for	IN	_	_	_
24	2	2	CD	_	_	_
25	min	min	NN	_	_	_
26	at	at	IN	_	_	_
27	4	4	CD	_	_	_
28	°C	°c	NN	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	left	leave	VBN	_	_	_
5	to	to	TO	_	_	_
6	stand	stand	VB	_	_	_
7	on	on	IN	_	_	_
8	ice	ice	NN	_	_	_
9	for	for	IN	_	_	_
10	1	1	CD	_	_	_
11	min	min	NN	_	_	_
12	before	before	IN	_	_	_
13	removing	remove	VBG	_	_	_
14	the	the	DT	_	_	_
15	supernatant	supernatant	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	washes	wash	NNS	_	_	_
3	were	be	VBD	_	_	_
4	carried	carry	VBN	_	_	_
5	out	out	RP	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	following	following	JJ	_	_	_
9	sequence	sequence	NN	_	_	_
10	:	:	:	_	_	_
11	The	the	DT	_	_	_
12	beads	bead	NNS	_	_	_
13	were	be	VBD	_	_	_
14	washed	wash	VBN	_	_	_
15	twice	twice	RB	_	_	_
16	with	with	IN	_	_	_
17	750	750	CD	_	_	_
18	µl	µl	NN	_	_	_
19	of	of	IN	_	_	_
20	cold	cold	JJ	_	_	_
21	IP	IP	NNP	_	_	_
22	wash	wash	NN	_	_	_
23	buffer	buffer	NN	_	_	_
24	1	1	CD	_	_	_
25	containing	contain	VBG	_	_	_
26	20	20	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	Tris-HCl	tris-hcl	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	pH	ph	NN	_	_	_
31	8.1	8.1	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	,	,	,	_	_	_
34	50	50	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	NaCl	nacl	NN	_	_	_
37	,	,	,	_	_	_
38	2mM	2mm	NN	_	_	_
39	EDTA	edta	NN	_	_	_
40	,	,	,	_	_	_
41	1	1	CD	_	_	_
42	%	%	NN	_	_	_
43	Triton	Triton	NNP	_	_	_
44	X-100	x-100	NN	_	_	_
45	,	,	,	_	_	_
46	0.1	0.1	CD	_	_	_
47	%	%	NN	_	_	_
48	SDS	sds	NN	_	_	_
49	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	transferred	transfer	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	1.5	1.5	CD	_	_	_
8	ml	ml	NN	_	_	_
9	microfuge	microfuge	NN	_	_	_
10	tube	tube	NN	_	_	_
11	after	after	IN	_	_	_
12	the	the	DT	_	_	_
13	first	first	JJ	_	_	_
14	wash	wash	NN	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	750	750	CD	_	_	_
8	µl	µl	NN	_	_	_
9	of	of	IN	_	_	_
10	cold	cold	JJ	_	_	_
11	IP	IP	NNP	_	_	_
12	wash	wash	NN	_	_	_
13	buffer	buffer	NN	_	_	_
14	2	2	CD	_	_	_
15	containing	contain	VBG	_	_	_
16	10	10	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	Tris-HCl	tris-hcl	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	pH	ph	NN	_	_	_
21	8.1	8.1	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	250	250	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	LiCl	licl	NN	_	_	_
27	,	,	,	_	_	_
28	1	1	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	EDTA	edta	NN	_	_	_
31	,	,	,	_	_	_
32	1	1	CD	_	_	_
33	%	%	NN	_	_	_
34	NP-40	np-40	NN	_	_	_
35	,	,	,	_	_	_
36	1	1	CD	_	_	_
37	%	%	NN	_	_	_
38	deoxycholic	deoxycholic	JJ	_	_	_
39	acid	acid	NN	_	_	_
40	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	twice	twice	RB	_	_	_
6	with	with	IN	_	_	_
7	750	750	CD	_	_	_
8	µl	µl	NN	_	_	_
9	of	of	IN	_	_	_
10	ice-cold	ice-cold	JJ	_	_	_
11	TE	TE	NNP	_	_	_
12	buffer	buffer	NN	_	_	_
13	containing	contain	VBG	_	_	_
14	10	10	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	Tris	Tris	NNP	_	_	_
17	base	base	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	pH	ph	NN	_	_	_
20	8	8	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	1	1	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	EDTA	edta	NN	_	_	_
26	.	.	.	_	_	_

1	DNA-protein-antibody	dna-protein-antibody	JJ	_	_	_
2	complexes	complex	NNS	_	_	_
3	were	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	protein	protein	NN	_	_	_
8	G-agarose	g-agarose	NN	_	_	_
9	beads	bead	NNS	_	_	_
10	by	by	IN	_	_	_
11	adding	add	VBG	_	_	_
12	225	225	CD	_	_	_
13	µl	µl	NN	_	_	_
14	of	of	IN	_	_	_
15	IP	IP	NNP	_	_	_
16	elution	elution	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	containing	contain	VBG	_	_	_
19	100	100	CD	_	_	_
20	mM	mm	NN	KWSUPP	_	_
21	NaHCO3	nahco3	NN	_	_	_
22	and	and	CC	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	SDS	sds	NN	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	IP	IP	NNP	_	_	_
7	elution	elution	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	,	,	,	_	_	_
10	briefly	briefly	NN	_	_	_
11	vortexed	vortex	VBD	_	_	_
12	and	and	CC	_	_	_
13	centrifuged	centrifuge	VBD	_	_	_
14	at	at	IN	_	_	_
15	7,500	7,500	CD	_	_	_
16	rpm	rpm	NN	_	_	_
17	for	for	IN	_	_	_
18	2	2	CD	_	_	_
19	min	min	NN	_	_	_
20	at	at	IN	_	_	_
21	room	room	NN	_	_	_
22	temperature	temperature	NN	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	in	in	IN	_	_	_
6	fresh	fresh	JJ	_	_	_
7	1.5	1.5	CD	_	_	_
8	ml	ml	NN	_	_	_
9	microfuge	microfuge	NN	_	_	_
10	tubes	tube	NNS	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bead	bead	NN	_	_	_
3	pellets	pellet	NNS	_	_	_
4	in	in	IN	_	_	_
5	the	the	DT	_	_	_
6	original	original	JJ	_	_	_
7	tubes	tube	NNS	_	_	_
8	were	be	VBD	_	_	_
9	resuspended	resuspend	VBN	_	_	_
10	in	in	IN	_	_	_
11	225	225	CD	_	_	_
12	µl	µl	NN	_	_	_
13	of	of	IN	_	_	_
14	IP	IP	NNP	_	_	_
15	elution	elution	NN	_	_	_
16	buffer	buffer	NN	_	_	_
17	again	again	RB	_	_	_
18	and	and	CC	_	_	_
19	briefly	briefly	RB	_	_	_
20	vortexed	vortex	VBN	_	_	_
21	and	and	CC	_	_	_
22	centrifuged	centrifuge	VBN	_	_	_
23	at	at	IN	_	_	_
24	7,500	7,500	CD	_	_	_
25	rpm	rpm	NN	_	_	_
26	for	for	IN	_	_	_
27	2	2	CD	_	_	_
28	min	min	NN	_	_	_
29	.	.	.	_	_	_

1	IP	IP	NNP	_	_	_
2	and	and	CC	_	_	_
3	input	input	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	thawed	thaw	VBN	_	_	_
7	on	on	IN	_	_	_
8	ice	ice	NN	_	_	_
9	.	.	.	_	_	_

1	0.1	0.1	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	RNase	rnase	NN	_	_	_
5	A	a	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	10	10	CD	_	_	_
8	mg/ml	mg/ml	NN	_	_	_
9	,	,	,	_	_	_
10	ICN	ICN	NNP	_	_	_
11	Biochemicals	Biochemicals	NNPS	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	16	16	CD	_	_	_
15	µl	µl	NN	_	_	_
16	of	of	IN	_	_	_
17	5	5	CD	_	_	_
18	M	m	NN	_	_	_
19	NaCl	nacl	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	to	to	TO	_	_	_
22	a	a	DT	_	_	_
23	final	final	JJ	_	_	_
24	concentration	concentration	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	M	m	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	was	be	VBD	_	_	_
30	added	add	VBN	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	input	input	NN	_	_	_
34	sample	sample	NN	_	_	_
35	.	.	.	_	_	_

1	Similarly	similarly	RB	_	_	_
2	,	,	,	_	_	_
3	0.2	0.2	CD	_	_	_
4	µl	µl	NN	_	_	_
5	of	of	IN	_	_	_
6	RNase	rnase	NN	_	_	_
7	A	a	NN	_	_	_
8	and	and	CC	_	_	_
9	27	27	CD	_	_	_
10	µl	µl	NN	_	_	_
11	of	of	IN	_	_	_
12	5	5	CD	_	_	_
13	M	m	NN	_	_	_
14	NaCl	nacl	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	to	to	TO	_	_	_
17	a	a	DT	_	_	_
18	final	final	JJ	_	_	_
19	concentration	concentration	NN	_	_	_
20	of	of	IN	_	_	_
21	0.3	0.3	CD	_	_	_
22	M	m	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	was	be	VBD	_	_	_
25	added	add	VBN	_	_	_
26	to	to	TO	_	_	_
27	each	each	DT	_	_	_
28	IP	IP	NNP	_	_	_
29	sample	sample	NN	_	_	_
30	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	including	include	VBG	_	_	_
4	the	the	DT	_	_	_
5	input	input	NN	_	_	_
6	DNA	dna	NN	_	_	_
7	were	be	VBD	_	_	_
8	incubated	incubate	VBN	_	_	_
9	at	at	IN	_	_	_
10	65	65	CD	_	_	_
11	°C	°c	NN	_	_	_
12	for	for	IN	_	_	_
13	6	6	CD	_	_	_
14	h	h	NN	_	_	_
15	to	to	TO	_	_	_
16	reverse	reverse	VB	_	_	_
17	cross-links	cross-link	NNS	_	_	_
18	.	.	.	_	_	_

1	9	9	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	Proteinase	Proteinase	NNP	_	_	_
5	K	K	NNP	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	10	10	CD	_	_	_
8	mg/ml	mg/ml	NN	_	_	_
9	,	,	,	_	_	_
10	GibcoBRL	gibcobrl	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	added	add	VBN	_	_	_
14	to	to	TO	_	_	_
15	each	each	DT	_	_	_
16	sample	sample	NN	_	_	_
17	and	and	CC	_	_	_
18	incubated	incubate	VBN	_	_	_
19	overnight	overnight	JJ	_	_	_
20	at	at	IN	_	_	_
21	45	45	CD	_	_	_
22	°C	°c	NN	_	_	_
23	.	.	.	_	_	_

1	2	2	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	yeast	yeast	NN	_	_	_
5	tRNA	trna	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	5mg/ml	5mg/ml	NN	_	_	_
8	,	,	,	_	_	_
9	Invitrogen	Invitrogen	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	each	each	DT	_	_	_
15	sample	sample	NN	_	_	_
16	followed	follow	VBN	_	_	_
17	by	by	IN	_	_	_
18	250	250	CD	_	_	_
19	µl	µl	NN	_	_	_
20	of	of	IN	_	_	_
21	phenol	phenol	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	pH	ph	NN	_	_	_
24	8	8	CD	_	_	_
25	,	,	,	_	_	_
26	Sigma	Sigma	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	250	250	CD	_	_	_
30	µl	µl	NN	_	_	_
31	of	of	IN	_	_	_
32	chloroform	chloroform	NN	_	_	_
33	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	centrifuged	centrifuge	VBN	_	_	_
4	at	at	IN	_	_	_
5	13,000	13,000	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	for	for	IN	_	_	_
8	5	5	CD	_	_	_
9	min	min	NN	_	_	_
10	at	at	IN	_	_	_
11	room	room	NN	_	_	_
12	temperature	temperature	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	aqueous	aqueous	JJ	_	_	_
3	layer	layer	NN	_	_	_
4	was	be	VBD	_	_	_
5	collected	collect	VBN	_	_	_
6	in	in	IN	_	_	_
7	fresh	fresh	JJ	_	_	_
8	1.5	1.5	CD	_	_	_
9	ml	ml	NN	_	_	_
10	centrifuge	centrifuge	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	and	and	CC	_	_	_
13	500	500	CD	_	_	_
14	µl	µl	NN	_	_	_
15	of	of	IN	_	_	_
16	chloroform	chloroform	NN	_	_	_
17	was	be	VBD	_	_	_
18	added	add	VBN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	vortexed	vortex	VBN	_	_	_
5	and	and	CC	_	_	_
6	centrifuged	centrifuge	VBN	_	_	_
7	at	at	IN	_	_	_
8	13,000	13,000	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	for	for	IN	_	_	_
11	5	5	CD	_	_	_
12	min	min	NN	_	_	_
13	and	and	CC	_	_	_
14	room	room	NN	_	_	_
15	temperature	temperature	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	aqueous	aqueous	JJ	_	_	_
3	layer	layer	NN	_	_	_
4	was	be	VBD	_	_	_
5	transferred	transfer	VBN	_	_	_
6	to	to	TO	_	_	_
7	a	a	DT	_	_	_
8	2	2	CD	_	_	_
9	ml	ml	NN	_	_	_
10	microfuge	microfuge	NN	_	_	_
11	tube	tube	NN	_	_	_
12	.	.	.	_	_	_

1	5	5	CD	_	_	_
2	µg	µg	NN	_	_	_
3	of	of	IN	_	_	_
4	glycogen	glycogen	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	5	5	CD	_	_	_
7	mg/ml	mg/ml	NN	_	_	_
8	,	,	,	_	_	_
9	Roche	Roche	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	1	1	CD	_	_	_
13	µl	µl	NN	_	_	_
14	of	of	IN	_	_	_
15	tRNA	trna	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	5	5	CD	_	_	_
18	mg/ml	mg/ml	NN	_	_	_
19	,	,	,	_	_	_
20	Invitrogen	Invitrogen	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	50	50	CD	_	_	_
24	µl	µl	NN	_	_	_
25	of	of	IN	_	_	_
26	3	3	CD	_	_	_
27	M	m	NN	_	_	_
28	NaAc	naac	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	pH	ph	NN	_	_	_
31	5.2	5.2	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	was	be	VBD	_	_	_
34	added	add	VBN	_	_	_
35	to	to	TO	_	_	_
36	each	each	DT	_	_	_
37	sample	sample	NN	_	_	_
38	and	and	CC	_	_	_
39	mixed	mixed	JJ	_	_	_
40	well	well	RB	_	_	_
41	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	precipitated	precipitate	VBN	_	_	_
5	with	with	IN	_	_	_
6	1,375	1,375	CD	_	_	_
7	µl	µl	NN	_	_	_
8	of	of	IN	_	_	_
9	95	95	CD	_	_	_
10	%	%	NN	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	and	and	CC	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	-80	-80	CD	_	_	_
16	°C	°c	NN	_	_	_
17	for	for	IN	_	_	_
18	1	1	CD	_	_	_
19	h	h	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	at	at	IN	_	_	_
6	13,000	13,000	CD	_	_	_
7	rpm	rpm	NN	_	_	_
8	for	for	IN	_	_	_
9	20	20	CD	_	_	_
10	min	min	NN	_	_	_
11	at	at	IN	_	_	_
12	4	4	CD	_	_	_
13	°C	°c	NN	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	DNA	dna	NN	_	_	_
3	pellets	pellet	NNS	_	_	_
4	were	be	VBD	_	_	_
5	washed	wash	VBN	_	_	_
6	with	with	IN	_	_	_
7	500	500	CD	_	_	_
8	µl	µl	NN	_	_	_
9	of	of	IN	_	_	_
10	ice-cold	ice-cold	JJ	_	_	_
11	70	70	CD	_	_	_
12	%	%	NN	_	_	_
13	ethanol	ethanol	NN	_	_	_
14	and	and	CC	_	_	_
15	centrifuged	centrifuge	VBN	_	_	_
16	at	at	IN	_	_	_
17	13,000	13,000	CD	_	_	_
18	rpm	rpm	NN	_	_	_
19	for	for	IN	_	_	_
20	5	5	CD	_	_	_
21	min	min	NN	_	_	_
22	at	at	IN	_	_	_
23	4	4	CD	_	_	_
24	°C	°c	NN	_	_	_
25	.	.	.	_	_	_

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	samples	sample	NNS	_	_	_
8	were	be	VBD	_	_	_
9	air-dried	air-dried	JJ	_	_	_
10	for	for	IN	_	_	_
11	10-15	10-15	CD	_	_	_
12	min	min	NN	_	_	_
13	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	of	of	IN	_	_	_
4	IP	IP	NNP	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	resuspended	resuspend	VBN	_	_	_
8	in	in	IN	_	_	_
9	50	50	CD	_	_	_
10	µl	µl	NN	_	_	_
11	nuclease-free	nuclease-free	JJ	_	_	_
12	H2O	h2o	NN	_	_	_
13	.	.	.	_	_	_

1	Input	input	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	resuspended	resuspend	VBN	_	_	_
6	in	in	IN	_	_	_
7	100	100	CD	_	_	_
8	µl	µl	NN	_	_	_
9	of	of	IN	_	_	_
10	nuclease-free	nuclease-free	JJ	_	_	_
11	H2O	h2o	NN	_	_	_
12	.	.	.	_	_	_

1	Samples	sample	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	1	1	CD	_	_	_
9	h.	h.	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	OD	od	NN	_	_	_
12	:	:	:	_	_	_
13	OD	od	NN	_	_	_
14	0.1	0.1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	of	of	IN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	F	f	NN	_	_	_
19	_	_	CD	_	_	_
20	r-B	r-b	NN	_	_	_
21	_	_	NN	_	_	_
22	r	r	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	/	/	:	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	F	f	NN	_	_	_
27	_	_	CD	_	_	_
28	g-B	g-b	NN	_	_	_
29	_	_	CD	_	_	_
30	g	g	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	,	,	,	_	_	_
33	where	where	WRB	_	_	_
34	F	f	NN	_	_	_
35	_	_	NN	_	_	_
36	r	r	NN	_	_	_
37	,	,	,	_	_	_
38	B	b	NN	_	_	_
39	_	_	NN	_	_	_
40	r	r	NN	_	_	_
41	,	,	,	_	_	_
42	F	f	NN	_	_	_
43	_	_	CD	_	_	_
44	g	g	NN	_	_	_
45	and	and	CC	_	_	_
46	B	b	NN	_	_	_
47	_	_	CD	_	_	_
48	g	g	NN	_	_	_
49	represent	represent	VBP	_	_	_
50	the	the	DT	_	_	_
51	median	median	JJ	_	_	_
52	Cy5	cy5	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	red	red	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Omega17	omega17	NN	_	_	_
58	_	_	NN	_	_	_
59	1	1	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Omega17	omega17	NN	_	_	_
62	_	_	NN	_	_	_
63	2	2	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Omega76	omega76	NN	_	_	_
66	_	_	NN	_	_	_
67	1	1	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Omega76	omega76	NN	_	_	_
70	_	_	NN	_	_	_
71	2	2	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	OmpFrecode	ompfrecode	NN	_	_	_
74	_	_	CD	_	_	_
75	f.wig	f.wig	NN	_	_	_
76	:	:	:	_	_	_
77	NC	nc	NN	_	_	_
78	_	_	SYM	_	_	_
79	000913.2	000913.2	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	OmpFrecode	ompfrecode	NN	_	_	_
82	_	_	CD	_	_	_
83	r.wig	r.wig	NN	_	_	_
84	:	:	:	_	_	_
85	NC	nc	NN	_	_	_
86	_	_	SYM	_	_	_
87	000913.2	000913.2	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	ompR	ompr	NN	GEN	_	_
90	_	_	NN	_	_	_
91	1	1	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	ompR	ompr	NN	GEN	_	_
94	_	_	NN	_	_	_
95	2	2	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	OmpR	ompr	NN	TF	_	_
98	_	_	CD	_	_	_
99	ChIPSeq	chipseq	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	ompR	ompr	NN	GEN	_	_
102	mutant	mutant	JJ	_	_	_
103	rep	rep	NN	GEN	_	_
104	1	1	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	ompR	ompr	NN	GEN	_	_
107	mutant	mutant	JJ	_	_	_
108	rep	rep	NN	GEN	_	_
109	2	2	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	OmpR	ompr	NN	TF	_	_
112	NaCl	nacl	NN	_	_	_
113	1	1	CD	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	OmpR	ompr	NN	TF	_	_
116	NaCl	nacl	NN	_	_	_
117	2	2	CD	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	∆	∆	CD	_	_	_
120	ompR	ompr	NN	GEN	_	_
121	pH	ph	NN	_	_	_
122	5.6	5.6	CD	_	_	_
123	A	a	DT	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	∆	∆	CD	_	_	_
126	ompR	ompr	NN	GEN	_	_
127	pH	ph	NN	_	_	_
128	5.6	5.6	CD	_	_	_
129	B	b	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	∆	∆	CD	_	_	_
132	ompR	ompr	NN	GEN	_	_
133	pH	ph	NN	_	_	_
134	5.6	5.6	CD	_	_	_
135	C	c	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	∆	∆	CD	_	_	_
138	ompR	ompr	NN	GEN	_	_
139	pH	ph	NN	_	_	_
140	7.2	7.2	CD	_	_	_
141	+15	+15	CD	_	_	_
142	%	%	NN	_	_	_
143	sucrose	sucrose	NN	_	_	_
144	A	a	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	∆	∆	CD	_	_	_
147	ompR	ompr	NN	GEN	_	_
148	pH	ph	NN	_	_	_
149	7.2	7.2	CD	_	_	_
150	+15	+15	CD	_	_	_
151	%	%	NN	_	_	_
152	sucrose	sucrose	NN	_	_	_
153	B	b	NN	_	_	_
154	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
155	One	one	CD	_	_	_
156	cell	cell	NN	_	_	_
157	pellet	pellet	NN	_	_	_
158	from	from	IN	_	_	_
159	each	each	DT	_	_	_
160	condition	condition	NN	_	_	_
161	and	and	CC	_	_	_
162	sampling	sampling	NN	_	_	_
163	time	time	NN	_	_	_
164	was	be	VBD	_	_	_
165	thawed	thaw	VBN	_	_	_
166	on	on	IN	_	_	_
167	ice	ice	NN	_	_	_
168	;	;	:	_	_	_
169	total	total	JJ	_	_	_
170	RNA	rna	NN	_	_	_
171	was	be	VBD	_	_	_
172	isolated	isolate	VBN	_	_	_
173	by	by	IN	_	_	_
174	RNAsnap	rnasnap	NN	_	_	_
175	™	™	NN	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	Stead	stead	NN	_	_	_
178	et	et	FW	_	_	_
179	al.	al.	FW	_	_	_
180	,	,	,	_	_	_
181	2012	2012	CD	_	_	_
182	,	,	,	_	_	_
183	Nucleic	Nucleic	NNP	_	_	_
184	Acids	Acids	NNP	_	_	_
185	Res	Res	NNP	_	_	_
186	-RRB-	-rrb-	-RRB-	_	_	_
187	.	.	.	_	_	_

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	One	one	CD	_	_	_
3	conditions	condition	NNS	_	_	_
4	:	:	:	_	_	_
5	1	1	CD	_	_	_
6	%	%	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	v/v	v/v	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	hydrogen	hydrogen	NN	SUPP	_	_
11	peroxide	peroxide	NN	SUPP	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	H2O2	h2o2	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	37	37	CD	_	_	_
17	Ceilsus	Ceilsus	NNP	_	_	_
18	degree	degree	NN	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	One	one	CD	_	_	_
21	conditions	condition	NNS	_	_	_
22	:	:	:	_	_	_
23	5	5	CD	_	_	_
24	%	%	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	v/v	v/v	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	isooctane	isooctane	NN	_	_	_
29	,	,	,	_	_	_
30	37	37	CD	_	_	_
31	Ceilsus	ceilsus	NN	_	_	_
32	degree	degree	NN	_	_	_
33	,	,	,	_	_	_
34	250rpm	250rpm	JJ	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	One	one	CD	_	_	_
37	hundred	hundred	CD	_	_	_
38	µl	µl	NN	_	_	_
39	tris-EDTA	tris-edta	NN	_	_	_
40	buffer	buffer	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	10	10	CD	_	_	_
43	mM	mm	NN	KWSUPP	_	_
44	Tris-Cl	tris-cl	NN	_	_	_
45	,	,	,	_	_	_
46	1	1	CD	_	_	_
47	mM	mm	NN	KWSUPP	_	_
48	EDTA	edta	NN	_	_	_
49	,	,	,	_	_	_
50	ph	ph	NN	_	_	_
51	8.0	8.0	CD	_	_	_
52	;	;	:	_	_	_
53	Promega	Promega	NNP	_	_	_
54	;	;	:	_	_	_
55	Madison	Madison	NNP	_	_	_
56	,	,	,	_	_	_
57	WI	WI	NNP	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	containing	contain	VBG	_	_	_
60	lysozyme	lysozyme	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	3	3	CD	_	_	_
63	mg/ml	mg/ml	NN	_	_	_
64	;	;	:	_	_	_
65	Sigma-Aldrich	Sigma-Aldrich	NNP	_	_	_
66	;	;	:	_	_	_
67	St.	St.	NNP	_	_	_
68	Louis	Louis	NNP	_	_	_
69	,	,	,	_	_	_
70	MO	MO	NNP	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	was	be	VBD	_	_	_
73	added	add	VBN	_	_	_
74	to	to	TO	_	_	_
75	each	each	DT	_	_	_
76	cell	cell	NN	_	_	_
77	pellet	pellet	NN	_	_	_
78	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	thoroughly	thoroughly	RB	_	_	_
5	mixed	mixed	JJ	_	_	_
6	and	and	CC	_	_	_
7	incubated	incubate	VBN	_	_	_
8	at	at	IN	_	_	_
9	room	room	NN	_	_	_
10	temperature	temperature	NN	_	_	_
11	for	for	IN	_	_	_
12	10	10	CD	_	_	_
13	min	min	NN	_	_	_
14	.	.	.	_	_	_

1	Buffer	buffer	NN	_	_	_
2	RLT	rlt	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	350	350	CD	_	_	_
5	µl	µl	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	combined	combine	VBN	_	_	_
9	with	with	IN	_	_	_
10	the	the	DT	_	_	_
11	tris-EDTA/lysozyme	tris-edta/lysozyme	NN	_	_	_
12	cell	cell	NN	_	_	_
13	suspension	suspension	NN	_	_	_
14	to	to	TO	_	_	_
15	further	further	JJ	_	_	_
16	lyse	lyse	NN	_	_	_
17	cells	cell	NNS	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	total	total	JJ	_	_	_
3	volume	volume	NN	_	_	_
4	was	be	VBD	_	_	_
5	combined	combine	VBN	_	_	_
6	with	with	IN	_	_	_
7	250	250	CD	_	_	_
8	µl	µl	NN	_	_	_
9	of	of	IN	_	_	_
10	200	200	CD	_	_	_
11	proof	proof	NN	_	_	_
12	ethanol	ethanol	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Aaper	Aaper	NNP	_	_	_
15	Alcohol	Alcohol	NNP	_	_	_
16	;	;	:	_	_	_
17	Shelbyville	Shelbyville	NNP	_	_	_
18	,	,	,	_	_	_
19	KY	ky	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	to	to	TO	_	_	_
22	solubilize	solubilize	VB	_	_	_
23	the	the	DT	_	_	_
24	cell	cell	NN	_	_	_
25	lysate	lysate	NN	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	the	the	DT	_	_	_
29	entire	entire	JJ	_	_	_
30	sample	sample	NN	_	_	_
31	was	be	VBD	_	_	_
32	transferred	transfer	VBN	_	_	_
33	to	to	TO	_	_	_
34	the	the	DT	_	_	_
35	RNeasy	RNeasy	NNP	_	_	_
36	Mini	Mini	NNP	_	_	_
37	Spin	Spin	NNP	_	_	_
38	Column	Column	NNP	_	_	_
39	in	in	IN	_	_	_
40	a	a	DT	_	_	_
41	collection	collection	NN	_	_	_
42	tube	tube	NN	_	_	_
43	and	and	CC	_	_	_
44	centrifuged	centrifuge	VBN	_	_	_
45	at	at	IN	_	_	_
46	8000	8000	CD	_	_	_
47	x	x	CC	_	_	_
48	g	g	NN	_	_	_
49	for	for	IN	_	_	_
50	15	15	CD	_	_	_
51	sec	sec	NN	_	_	_
52	at	at	IN	_	_	_
53	room	room	NN	_	_	_
54	temperature	temperature	NN	_	_	_
55	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	silica-based	silica-based	JJ	_	_	_
3	membrane	membrane	NN	_	_	_
4	efficiently	efficiently	RB	_	_	_
5	binds	bind	VBZ	_	_	_
6	up	up	RP	_	_	_
7	to	to	TO	_	_	_
8	100	100	CD	_	_	_
9	µg	µg	NN	_	_	_
10	of	of	IN	_	_	_
11	RNA	rna	NN	_	_	_
12	longer	longer	RBR	_	_	_
13	than	than	IN	_	_	_
14	200	200	CD	_	_	_
15	bases	basis	NNS	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	collection	collection	NN	_	_	_
3	tube	tube	NN	_	_	_
4	and	and	CC	_	_	_
5	eluate	eluate	NN	_	_	_
6	were	be	VBD	_	_	_
7	discarded	discard	VBN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	spin	spin	NN	_	_	_
12	column	column	NN	_	_	_
13	was	be	VBD	_	_	_
14	placed	place	VBN	_	_	_
15	in	in	IN	_	_	_
16	a	a	DT	_	_	_
17	new	new	JJ	_	_	_
18	collection	collection	NN	_	_	_
19	tube	tube	NN	_	_	_
20	.	.	.	_	_	_

1	Buffer	buffer	NN	_	_	_
2	RW1	rw1	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	700	700	CD	_	_	_
5	µl	µl	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	applied	apply	VBN	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	column	column	NN	_	_	_
12	,	,	,	_	_	_
13	centrifuged	centrifuge	VBN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	flow-through	flow-through	JJ	_	_	_
17	was	be	VBD	_	_	_
18	discarded	discard	VBN	_	_	_
19	as	as	IN	_	_	_
20	described	describe	VBN	_	_	_
21	previously	previously	RB	_	_	_
22	.	.	.	_	_	_

1	Twice	twice	RB	_	_	_
2	,	,	,	_	_	_
3	500	500	CD	_	_	_
4	µl	µl	NN	_	_	_
5	of	of	IN	_	_	_
6	buffer	buffer	NN	_	_	_
7	RPE	rpe	NN	_	_	_
8	was	be	VBD	_	_	_
9	applied	apply	VBN	_	_	_
10	to	to	TO	_	_	_
11	the	the	DT	_	_	_
12	spin	spin	NN	_	_	_
13	column	column	NN	_	_	_
14	allowing	allow	VBG	_	_	_
15	5	5	CD	_	_	_
16	min	min	NN	_	_	_
17	prior	prior	RB	_	_	_
18	to	to	TO	_	_	_
19	centrifugation	centrifugation	NN	_	_	_
20	at	at	IN	_	_	_
21	8000	8000	CD	_	_	_
22	x	x	CC	_	_	_
23	g	g	NN	_	_	_
24	for	for	IN	_	_	_
25	15	15	CD	_	_	_
26	sec	sec	NN	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	spin	spin	NN	_	_	_
3	column	column	NN	_	_	_
4	was	be	VBD	_	_	_
5	placed	place	VBN	_	_	_
6	in	in	IN	_	_	_
7	a	a	DT	_	_	_
8	1.5	1.5	CD	_	_	_
9	ml	ml	NN	_	_	_
10	collection	collection	NN	_	_	_
11	tube	tube	NN	_	_	_
12	that	that	WDT	_	_	_
13	was	be	VBD	_	_	_
14	used	use	VBN	_	_	_
15	for	for	IN	_	_	_
16	long-term	long-term	JJ	_	_	_
17	storage	storage	NN	_	_	_
18	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	order	order	NN	_	_	_
3	to	to	TO	_	_	_
4	elute	elute	VB	_	_	_
5	RNA	rna	NN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	spin	spin	NN	_	_	_
9	column	column	NN	_	_	_
10	,	,	,	_	_	_
11	30	30	CD	_	_	_
12	µl	µl	NN	_	_	_
13	RNase-free	rnase-free	NN	_	_	_
14	water	water	NN	_	_	_
15	was	be	VBD	_	_	_
16	applied	apply	VBN	_	_	_
17	directly	directly	RB	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	membrane	membrane	NN	_	_	_
21	and	and	CC	_	_	_
22	centrifuged	centrifuge	VBN	_	_	_
23	at	at	IN	_	_	_
24	8000	8000	CD	_	_	_
25	x	x	CC	_	_	_
26	g	g	NN	_	_	_
27	for	for	IN	_	_	_
28	15	15	CD	_	_	_
29	sec	sec	NN	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	eluate	eluate	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	evaluated	evaluate	VBN	_	_	_
11	for	for	IN	_	_	_
12	quantity	quantity	NN	_	_	_
13	,	,	,	_	_	_
14	quality	quality	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	purity	purity	NN	_	_	_
18	.	.	.	_	_	_

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	NNP	_	_	_
2	One	one	CD	_	_	_
3	volume	volume	NN	_	_	_
4	of	of	IN	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	added	add	VBN	_	_	_
9	to	to	TO	_	_	_
10	two	two	CD	_	_	_
11	volumes	volume	NNS	_	_	_
12	of	of	IN	_	_	_
13	RNAprotect	rnaprotect	NN	_	_	_
14	Bacteria	bacterium	NNS	_	_	_
15	Reagent	reagent	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	qiagen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	RNA	rna	NN	_	_	_
21	was	be	VBD	_	_	_
22	extracted	extract	VBN	_	_	_
23	using	use	VBG	_	_	_
24	RNeasy	RNeasy	NNP	_	_	_
25	mini	minus	NNS	_	_	_
26	kit	kit	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Qiagen	qiagen	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

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	NNP	_	_	_
10	Only	only	RB	_	_	_
11	ideal	ideal	JJ	_	_	_
12	correspondence	correspondence	NN	_	_	_
13	of	of	IN	_	_	_
14	sequence	sequence	NN	_	_	_
15	reads	read	VBZ	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	genome	genome	NN	_	_	_
19	in	in	IN	_	_	_
20	both	both	DT	_	_	_
21	cases	case	NNS	_	_	_
22	was	be	VBD	_	_	_
23	permitted	permit	VBN	_	_	_
24	.	.	.	_	_	_

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	NN	_	_	_
2	optA1	opta1	NN	_	_	_
3	_	_	NN	_	_	_
4	0	0	CD	_	_	_
5	_	_	NN	_	_	_
6	Hx	hx	NN	_	_	_
7	Rep1	rep1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	optA1	opta1	NN	_	_	_
10	_	_	NN	_	_	_
11	0	0	CD	_	_	_
12	_	_	SYM	_	_	_
13	Hx	hx	FW	_	_	_
14	Rep2	rep2	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	optA1	opta1	NN	_	_	_
17	_	_	NN	_	_	_
18	0	0	CD	_	_	_
19	_	_	SYM	_	_	_
20	Hx	hx	FW	_	_	_
21	Rep3	rep3	JJ	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	optA1	opta1	NN	_	_	_
24	_	_	NN	_	_	_
25	120	120	CD	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Low	low	JJ	_	_	_
28	Dilution	dilution	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	Rep1	rep1	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	optA1	opta1	NN	_	_	_
33	_	_	NN	_	_	_
34	120	120	CD	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Low	low	JJ	_	_	_
37	Dilution	dilution	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	Rep2	rep2	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	optA1	opta1	NN	_	_	_
42	_	_	NN	_	_	_
43	120	120	CD	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Low	low	JJ	_	_	_
46	Dilution	dilution	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	Rep3	rep3	JJ	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	optA1	opta1	NN	_	_	_
51	_	_	CD	_	_	_
52	15	15	CD	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	Low	low	JJ	_	_	_
55	Dilution	dilution	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	Rep1	rep1	JJ	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	optA1	opta1	NN	_	_	_
60	_	_	CD	_	_	_
61	15	15	CD	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Low	low	JJ	_	_	_
64	Dilution	dilution	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	Rep2	rep2	JJ	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	optA1	opta1	NN	_	_	_
69	_	_	CD	_	_	_
70	15	15	CD	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	Low	low	JJ	_	_	_
73	Dilution	dilution	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	Rep3	rep3	JJ	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	optA1	opta1	NN	_	_	_
78	_	_	CD	_	_	_
79	30	30	CD	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	Low	low	JJ	_	_	_
82	Dilution	dilution	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	Rep1	rep1	JJ	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	optA1	opta1	NN	_	_	_
87	_	_	CD	_	_	_
88	30	30	CD	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	Low	low	JJ	_	_	_
91	Dilution	dilution	NN	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	Rep2	rep2	JJ	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	optA1	opta1	NN	_	_	_
96	_	_	CD	_	_	_
97	30	30	CD	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	Low	low	JJ	_	_	_
100	Dilution	dilution	NN	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	Rep3	rep3	JJ	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	optA1	opta1	NN	_	_	_
105	_	_	CD	_	_	_
106	45	45	CD	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	Low	low	JJ	_	_	_
109	Dilution	dilution	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	Rep1	rep1	JJ	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	optA1	opta1	NN	_	_	_
114	_	_	CD	_	_	_
115	45	45	CD	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	Low	low	JJ	_	_	_
118	Dilution	dilution	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	Rep2	rep2	JJ	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	optA1	opta1	NN	_	_	_
123	_	_	CD	_	_	_
124	45	45	CD	_	_	_
125	-LRB-	-lrb-	-LRB-	_	_	_
126	Low	low	JJ	_	_	_
127	Dilution	dilution	NN	_	_	_
128	-RRB-	-rrb-	-RRB-	_	_	_
129	Rep3	rep3	JJ	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	optA1	opta1	NN	_	_	_
132	_	_	CD	_	_	_
133	60	60	CD	_	_	_
134	-LRB-	-lrb-	-LRB-	_	_	_
135	Low	low	JJ	_	_	_
136	Dilution	dilution	NN	_	_	_
137	-RRB-	-rrb-	-RRB-	_	_	_
138	Rep1	rep1	JJ	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	optA1	opta1	NN	_	_	_
141	_	_	CD	_	_	_
142	60	60	CD	_	_	_
143	-LRB-	-lrb-	-LRB-	_	_	_
144	Low	low	JJ	_	_	_
145	Dilution	dilution	NN	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	Rep2	rep2	JJ	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	optA1	opta1	NN	_	_	_
150	_	_	CD	_	_	_
151	60	60	CD	_	_	_
152	-LRB-	-lrb-	-LRB-	_	_	_
153	Low	low	JJ	_	_	_
154	Dilution	dilution	NN	_	_	_
155	-RRB-	-rrb-	-RRB-	_	_	_
156	Rep3	rep3	JJ	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	optA1	opta1	NN	_	_	_
159	_	_	CD	_	_	_
160	gpt	gpt	NN	GEN	_	_
161	_	_	NN	_	_	_
162	0	0	CD	_	_	_
163	_	_	NN	_	_	_
164	Hx	hx	NN	_	_	_
165	Rep1	rep1	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	optA1	opta1	NN	_	_	_
168	_	_	CD	_	_	_
169	gpt	gpt	NN	GEN	_	_
170	_	_	NN	_	_	_
171	0	0	CD	_	_	_
172	_	_	SYM	_	_	_
173	Hx	hx	FW	_	_	_
174	Rep2	rep2	JJ	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	optA1	opta1	NN	_	_	_
177	_	_	CD	_	_	_
178	gpt	gpt	NN	GEN	_	_
179	_	_	NN	_	_	_
180	0	0	CD	_	_	_
181	_	_	SYM	_	_	_
182	Hx	hx	FW	_	_	_
183	Rep3	rep3	JJ	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	optA1	opta1	NN	_	_	_
186	_	_	CD	_	_	_
187	gpt	gpt	NN	GEN	_	_
188	_	_	NN	_	_	_
189	120	120	CD	_	_	_
190	-LRB-	-lrb-	-LRB-	_	_	_
191	High	high	JJ	_	_	_
192	Dilution	dilution	NN	_	_	_
193	-RRB-	-rrb-	-RRB-	_	_	_
194	Rep1	rep1	JJ	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	optA1	opta1	NN	_	_	_
197	_	_	CD	_	_	_
198	gpt	gpt	NN	GEN	_	_
199	_	_	NN	_	_	_
200	120	120	CD	_	_	_
201	-LRB-	-lrb-	-LRB-	_	_	_
202	High	high	JJ	_	_	_
203	Dilution	dilution	NN	_	_	_
204	-RRB-	-rrb-	-RRB-	_	_	_
205	Rep2	rep2	JJ	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	optA1	opta1	NN	_	_	_
208	_	_	CD	_	_	_
209	gpt	gpt	NN	GEN	_	_
210	_	_	NN	_	_	_
211	120	120	CD	_	_	_
212	-LRB-	-lrb-	-LRB-	_	_	_
213	High	high	JJ	_	_	_
214	Dilution	dilution	NN	_	_	_
215	-RRB-	-rrb-	-RRB-	_	_	_
216	Rep3	rep3	JJ	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	optA1	opta1	NN	_	_	_
219	_	_	CD	_	_	_
220	gpt	gpt	NN	GEN	_	_
221	_	_	NN	_	_	_
222	120	120	CD	_	_	_
223	-LRB-	-lrb-	-LRB-	_	_	_
224	Low	low	JJ	_	_	_
225	Dilution	dilution	NN	_	_	_
226	-RRB-	-rrb-	-RRB-	_	_	_
227	Rep1	rep1	JJ	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	optA1	opta1	NN	_	_	_
230	_	_	CD	_	_	_
231	gpt	gpt	NN	GEN	_	_
232	_	_	NN	_	_	_
233	120	120	CD	_	_	_
234	-LRB-	-lrb-	-LRB-	_	_	_
235	Low	low	JJ	_	_	_
236	Dilution	dilution	NN	_	_	_
237	-RRB-	-rrb-	-RRB-	_	_	_
238	Rep2	rep2	JJ	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	optA1	opta1	NN	_	_	_
241	_	_	CD	_	_	_
242	gpt	gpt	NN	GEN	_	_
243	_	_	NN	_	_	_
244	120	120	CD	_	_	_
245	-LRB-	-lrb-	-LRB-	_	_	_
246	Low	low	JJ	_	_	_
247	Dilution	dilution	NN	_	_	_
248	-RRB-	-rrb-	-RRB-	_	_	_
249	Rep3	rep3	JJ	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	optA1	opta1	NN	_	_	_
252	_	_	SYM	_	_	_
253	gpt	gpt	FW	GEN	_	_
254	_	_	FW	_	_	_
255	15	15	CD	_	_	_
256	-LRB-	-lrb-	-LRB-	_	_	_
257	Low	low	JJ	_	_	_
258	Dilution	dilution	NN	_	_	_
259	-RRB-	-rrb-	-RRB-	_	_	_
260	Rep1	rep1	JJ	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	optA1	opta1	NN	_	_	_
263	_	_	SYM	_	_	_
264	gpt	gpt	FW	GEN	_	_
265	_	_	FW	_	_	_
266	15	15	CD	_	_	_
267	-LRB-	-lrb-	-LRB-	_	_	_
268	Low	low	JJ	_	_	_
269	Dilution	dilution	NN	_	_	_
270	-RRB-	-rrb-	-RRB-	_	_	_
271	Rep2	rep2	JJ	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	optA1	opta1	NN	_	_	_
274	_	_	SYM	_	_	_
275	gpt	gpt	FW	GEN	_	_
276	_	_	FW	_	_	_
277	15	15	CD	_	_	_
278	-LRB-	-lrb-	-LRB-	_	_	_
279	Low	low	JJ	_	_	_
280	Dilution	dilution	NN	_	_	_
281	-RRB-	-rrb-	-RRB-	_	_	_
282	Rep3	rep3	JJ	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	optA1	opta1	NN	_	_	_
285	_	_	CD	_	_	_
286	gpt	gpt	NN	GEN	_	_
287	_	_	NN	_	_	_
288	180	180	CD	_	_	_
289	-LRB-	-lrb-	-LRB-	_	_	_
290	High	high	JJ	_	_	_
291	Dilution	dilution	NN	_	_	_
292	-RRB-	-rrb-	-RRB-	_	_	_
293	Rep1	rep1	JJ	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	optA1	opta1	NN	_	_	_
296	_	_	CD	_	_	_
297	gpt	gpt	NN	GEN	_	_
298	_	_	NN	_	_	_
299	180	180	CD	_	_	_
300	-LRB-	-lrb-	-LRB-	_	_	_
301	High	high	JJ	_	_	_
302	Dilution	dilution	NN	_	_	_
303	-RRB-	-rrb-	-RRB-	_	_	_
304	Rep2	rep2	JJ	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	optA1	opta1	NN	_	_	_
307	_	_	CD	_	_	_
308	gpt	gpt	NN	GEN	_	_
309	_	_	NN	_	_	_
310	180	180	CD	_	_	_
311	-LRB-	-lrb-	-LRB-	_	_	_
312	High	high	JJ	_	_	_
313	Dilution	dilution	NN	_	_	_
314	-RRB-	-rrb-	-RRB-	_	_	_
315	Rep3	rep3	JJ	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	optA1	opta1	NN	_	_	_
318	_	_	CD	_	_	_
319	gpt	gpt	NN	GEN	_	_
320	_	_	NN	_	_	_
321	240	240	CD	_	_	_
322	-LRB-	-lrb-	-LRB-	_	_	_
323	High	high	JJ	_	_	_
324	Dilution	dilution	NN	_	_	_
325	-RRB-	-rrb-	-RRB-	_	_	_
326	Rep1	rep1	JJ	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	optA1	opta1	NN	_	_	_
329	_	_	CD	_	_	_
330	gpt	gpt	NN	GEN	_	_
331	_	_	NN	_	_	_
332	240	240	CD	_	_	_
333	-LRB-	-lrb-	-LRB-	_	_	_
334	High	high	JJ	_	_	_
335	Dilution	dilution	NN	_	_	_
336	-RRB-	-rrb-	-RRB-	_	_	_
337	Rep2	rep2	JJ	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	optA1	opta1	NN	_	_	_
340	_	_	CD	_	_	_
341	gpt	gpt	NN	GEN	_	_
342	_	_	NN	_	_	_
343	240	240	CD	_	_	_
344	-LRB-	-lrb-	-LRB-	_	_	_
345	High	high	JJ	_	_	_
346	Dilution	dilution	NN	_	_	_
347	-RRB-	-rrb-	-RRB-	_	_	_
348	Rep3	rep3	JJ	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	optA1	opta1	NN	_	_	_
351	_	_	CD	_	_	_
352	gpt	gpt	NN	GEN	_	_
353	_	_	NN	_	_	_
354	300	300	CD	_	_	_
355	-LRB-	-lrb-	-LRB-	_	_	_
356	High	high	JJ	_	_	_
357	Dilution	dilution	NN	_	_	_
358	-RRB-	-rrb-	-RRB-	_	_	_
359	Rep1	rep1	JJ	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	optA1	opta1	NN	_	_	_
362	_	_	CD	_	_	_
363	gpt	gpt	NN	GEN	_	_
364	_	_	NN	_	_	_
365	300	300	CD	_	_	_
366	-LRB-	-lrb-	-LRB-	_	_	_
367	High	high	JJ	_	_	_
368	Dilution	dilution	NN	_	_	_
369	-RRB-	-rrb-	-RRB-	_	_	_
370	Rep2	rep2	JJ	_	_	_
371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
372	optA1	opta1	NN	_	_	_
373	_	_	CD	_	_	_
374	gpt	gpt	NN	GEN	_	_
375	_	_	NN	_	_	_
376	300	300	CD	_	_	_
377	-LRB-	-lrb-	-LRB-	_	_	_
378	High	high	JJ	_	_	_
379	Dilution	dilution	NN	_	_	_
380	-RRB-	-rrb-	-RRB-	_	_	_
381	Rep3	rep3	JJ	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	optA1	opta1	NN	_	_	_
384	_	_	SYM	_	_	_
385	gpt	gpt	FW	GEN	_	_
386	_	_	FW	_	_	_
387	30	30	CD	_	_	_
388	-LRB-	-lrb-	-LRB-	_	_	_
389	Low	low	JJ	_	_	_
390	Dilution	dilution	NN	_	_	_
391	-RRB-	-rrb-	-RRB-	_	_	_
392	Rep1	rep1	JJ	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	optA1	opta1	NN	_	_	_
395	_	_	SYM	_	_	_
396	gpt	gpt	FW	GEN	_	_
397	_	_	FW	_	_	_
398	30	30	CD	_	_	_
399	-LRB-	-lrb-	-LRB-	_	_	_
400	Low	low	JJ	_	_	_
401	Dilution	dilution	NN	_	_	_
402	-RRB-	-rrb-	-RRB-	_	_	_
403	Rep2	rep2	JJ	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
405	optA1	opta1	NN	_	_	_
406	_	_	SYM	_	_	_
407	gpt	gpt	FW	GEN	_	_
408	_	_	FW	_	_	_
409	30	30	CD	_	_	_
410	-LRB-	-lrb-	-LRB-	_	_	_
411	Low	low	JJ	_	_	_
412	Dilution	dilution	NN	_	_	_
413	-RRB-	-rrb-	-RRB-	_	_	_
414	Rep3	rep3	JJ	_	_	_
415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
416	optA1	opta1	NN	_	_	_
417	_	_	CD	_	_	_
418	gpt	gpt	NN	GEN	_	_
419	_	_	NN	_	_	_
420	360	360	CD	_	_	_
421	-LRB-	-lrb-	-LRB-	_	_	_
422	High	high	JJ	_	_	_
423	Dilution	dilution	NN	_	_	_
424	-RRB-	-rrb-	-RRB-	_	_	_
425	Rep1	rep1	JJ	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	optA1	opta1	NN	_	_	_
428	_	_	CD	_	_	_
429	gpt	gpt	NN	GEN	_	_
430	_	_	NN	_	_	_
431	360	360	CD	_	_	_
432	-LRB-	-lrb-	-LRB-	_	_	_
433	High	high	JJ	_	_	_
434	Dilution	dilution	NN	_	_	_
435	-RRB-	-rrb-	-RRB-	_	_	_
436	Rep2	rep2	JJ	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	optA1	opta1	NN	_	_	_
439	_	_	CD	_	_	_
440	gpt	gpt	NN	GEN	_	_
441	_	_	NN	_	_	_
442	360	360	CD	_	_	_
443	-LRB-	-lrb-	-LRB-	_	_	_
444	High	high	JJ	_	_	_
445	Dilution	dilution	NN	_	_	_
446	-RRB-	-rrb-	-RRB-	_	_	_
447	Rep3	rep3	JJ	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	optA1	opta1	NN	_	_	_
450	_	_	CD	_	_	_
451	gpt	gpt	NN	GEN	_	_
452	_	_	NN	_	_	_
453	360	360	CD	_	_	_
454	-LRB-	-lrb-	-LRB-	_	_	_
455	Low	low	JJ	_	_	_
456	Dilution	dilution	NN	_	_	_
457	-RRB-	-rrb-	-RRB-	_	_	_
458	Rep1	rep1	JJ	_	_	_
459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
460	optA1	opta1	NN	_	_	_
461	_	_	CD	_	_	_
462	gpt	gpt	NN	GEN	_	_
463	_	_	NN	_	_	_
464	360	360	CD	_	_	_
465	-LRB-	-lrb-	-LRB-	_	_	_
466	Low	low	JJ	_	_	_
467	Dilution	dilution	NN	_	_	_
468	-RRB-	-rrb-	-RRB-	_	_	_
469	Rep2	rep2	JJ	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	optA1	opta1	NN	_	_	_
472	_	_	CD	_	_	_
473	gpt	gpt	NN	GEN	_	_
474	_	_	NN	_	_	_
475	360	360	CD	_	_	_
476	-LRB-	-lrb-	-LRB-	_	_	_
477	Low	low	JJ	_	_	_
478	Dilution	dilution	NN	_	_	_
479	-RRB-	-rrb-	-RRB-	_	_	_
480	Rep3	rep3	JJ	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	optA1	opta1	NN	_	_	_
483	_	_	SYM	_	_	_
484	gpt	gpt	FW	GEN	_	_
485	_	_	FW	_	_	_
486	45	45	CD	_	_	_
487	-LRB-	-lrb-	-LRB-	_	_	_
488	Low	low	JJ	_	_	_
489	Dilution	dilution	NN	_	_	_
490	-RRB-	-rrb-	-RRB-	_	_	_
491	Rep1	rep1	JJ	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
493	optA1	opta1	NN	_	_	_
494	_	_	SYM	_	_	_
495	gpt	gpt	FW	GEN	_	_
496	_	_	FW	_	_	_
497	45	45	CD	_	_	_
498	-LRB-	-lrb-	-LRB-	_	_	_
499	Low	low	JJ	_	_	_
500	Dilution	dilution	NN	_	_	_
501	-RRB-	-rrb-	-RRB-	_	_	_
502	Rep2	rep2	JJ	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	optA1	opta1	NN	_	_	_
505	_	_	SYM	_	_	_
506	gpt	gpt	FW	GEN	_	_
507	_	_	FW	_	_	_
508	45	45	CD	_	_	_
509	-LRB-	-lrb-	-LRB-	_	_	_
510	Low	low	JJ	_	_	_
511	Dilution	dilution	NN	_	_	_
512	-RRB-	-rrb-	-RRB-	_	_	_
513	Rep3	rep3	JJ	_	_	_
514	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
515	optA1	opta1	NN	_	_	_
516	_	_	SYM	_	_	_
517	gpt	gpt	FW	GEN	_	_
518	_	_	FW	_	_	_
519	60	60	CD	_	_	_
520	-LRB-	-lrb-	-LRB-	_	_	_
521	Low	low	JJ	_	_	_
522	Dilution	dilution	NN	_	_	_
523	-RRB-	-rrb-	-RRB-	_	_	_
524	Rep1	rep1	JJ	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	optA1	opta1	NN	_	_	_
527	_	_	SYM	_	_	_
528	gpt	gpt	FW	GEN	_	_
529	_	_	FW	_	_	_
530	60	60	CD	_	_	_
531	-LRB-	-lrb-	-LRB-	_	_	_
532	Low	low	JJ	_	_	_
533	Dilution	dilution	NN	_	_	_
534	-RRB-	-rrb-	-RRB-	_	_	_
535	Rep2	rep2	JJ	_	_	_
536	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
537	optA1	opta1	NN	_	_	_
538	_	_	SYM	_	_	_
539	gpt	gpt	FW	GEN	_	_
540	_	_	FW	_	_	_
541	60	60	CD	_	_	_
542	-LRB-	-lrb-	-LRB-	_	_	_
543	Low	low	JJ	_	_	_
544	Dilution	dilution	NN	_	_	_
545	-RRB-	-rrb-	-RRB-	_	_	_
546	Rep3	rep3	JJ	_	_	_
547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
548	optA1	opta1	NN	_	_	_
549	gpt	gpt	NN	GEN	_	_
550	strain	strain	NN	_	_	_
551	with	with	IN	_	_	_
552	hypoxanthine	hypoxanthine	NN	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	optA1	opta1	NN	_	_	_
555	gpt	gpt	NN	GEN	_	_
556	strain	strain	NN	_	_	_
557	w/o	w/o	NN	_	_	_
558	hypoxanthine	hypoxanthine	NN	_	_	_
559	120	120	CD	_	_	_
560	min	min	NN	_	_	_
561	at	at	IN	_	_	_
562	high	high	JJ	_	_	_
563	dilution	dilution	NN	_	_	_
564	protocol	protocol	NN	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	optA1	opta1	NN	_	_	_
567	gpt	gpt	NN	GEN	_	_
568	strain	strain	NN	_	_	_
569	w/o	w/o	NN	_	_	_
570	hypoxanthine	hypoxanthine	NN	_	_	_
571	120	120	CD	_	_	_
572	min	min	NN	_	_	_
573	at	at	IN	_	_	_
574	low	low	JJ	_	_	_
575	dilution	dilution	NN	_	_	_
576	protocol	protocol	NN	_	_	_
577	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
578	optA1	opta1	NN	_	_	_
579	gpt	gpt	NN	GEN	_	_
580	strain	strain	NN	_	_	_
581	w/o	w/o	NN	_	_	_
582	hypoxanthine	hypoxanthine	NN	_	_	_
583	15	15	CD	_	_	_
584	min	min	NN	_	_	_
585	at	at	IN	_	_	_
586	low	low	JJ	_	_	_
587	dilution	dilution	NN	_	_	_
588	protocol	protocol	NN	_	_	_
589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
590	optA1	opta1	NN	_	_	_
591	gpt	gpt	NN	GEN	_	_
592	strain	strain	NN	_	_	_
593	w/o	w/o	NN	_	_	_
594	hypoxanthine	hypoxanthine	NN	_	_	_
595	180	180	CD	_	_	_
596	min	min	NN	_	_	_
597	at	at	IN	_	_	_
598	high	high	JJ	_	_	_
599	dilution	dilution	NN	_	_	_
600	protocol	protocol	NN	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	optA1	opta1	NN	_	_	_
603	gpt	gpt	NN	GEN	_	_
604	strain	strain	NN	_	_	_
605	w/o	w/o	NN	_	_	_
606	hypoxanthine	hypoxanthine	NN	_	_	_
607	240	240	CD	_	_	_
608	min	min	NN	_	_	_
609	at	at	IN	_	_	_
610	high	high	JJ	_	_	_
611	dilution	dilution	NN	_	_	_
612	protocol	protocol	NN	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	optA1	opta1	NN	_	_	_
615	gpt	gpt	NN	GEN	_	_
616	strain	strain	NN	_	_	_
617	w/o	w/o	NN	_	_	_
618	hypoxanthine	hypoxanthine	NN	_	_	_
619	300	300	CD	_	_	_
620	min	min	NN	_	_	_
621	at	at	IN	_	_	_
622	high	high	JJ	_	_	_
623	dilution	dilution	NN	_	_	_
624	protocol	protocol	NN	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	optA1	opta1	NN	_	_	_
627	gpt	gpt	NN	GEN	_	_
628	strain	strain	NN	_	_	_
629	w/o	w/o	NN	_	_	_
630	hypoxanthine	hypoxanthine	NN	_	_	_
631	30	30	CD	_	_	_
632	min	min	NN	_	_	_
633	at	at	IN	_	_	_
634	low	low	JJ	_	_	_
635	dilution	dilution	NN	_	_	_
636	protocol	protocol	NN	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
638	optA1	opta1	NN	_	_	_
639	gpt	gpt	NN	GEN	_	_
640	strain	strain	NN	_	_	_
641	w/o	w/o	NN	_	_	_
642	hypoxanthine	hypoxanthine	NN	_	_	_
643	360	360	CD	_	_	_
644	min	min	NN	_	_	_
645	at	at	IN	_	_	_
646	high	high	JJ	_	_	_
647	dilution	dilution	NN	_	_	_
648	protocol	protocol	NN	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	optA1	opta1	NN	_	_	_
651	gpt	gpt	NN	GEN	_	_
652	strain	strain	NN	_	_	_
653	w/o	w/o	NN	_	_	_
654	hypoxanthine	hypoxanthine	NN	_	_	_
655	360	360	CD	_	_	_
656	min	min	NN	_	_	_
657	at	at	IN	_	_	_
658	low	low	JJ	_	_	_
659	dilution	dilution	NN	_	_	_
660	protocol	protocol	NN	_	_	_
661	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
662	optA1	opta1	NN	_	_	_
663	gpt	gpt	NN	GEN	_	_
664	strain	strain	NN	_	_	_
665	w/o	w/o	NN	_	_	_
666	hypoxanthine	hypoxanthine	NN	_	_	_
667	45	45	CD	_	_	_
668	min	min	NN	_	_	_
669	at	at	IN	_	_	_
670	low	low	JJ	_	_	_
671	dilution	dilution	NN	_	_	_
672	protocol	protocol	NN	_	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
674	optA1	opta1	NN	_	_	_
675	gpt	gpt	NN	GEN	_	_
676	strain	strain	NN	_	_	_
677	w/o	w/o	NN	_	_	_
678	hypoxanthine	hypoxanthine	NN	_	_	_
679	60	60	CD	_	_	_
680	min	min	NN	_	_	_
681	at	at	IN	_	_	_
682	low	low	JJ	_	_	_
683	dilution	dilution	NN	_	_	_
684	protocol	protocol	NN	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
686	optA1	opta1	NN	_	_	_
687	strain	strain	NN	_	_	_
688	with	with	IN	_	_	_
689	hypoxanthine	hypoxanthine	NN	_	_	_
690	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
691	optA1	opta1	NN	_	_	_
692	strain	strain	NN	_	_	_
693	w/o	w/o	NN	_	_	_
694	hypoxanthine	hypoxanthine	NN	_	_	_
695	120	120	CD	_	_	_
696	min	min	NN	_	_	_
697	at	at	IN	_	_	_
698	low	low	JJ	_	_	_
699	dilution	dilution	NN	_	_	_
700	protocol	protocol	NN	_	_	_
701	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
702	optA1	opta1	NN	_	_	_
703	strain	strain	NN	_	_	_
704	w/o	w/o	NN	_	_	_
705	hypoxanthine	hypoxanthine	NN	_	_	_
706	15	15	CD	_	_	_
707	min	min	NN	_	_	_
708	at	at	IN	_	_	_
709	low	low	JJ	_	_	_
710	dilution	dilution	NN	_	_	_
711	protocol	protocol	NN	_	_	_
712	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
713	optA1	opta1	NN	_	_	_
714	strain	strain	NN	_	_	_
715	w/o	w/o	NN	_	_	_
716	hypoxanthine	hypoxanthine	NN	_	_	_
717	30	30	CD	_	_	_
718	min	min	NN	_	_	_
719	at	at	IN	_	_	_
720	low	low	JJ	_	_	_
721	dilution	dilution	NN	_	_	_
722	protocol	protocol	NN	_	_	_
723	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
724	optA1	opta1	NN	_	_	_
725	strain	strain	NN	_	_	_
726	w/o	w/o	NN	_	_	_
727	hypoxanthine	hypoxanthine	NN	_	_	_
728	45	45	CD	_	_	_
729	min	min	NN	_	_	_
730	at	at	IN	_	_	_
731	low	low	JJ	_	_	_
732	dilution	dilution	NN	_	_	_
733	protocol	protocol	NN	_	_	_
734	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
735	optA1	opta1	NN	_	_	_
736	strain	strain	NN	_	_	_
737	w/o	w/o	NN	_	_	_
738	hypoxanthine	hypoxanthine	NN	_	_	_
739	60	60	CD	_	_	_
740	min	min	NN	_	_	_
741	at	at	IN	_	_	_
742	low	low	JJ	_	_	_
743	dilution	dilution	NN	_	_	_
744	protocol	protocol	NN	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
746	ORF1	orf1	NN	_	_	_
747	_	_	NN	_	_	_
748	1	1	CD	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
750	ORF1	orf1	NN	_	_	_
751	_	_	NN	_	_	_
752	1	1	CD	_	_	_
753	_	_	CD	_	_	_
754	IPTG	iptg	NN	_	_	_
755	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
756	ORF1	orf1	NN	_	_	_
757	_	_	NN	_	_	_
758	2	2	CD	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
760	ORF1	orf1	NN	_	_	_
761	_	_	NN	_	_	_
762	2	2	CD	_	_	_
763	_	_	CD	_	_	_
764	IPTG	iptg	NN	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
766	Original	original	JJ	_	_	_
767	prototroph	prototroph	NN	_	_	_
768	DH1	dh1	NN	_	_	_
769	cells	cell	NNS	_	_	_
770	at	at	IN	_	_	_
771	log	log	NN	_	_	_
772	phase	phase	NN	_	_	_
773	in	in	IN	_	_	_
774	monoculture	monoculture	NN	_	_	_
775	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
776	Original	original	JJ	_	_	_
777	prototroph	prototroph	NN	_	_	_
778	DH1	dh1	NN	_	_	_
779	cells	cell	NNS	_	_	_
780	at	at	IN	_	_	_
781	log	log	NN	_	_	_
782	phase	phase	NN	_	_	_
783	in	in	IN	_	_	_
784	monoculture	monoculture	NN	_	_	_
785	,	,	,	_	_	_
786	a	a	DT	_	_	_
787	technical	technical	JJ	_	_	_
788	replicate	replicate	VBP	_	_	_
789	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
790	originate	originate	VB	_	_	_
791	during	during	IN	_	_	_
792	array	array	NN	_	_	_
793	printing	printing	NN	_	_	_
794	,	,	,	_	_	_
795	as	as	RB	_	_	_
796	well	well	RB	_	_	_
797	as	as	IN	_	_	_
798	during	during	IN	_	_	_
799	the	the	DT	_	_	_
800	collection	collection	NN	_	_	_
801	and	and	CC	_	_	_
802	processing	processing	NN	_	_	_
803	of	of	IN	_	_	_
804	samples	sample	NNS	_	_	_
805	,	,	,	_	_	_
806	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
807	origin	origin	NN	_	_	_
808	of	of	IN	_	_	_
809	isolation	isolation	NN	_	_	_
810	:	:	:	_	_	_
811	patient	patient	NN	_	_	_
812	with	with	IN	_	_	_
813	hemolytic	hemolytic	JJ	_	_	_
814	uremic	uremic	JJ	_	_	_
815	syndrome	syndrome	NN	_	_	_
816	-LRB-	-lrb-	-LRB-	_	_	_
817	HUS	hus	NN	_	_	_
818	-RRB-	-rrb-	-RRB-	_	_	_
819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
820	OSU11	osu11	NN	_	_	_
821	,	,	,	_	_	_
822	histidine	histidine	NN	_	_	_
823	depleted	deplete	VBN	_	_	_
824	,	,	,	_	_	_
825	>	>	JJR	_	_	_
826	10	10	CD	_	_	_
827	hrs	hr	NNS	_	_	_
828	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
829	OSU11	osu11	NN	_	_	_
830	,	,	,	_	_	_
831	histidine	histidine	NN	_	_	_
832	depleted	deplete	VBN	_	_	_
833	,	,	,	_	_	_
834	>	>	JJR	_	_	_
835	10	10	CD	_	_	_
836	hrs	hr	NNS	_	_	_
837	,	,	,	_	_	_
838	rep	rep	NN	GEN	_	_
839	1	1	CD	_	_	_
840	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
841	OSU11	osu11	NN	_	_	_
842	,	,	,	_	_	_
843	histidine	histidine	NN	_	_	_
844	depleted	deplete	VBN	_	_	_
845	,	,	,	_	_	_
846	>	>	JJR	_	_	_
847	10	10	CD	_	_	_
848	hrs	hr	NNS	_	_	_
849	,	,	,	_	_	_
850	rep	rep	NN	GEN	_	_
851	2	2	CD	_	_	_
852	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
853	OSU11	osu11	NN	_	_	_
854	,	,	,	_	_	_
855	histidine	histidine	NN	_	_	_
856	depleted	deplete	VBN	_	_	_
857	,	,	,	_	_	_
858	>	>	JJR	_	_	_
859	10	10	CD	_	_	_
860	hrs	hr	NNS	_	_	_
861	,	,	,	_	_	_
862	rep	rep	NN	GEN	_	_
863	3	3	CD	_	_	_
864	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
865	OSU11	osu11	NN	_	_	_
866	,	,	,	_	_	_
867	histidine	histidine	NN	_	_	_
868	depleted	deplete	VBN	_	_	_
869	,	,	,	_	_	_
870	10	10	CD	_	_	_
871	min	min	NN	_	_	_
872	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
873	OSU11	osu11	NN	_	_	_
874	,	,	,	_	_	_
875	histidine	histidine	NN	_	_	_
876	depleted	deplete	VBN	_	_	_
877	,	,	,	_	_	_
878	10	10	CD	_	_	_
879	min	min	NN	_	_	_
880	,	,	,	_	_	_
881	rep	rep	NN	GEN	_	_
882	1	1	CD	_	_	_
883	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
884	OSU11	osu11	NN	_	_	_
885	,	,	,	_	_	_
886	histidine	histidine	NN	_	_	_
887	depleted	deplete	VBN	_	_	_
888	,	,	,	_	_	_
889	10	10	CD	_	_	_
890	min	min	NN	_	_	_
891	,	,	,	_	_	_
892	rep	rep	NN	GEN	_	_
893	2	2	CD	_	_	_
894	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
895	OSU11	osu11	NN	_	_	_
896	,	,	,	_	_	_
897	histidine	histidine	NN	_	_	_
898	depleted	deplete	VBN	_	_	_
899	,	,	,	_	_	_
900	10	10	CD	_	_	_
901	min	min	NN	_	_	_
902	,	,	,	_	_	_
903	rep	rep	NN	GEN	_	_
904	3	3	CD	_	_	_
905	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
906	OSU11	osu11	NN	_	_	_
907	,	,	,	_	_	_
908	histidine	histidine	NN	_	_	_
909	depleted	deplete	VBN	_	_	_
910	,	,	,	_	_	_
911	2	2	CD	_	_	_
912	hrs	hr	NNS	_	_	_
913	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
914	OSU11	osu11	NN	_	_	_
915	,	,	,	_	_	_
916	histidine	histidine	NN	_	_	_
917	depleted	deplete	VBN	_	_	_
918	,	,	,	_	_	_
919	2	2	CD	_	_	_
920	hrs	hr	NNS	_	_	_
921	,	,	,	_	_	_
922	rep	rep	NN	GEN	_	_
923	1	1	CD	_	_	_
924	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
925	OSU11	osu11	NN	_	_	_
926	,	,	,	_	_	_
927	histidine	histidine	NN	_	_	_
928	depleted	deplete	VBN	_	_	_
929	,	,	,	_	_	_
930	2	2	CD	_	_	_
931	hrs	hr	NNS	_	_	_
932	,	,	,	_	_	_
933	rep	rep	NN	GEN	_	_
934	2	2	CD	_	_	_
935	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
936	OSU11	osu11	NN	_	_	_
937	,	,	,	_	_	_
938	histidine	histidine	NN	_	_	_
939	depleted	deplete	VBN	_	_	_
940	,	,	,	_	_	_
941	2	2	CD	_	_	_
942	hrs	hr	NNS	_	_	_
943	,	,	,	_	_	_
944	rep	rep	NN	GEN	_	_
945	3	3	CD	_	_	_
946	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
947	OSU11	osu11	NN	_	_	_
948	,	,	,	_	_	_
949	histidine	histidine	NN	_	_	_
950	supplied	supply	VBD	_	_	_
951	,	,	,	_	_	_
952	1	1	CD	_	_	_
953	mM	mm	NN	KWSUPP	_	_
954	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
955	OSU11	osu11	NN	_	_	_
956	,	,	,	_	_	_
957	histidine	histidine	NN	_	_	_
958	supplied	supply	VBD	_	_	_
959	,	,	,	_	_	_
960	1	1	CD	_	_	_
961	mM	mm	NN	KWSUPP	_	_
962	,	,	,	_	_	_
963	rep	rep	NN	GEN	_	_
964	1	1	CD	_	_	_
965	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
966	OSU11	osu11	NN	_	_	_
967	,	,	,	_	_	_
968	histidine	histidine	NN	_	_	_
969	supplied	supply	VBD	_	_	_
970	,	,	,	_	_	_
971	1	1	CD	_	_	_
972	mM	mm	NN	KWSUPP	_	_
973	,	,	,	_	_	_
974	rep	rep	NN	GEN	_	_
975	2	2	CD	_	_	_
976	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
977	OSU11	osu11	NN	_	_	_
978	,	,	,	_	_	_
979	histidine	histidine	NN	_	_	_
980	supplied	supply	VBD	_	_	_
981	,	,	,	_	_	_
982	1	1	CD	_	_	_
983	mM	mm	NN	KWSUPP	_	_
984	,	,	,	_	_	_
985	rep	rep	NN	GEN	_	_
986	3	3	CD	_	_	_
987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
988	OSU11	osu11	NN	_	_	_
989	,	,	,	_	_	_
990	nurishment	nurishment	NN	_	_	_
991	,	,	,	_	_	_
992	biological	biological	JJ	_	_	_
993	rep	rep	NN	GEN	_	_
994	1	1	CD	_	_	_
995	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
996	OSU11	osu11	NN	_	_	_
997	,	,	,	_	_	_
998	nurishment	nurishment	NN	_	_	_
999	,	,	,	_	_	_
1000	biological	biological	JJ	_	_	_
1001	rep	rep	NN	GEN	_	_
1002	2	2	CD	_	_	_
1003	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1004	OSU11	osu11	NN	_	_	_
1005	,	,	,	_	_	_
1006	nurishment	nurishment	NN	_	_	_
1007	,	,	,	_	_	_
1008	biological	biological	JJ	_	_	_
1009	rep	rep	NN	GEN	_	_
1010	3	3	CD	_	_	_
1011	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1012	OSU11	osu11	NN	_	_	_
1013	,	,	,	_	_	_
1014	starved	starve	VBN	_	_	_
1015	,	,	,	_	_	_
1016	biological	biological	JJ	_	_	_
1017	rep	rep	NN	GEN	_	_
1018	1	1	CD	_	_	_
1019	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1020	OSU11	osu11	NN	_	_	_
1021	,	,	,	_	_	_
1022	starved	starve	VBN	_	_	_
1023	,	,	,	_	_	_
1024	biological	biological	JJ	_	_	_
1025	rep	rep	NN	GEN	_	_
1026	2	2	CD	_	_	_
1027	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1028	OSU11	osu11	NN	_	_	_
1029	,	,	,	_	_	_
1030	starved	starve	VBN	_	_	_
1031	,	,	,	_	_	_
1032	biological	biological	JJ	_	_	_
1033	rep	rep	NN	GEN	_	_
1034	3	3	CD	_	_	_
1035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1036	OSU12-hisA	osu12-hisa	NN	_	_	_
1037	,	,	,	_	_	_
1038	histidine	histidine	NN	_	_	_
1039	depleted	deplete	VBN	_	_	_
1040	,	,	,	_	_	_
1041	>	>	JJR	_	_	_
1042	10	10	CD	_	_	_
1043	hrs	hr	NNS	_	_	_
1044	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1045	OSU12-hisA	osu12-hisa	NN	_	_	_
1046	,	,	,	_	_	_
1047	histidine	histidine	NN	_	_	_
1048	depleted	deplete	VBN	_	_	_
1049	,	,	,	_	_	_
1050	>	>	JJR	_	_	_
1051	10	10	CD	_	_	_
1052	hrs	hr	NNS	_	_	_
1053	,	,	,	_	_	_
1054	rep	rep	NN	GEN	_	_
1055	1	1	CD	_	_	_
1056	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1057	OSU12-hisA	osu12-hisa	NN	_	_	_
1058	,	,	,	_	_	_
1059	histidine	histidine	NN	_	_	_
1060	depleted	deplete	VBN	_	_	_
1061	,	,	,	_	_	_
1062	>	>	JJR	_	_	_
1063	10	10	CD	_	_	_
1064	hrs	hr	NNS	_	_	_
1065	,	,	,	_	_	_
1066	rep	rep	NN	GEN	_	_
1067	2	2	CD	_	_	_
1068	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1069	OSU12-hisA	osu12-hisa	NN	_	_	_
1070	,	,	,	_	_	_
1071	histidine	histidine	NN	_	_	_
1072	depleted	deplete	VBN	_	_	_
1073	,	,	,	_	_	_
1074	>	>	JJR	_	_	_
1075	10	10	CD	_	_	_
1076	hrs	hr	NNS	_	_	_
1077	,	,	,	_	_	_
1078	rep	rep	NN	GEN	_	_
1079	3	3	CD	_	_	_
1080	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1081	OSU12-hisA	osu12-hisa	NN	_	_	_
1082	,	,	,	_	_	_
1083	histidine	histidine	NN	_	_	_
1084	depleted	deplete	VBN	_	_	_
1085	,	,	,	_	_	_
1086	10	10	CD	_	_	_
1087	min	min	NN	_	_	_
1088	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1089	OSU12-hisA	osu12-hisa	NN	_	_	_
1090	,	,	,	_	_	_
1091	histidine	histidine	NN	_	_	_
1092	depleted	deplete	VBN	_	_	_
1093	,	,	,	_	_	_
1094	10	10	CD	_	_	_
1095	min	min	NN	_	_	_
1096	,	,	,	_	_	_
1097	rep	rep	NN	GEN	_	_
1098	1	1	CD	_	_	_
1099	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1100	OSU12-hisA	osu12-hisa	NN	_	_	_
1101	,	,	,	_	_	_
1102	histidine	histidine	NN	_	_	_
1103	depleted	deplete	VBN	_	_	_
1104	,	,	,	_	_	_
1105	10	10	CD	_	_	_
1106	min	min	NN	_	_	_
1107	,	,	,	_	_	_
1108	rep	rep	NN	GEN	_	_
1109	2	2	CD	_	_	_
1110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1111	OSU12-hisA	osu12-hisa	NN	_	_	_
1112	,	,	,	_	_	_
1113	histidine	histidine	NN	_	_	_
1114	depleted	deplete	VBN	_	_	_
1115	,	,	,	_	_	_
1116	10	10	CD	_	_	_
1117	min	min	NN	_	_	_
1118	,	,	,	_	_	_
1119	rep	rep	NN	GEN	_	_
1120	3	3	CD	_	_	_
1121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1122	OSU12-hisA	osu12-hisa	NN	_	_	_
1123	,	,	,	_	_	_
1124	histidine	histidine	NN	_	_	_
1125	depleted	deplete	VBN	_	_	_
1126	,	,	,	_	_	_
1127	2	2	CD	_	_	_
1128	hrs	hr	NNS	_	_	_
1129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1130	OSU12-hisA	osu12-hisa	NN	_	_	_
1131	,	,	,	_	_	_
1132	histidine	histidine	NN	_	_	_
1133	depleted	deplete	VBN	_	_	_
1134	,	,	,	_	_	_
1135	2	2	CD	_	_	_
1136	hrs	hr	NNS	_	_	_
1137	,	,	,	_	_	_
1138	rep	rep	NN	GEN	_	_
1139	1	1	CD	_	_	_
1140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1141	OSU12-hisA	osu12-hisa	NN	_	_	_
1142	,	,	,	_	_	_
1143	histidine	histidine	NN	_	_	_
1144	depleted	deplete	VBN	_	_	_
1145	,	,	,	_	_	_
1146	2	2	CD	_	_	_
1147	hrs	hr	NNS	_	_	_
1148	,	,	,	_	_	_
1149	rep	rep	NN	GEN	_	_
1150	2	2	CD	_	_	_
1151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1152	OSU12-hisA	osu12-hisa	NN	_	_	_
1153	,	,	,	_	_	_
1154	histidine	histidine	NN	_	_	_
1155	depleted	deplete	VBN	_	_	_
1156	,	,	,	_	_	_
1157	2	2	CD	_	_	_
1158	hrs	hr	NNS	_	_	_
1159	,	,	,	_	_	_
1160	rep	rep	NN	GEN	_	_
1161	3	3	CD	_	_	_
1162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1163	OSU12-hisA	osu12-hisa	NN	_	_	_
1164	,	,	,	_	_	_
1165	histidine	histidine	NN	_	_	_
1166	supplied	supply	VBD	_	_	_
1167	,	,	,	_	_	_
1168	1	1	CD	_	_	_
1169	mM	mm	NN	KWSUPP	_	_
1170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1171	OSU12-hisA	osu12-hisa	NN	_	_	_
1172	,	,	,	_	_	_
1173	histidine	histidine	NN	_	_	_
1174	supplied	supply	VBD	_	_	_
1175	,	,	,	_	_	_
1176	1	1	CD	_	_	_
1177	mM	mm	NN	KWSUPP	_	_
1178	,	,	,	_	_	_
1179	rep	rep	NN	GEN	_	_
1180	1	1	CD	_	_	_
1181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1182	OSU12-hisA	osu12-hisa	NN	_	_	_
1183	,	,	,	_	_	_
1184	histidine	histidine	NN	_	_	_
1185	supplied	supply	VBD	_	_	_
1186	,	,	,	_	_	_
1187	1	1	CD	_	_	_
1188	mM	mm	NN	KWSUPP	_	_
1189	,	,	,	_	_	_
1190	rep	rep	NN	GEN	_	_
1191	2	2	CD	_	_	_
1192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1193	OSU12-hisA	osu12-hisa	NN	_	_	_
1194	,	,	,	_	_	_
1195	histidine	histidine	NN	_	_	_
1196	supplied	supply	VBD	_	_	_
1197	,	,	,	_	_	_
1198	1	1	CD	_	_	_
1199	mM	mm	NN	KWSUPP	_	_
1200	,	,	,	_	_	_
1201	rep	rep	NN	GEN	_	_
1202	3	3	CD	_	_	_
1203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1204	OSU12-hisB	osu12-hisb	NN	_	_	_
1205	,	,	,	_	_	_
1206	histidine	histidine	NN	_	_	_
1207	depleted	deplete	VBN	_	_	_
1208	,	,	,	_	_	_
1209	>	>	JJR	_	_	_
1210	10	10	CD	_	_	_
1211	hrs	hr	NNS	_	_	_
1212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1213	OSU12-hisB	osu12-hisb	NN	_	_	_
1214	,	,	,	_	_	_
1215	histidine	histidine	NN	_	_	_
1216	depleted	deplete	VBN	_	_	_
1217	,	,	,	_	_	_
1218	>	>	JJR	_	_	_
1219	10	10	CD	_	_	_
1220	hrs	hr	NNS	_	_	_
1221	,	,	,	_	_	_
1222	rep	rep	NN	GEN	_	_
1223	1	1	CD	_	_	_
1224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1225	OSU12-hisB	osu12-hisb	NN	_	_	_
1226	,	,	,	_	_	_
1227	histidine	histidine	NN	_	_	_
1228	depleted	deplete	VBN	_	_	_
1229	,	,	,	_	_	_
1230	>	>	JJR	_	_	_
1231	10	10	CD	_	_	_
1232	hrs	hr	NNS	_	_	_
1233	,	,	,	_	_	_
1234	rep	rep	NN	GEN	_	_
1235	2	2	CD	_	_	_
1236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1237	OSU12-hisB	osu12-hisb	NN	_	_	_
1238	,	,	,	_	_	_
1239	histidine	histidine	NN	_	_	_
1240	depleted	deplete	VBN	_	_	_
1241	,	,	,	_	_	_
1242	>	>	JJR	_	_	_
1243	10	10	CD	_	_	_
1244	hrs	hr	NNS	_	_	_
1245	,	,	,	_	_	_
1246	rep	rep	NN	GEN	_	_
1247	3	3	CD	_	_	_
1248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1249	OSU12-hisB	osu12-hisb	NN	_	_	_
1250	,	,	,	_	_	_
1251	histidine	histidine	NN	_	_	_
1252	depleted	deplete	VBN	_	_	_
1253	,	,	,	_	_	_
1254	10	10	CD	_	_	_
1255	min	min	NN	_	_	_
1256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1257	OSU12-hisB	osu12-hisb	NN	_	_	_
1258	,	,	,	_	_	_
1259	histidine	histidine	NN	_	_	_
1260	depleted	deplete	VBN	_	_	_
1261	,	,	,	_	_	_
1262	10	10	CD	_	_	_
1263	min	min	NN	_	_	_
1264	,	,	,	_	_	_
1265	rep	rep	NN	GEN	_	_
1266	1	1	CD	_	_	_
1267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1268	OSU12-hisB	osu12-hisb	NN	_	_	_
1269	,	,	,	_	_	_
1270	histidine	histidine	NN	_	_	_
1271	depleted	deplete	VBN	_	_	_
1272	,	,	,	_	_	_
1273	10	10	CD	_	_	_
1274	min	min	NN	_	_	_
1275	,	,	,	_	_	_
1276	rep	rep	NN	GEN	_	_
1277	2	2	CD	_	_	_
1278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1279	OSU12-hisB	osu12-hisb	NN	_	_	_
1280	,	,	,	_	_	_
1281	histidine	histidine	NN	_	_	_
1282	depleted	deplete	VBN	_	_	_
1283	,	,	,	_	_	_
1284	10	10	CD	_	_	_
1285	min	min	NN	_	_	_
1286	,	,	,	_	_	_
1287	rep	rep	NN	GEN	_	_
1288	3	3	CD	_	_	_
1289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1290	OSU12-hisB	osu12-hisb	NN	_	_	_
1291	,	,	,	_	_	_
1292	histidine	histidine	NN	_	_	_
1293	depleted	deplete	VBN	_	_	_
1294	,	,	,	_	_	_
1295	2	2	CD	_	_	_
1296	hrs	hr	NNS	_	_	_
1297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1298	OSU12-hisB	osu12-hisb	NN	_	_	_
1299	,	,	,	_	_	_
1300	histidine	histidine	NN	_	_	_
1301	depleted	deplete	VBN	_	_	_
1302	,	,	,	_	_	_
1303	2	2	CD	_	_	_
1304	hrs	hr	NNS	_	_	_
1305	,	,	,	_	_	_
1306	rep	rep	NN	GEN	_	_
1307	1	1	CD	_	_	_
1308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1309	OSU12-hisB	osu12-hisb	NN	_	_	_
1310	,	,	,	_	_	_
1311	histidine	histidine	NN	_	_	_
1312	depleted	deplete	VBN	_	_	_
1313	,	,	,	_	_	_
1314	2	2	CD	_	_	_
1315	hrs	hr	NNS	_	_	_
1316	,	,	,	_	_	_
1317	rep	rep	NN	GEN	_	_
1318	2	2	CD	_	_	_
1319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1320	OSU12-hisB	osu12-hisb	NN	_	_	_
1321	,	,	,	_	_	_
1322	histidine	histidine	NN	_	_	_
1323	depleted	deplete	VBN	_	_	_
1324	,	,	,	_	_	_
1325	2	2	CD	_	_	_
1326	hrs	hr	NNS	_	_	_
1327	,	,	,	_	_	_
1328	rep	rep	NN	GEN	_	_
1329	3	3	CD	_	_	_
1330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1331	OSU12-hisB	osu12-hisb	NN	_	_	_
1332	,	,	,	_	_	_
1333	histidine	histidine	NN	_	_	_
1334	supplied	supply	VBD	_	_	_
1335	,	,	,	_	_	_
1336	1	1	CD	_	_	_
1337	mM	mm	NN	KWSUPP	_	_
1338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1339	OSU12-hisB	osu12-hisb	NN	_	_	_
1340	,	,	,	_	_	_
1341	histidine	histidine	NN	_	_	_
1342	supplied	supply	VBD	_	_	_
1343	,	,	,	_	_	_
1344	1	1	CD	_	_	_
1345	mM	mm	NN	KWSUPP	_	_
1346	,	,	,	_	_	_
1347	rep	rep	NN	GEN	_	_
1348	1	1	CD	_	_	_
1349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1350	OSU12-hisB	osu12-hisb	NN	_	_	_
1351	,	,	,	_	_	_
1352	histidine	histidine	NN	_	_	_
1353	supplied	supply	VBD	_	_	_
1354	,	,	,	_	_	_
1355	1	1	CD	_	_	_
1356	mM	mm	NN	KWSUPP	_	_
1357	,	,	,	_	_	_
1358	rep	rep	NN	GEN	_	_
1359	2	2	CD	_	_	_
1360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1361	OSU12-hisB	osu12-hisb	NN	_	_	_
1362	,	,	,	_	_	_
1363	histidine	histidine	NN	_	_	_
1364	supplied	supply	VBD	_	_	_
1365	,	,	,	_	_	_
1366	1	1	CD	_	_	_
1367	mM	mm	NN	KWSUPP	_	_
1368	,	,	,	_	_	_
1369	rep	rep	NN	GEN	_	_
1370	3	3	CD	_	_	_
1371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1372	OSU12-hisC	osu12-hisc	NN	_	_	_
1373	,	,	,	_	_	_
1374	histidine	histidine	NN	_	_	_
1375	depleted	deplete	VBN	_	_	_
1376	,	,	,	_	_	_
1377	>	>	JJR	_	_	_
1378	10	10	CD	_	_	_
1379	hrs	hr	NNS	_	_	_
1380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1381	OSU12-hisC	osu12-hisc	NN	_	_	_
1382	,	,	,	_	_	_
1383	histidine	histidine	NN	_	_	_
1384	depleted	deplete	VBN	_	_	_
1385	,	,	,	_	_	_
1386	>	>	JJR	_	_	_
1387	10	10	CD	_	_	_
1388	hrs	hr	NNS	_	_	_
1389	,	,	,	_	_	_
1390	rep	rep	NN	GEN	_	_
1391	1	1	CD	_	_	_
1392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1393	OSU12-hisC	osu12-hisc	NN	_	_	_
1394	,	,	,	_	_	_
1395	histidine	histidine	NN	_	_	_
1396	depleted	deplete	VBN	_	_	_
1397	,	,	,	_	_	_
1398	>	>	JJR	_	_	_
1399	10	10	CD	_	_	_
1400	hrs	hr	NNS	_	_	_
1401	,	,	,	_	_	_
1402	rep	rep	NN	GEN	_	_
1403	2	2	CD	_	_	_
1404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1405	OSU12-hisC	osu12-hisc	NN	_	_	_
1406	,	,	,	_	_	_
1407	histidine	histidine	NN	_	_	_
1408	depleted	deplete	VBN	_	_	_
1409	,	,	,	_	_	_
1410	>	>	JJR	_	_	_
1411	10	10	CD	_	_	_
1412	hrs	hr	NNS	_	_	_
1413	,	,	,	_	_	_
1414	rep	rep	NN	GEN	_	_
1415	3	3	CD	_	_	_
1416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1417	OSU12-hisC	osu12-hisc	NN	_	_	_
1418	,	,	,	_	_	_
1419	histidine	histidine	NN	_	_	_
1420	depleted	deplete	VBN	_	_	_
1421	,	,	,	_	_	_
1422	10	10	CD	_	_	_
1423	min	min	NN	_	_	_
1424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1425	OSU12-hisC	osu12-hisc	NN	_	_	_
1426	,	,	,	_	_	_
1427	histidine	histidine	NN	_	_	_
1428	depleted	deplete	VBN	_	_	_
1429	,	,	,	_	_	_
1430	10	10	CD	_	_	_
1431	min	min	NN	_	_	_
1432	,	,	,	_	_	_
1433	rep	rep	NN	GEN	_	_
1434	1	1	CD	_	_	_
1435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1436	OSU12-hisC	osu12-hisc	NN	_	_	_
1437	,	,	,	_	_	_
1438	histidine	histidine	NN	_	_	_
1439	depleted	deplete	VBN	_	_	_
1440	,	,	,	_	_	_
1441	10	10	CD	_	_	_
1442	min	min	NN	_	_	_
1443	,	,	,	_	_	_
1444	rep	rep	NN	GEN	_	_
1445	2	2	CD	_	_	_
1446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1447	OSU12-hisC	osu12-hisc	NN	_	_	_
1448	,	,	,	_	_	_
1449	histidine	histidine	NN	_	_	_
1450	depleted	deplete	VBN	_	_	_
1451	,	,	,	_	_	_
1452	10	10	CD	_	_	_
1453	min	min	NN	_	_	_
1454	,	,	,	_	_	_
1455	rep	rep	NN	GEN	_	_
1456	3	3	CD	_	_	_
1457	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1458	OSU12-hisC	osu12-hisc	NN	_	_	_
1459	,	,	,	_	_	_
1460	histidine	histidine	NN	_	_	_
1461	depleted	deplete	VBN	_	_	_
1462	,	,	,	_	_	_
1463	2	2	CD	_	_	_
1464	hrs	hr	NNS	_	_	_
1465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1466	OSU12-hisC	osu12-hisc	NN	_	_	_
1467	,	,	,	_	_	_
1468	histidine	histidine	NN	_	_	_
1469	depleted	deplete	VBN	_	_	_
1470	,	,	,	_	_	_
1471	2	2	CD	_	_	_
1472	hrs	hr	NNS	_	_	_
1473	,	,	,	_	_	_
1474	rep	rep	NN	GEN	_	_
1475	1	1	CD	_	_	_
1476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1477	OSU12-hisC	osu12-hisc	NN	_	_	_
1478	,	,	,	_	_	_
1479	histidine	histidine	NN	_	_	_
1480	depleted	deplete	VBN	_	_	_
1481	,	,	,	_	_	_
1482	2	2	CD	_	_	_
1483	hrs	hr	NNS	_	_	_
1484	,	,	,	_	_	_
1485	rep	rep	NN	GEN	_	_
1486	2	2	CD	_	_	_
1487	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1488	OSU12-hisC	osu12-hisc	NN	_	_	_
1489	,	,	,	_	_	_
1490	histidine	histidine	NN	_	_	_
1491	depleted	deplete	VBN	_	_	_
1492	,	,	,	_	_	_
1493	2	2	CD	_	_	_
1494	hrs	hr	NNS	_	_	_
1495	,	,	,	_	_	_
1496	rep	rep	NN	GEN	_	_
1497	3	3	CD	_	_	_
1498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1499	OSU12-hisC	osu12-hisc	NN	_	_	_
1500	,	,	,	_	_	_
1501	histidine	histidine	NN	_	_	_
1502	supplied	supply	VBD	_	_	_
1503	,	,	,	_	_	_
1504	1	1	CD	_	_	_
1505	mM	mm	NN	KWSUPP	_	_
1506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1507	OSU12-hisC	osu12-hisc	NN	_	_	_
1508	,	,	,	_	_	_
1509	histidine	histidine	NN	_	_	_
1510	supplied	supply	VBD	_	_	_
1511	,	,	,	_	_	_
1512	1	1	CD	_	_	_
1513	mM	mm	NN	KWSUPP	_	_
1514	,	,	,	_	_	_
1515	rep	rep	NN	GEN	_	_
1516	1	1	CD	_	_	_
1517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1518	OSU12-hisC	osu12-hisc	NN	_	_	_
1519	,	,	,	_	_	_
1520	histidine	histidine	NN	_	_	_
1521	supplied	supply	VBD	_	_	_
1522	,	,	,	_	_	_
1523	1	1	CD	_	_	_
1524	mM	mm	NN	KWSUPP	_	_
1525	,	,	,	_	_	_
1526	rep	rep	NN	GEN	_	_
1527	2	2	CD	_	_	_
1528	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1529	OSU12-hisC	osu12-hisc	NN	_	_	_
1530	,	,	,	_	_	_
1531	histidine	histidine	NN	_	_	_
1532	supplied	supply	VBD	_	_	_
1533	,	,	,	_	_	_
1534	1	1	CD	_	_	_
1535	mM	mm	NN	KWSUPP	_	_
1536	,	,	,	_	_	_
1537	rep	rep	NN	GEN	_	_
1538	3	3	CD	_	_	_
1539	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1540	OSU12-hisC	osu12-hisc	NN	_	_	_
1541	,	,	,	_	_	_
1542	nurishment	nurishment	NN	_	_	_
1543	,	,	,	_	_	_
1544	biological	biological	JJ	_	_	_
1545	rep	rep	NN	GEN	_	_
1546	1	1	CD	_	_	_
1547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1548	OSU12-hisC	osu12-hisc	NN	_	_	_
1549	,	,	,	_	_	_
1550	nurishment	nurishment	NN	_	_	_
1551	,	,	,	_	_	_
1552	biological	biological	JJ	_	_	_
1553	rep	rep	NN	GEN	_	_
1554	2	2	CD	_	_	_
1555	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1556	OSU12-hisC	osu12-hisc	NN	_	_	_
1557	,	,	,	_	_	_
1558	nurishment	nurishment	NN	_	_	_
1559	,	,	,	_	_	_
1560	biological	biological	JJ	_	_	_
1561	rep	rep	NN	GEN	_	_
1562	3	3	CD	_	_	_
1563	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1564	OSU12-hisC	osu12-hisc	NN	_	_	_
1565	,	,	,	_	_	_
1566	starved	starve	VBN	_	_	_
1567	,	,	,	_	_	_
1568	biological	biological	JJ	_	_	_
1569	rep	rep	NN	GEN	_	_
1570	1	1	CD	_	_	_
1571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1572	OSU12-hisC	osu12-hisc	NN	_	_	_
1573	,	,	,	_	_	_
1574	starved	starve	VBN	_	_	_
1575	,	,	,	_	_	_
1576	biological	biological	JJ	_	_	_
1577	rep	rep	NN	GEN	_	_
1578	2	2	CD	_	_	_
1579	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1580	OSU12-hisC	osu12-hisc	NN	_	_	_
1581	,	,	,	_	_	_
1582	starved	starve	VBN	_	_	_
1583	,	,	,	_	_	_
1584	biological	biological	JJ	_	_	_
1585	rep	rep	NN	GEN	_	_
1586	3	3	CD	_	_	_
1587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1588	OSU12-hisD	osu12-hisd	NN	_	_	_
1589	,	,	,	_	_	_
1590	histidine	histidine	NN	_	_	_
1591	depleted	deplete	VBN	_	_	_
1592	,	,	,	_	_	_
1593	10	10	CD	_	_	_
1594	min	min	NN	_	_	_
1595	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1596	OSU12-hisD	osu12-hisd	NN	_	_	_
1597	,	,	,	_	_	_
1598	histidine	histidine	NN	_	_	_
1599	depleted	deplete	VBN	_	_	_
1600	,	,	,	_	_	_
1601	10	10	CD	_	_	_
1602	min	min	NN	_	_	_
1603	,	,	,	_	_	_
1604	rep	rep	NN	GEN	_	_
1605	1	1	CD	_	_	_
1606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1607	OSU12-hisD	osu12-hisd	NN	_	_	_
1608	,	,	,	_	_	_
1609	histidine	histidine	NN	_	_	_
1610	depleted	deplete	VBN	_	_	_
1611	,	,	,	_	_	_
1612	10	10	CD	_	_	_
1613	min	min	NN	_	_	_
1614	,	,	,	_	_	_
1615	rep	rep	NN	GEN	_	_
1616	2	2	CD	_	_	_
1617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1618	OSU12-hisD	osu12-hisd	NN	_	_	_
1619	,	,	,	_	_	_
1620	histidine	histidine	NN	_	_	_
1621	depleted	deplete	VBN	_	_	_
1622	,	,	,	_	_	_
1623	10	10	CD	_	_	_
1624	min	min	NN	_	_	_
1625	,	,	,	_	_	_
1626	rep	rep	NN	GEN	_	_
1627	3	3	CD	_	_	_
1628	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1629	OSU12-hisD	osu12-hisd	NN	_	_	_
1630	,	,	,	_	_	_
1631	histidine	histidine	NN	_	_	_
1632	depleted	deplete	VBN	_	_	_
1633	,	,	,	_	_	_
1634	2	2	CD	_	_	_
1635	hrs	hr	NNS	_	_	_
1636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1637	OSU12-hisD	osu12-hisd	NN	_	_	_
1638	,	,	,	_	_	_
1639	histidine	histidine	NN	_	_	_
1640	depleted	deplete	VBN	_	_	_
1641	,	,	,	_	_	_
1642	2	2	CD	_	_	_
1643	hrs	hr	NNS	_	_	_
1644	,	,	,	_	_	_
1645	rep	rep	NN	GEN	_	_
1646	1	1	CD	_	_	_
1647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1648	OSU12-hisD	osu12-hisd	NN	_	_	_
1649	,	,	,	_	_	_
1650	histidine	histidine	NN	_	_	_
1651	depleted	deplete	VBN	_	_	_
1652	,	,	,	_	_	_
1653	2	2	CD	_	_	_
1654	hrs	hr	NNS	_	_	_
1655	,	,	,	_	_	_
1656	rep	rep	NN	GEN	_	_
1657	2	2	CD	_	_	_
1658	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1659	OSU12-hisD	osu12-hisd	NN	_	_	_
1660	,	,	,	_	_	_
1661	histidine	histidine	NN	_	_	_
1662	depleted	deplete	VBN	_	_	_
1663	,	,	,	_	_	_
1664	2	2	CD	_	_	_
1665	hrs	hr	NNS	_	_	_
1666	,	,	,	_	_	_
1667	rep	rep	NN	GEN	_	_
1668	3	3	CD	_	_	_
1669	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1670	OSU12-hisD	osu12-hisd	NN	_	_	_
1671	,	,	,	_	_	_
1672	histidine	histidine	NN	_	_	_
1673	supplied	supply	VBD	_	_	_
1674	,	,	,	_	_	_
1675	1	1	CD	_	_	_
1676	mM	mm	NN	KWSUPP	_	_
1677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1678	OSU12-hisD	osu12-hisd	NN	_	_	_
1679	,	,	,	_	_	_
1680	histidine	histidine	NN	_	_	_
1681	supplied	supply	VBD	_	_	_
1682	,	,	,	_	_	_
1683	1	1	CD	_	_	_
1684	mM	mm	NN	KWSUPP	_	_
1685	,	,	,	_	_	_
1686	rep	rep	NN	GEN	_	_
1687	1	1	CD	_	_	_
1688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1689	OSU12-hisD	osu12-hisd	NN	_	_	_
1690	,	,	,	_	_	_
1691	histidine	histidine	NN	_	_	_
1692	supplied	supply	VBD	_	_	_
1693	,	,	,	_	_	_
1694	1	1	CD	_	_	_
1695	mM	mm	NN	KWSUPP	_	_
1696	,	,	,	_	_	_
1697	rep	rep	NN	GEN	_	_
1698	2	2	CD	_	_	_
1699	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1700	OSU12-hisD	osu12-hisd	NN	_	_	_
1701	,	,	,	_	_	_
1702	histidine	histidine	NN	_	_	_
1703	supplied	supply	VBD	_	_	_
1704	,	,	,	_	_	_
1705	1	1	CD	_	_	_
1706	mM	mm	NN	KWSUPP	_	_
1707	,	,	,	_	_	_
1708	rep	rep	NN	GEN	_	_
1709	3	3	CD	_	_	_
1710	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1711	OSU12-hisF	osu12-hisf	NN	_	_	_
1712	,	,	,	_	_	_
1713	histidine	histidine	NN	_	_	_
1714	depleted	deplete	VBN	_	_	_
1715	,	,	,	_	_	_
1716	>	>	JJR	_	_	_
1717	10	10	CD	_	_	_
1718	hrs	hr	NNS	_	_	_
1719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1720	OSU12-hisF	osu12-hisf	NN	_	_	_
1721	,	,	,	_	_	_
1722	histidine	histidine	NN	_	_	_
1723	depleted	deplete	VBN	_	_	_
1724	,	,	,	_	_	_
1725	>	>	JJR	_	_	_
1726	10	10	CD	_	_	_
1727	hrs	hr	NNS	_	_	_
1728	,	,	,	_	_	_
1729	rep	rep	NN	GEN	_	_
1730	1	1	CD	_	_	_
1731	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1732	OSU12-hisF	osu12-hisf	NN	_	_	_
1733	,	,	,	_	_	_
1734	histidine	histidine	NN	_	_	_
1735	depleted	deplete	VBN	_	_	_
1736	,	,	,	_	_	_
1737	>	>	JJR	_	_	_
1738	10	10	CD	_	_	_
1739	hrs	hr	NNS	_	_	_
1740	,	,	,	_	_	_
1741	rep	rep	NN	GEN	_	_
1742	2	2	CD	_	_	_
1743	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1744	OSU12-hisF	osu12-hisf	NN	_	_	_
1745	,	,	,	_	_	_
1746	histidine	histidine	NN	_	_	_
1747	depleted	deplete	VBN	_	_	_
1748	,	,	,	_	_	_
1749	>	>	JJR	_	_	_
1750	10	10	CD	_	_	_
1751	hrs	hr	NNS	_	_	_
1752	,	,	,	_	_	_
1753	rep	rep	NN	GEN	_	_
1754	3	3	CD	_	_	_
1755	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1756	OSU12-hisF	osu12-hisf	NN	_	_	_
1757	,	,	,	_	_	_
1758	histidine	histidine	NN	_	_	_
1759	depleted	deplete	VBN	_	_	_
1760	,	,	,	_	_	_
1761	10	10	CD	_	_	_
1762	min	min	NN	_	_	_
1763	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1764	OSU12-hisF	osu12-hisf	NN	_	_	_
1765	,	,	,	_	_	_
1766	histidine	histidine	NN	_	_	_
1767	depleted	deplete	VBN	_	_	_
1768	,	,	,	_	_	_
1769	10	10	CD	_	_	_
1770	min	min	NN	_	_	_
1771	,	,	,	_	_	_
1772	rep	rep	NN	GEN	_	_
1773	1	1	CD	_	_	_
1774	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1775	OSU12-hisF	osu12-hisf	NN	_	_	_
1776	,	,	,	_	_	_
1777	histidine	histidine	NN	_	_	_
1778	depleted	deplete	VBN	_	_	_
1779	,	,	,	_	_	_
1780	10	10	CD	_	_	_
1781	min	min	NN	_	_	_
1782	,	,	,	_	_	_
1783	rep	rep	NN	GEN	_	_
1784	2	2	CD	_	_	_
1785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1786	OSU12-hisF	osu12-hisf	NN	_	_	_
1787	,	,	,	_	_	_
1788	histidine	histidine	NN	_	_	_
1789	depleted	deplete	VBN	_	_	_
1790	,	,	,	_	_	_
1791	10	10	CD	_	_	_
1792	min	min	NN	_	_	_
1793	,	,	,	_	_	_
1794	rep	rep	NN	GEN	_	_
1795	3	3	CD	_	_	_
1796	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1797	OSU12-hisF	osu12-hisf	NN	_	_	_
1798	,	,	,	_	_	_
1799	histidine	histidine	NN	_	_	_
1800	depleted	deplete	VBN	_	_	_
1801	,	,	,	_	_	_
1802	2	2	CD	_	_	_
1803	hrs	hr	NNS	_	_	_
1804	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1805	OSU12-hisF	osu12-hisf	NN	_	_	_
1806	,	,	,	_	_	_
1807	histidine	histidine	NN	_	_	_
1808	depleted	deplete	VBN	_	_	_
1809	,	,	,	_	_	_
1810	2	2	CD	_	_	_
1811	hrs	hr	NNS	_	_	_
1812	,	,	,	_	_	_
1813	rep	rep	NN	GEN	_	_
1814	1	1	CD	_	_	_
1815	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1816	OSU12-hisF	osu12-hisf	NN	_	_	_
1817	,	,	,	_	_	_
1818	histidine	histidine	NN	_	_	_
1819	depleted	deplete	VBN	_	_	_
1820	,	,	,	_	_	_
1821	2	2	CD	_	_	_
1822	hrs	hr	NNS	_	_	_
1823	,	,	,	_	_	_
1824	rep	rep	NN	GEN	_	_
1825	2	2	CD	_	_	_
1826	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1827	OSU12-hisF	osu12-hisf	NN	_	_	_
1828	,	,	,	_	_	_
1829	histidine	histidine	NN	_	_	_
1830	depleted	deplete	VBN	_	_	_
1831	,	,	,	_	_	_
1832	2	2	CD	_	_	_
1833	hrs	hr	NNS	_	_	_
1834	,	,	,	_	_	_
1835	rep	rep	NN	GEN	_	_
1836	3	3	CD	_	_	_
1837	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1838	OSU12-hisF	osu12-hisf	NN	_	_	_
1839	,	,	,	_	_	_
1840	histidine	histidine	NN	_	_	_
1841	supplied	supply	VBD	_	_	_
1842	,	,	,	_	_	_
1843	1	1	CD	_	_	_
1844	mM	mm	NN	KWSUPP	_	_
1845	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1846	OSU12-hisF	osu12-hisf	NN	_	_	_
1847	,	,	,	_	_	_
1848	histidine	histidine	NN	_	_	_
1849	supplied	supply	VBD	_	_	_
1850	,	,	,	_	_	_
1851	1	1	CD	_	_	_
1852	mM	mm	NN	KWSUPP	_	_
1853	,	,	,	_	_	_
1854	rep	rep	NN	GEN	_	_
1855	1	1	CD	_	_	_
1856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1857	OSU12-hisF	osu12-hisf	NN	_	_	_
1858	,	,	,	_	_	_
1859	histidine	histidine	NN	_	_	_
1860	supplied	supply	VBD	_	_	_
1861	,	,	,	_	_	_
1862	1	1	CD	_	_	_
1863	mM	mm	NN	KWSUPP	_	_
1864	,	,	,	_	_	_
1865	rep	rep	NN	GEN	_	_
1866	2	2	CD	_	_	_
1867	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1868	OSU12-hisF	osu12-hisf	NN	_	_	_
1869	,	,	,	_	_	_
1870	histidine	histidine	NN	_	_	_
1871	supplied	supply	VBD	_	_	_
1872	,	,	,	_	_	_
1873	1	1	CD	_	_	_
1874	mM	mm	NN	KWSUPP	_	_
1875	,	,	,	_	_	_
1876	rep	rep	NN	GEN	_	_
1877	3	3	CD	_	_	_
1878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1879	OSU12-hisG	osu12-hisg	NN	_	_	_
1880	,	,	,	_	_	_
1881	histidine	histidine	NN	_	_	_
1882	depleted	deplete	VBN	_	_	_
1883	,	,	,	_	_	_
1884	10	10	CD	_	_	_
1885	min	min	NN	_	_	_
1886	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1887	OSU12-hisG	osu12-hisg	NN	_	_	_
1888	,	,	,	_	_	_
1889	histidine	histidine	NN	_	_	_
1890	depleted	deplete	VBN	_	_	_
1891	,	,	,	_	_	_
1892	10	10	CD	_	_	_
1893	min	min	NN	_	_	_
1894	,	,	,	_	_	_
1895	rep	rep	NN	GEN	_	_
1896	1	1	CD	_	_	_
1897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1898	OSU12-hisG	osu12-hisg	NN	_	_	_
1899	,	,	,	_	_	_
1900	histidine	histidine	NN	_	_	_
1901	depleted	deplete	VBN	_	_	_
1902	,	,	,	_	_	_
1903	10	10	CD	_	_	_
1904	min	min	NN	_	_	_
1905	,	,	,	_	_	_
1906	rep	rep	NN	GEN	_	_
1907	2	2	CD	_	_	_
1908	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1909	OSU12-hisG	osu12-hisg	NN	_	_	_
1910	,	,	,	_	_	_
1911	histidine	histidine	NN	_	_	_
1912	depleted	deplete	VBN	_	_	_
1913	,	,	,	_	_	_
1914	10	10	CD	_	_	_
1915	min	min	NN	_	_	_
1916	,	,	,	_	_	_
1917	rep	rep	NN	GEN	_	_
1918	3	3	CD	_	_	_
1919	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1920	OSU12-hisG	osu12-hisg	NN	_	_	_
1921	,	,	,	_	_	_
1922	histidine	histidine	NN	_	_	_
1923	depleted	deplete	VBN	_	_	_
1924	,	,	,	_	_	_
1925	2	2	CD	_	_	_
1926	hrs	hr	NNS	_	_	_
1927	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1928	OSU12-hisG	osu12-hisg	NN	_	_	_
1929	,	,	,	_	_	_
1930	histidine	histidine	NN	_	_	_
1931	depleted	deplete	VBN	_	_	_
1932	,	,	,	_	_	_
1933	2	2	CD	_	_	_
1934	hrs	hr	NNS	_	_	_
1935	,	,	,	_	_	_
1936	rep	rep	NN	GEN	_	_
1937	1	1	CD	_	_	_
1938	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1939	OSU12-hisG	osu12-hisg	NN	_	_	_
1940	,	,	,	_	_	_
1941	histidine	histidine	NN	_	_	_
1942	depleted	deplete	VBN	_	_	_
1943	,	,	,	_	_	_
1944	2	2	CD	_	_	_
1945	hrs	hr	NNS	_	_	_
1946	,	,	,	_	_	_
1947	rep	rep	NN	GEN	_	_
1948	2	2	CD	_	_	_
1949	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1950	OSU12-hisG	osu12-hisg	NN	_	_	_
1951	,	,	,	_	_	_
1952	histidine	histidine	NN	_	_	_
1953	depleted	deplete	VBN	_	_	_
1954	,	,	,	_	_	_
1955	2	2	CD	_	_	_
1956	hrs	hr	NNS	_	_	_
1957	,	,	,	_	_	_
1958	rep	rep	NN	GEN	_	_
1959	3	3	CD	_	_	_
1960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1961	OSU12-hisG	osu12-hisg	NN	_	_	_
1962	,	,	,	_	_	_
1963	histidine	histidine	NN	_	_	_
1964	supplied	supply	VBD	_	_	_
1965	,	,	,	_	_	_
1966	1	1	CD	_	_	_
1967	mM	mm	NN	KWSUPP	_	_
1968	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1969	OSU12-hisG	osu12-hisg	NN	_	_	_
1970	,	,	,	_	_	_
1971	histidine	histidine	NN	_	_	_
1972	supplied	supply	VBD	_	_	_
1973	,	,	,	_	_	_
1974	1	1	CD	_	_	_
1975	mM	mm	NN	KWSUPP	_	_
1976	,	,	,	_	_	_
1977	rep	rep	NN	GEN	_	_
1978	1	1	CD	_	_	_
1979	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1980	OSU12-hisG	osu12-hisg	NN	_	_	_
1981	,	,	,	_	_	_
1982	histidine	histidine	NN	_	_	_
1983	supplied	supply	VBD	_	_	_
1984	,	,	,	_	_	_
1985	1	1	CD	_	_	_
1986	mM	mm	NN	KWSUPP	_	_
1987	,	,	,	_	_	_
1988	rep	rep	NN	GEN	_	_
1989	2	2	CD	_	_	_
1990	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1991	OSU12-hisG	osu12-hisg	NN	_	_	_
1992	,	,	,	_	_	_
1993	histidine	histidine	NN	_	_	_
1994	supplied	supply	VBD	_	_	_
1995	,	,	,	_	_	_
1996	1	1	CD	_	_	_
1997	mM	mm	NN	KWSUPP	_	_
1998	,	,	,	_	_	_
1999	rep	rep	NN	GEN	_	_
2000	3	3	CD	_	_	_
2001	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2002	OSU12-hisI	osu12-hisi	NN	_	_	_
2003	,	,	,	_	_	_
2004	histidine	histidine	NN	_	_	_
2005	depleted	deplete	VBN	_	_	_
2006	,	,	,	_	_	_
2007	>	>	JJR	_	_	_
2008	10	10	CD	_	_	_
2009	hrs	hr	NNS	_	_	_
2010	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2011	OSU12-hisI	osu12-hisi	NN	_	_	_
2012	,	,	,	_	_	_
2013	histidine	histidine	NN	_	_	_
2014	depleted	deplete	VBN	_	_	_
2015	,	,	,	_	_	_
2016	>	>	JJR	_	_	_
2017	10	10	CD	_	_	_
2018	hrs	hr	NNS	_	_	_
2019	,	,	,	_	_	_
2020	rep	rep	NN	GEN	_	_
2021	1	1	CD	_	_	_
2022	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2023	OSU12-hisI	osu12-hisi	NN	_	_	_
2024	,	,	,	_	_	_
2025	histidine	histidine	NN	_	_	_
2026	depleted	deplete	VBN	_	_	_
2027	,	,	,	_	_	_
2028	>	>	JJR	_	_	_
2029	10	10	CD	_	_	_
2030	hrs	hr	NNS	_	_	_
2031	,	,	,	_	_	_
2032	rep	rep	NN	GEN	_	_
2033	2	2	CD	_	_	_
2034	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2035	OSU12-hisI	osu12-hisi	NN	_	_	_
2036	,	,	,	_	_	_
2037	histidine	histidine	NN	_	_	_
2038	depleted	deplete	VBN	_	_	_
2039	,	,	,	_	_	_
2040	>	>	JJR	_	_	_
2041	10	10	CD	_	_	_
2042	hrs	hr	NNS	_	_	_
2043	,	,	,	_	_	_
2044	rep	rep	NN	GEN	_	_
2045	3	3	CD	_	_	_
2046	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2047	OSU12-hisI	osu12-hisi	NN	_	_	_
2048	,	,	,	_	_	_
2049	histidine	histidine	NN	_	_	_
2050	depleted	deplete	VBN	_	_	_
2051	,	,	,	_	_	_
2052	10	10	CD	_	_	_
2053	min	min	NN	_	_	_
2054	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2055	OSU12-hisI	osu12-hisi	NN	_	_	_
2056	,	,	,	_	_	_
2057	histidine	histidine	NN	_	_	_
2058	depleted	deplete	VBN	_	_	_
2059	,	,	,	_	_	_
2060	10	10	CD	_	_	_
2061	min	min	NN	_	_	_
2062	,	,	,	_	_	_
2063	rep	rep	NN	GEN	_	_
2064	1	1	CD	_	_	_
2065	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2066	OSU12-hisI	osu12-hisi	NN	_	_	_
2067	,	,	,	_	_	_
2068	histidine	histidine	NN	_	_	_
2069	depleted	deplete	VBN	_	_	_
2070	,	,	,	_	_	_
2071	10	10	CD	_	_	_
2072	min	min	NN	_	_	_
2073	,	,	,	_	_	_
2074	rep	rep	NN	GEN	_	_
2075	2	2	CD	_	_	_
2076	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2077	OSU12-hisI	osu12-hisi	NN	_	_	_
2078	,	,	,	_	_	_
2079	histidine	histidine	NN	_	_	_
2080	depleted	deplete	VBN	_	_	_
2081	,	,	,	_	_	_
2082	10	10	CD	_	_	_
2083	min	min	NN	_	_	_
2084	,	,	,	_	_	_
2085	rep	rep	NN	GEN	_	_
2086	3	3	CD	_	_	_
2087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2088	OSU12-hisI	osu12-hisi	NN	_	_	_
2089	,	,	,	_	_	_
2090	histidine	histidine	NN	_	_	_
2091	depleted	deplete	VBN	_	_	_
2092	,	,	,	_	_	_
2093	2	2	CD	_	_	_
2094	hrs	hr	NNS	_	_	_
2095	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2096	OSU12-hisI	osu12-hisi	NN	_	_	_
2097	,	,	,	_	_	_
2098	histidine	histidine	NN	_	_	_
2099	depleted	deplete	VBN	_	_	_
2100	,	,	,	_	_	_
2101	2	2	CD	_	_	_
2102	hrs	hr	NNS	_	_	_
2103	,	,	,	_	_	_
2104	rep	rep	NN	GEN	_	_
2105	1	1	CD	_	_	_
2106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2107	OSU12-hisI	osu12-hisi	NN	_	_	_
2108	,	,	,	_	_	_
2109	histidine	histidine	NN	_	_	_
2110	depleted	deplete	VBN	_	_	_
2111	,	,	,	_	_	_
2112	2	2	CD	_	_	_
2113	hrs	hr	NNS	_	_	_
2114	,	,	,	_	_	_
2115	rep	rep	NN	GEN	_	_
2116	2	2	CD	_	_	_
2117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2118	OSU12-hisI	osu12-hisi	NN	_	_	_
2119	,	,	,	_	_	_
2120	histidine	histidine	NN	_	_	_
2121	depleted	deplete	VBN	_	_	_
2122	,	,	,	_	_	_
2123	2	2	CD	_	_	_
2124	hrs	hr	NNS	_	_	_
2125	,	,	,	_	_	_
2126	rep	rep	NN	GEN	_	_
2127	3	3	CD	_	_	_
2128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2129	OSU12-hisI	osu12-hisi	NN	_	_	_
2130	,	,	,	_	_	_
2131	histidine	histidine	NN	_	_	_
2132	supplied	supply	VBD	_	_	_
2133	,	,	,	_	_	_
2134	1	1	CD	_	_	_
2135	mM	mm	NN	KWSUPP	_	_
2136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2137	OSU12-hisI	osu12-hisi	NN	_	_	_
2138	,	,	,	_	_	_
2139	histidine	histidine	NN	_	_	_
2140	supplied	supply	VBD	_	_	_
2141	,	,	,	_	_	_
2142	1	1	CD	_	_	_
2143	mM	mm	NN	KWSUPP	_	_
2144	,	,	,	_	_	_
2145	rep	rep	NN	GEN	_	_
2146	1	1	CD	_	_	_
2147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2148	OSU12-hisI	osu12-hisi	NN	_	_	_
2149	,	,	,	_	_	_
2150	histidine	histidine	NN	_	_	_
2151	supplied	supply	VBD	_	_	_
2152	,	,	,	_	_	_
2153	1	1	CD	_	_	_
2154	mM	mm	NN	KWSUPP	_	_
2155	,	,	,	_	_	_
2156	rep	rep	NN	GEN	_	_
2157	2	2	CD	_	_	_
2158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2159	OSU12-hisI	osu12-hisi	NN	_	_	_
2160	,	,	,	_	_	_
2161	histidine	histidine	NN	_	_	_
2162	supplied	supply	VBD	_	_	_
2163	,	,	,	_	_	_
2164	1	1	CD	_	_	_
2165	mM	mm	NN	KWSUPP	_	_
2166	,	,	,	_	_	_
2167	rep	rep	NN	GEN	_	_
2168	3	3	CD	_	_	_
2169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2170	OTHER	other	NN	_	_	_
2171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2172	other	other	JJ	_	_	_
2173	extracted	extract	VBN	_	_	_
2174	using	use	VBG	_	_	_
2175	alkalyne	alkalyne	JJ	_	_	_
2176	lysis	lysis	NN	_	_	_
2177	preparation	preparation	NN	_	_	_
2178	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
15	outbreak	outbreak	NN	_	_	_
16	:	:	:	_	_	_
17	2011	2011	CD	_	_	_
18	outbreak	outbreak	NN	_	_	_
19	centered	center	VBN	_	_	_
20	in	in	IN	_	_	_
21	Northern	Northern	NNP	_	_	_
22	Germany	Germany	NNP	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	overexpression	overexpression	NN	_	_	_
25	:	:	:	_	_	_
26	-	-	:	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	overexpression	overexpression	NN	_	_	_
29	:	:	:	_	_	_
30	BglJ	bglj	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	overexpression	overexpression	NN	_	_	_
33	:	:	:	_	_	_
34	LeuO	leuo	NN	TF	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	overexpression	overexpression	NN	_	_	_
37	of	of	IN	_	_	_
38	arT	art	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	pCA24N	pca24n	NN	_	_	_
41	_	_	CD	_	_	_
42	arT	art	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	overexpression	overexpression	NN	_	_	_
46	of	of	IN	_	_	_
47	dosP	dosp	NN	GEN	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	pCA24N	pca24n	NN	_	_	_
50	_	_	CD	_	_	_
51	dosP	dosp	NN	GEN	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	overexpression	overexpression	NN	_	_	_
55	of	of	IN	_	_	_
56	empty	empty	JJ	_	_	_
57	vector	vector	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	pCA24N	pca24n	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Overnight	overnight	JJ	_	_	_
63	bacterial	bacterial	JJ	_	_	_
64	culture	culture	NN	_	_	_
65	in	in	IN	_	_	_
66	BHI	BHI	NNP	_	_	_
67	broth	broth	NN	_	_	_
68	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	overnight	overnight	JJ	_	_	_
3	bacterial	bacterial	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	in	in	IN	_	_	_
6	Luria	Luria	NNP	_	_	_
7	Broth	Broth	NNP	_	_	_
8	at	at	IN	_	_	_
9	37C	37c	NN	_	_	_
10	with	with	IN	_	_	_
11	shaking	shake	VBG	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	overnight	overnight	JJ	_	_	_
14	colony	colony	NN	_	_	_
15	growth	growth	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Overnight	Overnight	NNP	_	_	_
18	culture	culture	NN	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Overnight	overnight	JJ	_	_	_
21	culture	culture	NN	_	_	_
22	in	in	IN	_	_	_
23	LB	lb	NN	MED	_	_
24	medium	medium	NN	MED	_	_
25	was	be	VBD	_	_	_
26	innoculated	innoculate	VBN	_	_	_
27	from	from	IN	_	_	_
28	a	a	DT	_	_	_
29	single	single	JJ	_	_	_
30	colony	colony	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	overnight	overnight	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	diluted	dilute	VBN	_	_	_
6	1/200	1/200	CD	_	_	_
7	into	into	IN	_	_	_
8	MOPS	mop	NNS	MED	_	_
9	minimal	minimal	JJ	_	_	_
10	medium	medium	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Neidhardt	Neidhardt	NNP	_	_	_
13	,	,	,	_	_	_
14	J.	J.	NNP	_	_	_
15	Bacteriol.	Bacteriol.	NNP	_	_	_
16	,	,	,	_	_	_
17	1974	1974	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	incubated	incubate	VBN	_	_	_
21	with	with	IN	_	_	_
22	shaking	shake	VBG	_	_	_
23	at	at	IN	_	_	_
24	37	37	CD	_	_	_
25	C	c	NN	_	_	_
26	until	until	IN	_	_	_
27	OD600	od600	NN	_	_	_
28	=	=	JJ	_	_	_
29	0.5	0.5	CD	_	_	_
30	or	or	CC	_	_	_
31	OD600	od600	NN	_	_	_
32	=	=	JJ	_	_	_
33	0.3	0.3	CD	_	_	_
34	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	volume	volume	NN	_	_	_
4	10	10	CD	_	_	_
5	ml	ml	NN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Overnight	overnight	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	of	of	IN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	BW25113	bw25113	NN	_	_	_
8	in	in	IN	_	_	_
9	LB	lb	NN	_	_	_
10	was	be	VBD	_	_	_
11	diluted	dilute	VBN	_	_	_
12	in	in	IN	_	_	_
13	M9	m9	NN	MED	_	_
14	minimal	minimal	JJ	MED	_	_
15	medium	medium	NN	MED	_	_
16	with	with	IN	_	_	_
17	supplements	supplement	NNS	_	_	_
18	to	to	TO	_	_	_
19	OD600	od600	NN	_	_	_
20	=	=	JJ	_	_	_
21	0.02	0.02	CD	_	_	_
22	and	and	CC	_	_	_
23	was	be	VBD	_	_	_
24	incubated	incubate	VBN	_	_	_
25	at	at	IN	_	_	_
26	37	37	CD	_	_	_
27	Ceilsus	ceilsus	NN	_	_	_
28	degree	degree	NN	_	_	_
29	with	with	IN	_	_	_
30	shaking	shake	VBG	_	_	_
31	at	at	IN	_	_	_
32	250rpm	250rpm	NN	_	_	_
33	until	until	IN	_	_	_
34	its	its	PRP$	_	_	_
35	OD600	od600	NN	_	_	_
36	reached	reach	VBD	_	_	_
37	0.1	0.1	CD	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Overnight	overnight	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	of	of	IN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	in	in	IN	_	_	_
8	LB	lb	NN	_	_	_
9	was	be	VBD	_	_	_
10	diluted	dilute	VBN	_	_	_
11	in	in	IN	_	_	_
12	LB	lb	NN	_	_	_
13	supplemented	supplement	VBN	_	_	_
14	with	with	IN	_	_	_
15	0.8	0.8	CD	_	_	_
16	%	%	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	to	to	TO	_	_	_
19	OD600	od600	NN	_	_	_
20	=	=	JJ	_	_	_
21	0.02	0.02	CD	_	_	_
22	and	and	CC	_	_	_
23	was	be	VBD	_	_	_
24	continuously	continuously	RB	_	_	_
25	incubated	incubate	VBN	_	_	_
26	at	at	IN	_	_	_
27	30	30	CD	_	_	_
28	degree	degree	NN	_	_	_
29	celcius	celcius	NNS	_	_	_
30	with	with	IN	_	_	_
31	shaking	shake	VBG	_	_	_
32	until	until	IN	_	_	_
33	its	its	PRP$	_	_	_
34	OD600	od600	NN	_	_	_
35	reached	reach	VBD	_	_	_
36	1.0	1.0	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	Overnight	overnight	JJ	_	_	_
39	culture	culture	NN	_	_	_
40	of	of	IN	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	W3110	w3110	NN	_	_	_
44	in	in	IN	_	_	_
45	LB	lb	NN	_	_	_
46	was	be	VBD	_	_	_
47	diluted	dilute	VBN	_	_	_
48	in	in	IN	_	_	_
49	M9	m9	NN	MED	_	_
50	minimal	minimal	JJ	MED	_	_
51	medium	medium	NN	MED	_	_
52	with	with	IN	_	_	_
53	supplements	supplement	NNS	_	_	_
54	to	to	TO	_	_	_
55	OD600	od600	NN	_	_	_
56	=	=	JJ	_	_	_
57	0.01	0.01	CD	_	_	_
58	and	and	CC	_	_	_
59	was	be	VBD	_	_	_
60	incubated	incubate	VBN	_	_	_
61	at	at	IN	_	_	_
62	37	37	CD	_	_	_
63	Ceilsus	ceilsus	NN	_	_	_
64	degree	degree	NN	_	_	_
65	witouth	witouth	NN	_	_	_
66	shaking	shake	VBG	_	_	_
67	until	until	IN	_	_	_
68	its	its	PRP$	_	_	_
69	OD600	od600	NN	_	_	_
70	reached	reach	VBD	_	_	_
71	0.1	0.1	CD	_	_	_
72	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Overnight	Overnight	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	from	from	IN	_	_	_
5	isolated	isolate	VBN	_	_	_
6	colonies	colony	NNS	_	_	_
7	were	be	VBD	_	_	_
8	diluted	dilute	VBN	_	_	_
9	in	in	IN	_	_	_
10	fresh	fresh	JJ	_	_	_
11	medium	medium	NN	_	_	_
12	to	to	TO	_	_	_
13	an	a	DT	_	_	_
14	initial	initial	JJ	_	_	_
15	OD600	od600	NN	_	_	_
16	~	~	NN	_	_	_
17	0.03	0.03	CD	_	_	_
18	and	and	CC	_	_	_
19	grown	grow	VBN	_	_	_
20	to	to	TO	_	_	_
21	exponential	exponential	JJ	GrowthPhase	_	_
22	phase	phase	NN	GrowthPhase	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	OD600	od600	NN	_	_	_
25	~	~	NN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	at	at	IN	_	_	_
29	37ºC	37ºc	NN	_	_	_
30	,	,	,	_	_	_
31	with	with	IN	_	_	_
32	shaking	shake	VBG	_	_	_
33	at	at	IN	_	_	_
34	200	200	CD	_	_	_
35	rpm	rpm	NN	_	_	_
36	in	in	IN	_	_	_
37	Luria-Bertani	Luria-Bertani	NNP	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	LB	LB	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	medium	medium	NN	_	_	_
42	supplemented	supplement	VBN	_	_	_
43	with	with	IN	_	_	_
44	thymine	thymine	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	50	50	CD	_	_	_
47	mg	mg	NN	_	_	_
48	ml-1	ml-1	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	.	.	.	_	_	_

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/spectinomycin	streptomycin/spectinomycin	NNP	_	_	_
25	20	20	CD	_	_	_
26	µg	µg	NN	_	_	_
27	ml-1	ml-1	NN	_	_	_
28	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Overnight	Overnight	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	of	of	IN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	MG1655	mg1655	NN	_	_	_
8	grown	grow	VBN	_	_	_
9	at	at	IN	_	_	_
10	37	37	CD	_	_	_
11	°C	°c	NN	_	_	_
12	with	with	IN	_	_	_
13	shaking	shake	VBG	_	_	_
14	at	at	IN	_	_	_
15	200	200	CD	_	_	_
16	rpm	rpm	NN	_	_	_
17	were	be	VBD	_	_	_
18	diluted	dilute	VBN	_	_	_
19	1:625	1:625	CD	_	_	_
20	into	into	IN	_	_	_
21	50	50	CD	_	_	_
22	ml	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	LB	lb	NN	MED	_	_
25	broth	broth	NN	MED	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Roth	Roth	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	incubated	incubate	VBN	_	_	_
32	at	at	IN	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	with	with	IN	_	_	_
36	shaking	shake	VBG	_	_	_
37	at	at	IN	_	_	_
38	200	200	CD	_	_	_
39	rpm	rpm	NN	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Overnight	Overnight	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	of	of	IN	_	_	_
5	ESBL7	esbl7	NN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	original	original	JJ	_	_	_
9	isolate	isolate	NN	_	_	_
10	,	,	,	_	_	_
11	or	or	CC	_	_	_
12	isolates	isolate	NNS	_	_	_
13	pre-exposed	pre-expose	VBN	_	_	_
14	20	20	CD	_	_	_
15	times	time	NNS	_	_	_
16	to	to	TO	_	_	_
17	CORM-2	corm-2	NN	_	_	_
18	or	or	CC	_	_	_
19	vehicle	vehicle	NN	_	_	_
20	,	,	,	_	_	_
21	were	be	VBD	_	_	_
22	used	use	VBN	_	_	_
23	to	to	TO	_	_	_
24	inoculate	inoculate	VB	_	_	_
25	MS-medium	ms-medium	NN	_	_	_
26	,	,	,	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	OD620	od620	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	of	of	IN	_	_	_
31	0.1	0.1	CD	_	_	_
32	,	,	,	_	_	_
33	followed	follow	VBN	_	_	_
34	by	by	IN	_	_	_
35	exposure	exposure	NN	_	_	_
36	to	to	TO	_	_	_
37	CORM-2	corm-2	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	250	250	CD	_	_	_
40	µM	µm	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	or	or	CC	_	_	_
43	vehicle	vehicle	NN	_	_	_
44	for	for	IN	_	_	_
45	30	30	CD	_	_	_
46	min	min	NN	_	_	_
47	at	at	IN	_	_	_
48	37	37	CD	_	_	_
49	°C	°c	NN	_	_	_
50	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Overnight	Overnight	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	of	of	IN	_	_	_
5	strain	strain	NN	_	_	_
6	JM83	jm83	NN	_	_	_
7	were	be	VBD	_	_	_
8	diluted	dilute	VBN	_	_	_
9	1/100	1/100	CD	_	_	_
10	in	in	IN	_	_	_
11	LB	lb	NN	MED	_	_
12	medium	medium	NN	MED	_	_
13	and	and	CC	_	_	_
14	grown	grow	VBN	_	_	_
15	in	in	IN	_	_	_
16	microtiter	microtiter	NN	_	_	_
17	plates	plate	NNS	_	_	_
18	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	study	study	VB	_	_	_
3	the	the	DT	_	_	_
4	effects	effect	NNS	_	_	_
5	of	of	IN	_	_	_
6	trimethoprim	trimethoprim	NN	_	_	_
7	,	,	,	_	_	_
8	cells	cell	NNS	_	_	_
9	grown	grow	VBN	_	_	_
10	without	without	IN	_	_	_
11	antibiotics	antibiotic	NNS	_	_	_
12	were	be	VBD	_	_	_
13	compared	compare	VBN	_	_	_
14	to	to	TO	_	_	_
15	cells	cell	NNS	_	_	_
16	grown	grow	VBN	_	_	_
17	with	with	IN	_	_	_
18	0.5	0.5	CD	_	_	_
19	μg/ml	μg/ml	NN	_	_	_
20	trimethoprim	trimethoprim	NN	_	_	_
21	.	.	.	_	_	_

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

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	NN	_	_	_
2	overnight	overnight	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	subcultured	subculture	VBN	_	_	_
5	in	in	IN	_	_	_
6	either	either	DT	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	SCFA	scfa	NN	_	_	_
10	mixes	mix	VBZ	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	or	or	CC	_	_	_
13	the	the	DT	_	_	_
14	sodium	sodium	NN	SUPP	_	_
15	chloride	chloride	NN	SUPP	_	_
16	controls	control	NNS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	at	at	IN	_	_	_
19	37C	37c	NN	_	_	_
20	,	,	,	_	_	_
21	static	static	JJ	_	_	_
22	with	with	IN	_	_	_
23	5	5	CD	_	_	_
24	%	%	NN	_	_	_
25	CO2	co2	NN	_	_	_
26	to	to	TO	_	_	_
27	OD600	od600	NN	_	_	_
28	of	of	IN	_	_	_
29	1	1	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Overnight	overnight	NN	_	_	_
32	cultures	culture	NNS	_	_	_
33	were	be	VBD	_	_	_
34	inoculated	inoculate	VBN	_	_	_
35	1:100	1:100	CD	_	_	_
36	into	into	IN	_	_	_
37	20	20	CD	_	_	_
38	ml	ml	NN	_	_	_
39	of	of	IN	_	_	_
40	EZ	ez	NN	_	_	_
41	Rich	rich	JJ	_	_	_
42	Defined	defined	JJ	_	_	_
43	Medium	medium	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Neidhardt	Neidhardt	NNP	_	_	_
46	et	et	FW	_	_	_
47	al.	al.	FW	_	_	_
48	,	,	,	_	_	_
49	1974	1974	CD	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	in	in	IN	_	_	_
52	125	125	CD	_	_	_
53	ml	ml	NN	_	_	_
54	Erlenmeyer	erlenmeyer	NN	_	_	_
55	flasks	flask	NNS	_	_	_
56	and	and	CC	_	_	_
57	grown	grow	VBN	_	_	_
58	at	at	IN	_	_	_
59	37oC	37oc	NN	_	_	_
60	and	and	CC	_	_	_
61	250	250	CD	_	_	_
62	rpm	rpm	NN	_	_	_
63	in	in	IN	_	_	_
64	a	a	DT	_	_	_
65	reciprocating	reciprocate	VBG	_	_	_
66	water	water	NN	_	_	_
67	bath	bath	NN	_	_	_
68	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Overnight	Overnight	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	resuspended	resuspend	VBN	_	_	_
6	in	in	IN	_	_	_
7	fresh	fresh	JJ	_	_	_
8	medium	medium	NN	_	_	_
9	and	and	CC	_	_	_
10	TMP	tmp	NN	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	when	when	WRB	_	_	_
14	the	the	DT	_	_	_
15	optical	optical	JJ	_	_	_
16	density	density	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	O.D.	o.d.	NN	_	_	_
19	600	600	CD	_	_	_
20	nm	nm	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	of	of	IN	_	_	_
23	the	the	DT	_	_	_
24	culture	culture	NN	_	_	_
25	reached	reach	VBD	_	_	_
26	0.3-0.4	0.3-0.4	CD	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	overnight	overnight	JJ	_	_	_
3	in	in	IN	_	_	_
4	Luria-Bertani	Luria-Bertani	NNP	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	LB	LB	NNP	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	broth	broth	NN	_	_	_
9	with	with	IN	_	_	_
10	continuous	continuous	JJ	_	_	_
11	agitation	agitation	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	overnight	overnight	JJ	_	_	_
14	in	in	IN	_	_	_
15	Lurie-Bertani	Lurie-Bertani	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	LB	LB	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	broth	broth	NN	_	_	_
20	with	with	IN	_	_	_
21	continuous	continuous	JJ	_	_	_
22	agitation	agitation	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	oxic/anoxic	oxic/anoxic	JJ	_	_	_
25	:	:	:	_	_	_
26	anoxic	anoxic	JJ	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	NO3	no3	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	oxic/anoxic	oxic/anoxic	NN	_	_	_
32	:	:	:	_	_	_
33	oxic	oxic	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
35	Oxidative	oxidative	JJ	_	_	_
36	stress	stress	NN	_	_	_
37	200	200	CD	_	_	_
38	ug/ml	ug/ml	NN	_	_	_
39	of	of	IN	_	_	_
40	30	30	CD	_	_	_
41	%	%	NN	_	_	_
42	pre-warmed	pre-warmed	JJ	_	_	_
43	hydrogen	hydrogen	NN	SUPP	_	_
44	peroxide	peroxide	NN	SUPP	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	Fluka	fluka	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	was	be	VBD	_	_	_
49	added	add	VBN	_	_	_
50	to	to	TO	_	_	_
51	150	150	CD	_	_	_
52	ml	ml	NN	_	_	_
53	constantly	constantly	RB	_	_	_
54	stirred	stir	VBD	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	330	330	CD	_	_	_
57	rpm	rpm	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	cultures	culture	NNS	_	_	_
60	kept	keep	VBD	_	_	_
61	in	in	IN	_	_	_
62	1000	1000	CD	_	_	_
63	ml	ml	NN	_	_	_
64	flasks	flask	NNS	_	_	_
65	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	stress	stress	NN	_	_	_
3	Cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	transferred	transfer	VBN	_	_	_
6	from	from	IN	_	_	_
7	37oC	37oc	NN	_	_	_
8	into	into	IN	_	_	_
9	an	a	DT	_	_	_
10	ice	ice	NN	_	_	_
11	cold	cold	JJ	_	_	_
12	water	water	NN	_	_	_
13	bath	bath	NN	_	_	_
14	in	in	IN	_	_	_
15	order	order	NN	_	_	_
16	to	to	TO	_	_	_
17	lower	lower	VB	_	_	_
18	the	the	DT	_	_	_
19	temperature	temperature	NN	_	_	_
20	,	,	,	_	_	_
21	while	while	IN	_	_	_
22	stirring	stir	VBG	_	_	_
23	,	,	,	_	_	_
24	to	to	TO	_	_	_
25	16oC	16oc	NN	_	_	_
26	in	in	IN	_	_	_
27	less	less	JJR	_	_	_
28	than	than	IN	_	_	_
29	2	2	CD	_	_	_
30	min	min	NN	_	_	_
31	,	,	,	_	_	_
32	heat	heat	NN	_	_	_
33	stress	stress	NN	_	_	_
34	Cultures	culture	NNS	_	_	_
35	were	be	VBD	_	_	_
36	transferred	transfer	VBN	_	_	_
37	from	from	IN	_	_	_
38	37oC	37oc	NN	_	_	_
39	to	to	TO	_	_	_
40	a	a	DT	_	_	_
41	50oC	50oc	NN	_	_	_
42	water	water	NN	_	_	_
43	bath	bath	NN	_	_	_
44	.	.	.	_	_	_

1	While	while	IN	_	_	_
2	stirring	stir	VBG	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	temperature	temperature	NN	_	_	_
6	of	of	IN	_	_	_
7	each	each	DT	_	_	_
8	culture	culture	NN	_	_	_
9	was	be	VBD	_	_	_
10	raised	raise	VBN	_	_	_
11	to	to	TO	_	_	_
12	45oC	45oc	NN	_	_	_
13	in	in	IN	_	_	_
14	less	less	JJR	_	_	_
15	than	than	IN	_	_	_
16	2	2	CD	_	_	_
17	min	min	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	constantly	constantly	RB	_	_	_
3	stirring	stir	VBG	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	330rpm	330rpm	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	cultures	culture	NNS	_	_	_
8	were	be	VBD	_	_	_
9	then	then	RB	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	a	a	DT	_	_	_
13	45oC	45oc	NN	_	_	_
14	water	water	NN	_	_	_
15	bath	bath	NN	_	_	_
16	to	to	TO	_	_	_
17	maintain	maintain	VB	_	_	_
18	this	this	DT	_	_	_
19	temperature	temperature	NN	_	_	_
20	glucose	glucose	NN	SUPP	_	_
21	lactose	lactose	NN	_	_	_
22	shift	shift	NN	_	_	_
23	Carbon	Carbon	NNP	_	_	_
24	source	source	NN	_	_	_
25	concentrations	concentration	NNS	_	_	_
26	of	of	IN	_	_	_
27	0.15	0.15	CD	_	_	_
28	%	%	NN	_	_	_
29	lactose	lactose	NN	_	_	_
30	and	and	CC	_	_	_
31	0.05	0.05	CD	_	_	_
32	%	%	NN	_	_	_
33	glucose	glucose	NN	SUPP	_	_
34	were	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	150	150	CD	_	_	_
38	ml	ml	NN	_	_	_
39	culture	culture	NN	_	_	_
40	in	in	IN	_	_	_
41	1000	1000	CD	_	_	_
42	ml	ml	NN	_	_	_
43	flasks	flask	NNS	_	_	_
44	,	,	,	_	_	_
45	330	330	CD	_	_	_
46	rpm	rpm	NN	_	_	_
47	stirring	stir	VBG	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Oxidative	oxidative	JJ	_	_	_
3	stress	stress	NN	_	_	_
4	in	in	IN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	K-12	k-12	NN	_	_	_
8	#	#	#	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Oxidative	oxidative	JJ	_	_	_
12	stress	stress	NN	_	_	_
13	in	in	IN	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	K-12	k-12	NN	_	_	_
17	#	#	#	_	_	_
18	2	2	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	3	3	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	O157	o157	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Sakai	Sakai	NNP	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	#	#	#	_	_	_
39	1	1	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Oxidative	oxidative	JJ	_	_	_
42	stress	stress	NN	_	_	_
43	in	in	IN	_	_	_
44	E.	e.	FW	_	_	_
45	coli	coli	FW	_	_	_
46	O157	o157	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Sakai	Sakai	NNP	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	#	#	#	_	_	_
51	2	2	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
53	Oxidative	oxidative	JJ	_	_	_
54	stress	stress	NN	_	_	_
55	in	in	IN	_	_	_
56	E.	e.	FW	_	_	_
57	coli	coli	FW	_	_	_
58	O157	o157	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	Sakai	Sakai	NNP	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	#	#	#	_	_	_
63	3	3	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Oxo	Oxo	NNP	_	_	_
66	_	_	NNP	_	_	_
67	IN	in	IN	_	_	_
68	_	_	CD	_	_	_
69	120mkM	120mkm	NN	_	_	_
70	_	_	NN	_	_	_
71	3	3	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	Oxo	Oxo	NNP	_	_	_
74	_	_	NNP	_	_	_
75	IN	in	IN	_	_	_
76	_	_	SYM	_	_	_
77	Mu	mu	FW	_	_	_
78	_	_	FW	_	_	_
79	120mkM	120mkm	NN	_	_	_
80	_	_	NN	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Oxo	Oxo	NNP	_	_	_
84	_	_	NNP	_	_	_
85	IN	in	IN	_	_	_
86	_	_	SYM	_	_	_
87	Mu	mu	FW	_	_	_
88	_	_	FW	_	_	_
89	120mkM	120mkm	NN	_	_	_
90	_	_	NN	_	_	_
91	2	2	CD	_	_	_
92	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
93	Oxo	Oxo	NNP	_	_	_
94	_	_	NNP	_	_	_
95	IP	IP	NNP	_	_	_
96	_	_	SYM	_	_	_
97	120mkM	120mkm	NN	_	_	_
98	_	_	NN	_	_	_
99	3	3	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	Oxo	Oxo	NNP	_	_	_
102	_	_	NNP	_	_	_
103	IP	IP	NNP	_	_	_
104	_	_	SYM	_	_	_
105	Mu	mu	FW	_	_	_
106	_	_	FW	_	_	_
107	120mkM	120mkm	NN	_	_	_
108	_	_	NN	_	_	_
109	1	1	CD	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	Oxo	Oxo	NNP	_	_	_
112	_	_	NNP	_	_	_
113	IP	IP	NNP	_	_	_
114	_	_	SYM	_	_	_
115	Mu	mu	FW	_	_	_
116	_	_	FW	_	_	_
117	120mkM	120mkm	NN	_	_	_
118	_	_	NN	_	_	_
119	2	2	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Oxolinic	oxolinic	JJ	_	_	_
122	acid	acid	NN	_	_	_
123	Rep	Rep	NNP	_	_	_
124	1	1	CD	_	_	_
125	+	+	CC	_	_	_
126	A-IP	a-ip	JJ	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Oxolinic	oxolinic	JJ	_	_	_
129	acid	acid	NN	_	_	_
130	Rep	Rep	NNP	_	_	_
131	1	1	CD	_	_	_
132	+	+	CC	_	_	_
133	A+IP	A+IP	NNP	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	Oxolinic	oxolinic	JJ	_	_	_
136	acid	acid	NN	_	_	_
137	Rep	Rep	NNP	_	_	_
138	2	2	CD	_	_	_
139	+	+	CC	_	_	_
140	A-IP	a-ip	JJ	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	Oxolinic	oxolinic	JJ	_	_	_
143	acid	acid	NN	_	_	_
144	Rep	Rep	NNP	_	_	_
145	2	2	CD	_	_	_
146	+	+	CC	_	_	_
147	A+IP	A+IP	NNP	_	_	_
148	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
149	Oxolinic	oxolinic	JJ	_	_	_
150	acid	acid	NN	_	_	_
151	Rep	Rep	NNP	_	_	_
152	3	3	CD	_	_	_
153	+	+	CC	_	_	_
154	A-IP	a-ip	JJ	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	Oxolinic	oxolinic	JJ	_	_	_
157	acid	acid	NN	_	_	_
158	Rep	Rep	NNP	_	_	_
159	3	3	CD	_	_	_
160	+	+	CC	_	_	_
161	A+IP	A+IP	NNP	_	_	_
162	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
163	oxygen	oxygen	NN	_	_	_
164	condition	condition	NN	_	_	_
165	:	:	:	_	_	_
166	aerobic	aerobic	JJ	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	oxygen	oxygen	NN	_	_	_
169	condition	condition	NN	_	_	_
170	:	:	:	_	_	_
171	anaerobic	anaerobic	JJ	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	oxygen	oxygen	NN	_	_	_
174	_	_	CD	_	_	_
175	down	down	IN	_	_	_
176	_	_	CD	_	_	_
177	0	0	CD	_	_	_
178	min	min	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	oxygen	oxygen	NN	_	_	_
181	_	_	CD	_	_	_
182	down	down	IN	_	_	_
183	_	_	CD	_	_	_
184	12	12	CD	_	_	_
185	min	min	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	oxygen	oxygen	NN	_	_	_
188	_	_	CD	_	_	_
189	down	down	IN	_	_	_
190	_	_	CD	_	_	_
191	20	20	CD	_	_	_
192	min	min	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	oxygen	oxygen	NN	_	_	_
195	_	_	CD	_	_	_
196	down	down	IN	_	_	_
197	_	_	CD	_	_	_
198	28	28	CD	_	_	_
199	min	min	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	oxygen	oxygen	NN	_	_	_
202	_	_	CD	_	_	_
203	down	down	IN	_	_	_
204	_	_	CD	_	_	_
205	44	44	CD	_	_	_
206	min	min	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	oxygen	oxygen	NN	_	_	_
209	_	_	CD	_	_	_
210	down	down	IN	_	_	_
211	_	_	CD	_	_	_
212	4	4	CD	_	_	_
213	min	min	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	oxygen	oxygen	NN	_	_	_
216	_	_	CD	_	_	_
217	down	down	IN	_	_	_
218	_	_	CD	_	_	_
219	8	8	CD	_	_	_
220	min	min	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	oxygen	oxygen	NN	_	_	_
223	down	down	IN	_	_	_
224	shift	shift	NN	_	_	_
225	,	,	,	_	_	_
226	0	0	CD	_	_	_
227	min	min	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	oxygen	oxygen	NN	_	_	_
230	down	down	IN	_	_	_
231	shift	shift	NN	_	_	_
232	,	,	,	_	_	_
233	12	12	CD	_	_	_
234	min	min	NN	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	oxygen	oxygen	NN	_	_	_
237	down	down	IN	_	_	_
238	shift	shift	NN	_	_	_
239	,	,	,	_	_	_
240	20	20	CD	_	_	_
241	min	min	NN	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	oxygen	oxygen	NN	_	_	_
244	down	down	IN	_	_	_
245	shift	shift	NN	_	_	_
246	,	,	,	_	_	_
247	28	28	CD	_	_	_
248	min	min	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	oxygen	oxygen	NN	_	_	_
251	down	down	IN	_	_	_
252	shift	shift	NN	_	_	_
253	,	,	,	_	_	_
254	44	44	CD	_	_	_
255	min	min	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	oxygen	oxygen	NN	_	_	_
258	down	down	IN	_	_	_
259	shift	shift	NN	_	_	_
260	,	,	,	_	_	_
261	4	4	CD	_	_	_
262	min	min	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	oxygen	oxygen	NN	_	_	_
265	down	down	IN	_	_	_
266	shift	shift	NN	_	_	_
267	,	,	,	_	_	_
268	8	8	CD	_	_	_
269	min	min	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	oxygen	oxygen	NN	_	_	_
272	regime	regime	NN	_	_	_
273	:	:	:	_	_	_
274	daily	daily	JJ	_	_	_
275	shift	shift	NN	_	_	_
276	between	between	IN	_	_	_
277	shaking	shake	VBG	_	_	_
278	and	and	CC	_	_	_
279	static	static	JJ	_	_	_
280	-LRB-	-lrb-	-LRB-	_	_	_
281	no	no	DT	_	_	_
282	shaking	shake	VBG	_	_	_
283	-RRB-	-rrb-	-RRB-	_	_	_
284	conditions	condition	NNS	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
286	oxygen	oxygen	NN	_	_	_
287	regime	regime	NN	_	_	_
288	:	:	:	_	_	_
289	transfers	transfer	NNS	_	_	_
290	in	in	IN	_	_	_
291	constant	constant	JJ	_	_	_
292	static	static	JJ	_	_	_
293	conditions	condition	NNS	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
295	oxygen	oxygen	NN	_	_	_
296	regime	regime	NN	_	_	_
297	:	:	:	_	_	_
298	transfers	transfer	NNS	_	_	_
299	under	under	IN	_	_	_
300	constant	constant	JJ	_	_	_
301	shaking	shake	VBG	_	_	_
302	-LRB-	-lrb-	-LRB-	_	_	_
303	200rpm	200rpm	NN	_	_	_
304	-RRB-	-rrb-	-RRB-	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	oxygen	oxygen	NN	_	_	_
307	_	_	CD	_	_	_
308	Up	up	IN	_	_	_
309	_	_	CD	_	_	_
310	0	0	CD	_	_	_
311	min	min	NN	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	oxygen	oxygen	NN	_	_	_
314	_	_	CD	_	_	_
315	Up	up	IN	_	_	_
316	_	_	CD	_	_	_
317	12	12	CD	_	_	_
318	min	min	NN	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	oxygen	oxygen	NN	_	_	_
321	_	_	CD	_	_	_
322	Up	up	IN	_	_	_
323	_	_	CD	_	_	_
324	20	20	CD	_	_	_
325	min	min	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	oxygen	oxygen	NN	_	_	_
328	_	_	CD	_	_	_
329	Up	up	IN	_	_	_
330	_	_	CD	_	_	_
331	28	28	CD	_	_	_
332	min	min	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	oxygen	oxygen	NN	_	_	_
335	_	_	CD	_	_	_
336	Up	up	IN	_	_	_
337	_	_	CD	_	_	_
338	44	44	CD	_	_	_
339	min	min	NN	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	oxygen	oxygen	NN	_	_	_
342	_	_	CD	_	_	_
343	Up	up	IN	_	_	_
344	_	_	CD	_	_	_
345	4	4	CD	_	_	_
346	min	min	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	oxygen	oxygen	NN	_	_	_
349	_	_	CD	_	_	_
350	Up	up	IN	_	_	_
351	_	_	CD	_	_	_
352	8	8	CD	_	_	_
353	min	min	NN	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	oxygen	oxygen	NN	_	_	_
356	up	up	IN	_	_	_
357	shift	shift	NN	_	_	_
358	,	,	,	_	_	_
359	0	0	CD	_	_	_
360	min	min	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	oxygen	oxygen	NN	_	_	_
363	up	up	IN	_	_	_
364	shift	shift	NN	_	_	_
365	,	,	,	_	_	_
366	12	12	CD	_	_	_
367	min	min	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	oxygen	oxygen	NN	_	_	_
370	up	up	IN	_	_	_
371	shift	shift	NN	_	_	_
372	,	,	,	_	_	_
373	20	20	CD	_	_	_
374	min	min	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	oxygen	oxygen	NN	_	_	_
377	up	up	IN	_	_	_
378	shift	shift	NN	_	_	_
379	,	,	,	_	_	_
380	28	28	CD	_	_	_
381	min	min	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	oxygen	oxygen	NN	_	_	_
384	up	up	IN	_	_	_
385	shift	shift	NN	_	_	_
386	,	,	,	_	_	_
387	44	44	CD	_	_	_
388	min	min	NN	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	oxygen	oxygen	NN	_	_	_
391	up	up	IN	_	_	_
392	shift	shift	NN	_	_	_
393	,	,	,	_	_	_
394	4	4	CD	_	_	_
395	min	min	NN	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
397	oxygen	oxygen	NN	_	_	_
398	up	up	IN	_	_	_
399	shift	shift	NN	_	_	_
400	,	,	,	_	_	_
401	8	8	CD	_	_	_
402	min	min	NN	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	oxyR-8myc-tagged	oxyr-8myc-tagged	JJ	_	_	_
405	_	_	NN	_	_	_
406	PQ	pq	NN	_	_	_
407	treated	treat	VBN	_	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	OxyR	oxyr	NN	TF	_	_
410	PQ	pq	NN	_	_	_
411	1	1	CD	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	OxyR	oxyr	NN	TF	_	_
414	PQ	pq	NN	_	_	_
415	2	2	CD	_	_	_
416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
417	P2-08	p2-08	NN	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	P2-08	p2-08	NN	_	_	_
420	_	_	CD	_	_	_
421	R1	r1	NN	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	P2-08	p2-08	NN	_	_	_
424	_	_	CD	_	_	_
425	R2	r2	NN	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	P2-08	p2-08	NN	_	_	_
428	_	_	CD	_	_	_
429	R3	r3	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	P2-51	p2-51	NN	_	_	_
432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
433	P2-51	p2-51	NN	_	_	_
434	_	_	CD	_	_	_
435	R1	r1	NN	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	P2-51	p2-51	NN	_	_	_
438	_	_	CD	_	_	_
439	R2	r2	NN	_	_	_
440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
441	P2-51	p2-51	NN	_	_	_
442	_	_	CD	_	_	_
443	R3	r3	NN	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	P2-58	p2-58	NN	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	P2-58	p2-58	NN	_	_	_
448	_	_	CD	_	_	_
449	R1	r1	NN	_	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
451	P2-58	p2-58	NN	_	_	_
452	_	_	CD	_	_	_
453	R2	r2	NN	_	_	_
454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
455	P2-58	p2-58	NN	_	_	_
456	_	_	CD	_	_	_
457	R3	r3	NN	_	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	P2-66	p2-66	NN	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	P2-66	p2-66	NN	_	_	_
462	_	_	CD	_	_	_
463	R1	r1	NN	_	_	_
464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
465	P2-66	p2-66	NN	_	_	_
466	_	_	CD	_	_	_
467	R2	r2	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	P2-66	p2-66	NN	_	_	_
470	_	_	CD	_	_	_
471	R3	r3	NN	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	P2-77	p2-77	NN	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	P2-77	p2-77	NN	_	_	_
476	_	_	CD	_	_	_
477	R1	r1	NN	_	_	_
478	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
479	P2-77	p2-77	NN	_	_	_
480	_	_	CD	_	_	_
481	R2	r2	NN	_	_	_
482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
483	P2-77	p2-77	NN	_	_	_
484	_	_	CD	_	_	_
485	R3	r3	NN	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	P4XB2	p4xb2	NN	_	_	_
488	Mutant	mutant	JJ	_	_	_
489	-LRB-	-lrb-	-LRB-	_	_	_
490	1992	1992	CD	_	_	_
491	-RRB-	-rrb-	-RRB-	_	_	_
492	in	in	IN	_	_	_
493	Arginine	arginine	NN	_	_	_
494	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
495	P4XB2	p4xb2	NN	_	_	_
496	Mutant	mutant	JJ	_	_	_
497	-LRB-	-lrb-	-LRB-	_	_	_
498	1993	1993	CD	_	_	_
499	-RRB-	-rrb-	-RRB-	_	_	_
500	in	in	IN	_	_	_
501	Arginine	arginine	NN	_	_	_
502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
503	P4XB2	p4xb2	NN	_	_	_
504	Mutant	mutant	JJ	_	_	_
505	-LRB-	-lrb-	-LRB-	_	_	_
506	1994	1994	CD	_	_	_
507	-RRB-	-rrb-	-RRB-	_	_	_
508	in	in	IN	_	_	_
509	Arginine	arginine	NN	_	_	_
510	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
511	P4X	p4x	NN	_	_	_
512	Wild	Wild	NNP	_	_	_
513	Type	type	NN	_	_	_
514	-LRB-	-lrb-	-LRB-	_	_	_
515	1753	1753	CD	_	_	_
516	-RRB-	-rrb-	-RRB-	_	_	_
517	Reference	Reference	NNP	_	_	_
518	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
519	P4X	P4X	NNP	_	_	_
520	Wild	Wild	NNP	_	_	_
521	Type	type	NN	_	_	_
522	-LRB-	-lrb-	-LRB-	_	_	_
523	1754	1754	CD	_	_	_
524	-RRB-	-rrb-	-RRB-	_	_	_
525	in	in	IN	_	_	_
526	Arginine	arginine	NN	_	_	_
527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
528	P4X	p4x	NN	_	_	_
529	Wild	Wild	NNP	_	_	_
530	Type	type	NN	_	_	_
531	-LRB-	-lrb-	-LRB-	_	_	_
532	1765	1765	CD	_	_	_
533	-RRB-	-rrb-	-RRB-	_	_	_
534	Reference	Reference	NNP	_	_	_
535	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
536	P4X	P4X	NNP	_	_	_
537	Wild	Wild	NNP	_	_	_
538	Type	type	NN	_	_	_
539	-LRB-	-lrb-	-LRB-	_	_	_
540	1766	1766	CD	_	_	_
541	-RRB-	-rrb-	-RRB-	_	_	_
542	in	in	IN	_	_	_
543	Arginine	arginine	NN	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	P4X	p4x	NN	_	_	_
546	Wild	Wild	NNP	_	_	_
547	Type	type	NN	_	_	_
548	-LRB-	-lrb-	-LRB-	_	_	_
549	1989	1989	CD	_	_	_
550	-RRB-	-rrb-	-RRB-	_	_	_
551	Reference	Reference	NNP	_	_	_
552	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
553	P4X	P4X	NNP	_	_	_
554	Wild	Wild	NNP	_	_	_
555	Type	type	NN	_	_	_
556	-LRB-	-lrb-	-LRB-	_	_	_
557	1990	1990	CD	_	_	_
558	-RRB-	-rrb-	-RRB-	_	_	_
559	in	in	IN	_	_	_
560	Arginine	arginine	NN	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	P500	p500	CD	_	_	_
563	_	_	NN	_	_	_
564	1	1	CD	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	PA20	pa20	NN	_	_	_
567	cultures	culture	NNS	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	PA20	pa20	NN	_	_	_
570	cultures	culture	NNS	_	_	_
571	for	for	IN	_	_	_
572	RNA-seq	rna-seq	NN	_	_	_
573	were	be	VBD	_	_	_
574	grown	grow	VBN	_	_	_
575	on	on	IN	_	_	_
576	T-agar	t-agar	JJ	_	_	_
577	with	with	IN	_	_	_
578	and	and	CC	_	_	_
579	without	without	IN	_	_	_
580	added	add	VBN	_	_	_
581	Sulfamethoxazole	Sulfamethoxazole	NNP	_	_	_
582	-	-	:	_	_	_
583	Trimethoprim	Trimethoprim	NNP	_	_	_
584	at	at	IN	_	_	_
585	designated	designate	VBN	_	_	_
586	levels	level	NNS	_	_	_
587	for	for	IN	_	_	_
588	the	the	DT	_	_	_
589	indicated	indicated	JJ	_	_	_
590	times	time	NNS	_	_	_
591	and	and	CC	_	_	_
592	temperatures	temperature	NNS	_	_	_
593	.	.	.	_	_	_

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	Paired-end	paired-end	NN	_	_	_
3	reads	read	VBZ	_	_	_
4	mapped	map	VBN	_	_	_
5	to	to	TO	_	_	_
6	MG1655	mg1655	NN	_	_	_
7	genome	genome	NN	_	_	_
8	using	use	VBG	_	_	_
9	bowtie2	bowtie2	NN	_	_	_
10	with	with	IN	_	_	_
11	default	default	NN	_	_	_
12	settings	setting	NNS	_	_	_
13	.	.	.	_	_	_

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	paired	paired	JJ	_	_	_
3	end	end	NN	_	_	_
4	sequencing	sequencing	NN	_	_	_
5	with	with	IN	_	_	_
6	Illumina	Illumina	NNP	_	_	_
7	HiSeq	HiSeq	NNP	_	_	_
8	2500	2500	CD	_	_	_
9	Sequencer	Sequencer	NNP	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Paired-end	paired-end	NN	_	_	_
12	,	,	,	_	_	_
13	strand-specific	strand-specific	JJ	_	_	_
14	RNAseq	rnaseq	NN	_	_	_
15	libraries	library	NNS	_	_	_
16	were	be	VBD	_	_	_
17	generated	generate	VBN	_	_	_
18	using	use	VBG	_	_	_
19	the	the	DT	_	_	_
20	dUTP	dutp	NN	_	_	_
21	method	method	NN	_	_	_
22	-LCB-	-lcb-	-LRB-	_	_	_
23	Levin	Levin	NNP	_	_	_
24	JZ	JZ	NNP	_	_	_
25	et	et	FW	_	_	_
26	al.	al.	FW	_	_	_
27	2010	2010	CD	_	_	_
28	,	,	,	_	_	_
29	Nat	Nat	NNP	_	_	_
30	Methods	method	NNS	_	_	_
31	-RCB-	-rcb-	-RRB-	_	_	_
32	with	with	IN	_	_	_
33	the	the	DT	_	_	_
34	following	follow	VBG	_	_	_
35	modifications	modification	NNS	_	_	_
36	.	.	.	_	_	_

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	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	Paraquat	paraquat	NN	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	growing	grow	VBG	_	_	_
15	cultures	culture	NNS	_	_	_
16	at	at	IN	_	_	_
17	a	a	DT	_	_	_
18	final	final	JJ	_	_	_
19	concentration	concentration	NN	_	_	_
20	of	of	IN	_	_	_
21	250	250	CD	_	_	_
22	?	?	.	_	_	_

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	parental	parental	JJ	_	_	_
16	_	_	NN	_	_	_
17	temperature	temperature	NN	_	_	_
18	_	_	CD	_	_	_
19	Up	up	IN	_	_	_
20	_	_	CD	_	_	_
21	0	0	CD	_	_	_
22	min	min	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	parental	parental	JJ	_	_	_
25	_	_	NN	_	_	_
26	temperature	temperature	NN	_	_	_
27	_	_	VBD	_	_	_
28	Up	up	RP	_	_	_
29	_	_	SYM	_	_	_
30	16	16	CD	_	_	_
31	min	min	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	parental	parental	JJ	_	_	_
34	_	_	NN	_	_	_
35	temperature	temperature	NN	_	_	_
36	_	_	VBD	_	_	_
37	Up	up	RP	_	_	_
38	_	_	SYM	_	_	_
39	44	44	CD	_	_	_
40	min	min	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	parental	parental	JJ	_	_	_
43	temperature	temperature	NN	_	_	_
44	up	up	IN	_	_	_
45	shift	shift	NN	_	_	_
46	0	0	CD	_	_	_
47	min	min	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
49	parental	parental	JJ	_	_	_
50	temperature	temperature	NN	_	_	_
51	up	up	IN	_	_	_
52	shift	shift	NN	_	_	_
53	16	16	CD	_	_	_
54	min	min	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
56	parental	parental	JJ	_	_	_
57	temperature	temperature	NN	_	_	_
58	up	up	IN	_	_	_
59	shift	shift	NN	_	_	_
60	44	44	CD	_	_	_
61	min	min	NN	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Parent	Parent	NNP	_	_	_
64	LB	LB	NNP	_	_	_
65	rep1	rep1	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Parent	Parent	NNP	_	_	_
68	LB	LB	NNP	_	_	_
69	rep2	rep2	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Parent	Parent	NNP	_	_	_
72	M9	M9	NNP	_	_	_
73	rep1	rep1	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	Parent	Parent	NNP	_	_	_
76	M9	M9	NNP	_	_	_
77	rep2	rep2	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	parent	parent	NN	_	_	_
80	strain	strain	NN	_	_	_
81	:	:	:	_	_	_
82	BW27785	bw27785	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Parent	Parent	NNP	_	_	_
85	strain	strain	NN	_	_	_
86	of	of	IN	_	_	_
87	experimental	experimental	JJ	_	_	_
88	evolution	evolution	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Parent	Parent	NNP	_	_	_
91	strain	strain	NN	_	_	_
92	of	of	IN	_	_	_
93	experimental	experimental	JJ	_	_	_
94	evolution	evolution	NN	_	_	_
95	as	as	IN	_	_	_
96	adaptive	adaptive	JJ	_	_	_
97	evolved	evolve	VBD	_	_	_
98	E.	e.	FW	_	_	_
99	coli	coli	FW	_	_	_
100	W3110	w3110	NN	_	_	_
101	strain	strain	NN	_	_	_
102	to	to	TO	_	_	_
103	M9	m9	NN	_	_	_
104	synthetic	synthetic	JJ	_	_	_
105	medium	medium	NN	_	_	_
106	without	without	IN	_	_	_
107	ethanol	ethanol	NN	_	_	_
108	stress	stress	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	passage	passage	NN	_	_	_
111	:	:	:	_	_	_
112	4	4	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	Pause	pause	NN	_	_	_
115	sites	site	NNS	_	_	_
116	in	in	IN	_	_	_
117	E.	e.	FW	_	_	_
118	coli	coli	FW	_	_	_
119	wild-type	wild-type	JJ	_	_	_
120	strain	strain	NN	_	_	_
121	identified	identify	VBN	_	_	_
122	by	by	IN	_	_	_
123	RNET-seq	rnet-seq	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Pause	pause	NN	_	_	_
126	sites	site	NNS	_	_	_
127	in	in	IN	_	_	_
128	E.	e.	FW	_	_	_
129	coli	coli	FW	_	_	_
130	ΔgreAB	δgreab	NN	_	_	_
131	strain	strain	NN	_	_	_
132	identified	identify	VBN	_	_	_
133	by	by	IN	_	_	_
134	RNET-seq	rnet-seq	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	PC	pc	NN	_	_	_
137	1	1	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	PC	pc	NN	_	_	_
140	2	2	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	PC	pc	NN	_	_	_
143	3	3	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	pCA24N-hns	pca24n-hn	NNS	_	_	_
146	biofilm	biofilm	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	pCA24N-hnsK57N	pca24n-hnsk57n	NN	_	_	_
149	biofilm	biofilm	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	PCA	pca	NN	_	_	_
152	analysis	analysis	NN	_	_	_
153	was	be	VBD	_	_	_
154	performed	perform	VBN	_	_	_
155	using	use	VBG	_	_	_
156	the	the	DT	_	_	_
157	top	top	JJ	_	_	_
158	500	500	CD	_	_	_
159	genes	gene	NNS	_	_	_
160	with	with	IN	_	_	_
161	the	the	DT	_	_	_
162	most	most	RBS	_	_	_
163	variations	variation	NNS	_	_	_
164	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	PCK	pck	NN	_	_	_
3	_	_	CD	_	_	_
4	glucose-minimal	glucose-minimal	JJ	_	_	_
5	medium	medium	NN	_	_	_
6	_	_	NN	_	_	_
7	early	early	JJ	_	_	_
8	log	log	NN	_	_	_
9	phase	phase	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	PCK	pck	NN	_	_	_
12	_	_	CD	_	_	_
13	LB-GlC	lb-glc	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	_	_	NN	_	_	_
16	D	d	NN	_	_	_
17	=	=	JJ	_	_	_
18	0.1	0.1	CD	_	_	_
19	h-1	h-1	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	PCK	pck	NN	_	_	_
22	over	over	IN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	pControl	pcontrol	NN	_	_	_
25	_	_	CD	_	_	_
26	exponential	exponential	JJ	_	_	_
27	growth	growth	NN	_	_	_
28	phase	phase	NN	_	_	_
29	_	_	NN	_	_	_
30	1	1	CD	_	_	_
31	ml	ml	NN	_	_	_
32	cell	cell	NN	_	_	_
33	pellet	pellet	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	pControl	pcontrol	NN	_	_	_
36	_	_	CD	_	_	_
37	stationary	stationary	JJ	_	_	_
38	growth	growth	NN	_	_	_
39	phase	phase	NN	_	_	_
40	_	_	NN	_	_	_
41	1	1	CD	_	_	_
42	ml	ml	NN	_	_	_
43	cell	cell	NN	_	_	_
44	pellet	pellet	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	pControl	pcontrol	NN	_	_	_
47	_	_	CD	_	_	_
48	transition	transition	NN	_	_	_
49	growth	growth	NN	_	_	_
50	phase	phase	NN	_	_	_
51	_	_	NN	_	_	_
52	1	1	CD	_	_	_
53	ml	ml	NN	_	_	_
54	cell	cell	NN	_	_	_
55	pellet	pellet	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Peak	peak	JJ	_	_	_
58	calling	calling	NN	_	_	_
59	was	be	VBD	_	_	_
60	done	do	VBN	_	_	_
61	using	use	VBG	_	_	_
62	SPAT	spat	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Peak-calls	peak-call	NNS	_	_	_
65	were	be	VBD	_	_	_
66	done	do	VBN	_	_	_
67	using	use	VBG	_	_	_
68	GPS	gps	NN	_	_	_
69	within	within	IN	_	_	_
70	the	the	DT	_	_	_
71	GEMS	gem	NNS	_	_	_
72	software	software	NN	_	_	_
73	package	package	NN	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	v2	v2	NN	_	_	_
76	.3	.3	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	adapted	adapt	VBD	_	_	_
79	for	for	IN	_	_	_
80	ChIP-exo	ChIP-exo	NNP	_	_	_
81	data	datum	NNS	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
83	Peak	peak	JJ	_	_	_
84	detection	detection	NN	_	_	_
85	and	and	CC	_	_	_
86	count	count	NN	_	_	_
87	of	of	IN	_	_	_
88	coverage	coverage	NN	_	_	_
89	were	be	VBD	_	_	_
90	done	do	VBN	_	_	_
91	using	use	VBG	_	_	_
92	SEQMONK	SEQMONK	NNP	_	_	_
93	version	version	NN	_	_	_
94	0.21.0	0.21.0	CD	_	_	_
95	by	by	IN	_	_	_
96	Fasteris	Fasteris	NNP	_	_	_
97	SA	SA	NNP	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	Peaks	Peaks	NNPS	_	_	_
100	on	on	IN	_	_	_
101	opposing	oppose	VBG	_	_	_
102	strands	strand	NNS	_	_	_
103	were	be	VBD	_	_	_
104	paired	pair	VBN	_	_	_
105	with	with	IN	_	_	_
106	Genetrack	genetrack	NN	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	u	u	NN	_	_	_
109	=	=	JJ	_	_	_
110	0	0	CD	_	_	_
111	,	,	,	_	_	_
112	d	d	NN	_	_	_
113	=	=	JJ	_	_	_
114	80	80	CD	_	_	_
115	,	,	,	_	_	_
116	b	b	NN	_	_	_
117	=	=	JJ	_	_	_
118	2	2	CD	_	_	_
119	,	,	,	_	_	_
120	m	m	NN	_	_	_
121	=	=	JJ	_	_	_
122	mode	mode	NN	_	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	peaks	peak	NNS	_	_	_
126	were	be	VBD	_	_	_
127	called	call	VBN	_	_	_
128	using	use	VBG	_	_	_
129	MACS2	macs2	NN	_	_	_
130	with	with	IN	_	_	_
131	default	default	NN	_	_	_
132	parameters	parameter	NNS	_	_	_
133	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
134	Peaks	Peaks	NNPS	_	_	_
135	were	be	VBD	_	_	_
136	called	call	VBN	_	_	_
137	with	with	IN	_	_	_
138	GeneTrack	genetrack	NN	_	_	_
139	1.0.3	1.0.3	CD	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	s	s	NN	_	_	_
142	=	=	JJ	_	_	_
143	5	5	CD	_	_	_
144	,	,	,	_	_	_
145	e	e	SYM	_	_	_
146	=	=	JJ	_	_	_
147	10	10	CD	_	_	_
148	-RRB-	-rrb-	-RRB-	_	_	_
149	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
150	Peconic	Peconic	NNP	_	_	_
151	LLC	LLC	NNP	_	_	_
152	performed	perform	VBD	_	_	_
153	data	datum	NNS	_	_	_
154	processing	processing	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	PEN205	pen205	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	PEN205	pen205	NN	_	_	_
159	strain	strain	NN	_	_	_
160	first	first	JJ	_	_	_
161	repetition	repetition	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	PEN205	pen205	NN	_	_	_
164	strain	strain	NN	_	_	_
165	second	second	JJ	_	_	_
166	repetition	repetition	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	PEN205	pen205	NN	_	_	_
169	strain	strain	NN	_	_	_
170	third	third	JJ	_	_	_
171	repetition	repetition	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	PF2-04	pf2-04	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	PF2-04	pf2-04	NN	_	_	_
176	_	_	CD	_	_	_
177	R1	r1	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	PF2-04	pf2-04	NN	_	_	_
180	_	_	CD	_	_	_
181	R2	r2	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	PF2-04	pf2-04	NN	_	_	_
184	_	_	CD	_	_	_
185	R3	r3	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	PF2-08	pf2-08	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	PF2-08	pf2-08	NN	_	_	_
190	_	_	CD	_	_	_
191	R1	r1	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	PF2-08	pf2-08	NN	_	_	_
194	_	_	CD	_	_	_
195	R2	r2	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	PF2-08	pf2-08	NN	_	_	_
198	_	_	CD	_	_	_
199	R3	r3	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	PF2-12	pf2-12	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	PF2-12	pf2-12	NN	_	_	_
204	_	_	CD	_	_	_
205	R1	r1	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	PF2-12	pf2-12	NN	_	_	_
208	_	_	CD	_	_	_
209	R2	r2	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	PF2-12	pf2-12	NN	_	_	_
212	_	_	CD	_	_	_
213	R3	r3	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	pFlag-only	pflag-only	NN	_	_	_
216	control	control	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	pgi-ala-1	pgi-ala-1	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	pgi-ala-2	pgi-ala-2	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	pgi	pgi	NN	GEN	_	_
223	mutantin	mutantin	NN	_	_	_
224	Ala	ala	NN	_	_	_
225	media	media	NNS	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	pgi	pgi	NN	GEN	_	_
228	mutantin	mutantin	NN	_	_	_
229	Gln	gln	NN	_	_	_
230	media	media	NNS	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	pGIT1	pgit1	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	pGIT1	pgit1	NN	_	_	_
235	.1	.1	CD	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	pGIT1	pgit1	NN	_	_	_
238	.1	.1	NN	_	_	_
239	+	+	CC	_	_	_
240	NO2	no2	NN	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	pGIT1	pgit1	NN	_	_	_
243	.2	.2	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	pGIT1	pgit1	NN	_	_	_
246	.2	.2	NN	_	_	_
247	+	+	CC	_	_	_
248	NO2	no2	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	pGIT1	pgit1	NN	_	_	_
251	.3	.3	NN	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	pGIT1	pgit1	NN	_	_	_
254	.3	.3	NN	_	_	_
255	+	+	CC	_	_	_
256	NO2	no2	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	pGIT1	pgit1	NN	_	_	_
259	.4	.4	CD	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	pGIT1	pgit1	NN	_	_	_
262	.4	.4	NN	_	_	_
263	+	+	CC	_	_	_
264	NO2	no2	NN	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	pGIT1	pgit1	NN	_	_	_
267	+	+	CC	_	_	_
268	NO2	no2	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	pGIT8	pgit8	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	pGIT8	pgit8	NN	_	_	_
273	.1	.1	NN	_	_	_
274	+	+	CC	_	_	_
275	NO2	no2	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	pGIT8	pgit8	NN	_	_	_
278	.2	.2	NN	_	_	_
279	+	+	CC	_	_	_
280	NO2	no2	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	pGIT8	pgit8	NN	_	_	_
283	.3	.3	NN	_	_	_
284	+	+	CC	_	_	_
285	NO2	no2	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	pGIT8	pgit8	NN	_	_	_
288	.4	.4	NN	_	_	_
289	+	+	CC	_	_	_
290	NO2	no2	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	pGIT8	pgit8	NN	_	_	_
293	+	+	CC	_	_	_
294	NO2	no2	NN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	PGRP-1	pgrp-1	NN	_	_	_
297	,	,	,	_	_	_
298	biological	biological	JJ	_	_	_
299	rep1	rep1	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	PGRP-2	pgrp-2	NN	_	_	_
302	,	,	,	_	_	_
303	biological	biological	JJ	_	_	_
304	rep2	rep2	NN	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	PGRP-3	pgrp-3	NN	_	_	_
307	,	,	,	_	_	_
308	biological	biological	JJ	_	_	_
309	rep3	rep3	NN	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	pH	ph	NN	_	_	_
312	=	=	JJ	_	_	_
313	5.3	5.3	CD	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	ph	ph	NN	_	_	_
316	:	:	:	_	_	_
317	5.6	5.6	CD	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
319	pH	ph	NN	_	_	_
320	=	=	JJ	_	_	_
321	5.7	5.7	CD	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	ph	ph	NN	_	_	_
324	:	:	:	_	_	_
325	7.2	7.2	CD	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	phage	phage	NN	_	_	_
328	DNA	dna	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	phage	phage	NN	_	_	_
331	:	:	:	_	_	_
332	Lambda	Lambda	NNP	_	_	_
333	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
334	phase	phase	NN	_	_	_
335	:	:	:	_	_	_
336	early	early	JJ	GrowthPhase	_	_
337	stationary	stationary	JJ	GrowthPhase	_	_
338	phase	phase	NN	GrowthPhase	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	phase	phase	NN	_	_	_
341	:	:	:	_	_	_
342	logarithmic	logarithmic	JJ	_	_	_
343	phase	phase	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	phase	phase	NN	_	_	_
346	:	:	:	_	_	_
347	log	log	NN	_	_	_
348	phase	phase	NN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	phase	phase	NN	_	_	_
351	of	of	IN	_	_	_
352	growth	growth	NN	_	_	_
353	:	:	:	_	_	_
354	15	15	CD	_	_	_
355	min	min	NN	_	_	_
356	post	post	NN	_	_	_
357	stationary	stationary	JJ	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	phase	phase	NN	_	_	_
360	of	of	IN	_	_	_
361	growth	growth	NN	_	_	_
362	:	:	:	_	_	_
363	180	180	CD	_	_	_
364	min	min	NN	_	_	_
365	post	post	NN	_	_	_
366	stationary	stationary	JJ	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	phase	phase	NN	_	_	_
369	of	of	IN	_	_	_
370	growth	growth	NN	_	_	_
371	:	:	:	_	_	_
372	30	30	CD	_	_	_
373	min	min	NN	_	_	_
374	post	post	NN	_	_	_
375	stationary	stationary	JJ	_	_	_
376	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
377	phase	phase	NN	_	_	_
378	of	of	IN	_	_	_
379	growth	growth	NN	_	_	_
380	:	:	:	_	_	_
381	Late	late	JJ	_	_	_
382	log	log	NN	_	_	_
383	phase	phase	NN	_	_	_
384	OD	od	NN	_	_	_
385	1.6	1.6	CD	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	phase	phase	NN	_	_	_
388	of	of	IN	_	_	_
389	growth	growth	NN	_	_	_
390	:	:	:	_	_	_
391	Log	log	VB	_	_	_
392	phase	phase	NN	_	_	_
393	OD	od	NN	_	_	_
394	0.1	0.1	CD	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	phase	phase	NN	_	_	_
397	of	of	IN	_	_	_
398	growth	growth	NN	_	_	_
399	:	:	:	_	_	_
400	Log	log	VB	_	_	_
401	phase	phase	NN	_	_	_
402	OD	od	NN	_	_	_
403	0.2	0.2	CD	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
405	phase	phase	NN	_	_	_
406	of	of	IN	_	_	_
407	growth	growth	NN	_	_	_
408	:	:	:	_	_	_
409	Log	log	VB	_	_	_
410	phase	phase	NN	_	_	_
411	OD	od	NN	_	_	_
412	0.3	0.3	CD	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	phase	phase	NN	_	_	_
415	of	of	IN	_	_	_
416	growth	growth	NN	_	_	_
417	:	:	:	_	_	_
418	Log	log	VB	_	_	_
419	phase	phase	NN	_	_	_
420	OD	od	NN	_	_	_
421	0.4	0.4	CD	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	phase	phase	NN	_	_	_
424	of	of	IN	_	_	_
425	growth	growth	NN	_	_	_
426	:	:	:	_	_	_
427	Log	log	VB	_	_	_
428	phase	phase	NN	_	_	_
429	OD	od	NN	_	_	_
430	0.8	0.8	CD	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	phase	phase	NN	_	_	_
433	of	of	IN	_	_	_
434	growth	growth	NN	_	_	_
435	:	:	:	_	_	_
436	Log	log	VB	_	_	_
437	phase	phase	NN	_	_	_
438	OD	od	NN	_	_	_
439	1.4	1.4	CD	_	_	_
440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
441	pHDB3	phdb3	NN	_	_	_
442	_	_	NN	_	_	_
443	1	1	CD	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	pHDB3	phdb3	NN	_	_	_
446	_	_	NN	_	_	_
447	2	2	CD	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	pHDB3	phdb3	NN	_	_	_
450	_	_	CD	_	_	_
451	3	3	CD	_	_	_
452	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
453	phenotype	phenotype	NN	_	_	_
454	:	:	:	_	_	_
455	0.6	0.6	CD	_	_	_
456	%	%	NN	_	_	_
457	n-butanol	n-butanol	NN	_	_	_
458	tolerance	tolerance	NN	_	_	_
459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
460	phenotype	phenotype	NN	_	_	_
461	:	:	:	_	_	_
462	2	2	CD	_	_	_
463	%	%	NN	_	_	_
464	n-butanol	n-butanol	NN	_	_	_
465	tolerance	tolerance	NN	_	_	_
466	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
467	phenotype	phenotype	NN	_	_	_
468	:	:	:	_	_	_
469	Blue	Blue	NNP	_	_	_
470	colony-color	colony-color	NN	_	_	_
471	-LRB-	-lrb-	-LRB-	_	_	_
472	prion-containing	prion-containing	JJ	_	_	_
473	-RRB-	-rrb-	-RRB-	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	phenotype	phenotype	NN	_	_	_
476	:	:	:	_	_	_
477	lacking	lack	VBG	_	_	_
478	FNR	fnr	NN	TF	_	_
479	protein	protein	NN	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	phenotype	phenotype	NN	_	_	_
482	:	:	:	_	_	_
483	normal	normal	JJ	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	phenotype	phenotype	NN	_	_	_
486	:	:	:	_	_	_
487	Pale	Pale	NNP	_	_	_
488	colony-color	colony-color	NN	_	_	_
489	-LRB-	-lrb-	-LRB-	_	_	_
490	prion-lacking	prion-lacking	NN	_	_	_
491	-RRB-	-rrb-	-RRB-	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
493	phenotype	phenotype	NN	_	_	_
494	:	:	:	_	_	_
495	small	small	JJ	_	_	_
496	improvement	improvement	NN	_	_	_
497	in	in	IN	_	_	_
498	methyl	methyl	NN	_	_	_
499	ketone	ketone	NN	_	_	_
500	production	production	NN	_	_	_
501	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
502	Phenylalanine	Phenylalanine	NNP	_	_	_
503	addition	addition	NN	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	phoA	phoa	NN	GEN	_	_
506	_	_	NN	_	_	_
507	0	0	CD	_	_	_
508	min	min	NN	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	phoA	phoa	NN	GEN	_	_
511	_	_	CD	_	_	_
512	10	10	CD	_	_	_
513	min	min	NN	_	_	_
514	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
515	phoA	phoa	NN	GEN	_	_
516	_	_	CD	_	_	_
517	15	15	CD	_	_	_
518	min	min	NN	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	phoA	phoa	NN	GEN	_	_
521	_	_	NN	_	_	_
522	1	1	CD	_	_	_
523	min	min	NN	_	_	_
524	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
525	phoA	phoa	NN	GEN	_	_
526	_	_	NN	_	_	_
527	2	2	CD	_	_	_
528	min	min	NN	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	phoA	phoa	NN	GEN	_	_
531	_	_	CD	_	_	_
532	4	4	CD	_	_	_
533	min	min	NN	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	phoA	phoa	NN	GEN	_	_
536	_	_	CD	_	_	_
537	6	6	CD	_	_	_
538	min	min	NN	_	_	_
539	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
540	phoA	phoa	NN	GEN	_	_
541	_	_	CD	_	_	_
542	8	8	CD	_	_	_
543	min	min	NN	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	PhoB	phob	NN	TF	_	_
546	_	_	CD	_	_	_
547	ChIP	chip	NN	_	_	_
548	,	,	,	_	_	_
549	rep1	rep1	NN	_	_	_
550	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
551	PhoB	phob	NN	TF	_	_
552	_	_	CD	_	_	_
553	ChIP	chip	NN	_	_	_
554	,	,	,	_	_	_
555	rep2	rep2	NN	_	_	_
556	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
557	PhoB	phob	NN	TF	_	_
558	_	_	CD	_	_	_
559	ChIP	chip	NN	_	_	_
560	,	,	,	_	_	_
561	rep3	rep3	NN	_	_	_
562	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
563	PhoB	phob	NN	TF	_	_
564	knock-out	knock-out	JJ	_	_	_
565	strain	strain	NN	_	_	_
566	,	,	,	_	_	_
567	rep1	rep1	NN	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	PhoB	phob	NN	TF	_	_
570	knock-out	knock-out	JJ	_	_	_
571	strain	strain	NN	_	_	_
572	,	,	,	_	_	_
573	rep2	rep2	NN	_	_	_
574	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
575	phoU	phou	NN	GEN	_	_
576	_	_	NN	_	_	_
577	1	1	CD	_	_	_
578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
579	phoU	phou	NN	GEN	_	_
580	_	_	NN	_	_	_
581	2	2	CD	_	_	_
582	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
583	phoU	phou	NN	GEN	_	_
584	_	_	CD	_	_	_
585	3	3	CD	_	_	_
586	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
587	phoU	phou	NN	GEN	_	_
588	gene	gene	NN	_	_	_
589	mutant	mutant	JJ	_	_	_
590	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
591	phoU	phou	NN	GEN	_	_
592	gene	gene	NN	_	_	_
593	mutant	mutant	NN	_	_	_
594	;	;	:	_	_	_
595	minimal	minimal	JJ	_	_	_
596	medium	medium	NN	_	_	_
597	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
598	Physiological	physiological	JJ	_	_	_
599	perturbations	perturbation	NNS	_	_	_
600	were	be	VBD	_	_	_
601	carried	carry	VBN	_	_	_
602	out	out	RP	_	_	_
603	under	under	IN	_	_	_
604	a	a	DT	_	_	_
605	controlled	controlled	JJ	_	_	_
606	environment	environment	NN	_	_	_
607	in	in	IN	_	_	_
608	the	the	DT	_	_	_
609	context	context	NN	_	_	_
610	of	of	IN	_	_	_
611	bioreactor	bioreactor	NN	_	_	_
612	-LRB-	-lrb-	-LRB-	_	_	_
613	Bioflo	bioflo	NN	_	_	_
614	110	110	CD	_	_	_
615	,	,	,	_	_	_
616	New	New	NNP	_	_	_
617	Brunswick	Brunswick	NNP	_	_	_
618	Scientific	Scientific	NNP	_	_	_
619	-RRB-	-rrb-	-RRB-	_	_	_
620	growth	growth	NN	_	_	_
621	.	.	.	_	_	_

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	P	p	NN	_	_	_
3	is	be	VBZ	_	_	_
4	defined	define	VBN	_	_	_
5	by	by	IN	_	_	_
6	the	the	DT	_	_	_
7	pair	pair	NN	_	_	_
8	of	of	IN	_	_	_
9	integers	integer	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	X	x	NN	_	_	_
12	,	,	,	_	_	_
13	Y	y	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

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	NNP	_	_	_
11	Pixel	Pixel	NNP	_	_	_
12	intensities	intensity	NNS	_	_	_
13	were	be	VBD	_	_	_
14	extracted	extract	VBN	_	_	_
15	using	use	VBG	_	_	_
16	the	the	DT	_	_	_
17	``	``	``	_	_	_
18	Feature	Feature	NNP	_	_	_
19	Extraction	Extraction	NNP	_	_	_
20	''	''	''	_	_	_
21	software	software	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Agilent	Agilent	NNP	_	_	_
24	Technologies	Technologies	NNPS	_	_	_
25	,	,	,	_	_	_
26	Palo	Palo	NNP	_	_	_
27	Alto	Alto	NNP	_	_	_
28	,	,	,	_	_	_
29	CA	CA	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	planktonic	planktonic	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
5	Planktonic	planktonic	JJ	_	_	_
6	cultures	culture	NNS	_	_	_
7	of	of	IN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	were	be	VBD	_	_	_
11	harvested	harvest	VBN	_	_	_
12	and	and	CC	_	_	_
13	resuspended	resuspend	VBN	_	_	_
14	in	in	IN	_	_	_
15	RNAlater	rnalater	NN	_	_	_
16	and	and	CC	_	_	_
17	kept	keep	VBD	_	_	_
18	in	in	IN	_	_	_
19	4C	4c	NN	_	_	_
20	fridge	fridge	NN	_	_	_
21	overnight	overnight	JJ	_	_	_
22	.	.	.	_	_	_

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	plasmid	plasmid	NN	_	_	_
3	cured	cure	VBD	_	_	_
4	rep1	rep1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	plasmid	plasmid	NN	_	_	_
7	cured	cure	VBD	_	_	_
8	rep2	rep2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Plasmid	plasmid	NN	_	_	_
11	DNA	dna	NN	_	_	_
12	,	,	,	_	_	_
13	after	after	IN	_	_	_
14	n-butanol	n-butanol	NN	_	_	_
15	selection	selection	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Plasmid	plasmid	NN	_	_	_
18	DNA	dna	NN	_	_	_
19	,	,	,	_	_	_
20	BWG	BWG	NNP	_	_	_
21	post	post	NN	_	_	_
22	conjugation	conjugation	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Plasmid	plasmid	NN	_	_	_
25	DNA	dna	NN	_	_	_
26	,	,	,	_	_	_
27	BWY	BWY	NNP	_	_	_
28	post	post	NN	_	_	_
29	conjugation	conjugation	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Plasmid	plasmid	NN	_	_	_
32	DNA	dna	NN	_	_	_
33	,	,	,	_	_	_
34	donor	donor	NN	_	_	_
35	,	,	,	_	_	_
36	XL1-Blue	xl1-blue	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	Plasmid	plasmid	NN	_	_	_
39	DNA	dna	NN	_	_	_
40	,	,	,	_	_	_
41	post	post	NN	_	_	_
42	conjugation	conjugation	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	plasmid	plasmid	NN	_	_	_
45	:	:	:	_	_	_
46	Donor	Donor	NNP	_	_	_
47	Library	Library	NNP	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	plasmid	plasmid	NN	_	_	_
50	:	:	:	_	_	_
51	empty	empty	JJ	_	_	_
52	vector	vector	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	plasmid	plasmid	NN	_	_	_
55	:	:	:	_	_	_
56	G181D	g181d	NN	_	_	_
57	NusA	nusa	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	plasmid	plasmid	NN	_	_	_
60	:	:	:	_	_	_
61	G324D	g324d	NN	_	_	_
62	Rho	rho	NN	_	_	_
63	mutant	mutant	JJ	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	plasmid	plasmid	NN	_	_	_
66	:	:	:	_	_	_
67	Initial	initial	JJ	_	_	_
68	Recipient	Recipient	NNP	_	_	_
69	Library	Library	NNP	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	BWG	BWG	NNP	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	plasmid	plasmid	NN	_	_	_
75	:	:	:	_	_	_
76	Initial	initial	JJ	_	_	_
77	Recipient	Recipient	NNP	_	_	_
78	Library	Library	NNP	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	BWY	BWY	NNP	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	plasmid	plasmid	NN	_	_	_
84	:	:	:	_	_	_
85	N340S	n340s	NN	_	_	_
86	Rho	rho	NN	_	_	_
87	mutant	mutant	JJ	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	plasmid	plasmid	NN	_	_	_
90	:	:	:	_	_	_
91	None	none	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	plasmid	plasmid	NN	_	_	_
94	:	:	:	_	_	_
95	pBAD	pbad	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	plasmid	plasmid	NN	_	_	_
98	:	:	:	_	_	_
99	pBAD30-empty	pbad30-empty	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	plasmid	plasmid	NN	_	_	_
102	:	:	:	_	_	_
103	pBAD30-MazF	pbad30-mazf	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	plasmid	plasmid	NN	_	_	_
106	:	:	:	_	_	_
107	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	plasmid	plasmid	NN	_	_	_
110	:	:	:	_	_	_
111	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	plasmid	plasmid	NN	_	_	_
114	:	:	:	_	_	_
115	pBAD-tosR	pbad-tosr	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	plasmid	plasmid	NN	_	_	_
118	:	:	:	_	_	_
119	pControl	pcontrol	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	plasmid	plasmid	NN	_	_	_
122	:	:	:	_	_	_
123	PD864	pd864	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	plasmid	plasmid	NN	_	_	_
126	:	:	:	_	_	_
127	pKEDR13	pkedr13	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	plasmid	plasmid	NN	_	_	_
130	:	:	:	_	_	_
131	pKESK22	pkesk22	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	plasmid	plasmid	NN	_	_	_
134	:	:	:	_	_	_
135	pKETS1	pkets1	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	plasmid	plasmid	NN	_	_	_
138	:	:	:	_	_	_
139	pLCenvZM	plcenvzm	NN	_	_	_
140	,	,	,	_	_	_
141	pPCB	ppcb	NN	_	_	_
142	-LRB-	-lrb-	-LRB-	_	_	_
143	mutation	mutation	NN	_	_	_
144	-RRB-	-rrb-	-RRB-	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	Plasmid	plasmid	NN	_	_	_
147	pLCenvZ	plcenvz	NN	_	_	_
148	or	or	CC	_	_	_
149	pLCenvZM	plcenvzm	NN	_	_	_
150	was	be	VBD	_	_	_
151	co-transformed	co-transform	VBN	_	_	_
152	with	with	IN	_	_	_
153	pPCB	ppcb	NN	_	_	_
154	into	into	IN	_	_	_
155	the	the	DT	_	_	_
156	competent	competent	JJ	_	_	_
157	cells	cell	NNS	_	_	_
158	of	of	IN	_	_	_
159	E.	e.	FW	_	_	_
160	coli	coli	FW	_	_	_
161	JW3367	jw3367	NN	_	_	_
162	and	and	CC	_	_	_
163	spread	spread	NN	_	_	_
164	on	on	IN	_	_	_
165	LB	LB	NNP	_	_	_
166	agar	agar	NN	_	_	_
167	plates	plate	NNS	_	_	_
168	containing	contain	VBG	_	_	_
169	Ampicillin	ampicillin	NN	_	_	_
170	-LRB-	-lrb-	-LRB-	_	_	_
171	50	50	CD	_	_	_
172	ng/μl	ng/μl	NN	_	_	_
173	-RRB-	-rrb-	-RRB-	_	_	_
174	and	and	CC	_	_	_
175	Chloramphenicol	chloramphenicol	NN	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	170	170	CD	_	_	_
178	ng/μl	ng/μl	NN	_	_	_
179	-RRB-	-rrb-	-RRB-	_	_	_
180	at	at	IN	_	_	_
181	37	37	CD	_	_	_
182	°C	°c	NN	_	_	_
183	overnight	overnight	JJ	_	_	_
184	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	single	single	JJ	_	_	_
3	colony	colony	NN	_	_	_
4	was	be	VBD	_	_	_
5	diluted	dilute	VBN	_	_	_
6	in	in	IN	_	_	_
7	2.5	2.5	CD	_	_	_
8	ml	ml	NN	_	_	_
9	LB	lb	NN	MED	_	_
10	medium	medium	NN	MED	_	_
11	containing	contain	VBG	_	_	_
12	Ampicillin	ampicillin	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	50	50	CD	_	_	_
15	ng/μl	ng/μl	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	Chloramphenicol	chloramphenicol	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	170	170	CD	_	_	_
21	ng/μl	ng/μl	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	was	be	VBD	_	_	_
25	shaken	shake	VBN	_	_	_
26	at	at	IN	_	_	_
27	250	250	CD	_	_	_
28	rpm	rpm	NN	_	_	_
29	and	and	CC	_	_	_
30	37	37	CD	_	_	_
31	°C	°c	NN	_	_	_
32	overnight	overnight	JJ	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	plasmid	plasmid	NN	_	_	_
3	:	:	:	_	_	_
4	pLCenvZ	plcenvz	NN	_	_	_
5	,	,	,	_	_	_
6	pPCB	ppcb	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	wild	wild	JJ	_	_	_
9	type	type	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	plasmid	plasmid	NN	_	_	_
13	:	:	:	_	_	_
14	pLPLσ	plplσ	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	plasmid	plasmid	NN	_	_	_
17	:	:	:	_	_	_
18	PLYS	plys	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	plasmid	plasmid	NN	_	_	_
21	:	:	:	_	_	_
22	pMicL	pmicl	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	plasmid	plasmid	NN	_	_	_
25	:	:	:	_	_	_
26	pMicL-S	pmicl-s	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Plasmid	plasmid	NN	_	_	_
29	pool	pool	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	plasmid	plasmid	NN	_	_	_
32	:	:	:	_	_	_
33	pPROEx-CAT	pproex-cat	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	plasmid	plasmid	NN	_	_	_
36	:	:	:	_	_	_
37	PSB1C3	psb1c3	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	plasmid	plasmid	NN	_	_	_
40	:	:	:	_	_	_
41	R258C	r258c	NN	_	_	_
42	NusA	nusa	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	plasmid	plasmid	NN	_	_	_
45	:	:	:	_	_	_
46	R258C	r258c	NN	_	_	_
47	NuSA	nusa	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	plasmid	plasmid	NN	_	_	_
50	source	source	NN	_	_	_
51	:	:	:	_	_	_
52	Initial	initial	JJ	_	_	_
53	Recipient	Recipient	NNP	_	_	_
54	Library	Library	NNP	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	plasmid	plasmid	NN	_	_	_
57	source	source	NN	_	_	_
58	:	:	:	_	_	_
59	Post	Post	NNP	_	_	_
60	Selection	selection	NN	_	_	_
61	Library	Library	NNP	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	plasmid	plasmid	NN	_	_	_
64	:	:	:	_	_	_
65	wild	wild	JJ	_	_	_
66	type	type	NN	_	_	_
67	NusA	nusa	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	plasmid	plasmid	NN	_	_	_
70	:	:	:	_	_	_
71	WT	WT	NNP	_	_	_
72	Rho	rho	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	platform	platform	NN	_	_	_
75	_	_	CD	_	_	_
76	id	id	NN	_	_	_
77	design	design	NN	_	_	_
78	:	:	:	_	_	_
79	EcFS	ecfs	NN	_	_	_
80	_	_	NN	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	platform	platform	NN	_	_	_
84	_	_	CD	_	_	_
85	id	id	NN	_	_	_
86	design	design	NN	_	_	_
87	:	:	:	_	_	_
88	EcFS	ecfs	NN	_	_	_
89	_	_	NN	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	platform	platform	NN	_	_	_
93	_	_	CD	_	_	_
94	id	id	NN	_	_	_
95	_	_	CD	_	_	_
96	id	id	NN	_	_	_
97	design	design	NN	_	_	_
98	:	:	:	_	_	_
99	EcFS	ecfs	NN	_	_	_
100	_	_	NN	_	_	_
101	1	1	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	platform	platform	NN	_	_	_
104	_	_	CD	_	_	_
105	id	id	NN	_	_	_
106	_	_	CD	_	_	_
107	id	id	NN	_	_	_
108	design	design	NN	_	_	_
109	:	:	:	_	_	_
110	EcFS	ecfs	NN	_	_	_
111	_	_	NN	_	_	_
112	2	2	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	platform	platform	NN	_	_	_
115	_	_	CD	_	_	_
116	id	id	NN	_	_	_
117	_	_	CD	_	_	_
118	id	id	NN	_	_	_
119	design	design	NN	_	_	_
120	:	:	:	_	_	_
121	EcFS	ecfs	NN	_	_	_
122	_	_	NN	_	_	_
123	3	3	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	pLCV1	plcv1	NN	_	_	_
126	_	_	NN	_	_	_
127	1	1	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	pLCV1	plcv1	NN	_	_	_
130	_	_	NN	_	_	_
131	2	2	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	pLCV1	plcv1	NN	_	_	_
134	_	_	CD	_	_	_
135	3	3	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	pLPLσ	plplσ	NN	_	_	_
138	_	_	CD	_	_	_
139	exponential	exponential	JJ	_	_	_
140	growth	growth	NN	_	_	_
141	phase	phase	NN	_	_	_
142	_	_	NN	_	_	_
143	1	1	CD	_	_	_
144	ml	ml	NN	_	_	_
145	cell	cell	NN	_	_	_
146	pellet	pellet	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	pLPLσ	plplσ	NN	_	_	_
149	_	_	CD	_	_	_
150	stationary	stationary	JJ	_	_	_
151	growth	growth	NN	_	_	_
152	phase	phase	NN	_	_	_
153	_	_	NN	_	_	_
154	1	1	CD	_	_	_
155	ml	ml	NN	_	_	_
156	cell	cell	NN	_	_	_
157	pellet	pellet	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	pLPLσ	plplσ	NN	_	_	_
160	_	_	CD	_	_	_
161	transition	transition	NN	_	_	_
162	growth	growth	NN	_	_	_
163	phase	phase	NN	_	_	_
164	_	_	NN	_	_	_
165	1	1	CD	_	_	_
166	ml	ml	NN	_	_	_
167	cell	cell	NN	_	_	_
168	pellet	pellet	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	plus	plus	CC	_	_	_
171	Symbioflor	symbioflor	JJ	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	∆	∆	CD	_	_	_
174	pnp	pnp	NN	GEN	_	_
175	_	_	CD	_	_	_
176	RNA-Seq	rna-seq	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
178	Pnp	pnp	NN	_	_	_
179	-	-	:	_	_	_
180	-LRB-	-lrb-	-LRB-	_	_	_
181	YHC012	yhc012	NN	_	_	_
182	-RRB-	-rrb-	-RRB-	_	_	_
183	in	in	IN	_	_	_
184	M9	m9	NN	_	_	_
185	+	+	CC	_	_	_
186	0.2	0.2	CD	_	_	_
187	%	%	NN	_	_	_
188	Glycerol	glycerol	NN	_	_	_
189	,	,	,	_	_	_
190	0.2	0.2	CD	_	_	_
191	%	%	NN	_	_	_
192	Tryptone	tryptone	NN	_	_	_
193	at	at	IN	_	_	_
194	30	30	CD	_	_	_
195	C	c	NN	_	_	_
196	Mid	Mid	NNP	_	_	_
197	Log	Log	NNP	_	_	_
198	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
199	Pnp	Pnp	NNP	_	_	_
200	-	-	:	_	_	_
201	-LRB-	-lrb-	-LRB-	_	_	_
202	YHC012	yhc012	NN	_	_	_
203	-RRB-	-rrb-	-RRB-	_	_	_
204	in	in	IN	_	_	_
205	M9	m9	NN	_	_	_
206	+	+	CC	_	_	_
207	0.2	0.2	CD	_	_	_
208	%	%	NN	_	_	_
209	Glycerol	glycerol	NN	_	_	_
210	,	,	,	_	_	_
211	0.2	0.2	CD	_	_	_
212	%	%	NN	_	_	_
213	Tryptone	tryptone	NN	_	_	_
214	at	at	IN	_	_	_
215	30	30	CD	_	_	_
216	C	c	NN	_	_	_
217	Mid	Mid	NNP	_	_	_
218	Log	Log	NNP	_	_	_
219	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
220	Pnp	Pnp	NNP	_	_	_
221	-	-	:	_	_	_
222	-LRB-	-lrb-	-LRB-	_	_	_
223	YHC012	yhc012	NN	_	_	_
224	-RRB-	-rrb-	-RRB-	_	_	_
225	in	in	IN	_	_	_
226	M9	m9	NN	_	_	_
227	+	+	CC	_	_	_
228	0.2	0.2	CD	_	_	_
229	%	%	NN	_	_	_
230	Glycerol	glycerol	NN	_	_	_
231	,	,	,	_	_	_
232	0.2	0.2	CD	_	_	_
233	%	%	NN	_	_	_
234	Tryptone	tryptone	NN	_	_	_
235	at	at	IN	_	_	_
236	30	30	CD	_	_	_
237	C	c	NN	_	_	_
238	Mid	Mid	NNP	_	_	_
239	Log	Log	NNP	_	_	_
240	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
241	Pnp	Pnp	NNP	_	_	_
242	-	-	:	_	_	_
243	-LRB-	-lrb-	-LRB-	_	_	_
244	YHC012	yhc012	NN	_	_	_
245	-RRB-	-rrb-	-RRB-	_	_	_
246	in	in	IN	_	_	_
247	M9	m9	NN	_	_	_
248	+	+	CC	_	_	_
249	0.2	0.2	CD	_	_	_
250	%	%	NN	_	_	_
251	Glycerol	glycerol	NN	_	_	_
252	,	,	,	_	_	_
253	0.2	0.2	CD	_	_	_
254	%	%	NN	_	_	_
255	Tryptone	tryptone	NN	_	_	_
256	at	at	IN	_	_	_
257	30	30	CD	_	_	_
258	C	c	NN	_	_	_
259	Mid	Mid	NNP	_	_	_
260	Log	Log	NNP	_	_	_
261	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
262	Pnp	Pnp	NNP	_	_	_
263	-	-	:	_	_	_
264	-LRB-	-lrb-	-LRB-	_	_	_
265	YHC012	yhc012	NN	_	_	_
266	-RRB-	-rrb-	-RRB-	_	_	_
267	-RRB-	-rrb-	-RRB-	_	_	_
268	in	in	IN	_	_	_
269	M9	m9	NN	_	_	_
270	+	+	CC	_	_	_
271	0.2	0.2	CD	_	_	_
272	%	%	NN	_	_	_
273	Glycerol	glycerol	NN	_	_	_
274	,	,	,	_	_	_
275	0.2	0.2	CD	_	_	_
276	%	%	NN	_	_	_
277	Tryptone	tryptone	NN	_	_	_
278	at	at	IN	_	_	_
279	30	30	CD	_	_	_
280	C	c	NN	_	_	_
281	Mid	Mid	NNP	_	_	_
282	Log	Log	NNP	_	_	_
283	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
284	Pnp	Pnp	NNP	_	_	_
285	-	-	:	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	YHC012	yhc012	NN	_	_	_
288	-RRB-	-rrb-	-RRB-	_	_	_
289	in	in	IN	_	_	_
290	M9	m9	NN	_	_	_
291	+	+	CC	_	_	_
292	0.2	0.2	CD	_	_	_
293	%	%	NN	_	_	_
294	Glycerol	glycerol	NN	_	_	_
295	,	,	,	_	_	_
296	0.2	0.2	CD	_	_	_
297	%	%	NN	_	_	_
298	Tryptone	tryptone	NN	_	_	_
299	at	at	IN	_	_	_
300	30	30	CD	_	_	_
301	C	c	NN	_	_	_
302	Mid	Mid	NNP	_	_	_
303	Log	Log	NNP	_	_	_
304	1.5	1.5	CD	_	_	_
305	'	'	''	_	_	_
306	post	post	JJ	_	_	_
307	rif	rif	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	Pnp	pnp	NN	_	_	_
310	-	-	:	_	_	_
311	-LRB-	-lrb-	-LRB-	_	_	_
312	YHC012	yhc012	NN	_	_	_
313	-RRB-	-rrb-	-RRB-	_	_	_
314	in	in	IN	_	_	_
315	M9	m9	NN	_	_	_
316	+	+	CC	_	_	_
317	0.2	0.2	CD	_	_	_
318	%	%	NN	_	_	_
319	Glycerol	glycerol	NN	_	_	_
320	,	,	,	_	_	_
321	0.2	0.2	CD	_	_	_
322	%	%	NN	_	_	_
323	Tryptone	tryptone	NN	_	_	_
324	at	at	IN	_	_	_
325	30	30	CD	_	_	_
326	C	c	NN	_	_	_
327	Mid	Mid	NNP	_	_	_
328	Log	Log	NNP	_	_	_
329	3	3	CD	_	_	_
330	'	'	''	_	_	_
331	post	post	JJ	_	_	_
332	rif	rif	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	Pnp	pnp	NN	_	_	_
335	-	-	:	_	_	_
336	-LRB-	-lrb-	-LRB-	_	_	_
337	YHC012	yhc012	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	4.5	4.5	CD	_	_	_
355	'	'	''	_	_	_
356	post	post	JJ	_	_	_
357	rif	rif	NN	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	Pnp	pnp	NN	_	_	_
360	-	-	:	_	_	_
361	-LRB-	-lrb-	-LRB-	_	_	_
362	YHC012	yhc012	NN	_	_	_
363	-RRB-	-rrb-	-RRB-	_	_	_
364	in	in	IN	_	_	_
365	M9	m9	NN	_	_	_
366	+	+	CC	_	_	_
367	0.2	0.2	CD	_	_	_
368	%	%	NN	_	_	_
369	Glycerol	glycerol	NN	_	_	_
370	,	,	,	_	_	_
371	0.2	0.2	CD	_	_	_
372	%	%	NN	_	_	_
373	Tryptone	tryptone	NN	_	_	_
374	at	at	IN	_	_	_
375	30	30	CD	_	_	_
376	C	c	NN	_	_	_
377	Mid	Mid	NNP	_	_	_
378	Log	Log	NNP	_	_	_
379	6	6	CD	_	_	_
380	'	'	''	_	_	_
381	post	post	JJ	_	_	_
382	rif	rif	NN	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	Poly	poly	NN	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	Polyclonal	polyclonal	JJ	_	_	_
387	antibody	antibody	NN	_	_	_
388	for	for	IN	_	_	_
389	NusG	nusg	NN	_	_	_
390	-LRB-	-lrb-	-LRB-	_	_	_
391	raised	raise	VBN	_	_	_
392	for	for	IN	_	_	_
393	this	this	DT	_	_	_
394	study	study	NN	_	_	_
395	-RRB-	-rrb-	-RRB-	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
397	Polyclonal	polyclonal	JJ	_	_	_
398	antibody	antibody	NN	_	_	_
399	for	for	IN	_	_	_
400	Rho	rho	NN	_	_	_
401	-LRB-	-lrb-	-LRB-	_	_	_
402	gift	gift	NN	_	_	_
403	from	from	IN	_	_	_
404	Jeff	Jeff	NNP	_	_	_
405	Roberts	Roberts	NNP	_	_	_
406	-RRB-	-rrb-	-RRB-	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	polyphosphate	polyphosphate	NN	_	_	_
409	kinase	kinase	NN	_	_	_
410	1	1	CD	_	_	_
411	-LRB-	-lrb-	-LRB-	_	_	_
412	PPK1	ppk1	NN	_	_	_
413	-RRB-	-rrb-	-RRB-	_	_	_
414	mutant	mutant	JJ	_	_	_
415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
416	Polysomes	polysome	NNS	_	_	_
417	were	be	VBD	_	_	_
418	digested	digest	VBN	_	_	_
419	with	with	IN	_	_	_
420	MNase	mnase	NN	_	_	_
421	,	,	,	_	_	_
422	monosomes	monosome	NNS	_	_	_
423	were	be	VBD	_	_	_
424	purified	purify	VBN	_	_	_
425	by	by	IN	_	_	_
426	sucrose	sucrose	NN	_	_	_
427	gradient	gradient	NN	_	_	_
428	ultracentrifugation	ultracentrifugation	NN	_	_	_
429	,	,	,	_	_	_
430	and	and	CC	_	_	_
431	the	the	DT	_	_	_
432	resulting	result	VBG	_	_	_
433	mRNA	mrna	NN	_	_	_
434	fragments	fragment	NNS	_	_	_
435	were	be	VBD	_	_	_
436	extracted	extract	VBN	_	_	_
437	with	with	IN	_	_	_
438	phenol	phenol	NN	_	_	_
439	chloroform	chloroform	NN	_	_	_
440	and	and	CC	_	_	_
441	gel-purified	gel-purified	JJ	_	_	_
442	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	pooled	pool	VBD	_	_	_
3	reference	reference	NN	_	_	_
4	RNA	rna	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	pooled	pool	VBD	_	_	_
7	RNA	rna	NN	_	_	_
8	from	from	IN	_	_	_
9	all	all	DT	_	_	_
10	conditions	condition	NNS	_	_	_
11	including	include	VBG	_	_	_
12	the	the	DT	_	_	_
13	control	control	NN	_	_	_
14	,	,	,	_	_	_
15	reference	reference	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	pool	pool	NN	_	_	_
18	of	of	IN	_	_	_
19	aliquots	aliquot	NNS	_	_	_
20	from	from	IN	_	_	_
21	all	all	DT	_	_	_
22	samples	sample	NNS	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Pool	Pool	NNP	_	_	_
25	of	of	IN	_	_	_
26	eight	eight	CD	_	_	_
27	independent	independent	JJ	_	_	_
28	cultures	culture	NNS	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
30	population	population	NN	_	_	_
31	:	:	:	_	_	_
32	1	1	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	population	population	NN	_	_	_
35	:	:	:	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	population	population	NN	_	_	_
39	:	:	:	_	_	_
40	3	3	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	population	population	NN	_	_	_
43	:	:	:	_	_	_
44	4	4	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	population	population	NN	_	_	_
47	:	:	:	_	_	_
48	5	5	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	population	population	NN	_	_	_
51	:	:	:	_	_	_
52	6	6	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
54	population	population	NN	_	_	_
55	:	:	:	_	_	_
56	7	7	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	population	population	NN	_	_	_
59	:	:	:	_	_	_
60	A2	a2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	population	population	NN	_	_	_
63	:	:	:	_	_	_
64	A4	a4	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
66	population	population	NN	_	_	_
67	:	:	:	_	_	_
68	G2	g2	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	population	population	NN	_	_	_
71	:	:	:	_	_	_
72	G3	g3	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
74	population	population	NN	_	_	_
75	:	:	:	_	_	_
76	G5	g5	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
78	population	population	NN	_	_	_
79	:	:	:	_	_	_
80	G6	g6	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Post-processing	post-processing	NN	_	_	_
83	of	of	IN	_	_	_
84	the	the	DT	_	_	_
85	sequencing	sequencing	NN	_	_	_
86	reads	read	VBZ	_	_	_
87	from	from	IN	_	_	_
88	RNA-seq	rna-seq	NN	_	_	_
89	experiments	experiment	NNS	_	_	_
90	for	for	IN	_	_	_
91	each	each	DT	_	_	_
92	sample	sample	NN	_	_	_
93	was	be	VBD	_	_	_
94	performed	perform	VBN	_	_	_
95	using	use	VBG	_	_	_
96	HudsonAlpha	HudsonAlpha	NNP	_	_	_
97	's	's	POS	_	_	_
98	unique	unique	JJ	_	_	_
99	in-house	in-house	JJ	_	_	_
100	RNA-seq	rna-seq	NN	_	_	_
101	data	data	NN	_	_	_
102	analysis	analysis	NN	_	_	_
103	pipeline	pipeline	NN	_	_	_
104	.	.	.	_	_	_

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	NN	_	_	_
2	postscript	postscript	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	file	file	NN	_	_	_
5	=\	=\	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	PPC	PPC	NNP	_	_	_
8	_	_	SYM	_	_	_
9	glucose-minimal	glucose-minimal	JJ	_	_	_
10	medium	medium	NN	_	_	_
11	_	_	NN	_	_	_
12	early	early	JJ	_	_	_
13	log	log	NN	_	_	_
14	phase	phase	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	PPC	PPC	NNP	_	_	_
17	_	_	SYM	_	_	_
18	LB-GlC	lb-glc	JJ	_	_	_
19	medium	medium	NN	_	_	_
20	_	_	NN	_	_	_
21	D	d	NN	_	_	_
22	=	=	JJ	_	_	_
23	0.1	0.1	CD	_	_	_
24	h-1	h-1	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	PPK1-PPX	ppk1-ppx	NN	_	_	_
27	double	double	JJ	_	_	_
28	mutant	mutant	JJ	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	ppk	ppk	NN	GEN	_	_
31	KO	KO	NNP	_	_	_
32	LB	LB	NNP	_	_	_
33	rep1	rep1	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	ppk	ppk	NN	GEN	_	_
36	KO	KO	NNP	_	_	_
37	LB	LB	NNP	_	_	_
38	rep2	rep2	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	ppk	ppk	NN	GEN	_	_
41	KO	ko	NN	_	_	_
42	M9	m9	NN	_	_	_
43	rep1	rep1	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	ppk	ppk	NN	GEN	_	_
46	KO	ko	NN	_	_	_
47	M9	m9	NN	_	_	_
48	rep2	rep2	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	∆	∆	CD	_	_	_
51	ppk	ppk	NN	GEN	_	_
52	parent	parent	NN	_	_	_
53	Sample	sample	NN	_	_	_
54	24	24	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	∆	∆	CD	_	_	_
57	ppk	ppk	NN	GEN	_	_
58	parent	parent	NN	_	_	_
59	Sample	sample	NN	_	_	_
60	43	43	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	∆	∆	CD	_	_	_
63	ppk	ppk	NN	GEN	_	_
64	parent	parent	NN	_	_	_
65	Sample	sample	NN	_	_	_
66	5	5	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	ppk	ppk	NN	GEN	_	_
69	suppressor	suppressor	NN	_	_	_
70	1-1	1-1	CD	_	_	_
71	Sample	sample	NN	_	_	_
72	25	25	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	ppk	ppk	NN	GEN	_	_
75	suppressor	suppressor	NN	_	_	_
76	1-1	1-1	CD	_	_	_
77	Sample	sample	NN	_	_	_
78	44	44	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	ppk	ppk	NN	GEN	_	_
81	suppressor	suppressor	NN	_	_	_
82	1-1	1-1	CD	_	_	_
83	Sample	sample	NN	_	_	_
84	6	6	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	ppk	ppk	NN	GEN	_	_
87	suppressor	suppressor	NN	_	_	_
88	2-1	2-1	CD	_	_	_
89	Sample	sample	NN	_	_	_
90	26	26	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	ppk	ppk	NN	GEN	_	_
93	suppressor	suppressor	NN	_	_	_
94	2-1	2-1	CD	_	_	_
95	Sample	sample	NN	_	_	_
96	45	45	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	ppk	ppk	NN	GEN	_	_
99	suppressor	suppressor	NN	_	_	_
100	2-1	2-1	CD	_	_	_
101	Sample	sample	NN	_	_	_
102	7	7	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	ppk	ppk	NN	GEN	_	_
105	suppressor	suppressor	NN	_	_	_
106	3-1	3-1	CD	_	_	_
107	Sample	sample	NN	_	_	_
108	27	27	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	ppk	ppk	NN	GEN	_	_
111	suppressor	suppressor	NN	_	_	_
112	3-1	3-1	CD	_	_	_
113	Sample	sample	NN	_	_	_
114	46	46	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	ppk	ppk	NN	GEN	_	_
117	suppressor	suppressor	NN	_	_	_
118	3-1	3-1	CD	_	_	_
119	Sample	sample	NN	_	_	_
120	8	8	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	ppsA	ppsa	NN	GEN	_	_
123	mutant	mutant	JJ	_	_	_
124	15	15	CD	_	_	_
125	min	min	NN	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	1	1	CD	_	_	_
128	-RRB-	-rrb-	-RRB-	_	_	_
129	slide	slide	NN	_	_	_
130	1	1	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	ppsA	ppsa	NN	GEN	_	_
133	mutant	mutant	JJ	_	_	_
134	15	15	CD	_	_	_
135	min	min	NN	_	_	_
136	-LRB-	-lrb-	-LRB-	_	_	_
137	1	1	CD	_	_	_
138	-RRB-	-rrb-	-RRB-	_	_	_
139	slide	slide	NN	_	_	_
140	2	2	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	ppsA	ppsa	NN	GEN	_	_
143	mutant	mutant	NN	_	_	_
144	1	1	CD	_	_	_
145	hour	hour	NN	_	_	_
146	-LRB-	-lrb-	-LRB-	_	_	_
147	1	1	CD	_	_	_
148	-RRB-	-rrb-	-RRB-	_	_	_
149	slide	slide	NN	_	_	_
150	1	1	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	ppsA	ppsa	NN	GEN	_	_
153	mutant	mutant	NN	_	_	_
154	1	1	CD	_	_	_
155	hour	hour	NN	_	_	_
156	-LRB-	-lrb-	-LRB-	_	_	_
157	1	1	CD	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	slide	slide	NN	_	_	_
160	2	2	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	ppsA	ppsa	NN	GEN	_	_
163	mutant	mutant	NN	_	_	_
164	1	1	CD	_	_	_
165	hour	hour	NN	_	_	_
166	-LRB-	-lrb-	-LRB-	_	_	_
167	2	2	CD	_	_	_
168	-RRB-	-rrb-	-RRB-	_	_	_
169	slide	slide	NN	_	_	_
170	1	1	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	ppsA	ppsa	NN	GEN	_	_
173	mutant	mutant	NN	_	_	_
174	1	1	CD	_	_	_
175	hour	hour	NN	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	2	2	CD	_	_	_
178	-RRB-	-rrb-	-RRB-	_	_	_
179	slide	slide	NN	_	_	_
180	2	2	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	ppsA	ppsa	NN	GEN	_	_
183	mutant	mutant	NN	_	_	_
184	1	1	CD	_	_	_
185	hour	hour	NN	_	_	_
186	-LRB-	-lrb-	-LRB-	_	_	_
187	3	3	CD	_	_	_
188	-RRB-	-rrb-	-RRB-	_	_	_
189	slide	slide	NN	_	_	_
190	1	1	CD	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	ppsA	ppsa	NN	GEN	_	_
193	mutant	mutant	NN	_	_	_
194	1	1	CD	_	_	_
195	hour	hour	NN	_	_	_
196	-LRB-	-lrb-	-LRB-	_	_	_
197	3	3	CD	_	_	_
198	-RRB-	-rrb-	-RRB-	_	_	_
199	slide	slide	NN	_	_	_
200	2	2	CD	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	ppsA	ppsa	NN	GEN	_	_
203	mutant	mutant	NN	_	_	_
204	2	2	CD	_	_	_
205	hour	hour	NN	_	_	_
206	-LRB-	-lrb-	-LRB-	_	_	_
207	1	1	CD	_	_	_
208	-RRB-	-rrb-	-RRB-	_	_	_
209	slide	slide	NN	_	_	_
210	1	1	CD	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	ppsA	ppsa	NN	GEN	_	_
213	mutant	mutant	NN	_	_	_
214	2	2	CD	_	_	_
215	hour	hour	NN	_	_	_
216	-LRB-	-lrb-	-LRB-	_	_	_
217	1	1	CD	_	_	_
218	-RRB-	-rrb-	-RRB-	_	_	_
219	slide	slide	NN	_	_	_
220	2	2	CD	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	ppsA	ppsa	NN	GEN	_	_
223	mutant	mutant	NN	_	_	_
224	2	2	CD	_	_	_
225	hour	hour	NN	_	_	_
226	-LRB-	-lrb-	-LRB-	_	_	_
227	2	2	CD	_	_	_
228	-RRB-	-rrb-	-RRB-	_	_	_
229	slide	slide	NN	_	_	_
230	1	1	CD	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	ppsA	ppsa	NN	GEN	_	_
233	mutant	mutant	NN	_	_	_
234	2	2	CD	_	_	_
235	hour	hour	NN	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	2	2	CD	_	_	_
238	-RRB-	-rrb-	-RRB-	_	_	_
239	slide	slide	NN	_	_	_
240	2	2	CD	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	ppsA	ppsa	NN	GEN	_	_
243	mutant	mutant	NN	_	_	_
244	2	2	CD	_	_	_
245	hour	hour	NN	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	3	3	CD	_	_	_
248	-RRB-	-rrb-	-RRB-	_	_	_
249	slide	slide	NN	_	_	_
250	1	1	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	ppsA	ppsa	NN	GEN	_	_
253	mutant	mutant	NN	_	_	_
254	2	2	CD	_	_	_
255	hour	hour	NN	_	_	_
256	-LRB-	-lrb-	-LRB-	_	_	_
257	3	3	CD	_	_	_
258	-RRB-	-rrb-	-RRB-	_	_	_
259	slide	slide	NN	_	_	_
260	2	2	CD	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	ppsA	ppsa	NN	GEN	_	_
263	mutant	mutant	JJ	_	_	_
264	30	30	CD	_	_	_
265	min	min	NN	_	_	_
266	-LRB-	-lrb-	-LRB-	_	_	_
267	1	1	CD	_	_	_
268	-RRB-	-rrb-	-RRB-	_	_	_
269	slide	slide	NN	_	_	_
270	1	1	CD	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	ppsA	ppsa	NN	GEN	_	_
273	mutant	mutant	JJ	_	_	_
274	30	30	CD	_	_	_
275	min	min	NN	_	_	_
276	-LRB-	-lrb-	-LRB-	_	_	_
277	1	1	CD	_	_	_
278	-RRB-	-rrb-	-RRB-	_	_	_
279	slide	slide	NN	_	_	_
280	2	2	CD	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	ppsA	ppsa	NN	GEN	_	_
283	mutant	mutant	JJ	_	_	_
284	3	3	CD	_	_	_
285	hour	hour	NN	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	1	1	CD	_	_	_
288	-RRB-	-rrb-	-RRB-	_	_	_
289	slide	slide	NN	_	_	_
290	1	1	CD	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	ppsA	ppsa	NN	GEN	_	_
293	mutant	mutant	JJ	_	_	_
294	3	3	CD	_	_	_
295	hour	hour	NN	_	_	_
296	-LRB-	-lrb-	-LRB-	_	_	_
297	1	1	CD	_	_	_
298	-RRB-	-rrb-	-RRB-	_	_	_
299	slide	slide	NN	_	_	_
300	2	2	CD	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	ppsA	ppsa	NN	GEN	_	_
303	mutant	mutant	JJ	_	_	_
304	3	3	CD	_	_	_
305	hour	hour	NN	_	_	_
306	-LRB-	-lrb-	-LRB-	_	_	_
307	2	2	CD	_	_	_
308	-RRB-	-rrb-	-RRB-	_	_	_
309	slide	slide	NN	_	_	_
310	1	1	CD	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	ppsA	ppsa	NN	GEN	_	_
313	mutant	mutant	JJ	_	_	_
314	3	3	CD	_	_	_
315	hour	hour	NN	_	_	_
316	-LRB-	-lrb-	-LRB-	_	_	_
317	2	2	CD	_	_	_
318	-RRB-	-rrb-	-RRB-	_	_	_
319	slide	slide	NN	_	_	_
320	2	2	CD	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	ppsA	ppsa	NN	GEN	_	_
323	mutant	mutant	JJ	_	_	_
324	3	3	CD	_	_	_
325	hour	hour	NN	_	_	_
326	-LRB-	-lrb-	-LRB-	_	_	_
327	3	3	CD	_	_	_
328	-RRB-	-rrb-	-RRB-	_	_	_
329	slide	slide	NN	_	_	_
330	1	1	CD	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	ppsA	ppsa	NN	GEN	_	_
333	mutant	mutant	JJ	_	_	_
334	3	3	CD	_	_	_
335	hour	hour	NN	_	_	_
336	-LRB-	-lrb-	-LRB-	_	_	_
337	3	3	CD	_	_	_
338	-RRB-	-rrb-	-RRB-	_	_	_
339	slide	slide	NN	_	_	_
340	2	2	CD	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	ppsA	ppsa	NN	GEN	_	_
343	mutant	mutant	JJ	_	_	_
344	4	4	CD	_	_	_
345	hour	hour	NN	_	_	_
346	-LRB-	-lrb-	-LRB-	_	_	_
347	1	1	CD	_	_	_
348	-RRB-	-rrb-	-RRB-	_	_	_
349	slide	slide	NN	_	_	_
350	1	1	CD	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	ppsA	ppsa	NN	GEN	_	_
353	mutant	mutant	JJ	_	_	_
354	4	4	CD	_	_	_
355	hour	hour	NN	_	_	_
356	-LRB-	-lrb-	-LRB-	_	_	_
357	1	1	CD	_	_	_
358	-RRB-	-rrb-	-RRB-	_	_	_
359	slide	slide	NN	_	_	_
360	2	2	CD	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	ppsA	ppsa	NN	GEN	_	_
363	mutant	mutant	JJ	_	_	_
364	4	4	CD	_	_	_
365	hour	hour	NN	_	_	_
366	-LRB-	-lrb-	-LRB-	_	_	_
367	2	2	CD	_	_	_
368	-RRB-	-rrb-	-RRB-	_	_	_
369	slide	slide	NN	_	_	_
370	1	1	CD	_	_	_
371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
372	ppsA	ppsa	NN	GEN	_	_
373	mutant	mutant	JJ	_	_	_
374	4	4	CD	_	_	_
375	hour	hour	NN	_	_	_
376	-LRB-	-lrb-	-LRB-	_	_	_
377	2	2	CD	_	_	_
378	-RRB-	-rrb-	-RRB-	_	_	_
379	slide	slide	NN	_	_	_
380	2	2	CD	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	ppsA	ppsa	NN	GEN	_	_
383	mutant	mutant	JJ	_	_	_
384	4	4	CD	_	_	_
385	hour	hour	NN	_	_	_
386	-LRB-	-lrb-	-LRB-	_	_	_
387	3	3	CD	_	_	_
388	-RRB-	-rrb-	-RRB-	_	_	_
389	slide	slide	NN	_	_	_
390	1	1	CD	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	ppsA	ppsa	NN	GEN	_	_
393	mutant	mutant	JJ	_	_	_
394	4	4	CD	_	_	_
395	hour	hour	NN	_	_	_
396	-LRB-	-lrb-	-LRB-	_	_	_
397	3	3	CD	_	_	_
398	-RRB-	-rrb-	-RRB-	_	_	_
399	slide	slide	NN	_	_	_
400	2	2	CD	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	ppsA	ppsa	NN	GEN	_	_
403	mutant	mutant	JJ	_	_	_
404	5	5	CD	_	_	_
405	hour	hour	NN	_	_	_
406	-LRB-	-lrb-	-LRB-	_	_	_
407	1	1	CD	_	_	_
408	-RRB-	-rrb-	-RRB-	_	_	_
409	slide	slide	NN	_	_	_
410	1	1	CD	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	ppsA	ppsa	NN	GEN	_	_
413	mutant	mutant	JJ	_	_	_
414	5	5	CD	_	_	_
415	hour	hour	NN	_	_	_
416	-LRB-	-lrb-	-LRB-	_	_	_
417	1	1	CD	_	_	_
418	-RRB-	-rrb-	-RRB-	_	_	_
419	slide	slide	NN	_	_	_
420	2	2	CD	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	ppsA	ppsa	NN	GEN	_	_
423	mutant	mutant	JJ	_	_	_
424	5	5	CD	_	_	_
425	hour	hour	NN	_	_	_
426	-LRB-	-lrb-	-LRB-	_	_	_
427	2	2	CD	_	_	_
428	-RRB-	-rrb-	-RRB-	_	_	_
429	slide	slide	NN	_	_	_
430	1	1	CD	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	ppsA	ppsa	NN	GEN	_	_
433	mutant	mutant	JJ	_	_	_
434	5	5	CD	_	_	_
435	hour	hour	NN	_	_	_
436	-LRB-	-lrb-	-LRB-	_	_	_
437	2	2	CD	_	_	_
438	-RRB-	-rrb-	-RRB-	_	_	_
439	slide	slide	NN	_	_	_
440	2	2	CD	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	ppsA	ppsa	NN	GEN	_	_
443	mutant	mutant	JJ	_	_	_
444	5	5	CD	_	_	_
445	min	min	NN	_	_	_
446	-LRB-	-lrb-	-LRB-	_	_	_
447	1	1	CD	_	_	_
448	-RRB-	-rrb-	-RRB-	_	_	_
449	slide	slide	NN	_	_	_
450	1	1	CD	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	ppsA	ppsa	NN	GEN	_	_
453	mutant	mutant	JJ	_	_	_
454	5	5	CD	_	_	_
455	min	min	NN	_	_	_
456	-LRB-	-lrb-	-LRB-	_	_	_
457	1	1	CD	_	_	_
458	-RRB-	-rrb-	-RRB-	_	_	_
459	slide	slide	NN	_	_	_
460	2	2	CD	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	ppsA	ppsa	NN	GEN	_	_
463	mutant	mutant	JJ	_	_	_
464	6	6	CD	_	_	_
465	hour	hour	NN	_	_	_
466	-LRB-	-lrb-	-LRB-	_	_	_
467	1	1	CD	_	_	_
468	-RRB-	-rrb-	-RRB-	_	_	_
469	slide	slide	NN	_	_	_
470	1	1	CD	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	ppsA	ppsa	NN	GEN	_	_
473	mutant	mutant	JJ	_	_	_
474	6	6	CD	_	_	_
475	hour	hour	NN	_	_	_
476	-LRB-	-lrb-	-LRB-	_	_	_
477	1	1	CD	_	_	_
478	-RRB-	-rrb-	-RRB-	_	_	_
479	slide	slide	NN	_	_	_
480	2	2	CD	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	ppsA	ppsa	NN	GEN	_	_
483	mutant	mutant	JJ	_	_	_
484	6	6	CD	_	_	_
485	hour	hour	NN	_	_	_
486	-LRB-	-lrb-	-LRB-	_	_	_
487	2	2	CD	_	_	_
488	-RRB-	-rrb-	-RRB-	_	_	_
489	slide	slide	NN	_	_	_
490	1	1	CD	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	ppsA	ppsa	NN	GEN	_	_
493	mutant	mutant	JJ	_	_	_
494	6	6	CD	_	_	_
495	hour	hour	NN	_	_	_
496	-LRB-	-lrb-	-LRB-	_	_	_
497	2	2	CD	_	_	_
498	-RRB-	-rrb-	-RRB-	_	_	_
499	slide	slide	NN	_	_	_
500	2	2	CD	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	preprocessed	preprocessed	JJ	_	_	_
503	RNA-Seq	rna-seq	NN	_	_	_
504	reads	read	VBZ	_	_	_
505	were	be	VBD	_	_	_
506	mapped	map	VBN	_	_	_
507	to	to	TO	_	_	_
508	the	the	DT	_	_	_
509	reference	reference	NN	_	_	_
510	Escherichia	escherichia	FW	Organism	_	_
511	coli	coli	FW	Organism	_	_
512	strain	strain	NN	_	_	_
513	K12	k12	NN	_	_	_
514	sub-strain	sub-strain	JJ	_	_	_
515	MG1655	mg1655	NN	_	_	_
516	genome	genome	NN	_	_	_
517	-LRB-	-lrb-	-LRB-	_	_	_
518	GenBank	genbank	NN	_	_	_
519	accession	accession	NN	_	_	_
520	no	no	DT	_	_	_
521	.	.	.	_	_	_

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	print	print	NN	_	_	_
21	tip	tip	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	subtracting	subtract	VBG	_	_	_
25	the	the	DT	_	_	_
26	resulting	result	VBG	_	_	_
27	average	average	NN	_	_	_
28	from	from	IN	_	_	_
29	all	all	DT	_	_	_
30	the	the	DT	_	_	_
31	individual	individual	JJ	_	_	_
32	log	log	NN	_	_	_
33	ratios	ratio	NNS	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	Prior	prior	RB	_	_	_
36	to	to	TO	_	_	_
37	total	total	JJ	_	_	_
38	RNA	rna	NN	_	_	_
39	extraction	extraction	NN	_	_	_
40	harvested	harvest	VBN	_	_	_
41	bacterial	bacterial	JJ	_	_	_
42	cells	cell	NNS	_	_	_
43	were	be	VBD	_	_	_
44	stored	store	VBN	_	_	_
45	at	at	IN	_	_	_
46	-80.0	-80.0	CD	_	_	_
47	°C	°c	NN	_	_	_
48	in	in	IN	_	_	_
49	an	a	DT	_	_	_
50	equal	equal	JJ	_	_	_
51	volume	volume	NN	_	_	_
52	of	of	IN	_	_	_
53	RNAlater	rnalater	NN	_	_	_
54	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Probabilistic	Probabilistic	NNP	_	_	_
3	expression	expression	NN	_	_	_
4	counting	counting	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	RNA-Seq	rna-seq	NN	_	_	_
10	by	by	IN	_	_	_
11	Expectation-Maximization	expectation-maximization	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	RSEM	rsem	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	version	version	NN	_	_	_
16	1.2.4	1.2.4	CD	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Li	Li	NNP	_	_	_
19	and	and	CC	_	_	_
20	Dewey	Dewey	NNP	_	_	_
21	,	,	,	_	_	_
22	2011	2011	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Probe	Probe	NNP	_	_	_
26	signal	signal	NN	_	_	_
27	intensities	intensity	NNS	_	_	_
28	were	be	VBD	_	_	_
29	preprocessed	preprocess	VBN	_	_	_
30	using	use	VBG	_	_	_
31	robust	robust	JJ	_	_	_
32	multichip	multichip	NN	_	_	_
33	averaging	averaging	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	RMA	rma	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	in	in	IN	_	_	_
38	the	the	DT	_	_	_
39	program	program	NN	_	_	_
40	ArrayStar	arraystar	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	DNASTAR	dnastar	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	,	,	,	_	_	_
45	and	and	CC	_	_	_
46	the	the	DT	_	_	_
47	resulting	result	VBG	_	_	_
48	gene	gene	NN	_	_	_
49	expression	expression	NN	_	_	_
50	signals	signal	NNS	_	_	_
51	were	be	VBD	_	_	_
52	quantile-normalized	quantile-normalize	VBN	_	_	_
53	across	across	IN	_	_	_
54	all	all	DT	_	_	_
55	samples	sample	NNS	_	_	_
56	using	use	VBG	_	_	_
57	the	the	DT	_	_	_
58	normalize.quantiles	normalize.quantiles	JJ	_	_	_
59	function	function	NN	_	_	_
60	in	in	IN	_	_	_
61	the	the	DT	_	_	_
62	Bioconductor	Bioconductor	NNP	_	_	_
63	package	package	NN	_	_	_
64	for	for	IN	_	_	_
65	R.	R.	NNP	_	_	_
66	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
67	Procedures	procedure	NNS	_	_	_
68	to	to	TO	_	_	_
69	calculate	calculate	VB	_	_	_
70	the	the	DT	_	_	_
71	value	value	NN	_	_	_
72	of	of	IN	_	_	_
73	log2	log2	NN	_	_	_
74	ratio	ratio	NN	_	_	_
75	:	:	:	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	product	product	NN	_	_	_
78	:	:	:	_	_	_
79	Butanol	Butanol	NNP	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Progesterone	progesterone	NN	_	_	_
82	Treatment	treatment	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Proline	proline	NN	_	_	_
85	addition	addition	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Promega	Promega	NNP	_	_	_
88	RNase-free	RNase-free	NNP	_	_	_
89	DNase	dnase	NN	_	_	_
90	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
91	Protein	protein	NN	_	_	_
92	DNA	dna	NN	_	_	_
93	interactions	interaction	NNS	_	_	_
94	were	be	VBD	_	_	_
95	crosslinked	crosslink	VBN	_	_	_
96	for	for	IN	_	_	_
97	10	10	CD	_	_	_
98	min	min	NN	_	_	_
99	at	at	IN	_	_	_
100	22.5	22.5	CD	_	_	_
101	C	c	NN	_	_	_
102	with	with	IN	_	_	_
103	1	1	CD	_	_	_
104	%	%	NN	_	_	_
105	formaldehyde	formaldehyde	NN	_	_	_
106	and	and	CC	_	_	_
107	quenched	quench	VBN	_	_	_
108	using	use	VBG	_	_	_
109	glycine	glycine	NN	_	_	_
110	to	to	TO	_	_	_
111	a	a	DT	_	_	_
112	final	final	JJ	_	_	_
113	concentration	concentration	NN	_	_	_
114	of	of	IN	_	_	_
115	0.5	0.5	CD	_	_	_
116	M	m	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	protein	protein	NN	_	_	_
119	:	:	:	_	_	_
120	GST	gst	NN	_	_	_
121	expressed	express	VBN	_	_	_
122	in	in	IN	_	_	_
123	E.	e.	FW	_	_	_
124	coli	coli	FW	_	_	_
125	BL21	bl21	NN	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	DE3	de3	NN	_	_	_
128	-RRB-	-rrb-	-RRB-	_	_	_
129	from	from	IN	_	_	_
130	pGEX-4T-3	pgex-4t-3	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	protocol	protocol	NN	_	_	_
133	:	:	:	_	_	_
134	late	late	JJ	_	_	_
135	log	log	NN	_	_	_
136	phase	phase	NN	_	_	_
137	,	,	,	_	_	_
138	LB	lb	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	protocol	protocol	NN	_	_	_
141	:	:	:	_	_	_
142	late	late	JJ	_	_	_
143	log	log	NN	_	_	_
144	phase	phase	NN	_	_	_
145	,	,	,	_	_	_
146	LB	lb	NN	_	_	_
147	,	,	,	_	_	_
148	30	30	CD	_	_	_
149	min	min	NN	_	_	_
150	after	after	IN	_	_	_
151	butanol	butanol	NN	_	_	_
152	treatment	treatment	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	protocol	protocol	NN	_	_	_
155	:	:	:	_	_	_
156	M9	m9	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	protocol	protocol	NN	_	_	_
159	:	:	:	_	_	_
160	M9	m9	NN	_	_	_
161	supplemented	supplement	VBN	_	_	_
162	with	with	IN	_	_	_
163	0.6	0.6	CD	_	_	_
164	M	m	NN	_	_	_
165	NaCl	nacl	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	protocol	protocol	NN	_	_	_
168	:	:	:	_	_	_
169	small	small	JJ	_	_	_
170	RNA	rna	NN	_	_	_
171	DicF	dicf	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	protocol	protocol	NN	_	_	_
174	:	:	:	_	_	_
175	vector	vector	NN	_	_	_
176	control	control	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	pseudoalignment	pseudoalignment	NN	_	_	_
179	and	and	CC	_	_	_
180	quantitation	quantitation	NN	_	_	_
181	with	with	IN	_	_	_
182	kallisto	kallisto	FW	_	_	_
183	v0	v0	FW	_	_	_
184	.42.5	.42.5	CD	_	_	_
185	with	with	IN	_	_	_
186	parameters	parameter	NNS	_	_	_
187	--	--	:	_	_	_
188	single	single	JJ	_	_	_
189	-	-	:	_	_	_
190	l	l	NN	_	_	_
191	450	450	CD	_	_	_
192	-	-	:	_	_	_
193	s	s	NNS	_	_	_
194	250	250	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
196	Ptac	ptac	NN	_	_	_
197	:	:	:	_	_	_
198	:	:	:	_	_	_
199	fnr	fnr	SYM	GEN	_	_
200	-	-	:	_	_	_
201	A	a	NN	_	_	_
202	-	-	:	_	_	_
203	16	16	CD	_	_	_
204	µM	µm	NN	_	_	_
205	IPTG	iptg	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	Ptac	ptac	NN	_	_	_
208	:	:	:	_	_	_
209	:	:	:	_	_	_
210	fnr	fnr	SYM	GEN	_	_
211	-	-	:	_	_	_
212	A	a	NN	_	_	_
213	-	-	:	_	_	_
214	4	4	CD	_	_	_
215	µM	µm	NN	_	_	_
216	IPTG	iptg	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	Ptac	ptac	NN	_	_	_
219	:	:	:	_	_	_
220	:	:	:	_	_	_
221	fnr	fnr	SYM	GEN	_	_
222	-	-	:	_	_	_
223	A	a	NN	_	_	_
224	-	-	:	_	_	_
225	8	8	CD	_	_	_
226	µM	µm	NN	_	_	_
227	IPTG	iptg	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	Ptac	ptac	NN	_	_	_
230	:	:	:	_	_	_
231	:	:	:	_	_	_
232	fnr	fnr	SYM	GEN	_	_
233	-	-	:	_	_	_
234	B	b	NN	_	_	_
235	-	-	:	_	_	_
236	16	16	CD	_	_	_
237	µM	µm	NN	_	_	_
238	IPTG	iptg	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	Ptac	ptac	NN	_	_	_
241	:	:	:	_	_	_
242	:	:	:	_	_	_
243	fnr	fnr	SYM	GEN	_	_
244	-	-	:	_	_	_
245	B	b	NN	_	_	_
246	-	-	:	_	_	_
247	4	4	CD	_	_	_
248	µM	µm	NN	_	_	_
249	IPTG	iptg	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	Ptac	ptac	NN	_	_	_
252	:	:	:	_	_	_
253	:	:	:	_	_	_
254	fnr	fnr	SYM	GEN	_	_
255	-	-	:	_	_	_
256	B	b	NN	_	_	_
257	-	-	:	_	_	_
258	8	8	CD	_	_	_
259	µM	µm	NN	_	_	_
260	IPTG	iptg	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	Ptac	ptac	NN	_	_	_
263	:	:	:	_	_	_
264	:	:	:	_	_	_
265	fnr	fnr	SYM	GEN	_	_
266	-	-	:	_	_	_
267	C	c	NN	_	_	_
268	-	-	:	_	_	_
269	16	16	CD	_	_	_
270	µM	µm	NN	_	_	_
271	IPTG	iptg	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	ptsN	ptsn	NN	GEN	_	_
274	mutant	mutant	NN	_	_	_
275	replicate	replicate	VBP	_	_	_
276	1	1	CD	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	ptsN	ptsn	NN	GEN	_	_
279	mutant	mutant	NN	_	_	_
280	replicate	replicate	VBP	_	_	_
281	2	2	CD	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
283	Pure	pure	JJ	_	_	_
284	culture	culture	NN	_	_	_
285	in	in	IN	_	_	_
286	LB	LB	NNP	_	_	_
287	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
288	purification	purification	NN	_	_	_
289	:	:	:	_	_	_
290	Protein	protein	NN	_	_	_
291	purified	purify	VBN	_	_	_
292	using	use	VBG	_	_	_
293	GSH-sepharose	gsh-sepharose	JJ	_	_	_
294	4b	4b	NN	_	_	_
295	-LRB-	-lrb-	-LRB-	_	_	_
296	GE	GE	NNP	_	_	_
297	Life	Life	NNP	_	_	_
298	Sciences	Sciences	NNP	_	_	_
299	-RRB-	-rrb-	-RRB-	_	_	_
300	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
301	Purified	purify	VBN	_	_	_
302	total	total	JJ	_	_	_
303	RNA	rna	NN	_	_	_
304	was	be	VBD	_	_	_
305	depleted	deplete	VBN	_	_	_
306	of	of	IN	_	_	_
307	rRNA	rrna	NN	_	_	_
308	using	use	VBG	_	_	_
309	a	a	DT	_	_	_
310	Ribo-Zero	ribo-zero	NN	_	_	_
311	-LRB-	-lrb-	-LRB-	_	_	_
312	Bacteria	bacterium	NNS	_	_	_
313	-RRB-	-rrb-	-RRB-	_	_	_
314	rRNA	rrna	NN	_	_	_
315	Removal	removal	NN	_	_	_
316	Kit	kit	NN	_	_	_
317	-LRB-	-lrb-	-LRB-	_	_	_
318	Illumina	Illumina	NNP	_	_	_
319	-RRB-	-rrb-	-RRB-	_	_	_
320	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	PurR	purr	NN	TF	_	_
3	_	_	CD	_	_	_
4	Adenine	Adenine	NNP	_	_	_
5	_	_	SYM	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	PurR	purr	NN	TF	_	_
9	_	_	CD	_	_	_
10	Adenine	Adenine	NNP	_	_	_
11	_	_	NN	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	PurR	purr	NN	TF	_	_
15	_	_	CD	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	_	_	NN	_	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	PurR	purr	NN	TF	_	_
21	_	_	CD	_	_	_
22	glucose	glucose	NN	SUPP	_	_
23	_	_	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	putP	putp	NN	GEN	_	_
27	KO	ko	NN	_	_	_
28	rep1	rep1	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	putP	putp	NN	GEN	_	_
31	KO	ko	NN	_	_	_
32	rep2	rep2	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	putP	putp	NN	GEN	_	_
35	KO	ko	NN	_	_	_
36	rep3	rep3	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	pyrC	pyrc	NN	GEN	_	_
39	__	__	CD	_	_	_
40	U	U	NNP	_	_	_
41	_	_	NNP	_	_	_
42	N0075	N0075	NNP	_	_	_
43	_	_	VBD	_	_	_
44	r1	r1	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	pyrC	pyrc	NN	GEN	_	_
47	__	__	CD	_	_	_
48	U	U	NNP	_	_	_
49	_	_	NNP	_	_	_
50	N0075	N0075	NNP	_	_	_
51	_	_	VBD	_	_	_
52	r2	r2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	pyrC	pyrc	NN	GEN	_	_
55	__	__	CD	_	_	_
56	U	U	NNP	_	_	_
57	_	_	NNP	_	_	_
58	N0075	N0075	NNP	_	_	_
59	_	_	SYM	_	_	_
60	r3	r3	FW	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
62	pyrC	pyrc	NN	GEN	_	_
63	upregulation	upregulation	NN	_	_	_
64	,	,	,	_	_	_
65	0.075	0.075	CD	_	_	_
66	mg/mL	mg/ml	NN	_	_	_
67	norfloxacin	norfloxacin	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	qC	qc	NN	_	_	_
70	:	:	:	_	_	_
71	We	we	PRP	_	_	_
72	checked	check	VBD	_	_	_
73	the	the	DT	_	_	_
74	quality	quality	NN	_	_	_
75	of	of	IN	_	_	_
76	the	the	DT	_	_	_
77	raw	raw	JJ	_	_	_
78	reads	read	VBZ	_	_	_
79	data	datum	NNS	_	_	_
80	for	for	IN	_	_	_
81	each	each	DT	_	_	_
82	sample	sample	NN	_	_	_
83	using	use	VBG	_	_	_
84	FastQC	fastqc	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	version	version	NN	_	_	_
87	0.11.3	0.11.3	CD	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	to	to	TO	_	_	_
90	identify	identify	VB	_	_	_
91	features	feature	NNS	_	_	_
92	of	of	IN	_	_	_
93	the	the	DT	_	_	_
94	data	datum	NNS	_	_	_
95	that	that	WDT	_	_	_
96	may	may	MD	_	_	_
97	indicate	indicate	VB	_	_	_
98	quality	quality	NN	_	_	_
99	problems	problem	NNS	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	e.g.	e.g.	FW	_	_	_
102	low	low	JJ	_	_	_
103	quality	quality	NN	_	_	_
104	scores	score	NNS	_	_	_
105	,	,	,	_	_	_
106	over-represented	over-represented	JJ	_	_	_
107	sequences	sequence	NNS	_	_	_
108	,	,	,	_	_	_
109	inappropriate	inappropriate	JJ	_	_	_
110	GC	gc	NN	_	_	_
111	content	content	NN	_	_	_
112	,	,	,	_	_	_
113	etc.	etc.	FW	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Qiagen	Qiagen	NNP	_	_	_
3	Genomic	genomic	JJ	_	_	_
4	Tip	tip	NN	_	_	_
5	500/G	500/g	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	,	,	,	_	_	_
9	Hilden	Hilden	NNP	_	_	_
10	,	,	,	_	_	_
11	Germany	Germany	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	Genomic	genomic	JJ	_	_	_
16	DNA	dna	NN	_	_	_
17	Buffer	buffer	NN	_	_	_
18	set	set	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Qiagen	qiagen	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Qiagen	qiagen	NN	_	_	_
24	RNA	rna	NN	_	_	_
25	extraction	extraction	NN	_	_	_
26	kit	kit	NN	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Qiagen	Qiagen	NNP	_	_	_
29	Rneasy	Rneasy	NNP	_	_	_
30	column	column	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Qiagen	Qiagen	NNP	_	_	_
33	RNeasy	RNeasy	NNP	_	_	_
34	Midikit	Midikit	NNP	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	Qiagen	Qiagen	NNP	_	_	_
37	Rneasy	Rneasy	NNP	_	_	_
38	mini	minus	NNS	_	_	_
39	kit	kit	NN	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Qiagen	Qiagen	NNP	_	_	_
42	RNeasy	RNeasy	NNP	_	_	_
43	mini	minus	NNS	_	_	_
44	Kit	kit	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Quality	quality	JJ	_	_	_
47	and	and	CC	_	_	_
48	adapter	adapter	NN	_	_	_
49	trimming	trim	VBG	_	_	_
50	was	be	VBD	_	_	_
51	performed	perform	VBN	_	_	_
52	with	with	IN	_	_	_
53	the	the	DT	_	_	_
54	CLC	clc	NN	_	_	_
55	Genomics	genomic	NNS	_	_	_
56	Workbench	workbench	JJ	_	_	_
57	9.0	9.0	CD	_	_	_
58	software	software	NN	_	_	_
59	package	package	NN	_	_	_
60	using	use	VBG	_	_	_
61	the	the	DT	_	_	_
62	`	`	``	_	_	_
63	Trim	Trim	NNP	_	_	_
64	Sequences	sequence	NNS	_	_	_
65	'	'	POS	_	_	_
66	tool	tool	NN	_	_	_
67	with	with	IN	_	_	_
68	standard	standard	JJ	_	_	_
69	parameters	parameter	NNS	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Quality	Quality	NNP	_	_	_
3	control	control	NN	_	_	_
4	and	and	CC	_	_	_
5	microarray	microarray	NN	_	_	_
6	data	data	NN	_	_	_
7	analysis	analysis	NN	_	_	_
8	of	of	IN	_	_	_
9	all	all	DT	_	_	_
10	60	60	CD	_	_	_
11	chips	chip	NNS	_	_	_
12	was	be	VBD	_	_	_
13	done	do	VBN	_	_	_
14	using	use	VBG	_	_	_
15	R/Bioconductor	r/bioconductor	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	http://www.bioconductor.org/	http://www.bioconductor.org/	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Signal	signal	NN	_	_	_
2	intensity	intensity	NN	_	_	_
3	files	file	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	CEL	cel	NN	_	_	_
6	files	file	NNS	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	of	of	IN	_	_	_
9	all	all	DT	_	_	_
10	60	60	CD	_	_	_
11	chips	chip	NNS	_	_	_
12	were	be	VBD	_	_	_
13	summarized	summarize	VBN	_	_	_
14	using	use	VBG	_	_	_
15	RMA	rma	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	robust	robust	JJ	_	_	_
18	multi	multus	NNS	_	_	_
19	array	array	NN	_	_	_
20	average	average	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	as	as	IN	_	_	_
23	processing	processing	NN	_	_	_
24	algorithm	algorithm	NN	_	_	_
25	and	and	CC	_	_	_
26	quantile	quantile	NN	_	_	_
27	normalization	normalization	NN	_	_	_
28	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	modified	modify	VBN	_	_	_
3	t-test	t-test	NN	_	_	_
4	using	use	VBG	_	_	_
5	limma	limma	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	for	for	IN	_	_	_
9	comparison	comparison	NN	_	_	_
10	of	of	IN	_	_	_
11	experimental	experimental	JJ	_	_	_
12	conditions	condition	NNS	_	_	_
13	.	.	.	_	_	_

1	See	see	VB	_	_	_
2	also	also	RB	_	_	_
3	additional	additional	JJ	_	_	_
4	files	file	NNS	_	_	_
5	containing	contain	VBG	_	_	_
6	only	only	RB	_	_	_
7	E.coli	e.coli	JJ	_	_	_
8	K-12	k-12	NN	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	probes	probe	NNS	_	_	_
11	with	with	IN	_	_	_
12	P-values	p-value	NNS	_	_	_
13	and	and	CC	_	_	_
14	ratio	ratio	NN	_	_	_
15	.	.	.	_	_	_

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://galaxyproject.org	https://galaxyproject.org	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	FASTX	fastx	NN	_	_	_
3	tools	tool	NNS	_	_	_
4	in	in	IN	_	_	_
5	Galaxy	galaxy	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	http://hannonlab.cshl.edu/fastx_toolkit	http://hannonlab.cshl.edu/fastx_toolkit	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	were	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	for	for	IN	_	_	_
12	filtering	filter	VBG	_	_	_
13	by	by	IN	_	_	_
14	quality	quality	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	80	80	CD	_	_	_
17	%	%	NN	_	_	_
18	of	of	IN	_	_	_
19	sequence	sequence	NN	_	_	_
20	>	>	JJR	_	_	_
21	quality	quality	NN	_	_	_
22	score	score	NN	_	_	_
23	of	of	IN	_	_	_
24	20	20	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	then	then	RB	_	_	_
28	reads	read	VBZ	_	_	_
29	were	be	VBD	_	_	_
30	trimmed	trim	VBN	_	_	_
31	at	at	IN	_	_	_
32	both	both	DT	_	_	_
33	5	5	CD	_	_	_
34	'	'	''	_	_	_
35	and	and	CC	_	_	_
36	3	3	CD	_	_	_
37	'	'	''	_	_	_
38	ends	end	VBZ	_	_	_
39	using	use	VBG	_	_	_
40	a	a	DT	_	_	_
41	window	window	NN	_	_	_
42	and	and	CC	_	_	_
43	step	step	NN	_	_	_
44	size	size	NN	_	_	_
45	of	of	IN	_	_	_
46	1	1	CD	_	_	_
47	with	with	IN	_	_	_
48	quality	quality	NN	_	_	_
49	score	score	NN	_	_	_
50	>	>	JJR	_	_	_
51	20	20	CD	_	_	_
52	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Quality	Quality	NNP	_	_	_
3	trimming	trim	VBG	_	_	_
4	of	of	IN	_	_	_
5	3	3	CD	_	_	_
6	'	'	''	_	_	_
7	end	end	NN	_	_	_
8	at	at	IN	_	_	_
9	Read	Read	NNP	_	_	_
10	Segment	Segment	NNP	_	_	_
11	Quality	Quality	NNP	_	_	_
12	Control	Control	NNP	_	_	_
13	Indicator	Indicator	NNP	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Quality	Quality	NNP	_	_	_
3	trimming	trim	VBG	_	_	_
4	using	use	VBG	_	_	_
5	FASTX-toolkit	fastx-toolkit	NN	_	_	_
6	,	,	,	_	_	_
7	version	version	NN	_	_	_
8	0.0.13.2	0.0.13.2	CD	_	_	_
9	,	,	,	_	_	_
10	parameters	parameter	NNS	_	_	_
11	-	-	:	_	_	_
12	v	v	LS	_	_	_
13	-	-	:	_	_	_
14	t	t	NN	_	_	_
15	20	20	CD	_	_	_
16	-	-	:	_	_	_
17	l	l	NN	_	_	_
18	10	10	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Quantification	quantification	NN	_	_	_
21	of	of	IN	_	_	_
22	gene	gene	NN	_	_	_
23	expression	expression	NN	_	_	_
24	and	and	CC	_	_	_
25	analysis	analysis	NN	_	_	_
26	of	of	IN	_	_	_
27	gene	gene	NN	_	_	_
28	differential	differential	JJ	_	_	_
29	expression	expression	NN	_	_	_
30	were	be	VBD	_	_	_
31	performed	perform	VBN	_	_	_
32	using	use	VBG	_	_	_
33	Fragment	fragment	NN	_	_	_
34	Per	per	IN	_	_	_
35	Kilo	Kilo	NNP	_	_	_
36	bases	basis	NNS	_	_	_
37	per	per	IN	_	_	_
38	Million	Million	NNP	_	_	_
39	reads	read	VBZ	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	FPKM	fpkm	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	value	value	NN	_	_	_
44	based	base	VBN	_	_	_
45	rsem	rsem	NN	_	_	_
46	software	software	NN	_	_	_
47	version	version	NN	_	_	_
48	1.2.4	1.2.4	CD	_	_	_
49	and	and	CC	_	_	_
50	edgeR	edger	NN	_	_	_
51	version	version	NN	_	_	_
52	3.4.2	3.4.2	CD	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	Bioconductor	bioconductor	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	,	,	,	_	_	_
57	respectively	respectively	RB	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	Quantification	quantification	NN	_	_	_
60	of	of	IN	_	_	_
61	the	the	DT	_	_	_
62	scans	scan	NNS	_	_	_
63	were	be	VBD	_	_	_
64	performed	perform	VBN	_	_	_
65	with	with	IN	_	_	_
66	ImaGene	imagene	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Version	version	NN	_	_	_
69	6.0.1	6.0.1	CD	_	_	_
70	;	;	:	_	_	_
71	BioDiscovery	BioDiscovery	NNP	_	_	_
72	;	;	:	_	_	_
73	El	El	NNP	_	_	_
74	Segundo	Segundo	NNP	_	_	_
75	,	,	,	_	_	_
76	CA	CA	NNP	_	_	_
77	;	;	:	_	_	_
78	www.biodiscovery.com	www.biodiscovery.com	NNP	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	;	;	:	_	_	_
81	with	with	IN	_	_	_
82	the	the	DT	_	_	_
83	results	result	NNS	_	_	_
84	presented	present	VBN	_	_	_
85	in	in	IN	_	_	_
86	the	the	DT	_	_	_
87	associated	associate	VBN	_	_	_
88	text	text	NN	_	_	_
89	files	file	NNS	_	_	_
90	.	.	.	_	_	_

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/lcDNA	receptor.seas.ucla.edu/lcdna	NN	_	_	_
21	;	;	:	_	_	_
22	Hyduke	Hyduke	NNP	_	_	_
23	DR	dr	NN	_	_	_
24	,	,	,	_	_	_
25	Rohlin	Rohlin	NNP	_	_	_
26	L	L	NNP	_	_	_
27	,	,	,	_	_	_
28	Kao	Kao	NNP	_	_	_
29	KC	KC	NNP	_	_	_
30	,	,	,	_	_	_
31	Liao	Liao	NNP	_	_	_
32	JC	JC	NNP	_	_	_
33	.	.	.	_	_	_

1	2003	2003	CD	_	_	_
2	A	a	DT	_	_	_
3	software	software	NN	_	_	_
4	package	package	NN	_	_	_
5	for	for	IN	_	_	_
6	cDNA	cdna	NN	_	_	_
7	microarray	microarray	NN	_	_	_
8	data	datum	NNS	_	_	_
9	normalization	normalization	NN	_	_	_
10	and	and	CC	_	_	_
11	assessing	assess	VBG	_	_	_
12	confidence	confidence	NN	_	_	_
13	intervals	interval	NNS	_	_	_
14	.	.	.	_	_	_

1	OMICS	omics	NN	_	_	_
2	7	7	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	3	3	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	227-234	227-234	CD	_	_	_
8	.	.	.	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Quantification	quantification	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	scans	scan	NNS	_	_	_
6	were	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	with	with	IN	_	_	_
9	ImaGene	imagene	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Version	version	NN	_	_	_
12	6.0.1	6.0.1	CD	_	_	_
13	;	;	:	_	_	_
14	BioDiscovery	BioDiscovery	NNP	_	_	_
15	;	;	:	_	_	_
16	El	El	NNP	_	_	_
17	Segundo	Segundo	NNP	_	_	_
18	,	,	,	_	_	_
19	CA	CA	NNP	_	_	_
20	;	;	:	_	_	_
21	www.biodiscovery.com	www.biodiscovery.com	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	;	;	:	_	_	_
24	with	with	IN	_	_	_
25	the	the	DT	_	_	_
26	results	result	NNS	_	_	_
27	presented	present	VBN	_	_	_
28	in	in	IN	_	_	_
29	the	the	DT	_	_	_
30	associated	associate	VBN	_	_	_
31	text	text	NN	_	_	_
32	files	file	NNS	_	_	_
33	.	.	.	_	_	_

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/lcDNA	receptor.seas.ucla.edu/lcdna	NN	_	_	_
21	;	;	:	_	_	_
22	Hyduke	Hyduke	NNP	_	_	_
23	DR	dr	NN	_	_	_
24	,	,	,	_	_	_
25	Rohlin	Rohlin	NNP	_	_	_
26	L	L	NNP	_	_	_
27	,	,	,	_	_	_
28	Kao	Kao	NNP	_	_	_
29	KC	KC	NNP	_	_	_
30	,	,	,	_	_	_
31	Liao	Liao	NNP	_	_	_
32	JC	JC	NNP	_	_	_
33	.	.	.	_	_	_

1	2003	2003	CD	_	_	_
2	A	a	DT	_	_	_
3	software	software	NN	_	_	_
4	package	package	NN	_	_	_
5	for	for	IN	_	_	_
6	cDNA	cdna	NN	_	_	_
7	microarray	microarray	NN	_	_	_
8	data	datum	NNS	_	_	_
9	normalization	normalization	NN	_	_	_
10	and	and	CC	_	_	_
11	assessing	assess	VBG	_	_	_
12	confidence	confidence	NN	_	_	_
13	intervals	interval	NNS	_	_	_
14	.	.	.	_	_	_

1	OMICS	omics	NN	_	_	_
2	7	7	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	3	3	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	227-234	227-234	CD	_	_	_
8	.	.	.	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	R11	r11	NN	_	_	_
3	DH10BGFP	dh10bgfp	NN	_	_	_
4	_	_	CD	_	_	_
5	pLys	ply	VBZ	_	_	_
6	_	_	SYM	_	_	_
7	1	1	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	R16	r16	NN	_	_	_
10	MG1655GFP	mg1655gfp	NN	_	_	_
11	_	_	CD	_	_	_
12	pLys	ply	VBZ	_	_	_
13	_	_	SYM	_	_	_
14	M1	m1	NN	_	_	_
15	_	_	NN	_	_	_
16	1	1	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	R19	r19	NN	_	_	_
19	MG1655GFP	mg1655gfp	NN	_	_	_
20	_	_	CD	_	_	_
21	Lux	lux	FW	_	_	_
22	_	_	FW	_	_	_
23	1	1	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	R26	r26	NN	_	_	_
26	MG1655GFP	mg1655gfp	NN	_	_	_
27	_	_	CD	_	_	_
28	Lux	lux	FW	_	_	_
29	_	_	FW	_	_	_
30	1	1	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	R27	r27	NN	_	_	_
33	MG1655GFP	mg1655gfp	NN	_	_	_
34	_	_	CD	_	_	_
35	pD864	pd864	NN	_	_	_
36	_	_	CD	_	_	_
37	LacZ	lacz	NN	_	_	_
38	_	_	NN	_	_	_
39	1	1	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	R29	r29	NN	_	_	_
42	DH10BGFP	dh10bgfp	NN	_	_	_
43	_	_	CD	_	_	_
44	None	none	NN	_	_	_
45	_	_	NN	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	R2	r2	NN	_	_	_
49	DH10BGFP	dh10bgfp	NN	_	_	_
50	_	_	CD	_	_	_
51	pLys	ply	VBZ	_	_	_
52	_	_	SYM	_	_	_
53	M1	m1	NN	_	_	_
54	_	_	NN	_	_	_
55	1	1	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	R3	r3	NN	_	_	_
58	DH10BGFP	dh10bgfp	NN	_	_	_
59	_	_	CD	_	_	_
60	pSB1C3	psb1c3	NN	_	_	_
61	_	_	NN	_	_	_
62	1	1	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	R6	r6	NN	_	_	_
65	DH10BGFP	dh10bgfp	NN	_	_	_
66	_	_	CD	_	_	_
67	pD864	pd864	NN	_	_	_
68	_	_	CD	_	_	_
69	LacZ	lacz	NN	_	_	_
70	_	_	NN	_	_	_
71	1	1	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	ration	ration	NN	_	_	_
74	of	of	IN	_	_	_
75	median	median	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	635/532	635/532	CD	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	Ratio	Ratio	NNP	_	_	_
81	of	of	IN	_	_	_
82	median	median	JJ	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
84	ratio	ratio	NN	_	_	_
85	set	set	VBN	_	_	_
86	to	to	TO	_	_	_
87	missing	miss	VBG	_	_	_
88	where	where	WRB	_	_	_
89	SNR	snr	NN	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	feature	feature	NN	_	_	_
92	mean	mean	NN	_	_	_
93	-	-	:	_	_	_
94	backround	backround	NN	_	_	_
95	mean	mean	VB	_	_	_
96	/	/	:	_	_	_
97	background	background	NN	_	_	_
98	SD	sd	NN	_	_	_
99	-RRB-	-rrb-	-RRB-	_	_	_
100	less	less	JJR	_	_	_
101	than	than	IN	_	_	_
102	2	2	CD	_	_	_
103	in	in	IN	_	_	_
104	both	both	CC	_	_	_
105	channels	channel	NNS	_	_	_
106	;	;	:	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	Raw	raw	NN	_	_	_
109	CEL	cel	NN	_	_	_
110	files	file	NNS	_	_	_
111	were	be	VBD	_	_	_
112	analyzed	analyze	VBN	_	_	_
113	using	use	VBG	_	_	_
114	robust	robust	JJ	_	_	_
115	multi-array	multi-array	JJ	_	_	_
116	average	average	NN	_	_	_
117	for	for	IN	_	_	_
118	normalization	normalization	NN	_	_	_
119	and	and	CC	_	_	_
120	calculation	calculation	NN	_	_	_
121	of	of	IN	_	_	_
122	probe	probe	NN	_	_	_
123	intensities	intensity	NNS	_	_	_
124	.	.	.	_	_	_

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	Raw	raw	NN	_	_	_
18	counts	count	NNS	_	_	_
19	of	of	IN	_	_	_
20	mapped	map	VBN	_	_	_
21	reads	read	VBZ	_	_	_
22	per	per	IN	_	_	_
23	reference	reference	NN	_	_	_
24	base	base	NN	_	_	_
25	pair	pair	NN	_	_	_
26	were	be	VBD	_	_	_
27	then	then	RB	_	_	_
28	calculated	calculate	VBN	_	_	_
29	using	use	VBG	_	_	_
30	SAMtools	samtool	NNS	_	_	_
31	software	software	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	with	with	IN	_	_	_
34	parameter	parameter	NN	_	_	_
35	--	--	:	_	_	_
36	d	d	NN	_	_	_
37	set	set	VBN	_	_	_
38	to	to	TO	_	_	_
39	10	10	CD	_	_	_
40	^	^	CD	_	_	_
41	6	6	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	.	.	.	_	_	_

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://genome.ucsc.edu	http://genome.ucsc.edu	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	for	for	IN	_	_	_
23	the	the	DT	_	_	_
24	chosen	choose	VBN	_	_	_
25	reference	reference	NN	_	_	_
26	sequence	sequence	NN	_	_	_
27	applying	apply	VBG	_	_	_
28	HTseq-count	htseq-count	JJ	_	_	_
29	v.	v.	CC	_	_	_
30	0.6.1	0.6.1	CD	_	_	_
31	in	in	IN	_	_	_
32	the	the	DT	_	_	_
33	intersection-nonempty	intersection-nonempty	JJ	_	_	_
34	mode	mode	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	data	datum	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	.	.	.	_	_	_

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

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	and	and	CC	_	_	_
7	log2	log2	NN	_	_	_
8	transformed	transform	VBN	_	_	_
9	with	with	IN	_	_	_
10	the	the	DT	_	_	_
11	Acuity	acuity	NN	_	_	_
12	4.0	4.0	CD	_	_	_
13	software	software	NN	_	_	_
14	package	package	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	data	datum	NNS	_	_	_
18	with	with	IN	_	_	_
19	low	low	JJ	_	_	_
20	fluorescence	fluorescence	NN	_	_	_
21	intensities	intensity	NNS	_	_	_
22	were	be	VBD	_	_	_
23	eliminated	eliminate	VBN	_	_	_
24	.	.	.	_	_	_

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	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	quantile	quantile	JJ	_	_	_
8	method	method	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	,	,	,	_	_	_
11	merged	merged	JJ	_	_	_
12	and	and	CC	_	_	_
13	filtered	filter	VBN	_	_	_
14	by	by	IN	_	_	_
15	Feature	Feature	NNP	_	_	_
16	Extraction	Extraction	NNP	_	_	_
17	Software	Software	NNP	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Agilent	Agilent	NNP	_	_	_
20	Technologies	Technologies	NNPS	_	_	_
21	Inc.	Inc.	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	.	.	.	_	_	_

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	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://cran.r-project.org/	http://cran.r-project.org/	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	Limma	limma	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Bioconductor	bioconductor	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	package	package	NN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Raw	raw	NN	_	_	_
22	Microarray	Microarray	NNP	_	_	_
23	data	datum	NNS	_	_	_
24	evaluation	evaluation	NN	_	_	_
25	including	include	VBG	_	_	_
26	preprocessing	preprocessing	NN	_	_	_
27	,	,	,	_	_	_
28	normalization	normalization	NN	_	_	_
29	,	,	,	_	_	_
30	grouping	group	VBG	_	_	_
31	the	the	DT	_	_	_
32	differentially	differentially	RB	_	_	_
33	expressed	express	VBN	_	_	_
34	genes	gene	NNS	_	_	_
35	and	and	CC	_	_	_
36	statistical	statistical	JJ	_	_	_
37	analyses	analysis	NNS	_	_	_
38	with	with	IN	_	_	_
39	Moderated	moderate	VBN	_	_	_
40	T-test	t-test	NN	_	_	_
41	and	and	CC	_	_	_
42	Bonferroni	Bonferroni	NNP	_	_	_
43	FWER	FWER	NNP	_	_	_
44	was	be	VBD	_	_	_
45	carried	carry	VBN	_	_	_
46	out	out	RP	_	_	_
47	with	with	IN	_	_	_
48	GeneSpring	genespring	NN	_	_	_
49	13.0	13.0	CD	_	_	_
50	Software	Software	NNP	_	_	_
51	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	microarray	microarray	NN	_	_	_
4	intensity	intensity	NN	_	_	_
5	data	datum	NNS	_	_	_
6	were	be	VBD	_	_	_
7	normalized	normalize	VBN	_	_	_
8	per	per	IN	_	_	_
9	chip	chip	NN	_	_	_
10	to	to	TO	_	_	_
11	the	the	DT	_	_	_
12	same	same	JJ	_	_	_
13	mean	mean	NN	_	_	_
14	value	value	NN	_	_	_
15	,	,	,	_	_	_
16	which	which	WDT	_	_	_
17	is	be	VBZ	_	_	_
18	recommended	recommend	VBN	_	_	_
19	by	by	IN	_	_	_
20	the	the	DT	_	_	_
21	manufacturer	manufacturer	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	,	,	,	_	_	_
4	not	not	RB	_	_	_
5	normalised	normalised	JJ	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Raw	raw	NN	_	_	_
8	probe	probe	NN	_	_	_
9	intensities	intensity	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	probe	probe	NN	_	_	_
4	intensities	intensity	NNS	_	_	_
5	were	be	VBD	_	_	_
6	normalized	normalize	VBN	_	_	_
7	across	across	IN	_	_	_
8	all	all	DT	_	_	_
9	samples	sample	NNS	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	Robust	Robust	NNP	_	_	_
13	Multichip	Multichip	NNP	_	_	_
14	Average	Average	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	RMA	RMA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	algorithm	algorithm	NN	_	_	_
19	in	in	IN	_	_	_
20	the	the	DT	_	_	_
21	NimbleScan	NimbleScan	NNP	_	_	_
22	software	software	NN	_	_	_
23	package	package	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	version	version	NN	_	_	_
26	2.5	2.5	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	probe	probe	NN	_	_	_
4	intensities	intensity	NNS	_	_	_
5	were	be	VBD	_	_	_
6	normalized	normalize	VBN	_	_	_
7	across	across	IN	_	_	_
8	samples	sample	NNS	_	_	_
9	using	use	VBG	_	_	_
10	RMA	rma	NN	_	_	_
11	analysis	analysis	NN	_	_	_
12	implemented	implement	VBD	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	NimbleScan	NimbleScan	NNP	_	_	_
16	software	software	NN	_	_	_
17	package	package	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	v.	v.	CC	_	_	_
20	2.4	2.4	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	read	read	VBD	_	_	_
4	counts	count	NNS	_	_	_
5	of	of	IN	_	_	_
6	transcripts	transcript	NNS	_	_	_
7	were	be	VBD	_	_	_
8	obtained	obtain	VBN	_	_	_
9	by	by	IN	_	_	_
10	aligning	align	VBG	_	_	_
11	samples	sample	NNS	_	_	_
12	1-14	1-14	CD	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	reference	reference	NN	_	_	_
16	genome	genome	NN	_	_	_
17	and	and	CC	_	_	_
18	counting	count	VBG	_	_	_
19	mapped	map	VBN	_	_	_
20	reads	read	VBZ	_	_	_
21	per	per	IN	_	_	_
22	feature	feature	NN	_	_	_
23	using	use	VBG	_	_	_
24	Rockhopper	Rockhopper	NNP	_	_	_
25	v2	v2	NN	_	_	_
26	.0.3	.0.3	CD	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	aligned	align	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	w3110	w3110	NN	_	_	_
11	MuSGS	musgs	NN	_	_	_
12	genome	genome	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	containing	contain	VBG	_	_	_
15	a	a	DT	_	_	_
16	strong	strong	JJ	_	_	_
17	gyrase	gyrase	NN	_	_	_
18	binding	binding	NN	_	_	_
19	site	site	NN	_	_	_
20	from	from	IN	_	_	_
21	bacteriophage	bacteriophage	NN	_	_	_
22	Mu	mu	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	with	with	IN	_	_	_
25	BWA	bwa	NN	_	_	_
26	MEM	mem	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	default	default	NN	_	_	_
29	settings	setting	NNS	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	Raw	raw	NN	_	_	_
33	reads	read	VBZ	_	_	_
34	were	be	VBD	_	_	_
35	trimmed	trim	VBN	_	_	_
36	by	by	IN	_	_	_
37	two	two	CD	_	_	_
38	nt	nt	NNS	_	_	_
39	from	from	IN	_	_	_
40	the	the	DT	_	_	_
41	5	5	CD	_	_	_
42	'	'	''	_	_	_
43	end	end	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	to	to	TO	_	_	_
46	remove	remove	VB	_	_	_
47	any	any	DT	_	_	_
48	non-templated	non-templated	JJ	_	_	_
49	nts	nt	NNS	_	_	_
50	added	add	VBN	_	_	_
51	by	by	IN	_	_	_
52	reverse	reverse	JJ	_	_	_
53	transcriptase	transcriptase	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	,	,	,	_	_	_
56	and	and	CC	_	_	_
57	were	be	VBD	_	_	_
58	then	then	RB	_	_	_
59	mapped	map	VBN	_	_	_
60	using	use	VBG	_	_	_
61	the	the	DT	_	_	_
62	Burrows-Wheeler	Burrows-Wheeler	NNP	_	_	_
63	Aligner	Aligner	NNP	_	_	_
64	to	to	TO	_	_	_
65	the	the	DT	_	_	_
66	Escherichia	escherichia	FW	Organism	_	_
67	coli	coli	FW	Organism	_	_
68	MG1655	mg1655	NN	_	_	_
69	genome	genome	NN	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	NCBI	ncbi	NN	_	_	_
72	accession	accession	NN	_	_	_
73	NC	nc	NN	_	_	_
74	_	_	SYM	_	_	_
75	000913	000913	CD	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	.	.	.	_	_	_

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	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	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	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	reads	read	VBZ	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	FASTQ	fastq	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	were	be	VBD	_	_	_
9	processed	process	VBN	_	_	_
10	by	by	IN	_	_	_
11	Xpression	xpression	NN	_	_	_
12	and	and	CC	_	_	_
13	only	only	RB	_	_	_
14	the	the	DT	_	_	_
15	uniquely	uniquely	RB	_	_	_
16	mapped	map	VBN	_	_	_
17	reads	read	VBZ	_	_	_
18	were	be	VBD	_	_	_
19	subjected	subject	VBN	_	_	_
20	to	to	TO	_	_	_
21	further	further	JJ	_	_	_
22	analysis	analysis	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	signal	signal	NN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	extracted	extract	VBN	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	TIFF	tiff	NN	_	_	_
10	image	image	NN	_	_	_
11	with	with	IN	_	_	_
12	Agilent	Agilent	NNP	_	_	_
13	Feature	Feature	NNP	_	_	_
14	Extraction	Extraction	NNP	_	_	_
15	Software	Software	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	V10	V10	NNP	_	_	_
18	.7.1.1	.7.1.1	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Read	Read	NNP	_	_	_
3	counting	count	VBG	_	_	_
4	using	use	VBG	_	_	_
5	bedtools	bedtool	NNS	_	_	_
6	,	,	,	_	_	_
7	version	version	NN	_	_	_
8	2.17.0	2.17.0	CD	_	_	_
9	,	,	,	_	_	_
10	parameter	parameter	NN	_	_	_
11	:	:	:	_	_	_
12	-	-	:	_	_	_
13	s	s	NNS	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	middle	middle	JJ	_	_	_
17	nucleotide	nucleotide	NN	_	_	_
18	of	of	IN	_	_	_
19	each	each	DT	_	_	_
20	read	read	NN	_	_	_
21	was	be	VBD	_	_	_
22	taken	take	VBN	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Read	Read	NNP	_	_	_
25	counts	count	VBZ	_	_	_
26	for	for	IN	_	_	_
27	each	each	DT	_	_	_
28	host	host	NN	_	_	_
29	and	and	CC	_	_	_
30	circuit	circuit	NN	_	_	_
31	gene	gene	NN	_	_	_
32	was	be	VBD	_	_	_
33	carried	carry	VBN	_	_	_
34	out	out	RP	_	_	_
35	using	use	VBG	_	_	_
36	the	the	DT	_	_	_
37	htseq-count	htseq-count	JJ	_	_	_
38	command	command	NN	_	_	_
39	of	of	IN	_	_	_
40	the	the	DT	_	_	_
41	HTSeq	htseq	NN	_	_	_
42	toolkit	toolkit	NN	_	_	_
43	with	with	IN	_	_	_
44	user-defined	user-defined	JJ	_	_	_
45	GFF	gff	NN	_	_	_
46	annotations	annotation	NNS	_	_	_
47	of	of	IN	_	_	_
48	the	the	DT	_	_	_
49	reference	reference	NN	_	_	_
50	sequences	sequence	NNS	_	_	_
51	and	and	CC	_	_	_
52	the	the	DT	_	_	_
53	options	option	NNS	_	_	_
54	'	'	POS	_	_	_
55	-	-	:	_	_	_
56	s	s	NNS	_	_	_
57	reverse	reverse	JJ	_	_	_
58	-	-	:	_	_	_
59	a	a	DT	_	_	_
60	10	10	CD	_	_	_
61	-	-	:	_	_	_
62	m	m	NN	_	_	_
63	union	union	NN	_	_	_
64	'	'	''	_	_	_
65	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Read	Read	NNP	_	_	_
3	counts	count	VBZ	_	_	_
4	per	per	IN	_	_	_
5	gene	gene	NN	_	_	_
6	determined	determine	VBN	_	_	_
7	using	use	VBG	_	_	_
8	HTseq	htseq	NN	_	_	_
9	count	count	NN	_	_	_
10	before	before	IN	_	_	_
11	normalized	normalize	VBN	_	_	_
12	using	use	VBG	_	_	_
13	DESeq2	deseq2	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	Read	read	VBP	_	_	_
16	counts	count	NNS	_	_	_
17	were	be	VBD	_	_	_
18	normalized	normalize	VBN	_	_	_
19	by	by	IN	_	_	_
20	million	million	CD	_	_	_
21	mapped	map	VBD	_	_	_
22	reads	read	VBZ	_	_	_
23	for	for	IN	_	_	_
24	each	each	DT	_	_	_
25	nucleotide	nucleotide	NN	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Read	Read	NNP	_	_	_
28	count	count	NN	_	_	_
29	was	be	VBD	_	_	_
30	calculated	calculate	VBN	_	_	_
31	for	for	IN	_	_	_
32	each	each	DT	_	_	_
33	genomic	genomic	JJ	_	_	_
34	position	position	NN	_	_	_
35	from	from	IN	_	_	_
36	sequence	sequence	NN	_	_	_
37	alignment	alignment	NN	_	_	_
38	,	,	,	_	_	_
39	and	and	CC	_	_	_
40	95	95	CD	_	_	_
41	%	%	NN	_	_	_
42	strongest	strongest	JJS	_	_	_
43	intensity	intensity	NN	_	_	_
44	was	be	VBD	_	_	_
45	used	use	VBN	_	_	_
46	as	as	IN	_	_	_
47	background	background	NN	_	_	_
48	intensity	intensity	NN	_	_	_
49	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Read	Read	NNP	_	_	_
3	coverage	coverage	NN	_	_	_
4	maps	map	NNS	_	_	_
5	and	and	CC	_	_	_
6	RPKM	RPKM	NNP	_	_	_
7	data	datum	NNS	_	_	_
8	was	be	VBD	_	_	_
9	subsequently	subsequently	RB	_	_	_
10	generated	generate	VBN	_	_	_
11	by	by	IN	_	_	_
12	Geneious	Geneious	NNP	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Read	Read	NNP	_	_	_
3	mapping	mapping	NN	_	_	_
4	using	use	VBG	_	_	_
5	segemehl	segemehl	NN	_	_	_
6	version	version	NN	_	_	_
7	0.13	0.13	CD	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	TRAPL	trapl	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Read	read	VB	_	_	_
13	mapping	mapping	NN	_	_	_
14	using	use	VBG	_	_	_
15	segemehl	segemehl	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	via	via	IN	_	_	_
18	READemption	reademption	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Read-mapping	read-mapping	NN	_	_	_
22	was	be	VBD	_	_	_
23	done	do	VBN	_	_	_
24	with	with	IN	_	_	_
25	soap2	soap2	NN	_	_	_
26	.21	.21	CD	_	_	_
27	.	.	.	_	_	_

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	reads	read	VBZ	_	_	_
33	aligned	align	VBN	_	_	_
34	to	to	TO	_	_	_
35	the	the	DT	_	_	_
36	reference	reference	NN	_	_	_
37	genome	genome	NN	_	_	_
38	of	of	IN	_	_	_
39	E.	e.	FW	_	_	_
40	coli	coli	FW	_	_	_
41	K-12	k-12	NN	_	_	_
42	Mg1655	mg1655	NN	_	_	_
43	using	use	VBG	_	_	_
44	BWA	BWA	NNP	_	_	_
45	,	,	,	_	_	_
46	with	with	IN	_	_	_
47	quality	quality	NN	_	_	_
48	threshold	threshold	NN	_	_	_
49	of	of	IN	_	_	_
50	20	20	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	Reads	read	VBZ	_	_	_
53	aligning	align	VBG	_	_	_
54	to	to	TO	_	_	_
55	each	each	DT	_	_	_
56	protein-encoding	protein-encoding	JJ	_	_	_
57	gene	gene	NN	_	_	_
58	family	family	NN	_	_	_
59	with	with	IN	_	_	_
60	strand-specific	strand-specific	JJ	_	_	_
61	mapping	mapping	NN	_	_	_
62	quality	quality	NN	_	_	_
63	above	above	IN	_	_	_
64	23	23	CD	_	_	_
65	were	be	VBD	_	_	_
66	counted	count	VBN	_	_	_
67	using	use	VBG	_	_	_
68	HTSeq-count	htseq-count	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	Reads	read	VBZ	_	_	_
71	longer	longer	JJR	_	_	_
72	than	than	IN	_	_	_
73	25	25	CD	_	_	_
74	nt	nt	NNS	_	_	_
75	and	and	CC	_	_	_
76	≤	≤	NN	_	_	_
77	2	2	CD	_	_	_
78	N	n	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	ambiguous	ambiguous	JJ	_	_	_
81	nucleotides	nucleotide	NNS	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	were	be	VBD	_	_	_
84	preserved	preserve	VBN	_	_	_
85	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	read	VBZ	_	_	_
3	mapped	map	VBN	_	_	_
4	to	to	TO	_	_	_
5	more	more	JJR	_	_	_
6	than	than	IN	_	_	_
7	one	one	CD	_	_	_
8	locus	locus	NN	_	_	_
9	were	be	VBD	_	_	_
10	discarded	discard	VBN	_	_	_
11	.	.	.	_	_	_

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	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	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Reads	read	VBZ	_	_	_
15	per	per	IN	_	_	_
16	kilobase	kilobase	NN	_	_	_
17	of	of	IN	_	_	_
18	exon	exon	NN	_	_	_
19	model	model	NN	_	_	_
20	per	per	IN	_	_	_
21	million	million	CD	_	_	_
22	mapped	map	VBD	_	_	_
23	reads	read	VBZ	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	RPKM	rpkm	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	was	be	VBD	_	_	_
28	used	use	VBN	_	_	_
29	as	as	IN	_	_	_
30	a	a	DT	_	_	_
31	normalized	normalize	VBN	_	_	_
32	metric	metric	JJ	_	_	_
33	to	to	TO	_	_	_
34	present	present	VB	_	_	_
35	the	the	DT	_	_	_
36	gene	gene	NN	_	_	_
37	expression	expression	NN	_	_	_
38	levels	level	NNS	_	_	_
39	.	.	.	_	_	_

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	NNP	_	_	_
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	a	a	DT	_	_	_
28	protocol	protocol	NN	_	_	_
29	from	from	IN	_	_	_
30	Chepelev	Chepelev	NNP	_	_	_
31	et	et	FW	_	_	_
32	al.	al.	FW	_	_	_
33	,	,	,	_	_	_
34	Nucleic	Nucleic	NNP	_	_	_
35	Acids	Acids	NNP	_	_	_
36	Research	Research	NNP	_	_	_
37	,	,	,	_	_	_
38	2009	2009	CD	_	_	_
39	.	.	.	_	_	_

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	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	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	cufflinks	cufflink	NNS	_	_	_
19	v.	v.	CC	_	_	_
20	1.3.0	1.3.0	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	Reads	read	VBZ	_	_	_
23	per	per	IN	_	_	_
24	kilobase	kilobase	NN	_	_	_
25	of	of	IN	_	_	_
26	gene	gene	NN	_	_	_
27	per	per	IN	_	_	_
28	million	million	CD	_	_	_
29	mapped	map	VBN	_	_	_
30	sequence	sequence	NN	_	_	_
31	reads	read	VBZ	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	RPKM	rpkm	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	were	be	VBD	_	_	_
36	calculated	calculate	VBN	_	_	_
37	for	for	IN	_	_	_
38	normalization	normalization	NN	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	Reads	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	adapter	adapter	NN	_	_	_
5	removed	remove	VBN	_	_	_
6	and	and	CC	_	_	_
7	trimmed	trim	VBN	_	_	_
8	to	to	TO	_	_	_
9	40Bp	40bp	NN	_	_	_
10	using	use	VBG	_	_	_
11	trimmomatic	trimmomatic	JJ	_	_	_
12	0.32	0.32	CD	_	_	_
13	with	with	IN	_	_	_
14	parameters	parameter	NNS	_	_	_
15	ILLUMINACLIP	ILLUMINACLIP	NNP	_	_	_
16	:	:	:	_	_	_
17	/	/	:	_	_	_
18	Trimmomatic-0.32	trimmomatic-0.32	NN	_	_	_
19	/	/	:	_	_	_
20	adapters/TruSeq3-PE	adapters/truseq3-pe	JJ	_	_	_
21	-2	-2	CD	_	_	_
22	.	.	.	_	_	_

1	fa	fa	NN	_	_	_
2	:	:	:	_	_	_
3	2:30:10	2:30:10	CD	_	_	_
4	HEADCROP	headcrop	NN	_	_	_
5	:	:	:	_	_	_
6	8	8	CD	_	_	_
7	CROP	crop	NN	_	_	_
8	:	:	:	_	_	_
9	40	40	CD	_	_	_
10	SLIDINGWINDOW	SLIDINGWINDOW	NNP	_	_	_
11	:	:	:	_	_	_
12	6:5	6:5	CD	_	_	_
13	MINLEN	MINLEN	NNP	_	_	_
14	:	:	:	_	_	_
15	40	40	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Reads	read	NNS	_	_	_
18	were	be	VBD	_	_	_
19	aligned	align	VBN	_	_	_
20	to	to	TO	_	_	_
21	E.coli	e.coli	VB	_	_	_
22	rRNA	rrna	NN	_	_	_
23	and	and	CC	_	_	_
24	tRNA	trna	NN	_	_	_
25	using	use	VBG	_	_	_
26	Bowtie	Bowtie	NNP	_	_	_
27	v.	v.	CC	_	_	_
28	0.12.0	0.12.0	CD	_	_	_
29	allowing	allow	VBG	_	_	_
30	for	for	IN	_	_	_
31	one	one	CD	_	_	_
32	mismatch	mismatch	NN	_	_	_
33	and	and	CC	_	_	_
34	reads	read	VBZ	_	_	_
35	aligning	align	VBG	_	_	_
36	to	to	TO	_	_	_
37	more	more	JJR	_	_	_
38	than	than	IN	_	_	_
39	one	one	CD	_	_	_
40	position	position	NN	_	_	_
41	in	in	IN	_	_	_
42	the	the	DT	_	_	_
43	genome	genome	NN	_	_	_
44	were	be	VBD	_	_	_
45	randomly	randomly	RB	_	_	_
46	assigned	assign	VBN	_	_	_
47	to	to	TO	_	_	_
48	one	one	CD	_	_	_
49	of	of	IN	_	_	_
50	those	those	DT	_	_	_
51	positions	position	NNS	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	Reads	Reads	NNPS	_	_	_
54	were	be	VBD	_	_	_
55	aligned	align	VBN	_	_	_
56	to	to	TO	_	_	_
57	GenBank	genbank	NN	_	_	_
58	ID	id	NN	_	_	_
59	U00096	u00096	NN	_	_	_
60	.2	.2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Reads	read	NNS	_	_	_
63	were	be	VBD	_	_	_
64	aligned	align	VBN	_	_	_
65	to	to	TO	_	_	_
66	the	the	DT	_	_	_
67	MG1655	mg1655	NN	_	_	_
68	genome	genome	NN	_	_	_
69	with	with	IN	_	_	_
70	Bowtie	Bowtie	NNP	_	_	_
71	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	Reads	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	aligned	align	VBN	_	_	_
5	using	use	VBG	_	_	_
6	MG15655	mg15655	NN	_	_	_
7	as	as	IN	_	_	_
8	reference	reference	NN	_	_	_
9	genome	genome	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	NC000913	nc000913	NN	_	_	_
12	.2	.2	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	using	use	VBG	_	_	_
15	Bowtie2	bowtie2	NN	_	_	_
16	tool	tool	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	Reads	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	end-to-end	end-to-end	JJ	_	_	_
5	aligned	align	VBN	_	_	_
6	,	,	,	_	_	_
7	with	with	IN	_	_	_
8	no	no	DT	_	_	_
9	mismatches	mismatch	NNS	_	_	_
10	allowed	allow	VBN	_	_	_
11	,	,	,	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	respective	respective	JJ	_	_	_
15	draft	draft	NN	_	_	_
16	genomes	genome	NNS	_	_	_
17	using	use	VBG	_	_	_
18	Bowtie2	bowtie2	NN	_	_	_
19	with	with	IN	_	_	_
20	default	default	NN	_	_	_
21	settings	setting	NNS	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	reads	read	VBZ	_	_	_
24	were	be	VBD	_	_	_
25	mapped	map	VBN	_	_	_
26	to	to	TO	_	_	_
27	the	the	DT	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	K12	k12	NN	_	_	_
31	MG1655	mg1655	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	NC000913	nc000913	NN	_	_	_
34	.3	.3	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	genome	genome	NN	_	_	_
37	using	use	VBG	_	_	_
38	Novoalign	novoalign	JJ	_	_	_
39	version	version	NN	_	_	_
40	2.07	2.07	CD	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	www.novocraft.com	www.novocraft.com	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	-	-	:	_	_	_
45	Example	example	NN	_	_	_
46	:	:	:	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	novoalign	novoalign	JJ	_	_	_
49	-	-	:	_	_	_
50	f	f	FW	_	_	_
51	DL4900	dl4900	FW	_	_	_
52	_	_	SYM	_	_	_
53	clip	clip	VB	_	_	_
54	_	_	SYM	_	_	_
55	clp.fasta	clp.fasta	SYM	_	_	_
56	-	-	:	_	_	_
57	d	d	NN	_	_	_
58	NC000913	nc000913	NN	_	_	_
59	.3	.3	NN	_	_	_
60	.	.	.	_	_	_

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	Reads	read	NNS	_	_	_
10	were	be	VBD	_	_	_
11	mapped	map	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	NC	NC	NNP	_	_	_
15	_	_	SYM	_	_	_
16	000913.2	000913.2	CD	_	_	_
17	reference	reference	NN	_	_	_
18	genome	genome	NN	_	_	_
19	using	use	VBG	_	_	_
20	the	the	DT	_	_	_
21	default	default	NN	_	_	_
22	settings	setting	NNS	_	_	_
23	in	in	IN	_	_	_
24	bowtie2	bowtie2	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Langmead	langmead	NN	_	_	_
27	and	and	CC	_	_	_
28	Salzberg	Salzberg	NNP	_	_	_
29	,	,	,	_	_	_
30	2012	2012	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

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	NNP	_	_	_
2	Reads	Reads	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	mapped	map	VBN	_	_	_
5	using	use	VBG	_	_	_
6	BWA	BWA	NNP	_	_	_
7	0.7.5	0.7.5	CD	_	_	_
8	a	a	DT	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Reads	read	NNS	_	_	_
11	were	be	VBD	_	_	_
12	trimmed	trim	VBN	_	_	_
13	and	and	CC	_	_	_
14	adaptors	adaptor	NNS	_	_	_
15	removed	remove	VBN	_	_	_
16	using	use	VBG	_	_	_
17	the	the	DT	_	_	_
18	fastx	fastx	NN	_	_	_
19	_	_	NN	_	_	_
20	toolkit	toolkit	NN	_	_	_
21	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
17	Read	read	VBP	_	_	_
18	using	use	VBG	_	_	_
19	bedtools	bedtool	NNS	_	_	_
20	,	,	,	_	_	_
21	version	version	NN	_	_	_
22	2.17.0	2.17.0	CD	_	_	_
23	,	,	,	_	_	_
24	parameter	parameter	NN	_	_	_
25	:	:	:	_	_	_
26	-	-	:	_	_	_
27	s	s	NNS	_	_	_
28	,	,	,	_	_	_
29	for	for	IN	_	_	_
30	samples	sample	NNS	_	_	_
31	1-5	1-5	CD	_	_	_
32	the	the	DT	_	_	_
33	middle	middle	NN	_	_	_
34	nucleotide	nucleotide	NN	_	_	_
35	of	of	IN	_	_	_
36	each	each	DT	_	_	_
37	read	read	NN	_	_	_
38	was	be	VBD	_	_	_
39	taken	take	VBN	_	_	_
40	,	,	,	_	_	_
41	for	for	IN	_	_	_
42	samples	sample	NNS	_	_	_
43	6-9	6-9	CD	_	_	_
44	the	the	DT	_	_	_
45	first	first	JJ	_	_	_
46	nucleotide	nucleotide	NN	_	_	_
47	was	be	VBD	_	_	_
48	taken	take	VBN	_	_	_
49	and	and	CC	_	_	_
50	the	the	DT	_	_	_
51	read	read	NN	_	_	_
52	count	count	NN	_	_	_
53	was	be	VBD	_	_	_
54	assigned	assign	VBN	_	_	_
55	to	to	TO	_	_	_
56	the	the	DT	_	_	_
57	nucleotide	nucleotide	NN	_	_	_
58	5	5	CD	_	_	_
59	'	'	''	_	_	_
60	of	of	IN	_	_	_
61	the	the	DT	_	_	_
62	first	first	JJ	_	_	_
63	nucleotide	nucleotide	NN	_	_	_
64	see	see	VB	_	_	_
65	-LCB-	-lcb-	-LRB-	_	_	_
66	Kertesz	Kertesz	NNP	_	_	_
67	,	,	,	_	_	_
68	2010	2010	CD	_	_	_
69	-RCB-	-rcb-	-RRB-	_	_	_
70	for	for	IN	_	_	_
71	details	detail	NNS	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	recA730	reca730	NN	_	_	_
74	_	_	CD	_	_	_
75	vs	vs	CC	_	_	_
76	_	_	CD	_	_	_
77	recA730	reca730	NN	_	_	_
78	,	,	,	_	_	_
79	dcd	dcd	NN	GEN	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	recA730	reca730	NN	_	_	_
82	_	_	CD	_	_	_
83	vs	vs	CC	_	_	_
84	_	_	CD	_	_	_
85	recA730	reca730	NN	_	_	_
86	,	,	,	_	_	_
87	ndk	ndk	NN	GEN	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	recA	reca	NN	GEN	_	_
90	deletion	deletion	NN	_	_	_
91	0.05	0.05	CD	_	_	_
92	ug/ml	ug/ml	NN	_	_	_
93	norfloxacin	norfloxacin	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	recA	reca	NN	GEN	_	_
96	deletion	deletion	NN	_	_	_
97	0	0	CD	_	_	_
98	ug/ml	ug/ml	NN	_	_	_
99	norfloxacin	norfloxacin	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	recA	reca	NN	GEN	_	_
102	deletion	deletion	NN	_	_	_
103	1.0	1.0	CD	_	_	_
104	ug/ml	ug/ml	NN	_	_	_
105	norfloxacin	norfloxacin	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	recA	reca	NN	GEN	_	_
108	_	_	NN	_	_	_
109	D	d	NN	_	_	_
110	_	_	CD	_	_	_
111	N0000	n0000	NN	_	_	_
112	_	_	CD	_	_	_
113	r1	r1	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	recA	reca	NN	GEN	_	_
116	_	_	NN	_	_	_
117	D	d	NN	_	_	_
118	_	_	CD	_	_	_
119	N0000	n0000	NN	_	_	_
120	_	_	CD	_	_	_
121	r2	r2	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	recA	reca	NN	GEN	_	_
124	_	_	NN	_	_	_
125	D	d	NN	_	_	_
126	_	_	CD	_	_	_
127	N0050	n0050	NN	_	_	_
128	_	_	CD	_	_	_
129	r1	r1	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	recA	reca	NN	GEN	_	_
132	_	_	NN	_	_	_
133	D	d	NN	_	_	_
134	_	_	CD	_	_	_
135	N0050	n0050	NN	_	_	_
136	_	_	CD	_	_	_
137	r2	r2	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	recA	reca	NN	GEN	_	_
140	_	_	NN	_	_	_
141	D	d	NN	_	_	_
142	_	_	CD	_	_	_
143	N1000	n1000	NN	_	_	_
144	_	_	CD	_	_	_
145	r1	r1	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	recA	reca	NN	GEN	_	_
148	_	_	NN	_	_	_
149	D	d	NN	_	_	_
150	_	_	CD	_	_	_
151	N1000	n1000	NN	_	_	_
152	_	_	CD	_	_	_
153	r2	r2	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	recA	reca	NN	GEN	_	_
156	___	___	CD	_	_	_
157	U	U	NNP	_	_	_
158	_	_	NNP	_	_	_
159	N0025	N0025	NNP	_	_	_
160	_	_	NNP	_	_	_
161	r1	r1	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	recA	reca	NN	GEN	_	_
164	___	___	CD	_	_	_
165	U	U	NNP	_	_	_
166	_	_	NNP	_	_	_
167	N0025	N0025	NNP	_	_	_
168	_	_	SYM	_	_	_
169	r2	r2	FW	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
171	recA	reca	NN	GEN	_	_
172	___	___	CD	_	_	_
173	U	U	NNP	_	_	_
174	_	_	NNP	_	_	_
175	N0025	N0025	NNP	_	_	_
176	_	_	SYM	_	_	_
177	r3	r3	FW	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
179	recA	reca	NN	GEN	_	_
180	upregulation	upregulation	NN	_	_	_
181	,	,	,	_	_	_
182	amp	amp	NN	_	_	_
183	50ug/ml	50ug/ml	NN	_	_	_
184	,	,	,	_	_	_
185	0.0125	0.0125	CD	_	_	_
186	%	%	NN	_	_	_
187	arabinose	arabinose	NN	_	_	_
188	,	,	,	_	_	_
189	0.025	0.025	CD	_	_	_
190	ug/ml	ug/ml	NN	_	_	_
191	norfloxacin	norfloxacin	NN	_	_	_
192	OD	od	NN	_	_	_
193	~	~	NN	_	_	_
194	0.3	0.3	CD	_	_	_
195	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
196	Recombinant	recombinant	JJ	_	_	_
197	,	,	,	_	_	_
198	high	high	JJ	_	_	_
199	cell	cell	NN	_	_	_
200	density	density	NN	_	_	_
201	,	,	,	_	_	_
202	Time	Time	NNP	_	_	_
203	0	0	CD	_	_	_
204	,	,	,	_	_	_
205	no	no	DT	_	_	_
206	IPTG	iptg	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	Recombinant	recombinant	JJ	_	_	_
209	,	,	,	_	_	_
210	high	high	JJ	_	_	_
211	cell	cell	NN	_	_	_
212	density	density	NN	_	_	_
213	,	,	,	_	_	_
214	Time	Time	NNP	_	_	_
215	1	1	CD	_	_	_
216	h	h	NN	_	_	_
217	,	,	,	_	_	_
218	5	5	CD	_	_	_
219	mM	mm	NN	KWSUPP	_	_
220	IPTG	iptg	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	Recombinant	recombinant	JJ	_	_	_
223	,	,	,	_	_	_
224	high	high	JJ	_	_	_
225	cell	cell	NN	_	_	_
226	density	density	NN	_	_	_
227	,	,	,	_	_	_
228	Time	Time	NNP	_	_	_
229	1	1	CD	_	_	_
230	h	h	NN	_	_	_
231	,	,	,	_	_	_
232	no	no	DT	_	_	_
233	IPTG	iptg	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	Recombinant	recombinant	JJ	_	_	_
236	,	,	,	_	_	_
237	high	high	JJ	_	_	_
238	cell	cell	NN	_	_	_
239	density	density	NN	_	_	_
240	,	,	,	_	_	_
241	Time	Time	NNP	_	_	_
242	4	4	CD	_	_	_
243	h	h	NN	_	_	_
244	,	,	,	_	_	_
245	no	no	DT	_	_	_
246	IPTG	iptg	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	Recombinant	recombinant	JJ	_	_	_
249	,	,	,	_	_	_
250	high	high	JJ	_	_	_
251	cell	cell	NN	_	_	_
252	density	density	NN	_	_	_
253	,	,	,	_	_	_
254	Time	Time	NNP	_	_	_
255	S0	S0	NNP	_	_	_
256	,	,	,	_	_	_
257	no	no	DT	_	_	_
258	IPTG	iptg	NN	_	_	_
259	,	,	,	_	_	_
260	1	1	CD	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	Recombinant	recombinant	JJ	_	_	_
263	,	,	,	_	_	_
264	high	high	JJ	_	_	_
265	cell	cell	NN	_	_	_
266	density	density	NN	_	_	_
267	,	,	,	_	_	_
268	Time	Time	NNP	_	_	_
269	S0	S0	NNP	_	_	_
270	,	,	,	_	_	_
271	no	no	DT	_	_	_
272	IPTG	iptg	NN	_	_	_
273	,	,	,	_	_	_
274	2	2	CD	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
276	Recombinant	recombinant	JJ	_	_	_
277	,	,	,	_	_	_
278	high	high	JJ	_	_	_
279	cell	cell	NN	_	_	_
280	density	density	NN	_	_	_
281	,	,	,	_	_	_
282	Time	Time	NNP	_	_	_
283	S0	S0	NNP	_	_	_
284	,	,	,	_	_	_
285	no	no	DT	_	_	_
286	IPTG	iptg	NN	_	_	_
287	,	,	,	_	_	_
288	3	3	CD	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	Recombinant	recombinant	JJ	_	_	_
291	,	,	,	_	_	_
292	high	high	JJ	_	_	_
293	cell	cell	NN	_	_	_
294	density	density	NN	_	_	_
295	,	,	,	_	_	_
296	Time	Time	NNP	_	_	_
297	S1	s1	NN	_	_	_
298	,	,	,	_	_	_
299	IPTG	iptg	NN	_	_	_
300	,	,	,	_	_	_
301	1	1	CD	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	Recombinant	recombinant	JJ	_	_	_
304	,	,	,	_	_	_
305	high	high	JJ	_	_	_
306	cell	cell	NN	_	_	_
307	density	density	NN	_	_	_
308	,	,	,	_	_	_
309	Time	Time	NNP	_	_	_
310	S1	s1	NN	_	_	_
311	,	,	,	_	_	_
312	IPTG	iptg	NN	_	_	_
313	,	,	,	_	_	_
314	2	2	CD	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
316	Recombinant	recombinant	JJ	_	_	_
317	,	,	,	_	_	_
318	high	high	JJ	_	_	_
319	cell	cell	NN	_	_	_
320	density	density	NN	_	_	_
321	,	,	,	_	_	_
322	Time	Time	NNP	_	_	_
323	S1	s1	NN	_	_	_
324	,	,	,	_	_	_
325	IPTG	iptg	NN	_	_	_
326	,	,	,	_	_	_
327	3	3	CD	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	Recombinant	recombinant	JJ	_	_	_
330	,	,	,	_	_	_
331	high	high	JJ	_	_	_
332	cell	cell	NN	_	_	_
333	density	density	NN	_	_	_
334	,	,	,	_	_	_
335	Time	Time	NNP	_	_	_
336	S1	s1	NN	_	_	_
337	,	,	,	_	_	_
338	no	no	DT	_	_	_
339	IPTG	iptg	NN	_	_	_
340	,	,	,	_	_	_
341	1	1	CD	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	Recombinant	recombinant	JJ	_	_	_
344	,	,	,	_	_	_
345	high	high	JJ	_	_	_
346	cell	cell	NN	_	_	_
347	density	density	NN	_	_	_
348	,	,	,	_	_	_
349	Time	Time	NNP	_	_	_
350	S1	s1	NN	_	_	_
351	,	,	,	_	_	_
352	no	no	DT	_	_	_
353	IPTG	iptg	NN	_	_	_
354	,	,	,	_	_	_
355	2	2	CD	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
357	Recombinant	recombinant	JJ	_	_	_
358	,	,	,	_	_	_
359	high	high	JJ	_	_	_
360	cell	cell	NN	_	_	_
361	density	density	NN	_	_	_
362	,	,	,	_	_	_
363	Time	Time	NNP	_	_	_
364	S1	s1	NN	_	_	_
365	,	,	,	_	_	_
366	no	no	DT	_	_	_
367	IPTG	iptg	NN	_	_	_
368	,	,	,	_	_	_
369	3	3	CD	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	Recombinant	recombinant	JJ	_	_	_
372	,	,	,	_	_	_
373	high	high	JJ	_	_	_
374	cell	cell	NN	_	_	_
375	density	density	NN	_	_	_
376	,	,	,	_	_	_
377	Time	Time	NNP	_	_	_
378	S4	S4	NNP	_	_	_
379	,	,	,	_	_	_
380	no	no	DT	_	_	_
381	IPTG	iptg	NN	_	_	_
382	,	,	,	_	_	_
383	1	1	CD	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	Recombinant	recombinant	JJ	_	_	_
386	,	,	,	_	_	_
387	high	high	JJ	_	_	_
388	cell	cell	NN	_	_	_
389	density	density	NN	_	_	_
390	,	,	,	_	_	_
391	Time	Time	NNP	_	_	_
392	S4	S4	NNP	_	_	_
393	,	,	,	_	_	_
394	no	no	DT	_	_	_
395	IPTG	iptg	NN	_	_	_
396	,	,	,	_	_	_
397	2	2	CD	_	_	_
398	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
399	Recombinant	recombinant	JJ	_	_	_
400	,	,	,	_	_	_
401	high	high	JJ	_	_	_
402	cell	cell	NN	_	_	_
403	density	density	NN	_	_	_
404	,	,	,	_	_	_
405	Time	Time	NNP	_	_	_
406	S4	S4	NNP	_	_	_
407	,	,	,	_	_	_
408	no	no	DT	_	_	_
409	IPTG	iptg	NN	_	_	_
410	,	,	,	_	_	_
411	3	3	CD	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	Reduced	reduce	VBN	_	_	_
414	genome	genome	NN	_	_	_
415	strain	strain	NN	_	_	_
416	MDS42	mds42	NN	_	_	_
417	,	,	,	_	_	_
418	100	100	CD	_	_	_
419	mcg/ml	mcg/ml	NN	_	_	_
420	bicyclomycin	bicyclomycin	NN	_	_	_
421	20	20	CD	_	_	_
422	min	min	NN	_	_	_
423	,	,	,	_	_	_
424	exponential	exponential	JJ	GrowthPhase	_	_
425	phase	phase	NN	GrowthPhase	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	Reduced	reduce	VBN	_	_	_
428	genome	genome	NN	_	_	_
429	strain	strain	NN	_	_	_
430	MDS42	mds42	NN	_	_	_
431	,	,	,	_	_	_
432	control	control	NN	_	_	_
433	sample	sample	NN	_	_	_
434	,	,	,	_	_	_
435	exponential	exponential	JJ	GrowthPhase	_	_
436	phase	phase	NN	GrowthPhase	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	Reduced	reduce	VBN	_	_	_
439	genome	genome	NN	_	_	_
440	strain	strain	NN	_	_	_
441	MDS42	mds42	NN	_	_	_
442	,	,	,	_	_	_
443	deletion	deletion	NN	_	_	_
444	of	of	IN	_	_	_
445	nusA	nusa	NN	GEN	_	_
446	gene	gene	NN	_	_	_
447	,	,	,	_	_	_
448	OD600	od600	NN	_	_	_
449	=	=	JJ	_	_	_
450	0.3	0.3	CD	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	Reduced	reduce	VBN	_	_	_
453	genome	genome	NN	_	_	_
454	strain	strain	NN	_	_	_
455	MDS42	mds42	NN	_	_	_
456	,	,	,	_	_	_
457	deletion	deletion	NN	_	_	_
458	of	of	IN	_	_	_
459	nusG	nusg	NN	GEN	_	_
460	gene	gene	NN	_	_	_
461	,	,	,	_	_	_
462	OD600	od600	NN	_	_	_
463	=	=	JJ	_	_	_
464	0.3	0.3	CD	_	_	_
465	,	,	,	_	_	_
466	overnight	overnight	JJ	_	_	_
467	culture	culture	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	referece	referece	NN	_	_	_
470	:	:	:	_	_	_
471	The	the	DT	_	_	_
472	three	three	CD	_	_	_
473	genomes	genome	NNS	_	_	_
474	contributing	contribute	VBG	_	_	_
475	to	to	TO	_	_	_
476	the	the	DT	_	_	_
477	ORFs	orf	NNS	_	_	_
478	on	on	IN	_	_	_
479	the	the	DT	_	_	_
480	microarray	microarray	NN	_	_	_
481	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	reference	reference	NN	_	_	_
3	0	0	CD	_	_	_
4	'	'	''	_	_	_
5	,	,	,	_	_	_
6	min	min	NN	_	_	_
7	+.2	+.2	CD	_	_	_
8	%	%	NN	_	_	_
9	glu	glu	NN	_	_	_
10	,	,	,	_	_	_
11	25	25	CD	_	_	_
12	ug	ug	NN	_	_	_
13	RNA	rna	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Reference	Reference	NNP	_	_	_
16	Design	Design	NNP	_	_	_
17	timecourse	timecourse	NN	_	_	_
18	c	c	NN	_	_	_
19	_	_	CD	_	_	_
20	t10	t10	NN	_	_	_
21	.1	.1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Reference	Reference	NNP	_	_	_
24	Design	design	NN	_	_	_
25	timecourse	timecourse	NN	_	_	_
26	c	c	NN	_	_	_
27	_	_	CD	_	_	_
28	t10	t10	NN	_	_	_
29	.2	.2	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	Reference	Reference	NNP	_	_	_
32	Design	design	NN	_	_	_
33	timecourse	timecourse	NN	_	_	_
34	c	c	NN	_	_	_
35	_	_	CD	_	_	_
36	t1	t1	NN	_	_	_
37	.1	.1	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
39	Reference	Reference	NNP	_	_	_
40	Design	design	NN	_	_	_
41	timecourse	timecourse	NN	_	_	_
42	c	c	NN	_	_	_
43	_	_	CD	_	_	_
44	t11	t11	NN	_	_	_
45	.1	.1	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	Reference	Reference	NNP	_	_	_
48	Design	design	NN	_	_	_
49	timecourse	timecourse	NN	_	_	_
50	c	c	NN	_	_	_
51	_	_	CD	_	_	_
52	t11	t11	NN	_	_	_
53	.2	.2	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	Reference	Reference	NNP	_	_	_
56	Design	design	NN	_	_	_
57	timecourse	timecourse	NN	_	_	_
58	c	c	NN	_	_	_
59	_	_	CD	_	_	_
60	t1	t1	NN	_	_	_
61	.2	.2	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
63	Reference	Reference	NNP	_	_	_
64	Design	design	NN	_	_	_
65	timecourse	timecourse	NN	_	_	_
66	c	c	NN	_	_	_
67	_	_	CD	_	_	_
68	t2	t2	NN	_	_	_
69	.1	.1	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
71	Reference	Reference	NNP	_	_	_
72	Design	design	NN	_	_	_
73	timecourse	timecourse	NN	_	_	_
74	c	c	NN	_	_	_
75	_	_	CD	_	_	_
76	t2	t2	NN	_	_	_
77	.2	.2	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
79	Reference	Reference	NNP	_	_	_
80	Design	design	NN	_	_	_
81	timecourse	timecourse	NN	_	_	_
82	c	c	NN	_	_	_
83	_	_	CD	_	_	_
84	t3	t3	NN	_	_	_
85	.1	.1	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
87	Reference	Reference	NNP	_	_	_
88	Design	design	NN	_	_	_
89	timecourse	timecourse	NN	_	_	_
90	c	c	NN	_	_	_
91	_	_	CD	_	_	_
92	t3	t3	NN	_	_	_
93	.2	.2	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
95	Reference	Reference	NNP	_	_	_
96	Design	design	NN	_	_	_
97	timecourse	timecourse	NN	_	_	_
98	c	c	NN	_	_	_
99	_	_	CD	_	_	_
100	t4	t4	NN	_	_	_
101	.1	.1	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
103	Reference	Reference	NNP	_	_	_
104	Design	design	NN	_	_	_
105	timecourse	timecourse	NN	_	_	_
106	c	c	NN	_	_	_
107	_	_	CD	_	_	_
108	t4	t4	NN	_	_	_
109	.2	.2	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
111	Reference	Reference	NNP	_	_	_
112	Design	design	NN	_	_	_
113	timecourse	timecourse	NN	_	_	_
114	c	c	NN	_	_	_
115	_	_	CD	_	_	_
116	t5	t5	NN	_	_	_
117	.1	.1	CD	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
119	Reference	Reference	NNP	_	_	_
120	Design	design	NN	_	_	_
121	timecourse	timecourse	NN	_	_	_
122	c	c	NN	_	_	_
123	_	_	CD	_	_	_
124	t5	t5	NN	_	_	_
125	.2	.2	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
127	Reference	Reference	NNP	_	_	_
128	Design	design	NN	_	_	_
129	timecourse	timecourse	NN	_	_	_
130	c	c	NN	_	_	_
131	_	_	CD	_	_	_
132	t6	t6	NN	_	_	_
133	.1	.1	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
135	Reference	Reference	NNP	_	_	_
136	Design	design	NN	_	_	_
137	timecourse	timecourse	NN	_	_	_
138	c	c	NN	_	_	_
139	_	_	CD	_	_	_
140	t6	t6	NN	_	_	_
141	.2	.2	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
143	Reference	Reference	NNP	_	_	_
144	Design	design	NN	_	_	_
145	timecourse	timecourse	NN	_	_	_
146	c	c	NN	_	_	_
147	_	_	CD	_	_	_
148	t7	t7	NN	_	_	_
149	.1	.1	CD	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
151	Reference	Reference	NNP	_	_	_
152	Design	design	NN	_	_	_
153	timecourse	timecourse	NN	_	_	_
154	c	c	NN	_	_	_
155	_	_	CD	_	_	_
156	t7	t7	NN	_	_	_
157	.2	.2	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
159	Reference	Reference	NNP	_	_	_
160	Design	design	NN	_	_	_
161	timecourse	timecourse	NN	_	_	_
162	c	c	NN	_	_	_
163	_	_	CD	_	_	_
164	t8	t8	NN	_	_	_
165	.1	.1	CD	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
167	Reference	Reference	NNP	_	_	_
168	Design	design	NN	_	_	_
169	timecourse	timecourse	NN	_	_	_
170	c	c	NN	_	_	_
171	_	_	CD	_	_	_
172	t8	t8	NN	_	_	_
173	.2	.2	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
175	Reference	Reference	NNP	_	_	_
176	Design	design	NN	_	_	_
177	timecourse	timecourse	NN	_	_	_
178	c	c	NN	_	_	_
179	_	_	CD	_	_	_
180	t9	t9	NN	_	_	_
181	.1	.1	CD	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
183	Reference	Reference	NNP	_	_	_
184	Design	design	NN	_	_	_
185	timecourse	timecourse	NN	_	_	_
186	c	c	NN	_	_	_
187	_	_	CD	_	_	_
188	t9	t9	NN	_	_	_
189	.2	.2	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	reference	reference	NN	_	_	_
192	DNA	dna	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	Reference	Reference	NNP	_	_	_
195	DNA	DNA	NNP	_	_	_
196	genomic	genomic	JJ	_	_	_
197	DNA	dna	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	reference	reference	NN	_	_	_
200	:	:	:	_	_	_
201	E.	e.	FW	_	_	_
202	coli	coli	FW	_	_	_
203	TOP10	top10	NN	_	_	_
204	containing	contain	VBG	_	_	_
205	pBAD18	pbad18	NN	_	_	_
206	vector	vector	NN	_	_	_
207	with	with	IN	_	_	_
208	no	no	DT	_	_	_
209	arabinose	arabinose	NN	_	_	_
210	added	add	VBD	_	_	_
211	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
212	Reference	Reference	NNP	_	_	_
213	files	file	VBZ	_	_	_
214	for	for	IN	_	_	_
215	the	the	DT	_	_	_
216	genome	genome	NN	_	_	_
217	sequence	sequence	NN	_	_	_
218	being	be	VBG	_	_	_
219	queried	query	VBN	_	_	_
220	,	,	,	_	_	_
221	Escherichia	escherichia	FW	Organism	_	_
222	coli	coli	FW	Organism	_	_
223	BL21	bl21	NN	_	_	_
224	-LRB-	-lrb-	-LRB-	_	_	_
225	DE3	de3	NN	_	_	_
226	-RRB-	-rrb-	-RRB-	_	_	_
227	genome	genome	NN	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	NC	nc	NN	_	_	_
230	_	_	CD	_	_	_
231	012971	012971	CD	_	_	_
232	-RRB-	-rrb-	-RRB-	_	_	_
233	were	be	VBD	_	_	_
234	uploaded	upload	VBN	_	_	_
235	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	reference	reference	NN	_	_	_
3	genome	genome	NN	_	_	_
4	:	:	:	_	_	_
5	U00096	u00096	NN	_	_	_
6	.2	.2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Reference	Reference	NNP	_	_	_
9	genome	genome	NN	_	_	_
10	used	use	VBN	_	_	_
11	:	:	:	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	K12	k12	NN	_	_	_
15	MG1655	mg1655	NN	_	_	_
16	,	,	,	_	_	_
17	version	version	NN	_	_	_
18	:	:	:	_	_	_
19	iGenome	iGenome	NNP	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Reference	Reference	NNP	_	_	_
22	genomic	genomic	JJ	_	_	_
23	DNA	dna	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Reference	Reference	NNP	_	_	_
26	Genomic	genomic	JJ	_	_	_
27	DNA	dna	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	REference	reference	NN	_	_	_
30	genomic	genomic	JJ	_	_	_
31	DNA	dna	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	reference	reference	NN	_	_	_
34	:	:	:	_	_	_
35	Input	input	NN	_	_	_
36	DNA	dna	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	reference	reference	NN	_	_	_
39	:	:	:	_	_	_
40	input	input	NN	_	_	_
41	Genomic	genomic	JJ	_	_	_
42	DNA	dna	NN	_	_	_
43	control	control	NN	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	Reference	Reference	NNP	_	_	_
46	Pool	Pool	NNP	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	References	References	NNPS	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	References	References	NNPS	_	_	_
51	:	:	:	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	reference	reference	NN	_	_	_
54	sample	sample	NN	_	_	_
55	harvested	harvest	VBN	_	_	_
56	immediately	immediately	RB	_	_	_
57	prior	prior	RB	_	_	_
58	to	to	TO	_	_	_
59	glucose	glucose	NN	SUPP	_	_
60	to	to	TO	_	_	_
61	acetate	acetate	NN	SUPP	_	_
62	shift	shift	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
64	Reformat	reformat	VB	_	_	_
65	Illumina	Illumina	NNP	_	_	_
66	files	file	NNS	_	_	_
67	to	to	TO	_	_	_
68	Sanger	Sanger	NNP	_	_	_
69	format	format	NN	_	_	_
70	,	,	,	_	_	_
71	FASTQ	FASTQ	NNP	_	_	_
72	Groomer	Groomer	NNP	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	REL606	REL606	NNP	_	_	_
75	,	,	,	_	_	_
76	exponential	exponential	JJ	GrowthPhase	_	_
77	phase	phase	NN	GrowthPhase	_	_
78	,	,	,	_	_	_
79	LB	lb	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	REL606	rel606	NN	_	_	_
82	_	_	CD	_	_	_
83	glucose-limited	glucose-limited	JJ	_	_	_
84	minimal	minimal	JJ	_	_	_
85	medium	medium	NN	_	_	_
86	_	_	NN	_	_	_
87	168	168	CD	_	_	_
88	hr	hr	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	REL606	rel606	NN	_	_	_
91	_	_	CD	_	_	_
92	glucose-limited	glucose-limited	JJ	_	_	_
93	minimal	minimal	JJ	_	_	_
94	medium	medium	NN	_	_	_
95	_	_	NN	_	_	_
96	168	168	CD	_	_	_
97	hr	hr	NN	_	_	_
98	_	_	NN	_	_	_
99	rRNA	rrna	NN	_	_	_
100	not	not	RB	_	_	_
101	depleted	deplete	VBN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	REL606	rel606	NN	_	_	_
104	_	_	CD	_	_	_
105	glucose-limited	glucose-limited	JJ	_	_	_
106	minimal	minimal	JJ	_	_	_
107	medium	medium	NN	_	_	_
108	_	_	NN	_	_	_
109	24	24	CD	_	_	_
110	hr	hr	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	REL606	rel606	NN	_	_	_
113	_	_	CD	_	_	_
114	glucose-limited	glucose-limited	JJ	_	_	_
115	minimal	minimal	JJ	_	_	_
116	medium	medium	NN	_	_	_
117	_	_	NN	_	_	_
118	24	24	CD	_	_	_
119	hr	hr	NN	_	_	_
120	_	_	NN	_	_	_
121	rRNA	rrna	NN	_	_	_
122	not	not	RB	_	_	_
123	depleted	deplete	VBN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	REL606	rel606	NN	_	_	_
126	_	_	CD	_	_	_
127	glucose-limited	glucose-limited	JJ	_	_	_
128	minimal	minimal	JJ	_	_	_
129	medium	medium	NN	_	_	_
130	_	_	NN	_	_	_
131	336	336	CD	_	_	_
132	hr	hr	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	REL606	rel606	NN	_	_	_
135	_	_	CD	_	_	_
136	glucose-limited	glucose-limited	JJ	_	_	_
137	minimal	minimal	JJ	_	_	_
138	medium	medium	NN	_	_	_
139	_	_	NN	_	_	_
140	336	336	CD	_	_	_
141	hr	hr	NN	_	_	_
142	_	_	NN	_	_	_
143	rRNA	rrna	NN	_	_	_
144	not	not	RB	_	_	_
145	depleted	deplete	VBN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	REL606	rel606	NN	_	_	_
148	_	_	CD	_	_	_
149	glucose-limited	glucose-limited	JJ	_	_	_
150	minimal	minimal	JJ	_	_	_
151	medium	medium	NN	_	_	_
152	_	_	NN	_	_	_
153	3	3	CD	_	_	_
154	hr	hr	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	REL606	rel606	NN	_	_	_
157	_	_	CD	_	_	_
158	glucose-limited	glucose-limited	JJ	_	_	_
159	minimal	minimal	JJ	_	_	_
160	medium	medium	NN	_	_	_
161	_	_	NN	_	_	_
162	3	3	CD	_	_	_
163	hr	hr	NN	_	_	_
164	_	_	NN	_	_	_
165	rRNA	rrna	NN	_	_	_
166	not	not	RB	_	_	_
167	depleted	deplete	VBN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	REL606	rel606	NN	_	_	_
170	_	_	CD	_	_	_
171	glucose-limited	glucose-limited	JJ	_	_	_
172	minimal	minimal	JJ	_	_	_
173	medium	medium	NN	_	_	_
174	_	_	NN	_	_	_
175	48	48	CD	_	_	_
176	hr	hr	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	REL606	rel606	NN	_	_	_
179	_	_	CD	_	_	_
180	glucose-limited	glucose-limited	JJ	_	_	_
181	minimal	minimal	JJ	_	_	_
182	medium	medium	NN	_	_	_
183	_	_	NN	_	_	_
184	48	48	CD	_	_	_
185	hr	hr	NN	_	_	_
186	_	_	NN	_	_	_
187	rRNA	rrna	NN	_	_	_
188	not	not	RB	_	_	_
189	depleted	deplete	VBN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	REL606	rel606	NN	_	_	_
192	_	_	CD	_	_	_
193	glucose-limited	glucose-limited	JJ	_	_	_
194	minimal	minimal	JJ	_	_	_
195	medium	medium	NN	_	_	_
196	_	_	NN	_	_	_
197	4	4	CD	_	_	_
198	hr	hr	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	REL606	rel606	NN	_	_	_
201	_	_	CD	_	_	_
202	glucose-limited	glucose-limited	JJ	_	_	_
203	minimal	minimal	JJ	_	_	_
204	medium	medium	NN	_	_	_
205	_	_	NN	_	_	_
206	4	4	CD	_	_	_
207	hr	hr	NN	_	_	_
208	_	_	NN	_	_	_
209	rRNA	rrna	NN	_	_	_
210	not	not	RB	_	_	_
211	depleted	deplete	VBN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	REL606	rel606	NN	_	_	_
214	_	_	CD	_	_	_
215	glucose-limited	glucose-limited	JJ	_	_	_
216	minimal	minimal	JJ	_	_	_
217	medium	medium	NN	_	_	_
218	_	_	SYM	_	_	_
219	5	5	CD	_	_	_
220	hr	hr	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	REL606	rel606	NN	_	_	_
223	_	_	CD	_	_	_
224	glucose-limited	glucose-limited	JJ	_	_	_
225	minimal	minimal	JJ	_	_	_
226	medium	medium	NN	_	_	_
227	_	_	SYM	_	_	_
228	5	5	CD	_	_	_
229	hr	hr	NN	_	_	_
230	_	_	NN	_	_	_
231	rRNA	rrna	NN	_	_	_
232	not	not	RB	_	_	_
233	depleted	deplete	VBN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	REL606	rel606	NN	_	_	_
236	_	_	CD	_	_	_
237	glucose-limited	glucose-limited	JJ	_	_	_
238	minimal	minimal	JJ	_	_	_
239	medium	medium	NN	_	_	_
240	_	_	NN	_	_	_
241	6	6	CD	_	_	_
242	hr	hr	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	REL606	rel606	NN	_	_	_
245	_	_	CD	_	_	_
246	glucose-limited	glucose-limited	JJ	_	_	_
247	minimal	minimal	JJ	_	_	_
248	medium	medium	NN	_	_	_
249	_	_	NN	_	_	_
250	6	6	CD	_	_	_
251	hr	hr	NN	_	_	_
252	_	_	NN	_	_	_
253	rRNA	rrna	NN	_	_	_
254	not	not	RB	_	_	_
255	depleted	deplete	VBN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	REL606	rel606	NN	_	_	_
258	_	_	CD	_	_	_
259	glucose-limited	glucose-limited	JJ	_	_	_
260	minimal	minimal	JJ	_	_	_
261	medium	medium	NN	_	_	_
262	_	_	NN	_	_	_
263	8	8	CD	_	_	_
264	hr	hr	NN	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	REL606	rel606	NN	_	_	_
267	_	_	CD	_	_	_
268	glucose-limited	glucose-limited	JJ	_	_	_
269	minimal	minimal	JJ	_	_	_
270	medium	medium	NN	_	_	_
271	_	_	NN	_	_	_
272	8	8	CD	_	_	_
273	hr	hr	NN	_	_	_
274	_	_	NN	_	_	_
275	rRNA	rrna	NN	_	_	_
276	not	not	RB	_	_	_
277	depleted	deplete	VBN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	REL606	rel606	NN	_	_	_
280	,	,	,	_	_	_
281	stationary	stationary	JJ	GrowthPhase	_	_
282	phase	phase	NN	GrowthPhase	_	_
283	,	,	,	_	_	_
284	LB	lb	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	relE	rele	NN	GEN	_	_
287	___	___	CD	_	_	_
288	U	U	NNP	_	_	_
289	_	_	NNP	_	_	_
290	N0025	N0025	NNP	_	_	_
291	_	_	VBD	_	_	_
292	r1	r1	NN	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	relE	rele	NN	GEN	_	_
295	___	___	CD	_	_	_
296	U	U	NNP	_	_	_
297	_	_	NNP	_	_	_
298	N0025	N0025	NNP	_	_	_
299	_	_	VBD	_	_	_
300	r2	r2	NN	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	relE	rele	NN	GEN	_	_
303	___	___	CD	_	_	_
304	U	U	NNP	_	_	_
305	_	_	NNP	_	_	_
306	N0025	N0025	NNP	_	_	_
307	_	_	VBD	_	_	_
308	r3	r3	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	relE	rele	NN	GEN	_	_
311	upregulation	upregulation	NN	_	_	_
312	,	,	,	_	_	_
313	amp	amp	NN	_	_	_
314	50ug/ml	50ug/ml	NN	_	_	_
315	,	,	,	_	_	_
316	0.0125	0.0125	CD	_	_	_
317	%	%	NN	_	_	_
318	arabinose	arabinose	NN	_	_	_
319	,	,	,	_	_	_
320	0.025	0.025	CD	_	_	_
321	ug/ml	ug/ml	NN	_	_	_
322	norfloxacin	norfloxacin	NN	_	_	_
323	OD	od	NN	_	_	_
324	~	~	NN	_	_	_
325	0.3	0.3	CD	_	_	_
326	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
327	Remaining	remain	VBG	_	_	_
328	linker-1	linker-1	NN	_	_	_
329	reads	read	VBZ	_	_	_
330	-LRB-	-lrb-	-LRB-	_	_	_
331	CTGTAGGCACCATCAAT	ctgtaggcaccatcaat	NN	_	_	_
332	-RRB-	-rrb-	-RRB-	_	_	_
333	were	be	VBD	_	_	_
334	removed	remove	VBN	_	_	_
335	from	from	IN	_	_	_
336	fastq	fastq	NN	_	_	_
337	files	file	NNS	_	_	_
338	using	use	VBG	_	_	_
339	fastx	fastx	NN	_	_	_
340	_	_	NN	_	_	_
341	clipper	clipper	NN	_	_	_
342	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
343	Removal	removal	NN	_	_	_
344	of	of	IN	_	_	_
345	PCR	pcr	NN	_	_	_
346	duplicates	duplicate	VBZ	_	_	_
347	based	base	VBN	_	_	_
348	on	on	IN	_	_	_
349	the	the	DT	_	_	_
350	20	20	CD	_	_	_
351	first	first	JJ	_	_	_
352	bp	bp	NN	_	_	_
353	of	of	IN	_	_	_
354	the	the	DT	_	_	_
355	read	read	NN	_	_	_
356	containing	contain	VBG	_	_	_
357	a	a	DT	_	_	_
358	6	6	CD	_	_	_
359	nt	nt	NN	_	_	_
360	random	random	JJ	_	_	_
361	tag	tag	NN	GEN	_	_
362	-LRB-	-lrb-	-LRB-	_	_	_
363	home	home	NN	_	_	_
364	made	make	VBN	_	_	_
365	script	script	NN	_	_	_
366	-RRB-	-rrb-	-RRB-	_	_	_
367	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Remove	remove	VBP	_	_	_
3	non-protein	non-protein	JJ	_	_	_
4	coding	code	VBG	_	_	_
5	counts	count	NNS	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	replicate	replicate	VBP	_	_	_
8	:	:	:	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Replicate	replicate	VB	_	_	_
12	1	1	LS	_	_	_
13	-	-	:	_	_	_
14	timepoint	timepoint	NN	_	_	_
15	1	1	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	4.5	4.5	CD	_	_	_
18	h	h	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Replicate	replicate	VB	_	_	_
22	1	1	LS	_	_	_
23	-	-	:	_	_	_
24	timepoint	timepoint	NN	_	_	_
25	1	1	CD	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	4.5	4.5	CD	_	_	_
28	h	h	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	-	-	:	_	_	_
31	dye	dye	VB	_	_	_
32	swap	swap	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Replicate	replicate	VB	_	_	_
35	1	1	LS	_	_	_
36	-	-	:	_	_	_
37	timepoint	timepoint	NN	_	_	_
38	2	2	CD	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	6h	6h	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Replicate	replicate	VB	_	_	_
44	1	1	LS	_	_	_
45	-	-	:	_	_	_
46	timepoint	timepoint	NN	_	_	_
47	2	2	CD	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	6h	6h	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	-	-	:	_	_	_
52	dye	dye	VB	_	_	_
53	swap	swap	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	Replicate	replicate	VB	_	_	_
56	1	1	LS	_	_	_
57	-	-	:	_	_	_
58	timepoint	timepoint	NN	_	_	_
59	3	3	CD	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	9h	9h	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Replicate	replicate	VB	_	_	_
65	1	1	LS	_	_	_
66	-	-	:	_	_	_
67	timepoint	timepoint	NN	_	_	_
68	3	3	CD	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	9h	9h	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	-	-	:	_	_	_
73	dye	dye	VB	_	_	_
74	swap	swap	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
76	replicate	replicate	VBP	_	_	_
77	:	:	:	_	_	_
78	2	2	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
80	Replicate	replicate	VB	_	_	_
81	2	2	LS	_	_	_
82	-	-	:	_	_	_
83	timepoint	timepoint	NN	_	_	_
84	1	1	CD	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	4.5	4.5	CD	_	_	_
87	h	h	NN	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Replicate	replicate	VB	_	_	_
91	2	2	LS	_	_	_
92	-	-	:	_	_	_
93	timepoint	timepoint	NN	_	_	_
94	1	1	CD	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	4.5	4.5	CD	_	_	_
97	h	h	NN	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	-	-	:	_	_	_
100	dye	dye	VB	_	_	_
101	swap	swap	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	Replicate	replicate	VB	_	_	_
104	2	2	LS	_	_	_
105	-	-	:	_	_	_
106	timepoint	timepoint	NN	_	_	_
107	2	2	CD	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	6h	6h	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Replicate	replicate	VB	_	_	_
113	2	2	LS	_	_	_
114	-	-	:	_	_	_
115	timepoint	timepoint	NN	_	_	_
116	2	2	CD	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	6h	6h	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	-	-	:	_	_	_
121	dye	dye	VB	_	_	_
122	swap	swap	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	Replicate	replicate	VB	_	_	_
125	2	2	LS	_	_	_
126	-	-	:	_	_	_
127	timepoint	timepoint	NN	_	_	_
128	3	3	CD	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	9h	9h	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	Replicate	replicate	VB	_	_	_
134	2	2	LS	_	_	_
135	-	-	:	_	_	_
136	timepoint	timepoint	NN	_	_	_
137	3	3	CD	_	_	_
138	-LRB-	-lrb-	-LRB-	_	_	_
139	9h	9h	NN	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	-	-	:	_	_	_
142	dye	dye	VB	_	_	_
143	swap	swap	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
145	replicate	replicate	VBP	_	_	_
146	:	:	:	_	_	_
147	3	3	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	replicate	replicate	VB	_	_	_
150	:	:	:	_	_	_
151	4	4	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	replicates	replicate	VBZ	_	_	_
154	:	:	:	_	_	_
155	ORF1	orf1	NN	_	_	_
156	replicate	replicate	VB	_	_	_
157	1	1	CD	_	_	_
158	/	/	:	_	_	_
159	induced	induce	VBN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	replicates	replicate	VBZ	_	_	_
162	:	:	:	_	_	_
163	ORF1	orf1	NN	_	_	_
164	replicate	replicate	VB	_	_	_
165	1	1	CD	_	_	_
166	/	/	:	_	_	_
167	not	not	RB	_	_	_
168	induced	induce	VBN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	replicates	replicate	VBZ	_	_	_
171	:	:	:	_	_	_
172	ORF1	orf1	NN	_	_	_
173	replicate	replicate	VB	_	_	_
174	2	2	CD	_	_	_
175	/	/	:	_	_	_
176	induced	induce	VBN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	replicates	replicate	VBZ	_	_	_
179	:	:	:	_	_	_
180	ORF1	orf1	NN	_	_	_
181	replicate	replicate	VB	_	_	_
182	2	2	CD	_	_	_
183	/	/	:	_	_	_
184	not	not	RB	_	_	_
185	induced	induce	VBN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	replicates	replicate	VBZ	_	_	_
188	:	:	:	_	_	_
189	Svi3-3	svi3-3	NN	_	_	_
190	replicate	replicate	VB	_	_	_
191	1	1	CD	_	_	_
192	/	/	:	_	_	_
193	induced	induce	VBN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	replicates	replicate	VBZ	_	_	_
196	:	:	:	_	_	_
197	Svi3-3	svi3-3	NN	_	_	_
198	replicate	replicate	VB	_	_	_
199	1	1	CD	_	_	_
200	/	/	:	_	_	_
201	not	not	RB	_	_	_
202	induced	induce	VBN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	replicates	replicate	VBZ	_	_	_
205	:	:	:	_	_	_
206	Svi3-3	svi3-3	NN	_	_	_
207	replicate	replicate	VB	_	_	_
208	2	2	CD	_	_	_
209	/	/	:	_	_	_
210	induced	induce	VBN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	replicates	replicate	VBZ	_	_	_
213	:	:	:	_	_	_
214	Svi3-3	svi3-3	NN	_	_	_
215	replicate	replicate	VB	_	_	_
216	2	2	CD	_	_	_
217	/	/	:	_	_	_
218	not	not	RB	_	_	_
219	induced	induce	VBN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	replicates	replicate	VBZ	_	_	_
222	:	:	:	_	_	_
223	WT	WT	NNP	_	_	_
224	replicate	replicate	VB	_	_	_
225	1	1	CD	_	_	_
226	/	/	:	_	_	_
227	induced	induce	VBN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	replicates	replicate	VBZ	_	_	_
230	:	:	:	_	_	_
231	WT	WT	NNP	_	_	_
232	replicate	replicate	VB	_	_	_
233	2	2	CD	_	_	_
234	/	/	:	_	_	_
235	induced	induce	VBN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	reporter	reporter	NN	_	_	_
238	:	:	:	_	_	_
239	CRE	cre	NN	_	_	_
240	multi-hit	multi-hit	JJ	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	reporter	reporter	NN	_	_	_
243	:	:	:	_	_	_
244	CRE	cre	NN	_	_	_
245	single-hit	single-hit	JJ	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	reporter	reporter	NN	_	_	_
248	:	:	:	_	_	_
249	IFNB	ifnb	NN	_	_	_
250	multi-hit	multi-hit	JJ	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	reporter	reporter	NN	_	_	_
253	:	:	:	_	_	_
254	IFNB	ifnb	NN	_	_	_
255	single-hit	single-hit	JJ	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
257	Require	require	VB	_	_	_
258	peaks	peak	NNS	_	_	_
259	to	to	TO	_	_	_
260	be	be	VB	_	_	_
261	present	present	JJ	_	_	_
262	in	in	IN	_	_	_
263	at	at	IN	_	_	_
264	least	least	JJS	_	_	_
265	2	2	CD	_	_	_
266	replicates	replicate	VBZ	_	_	_
267	and	and	CC	_	_	_
268	conform	conform	VB	_	_	_
269	to	to	TO	_	_	_
270	a	a	DT	_	_	_
271	peak	peak	JJ	_	_	_
272	shape	shape	NN	_	_	_
273	by	by	IN	_	_	_
274	visual	visual	JJ	_	_	_
275	inspection	inspection	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	Respiratory	respiratory	JJ	_	_	_
278	defecient	defecient	JJ	_	_	_
279	E.	e.	FW	_	_	_
280	coli	coli	FW	_	_	_
281	mutant	mutant	NN	_	_	_
282	-LRB-	-lrb-	-LRB-	_	_	_
283	ECOM4	ecom4	NN	_	_	_
284	-RRB-	-rrb-	-RRB-	_	_	_
285	,	,	,	_	_	_
286	M9	m9	NN	_	_	_
287	media	media	NNS	_	_	_
288	with	with	IN	_	_	_
289	4	4	CD	_	_	_
290	g/L	g/l	NN	_	_	_
291	glucose	glucose	NN	SUPP	_	_
292	,	,	,	_	_	_
293	aerobic	aerobic	JJ	_	_	_
294	,	,	,	_	_	_
295	log	log	NN	_	_	_
296	phase	phase	NN	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	Resulting	result	VBG	_	_	_
299	mRNA	mrna	NN	_	_	_
300	was	be	VBD	_	_	_
301	reverse-transcribed	reverse-transcribed	JJ	_	_	_
302	to	to	TO	_	_	_
303	cDNA	cdna	NN	_	_	_
304	libraries	library	NNS	_	_	_
305	via	via	IN	_	_	_
306	SuperScript	SuperScript	NNP	_	_	_
307	III	III	NNP	_	_	_
308	First	First	NNP	_	_	_
309	Strand	Strand	NNP	_	_	_
310	reverse	reverse	VB	_	_	_
311	transcription	transcription	NN	_	_	_
312	kit	kit	NN	_	_	_
313	-LRB-	-lrb-	-LRB-	_	_	_
314	Invitrogen	Invitrogen	NNP	_	_	_
315	,	,	,	_	_	_
316	Carlsbad	Carlsbad	NNP	_	_	_
317	,	,	,	_	_	_
318	CA	CA	NNP	_	_	_
319	,	,	,	_	_	_
320	18080051	18080051	CD	_	_	_
321	-RRB-	-rrb-	-RRB-	_	_	_
322	as	as	IN	_	_	_
323	per	per	IN	_	_	_
324	the	the	DT	_	_	_
325	manufacturer	manufacturer	NN	_	_	_
326	's	's	POS	_	_	_
327	instructions	instruction	NNS	_	_	_
328	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Resulting	Resulting	NNP	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	aligned	align	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	published	publish	VBN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	K-12	k-12	NN	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	genome	genome	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	U00096	u00096	NN	_	_	_
16	.2	.2	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	using	use	VBG	_	_	_
19	the	the	DT	_	_	_
20	software	software	NN	_	_	_
21	package	package	NN	_	_	_
22	SOAP	soap	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Li	Li	NNP	_	_	_
25	et	et	FW	_	_	_
26	al	al	FW	_	_	_
27	,	,	,	_	_	_
28	2009	2009	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	allowing	allow	VBG	_	_	_
32	no	no	RB	_	_	_
33	more	more	JJR	_	_	_
34	than	than	IN	_	_	_
35	two	two	CD	_	_	_
36	mismatches	mismatch	NNS	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Supplemental	Supplemental	NNP	_	_	_
39	File	File	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

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	NNP	_	_	_
2	Resulting	Resulting	NNP	_	_	_
3	SAM	SAM	NNP	_	_	_
4	files	file	NNS	_	_	_
5	were	be	VBD	_	_	_
6	processed	process	VBN	_	_	_
7	with	with	IN	_	_	_
8	custom	custom	NN	_	_	_
9	script	script	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	SAM_to_coverage_and_N5E_N3E.py	sam_to_coverage_and_n5e_n3e.py	NN	_	_	_
12	,	,	,	_	_	_
13	github	github	NN	_	_	_
14	:	:	:	_	_	_
15	https://github.com/sutormin94/Gyrase_Topo-seq	https://github.com/sutormin94/gyrase_topo-seq	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	giving	give	VBG	_	_	_
19	coverage	coverage	NN	_	_	_
20	depth	depth	NN	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	genome	genome	NN	_	_	_
24	and	and	CC	_	_	_
25	N3E	n3e	NN	_	_	_
26	values	value	NNS	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	number	number	NN	_	_	_
29	of	of	IN	_	_	_
30	DNA	dna	NN	_	_	_
31	fragments	fragment	NNS	_	_	_
32	3	3	CD	_	_	_
33	'	'	''	_	_	_
34	-	-	:	_	_	_
35	ends	end	NNS	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	for	for	IN	_	_	_
38	every	every	DT	_	_	_
39	position	position	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	re-suspended	re-suspended	JJ	_	_	_
42	in	in	IN	_	_	_
43	200	200	CD	_	_	_
44	ul	ul	NN	_	_	_
45	Trizol	trizol	NN	_	_	_
46	and	and	CC	_	_	_
47	combined	combine	VBN	_	_	_
48	for	for	IN	_	_	_
49	a	a	DT	_	_	_
50	total	total	JJ	_	_	_
51	volume	volume	NN	_	_	_
52	of	of	IN	_	_	_
53	1	1	CD	_	_	_
54	ml	ml	NN	_	_	_
55	,	,	,	_	_	_
56	then	then	RB	_	_	_
57	promptly	promptly	RB	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
59	RF2	rf2	NN	_	_	_
60	*	*	SYM	_	_	_
61	_	_	SYM	_	_	_
62	exp1	exp1	NN	_	_	_
63	_	_	NN	_	_	_
64	mRNA	mrna	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	RF2	rf2	NN	_	_	_
67	*	*	SYM	_	_	_
68	_	_	SYM	_	_	_
69	exp1	exp1	FW	_	_	_
70	_	_	FW	_	_	_
71	ribosome	ribosome	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	RF2	rf2	NN	_	_	_
74	*	*	SYM	_	_	_
75	_	_	SYM	_	_	_
76	exp3	exp3	FW	_	_	_
77	_	_	FW	_	_	_
78	mRNA	mrna	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	RF2	rf2	NN	_	_	_
81	*	*	SYM	_	_	_
82	_	_	SYM	_	_	_
83	exp3	exp3	FW	_	_	_
84	_	_	FW	_	_	_
85	ribosome	ribosome	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	RF2	rf2	NN	_	_	_
88	*	*	SYM	_	_	_
89	∆	∆	SYM	_	_	_
90	RF3	rf3	NN	_	_	_
91	_	_	SYM	_	_	_
92	exp2	exp2	FW	_	_	_
93	_	_	FW	_	_	_
94	repA	repa	NN	_	_	_
95	_	_	NN	_	_	_
96	mRNA	mrna	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	RF2	rf2	NN	_	_	_
99	*	*	SYM	_	_	_
100	∆	∆	SYM	_	_	_
101	RF3	rf3	NN	_	_	_
102	_	_	SYM	_	_	_
103	exp2	exp2	FW	_	_	_
104	_	_	FW	_	_	_
105	repA	repa	NN	_	_	_
106	_	_	NN	_	_	_
107	ribosome	ribosome	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	RF2	rf2	NN	_	_	_
110	*	*	SYM	_	_	_
111	∆	∆	SYM	_	_	_
112	RF3	rf3	NN	_	_	_
113	_	_	CD	_	_	_
114	exp2	exp2	NN	_	_	_
115	_	_	CD	_	_	_
116	repB	repb	NN	_	_	_
117	_	_	NN	_	_	_
118	mRNA	mrna	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	RF2	rf2	NN	_	_	_
121	*	*	SYM	_	_	_
122	∆	∆	SYM	_	_	_
123	RF3	rf3	NN	_	_	_
124	_	_	CD	_	_	_
125	exp2	exp2	NN	_	_	_
126	_	_	CD	_	_	_
127	repB	repb	NN	_	_	_
128	_	_	NN	_	_	_
129	ribosome	ribosome	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	RF2	rf2	NN	_	_	_
132	*	*	SYM	_	_	_
133	∆	∆	SYM	_	_	_
134	RF3	rf3	NN	_	_	_
135	_	_	CD	_	_	_
136	exp3	exp3	NN	_	_	_
137	_	_	NN	_	_	_
138	mRNA	mrna	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	RF2	rf2	NN	_	_	_
141	*	*	SYM	_	_	_
142	∆	∆	SYM	_	_	_
143	RF3	rf3	NN	_	_	_
144	_	_	CD	_	_	_
145	exp3	exp3	NN	_	_	_
146	_	_	NN	_	_	_
147	ribosome	ribosome	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	RF2	rf2	NN	_	_	_
150	*	*	SYM	_	_	_
151	∆	∆	SYM	_	_	_
152	RF3	rf3	NN	_	_	_
153	_	_	SYM	_	_	_
154	exp4	exp4	FW	_	_	_
155	_	_	FW	_	_	_
156	repA	repa	NN	_	_	_
157	_	_	NN	_	_	_
158	mRNA	mrna	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	RF2	rf2	NN	_	_	_
161	*	*	SYM	_	_	_
162	∆	∆	SYM	_	_	_
163	RF3	rf3	NN	_	_	_
164	_	_	SYM	_	_	_
165	exp4	exp4	FW	_	_	_
166	_	_	FW	_	_	_
167	repA	repa	NN	_	_	_
168	_	_	NN	_	_	_
169	ribosome	ribosome	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	RF2	rf2	NN	_	_	_
172	*	*	SYM	_	_	_
173	∆	∆	SYM	_	_	_
174	RF3	rf3	NN	_	_	_
175	_	_	CD	_	_	_
176	exp4	exp4	NN	_	_	_
177	_	_	CD	_	_	_
178	repB	repb	NN	_	_	_
179	_	_	NN	_	_	_
180	mRNA	mrna	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	RF2	rf2	NN	_	_	_
183	*	*	SYM	_	_	_
184	∆	∆	SYM	_	_	_
185	RF3	rf3	NN	_	_	_
186	_	_	CD	_	_	_
187	exp4	exp4	NN	_	_	_
188	_	_	CD	_	_	_
189	repB	repb	NN	_	_	_
190	_	_	NN	_	_	_
191	ribosome	ribosome	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	∆	∆	CD	_	_	_
194	RF3	rf3	NN	_	_	_
195	_	_	CD	_	_	_
196	exp1	exp1	NN	_	_	_
197	_	_	NN	_	_	_
198	mRNA	mrna	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	∆	∆	CD	_	_	_
201	RF3	rf3	NN	_	_	_
202	_	_	CD	_	_	_
203	exp1	exp1	NN	_	_	_
204	_	_	NN	_	_	_
205	ribosome	ribosome	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	∆	∆	CD	_	_	_
208	RF3	rf3	NN	_	_	_
209	_	_	CD	_	_	_
210	exp3	exp3	NN	_	_	_
211	_	_	NN	_	_	_
212	mRNA	mrna	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	∆	∆	CD	_	_	_
215	RF3	rf3	NN	_	_	_
216	_	_	CD	_	_	_
217	exp3	exp3	NN	_	_	_
218	_	_	NN	_	_	_
219	ribosome	ribosome	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	∆	∆	CD	_	_	_
222	RF3	rf3	NN	_	_	_
223	_	_	NN	_	_	_
224	minimal	minimal	JJ	_	_	_
225	_	_	NN	_	_	_
226	mRNA	mrna	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	∆	∆	CD	_	_	_
229	RF3	rf3	NN	_	_	_
230	_	_	NN	_	_	_
231	minimal	minimal	JJ	_	_	_
232	_	_	NN	_	_	_
233	ribosome	ribosome	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	rfbA	rfba	NN	GEN	_	_
236	KO	ko	NN	_	_	_
237	rep1	rep1	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	rfbA	rfba	NN	GEN	_	_
240	KO	ko	NN	_	_	_
241	rep2	rep2	NN	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	rfbA	rfba	NN	GEN	_	_
244	KO	ko	NN	_	_	_
245	rep3	rep3	NN	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	RhIB	rhib	NN	_	_	_
248	wild	wild	JJ	_	_	_
249	type	type	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	RhlBP238L	rhlbp238l	NN	_	_	_
252	mutant	mutant	JJ	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	RhlBP238L	rhlbp238l	NN	_	_	_
255	vs	vs	CC	_	_	_
256	flag	flag	NN	_	_	_
257	only	only	RB	_	_	_
258	1	1	CD	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	RhlBP238L	rhlbp238l	NN	_	_	_
261	vs	vs	CC	_	_	_
262	flag	flag	NN	_	_	_
263	only	only	RB	_	_	_
264	2	2	CD	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	RhlBP238L	rhlbp238l	NN	_	_	_
267	vs	vs	CC	_	_	_
268	flag	flag	NN	_	_	_
269	only	only	RB	_	_	_
270	3	3	CD	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	RhlB	rhlb	NN	_	_	_
273	-	-	:	_	_	_
274	-LRB-	-lrb-	-LRB-	_	_	_
275	SU02	su02	NN	_	_	_
276	-RRB-	-rrb-	-RRB-	_	_	_
277	in	in	IN	_	_	_
278	M9	m9	NN	_	_	_
279	0.2	0.2	CD	_	_	_
280	%	%	NN	_	_	_
281	Glycerol	glycerol	NN	_	_	_
282	,	,	,	_	_	_
283	0.2	0.2	CD	_	_	_
284	%	%	NN	_	_	_
285	Tryptone	tryptone	NN	_	_	_
286	at	at	IN	_	_	_
287	30	30	CD	_	_	_
288	C	c	NN	_	_	_
289	Mid	Mid	NNP	_	_	_
290	Log	Log	NNP	_	_	_
291	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
292	RhlB	rhlb	NN	_	_	_
293	-	-	:	_	_	_
294	-LRB-	-lrb-	-LRB-	_	_	_
295	SU02	su02	NN	_	_	_
296	-RRB-	-rrb-	-RRB-	_	_	_
297	in	in	IN	_	_	_
298	M9	m9	NN	_	_	_
299	+	+	CC	_	_	_
300	0.2	0.2	CD	_	_	_
301	%	%	NN	_	_	_
302	Glycerol	glycerol	NN	_	_	_
303	,	,	,	_	_	_
304	0.2	0.2	CD	_	_	_
305	%	%	NN	_	_	_
306	Tryptone	tryptone	NN	_	_	_
307	at	at	IN	_	_	_
308	30	30	CD	_	_	_
309	C	c	NN	_	_	_
310	Mid	Mid	NNP	_	_	_
311	Log	Log	NNP	_	_	_
312	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
313	RhlB	rhlb	NN	_	_	_
314	-	-	:	_	_	_
315	-LRB-	-lrb-	-LRB-	_	_	_
316	SU02	su02	NN	_	_	_
317	-RRB-	-rrb-	-RRB-	_	_	_
318	in	in	IN	_	_	_
319	M9	m9	NN	_	_	_
320	0.2	0.2	CD	_	_	_
321	%	%	NN	_	_	_
322	Glycerol	glycerol	NN	_	_	_
323	,	,	,	_	_	_
324	0.2	0.2	CD	_	_	_
325	%	%	NN	_	_	_
326	Tryptone	tryptone	NN	_	_	_
327	at	at	IN	_	_	_
328	30	30	CD	_	_	_
329	C	c	NN	_	_	_
330	Mid	Mid	NNP	_	_	_
331	Log	Log	NNP	_	_	_
332	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
333	RhlB	rhlb	NN	_	_	_
334	-	-	:	_	_	_
335	-LRB-	-lrb-	-LRB-	_	_	_
336	SU02	su02	NN	_	_	_
337	-RRB-	-rrb-	-RRB-	_	_	_
338	in	in	IN	_	_	_
339	M9	m9	NN	_	_	_
340	+	+	CC	_	_	_
341	0.2	0.2	CD	_	_	_
342	%	%	NN	_	_	_
343	Glycerol	glycerol	NN	_	_	_
344	,	,	,	_	_	_
345	0.2	0.2	CD	_	_	_
346	%	%	NN	_	_	_
347	Tryptone	tryptone	NN	_	_	_
348	at	at	IN	_	_	_
349	30	30	CD	_	_	_
350	C	c	NN	_	_	_
351	Mid	Mid	NNP	_	_	_
352	Log	Log	NNP	_	_	_
353	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
354	RhlB	rhlb	NN	_	_	_
355	-	-	:	_	_	_
356	-LRB-	-lrb-	-LRB-	_	_	_
357	SU02	su02	NN	_	_	_
358	-RRB-	-rrb-	-RRB-	_	_	_
359	in	in	IN	_	_	_
360	M9	m9	NN	_	_	_
361	+	+	CC	_	_	_
362	0.2	0.2	CD	_	_	_
363	%	%	NN	_	_	_
364	Glycerol	glycerol	NN	_	_	_
365	,	,	,	_	_	_
366	0.2	0.2	CD	_	_	_
367	%	%	NN	_	_	_
368	Tryptone	tryptone	NN	_	_	_
369	at	at	IN	_	_	_
370	30	30	CD	_	_	_
371	C	c	NN	_	_	_
372	Mid	Mid	NNP	_	_	_
373	Log	Log	NNP	_	_	_
374	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
375	RhlB	rhlb	NN	_	_	_
376	-	-	:	_	_	_
377	-LRB-	-lrb-	-LRB-	_	_	_
378	SU02	su02	NN	_	_	_
379	-RRB-	-rrb-	-RRB-	_	_	_
380	in	in	IN	_	_	_
381	M9	m9	NN	_	_	_
382	+	+	CC	_	_	_
383	0.2	0.2	CD	_	_	_
384	%	%	NN	_	_	_
385	Glycerol	glycerol	NN	_	_	_
386	,	,	,	_	_	_
387	0.2	0.2	CD	_	_	_
388	%	%	NN	_	_	_
389	Tryptone	tryptone	NN	_	_	_
390	at	at	IN	_	_	_
391	30	30	CD	_	_	_
392	C	c	NN	_	_	_
393	Mid	Mid	NNP	_	_	_
394	Log	Log	NNP	_	_	_
395	1.5	1.5	CD	_	_	_
396	'	'	''	_	_	_
397	post	post	JJ	_	_	_
398	rif	rif	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	RhlB	rhlb	NN	_	_	_
401	-	-	:	_	_	_
402	-LRB-	-lrb-	-LRB-	_	_	_
403	SU02	su02	NN	_	_	_
404	-RRB-	-rrb-	-RRB-	_	_	_
405	in	in	IN	_	_	_
406	M9	m9	NN	_	_	_
407	+	+	CC	_	_	_
408	0.2	0.2	CD	_	_	_
409	%	%	NN	_	_	_
410	Glycerol	glycerol	NN	_	_	_
411	,	,	,	_	_	_
412	0.2	0.2	CD	_	_	_
413	%	%	NN	_	_	_
414	Tryptone	tryptone	NN	_	_	_
415	at	at	IN	_	_	_
416	30	30	CD	_	_	_
417	C	c	NN	_	_	_
418	Mid	Mid	NNP	_	_	_
419	Log	Log	NNP	_	_	_
420	3	3	CD	_	_	_
421	'	'	''	_	_	_
422	post	post	JJ	_	_	_
423	rif	rif	NN	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	RhlB	rhlb	NN	_	_	_
426	-	-	:	_	_	_
427	-LRB-	-lrb-	-LRB-	_	_	_
428	SU02	su02	NN	_	_	_
429	-RRB-	-rrb-	-RRB-	_	_	_
430	in	in	IN	_	_	_
431	M9	m9	NN	_	_	_
432	+	+	CC	_	_	_
433	0.2	0.2	CD	_	_	_
434	%	%	NN	_	_	_
435	Glycerol	glycerol	NN	_	_	_
436	,	,	,	_	_	_
437	0.2	0.2	CD	_	_	_
438	%	%	NN	_	_	_
439	Tryptone	tryptone	NN	_	_	_
440	at	at	IN	_	_	_
441	30	30	CD	_	_	_
442	C	c	NN	_	_	_
443	Mid	Mid	NNP	_	_	_
444	Log	Log	NNP	_	_	_
445	3	3	CD	_	_	_
446	'	'	''	_	_	_
447	post	post	JJ	_	_	_
448	rif	rif	NN	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	RhlB	rhlb	NN	_	_	_
451	-	-	:	_	_	_
452	-LRB-	-lrb-	-LRB-	_	_	_
453	SU02	su02	NN	_	_	_
454	-RRB-	-rrb-	-RRB-	_	_	_
455	in	in	IN	_	_	_
456	M9	m9	NN	_	_	_
457	+	+	CC	_	_	_
458	0.2	0.2	CD	_	_	_
459	%	%	NN	_	_	_
460	Glycerol	glycerol	NN	_	_	_
461	,	,	,	_	_	_
462	0.2	0.2	CD	_	_	_
463	%	%	NN	_	_	_
464	Tryptone	tryptone	NN	_	_	_
465	at	at	IN	_	_	_
466	30	30	CD	_	_	_
467	C	c	NN	_	_	_
468	Mid	Mid	NNP	_	_	_
469	Log	Log	NNP	_	_	_
470	4.5	4.5	CD	_	_	_
471	'	'	''	_	_	_
472	post	post	JJ	_	_	_
473	rif	rif	NN	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	RhlB	rhlb	NN	_	_	_
476	-	-	:	_	_	_
477	-LRB-	-lrb-	-LRB-	_	_	_
478	SU02	su02	NN	_	_	_
479	-RRB-	-rrb-	-RRB-	_	_	_
480	in	in	IN	_	_	_
481	M9	m9	NN	_	_	_
482	+	+	CC	_	_	_
483	0.2	0.2	CD	_	_	_
484	%	%	NN	_	_	_
485	Glycerol	glycerol	NN	_	_	_
486	,	,	,	_	_	_
487	0.2	0.2	CD	_	_	_
488	%	%	NN	_	_	_
489	Tryptone	tryptone	NN	_	_	_
490	at	at	IN	_	_	_
491	30	30	CD	_	_	_
492	C	c	NN	_	_	_
493	Mid	Mid	NNP	_	_	_
494	Log	Log	NNP	_	_	_
495	6	6	CD	_	_	_
496	'	'	''	_	_	_
497	post	post	JJ	_	_	_
498	rif	rif	NN	_	_	_
499	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
500	RhlB	rhlb	NN	_	_	_
501	-	-	:	_	_	_
502	-LRB-	-lrb-	-LRB-	_	_	_
503	SU02	su02	NN	_	_	_
504	-RRB-	-rrb-	-RRB-	_	_	_
505	in	in	IN	_	_	_
506	M9	m9	NN	_	_	_
507	+	+	CC	_	_	_
508	0.2	0.2	CD	_	_	_
509	%	%	NN	_	_	_
510	Glycerol	glycerol	NN	_	_	_
511	,	,	,	_	_	_
512	0.2	0.2	CD	_	_	_
513	%	%	NN	_	_	_
514	Tryptone	tryptone	NN	_	_	_
515	at	at	IN	_	_	_
516	30	30	CD	_	_	_
517	Mid	Mid	NNP	_	_	_
518	Log	Log	NNP	_	_	_
519	6	6	CD	_	_	_
520	'	'	''	_	_	_
521	post	post	JJ	_	_	_
522	rif	rif	NN	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	RhlBwt	rhlbwt	NN	_	_	_
525	vs	vs	CC	_	_	_
526	flag	flag	NN	_	_	_
527	only	only	RB	_	_	_
528	1	1	CD	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	RhlBwt	rhlbwt	NN	_	_	_
531	vs	vs	CC	_	_	_
532	flag	flag	NN	_	_	_
533	only	only	RB	_	_	_
534	2	2	CD	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	RhlBwt	rhlbwt	NN	_	_	_
537	vs	vs	CC	_	_	_
538	flag	flag	NN	_	_	_
539	only	only	RB	_	_	_
540	3	3	CD	_	_	_
541	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
542	Rho	rho	NN	_	_	_
543	ChIP-chip	chip-chip	NN	_	_	_
544	in	in	IN	_	_	_
545	E.	e.	FW	_	_	_
546	coli	coli	FW	_	_	_
547	K-12	k-12	NN	_	_	_
548	MG1655	mg1655	NN	_	_	_
549	cells	cell	NNS	_	_	_
550	-LRB-	-lrb-	-LRB-	_	_	_
551	Dataset	Dataset	NNP	_	_	_
552	3421602	3421602	CD	_	_	_
553	-RRB-	-rrb-	-RRB-	_	_	_
554	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
555	Rho	rho	NN	_	_	_
556	ChIP-chip	chip-chip	NN	_	_	_
557	in	in	IN	_	_	_
558	E.	e.	FW	_	_	_
559	coli	coli	FW	_	_	_
560	K-12	k-12	NN	_	_	_
561	MG1655	mg1655	NN	_	_	_
562	cells	cell	NNS	_	_	_
563	-LRB-	-lrb-	-LRB-	_	_	_
564	Dataset	Dataset	NNP	_	_	_
565	70261	70261	CD	_	_	_
566	-RRB-	-rrb-	-RRB-	_	_	_
567	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
568	Rho	rho	NN	_	_	_
569	ChIP	chip	NN	_	_	_
570	in	in	IN	_	_	_
571	E.	e.	FW	_	_	_
572	coli	coli	FW	_	_	_
573	K-12	k-12	NN	_	_	_
574	MG1655	mg1655	NN	_	_	_
575	cells	cell	NNS	_	_	_
576	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
577	Rhodococcus	rhodococcus	NN	_	_	_
578	jostii	jostii	NN	_	_	_
579	RHA1	rha1	NN	_	_	_
580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
581	∆	∆	CD	_	_	_
582	rho	rho	NN	GEN	_	_
583	UvsW	uvsw	NN	_	_	_
584	_	_	CD	_	_	_
585	replicate1	replicate1	NN	_	_	_
586	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
587	∆	∆	CD	_	_	_
588	rho	rho	NN	GEN	_	_
589	UvsW	uvsw	NN	_	_	_
590	_	_	CD	_	_	_
591	replicate2	replicate2	NN	_	_	_
592	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
593	∆	∆	CD	_	_	_
594	rho	rho	NN	GEN	_	_
595	UvsW	uvsw	NN	_	_	_
596	_	_	CD	_	_	_
597	replicate3	replicate3	NN	_	_	_
598	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
599	Ribosomal	ribosomal	JJ	_	_	_
600	RNA	rna	NN	_	_	_
601	-LRB-	-lrb-	-LRB-	_	_	_
602	rRNA	rrna	NN	_	_	_
603	-RRB-	-rrb-	-RRB-	_	_	_
604	was	be	VBD	_	_	_
605	removed	remove	VBN	_	_	_
606	using	use	VBG	_	_	_
607	Ribo-Zero	Ribo-Zero	NNP	_	_	_
608	™	™	NNP	_	_	_
609	Gold	Gold	NNP	_	_	_
610	-LRB-	-lrb-	-LRB-	_	_	_
611	Yeast	yeast	NN	_	_	_
612	-RRB-	-rrb-	-RRB-	_	_	_
613	kit	kit	NN	_	_	_
614	-LRB-	-lrb-	-LRB-	_	_	_
615	Epicenter	epicenter	NN	_	_	_
616	,	,	,	_	_	_
617	Madison	Madison	NNP	_	_	_
618	,	,	,	_	_	_
619	WI	WI	NNP	_	_	_
620	-RRB-	-rrb-	-RRB-	_	_	_
621	using	use	VBG	_	_	_
622	manufacturer	manufacturer	NN	_	_	_
623	's	's	POS	_	_	_
624	recommended	recommend	VBN	_	_	_
625	protocol	protocol	NN	_	_	_
626	.	.	.	_	_	_

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	NNP	_	_	_
2	Ribosomal	ribosomal	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	first	first	JJ	_	_	_
6	removed	remove	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Ribozero	Ribozero	NNP	_	_	_
10	rRNA	rrna	NN	_	_	_
11	Removal	removal	NN	_	_	_
12	Meta-Bacteria	Meta-Bacteria	NNP	_	_	_
13	kit	kit	NN	_	_	_
14	.	.	.	_	_	_

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	NNP	_	_	_
19	Ribosomal	ribosomal	JJ	_	_	_
20	RNA	rna	NN	_	_	_
21	was	be	VBD	_	_	_
22	removed	remove	VBN	_	_	_
23	from	from	IN	_	_	_
24	1	1	CD	_	_	_
25	μg	μg	NN	_	_	_
26	of	of	IN	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	using	use	VBG	_	_	_
30	Ribozero	Ribozero	NNP	_	_	_
31	rRNA	rrna	NN	_	_	_
32	Removal	removal	NN	_	_	_
33	Meta-Bacteria	Meta-Bacteria	NNP	_	_	_
34	Kit	kit	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Epicentre	Epicentre	NNP	_	_	_
37	Biotechnologies	Biotechnologies	NNPS	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	and	and	CC	_	_	_
40	the	the	DT	_	_	_
41	mRNA-enriched	mrna-enriched	JJ	_	_	_
42	fraction	fraction	NN	_	_	_
43	was	be	VBD	_	_	_
44	converted	convert	VBN	_	_	_
45	to	to	TO	_	_	_
46	indexed	index	VBN	_	_	_
47	RNA-seq	rna-seq	NN	_	_	_
48	libraries	library	NNS	_	_	_
49	with	with	IN	_	_	_
50	the	the	DT	_	_	_
51	ScriptSeq	ScriptSeq	NNP	_	_	_
52	™	™	CD	_	_	_
53	v2	v2	NN	_	_	_
54	RNA-Seq	rna-seq	NN	_	_	_
55	Library	Library	NNP	_	_	_
56	Preparation	Preparation	NNP	_	_	_
57	Kit	kit	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	Epicentre	Epicentre	NNP	_	_	_
60	Biotechnologies	Biotechnologies	NNPS	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Ribosome	Ribosome	NNP	_	_	_
3	profiling	profile	VBG	_	_	_
4	10	10	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	WT	wt	JJ	_	_	_
13	cells	cell	NNS	_	_	_
14	_	_	VBP	_	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Ribosome	Ribosome	NNP	_	_	_
18	profiling	profile	VBG	_	_	_
19	10	10	CD	_	_	_
20	min	min	NN	_	_	_
21	after	after	IN	_	_	_
22	shift	shift	NN	_	_	_
23	to	to	TO	_	_	_
24	10	10	CD	_	_	_
25	°C	°c	NN	_	_	_
26	in	in	IN	_	_	_
27	WT	wt	JJ	_	_	_
28	cells	cell	NNS	_	_	_
29	_	_	VBP	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Ribosome	Ribosome	NNP	_	_	_
33	profiling	profile	VBG	_	_	_
34	15	15	CD	_	_	_
35	min	min	NN	_	_	_
36	after	after	IN	_	_	_
37	shift	shift	NN	_	_	_
38	to	to	TO	_	_	_
39	10	10	CD	_	_	_
40	°C	°c	NN	_	_	_
41	in	in	IN	_	_	_
42	WT	wt	JJ	_	_	_
43	cells	cell	NNS	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
45	Ribosome	ribosome	NN	_	_	_
46	profiling	profiling	NN	_	_	_
47	2	2	CD	_	_	_
48	hr	hr	NN	_	_	_
49	after	after	IN	_	_	_
50	shift	shift	NN	_	_	_
51	to	to	TO	_	_	_
52	10	10	CD	_	_	_
53	°C	°c	NN	_	_	_
54	in	in	IN	_	_	_
55	WT	wt	JJ	_	_	_
56	cells	cell	NNS	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Ribosome	Ribosome	NNP	_	_	_
59	profiling	profile	VBG	_	_	_
60	30	30	CD	_	_	_
61	min	min	NN	_	_	_
62	after	after	IN	_	_	_
63	shift	shift	NN	_	_	_
64	to	to	TO	_	_	_
65	10	10	CD	_	_	_
66	°C	°c	NN	_	_	_
67	in	in	IN	_	_	_
68	WT	wt	JJ	_	_	_
69	cells	cell	NNS	_	_	_
70	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
71	Ribosome	Ribosome	NNP	_	_	_
72	profiling	profile	VBG	_	_	_
73	3	3	CD	_	_	_
74	hr	hr	NN	_	_	_
75	after	after	IN	_	_	_
76	shift	shift	NN	_	_	_
77	to	to	TO	_	_	_
78	10	10	CD	_	_	_
79	°C	°c	NN	_	_	_
80	in	in	IN	_	_	_
81	WT	wt	JJ	_	_	_
82	cells	cell	NNS	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	Ribosome	Ribosome	NNP	_	_	_
85	profiling	profile	VBG	_	_	_
86	4	4	CD	_	_	_
87	hr	hr	NN	_	_	_
88	after	after	IN	_	_	_
89	shift	shift	NN	_	_	_
90	to	to	TO	_	_	_
91	10	10	CD	_	_	_
92	°C	°c	NN	_	_	_
93	in	in	IN	_	_	_
94	WT	wt	JJ	_	_	_
95	cells	cell	NNS	_	_	_
96	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
97	Ribosome	Ribosome	NNP	_	_	_
98	profiling	profile	VBG	_	_	_
99	5	5	CD	_	_	_
100	min	min	NN	_	_	_
101	after	after	IN	_	_	_
102	shift	shift	NN	_	_	_
103	to	to	TO	_	_	_
104	10	10	CD	_	_	_
105	°C	°c	NN	_	_	_
106	in	in	IN	_	_	_
107	WT	wt	JJ	_	_	_
108	cells	cell	NNS	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	Ribosome	Ribosome	NNP	_	_	_
111	profiling	profile	VBG	_	_	_
112	6	6	CD	_	_	_
113	hr	hr	NN	_	_	_
114	after	after	IN	_	_	_
115	shift	shift	NN	_	_	_
116	to	to	TO	_	_	_
117	10	10	CD	_	_	_
118	°C	°c	NN	_	_	_
119	in	in	IN	_	_	_
120	WT	wt	JJ	_	_	_
121	cells	cell	NNS	_	_	_
122	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
123	Ribosome	Ribosome	NNP	_	_	_
124	profiling	profile	VBG	_	_	_
125	8	8	CD	_	_	_
126	hr	hr	NN	_	_	_
127	after	after	IN	_	_	_
128	shift	shift	NN	_	_	_
129	to	to	TO	_	_	_
130	10	10	CD	_	_	_
131	°C	°c	NN	_	_	_
132	in	in	IN	_	_	_
133	∆	∆	CD	_	_	_
134	cspABEG	cspabeg	NN	_	_	_
135	cells	cell	NNS	_	_	_
136	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
137	Ribosome	Ribosome	NNP	_	_	_
138	profiling	profile	VBG	_	_	_
139	8	8	CD	_	_	_
140	hr	hr	NN	_	_	_
141	after	after	IN	_	_	_
142	shift	shift	NN	_	_	_
143	to	to	TO	_	_	_
144	10	10	CD	_	_	_
145	°C	°c	NN	_	_	_
146	in	in	IN	_	_	_
147	WT	wt	JJ	_	_	_
148	cells	cell	NNS	_	_	_
149	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
150	Ribosome	Ribosome	NNP	_	_	_
151	profiling	profile	VBG	_	_	_
152	at	at	IN	_	_	_
153	37	37	CD	_	_	_
154	°C	°c	NN	_	_	_
155	in	in	IN	_	_	_
156	∆	∆	CD	_	_	_
157	cspABCEG	cspabceg	NN	_	_	_
158	cells	cell	NNS	_	_	_
159	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
160	Ribosome	Ribosome	NNP	_	_	_
161	profiling	profile	VBG	_	_	_
162	at	at	IN	_	_	_
163	37	37	CD	_	_	_
164	°C	°c	NN	_	_	_
165	in	in	IN	_	_	_
166	WT	wt	JJ	_	_	_
167	cells	cell	NNS	_	_	_
168	_	_	VBP	_	_	_
169	1	1	CD	_	_	_
170	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
171	Ribosome	Ribosome	NNP	_	_	_
172	profiling	profile	VBG	_	_	_
173	at	at	IN	_	_	_
174	37	37	CD	_	_	_
175	°C	°c	NN	_	_	_
176	in	in	IN	_	_	_
177	WT	wt	JJ	_	_	_
178	cells	cell	NNS	_	_	_
179	_	_	VBP	_	_	_
180	2	2	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
182	ribosome	ribosome	NN	_	_	_
183	profiling	profiling	NN	_	_	_
184	in	in	IN	_	_	_
185	rich	rich	JJ	_	_	_
186	defined	define	VBN	_	_	_
187	media	media	NNS	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	ribosome	ribosome	NN	_	_	_
190	profiling	profile	VBG	_	_	_
191	MicL	micl	NN	_	_	_
192	t0	t0	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	ribosome	ribosome	NN	_	_	_
195	profiling	profile	VBG	_	_	_
196	MicL	micl	NN	_	_	_
197	t20	t20	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	Ribosome	ribosome	NN	_	_	_
200	protected	protect	VBD	_	_	_
201	and	and	CC	_	_	_
202	total	total	JJ	_	_	_
203	mRNA	mrna	NN	_	_	_
204	fragments	fragment	NNS	_	_	_
205	were	be	VBD	_	_	_
206	size	size	NN	_	_	_
207	selected	select	VBN	_	_	_
208	via	via	IN	_	_	_
209	gel	gel	NN	_	_	_
210	purification	purification	NN	_	_	_
211	.	.	.	_	_	_

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	NNP	_	_	_
2	Ribosome	Ribosome	NNP	_	_	_
3	protected	protect	VBD	_	_	_
4	mRNA	mrna	NN	_	_	_
5	fragments	fragment	NNS	_	_	_
6	were	be	VBD	_	_	_
7	size	size	NN	_	_	_
8	selected	select	VBN	_	_	_
9	via	via	IN	_	_	_
10	gel	gel	NN	_	_	_
11	purification	purification	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	ligated	ligate	VBN	_	_	_
15	to	to	TO	_	_	_
16	5	5	CD	_	_	_
17	'	'	''	_	_	_
18	adenylated	adenylate	VBN	_	_	_
19	DNA	dna	NN	_	_	_
20	oligo	oligo	JJ	_	_	_
21	.	.	.	_	_	_

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	NNP	_	_	_
2	Ribosome	Ribosome	NNP	_	_	_
3	protected	protect	VBD	_	_	_
4	mRNA	mrna	NN	_	_	_
5	fragments	fragment	NNS	_	_	_
6	were	be	VBD	_	_	_
7	size	size	NN	_	_	_
8	selected	select	VBN	_	_	_
9	via	via	IN	_	_	_
10	gel	gel	NN	_	_	_
11	purification	purification	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	ligated	ligate	VBN	_	_	_
15	to	to	TO	_	_	_
16	5	5	CD	_	_	_
17	'	'	''	_	_	_
18	adenylated	adenylate	VBN	_	_	_
19	DNA	dna	NN	_	_	_
20	oligo	oligo	JJ	_	_	_
21	.	.	.	_	_	_

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	ribosome-protected	ribosome-protected	JJ	_	_	_
20	:	:	:	_	_	_
21	No	no	DT	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	ribosome-protected	ribosome-protected	JJ	_	_	_
24	:	:	:	_	_	_
25	Yes	yes	UH	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	ribozero	ribozero	NN	_	_	_
28	:	:	:	_	_	_
29	No	no	DT	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	ribozero	ribozero	NN	_	_	_
32	:	:	:	_	_	_
33	Yes	yes	UH	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
35	Rifampicine	Rifampicine	NNP	_	_	_
36	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
37	Rep	Rep	NNP	_	_	_
38	1	1	LS	_	_	_
39	-	-	:	_	_	_
40	A-IP	a-ip	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Rifampicine	Rifampicine	NNP	_	_	_
43	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
44	Rep	Rep	NNP	_	_	_
45	1	1	CD	_	_	_
46	+	+	CC	_	_	_
47	A-IP	a-ip	JJ	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Rifampicine	Rifampicine	NNP	_	_	_
50	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
51	Rep	Rep	NNP	_	_	_
52	1	1	CD	_	_	_
53	+	+	CC	_	_	_
54	A+IP	A+IP	NNP	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Rifampicine	Rifampicine	NNP	_	_	_
57	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
58	Rep	Rep	NNP	_	_	_
59	2	2	CD	_	_	_
60	+	+	CC	_	_	_
61	A-IP	a-ip	JJ	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Rifampicine	Rifampicine	NNP	_	_	_
64	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
65	Rep	Rep	NNP	_	_	_
66	2	2	CD	_	_	_
67	+	+	CC	_	_	_
68	A+IP	A+IP	NNP	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Rifampicine	Rifampicine	NNP	_	_	_
71	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
72	Rep	Rep	NNP	_	_	_
73	3	3	CD	_	_	_
74	+	+	CC	_	_	_
75	A-IP	a-ip	JJ	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Rifampicine	Rifampicine	NNP	_	_	_
78	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
79	Rep	Rep	NNP	_	_	_
80	3	3	CD	_	_	_
81	+	+	CC	_	_	_
82	A+IP	A+IP	NNP	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	RifCfx	RifCfx	NNP	_	_	_
85	_	_	NNP	_	_	_
86	IN	in	IN	_	_	_
87	_	_	CD	_	_	_
88	Mu	mu	NN	_	_	_
89	_	_	NN	_	_	_
90	122mkM	122mkm	NN	_	_	_
91	_	_	CD	_	_	_
92	10mkM	10mkm	NN	_	_	_
93	_	_	NN	_	_	_
94	1	1	CD	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	RifCfx	rifcfx	NN	_	_	_
97	_	_	CD	_	_	_
98	IN	in	IN	_	_	_
99	_	_	CD	_	_	_
100	Mu	mu	NN	_	_	_
101	_	_	NN	_	_	_
102	122mkM	122mkm	NN	_	_	_
103	_	_	CD	_	_	_
104	10mkM	10mkm	NN	_	_	_
105	_	_	NN	_	_	_
106	2	2	CD	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	RifCfx	rifcfx	NN	_	_	_
109	_	_	CD	_	_	_
110	IN	in	IN	_	_	_
111	_	_	CD	_	_	_
112	Mu	mu	NN	_	_	_
113	_	_	NN	_	_	_
114	122mkM	122mkm	NN	_	_	_
115	_	_	CD	_	_	_
116	10mkM	10mkm	NN	_	_	_
117	_	_	NN	_	_	_
118	3	3	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	RifCfx	rifcfx	NN	_	_	_
121	_	_	CD	_	_	_
122	IP	IP	NNP	_	_	_
123	_	_	SYM	_	_	_
124	Mu	mu	FW	_	_	_
125	_	_	FW	_	_	_
126	122mkM	122mkm	NN	_	_	_
127	_	_	CD	_	_	_
128	10mkM	10mkm	NN	_	_	_
129	_	_	NN	_	_	_
130	1	1	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	RifCfx	rifcfx	NN	_	_	_
133	_	_	CD	_	_	_
134	IP	IP	NNP	_	_	_
135	_	_	SYM	_	_	_
136	Mu	mu	FW	_	_	_
137	_	_	FW	_	_	_
138	122mkM	122mkm	NN	_	_	_
139	_	_	CD	_	_	_
140	10mkM	10mkm	NN	_	_	_
141	_	_	NN	_	_	_
142	2	2	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	RifCfx	rifcfx	NN	_	_	_
145	_	_	CD	_	_	_
146	IP	IP	NNP	_	_	_
147	_	_	SYM	_	_	_
148	Mu	mu	FW	_	_	_
149	_	_	FW	_	_	_
150	122mkM	122mkm	NN	_	_	_
151	_	_	CD	_	_	_
152	10mkM	10mkm	NN	_	_	_
153	_	_	NN	_	_	_
154	3	3	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	Rif	rif	NN	_	_	_
157	_	_	CD	_	_	_
158	IN	in	IN	_	_	_
159	_	_	CD	_	_	_
160	Mu	mu	NN	_	_	_
161	_	_	CD	_	_	_
162	122mkM	122mkm	NN	_	_	_
163	_	_	NN	_	_	_
164	1	1	CD	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	rimI	rimi	NN	GEN	_	_
167	__	__	CD	_	_	_
168	U	U	NNP	_	_	_
169	_	_	NNP	_	_	_
170	N0075	N0075	NNP	_	_	_
171	_	_	SYM	_	_	_
172	r1	r1	FW	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
174	rimI	rimi	NN	GEN	_	_
175	__	__	CD	_	_	_
176	U	U	NNP	_	_	_
177	_	_	NNP	_	_	_
178	N0075	N0075	NNP	_	_	_
179	_	_	SYM	_	_	_
180	r2	r2	FW	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
182	rimI	rimi	NN	GEN	_	_
183	__	__	CD	_	_	_
184	U	U	NNP	_	_	_
185	_	_	NNP	_	_	_
186	N0075	N0075	NNP	_	_	_
187	_	_	SYM	_	_	_
188	r3	r3	FW	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
190	rimI	rimi	NN	GEN	_	_
191	upregulation	upregulation	NN	_	_	_
192	,	,	,	_	_	_
193	0.075	0.075	CD	_	_	_
194	mg/mL	mg/ml	NN	_	_	_
195	norfloxacin	norfloxacin	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
197	rip	rip	VBP	_	_	_
198	antibody	antibody	NN	_	_	_
199	:	:	:	_	_	_
200	Monoclonal	monoclonal	JJ	_	_	_
201	ANTI-FLAG	anti-flag	NN	_	_	_
202	^	^	NN	_	_	_
203	=	=	JJ	_	_	_
204	AE	ae	NN	_	_	_
205	M2	m2	NN	_	_	_
206	antibody	antibody	NN	_	_	_
207	produced	produce	VBN	_	_	_
208	in	in	IN	_	_	_
209	mouse	mouse	NN	_	_	_
210	,	,	,	_	_	_
211	Sigma	Sigma	NNP	_	_	_
212	,	,	,	_	_	_
213	F1804-200UG	f1804-200ug	NN	_	_	_
214	,	,	,	_	_	_
215	SLBG5673V	slbg5673v	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	riplot	riplot	NN	_	_	_
218	-LRB-	-lrb-	-LRB-	_	_	_
219	LogData	LogData	NNP	_	_	_
220	,	,	,	_	_	_
221	onScreen	onscreen	NN	_	_	_
222	=	=	JJ	_	_	_
223	FALSE	false	NN	_	_	_
224	-RRB-	-rrb-	-RRB-	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	riplot	riplot	NN	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	NormalData	NormalData	NNP	_	_	_
229	,	,	,	_	_	_
230	onScreen	onscreen	NN	_	_	_
231	=	=	JJ	_	_	_
232	FALSE	false	NN	_	_	_
233	-RRB-	-rrb-	-RRB-	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	RIP-Seq	rip-seq	JJ	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
237	RMA	rma	NN	_	_	_
238	normalization	normalization	NN	_	_	_
239	was	be	VBD	_	_	_
240	performed	perform	VBN	_	_	_
241	on	on	IN	_	_	_
242	CELL	cell	NN	_	_	_
243	files	files	NNS	_	_	_
244	using	use	VBG	_	_	_
245	the	the	DT	_	_	_
246	Partek	Partek	NNP	_	_	_
247	Genomic	genomic	JJ	_	_	_
248	Suite	suite	NN	_	_	_
249	6.5	6.5	CD	_	_	_
250	.	.	.	_	_	_

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	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	RMA	rma	NN	_	_	_
3	with	with	IN	_	_	_
4	quartile	quartile	JJ	_	_	_
5	normalization	normalization	NN	_	_	_
6	according	accord	VBG	_	_	_
7	to	to	TO	_	_	_
8	method	method	NN	_	_	_
9	of	of	IN	_	_	_
10	Irizarry	Irizarry	NNP	_	_	_
11	et	et	FW	_	_	_
12	al	al	FW	_	_	_
13	,	,	,	_	_	_
14	2003	2003	CD	_	_	_
15	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	_	_	NN	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	RNA	rna	NN	_	_	_
7	_	_	NN	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	RNA	rna	NN	_	_	_
11	degradation	degradation	NN	_	_	_
12	was	be	VBD	_	_	_
13	stopped	stop	VBN	_	_	_
14	using	use	VBG	_	_	_
15	Qiagen	Qiagen	NNP	_	_	_
16	's	's	POS	_	_	_
17	RNAprotect	rnaprotect	NN	_	_	_
18	reagent	reagent	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	RNAeasy	rnaeasy	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	RNAEasy	rnaeasy	NN	_	_	_
23	with	with	IN	_	_	_
24	RNAProtect	rnaprotect	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Qiagen	qiagen	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	RNA	rna	NN	_	_	_
30	extracted	extract	VBN	_	_	_
31	according	accord	VBG	_	_	_
32	to	to	TO	_	_	_
33	QiAgen	QiAgen	NNP	_	_	_
34	RNeasy	RNeasy	NNP	_	_	_
35	MiniKit	MiniKit	NNP	_	_	_
36	protocol	protocol	NN	_	_	_
37	for	for	IN	_	_	_
38	bacterial	bacterial	JJ	_	_	_
39	samples	sample	NNS	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	RNA	rna	NN	_	_	_
42	extracted	extract	VBN	_	_	_
43	by	by	IN	_	_	_
44	hot	hot	JJ	_	_	_
45	phenol	phenol	NN	_	_	_
46	choloroform	choloroform	NN	_	_	_
47	folled	foll	VBN	_	_	_
48	by	by	IN	_	_	_
49	Qiagen	Qiagen	NNP	_	_	_
50	RNA	rna	NN	_	_	_
51	Midi	midi	NN	_	_	_
52	column	column	NN	_	_	_
53	.	.	.	_	_	_

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	BW25113	bw25113	NN	_	_	_
9	wild	wild	JJ	_	_	_
10	type	type	NN	_	_	_
11	after	after	IN	_	_	_
12	24h	24h	NN	_	_	_
13	of	of	IN	_	_	_
14	growth	growth	NN	_	_	_
15	in	in	IN	_	_	_
16	LBglu	lbglu	NN	_	_	_
17	with	with	IN	_	_	_
18	glass	glass	NN	_	_	_
19	wool	wool	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	RNA	rna	NN	_	_	_
22	extracted	extract	VBN	_	_	_
23	from	from	IN	_	_	_
24	biofilm	biofilm	NN	_	_	_
25	cells	cell	NNS	_	_	_
26	of	of	IN	_	_	_
27	BW25113	bw25113	NN	_	_	_
28	ymgB	ymgb	NN	_	_	_
29	mutant	mutant	NN	_	_	_
30	after	after	IN	_	_	_
31	24h	24h	NN	_	_	_
32	of	of	IN	_	_	_
33	growth	growth	NN	_	_	_
34	in	in	IN	_	_	_
35	LBglu	lbglu	NN	_	_	_
36	with	with	IN	_	_	_
37	glass	glass	NN	_	_	_
38	wool	wool	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	RNA	rna	NN	_	_	_
41	extracted	extract	VBN	_	_	_
42	from	from	IN	_	_	_
43	biofilm	biofilm	NN	_	_	_
44	cells	cell	NNS	_	_	_
45	of	of	IN	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	K-12	k-12	NN	_	_	_
49	BW25113	bw25113	NN	_	_	_
50	tnaA	tnaa	NN	GEN	_	_
51	mutant	mutant	NN	_	_	_
52	after	after	IN	_	_	_
53	7	7	CD	_	_	_
54	hours	hour	NNS	_	_	_
55	of	of	IN	_	_	_
56	growth	growth	NN	_	_	_
57	in	in	IN	_	_	_
58	LB	lb	NN	_	_	_
59	with	with	IN	_	_	_
60	glasswool	glasswool	NN	_	_	_
61	and	and	CC	_	_	_
62	100	100	CD	_	_	_
63	uM	um	NN	_	_	_
64	indole	indole	NN	_	_	_
65	at	at	IN	_	_	_
66	37ºC	37ºc	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	RNA	rna	NN	_	_	_
69	extracted	extract	VBN	_	_	_
70	from	from	IN	_	_	_
71	biofilm	biofilm	NN	_	_	_
72	cells	cell	NNS	_	_	_
73	of	of	IN	_	_	_
74	E.	e.	FW	_	_	_
75	coli	coli	FW	_	_	_
76	K-12	k-12	NN	_	_	_
77	BW25113	bw25113	NN	_	_	_
78	tnaA	tnaa	NN	GEN	_	_
79	mutant	mutant	NN	_	_	_
80	after	after	IN	_	_	_
81	7	7	CD	_	_	_
82	hours	hour	NNS	_	_	_
83	of	of	IN	_	_	_
84	growth	growth	NN	_	_	_
85	in	in	IN	_	_	_
86	LB	lb	NN	_	_	_
87	with	with	IN	_	_	_
88	glasswool	glasswool	NN	_	_	_
89	and	and	CC	_	_	_
90	DMF	dmf	NN	_	_	_
91	at	at	IN	_	_	_
92	30ºC	30ºC	NNP	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	RNA	RNA	NNP	_	_	_
95	extracted	extract	VBN	_	_	_
96	from	from	IN	_	_	_
97	biofilm	biofilm	NN	_	_	_
98	cells	cell	NNS	_	_	_
99	of	of	IN	_	_	_
100	E.	e.	FW	_	_	_
101	coli	coli	FW	_	_	_
102	K-12	k-12	NN	_	_	_
103	BW25113	bw25113	NN	_	_	_
104	tnaA	tnaa	NN	GEN	_	_
105	mutant	mutant	NN	_	_	_
106	after	after	IN	_	_	_
107	7	7	CD	_	_	_
108	hours	hour	NNS	_	_	_
109	of	of	IN	_	_	_
110	growth	growth	NN	_	_	_
111	in	in	IN	_	_	_
112	LB	lb	NN	_	_	_
113	with	with	IN	_	_	_
114	glasswool	glasswool	NN	_	_	_
115	and	and	CC	_	_	_
116	DMF	dmf	NN	_	_	_
117	at	at	IN	_	_	_
118	37ºC	37ºc	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	RNA	rna	NN	_	_	_
121	extracted	extract	VBN	_	_	_
122	from	from	IN	_	_	_
123	biofilm	biofilm	NN	_	_	_
124	cells	cell	NNS	_	_	_
125	of	of	IN	_	_	_
126	E.	e.	FW	_	_	_
127	coli	coli	FW	_	_	_
128	K-12	k-12	NN	_	_	_
129	BW25113	bw25113	NN	_	_	_
130	tnaA	tnaa	NN	GEN	_	_
131	mutant	mutant	NN	_	_	_
132	after	after	IN	_	_	_
133	7	7	CD	_	_	_
134	hours	hour	NNS	_	_	_
135	of	of	IN	_	_	_
136	growth	growth	NN	_	_	_
137	in	in	IN	_	_	_
138	LB	lb	NN	_	_	_
139	with	with	IN	_	_	_
140	glasswool	glasswool	NN	_	_	_
141	and	and	CC	_	_	_
142	with	with	IN	_	_	_
143	100	100	CD	_	_	_
144	uM	um	NN	_	_	_
145	indole	indole	NN	_	_	_
146	at	at	IN	_	_	_
147	30ºC	30ºC	NNP	_	_	_
148	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
149	RNA	RNA	NNP	_	_	_
150	extracted	extract	VBN	_	_	_
151	from	from	IN	_	_	_
152	biofilm	biofilm	NN	_	_	_
153	cells	cell	NNS	_	_	_
154	of	of	IN	_	_	_
155	E.	e.	FW	_	_	_
156	coli	coli	FW	_	_	_
157	K-12	k-12	NN	_	_	_
158	BW25113	bw25113	NN	_	_	_
159	w/t	w/t	NN	_	_	_
160	after	after	IN	_	_	_
161	7	7	CD	_	_	_
162	hours	hour	NNS	_	_	_
163	of	of	IN	_	_	_
164	growth	growth	NN	_	_	_
165	in	in	IN	_	_	_
166	LB	lb	NN	_	_	_
167	with	with	IN	_	_	_
168	glasswool	glasswool	NN	_	_	_
169	at	at	IN	_	_	_
170	30ºC	30ºC	NNP	_	_	_
171	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
172	RNA	RNA	NNP	_	_	_
173	extracted	extract	VBN	_	_	_
174	from	from	IN	_	_	_
175	biofilm	biofilm	NN	_	_	_
176	cells	cell	NNS	_	_	_
177	of	of	IN	_	_	_
178	E.	e.	FW	_	_	_
179	coli	coli	FW	_	_	_
180	K-12	k-12	NN	_	_	_
181	hha	hha	NN	GEN	_	_
182	mutant	mutant	NN	_	_	_
183	after	after	IN	_	_	_
184	15	15	CD	_	_	_
185	hours	hour	NNS	_	_	_
186	of	of	IN	_	_	_
187	growth	growth	NN	_	_	_
188	at	at	IN	_	_	_
189	37C	37c	NN	_	_	_
190	in	in	IN	_	_	_
191	LB	LB	NNP	_	_	_
192	glu	glu	NN	_	_	_
193	with	with	IN	_	_	_
194	glasswool	glasswool	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	RNA	rna	NN	_	_	_
197	extracted	extract	VBN	_	_	_
198	from	from	IN	_	_	_
199	biofilm	biofilm	NN	_	_	_
200	cells	cell	NNS	_	_	_
201	of	of	IN	_	_	_
202	E.	e.	FW	_	_	_
203	coli	coli	FW	_	_	_
204	K-12	k-12	NN	_	_	_
205	hha	hha	NN	GEN	_	_
206	mutant	mutant	NN	_	_	_
207	after	after	IN	_	_	_
208	24	24	CD	_	_	_
209	hours	hour	NNS	_	_	_
210	of	of	IN	_	_	_
211	growth	growth	NN	_	_	_
212	at	at	IN	_	_	_
213	37C	37c	NN	_	_	_
214	in	in	IN	_	_	_
215	LB	LB	NNP	_	_	_
216	glu	glu	NN	_	_	_
217	with	with	IN	_	_	_
218	glasswool	glasswool	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	RNA	rna	NN	_	_	_
221	extracted	extract	VBN	_	_	_
222	from	from	IN	_	_	_
223	biofilm	biofilm	NN	_	_	_
224	cells	cell	NNS	_	_	_
225	of	of	IN	_	_	_
226	E.	e.	FW	_	_	_
227	coli	coli	FW	_	_	_
228	K-12	k-12	NN	_	_	_
229	hha	hha	NN	GEN	_	_
230	mutant	mutant	NN	_	_	_
231	after	after	IN	_	_	_
232	4	4	CD	_	_	_
233	hours	hour	NNS	_	_	_
234	of	of	IN	_	_	_
235	growth	growth	NN	_	_	_
236	at	at	IN	_	_	_
237	37C	37c	NN	_	_	_
238	in	in	IN	_	_	_
239	LB	LB	NNP	_	_	_
240	glu	glu	NN	_	_	_
241	with	with	IN	_	_	_
242	glasswool	glasswool	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	RNA	rna	NN	_	_	_
245	extracted	extract	VBN	_	_	_
246	from	from	IN	_	_	_
247	biofilm	biofilm	NN	_	_	_
248	cells	cell	NNS	_	_	_
249	of	of	IN	_	_	_
250	E.	e.	FW	_	_	_
251	coli	coli	FW	_	_	_
252	K-12	k-12	NN	_	_	_
253	hha	hha	NN	GEN	_	_
254	mutant	mutant	NN	_	_	_
255	after	after	IN	_	_	_
256	4	4	CD	_	_	_
257	hours	hour	NNS	_	_	_
258	of	of	IN	_	_	_
259	growth	growth	NN	_	_	_
260	at	at	IN	_	_	_
261	37C	37c	NN	_	_	_
262	in	in	IN	_	_	_
263	LB	lb	NN	_	_	_
264	with	with	IN	_	_	_
265	glasswool	glasswool	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	RNA	rna	NN	_	_	_
268	extracted	extract	VBN	_	_	_
269	from	from	IN	_	_	_
270	biofilm	biofilm	NN	_	_	_
271	cells	cell	NNS	_	_	_
272	of	of	IN	_	_	_
273	E.	e.	FW	_	_	_
274	coli	coli	FW	_	_	_
275	K-12	k-12	NN	_	_	_
276	sdiA	sdia	NN	GEN	_	_
277	mutant	mutant	NN	_	_	_
278	after	after	IN	_	_	_
279	7	7	CD	_	_	_
280	hours	hour	NNS	_	_	_
281	of	of	IN	_	_	_
282	growth	growth	NN	_	_	_
283	in	in	IN	_	_	_
284	LB	lb	NN	_	_	_
285	with	with	IN	_	_	_
286	glasswool	glasswool	NN	_	_	_
287	at	at	IN	_	_	_
288	30ºC	30ºc	NN	_	_	_
289	with	with	IN	_	_	_
290	1	1	CD	_	_	_
291	mM	mm	NN	KWSUPP	_	_
292	indole	indole	NN	_	_	_
293	presence	presence	NN	_	_	_
294	.	.	.	_	_	_

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	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	15	15	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	NNP	_	_	_
22	glu	glu	NN	_	_	_
23	with	with	IN	_	_	_
24	glasswool	glasswool	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	RNA	rna	NN	_	_	_
27	extracted	extract	VBN	_	_	_
28	from	from	IN	_	_	_
29	biofilm	biofilm	NN	_	_	_
30	cells	cell	NNS	_	_	_
31	of	of	IN	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	K-12	k-12	NN	_	_	_
35	wild	wild	JJ	_	_	_
36	type	type	NN	_	_	_
37	after	after	IN	_	_	_
38	24	24	CD	_	_	_
39	hours	hour	NNS	_	_	_
40	of	of	IN	_	_	_
41	growth	growth	NN	_	_	_
42	at	at	IN	_	_	_
43	37C	37c	NN	_	_	_
44	in	in	IN	_	_	_
45	LB	LB	NNP	_	_	_
46	glu	glu	NN	_	_	_
47	with	with	IN	_	_	_
48	glasswool	glasswool	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	RNA	rna	NN	_	_	_
51	extracted	extract	VBN	_	_	_
52	from	from	IN	_	_	_
53	biofilm	biofilm	NN	_	_	_
54	cells	cell	NNS	_	_	_
55	of	of	IN	_	_	_
56	E.	e.	FW	_	_	_
57	coli	coli	FW	_	_	_
58	K-12	k-12	NN	_	_	_
59	wild	wild	JJ	_	_	_
60	type	type	NN	_	_	_
61	after	after	IN	_	_	_
62	4	4	CD	_	_	_
63	hours	hour	NNS	_	_	_
64	of	of	IN	_	_	_
65	growth	growth	NN	_	_	_
66	at	at	IN	_	_	_
67	37C	37c	NN	_	_	_
68	in	in	IN	_	_	_
69	LB	LB	NNP	_	_	_
70	glu	glu	NN	_	_	_
71	with	with	IN	_	_	_
72	glasswool	glasswool	NN	_	_	_
73	.	.	.	_	_	_

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	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	EHEC	ehec	NN	_	_	_
9	wild	wild	JJ	_	_	_
10	type	type	NN	_	_	_
11	after	after	IN	_	_	_
12	7h	7h	NN	_	_	_
13	of	of	IN	_	_	_
14	growth	growth	NN	_	_	_
15	in	in	IN	_	_	_
16	LB	lb	NN	_	_	_
17	and	and	CC	_	_	_
18	0.1	0.1	CD	_	_	_
19	%	%	NN	_	_	_
20	DMF	dmf	NN	_	_	_
21	with	with	IN	_	_	_
22	glass	glass	NN	_	_	_
23	wool	wool	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	RNA	rna	NN	_	_	_
26	extracted	extract	VBN	_	_	_
27	from	from	IN	_	_	_
28	biofilm	biofilm	NN	_	_	_
29	cells	cell	NNS	_	_	_
30	of	of	IN	_	_	_
31	EHEC	ehec	NN	_	_	_
32	wild	wild	JJ	_	_	_
33	type	type	NN	_	_	_
34	after	after	IN	_	_	_
35	7h	7h	NN	_	_	_
36	of	of	IN	_	_	_
37	growth	growth	NN	_	_	_
38	in	in	IN	_	_	_
39	LB	lb	NN	_	_	_
40	and	and	CC	_	_	_
41	1000	1000	CD	_	_	_
42	micro	micro	JJ	_	_	_
43	M	m	NN	_	_	_
44	7-hydroxyindole	7-hydroxyindole	NN	_	_	_
45	with	with	IN	_	_	_
46	glass	glass	NN	_	_	_
47	wool	wool	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	RNA	rna	NN	_	_	_
50	extracted	extract	VBN	_	_	_
51	from	from	IN	_	_	_
52	biofilm	biofilm	NN	_	_	_
53	cells	cell	NNS	_	_	_
54	of	of	IN	_	_	_
55	EHEC	ehec	NN	_	_	_
56	wild	wild	JJ	_	_	_
57	type	type	NN	_	_	_
58	after	after	IN	_	_	_
59	7h	7h	NN	_	_	_
60	of	of	IN	_	_	_
61	growth	growth	NN	_	_	_
62	in	in	IN	_	_	_
63	LB	lb	NN	_	_	_
64	and	and	CC	_	_	_
65	250	250	CD	_	_	_
66	micro	micro	JJ	_	_	_
67	M	m	NN	_	_	_
68	isatin	isatin	NN	_	_	_
69	with	with	IN	_	_	_
70	glass	glass	NN	_	_	_
71	wool	wool	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	RNA	rna	NN	_	_	_
74	extracted	extract	VBN	_	_	_
75	from	from	IN	_	_	_
76	biofilm	biofilm	NN	_	_	_
77	cells	cell	NNS	_	_	_
78	of	of	IN	_	_	_
79	K-12	k-12	NN	_	_	_
80	sdiA-no	sdia-no	JJ	_	_	_
81	SdiA	sdia	NN	TF	_	_
82	1	1	CD	_	_	_
83	after	after	IN	_	_	_
84	12h	12h	NN	_	_	_
85	of	of	IN	_	_	_
86	growth	growth	NN	_	_	_
87	in	in	IN	_	_	_
88	LB	lb	NN	_	_	_
89	+	+	CC	_	_	_
90	1	1	CD	_	_	_
91	mMIPTG	mmiptg	NN	_	_	_
92	and	and	CC	_	_	_
93	30	30	CD	_	_	_
94	microM	microm	NN	_	_	_
95	Cm	cm	NN	_	_	_
96	with	with	IN	_	_	_
97	glass	glass	NN	_	_	_
98	wool	wool	NN	_	_	_
99	at	at	IN	_	_	_
100	30oC	30oC	NNP	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	RNA	RNA	NNP	_	_	_
103	extracted	extract	VBN	_	_	_
104	from	from	IN	_	_	_
105	biofilm	biofilm	NN	_	_	_
106	cells	cell	NNS	_	_	_
107	of	of	IN	_	_	_
108	K-12	k-12	NN	_	_	_
109	sdiA-SdiA1E11	sdia-sdia1e11	NN	_	_	_
110	after	after	IN	_	_	_
111	12h	12h	NN	_	_	_
112	of	of	IN	_	_	_
113	growth	growth	NN	_	_	_
114	in	in	IN	_	_	_
115	LB	lb	NN	_	_	_
116	+	+	CC	_	_	_
117	1	1	CD	_	_	_
118	mMIPTG	mmiptg	NN	_	_	_
119	and	and	CC	_	_	_
120	30	30	CD	_	_	_
121	microM	microm	NN	_	_	_
122	Cm	cm	NN	_	_	_
123	with	with	IN	_	_	_
124	glass	glass	NN	_	_	_
125	wool	wool	NN	_	_	_
126	at	at	IN	_	_	_
127	30oC	30oC	NNP	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	RNA	RNA	NNP	_	_	_
130	extracted	extract	VBN	_	_	_
131	from	from	IN	_	_	_
132	biofilm	biofilm	NN	_	_	_
133	cells	cell	NNS	_	_	_
134	of	of	IN	_	_	_
135	K-12	k-12	NN	_	_	_
136	sdiA-WTSdiA	sdia-wtsdia	NN	_	_	_
137	after	after	IN	_	_	_
138	12h	12h	NN	_	_	_
139	of	of	IN	_	_	_
140	growth	growth	NN	_	_	_
141	in	in	IN	_	_	_
142	LB	lb	NN	_	_	_
143	+	+	CC	_	_	_
144	1	1	CD	_	_	_
145	mMIPTG	mmiptg	NN	_	_	_
146	and	and	CC	_	_	_
147	30	30	CD	_	_	_
148	microM	microm	NN	_	_	_
149	Cm	cm	NN	_	_	_
150	with	with	IN	_	_	_
151	glass	glass	NN	_	_	_
152	wool	wool	NN	_	_	_
153	at	at	IN	_	_	_
154	30oC	30oC	NNP	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	RNA	RNA	NNP	_	_	_
157	extracted	extract	VBN	_	_	_
158	from	from	IN	_	_	_
159	cells	cell	NNS	_	_	_
160	of	of	IN	_	_	_
161	BW25113	bw25113	NN	_	_	_
162	at	at	IN	_	_	_
163	OD	od	NN	_	_	_
164	1.0	1.0	CD	_	_	_
165	after	after	IN	_	_	_
166	contacting	contact	VBG	_	_	_
167	for	for	IN	_	_	_
168	10	10	CD	_	_	_
169	min	min	NN	_	_	_
170	with	with	IN	_	_	_
171	2	2	CD	_	_	_
172	mM	mm	NN	KWSUPP	_	_
173	H2O2	h2o2	NN	_	_	_
174	in	in	IN	_	_	_
175	LB	lb	NN	_	_	_
176	at	at	IN	_	_	_
177	37oC	37oc	NN	_	_	_
178	.	.	.	_	_	_

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/pBS	tg1/pbs	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Kan	Kan	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	/	/	:	_	_	_
12	pMMB277	pmmb277	NN	_	_	_
13	after	after	IN	_	_	_
14	contacting	contact	VBG	_	_	_
15	for	for	IN	_	_	_
16	2	2	CD	_	_	_
17	h	h	NN	_	_	_
18	with	with	IN	_	_	_
19	cis-DCE	cis-dce	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	1	1	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	in	in	IN	_	_	_
25	Tris-HNO3	tris-hno3	NN	_	_	_
26	buffer	buffer	NN	_	_	_
27	with	with	IN	_	_	_
28	succinate	succinate	NN	SUPP	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	5	5	CD	_	_	_
31	mM	mm	NN	KWSUPP	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	,	,	,	_	_	_
34	IPTG	iptg	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	0.5	0.5	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	at	at	IN	_	_	_
40	37oC	37oc	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	RNA	rna	NN	_	_	_
43	extracted	extract	VBN	_	_	_
44	from	from	IN	_	_	_
45	cells	cell	NNS	_	_	_
46	of	of	IN	_	_	_
47	TG1/pBS	tg1/pbs	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	Kan	Kan	NNP	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	-	-	:	_	_	_
52	TOM-Green/pMMB277-IsoILR	tom-green/pmmb277-isoilr	NN	_	_	_
53	1-GSHI	1-gshi	NN	_	_	_
54	after	after	IN	_	_	_
55	contacting	contact	VBG	_	_	_
56	for	for	IN	_	_	_
57	2	2	CD	_	_	_
58	h	h	NN	_	_	_
59	with	with	IN	_	_	_
60	cis-DCE	cis-dce	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	1	1	CD	_	_	_
63	mM	mm	NN	KWSUPP	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	in	in	IN	_	_	_
66	Tris-HNO3	tris-hno3	NN	_	_	_
67	buffer	buffer	NN	_	_	_
68	with	with	IN	_	_	_
69	succinate	succinate	NN	SUPP	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	5	5	CD	_	_	_
72	mM	mm	NN	KWSUPP	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	,	,	,	_	_	_
75	IPTG	iptg	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	0.5	0.5	CD	_	_	_
78	mM	mm	NN	KWSUPP	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	at	at	IN	_	_	_
81	37oC	37oc	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	RNA	rna	NN	_	_	_
84	extracted	extract	VBN	_	_	_
85	from	from	IN	_	_	_
86	cells	cell	NNS	_	_	_
87	of	of	IN	_	_	_
88	TG1	tg1	NN	_	_	_
89	/	/	:	_	_	_
90	pMMB206-TOM-Green/pBS	pmmb206-tom-green/pbs	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	Kan	Kan	NNP	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	after	after	IN	_	_	_
95	contacting	contact	VBG	_	_	_
96	for	for	IN	_	_	_
97	2	2	CD	_	_	_
98	h	h	NN	_	_	_
99	with	with	IN	_	_	_
100	cis-DCE	cis-dce	NN	_	_	_
101	-LRB-	-lrb-	-LRB-	_	_	_
102	1	1	CD	_	_	_
103	mM	mm	NN	KWSUPP	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	in	in	IN	_	_	_
106	Tris-HNO3	tris-hno3	NN	_	_	_
107	buffer	buffer	NN	_	_	_
108	with	with	IN	_	_	_
109	succinate	succinate	NN	SUPP	_	_
110	-LRB-	-lrb-	-LRB-	_	_	_
111	5	5	CD	_	_	_
112	mM	mm	NN	KWSUPP	_	_
113	-RRB-	-rrb-	-RRB-	_	_	_
114	,	,	,	_	_	_
115	IPTG	iptg	NN	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	0.5	0.5	CD	_	_	_
118	mM	mm	NN	KWSUPP	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	at	at	IN	_	_	_
121	37oC	37oc	NN	_	_	_
122	.	.	.	_	_	_

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/pMMB206-TOM-Green/pBS	tg1/pmmb206-tom-green/pbs	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Kan	Kan	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	-	-	:	_	_	_
12	EchA	echa	NN	_	_	_
13	F108L/I219L/C248I	f108l/i219l/c248i	NN	_	_	_
14	after	after	IN	_	_	_
15	contacting	contact	VBG	_	_	_
16	for	for	IN	_	_	_
17	2	2	CD	_	_	_
18	h	h	NN	_	_	_
19	with	with	IN	_	_	_
20	cis-DCE	cis-dce	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	1	1	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	in	in	IN	_	_	_
26	Tris-HNO3	tris-hno3	NN	_	_	_
27	buffer	buffer	NN	_	_	_
28	with	with	IN	_	_	_
29	succinate	succinate	NN	SUPP	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	5	5	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	,	,	,	_	_	_
35	IPTG	iptg	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	0.5	0.5	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	at	at	IN	_	_	_
41	37oC	37oc	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	rna	rna	NN	GEN	_	_
44	extracted	extract	VBN	_	_	_
45	from	from	IN	_	_	_
46	e.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	o157	o157	NN	_	_	_
49	:	:	:	_	_	_
50	H7	h7	NN	_	_	_
51	EDL933	edl933	NN	_	_	_
52	cells	cell	NNS	_	_	_
53	grown	grow	VBN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	7	7	CD	_	_	_
56	hrs	hr	NNS	_	_	_
57	incubation	incubation	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	in	in	IN	_	_	_
60	LB	lb	NN	_	_	_
61	at	at	IN	_	_	_
62	37ºC	37ºc	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	rna	rna	NN	GEN	_	_
65	extracted	extract	VBN	_	_	_
66	from	from	IN	_	_	_
67	e.	e.	FW	_	_	_
68	coli	coli	FW	_	_	_
69	o157	o157	NN	_	_	_
70	:	:	:	_	_	_
71	H7	h7	NN	_	_	_
72	EDL933	edl933	NN	_	_	_
73	cells	cell	NNS	_	_	_
74	grown	grow	VBN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	7	7	CD	_	_	_
77	hrs	hr	NNS	_	_	_
78	incubation	incubation	NN	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	in	in	IN	_	_	_
81	LB	lb	NN	_	_	_
82	at	at	IN	_	_	_
83	37ºC	37ºc	NN	_	_	_
84	with	with	IN	_	_	_
85	0.05	0.05	CD	_	_	_
86	mg/ml	mg/ml	NN	_	_	_
87	Phloretin	phloretin	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	RNA	rna	NN	_	_	_
90	extracted	extract	VBN	_	_	_
91	from	from	IN	_	_	_
92	e.	e.	FW	_	_	_
93	coli	coli	FW	_	_	_
94	o157	o157	NN	_	_	_
95	:	:	:	_	_	_
96	H7	h7	NN	_	_	_
97	EDL933	edl933	NN	_	_	_
98	cells	cell	NNS	_	_	_
99	grown	grow	VBN	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	7	7	CD	_	_	_
102	hrs	hr	NNS	_	_	_
103	incubation	incubation	NN	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	in	in	IN	_	_	_
106	LB	lb	NN	_	_	_
107	at	at	IN	_	_	_
108	37ºC	37ºc	NN	_	_	_
109	with	with	IN	_	_	_
110	0.1	0.1	CD	_	_	_
111	mg/ml	mg/ml	NN	_	_	_
112	of	of	IN	_	_	_
113	IAAld	iaald	JJ	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	rna	rna	NN	GEN	_	_
116	extracted	extract	VBN	_	_	_
117	from	from	IN	_	_	_
118	e.	e.	FW	_	_	_
119	coli	coli	FW	_	_	_
120	o157	o157	NN	_	_	_
121	:	:	:	_	_	_
122	H7	h7	NN	_	_	_
123	EDL933	edl933	NN	_	_	_
124	cells	cell	NNS	_	_	_
125	grown	grow	VBN	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	7	7	CD	_	_	_
128	hrs	hr	NNS	_	_	_
129	incubation	incubation	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	in	in	IN	_	_	_
132	LB	lb	NN	_	_	_
133	at	at	IN	_	_	_
134	37ºC	37ºc	NN	_	_	_
135	with	with	IN	_	_	_
136	0.5	0.5	CD	_	_	_
137	%	%	NN	_	_	_
138	honey	honey	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	RNA	rna	NN	_	_	_
141	extracted	extract	VBN	_	_	_
142	from	from	IN	_	_	_
143	e.	e.	FW	_	_	_
144	coli	coli	FW	_	_	_
145	o157	o157	NN	_	_	_
146	:	:	:	_	_	_
147	H7	h7	NN	_	_	_
148	EDL933	edl933	NN	_	_	_
149	cells	cell	NNS	_	_	_
150	grown	grow	VBN	_	_	_
151	-LRB-	-lrb-	-LRB-	_	_	_
152	7	7	CD	_	_	_
153	hrs	hr	NNS	_	_	_
154	incubation	incubation	NN	_	_	_
155	-RRB-	-rrb-	-RRB-	_	_	_
156	in	in	IN	_	_	_
157	LB	lb	NN	_	_	_
158	at	at	IN	_	_	_
159	37ºC	37ºc	NN	_	_	_
160	with	with	IN	_	_	_
161	DMSO	dmso	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	RNA	rna	NN	_	_	_
164	extracted	extract	VBN	_	_	_
165	from	from	IN	_	_	_
166	free	free	JJ	_	_	_
167	living	living	NN	_	_	_
168	cells	cell	NNS	_	_	_
169	of	of	IN	_	_	_
170	E.	e.	FW	_	_	_
171	coli	coli	FW	_	_	_
172	K-12	k-12	NN	_	_	_
173	BW25113	bw25113	NN	_	_	_
174	luxS	luxs	NN	GEN	_	_
175	mutant	mutant	NN	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	when	when	WRB	_	_	_
178	growth	growth	NN	_	_	_
179	to	to	TO	_	_	_
180	OD600	od600	NN	_	_	_
181	0.5	0.5	CD	_	_	_
182	at	at	IN	_	_	_
183	30ºC	30ºC	NNP	_	_	_
184	in	in	IN	_	_	_
185	LB	LB	NNP	_	_	_
186	,	,	,	_	_	_
187	100	100	CD	_	_	_
188	uM	um	NN	_	_	_
189	AI2	ai2	NN	_	_	_
190	was	be	VBD	_	_	_
191	added	add	VBN	_	_	_
192	in	in	IN	_	_	_
193	and	and	CC	_	_	_
194	3-h	3-h	JJ	_	_	_
195	further	further	JJ	_	_	_
196	incubation	incubation	NN	_	_	_
197	was	be	VBD	_	_	_
198	applied	apply	VBN	_	_	_
199	-RRB-	-rrb-	-RRB-	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	RNA	rna	NN	_	_	_
202	extracted	extract	VBN	_	_	_
203	from	from	IN	_	_	_
204	free	free	JJ	_	_	_
205	living	living	NN	_	_	_
206	cells	cell	NNS	_	_	_
207	of	of	IN	_	_	_
208	E.	e.	FW	_	_	_
209	coli	coli	FW	_	_	_
210	K-12	k-12	NN	_	_	_
211	BW25113	bw25113	NN	_	_	_
212	luxS	luxs	NN	GEN	_	_
213	mutant	mutant	NN	_	_	_
214	-LRB-	-lrb-	-LRB-	_	_	_
215	when	when	WRB	_	_	_
216	growth	growth	NN	_	_	_
217	to	to	TO	_	_	_
218	OD600	od600	NN	_	_	_
219	0.5	0.5	CD	_	_	_
220	at	at	IN	_	_	_
221	30ºC	30ºC	NNP	_	_	_
222	in	in	IN	_	_	_
223	LB	LB	NNP	_	_	_
224	,	,	,	_	_	_
225	no	no	DT	_	_	_
226	AI2	ai2	NN	_	_	_
227	was	be	VBD	_	_	_
228	added	add	VBN	_	_	_
229	in	in	IN	_	_	_
230	and	and	CC	_	_	_
231	3-h	3-h	JJ	_	_	_
232	further	further	JJ	_	_	_
233	incubation	incubation	NN	_	_	_
234	was	be	VBD	_	_	_
235	applied	apply	VBN	_	_	_
236	-RRB-	-rrb-	-RRB-	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	RNA	rna	NN	_	_	_
239	extracted	extract	VBN	_	_	_
240	from	from	IN	_	_	_
241	free	free	JJ	_	_	_
242	living	living	NN	_	_	_
243	cells	cell	NNS	_	_	_
244	of	of	IN	_	_	_
245	E.	e.	FW	_	_	_
246	coli	coli	FW	_	_	_
247	K-12	k-12	NN	_	_	_
248	BW25113	bw25113	NN	_	_	_
249	luxS	luxs	NN	GEN	_	_
250	mutant	mutant	NN	_	_	_
251	-LRB-	-lrb-	-LRB-	_	_	_
252	when	when	WRB	_	_	_
253	growth	growth	NN	_	_	_
254	to	to	TO	_	_	_
255	OD600	od600	NN	_	_	_
256	0.5	0.5	CD	_	_	_
257	at	at	IN	_	_	_
258	37ºC	37ºc	NN	_	_	_
259	in	in	IN	_	_	_
260	LB	LB	NNP	_	_	_
261	,	,	,	_	_	_
262	100	100	CD	_	_	_
263	uM	um	NN	_	_	_
264	AI2	ai2	NN	_	_	_
265	was	be	VBD	_	_	_
266	added	add	VBN	_	_	_
267	in	in	IN	_	_	_
268	and	and	CC	_	_	_
269	3-h	3-h	JJ	_	_	_
270	further	further	JJ	_	_	_
271	incubation	incubation	NN	_	_	_
272	was	be	VBD	_	_	_
273	applied	apply	VBN	_	_	_
274	-RRB-	-rrb-	-RRB-	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	RNA	rna	NN	_	_	_
277	extracted	extract	VBN	_	_	_
278	from	from	IN	_	_	_
279	free	free	JJ	_	_	_
280	living	living	NN	_	_	_
281	cells	cell	NNS	_	_	_
282	of	of	IN	_	_	_
283	E.	e.	FW	_	_	_
284	coli	coli	FW	_	_	_
285	K-12	k-12	NN	_	_	_
286	BW25113	bw25113	NN	_	_	_
287	luxS	luxs	NN	GEN	_	_
288	mutant	mutant	NN	_	_	_
289	-LRB-	-lrb-	-LRB-	_	_	_
290	when	when	WRB	_	_	_
291	growth	growth	NN	_	_	_
292	to	to	TO	_	_	_
293	OD600	od600	NN	_	_	_
294	0.5	0.5	CD	_	_	_
295	at	at	IN	_	_	_
296	37ºC	37ºc	NN	_	_	_
297	in	in	IN	_	_	_
298	LB	LB	NNP	_	_	_
299	,	,	,	_	_	_
300	no	no	DT	_	_	_
301	AI2	ai2	NN	_	_	_
302	was	be	VBD	_	_	_
303	added	add	VBN	_	_	_
304	in	in	IN	_	_	_
305	and	and	CC	_	_	_
306	3-h	3-h	JJ	_	_	_
307	further	further	JJ	_	_	_
308	incubation	incubation	NN	_	_	_
309	was	be	VBD	_	_	_
310	applied	apply	VBN	_	_	_
311	-RRB-	-rrb-	-RRB-	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	RNA	rna	NN	_	_	_
314	extracted	extract	VBN	_	_	_
315	from	from	IN	_	_	_
316	free	free	JJ	_	_	_
317	living	living	NN	_	_	_
318	cells	cell	NNS	_	_	_
319	of	of	IN	_	_	_
320	E.	e.	FW	_	_	_
321	coli	coli	FW	_	_	_
322	K-12	k-12	NN	_	_	_
323	BW25113	bw25113	NN	_	_	_
324	sdiA	sdia	NN	GEN	_	_
325	mutant	mutant	NN	_	_	_
326	when	when	WRB	_	_	_
327	growth	growth	NN	_	_	_
328	to	to	TO	_	_	_
329	OD600	od600	NN	_	_	_
330	4.0	4.0	CD	_	_	_
331	at	at	IN	_	_	_
332	30ºC	30ºC	NNP	_	_	_
333	in	in	IN	_	_	_
334	LB	LB	NNP	_	_	_
335	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
336	RNA	RNA	NNP	_	_	_
337	extracted	extract	VBN	_	_	_
338	from	from	IN	_	_	_
339	free	free	JJ	_	_	_
340	living	living	NN	_	_	_
341	cells	cell	NNS	_	_	_
342	of	of	IN	_	_	_
343	E.	e.	FW	_	_	_
344	coli	coli	FW	_	_	_
345	K-12	k-12	NN	_	_	_
346	BW25113	bw25113	NN	_	_	_
347	wild	wild	JJ	_	_	_
348	type	type	NN	_	_	_
349	when	when	WRB	_	_	_
350	growth	growth	NN	_	_	_
351	to	to	TO	_	_	_
352	OD600	od600	NN	_	_	_
353	4.0	4.0	CD	_	_	_
354	at	at	IN	_	_	_
355	30ºC	30ºC	NNP	_	_	_
356	in	in	IN	_	_	_
357	LB	LB	NNP	_	_	_
358	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
359	RNA	RNA	NNP	_	_	_
360	extracted	extract	VBN	_	_	_
361	from	from	IN	_	_	_
362	suspension	suspension	NN	_	_	_
363	cells	cell	NNS	_	_	_
364	of	of	IN	_	_	_
365	E.	e.	FW	_	_	_
366	coli	coli	FW	_	_	_
367	K-12	k-12	NN	_	_	_
368	BW25113	bw25113	NN	_	_	_
369	mqsR	mqsr	NN	GEN	_	_
370	deleted	delete	VBN	_	_	_
371	mutant	mutant	JJ	_	_	_
372	after	after	IN	_	_	_
373	OD600	od600	NN	_	_	_
374	=	=	JJ	_	_	_
375	0.5	0.5	CD	_	_	_
376	of	of	IN	_	_	_
377	growth	growth	NN	_	_	_
378	in	in	IN	_	_	_
379	LB	lb	NN	_	_	_
380	at	at	IN	_	_	_
381	37oC	37oc	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	RNA	rna	NN	_	_	_
384	extracted	extract	VBN	_	_	_
385	from	from	IN	_	_	_
386	suspension	suspension	NN	_	_	_
387	cells	cell	NNS	_	_	_
388	of	of	IN	_	_	_
389	E.	e.	FW	_	_	_
390	coli	coli	FW	_	_	_
391	K-12	k-12	NN	_	_	_
392	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
393	-LRB-	-lrb-	-LRB-	_	_	_
394	empty	empty	JJ	_	_	_
395	vector	vector	NN	_	_	_
396	-RRB-	-rrb-	-RRB-	_	_	_
397	after	after	IN	_	_	_
398	OD600	od600	NN	_	_	_
399	=	=	JJ	_	_	_
400	0.5	0.5	CD	_	_	_
401	of	of	IN	_	_	_
402	growth	growth	NN	_	_	_
403	,	,	,	_	_	_
404	then	then	RB	_	_	_
405	2	2	CD	_	_	_
406	mM	mm	NN	KWSUPP	_	_
407	IPTG	iptg	NN	_	_	_
408	for	for	IN	_	_	_
409	15	15	CD	_	_	_
410	min	min	NN	_	_	_
411	short	short	JJ	_	_	_
412	time	time	NN	_	_	_
413	in	in	IN	_	_	_
414	LB	lb	NN	_	_	_
415	at	at	IN	_	_	_
416	37oC	37oc	NN	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	RNA	rna	NN	_	_	_
419	extracted	extract	VBN	_	_	_
420	from	from	IN	_	_	_
421	suspension	suspension	NN	_	_	_
422	cells	cell	NNS	_	_	_
423	of	of	IN	_	_	_
424	E.	e.	FW	_	_	_
425	coli	coli	FW	_	_	_
426	K-12	k-12	NN	_	_	_
427	BW25113/pCA24N	bw25113/pca24n	NN	_	_	_
428	-LRB-	-lrb-	-LRB-	_	_	_
429	empty	empty	JJ	_	_	_
430	vector	vector	NN	_	_	_
431	-RRB-	-rrb-	-RRB-	_	_	_
432	after	after	IN	_	_	_
433	OD600	od600	NN	_	_	_
434	=	=	JJ	_	_	_
435	0.5	0.5	CD	_	_	_
436	of	of	IN	_	_	_
437	growth	growth	NN	_	_	_
438	with	with	IN	_	_	_
439	2	2	CD	_	_	_
440	mM	mm	NN	KWSUPP	_	_
441	IPTG	iptg	NN	_	_	_
442	in	in	IN	_	_	_
443	LB	lb	NN	_	_	_
444	at	at	IN	_	_	_
445	37oC	37oc	NN	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	RNA	rna	NN	_	_	_
448	extracted	extract	VBN	_	_	_
449	from	from	IN	_	_	_
450	suspension	suspension	NN	_	_	_
451	cells	cell	NNS	_	_	_
452	of	of	IN	_	_	_
453	E.	e.	FW	_	_	_
454	coli	coli	FW	_	_	_
455	K-12	k-12	NN	_	_	_
456	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
457	after	after	IN	_	_	_
458	OD600	od600	NN	_	_	_
459	=	=	JJ	_	_	_
460	0.5	0.5	CD	_	_	_
461	of	of	IN	_	_	_
462	growth	growth	NN	_	_	_
463	,	,	,	_	_	_
464	then	then	RB	_	_	_
465	2	2	CD	_	_	_
466	mM	mm	NN	KWSUPP	_	_
467	IPTG	iptg	NN	_	_	_
468	for	for	IN	_	_	_
469	15	15	CD	_	_	_
470	min	min	NN	_	_	_
471	short	short	JJ	_	_	_
472	time	time	NN	_	_	_
473	in	in	IN	_	_	_
474	LB	lb	NN	_	_	_
475	at	at	IN	_	_	_
476	37oC	37oc	NN	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	RNA	rna	NN	_	_	_
479	extracted	extract	VBN	_	_	_
480	from	from	IN	_	_	_
481	suspension	suspension	NN	_	_	_
482	cells	cell	NNS	_	_	_
483	of	of	IN	_	_	_
484	E.	e.	FW	_	_	_
485	coli	coli	FW	_	_	_
486	K-12	k-12	NN	_	_	_
487	BW25113/pCA24N-mqsR	bw25113/pca24n-mqsr	NN	_	_	_
488	after	after	IN	_	_	_
489	OD600	od600	NN	_	_	_
490	=	=	JJ	_	_	_
491	0.5	0.5	CD	_	_	_
492	of	of	IN	_	_	_
493	growth	growth	NN	_	_	_
494	with	with	IN	_	_	_
495	2	2	CD	_	_	_
496	mM	mm	NN	KWSUPP	_	_
497	IPTG	iptg	NN	_	_	_
498	in	in	IN	_	_	_
499	LB	lb	NN	_	_	_
500	at	at	IN	_	_	_
501	37oC	37oc	NN	_	_	_
502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
503	RNA	rna	NN	_	_	_
504	extracted	extract	VBN	_	_	_
505	from	from	IN	_	_	_
506	suspension	suspension	NN	_	_	_
507	cells	cell	NNS	_	_	_
508	of	of	IN	_	_	_
509	E.	e.	FW	_	_	_
510	coli	coli	FW	_	_	_
511	K-12	k-12	NN	_	_	_
512	BW25113	bw25113	NN	_	_	_
513	wild	wild	JJ	_	_	_
514	type	type	NN	_	_	_
515	after	after	IN	_	_	_
516	OD600	od600	NN	_	_	_
517	=	=	JJ	_	_	_
518	0.5	0.5	CD	_	_	_
519	of	of	IN	_	_	_
520	growth	growth	NN	_	_	_
521	in	in	IN	_	_	_
522	LB	lb	NN	_	_	_
523	at	at	IN	_	_	_
524	37oC	37oc	NN	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	RNA	rna	NN	_	_	_
527	extracted	extract	VBN	_	_	_
528	from	from	IN	_	_	_
529	suspension	suspension	NN	_	_	_
530	cells	cell	NNS	_	_	_
531	of	of	IN	_	_	_
532	E.	e.	FW	_	_	_
533	coli	coli	FW	_	_	_
534	K-12	k-12	NN	_	_	_
535	BW25113	bw25113	NN	_	_	_
536	w/t	w/t	NN	_	_	_
537	after	after	IN	_	_	_
538	7	7	CD	_	_	_
539	hours	hour	NNS	_	_	_
540	of	of	IN	_	_	_
541	growth	growth	NN	_	_	_
542	in	in	IN	_	_	_
543	LB	lb	NN	_	_	_
544	with	with	IN	_	_	_
545	glasswool	glasswool	NN	_	_	_
546	at	at	IN	_	_	_
547	30ºC	30ºC	NNP	_	_	_
548	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
549	RNA	RNA	NNP	_	_	_
550	extracted	extract	VBN	_	_	_
551	from	from	IN	_	_	_
552	suspension	suspension	NN	_	_	_
553	cells	cell	NNS	_	_	_
554	of	of	IN	_	_	_
555	EHEC	ehec	NN	_	_	_
556	wild	wild	JJ	_	_	_
557	type	type	NN	_	_	_
558	after	after	IN	_	_	_
559	7	7	CD	_	_	_
560	h	h	NN	_	_	_
561	of	of	IN	_	_	_
562	growth	growth	NN	_	_	_
563	in	in	IN	_	_	_
564	LB	lb	NN	_	_	_
565	and	and	CC	_	_	_
566	0.1	0.1	CD	_	_	_
567	%	%	NN	_	_	_
568	DMF	dmf	NN	_	_	_
569	with	with	IN	_	_	_
570	glass	glass	NN	_	_	_
571	wool	wool	NN	_	_	_
572	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
573	RNA	rna	NN	_	_	_
574	extraction	extraction	NN	_	_	_
575	:	:	:	_	_	_
576	A	a	DT	_	_	_
577	hot-phenol	hot-phenol	NN	_	_	_
578	procedure	procedure	NN	_	_	_
579	was	be	VBD	_	_	_
580	used	use	VBN	_	_	_
581	to	to	TO	_	_	_
582	extract	extract	VB	_	_	_
583	total	total	JJ	_	_	_
584	RNA	rna	NN	_	_	_
585	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	sequentially	sequentially	RB	_	_	_
6	with	with	IN	_	_	_
7	phenol/chloroform	phenol/chloroform	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	preheated	preheated	JJ	_	_	_
10	to	to	TO	_	_	_
11	640	640	CD	_	_	_
12	C	c	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	followed	follow	VBN	_	_	_
16	by	by	IN	_	_	_
17	chloroform/isoamyl	chloroform/isoamyl	JJ	_	_	_
18	alcohol	alcohol	NN	_	_	_
19	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitate	VBN	_	_	_
4	with	with	IN	_	_	_
5	1/10	1/10	CD	_	_	_
6	volume	volume	NN	_	_	_
7	of	of	IN	_	_	_
8	3M	3M	NNP	_	_	_
9	NaOAc	naoac	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	pH	ph	NN	_	_	_
12	5.2	5.2	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	2	2	CD	_	_	_
16	volumes	volume	NNS	_	_	_
17	of	of	IN	_	_	_
18	ethanol	ethanol	NN	_	_	_
19	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubating	incubate	VBG	_	_	_
3	overnight	overnight	JJ	_	_	_
4	at	at	IN	_	_	_
5	--	--	:	_	_	_
6	200	200	CD	_	_	_
7	C	c	NN	_	_	_
8	,	,	,	_	_	_
9	samples	sample	NNS	_	_	_
10	were	be	VBD	_	_	_
11	spun	spin	VBN	_	_	_
12	down	down	RB	_	_	_
13	and	and	CC	_	_	_
14	pellets	pellet	NNS	_	_	_
15	were	be	VBD	_	_	_
16	washed	wash	VBN	_	_	_
17	with	with	IN	_	_	_
18	ice	ice	NN	_	_	_
19	cold	cold	JJ	_	_	_
20	70	70	CD	_	_	_
21	%	%	NN	_	_	_
22	ethanol	ethanol	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	prepared	prepare	VBN	_	_	_
25	with	with	IN	_	_	_
26	DEPC	depc	NN	_	_	_
27	-	-	:	_	_	_
28	H2O	h2o	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	resuspended	resuspend	VBN	_	_	_
4	in	in	IN	_	_	_
5	water	water	NN	_	_	_
6	,	,	,	_	_	_
7	DNase	dnase	NN	_	_	_
8	treated	treat	VBN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	RQ1	rq1	NN	_	_	_
11	RNase-free	rnase-free	NN	_	_	_
12	DNase	dnase	NN	_	_	_
13	/	/	:	_	_	_
14	Promega	Promega	NNP	_	_	_
15	,	,	,	_	_	_
16	WI	WI	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	purified	purify	VBN	_	_	_
20	using	use	VBG	_	_	_
21	an	a	DT	_	_	_
22	RNeasy	rneasy	NN	_	_	_
23	purification	purification	NN	_	_	_
24	kit	kit	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Qiagen	Qiagen	NNP	_	_	_
27	,	,	,	_	_	_
28	CA	CA	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	Kit	kit	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	RNA	rna	NN	_	_	_
7	extractions	extraction	NNS	_	_	_
8	were	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	using	use	VBG	_	_	_
11	RiboPure	RiboPure	NNP	_	_	_
12	™	™	CD	_	_	_
13	Bacteria	bacterium	NNS	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Ambion	Ambion	NNP	_	_	_
17	,	,	,	_	_	_
18	Austin	Austin	NNP	_	_	_
19	,	,	,	_	_	_
20	TX	TX	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	according	accord	VBG	_	_	_
24	to	to	TO	_	_	_
25	the	the	DT	_	_	_
26	manufacturer	manufacturer	NN	_	_	_
27	's	's	POS	_	_	_
28	recommendations	recommendation	NNS	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
30	RNA	rna	NN	_	_	_
31	extraction	extraction	NN	_	_	_
32	was	be	VBD	_	_	_
33	performed	perform	VBN	_	_	_
34	according	accord	VBG	_	_	_
35	to	to	TO	_	_	_
36	the	the	DT	_	_	_
37	manufacturer	manufacturer	NN	_	_	_
38	's	's	POS	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Qiagen	Qiagen	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	instructions	instruction	NNS	_	_	_
43	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	RiboPure-BacteriaTM	RiboPure-BacteriaTM	NNP	_	_	_
8	Bacteria	bacterium	NNS	_	_	_
9	kit	kit	NN	_	_	_
10	according	accord	VBG	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	manufacturer	manufacturer	NN	_	_	_
14	's	's	POS	_	_	_
15	protocol	protocol	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Ambion	Ambion	NNP	_	_	_
18	,	,	,	_	_	_
19	Life	Life	NNP	_	_	_
20	Technologies	Technologies	NNPS	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

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	extraction	extraction	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	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	,	,	,	_	_	_
14	Hilden	Hilden	NNP	_	_	_
15	,	,	,	_	_	_
16	Germany	Germany	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	from	from	IN	_	_	_
4	1	1	CD	_	_	_
5	%	%	NN	_	_	_
6	isobutanol	isobutanol	NN	_	_	_
7	treated	treat	VBN	_	_	_
8	sample	sample	NN	_	_	_
9	and	and	CC	_	_	_
10	untreated	untreated	JJ	_	_	_
11	sample	sample	NN	_	_	_
12	were	be	VBD	_	_	_
13	mixed	mix	VBN	_	_	_
14	after	after	IN	_	_	_
15	RNA	rna	NN	_	_	_
16	purification	purification	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	RNA	rna	NN	_	_	_
19	from	from	IN	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	0.5	0.5	CD	_	_	_
23	hours	hour	NNS	_	_	_
24	after	after	IN	_	_	_
25	inoculation	inoculation	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	RNA	rna	NN	_	_	_
28	from	from	IN	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	1.5	1.5	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	2	2	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	3.5	3.5	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	3	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	4	4	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	expressing	express	VBG	_	_	_
77	synthetic	synthetic	JJ	_	_	_
78	protein	protein	NN	_	_	_
79	DX	DX	NNP	_	_	_
80	for	for	IN	_	_	_
81	0.5	0.5	CD	_	_	_
82	hours	hour	NNS	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	RNA	rna	NN	_	_	_
85	from	from	IN	_	_	_
86	E.	e.	FW	_	_	_
87	coli	coli	FW	_	_	_
88	expressing	express	VBG	_	_	_
89	synthetic	synthetic	JJ	_	_	_
90	protein	protein	NN	_	_	_
91	DX	DX	NNP	_	_	_
92	for	for	IN	_	_	_
93	1.5	1.5	CD	_	_	_
94	hours	hour	NNS	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	RNA	rna	NN	_	_	_
97	from	from	IN	_	_	_
98	E.	e.	FW	_	_	_
99	coli	coli	FW	_	_	_
100	expressing	express	VBG	_	_	_
101	synthetic	synthetic	JJ	_	_	_
102	protein	protein	NN	_	_	_
103	DX	DX	NNP	_	_	_
104	for	for	IN	_	_	_
105	1	1	CD	_	_	_
106	hours	hour	NNS	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	RNA	rna	NN	_	_	_
109	from	from	IN	_	_	_
110	E.	e.	FW	_	_	_
111	coli	coli	FW	_	_	_
112	expressing	express	VBG	_	_	_
113	synthetic	synthetic	JJ	_	_	_
114	protein	protein	NN	_	_	_
115	DX	DX	NNP	_	_	_
116	for	for	IN	_	_	_
117	2	2	CD	_	_	_
118	hours	hour	NNS	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	RNA	rna	NN	_	_	_
121	from	from	IN	_	_	_
122	E.	e.	FW	_	_	_
123	coli	coli	FW	_	_	_
124	expressing	express	VBG	_	_	_
125	synthetic	synthetic	JJ	_	_	_
126	protein	protein	NN	_	_	_
127	DX	DX	NNP	_	_	_
128	for	for	IN	_	_	_
129	3.5	3.5	CD	_	_	_
130	hours	hour	NNS	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	RNA	rna	NN	_	_	_
133	from	from	IN	_	_	_
134	E.	e.	FW	_	_	_
135	coli	coli	FW	_	_	_
136	expressing	express	VBG	_	_	_
137	synthetic	synthetic	JJ	_	_	_
138	protein	protein	NN	_	_	_
139	DX	DX	NNP	_	_	_
140	for	for	IN	_	_	_
141	3	3	CD	_	_	_
142	hours	hour	NNS	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	RNA	rna	NN	_	_	_
145	from	from	IN	_	_	_
146	E.	e.	FW	_	_	_
147	coli	coli	FW	_	_	_
148	expressing	express	VBG	_	_	_
149	synthetic	synthetic	JJ	_	_	_
150	protein	protein	NN	_	_	_
151	DX	DX	NNP	_	_	_
152	for	for	IN	_	_	_
153	4	4	CD	_	_	_
154	hours	hour	NNS	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	RNA	rna	NN	_	_	_
157	from	from	IN	_	_	_
158	Escherichia	escherichia	FW	Organism	_	_
159	coli	coli	FW	Organism	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	RNA	rna	NN	_	_	_
162	from	from	IN	_	_	_
163	late	late	JJ	_	_	_
164	log	log	NN	_	_	_
165	phase	phase	NN	_	_	_
166	E	e	NN	_	_	_
167	coli	coli	NN	_	_	_
168	EDL933	edl933	NN	_	_	_
169	pooled	pool	VBD	_	_	_
170	reference	reference	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	RNA	rna	NN	_	_	_
173	from	from	IN	_	_	_
174	late	late	JJ	_	_	_
175	log	log	NN	_	_	_
176	phase	phase	NN	_	_	_
177	E	e	NN	_	_	_
178	coli	coli	NN	_	_	_
179	FRIK2000	frik2000	NN	_	_	_
180	rep	rep	NN	GEN	_	_
181	1	1	CD	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	RNA	rna	NN	_	_	_
184	from	from	IN	_	_	_
185	late	late	JJ	_	_	_
186	log	log	NN	_	_	_
187	phase	phase	NN	_	_	_
188	E	e	NN	_	_	_
189	coli	coli	NN	_	_	_
190	FRIK2000	frik2000	NN	_	_	_
191	rep	rep	NN	GEN	_	_
192	2	2	CD	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	RNA	rna	NN	_	_	_
195	from	from	IN	_	_	_
196	late	late	JJ	_	_	_
197	log	log	NN	_	_	_
198	phase	phase	NN	_	_	_
199	E	e	NN	_	_	_
200	coli	coli	NN	_	_	_
201	FRIK2000	frik2000	NN	_	_	_
202	rep	rep	NN	GEN	_	_
203	3	3	CD	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	RNA	rna	NN	_	_	_
206	from	from	IN	_	_	_
207	late	late	JJ	_	_	_
208	log	log	NN	_	_	_
209	phase	phase	NN	_	_	_
210	E	e	NN	_	_	_
211	coli	coli	NN	_	_	_
212	FRIK2000	frik2000	NN	_	_	_
213	rep	rep	NN	GEN	_	_
214	4	4	CD	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	RNA	rna	NN	_	_	_
217	from	from	IN	_	_	_
218	late	late	JJ	_	_	_
219	log	log	NN	_	_	_
220	phase	phase	NN	_	_	_
221	E	e	NN	_	_	_
222	coli	coli	NN	_	_	_
223	FRIK966	frik966	NN	_	_	_
224	rep	rep	NN	GEN	_	_
225	1	1	CD	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	RNA	rna	NN	_	_	_
228	from	from	IN	_	_	_
229	late	late	JJ	_	_	_
230	log	log	NN	_	_	_
231	phase	phase	NN	_	_	_
232	E	e	NN	_	_	_
233	coli	coli	NN	_	_	_
234	FRIK966	frik966	NN	_	_	_
235	rep	rep	NN	GEN	_	_
236	2	2	CD	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	RNA	rna	NN	_	_	_
239	from	from	IN	_	_	_
240	late	late	JJ	_	_	_
241	log	log	NN	_	_	_
242	phase	phase	NN	_	_	_
243	E	e	NN	_	_	_
244	coli	coli	NN	_	_	_
245	FRIK966	frik966	NN	_	_	_
246	rep	rep	NN	GEN	_	_
247	3	3	CD	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	RNA	rna	NN	_	_	_
250	from	from	IN	_	_	_
251	late	late	JJ	_	_	_
252	log	log	NN	_	_	_
253	phase	phase	NN	_	_	_
254	E	e	NN	_	_	_
255	coli	coli	NN	_	_	_
256	FRIK966	frik966	NN	_	_	_
257	rep	rep	NN	GEN	_	_
258	4	4	CD	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	RNA	rna	NN	_	_	_
261	isolation	isolation	NN	_	_	_
262	was	be	VBD	_	_	_
263	performed	perform	VBN	_	_	_
264	using	use	VBG	_	_	_
265	an	a	DT	_	_	_
266	RNeasy	rneasy	NN	_	_	_
267	mini	minus	NNS	_	_	_
268	kit	kit	NN	_	_	_
269	-LRB-	-lrb-	-LRB-	_	_	_
270	Qiagen	Qiagen	NNP	_	_	_
271	Technologies	Technologies	NNPS	_	_	_
272	,	,	,	_	_	_
273	Hilden	Hilden	NNP	_	_	_
274	,	,	,	_	_	_
275	Germany	Germany	NNP	_	_	_
276	-RRB-	-rrb-	-RRB-	_	_	_
277	,	,	,	_	_	_
278	according	accord	VBG	_	_	_
279	to	to	TO	_	_	_
280	the	the	DT	_	_	_
281	manufacturer	manufacturer	NN	_	_	_
282	's	's	POS	_	_	_
283	protocol	protocol	NN	_	_	_
284	.	.	.	_	_	_

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/A230	a260/a230	NN	_	_	_
56	and	and	CC	_	_	_
57	A260/A280	a260/a280	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	had	have	VBD	_	_	_
4	A260/A230	a260/a230	NN	_	_	_
5	and	and	CC	_	_	_
6	A260/A280	a260/a280	NN	_	_	_
7	ratios	ratio	NNS	_	_	_
8	above	above	IN	_	_	_
9	1.9	1.9	CD	_	_	_
10	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	integrity	integrity	NN	_	_	_
4	was	be	VBD	_	_	_
5	analysed	analyse	VBN	_	_	_
6	using	use	VBG	_	_	_
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	Palo	Palo	NNP	_	_	_
15	Alto	Alto	NNP	_	_	_
16	,	,	,	_	_	_
17	CA	CA	NNP	_	_	_
18	,	,	,	_	_	_
19	USA	USA	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	in	in	IN	_	_	_
22	conjunction	conjunction	NN	_	_	_
23	with	with	IN	_	_	_
24	RNA	rna	NN	_	_	_
25	6000	6000	CD	_	_	_
26	Nano	Nano	NNP	_	_	_
27	LabChip	LabChip	NNP	_	_	_
28	kit	kit	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Agilent	Agilent	NNP	_	_	_
31	Technologies	Technologies	NNPS	_	_	_
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	protocol	protocol	NN	_	_	_
39	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	integrity	integrity	NN	_	_	_
3	number	number	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	RIN	rin	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	values	value	NNS	_	_	_
8	were	be	VBD	_	_	_
9	>	>	JJR	_	_	_
10	8.5	8.5	CD	_	_	_
11	for	for	IN	_	_	_
12	all	all	DT	_	_	_
13	samples	sample	NNS	_	_	_
14	.	.	.	_	_	_

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/A230	a260/a230	NN	_	_	_
56	and	and	CC	_	_	_
57	A260/A280	a260/a280	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	had	have	VBD	_	_	_
4	A260/A230	a260/a230	NN	_	_	_
5	and	and	CC	_	_	_
6	A260/A280	a260/a280	NN	_	_	_
7	ratios	ratio	NNS	_	_	_
8	above	above	IN	_	_	_
9	1.9	1.9	CD	_	_	_
10	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	integrity	integrity	NN	_	_	_
4	was	be	VBD	_	_	_
5	analysed	analyse	VBN	_	_	_
6	using	use	VBG	_	_	_
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	Palo	Palo	NNP	_	_	_
15	Alto	Alto	NNP	_	_	_
16	,	,	,	_	_	_
17	CA	CA	NNP	_	_	_
18	,	,	,	_	_	_
19	USA	USA	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	in	in	IN	_	_	_
22	conjunction	conjunction	NN	_	_	_
23	with	with	IN	_	_	_
24	RNA	rna	NN	_	_	_
25	6000	6000	CD	_	_	_
26	Nano	Nano	NNP	_	_	_
27	LabChip	LabChip	NNP	_	_	_
28	kit	kit	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Agilent	Agilent	NNP	_	_	_
31	Technologies	Technologies	NNPS	_	_	_
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	protocol	protocol	NN	_	_	_
39	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	integrity	integrity	NN	_	_	_
3	number	number	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	RIN	rin	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	values	value	NNS	_	_	_
8	were	be	VBD	_	_	_
9	>	>	JJR	_	_	_
10	9	9	CD	_	_	_
11	for	for	IN	_	_	_
12	all	all	DT	_	_	_
13	samples	sample	NNS	_	_	_
14	.	.	.	_	_	_

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/phenol	sds/phenol	NN	_	_	_
11	protocol	protocol	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	http://www.genome.wisc.edu/pub/reprints/	http://www.genome.wisc.edu/pub/reprints/	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	with	with	IN	_	_	_
16	an	a	DT	_	_	_
17	additional	additional	JJ	_	_	_
18	1-min	1-min	JJ	_	_	_
19	bead-beating	bead-beating	NN	_	_	_
20	.	.	.	_	_	_

1	Chemical	Chemical	NNP	_	_	_
2	extractions	extraction	NNS	_	_	_
3	were	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	in	in	IN	_	_	_
6	phase	phase	NN	_	_	_
7	lock	lock	NN	_	_	_
8	gels	gel	NNS	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Fisher	Fisher	NNP	_	_	_
11	Scientific	Scientific	NNP	_	_	_
12	,	,	,	_	_	_
13	Pittsburgh	Pittsburgh	NNP	_	_	_
14	,	,	,	_	_	_
15	PA	pa	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
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	by	by	IN	_	_	_
9	the	the	DT	_	_	_
10	company	company	NN	_	_	_
11	Vertis	Vertis	NNP	_	_	_
12	Biotechnologie	Biotechnologie	NNP	_	_	_
13	AG	AG	NNP	_	_	_
14	in	in	IN	_	_	_
15	Germany	Germany	NNP	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
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	pgcgrowthconditions	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	libraries	library	NNS	_	_	_
30	were	be	VBD	_	_	_
31	prepared	prepare	VBN	_	_	_
32	for	for	IN	_	_	_
33	sequencing	sequencing	NN	_	_	_
34	using	use	VBG	_	_	_
35	standard	standard	JJ	_	_	_
36	Illumina	Illumina	NNP	_	_	_
37	protocols	protocol	NNS	_	_	_
38	.	.	.	_	_	_

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	RNAP	rnap	NN	_	_	_
3	beta	beta	NN	_	_	_
4	subunit	subunit	NN	_	_	_
5	ChIP	chip	NN	_	_	_
6	DNA	dna	NN	_	_	_
7	from	from	IN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	CC72	cc72	NN	_	_	_
11	10	10	CD	_	_	_
12	min	min	NN	_	_	_
13	after	after	IN	_	_	_
14	osmotic	osmotic	JJ	_	_	_
15	stress	stress	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	RNAP	rnap	NN	_	_	_
18	beta	beta	NN	_	_	_
19	subunit	subunit	NN	_	_	_
20	ChIP	chip	NN	_	_	_
21	DNA	dna	NN	_	_	_
22	from	from	IN	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	CC72	cc72	NN	_	_	_
26	20	20	CD	_	_	_
27	min	min	NN	_	_	_
28	after	after	IN	_	_	_
29	osmotic	osmotic	JJ	_	_	_
30	stress	stress	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	RNAP	rnap	NN	_	_	_
33	beta	beta	NN	_	_	_
34	subunit	subunit	NN	_	_	_
35	ChIP	chip	NN	_	_	_
36	DNA	dna	NN	_	_	_
37	from	from	IN	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	CC72	cc72	NN	_	_	_
41	45	45	CD	_	_	_
42	min	min	NN	_	_	_
43	after	after	IN	_	_	_
44	osmotic	osmotic	JJ	_	_	_
45	stress	stress	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	RNAP	rnap	NN	_	_	_
48	beta	beta	NN	_	_	_
49	subunit	subunit	NN	_	_	_
50	ChIP	chip	NN	_	_	_
51	DNA	dna	NN	_	_	_
52	from	from	IN	_	_	_
53	E.	e.	FW	_	_	_
54	coli	coli	FW	_	_	_
55	CC72	cc72	NN	_	_	_
56	at	at	IN	_	_	_
57	early-exponential	early-exponential	JJ	_	_	_
58	phase	phase	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	RNAP	rnap	NN	_	_	_
61	ChIP	chip	NN	_	_	_
62	DNA	dna	NN	_	_	_
63	from	from	IN	_	_	_
64	DdksA	ddksa	NN	_	_	_
65	cells	cell	NNS	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
67	RNAP	rnap	NN	_	_	_
68	ChIP	chip	NN	_	_	_
69	DNA	dna	NN	_	_	_
70	from	from	IN	_	_	_
71	MDS42	mds42	NN	_	_	_
72	cells	cell	NNS	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
74	RNAP	rnap	NN	_	_	_
75	ChIP	chip	NN	_	_	_
76	DNA	dna	NN	_	_	_
77	from	from	IN	_	_	_
78	MDS42	mds42	NN	_	_	_
79	ΔnusA	δnusa	NN	_	_	_
80	*	*	NN	_	_	_
81	cells	cell	NNS	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
83	RNAP	rnap	NN	_	_	_
84	ChIP	chip	NN	_	_	_
85	DNA	dna	NN	_	_	_
86	from	from	IN	_	_	_
87	MDS42	mds42	NN	_	_	_
88	ΔnusG	δnusg	NN	_	_	_
89	cells	cell	NNS	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
91	RNAP	rnap	NN	_	_	_
92	ChIP	chip	NN	_	_	_
93	DNA	dna	NN	_	_	_
94	from	from	IN	_	_	_
95	MG1655	mg1655	NN	_	_	_
96	cells	cell	NNS	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
98	RNAP	rnap	NN	_	_	_
99	ChIP	chip	NN	_	_	_
100	DNA	dna	NN	_	_	_
101	from	from	IN	_	_	_
102	MG1655	mg1655	NN	_	_	_
103	Δhns	δhns	NN	_	_	_
104	cells	cell	NNS	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
106	RNAP	rnap	NN	_	_	_
107	ChIP	chip	NN	_	_	_
108	DNA	dna	NN	_	_	_
109	from	from	IN	_	_	_
110	starved	starve	VBN	_	_	_
111	DdksA	ddksa	NN	_	_	_
112	cells	cell	NNS	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
114	RNAP	rnap	NN	_	_	_
115	ChIP	chip	NN	_	_	_
116	DNA	dna	NN	_	_	_
117	from	from	IN	_	_	_
118	starved	starve	VBN	_	_	_
119	wt	wt	JJ	_	_	_
120	cells	cell	NNS	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
122	RNAP	rnap	NN	_	_	_
123	ChIP	chip	NN	_	_	_
124	DNA	dna	NN	_	_	_
125	from	from	IN	_	_	_
126	wt	wt	JJ	_	_	_
127	cells	cell	NNS	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
129	RNAP	rnap	NN	_	_	_
130	ChIP	chip	NN	_	_	_
131	DNA	dna	NN	_	_	_
132	,	,	,	_	_	_
133	old	old	JJ	_	_	_
134	protocol	protocol	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	RNAP	rnap	NN	_	_	_
137	_	_	CD	_	_	_
138	DdksA	ddksa	NN	_	_	_
139	_	_	CD	_	_	_
140	SHX	SHX	NNP	_	_	_
141	_	_	CD	_	_	_
142	rep1	rep1	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	RNAP	rnap	NN	_	_	_
145	_	_	CD	_	_	_
146	DdksA	ddksa	NN	_	_	_
147	_	_	CD	_	_	_
148	SHX	SHX	NNP	_	_	_
149	_	_	CD	_	_	_
150	rep2	rep2	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	RNAP	rnap	NN	_	_	_
153	_	_	CD	_	_	_
154	DdksA	ddksa	NN	_	_	_
155	_	_	NN	_	_	_
156	untreated	untreated	JJ	_	_	_
157	_	_	NN	_	_	_
158	rep1	rep1	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	RNAP	rnap	NN	_	_	_
161	_	_	CD	_	_	_
162	DdksA	ddksa	NN	_	_	_
163	_	_	NN	_	_	_
164	untreated	untreated	JJ	_	_	_
165	_	_	NN	_	_	_
166	rep2	rep2	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	RNAP	rnap	NN	_	_	_
169	old	old	JJ	_	_	_
170	rep1	rep1	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	RNAP	rnap	NN	_	_	_
173	old	old	JJ	_	_	_
174	rep2	rep2	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	RNA	rna	NN	_	_	_
177	polymerase	polymerase	NN	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	Beta	beta	NN	_	_	_
180	'	'	''	_	_	_
181	-RRB-	-rrb-	-RRB-	_	_	_
182	ChIP-chip	chip-chip	NN	_	_	_
183	in	in	IN	_	_	_
184	E.	e.	FW	_	_	_
185	coli	coli	FW	_	_	_
186	K-12	k-12	NN	_	_	_
187	MG1655	mg1655	NN	_	_	_
188	cells	cell	NNS	_	_	_
189	-LRB-	-lrb-	-LRB-	_	_	_
190	Dataset	Dataset	NNP	_	_	_
191	100040	100040	CD	_	_	_
192	-RRB-	-rrb-	-RRB-	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	RNA	rna	NN	_	_	_
195	polymerase	polymerase	NN	_	_	_
196	-LRB-	-lrb-	-LRB-	_	_	_
197	Beta	beta	NN	_	_	_
198	-RRB-	-rrb-	-RRB-	_	_	_
199	ChIP-chip	chip-chip	NN	_	_	_
200	in	in	IN	_	_	_
201	E.	e.	FW	_	_	_
202	coli	coli	FW	_	_	_
203	K-12	k-12	NN	_	_	_
204	MG1655	mg1655	NN	_	_	_
205	cells	cell	NNS	_	_	_
206	-LRB-	-lrb-	-LRB-	_	_	_
207	Dataset	Dataset	NNP	_	_	_
208	3427302	3427302	CD	_	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	RNA	rna	NN	_	_	_
212	polymerase	polymerase	NN	_	_	_
213	-LRB-	-lrb-	-LRB-	_	_	_
214	Beta	beta	NN	_	_	_
215	'	'	''	_	_	_
216	-RRB-	-rrb-	-RRB-	_	_	_
217	ChIP-chip	chip-chip	NN	_	_	_
218	in	in	IN	_	_	_
219	E.	e.	FW	_	_	_
220	coli	coli	FW	_	_	_
221	K-12	k-12	NN	_	_	_
222	MG1655	mg1655	NN	_	_	_
223	cells	cell	NNS	_	_	_
224	-LRB-	-lrb-	-LRB-	_	_	_
225	Dataset	Dataset	NNP	_	_	_
226	56706	56706	CD	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	RNA	rna	NN	_	_	_
230	polymerase	polymerase	NN	_	_	_
231	-LRB-	-lrb-	-LRB-	_	_	_
232	Beta	beta	NN	_	_	_
233	'	'	''	_	_	_
234	-RRB-	-rrb-	-RRB-	_	_	_
235	ChIP-chip	chip-chip	NN	_	_	_
236	in	in	IN	_	_	_
237	E.	e.	FW	_	_	_
238	coli	coli	FW	_	_	_
239	K-12	k-12	NN	_	_	_
240	MG1655	mg1655	NN	_	_	_
241	cells	cell	NNS	_	_	_
242	-LRB-	-lrb-	-LRB-	_	_	_
243	Dataset	Dataset	NNP	_	_	_
244	62215	62215	CD	_	_	_
245	-RRB-	-rrb-	-RRB-	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	RNA	rna	NN	_	_	_
248	polymerase	polymerase	NN	_	_	_
249	-LRB-	-lrb-	-LRB-	_	_	_
250	Beta	beta	NN	_	_	_
251	'	'	''	_	_	_
252	-RRB-	-rrb-	-RRB-	_	_	_
253	ChIP-chip	chip-chip	NN	_	_	_
254	in	in	IN	_	_	_
255	E.	e.	FW	_	_	_
256	coli	coli	FW	_	_	_
257	K-12	k-12	NN	_	_	_
258	MG1655	mg1655	NN	_	_	_
259	cells	cell	NNS	_	_	_
260	treated	treat	VBN	_	_	_
261	with	with	IN	_	_	_
262	100ug/ml	100ug/ml	JJ	_	_	_
263	rifampicin	rifampicin	NN	SUPP	_	_
264	-LRB-	-lrb-	-LRB-	_	_	_
265	Dataset	dataset	NN	_	_	_
266	81586	81586	CD	_	_	_
267	-RRB-	-rrb-	-RRB-	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	RNA	rna	NN	_	_	_
270	polymerase	polymerase	NN	_	_	_
271	-LRB-	-lrb-	-LRB-	_	_	_
272	Beta	beta	NN	_	_	_
273	-RRB-	-rrb-	-RRB-	_	_	_
274	ChIP-chip	chip-chip	NN	_	_	_
275	in	in	IN	_	_	_
276	E.	e.	FW	_	_	_
277	coli	coli	FW	_	_	_
278	K-12	k-12	NN	_	_	_
279	MG1655	mg1655	NN	_	_	_
280	cells	cell	NNS	_	_	_
281	treated	treat	VBN	_	_	_
282	with	with	IN	_	_	_
283	20ug/ml	20ug/ml	JJ	_	_	_
284	bicyclomycin	bicyclomycin	NN	_	_	_
285	-LRB-	-lrb-	-LRB-	_	_	_
286	Dataset	dataset	NN	_	_	_
287	3428302	3428302	CD	_	_	_
288	-RRB-	-rrb-	-RRB-	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	RNA	rna	NN	_	_	_
291	polymerase	polymerase	NN	_	_	_
292	-LRB-	-lrb-	-LRB-	_	_	_
293	Beta	beta	NN	_	_	_
294	'	'	''	_	_	_
295	-RRB-	-rrb-	-RRB-	_	_	_
296	ChIP-chip	chip-chip	NN	_	_	_
297	in	in	IN	_	_	_
298	E.	e.	FW	_	_	_
299	coli	coli	FW	_	_	_
300	K-12	k-12	NN	_	_	_
301	MG1655	mg1655	NN	_	_	_
302	cells	cell	NNS	_	_	_
303	treated	treat	VBN	_	_	_
304	with	with	IN	_	_	_
305	20ug/ml	20ug/ml	JJ	_	_	_
306	bicyclomycin	bicyclomycin	NN	_	_	_
307	-LRB-	-lrb-	-LRB-	_	_	_
308	Dataset	dataset	NN	_	_	_
309	94828	94828	CD	_	_	_
310	-RRB-	-rrb-	-RRB-	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	RNA	rna	NN	_	_	_
313	polymerase	polymerase	NN	_	_	_
314	-LRB-	-lrb-	-LRB-	_	_	_
315	Beta	beta	NN	_	_	_
316	'	'	''	_	_	_
317	-RRB-	-rrb-	-RRB-	_	_	_
318	ChIP	chip	NN	_	_	_
319	in	in	IN	_	_	_
320	E.	e.	FW	_	_	_
321	coli	coli	FW	_	_	_
322	K-12	k-12	NN	_	_	_
323	MG1655	mg1655	NN	_	_	_
324	cells	cell	NNS	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	RNA	rna	NN	_	_	_
327	polymerase	polymerase	NN	_	_	_
328	-LRB-	-lrb-	-LRB-	_	_	_
329	Beta	beta	NN	_	_	_
330	'	'	''	_	_	_
331	-RRB-	-rrb-	-RRB-	_	_	_
332	ChIP	chip	NN	_	_	_
333	in	in	IN	_	_	_
334	E.	e.	FW	_	_	_
335	coli	coli	FW	_	_	_
336	K-12	k-12	NN	_	_	_
337	MG1655	mg1655	NN	_	_	_
338	cells	cell	NNS	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	RNA	rna	NN	_	_	_
341	polymerase	polymerase	NN	_	_	_
342	-LRB-	-lrb-	-LRB-	_	_	_
343	Beta	beta	NN	_	_	_
344	'	'	''	_	_	_
345	-RRB-	-rrb-	-RRB-	_	_	_
346	ChIP	chip	NN	_	_	_
347	in	in	IN	_	_	_
348	E.	e.	FW	_	_	_
349	coli	coli	FW	_	_	_
350	K-12	k-12	NN	_	_	_
351	MG1655	mg1655	NN	_	_	_
352	cells	cell	NNS	_	_	_
353	treated	treat	VBN	_	_	_
354	with	with	IN	_	_	_
355	100ug/ml	100ug/ml	JJ	_	_	_
356	rifampicin	rifampicin	NN	SUPP	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	RNA	rna	NN	_	_	_
359	polymerase	polymerase	NN	_	_	_
360	-LRB-	-lrb-	-LRB-	_	_	_
361	Beta	beta	NN	_	_	_
362	'	'	''	_	_	_
363	-RRB-	-rrb-	-RRB-	_	_	_
364	ChIP	chip	NN	_	_	_
365	in	in	IN	_	_	_
366	E.	e.	FW	_	_	_
367	coli	coli	FW	_	_	_
368	K-12	k-12	NN	_	_	_
369	MG1655	mg1655	NN	_	_	_
370	cells	cell	NNS	_	_	_
371	treated	treat	VBN	_	_	_
372	with	with	IN	_	_	_
373	20ug/ml	20ug/ml	JJ	_	_	_
374	bicyclomycin	bicyclomycin	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	RNA	rna	NN	_	_	_
377	polymerase	polymerase	NN	_	_	_
378	-LRB-	-lrb-	-LRB-	_	_	_
379	Beta	beta	NN	_	_	_
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	treated	treat	VBN	_	_	_
389	with	with	IN	_	_	_
390	20ug/ml	20ug/ml	JJ	_	_	_
391	bicyclomycin	bicyclomycin	NN	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
393	RNA	rna	NN	_	_	_
394	polymerase	polymerase	NN	_	_	_
395	-LRB-	-lrb-	-LRB-	_	_	_
396	Beta	beta	NN	_	_	_
397	'	'	''	_	_	_
398	-RRB-	-rrb-	-RRB-	_	_	_
399	ChIP	chip	NN	_	_	_
400	in	in	IN	_	_	_
401	E.	e.	FW	_	_	_
402	coli	coli	FW	_	_	_
403	K-12	k-12	NN	_	_	_
404	MG1655	mg1655	NN	_	_	_
405	cells	cell	NNS	_	_	_
406	,	,	,	_	_	_
407	untreated	untreated	JJ	_	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	RNA	rna	NN	_	_	_
410	polymerase	polymerase	NN	_	_	_
411	-LRB-	-lrb-	-LRB-	_	_	_
412	Beta	beta	NN	_	_	_
413	-RRB-	-rrb-	-RRB-	_	_	_
414	ChIP	chip	NN	_	_	_
415	in	in	IN	_	_	_
416	E.	e.	FW	_	_	_
417	coli	coli	FW	_	_	_
418	K-12	k-12	NN	_	_	_
419	MG1655	mg1655	NN	_	_	_
420	cells	cell	NNS	_	_	_
421	,	,	,	_	_	_
422	untreated	untreated	JJ	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	RNA	rna	NN	_	_	_
425	produced	produce	VBN	_	_	_
426	by	by	IN	_	_	_
427	in	in	FW	_	_	_
428	vitro	vitro	FW	_	_	_
429	transcription	transcription	NN	_	_	_
430	,	,	,	_	_	_
431	with	with	IN	_	_	_
432	RNA	rna	NN	_	_	_
433	polymerase	polymerase	NN	_	_	_
434	E	e	NN	_	_	_
435	σ70	σ70	NN	_	_	_
436	,	,	,	_	_	_
437	of	of	IN	_	_	_
438	2	2	CD	_	_	_
439	ug	ug	NN	_	_	_
440	of	of	IN	_	_	_
441	genomic	genomic	JJ	_	_	_
442	DNA	dna	NN	_	_	_
443	from	from	IN	_	_	_
444	E.	e.	FW	_	_	_
445	coli	coli	FW	_	_	_
446	MG1655	mg1655	NN	_	_	_
447	digested	digest	VBN	_	_	_
448	with	with	IN	_	_	_
449	EcoRI	ecori	NN	_	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
451	RNA	rna	NN	_	_	_
452	produced	produce	VBN	_	_	_
453	by	by	IN	_	_	_
454	in	in	FW	_	_	_
455	vitro	vitro	FW	_	_	_
456	transcription	transcription	NN	_	_	_
457	,	,	,	_	_	_
458	with	with	IN	_	_	_
459	RNA	rna	NN	_	_	_
460	polymerase	polymerase	NN	_	_	_
461	E	e	NN	_	_	_
462	σS	σs	NN	_	_	_
463	,	,	,	_	_	_
464	of	of	IN	_	_	_
465	2	2	CD	_	_	_
466	ug	ug	NN	_	_	_
467	of	of	IN	_	_	_
468	genomic	genomic	JJ	_	_	_
469	DNA	dna	NN	_	_	_
470	from	from	IN	_	_	_
471	E.	e.	FW	_	_	_
472	coli	coli	FW	_	_	_
473	MG1655	mg1655	NN	_	_	_
474	digested	digest	VBN	_	_	_
475	with	with	IN	_	_	_
476	EcoRI	ecori	NN	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	RNAP	rnap	NN	_	_	_
479	_	_	CD	_	_	_
480	wt	wt	JJ	_	_	_
481	_	_	NN	_	_	_
482	SHX	shx	NN	_	_	_
483	_	_	CD	_	_	_
484	rep1	rep1	NN	_	_	_
485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
486	RNAP	rnap	NN	_	_	_
487	_	_	CD	_	_	_
488	wt	wt	JJ	_	_	_
489	_	_	NN	_	_	_
490	SHX	shx	NN	_	_	_
491	_	_	CD	_	_	_
492	rep2	rep2	NN	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	RNAP	rnap	NN	_	_	_
495	_	_	CD	_	_	_
496	wt	wt	JJ	_	_	_
497	_	_	NN	_	_	_
498	untreated	untreated	JJ	_	_	_
499	_	_	NN	_	_	_
500	rep1	rep1	NN	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	RNAP	rnap	NN	_	_	_
503	_	_	CD	_	_	_
504	wt	wt	JJ	_	_	_
505	_	_	NN	_	_	_
506	untreated	untreated	JJ	_	_	_
507	_	_	NN	_	_	_
508	rep2	rep2	NN	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	RNA	rna	NN	_	_	_
511	quality	quality	NN	_	_	_
512	was	be	VBD	_	_	_
513	confirmed	confirm	VBN	_	_	_
514	with	with	IN	_	_	_
515	the	the	DT	_	_	_
516	Bioanalyzer	Bioanalyzer	NNP	_	_	_
517	system	system	NN	_	_	_
518	-LRB-	-lrb-	-LRB-	_	_	_
519	Agilent	Agilent	NNP	_	_	_
520	Technologies	Technologies	NNPS	_	_	_
521	,	,	,	_	_	_
522	Santa	Santa	NNP	_	_	_
523	Clara	Clara	NNP	_	_	_
524	,	,	,	_	_	_
525	CA	CA	NNP	_	_	_
526	,	,	,	_	_	_
527	USA	USA	NNP	_	_	_
528	-RRB-	-rrb-	-RRB-	_	_	_
529	and	and	CC	_	_	_
530	sequencing	sequencing	NN	_	_	_
531	-LRB-	-lrb-	-LRB-	_	_	_
532	50	50	CD	_	_	_
533	cycles	cycle	NNS	_	_	_
534	,	,	,	_	_	_
535	pooling	pool	VBG	_	_	_
536	eight	eight	CD	_	_	_
537	bar-coded	bar-coded	JJ	_	_	_
538	samples	sample	NNS	_	_	_
539	per	per	IN	_	_	_
540	lane	lane	NN	_	_	_
541	-RRB-	-rrb-	-RRB-	_	_	_
542	was	be	VBD	_	_	_
543	performed	perform	VBN	_	_	_
544	on	on	IN	_	_	_
545	the	the	DT	_	_	_
546	Illumina	Illumina	NNP	_	_	_
547	HiSeq	HiSeq	NNP	_	_	_
548	platform	platform	NN	_	_	_
549	-LRB-	-lrb-	-LRB-	_	_	_
550	Illumina	Illumina	NNP	_	_	_
551	,	,	,	_	_	_
552	San	San	NNP	_	_	_
553	Diego	Diego	NNP	_	_	_
554	,	,	,	_	_	_
555	CA	CA	NNP	_	_	_
556	,	,	,	_	_	_
557	USA	USA	NNP	_	_	_
558	-RRB-	-rrb-	-RRB-	_	_	_
559	at	at	IN	_	_	_
560	the	the	DT	_	_	_
561	Research	Research	NNP	_	_	_
562	Technology	Technology	NNP	_	_	_
563	Support	support	NN	_	_	_
564	Facility	facility	NN	_	_	_
565	-LRB-	-lrb-	-LRB-	_	_	_
566	RTSF	rtsf	NN	_	_	_
567	-RRB-	-rrb-	-RRB-	_	_	_
568	at	at	IN	_	_	_
569	Michigan	Michigan	NNP	_	_	_
570	State	State	NNP	_	_	_
571	University	University	NNP	_	_	_
572	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	via	via	IN	_	_	_
7	Invitrogen	Invitrogen	NNP	_	_	_
8	RNAeasy	RNAeasy	NNP	_	_	_
9	Kit	kit	NN	_	_	_
10	and	and	CC	_	_	_
11	treated	treat	VBN	_	_	_
12	with	with	IN	_	_	_
13	DNaseI	dnasei	NN	_	_	_
14	to	to	TO	_	_	_
15	remove	remove	VB	_	_	_
16	all	all	DT	_	_	_
17	DNA	dna	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	RNA-Seq	rna-seq	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	RNA-seq	rna-seq	NN	_	_	_
22	37C	37c	NN	_	_	_
23	LB	lb	NN	_	_	_
24	rep1	rep1	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	RNA-seq	rna-seq	NN	_	_	_
27	37C	37c	NN	_	_	_
28	LB	lb	NN	_	_	_
29	rep2	rep2	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	RNA-seq	rna-seq	NN	_	_	_
32	data	datum	NNS	_	_	_
33	were	be	VBD	_	_	_
34	mapped	map	VBN	_	_	_
35	to	to	TO	_	_	_
36	the	the	DT	_	_	_
37	E.	e.	FW	_	_	_
38	coli	coli	FW	_	_	_
39	O157	o157	NN	_	_	_
40	:	:	:	_	_	_
41	H7	h7	NN	_	_	_
42	Sakai	Sakai	NNP	_	_	_
43	genome	genome	NN	_	_	_
44	using	use	VBG	_	_	_
45	the	the	DT	_	_	_
46	Subjunc	subjunc	NN	_	_	_
47	aligner	aligner	NN	_	_	_
48	program	program	NN	_	_	_
49	from	from	IN	_	_	_
50	the	the	DT	_	_	_
51	Subread	Subread	NNP	_	_	_
52	package	package	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	v1	v1	NN	_	_	_
55	.4.6	.4.6	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	http://bioinf.wehi.edu.au/subread/	http://bioinf.wehi.edu.au/subread/	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNAseq	rnaseq	NN	_	_	_
3	_	_	CD	_	_	_
4	delAr1delAr2	delar1delar2	NN	_	_	_
5	_	_	NN	_	_	_
6	glycerol	glycerol	NN	SUPP	_	_
7	_	_	CD	_	_	_
8	NH4Cl	nh4cl	NN	_	_	_
9	_	_	CD	_	_	_
10	O2	o2	CD	_	_	_
11	_	_	NN	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	RNAseq	rnaseq	NN	_	_	_
15	_	_	CD	_	_	_
16	delAr1delAr2	delar1delar2	NN	_	_	_
17	_	_	NN	_	_	_
18	glycerol	glycerol	NN	SUPP	_	_
19	_	_	CD	_	_	_
20	NH4Cl	nh4cl	NN	_	_	_
21	_	_	CD	_	_	_
22	O2	o2	CD	_	_	_
23	_	_	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	RNAseq	rnaseq	NN	_	_	_
27	_	_	CD	_	_	_
28	delAr1delAr2	delar1delar2	NN	_	_	_
29	_	_	NN	_	_	_
30	glycerol	glycerol	NN	SUPP	_	_
31	_	_	CD	_	_	_
32	NH4Cl	nh4cl	NN	_	_	_
33	_	_	CD	_	_	_
34	O2	o2	CD	_	_	_
35	_	_	NN	_	_	_
36	3	3	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	RNAseq	rnaseq	NN	_	_	_
39	_	_	CD	_	_	_
40	delAr1	delar1	NN	_	_	_
41	_	_	NN	_	_	_
42	glycerol	glycerol	NN	SUPP	_	_
43	_	_	CD	_	_	_
44	NH4Cl	nh4cl	NN	_	_	_
45	_	_	CD	_	_	_
46	O2	o2	CD	_	_	_
47	_	_	NN	_	_	_
48	1	1	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	RNAseq	rnaseq	NN	_	_	_
51	_	_	CD	_	_	_
52	delAr1	delar1	NN	_	_	_
53	_	_	NN	_	_	_
54	glycerol	glycerol	NN	SUPP	_	_
55	_	_	CD	_	_	_
56	NH4Cl	nh4cl	NN	_	_	_
57	_	_	CD	_	_	_
58	O2	o2	CD	_	_	_
59	_	_	NN	_	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	RNAseq	rnaseq	NN	_	_	_
63	_	_	CD	_	_	_
64	delAr1	delar1	NN	_	_	_
65	_	_	NN	_	_	_
66	glycerol	glycerol	NN	SUPP	_	_
67	_	_	CD	_	_	_
68	NH4Cl	nh4cl	NN	_	_	_
69	_	_	CD	_	_	_
70	O2	o2	CD	_	_	_
71	_	_	NN	_	_	_
72	3	3	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	RNAseq	rnaseq	NN	_	_	_
75	_	_	CD	_	_	_
76	delAr2	delar2	NN	_	_	_
77	_	_	NN	_	_	_
78	glycerol	glycerol	NN	SUPP	_	_
79	_	_	CD	_	_	_
80	NH4Cl	nh4cl	NN	_	_	_
81	_	_	CD	_	_	_
82	O2	o2	CD	_	_	_
83	_	_	NN	_	_	_
84	1	1	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	RNAseq	rnaseq	NN	_	_	_
87	_	_	CD	_	_	_
88	delAr2	delar2	NN	_	_	_
89	_	_	NN	_	_	_
90	glycerol	glycerol	NN	SUPP	_	_
91	_	_	CD	_	_	_
92	NH4Cl	nh4cl	NN	_	_	_
93	_	_	CD	_	_	_
94	O2	o2	CD	_	_	_
95	_	_	NN	_	_	_
96	2	2	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	RNAseq	rnaseq	NN	_	_	_
99	_	_	CD	_	_	_
100	delAr2	delar2	NN	_	_	_
101	_	_	NN	_	_	_
102	glycerol	glycerol	NN	SUPP	_	_
103	_	_	CD	_	_	_
104	NH4Cl	nh4cl	NN	_	_	_
105	_	_	CD	_	_	_
106	O2	o2	CD	_	_	_
107	_	_	NN	_	_	_
108	3	3	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	RNAseq	rnaseq	NN	_	_	_
111	_	_	CD	_	_	_
112	delta-crp	delta-crp	JJ	_	_	_
113	_	_	NN	_	_	_
114	fructose	fructose	NN	_	_	_
115	_	_	CD	_	_	_
116	NH4Cl	nh4cl	NN	_	_	_
117	_	_	CD	_	_	_
118	O2	o2	CD	_	_	_
119	_	_	NN	_	_	_
120	1	1	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	RNAseq	rnaseq	NN	_	_	_
123	_	_	CD	_	_	_
124	delta-crp	delta-crp	JJ	_	_	_
125	_	_	NN	_	_	_
126	fructose	fructose	NN	_	_	_
127	_	_	CD	_	_	_
128	NH4Cl	nh4cl	NN	_	_	_
129	_	_	CD	_	_	_
130	O2	o2	CD	_	_	_
131	_	_	NN	_	_	_
132	2	2	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	RNAseq	rnaseq	NN	_	_	_
135	_	_	CD	_	_	_
136	delta-crp	delta-crp	JJ	_	_	_
137	_	_	NN	_	_	_
138	fructose	fructose	NN	_	_	_
139	_	_	CD	_	_	_
140	NH4Cl	nh4cl	NN	_	_	_
141	_	_	CD	_	_	_
142	O2	o2	CD	_	_	_
143	_	_	NN	_	_	_
144	3	3	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	RNAseq	rnaseq	NN	_	_	_
147	_	_	CD	_	_	_
148	delta-crp	delta-crp	JJ	_	_	_
149	_	_	NN	_	_	_
150	glucose	glucose	NN	SUPP	_	_
151	_	_	CD	_	_	_
152	NH4Cl	nh4cl	NN	_	_	_
153	_	_	CD	_	_	_
154	O2	o2	CD	_	_	_
155	_	_	NN	_	_	_
156	1	1	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	RNAseq	rnaseq	NN	_	_	_
159	_	_	CD	_	_	_
160	delta-crp	delta-crp	JJ	_	_	_
161	_	_	NN	_	_	_
162	glucose	glucose	NN	SUPP	_	_
163	_	_	CD	_	_	_
164	NH4Cl	nh4cl	NN	_	_	_
165	_	_	CD	_	_	_
166	O2	o2	CD	_	_	_
167	_	_	NN	_	_	_
168	2	2	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	RNAseq	rnaseq	NN	_	_	_
171	_	_	CD	_	_	_
172	delta-crp	delta-crp	JJ	_	_	_
173	_	_	NN	_	_	_
174	glucose	glucose	NN	SUPP	_	_
175	_	_	CD	_	_	_
176	NH4Cl	nh4cl	NN	_	_	_
177	_	_	CD	_	_	_
178	O2	o2	CD	_	_	_
179	_	_	NN	_	_	_
180	3	3	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	RNAseq	rnaseq	NN	_	_	_
183	_	_	CD	_	_	_
184	delta-crp	delta-crp	JJ	_	_	_
185	_	_	NN	_	_	_
186	glycerol	glycerol	NN	SUPP	_	_
187	_	_	CD	_	_	_
188	NH4Cl	nh4cl	NN	_	_	_
189	_	_	CD	_	_	_
190	O2	o2	CD	_	_	_
191	_	_	NN	_	_	_
192	1	1	CD	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	RNAseq	rnaseq	NN	_	_	_
195	_	_	CD	_	_	_
196	delta-crp	delta-crp	JJ	_	_	_
197	_	_	NN	_	_	_
198	glycerol	glycerol	NN	SUPP	_	_
199	_	_	CD	_	_	_
200	NH4Cl	nh4cl	NN	_	_	_
201	_	_	CD	_	_	_
202	O2	o2	CD	_	_	_
203	_	_	NN	_	_	_
204	2	2	CD	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	RNAseq	rnaseq	NN	_	_	_
207	_	_	CD	_	_	_
208	delta-crp	delta-crp	JJ	_	_	_
209	_	_	NN	_	_	_
210	glycerol	glycerol	NN	SUPP	_	_
211	_	_	CD	_	_	_
212	NH4Cl	nh4cl	NN	_	_	_
213	_	_	CD	_	_	_
214	O2	o2	CD	_	_	_
215	_	_	NN	_	_	_
216	3	3	CD	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	RNA-seq	rna-seq	NN	_	_	_
219	libraries	library	NNS	_	_	_
220	were	be	VBD	_	_	_
221	prepared	prepare	VBN	_	_	_
222	by	by	IN	_	_	_
223	Vertis	Vertis	NNP	_	_	_
224	AG	AG	NNP	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	Freising-Weihenstephan	Freising-Weihenstephan	NNP	_	_	_
227	,	,	,	_	_	_
228	Germany	Germany	NNP	_	_	_
229	-RRB-	-rrb-	-RRB-	_	_	_
230	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	were	be	VBD	_	_	_
7	done	do	VBN	_	_	_
8	using	use	VBG	_	_	_
9	blind	blind	JJ	_	_	_
10	and	and	CC	_	_	_
11	fit-only	fit-only	JJ	_	_	_
12	parameter	parameter	NN	_	_	_
13	in	in	IN	_	_	_
14	DE-Seq	de-seq	NN	_	_	_
15	pakage	pakage	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	RNA-seq	rna-seq	NN	_	_	_
18	of	of	IN	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	wt	wt	JJ	_	_	_
22	cells	cell	NNS	_	_	_
23	in	in	IN	_	_	_
24	stationary	stationary	JJ	GrowthPhase	_	_
25	phase	phase	NN	GrowthPhase	_	_
26	30	30	CD	_	_	_
27	°C	°c	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	30h	30h	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	RNA-seq	rna-seq	NN	_	_	_
33	of	of	IN	_	_	_
34	E.	e.	FW	_	_	_
35	coli	coli	FW	_	_	_
36	wt	wt	JJ	_	_	_
37	cells	cell	NNS	_	_	_
38	in	in	IN	_	_	_
39	stationary	stationary	JJ	GrowthPhase	_	_
40	phase	phase	NN	GrowthPhase	_	_
41	30	30	CD	_	_	_
42	°C	°c	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	30h	30h	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	-	-	:	_	_	_
47	Replicate	replicate	VB	_	_	_
48	1	1	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	RNA-seq	rna-seq	NN	_	_	_
51	reads	read	VBZ	_	_	_
52	were	be	VBD	_	_	_
53	aligned	align	VBN	_	_	_
54	to	to	TO	_	_	_
55	the	the	DT	_	_	_
56	CFT073	cft073	NN	_	_	_
57	genome	genome	NN	_	_	_
58	using	use	VBG	_	_	_
59	bowtie	bowtie	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	version	version	NN	_	_	_
62	0.12.8	0.12.8	CD	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	RNA-seq	rna-seq	NN	_	_	_
66	reads	read	VBZ	_	_	_
67	were	be	VBD	_	_	_
68	aligned	align	VBN	_	_	_
69	to	to	TO	_	_	_
70	the	the	DT	_	_	_
71	W3110	w3110	NN	_	_	_
72	genome	genome	NN	_	_	_
73	using	use	VBG	_	_	_
74	CASAVA	CASAVA	NNP	_	_	_
75	1.8.2	1.8.2	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	RNA-seq	rna-seq	NN	_	_	_
78	reads	read	VBZ	_	_	_
79	were	be	VBD	_	_	_
80	mapped	map	VBN	_	_	_
81	to	to	TO	_	_	_
82	the	the	DT	_	_	_
83	E.	e.	FW	_	_	_
84	coli	coli	FW	_	_	_
85	K-12	k-12	NN	_	_	_
86	MG1655	mg1655	NN	_	_	_
87	genome	genome	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	GenBank	genbank	NN	_	_	_
90	ID	id	NN	_	_	_
91	U00096	u00096	NN	_	_	_
92	.2	.2	NN	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	using	use	VBG	_	_	_
95	short	short	JJ	_	_	_
96	oligonucleotide	oligonucleotide	NN	_	_	_
97	alignment	alignment	NN	_	_	_
98	program	program	NN	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	SOAP	soap	NN	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	RNA-Seq	rna-seq	NN	_	_	_
104	reads	read	VBZ	_	_	_
105	were	be	VBD	_	_	_
106	mapped	map	VBN	_	_	_
107	to	to	TO	_	_	_
108	the	the	DT	_	_	_
109	reference	reference	NN	_	_	_
110	genome	genome	NN	_	_	_
111	using	use	VBG	_	_	_
112	EDGE-Pro	edge-pro	NN	_	_	_
113	-LRB-	-lrb-	-LRB-	_	_	_
114	Magoc	magoc	NN	_	_	_
115	T	t	NN	_	_	_
116	,	,	,	_	_	_
117	Wood	Wood	NNP	_	_	_
118	D	D	NNP	_	_	_
119	and	and	CC	_	_	_
120	Salzberg	Salzberg	NNP	_	_	_
121	SL	SL	NNP	_	_	_
122	,	,	,	_	_	_
123	2013	2013	CD	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	with	with	IN	_	_	_
127	default	default	NN	_	_	_
128	parameters	parameter	NNS	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
130	RNA	rna	NN	_	_	_
131	sequences	sequence	NNS	_	_	_
132	from	from	IN	_	_	_
133	each	each	DT	_	_	_
134	of	of	IN	_	_	_
135	the	the	DT	_	_	_
136	two	two	CD	_	_	_
137	differential	differential	JJ	_	_	_
138	analyses	analysis	NNS	_	_	_
139	were	be	VBD	_	_	_
140	processed	process	VBN	_	_	_
141	and	and	CC	_	_	_
142	mapped	map	VBN	_	_	_
143	to	to	TO	_	_	_
144	the	the	DT	_	_	_
145	corresponding	corresponding	JJ	_	_	_
146	genomes	genome	NNS	_	_	_
147	as	as	IN	_	_	_
148	a	a	DT	_	_	_
149	service	service	NN	_	_	_
150	provided	provide	VBN	_	_	_
151	by	by	IN	_	_	_
152	vertis	vertis	NN	_	_	_
153	Biotechnologie	Biotechnologie	NNP	_	_	_
154	AG	AG	NNP	_	_	_
155	,	,	,	_	_	_
156	Germany	Germany	NNP	_	_	_
157	-LRB-	-lrb-	-LRB-	_	_	_
158	www.vertis-biotech.com	www.vertis-biotech.com	NNP	_	_	_
159	-RRB-	-rrb-	-RRB-	_	_	_
160	.	.	.	_	_	_

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	sequences	sequence	NNS	_	_	_
4	were	be	VBD	_	_	_
5	quality	quality	JJ	_	_	_
6	assessed	assess	VBN	_	_	_
7	and	and	CC	_	_	_
8	trimmed	trim	VBN	_	_	_
9	using	use	VBG	_	_	_
10	FastQC	fastqc	NN	_	_	_
11	version	version	NN	_	_	_
12	0.10.1	0.10.1	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	www.bioinformatics.babraham.ac.uk/projects/fastqc/	www.bioinformatics.babraham.ac.uk/projects/fastqc/	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	identification	identification	NN	_	_	_
3	of	of	IN	_	_	_
4	differentially	differentially	RB	_	_	_
5	expressed	express	VBN	_	_	_
6	genes	gene	NNS	_	_	_
7	was	be	VBD	_	_	_
8	performed	perform	VBN	_	_	_
9	using	use	VBG	_	_	_
10	cufflinks	cufflink	NNS	_	_	_
11	version	version	NN	_	_	_
12	2.0.2	2.0.2	CD	_	_	_
13	to	to	TO	_	_	_
14	analyse	analyse	VB	_	_	_
15	the	the	DT	_	_	_
16	trimmed	trimmed	RBR	_	_	_
17	sequences	sequence	NNS	_	_	_
18	as	as	IN	_	_	_
19	a	a	DT	_	_	_
20	time	time	NN	_	_	_
21	course	course	NN	_	_	_
22	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	trimmed	trim	VBD	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	aligned	align	VBN	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	reference	reference	NN	_	_	_
13	genome	genome	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	NC	nc	NN	_	_	_
16	_	_	CD	_	_	_
17	000913	000913	CD	_	_	_
18	13-Feb-2011	13-feb-2011	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	using	use	VBG	_	_	_
21	Tophat	Tophat	NNP	_	_	_
22	version	version	NN	_	_	_
23	2.0.7	2.0.7	CD	_	_	_
24	.	.	.	_	_	_

1	Aligned	align	VBN	_	_	_
2	reads	read	VBZ	_	_	_
3	were	be	VBD	_	_	_
4	assembled	assemble	VBN	_	_	_
5	for	for	IN	_	_	_
6	differential	differential	JJ	_	_	_
7	expression	expression	NN	_	_	_
8	using	use	VBG	_	_	_
9	cufflinks	cufflink	NNS	_	_	_
10	version	version	NN	_	_	_
11	and	and	CC	_	_	_
12	merged	merge	VBD	_	_	_
13	using	use	VBG	_	_	_
14	cuffmerge	cuffmerge	NN	_	_	_
15	with	with	IN	_	_	_
16	an	a	DT	_	_	_
17	`	`	``	_	_	_
18	assemblies	assembly	NNS	_	_	_
19	'	'	POS	_	_	_
20	file	file	NN	_	_	_
21	containing	contain	VBG	_	_	_
22	the	the	DT	_	_	_
23	transcript.gtf	transcript.gtf	JJ	_	_	_
24	output	output	NN	_	_	_
25	files	file	NNS	_	_	_
26	from	from	IN	_	_	_
27	culfflinks	culfflink	NNS	_	_	_
28	.	.	.	_	_	_

1	Differential	differential	JJ	_	_	_
2	expression	expression	NN	_	_	_
3	analysis	analysis	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	merged.gtf	merged.gtf	JJ	_	_	_
9	output	output	NN	_	_	_
10	file	file	NN	_	_	_
11	from	from	IN	_	_	_
12	cuffmerge	cuffmerge	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	by	by	IN	_	_	_
6	the	the	DT	_	_	_
7	DOE	DOE	NNP	_	_	_
8	Joint	Joint	NNP	_	_	_
9	Genome	Genome	NNP	_	_	_
10	Institute	Institute	NNP	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	dUTP	dutp	NN	_	_	_
14	method	method	NN	_	_	_
15	.	.	.	_	_	_

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	85/100	85/100	CD	_	_	_
15	,	,	,	_	_	_
16	then	then	RB	_	_	_
17	140/100	140/100	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	selected	select	VBN	_	_	_
20	cDNAs	cdna	NNS	_	_	_
21	in	in	IN	_	_	_
22	a	a	DT	_	_	_
23	range	range	NN	_	_	_
24	between	between	IN	_	_	_
25	150-350	150-350	CD	_	_	_
26	bp	bp	NN	_	_	_
27	.	.	.	_	_	_

1	cDNAs	cdna	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	A-tailed	a-tailed	JJ	_	_	_
5	using	use	VBG	_	_	_
6	Exo	Exo	NNP	_	_	_
7	-	-	:	_	_	_
8	Klenow	Klenow	NNP	_	_	_
9	,	,	,	_	_	_
10	followed	follow	VBN	_	_	_
11	by	by	IN	_	_	_
12	ligation	ligation	NN	_	_	_
13	of	of	IN	_	_	_
14	sequencing	sequencing	NN	_	_	_
15	adapter	adapter	NN	_	_	_
16	oligos	oligo	NNS	_	_	_
17	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	bead	bead	NN	_	_	_
3	purification	purification	NN	_	_	_
4	,	,	,	_	_	_
5	dUTP	dutp	NN	_	_	_
6	was	be	VBD	_	_	_
7	cleaved	cleave	VBN	_	_	_
8	from	from	IN	_	_	_
9	the	the	DT	_	_	_
10	second	second	JJ	_	_	_
11	strand	strand	NN	_	_	_
12	using	use	VBG	_	_	_
13	AmpErase	AmpErase	NNP	_	_	_
14	Uracil	Uracil	NNP	_	_	_
15	N-glycosylase	n-glycosylase	NN	_	_	_
16	,	,	,	_	_	_
17	resulting	result	VBG	_	_	_
18	in	in	IN	_	_	_
19	adaptor	adaptor	NN	_	_	_
20	ligated	ligate	VBD	_	_	_
21	single	single	JJ	_	_	_
22	stranded	strand	VBN	_	_	_
23	cDNAs	cdna	NNS	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNAseq	rnaseq	NN	_	_	_
3	_	_	CD	_	_	_
4	wt	wt	JJ	_	_	_
5	_	_	NN	_	_	_
6	fructose	fructose	NN	_	_	_
7	_	_	CD	_	_	_
8	NH4Cl	nh4cl	NN	_	_	_
9	_	_	CD	_	_	_
10	O2	o2	CD	_	_	_
11	_	_	NN	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	RNAseq	rnaseq	NN	_	_	_
15	_	_	CD	_	_	_
16	wt	wt	JJ	_	_	_
17	_	_	NN	_	_	_
18	fructose	fructose	NN	_	_	_
19	_	_	CD	_	_	_
20	NH4Cl	nh4cl	NN	_	_	_
21	_	_	CD	_	_	_
22	O2	o2	CD	_	_	_
23	_	_	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	RNAseq	rnaseq	NN	_	_	_
27	_	_	CD	_	_	_
28	wt	wt	JJ	_	_	_
29	_	_	NN	_	_	_
30	glucose	glucose	NN	SUPP	_	_
31	_	_	CD	_	_	_
32	NH4Cl	nh4cl	NN	_	_	_
33	_	_	CD	_	_	_
34	O2	o2	CD	_	_	_
35	_	_	NN	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	RNAseq	rnaseq	NN	_	_	_
39	_	_	CD	_	_	_
40	wt	wt	JJ	_	_	_
41	_	_	NN	_	_	_
42	glucose	glucose	NN	SUPP	_	_
43	_	_	CD	_	_	_
44	NH4Cl	nh4cl	NN	_	_	_
45	_	_	CD	_	_	_
46	O2	o2	CD	_	_	_
47	_	_	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	RNAseq	rnaseq	NN	_	_	_
51	_	_	CD	_	_	_
52	wt	wt	JJ	_	_	_
53	_	_	NN	_	_	_
54	glucose	glucose	NN	SUPP	_	_
55	_	_	CD	_	_	_
56	NH4Cl	nh4cl	NN	_	_	_
57	_	_	CD	_	_	_
58	O2	o2	CD	_	_	_
59	_	_	NN	_	_	_
60	3	3	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	RNAseq	rnaseq	NN	_	_	_
63	_	_	CD	_	_	_
64	wt	wt	JJ	_	_	_
65	_	_	NN	_	_	_
66	glycerol	glycerol	NN	SUPP	_	_
67	_	_	CD	_	_	_
68	NH4Cl	nh4cl	NN	_	_	_
69	_	_	CD	_	_	_
70	O2	o2	CD	_	_	_
71	_	_	NN	_	_	_
72	1	1	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	RNAseq	rnaseq	NN	_	_	_
75	_	_	CD	_	_	_
76	wt	wt	JJ	_	_	_
77	_	_	NN	_	_	_
78	glycerol	glycerol	NN	SUPP	_	_
79	_	_	CD	_	_	_
80	NH4Cl	nh4cl	NN	_	_	_
81	_	_	CD	_	_	_
82	O2	o2	CD	_	_	_
83	_	_	NN	_	_	_
84	2	2	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	RNA-size	rna-size	NN	_	_	_
87	selection	selection	NN	_	_	_
88	and	and	CC	_	_	_
89	generation	generation	NN	_	_	_
90	of	of	IN	_	_	_
91	the	the	DT	_	_	_
92	cDNA	cdna	NN	_	_	_
93	libraries	library	NNS	_	_	_
94	was	be	VBD	_	_	_
95	performed	perform	VBN	_	_	_
96	as	as	IN	_	_	_
97	described	describe	VBN	_	_	_
98	-LCB-	-lcb-	-LRB-	_	_	_
99	Ingolia	Ingolia	NNP	_	_	_
100	,	,	,	_	_	_
101	2009	2009	CD	_	_	_
102	-RCB-	-rcb-	-RRB-	_	_	_
103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
104	RNAsnap	rnasnap	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	RNAsnap	rnasnap	NN	_	_	_
107	followed	follow	VBN	_	_	_
108	by	by	IN	_	_	_
109	purification	purification	NN	_	_	_
110	through	through	IN	_	_	_
111	Zymo	Zymo	NNP	_	_	_
112	RNA	rna	NN	_	_	_
113	clean	clean	JJ	_	_	_
114	and	and	CC	_	_	_
115	concentrator	concentrator	NN	_	_	_
116	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNAsnap	rnasnap	NN	_	_	_
3	followed	follow	VBN	_	_	_
4	by	by	IN	_	_	_
5	RiboZero	RiboZero	NNP	_	_	_
6	rRNA	rrna	NN	_	_	_
7	removal	removal	NN	_	_	_
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	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	rna	rna	NN	GEN	_	_
17	treatment	treatment	NN	_	_	_
18	:	:	:	_	_	_
19	no	no	DT	_	_	_
20	RNA	rna	NN	_	_	_
21	treatment	treatment	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	rna	rna	NN	GEN	_	_
24	treatment	treatment	NN	_	_	_
25	:	:	:	_	_	_
26	rRNA	rrna	NN	_	_	_
27	depleted	deplete	VBD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	rna	rna	NN	GEN	_	_
30	treatment	treatment	NN	_	_	_
31	:	:	:	_	_	_
32	rRNA	rrna	NN	_	_	_
33	depleted	deplete	VBN	_	_	_
34	;	;	:	_	_	_
35	Terminal	terminal	JJ	_	_	_
36	Exonuclease	exonuclease	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	RNA	rna	NN	_	_	_
39	was	be	VBD	_	_	_
40	dephosphorylated	dephosphorylate	VBN	_	_	_
41	,	,	,	_	_	_
42	ligated	ligate	VBN	_	_	_
43	to	to	TO	_	_	_
44	an	a	DT	_	_	_
45	adaptor	adaptor	NN	_	_	_
46	,	,	,	_	_	_
47	reverse	reverse	JJ	_	_	_
48	transcribed	transcribe	VBN	_	_	_
49	,	,	,	_	_	_
50	circularized	circularize	VBN	_	_	_
51	then	then	RB	_	_	_
52	amplified	amplify	VBN	_	_	_
53	with	with	IN	_	_	_
54	Illumina	Illumina	NNP	_	_	_
55	adaptors	adaptor	NNS	_	_	_
56	and	and	CC	_	_	_
57	barcodes	barcode	NNS	_	_	_
58	.	.	.	_	_	_

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	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	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	each	each	DT	_	_	_
7	sample	sample	NN	_	_	_
8	using	use	VBG	_	_	_
9	a	a	DT	_	_	_
10	QIAGEN	QIAGEN	NNP	_	_	_
11	RNA	rna	NN	_	_	_
12	extraction	extraction	NN	_	_	_
13	kit	kit	NN	_	_	_
14	according	accord	VBG	_	_	_
15	to	to	TO	_	_	_
16	the	the	DT	_	_	_
17	manufacturer	manufacturer	NN	_	_	_
18	's	's	POS	_	_	_
19	instruction	instruction	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	RNA	rna	NN	_	_	_
22	was	be	VBD	_	_	_
23	extracted	extract	VBN	_	_	_
24	from	from	IN	_	_	_
25	harvested	harvest	VBN	_	_	_
26	cultures	culture	NNS	_	_	_
27	using	use	VBG	_	_	_
28	a	a	DT	_	_	_
29	hot	hot	JJ	_	_	_
30	lysis	lysis	NN	_	_	_
31	buffer	buffer	NN	_	_	_
32	and	and	CC	_	_	_
33	acid	acid	NN	_	_	_
34	phenol-based	phenol-based	JJ	_	_	_
35	extraction	extraction	NN	_	_	_
36	method	method	NN	_	_	_
37	and	and	CC	_	_	_
38	isopropanol	isopropanol	NN	_	_	_
39	precipitation	precipitation	NN	_	_	_
40	.	.	.	_	_	_

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	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	samples	sample	NNS	_	_	_
7	using	use	VBG	_	_	_
8	hot	hot	JJ	_	_	_
9	phenol	phenol	NN	_	_	_
10	.	.	.	_	_	_

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

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	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	two	two	CD	_	_	_
7	biological	biological	JJ	_	_	_
8	replicates	replicate	VBZ	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	30	30	CD	_	_	_
11	mL	ml	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	of	of	IN	_	_	_
14	each	each	DT	_	_	_
15	bacterial	bacterial	JJ	_	_	_
16	culture	culture	NN	_	_	_
17	isolated	isolate	VBN	_	_	_
18	at	at	IN	_	_	_
19	each	each	DT	_	_	_
20	time	time	NN	_	_	_
21	point	point	NN	_	_	_
22	.	.	.	_	_	_

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/Phenol	etoh/phenol	NN	_	_	_
18	stop	stop	VB	_	_	_
19	solution	solution	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	5	5	CD	_	_	_
22	%	%	NN	_	_	_
23	water-saturated	water-saturated	JJ	_	_	_
24	phenol	phenol	NN	_	_	_
25	pH	ph	NN	_	_	_
26	4.2	4.2	CD	_	_	_
27	-LSB-	-lsb-	-LRB-	_	_	_
28	Invitrogen	invitrogen	NN	_	_	_
29	-RSB-	-rsb-	-RRB-	_	_	_
30	in	in	IN	_	_	_
31	100	100	CD	_	_	_
32	%	%	NN	_	_	_
33	ethanol	ethanol	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	4,000	4,000	CD	_	_	_
8	rpm	rpm	NN	_	_	_
9	,	,	,	_	_	_
10	5	5	CD	_	_	_
11	min	min	NN	_	_	_
12	,	,	,	_	_	_
13	4	4	CD	_	_	_
14	°C	°c	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	pellet	pellet	NN	_	_	_
19	suspended	suspend	VBN	_	_	_
20	in	in	IN	_	_	_
21	800	800	CD	_	_	_
22	µL	µl	NN	_	_	_
23	TE	TE	NNP	_	_	_
24	pH	ph	NN	_	_	_
25	8.0	8.0	CD	_	_	_
26	supplemented	supplement	VBN	_	_	_
27	with	with	IN	_	_	_
28	0.5	0.5	CD	_	_	_
29	mg/mL	mg/ml	NN	_	_	_
30	lysozyme	lysozyme	NN	_	_	_
31	.	.	.	_	_	_

1	SDS	sds	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	80	80	CD	_	_	_
4	µL	µl	NN	_	_	_
5	at	at	IN	_	_	_
6	10	10	CD	_	_	_
7	%	%	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	w/v	w/v	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	added	add	VBN	_	_	_
14	,	,	,	_	_	_
15	samples	sample	NNS	_	_	_
16	mixed	mix	VBN	_	_	_
17	by	by	IN	_	_	_
18	inversion	inversion	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	incubated	incubate	VBN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	65	65	CD	_	_	_
24	°C	°c	NN	_	_	_
25	,	,	,	_	_	_
26	2	2	CD	_	_	_
27	min	min	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	,	,	,	_	_	_
30	before	before	IN	_	_	_
31	the	the	DT	_	_	_
32	addition	addition	NN	_	_	_
33	of	of	IN	_	_	_
34	88	88	CD	_	_	_
35	µL	µl	NN	_	_	_
36	1	1	CD	_	_	_
37	M	m	NN	_	_	_
38	NaOAc	naoac	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	pH	ph	NN	_	_	_
41	5.2	5.2	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	an	a	DT	_	_	_
7	equal	equal	JJ	_	_	_
8	volume	volume	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	1mL	1ml	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	of	of	IN	_	_	_
13	water-saturated	water-saturated	JJ	_	_	_
14	phenol	phenol	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	pH	ph	NN	_	_	_
17	4.2	4.2	CD	_	_	_
18	,	,	,	_	_	_
19	65	65	CD	_	_	_
20	°C	°c	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	incubated	incubate	VBN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	65	65	CD	_	_	_
26	°C	°c	NN	_	_	_
27	,	,	,	_	_	_
28	6	6	CD	_	_	_
29	min	min	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	solution	solution	NN	_	_	_
3	was	be	VBD	_	_	_
4	separated	separate	VBN	_	_	_
5	into	into	IN	_	_	_
6	layers	layer	NNS	_	_	_
7	by	by	IN	_	_	_
8	centrifugation	centrifugation	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	14,000	14,000	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	,	,	,	_	_	_
13	10	10	CD	_	_	_
14	min	min	NN	_	_	_
15	,	,	,	_	_	_
16	4	4	CD	_	_	_
17	°C	°c	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	the	the	DT	_	_	_
21	upper	upper	JJ	_	_	_
22	aqueous	aqueous	JJ	_	_	_
23	RNA	rna	NN	_	_	_
24	containing	contain	VBG	_	_	_
25	layer	layer	NN	_	_	_
26	removed	remove	VBD	_	_	_
27	and	and	CC	_	_	_
28	transferred	transfer	VBD	_	_	_
29	into	into	IN	_	_	_
30	a	a	DT	_	_	_
31	fresh	fresh	JJ	_	_	_
32	tube	tube	NN	_	_	_
33	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	cleaned	clean	VBN	_	_	_
4	by	by	IN	_	_	_
5	three	three	CD	_	_	_
6	extractions	extraction	NNS	_	_	_
7	with	with	IN	_	_	_
8	phenol	phenol	NN	_	_	_
9	:	:	:	_	_	_
10	CHCl3	chcl3	NN	_	_	_
11	:	:	:	_	_	_
12	IAA	iaa	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	25:24:1	25:24:1	CD	_	_	_
15	,	,	,	_	_	_
16	pH	ph	NN	_	_	_
17	8.0	8.0	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	before	before	IN	_	_	_
20	being	be	VBG	_	_	_
21	precipitated	precipitated	JJ	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	-80	-80	CD	_	_	_
24	°C	°c	NN	_	_	_
25	,	,	,	_	_	_
26	O/N	o/n	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	following	follow	VBG	_	_	_
29	the	the	DT	_	_	_
30	addition	addition	NN	_	_	_
31	of	of	IN	_	_	_
32	1/10	1/10	CD	_	_	_
33	volume	volume	NN	_	_	_
34	of	of	IN	_	_	_
35	3M	3M	NNP	_	_	_
36	NaOAc	naoac	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	pH	ph	NN	_	_	_
39	5.2	5.2	CD	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	and	and	CC	_	_	_
42	2	2	CD	_	_	_
43	volumes	volume	NNS	_	_	_
44	of	of	IN	_	_	_
45	ice	ice	NN	_	_	_
46	cold	cold	JJ	_	_	_
47	100	100	CD	_	_	_
48	%	%	NN	_	_	_
49	EtOH	etoh	NN	_	_	_
50	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	pelleted	pelleted	JJ	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	14,000	14,000	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	,	,	,	_	_	_
8	25	25	CD	_	_	_
9	min	min	NN	_	_	_
10	,	,	,	_	_	_
11	4	4	CD	_	_	_
12	°C	°c	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	supernatant	supernatant	JJ	_	_	_
17	removed	remove	VBN	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	washed	wash	VBN	_	_	_
22	with	with	IN	_	_	_
23	1	1	CD	_	_	_
24	mL	ml	NN	_	_	_
25	75	75	CD	_	_	_
26	%	%	NN	_	_	_
27	cold	cold	JJ	_	_	_
28	EtOH	etoh	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	made	make	VBN	_	_	_
31	with	with	IN	_	_	_
32	DEPC-treated	depc-treated	JJ	_	_	_
33	water	water	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	two	two	CD	_	_	_
7	biological	biological	JJ	_	_	_
8	replicates	replicate	VBZ	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	30	30	CD	_	_	_
11	mL	ml	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	of	of	IN	_	_	_
14	each	each	DT	_	_	_
15	bacterial	bacterial	JJ	_	_	_
16	culture	culture	NN	_	_	_
17	isolated	isolate	VBN	_	_	_
18	at	at	IN	_	_	_
19	each	each	DT	_	_	_
20	time	time	NN	_	_	_
21	point	point	NN	_	_	_
22	.	.	.	_	_	_

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/Phenol	etoh/phenol	NN	_	_	_
18	stop	stop	VB	_	_	_
19	solution	solution	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	5	5	CD	_	_	_
22	%	%	NN	_	_	_
23	water-saturated	water-saturated	JJ	_	_	_
24	phenol	phenol	NN	_	_	_
25	pH	ph	NN	_	_	_
26	4.2	4.2	CD	_	_	_
27	-LSB-	-lsb-	-LRB-	_	_	_
28	Invitrogen	invitrogen	NN	_	_	_
29	-RSB-	-rsb-	-RRB-	_	_	_
30	in	in	IN	_	_	_
31	100	100	CD	_	_	_
32	%	%	NN	_	_	_
33	ethanol	ethanol	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	4,000	4,000	CD	_	_	_
8	rpm	rpm	NN	_	_	_
9	,	,	,	_	_	_
10	5	5	CD	_	_	_
11	min	min	NN	_	_	_
12	,	,	,	_	_	_
13	4	4	CD	_	_	_
14	°C	°c	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	pellet	pellet	NN	_	_	_
19	suspended	suspend	VBN	_	_	_
20	in	in	IN	_	_	_
21	800	800	CD	_	_	_
22	µL	µl	NN	_	_	_
23	TE	TE	NNP	_	_	_
24	pH	ph	NN	_	_	_
25	8.0	8.0	CD	_	_	_
26	supplemented	supplement	VBN	_	_	_
27	with	with	IN	_	_	_
28	0.5	0.5	CD	_	_	_
29	mg/mL	mg/ml	NN	_	_	_
30	lysozyme	lysozyme	NN	_	_	_
31	.	.	.	_	_	_

1	SDS	sds	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	80	80	CD	_	_	_
4	µL	µl	NN	_	_	_
5	at	at	IN	_	_	_
6	10	10	CD	_	_	_
7	%	%	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	w/v	w/v	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	added	add	VBN	_	_	_
14	,	,	,	_	_	_
15	samples	sample	NNS	_	_	_
16	mixed	mix	VBN	_	_	_
17	by	by	IN	_	_	_
18	inversion	inversion	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	incubated	incubate	VBN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	65	65	CD	_	_	_
24	°C	°c	NN	_	_	_
25	,	,	,	_	_	_
26	2	2	CD	_	_	_
27	min	min	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	,	,	,	_	_	_
30	before	before	IN	_	_	_
31	the	the	DT	_	_	_
32	addition	addition	NN	_	_	_
33	of	of	IN	_	_	_
34	88	88	CD	_	_	_
35	µL	µl	NN	_	_	_
36	1	1	CD	_	_	_
37	M	m	NN	_	_	_
38	NaOAc	naoac	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	pH	ph	NN	_	_	_
41	5.2	5.2	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	an	a	DT	_	_	_
7	equal	equal	JJ	_	_	_
8	volume	volume	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	1mL	1ml	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	of	of	IN	_	_	_
13	water-saturated	water-saturated	JJ	_	_	_
14	phenol	phenol	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	pH	ph	NN	_	_	_
17	4.2	4.2	CD	_	_	_
18	,	,	,	_	_	_
19	65	65	CD	_	_	_
20	°C	°c	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	incubated	incubate	VBN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	65	65	CD	_	_	_
26	°C	°c	NN	_	_	_
27	,	,	,	_	_	_
28	6	6	CD	_	_	_
29	min	min	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	solution	solution	NN	_	_	_
3	was	be	VBD	_	_	_
4	separated	separate	VBN	_	_	_
5	into	into	IN	_	_	_
6	layers	layer	NNS	_	_	_
7	by	by	IN	_	_	_
8	centrifugation	centrifugation	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	14,000	14,000	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	,	,	,	_	_	_
13	10	10	CD	_	_	_
14	min	min	NN	_	_	_
15	,	,	,	_	_	_
16	4	4	CD	_	_	_
17	°C	°c	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	the	the	DT	_	_	_
21	upper	upper	JJ	_	_	_
22	aqueous	aqueous	JJ	_	_	_
23	RNA	rna	NN	_	_	_
24	containing	contain	VBG	_	_	_
25	layer	layer	NN	_	_	_
26	removed	remove	VBD	_	_	_
27	and	and	CC	_	_	_
28	transferred	transfer	VBD	_	_	_
29	into	into	IN	_	_	_
30	a	a	DT	_	_	_
31	fresh	fresh	JJ	_	_	_
32	tube	tube	NN	_	_	_
33	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	cleaned	clean	VBN	_	_	_
4	by	by	IN	_	_	_
5	three	three	CD	_	_	_
6	extractions	extraction	NNS	_	_	_
7	with	with	IN	_	_	_
8	phenol	phenol	NN	_	_	_
9	:	:	:	_	_	_
10	CHCl3	chcl3	NN	_	_	_
11	:	:	:	_	_	_
12	IAA	iaa	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	25:24:1	25:24:1	CD	_	_	_
15	,	,	,	_	_	_
16	pH	ph	NN	_	_	_
17	8.0	8.0	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	before	before	IN	_	_	_
20	being	be	VBG	_	_	_
21	precipitated	precipitated	JJ	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	-80	-80	CD	_	_	_
24	°C	°c	NN	_	_	_
25	,	,	,	_	_	_
26	O/N	o/n	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	following	follow	VBG	_	_	_
29	the	the	DT	_	_	_
30	addition	addition	NN	_	_	_
31	of	of	IN	_	_	_
32	1/10	1/10	CD	_	_	_
33	volume	volume	NN	_	_	_
34	of	of	IN	_	_	_
35	3M	3M	NNP	_	_	_
36	NaOAc	naoac	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	pH	ph	NN	_	_	_
39	5.2	5.2	CD	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	and	and	CC	_	_	_
42	2	2	CD	_	_	_
43	volumes	volume	NNS	_	_	_
44	of	of	IN	_	_	_
45	ice	ice	NN	_	_	_
46	cold	cold	JJ	_	_	_
47	100	100	CD	_	_	_
48	%	%	NN	_	_	_
49	EtOH	etoh	NN	_	_	_
50	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	pelleted	pelleted	JJ	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	14,000	14,000	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	,	,	,	_	_	_
8	25	25	CD	_	_	_
9	min	min	NN	_	_	_
10	,	,	,	_	_	_
11	4	4	CD	_	_	_
12	°C	°c	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	supernatant	supernatant	JJ	_	_	_
17	removed	remove	VBN	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	washed	wash	VBN	_	_	_
22	with	with	IN	_	_	_
23	1	1	CD	_	_	_
24	mL	ml	NN	_	_	_
25	75	75	CD	_	_	_
26	%	%	NN	_	_	_
27	cold	cold	JJ	_	_	_
28	EtOH	etoh	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	made	make	VBN	_	_	_
31	with	with	IN	_	_	_
32	DEPC-treated	depc-treated	JJ	_	_	_
33	water	water	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	pelleted	pelleted	JJ	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	14,000	14,000	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	,	,	,	_	_	_
8	5	5	CD	_	_	_
9	min	min	NN	_	_	_
10	,	,	,	_	_	_
11	4	4	CD	_	_	_
12	°C	°c	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	air	air	NN	_	_	_
16	dried	dry	VBD	_	_	_
17	before	before	IN	_	_	_
18	suspension	suspension	NN	_	_	_
19	in	in	IN	_	_	_
20	80	80	CD	_	_	_
21	µL	µl	NN	_	_	_
22	RNAse	rnase	NN	_	_	_
23	free	free	JJ	_	_	_
24	water	water	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Invitrogen	invitrogen	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	treatment	treatment	NN	_	_	_
30	with	with	IN	_	_	_
31	TURBO	TURBO	NNP	_	_	_
32	DNAse	dnase	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Ambion	ambion	NN	_	_	_
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	instructions	instruction	NNS	_	_	_
42	.	.	.	_	_	_

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	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	an	a	DT	_	_	_
7	RNeasy	rneasy	JJ	_	_	_
8	kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	qiagen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	after	after	IN	_	_	_
14	1st	1st	JJ	_	_	_
15	and	and	CC	_	_	_
16	2nd	2nd	JJ	_	_	_
17	strand	strand	NN	_	_	_
18	cDNA	cdna	NN	_	_	_
19	synthesis	synthesis	NN	_	_	_
20	,	,	,	_	_	_
21	linker	linker	NN	_	_	_
22	ligation	ligation	NN	_	_	_
23	and	and	CC	_	_	_
24	size	size	NN	_	_	_
25	selection	selection	NN	_	_	_
26	subjected	subject	VBN	_	_	_
27	to	to	TO	_	_	_
28	shotgun	shotgun	NN	_	_	_
29	sequencing	sequencing	NN	_	_	_
30	using	use	VBG	_	_	_
31	single	single	JJ	_	_	_
32	read	read	NN	_	_	_
33	40bp	40bp	JJ	_	_	_
34	read	read	NN	_	_	_
35	length	length	NN	_	_	_
36	runs	run	VBZ	_	_	_
37	on	on	IN	_	_	_
38	an	a	DT	_	_	_
39	Illumina	Illumina	NNP	_	_	_
40	Genome	Genome	NNP	_	_	_
41	Analyzer	Analyzer	NNP	_	_	_
42	GAII	GAII	NNP	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	QIAGEN	QIAGEN	NNP	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	Mini	Mini	NNP	_	_	_
9	Kit	kit	NN	_	_	_
10	following	follow	VBG	_	_	_
11	manufacturer	manufacturer	NN	_	_	_
12	's	's	POS	_	_	_
13	instructions	instruction	NNS	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Qiagen	Qiagen	NNP	_	_	_
7	's	's	POS	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	minikit	minikit	NN	_	_	_
10	Cat	cat	NN	_	_	_
11	#	#	#	_	_	_
12	74106	74106	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	RNA	rna	NN	_	_	_
15	was	be	VBD	_	_	_
16	extracted	extract	VBN	_	_	_
17	using	use	VBG	_	_	_
18	RNAeasy	rnaeasy	NN	_	_	_
19	columns	column	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Qiagen	Qiagen	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	following	follow	VBG	_	_	_
24	the	the	DT	_	_	_
25	manufacturer	manufacturer	NN	_	_	_
26	's	's	POS	_	_	_
27	recommendations	recommendation	NNS	_	_	_
28	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNAeasy	rnaeasy	NN	_	_	_
7	mini-Kit	mini-kit	NN	_	_	_
8	Qiagen	Qiagen	NNP	_	_	_
9	and	and	CC	_	_	_
10	hybridizated	hybridizate	VBN	_	_	_
11	on	on	IN	_	_	_
12	Affymatrix	Affymatrix	NNP	_	_	_
13	microarrays	microarray	NNS	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Mini	Mini	NNP	_	_	_
10	Kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	74104	74104	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	mechanical	mechanical	JJ	_	_	_
16	cell	cell	NN	_	_	_
17	disruption	disruption	NN	_	_	_
18	with	with	IN	_	_	_
19	glass	glass	NN	_	_	_
20	beads	bead	NNS	_	_	_
21	but	but	CC	_	_	_
22	without	without	IN	_	_	_
23	enzymatic	enzymatic	JJ	_	_	_
24	lysis	lysis	NN	_	_	_
25	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	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	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Trizol	Trizol	NNP	_	_	_
7	and	and	CC	_	_	_
8	chloroform	chloroform	NN	_	_	_
9	in	in	IN	_	_	_
10	conjunction	conjunction	NN	_	_	_
11	with	with	IN	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	's	's	POS	_	_	_
14	RNeasy	RNeasy	NNP	_	_	_
15	Mini	Mini	NNP	_	_	_
16	kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	Qiagen	NNP	_	_	_
19	,	,	,	_	_	_
20	Valencia	Valencia	NNP	_	_	_
21	,	,	,	_	_	_
22	CA	CA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	following	follow	VBG	_	_	_
25	the	the	DT	_	_	_
26	A.	a.	NN	_	_	_
27	Untergasser	Untergasser	NNP	_	_	_
28	protocol	protocol	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm	http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	with	with	IN	_	_	_
33	one	one	CD	_	_	_
34	modification	modification	NN	_	_	_
35	:	:	:	_	_	_
36	Phase	phase	NN	_	_	_
37	Lock	lock	NN	_	_	_
38	Gel	gel	NN	_	_	_
39	tubes	tube	NNS	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Eppendorf	Eppendorf	NNP	_	_	_
42	,	,	,	_	_	_
43	Westbury	Westbury	NNP	_	_	_
44	,	,	,	_	_	_
45	NY	NY	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	were	be	VBD	_	_	_
48	used	use	VBN	_	_	_
49	to	to	TO	_	_	_
50	better	better	JJR	_	_	_
51	separate	separate	JJ	_	_	_
52	organic	organic	JJ	_	_	_
53	and	and	CC	_	_	_
54	aqueous	aqueous	JJ	_	_	_
55	phases	phase	NNS	_	_	_
56	after	after	IN	_	_	_
57	the	the	DT	_	_	_
58	addition	addition	NN	_	_	_
59	of	of	IN	_	_	_
60	chloroform	chloroform	NN	_	_	_
61	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	digested	digest	VBN	_	_	_
4	with	with	IN	_	_	_
5	Ambion	Ambion	NNP	_	_	_
6	rDNAse	rDNAse	NNP	_	_	_
7	I	I	NNP	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Life	Life	NNP	_	_	_
10	Technologies	Technologies	NNPS	_	_	_
11	,	,	,	_	_	_
12	Carlsbad	Carlsbad	NNP	_	_	_
13	,	,	,	_	_	_
14	CA	CA	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	for	for	IN	_	_	_
17	30	30	CD	_	_	_
18	min	min	NN	_	_	_
19	at	at	IN	_	_	_
20	37	37	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	further	further	JJ	_	_	_
5	cleaned	clean	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Mini	Mini	NNP	_	_	_
10	kit	kit	NN	_	_	_
11	and	and	CC	_	_	_
12	quality	quality	NN	_	_	_
13	was	be	VBD	_	_	_
14	assessed	assess	VBN	_	_	_
15	by	by	IN	_	_	_
16	the	the	DT	_	_	_
17	RNA	rna	NN	_	_	_
18	ScreenTape	screentape	NN	_	_	_
19	Assay	assay	NN	_	_	_
20	on	on	IN	_	_	_
21	the	the	DT	_	_	_
22	TapeStation	TapeStation	NNP	_	_	_
23	2200	2200	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Agilent	Agilent	NNP	_	_	_
26	Technologies	Technologies	NNPS	_	_	_
27	,	,	,	_	_	_
28	Santa	Santa	NNP	_	_	_
29	Clara	Clara	NNP	_	_	_
30	,	,	,	_	_	_
31	CA	CA	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	with	with	IN	_	_	_
3	RIN	rin	NN	_	_	_
4	values	value	NNS	_	_	_
5	greater	greater	JJR	_	_	_
6	than	than	IN	_	_	_
7	8.0	8.0	CD	_	_	_
8	were	be	VBD	_	_	_
9	treated	treat	VBN	_	_	_
10	with	with	IN	_	_	_
11	the	the	DT	_	_	_
12	Ambion	Ambion	NNP	_	_	_
13	MICROBExpress	MICROBExpress	NNPS	_	_	_
14	Bacterial	bacterial	JJ	_	_	_
15	mRNA	mrna	NN	_	_	_
16	Enrichment	Enrichment	NNP	_	_	_
17	Kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Life	Life	NNP	_	_	_
20	Technologies	Technologies	NNPS	_	_	_
21	,	,	,	_	_	_
22	Carlsbad	Carlsbad	NNP	_	_	_
23	,	,	,	_	_	_
24	CA	CA	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	were	be	VBD	_	_	_
28	used	use	VBN	_	_	_
29	for	for	IN	_	_	_
30	library	library	NN	_	_	_
31	construction	construction	NN	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Trizol	trizol	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Invitrogen	invitrogen	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	RNA	rna	NN	_	_	_
12	was	be	VBD	_	_	_
13	extracted	extract	VBN	_	_	_
14	using	use	VBG	_	_	_
15	Trizol	Trizol	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Invitrogen	Invitrogen	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	Direct-zol	direct-zol	NN	_	_	_
21	RNA	rna	NN	_	_	_
22	MiniPrep	MiniPrep	NNP	_	_	_
23	kit	kit	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Zymo	zymo	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	TRIzol	trizol	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Invitrogen	invitrogen	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	,	,	,	_	_	_
11	following	follow	VBG	_	_	_
12	the	the	DT	_	_	_
13	manufacturer	manufacturer	NN	_	_	_
14	's	's	POS	_	_	_
15	protocol	protocol	NN	_	_	_
16	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	fragmented	fragmented	JJ	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	NEBNext	nebnext	NN	_	_	_
8	Magnesium	magnesium	NN	_	_	_
9	RNA	rna	NN	_	_	_
10	Fragmentation	fragmentation	NN	_	_	_
11	Module	module	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	New	New	NNP	_	_	_
14	England	England	NNP	_	_	_
15	Biolabs	Biolabs	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	following	follow	VBG	_	_	_
6	cell	cell	NN	_	_	_
7	lysis	lysis	NN	_	_	_
8	and	and	CC	_	_	_
9	phenol	phenol	NN	_	_	_
10	:	:	:	_	_	_
11	chloroform	chloroform	NN	_	_	_
12	extraction	extraction	NN	_	_	_
13	as	as	IN	_	_	_
14	previously	previously	RB	_	_	_
15	described	describe	VBN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Andrade	Andrade	NNP	_	_	_
18	,	,	,	_	_	_
19	Pobre	Pobre	NNP	_	_	_
20	et	et	FW	_	_	_
21	al.	al.	FW	_	_	_
22	2012	2012	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

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	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	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	samples	sample	NNS	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	RNeasy	RNeasy	NNP	_	_	_
10	Mini	Mini	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

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	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	culture	culture	NN	_	_	_
8	by	by	IN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	Qiagen	Qiagen	NNP	_	_	_
12	RNeasy	RNeasy	NNP	_	_	_
13	mini-prep	mini-prep	NN	_	_	_
14	kit.cDNA	kit.cdna	NN	_	_	_
15	was	be	VBD	_	_	_
16	synthesized	synthesize	VBN	_	_	_
17	using	use	VBG	_	_	_
18	5-10	5-10	CD	_	_	_
19	µg/ml	µg/ml	NN	_	_	_
20	of	of	IN	_	_	_
21	RNA	rna	NN	_	_	_
22	and	and	CC	_	_	_
23	the	the	DT	_	_	_
24	first	first	JJ	_	_	_
25	strand	strand	NN	_	_	_
26	cDNA	cdna	NN	_	_	_
27	synthesis	synthesis	NN	_	_	_
28	kit	kit	NN	_	_	_
29	from	from	IN	_	_	_
30	Invitrogen	Invitrogen	NNP	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Invitrogen	Invitrogen	NNP	_	_	_
33	Bioservices	Bioservices	NNP	_	_	_
34	India	India	NNP	_	_	_
35	Pvt.	Pvt.	NNP	_	_	_
36	Ltd.	Ltd.	NNP	_	_	_
37	,	,	,	_	_	_
38	Bangalore	Bangalore	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

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/s	m/s	NNS	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	lysed	lyse	VBN	_	_	_
4	by	by	IN	_	_	_
5	three	three	CD	_	_	_
6	cycles	cycle	NNS	_	_	_
7	of	of	IN	_	_	_
8	homogenisation	homogenisation	NN	_	_	_
9	for	for	IN	_	_	_
10	1	1	CD	_	_	_
11	min	min	NN	_	_	_
12	with	with	IN	_	_	_
13	cooling	cooling	NN	_	_	_
14	between	between	IN	_	_	_
15	each	each	DT	_	_	_
16	cycle	cycle	NN	_	_	_
17	in	in	IN	_	_	_
18	an	a	DT	_	_	_
19	ice-water	ice-water	JJ	_	_	_
20	bath	bath	NN	_	_	_
21	for	for	IN	_	_	_
22	1	1	CD	_	_	_
23	min	min	NN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysates	lysate	NNS	_	_	_
3	were	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	an	a	DT	_	_	_
7	equal	equal	JJ	_	_	_
8	volume	volume	NN	_	_	_
9	of	of	IN	_	_	_
10	acidic	acidic	JJ	_	_	_
11	phenol	phenol	NN	_	_	_
12	:	:	:	_	_	_
13	chloroform	chloroform	NN	_	_	_
14	:	:	:	_	_	_
15	isoamyl	isoamyl	NN	_	_	_
16	alcohol	alcohol	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	50	50	CD	_	_	_
19	:	:	:	_	_	_
20	50	50	CD	_	_	_
21	:	:	:	_	_	_
22	1	1	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	then	then	RB	_	_	_
26	chloroform	chloroform	NN	_	_	_
27	:	:	:	_	_	_
28	isoamyl	isoamyl	NN	_	_	_
29	alcohol	alcohol	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	49	49	CD	_	_	_
32	:	:	:	_	_	_
33	1	1	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	Nucleic	nucleic	JJ	_	_	_
2	acid	acid	NN	_	_	_
3	in	in	IN	_	_	_
4	the	the	DT	_	_	_
5	aqueous	aqueous	JJ	_	_	_
6	phase	phase	NN	_	_	_
7	was	be	VBD	_	_	_
8	precipitated	precipitate	VBN	_	_	_
9	by	by	IN	_	_	_
10	adding	add	VBG	_	_	_
11	NaCl	nacl	NN	_	_	_
12	to	to	TO	_	_	_
13	150	150	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	and	and	CC	_	_	_
16	2.5	2.5	CD	_	_	_
17	x	x	CC	_	_	_
18	volumes	volume	NNS	_	_	_
19	of	of	IN	_	_	_
20	100	100	CD	_	_	_
21	%	%	NN	_	_	_
22	-LSB-	-lsb-	-LRB-	_	_	_
23	v/v	v/v	NN	_	_	_
24	-RSB-	-rsb-	-RRB-	_	_	_
25	ethanol	ethanol	NN	_	_	_
26	,	,	,	_	_	_
27	chilling	chill	VBG	_	_	_
28	at	at	IN	_	_	_
29	-20	-20	CD	_	_	_
30	°C	°c	NN	_	_	_
31	for	for	IN	_	_	_
32	1	1	CD	_	_	_
33	h	h	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	then	then	RB	_	_	_
37	harvested	harvest	VBN	_	_	_
38	by	by	IN	_	_	_
39	centrifugation	centrifugation	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	13,000	13,000	CD	_	_	_
42	x	x	CC	_	_	_
43	g	g	NN	_	_	_
44	for	for	IN	_	_	_
45	30	30	CD	_	_	_
46	min	min	NN	_	_	_
47	at	at	IN	_	_	_
48	4	4	CD	_	_	_
49	°C	°c	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	nucleic	nucleic	JJ	_	_	_
3	acid	acid	NN	_	_	_
4	pellet	pellet	NN	_	_	_
5	was	be	VBD	_	_	_
6	washed	wash	VBN	_	_	_
7	twice	twice	RB	_	_	_
8	with	with	IN	_	_	_
9	700	700	CD	_	_	_
10	µL	µl	NN	_	_	_
11	of	of	IN	_	_	_
12	70	70	CD	_	_	_
13	%	%	NN	_	_	_
14	-LSB-	-lsb-	-LRB-	_	_	_
15	v/v	v/v	NN	_	_	_
16	-RSB-	-rsb-	-RRB-	_	_	_
17	ethanol	ethanol	NN	_	_	_
18	,	,	,	_	_	_
19	air	air	NN	_	_	_
20	dried	dry	VBD	_	_	_
21	for	for	IN	_	_	_
22	5	5	CD	_	_	_
23	min	min	NN	_	_	_
24	and	and	CC	_	_	_
25	resuspended	resuspend	VBN	_	_	_
26	in	in	IN	_	_	_
27	RNase-free	rnase-free	JJ	_	_	_
28	water	water	NN	_	_	_
29	.	.	.	_	_	_

1	Contaminating	contaminate	VBG	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	from	from	IN	_	_	_
6	both	both	DT	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	and	and	CC	_	_	_
10	S.	s.	FW	_	_	_
11	coelicolor	coelicolor	FW	_	_	_
12	by	by	IN	_	_	_
13	incubating	incubate	VBG	_	_	_
14	with	with	IN	_	_	_
15	DNase	dnase	NN	_	_	_
16	as	as	IN	_	_	_
17	described	describe	VBN	_	_	_
18	by	by	IN	_	_	_
19	the	the	DT	_	_	_
20	vendor	vendor	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Ambion	ambion	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	extracted	extract	VBN	_	_	_
26	with	with	IN	_	_	_
27	phenol	phenol	NN	_	_	_
28	:	:	:	_	_	_
29	chloroform	chloroform	NN	_	_	_
30	as	as	IN	_	_	_
31	described	describe	VBN	_	_	_
32	above	above	IN	_	_	_
33	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	concentration	concentration	NN	_	_	_
3	and	and	CC	_	_	_
4	integrity	integrity	NN	_	_	_
5	of	of	IN	_	_	_
6	RNA	rna	NN	_	_	_
7	samples	sample	NNS	_	_	_
8	were	be	VBD	_	_	_
9	determined	determine	VBN	_	_	_
10	using	use	VBG	_	_	_
11	a	a	DT	_	_	_
12	NanoDropTM	nanodroptm	NN	_	_	_
13	1000	1000	CD	_	_	_
14	spectrophotometer	spectrophotometer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Thermo	Thermo	NNP	_	_	_
17	Fisher	Fisher	NNP	_	_	_
18	Scientific	Scientific	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	agarose	agarose	NN	_	_	_
22	gel	gel	NN	_	_	_
23	electrophoresis	electrophoresis	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Kime	Kime	NNP	_	_	_
26	et	et	FW	_	_	_
27	al.	al.	FW	_	_	_
28	2008	2008	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	respectively	respectively	RB	_	_	_
32	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	enriched	enrich	VBN	_	_	_
4	for	for	IN	_	_	_
5	mRNA	mrna	NN	_	_	_
6	using	use	VBG	_	_	_
7	MICROBExpress-Bacteria	microbexpress-bacteria	JJ	_	_	_
8	beads	bead	NNS	_	_	_
9	,	,	,	_	_	_
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	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	standard	standard	JJ	_	_	_
7	Trizol	trizol	NN	_	_	_
8	lysis	lysis	NN	_	_	_
9	and	and	CC	_	_	_
10	aqueous	aqueous	JJ	_	_	_
11	extraction	extraction	NN	_	_	_
12	,	,	,	_	_	_
13	followed	follow	VBN	_	_	_
14	by	by	IN	_	_	_
15	further	further	JJ	_	_	_
16	purification	purification	NN	_	_	_
17	using	use	VBG	_	_	_
18	a	a	DT	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	RNAeasy	RNAeasy	NNP	_	_	_
21	kit	kit	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	Protect	Protect	NNP	_	_	_
9	Bacteria	bacterium	NNS	_	_	_
10	Mini	Mini	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	following	follow	VBG	_	_	_
17	manufacturer	manufacturer	NN	_	_	_
18	's	's	POS	_	_	_
19	instructions	instruction	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Trizol	Trizol	NNP	_	_	_
7	reagent	reagent	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Thermo	Thermo	NNP	_	_	_
10	Fisher	Fisher	NNP	_	_	_
11	Scientific	Scientific	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	RNA	rna	NN	_	_	_
15	was	be	VBD	_	_	_
16	obtained	obtain	VBN	_	_	_
17	from	from	IN	_	_	_
18	cells	cell	NNS	_	_	_
19	pellets	pellet	NNS	_	_	_
20	by	by	IN	_	_	_
21	lysozyme	lysozyme	NN	_	_	_
22	treatment	treatment	NN	_	_	_
23	and	and	CC	_	_	_
24	phenol-chloroform	phenol-chloroform	JJ	_	_	_
25	extraction	extraction	NN	_	_	_
26	,	,	,	_	_	_
27	analyzed	analyze	VBN	_	_	_
28	by	by	IN	_	_	_
29	agarose	agarose	NN	_	_	_
30	gel	gel	NN	_	_	_
31	electrophoresis	electrophoresis	NN	_	_	_
32	to	to	TO	_	_	_
33	confirm	confirm	VB	_	_	_
34	integrity	integrity	NN	_	_	_
35	,	,	,	_	_	_
36	quantified	quantify	VBN	_	_	_
37	using	use	VBG	_	_	_
38	a	a	DT	_	_	_
39	Nanodrop	Nanodrop	NNP	_	_	_
40	spectrophotometer	spectrophotometer	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	Thermo	Thermo	NNP	_	_	_
43	Scientific	Scientific	NNP	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	,	,	,	_	_	_
46	and	and	CC	_	_	_
47	stored	store	VBD	_	_	_
48	at	at	IN	_	_	_
49	-80	-80	CD	_	_	_
50	°C	°c	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	RNA	rna	NN	_	_	_
53	was	be	VBD	_	_	_
54	obtained	obtain	VBN	_	_	_
55	from	from	IN	_	_	_
56	each	each	DT	_	_	_
57	culture	culture	NN	_	_	_
58	using	use	VBG	_	_	_
59	Ambion	Ambion	NNP	_	_	_
60	RiboPureTM-bacteria	RiboPureTM-bacteria	NNP	_	_	_
61	RNA	rna	NN	_	_	_
62	extraction	extraction	NN	_	_	_
63	kit	kit	NN	_	_	_
64	according	accord	VBG	_	_	_
65	to	to	TO	_	_	_
66	the	the	DT	_	_	_
67	manufacturer	manufacturer	NN	_	_	_
68	's	's	POS	_	_	_
69	instructions	instruction	NNS	_	_	_
70	.	.	.	_	_	_

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	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	pelleted	pelleted	JJ	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	14,000	14,000	CD	_	_	_
7	rpm	rpm	NN	_	_	_
8	,	,	,	_	_	_
9	5	5	CD	_	_	_
10	min	min	NN	_	_	_
11	,	,	,	_	_	_
12	4	4	CD	_	_	_
13	°C	°c	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	air	air	NN	_	_	_
17	dried	dry	VBD	_	_	_
18	before	before	IN	_	_	_
19	suspension	suspension	NN	_	_	_
20	in	in	IN	_	_	_
21	80	80	CD	_	_	_
22	µL	µl	NN	_	_	_
23	RNAse	rnase	NN	_	_	_
24	free	free	JJ	_	_	_
25	water	water	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Invitrogen	invitrogen	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	treatment	treatment	NN	_	_	_
31	with	with	IN	_	_	_
32	TURBO	TURBO	NNP	_	_	_
33	DNAse	dnase	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Ambion	ambion	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	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	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	prepared	prepare	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	Trizol	Trizol	NNP	_	_	_
8	Reagent	Reagent	NNP	_	_	_
9	and	and	CC	_	_	_
10	a	a	DT	_	_	_
11	RiboPure	RiboPure	NNP	_	_	_
12	kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Invitrogen	Invitrogen	NNP	_	_	_
15	,	,	,	_	_	_
16	Carlsbad	Carlsbad	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	,	,	,	_	_	_
20	USA	USA	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	following	follow	VBG	_	_	_
23	the	the	DT	_	_	_
24	manufacturer	manufacturer	NN	_	_	_
25	's	's	POS	_	_	_
26	protocol	protocol	NN	_	_	_
27	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	by	by	IN	_	_	_
6	a	a	DT	_	_	_
7	standard	standard	JJ	_	_	_
8	protocol	protocol	NN	_	_	_
9	using	use	VBG	_	_	_
10	Phenol	Phenol	NNP	_	_	_
11	Chloroform	Chloroform	NNP	_	_	_
12	.	.	.	_	_	_

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	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	from	from	IN	_	_	_
6	200	200	CD	_	_	_
7	µL	µl	NN	_	_	_
8	of	of	IN	_	_	_
9	overnight	overnight	JJ	_	_	_
10	culture	culture	NN	_	_	_
11	by	by	IN	_	_	_
12	pelleting	pelleting	NN	_	_	_
13	and	and	CC	_	_	_
14	resuspeding	resuspeding	NN	_	_	_
15	in	in	IN	_	_	_
16	500	500	CD	_	_	_
17	µL	µl	NN	_	_	_
18	of	of	IN	_	_	_
19	Trizol	trizol	NN	_	_	_
20	at	at	IN	_	_	_
21	65	65	CD	_	_	_
22	°C	°c	NN	_	_	_
23	,	,	,	_	_	_
24	followed	follow	VBN	_	_	_
25	by	by	IN	_	_	_
26	purification	purification	NN	_	_	_
27	on	on	IN	_	_	_
28	a	a	DT	_	_	_
29	column	column	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Direct-Zol	Direct-Zol	NNP	_	_	_
32	,	,	,	_	_	_
33	Zymo	Zymo	NNP	_	_	_
34	Research	Research	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

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	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	from	from	IN	_	_	_
6	lysates	lysate	NNS	_	_	_
7	by	by	IN	_	_	_
8	phenol/chloroform	phenol/chloroform	NN	_	_	_
9	method	method	NN	_	_	_
10	.	.	.	_	_	_

1	rRNA	rrna	NN	_	_	_
2	was	be	VBD	_	_	_
3	first	first	JJ	_	_	_
4	removed	remove	VBN	_	_	_
5	using	use	VBG	_	_	_
6	MICROBExpress	microbexpress	NN	_	_	_
7	following	follow	VBG	_	_	_
8	manufacturer	manufacturer	NN	_	_	_
9	's	's	POS	_	_	_
10	protocol	protocol	NN	_	_	_
11	,	,	,	_	_	_
12	except	except	IN	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	collected	collect	VBN	_	_	_
16	using	use	VBG	_	_	_
17	Zymo	Zymo	NNP	_	_	_
18	's	's	POS	_	_	_
19	RNA	rna	NN	_	_	_
20	columns	column	NNS	_	_	_
21	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	second	second	JJ	_	_	_
3	rRNA	rrna	NN	_	_	_
4	removal	removal	NN	_	_	_
5	step	step	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	following	follow	VBG	_	_	_
9	the	the	DT	_	_	_
10	protocol	protocol	NN	_	_	_
11	described	describe	VBN	_	_	_
12	in	in	IN	_	_	_
13	Affymetrix	Affymetrix	NNP	_	_	_
14	Expression	expression	NN	_	_	_
15	Handbook	handbook	NN	_	_	_
16	,	,	,	_	_	_
17	substituting	substitute	VBG	_	_	_
18	enzymes	enzyme	NNS	_	_	_
19	MMLV	mmlv	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Ambion	ambion	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	RNase	rnase	NN	_	_	_
25	H	h	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	NEB	neb	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	DnaseI	dnasei	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Amplification	amplification	NN	_	_	_
34	grade	grade	NN	_	_	_
35	,	,	,	_	_	_
36	Invitrogen	Invitrogen	NNP	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	on	on	IN	_	_	_
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	following	follow	VBG	_	_	_
14	manufacturer	manufacturer	NN	_	_	_
15	's	's	POS	_	_	_
16	instructions	instruction	NNS	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	eluted	elute	VBN	_	_	_
20	in	in	IN	_	_	_
21	6	6	CD	_	_	_
22	μl	μl	NN	_	_	_
23	of	of	IN	_	_	_
24	nuclease-free	nuclease-free	JJ	_	_	_
25	water	water	NN	_	_	_
26	.	.	.	_	_	_

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/μl	μg/μl	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	resuspended	resuspend	VBN	_	_	_
22	in	in	IN	_	_	_
23	6	6	CD	_	_	_
24	μl	μl	NN	_	_	_
25	nuclease-free	nuclease-free	JJ	_	_	_
26	water	water	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	were	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	wild	wild	JJ	_	_	_
7	type	type	NN	_	_	_
8	and	and	CC	_	_	_
9	mutants	mutant	NNS	_	_	_
10	.	.	.	_	_	_

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	∆	∆	SYM	_	_	_
3	rnb	rnb	FW	GEN	_	_
4	_	_	FW	_	_	_
5	RNA-Seq	rna-seq	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	rnc	rnc	SYM	GEN	_	_
8	-	-	:	_	_	_
9	_	_	SYM	_	_	_
10	time0	time0	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	rnc	rnc	SYM	GEN	_	_
13	-	-	:	_	_	_
14	_	_	SYM	_	_	_
15	time10	time10	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	rnc	rnc	SYM	GEN	_	_
18	-	-	:	_	_	_
19	_	_	SYM	_	_	_
20	time20	time20	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	rnc	rnc	SYM	GEN	_	_
23	-	-	:	_	_	_
24	_	_	SYM	_	_	_
25	time2	time2	CD	_	_	_
26	.5	.5	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	rnc	rnc	SYM	GEN	_	_
29	-	-	:	_	_	_
30	_	_	SYM	_	_	_
31	time5	time5	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	rnc	rnc	SYM	GEN	_	_
34	-	-	:	_	_	_
35	_	_	SYM	_	_	_
36	time7	time7	CD	_	_	_
37	.5	.5	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	rne-3071	rne-3071	NN	_	_	_
40	ts	t	NNS	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	RNeasy	rneasy	NN	_	_	_
43	Mini	Mini	NNP	_	_	_
44	Kit	kit	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	Qiagen	Qiagen	NNP	_	_	_
47	,	,	,	_	_	_
48	Austin	Austin	NNP	_	_	_
49	,	,	,	_	_	_
50	TX	TX	NNP	_	_	_
51	,	,	,	_	_	_
52	USA	USA	NNP	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	with	with	IN	_	_	_
55	on-column	on-column	JJ	_	_	_
56	DNase	dnase	NN	_	_	_
57	treatment	treatment	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	RNase-Free	rnase-free	JJ	_	_	_
60	DNase	dnase	NN	_	_	_
61	Set	set	VB	_	_	_
62	,	,	,	_	_	_
63	Qiagen	Qiagen	NNP	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	rne	rne	NN	GEN	_	_
3	wild-type	wild-type	JJ	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	rng	rng	NN	GEN	_	_
6	mutant	mutant	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	rng	rng	NN	GEN	_	_
9	wild-type	wild-type	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	rnpB	rnpb	NN	GEN	_	_
12	SPET-seq	spet-seq	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	in	in	FW	_	_	_
15	vitro	vitro	FW	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	∆	∆	CD	_	_	_
19	rnr	rnr	NN	GEN	_	_
20	_	_	CD	_	_	_
21	RNA-Seq	rna-seq	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Rockhopper	rockhopper	NN	_	_	_
24	version	version	NN	_	_	_
25	1.20	1.20	CD	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	manuscript	manuscript	NN	_	_	_
28	submitted	submit	VBN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	was	be	VBD	_	_	_
31	used	use	VBN	_	_	_
32	for	for	IN	_	_	_
33	alignment	alignment	NN	_	_	_
34	,	,	,	_	_	_
35	normalization	normalization	NN	_	_	_
36	,	,	,	_	_	_
37	and	and	CC	_	_	_
38	quantification	quantification	NN	_	_	_
39	.	.	.	_	_	_

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://cs.wellesley.edu/~btjaden/Rockhopper	http://cs.wellesley.edu/~btjaden/rockhopper	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Rodrigue	Rodrigue	NNP	_	_	_
10	_	_	SYM	_	_	_
11	10-WT-Ni-3	10-wt-ni-3	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Rodrigue	Rodrigue	NNP	_	_	_
14	_	_	SYM	_	_	_
15	1-WT-phiNi-1	1-wt-phini-1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Rodrigue	Rodrigue	NNP	_	_	_
18	_	_	SYM	_	_	_
19	2-WT-Ni-1	2-wt-ni-1	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Rodrigue	Rodrigue	NNP	_	_	_
22	_	_	SYM	_	_	_
23	5-WT-Ni-2	5-wt-ni-2	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Rodrigue	Rodrigue	NNP	_	_	_
26	_	_	SYM	_	_	_
27	6-WT-phiNi-2	6-wt-phini-2	JJ	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Rodrigue	Rodrigue	NNP	_	_	_
30	_	_	SYM	_	_	_
31	9-WT-phiNi-3	9-wt-phini-3	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Roemerine	roemerine	JJ	_	_	_
34	_	_	NN	_	_	_
35	0	0	CD	_	_	_
36	min	min	NN	_	_	_
37	_	_	CD	_	_	_
38	rep1	rep1	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Roemerine	roemerine	JJ	_	_	_
41	_	_	NN	_	_	_
42	0	0	CD	_	_	_
43	min	min	NN	_	_	_
44	_	_	CD	_	_	_
45	rep2	rep2	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Roemerine	roemerine	JJ	_	_	_
48	_	_	NN	_	_	_
49	0	0	CD	_	_	_
50	min	min	NN	_	_	_
51	_	_	CD	_	_	_
52	rep3	rep3	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Roemerine	roemerine	JJ	_	_	_
55	_	_	NN	_	_	_
56	60	60	CD	_	_	_
57	min	min	NN	_	_	_
58	_	_	CD	_	_	_
59	rep1	rep1	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Roemerine	roemerine	JJ	_	_	_
62	_	_	NN	_	_	_
63	60	60	CD	_	_	_
64	min	min	NN	_	_	_
65	_	_	CD	_	_	_
66	rep2	rep2	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Roemerine	roemerine	JJ	_	_	_
69	_	_	NN	_	_	_
70	60	60	CD	_	_	_
71	min	min	NN	_	_	_
72	_	_	CD	_	_	_
73	rep3	rep3	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	-	-	:	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	-	-	:	_	_	_
79	Roemerine	roemerine	NN	_	_	_
80	treatment	treatment	NN	_	_	_
81	,	,	,	_	_	_
82	0	0	CD	_	_	_
83	min	min	NN	_	_	_
84	,	,	,	_	_	_
85	replicate	replicate	VB	_	_	_
86	1	1	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	-	-	:	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	-	-	:	_	_	_
92	Roemerine	roemerine	NN	_	_	_
93	treatment	treatment	NN	_	_	_
94	,	,	,	_	_	_
95	0	0	CD	_	_	_
96	min	min	NN	_	_	_
97	,	,	,	_	_	_
98	replicate	replicate	VB	_	_	_
99	2	2	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
101	-LRB-	-lrb-	-LRB-	_	_	_
102	-	-	:	_	_	_
103	-RRB-	-rrb-	-RRB-	_	_	_
104	-	-	:	_	_	_
105	Roemerine	roemerine	NN	_	_	_
106	treatment	treatment	NN	_	_	_
107	,	,	,	_	_	_
108	0	0	CD	_	_	_
109	min	min	NN	_	_	_
110	,	,	,	_	_	_
111	replicate	replicate	VB	_	_	_
112	3	3	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	-LRB-	-lrb-	-LRB-	_	_	_
115	-	-	:	_	_	_
116	-RRB-	-rrb-	-RRB-	_	_	_
117	-	-	:	_	_	_
118	Roemerine	roemerine	NN	_	_	_
119	treatment	treatment	NN	_	_	_
120	,	,	,	_	_	_
121	60	60	CD	_	_	_
122	min	min	NN	_	_	_
123	,	,	,	_	_	_
124	replicate	replicate	VB	_	_	_
125	1	1	CD	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	-	-	:	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	-	-	:	_	_	_
131	Roemerine	roemerine	NN	_	_	_
132	treatment	treatment	NN	_	_	_
133	,	,	,	_	_	_
134	60	60	CD	_	_	_
135	min	min	NN	_	_	_
136	,	,	,	_	_	_
137	replicate	replicate	VB	_	_	_
138	2	2	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	-	-	:	_	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	-	-	:	_	_	_
144	Roemerine	roemerine	NN	_	_	_
145	treatment	treatment	NN	_	_	_
146	,	,	,	_	_	_
147	60	60	CD	_	_	_
148	min	min	NN	_	_	_
149	,	,	,	_	_	_
150	replicate	replicate	VB	_	_	_
151	3	3	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	RP437	rp437	NN	_	_	_
154	persisters	persister	NNS	_	_	_
155	treated	treat	VBN	_	_	_
156	with	with	IN	_	_	_
157	BF8	bf8	NN	_	_	_
158	at	at	IN	_	_	_
159	5	5	CD	_	_	_
160	µg/mL	µg/ml	NN	_	_	_
161	for	for	IN	_	_	_
162	1	1	CD	_	_	_
163	hour	hour	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	RP437	rp437	NN	_	_	_
166	was	be	VBD	_	_	_
167	inoculated	inoculate	VBN	_	_	_
168	in	in	IN	_	_	_
169	100	100	CD	_	_	_
170	mL	ml	NN	_	_	_
171	LB	lb	NN	_	_	_
172	and	and	CC	_	_	_
173	grown	grow	VBN	_	_	_
174	for	for	IN	_	_	_
175	18	18	CD	_	_	_
176	h	h	NN	_	_	_
177	-LRB-	-lrb-	-LRB-	_	_	_
178	200	200	CD	_	_	_
179	rpm	rpm	NN	_	_	_
180	,	,	,	_	_	_
181	37oC	37oc	NN	_	_	_
182	-RRB-	-rrb-	-RRB-	_	_	_
183	.	.	.	_	_	_

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/mL	µg/ml	NN	_	_	_
13	Ofloxacin	ofloxacin	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	3.5	3.5	CD	_	_	_
16	h	h	NN	_	_	_
17	,	,	,	_	_	_
18	200	200	CD	_	_	_
19	rpm	rpm	NN	_	_	_
20	,	,	,	_	_	_
21	37oC	37oc	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	followed	follow	VBN	_	_	_
25	by	by	IN	_	_	_
26	centrifugation	centrifugation	NN	_	_	_
27	and	and	CC	_	_	_
28	washing	wash	VBG	_	_	_
29	with	with	IN	_	_	_
30	0.85	0.85	CD	_	_	_
31	%	%	NN	_	_	_
32	NaCl	nacl	NN	_	_	_
33	solution	solution	NN	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RPMI	rpmi	NN	_	_	_
3	1A	1a	NN	_	_	_
4	,	,	,	_	_	_
5	Microarray	Microarray	NNP	_	_	_
6	#	#	#	_	_	_
7	1	1	CD	_	_	_
8	first	first	JJ	_	_	_
9	duplicate	duplicate	VB	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	RPMI	rpmi	NN	_	_	_
12	1B	1b	NN	_	_	_
13	,	,	,	_	_	_
14	Microarray	Microarray	NNP	_	_	_
15	#	#	#	_	_	_
16	1	1	CD	_	_	_
17	second	second	JJ	_	_	_
18	replicate	replicate	VBP	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	RPMI	rpmi	NN	_	_	_
21	2A	2a	NN	_	_	_
22	,	,	,	_	_	_
23	Microarray	Microarray	NNP	_	_	_
24	#	#	#	_	_	_
25	2	2	CD	_	_	_
26	,	,	,	_	_	_
27	first	first	RB	_	_	_
28	replicate	replicate	VB	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	RPMI	rpmi	NN	_	_	_
31	2B	2b	NN	_	_	_
32	,	,	,	_	_	_
33	Microarray	Microarray	NNP	_	_	_
34	#	#	#	_	_	_
35	2	2	CD	_	_	_
36	second	second	JJ	_	_	_
37	replicate	replicate	VBP	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	RpoB	rpob	NN	_	_	_
40	∆	∆	CD	_	_	_
41	cra	cra	NN	GEN	_	_
42	1	1	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	RpoB	rpob	NN	_	_	_
45	∆	∆	CD	_	_	_
46	cra	cra	NN	GEN	_	_
47	2	2	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	RpoB	rpob	NN	_	_	_
50	∆	∆	CD	_	_	_
51	crp	crp	NN	GEN	_	_
52	1	1	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	RpoB	rpob	NN	_	_	_
55	∆	∆	CD	_	_	_
56	crp	crp	NN	GEN	_	_
57	2	2	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	RpoB	rpob	NN	_	_	_
60	with	with	IN	_	_	_
61	DPD	dpd	NN	_	_	_
62	1	1	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	2	2	CD	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	ChIP-exo	chip-exo	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	RpoB	rpob	NN	_	_	_
76	with	with	IN	_	_	_
77	DPD	dpd	NN	_	_	_
78	and	and	CC	_	_	_
79	rifampicin	rifampicin	NN	SUPP	_	_
80	1	1	CD	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	ChIP-exo	chip-exo	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	RpoB	rpob	NN	_	_	_
86	with	with	IN	_	_	_
87	DPD	dpd	NN	_	_	_
88	and	and	CC	_	_	_
89	rifampicin	rifampicin	NN	SUPP	_	_
90	2	2	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	1	1	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	2	2	CD	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	ChIP-exo	chip-exo	NN	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	RpoB	rpob	NN	_	_	_
112	with	with	IN	_	_	_
113	Fe	Fe	NNP	_	_	_
114	and	and	CC	_	_	_
115	rifampicin	rifampicin	NN	SUPP	_	_
116	1	1	CD	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	ChIP-exo	chip-exo	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	RpoB	rpob	NN	_	_	_
122	with	with	IN	_	_	_
123	Fe	Fe	NNP	_	_	_
124	and	and	CC	_	_	_
125	rifampicin	rifampicin	NN	SUPP	_	_
126	2	2	CD	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	ChIP-exo	chip-exo	NN	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	RpoB	rpob	NN	_	_	_
132	WT	wt	NN	_	_	_
133	1	1	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	RpoB	rpob	NN	_	_	_
136	WT	wt	NN	_	_	_
137	2	2	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	rpo	rpo	NN	_	_	_
140	,	,	,	_	_	_
141	delfis	delfis	NN	_	_	_
142	,	,	,	_	_	_
143	ME	me	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	rpo	rpo	NN	_	_	_
146	,	,	,	_	_	_
147	delhns	delhn	NNS	_	_	_
148	,	,	,	_	_	_
149	ME	me	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	RpoE	rpoe	NN	_	_	_
152	induced	induce	VBN	_	_	_
153	-LRB-	-lrb-	-LRB-	_	_	_
154	0	0	CD	_	_	_
155	min	min	NN	_	_	_
156	-RRB-	-rrb-	-RRB-	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	RpoE	rpoe	NN	_	_	_
159	induced	induce	VBN	_	_	_
160	-LRB-	-lrb-	-LRB-	_	_	_
161	10	10	CD	_	_	_
162	min	min	NN	_	_	_
163	-RRB-	-rrb-	-RRB-	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	RpoE	rpoe	NN	_	_	_
166	induced	induce	VBN	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	15	15	CD	_	_	_
169	min	min	NN	_	_	_
170	-RRB-	-rrb-	-RRB-	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	RpoE	rpoe	NN	_	_	_
173	induced	induce	VBN	_	_	_
174	-LRB-	-lrb-	-LRB-	_	_	_
175	15	15	CD	_	_	_
176	min	min	NN	_	_	_
177	-RRB-	-rrb-	-RRB-	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	RpoE	rpoe	NN	_	_	_
180	induced	induce	VBN	_	_	_
181	-LRB-	-lrb-	-LRB-	_	_	_
182	20	20	CD	_	_	_
183	min	min	NN	_	_	_
184	-RRB-	-rrb-	-RRB-	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	RpoE	rpoe	NN	_	_	_
187	induced	induce	VBN	_	_	_
188	-LRB-	-lrb-	-LRB-	_	_	_
189	2.5	2.5	CD	_	_	_
190	min	min	NN	_	_	_
191	-RRB-	-rrb-	-RRB-	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	RpoE	rpoe	NN	_	_	_
194	induced	induce	VBN	_	_	_
195	-LRB-	-lrb-	-LRB-	_	_	_
196	30	30	CD	_	_	_
197	min	min	NN	_	_	_
198	-RRB-	-rrb-	-RRB-	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	RpoE	rpoe	NN	_	_	_
201	induced	induce	VBN	_	_	_
202	-LRB-	-lrb-	-LRB-	_	_	_
203	5	5	CD	_	_	_
204	min	min	NN	_	_	_
205	-RRB-	-rrb-	-RRB-	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	RpoE	rpoe	NN	_	_	_
208	induced	induce	VBN	_	_	_
209	-LRB-	-lrb-	-LRB-	_	_	_
210	5	5	CD	_	_	_
211	min	min	NN	_	_	_
212	-RRB-	-rrb-	-RRB-	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	RpoE	rpoe	NN	_	_	_
215	induced	induce	VBN	_	_	_
216	-LRB-	-lrb-	-LRB-	_	_	_
217	60	60	CD	_	_	_
218	min	min	NN	_	_	_
219	-RRB-	-rrb-	-RRB-	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	RpoH	rpoh	NN	_	_	_
222	induced	induce	VBN	_	_	_
223	-LRB-	-lrb-	-LRB-	_	_	_
224	0	0	CD	_	_	_
225	min	min	NN	_	_	_
226	-RRB-	-rrb-	-RRB-	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	RpoH	rpoh	NN	_	_	_
229	induced	induce	VBN	_	_	_
230	-LRB-	-lrb-	-LRB-	_	_	_
231	10	10	CD	_	_	_
232	min	min	NN	_	_	_
233	-RRB-	-rrb-	-RRB-	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	RpoH	rpoh	NN	_	_	_
236	induced	induce	VBN	_	_	_
237	-LRB-	-lrb-	-LRB-	_	_	_
238	20	20	CD	_	_	_
239	min	min	NN	_	_	_
240	-RRB-	-rrb-	-RRB-	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	RpoH	rpoh	NN	_	_	_
243	induced	induce	VBN	_	_	_
244	-LRB-	-lrb-	-LRB-	_	_	_
245	2.5	2.5	CD	_	_	_
246	min	min	NN	_	_	_
247	-RRB-	-rrb-	-RRB-	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	RpoH	rpoh	NN	_	_	_
250	induced	induce	VBN	_	_	_
251	-LRB-	-lrb-	-LRB-	_	_	_
252	5	5	CD	_	_	_
253	min	min	NN	_	_	_
254	-RRB-	-rrb-	-RRB-	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	rpoN	rpon	NN	GEN	_	_
257	mutant	mutant	JJ	_	_	_
258	grown	grow	VBN	_	_	_
259	to	to	TO	_	_	_
260	logarithmic	logarithmic	JJ	_	_	_
261	phase	phase	NN	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	rpoN	rpon	NN	GEN	_	_
264	mutant	mutant	JJ	_	_	_
265	grown	grow	VBN	_	_	_
266	to	to	TO	_	_	_
267	transition	transition	NN	_	_	_
268	phase	phase	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	rpoS	rpos	NN	GEN	_	_
271	_	_	CD	_	_	_
272	04	04	CD	_	_	_
273	_	_	NN	_	_	_
274	rep1	rep1	NN	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	rpoS	rpos	NN	GEN	_	_
277	_	_	CD	_	_	_
278	04	04	CD	_	_	_
279	_	_	NN	_	_	_
280	rep2	rep2	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	rpoS	rpos	NN	GEN	_	_
283	_	_	CD	_	_	_
284	04	04	CD	_	_	_
285	_	_	SYM	_	_	_
286	TEX	TEX	NNP	_	_	_
287	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
288	rpoS	rpos	NN	GEN	_	_
289	_	_	CD	_	_	_
290	15	15	CD	_	_	_
291	min	min	NN	_	_	_
292	_	_	CD	_	_	_
293	rep1	rep1	NN	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	rpoS	rpos	NN	GEN	_	_
296	_	_	CD	_	_	_
297	16	16	CD	_	_	_
298	_	_	NN	_	_	_
299	rep1	rep1	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	rpoS	rpos	NN	GEN	_	_
302	_	_	NN	_	_	_
303	180	180	CD	_	_	_
304	min	min	NN	_	_	_
305	_	_	CD	_	_	_
306	rep1	rep1	NN	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	rpoS	rpos	NN	GEN	_	_
309	_	_	CD	_	_	_
310	30	30	CD	_	_	_
311	min	min	NN	_	_	_
312	_	_	CD	_	_	_
313	rep1	rep1	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	rpoS	rpos	NN	GEN	_	_
316	_	_	CD	_	_	_
317	30	30	CD	_	_	_
318	min	min	NN	_	_	_
319	_	_	CD	_	_	_
320	rep2	rep2	NN	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	rpoS	rpos	NN	GEN	_	_
323	_	_	CD	_	_	_
324	30	30	CD	_	_	_
325	min	min	NN	_	_	_
326	_	_	CD	_	_	_
327	TEX	TEX	NNP	_	_	_
328	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
329	rpoS	rpos	NN	GEN	_	_
330	_	_	CD	_	_	_
331	EE	ee	NN	_	_	_
332	_	_	NN	_	_	_
333	1	1	CD	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	rpoS	rpos	NN	GEN	_	_
336	_	_	CD	_	_	_
337	EE	ee	NN	_	_	_
338	_	_	NN	_	_	_
339	2	2	CD	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	rpos	rpo	NNS	_	_	_
342	level	level	NN	_	_	_
343	:	:	:	_	_	_
344	0	0	CD	_	_	_
345	%	%	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	rpos	rpo	NNS	_	_	_
348	level	level	NN	_	_	_
349	:	:	:	_	_	_
350	100	100	CD	_	_	_
351	%	%	NN	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
353	rpos	rpo	NNS	_	_	_
354	level	level	NN	_	_	_
355	:	:	:	_	_	_
356	26	26	CD	_	_	_
357	%	%	NN	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	rpoS	rpos	NN	GEN	_	_
360	_	_	NN	_	_	_
361	LS	ls	NN	_	_	_
362	_	_	NN	_	_	_
363	1	1	CD	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	rpoS	rpos	NN	GEN	_	_
366	_	_	NN	_	_	_
367	LS	ls	NN	_	_	_
368	_	_	NN	_	_	_
369	2	2	CD	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	rpoS	rpos	NN	GEN	_	_
372	_	_	CD	_	_	_
373	ME	me	NN	_	_	_
374	_	_	NN	_	_	_
375	1	1	CD	_	_	_
376	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
377	rpoS	rpos	NN	GEN	_	_
378	_	_	CD	_	_	_
379	ME	me	NN	_	_	_
380	_	_	NN	_	_	_
381	2	2	CD	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	rpoS	rpos	NN	GEN	_	_
384	mutant	mutant	JJ	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	rpoS	rpos	NN	GEN	_	_
387	_	_	CD	_	_	_
388	N	n	NN	_	_	_
389	_	_	CD	_	_	_
390	strv	strv	NN	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	rpoS	rpos	NN	GEN	_	_
393	_	_	CD	_	_	_
394	N	n	NN	_	_	_
395	_	_	SYM	_	_	_
396	strv	strv	FW	_	_	_
397	_	_	FW	_	_	_
398	TEX	tex	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	rpoS	rpos	NN	GEN	_	_
401	_	_	CD	_	_	_
402	S	s	NN	_	_	_
403	_	_	NN	_	_	_
404	1	1	CD	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	rpoS	rpos	NN	GEN	_	_
407	_	_	CD	_	_	_
408	S	s	NN	_	_	_
409	_	_	NN	_	_	_
410	2	2	CD	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	rpoS	rpos	NN	GEN	_	_
413	_	_	CD	_	_	_
414	TS	ts	NN	_	_	_
415	_	_	NN	_	_	_
416	1	1	CD	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	rpoS	rpos	NN	GEN	_	_
419	_	_	CD	_	_	_
420	TS	ts	NN	_	_	_
421	_	_	NN	_	_	_
422	2	2	CD	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	rpo	rpo	NN	_	_	_
425	,	,	,	_	_	_
426	wt	wt	JJ	_	_	_
427	,	,	,	_	_	_
428	ME	me	JJ	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	rraA	rraa	NN	GEN	_	_
431	deletion	deletion	NN	_	_	_
432	,	,	,	_	_	_
433	OD600	od600	NN	_	_	_
434	=	=	JJ	_	_	_
435	0.3	0.3	CD	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	rraA	rraa	NN	GEN	_	_
438	deletion	deletion	NN	_	_	_
439	,	,	,	_	_	_
440	OD600	od600	NN	_	_	_
441	=	=	JJ	_	_	_
442	0.5	0.5	CD	_	_	_
443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
444	rraA	rraa	NN	GEN	_	_
445	deletion	deletion	NN	_	_	_
446	,	,	,	_	_	_
447	OD600	od600	NN	_	_	_
448	=	=	JJ	_	_	_
449	1.0	1.0	CD	_	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
451	rRNA	rrna	NN	_	_	_
452	depleted	deplete	VBN	_	_	_
453	RNA	rna	NN	_	_	_
454	was	be	VBD	_	_	_
455	then	then	RB	_	_	_
456	primed	prime	VBN	_	_	_
457	using	use	VBG	_	_	_
458	random	random	JJ	_	_	_
459	hexamers	hexamer	NNS	_	_	_
460	and	and	CC	_	_	_
461	reverse	reverse	VB	_	_	_
462	transcribed	transcribe	VBN	_	_	_
463	using	use	VBG	_	_	_
464	SuperScript	SuperScript	NNP	_	_	_
465	III	III	NNP	_	_	_
466	-LRB-	-lrb-	-LRB-	_	_	_
467	Life	Life	NNP	_	_	_
468	Technologies	Technologies	NNPS	_	_	_
469	-RRB-	-rrb-	-RRB-	_	_	_
470	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	rRNA	rrna	NN	_	_	_
3	depletion	depletion	NN	_	_	_
4	,	,	,	_	_	_
5	fragmentation	fragmentation	NN	_	_	_
6	,	,	,	_	_	_
7	reverse	reverse	JJ	_	_	_
8	transcription	transcription	NN	_	_	_
9	,	,	,	_	_	_
10	tagging	tagging	NN	_	_	_
11	,	,	,	_	_	_
12	barcoding	barcoding	NN	_	_	_
13	,	,	,	_	_	_
14	limited	limited	JJ	_	_	_
15	cycle	cycle	NN	_	_	_
16	PCR	pcr	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Illumina	Illumina	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	rRNA	rrna	NN	_	_	_
22	depletion	depletion	NN	_	_	_
23	:	:	:	_	_	_
24	Genomic	genomic	JJ	_	_	_
25	DNA	dna	NN	_	_	_
26	was	be	VBD	_	_	_
27	removed	remove	VBN	_	_	_
28	with	with	IN	_	_	_
29	TURBO	TURBO	NNP	_	_	_
30	DNAse	dnase	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Ambion	ambion	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	then	then	RB	_	_	_
37	total	total	JJ	_	_	_
38	RNA	rna	NN	_	_	_
39	was	be	VBD	_	_	_
40	run	run	VBN	_	_	_
41	over	over	IN	_	_	_
42	two	two	CD	_	_	_
43	MEGAClear	megaclear	NN	_	_	_
44	columns	column	NNS	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	Ambion	Ambion	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	to	to	TO	_	_	_
49	deplete	deplete	VB	_	_	_
50	tRNAs	trna	NNS	_	_	_
51	and	and	CC	_	_	_
52	5S	5s	NN	_	_	_
53	rRNA	rrna	NN	_	_	_
54	.	.	.	_	_	_

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	rRNA	rrna	NN	_	_	_
3	reduction	reduction	NN	_	_	_
4	with	with	IN	_	_	_
5	EpiCentre	EpiCentre	NNP	_	_	_
6	Ribo-Zero	Ribo-Zero	NNP	_	_	_
7	Gram	Gram	NNP	_	_	_
8	Negative	negative	JJ	_	_	_
9	Ribosomal	ribosomal	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	reduction	reduction	NN	_	_	_
12	kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	2.5	2.5	CD	_	_	_
15	ug	ug	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	&	&	CC	_	_	_
18	TruSeq	TruSeq	NNP	_	_	_
19	RNA	rna	NN	_	_	_
20	Library	Library	NNP	_	_	_
21	Prep	Prep	NNP	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	rRNA	rrna	NN	_	_	_
24	was	be	VBD	_	_	_
25	removed	remove	VBN	_	_	_
26	from	from	IN	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	by	by	IN	_	_	_
30	using	use	VBG	_	_	_
31	the	the	DT	_	_	_
32	Ribo-Zero	Ribo-Zero	NNP	_	_	_
33	rRNA	rrna	NN	_	_	_
34	removal	removal	NN	_	_	_
35	kit	kit	NN	_	_	_
36	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	R	r	NN	_	_	_
3	scripts	script	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	Bioconductor	bioconductor	NN	_	_	_
6	GenomicRanges	genomicrange	NNS	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	and	and	CC	_	_	_
9	custom	custom	NN	_	_	_
10	scripts	script	NNS	_	_	_
11	were	be	VBD	_	_	_
12	used	use	VBN	_	_	_
13	to	to	TO	_	_	_
14	calculate	calculate	VB	_	_	_
15	RPKMs	rpkm	NNS	_	_	_
16	.	.	.	_	_	_

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	rsd	rsd	NN	GEN	_	_
3	_	_	CD	_	_	_
4	EE	ee	NN	_	_	_
5	_	_	NN	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	rsd	rsd	NN	GEN	_	_
9	_	_	CD	_	_	_
10	EE	ee	NN	_	_	_
11	_	_	NN	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	rsd	rsd	NN	GEN	_	_
15	_	_	NN	_	_	_
16	LS	ls	NN	_	_	_
17	_	_	NN	_	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	rsd	rsd	NN	GEN	_	_
21	_	_	NN	_	_	_
22	LS	ls	NN	_	_	_
23	_	_	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	rsd	rsd	NN	GEN	_	_
27	_	_	CD	_	_	_
28	ME	me	NN	_	_	_
29	_	_	NN	_	_	_
30	1	1	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	rsd	rsd	NN	GEN	_	_
33	_	_	CD	_	_	_
34	ME	me	NN	_	_	_
35	_	_	NN	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	rsd	rsd	NN	GEN	_	_
39	_	_	CD	_	_	_
40	S	s	NN	_	_	_
41	_	_	NN	_	_	_
42	1	1	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	rsd	rsd	NN	GEN	_	_
45	_	_	CD	_	_	_
46	S	s	NN	_	_	_
47	_	_	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	rsdssrS	rsdssrs	NN	_	_	_
51	_	_	CD	_	_	_
52	EE	ee	NN	_	_	_
53	_	_	NN	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	rsdssrS	rsdssrs	NN	_	_	_
57	_	_	CD	_	_	_
58	EE	ee	NN	_	_	_
59	_	_	NN	_	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	rsdssrS	rsdssrs	NN	_	_	_
63	_	_	NN	_	_	_
64	LS	ls	NN	_	_	_
65	_	_	NN	_	_	_
66	1	1	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	rsdssrS	rsdssrs	NN	_	_	_
69	_	_	NN	_	_	_
70	LS	ls	NN	_	_	_
71	_	_	NN	_	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	rsdssrS	rsdssrs	NN	_	_	_
75	_	_	CD	_	_	_
76	ME	me	NN	_	_	_
77	_	_	NN	_	_	_
78	1	1	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	rsdssrS	rsdssrs	NN	_	_	_
81	_	_	CD	_	_	_
82	ME	me	NN	_	_	_
83	_	_	NN	_	_	_
84	2	2	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	rsdssrS	rsdssrs	NN	_	_	_
87	_	_	CD	_	_	_
88	S	s	NN	_	_	_
89	_	_	NN	_	_	_
90	1	1	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	rsdssrS	rsdssrs	NN	_	_	_
93	_	_	CD	_	_	_
94	S	s	NN	_	_	_
95	_	_	NN	_	_	_
96	2	2	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	rsdssrS	rsdssrs	NN	_	_	_
99	_	_	CD	_	_	_
100	TS	ts	NN	_	_	_
101	_	_	NN	_	_	_
102	1	1	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	rsdssrS	rsdssrs	NN	_	_	_
105	_	_	CD	_	_	_
106	TS	ts	NN	_	_	_
107	_	_	NN	_	_	_
108	2	2	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	rsd	rsd	NN	GEN	_	_
111	_	_	CD	_	_	_
112	TS	ts	NN	_	_	_
113	_	_	NN	_	_	_
114	1	1	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	rsd	rsd	NN	GEN	_	_
117	_	_	CD	_	_	_
118	TS	ts	NN	_	_	_
119	_	_	NN	_	_	_
120	2	2	CD	_	_	_
121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
122	R.	R.	NNP	_	_	_
123	sphaeroides	sphaeroide	NNS	_	_	_
124	was	be	VBD	_	_	_
125	phototrophically	phototrophically	RB	_	_	_
126	grown	grow	VBN	_	_	_
127	to	to	TO	_	_	_
128	mid-log	mid-log	JJ	_	_	_
129	phase	phase	NN	_	_	_
130	-LRB-	-lrb-	-LRB-	_	_	_
131	100-150	100-150	CD	_	_	_
132	kletts	klett	NNS	_	_	_
133	-RRB-	-rrb-	-RRB-	_	_	_
134	in	in	IN	_	_	_
135	Sistrom	Sistrom	NNP	_	_	_
136	's	's	POS	_	_	_
137	minimal	minimal	JJ	_	_	_
138	medium	medium	NN	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	Sistrom	sistrom	NN	_	_	_
141	,	,	,	_	_	_
142	W.	W.	NNP	_	_	_
143	1960	1960	CD	_	_	_
144	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	rstB	rstb	NN	GEN	_	_
3	__	__	CD	_	_	_
4	U	U	NNP	_	_	_
5	_	_	NNP	_	_	_
6	N0075	N0075	NNP	_	_	_
7	_	_	VBD	_	_	_
8	r1	r1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	rstB	rstb	NN	GEN	_	_
11	__	__	CD	_	_	_
12	U	U	NNP	_	_	_
13	_	_	NNP	_	_	_
14	N0075	N0075	NNP	_	_	_
15	_	_	VBD	_	_	_
16	r2	r2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	rstB	rstb	NN	GEN	_	_
19	__	__	CD	_	_	_
20	U	U	NNP	_	_	_
21	_	_	NNP	_	_	_
22	N0075	N0075	NNP	_	_	_
23	_	_	SYM	_	_	_
24	r3	r3	FW	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
26	rstB	rstb	NN	GEN	_	_
27	upregulation	upregulation	NN	_	_	_
28	,	,	,	_	_	_
29	0.075	0.075	CD	_	_	_
30	mg/mL	mg/ml	NN	_	_	_
31	norfloxacin	norfloxacin	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	ruvA	ruva	NN	GEN	_	_
34	___	___	CD	_	_	_
35	U	U	NNP	_	_	_
36	_	_	NNP	_	_	_
37	N0025	N0025	NNP	_	_	_
38	_	_	VBD	_	_	_
39	r1	r1	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	ruvA	ruva	NN	GEN	_	_
42	___	___	CD	_	_	_
43	U	U	NNP	_	_	_
44	_	_	NNP	_	_	_
45	N0025	N0025	NNP	_	_	_
46	_	_	VBD	_	_	_
47	r2	r2	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	ruvA	ruva	NN	GEN	_	_
50	___	___	CD	_	_	_
51	U	U	NNP	_	_	_
52	_	_	NNP	_	_	_
53	N0025	N0025	NNP	_	_	_
54	_	_	SYM	_	_	_
55	r3	r3	FW	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
57	ruvA	ruva	NN	GEN	_	_
58	upregulation	upregulation	NN	_	_	_
59	,	,	,	_	_	_
60	amp	amp	NN	_	_	_
61	50ug/ml	50ug/ml	NN	_	_	_
62	,	,	,	_	_	_
63	0.0125	0.0125	CD	_	_	_
64	%	%	NN	_	_	_
65	arabinose	arabinose	NN	_	_	_
66	,	,	,	_	_	_
67	0.025	0.025	CD	_	_	_
68	ug/ml	ug/ml	NN	_	_	_
69	norfloxacin	norfloxacin	NN	_	_	_
70	OD	od	NN	_	_	_
71	~	~	NN	_	_	_
72	0.3	0.3	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	ruvC	ruvc	NN	GEN	_	_
75	__	__	CD	_	_	_
76	U	U	NNP	_	_	_
77	_	_	NNP	_	_	_
78	N0075	N0075	NNP	_	_	_
79	_	_	VBD	_	_	_
80	r1	r1	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	ruvC	ruvc	NN	GEN	_	_
83	__	__	CD	_	_	_
84	U	U	NNP	_	_	_
85	_	_	NNP	_	_	_
86	N0075	N0075	NNP	_	_	_
87	_	_	VBD	_	_	_
88	r2	r2	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	ruvC	ruvc	NN	GEN	_	_
91	__	__	CD	_	_	_
92	U	U	NNP	_	_	_
93	_	_	NNP	_	_	_
94	N0075	N0075	NNP	_	_	_
95	_	_	SYM	_	_	_
96	r3	r3	FW	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
98	ruvC	ruvc	NN	GEN	_	_
99	upregulation	upregulation	NN	_	_	_
100	,	,	,	_	_	_
101	0.075	0.075	CD	_	_	_
102	mg/mL	mg/ml	NN	_	_	_
103	norfloxacin	norfloxacin	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	∆	∆	CD	_	_	_
106	ryhB	ryhb	NN	GEN	_	_
107	Aerobic	aerobic	JJ	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	∆	∆	CD	_	_	_
110	ryhB	ryhb	NN	GEN	_	_
111	Anaerobic	anaerobic	JJ	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	RyhB-minus_cDNA_Aerobic_WIG.txt	ryhb-minus_cdna_aerobic_wig.txt	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	RyhB-minus_cDNA_Anaerobic_WIG.txt	ryhb-minus_cdna_anaerobic_wig.txt	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	s70	s70	NN	_	_	_
118	ChIP	chip	NN	_	_	_
119	DNA	dna	NN	_	_	_
120	from	from	IN	_	_	_
121	DdksA	ddksa	NN	_	_	_
122	cells	cell	NNS	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
124	s70	s70	NN	_	_	_
125	ChIP	chip	NN	_	_	_
126	DNA	dna	NN	_	_	_
127	from	from	IN	_	_	_
128	starved	starve	VBN	_	_	_
129	DdksA	ddksa	NN	_	_	_
130	cells	cell	NNS	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
132	s70	s70	NN	_	_	_
133	ChIP	chip	NN	_	_	_
134	DNA	dna	NN	_	_	_
135	from	from	IN	_	_	_
136	starved	starve	VBN	_	_	_
137	wt	wt	JJ	_	_	_
138	cells	cell	NNS	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	s70	s70	NN	_	_	_
141	ChIP	chip	NN	_	_	_
142	DNA	dna	NN	_	_	_
143	from	from	IN	_	_	_
144	wt	wt	JJ	_	_	_
145	cells	cell	NNS	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	s70	s70	NN	_	_	_
148	_	_	CD	_	_	_
149	DdksA	ddksa	NN	_	_	_
150	_	_	CD	_	_	_
151	SHX	SHX	NNP	_	_	_
152	_	_	CD	_	_	_
153	rep1	rep1	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	s70	s70	NN	_	_	_
156	_	_	CD	_	_	_
157	DdksA	ddksa	NN	_	_	_
158	_	_	CD	_	_	_
159	SHX	SHX	NNP	_	_	_
160	_	_	CD	_	_	_
161	rep2	rep2	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	s70	s70	NN	_	_	_
164	_	_	CD	_	_	_
165	DdksA	ddksa	NN	_	_	_
166	_	_	NN	_	_	_
167	untreated	untreated	JJ	_	_	_
168	_	_	NN	_	_	_
169	rep1	rep1	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	s70	s70	NN	_	_	_
172	_	_	CD	_	_	_
173	DdksA	ddksa	NN	_	_	_
174	_	_	NN	_	_	_
175	untreated	untreated	JJ	_	_	_
176	_	_	NN	_	_	_
177	rep2	rep2	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	s70	s70	NN	_	_	_
180	_	_	CD	_	_	_
181	wt	wt	JJ	_	_	_
182	_	_	NN	_	_	_
183	SHX	shx	NN	_	_	_
184	_	_	CD	_	_	_
185	rep1	rep1	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	s70	s70	NN	_	_	_
188	_	_	CD	_	_	_
189	wt	wt	JJ	_	_	_
190	_	_	NN	_	_	_
191	SHX	shx	NN	_	_	_
192	_	_	CD	_	_	_
193	rep2	rep2	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	s70	s70	NN	_	_	_
196	_	_	CD	_	_	_
197	wt	wt	JJ	_	_	_
198	_	_	NN	_	_	_
199	untreated	untreated	JJ	_	_	_
200	_	_	NN	_	_	_
201	rep1	rep1	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	s70	s70	NN	_	_	_
204	_	_	CD	_	_	_
205	wt	wt	JJ	_	_	_
206	_	_	NN	_	_	_
207	untreated	untreated	JJ	_	_	_
208	_	_	NN	_	_	_
209	rep2	rep2	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	Sakai	Sakai	NNP	_	_	_
212	grown	grow	VBN	_	_	_
213	to	to	TO	_	_	_
214	OD600	od600	NN	_	_	_
215	=	=	JJ	_	_	_
216	1.8	1.8	CD	_	_	_
217	in	in	IN	_	_	_
218	DMEM-MOPS	dmem-mops	NN	_	_	_
219	0.4	0.4	CD	_	_	_
220	%	%	NN	_	_	_
221	glucose	glucose	NN	SUPP	_	_
222	at	at	IN	_	_	_
223	a	a	DT	_	_	_
224	10:1	10:1	CD	_	_	_
225	flask-to-media	flask-to-media	NN	_	_	_
226	volume	volume	NN	_	_	_
227	in	in	IN	_	_	_
228	a	a	DT	_	_	_
229	rotary	rotary	JJ	_	_	_
230	shaker	shaker	NN	_	_	_
231	-LRB-	-lrb-	-LRB-	_	_	_
232	180	180	CD	_	_	_
233	RPM	rpm	NN	_	_	_
234	-RRB-	-rrb-	-RRB-	_	_	_
235	.	.	.	_	_	_

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	same	same	JJ	_	_	_
10	cultures	culture	NNS	_	_	_
11	used	use	VBN	_	_	_
12	for	for	IN	_	_	_
13	the	the	DT	_	_	_
14	viability	viability	NN	_	_	_
15	assay	assay	NN	_	_	_
16	.	.	.	_	_	_

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	NNP	_	_	_
10	SAM	SAM	NNP	_	_	_
11	files	file	VBZ	_	_	_
12	thus	thus	RB	_	_	_
13	obtained	obtain	VBN	_	_	_
14	were	be	VBD	_	_	_
15	converted	convert	VBN	_	_	_
16	to	to	TO	_	_	_
17	BAM	BAM	NNP	_	_	_
18	files	file	NNS	_	_	_
19	using	use	VBG	_	_	_
20	samtools	samtool	NNS	_	_	_
21	view	view	VBP	_	_	_
22	command	command	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Sample	sample	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Sample	sample	NN	_	_	_
27	1	1	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	sample	sample	NN	_	_	_
30	:	:	:	_	_	_
31	1A	1a	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Sample	sample	NN	_	_	_
34	2	2	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	sample	sample	NN	_	_	_
37	:	:	:	_	_	_
38	23S	23s	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	sample	sample	NN	_	_	_
41	:	:	:	_	_	_
42	2A	2a	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	sample	sample	NN	_	_	_
45	:	:	:	_	_	_
46	32D	32d	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	sample	sample	NN	_	_	_
49	:	:	:	_	_	_
50	33D	33d	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	sample	sample	NN	_	_	_
53	:	:	:	_	_	_
54	35B	35b	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	sample	sample	NN	_	_	_
57	:	:	:	_	_	_
58	3A	3a	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	sample	sample	NN	_	_	_
61	:	:	:	_	_	_
62	4A	4a	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	sample	sample	NN	_	_	_
65	:	:	:	_	_	_
66	5A	5a	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	sample	sample	NN	_	_	_
69	:	:	:	_	_	_
70	#	#	#	_	_	_
71	6	6	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	sample	sample	NN	_	_	_
74	:	:	:	_	_	_
75	6A	6a	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Sample	sample	NN	_	_	_
78	79	79	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	sample	sample	NN	_	_	_
81	:	:	:	_	_	_
82	9A	9a	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	sample	sample	NN	_	_	_
85	:	:	:	_	_	_
86	Bio-1	bio-1	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	sample	sample	NN	_	_	_
89	:	:	:	_	_	_
90	Bio-2	bio-2	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	sample	sample	NN	_	_	_
93	:	:	:	_	_	_
94	Bio-3	bio-3	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	sample	sample	NN	_	_	_
97	:	:	:	_	_	_
98	Bio-4	bio-4	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	sample	sample	NN	_	_	_
101	:	:	:	_	_	_
102	Biopile	Biopile	NNP	_	_	_
103	control	control	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	sample	sample	NN	_	_	_
106	:	:	:	_	_	_
107	BZ-NT	bz-nt	JJ	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Sample	sample	NN	_	_	_
110	collection	collection	NN	_	_	_
111	from	from	IN	_	_	_
112	M9	m9	NN	_	_	_
113	medium	medium	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	sample	sample	NN	_	_	_
116	:	:	:	_	_	_
117	Composite	Composite	NNP	_	_	_
118	A	A	NNP	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	sample	sample	NN	_	_	_
121	:	:	:	_	_	_
122	Composite	Composite	NNP	_	_	_
123	B	B	NNP	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	sample	sample	NN	_	_	_
126	id	id	NN	_	_	_
127	:	:	:	_	_	_
128	1a	1a	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	sample	sample	NN	_	_	_
131	id	id	NN	_	_	_
132	:	:	:	_	_	_
133	1b	1b	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	sample	sample	NN	_	_	_
136	id	id	NN	_	_	_
137	:	:	:	_	_	_
138	1c	1c	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	sample	sample	NN	_	_	_
141	id	id	NN	_	_	_
142	:	:	:	_	_	_
143	1d	1d	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	sample	sample	NN	_	_	_
146	id	id	NN	_	_	_
147	:	:	:	_	_	_
148	2a	2a	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	sample	sample	NN	_	_	_
151	id	id	NN	_	_	_
152	:	:	:	_	_	_
153	2b	2b	JJ	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	sample	sample	NN	_	_	_
156	id	id	NN	_	_	_
157	:	:	:	_	_	_
158	2c	2c	JJ	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	sample	sample	NN	_	_	_
161	id	id	NN	_	_	_
162	:	:	:	_	_	_
163	2d	2d	JJ	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	sample	sample	NN	_	_	_
166	id	id	NN	_	_	_
167	:	:	:	_	_	_
168	3a	3a	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	sample	sample	NN	_	_	_
171	id	id	NN	_	_	_
172	:	:	:	_	_	_
173	3b	3b	CD	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	sample	sample	NN	_	_	_
176	id	id	NN	_	_	_
177	:	:	:	_	_	_
178	3c	3c	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	sample	sample	NN	_	_	_
181	id	id	NN	_	_	_
182	:	:	:	_	_	_
183	3d	3d	JJ	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	sample	sample	NN	_	_	_
186	id	id	NN	_	_	_
187	:	:	:	_	_	_
188	4a	4a	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	sample	sample	NN	_	_	_
191	id	id	NN	_	_	_
192	:	:	:	_	_	_
193	4b	4b	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	sample	sample	NN	_	_	_
196	id	id	NN	_	_	_
197	:	:	:	_	_	_
198	4c	4c	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	sample	sample	NN	_	_	_
201	id	id	NN	_	_	_
202	:	:	:	_	_	_
203	4d	4d	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	sample	sample	NN	_	_	_
206	id	id	NN	_	_	_
207	:	:	:	_	_	_
208	5a	5a	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	sample	sample	NN	_	_	_
211	id	id	NN	_	_	_
212	:	:	:	_	_	_
213	5b	5b	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	sample	sample	NN	_	_	_
216	id	id	NN	_	_	_
217	:	:	:	_	_	_
218	5c	5c	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	sample	sample	NN	_	_	_
221	id	id	NN	_	_	_
222	:	:	:	_	_	_
223	5d	5d	JJ	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	sample	sample	NN	_	_	_
226	id	id	NN	_	_	_
227	:	:	:	_	_	_
228	6a	6a	FW	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
230	sample	sample	NN	_	_	_
231	id	id	NN	_	_	_
232	:	:	:	_	_	_
233	6b	6b	JJ	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	sample	sample	NN	_	_	_
236	id	id	NN	_	_	_
237	:	:	:	_	_	_
238	6c	6c	JJ	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	sample	sample	NN	_	_	_
241	id	id	NN	_	_	_
242	:	:	:	_	_	_
243	6d	6d	JJ	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	sample	sample	NN	_	_	_
246	id	id	NN	_	_	_
247	:	:	:	_	_	_
248	7a	7a	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	sample	sample	NN	_	_	_
251	id	id	NN	_	_	_
252	:	:	:	_	_	_
253	7b	7b	CD	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	sample	sample	NN	_	_	_
256	id	id	NN	_	_	_
257	:	:	:	_	_	_
258	7c	7c	CD	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	sample	sample	NN	_	_	_
261	id	id	NN	_	_	_
262	:	:	:	_	_	_
263	7d	7d	CD	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
265	sample	sample	NN	_	_	_
266	:	:	:	_	_	_
267	LC-1	lc-1	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	sample	sample	NN	_	_	_
270	:	:	:	_	_	_
271	NC	nc	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	sample	sample	NN	_	_	_
274	:	:	:	_	_	_
275	NF-NT	nf-nt	JJ	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	sample	sample	NN	_	_	_
278	:	:	:	_	_	_
279	Polygons	polygon	NNS	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	sample	sample	NN	_	_	_
282	port	port	NN	_	_	_
283	:	:	:	_	_	_
284	PFR	pfr	NN	_	_	_
285	P1	p1	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	sample	sample	NN	_	_	_
288	port	port	NN	_	_	_
289	:	:	:	_	_	_
290	PFR	pfr	NN	_	_	_
291	P3	p3	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	sample	sample	NN	_	_	_
294	port	port	NN	_	_	_
295	:	:	:	_	_	_
296	PFR	pfr	NN	_	_	_
297	P5	p5	NN	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	sample	sample	NN	_	_	_
300	port	port	NN	_	_	_
301	:	:	:	_	_	_
302	STR	str	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	Samples	sample	NNS	_	_	_
305	-LRB-	-lrb-	-LRB-	_	_	_
306	200-ml	200-ml	JJ	_	_	_
307	-RRB-	-rrb-	-RRB-	_	_	_
308	of	of	IN	_	_	_
309	the	the	DT	_	_	_
310	above	above	JJ	_	_	_
311	cultures	culture	NNS	_	_	_
312	for	for	IN	_	_	_
313	each	each	DT	_	_	_
314	strain	strain	NN	_	_	_
315	were	be	VBD	_	_	_
316	split	split	VBN	_	_	_
317	into	into	IN	_	_	_
318	two	two	CD	_	_	_
319	aliquots	aliquot	NNS	_	_	_
320	-LRB-	-lrb-	-LRB-	_	_	_
321	each	each	DT	_	_	_
322	100	100	CD	_	_	_
323	ml	ml	NN	_	_	_
324	-RRB-	-rrb-	-RRB-	_	_	_
325	,	,	,	_	_	_
326	and	and	CC	_	_	_
327	the	the	DT	_	_	_
328	aliquots	aliquot	NNS	_	_	_
329	were	be	VBD	_	_	_
330	then	then	RB	_	_	_
331	incubated	incubate	VBN	_	_	_
332	at	at	IN	_	_	_
333	30	30	CD	_	_	_
334	°C	°c	NN	_	_	_
335	or	or	CC	_	_	_
336	42	42	CD	_	_	_
337	°C	°c	NN	_	_	_
338	for	for	IN	_	_	_
339	another	another	DT	_	_	_
340	60	60	CD	_	_	_
341	min	min	NN	_	_	_
342	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	30	30	CD	_	_	_
5	ml	ml	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	were	be	VBD	_	_	_
8	harvested	harvest	VBN	_	_	_
9	directly	directly	RB	_	_	_
10	into	into	IN	_	_	_
11	cold	cold	JJ	_	_	_
12	phenol	phenol	NN	_	_	_
13	ethanol	ethanol	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	187	187	CD	_	_	_
16	µl	µl	NN	_	_	_
17	phenol	phenol	NN	_	_	_
18	,	,	,	_	_	_
19	3.56	3.56	CD	_	_	_
20	ml	ml	NN	_	_	_
21	ethanol	ethanol	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	to	to	TO	_	_	_
24	stabilize	stabilize	VB	_	_	_
25	RNA	rna	NN	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	total	total	JJ	_	_	_
29	RNA	rna	NN	_	_	_
30	was	be	VBD	_	_	_
31	purified	purify	VBN	_	_	_
32	using	use	VBG	_	_	_
33	Qiagen	Qiagen	NNP	_	_	_
34	's	's	POS	_	_	_
35	RNeasy	RNeasy	NNP	_	_	_
36	Mini	Mini	NNP	_	_	_
37	kit	kit	NN	_	_	_
38	as	as	IN	_	_	_
39	recommended	recommend	VBN	_	_	_
40	by	by	IN	_	_	_
41	suppliers	supplier	NNS	_	_	_
42	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	931	931	CD	_	_	_
4	,	,	,	_	_	_
5	933	933	CD	_	_	_
6	,	,	,	_	_	_
7	935	935	CD	_	_	_
8	and	and	CC	_	_	_
9	937	937	CD	_	_	_
10	were	be	VBD	_	_	_
11	aligned	align	VBN	_	_	_
12	with	with	IN	_	_	_
13	bowtie	bowtie	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	V	v	NN	_	_	_
16	1.1.2	1.1.2	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	with	with	IN	_	_	_
19	parameters	parameter	NNS	_	_	_
20	--	--	:	_	_	_
21	wrapper	wrapper	NN	_	_	_
22	basic-0	basic-0	NN	_	_	_
23	-	-	:	_	_	_
24	q	q	SYM	_	_	_
25	-	-	:	_	_	_
26	m	m	NN	_	_	_
27	1	1	CD	_	_	_
28	-	-	:	_	_	_
29	l	l	NN	_	_	_
30	55	55	CD	_	_	_
31	-	-	:	_	_	_
32	k	k	NN	_	_	_
33	1	1	CD	_	_	_
34	-5	-5	CD	_	_	_
35	3	3	CD	_	_	_
36	-3	-3	CD	_	_	_
37	40	40	CD	_	_	_
38	--	--	:	_	_	_
39	best	best	JJS	_	_	_
40	-	-	:	_	_	_
41	S	s	NN	_	_	_
42	-	-	:	_	_	_
43	p	p	NN	_	_	_
44	24	24	CD	_	_	_
45	,	,	,	_	_	_
46	and	and	CC	_	_	_
47	samples	sample	NNS	_	_	_
48	1311	1311	CD	_	_	_
49	,	,	,	_	_	_
50	1314	1314	CD	_	_	_
51	,	,	,	_	_	_
52	1317	1317	CD	_	_	_
53	and	and	CC	_	_	_
54	1320	1320	CD	_	_	_
55	were	be	VBD	_	_	_
56	aligned	align	VBN	_	_	_
57	with	with	IN	_	_	_
58	bowtie	bowtie	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	V	v	NN	_	_	_
61	1.1.2	1.1.2	CD	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	with	with	IN	_	_	_
64	paramters	paramter	NNS	_	_	_
65	--	--	:	_	_	_
66	wrapper	wrapper	NN	_	_	_
67	basic-0	basic-0	NN	_	_	_
68	-	-	:	_	_	_
69	q	q	SYM	_	_	_
70	-	-	:	_	_	_
71	m	m	NN	_	_	_
72	1	1	CD	_	_	_
73	-	-	:	_	_	_
74	v	v	LS	_	_	_
75	2	2	CD	_	_	_
76	--	--	:	_	_	_
77	best	best	JJS	_	_	_
78	-	-	:	_	_	_
79	p	p	NN	_	_	_
80	24	24	CD	_	_	_
81	-	-	:	_	_	_
82	S	s	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Samples	sample	NNS	_	_	_
85	for	for	IN	_	_	_
86	microarray	microarray	NN	_	_	_
87	analyses	analysis	NNS	_	_	_
88	were	be	VBD	_	_	_
89	taken	take	VBN	_	_	_
90	before	before	IN	_	_	_
91	ciprofloxacin	ciprofloxacin	NN	_	_	_
92	treatment	treatment	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	t0	t0	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	and	and	CC	_	_	_
97	then	then	RB	_	_	_
98	at	at	IN	_	_	_
99	1	1	CD	_	_	_
100	hour	hour	NN	_	_	_
101	post-treatment	post-treatment	JJ	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	t1	t1	NN	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	.	.	.	_	_	_

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/ml	cells/ml	NNS	_	_	_
8	and	and	CC	_	_	_
9	cultures	culture	NNS	_	_	_
10	were	be	VBD	_	_	_
11	treated	treat	VBN	_	_	_
12	with	with	IN	_	_	_
13	ciprofloxacin	ciprofloxacin	NN	_	_	_
14	in	in	IN	_	_	_
15	Erlenmeyer	Erlenmeyer	NNP	_	_	_
16	flasks	flask	NNS	_	_	_
17	using	use	VBG	_	_	_
18	20	20	CD	_	_	_
19	ml	ml	NN	_	_	_
20	fresh	fresh	JJ	_	_	_
21	LB	lb	NN	_	_	_
22	.	.	.	_	_	_

1	~	~	NN	_	_	_
2	109	109	CD	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	taken	take	VBN	_	_	_
6	at	at	IN	_	_	_
7	each	each	DT	_	_	_
8	timepoint	timepoint	NN	_	_	_
9	as	as	IN	_	_	_
10	samples	sample	NNS	_	_	_
11	for	for	IN	_	_	_
12	RNA	rna	NN	_	_	_
13	isolation	isolation	NN	_	_	_
14	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	order	order	NN	_	_	_
3	to	to	TO	_	_	_
4	stabilize	stabilize	VB	_	_	_
5	RNA	rna	NN	_	_	_
6	,	,	,	_	_	_
7	RNA	rna	NN	_	_	_
8	Bacteria	bacterium	NNS	_	_	_
9	Protect	protect	VB	_	_	_
10	Reagent	reagent	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	was	be	VBD	_	_	_
15	added	add	VBN	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	samples	sample	NNS	_	_	_
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	and	and	CC	_	_	_
27	then	then	RB	_	_	_
28	samples	sample	NNS	_	_	_
29	were	be	VBD	_	_	_
30	stored	store	VBN	_	_	_
31	overnight	overnight	RB	_	_	_
32	at	at	IN	_	_	_
33	-80	-80	CD	_	_	_
34	°C	°c	NN	_	_	_
35	.	.	.	_	_	_

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	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	instructions	instruction	NNS	_	_	_
19	.	.	.	_	_	_

1	Sample	sample	VB	_	_	_
2	concentration	concentration	NN	_	_	_
3	was	be	VBD	_	_	_
4	estimated	estimate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	NanoDrop	NanoDrop	NNP	_	_	_
8	1000	1000	CD	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Thermoscientific	thermoscientific	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	spectrophotometer	spectrophotometer	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	for	for	IN	_	_	_
4	microarray	microarray	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	were	be	VBD	_	_	_
7	collected	collect	VBN	_	_	_
8	as	as	IN	_	_	_
9	described	describe	VBN	_	_	_
10	earlier	earlier	JJR	_	_	_
11	-LSB-	-lsb-	-LRB-	_	_	_
12	1	1	CD	_	_	_
13	-RSB-	-rsb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	shortly	shortly	RB	_	_	_
19	mixed	mix	VBN	_	_	_
20	by	by	IN	_	_	_
21	vortexing	vortex	VBG	_	_	_
22	,	,	,	_	_	_
23	divided	divide	VBN	_	_	_
24	in	in	IN	_	_	_
25	0.5	0.5	CD	_	_	_
26	mL	ml	NN	_	_	_
27	aliquots	aliquot	NNS	_	_	_
28	and	and	CC	_	_	_
29	1	1	CD	_	_	_
30	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	for	for	IN	_	_	_
4	transcriptome	transcriptome	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	were	be	VBD	_	_	_
7	taken	take	VBN	_	_	_
8	from	from	IN	_	_	_
9	exponentially	exponentially	RB	_	_	_
10	growing	grow	VBG	_	_	_
11	cells	cell	NNS	_	_	_
12	.	.	.	_	_	_

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	Samples	sample	NNS	_	_	_
3	of	of	IN	_	_	_
4	~	~	NN	_	_	_
5	7.2	7.2	CD	_	_	_
6	ml	ml	NN	_	_	_
7	bacterial	bacterial	JJ	_	_	_
8	culture	culture	NN	_	_	_
9	were	be	VBD	_	_	_
10	mixed	mix	VBN	_	_	_
11	with	with	IN	_	_	_
12	0.8	0.8	CD	_	_	_
13	ml	ml	NN	_	_	_
14	stop	stop	NN	_	_	_
15	solution	solution	NN	_	_	_
16	,	,	,	_	_	_
17	pelleted	pelleted	JJ	_	_	_
18	and	and	CC	_	_	_
19	total	total	JJ	_	_	_
20	RNA	rna	NN	_	_	_
21	was	be	VBD	_	_	_
22	purified	purify	VBN	_	_	_
23	using	use	VBG	_	_	_
24	RNeasy	RNeasy	NNP	_	_	_
25	Mini	Mini	NNP	_	_	_
26	Kit	kit	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Qiagen	qiagen	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

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	/	/	:	_	_	_
31	µl	µl	NN	_	_	_
32	,	,	,	_	_	_
33	Amersham	Amersham	NNP	_	_	_
34	Pharmacia	Pharmacia	NNP	_	_	_
35	Biotech	Biotech	NNP	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	in	in	IN	_	_	_
38	nuclease-free	nuclease-free	JJ	_	_	_
39	water	water	NN	_	_	_
40	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	4	4	CD	_	_	_
5	min	min	NN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	,	,	,	_	_	_
10	DNase	dnase	NN	_	_	_
11	I	i	CD	_	_	_
12	was	be	VBD	_	_	_
13	heat	heat	NN	_	_	_
14	inactivated	inactivate	VBN	_	_	_
15	at	at	IN	_	_	_
16	98	98	CD	_	_	_
17	°C	°c	NN	_	_	_
18	for	for	IN	_	_	_
19	10	10	CD	_	_	_
20	min	min	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	of	of	IN	_	_	_
4	magnetic	magnetic	JJ	_	_	_
5	field-treated	field-treated	JJ	_	_	_
6	or	or	CC	_	_	_
7	sham-treated	sham-treated	JJ	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	withdrawn	withdraw	VBN	_	_	_
11	as	as	IN	_	_	_
12	fast	fast	JJ	_	_	_
13	as	as	IN	_	_	_
14	possible	possible	JJ	_	_	_
15	from	from	IN	_	_	_
16	the	the	DT	_	_	_
17	bioreactor	bioreactor	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	not	not	RB	_	_	_
20	later	later	RB	_	_	_
21	than	than	IN	_	_	_
22	3	3	CD	_	_	_
23	min	min	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	after	after	IN	_	_	_
26	the	the	DT	_	_	_
27	specified	specify	VBN	_	_	_
28	treatement	treatement	NN	_	_	_
29	period	period	NN	_	_	_
30	.	.	.	_	_	_

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	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	Samples	sample	NNS	_	_	_
43	were	be	VBD	_	_	_
44	aligned	align	VBN	_	_	_
45	to	to	TO	_	_	_
46	the	the	DT	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	K	k	NN	_	_	_
50	12	12	CD	_	_	_
51	MG1655	mg1655	NN	_	_	_
52	reference	reference	NN	_	_	_
53	sequence	sequence	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	version	version	NN	_	_	_
56	NC000913	nc000913	NN	_	_	_
57	.2	.2	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	,	,	,	_	_	_
60	using	use	VBG	_	_	_
61	BWA	bwa	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	version	version	NN	_	_	_
64	0.5	0.5	CD	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	WITH	with	IN	_	_	_
67	-	-	:	_	_	_
68	q	q	NN	_	_	_
69	30	30	CD	_	_	_
70	parameter	parameter	NN	_	_	_
71	for	for	IN	_	_	_
72	trimming	trim	VBG	_	_	_
73	of	of	IN	_	_	_
74	reads	read	VBZ	_	_	_
75	below	below	IN	_	_	_
76	PHRED	PHRED	NNP	_	_	_
77	quality	quality	NN	_	_	_
78	score	score	NN	_	_	_
79	of	of	IN	_	_	_
80	30	30	CD	_	_	_
81	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	background	background	NN	_	_	_
5	corrected	correct	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	normexp	normexp	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	function	function	NN	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	Limma	Limma	NNP	_	_	_
15	package	package	NN	_	_	_
16	in	in	IN	_	_	_
17	R	r	NN	_	_	_
18	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:1	1:1	CD	_	_	_
6	in	in	IN	_	_	_
7	RNA	rna	NN	_	_	_
8	Protect	protect	VB	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	Qiagen	NNP	_	_	_
11	,	,	,	_	_	_
12	Carlsbad	Carlsbad	NNP	_	_	_
13	,	,	,	_	_	_
14	CA	CA	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	to	to	TO	_	_	_
17	inhibit	inhibit	VB	_	_	_
18	RNase	rnase	NN	_	_	_
19	activity	activity	NN	_	_	_
20	and	and	CC	_	_	_
21	then	then	RB	_	_	_
22	centrifuged	centrifuge	VBD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	5000	5000	CD	_	_	_
25	x	x	CC	_	_	_
26	g	g	NN	_	_	_
27	,	,	,	_	_	_
28	10	10	CD	_	_	_
29	min	min	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	Pellets	pellet	NNS	_	_	_
2	were	be	VBD	_	_	_
3	resuspended	resuspend	VBN	_	_	_
4	in	in	IN	_	_	_
5	TE/lysozyme	te/lysozyme	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	10	10	CD	_	_	_
8	mg/ml	mg/ml	NN	_	_	_
9	lysozyme	lysozyme	NN	_	_	_
10	,	,	,	_	_	_
11	0.5	0.5	CD	_	_	_
12	%	%	NN	_	_	_
13	SDS	sds	NN	_	_	_
14	,	,	,	_	_	_
15	pH	ph	NN	_	_	_
16	8.0	8.0	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	with	with	IN	_	_	_
19	added	add	VBN	_	_	_
20	proteinase	proteinase	NN	_	_	_
21	K	k	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	1.5	1.5	CD	_	_	_
24	mg/ml	mg/ml	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	's	's	POS	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	kit	kit	NN	_	_	_
9	according	accord	VBG	_	_	_
10	to	to	TO	_	_	_
11	manufacturer	manufacturer	NN	_	_	_
12	instructions	instruction	NNS	_	_	_
13	with	with	IN	_	_	_
14	slight	slight	JJ	_	_	_
15	modification	modification	NN	_	_	_
16	.	.	.	_	_	_

1	Before	before	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	,	,	,	_	_	_
4	β-mercaptoethanol	β-mercaptoethanol	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	kit	kit	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	RLT	rlt	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	10	10	CD	_	_	_
14	%	%	NN	_	_	_
15	v/v	v/v	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	Additionally	additionally	RB	_	_	_
2	,	,	,	_	_	_
3	during	during	IN	_	_	_
4	the	the	DT	_	_	_
5	wash	wash	NN	_	_	_
6	step	step	NN	_	_	_
7	RNase-free	rnase-free	JJ	_	_	_
8	DNase	dnase	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	Qiagen	NNP	_	_	_
11	,	,	,	_	_	_
12	Carlsbad	Carlsbad	NNP	_	_	_
13	,	,	,	_	_	_
14	CA	CA	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	was	be	VBD	_	_	_
17	diluted	dilute	VBN	_	_	_
18	in	in	IN	_	_	_
19	RNeasy	RNeasy	NNP	_	_	_
20	kit	kit	NN	_	_	_
21	buffer	buffer	NN	_	_	_
22	RDD	rdd	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	310	310	CD	_	_	_
25	Kunitz	Kunitz	NNP	_	_	_
26	units/mL	units/ml	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	,	,	,	_	_	_
29	added	add	VBD	_	_	_
30	to	to	TO	_	_	_
31	the	the	DT	_	_	_
32	purification	purification	NN	_	_	_
33	column	column	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	incubated	incubate	VBN	_	_	_
37	for	for	IN	_	_	_
38	15	15	CD	_	_	_
39	minutes	minute	NNS	_	_	_
40	at	at	IN	_	_	_
41	room	room	NN	_	_	_
42	temperature	temperature	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	RT	rt	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	isolation	isolation	NN	_	_	_
3	,	,	,	_	_	_
4	spectrophotometric	spectrophotometric	JJ	_	_	_
5	NanoDrop	NanoDrop	NNP	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	NanoDrop	NanoDrop	NNP	_	_	_
8	1000	1000	CD	_	_	_
9	v3	v3	NN	_	_	_
10	.8.1	.8.1	CD	_	_	_
11	;	;	:	_	_	_
12	Thermo	Thermo	NNP	_	_	_
13	Fisher	Fisher	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	curves	curve	NNS	_	_	_
16	were	be	VBD	_	_	_
17	obtained	obtain	VBN	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	total	total	JJ	_	_	_
21	RNA	rna	NN	_	_	_
22	sample	sample	NN	_	_	_
23	and	and	CC	_	_	_
24	verified	verify	VBN	_	_	_
25	for	for	IN	_	_	_
26	purity	purity	NN	_	_	_
27	,	,	,	_	_	_
28	as	as	IN	_	_	_
29	defined	define	VBN	_	_	_
30	by	by	IN	_	_	_
31	absorbance	absorbance	NN	_	_	_
32	ratios	ratio	NNS	_	_	_
33	at	at	IN	_	_	_
34	260/280	260/280	CD	_	_	_
35	nm	nm	NN	_	_	_
36	and	and	CC	_	_	_
37	260/230	260/230	CD	_	_	_
38	nm	nm	NN	_	_	_
39	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	sent	send	VBN	_	_	_
6	to	to	TO	_	_	_
7	Oregon	Oregon	NNP	_	_	_
8	State	State	NNP	_	_	_
9	University	University	NNP	_	_	_
10	's	's	POS	_	_	_
11	Center	Center	NNP	_	_	_
12	for	for	IN	_	_	_
13	Genome	Genome	NNP	_	_	_
14	Research	Research	NNP	_	_	_
15	and	and	CC	_	_	_
16	Biocomputing	Biocomputing	NNP	_	_	_
17	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	integrity	integrity	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	RIN	rin	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	measurements	measurement	NNS	_	_	_
7	were	be	VBD	_	_	_
8	taken	take	VBN	_	_	_
9	using	use	VBG	_	_	_
10	an	a	DT	_	_	_
11	Agilent	Agilent	NNP	_	_	_
12	Bioanalyzer	Bioanalyzer	NNP	_	_	_
13	,	,	,	_	_	_
14	resulting	result	VBG	_	_	_
15	in	in	IN	_	_	_
16	RIN	RIN	NNP	_	_	_
17	scores	score	NNS	_	_	_
18	of	of	IN	_	_	_
19	10	10	CD	_	_	_
20	,	,	,	_	_	_
21	out	out	IN	_	_	_
22	of	of	IN	_	_	_
23	a	a	DT	_	_	_
24	possible	possible	JJ	_	_	_
25	10	10	CD	_	_	_
26	,	,	,	_	_	_
27	for	for	IN	_	_	_
28	each	each	DT	_	_	_
29	sample	sample	NN	_	_	_
30	.	.	.	_	_	_

1	Ribosomal	ribosomal	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	depleted	deplete	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	RiboZero	RiboZero	NNP	_	_	_
8	rRNA	rrna	NN	_	_	_
9	removal	removal	NN	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Life	Life	NNP	_	_	_
13	Technologies	Technologies	NNPS	_	_	_
14	,	,	,	_	_	_
15	Eugene	Eugene	NNP	_	_	_
16	,	,	,	_	_	_
17	OR	or	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	aerobically	aerobically	RB	_	_	_
6	in	in	IN	_	_	_
7	rich	rich	JJ	MED	_	_
8	media	media	NNS	MED	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Samples	sample	NNS	_	_	_
11	were	be	VBD	_	_	_
12	grown	grow	VBN	_	_	_
13	anaerobically	anaerobically	RB	_	_	_
14	in	in	IN	_	_	_
15	MOPS	mop	NNS	MED	_	_
16	minimal	minimal	JJ	_	_	_
17	media	media	NNS	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	casamino	casamino	NN	SUPP	_	_
21	acids	acid	NNS	SUPP	_	_
22	using	use	VBG	_	_	_
23	glucose	glucose	NN	SUPP	_	_
24	as	as	IN	_	_	_
25	the	the	DT	_	_	_
26	carbon	carbon	NN	_	_	_
27	source	source	NN	_	_	_
28	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	mid	mid	JJ	GrowthPhase	_	_
7	exponential	exponential	JJ	GrowthPhase	_	_
8	phase	phase	NN	GrowthPhase	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	OD	od	NN	_	_	_
11	approx	approx	RB	_	_	_
12	0.5	0.5	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

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	Samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	grown	grow	VBN	_	_	_
19	to	to	TO	_	_	_
20	mid	mid	JJ	GrowthPhase	_	_
21	exponential	exponential	JJ	GrowthPhase	_	_
22	phase	phase	NN	GrowthPhase	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	OD	od	NN	_	_	_
25	approx	approx	RB	_	_	_
26	0.5	0.5	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

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/isopropanol	ice/isopropanol	NN	_	_	_
13	bath	bath	NN	_	_	_
14	,	,	,	_	_	_
15	harvested	harvest	VBN	_	_	_
16	by	by	IN	_	_	_
17	centrifugation	centrifugation	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	4470	4470	CD	_	_	_
20	×	×	CD	_	_	_
21	g	g	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	at	at	IN	_	_	_
24	4	4	CD	_	_	_
25	ºC	ºc	NN	_	_	_
26	and	and	CC	_	_	_
27	resuspended	resuspend	VBN	_	_	_
28	in	in	IN	_	_	_
29	RNALater	rnalater	NN	_	_	_
30	to	to	TO	_	_	_
31	stop	stop	VB	_	_	_
32	RNA	rna	NN	_	_	_
33	degradation	degradation	NN	_	_	_
34	.	.	.	_	_	_

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	Samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	mixed	mixed	JJ	_	_	_
19	,	,	,	_	_	_
20	incubated	incubate	VBN	_	_	_
21	on	on	IN	_	_	_
22	ice	ice	NN	_	_	_
23	for	for	IN	_	_	_
24	10	10	CD	_	_	_
25	min	min	NN	_	_	_
26	after	after	IN	_	_	_
27	which	which	WDT	_	_	_
28	cells	cell	NNS	_	_	_
29	were	be	VBD	_	_	_
30	collected	collect	VBN	_	_	_
31	by	by	IN	_	_	_
32	centrifugation	centrifugation	NN	_	_	_
33	at	at	IN	_	_	_
34	4150	4150	CD	_	_	_
35	rpm	rpm	NN	_	_	_
36	at	at	IN	_	_	_
37	4	4	CD	_	_	_
38	˚C	˚c	NN	_	_	_
39	for	for	IN	_	_	_
40	10	10	CD	_	_	_
41	min	min	NN	_	_	_
42	.	.	.	_	_	_

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/dry	ethanol/dry	NN	_	_	_
9	ice	ice	NN	_	_	_
10	slurry	slurry	NN	_	_	_
11	and	and	CC	_	_	_
12	stored	store	VBD	_	_	_
13	at	at	IN	_	_	_
14	-80	-80	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	total	total	JJ	_	_	_
18	RNA	rna	NN	_	_	_
19	could	could	MD	_	_	_
20	be	be	VB	_	_	_
21	extracted	extract	VBN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	sent	send	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	International	International	NNP	_	_	_
8	Space	Space	NNP	_	_	_
9	Station	Station	NNP	_	_	_
10	at	at	IN	_	_	_
11	4C	4c	NN	_	_	_
12	in	in	IN	_	_	_
13	FPAs	fpa	NNS	_	_	_
14	,	,	,	_	_	_
15	as	as	IN	_	_	_
16	described	describe	VBN	_	_	_
17	above	above	IN	_	_	_
18	.	.	.	_	_	_

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/L	g/l	NN	_	_	_
45	glucose	glucose	NN	SUPP	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	,	,	,	_	_	_
48	yielding	yield	VBG	_	_	_
49	3.25	3.25	CD	_	_	_
50	mL	ml	NN	_	_	_
51	of	of	IN	_	_	_
52	a	a	DT	_	_	_
53	culture	culture	NN	_	_	_
54	with	with	IN	_	_	_
55	a	a	DT	_	_	_
56	starting	start	VBG	_	_	_
57	cell	cell	NN	_	_	_
58	concentration	concentration	NN	_	_	_
59	of	of	IN	_	_	_
60	1.22	1.22	CD	_	_	_
61	e6	e6	NN	_	_	_
62	cell/mL	cell/ml	NN	_	_	_
63	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	Prokaryotic	Prokaryotic	NNP	_	_	_
7	Target	target	NN	_	_	_
8	Preparation	preparation	NN	_	_	_
9	protocol	protocol	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	GeneChip	genechip	NN	_	_	_
12	Expression	expression	NN	_	_	_
13	Analysis	analysis	NN	_	_	_
14	Technical	Technical	NNP	_	_	_
15	Manual	Manual	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	RNAprotect	rnaprotect	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Qiagen	Qiagen	NNP	_	_	_
9	,	,	,	_	_	_
10	Hilden	Hilden	NNP	_	_	_
11	,	,	,	_	_	_
12	Germany	Germany	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	stored	store	VBN	_	_	_
16	at	at	IN	_	_	_
17	-80	-80	CD	_	_	_
18	°C	°c	NN	_	_	_
19	until	until	IN	_	_	_
20	preparation	preparation	NN	_	_	_
21	.	.	.	_	_	_

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	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Samples	sample	NNS	_	_	_
35	were	be	VBD	_	_	_
36	used	use	VBN	_	_	_
37	for	for	IN	_	_	_
38	on-bead	on-bead	JJ	_	_	_
39	enzymatic	enzymatic	JJ	_	_	_
40	reactions	reaction	NNS	_	_	_
41	of	of	IN	_	_	_
42	the	the	DT	_	_	_
43	ChIP-exo	ChIP-exo	NNP	_	_	_
44	procedure	procedure	NN	_	_	_
45	and	and	CC	_	_	_
46	Illumina	Illumina	NNP	_	_	_
47	Tru-seq	tru-seq	JJ	_	_	_
48	sequencing	sequencing	NN	_	_	_
49	libraries	library	NNS	_	_	_
50	were	be	VBD	_	_	_
51	construction	construction	NN	_	_	_
52	as	as	IN	_	_	_
53	described	describe	VBN	_	_	_
54	in	in	IN	_	_	_
55	Rhee	Rhee	NNP	_	_	_
56	and	and	CC	_	_	_
57	Pugh	Pugh	NNP	_	_	_
58	,	,	,	_	_	_
59	2012	2012	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
61	sample	sample	NN	_	_	_
62	type	type	NN	_	_	_
63	:	:	:	_	_	_
64	AT1	at1	NN	_	_	_
65	digested	digest	VBD	_	_	_
66	total	total	JJ	_	_	_
67	RNA	rna	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	sample	sample	NN	_	_	_
70	type	type	NN	_	_	_
71	:	:	:	_	_	_
72	cDNA	cdna	NN	_	_	_
73	produced	produce	VBN	_	_	_
74	by	by	IN	_	_	_
75	RT	rt	NN	_	_	_
76	of	of	IN	_	_	_
77	RNA	rna	NN	_	_	_
78	deriving	derive	VBG	_	_	_
79	from	from	IN	_	_	_
80	vitro	vitro	FW	_	_	_
81	transcription	transcription	NN	_	_	_
82	,	,	,	_	_	_
83	with	with	IN	_	_	_
84	RNA	rna	NN	_	_	_
85	polymerase	polymerase	NN	_	_	_
86	E	e	NN	_	_	_
87	σ70	σ70	NN	_	_	_
88	,	,	,	_	_	_
89	of	of	IN	_	_	_
90	2	2	CD	_	_	_
91	ug	ug	NN	_	_	_
92	of	of	IN	_	_	_
93	genomic	genomic	JJ	_	_	_
94	DNA	dna	NN	_	_	_
95	from	from	IN	_	_	_
96	E.	e.	FW	_	_	_
97	coli	coli	FW	_	_	_
98	MG1655	mg1655	NN	_	_	_
99	digested	digest	VBN	_	_	_
100	with	with	IN	_	_	_
101	EcoRI	ecori	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	sample	sample	NN	_	_	_
104	type	type	NN	_	_	_
105	:	:	:	_	_	_
106	cDNA	cdna	NN	_	_	_
107	produced	produce	VBN	_	_	_
108	by	by	IN	_	_	_
109	RT	rt	NN	_	_	_
110	of	of	IN	_	_	_
111	RNA	rna	NN	_	_	_
112	deriving	derive	VBG	_	_	_
113	from	from	IN	_	_	_
114	vitro	vitro	FW	_	_	_
115	transcription	transcription	NN	_	_	_
116	,	,	,	_	_	_
117	with	with	IN	_	_	_
118	RNA	rna	NN	_	_	_
119	polymerase	polymerase	NN	_	_	_
120	E	e	NN	_	_	_
121	σS	σs	NN	_	_	_
122	,	,	,	_	_	_
123	of	of	IN	_	_	_
124	2	2	CD	_	_	_
125	ug	ug	NN	_	_	_
126	of	of	IN	_	_	_
127	genomic	genomic	JJ	_	_	_
128	DNA	dna	NN	_	_	_
129	from	from	IN	_	_	_
130	E.	e.	FW	_	_	_
131	coli	coli	FW	_	_	_
132	MG1655	mg1655	NN	_	_	_
133	digested	digest	VBN	_	_	_
134	with	with	IN	_	_	_
135	EcoRI	ecori	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	sample	sample	NN	_	_	_
138	type	type	NN	_	_	_
139	:	:	:	_	_	_
140	control	control	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
142	sample	sample	NN	_	_	_
143	type	type	NN	_	_	_
144	:	:	:	_	_	_
145	E.	e.	FW	_	_	_
146	coli	coli	FW	_	_	_
147	strain	strain	NN	_	_	_
148	MC4100relA	mc4100rela	NN	_	_	_
149	+	+	CC	_	_	_
150	in	in	IN	_	_	_
151	mid	mid	JJ	_	_	_
152	log	log	NN	_	_	_
153	phase	phase	NN	_	_	_
154	incubated	incubate	VBN	_	_	_
155	at	at	IN	_	_	_
156	37ºC	37ºc	NN	_	_	_
157	for	for	IN	_	_	_
158	4	4	CD	_	_	_
159	hours	hour	NNS	_	_	_
160	with	with	IN	_	_	_
161	100	100	CD	_	_	_
162	μg/ml	μg/ml	NN	_	_	_
163	NA	na	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	sample	sample	NN	_	_	_
166	type	type	NN	_	_	_
167	:	:	:	_	_	_
168	E.	e.	FW	_	_	_
169	coli	coli	FW	_	_	_
170	strain	strain	NN	_	_	_
171	MC4100relA	mc4100rela	NN	_	_	_
172	+	+	CC	_	_	_
173	in	in	IN	_	_	_
174	mid	mid	JJ	_	_	_
175	log	log	NN	_	_	_
176	phase	phase	NN	_	_	_
177	incubated	incubate	VBN	_	_	_
178	at	at	IN	_	_	_
179	37ºC	37ºc	NN	_	_	_
180	for	for	IN	_	_	_
181	4	4	CD	_	_	_
182	hours	hour	NNS	_	_	_
183	with	with	IN	_	_	_
184	10	10	CD	_	_	_
185	μg/ml	μg/ml	NN	_	_	_
186	NA	na	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	sample	sample	NN	_	_	_
189	type	type	NN	_	_	_
190	:	:	:	_	_	_
191	E.	e.	FW	_	_	_
192	coli	coli	FW	_	_	_
193	strain	strain	NN	_	_	_
194	MC4100relA	mc4100rela	NN	_	_	_
195	+	+	CC	_	_	_
196	in	in	IN	_	_	_
197	mid	mid	JJ	_	_	_
198	log	log	NN	_	_	_
199	phase	phase	NN	_	_	_
200	incubated	incubate	VBN	_	_	_
201	at	at	IN	_	_	_
202	37ºC	37ºc	NN	_	_	_
203	for	for	IN	_	_	_
204	4	4	CD	_	_	_
205	hours	hour	NNS	_	_	_
206	without	without	IN	_	_	_
207	treatment	treatment	NN	_	_	_
208	.	.	.	_	_	_

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/ml	μg/ml	NN	_	_	_
25	NA	na	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	sample	sample	NN	_	_	_
28	type	type	NN	_	_	_
29	:	:	:	_	_	_
30	E.	e.	FW	_	_	_
31	coli	coli	FW	_	_	_
32	strain	strain	NN	_	_	_
33	MC4100relA	mc4100rela	NN	_	_	_
34	+	+	CC	_	_	_
35	∆	∆	SYM	_	_	_
36	mazEF	mazef	NN	_	_	_
37	in	in	IN	_	_	_
38	mid	mid	JJ	_	_	_
39	log	log	NN	_	_	_
40	phase	phase	NN	_	_	_
41	incubated	incubate	VBN	_	_	_
42	at	at	IN	_	_	_
43	37ºC	37ºc	NN	_	_	_
44	for	for	IN	_	_	_
45	4	4	CD	_	_	_
46	hours	hour	NNS	_	_	_
47	with	with	IN	_	_	_
48	10	10	CD	_	_	_
49	μg/ml	μg/ml	NN	_	_	_
50	NA	na	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	sample	sample	NN	_	_	_
53	type	type	NN	_	_	_
54	:	:	:	_	_	_
55	E.	e.	FW	_	_	_
56	coli	coli	FW	_	_	_
57	strain	strain	NN	_	_	_
58	MC4100relA	mc4100rela	NN	_	_	_
59	+	+	CC	_	_	_
60	∆	∆	SYM	_	_	_
61	mazEF	mazef	NN	_	_	_
62	in	in	IN	_	_	_
63	mid	mid	JJ	_	_	_
64	log	log	NN	_	_	_
65	phase	phase	NN	_	_	_
66	incubated	incubate	VBN	_	_	_
67	at	at	IN	_	_	_
68	37ºC	37ºc	NN	_	_	_
69	for	for	IN	_	_	_
70	4	4	CD	_	_	_
71	hours	hour	NNS	_	_	_
72	without	without	IN	_	_	_
73	treatment	treatment	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	sample	sample	NN	_	_	_
76	type	type	NN	_	_	_
77	:	:	:	_	_	_
78	E.	e.	FW	_	_	_
79	coli	coli	FW	_	_	_
80	strain	strain	NN	_	_	_
81	MC4100relA	mc4100rela	NN	_	_	_
82	+	+	CC	_	_	_
83	∆	∆	SYM	_	_	_
84	mazEFlexA3	mazeflexa3	NN	_	_	_
85	in	in	IN	_	_	_
86	mid	mid	JJ	_	_	_
87	log	log	NN	_	_	_
88	phase	phase	NN	_	_	_
89	incubated	incubate	VBN	_	_	_
90	at	at	IN	_	_	_
91	37ºC	37ºc	NN	_	_	_
92	for	for	IN	_	_	_
93	4	4	CD	_	_	_
94	hours	hour	NNS	_	_	_
95	with	with	IN	_	_	_
96	100	100	CD	_	_	_
97	μg/ml	μg/ml	NN	_	_	_
98	NA	na	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	sample	sample	NN	_	_	_
101	type	type	NN	_	_	_
102	:	:	:	_	_	_
103	E.	e.	FW	_	_	_
104	coli	coli	FW	_	_	_
105	strain	strain	NN	_	_	_
106	MC4100relA	mc4100rela	NN	_	_	_
107	+	+	CC	_	_	_
108	∆	∆	SYM	_	_	_
109	mazEFlexA3	mazeflexa3	NN	_	_	_
110	in	in	IN	_	_	_
111	mid	mid	JJ	_	_	_
112	log	log	NN	_	_	_
113	phase	phase	NN	_	_	_
114	incubated	incubate	VBN	_	_	_
115	at	at	IN	_	_	_
116	37ºC	37ºc	NN	_	_	_
117	for	for	IN	_	_	_
118	4	4	CD	_	_	_
119	hours	hour	NNS	_	_	_
120	with	with	IN	_	_	_
121	10	10	CD	_	_	_
122	μg/ml	μg/ml	NN	_	_	_
123	NA	na	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	sample	sample	NN	_	_	_
126	type	type	NN	_	_	_
127	:	:	:	_	_	_
128	E.	e.	FW	_	_	_
129	coli	coli	FW	_	_	_
130	strain	strain	NN	_	_	_
131	MC4100relA	mc4100rela	NN	_	_	_
132	+	+	CC	_	_	_
133	∆	∆	SYM	_	_	_
134	mazEFlexA3	mazeflexa3	NN	_	_	_
135	in	in	IN	_	_	_
136	mid	mid	JJ	_	_	_
137	log	log	NN	_	_	_
138	phase	phase	NN	_	_	_
139	incubated	incubate	VBN	_	_	_
140	at	at	IN	_	_	_
141	37ºC	37ºc	NN	_	_	_
142	for	for	IN	_	_	_
143	4	4	CD	_	_	_
144	hours	hour	NNS	_	_	_
145	without	without	IN	_	_	_
146	treatment	treatment	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	sample	sample	NN	_	_	_
149	type	type	NN	_	_	_
150	:	:	:	_	_	_
151	input	input	NN	_	_	_
152	control	control	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
154	sample	sample	NN	_	_	_
155	type	type	NN	_	_	_
156	:	:	:	_	_	_
157	input	input	NN	_	_	_
158	DNA	dna	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	sample	sample	NN	_	_	_
161	type	type	NN	_	_	_
162	:	:	:	_	_	_
163	mock	mock	JJ	_	_	_
164	community	community	NN	_	_	_
165	-LSB-	-lsb-	-LRB-	_	_	_
166	artificial	artificial	JJ	_	_	_
167	bacterial	bacterial	JJ	_	_	_
168	DNA	dna	NN	_	_	_
169	mix	mix	NN	_	_	_
170	-RSB-	-rsb-	-RRB-	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	sample	sample	NN	_	_	_
173	type	type	NN	_	_	_
174	:	:	:	_	_	_
175	no	no	DT	_	_	_
176	RNA	rna	NN	_	_	_
177	treatment	treatment	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	sample	sample	NN	_	_	_
180	type	type	NN	_	_	_
181	:	:	:	_	_	_
182	plasmid	plasmid	NN	_	_	_
183	pool	pool	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	sample	sample	NN	_	_	_
186	type	type	NN	_	_	_
187	:	:	:	_	_	_
188	ribosome	ribosome	NN	_	_	_
189	protected	protect	VBD	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	sample	sample	NN	_	_	_
192	type	type	NN	_	_	_
193	:	:	:	_	_	_
194	test	test	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	sample	sample	NN	_	_	_
197	type	type	NN	_	_	_
198	:	:	:	_	_	_
199	V1	v1	NN	_	_	_
200	digested	digest	VBD	_	_	_
201	total	total	JJ	_	_	_
202	RNA	rna	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	sample	sample	NN	_	_	_
205	:	:	:	_	_	_
206	Vegetated	vegetated	JJ	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
208	Sampling	sample	VBG	_	_	_
209	by	by	IN	_	_	_
210	directly	directly	RB	_	_	_
211	placing	place	VBG	_	_	_
212	the	the	DT	_	_	_
213	culture	culture	NN	_	_	_
214	sample	sample	NN	_	_	_
215	into	into	IN	_	_	_
216	RNAprotect	rnaprotect	NN	_	_	_
217	Bacteria	bacterium	NNS	_	_	_
218	Reagent	reagent	NN	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	Qiagen	Qiagen	NNP	_	_	_
221	,	,	,	_	_	_
222	Hilden	Hilden	NNP	_	_	_
223	,	,	,	_	_	_
224	Germany	Germany	NNP	_	_	_
225	-RRB-	-rrb-	-RRB-	_	_	_
226	,	,	,	_	_	_
227	following	follow	VBG	_	_	_
228	short	short	JJ	_	_	_
229	centrifugation	centrifugation	NN	_	_	_
230	the	the	DT	_	_	_
231	pellet	pellet	NN	_	_	_
232	was	be	VBD	_	_	_
233	stored	store	VBN	_	_	_
234	at	at	IN	_	_	_
235	−	−	CD	_	_	_
236	70	70	CD	_	_	_
237	°C	°c	NN	_	_	_
238	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	SA	SA	NNP	_	_	_
3	_	_	NNP	_	_	_
4	TP1	tp1	NN	_	_	_
5	_	_	CD	_	_	_
6	repl1	repl1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	SA	SA	NNP	_	_	_
9	_	_	NNP	_	_	_
10	TP1	tp1	NN	_	_	_
11	_	_	CD	_	_	_
12	repl2	repl2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	SA	SA	NNP	_	_	_
15	_	_	NNP	_	_	_
16	TP1	tp1	NN	_	_	_
17	_	_	CD	_	_	_
18	repl3	repl3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	SA	SA	NNP	_	_	_
21	_	_	NNP	_	_	_
22	TP1	tp1	NN	_	_	_
23	_	_	CD	_	_	_
24	repl4	repl4	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	SA	SA	NNP	_	_	_
27	_	_	NNP	_	_	_
28	TP1	tp1	NN	_	_	_
29	_	_	CD	_	_	_
30	repl5	repl5	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	SA	SA	NNP	_	_	_
33	_	_	SYM	_	_	_
34	TP2	tp2	NN	_	_	_
35	_	_	CD	_	_	_
36	repl1	repl1	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	SA	SA	NNP	_	_	_
39	_	_	SYM	_	_	_
40	TP2	tp2	NN	_	_	_
41	_	_	CD	_	_	_
42	repl2	repl2	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	SA	SA	NNP	_	_	_
45	_	_	SYM	_	_	_
46	TP2	tp2	NN	_	_	_
47	_	_	CD	_	_	_
48	repl3	repl3	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	SA	SA	NNP	_	_	_
51	_	_	SYM	_	_	_
52	TP2	tp2	NN	_	_	_
53	_	_	CD	_	_	_
54	repl4	repl4	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	SA	SA	NNP	_	_	_
57	_	_	SYM	_	_	_
58	TP2	tp2	NN	_	_	_
59	_	_	CD	_	_	_
60	repl5	repl5	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	SA	SA	NNP	_	_	_
63	_	_	SYM	_	_	_
64	TP3	tp3	NN	_	_	_
65	_	_	CD	_	_	_
66	repl1	repl1	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	SA	SA	NNP	_	_	_
69	_	_	SYM	_	_	_
70	TP3	tp3	NN	_	_	_
71	_	_	CD	_	_	_
72	repl2	repl2	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	SA	SA	NNP	_	_	_
75	_	_	SYM	_	_	_
76	TP3	tp3	NN	_	_	_
77	_	_	CD	_	_	_
78	repl3	repl3	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	SA	SA	NNP	_	_	_
81	_	_	SYM	_	_	_
82	TP3	tp3	NN	_	_	_
83	_	_	CD	_	_	_
84	repl4	repl4	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	SA	SA	NNP	_	_	_
87	_	_	SYM	_	_	_
88	TP3	tp3	NN	_	_	_
89	_	_	CD	_	_	_
90	repl5	repl5	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	SA	SA	NNP	_	_	_
93	_	_	SYM	_	_	_
94	TP4	tp4	NN	_	_	_
95	_	_	CD	_	_	_
96	repl1	repl1	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	SA	SA	NNP	_	_	_
99	_	_	SYM	_	_	_
100	TP4	tp4	NN	_	_	_
101	_	_	CD	_	_	_
102	repl2	repl2	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	SA	SA	NNP	_	_	_
105	_	_	SYM	_	_	_
106	TP4	tp4	NN	_	_	_
107	_	_	CD	_	_	_
108	repl3	repl3	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	SA	SA	NNP	_	_	_
111	_	_	SYM	_	_	_
112	TP4	tp4	NN	_	_	_
113	_	_	CD	_	_	_
114	repl4	repl4	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	SA	SA	NNP	_	_	_
117	_	_	SYM	_	_	_
118	TP4	tp4	NN	_	_	_
119	_	_	CD	_	_	_
120	repl5	repl5	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	Saturated	Saturated	NNP	_	_	_
123	E.	E.	NNP	_	_	_
124	coli	coli	NN	_	_	_
125	cultures	culture	NNS	_	_	_
126	were	be	VBD	_	_	_
127	diluted	dilute	VBN	_	_	_
128	in	in	IN	_	_	_
129	LB	lb	NN	_	_	_
130	to	to	TO	_	_	_
131	an	a	DT	_	_	_
132	OD.of	od.of	JJ	_	_	_
133	0.05	0.05	CD	_	_	_
134	OD600	od600	NN	_	_	_
135	,	,	,	_	_	_
136	grown	grow	VBN	_	_	_
137	at	at	IN	_	_	_
138	37	37	CD	_	_	_
139	degrees	degree	NNS	_	_	_
140	Celsius	Celsius	NNP	_	_	_
141	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
142	Saturated	Saturated	NNP	_	_	_
143	E.	E.	NNP	_	_	_
144	coli	coli	NN	_	_	_
145	cultures	culture	NNS	_	_	_
146	were	be	VBD	_	_	_
147	diluted	dilute	VBN	_	_	_
148	in	in	IN	_	_	_
149	LB	LB	NNP	_	_	_
150	toan	toan	NN	_	_	_
151	OD.of	od.of	NN	_	_	_
152	0.05	0.05	CD	_	_	_
153	OD600	od600	NN	_	_	_
154	,	,	,	_	_	_
155	grown	grow	VBN	_	_	_
156	at	at	IN	_	_	_
157	37	37	CD	_	_	_
158	degrees	degree	NNS	_	_	_
159	Celsius	Celsius	NNP	_	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
161	SB10	sb10	NN	_	_	_
162	_	_	NN	_	_	_
163	1	1	CD	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	SB10	sb10	NN	_	_	_
166	_	_	NN	_	_	_
167	2	2	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	SB10	sb10	NN	_	_	_
170	_	_	CD	_	_	_
171	3	3	CD	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	SB1	sb1	NN	_	_	_
174	_	_	NN	_	_	_
175	1	1	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	SB11	sb11	NN	_	_	_
178	_	_	NN	_	_	_
179	1	1	CD	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	SB11	sb11	NN	_	_	_
182	_	_	NN	_	_	_
183	2	2	CD	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	SB11	sb11	NN	_	_	_
186	_	_	CD	_	_	_
187	3	3	CD	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	SB1	sb1	NN	_	_	_
190	_	_	NN	_	_	_
191	2	2	CD	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	SB12	sb12	NN	_	_	_
194	_	_	NN	_	_	_
195	1	1	CD	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	SB12	sb12	NN	_	_	_
198	_	_	NN	_	_	_
199	2	2	CD	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	SB12	sb12	NN	_	_	_
202	_	_	CD	_	_	_
203	3	3	CD	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	SB1	sb1	NN	_	_	_
206	_	_	CD	_	_	_
207	3	3	CD	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	SB13	sb13	NN	_	_	_
210	_	_	NN	_	_	_
211	1	1	CD	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	SB13	sb13	NN	_	_	_
214	_	_	NN	_	_	_
215	2	2	CD	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	SB13	sb13	NN	_	_	_
218	_	_	CD	_	_	_
219	3	3	CD	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	SB14	sb14	NN	_	_	_
222	_	_	NN	_	_	_
223	1	1	CD	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	SB14	sb14	NN	_	_	_
226	_	_	NN	_	_	_
227	2	2	CD	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	SB14	sb14	NN	_	_	_
230	_	_	CD	_	_	_
231	3	3	CD	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	SB15	sb15	NN	_	_	_
234	_	_	NN	_	_	_
235	1	1	CD	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	SB15	sb15	NN	_	_	_
238	_	_	NN	_	_	_
239	2	2	CD	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	SB15	sb15	NN	_	_	_
242	_	_	CD	_	_	_
243	3	3	CD	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	SB16	sb16	NN	_	_	_
246	_	_	NN	_	_	_
247	1	1	CD	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	SB16	sb16	NN	_	_	_
250	_	_	NN	_	_	_
251	2	2	CD	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	SB16	sb16	NN	_	_	_
254	_	_	CD	_	_	_
255	3	3	CD	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	SB17	sb17	NN	_	_	_
258	_	_	NN	_	_	_
259	1	1	CD	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	SB17	sb17	NN	_	_	_
262	_	_	NN	_	_	_
263	2	2	CD	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	SB17	sb17	NN	_	_	_
266	_	_	CD	_	_	_
267	3	3	CD	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	SB18	sb18	NN	_	_	_
270	_	_	NN	_	_	_
271	1	1	CD	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	SB18	sb18	NN	_	_	_
274	_	_	NN	_	_	_
275	2	2	CD	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	SB18	sb18	NN	_	_	_
278	_	_	CD	_	_	_
279	3	3	CD	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	SB1	sb1	NN	_	_	_
282	genomic	genomic	JJ	_	_	_
283	DNA	dna	NN	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	SB2	sb2	NN	_	_	_
286	_	_	NN	_	_	_
287	1	1	CD	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	SB2	sb2	NN	_	_	_
290	_	_	NN	_	_	_
291	2	2	CD	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	SB2	sb2	NN	_	_	_
294	_	_	CD	_	_	_
295	3	3	CD	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	SB3	sb3	NN	_	_	_
298	_	_	NN	_	_	_
299	1	1	CD	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	SB3	sb3	NN	_	_	_
302	_	_	NN	_	_	_
303	2	2	CD	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	SB3	sb3	NN	_	_	_
306	_	_	CD	_	_	_
307	3	3	CD	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	SB5	sb5	NN	_	_	_
310	_	_	NN	_	_	_
311	1	1	CD	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	SB5	sb5	NN	_	_	_
314	_	_	NN	_	_	_
315	2	2	CD	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	SB5	sb5	NN	_	_	_
318	_	_	CD	_	_	_
319	3	3	CD	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	SB6	sb6	NN	_	_	_
322	_	_	NN	_	_	_
323	1	1	CD	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	SB6	sb6	NN	_	_	_
326	_	_	NN	_	_	_
327	2	2	CD	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	SB6	sb6	NN	_	_	_
330	_	_	CD	_	_	_
331	3	3	CD	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	SB7	sb7	NN	_	_	_
334	_	_	NN	_	_	_
335	1	1	CD	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	SB7	sb7	NN	_	_	_
338	_	_	NN	_	_	_
339	2	2	CD	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	SB7	sb7	NN	_	_	_
342	_	_	CD	_	_	_
343	3	3	CD	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	SB8	sb8	NN	_	_	_
346	_	_	NN	_	_	_
347	1	1	CD	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	SB8	sb8	NN	_	_	_
350	_	_	NN	_	_	_
351	2	2	CD	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
353	SB8	sb8	NN	_	_	_
354	_	_	CD	_	_	_
355	3	3	CD	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	SB9	sb9	NN	_	_	_
358	_	_	CD	_	_	_
359	1	1	CD	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	SB9	sb9	NN	_	_	_
362	_	_	NN	_	_	_
363	2	2	CD	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
365	SB9	sb9	NN	_	_	_
366	_	_	SYM	_	_	_
367	3	3	CD	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	sbcB	sbcb	NN	GEN	_	_
370	__	__	CD	_	_	_
371	U	U	NNP	_	_	_
372	_	_	NNP	_	_	_
373	N0075	N0075	NNP	_	_	_
374	_	_	VBD	_	_	_
375	r1	r1	NN	_	_	_
376	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
377	sbcB	sbcb	NN	GEN	_	_
378	__	__	CD	_	_	_
379	U	U	NNP	_	_	_
380	_	_	NNP	_	_	_
381	N0075	N0075	NNP	_	_	_
382	_	_	VBD	_	_	_
383	r2	r2	NN	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	sbcB	sbcb	NN	GEN	_	_
386	__	__	CD	_	_	_
387	U	U	NNP	_	_	_
388	_	_	NNP	_	_	_
389	N0075	N0075	NNP	_	_	_
390	_	_	SYM	_	_	_
391	r3	r3	FW	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
393	sbcB	sbcb	NN	GEN	_	_
394	upregulation	upregulation	NN	_	_	_
395	,	,	,	_	_	_
396	0.075	0.075	CD	_	_	_
397	mg/mL	mg/ml	NN	_	_	_
398	norfloxacin	norfloxacin	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	Scale	Scale	NNP	_	_	_
401	data	datum	NNS	_	_	_
402	set	set	VBN	_	_	_
403	to	to	TO	_	_	_
404	20	20	CD	_	_	_
405	million	million	CD	_	_	_
406	reads	read	VBZ	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	Scanned	scan	VBN	_	_	_
409	arrays	array	NNS	_	_	_
410	were	be	VBD	_	_	_
411	analyzed	analyze	VBN	_	_	_
412	with	with	IN	_	_	_
413	Affymetrix	Affymetrix	NNP	_	_	_
414	GCOS	GCOS	NNP	_	_	_
415	1.4	1.4	CD	_	_	_
416	software	software	NN	_	_	_
417	to	to	TO	_	_	_
418	obtain	obtain	VB	_	_	_
419	Detection	detection	NN	_	_	_
420	calls	call	NNS	_	_	_
421	and	and	CC	_	_	_
422	Expression	expression	NN	_	_	_
423	values	value	NNS	_	_	_
424	based	base	VBN	_	_	_
425	on	on	IN	_	_	_
426	MAS	MAS	NNP	_	_	_
427	5.0	5.0	CD	_	_	_
428	algorithms	algorithm	NNS	_	_	_
429	.	.	.	_	_	_

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	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	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	pgcgrowthconditions	NN	_	_	_
2	Scanned	scan	VBD	_	_	_
3	spot	spot	NN	_	_	_
4	signals	signal	NNS	_	_	_
5	were	be	VBD	_	_	_
6	normalized	normalize	VBN	_	_	_
7	using	use	VBG	_	_	_
8	internal	internal	JJ	_	_	_
9	Protoarray	Protoarray	NNP	_	_	_
10	control	control	NN	_	_	_
11	proteins	protein	NNS	_	_	_
12	and	and	CC	_	_	_
13	Z	z	NN	_	_	_
14	scores	score	NNS	_	_	_
15	subsequently	subsequently	RB	_	_	_
16	determined	determine	VBD	_	_	_
17	based	base	VBN	_	_	_
18	on	on	IN	_	_	_
19	comparisons	comparison	NNS	_	_	_
20	of	of	IN	_	_	_
21	mean	mean	NN	_	_	_
22	signals	signal	NNS	_	_	_
23	for	for	IN	_	_	_
24	each	each	DT	_	_	_
25	spot	spot	NN	_	_	_
26	pair	pair	NN	_	_	_
27	to	to	TO	_	_	_
28	the	the	DT	_	_	_
29	mean	mean	NN	_	_	_
30	spot	spot	NN	_	_	_
31	intensity	intensity	NN	_	_	_
32	for	for	IN	_	_	_
33	the	the	DT	_	_	_
34	array	array	NN	_	_	_
35	.	.	.	_	_	_

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	Scatter	Scatter	NNP	_	_	_
11	signal	signal	NN	_	_	_
12	intensity	intensity	NN	_	_	_
13	after	after	IN	_	_	_
14	illumination	illumination	NN	_	_	_
15	at	at	IN	_	_	_
16	150	150	CD	_	_	_
17	ms	m	NNS	_	_	_
18	exposure	exposure	NN	_	_	_
19	without	without	IN	_	_	_
20	normalization	normalization	NN	_	_	_
21	,	,	,	_	_	_
22	without	without	IN	_	_	_
23	transformation	transformation	NN	_	_	_
24	.	.	.	_	_	_

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	scraping	scrape	VBG	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	,	,	,	_	_	_
5	opening	open	VBG	_	_	_
6	with	with	IN	_	_	_
7	bead	bead	NN	_	_	_
8	beating	beating	NN	_	_	_
9	,	,	,	_	_	_
10	Trizol-based	trizol-based	JJ	_	_	_
11	RNA	rna	NN	_	_	_
12	isolation	isolation	NN	_	_	_
13	,	,	,	_	_	_
14	rRNA	rrna	NN	_	_	_
15	depletion	depletion	NN	_	_	_
16	with	with	IN	_	_	_
17	RiboZero	RiboZero	NNP	_	_	_
18	,	,	,	_	_	_
19	DNA	DNA	NNP	_	_	_
20	digest	digest	VB	_	_	_
21	,	,	,	_	_	_
22	SoLiD	solid	JJ	_	_	_
23	seq	seq	NN	_	_	_
24	by	by	IN	_	_	_
25	CeGaT	cegat	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Tübingen	tübingen	NN	_	_	_
28	,	,	,	_	_	_
29	Germany	Germany	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	ScriptSeq	scriptseq	NN	_	_	_
33	v2	v2	NN	_	_	_
34	Complete	complete	JJ	_	_	_
35	Kit	kit	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	EpiCentre	EpiCentre	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	SD10	sd10	NN	_	_	_
41	_	_	NN	_	_	_
42	1	1	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	SD10	sd10	NN	_	_	_
45	_	_	NN	_	_	_
46	2	2	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	SD10	sd10	NN	_	_	_
49	_	_	CD	_	_	_
50	3	3	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	SD11	sd11	NN	_	_	_
53	_	_	NN	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	SD11	sd11	NN	_	_	_
57	_	_	NN	_	_	_
58	2	2	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	SD11	sd11	NN	_	_	_
61	_	_	CD	_	_	_
62	3	3	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	SD12	sd12	NN	_	_	_
65	_	_	NN	_	_	_
66	1	1	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	SD12	sd12	NN	_	_	_
69	_	_	NN	_	_	_
70	2	2	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	SD12	sd12	NN	_	_	_
73	_	_	CD	_	_	_
74	3	3	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	SD13	sd13	NN	_	_	_
77	_	_	NN	_	_	_
78	1	1	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	SD13	sd13	NN	_	_	_
81	_	_	NN	_	_	_
82	2	2	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	SD13	sd13	NN	_	_	_
85	_	_	CD	_	_	_
86	3	3	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	SD2	sd2	NN	_	_	_
89	_	_	NN	_	_	_
90	1	1	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	SD2	sd2	NN	_	_	_
93	_	_	NN	_	_	_
94	2	2	CD	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	SD2	sd2	NN	_	_	_
97	_	_	CD	_	_	_
98	3	3	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	SD3	sd3	NN	_	_	_
101	_	_	NN	_	_	_
102	1	1	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	SD3	sd3	NN	_	_	_
105	_	_	NN	_	_	_
106	2	2	CD	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	SD3	sd3	NN	_	_	_
109	_	_	CD	_	_	_
110	3	3	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	SD4	sd4	NN	_	_	_
113	_	_	NN	_	_	_
114	1	1	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	SD4	sd4	NN	_	_	_
117	_	_	NN	_	_	_
118	2	2	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	SD4	sd4	NN	_	_	_
121	_	_	CD	_	_	_
122	3	3	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	SD5	sd5	NN	_	_	_
125	_	_	NN	_	_	_
126	1	1	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	SD5	sd5	NN	_	_	_
129	_	_	NN	_	_	_
130	2	2	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	SD5	sd5	NN	_	_	_
133	_	_	CD	_	_	_
134	3	3	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	SD6	sd6	NN	_	_	_
137	_	_	NN	_	_	_
138	1	1	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	SD6	sd6	NN	_	_	_
141	_	_	NN	_	_	_
142	2	2	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	SD6	sd6	NN	_	_	_
145	_	_	CD	_	_	_
146	3	3	CD	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	SD7	sd7	NN	_	_	_
149	_	_	NN	_	_	_
150	1	1	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	SD7	sd7	NN	_	_	_
153	_	_	NN	_	_	_
154	2	2	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	SD7	sd7	NN	_	_	_
157	_	_	CD	_	_	_
158	3	3	CD	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	SD8	sd8	NN	_	_	_
161	_	_	NN	_	_	_
162	1	1	CD	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	SD8	sd8	NN	_	_	_
165	_	_	NN	_	_	_
166	2	2	CD	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	SD8	sd8	NN	_	_	_
169	_	_	CD	_	_	_
170	3	3	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	SD9	sd9	NN	_	_	_
173	_	_	NN	_	_	_
174	1	1	CD	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	SD9	sd9	NN	_	_	_
177	_	_	NN	_	_	_
178	2	2	CD	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	SD9	sd9	NN	_	_	_
181	_	_	CD	_	_	_
182	3	3	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	sdhA	sdha	NN	GEN	_	_
185	_	_	CD	_	_	_
186	FA	FA	NNP	_	_	_
187	_	_	SYM	_	_	_
188	I	I	PRP	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
190	sdhA	sdha	NN	GEN	_	_
191	_	_	CD	_	_	_
192	FA	FA	NNP	_	_	_
193	_	_	NNP	_	_	_
194	II	II	NNP	_	_	_
195	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
196	sdhA	sdhA	NNP	GEN	_	_
197	_	_	NNP	_	_	_
198	FA	FA	NNP	_	_	_
199	_	_	VBD	_	_	_
200	III	iii	CD	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	sdhA	sdha	NN	GEN	_	_
203	_	_	CD	_	_	_
204	LB	lb	NN	_	_	_
205	_	_	NN	_	_	_
206	I	I	PRP	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
208	sdhA	sdha	NN	GEN	_	_
209	_	_	CD	_	_	_
210	LB	lb	NN	_	_	_
211	_	_	NN	_	_	_
212	II	ii	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	sdhA	sdha	NN	GEN	_	_
215	_	_	CD	_	_	_
216	LB	LB	NNP	_	_	_
217	_	_	NNP	_	_	_
218	III	III	NNP	_	_	_
219	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
220	sdhC	sdhC	NNP	GEN	_	_
221	KO	KO	NNP	_	_	_
222	rep1	rep1	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	sdhC	sdhc	NN	GEN	_	_
225	KO	ko	NN	_	_	_
226	rep2	rep2	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	sdhC	sdhc	NN	GEN	_	_
229	KO	ko	NN	_	_	_
230	rep3	rep3	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	Second	second	JJ	_	_	_
233	biological	biological	JJ	_	_	_
234	repeat	repeat	NN	_	_	_
235	37	37	CD	_	_	_
236	°C	°c	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	Second	second	JJ	_	_	_
239	biological	biological	JJ	_	_	_
240	repeat	repeat	NN	_	_	_
241	50	50	CD	_	_	_
242	°C	°c	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
244	See	see	VB	_	_	_
245	publication	publication	NN	_	_	_
246	for	for	IN	_	_	_
247	complete	complete	JJ	_	_	_
248	protocol	protocol	NN	_	_	_
249	.	.	.	_	_	_

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	See	see	VB	_	_	_
3	the	the	DT	_	_	_
4	paper	paper	NN	_	_	_
5	Variation	variation	NN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	Genomic	genomic	JJ	_	_	_
9	islands	island	NNS	_	_	_
10	of	of	IN	_	_	_
11	porcine	porcine	NN	_	_	_
12	enteropathogenic	enteropathogenic	JJ	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	strains	strain	NNS	_	_	_
16	of	of	IN	_	_	_
17	serogroup	serogroup	NN	_	_	_
18	O45	o45	NN	_	_	_
19	revealed	reveal	VBN	_	_	_
20	by	by	IN	_	_	_
21	comparative	comparative	JJ	_	_	_
22	genomic	genomic	JJ	_	_	_
23	hybridization	hybridization	NN	_	_	_
24	and	and	CC	_	_	_
25	PCR	pcr	NN	_	_	_
26	by	by	IN	_	_	_
27	Bruant	Bruant	NNP	_	_	_
28	and	and	CC	_	_	_
29	Zhang	Zhang	NNP	_	_	_
30	et	et	FW	_	_	_
31	al.	al.	FW	_	_	_
32	2009	2009	CD	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Separate	separate	JJ	_	_	_
35	E.	e.	FW	_	_	_
36	coli	coli	FW	_	_	_
37	colonies	colony	NNS	_	_	_
38	were	be	VBD	_	_	_
39	picked	pick	VBN	_	_	_
40	from	from	IN	_	_	_
41	LB	LB	NNP	_	_	_
42	agar	agar	NN	_	_	_
43	plates	plate	NNS	_	_	_
44	for	for	IN	_	_	_
45	each	each	DT	_	_	_
46	replicate	replicate	VBP	_	_	_
47	.	.	.	_	_	_

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	SeqA	seqa	NN	_	_	_
3	ChIP	chip	NN	_	_	_
4	DNA	dna	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	SeqA	seqa	NN	_	_	_
7	ChIP	chip	NN	_	_	_
8	DNA	dna	NN	_	_	_
9	,	,	,	_	_	_
10	new	new	JJ	_	_	_
11	protocol	protocol	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	SeqA	seqa	NN	_	_	_
14	ChIP	chip	NN	_	_	_
15	DNA	dna	NN	_	_	_
16	,	,	,	_	_	_
17	old	old	JJ	_	_	_
18	protocol	protocol	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	SeqA	seqa	NN	_	_	_
21	in	in	IN	_	_	_
22	0	0	CD	_	_	_
23	min	min	NN	_	_	_
24	dnaC2	dnac2	NN	_	_	_
25	rep1	rep1	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	SeqA	seqa	NN	_	_	_
28	in	in	IN	_	_	_
29	0	0	CD	_	_	_
30	min	min	NN	_	_	_
31	dnaC2	dnac2	NN	_	_	_
32	rep2	rep2	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	SeqA	seqa	NN	_	_	_
35	in	in	IN	_	_	_
36	15	15	CD	_	_	_
37	min	min	NN	_	_	_
38	dnaC2	dnac2	NN	_	_	_
39	LB	lb	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	SeqA	seqa	NN	_	_	_
42	in	in	IN	_	_	_
43	15	15	CD	_	_	_
44	min	min	NN	_	_	_
45	dnaC2	dnac2	NN	_	_	_
46	LB	lb	NN	_	_	_
47	dam	dam	NN	GEN	_	_
48	+	+	CC	_	_	_
49	+	+	CC	_	_	_
50	rep1	rep1	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	SeqA	seqa	NN	_	_	_
53	in	in	IN	_	_	_
54	15	15	CD	_	_	_
55	min	min	NN	_	_	_
56	dnaC2	dnac2	NN	_	_	_
57	LB	lb	NN	_	_	_
58	dam	dam	NN	GEN	_	_
59	+	+	CC	_	_	_
60	+	+	CC	_	_	_
61	rep2	rep2	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	SeqA	seqa	NN	_	_	_
64	in	in	IN	_	_	_
65	15	15	CD	_	_	_
66	min	min	NN	_	_	_
67	dnaC2	dnac2	NN	_	_	_
68	rep1	rep1	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	SeqA	seqa	NN	_	_	_
71	in	in	IN	_	_	_
72	15	15	CD	_	_	_
73	min	min	NN	_	_	_
74	dnaC2	dnac2	NN	_	_	_
75	rep2	rep2	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	SeqA	seqa	NN	_	_	_
78	in	in	IN	_	_	_
79	15	15	CD	_	_	_
80	min	min	NN	_	_	_
81	dnaC2	dnac2	NN	_	_	_
82	rep3	rep3	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	SeqA	seqa	NN	_	_	_
85	in	in	IN	_	_	_
86	16	16	CD	_	_	_
87	min	min	NN	_	_	_
88	dnaC2	dnac2	NN	_	_	_
89	rep1	rep1	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	SeqA	seqa	NN	_	_	_
92	in	in	IN	_	_	_
93	16	16	CD	_	_	_
94	min	min	NN	_	_	_
95	dnaC2	dnac2	NN	_	_	_
96	rep2	rep2	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	SeqA	seqa	NN	_	_	_
99	in	in	IN	_	_	_
100	17	17	CD	_	_	_
101	min	min	NN	_	_	_
102	dnaC2	dnac2	NN	_	_	_
103	rep1	rep1	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	SeqA	seqa	NN	_	_	_
106	in	in	IN	_	_	_
107	17	17	CD	_	_	_
108	min	min	NN	_	_	_
109	dnaC2	dnac2	NN	_	_	_
110	rep2	rep2	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	SeqA	seqa	NN	_	_	_
113	in	in	IN	_	_	_
114	35	35	CD	_	_	_
115	min	min	NN	_	_	_
116	dnaC2	dnac2	NN	_	_	_
117	rep1	rep1	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	SeqA	seqa	NN	_	_	_
120	in	in	IN	_	_	_
121	35	35	CD	_	_	_
122	min	min	NN	_	_	_
123	dnaC2	dnac2	NN	_	_	_
124	rep2	rep2	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	SeqA	seqa	NN	_	_	_
127	in	in	IN	_	_	_
128	50	50	CD	_	_	_
129	min	min	NN	_	_	_
130	dnaC2	dnac2	NN	_	_	_
131	rep1	rep1	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	SeqA	seqa	NN	_	_	_
134	in	in	IN	_	_	_
135	50	50	CD	_	_	_
136	min	min	NN	_	_	_
137	dnaC2	dnac2	NN	_	_	_
138	rep2	rep2	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	SeqA	seqa	NN	_	_	_
141	in	in	IN	_	_	_
142	5	5	CD	_	_	_
143	min	min	NN	_	_	_
144	dnaC2	dnac2	NN	_	_	_
145	rep1	rep1	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	SeqA	seqa	NN	_	_	_
148	in	in	IN	_	_	_
149	5	5	CD	_	_	_
150	min	min	NN	_	_	_
151	dnaC2	dnac2	NN	_	_	_
152	rep2	rep2	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	SeqA	seqa	NN	_	_	_
155	in	in	IN	_	_	_
156	AB	AB	NNP	_	_	_
157	acetate	acetate	NN	SUPP	_	_
158	rep1	rep1	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	SeqA	seqa	NN	_	_	_
161	in	in	IN	_	_	_
162	AB	AB	NNP	_	_	_
163	acetate	acetate	NN	SUPP	_	_
164	rep2	rep2	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	SeqA	seqa	NN	_	_	_
167	in	in	IN	_	_	_
168	hisA	hisA	NNP	GEN	_	_
169	GATC	GATC	NNP	_	_	_
170	cluster	cluster	NN	_	_	_
171	rep1	rep1	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	SeqA	seqa	NN	_	_	_
174	in	in	IN	_	_	_
175	hisA	hisA	NNP	GEN	_	_
176	GATC	GATC	NNP	_	_	_
177	cluster	cluster	NN	_	_	_
178	rep2	rep2	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	SeqA	seqa	NN	_	_	_
181	in	in	IN	_	_	_
182	srlA	srla	NN	GEN	_	_
183	GATC	gatc	NN	_	_	_
184	cluster	cluster	NN	_	_	_
185	rep1	rep1	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	SeqA	seqa	NN	_	_	_
188	in	in	IN	_	_	_
189	srlA	srla	NN	GEN	_	_
190	GATC	gatc	NN	_	_	_
191	cluster	cluster	NN	_	_	_
192	rep2	rep2	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	SeqA	seqa	NN	_	_	_
195	in	in	IN	_	_	_
196	ter	ter	NN	_	_	_
197	GATC	gatc	NN	_	_	_
198	cluster	cluster	NN	_	_	_
199	rep1	rep1	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	SeqA	seqa	NN	_	_	_
202	in	in	IN	_	_	_
203	ter	ter	NN	_	_	_
204	GATC	gatc	NN	_	_	_
205	cluster	cluster	NN	_	_	_
206	rep2	rep2	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	SeqA	seqa	NN	_	_	_
209	in	in	IN	_	_	_
210	tnaA	tnaa	NN	GEN	_	_
211	GATC	gatc	NN	_	_	_
212	cluster	cluster	NN	_	_	_
213	rep1	rep1	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	SeqA	seqa	NN	_	_	_
216	in	in	IN	_	_	_
217	tnaA	tnaa	NN	GEN	_	_
218	GATC	gatc	NN	_	_	_
219	cluster	cluster	NN	_	_	_
220	rep2	rep2	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	SeqA	seqa	NN	_	_	_
223	new	new	JJ	_	_	_
224	deltaSeqA	deltaseqa	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	SeqA	seqa	NN	_	_	_
227	new	new	JJ	_	_	_
228	rep1	rep1	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	SeqA	seqa	NN	_	_	_
231	new	new	JJ	_	_	_
232	rep2	rep2	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	SeqA	seqa	NN	_	_	_
235	old	old	JJ	_	_	_
236	deltaSeqA	deltaseqa	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	SeqA	seqa	NN	_	_	_
239	old	old	JJ	_	_	_
240	rep1	rep1	NN	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	SeqA	seqa	NN	_	_	_
243	old	old	JJ	_	_	_
244	rep2	rep2	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	Sequence	sequence	NN	_	_	_
247	data	datum	NNS	_	_	_
248	from	from	IN	_	_	_
249	BGI	BGI	NNP	_	_	_
250	had	have	VBD	_	_	_
251	been	be	VBN	_	_	_
252	filtered	filter	VBN	_	_	_
253	to	to	TO	_	_	_
254	remove	remove	VB	_	_	_
255	reads	read	VBZ	_	_	_
256	containing	contain	VBG	_	_	_
257	≥	≥	SYM	_	_	_
258	10	10	CD	_	_	_
259	%	%	NN	_	_	_
260	unreadable	unreadable	JJ	_	_	_
261	bases	basis	NNS	_	_	_
262	,	,	,	_	_	_
263	≥	≥	SYM	_	_	_
264	20	20	CD	_	_	_
265	%	%	NN	_	_	_
266	low	low	JJ	_	_	_
267	quality	quality	NN	_	_	_
268	-LRB-	-lrb-	-LRB-	_	_	_
269	≤	≤	CD	_	_	_
270	Q20	q20	NN	_	_	_
271	-RRB-	-rrb-	-RRB-	_	_	_
272	bases	basis	NNS	_	_	_
273	,	,	,	_	_	_
274	adapter	adapter	NN	_	_	_
275	contamination	contamination	NN	_	_	_
276	or	or	CC	_	_	_
277	duplicate	duplicate	VB	_	_	_
278	read-pairs	read-pairs	JJ	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
280	Sequence	sequence	NN	_	_	_
281	data	datum	NNS	_	_	_
282	was	be	VBD	_	_	_
283	processed	process	VBN	_	_	_
284	by	by	IN	_	_	_
285	conversion	conversion	NN	_	_	_
286	of	of	IN	_	_	_
287	the	the	DT	_	_	_
288	sample	sample	NN	_	_	_
289	alignment	alignment	NN	_	_	_
290	-LRB-	-lrb-	-LRB-	_	_	_
291	BAM	bam	NN	_	_	_
292	-RRB-	-rrb-	-RRB-	_	_	_
293	files	file	VBZ	_	_	_
294	to	to	TO	_	_	_
295	strand-specific	strand-specific	JJ	_	_	_
296	base	base	NN	_	_	_
297	count	count	NN	_	_	_
298	-LRB-	-lrb-	-LRB-	_	_	_
299	BigWIG	bigwig	NN	_	_	_
300	-RRB-	-rrb-	-RRB-	_	_	_
301	files	file	NNS	_	_	_
302	.	.	.	_	_	_

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	NNP	_	_	_
2	Sequence	sequence	NN	_	_	_
3	data	datum	NNS	_	_	_
4	was	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	by	by	IN	_	_	_
7	conversion	conversion	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	sample	sample	NN	_	_	_
11	alignment	alignment	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	BAM	bam	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	files	file	VBZ	_	_	_
16	to	to	TO	_	_	_
17	strand-specific	strand-specific	JJ	_	_	_
18	base	base	NN	_	_	_
19	count	count	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	WIG	wig	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	files	file	NNS	_	_	_
24	.	.	.	_	_	_

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	Sequenced	sequence	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	mapped	map	VBN	_	_	_
6	onto	onto	IN	_	_	_
7	NC	nc	NN	_	_	_
8	_	_	CD	_	_	_
9	000913	000913	CD	_	_	_
10	reference	reference	NN	_	_	_
11	genome	genome	NN	_	_	_
12	sequence	sequence	NN	_	_	_
13	using	use	VBG	_	_	_
14	bowtie	bowtie	NN	_	_	_
15	v1	v1	NN	_	_	_
16	.0.0	.0.0	CD	_	_	_
17	with	with	IN	_	_	_
18	parameters	parameter	NNS	_	_	_
19	-	-	:	_	_	_
20	X	x	NN	_	_	_
21	1000	1000	CD	_	_	_
22	-	-	:	_	_	_
23	n	n	NN	_	_	_
24	2	2	CD	_	_	_
25	-3	-3	CD	_	_	_
26	3	3	LS	_	_	_
27	-	-	:	_	_	_
28	S	s	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Sequenced	sequence	VBN	_	_	_
31	reads	read	VBZ	_	_	_
32	were	be	VBD	_	_	_
33	trimmed	trim	VBN	_	_	_
34	for	for	IN	_	_	_
35	adaptor	adaptor	NN	_	_	_
36	sequence	sequence	NN	_	_	_
37	.	.	.	_	_	_

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	and	and	CC	_	_	_
10	low-quality	low-quality	JJ	_	_	_
11	sequence	sequence	NN	_	_	_
12	using	use	VBG	_	_	_
13	TrimGalore	trimgalore	NN	_	_	_
14	version	version	NN	_	_	_
15	0.4.1	0.4.1	CD	_	_	_
16	,	,	,	_	_	_
17	then	then	RB	_	_	_
18	mapped	map	VBD	_	_	_
19	to	to	TO	_	_	_
20	mm8	mm8	VB	_	_	_
21	whole	whole	JJ	_	_	_
22	genome	genome	NN	_	_	_
23	using	use	VBG	_	_	_
24	bwa	bwa	NN	_	_	_
25	mem	mem	NN	_	_	_
26	version	version	NN	_	_	_
27	0.7.12	0.7.12	CD	_	_	_
28	with	with	IN	_	_	_
29	default	default	NN	_	_	_
30	parameters	parameter	NNS	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Sequenced	sequence	VBN	_	_	_
33	reads	read	VBZ	_	_	_
34	were	be	VBD	_	_	_
35	trimmed	trim	VBN	_	_	_
36	for	for	IN	_	_	_
37	adaptor	adaptor	NN	_	_	_
38	sequence	sequence	NN	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	masked	mask	VBN	_	_	_
42	for	for	IN	_	_	_
43	low-complexity	low-complexity	NN	_	_	_
44	or	or	CC	_	_	_
45	low-quality	low-quality	JJ	_	_	_
46	sequence	sequence	NN	_	_	_
47	,	,	,	_	_	_
48	then	then	RB	_	_	_
49	mapped	map	VBD	_	_	_
50	to	to	TO	_	_	_
51	CP009273	CP009273	NNP	_	_	_
52	.1	.1	CD	_	_	_
53	whole	whole	JJ	_	_	_
54	genome	genome	NN	_	_	_
55	using	use	VBG	_	_	_
56	bowtie2	bowtie2	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Sequenced	sequence	VBN	_	_	_
59	reads	read	VBZ	_	_	_
60	were	be	VBD	_	_	_
61	trimmed	trim	VBN	_	_	_
62	for	for	IN	_	_	_
63	adaptor	adaptor	NN	_	_	_
64	sequence	sequence	NN	_	_	_
65	,	,	,	_	_	_
66	and	and	CC	_	_	_
67	masked	mask	VBN	_	_	_
68	for	for	IN	_	_	_
69	low-complexity	low-complexity	NN	_	_	_
70	or	or	CC	_	_	_
71	low-quality	low-quality	JJ	_	_	_
72	sequence	sequence	NN	_	_	_
73	,	,	,	_	_	_
74	then	then	RB	_	_	_
75	mapped	map	VBD	_	_	_
76	to	to	TO	_	_	_
77	E.coli	e.coli	VB	_	_	_
78	K2	k2	NN	_	_	_
79	BW25113	bw25113	NN	_	_	_
80	whole	whole	JJ	_	_	_
81	genome	genome	NN	_	_	_
82	using	use	VBG	_	_	_
83	bowtie	bowtie	NN	_	_	_
84	v0	v0	NN	_	_	_
85	.12.2	.12.2	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Sequenced	sequence	VBN	_	_	_
88	reads	read	VBZ	_	_	_
89	were	be	VBD	_	_	_
90	trimmed	trim	VBN	_	_	_
91	for	for	IN	_	_	_
92	adaptor	adaptor	NN	_	_	_
93	sequence	sequence	NN	_	_	_
94	,	,	,	_	_	_
95	and	and	CC	_	_	_
96	masked	mask	VBN	_	_	_
97	for	for	IN	_	_	_
98	low-complexity	low-complexity	NN	_	_	_
99	or	or	CC	_	_	_
100	low-quality	low-quality	JJ	_	_	_
101	sequence	sequence	NN	_	_	_
102	,	,	,	_	_	_
103	then	then	RB	_	_	_
104	mapped	map	VBD	_	_	_
105	to	to	TO	_	_	_
106	Escherichia	escherichia	FW	Organism	_	_
107	coli	coli	FW	Organism	_	_
108	ATCC8739	atcc8739	NN	_	_	_
109	genome	genome	NN	_	_	_
110	-LRB-	-lrb-	-LRB-	_	_	_
111	GenBank	genbank	NN	_	_	_
112	CP000946	cp000946	NN	_	_	_
113	.1	.1	NN	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	using	use	VBG	_	_	_
116	Bowtie	Bowtie	NNP	_	_	_
117	2	2	CD	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	version	version	NN	_	_	_
120	2.2.5	2.2.5	CD	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	Sequenced	sequence	VBN	_	_	_
124	reads	read	VBZ	_	_	_
125	were	be	VBD	_	_	_
126	trimmed	trim	VBN	_	_	_
127	for	for	IN	_	_	_
128	adaptor	adaptor	NN	_	_	_
129	sequence	sequence	NN	_	_	_
130	,	,	,	_	_	_
131	and	and	CC	_	_	_
132	masked	mask	VBN	_	_	_
133	for	for	IN	_	_	_
134	low-complexity	low-complexity	NN	_	_	_
135	or	or	CC	_	_	_
136	low-quality	low-quality	JJ	_	_	_
137	sequence	sequence	NN	_	_	_
138	,	,	,	_	_	_
139	then	then	RB	_	_	_
140	mapped	map	VBD	_	_	_
141	to	to	TO	_	_	_
142	Escherichia	escherichia	FW	Organism	_	_
143	coli	coli	FW	Organism	_	_
144	str	str	FW	_	_	_
145	.	.	.	_	_	_

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	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	using	use	VBG	_	_	_
18	FASTX-Toolkit	fastx-toolkit	NN	_	_	_
19	version	version	NN	_	_	_
20	0.0.13	0.0.13	CD	_	_	_
21	and	and	CC	_	_	_
22	Perl	Perl	NNP	_	_	_
23	version	version	NN	_	_	_
24	5.8.8	5.8.8	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Sequenced	sequence	VBN	_	_	_
27	reads	read	VBZ	_	_	_
28	were	be	VBD	_	_	_
29	trimmed	trim	VBN	_	_	_
30	for	for	IN	_	_	_
31	adaptor	adaptor	NN	_	_	_
32	sequence	sequence	NN	_	_	_
33	and	and	CC	_	_	_
34	masked	mask	VBN	_	_	_
35	for	for	IN	_	_	_
36	low-complexity	low-complexity	JJ	_	_	_
37	sequence	sequence	NN	_	_	_
38	,	,	,	_	_	_
39	then	then	RB	_	_	_
40	mapped	map	VBD	_	_	_
41	to	to	TO	_	_	_
42	E.coli	e.coli	VB	_	_	_
43	W3110	w3110	NN	_	_	_
44	whole	whole	JJ	_	_	_
45	genome	genome	NN	_	_	_
46	.	.	.	_	_	_

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	sequences	sequence	NNS	_	_	_
9	using	use	VBG	_	_	_
10	FastQC	fastqc	NN	_	_	_
11	v0	v0	NN	_	_	_
12	.11.2	.11.2	CD	_	_	_
13	.	.	.	_	_	_

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	then	then	RB	_	_	_
11	mapped	map	VBD	_	_	_
12	to	to	TO	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	K12	k12	NN	_	_	_
16	genome	genome	NN	_	_	_
17	using	use	VBG	_	_	_
18	bowtie	bowtie	NN	_	_	_
19	v0	v0	NN	_	_	_
20	.12.7	.12.7	CD	_	_	_
21	with	with	IN	_	_	_
22	parameters	parameter	NNS	_	_	_
23	bowtie	bowtie	VBP	_	_	_
24	-	-	:	_	_	_
25	t	t	NN	_	_	_
26	-	-	:	_	_	_
27	v	v	LS	_	_	_
28	3	3	LS	_	_	_
29	-	-	:	_	_	_
30	m	m	NN	_	_	_
31	1	1	CD	_	_	_
32	--	--	:	_	_	_
33	best	best	JJS	_	_	_
34	-	-	:	_	_	_
35	S	s	NN	_	_	_
36	-	-	:	_	_	_
37	p	p	NN	_	_	_
38	2	2	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Sequenced	sequence	VBN	_	_	_
41	reads	read	VBZ	_	_	_
42	were	be	VBD	_	_	_
43	trimmed	trim	VBN	_	_	_
44	for	for	IN	_	_	_
45	adaptor	adaptor	NN	_	_	_
46	sequence	sequence	NN	_	_	_
47	using	use	VBG	_	_	_
48	Cutadapt	Cutadapt	NNP	_	_	_
49	v.	v.	CC	_	_	_
50	1.8.3	1.8.3	CD	_	_	_
51	,	,	,	_	_	_
52	then	then	RB	_	_	_
53	mapped	map	VBD	_	_	_
54	to	to	TO	_	_	_
55	E.	e.	FW	_	_	_
56	coli	coli	FW	_	_	_
57	K12	k12	NN	_	_	_
58	substr	substr	NN	_	_	_
59	.	.	.	_	_	_

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.	IN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Sequenced	Sequenced	NNP	_	_	_
22	reads	read	VBZ	_	_	_
23	were	be	VBD	_	_	_
24	trimmed	trim	VBN	_	_	_
25	,	,	,	_	_	_
26	the	the	DT	_	_	_
27	mapped	map	VBN	_	_	_
28	to	to	TO	_	_	_
29	the	the	DT	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	K-12	k-12	NN	_	_	_
33	MG1655	mg1655	NN	_	_	_
34	genome	genome	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	U00096	u00096	NN	_	_	_
37	.2	.2	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	using	use	VBG	_	_	_
40	SOAP	soap	NN	_	_	_
41	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Sequence	sequence	NN	_	_	_
3	reads	read	VBZ	_	_	_
4	for	for	IN	_	_	_
5	cDNA	cdna	NN	_	_	_
6	libraries	library	NNS	_	_	_
7	were	be	VBD	_	_	_
8	aligned	align	VBN	_	_	_
9	onto	onto	IN	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	K12	k12	NN	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	genome	genome	NN	_	_	_
15	,	,	,	_	_	_
16	using	use	VBG	_	_	_
17	Mosaik	mosaik	NN	_	_	_
18	with	with	IN	_	_	_
19	following	follow	VBG	_	_	_
20	arguments	argument	NNS	_	_	_
21	:	:	:	_	_	_
22	hash	hash	VB	_	_	_
23	size	size	NN	_	_	_
24	=	=	JJ	_	_	_
25	10	10	CD	_	_	_
26	,	,	,	_	_	_
27	mismatch	mismatch	NN	_	_	_
28	=	=	JJ	_	_	_
29	0	0	CD	_	_	_
30	.	.	.	_	_	_

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	NNP	_	_	_
2	Sequence	sequence	NN	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	aligned	align	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	published	publish	VBN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	K-12	k-12	NN	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	genome	genome	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	U00096	u00096	NN	_	_	_
16	.2	.2	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	using	use	VBG	_	_	_
19	the	the	DT	_	_	_
20	software	software	NN	_	_	_
21	packages	package	NNS	_	_	_
22	SOAP	soap	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Li	Li	NNP	_	_	_
25	et	et	FW	_	_	_
26	al	al	FW	_	_	_
27	,	,	,	_	_	_
28	2009	2009	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	ELAND	ELAND	NNP	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	within	within	IN	_	_	_
34	the	the	DT	_	_	_
35	Illumina	Illumina	NNP	_	_	_
36	Genome	Genome	NNP	_	_	_
37	Analyzer	Analyzer	NNP	_	_	_
38	Pipeline	Pipeline	NNP	_	_	_
39	Software	Software	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	,	,	,	_	_	_
42	allowing	allow	VBG	_	_	_
43	at	at	IN	_	_	_
44	most	most	JJS	_	_	_
45	two	two	CD	_	_	_
46	mismatches	mismatch	NNS	_	_	_
47	.	.	.	_	_	_

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	NNP	_	_	_
2	Sequence	sequence	NN	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	obtained	obtain	VBN	_	_	_
6	and	and	CC	_	_	_
7	mapped	map	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	W3110	w3110	NN	_	_	_
11	genome	genome	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	NCBI	ncbi	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	using	use	VBG	_	_	_
16	the	the	DT	_	_	_
17	Illumina	Illumina	NNP	_	_	_
18	Genome	Genome	NNP	_	_	_
19	Analyzer	Analyzer	NNP	_	_	_
20	Pipeline	Pipeline	NNP	_	_	_
21	.	.	.	_	_	_

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	NNP	_	_	_
2	Sequence	sequence	NN	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	trimmed	trim	VBN	_	_	_
6	for	for	IN	_	_	_
7	adaptor	adaptor	NN	_	_	_
8	reads	read	VBZ	_	_	_
9	and	and	CC	_	_	_
10	mapped	map	VBN	_	_	_
11	to	to	TO	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	K12	k12	NN	_	_	_
15	MG1655	mg1655	NN	_	_	_
16	genome	genome	NN	_	_	_
17	using	use	VBG	_	_	_
18	CLC	clc	NN	_	_	_
19	Genomics	genomic	NNS	_	_	_
20	Workbench	workbench	JJ	_	_	_
21	6.0.1	6.0.1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Sequences	sequence	NNS	_	_	_
24	obtained	obtain	VBN	_	_	_
25	from	from	IN	_	_	_
26	the	the	DT	_	_	_
27	Illumina	Illumina	NNP	_	_	_
28	Genome	Genome	NNP	_	_	_
29	Analyzer	Analyzer	NNP	_	_	_
30	were	be	VBD	_	_	_
31	mapped	map	VBN	_	_	_
32	to	to	TO	_	_	_
33	both	both	DT	_	_	_
34	strands	strand	NNS	_	_	_
35	of	of	IN	_	_	_
36	the	the	DT	_	_	_
37	E.	e.	FW	_	_	_
38	coli	coli	FW	_	_	_
39	K12	k12	NN	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	genome	genome	NN	_	_	_
42	using	use	VBG	_	_	_
43	BLAT	BLAT	NNP	_	_	_
44	allowing	allow	VBG	_	_	_
45	no	no	DT	_	_	_
46	gaps	gap	NNS	_	_	_
47	and	and	CC	_	_	_
48	up	up	RB	_	_	_
49	to	to	TO	_	_	_
50	two	two	CD	_	_	_
51	mismatches	mismatch	NNS	_	_	_
52	.	.	.	_	_	_

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	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	NNP	_	_	_
41	Sequences	sequence	NNS	_	_	_
42	were	be	VBD	_	_	_
43	mapped	map	VBN	_	_	_
44	to	to	TO	_	_	_
45	NC	NC	NNP	_	_	_
46	_	_	SYM	_	_	_
47	000913.2	000913.2	CD	_	_	_
48	using	use	VBG	_	_	_
49	bowtie2	bowtie2	NN	_	_	_
50	v2	v2	NN	_	_	_
51	.2.2	.2.2	CD	_	_	_
52	with	with	IN	_	_	_
53	parameters	parameter	NNS	_	_	_
54	-	-	:	_	_	_
55	N	n	NN	_	_	_
56	0	0	CD	_	_	_
57	--	--	:	_	_	_
58	sensitive	sensitive	JJ	_	_	_
59	--	--	:	_	_	_
60	minins	minin	NNS	_	_	_
61	130	130	CD	_	_	_
62	--	--	:	_	_	_
63	maxins	maxin	NNS	_	_	_
64	780	780	CD	_	_	_
65	-	-	:	_	_	_
66	q	q	NN	_	_	_
67	--	--	:	_	_	_
68	no-mixed	no-mixed	JJ	_	_	_
69	--	--	:	_	_	_
70	no-discordant	no-discordant	JJ	_	_	_
71	--	--	:	_	_	_
72	no-unal	no-unal	JJ	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	sequencing	sequencing	NN	_	_	_
75	|	|	SYM	_	_	_
76	Immunoprecipitated	immunoprecipitate	VBN	_	_	_
77	samples	sample	NNS	_	_	_
78	and	and	CC	_	_	_
79	the	the	DT	_	_	_
80	sheared	sheared	JJ	_	_	_
81	DNA	dna	NN	_	_	_
82	following	follow	VBG	_	_	_
83	the	the	DT	_	_	_
84	Bioruptor	Bioruptor	NNP	_	_	_
85	were	be	VBD	_	_	_
86	de-crosslinked	de-crosslinked	JJ	_	_	_
87	in	in	IN	_	_	_
88	0.5	0.5	CD	_	_	_
89	x	x	CC	_	_	_
90	elution	elution	NN	_	_	_
91	buffer	buffer	NN	_	_	_
92	containing	contain	VBG	_	_	_
93	0.8	0.8	CD	_	_	_
94	mg/ml	mg/ml	NN	_	_	_
95	Pronase	Pronase	NNP	_	_	_
96	at	at	IN	_	_	_
97	42degree	42degree	CD	_	_	_
98	C	c	NN	_	_	_
99	for	for	IN	_	_	_
100	2	2	CD	_	_	_
101	h	h	NN	_	_	_
102	followed	follow	VBN	_	_	_
103	by	by	IN	_	_	_
104	65degree	65degree	CD	_	_	_
105	C	c	NN	_	_	_
106	for	for	IN	_	_	_
107	6	6	CD	_	_	_
108	h.	h.	NN	_	_	_
109	DNA	dna	NN	_	_	_
110	was	be	VBD	_	_	_
111	purified	purify	VBN	_	_	_
112	using	use	VBG	_	_	_
113	a	a	DT	_	_	_
114	PCR	pcr	NN	_	_	_
115	purification	purification	NN	_	_	_
116	kit	kit	NN	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	QIAGEN	qiagen	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	DNA	dna	NN	_	_	_
7	fragment	fragment	NN	_	_	_
8	sizes	size	NNS	_	_	_
9	were	be	VBD	_	_	_
10	checked	check	VBN	_	_	_
11	and	and	CC	_	_	_
12	gene-specific	gene-specific	JJ	_	_	_
13	quantitative	quantitative	JJ	_	_	_
14	PCR	pcr	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	qPCR	qpcr	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	was	be	VBD	_	_	_
19	carried	carry	VBN	_	_	_
20	out	out	RP	_	_	_
21	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	and	and	CC	_	_	_
3	post	post	VB	_	_	_
4	library	library	NN	_	_	_
5	construction	construction	NN	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	concentration	concentration	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	immunoprecipitated	immunoprecipitate	VBN	_	_	_
12	DNA	dna	NN	_	_	_
13	samples	sample	NNS	_	_	_
14	was	be	VBD	_	_	_
15	measured	measure	VBN	_	_	_
16	using	use	VBG	_	_	_
17	the	the	DT	_	_	_
18	Qubit	Qubit	NNP	_	_	_
19	HS	hs	NN	_	_	_
20	DNA	dna	NN	_	_	_
21	kit	kit	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Invitrogen	invitrogen	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	Library	Library	NNP	_	_	_
2	construction	construction	NN	_	_	_
3	and	and	CC	_	_	_
4	sequencing	sequencing	NN	_	_	_
5	was	be	VBD	_	_	_
6	done	do	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	ChIP-Seq	chip-seq	NN	_	_	_
10	Sample	Sample	NNP	_	_	_
11	Prep	Prep	NNP	_	_	_
12	kit	kit	NN	_	_	_
13	,	,	,	_	_	_
14	Reagent	Reagent	NNP	_	_	_
15	Preparation	Preparation	NNP	_	_	_
16	kit	kit	NN	_	_	_
17	and	and	CC	_	_	_
18	Cluster	Cluster	NNP	_	_	_
19	Station	Station	NNP	_	_	_
20	kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Illumina	Illumina	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	loaded	load	VBN	_	_	_
4	at	at	IN	_	_	_
5	a	a	DT	_	_	_
6	concentration	concentration	NN	_	_	_
7	of	of	IN	_	_	_
8	10	10	CD	_	_	_
9	pM	pm	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Sequencing	sequencing	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	constructed	construct	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	NEBNext	nebnext	NN	_	_	_
9	Ultra	ultra	NN	_	_	_
10	DNA	dna	NN	_	_	_
11	Library	Library	NNP	_	_	_
12	Prep	Prep	NNP	_	_	_
13	Kit	kit	NN	_	_	_
14	for	for	IN	_	_	_
15	Illumina	Illumina	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	#E7370	#E7370	NNP	_	_	_
18	,	,	,	_	_	_
19	NEB	NEB	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	for	for	IN	_	_	_
22	samples	sample	NNS	_	_	_
23	1	1	CD	_	_	_
24	to	to	TO	_	_	_
25	3	3	CD	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	37	37	CD	_	_	_
28	C	c	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	the	the	DT	_	_	_
32	WaferGen	WaferGen	NNP	_	_	_
33	PrepX	PrepX	NNP	_	_	_
34	ILM	ILM	NNP	_	_	_
35	ChiP-Seq	ChiP-Seq	NNP	_	_	_
36	Library	Library	NNP	_	_	_
37	Kit	kit	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	#	#	#	_	_	_
40	400075	400075	CD	_	_	_
41	,	,	,	_	_	_
42	WaferGen	WaferGen	NNP	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	on	on	IN	_	_	_
45	the	the	DT	_	_	_
46	Apollo	Apollo	NNP	_	_	_
47	324	324	CD	_	_	_
48	System	System	NNP	_	_	_
49	for	for	IN	_	_	_
50	samples	sample	NNS	_	_	_
51	4	4	CD	_	_	_
52	to	to	TO	_	_	_
53	10	10	CD	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	22	22	CD	_	_	_
56	C	c	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Sequencing	sequencing	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	with	with	IN	_	_	_
7	Accel	Accel	NNP	_	_	_
8	NGS	NGS	NNP	_	_	_
9	1S	1s	NN	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Swift	Swift	NNP	_	_	_
13	Bioscience	Bioscience	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	in	in	IN	_	_	_
16	accordanse	accordanse	NN	_	_	_
17	with	with	IN	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	protocol	protocol	NN	_	_	_
21	.	.	.	_	_	_

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	NN	_	_	_
21	Sequencing	sequencing	NN	_	_	_
22	reads	read	VBZ	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	approximately	approximately	RB	_	_	_
25	13	13	CD	_	_	_
26	to	to	TO	_	_	_
27	25	25	CD	_	_	_
28	million	million	CD	_	_	_
29	per	per	IN	_	_	_
30	sample	sample	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	were	be	VBD	_	_	_
33	imported	import	VBN	_	_	_
34	into	into	IN	_	_	_
35	Geneious	geneious	JJ	_	_	_
36	Pro	pro	FW	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Biomatters	biomatter	NNS	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	and	and	CC	_	_	_
41	assembled	assemble	VBN	_	_	_
42	to	to	TO	_	_	_
43	the	the	DT	_	_	_
44	reference	reference	NN	_	_	_
45	chromosome	chromosome	NN	_	_	_
46	MG1655	mg1655	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	GenBank	genbank	NN	_	_	_
49	Accession	Accession	NNP	_	_	_
50	Number	number	NN	_	_	_
51	000913.2	000913.2	CD	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	.	.	.	_	_	_

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/low	medium/low	VB	_	_	_
8	sensitivity	sensitivity	NN	_	_	_
9	on	on	IN	_	_	_
10	Geneious	Geneious	NNP	_	_	_
11	,	,	,	_	_	_
12	with	with	IN	_	_	_
13	the	the	DT	_	_	_
14	following	follow	VBG	_	_	_
15	parameters	parameter	NNS	_	_	_
16	:	:	:	_	_	_
17	10	10	CD	_	_	_
18	%	%	NN	_	_	_
19	gaps	gap	NNS	_	_	_
20	allowed	allow	VBD	_	_	_
21	per	per	IN	_	_	_
22	read	read	NN	_	_	_
23	;	;	:	_	_	_
24	word	word	NN	_	_	_
25	length	length	NN	_	_	_
26	of	of	IN	_	_	_
27	18	18	CD	_	_	_
28	;	;	:	_	_	_
29	index	index	NN	_	_	_
30	word	word	NN	_	_	_
31	length	length	NN	_	_	_
32	of	of	IN	_	_	_
33	13	13	CD	_	_	_
34	;	;	:	_	_	_
35	words	word	NNS	_	_	_
36	repeated	repeat	VBN	_	_	_
37	more	more	JJR	_	_	_
38	than	than	IN	_	_	_
39	12	12	CD	_	_	_
40	times	time	NNS	_	_	_
41	ignored	ignore	VBN	_	_	_
42	;	;	:	_	_	_
43	20	20	CD	_	_	_
44	%	%	NN	_	_	_
45	maximum	maximum	NN	_	_	_
46	mismatches	mismatch	NNS	_	_	_
47	per	per	IN	_	_	_
48	read	read	NN	_	_	_
49	;	;	:	_	_	_
50	and	and	CC	_	_	_
51	maximum	maximum	JJ	_	_	_
52	ambiguity	ambiguity	NN	_	_	_
53	of	of	IN	_	_	_
54	4	4	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
56	Sequencing	sequencing	NN	_	_	_
57	reads	read	VBZ	_	_	_
58	were	be	VBD	_	_	_
59	aligned	align	VBN	_	_	_
60	to	to	TO	_	_	_
61	the	the	DT	_	_	_
62	mg1655	mg1655	NN	_	_	_
63	genome	genome	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	NC	nc	NN	_	_	_
66	_	_	CD	_	_	_
67	000913.2	000913.2	CD	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	or	or	CC	_	_	_
70	a	a	DT	_	_	_
71	list	list	NN	_	_	_
72	of	of	IN	_	_	_
73	the	the	DT	_	_	_
74	designed	design	VBN	_	_	_
75	signal	signal	NN	_	_	_
76	peptide	peptide	NN	_	_	_
77	fusions	fusion	NNS	_	_	_
78	using	use	VBG	_	_	_
79	bowtie	bowtie	NN	_	_	_
80	0.12.9	0.12.9	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
82	Sequencing	sequencing	NN	_	_	_
83	reads	read	VBZ	_	_	_
84	were	be	VBD	_	_	_
85	mapped	map	VBN	_	_	_
86	to	to	TO	_	_	_
87	the	the	DT	_	_	_
88	E.	e.	FW	_	_	_
89	coli	coli	FW	_	_	_
90	genome	genome	NN	_	_	_
91	with	with	IN	_	_	_
92	bowtie2	bowtie2	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
94	Sequential	sequential	JJ	_	_	_
95	Design	design	NN	_	_	_
96	timecourse	timecourse	NN	_	_	_
97	t10	t10	NN	_	_	_
98	_	_	CD	_	_	_
99	t11	t11	NN	_	_	_
100	.1	.1	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
102	Sequential	sequential	JJ	_	_	_
103	Design	design	NN	_	_	_
104	timecourse	timecourse	NN	_	_	_
105	t10	t10	NN	_	_	_
106	_	_	CD	_	_	_
107	t11	t11	NN	_	_	_
108	.2	.2	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
110	Sequential	sequential	JJ	_	_	_
111	Design	design	NN	_	_	_
112	timecourse	timecourse	NN	_	_	_
113	t1	t1	NN	_	_	_
114	_	_	CD	_	_	_
115	t2	t2	NN	_	_	_
116	.1	.1	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
118	Sequential	sequential	JJ	_	_	_
119	Design	design	NN	_	_	_
120	timecourse	timecourse	NN	_	_	_
121	t1	t1	NN	_	_	_
122	_	_	CD	_	_	_
123	t2	t2	NN	_	_	_
124	.2	.2	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
126	Sequential	sequential	JJ	_	_	_
127	Design	design	NN	_	_	_
128	timecourse	timecourse	NN	_	_	_
129	t2	t2	NN	_	_	_
130	_	_	CD	_	_	_
131	t3	t3	NN	_	_	_
132	.1	.1	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
134	Sequential	sequential	JJ	_	_	_
135	Design	design	NN	_	_	_
136	timecourse	timecourse	NN	_	_	_
137	t2	t2	NN	_	_	_
138	_	_	CD	_	_	_
139	t3	t3	NN	_	_	_
140	.2	.2	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
142	Sequential	sequential	JJ	_	_	_
143	Design	design	NN	_	_	_
144	timecourse	timecourse	NN	_	_	_
145	t3	t3	NN	_	_	_
146	_	_	CD	_	_	_
147	t4	t4	NN	_	_	_
148	.1	.1	CD	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
150	Sequential	sequential	JJ	_	_	_
151	Design	design	NN	_	_	_
152	timecourse	timecourse	NN	_	_	_
153	t3	t3	NN	_	_	_
154	_	_	CD	_	_	_
155	t4	t4	NN	_	_	_
156	.2	.2	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
158	Sequential	sequential	JJ	_	_	_
159	Design	design	NN	_	_	_
160	timecourse	timecourse	NN	_	_	_
161	t4	t4	NN	_	_	_
162	_	_	CD	_	_	_
163	t5	t5	NN	_	_	_
164	.1	.1	CD	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
166	Sequential	sequential	JJ	_	_	_
167	Design	design	NN	_	_	_
168	timecourse	timecourse	NN	_	_	_
169	t4	t4	NN	_	_	_
170	_	_	CD	_	_	_
171	t5	t5	NN	_	_	_
172	.2	.2	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
174	Sequential	sequential	JJ	_	_	_
175	Design	design	NN	_	_	_
176	timecourse	timecourse	NN	_	_	_
177	t5	t5	NN	_	_	_
178	_	_	CD	_	_	_
179	t6	t6	NN	_	_	_
180	.1	.1	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
182	Sequential	sequential	JJ	_	_	_
183	Design	design	NN	_	_	_
184	timecourse	timecourse	NN	_	_	_
185	t5	t5	NN	_	_	_
186	_	_	CD	_	_	_
187	t6	t6	NN	_	_	_
188	.2	.2	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
190	Sequential	sequential	JJ	_	_	_
191	Design	design	NN	_	_	_
192	timecourse	timecourse	NN	_	_	_
193	t6	t6	NN	_	_	_
194	_	_	CD	_	_	_
195	t7	t7	NN	_	_	_
196	.1	.1	CD	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
198	Sequential	sequential	JJ	_	_	_
199	Design	design	NN	_	_	_
200	timecourse	timecourse	NN	_	_	_
201	t6	t6	NN	_	_	_
202	_	_	CD	_	_	_
203	t7	t7	NN	_	_	_
204	.2	.2	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
206	Sequential	sequential	JJ	_	_	_
207	Design	design	NN	_	_	_
208	timecourse	timecourse	NN	_	_	_
209	t7	t7	NN	_	_	_
210	_	_	CD	_	_	_
211	t8	t8	NN	_	_	_
212	.1	.1	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
214	Sequential	sequential	JJ	_	_	_
215	Design	design	NN	_	_	_
216	timecourse	timecourse	NN	_	_	_
217	t7	t7	NN	_	_	_
218	_	_	CD	_	_	_
219	t8	t8	NN	_	_	_
220	.2	.2	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
222	Sequential	sequential	JJ	_	_	_
223	Design	design	NN	_	_	_
224	timecourse	timecourse	NN	_	_	_
225	t8	t8	NN	_	_	_
226	_	_	CD	_	_	_
227	t9	t9	NN	_	_	_
228	.1	.1	CD	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
230	Sequential	sequential	JJ	_	_	_
231	Design	design	NN	_	_	_
232	timecourse	timecourse	NN	_	_	_
233	t8	t8	NN	_	_	_
234	_	_	CD	_	_	_
235	t9	t9	NN	_	_	_
236	.2	.2	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
238	Sequential	sequential	JJ	_	_	_
239	Design	design	NN	_	_	_
240	timecourse	timecourse	NN	_	_	_
241	t9	t9	NN	_	_	_
242	_	_	CD	_	_	_
243	t10	t10	NN	_	_	_
244	.1	.1	CD	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
246	Sequential	sequential	JJ	_	_	_
247	Design	design	NN	_	_	_
248	timecourse	timecourse	NN	_	_	_
249	t9	t9	NN	_	_	_
250	_	_	CD	_	_	_
251	t10	t10	NN	_	_	_
252	.2	.2	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	Serine	serine	NN	_	_	_
255	addition	addition	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	Serine	serine	NN	_	_	_
258	Hydroxamate	hydroxamate	NN	_	_	_
259	stressed	stress	VBD	_	_	_
260	,	,	,	_	_	_
261	replicate	replicate	VB	_	_	_
262	#	#	#	_	_	_
263	1	1	CD	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	Serine	serine	NN	_	_	_
266	Hydroxamate	hydroxamate	NN	_	_	_
267	stressed	stress	VBD	_	_	_
268	,	,	,	_	_	_
269	replicate	replicate	VB	_	_	_
270	#	#	#	_	_	_
271	2	2	CD	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	Serine	serine	NN	_	_	_
274	Hydroxamate	hydroxamate	NN	_	_	_
275	stressed	stress	VBD	_	_	_
276	,	,	,	_	_	_
277	replicate	replicate	VB	_	_	_
278	#	#	#	_	_	_
279	3	3	CD	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	Serine	serine	NN	_	_	_
282	hydrxamate	hydrxamate	NN	_	_	_
283	-LRB-	-lrb-	-LRB-	_	_	_
284	100	100	CD	_	_	_
285	mg/L	mg/l	NN	_	_	_
286	final	final	JJ	_	_	_
287	concentration	concentration	NN	_	_	_
288	-RRB-	-rrb-	-RRB-	_	_	_
289	was	be	VBD	_	_	_
290	added	add	VBN	_	_	_
291	to	to	TO	_	_	_
292	the	the	DT	_	_	_
293	cultures	culture	NNS	_	_	_
294	in	in	IN	_	_	_
295	the	the	DT	_	_	_
296	late-exponential	late-exponential	JJ	_	_	_
297	phase	phase	NN	_	_	_
298	at	at	IN	_	_	_
299	~	~	CD	_	_	_
300	11	11	CD	_	_	_
301	OD	od	NN	_	_	_
302	-LRB-	-lrb-	-LRB-	_	_	_
303	~	~	NN	_	_	_
304	5.5	5.5	CD	_	_	_
305	g	g	NN	_	_	_
306	g	g	NN	_	_	_
307	dry	dry	JJ	_	_	_
308	cell	cell	NN	_	_	_
309	weight	weight	NN	_	_	_
310	per	per	IN	_	_	_
311	liter	liter	NN	_	_	_
312	-RRB-	-rrb-	-RRB-	_	_	_
313	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	for	for	IN	_	_	_
3	DNA	dna	NN	_	_	_
4	microarray	microarray	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	were	be	VBD	_	_	_
7	taken	take	VBN	_	_	_
8	1	1	CD	_	_	_
9	hour	hour	NN	_	_	_
10	after	after	IN	_	_	_
11	the	the	DT	_	_	_
12	beginning	begin	VBG	_	_	_
13	the	the	DT	_	_	_
14	serine	serine	NN	_	_	_
15	hydrxamate	hydrxamate	NN	_	_	_
16	addition	addition	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	13.2	13.2	CD	_	_	_
19	OD	od	NN	_	_	_
20	,	,	,	_	_	_
21	~	~	NN	_	_	_
22	6.6	6.6	CD	_	_	_
23	g	g	NN	_	_	_
24	dry	dry	JJ	_	_	_
25	cell	cell	NN	_	_	_
26	weight	weight	NN	_	_	_
27	per	per	IN	_	_	_
28	liter	liter	NN	_	_	_
29	,	,	,	_	_	_
30	growth	growth	NN	_	_	_
31	rate	rate	NN	_	_	_
32	0.15	0.15	CD	_	_	_
33	1/h	1/h	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	serotype	serotype	NN	_	_	_
3	O157	o157	NN	_	_	_
4	:	:	:	_	_	_
5	H7	h7	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	serotype	serotype	NN	_	_	_
8	O157	o157	NN	_	_	_
9	:	:	:	_	_	_
10	H7	h7	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	serotype	serotype	NN	_	_	_
13	:	:	:	_	_	_
14	O157	o157	NN	_	_	_
15	:	:	:	_	_	_
16	H7	h7	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	serotype	serotype	NN	_	_	_
19	:	:	:	_	_	_
20	o157	o157	NN	_	_	_
21	:	:	:	_	_	_
22	H7	h7	NN	_	_	_
23	clade	clade	NN	_	_	_
24	2	2	CD	_	_	_
25	,	,	,	_	_	_
26	stx	stx	NN	_	_	_
27	1	1	CD	_	_	_
28	and	and	CC	_	_	_
29	2	2	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	serotype	serotype	NN	_	_	_
32	:	:	:	_	_	_
33	o157	o157	NN	_	_	_
34	:	:	:	_	_	_
35	H7	h7	NN	_	_	_
36	clade	clade	NN	_	_	_
37	2	2	CD	_	_	_
38	,	,	,	_	_	_
39	stx	stx	NN	_	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	serotype	serotype	NN	_	_	_
43	:	:	:	_	_	_
44	o157	o157	NN	_	_	_
45	:	:	:	_	_	_
46	H7	h7	NN	_	_	_
47	clade	clade	NN	_	_	_
48	8	8	CD	_	_	_
49	,	,	,	_	_	_
50	stx	stx	NN	_	_	_
51	2	2	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	serotype	serotype	NN	_	_	_
54	:	:	:	_	_	_
55	o157	o157	NN	_	_	_
56	:	:	:	_	_	_
57	H7	h7	NN	_	_	_
58	clade	clade	NN	_	_	_
59	8	8	CD	_	_	_
60	,	,	,	_	_	_
61	stx	stx	NN	_	_	_
62	2	2	CD	_	_	_
63	and	and	CC	_	_	_
64	2c	2c	JJ	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	serotype	serotype	NN	_	_	_
67	O175	o175	NN	_	_	_
68	:	:	:	_	_	_
69	H16	h16	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	serovar	serovar	NN	_	_	_
72	O157	o157	NN	_	_	_
73	:	:	:	_	_	_
74	H7	h7	NN	_	_	_
75	strain	strain	NN	_	_	_
76	EDL933	edl933	NN	_	_	_
77	;	;	:	_	_	_
78	GenBank	genbank	NN	_	_	_
79	accession	accession	NN	_	_	_
80	NC	nc	NN	_	_	_
81	_	_	CD	_	_	_
82	002655.2	002655.2	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	setwd	setwd	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	\	\	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	Seven	seven	CD	_	_	_
89	mililiter	mililiter	NN	_	_	_
90	of	of	IN	_	_	_
91	phenol/water	phenol/water	NN	_	_	_
92	were	be	VBD	_	_	_
93	added	add	VBN	_	_	_
94	before	before	IN	_	_	_
95	incubating	incubate	VBG	_	_	_
96	10	10	CD	_	_	_
97	min	min	NN	_	_	_
98	at	at	IN	_	_	_
99	67	67	CD	_	_	_
100	°C	°c	NN	_	_	_
101	with	with	IN	_	_	_
102	occasional	occasional	JJ	_	_	_
103	stirring	stir	VBG	_	_	_
104	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	cooled	cool	VBN	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	and	and	CC	_	_	_
8	spun	spin	VBD	_	_	_
9	10	10	CD	_	_	_
10	min	min	NN	_	_	_
11	at	at	IN	_	_	_
12	5000	5000	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	aqueous	aqueous	JJ	_	_	_
3	phase	phase	NN	_	_	_
4	was	be	VBD	_	_	_
5	separated	separate	VBN	_	_	_
6	and	and	CC	_	_	_
7	extracted	extract	VBN	_	_	_
8	again	again	RB	_	_	_
9	once	once	RB	_	_	_
10	the	the	DT	_	_	_
11	same	same	JJ	_	_	_
12	way	way	NN	_	_	_
13	and	and	CC	_	_	_
14	then	then	RB	_	_	_
15	once	once	RB	_	_	_
16	with	with	IN	_	_	_
17	phenol/chloroform	phenol/chloroform	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	v/v	v/v	NN	_	_	_
20	1:1	1:1	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	tenth	tenth	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	volume	volume	NN	_	_	_
6	of	of	IN	_	_	_
7	4M	4m	NN	_	_	_
8	NaCl	nacl	NN	_	_	_
9	and	and	CC	_	_	_
10	2.5	2.5	CD	_	_	_
11	volumes	volume	NNS	_	_	_
12	of	of	IN	_	_	_
13	cold	cold	JJ	_	_	_
14	ethanol	ethanol	NN	_	_	_
15	were	be	VBD	_	_	_
16	then	then	RB	_	_	_
17	added	add	VBN	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	aqueous	aqueous	JJ	_	_	_
21	phase	phase	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	tubes	tube	NNS	_	_	_
3	were	be	VBD	_	_	_
4	left	leave	VBN	_	_	_
5	at	at	IN	_	_	_
6	-20	-20	CD	_	_	_
7	°C	°c	NN	_	_	_
8	for	for	IN	_	_	_
9	two	two	CD	_	_	_
10	hours	hour	NNS	_	_	_
11	then	then	RB	_	_	_
12	spun	spin	VBD	_	_	_
13	at	at	IN	_	_	_
14	8500rpm	8500rpm	NN	_	_	_
15	at	at	IN	_	_	_
16	4	4	CD	_	_	_
17	°C	°c	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	with	with	IN	_	_	_
6	70	70	CD	_	_	_
7	%	%	NN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	,	,	,	_	_	_
10	dried	dry	VBN	_	_	_
11	under	under	IN	_	_	_
12	vacuum	vacuum	NN	_	_	_
13	and	and	CC	_	_	_
14	resuspened	resuspen	VBN	_	_	_
15	in	in	IN	_	_	_
16	300	300	CD	_	_	_
17	l	l	NN	_	_	_
18	sterile	sterile	JJ	_	_	_
19	water	water	NN	_	_	_
20	and	and	CC	_	_	_
21	transferred	transfer	VBN	_	_	_
22	to	to	TO	_	_	_
23	an	a	DT	_	_	_
24	eppendord	eppendord	NN	_	_	_
25	tube	tube	NN	_	_	_
26	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	amount	amount	NN	_	_	_
3	of	of	IN	_	_	_
4	34.5	34.5	CD	_	_	_
5	l	l	NN	_	_	_
6	Qiagen	Qiagen	NNP	_	_	_
7	RDD	RDD	NNP	_	_	_
8	buffer	buffer	NN	_	_	_
9	and	and	CC	_	_	_
10	9.37	9.37	CD	_	_	_
11	l	l	NN	_	_	_
12	of	of	IN	_	_	_
13	RNase	rnase	NN	_	_	_
14	free	free	JJ	_	_	_
15	DNase	dnase	NN	_	_	_
16	I	i	CD	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	qiagen	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	were	be	VBD	_	_	_
21	added	add	VBN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	15	15	CD	_	_	_
3	min	min	NN	_	_	_
4	at	at	IN	_	_	_
5	room	room	NN	_	_	_
6	temperature	temperature	NN	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	tubes	tube	NNS	_	_	_
10	were	be	VBD	_	_	_
11	mixed	mix	VBN	_	_	_
12	by	by	IN	_	_	_
13	inversion	inversion	NN	_	_	_
14	and	and	CC	_	_	_
15	deproteinized	deproteinize	VBN	_	_	_
16	as	as	IN	_	_	_
17	shown	show	VBN	_	_	_
18	above	above	IN	_	_	_
19	with	with	IN	_	_	_
20	300	300	CD	_	_	_
21	l	l	NN	_	_	_
22	phenol/H2O	phenol/h2o	NN	_	_	_
23	at	at	IN	_	_	_
24	room	room	NN	_	_	_
25	temperature	temperature	NN	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	precipitated	precipitate	VBN	_	_	_
6	with	with	IN	_	_	_
7	37.5	37.5	CD	_	_	_
8	µl	µl	NN	_	_	_
9	NaCl	nacl	NN	_	_	_
10	4M	4m	NN	_	_	_
11	and	and	CC	_	_	_
12	823µl	823µl	NN	_	_	_
13	cold	cold	JJ	_	_	_
14	ethanol	ethanol	NN	_	_	_
15	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	2	2	CD	_	_	_
3	hours	hour	NNS	_	_	_
4	at	at	IN	_	_	_
5	-20	-20	CD	_	_	_
6	°C	°c	NN	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	tubes	tube	NNS	_	_	_
10	were	be	VBD	_	_	_
11	centrifuged	centrifuge	VBN	_	_	_
12	30	30	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	10,000	10,000	CD	_	_	_
16	G	g	NN	_	_	_
17	at	at	IN	_	_	_
18	4	4	CD	_	_	_
19	°C	°c	NN	_	_	_
20	,	,	,	_	_	_
21	the	the	DT	_	_	_
22	pellets	pellet	NNS	_	_	_
23	were	be	VBD	_	_	_
24	then	then	RB	_	_	_
25	washed	wash	VBN	_	_	_
26	with	with	IN	_	_	_
27	70	70	CD	_	_	_
28	%	%	NN	_	_	_
29	ethanol	ethanol	NN	_	_	_
30	then	then	RB	_	_	_
31	dried	dry	VBD	_	_	_
32	under	under	IN	_	_	_
33	vacuum	vacuum	NN	_	_	_
34	and	and	CC	_	_	_
35	resuspended	resuspend	VBN	_	_	_
36	in	in	IN	_	_	_
37	60µl	60µl	JJ	_	_	_
38	sterile	sterile	JJ	_	_	_
39	water	water	NN	_	_	_
40	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNAs	rna	NNS	_	_	_
3	were	be	VBD	_	_	_
4	stored	store	VBN	_	_	_
5	at	at	IN	_	_	_
6	-20	-20	CD	_	_	_
7	°C	°c	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	SF1a	sf1a	NN	_	_	_
3	_	_	NN	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	SF1a	sf1a	NN	_	_	_
7	_	_	NN	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	SF1a	sf1a	NN	_	_	_
11	_	_	CD	_	_	_
12	3	3	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	SF1b	sf1b	NN	_	_	_
15	_	_	NN	_	_	_
16	1	1	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	SF1b	sf1b	NN	_	_	_
19	_	_	NN	_	_	_
20	2	2	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	SF1b	sf1b	NN	_	_	_
23	_	_	CD	_	_	_
24	3	3	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	SF2b	sf2b	NN	_	_	_
27	_	_	NN	_	_	_
28	1	1	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	SF2b	sf2b	NN	_	_	_
31	_	_	NN	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	SF2b	sf2b	NN	_	_	_
35	_	_	CD	_	_	_
36	3	3	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	SF3	sf3	NN	_	_	_
39	_	_	NN	_	_	_
40	1	1	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	SF3	sf3	NN	_	_	_
43	_	_	NN	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	SF3	sf3	NN	_	_	_
47	_	_	CD	_	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	SF4a	sf4a	NN	_	_	_
51	_	_	NN	_	_	_
52	1	1	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	SF4a	sf4a	NN	_	_	_
55	_	_	NN	_	_	_
56	2	2	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	SF4a	sf4a	NN	_	_	_
59	_	_	CD	_	_	_
60	3	3	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	SF4b	sf4b	NN	_	_	_
63	_	_	NN	_	_	_
64	1	1	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	SF4b	sf4b	NN	_	_	_
67	_	_	NN	_	_	_
68	2	2	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	SF4b	sf4b	NN	_	_	_
71	_	_	CD	_	_	_
72	3	3	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	SF5	sf5	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	SF5	sf5	NN	_	_	_
77	_	_	NN	_	_	_
78	2	2	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	SF5	sf5	NN	_	_	_
81	_	_	CD	_	_	_
82	3	3	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	SF6	sf6	NN	_	_	_
85	_	_	NN	_	_	_
86	1	1	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	SF6	sf6	NN	_	_	_
89	_	_	NN	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	SF6	sf6	NN	_	_	_
93	_	_	CD	_	_	_
94	3	3	CD	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	SFx	sfx	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	SFx	sfx	NN	_	_	_
99	_	_	NN	_	_	_
100	2	2	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
102	SFx	SFx	NNP	_	_	_
103	_	_	SYM	_	_	_
104	3	3	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	SFy	sfy	NN	_	_	_
107	_	_	NN	_	_	_
108	1	1	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	SFy	sfy	NN	_	_	_
111	_	_	NN	_	_	_
112	2	2	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	SFy	sfy	NN	_	_	_
115	_	_	CD	_	_	_
116	3	3	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	SgrR	sgrr	NN	TF	_	_
119	_	_	NN	_	_	_
120	1	1	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	SgrR	sgrr	NN	TF	_	_
123	_	_	NN	_	_	_
124	2	2	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	SgrR	sgrr	NN	TF	_	_
127	_	_	CD	_	_	_
128	3	3	CD	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	sgrS	sgrs	NN	GEN	_	_
131	_	_	CD	_	_	_
132	T	t	NN	_	_	_
133	_	_	NN	_	_	_
134	1	1	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	sgrS	sgrs	NN	GEN	_	_
137	_	_	CD	_	_	_
138	T	t	NN	_	_	_
139	_	_	NN	_	_	_
140	2	2	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	sgrS	sgrs	NN	GEN	_	_
143	_	_	CD	_	_	_
144	T	t	NN	_	_	_
145	_	_	NN	_	_	_
146	3	3	CD	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	sgrS	sgrs	NN	GEN	_	_
149	_	_	CD	_	_	_
150	un	un	NN	_	_	_
151	_	_	NN	_	_	_
152	1	1	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	sgrS	sgrs	NN	GEN	_	_
155	_	_	CD	_	_	_
156	un	un	NN	_	_	_
157	_	_	NN	_	_	_
158	2	2	CD	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	sgrS	sgrs	NN	GEN	_	_
161	_	_	CD	_	_	_
162	un	un	NN	_	_	_
163	_	_	NN	_	_	_
164	3	3	CD	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	SH0003	sh0003	NN	_	_	_
167	30h	30h	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	SH0012	sh0012	NN	_	_	_
170	20h	20h	JJ	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	SH0012	sh0012	NN	_	_	_
173	30h	30h	CD	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	Sh0012	sh0012	NN	_	_	_
176	40h	40h	CD	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	SH0012	sh0012	NN	_	_	_
179	and	and	CC	_	_	_
180	SH0003	sh0003	NN	_	_	_
181	were	be	VBD	_	_	_
182	fermented	ferment	VBN	_	_	_
183	in	in	IN	_	_	_
184	a	a	DT	_	_	_
185	5.0	5.0	CD	_	_	_
186	L	l	NN	_	_	_
187	jar-fermenter	jar-fermenter	NN	_	_	_
188	with	with	IN	_	_	_
189	a	a	DT	_	_	_
190	2.0	2.0	CD	_	_	_
191	working	work	VBG	_	_	_
192	voulume	voulume	NN	_	_	_
193	of	of	IN	_	_	_
194	modified	modify	VBN	_	_	_
195	R	r	NN	_	_	_
196	medium	medium	NN	_	_	_
197	-LRB-	-lrb-	-LRB-	_	_	_
198	20g/L	20g/l	NN	_	_	_
199	glucose	glucose	NN	SUPP	_	_
200	,	,	,	_	_	_
201	80	80	CD	_	_	_
202	g/L	g/l	NN	_	_	_
203	glycerol	glycerol	NN	SUPP	_	_
204	,	,	,	_	_	_
205	1.4	1.4	CD	_	_	_
206	g/L	g/l	NN	_	_	_
207	MgSDo4	mgsdo4	NN	_	_	_
208	,	,	,	_	_	_
209	13.5	13.5	CD	_	_	_
210	g/L	g/l	NN	_	_	_
211	KH2PO4	kh2po4	NN	_	_	_
212	,	,	,	_	_	_
213	4.0	4.0	CD	_	_	_
214	g/L	g/l	NN	_	_	_
215	-LRB-	-lrb-	-LRB-	_	_	_
216	NH4	nh4	NN	_	_	_
217	-RRB-	-rrb-	-RRB-	_	_	_
218	2HPO4	2hpo4	NN	_	_	_
219	and	and	CC	_	_	_
220	1.7	1.7	CD	_	_	_
221	g/L	g/l	NN	_	_	_
222	citric	citric	JJ	_	_	_
223	acid	acid	NN	_	_	_
224	at	at	IN	_	_	_
225	35	35	CD	_	_	_
226	°C	°c	NN	_	_	_
227	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	agitation	agitation	NN	_	_	_
3	was	be	VBD	_	_	_
4	at	at	IN	_	_	_
5	1200	1200	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	and	and	CC	_	_	_
8	pH	ph	NN	_	_	_
9	was	be	VBD	_	_	_
10	maintained	maintain	VBN	_	_	_
11	at	at	IN	_	_	_
12	7.0	7.0	CD	_	_	_
13	with	with	IN	_	_	_
14	5N	5n	NN	_	_	_
15	NH4OH	nh4oh	NN	_	_	_
16	.	.	.	_	_	_

1	with	with	IN	_	_	_
2	the	the	DT	_	_	_
3	depletion	depletion	NN	_	_	_
4	of	of	IN	_	_	_
5	initial	initial	JJ	_	_	_
6	glucose	glucose	NN	SUPP	_	_
7	,	,	,	_	_	_
8	feeding	feed	VBG	_	_	_
9	medium	medium	NN	_	_	_
10	of	of	IN	_	_	_
11	glycerol	glycerol	NN	SUPP	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	700g/L	700g/l	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	was	be	VBD	_	_	_
16	throughout	throughout	IN	_	_	_
17	fermentation	fermentation	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	SH0012	sh0012	NN	_	_	_
3	no	no	DT	_	_	_
4	rpm	rpm	NN	_	_	_
5	change	change	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	SH0012	sh0012	NN	_	_	_
8	no	no	DT	_	_	_
9	vitamin	vitamin	NN	_	_	_
10	B12	b12	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Shigella	shigella	NN	_	_	_
13	boydii	boydii	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Shigella	shigella	NN	_	_	_
16	boydii	boydii	NN	_	_	_
17	13	13	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Shigella	shigella	NN	_	_	_
20	boydii	boydii	NN	_	_	_
21	14	14	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Shigella	shigella	NN	_	_	_
24	boydii	boydii	NN	_	_	_
25	15	15	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Shigella	shigella	NN	_	_	_
28	boydii	boydii	NN	_	_	_
29	15	15	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Shigella	shigella	NN	_	_	_
32	boydii	boydii	NN	_	_	_
33	16	16	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Shigella	shigella	NN	_	_	_
36	boydii	boydii	NN	_	_	_
37	17	17	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	Shigella	shigella	NN	_	_	_
40	boydii	boydii	NN	_	_	_
41	18	18	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Shigella	shigella	NN	_	_	_
44	boydii	boydii	NN	_	_	_
45	serogroup	serogroup	NN	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Shigella	shigella	NN	_	_	_
49	boydii	boydii	NN	_	_	_
50	serogroup	serogroup	NN	_	_	_
51	2	2	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
53	Shigella	shigella	NN	_	_	_
54	boydii	boydii	NN	_	_	_
55	serotype	serotype	NN	_	_	_
56	1	1	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Shigella	shigella	NN	_	_	_
59	boydii	boydii	NN	_	_	_
60	serotype	serotype	NN	_	_	_
61	10	10	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
63	Shigella	shigella	NN	_	_	_
64	boydii	boydii	NN	_	_	_
65	serotype	serotype	NN	_	_	_
66	11	11	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	Shigella	shigella	NN	_	_	_
69	boydii	boydii	NN	_	_	_
70	serotype	serotype	NN	_	_	_
71	12	12	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	Shigella	shigella	NN	_	_	_
74	boydii	boydii	NN	_	_	_
75	serotype	serotype	NN	_	_	_
76	13	13	CD	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	Shigella	shigella	NN	_	_	_
79	boydii	boydii	NN	_	_	_
80	serotype2	serotype2	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Shigella	shigella	NN	_	_	_
83	boydii	boydii	NN	_	_	_
84	serotype	serotype	NN	_	_	_
85	2	2	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
87	Shigella	shigella	NN	_	_	_
88	boydii	boydii	NN	_	_	_
89	serotype3	serotype3	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	Shigella	shigella	NN	_	_	_
92	boydii	boydii	NN	_	_	_
93	serotype	serotype	NN	_	_	_
94	3	3	CD	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Shigella	shigella	NN	_	_	_
97	boydii	boydii	NN	_	_	_
98	serotype	serotype	NN	_	_	_
99	5	5	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
101	Shigella	shigella	NN	_	_	_
102	boydii	boydii	NN	_	_	_
103	serotype	serotype	NN	_	_	_
104	6	6	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	Shigella	shigella	NN	_	_	_
107	boydii	boydii	NN	_	_	_
108	serotype	serotype	NN	_	_	_
109	7	7	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	Shigella	shigella	NN	_	_	_
112	boydii	boydii	NN	_	_	_
113	serotype	serotype	NN	_	_	_
114	7	7	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Shigella	shigella	NN	_	_	_
117	boydii	boydii	NN	_	_	_
118	serotype	serotype	NN	_	_	_
119	8	8	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Shigella	shigella	NN	_	_	_
122	boydii	boydii	NN	_	_	_
123	serotype	serotype	NN	_	_	_
124	9	9	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	Shigella	shigella	NN	_	_	_
127	dysenteriae	dysenteriae	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Shigella	shigella	NN	_	_	_
130	dysenteriae	dysenteriae	NN	_	_	_
131	10	10	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
133	Shigella	shigella	NN	_	_	_
134	dysenteriae	dysenteriae	NN	_	_	_
135	11	11	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
137	Shigella	shigella	NN	_	_	_
138	dysenteriae	dysenteriae	NN	_	_	_
139	12	12	CD	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
141	Shigella	shigella	NN	_	_	_
142	dysenteriae	dysenteriae	NN	_	_	_
143	13	13	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
145	Shigella	shigella	NN	_	_	_
146	dysenteriae	dysenteriae	NN	_	_	_
147	2	2	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
149	Shigella	shigella	NN	_	_	_
150	dysenteriae	dysenteriae	NN	_	_	_
151	3	3	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	Shigella	shigella	NN	_	_	_
154	dysenteriae	dysenteriae	NN	_	_	_
155	4	4	CD	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
157	Shigella	shigella	NN	_	_	_
158	dysenteriae	dysenteriae	NN	_	_	_
159	5	5	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
161	Shigella	shigella	NN	_	_	_
162	dysenteriae	dysenteriae	NN	_	_	_
163	6	6	CD	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	Shigella	shigella	NN	_	_	_
166	dysenteriae	dysenteriae	NN	_	_	_
167	7	7	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	Shigella	shigella	NN	_	_	_
170	dysenteriae	dysenteriae	NN	_	_	_
171	8	8	CD	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	Shigella	shigella	NN	_	_	_
174	dysenteriae	dysenteria	NNS	_	_	_
175	9	9	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	Shigella	shigella	NN	_	_	_
178	flexneri	flexneri	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	Shigella	shigella	NN	_	_	_
181	flexneri	flexneri	NN	_	_	_
182	1a	1a	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	Shigella	shigella	NN	_	_	_
185	flexneri	flexneri	NN	_	_	_
186	1b	1b	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	Shigella	shigella	NN	_	_	_
189	flexneri	flexneri	NN	_	_	_
190	2b	2b	JJ	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	Shigella	shigella	NN	_	_	_
193	flexneri	flexneri	NN	_	_	_
194	3	3	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	Shigella	shigella	NN	_	_	_
197	flexneri	flexneri	NN	_	_	_
198	4a	4a	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	Shigella	shigella	NN	_	_	_
201	flexneri	flexneri	NN	_	_	_
202	4b	4b	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	Shigella	shigella	NN	_	_	_
205	flexneri	flexneri	NN	_	_	_
206	5	5	CD	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	Shigella	shigella	NN	_	_	_
209	flexneri	flexneri	NN	_	_	_
210	6	6	CD	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	Shigella	shigella	NN	_	_	_
213	flexneri	flexneri	NN	_	_	_
214	variant	variant	JJ	_	_	_
215	x	x	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	Shigella	shigella	NN	_	_	_
218	flexneri	flexneri	NN	_	_	_
219	variant	variant	JJ	_	_	_
220	y	y	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	SHX-treated	shx-treated	JJ	_	_	_
223	Delta	delta	NN	_	_	_
224	dksA	dksa	NN	GEN	_	_
225	Cells	cell	NNS	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	SHX-treated	shx-treated	JJ	_	_	_
228	Delta	delta	NN	_	_	_
229	dksA	dksa	NN	GEN	_	_
230	Cells	cell	NNS	_	_	_
231	Replicate	replicate	VB	_	_	_
232	1	1	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	SHX-treated	shx-treated	JJ	_	_	_
235	Delta	delta	NN	_	_	_
236	dksA	dksa	NN	GEN	_	_
237	Cells	cell	NNS	_	_	_
238	Replicate	replicate	VB	_	_	_
239	2	2	CD	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
241	SHX-treated	shx-treated	JJ	_	_	_
242	Delta	delta	NN	_	_	_
243	dksA	dksa	NN	GEN	_	_
244	Cells	cell	NNS	_	_	_
245	Replicate	replicate	VB	_	_	_
246	3	3	CD	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	SHX-treated	shx-treated	JJ	_	_	_
249	Wild-type	wild-type	JJ	_	_	_
250	Cells	cell	NNS	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	SHX-treated	shx-treated	JJ	_	_	_
253	Wild-type	wild-type	JJ	_	_	_
254	Cells	cell	NNS	_	_	_
255	Replicate	replicate	VB	_	_	_
256	1	1	CD	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	SHX-treated	shx-treated	JJ	_	_	_
259	Wild-type	wild-type	JJ	_	_	_
260	Cells	cell	NNS	_	_	_
261	Replicate	replicate	VB	_	_	_
262	2	2	CD	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
264	SHX-treated	shx-treated	JJ	_	_	_
265	Wild-type	wild-type	JJ	_	_	_
266	Cells	cell	NNS	_	_	_
267	Replicate	replicate	VB	_	_	_
268	3	3	CD	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	Sig70	sig70	NN	_	_	_
271	in	in	IN	_	_	_
272	E.	e.	FW	_	_	_
273	coli	coli	FW	_	_	_
274	_	_	SYM	_	_	_
275	exponential	exponential	JJ	_	_	_
276	aerobic	aerobic	JJ	_	_	_
277	growth	growth	NN	_	_	_
278	_	_	IN	_	_	_
279	no	no	DT	_	_	_
280	rifampicin	rifampicin	NN	SUPP	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Sig70	sig70	NN	_	_	_
283	in	in	IN	_	_	_
284	E.	e.	FW	_	_	_
285	coli	coli	FW	_	_	_
286	,	,	,	_	_	_
287	exponential	exponential	JJ	_	_	_
288	aerobic	aerobic	JJ	_	_	_
289	growth	growth	NN	_	_	_
290	,	,	,	_	_	_
291	no	no	DT	_	_	_
292	rifampicin	rifampicin	NN	SUPP	_	_
293	applied	apply	VBD	_	_	_
294	replicate	replicate	VB	_	_	_
295	1	1	CD	_	_	_
296	-LRB-	-lrb-	-LRB-	_	_	_
297	run	run	NN	_	_	_
298	299	299	CD	_	_	_
299	-RRB-	-rrb-	-RRB-	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	Sig70	sig70	NN	_	_	_
302	in	in	IN	_	_	_
303	E.	e.	FW	_	_	_
304	coli	coli	FW	_	_	_
305	,	,	,	_	_	_
306	exponential	exponential	JJ	_	_	_
307	aerobic	aerobic	JJ	_	_	_
308	growth	growth	NN	_	_	_
309	,	,	,	_	_	_
310	no	no	DT	_	_	_
311	rifampicin	rifampicin	NN	SUPP	_	_
312	applied	apply	VBD	_	_	_
313	replicate	replicate	VB	_	_	_
314	1	1	CD	_	_	_
315	-LRB-	-lrb-	-LRB-	_	_	_
316	run	run	NN	_	_	_
317	423	423	CD	_	_	_
318	-RRB-	-rrb-	-RRB-	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	Sig70	sig70	NN	_	_	_
321	in	in	IN	_	_	_
322	E.	e.	FW	_	_	_
323	coli	coli	FW	_	_	_
324	,	,	,	_	_	_
325	exponential	exponential	JJ	_	_	_
326	aerobic	aerobic	JJ	_	_	_
327	growth	growth	NN	_	_	_
328	,	,	,	_	_	_
329	no	no	DT	_	_	_
330	rifampicin	rifampicin	NN	SUPP	_	_
331	applied	apply	VBD	_	_	_
332	replicate	replicate	VB	_	_	_
333	2	2	CD	_	_	_
334	-LRB-	-lrb-	-LRB-	_	_	_
335	run	run	NN	_	_	_
336	299	299	CD	_	_	_
337	-RRB-	-rrb-	-RRB-	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	Sig70	sig70	NN	_	_	_
340	in	in	IN	_	_	_
341	E.	e.	FW	_	_	_
342	coli	coli	FW	_	_	_
343	,	,	,	_	_	_
344	exponential	exponential	JJ	_	_	_
345	aerobic	aerobic	JJ	_	_	_
346	growth	growth	NN	_	_	_
347	,	,	,	_	_	_
348	no	no	DT	_	_	_
349	rifampicin	rifampicin	NN	SUPP	_	_
350	applied	apply	VBD	_	_	_
351	replicate	replicate	VB	_	_	_
352	2	2	CD	_	_	_
353	-LRB-	-lrb-	-LRB-	_	_	_
354	run	run	NN	_	_	_
355	423	423	CD	_	_	_
356	-RRB-	-rrb-	-RRB-	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	Sig70	sig70	NN	_	_	_
359	in	in	IN	_	_	_
360	E.	e.	FW	_	_	_
361	coli	coli	FW	_	_	_
362	_	_	SYM	_	_	_
363	exponential	exponential	JJ	_	_	_
364	aerobic	aerobic	JJ	_	_	_
365	growth	growth	NN	_	_	_
366	_	_	NN	_	_	_
367	rifampicin	rifampicin	NN	SUPP	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	Sig70	sig70	NN	_	_	_
370	in	in	IN	_	_	_
371	E.	e.	FW	_	_	_
372	coli	coli	FW	_	_	_
373	,	,	,	_	_	_
374	exponential	exponential	JJ	_	_	_
375	aerobic	aerobic	JJ	_	_	_
376	growth	growth	NN	_	_	_
377	,	,	,	_	_	_
378	rifampicin	rifampicin	NN	SUPP	_	_
379	applied	apply	VBD	_	_	_
380	for	for	IN	_	_	_
381	20	20	CD	_	_	_
382	minutes	minute	NNS	_	_	_
383	,	,	,	_	_	_
384	replicate	replicate	VBP	_	_	_
385	1	1	CD	_	_	_
386	-LRB-	-lrb-	-LRB-	_	_	_
387	run	run	NN	_	_	_
388	423	423	CD	_	_	_
389	-RRB-	-rrb-	-RRB-	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	Sig70	sig70	NN	_	_	_
392	in	in	IN	_	_	_
393	E.	e.	FW	_	_	_
394	coli	coli	FW	_	_	_
395	,	,	,	_	_	_
396	exponential	exponential	JJ	_	_	_
397	aerobic	aerobic	JJ	_	_	_
398	growth	growth	NN	_	_	_
399	,	,	,	_	_	_
400	rifampicin	rifampicin	NN	SUPP	_	_
401	applied	apply	VBD	_	_	_
402	for	for	IN	_	_	_
403	20	20	CD	_	_	_
404	minutes	minute	NNS	_	_	_
405	,	,	,	_	_	_
406	replicate	replicate	VBP	_	_	_
407	2	2	CD	_	_	_
408	-LRB-	-lrb-	-LRB-	_	_	_
409	run	run	NN	_	_	_
410	423	423	CD	_	_	_
411	-RRB-	-rrb-	-RRB-	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	Sig70	sig70	NN	_	_	_
414	in	in	IN	_	_	_
415	E.	e.	FW	_	_	_
416	coli	coli	FW	_	_	_
417	_	_	SYM	_	_	_
418	static	static	JJ	_	_	_
419	aerobic	aerobic	JJ	_	_	_
420	growth	growth	NN	_	_	_
421	_	_	IN	_	_	_
422	no	no	DT	_	_	_
423	rifampicin	rifampicin	NN	SUPP	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	Sig70	sig70	NN	_	_	_
426	in	in	IN	_	_	_
427	E.	e.	FW	_	_	_
428	coli	coli	FW	_	_	_
429	,	,	,	_	_	_
430	static	static	JJ	_	_	_
431	aerobic	aerobic	JJ	_	_	_
432	growth	growth	NN	_	_	_
433	,	,	,	_	_	_
434	no	no	DT	_	_	_
435	rifampicin	rifampicin	NN	SUPP	_	_
436	applied	apply	VBD	_	_	_
437	replicate	replicate	VB	_	_	_
438	1	1	CD	_	_	_
439	-LRB-	-lrb-	-LRB-	_	_	_
440	run	run	NN	_	_	_
441	299	299	CD	_	_	_
442	-RRB-	-rrb-	-RRB-	_	_	_
443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
444	Sig70	sig70	NN	_	_	_
445	in	in	IN	_	_	_
446	E.	e.	FW	_	_	_
447	coli	coli	FW	_	_	_
448	,	,	,	_	_	_
449	static	static	JJ	_	_	_
450	aerobic	aerobic	JJ	_	_	_
451	growth	growth	NN	_	_	_
452	,	,	,	_	_	_
453	no	no	DT	_	_	_
454	rifampicin	rifampicin	NN	SUPP	_	_
455	applied	apply	VBD	_	_	_
456	replicate	replicate	VB	_	_	_
457	2	2	CD	_	_	_
458	-LRB-	-lrb-	-LRB-	_	_	_
459	run	run	NN	_	_	_
460	299	299	CD	_	_	_
461	-RRB-	-rrb-	-RRB-	_	_	_
462	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
463	Sigma70	sigma70	NN	_	_	_
464	_	_	CD	_	_	_
465	ChIP	chip	NN	_	_	_
466	_	_	CD	_	_	_
467	A	a	DT	_	_	_
468	_	_	NN	_	_	_
469	cy5	cy5	NN	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	Sigma70	sigma70	NN	_	_	_
472	_	_	CD	_	_	_
473	ChIP	chip	NN	_	_	_
474	_	_	NN	_	_	_
475	B	b	NN	_	_	_
476	_	_	CD	_	_	_
477	cy5	cy5	NN	_	_	_
478	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
479	Sigma70	sigma70	NN	_	_	_
480	ChIP-chip	chip-chip	NN	_	_	_
481	in	in	IN	_	_	_
482	E.	e.	FW	_	_	_
483	coli	coli	FW	_	_	_
484	K-12	k-12	NN	_	_	_
485	MG1655	mg1655	NN	_	_	_
486	cells	cell	NNS	_	_	_
487	-LRB-	-lrb-	-LRB-	_	_	_
488	Dataset	Dataset	NNP	_	_	_
489	56859	56859	CD	_	_	_
490	-RRB-	-rrb-	-RRB-	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	Sigma70	sigma70	NN	_	_	_
493	ChIP-chip	chip-chip	NN	_	_	_
494	in	in	IN	_	_	_
495	E.	e.	FW	_	_	_
496	coli	coli	FW	_	_	_
497	K-12	k-12	NN	_	_	_
498	MG1655	mg1655	NN	_	_	_
499	cells	cell	NNS	_	_	_
500	-LRB-	-lrb-	-LRB-	_	_	_
501	Dataset	Dataset	NNP	_	_	_
502	62214	62214	CD	_	_	_
503	-RRB-	-rrb-	-RRB-	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	Sigma70	sigma70	NN	_	_	_
506	ChIP-chip	chip-chip	NN	_	_	_
507	in	in	IN	_	_	_
508	E.	e.	FW	_	_	_
509	coli	coli	FW	_	_	_
510	K-12	k-12	NN	_	_	_
511	MG1655	mg1655	NN	_	_	_
512	cells	cell	NNS	_	_	_
513	-LRB-	-lrb-	-LRB-	_	_	_
514	Dataset	Dataset	NNP	_	_	_
515	64194	64194	CD	_	_	_
516	-RRB-	-rrb-	-RRB-	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	Sigma70	sigma70	NN	_	_	_
519	ChIP-chip	chip-chip	NN	_	_	_
520	in	in	IN	_	_	_
521	E.	e.	FW	_	_	_
522	coli	coli	FW	_	_	_
523	K-12	k-12	NN	_	_	_
524	MG1655	mg1655	NN	_	_	_
525	cells	cell	NNS	_	_	_
526	treated	treat	VBN	_	_	_
527	with	with	IN	_	_	_
528	100ug/ml	100ug/ml	JJ	_	_	_
529	rifampicin	rifampicin	NN	SUPP	_	_
530	-LRB-	-lrb-	-LRB-	_	_	_
531	Dataset	dataset	NN	_	_	_
532	84847	84847	CD	_	_	_
533	-RRB-	-rrb-	-RRB-	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	Sigma70	sigma70	NN	_	_	_
536	_	_	CD	_	_	_
537	ChIP	chip	NN	_	_	_
538	_	_	NN	_	_	_
539	control	control	NN	_	_	_
540	_	_	CD	_	_	_
541	A	a	DT	_	_	_
542	_	_	NN	_	_	_
543	cy3	cy3	NN	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	Sigma70	sigma70	NN	_	_	_
546	_	_	CD	_	_	_
547	ChIP	chip	NN	_	_	_
548	_	_	NN	_	_	_
549	control	control	NN	_	_	_
550	_	_	NN	_	_	_
551	B	b	NN	_	_	_
552	_	_	CD	_	_	_
553	cy3	cy3	NN	_	_	_
554	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
555	Sigma70	sigma70	NN	_	_	_
556	ChIP	chip	NN	_	_	_
557	in	in	IN	_	_	_
558	E.	e.	FW	_	_	_
559	coli	coli	FW	_	_	_
560	K-12	k-12	NN	_	_	_
561	MG1655	mg1655	NN	_	_	_
562	cells	cell	NNS	_	_	_
563	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
564	Sigma70	sigma70	NN	_	_	_
565	ChIP	chip	NN	_	_	_
566	in	in	IN	_	_	_
567	E.	e.	FW	_	_	_
568	coli	coli	FW	_	_	_
569	K-12	k-12	NN	_	_	_
570	MG1655	mg1655	NN	_	_	_
571	cells	cell	NNS	_	_	_
572	treated	treat	VBN	_	_	_
573	with	with	IN	_	_	_
574	100ug/ml	100ug/ml	JJ	_	_	_
575	rifampicin	rifampicin	NN	SUPP	_	_
576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
577	Sigma70	sigma70	NN	_	_	_
578	_	_	CD	_	_	_
579	IP	IP	NNP	_	_	_
580	_	_	SYM	_	_	_
581	ChIP-seq	ChIP-seq	NNP	_	_	_
582	_	_	NNP	_	_	_
583	Aerobic	Aerobic	NNP	_	_	_
584	_	_	SYM	_	_	_
585	A	a	DT	_	_	_
586	_	_	JJ	_	_	_
587	SET	SET	NNP	_	_	_
588	_	_	SYM	_	_	_
589	WIG.wig	WIG.wig	NNP	_	_	_
590	:	:	:	_	_	_
591	U00096	u00096	NN	_	_	_
592	.2	.2	NN	_	_	_
593	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
594	Sigma70	sigma70	NN	_	_	_
595	_	_	CD	_	_	_
596	IP	IP	NNP	_	_	_
597	_	_	SYM	_	_	_
598	ChIP-seq	ChIP-seq	NNP	_	_	_
599	_	_	SYM	_	_	_
600	Anaerobic	anaerobic	JJ	_	_	_
601	_	_	NN	_	_	_
602	A	a	DT	_	_	_
603	_	_	JJ	_	_	_
604	SET	SET	NNP	_	_	_
605	_	_	SYM	_	_	_
606	WIG.wig	WIG.wig	NNP	_	_	_
607	:	:	:	_	_	_
608	U00096	u00096	NN	_	_	_
609	.2	.2	NN	_	_	_
610	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
611	Sigma70	sigma70	NN	_	_	_
612	LB	lb	NN	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	Sigma70	sigma70	NN	_	_	_
615	LB-1	lb-1	NN	_	_	_
616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
617	Sigma70	sigma70	NN	_	_	_
618	LB-2	lb-2	NN	_	_	_
619	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
620	Sigma70	sigma70	NN	_	_	_
621	LB-3	lb-3	NN	_	_	_
622	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
623	Sigma70	sigma70	NN	_	_	_
624	LP	lp	NN	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	Sigma70	sigma70	NN	_	_	_
627	LP-1	lp-1	NN	_	_	_
628	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
629	Sigma70	sigma70	NN	_	_	_
630	LP-2	lp-2	NN	_	_	_
631	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
632	Sigma70	sigma70	NN	_	_	_
633	LP-3	lp-3	NN	_	_	_
634	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
635	Signal	signal	NN	_	_	_
636	and	and	CC	_	_	_
637	p-values	p-value	NNS	_	_	_
638	for	for	IN	_	_	_
639	each	each	DT	_	_	_
640	genomic	genomic	JJ	_	_	_
641	position	position	NN	_	_	_
642	interrogated	interrogate	VBN	_	_	_
643	.	.	.	_	_	_

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	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	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/MAANOVA	r/maanova	NN	_	_	_
10	microarray	microarray	NN	_	_	_
11	statistical	statistical	JJ	_	_	_
12	package	package	NN	_	_	_
13	,	,	,	_	_	_
14	available	available	JJ	_	_	_
15	at	at	IN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	http://www.jax.org/staff/churchill/labsite/	http://www.jax.org/staff/churchill/labsite/	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resulting	result	VBG	_	_	_
3	variety-by-gene	variety-by-gene	JJ	_	_	_
4	interaction	interaction	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	VG	vg	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	values	value	NNS	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	control	control	NN	_	_	_
12	and	and	CC	_	_	_
13	experimental	experimental	JJ	_	_	_
14	spot	spot	NN	_	_	_
15	intensities	intensity	NNS	_	_	_
16	were	be	VBD	_	_	_
17	combined	combine	VBN	_	_	_
18	with	with	IN	_	_	_
19	the	the	DT	_	_	_
20	residual	residual	JJ	_	_	_
21	noise	noise	NN	_	_	_
22	from	from	IN	_	_	_
23	each	each	DT	_	_	_
24	spot	spot	NN	_	_	_
25	to	to	TO	_	_	_
26	obtain	obtain	VB	_	_	_
27	the	the	DT	_	_	_
28	filtered	filter	VBN	_	_	_
29	and	and	CC	_	_	_
30	adjusted	adjust	VBN	_	_	_
31	expression	expression	NN	_	_	_
32	values	value	NNS	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Cui	cuus	NNS	_	_	_
35	.	.	.	_	_	_

1	et	et	FW	_	_	_
2	.	.	.	_	_	_

1	al	al	NNP	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	.	.	.	_	_	_

1	Duplicate	duplicate	VB	_	_	_
2	expression	expression	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	each	each	DT	_	_	_
6	array	array	NN	_	_	_
7	were	be	VBD	_	_	_
8	combined	combine	VBN	_	_	_
9	,	,	,	_	_	_
10	averaged	average	VBD	_	_	_
11	and	and	CC	_	_	_
12	values	value	NNS	_	_	_
13	from	from	IN	_	_	_
14	MAANOVA	MAANOVA	NNP	_	_	_
15	were	be	VBD	_	_	_
16	subsequently	subsequently	RB	_	_	_
17	subjected	subject	VBN	_	_	_
18	to	to	TO	_	_	_
19	significance	significance	NN	_	_	_
20	analysis	analysis	NN	_	_	_
21	of	of	IN	_	_	_
22	microarray	microarray	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	SAM	sam	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	data	datum	NNS	_	_	_
27	with	with	IN	_	_	_
28	the	the	DT	_	_	_
29	SAM	SAM	NNP	_	_	_
30	package	package	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Tusher	tusher	NN	_	_	_
33	.	.	.	_	_	_

1	et.al	et.al	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	.	.	.	_	_	_

1	Significantly	significantly	RB	_	_	_
2	up	up	IN	_	_	_
3	-	-	:	_	_	_
4	and	and	CC	_	_	_
5	down-regulated	down-regulate	VBD	_	_	_
6	genes	gene	NNS	_	_	_
7	were	be	VBD	_	_	_
8	identified	identify	VBN	_	_	_
9	based	base	VBN	_	_	_
10	on	on	IN	_	_	_
11	a	a	DT	_	_	_
12	1.5	1.5	CD	_	_	_
13	cutoff	cutoff	NN	_	_	_
14	threshold	threshold	NN	_	_	_
15	,	,	,	_	_	_
16	a	a	DT	_	_	_
17	global	global	JJ	_	_	_
18	false	false	JJ	_	_	_
19	discovery	discovery	NN	_	_	_
20	rate	rate	NN	_	_	_
21	lower	lower	JJR	_	_	_
22	than	than	IN	_	_	_
23	5	5	CD	_	_	_
24	%	%	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	p	p	NN	_	_	_
27	<	<	JJR	_	_	_
28	0.05	0.05	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	Six	six	CD	_	_	_
2	arrays	array	NNS	_	_	_
3	representing	represent	VBG	_	_	_
4	a	a	DT	_	_	_
5	total	total	NN	_	_	_
6	of	of	IN	_	_	_
7	12	12	CD	_	_	_
8	replicates	replicate	VBZ	_	_	_
9	were	be	VBD	_	_	_
10	analyzed	analyze	VBN	_	_	_
11	between	between	IN	_	_	_
12	a	a	DT	_	_	_
13	treatment	treatment	NN	_	_	_
14	and	and	CC	_	_	_
15	a	a	DT	_	_	_
16	control	control	NN	_	_	_
17	.	.	.	_	_	_

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	treat	VBN	_	_	_
41	group/average	group/average	NN	_	_	_
42	intensity	intensity	NN	_	_	_
43	in	in	IN	_	_	_
44	control	control	NN	_	_	_
45	group	group	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	the	the	DT	_	_	_
48	`	`	``	_	_	_
49	Avg	avg	NN	_	_	_
50	'	'	''	_	_	_
51	columns	column	NNS	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	.	.	.	_	_	_

1	Transformed	transform	VBN	_	_	_
2	Ln	ln	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	signal	signal	NN	_	_	_
5	intensity	intensity	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	values	value	NNS	_	_	_
8	,	,	,	_	_	_
9	shown	show	VBN	_	_	_
10	in	in	IN	_	_	_
11	columns	column	NNS	_	_	_
12	`	`	``	_	_	_
13	Ln	ln	NN	_	_	_
14	'	'	''	_	_	_
15	,	,	,	_	_	_
16	were	be	VBD	_	_	_
17	used	use	VBN	_	_	_
18	for	for	IN	_	_	_
19	direct	direct	JJ	_	_	_
20	statistical	statistical	JJ	_	_	_
21	comparisons	comparison	NNS	_	_	_
22	of	of	IN	_	_	_
23	expression	expression	NN	_	_	_
24	signals	signal	NNS	_	_	_
25	between	between	IN	_	_	_
26	treated	treated	JJ	_	_	_
27	and	and	CC	_	_	_
28	control	control	JJ	_	_	_
29	groups	group	NNS	_	_	_
30	by	by	IN	_	_	_
31	t-test	t-test	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	columns	column	NNS	_	_	_
34	`	`	``	_	_	_
35	t-test	t-test	NN	_	_	_
36	'	'	''	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	probes	probe	NNS	_	_	_
3	in	in	IN	_	_	_
4	the	the	DT	_	_	_
5	expressed_present_probes.txt	expressed_present_probes.txt	NN	_	_	_
6	are	be	VBP	_	_	_
7	arranged	arrange	VBN	_	_	_
8	in	in	IN	_	_	_
9	descending	descend	VBG	_	_	_
10	order	order	NN	_	_	_
11	from	from	IN	_	_	_
12	the	the	DT	_	_	_
13	highest	highest	JJS	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	lowest	lowest	JJS	_	_	_
17	ratio	ratio	NN	_	_	_
18	of	of	IN	_	_	_
19	gene	gene	NN	_	_	_
20	induction	induction	NN	_	_	_
21	in	in	IN	_	_	_
22	PGRP/control	pgrp/control	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	column	column	NN	_	_	_
25	`	`	``	_	_	_
26	Ratio	ratio	NN	_	_	_
27	'	'	''	_	_	_
28	in	in	IN	_	_	_
29	`	`	``	_	_	_
30	expressed_present_probes.txt	expressed_present_probes.txt	NN	_	_	_
31	'	'	''	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Single	single	JJ	_	_	_
3	colonies	colony	NNS	_	_	_
4	of	of	IN	_	_	_
5	P.	P.	NNP	_	_	_
6	putida	putida	NN	_	_	_
7	strain	strain	NN	_	_	_
8	DOT-T1E	dot-t1e	NN	_	_	_
9	and	and	CC	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	were	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	overnight	overnight	RB	_	_	_
16	in	in	IN	_	_	_
17	Luria	Luria	NNP	_	_	_
18	--	--	:	_	_	_
19	Bertani	Bertani	NNP	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	LB	LB	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	medium	medium	NN	_	_	_
24	at	at	IN	_	_	_
25	30	30	CD	_	_	_
26	°C	°c	NN	_	_	_
27	.	.	.	_	_	_

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/ml	µg/ml	NN	_	_	_
30	kanamycin	kanamycin	NN	_	_	_
31	,	,	,	_	_	_
32	300	300	CD	_	_	_
33	µg/ml	µg/ml	JJ	_	_	_
34	ampicillin	ampicillin	NN	_	_	_
35	,	,	,	_	_	_
36	150	150	CD	_	_	_
37	µg/ml	µg/ml	JJ	_	_	_
38	chloramphenicol	chloramphenicol	NN	_	_	_
39	,	,	,	_	_	_
40	4	4	CD	_	_	_
41	µg/ml	µg/ml	NN	_	_	_
42	tetracycline	tetracycline	NN	_	_	_
43	,	,	,	_	_	_
44	0.5	0.5	CD	_	_	_
45	µg/ml	µg/ml	JJ	_	_	_
46	ciprofloxacin	ciprofloxacin	NN	_	_	_
47	,	,	,	_	_	_
48	300	300	CD	_	_	_
49	µg/ml	µg/ml	NN	_	_	_
50	spectinomycin	spectinomycin	NN	_	_	_
51	,	,	,	_	_	_
52	500	500	CD	_	_	_
53	µg/ml	µg/ml	JJ	_	_	_
54	rifampicin	rifampicin	NN	SUPP	_	_
55	and	and	CC	_	_	_
56	2	2	CD	_	_	_
57	µg/ml	µg/ml	JJ	_	_	_
58	gentamicin	gentamicin	NN	_	_	_
59	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	under	under	IN	_	_	_
6	the	the	DT	_	_	_
7	same	same	JJ	_	_	_
8	conditions	condition	NNS	_	_	_
9	for	for	IN	_	_	_
10	one	one	CD	_	_	_
11	hour	hour	NN	_	_	_
12	more	more	RBR	_	_	_
13	.	.	.	_	_	_

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	8000	8000	CD	_	_	_
8	g	g	NN	_	_	_
9	for	for	IN	_	_	_
10	10	10	CD	_	_	_
11	min	min	NN	_	_	_
12	and	and	CC	_	_	_
13	suspended	suspend	VBN	_	_	_
14	immediately	immediately	RB	_	_	_
15	in	in	IN	_	_	_
16	stop	stop	NN	_	_	_
17	solution	solution	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	95	95	CD	_	_	_
20	%	%	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	v/v	v/v	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	ethanol	ethanol	NN	_	_	_
25	,	,	,	_	_	_
26	5	5	CD	_	_	_
27	%	%	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	v/v	v/v	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	phenol	phenol	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	and	and	CC	_	_	_
34	pelleted	pellete	VBN	_	_	_
35	by	by	IN	_	_	_
36	centrifugation	centrifugation	NN	_	_	_
37	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	that	that	DT	_	_	_
3	,	,	,	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	extracted	extract	VBN	_	_	_
8	with	with	IN	_	_	_
9	Trizol	trizol	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Invitrogen	invitrogen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	Removal	removal	NN	_	_	_
2	of	of	IN	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	carried	carry	VBN	_	_	_
6	out	out	RP	_	_	_
7	by	by	IN	_	_	_
8	treatment	treatment	NN	_	_	_
9	with	with	IN	_	_	_
10	DNase	dnase	NN	_	_	_
11	I	i	CD	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Fermentas	fermentas	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	in	in	IN	_	_	_
16	combination	combination	NN	_	_	_
17	with	with	IN	_	_	_
18	the	the	DT	_	_	_
19	RNase	rnase	NN	_	_	_
20	inhibitor	inhibitor	NN	_	_	_
21	RiboLock	ribolock	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Fermentas	fermentas	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	integrity	integrity	NN	_	_	_
3	and	and	CC	_	_	_
4	quality	quality	NN	_	_	_
5	of	of	IN	_	_	_
6	total	total	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	assessed	assess	VBN	_	_	_
10	with	with	IN	_	_	_
11	an	a	DT	_	_	_
12	Agilent	Agilent	NNP	_	_	_
13	2100	2100	CD	_	_	_
14	Bioanalyzer	Bioanalyzer	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Agilent	Agilent	NNP	_	_	_
17	Technologies	Technologies	NNPS	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Single	single	JJ	_	_	_
3	colonies	colony	NNS	_	_	_
4	were	be	VBD	_	_	_
5	inoculated	inoculate	VBN	_	_	_
6	into	into	IN	_	_	_
7	15x100	15x100	CD	_	_	_
8	mm	mm	NN	_	_	_
9	tubes	tube	NNS	_	_	_
10	containing	contain	VBG	_	_	_
11	4	4	CD	_	_	_
12	ml	ml	NN	_	_	_
13	LB	lb	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	grown	grow	VBN	_	_	_
17	at	at	IN	_	_	_
18	30ºC	30ºc	NN	_	_	_
19	and	and	CC	_	_	_
20	250	250	CD	_	_	_
21	rpm	rpm	NN	_	_	_
22	overnight	overnight	JJ	_	_	_
23	.	.	.	_	_	_

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	single	single	JJ	_	_	_
30	mutant	mutant	NN	_	_	_
31	in	in	IN	_	_	_
32	exopolyphosphatase	exopolyphosphatase	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	PPX	ppx	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	single	single	JJ	_	_	_
38	mutant	mutant	NN	_	_	_
39	in	in	IN	_	_	_
40	polyphosphate	polyphosphate	NN	_	_	_
41	kinase	kinase	NN	_	_	_
42	1	1	CD	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	PPK1	ppk1	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Singleton	Singleton	NNP	_	_	_
48	peaks	peak	NNS	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	standard	standard	JJ	_	_	_
51	deviation	deviation	NN	_	_	_
52	=	=	JJ	_	_	_
53	0	0	CD	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	and	and	CC	_	_	_
56	peaks	peak	VBZ	_	_	_
57	without	without	IN	_	_	_
58	matched	match	VBN	_	_	_
59	peaks	peak	NNS	_	_	_
60	on	on	IN	_	_	_
61	the	the	DT	_	_	_
62	opposing	oppose	VBG	_	_	_
63	strand	strand	NN	_	_	_
64	where	where	WRB	_	_	_
65	discarded	discard	VBN	_	_	_
66	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
67	Size	size	NN	_	_	_
68	filtering	filter	VBG	_	_	_
69	:	:	:	_	_	_
70	discarding	discard	VBG	_	_	_
71	reads	read	VBZ	_	_	_
72	shorter	shorter	JJR	_	_	_
73	than	than	IN	_	_	_
74	12	12	CD	_	_	_
75	nt	nt	NNS	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	TRAPL	trapl	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Size	size	NN	_	_	_
81	filtering	filter	VBG	_	_	_
82	:	:	:	_	_	_
83	discarding	discard	VBG	_	_	_
84	reads	read	VBZ	_	_	_
85	shorter	shorter	JJR	_	_	_
86	than	than	IN	_	_	_
87	12	12	CD	_	_	_
88	nt	nt	NNS	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	via	via	IN	_	_	_
91	READemption	reademption	NN	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Slide	slide	NN	_	_	_
95	10	10	CD	_	_	_
96	_	_	SYM	_	_	_
97	Anaerobic	anaerobic	JJ	_	_	_
98	culture	culture	NN	_	_	_
99	_	_	SYM	_	_	_
100	CORM-3	corm-3	NN	_	_	_
101	_	_	NN	_	_	_
102	biol	biol	NN	_	_	_
103	rep	rep	NN	GEN	_	_
104	1	1	CD	_	_	_
105	_	_	NN	_	_	_
106	Cy3	cy3	NN	_	_	_
107	0	0	CD	_	_	_
108	Cy5	cy5	NN	_	_	_
109	10	10	CD	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	Slide	Slide	NNP	_	_	_
112	10	10	CD	_	_	_
113	_	_	SYM	_	_	_
114	Anaerobic	anaerobic	JJ	_	_	_
115	culture	culture	NN	_	_	_
116	_	_	SYM	_	_	_
117	CORM-3	corm-3	NN	_	_	_
118	_	_	NN	_	_	_
119	biol	biol	NN	_	_	_
120	rep	rep	NN	GEN	_	_
121	1	1	CD	_	_	_
122	_	_	NN	_	_	_
123	Cy3	cy3	NN	_	_	_
124	0	0	CD	_	_	_
125	Cy5	cy5	NN	_	_	_
126	5	5	CD	_	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	Slide	Slide	NNP	_	_	_
129	10	10	CD	_	_	_
130	_	_	SYM	_	_	_
131	Anaerobic	anaerobic	JJ	_	_	_
132	culture	culture	NN	_	_	_
133	_	_	SYM	_	_	_
134	CORM-3	corm-3	NN	_	_	_
135	_	_	NN	_	_	_
136	biol	biol	NN	_	_	_
137	rep	rep	NN	GEN	_	_
138	2	2	CD	_	_	_
139	_	_	CD	_	_	_
140	Cy3	cy3	NN	_	_	_
141	0	0	CD	_	_	_
142	Cy5	cy5	NN	_	_	_
143	10	10	CD	_	_	_
144	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
145	Slide	Slide	NNP	_	_	_
146	10	10	CD	_	_	_
147	_	_	SYM	_	_	_
148	Anaerobic	anaerobic	JJ	_	_	_
149	culture	culture	NN	_	_	_
150	_	_	SYM	_	_	_
151	CORM-3	corm-3	NN	_	_	_
152	_	_	NN	_	_	_
153	biol	biol	NN	_	_	_
154	rep	rep	NN	GEN	_	_
155	2	2	CD	_	_	_
156	_	_	CD	_	_	_
157	Cy3	cy3	NN	_	_	_
158	0	0	CD	_	_	_
159	Cy5	cy5	NN	_	_	_
160	20	20	CD	_	_	_
161	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
162	Slide	Slide	NNP	_	_	_
163	10	10	CD	_	_	_
164	_	_	SYM	_	_	_
165	Anaerobic	anaerobic	JJ	_	_	_
166	culture	culture	NN	_	_	_
167	_	_	SYM	_	_	_
168	CORM-3	corm-3	NN	_	_	_
169	_	_	NN	_	_	_
170	biol	biol	NN	_	_	_
171	rep	rep	NN	GEN	_	_
172	2	2	CD	_	_	_
173	_	_	CD	_	_	_
174	Cy3	cy3	NN	_	_	_
175	0	0	CD	_	_	_
176	Cy5	cy5	NN	_	_	_
177	2.5	2.5	CD	_	_	_
178	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
179	Slide	Slide	NNP	_	_	_
180	10	10	CD	_	_	_
181	_	_	SYM	_	_	_
182	Anaerobic	anaerobic	JJ	_	_	_
183	culture	culture	NN	_	_	_
184	_	_	SYM	_	_	_
185	CORM-3	corm-3	NN	_	_	_
186	_	_	NN	_	_	_
187	biol	biol	NN	_	_	_
188	rep	rep	NN	GEN	_	_
189	2	2	CD	_	_	_
190	_	_	CD	_	_	_
191	Cy3	cy3	NN	_	_	_
192	0	0	CD	_	_	_
193	Cy5	cy5	NN	_	_	_
194	40	40	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	Slide	slide	NN	_	_	_
197	10	10	CD	_	_	_
198	_	_	SYM	_	_	_
199	Anaerobic	anaerobic	JJ	_	_	_
200	culture	culture	NN	_	_	_
201	_	_	SYM	_	_	_
202	CORM-3	corm-3	NN	_	_	_
203	_	_	NN	_	_	_
204	biol	biol	NN	_	_	_
205	rep	rep	NN	GEN	_	_
206	2	2	CD	_	_	_
207	_	_	CD	_	_	_
208	Cy3	cy3	NN	_	_	_
209	0	0	CD	_	_	_
210	Cy5	cy5	NN	_	_	_
211	5	5	CD	_	_	_
212	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
213	Slide	Slide	NNP	_	_	_
214	10	10	CD	_	_	_
215	_	_	SYM	_	_	_
216	Anaerobic	anaerobic	JJ	_	_	_
217	culture	culture	NN	_	_	_
218	_	_	SYM	_	_	_
219	CORM-3	corm-3	NN	_	_	_
220	_	_	NN	_	_	_
221	biol	biol	NN	_	_	_
222	rep	rep	NN	GEN	_	_
223	2	2	CD	_	_	_
224	_	_	CD	_	_	_
225	Cy3	cy3	NN	_	_	_
226	0	0	CD	_	_	_
227	Cy5	cy5	NN	_	_	_
228	80	80	CD	_	_	_
229	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
230	Slide	Slide	NNP	_	_	_
231	11	11	CD	_	_	_
232	_	_	SYM	_	_	_
233	Anaerobic	anaerobic	JJ	_	_	_
234	culture	culture	NN	_	_	_
235	_	_	SYM	_	_	_
236	CORM-3	corm-3	NN	_	_	_
237	_	_	NN	_	_	_
238	biol	biol	NN	_	_	_
239	rep	rep	NN	GEN	_	_
240	1	1	CD	_	_	_
241	_	_	CD	_	_	_
242	Cy3	cy3	NN	_	_	_
243	20	20	CD	_	_	_
244	Cy5	cy5	NN	_	_	_
245	0	0	CD	_	_	_
246	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
247	Slide	Slide	NNP	_	_	_
248	11	11	CD	_	_	_
249	_	_	SYM	_	_	_
250	Anaerobic	anaerobic	JJ	_	_	_
251	culture	culture	NN	_	_	_
252	_	_	SYM	_	_	_
253	CORM-3	corm-3	NN	_	_	_
254	_	_	NN	_	_	_
255	biol	biol	NN	_	_	_
256	rep	rep	NN	GEN	_	_
257	1	1	CD	_	_	_
258	_	_	CD	_	_	_
259	Cy3	cy3	NN	_	_	_
260	5	5	CD	_	_	_
261	Cy5	cy5	NN	_	_	_
262	0	0	CD	_	_	_
263	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
264	Slide	Slide	NNP	_	_	_
265	11	11	CD	_	_	_
266	_	_	SYM	_	_	_
267	Anaerobic	anaerobic	JJ	_	_	_
268	culture	culture	NN	_	_	_
269	_	_	SYM	_	_	_
270	CORM-3	corm-3	NN	_	_	_
271	_	_	NN	_	_	_
272	biol	biol	NN	_	_	_
273	rep	rep	NN	GEN	_	_
274	2	2	CD	_	_	_
275	_	_	CD	_	_	_
276	Cy3	cy3	NN	_	_	_
277	10	10	CD	_	_	_
278	Cy5	cy5	NN	_	_	_
279	0	0	CD	_	_	_
280	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
281	Slide	Slide	NNP	_	_	_
282	11	11	CD	_	_	_
283	_	_	SYM	_	_	_
284	Anaerobic	anaerobic	JJ	_	_	_
285	culture	culture	NN	_	_	_
286	_	_	SYM	_	_	_
287	CORM-3	corm-3	NN	_	_	_
288	_	_	NN	_	_	_
289	biol	biol	NN	_	_	_
290	rep	rep	NN	GEN	_	_
291	2	2	CD	_	_	_
292	_	_	CD	_	_	_
293	Cy3	cy3	NN	_	_	_
294	20	20	CD	_	_	_
295	Cy5	cy5	NN	_	_	_
296	0	0	CD	_	_	_
297	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
298	Slide	Slide	NNP	_	_	_
299	11	11	CD	_	_	_
300	_	_	SYM	_	_	_
301	Anaerobic	anaerobic	JJ	_	_	_
302	culture	culture	NN	_	_	_
303	_	_	SYM	_	_	_
304	CORM-3	corm-3	NN	_	_	_
305	_	_	NN	_	_	_
306	biol	biol	NN	_	_	_
307	rep	rep	NN	GEN	_	_
308	2	2	CD	_	_	_
309	_	_	CD	_	_	_
310	Cy3	cy3	NN	_	_	_
311	2.5	2.5	CD	_	_	_
312	Cy5	cy5	NN	_	_	_
313	0	0	CD	_	_	_
314	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
315	Slide	Slide	NNP	_	_	_
316	11	11	CD	_	_	_
317	_	_	SYM	_	_	_
318	Anaerobic	anaerobic	JJ	_	_	_
319	culture	culture	NN	_	_	_
320	_	_	SYM	_	_	_
321	CORM-3	corm-3	NN	_	_	_
322	_	_	NN	_	_	_
323	biol	biol	NN	_	_	_
324	rep	rep	NN	GEN	_	_
325	2	2	CD	_	_	_
326	_	_	CD	_	_	_
327	Cy3	cy3	NN	_	_	_
328	40	40	CD	_	_	_
329	Cy5	cy5	NN	_	_	_
330	0	0	CD	_	_	_
331	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
332	Slide	Slide	NNP	_	_	_
333	11	11	CD	_	_	_
334	_	_	SYM	_	_	_
335	Anaerobic	anaerobic	JJ	_	_	_
336	culture	culture	NN	_	_	_
337	_	_	SYM	_	_	_
338	CORM-3	corm-3	NN	_	_	_
339	_	_	NN	_	_	_
340	biol	biol	NN	_	_	_
341	rep	rep	NN	GEN	_	_
342	2	2	CD	_	_	_
343	_	_	CD	_	_	_
344	Cy3	cy3	NN	_	_	_
345	5	5	CD	_	_	_
346	Cy5	cy5	NN	_	_	_
347	0	0	CD	_	_	_
348	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
349	Slide	Slide	NNP	_	_	_
350	11	11	CD	_	_	_
351	_	_	SYM	_	_	_
352	Anaerobic	anaerobic	JJ	_	_	_
353	culture	culture	NN	_	_	_
354	_	_	SYM	_	_	_
355	CORM-3	corm-3	NN	_	_	_
356	_	_	NN	_	_	_
357	biol	biol	NN	_	_	_
358	rep	rep	NN	GEN	_	_
359	2	2	CD	_	_	_
360	_	_	CD	_	_	_
361	Cy3	cy3	NN	_	_	_
362	80	80	CD	_	_	_
363	Cy5	cy5	NN	_	_	_
364	0	0	CD	_	_	_
365	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
366	Slide	Slide	NNP	_	_	_
367	12	12	CD	_	_	_
368	_	_	SYM	_	_	_
369	Anaerobic	anaerobic	JJ	_	_	_
370	culture	culture	NN	_	_	_
371	_	_	SYM	_	_	_
372	CORM-3	corm-3	NN	_	_	_
373	_	_	NN	_	_	_
374	biol	biol	NN	_	_	_
375	rep	rep	NN	GEN	_	_
376	1	1	CD	_	_	_
377	_	_	NN	_	_	_
378	Cy3	cy3	NN	_	_	_
379	0	0	CD	_	_	_
380	Cy5	cy5	NN	_	_	_
381	20	20	CD	_	_	_
382	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
383	Slide	Slide	NNP	_	_	_
384	12	12	CD	_	_	_
385	_	_	SYM	_	_	_
386	Anaerobic	anaerobic	JJ	_	_	_
387	culture	culture	NN	_	_	_
388	_	_	SYM	_	_	_
389	CORM-3	corm-3	NN	_	_	_
390	_	_	NN	_	_	_
391	biol	biol	NN	_	_	_
392	rep	rep	NN	GEN	_	_
393	1	1	CD	_	_	_
394	_	_	NN	_	_	_
395	Cy3	cy3	NN	_	_	_
396	0	0	CD	_	_	_
397	Cy5	cy5	NN	_	_	_
398	2.5	2.5	CD	_	_	_
399	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
400	Slide	Slide	NNP	_	_	_
401	12	12	CD	_	_	_
402	_	_	SYM	_	_	_
403	Anaerobic	anaerobic	JJ	_	_	_
404	culture	culture	NN	_	_	_
405	_	_	SYM	_	_	_
406	CORM-3	corm-3	NN	_	_	_
407	_	_	NN	_	_	_
408	biol	biol	NN	_	_	_
409	rep	rep	NN	GEN	_	_
410	1	1	CD	_	_	_
411	_	_	NN	_	_	_
412	Cy3	cy3	NN	_	_	_
413	0	0	CD	_	_	_
414	Cy5	cy5	NN	_	_	_
415	40	40	CD	_	_	_
416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
417	Slide	slide	NN	_	_	_
418	12	12	CD	_	_	_
419	_	_	SYM	_	_	_
420	Anaerobic	anaerobic	JJ	_	_	_
421	culture	culture	NN	_	_	_
422	_	_	SYM	_	_	_
423	CORM-3	corm-3	NN	_	_	_
424	_	_	NN	_	_	_
425	biol	biol	NN	_	_	_
426	rep	rep	NN	GEN	_	_
427	1	1	CD	_	_	_
428	_	_	NN	_	_	_
429	Cy3	cy3	NN	_	_	_
430	0	0	CD	_	_	_
431	Cy5	cy5	NN	_	_	_
432	80	80	CD	_	_	_
433	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
434	Slide	Slide	NNP	_	_	_
435	12	12	CD	_	_	_
436	_	_	SYM	_	_	_
437	Anaerobic	anaerobic	JJ	_	_	_
438	culture	culture	NN	_	_	_
439	_	_	SYM	_	_	_
440	CORM-3	corm-3	NN	_	_	_
441	_	_	NN	_	_	_
442	biol	biol	NN	_	_	_
443	rep	rep	NN	GEN	_	_
444	1	1	CD	_	_	_
445	_	_	CD	_	_	_
446	Cy3	cy3	NN	_	_	_
447	10	10	CD	_	_	_
448	Cy5	cy5	NN	_	_	_
449	0	0	CD	_	_	_
450	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
451	Slide	Slide	NNP	_	_	_
452	12	12	CD	_	_	_
453	_	_	SYM	_	_	_
454	Anaerobic	anaerobic	JJ	_	_	_
455	culture	culture	NN	_	_	_
456	_	_	SYM	_	_	_
457	CORM-3	corm-3	NN	_	_	_
458	_	_	NN	_	_	_
459	biol	biol	NN	_	_	_
460	rep	rep	NN	GEN	_	_
461	1	1	CD	_	_	_
462	_	_	CD	_	_	_
463	Cy3	cy3	NN	_	_	_
464	2.5	2.5	CD	_	_	_
465	Cy5	cy5	NN	_	_	_
466	0	0	CD	_	_	_
467	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
468	Slide	Slide	NNP	_	_	_
469	12	12	CD	_	_	_
470	_	_	SYM	_	_	_
471	Anaerobic	anaerobic	JJ	_	_	_
472	culture	culture	NN	_	_	_
473	_	_	SYM	_	_	_
474	CORM-3	corm-3	NN	_	_	_
475	_	_	NN	_	_	_
476	biol	biol	NN	_	_	_
477	rep	rep	NN	GEN	_	_
478	1	1	CD	_	_	_
479	_	_	CD	_	_	_
480	Cy3	cy3	NN	_	_	_
481	40	40	CD	_	_	_
482	Cy5	cy5	NN	_	_	_
483	0	0	CD	_	_	_
484	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
485	Slide	Slide	NNP	_	_	_
486	12	12	CD	_	_	_
487	_	_	SYM	_	_	_
488	Anaerobic	anaerobic	JJ	_	_	_
489	culture	culture	NN	_	_	_
490	_	_	SYM	_	_	_
491	CORM-3	corm-3	NN	_	_	_
492	_	_	NN	_	_	_
493	biol	biol	NN	_	_	_
494	rep	rep	NN	GEN	_	_
495	1	1	CD	_	_	_
496	_	_	CD	_	_	_
497	Cy3	cy3	NN	_	_	_
498	80	80	CD	_	_	_
499	Cy5	cy5	NN	_	_	_
500	0	0	CD	_	_	_
501	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
502	Slide	Slide	NNP	_	_	_
503	13	13	CD	_	_	_
504	_	_	CD	_	_	_
505	Wild	Wild	NNP	_	_	_
506	type	type	NN	_	_	_
507	_	_	CD	_	_	_
508	CORM-3	corm-3	NN	_	_	_
509	_	_	NN	_	_	_
510	biol	biol	NN	_	_	_
511	rep	rep	NN	GEN	_	_
512	1	1	CD	_	_	_
513	_	_	NN	_	_	_
514	Cy3	cy3	NN	_	_	_
515	0	0	CD	_	_	_
516	Cy5	cy5	NN	_	_	_
517	120	120	CD	_	_	_
518	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
519	Slide	Slide	NNP	_	_	_
520	13	13	CD	_	_	_
521	_	_	CD	_	_	_
522	Wild	Wild	NNP	_	_	_
523	type	type	NN	_	_	_
524	_	_	CD	_	_	_
525	CORM-3	corm-3	NN	_	_	_
526	_	_	NN	_	_	_
527	biol	biol	NN	_	_	_
528	rep	rep	NN	GEN	_	_
529	1	1	CD	_	_	_
530	_	_	CD	_	_	_
531	Cy3	cy3	NN	_	_	_
532	10	10	CD	_	_	_
533	Cy5	cy5	NN	_	_	_
534	0	0	CD	_	_	_
535	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
536	Slide	Slide	NNP	_	_	_
537	13	13	CD	_	_	_
538	_	_	CD	_	_	_
539	Wild	Wild	NNP	_	_	_
540	type	type	NN	_	_	_
541	_	_	CD	_	_	_
542	CORM-3	corm-3	NN	_	_	_
543	_	_	NN	_	_	_
544	biol	biol	NN	_	_	_
545	rep	rep	NN	GEN	_	_
546	1	1	CD	_	_	_
547	_	_	CD	_	_	_
548	Cy3	cy3	NN	_	_	_
549	120	120	CD	_	_	_
550	Cy5	cy5	NN	_	_	_
551	0	0	CD	_	_	_
552	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
553	Slide	Slide	NNP	_	_	_
554	13	13	CD	_	_	_
555	_	_	CD	_	_	_
556	Wild	Wild	NNP	_	_	_
557	type	type	NN	_	_	_
558	_	_	CD	_	_	_
559	CORM-3	corm-3	NN	_	_	_
560	_	_	NN	_	_	_
561	biol	biol	NN	_	_	_
562	rep	rep	NN	GEN	_	_
563	1	1	CD	_	_	_
564	_	_	CD	_	_	_
565	Cy3	cy3	NN	_	_	_
566	20	20	CD	_	_	_
567	Cy5	cy5	NN	_	_	_
568	0	0	CD	_	_	_
569	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
570	Slide	Slide	NNP	_	_	_
571	13	13	CD	_	_	_
572	_	_	CD	_	_	_
573	Wild	Wild	NNP	_	_	_
574	type	type	NN	_	_	_
575	_	_	CD	_	_	_
576	CORM-3	corm-3	NN	_	_	_
577	_	_	NN	_	_	_
578	biol	biol	NN	_	_	_
579	rep	rep	NN	GEN	_	_
580	1	1	CD	_	_	_
581	_	_	CD	_	_	_
582	Cy3	cy3	NN	_	_	_
583	40	40	CD	_	_	_
584	Cy5	cy5	NN	_	_	_
585	0	0	CD	_	_	_
586	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
587	Slide	Slide	NNP	_	_	_
588	13	13	CD	_	_	_
589	_	_	CD	_	_	_
590	Wild	Wild	NNP	_	_	_
591	type	type	NN	_	_	_
592	_	_	CD	_	_	_
593	CORM-3	corm-3	NN	_	_	_
594	_	_	NN	_	_	_
595	biol	biol	NN	_	_	_
596	rep	rep	NN	GEN	_	_
597	1	1	CD	_	_	_
598	_	_	CD	_	_	_
599	Cy3	cy3	NN	_	_	_
600	60	60	CD	_	_	_
601	Cy5	cy5	NN	_	_	_
602	0	0	CD	_	_	_
603	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
604	Slide	Slide	NNP	_	_	_
605	13	13	CD	_	_	_
606	_	_	CD	_	_	_
607	Wild	Wild	NNP	_	_	_
608	type	type	NN	_	_	_
609	_	_	CD	_	_	_
610	CORM-3	corm-3	NN	_	_	_
611	_	_	NN	_	_	_
612	biol	biol	NN	_	_	_
613	rep	rep	NN	GEN	_	_
614	2	2	CD	_	_	_
615	_	_	CD	_	_	_
616	Cy3	cy3	NN	_	_	_
617	0	0	CD	_	_	_
618	Cy5	cy5	NN	_	_	_
619	10	10	CD	_	_	_
620	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
621	Slide	Slide	NNP	_	_	_
622	13	13	CD	_	_	_
623	_	_	CD	_	_	_
624	Wild	Wild	NNP	_	_	_
625	type	type	NN	_	_	_
626	_	_	CD	_	_	_
627	CORM-3	corm-3	NN	_	_	_
628	_	_	NN	_	_	_
629	biol	biol	NN	_	_	_
630	rep	rep	NN	GEN	_	_
631	2	2	CD	_	_	_
632	_	_	CD	_	_	_
633	Cy3	cy3	NN	_	_	_
634	0	0	CD	_	_	_
635	Cy5	cy5	NN	_	_	_
636	20	20	CD	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
638	Slide	slide	NN	_	_	_
639	14	14	CD	_	_	_
640	_	_	CD	_	_	_
641	Wild	Wild	NNP	_	_	_
642	type	type	NN	_	_	_
643	_	_	CD	_	_	_
644	CORM-3	corm-3	NN	_	_	_
645	_	_	NN	_	_	_
646	biol	biol	NN	_	_	_
647	rep	rep	NN	GEN	_	_
648	2	2	CD	_	_	_
649	_	_	CD	_	_	_
650	Cy3	cy3	NN	_	_	_
651	0	0	CD	_	_	_
652	Cy5	cy5	NN	_	_	_
653	120	120	CD	_	_	_
654	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
655	Slide	Slide	NNP	_	_	_
656	14	14	CD	_	_	_
657	_	_	CD	_	_	_
658	Wild	Wild	NNP	_	_	_
659	type	type	NN	_	_	_
660	_	_	CD	_	_	_
661	CORM-3	corm-3	NN	_	_	_
662	_	_	NN	_	_	_
663	biol	biol	NN	_	_	_
664	rep	rep	NN	GEN	_	_
665	2	2	CD	_	_	_
666	_	_	CD	_	_	_
667	Cy3	cy3	NN	_	_	_
668	0	0	CD	_	_	_
669	Cy5	cy5	NN	_	_	_
670	40	40	CD	_	_	_
671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
672	Slide	slide	NN	_	_	_
673	14	14	CD	_	_	_
674	_	_	CD	_	_	_
675	Wild	Wild	NNP	_	_	_
676	type	type	NN	_	_	_
677	_	_	CD	_	_	_
678	CORM-3	corm-3	NN	_	_	_
679	_	_	NN	_	_	_
680	biol	biol	NN	_	_	_
681	rep	rep	NN	GEN	_	_
682	2	2	CD	_	_	_
683	_	_	CD	_	_	_
684	Cy3	cy3	NN	_	_	_
685	0	0	CD	_	_	_
686	Cy5	cy5	NN	_	_	_
687	60	60	CD	_	_	_
688	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
689	Slide	Slide	NNP	_	_	_
690	14	14	CD	_	_	_
691	_	_	CD	_	_	_
692	Wild	Wild	NNP	_	_	_
693	type	type	NN	_	_	_
694	_	_	CD	_	_	_
695	CORM-3	corm-3	NN	_	_	_
696	_	_	NN	_	_	_
697	biol	biol	NN	_	_	_
698	rep	rep	NN	GEN	_	_
699	2	2	CD	_	_	_
700	_	_	CD	_	_	_
701	Cy3	cy3	NN	_	_	_
702	10	10	CD	_	_	_
703	Cy5	cy5	NN	_	_	_
704	0	0	CD	_	_	_
705	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
706	Slide	Slide	NNP	_	_	_
707	14	14	CD	_	_	_
708	_	_	CD	_	_	_
709	Wild	Wild	NNP	_	_	_
710	type	type	NN	_	_	_
711	_	_	CD	_	_	_
712	CORM-3	corm-3	NN	_	_	_
713	_	_	NN	_	_	_
714	biol	biol	NN	_	_	_
715	rep	rep	NN	GEN	_	_
716	2	2	CD	_	_	_
717	_	_	SYM	_	_	_
718	Cy3	cy3	NN	_	_	_
719	120	120	CD	_	_	_
720	Cy5	cy5	NN	_	_	_
721	0	0	CD	_	_	_
722	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
723	Slide	Slide	NNP	_	_	_
724	14	14	CD	_	_	_
725	_	_	CD	_	_	_
726	Wild	Wild	NNP	_	_	_
727	type	type	NN	_	_	_
728	_	_	CD	_	_	_
729	CORM-3	corm-3	NN	_	_	_
730	_	_	NN	_	_	_
731	biol	biol	NN	_	_	_
732	rep	rep	NN	GEN	_	_
733	2	2	CD	_	_	_
734	_	_	CD	_	_	_
735	Cy3	cy3	NN	_	_	_
736	20	20	CD	_	_	_
737	Cy5	cy5	NN	_	_	_
738	0	0	CD	_	_	_
739	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
740	Slide	Slide	NNP	_	_	_
741	14	14	CD	_	_	_
742	_	_	CD	_	_	_
743	Wild	Wild	NNP	_	_	_
744	type	type	NN	_	_	_
745	_	_	CD	_	_	_
746	CORM-3	corm-3	NN	_	_	_
747	_	_	NN	_	_	_
748	biol	biol	NN	_	_	_
749	rep	rep	NN	GEN	_	_
750	2	2	CD	_	_	_
751	_	_	CD	_	_	_
752	Cy3	cy3	NN	_	_	_
753	40	40	CD	_	_	_
754	Cy5	cy5	NN	_	_	_
755	0	0	CD	_	_	_
756	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
757	Slide	Slide	NNP	_	_	_
758	14	14	CD	_	_	_
759	_	_	CD	_	_	_
760	Wild	Wild	NNP	_	_	_
761	type	type	NN	_	_	_
762	_	_	CD	_	_	_
763	CORM-3	corm-3	NN	_	_	_
764	_	_	NN	_	_	_
765	biol	biol	NN	_	_	_
766	rep	rep	NN	GEN	_	_
767	2	2	CD	_	_	_
768	_	_	CD	_	_	_
769	Cy3	cy3	NN	_	_	_
770	60	60	CD	_	_	_
771	Cy5	cy5	NN	_	_	_
772	0	0	CD	_	_	_
773	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
774	Slide	Slide	NNP	_	_	_
775	15	15	CD	_	_	_
776	_	_	SYM	_	_	_
777	hemA	hema	NN	GEN	_	_
778	_	_	CD	_	_	_
779	CORM-3	corm-3	NN	_	_	_
780	_	_	NN	_	_	_
781	biol	biol	NN	_	_	_
782	rep	rep	NN	GEN	_	_
783	2	2	CD	_	_	_
784	_	_	SYM	_	_	_
785	Cy3	cy3	NN	_	_	_
786	120	120	CD	_	_	_
787	Cy5	cy5	NN	_	_	_
788	0	0	CD	_	_	_
789	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
790	Slide	Slide	NNP	_	_	_
791	15	15	CD	_	_	_
792	_	_	SYM	_	_	_
793	hemA	hema	NN	GEN	_	_
794	_	_	CD	_	_	_
795	CORM-3	corm-3	NN	_	_	_
796	_	_	NN	_	_	_
797	biol	biol	NN	_	_	_
798	rep	rep	NN	GEN	_	_
799	2	2	CD	_	_	_
800	_	_	CD	_	_	_
801	Cy3	cy3	NN	_	_	_
802	20	20	CD	_	_	_
803	Cy5	cy5	NN	_	_	_
804	0	0	CD	_	_	_
805	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
806	Slide	Slide	NNP	_	_	_
807	15	15	CD	_	_	_
808	_	_	SYM	_	_	_
809	hemA	hema	NN	GEN	_	_
810	_	_	CD	_	_	_
811	CORM-3	corm-3	NN	_	_	_
812	_	_	NN	_	_	_
813	biol	biol	NN	_	_	_
814	rep	rep	NN	GEN	_	_
815	2	2	CD	_	_	_
816	_	_	CD	_	_	_
817	Cy3	cy3	NN	_	_	_
818	40	40	CD	_	_	_
819	Cy5	cy5	NN	_	_	_
820	0	0	CD	_	_	_
821	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
822	Slide	Slide	NNP	_	_	_
823	15	15	CD	_	_	_
824	_	_	SYM	_	_	_
825	hemA	hema	NN	GEN	_	_
826	_	_	CD	_	_	_
827	CORM-3	corm-3	NN	_	_	_
828	_	_	NN	_	_	_
829	biol	biol	NN	_	_	_
830	rep	rep	NN	GEN	_	_
831	2	2	CD	_	_	_
832	_	_	CD	_	_	_
833	Cy3	cy3	NN	_	_	_
834	60	60	CD	_	_	_
835	Cy5	cy5	NN	_	_	_
836	0	0	CD	_	_	_
837	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
838	Slide	Slide	NNP	_	_	_
839	15	15	CD	_	_	_
840	_	_	CD	_	_	_
841	Wild	Wild	NNP	_	_	_
842	type	type	NN	_	_	_
843	_	_	CD	_	_	_
844	CORM-3	corm-3	NN	_	_	_
845	_	_	NN	_	_	_
846	biol	biol	NN	_	_	_
847	rep	rep	NN	GEN	_	_
848	1	1	CD	_	_	_
849	_	_	NN	_	_	_
850	Cy3	cy3	NN	_	_	_
851	0	0	CD	_	_	_
852	Cy5	cy5	NN	_	_	_
853	10	10	CD	_	_	_
854	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
855	Slide	Slide	NNP	_	_	_
856	15	15	CD	_	_	_
857	_	_	CD	_	_	_
858	Wild	Wild	NNP	_	_	_
859	type	type	NN	_	_	_
860	_	_	CD	_	_	_
861	CORM-3	corm-3	NN	_	_	_
862	_	_	NN	_	_	_
863	biol	biol	NN	_	_	_
864	rep	rep	NN	GEN	_	_
865	1	1	CD	_	_	_
866	_	_	NN	_	_	_
867	Cy3	cy3	NN	_	_	_
868	0	0	CD	_	_	_
869	Cy5	cy5	NN	_	_	_
870	20	20	CD	_	_	_
871	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
872	Slide	Slide	NNP	_	_	_
873	15	15	CD	_	_	_
874	_	_	CD	_	_	_
875	Wild	Wild	NNP	_	_	_
876	type	type	NN	_	_	_
877	_	_	CD	_	_	_
878	CORM-3	corm-3	NN	_	_	_
879	_	_	NN	_	_	_
880	biol	biol	NN	_	_	_
881	rep	rep	NN	GEN	_	_
882	1	1	CD	_	_	_
883	_	_	NN	_	_	_
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	15	15	CD	_	_	_
891	_	_	CD	_	_	_
892	Wild	Wild	NNP	_	_	_
893	type	type	NN	_	_	_
894	_	_	CD	_	_	_
895	CORM-3	corm-3	NN	_	_	_
896	_	_	NN	_	_	_
897	biol	biol	NN	_	_	_
898	rep	rep	NN	GEN	_	_
899	1	1	CD	_	_	_
900	_	_	NN	_	_	_
901	Cy3	cy3	NN	_	_	_
902	0	0	CD	_	_	_
903	Cy5	cy5	NN	_	_	_
904	60	60	CD	_	_	_
905	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
906	Slide	slide	NN	_	_	_
907	16	16	CD	_	_	_
908	_	_	NN	_	_	_
909	hemA	hema	NN	GEN	_	_
910	_	_	CD	_	_	_
911	CORM-3	corm-3	NN	_	_	_
912	_	_	NN	_	_	_
913	biol	biol	NN	_	_	_
914	rep	rep	NN	GEN	_	_
915	1	1	CD	_	_	_
916	_	_	CD	_	_	_
917	Cy3	cy3	NN	_	_	_
918	120	120	CD	_	_	_
919	Cy5	cy5	NN	_	_	_
920	0	0	CD	_	_	_
921	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
922	Slide	Slide	NNP	_	_	_
923	16	16	CD	_	_	_
924	_	_	SYM	_	_	_
925	hemA	hema	NN	GEN	_	_
926	_	_	CD	_	_	_
927	CORM-3	corm-3	NN	_	_	_
928	_	_	NN	_	_	_
929	biol	biol	NN	_	_	_
930	rep	rep	NN	GEN	_	_
931	1	1	CD	_	_	_
932	_	_	CD	_	_	_
933	Cy3	cy3	NN	_	_	_
934	60	60	CD	_	_	_
935	Cy5	cy5	NN	_	_	_
936	0	0	CD	_	_	_
937	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
938	Slide	Slide	NNP	_	_	_
939	16	16	CD	_	_	_
940	_	_	SYM	_	_	_
941	hemA	hema	NN	GEN	_	_
942	_	_	CD	_	_	_
943	CORM-3	corm-3	NN	_	_	_
944	_	_	NN	_	_	_
945	biol	biol	NN	_	_	_
946	rep	rep	NN	GEN	_	_
947	2	2	CD	_	_	_
948	_	_	CD	_	_	_
949	Cy3	cy3	NN	_	_	_
950	0	0	CD	_	_	_
951	Cy5	cy5	NN	_	_	_
952	10	10	CD	_	_	_
953	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
954	Slide	slide	NN	_	_	_
955	16	16	CD	_	_	_
956	_	_	NN	_	_	_
957	hemA	hema	NN	GEN	_	_
958	_	_	CD	_	_	_
959	CORM-3	corm-3	NN	_	_	_
960	_	_	NN	_	_	_
961	biol	biol	NN	_	_	_
962	rep	rep	NN	GEN	_	_
963	2	2	CD	_	_	_
964	_	_	CD	_	_	_
965	Cy3	cy3	NN	_	_	_
966	0	0	CD	_	_	_
967	Cy5	cy5	NN	_	_	_
968	120	120	CD	_	_	_
969	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
970	Slide	slide	NN	_	_	_
971	16	16	CD	_	_	_
972	_	_	NN	_	_	_
973	hemA	hema	NN	GEN	_	_
974	_	_	CD	_	_	_
975	CORM-3	corm-3	NN	_	_	_
976	_	_	NN	_	_	_
977	biol	biol	NN	_	_	_
978	rep	rep	NN	GEN	_	_
979	2	2	CD	_	_	_
980	_	_	CD	_	_	_
981	Cy3	cy3	NN	_	_	_
982	0	0	CD	_	_	_
983	Cy5	cy5	NN	_	_	_
984	20	20	CD	_	_	_
985	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
986	Slide	slide	NN	_	_	_
987	16	16	CD	_	_	_
988	_	_	NN	_	_	_
989	hemA	hema	NN	GEN	_	_
990	_	_	CD	_	_	_
991	CORM-3	corm-3	NN	_	_	_
992	_	_	NN	_	_	_
993	biol	biol	NN	_	_	_
994	rep	rep	NN	GEN	_	_
995	2	2	CD	_	_	_
996	_	_	CD	_	_	_
997	Cy3	cy3	NN	_	_	_
998	0	0	CD	_	_	_
999	Cy5	cy5	NN	_	_	_
1000	40	40	CD	_	_	_
1001	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1002	Slide	slide	NN	_	_	_
1003	16	16	CD	_	_	_
1004	_	_	NN	_	_	_
1005	hemA	hema	NN	GEN	_	_
1006	_	_	CD	_	_	_
1007	CORM-3	corm-3	NN	_	_	_
1008	_	_	NN	_	_	_
1009	biol	biol	NN	_	_	_
1010	rep	rep	NN	GEN	_	_
1011	2	2	CD	_	_	_
1012	_	_	CD	_	_	_
1013	Cy3	cy3	NN	_	_	_
1014	0	0	CD	_	_	_
1015	Cy5	cy5	NN	_	_	_
1016	60	60	CD	_	_	_
1017	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1018	Slide	slide	NN	_	_	_
1019	16	16	CD	_	_	_
1020	_	_	NN	_	_	_
1021	hemA	hema	NN	GEN	_	_
1022	_	_	CD	_	_	_
1023	CORM-3	corm-3	NN	_	_	_
1024	_	_	NN	_	_	_
1025	biol	biol	NN	_	_	_
1026	rep	rep	NN	GEN	_	_
1027	2	2	CD	_	_	_
1028	_	_	CD	_	_	_
1029	Cy3	cy3	NN	_	_	_
1030	10	10	CD	_	_	_
1031	Cy5	cy5	NN	_	_	_
1032	0	0	CD	_	_	_
1033	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1034	Slide	Slide	NNP	_	_	_
1035	17	17	CD	_	_	_
1036	_	_	SYM	_	_	_
1037	hemA	hema	NN	GEN	_	_
1038	_	_	CD	_	_	_
1039	CORM-3	corm-3	NN	_	_	_
1040	_	_	NN	_	_	_
1041	biol	biol	NN	_	_	_
1042	rep	rep	NN	GEN	_	_
1043	1	1	CD	_	_	_
1044	_	_	NN	_	_	_
1045	Cy3	cy3	NN	_	_	_
1046	0	0	CD	_	_	_
1047	Cy5	cy5	NN	_	_	_
1048	10	10	CD	_	_	_
1049	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1050	Slide	slide	NN	_	_	_
1051	17	17	CD	_	_	_
1052	_	_	NN	_	_	_
1053	hemA	hema	NN	GEN	_	_
1054	_	_	CD	_	_	_
1055	CORM-3	corm-3	NN	_	_	_
1056	_	_	NN	_	_	_
1057	biol	biol	NN	_	_	_
1058	rep	rep	NN	GEN	_	_
1059	1	1	CD	_	_	_
1060	_	_	NN	_	_	_
1061	Cy3	cy3	NN	_	_	_
1062	0	0	CD	_	_	_
1063	Cy5	cy5	NN	_	_	_
1064	120	120	CD	_	_	_
1065	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1066	Slide	slide	NN	_	_	_
1067	17	17	CD	_	_	_
1068	_	_	NN	_	_	_
1069	hemA	hema	NN	GEN	_	_
1070	_	_	CD	_	_	_
1071	CORM-3	corm-3	NN	_	_	_
1072	_	_	NN	_	_	_
1073	biol	biol	NN	_	_	_
1074	rep	rep	NN	GEN	_	_
1075	1	1	CD	_	_	_
1076	_	_	NN	_	_	_
1077	Cy3	cy3	NN	_	_	_
1078	0	0	CD	_	_	_
1079	Cy5	cy5	NN	_	_	_
1080	20	20	CD	_	_	_
1081	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1082	Slide	slide	NN	_	_	_
1083	17	17	CD	_	_	_
1084	_	_	NN	_	_	_
1085	hemA	hema	NN	GEN	_	_
1086	_	_	CD	_	_	_
1087	CORM-3	corm-3	NN	_	_	_
1088	_	_	NN	_	_	_
1089	biol	biol	NN	_	_	_
1090	rep	rep	NN	GEN	_	_
1091	1	1	CD	_	_	_
1092	_	_	NN	_	_	_
1093	Cy3	cy3	NN	_	_	_
1094	0	0	CD	_	_	_
1095	Cy5	cy5	NN	_	_	_
1096	40	40	CD	_	_	_
1097	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1098	Slide	slide	NN	_	_	_
1099	17	17	CD	_	_	_
1100	_	_	NN	_	_	_
1101	hemA	hema	NN	GEN	_	_
1102	_	_	CD	_	_	_
1103	CORM-3	corm-3	NN	_	_	_
1104	_	_	NN	_	_	_
1105	biol	biol	NN	_	_	_
1106	rep	rep	NN	GEN	_	_
1107	1	1	CD	_	_	_
1108	_	_	NN	_	_	_
1109	Cy3	cy3	NN	_	_	_
1110	0	0	CD	_	_	_
1111	Cy5	cy5	NN	_	_	_
1112	60	60	CD	_	_	_
1113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1114	Slide	slide	NN	_	_	_
1115	17	17	CD	_	_	_
1116	_	_	NN	_	_	_
1117	hemA	hema	NN	GEN	_	_
1118	_	_	CD	_	_	_
1119	CORM-3	corm-3	NN	_	_	_
1120	_	_	NN	_	_	_
1121	biol	biol	NN	_	_	_
1122	rep	rep	NN	GEN	_	_
1123	1	1	CD	_	_	_
1124	_	_	CD	_	_	_
1125	Cy3	cy3	NN	_	_	_
1126	10	10	CD	_	_	_
1127	Cy5	cy5	NN	_	_	_
1128	0	0	CD	_	_	_
1129	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1130	Slide	Slide	NNP	_	_	_
1131	17	17	CD	_	_	_
1132	_	_	SYM	_	_	_
1133	hemA	hema	NN	GEN	_	_
1134	_	_	CD	_	_	_
1135	CORM-3	corm-3	NN	_	_	_
1136	_	_	NN	_	_	_
1137	biol	biol	NN	_	_	_
1138	rep	rep	NN	GEN	_	_
1139	1	1	CD	_	_	_
1140	_	_	CD	_	_	_
1141	Cy3	cy3	NN	_	_	_
1142	20	20	CD	_	_	_
1143	Cy5	cy5	NN	_	_	_
1144	0	0	CD	_	_	_
1145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1146	Slide	Slide	NNP	_	_	_
1147	17	17	CD	_	_	_
1148	_	_	SYM	_	_	_
1149	hemA	hema	NN	GEN	_	_
1150	_	_	CD	_	_	_
1151	CORM-3	corm-3	NN	_	_	_
1152	_	_	NN	_	_	_
1153	biol	biol	NN	_	_	_
1154	rep	rep	NN	GEN	_	_
1155	1	1	CD	_	_	_
1156	_	_	CD	_	_	_
1157	Cy3	cy3	NN	_	_	_
1158	40	40	CD	_	_	_
1159	Cy5	cy5	NN	_	_	_
1160	0	0	CD	_	_	_
1161	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1162	Slide	Slide	NNP	_	_	_
1163	18	18	CD	_	_	_
1164	_	_	SYM	_	_	_
1165	Aerobic	aerobic	JJ	_	_	_
1166	culture	culture	NN	_	_	_
1167	_	_	SYM	_	_	_
1168	CORM-3	corm-3	NN	_	_	_
1169	_	_	NN	_	_	_
1170	biol	biol	NN	_	_	_
1171	rep	rep	NN	GEN	_	_
1172	1	1	CD	_	_	_
1173	_	_	NN	_	_	_
1174	Cy3	cy3	NN	_	_	_
1175	0	0	CD	_	_	_
1176	Cy5	cy5	NN	_	_	_
1177	10	10	CD	_	_	_
1178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1179	Slide	slide	NN	_	_	_
1180	18	18	CD	_	_	_
1181	_	_	SYM	_	_	_
1182	Aerobic	aerobic	JJ	_	_	_
1183	culture	culture	NN	_	_	_
1184	_	_	SYM	_	_	_
1185	CORM-3	corm-3	NN	_	_	_
1186	_	_	NN	_	_	_
1187	biol	biol	NN	_	_	_
1188	rep	rep	NN	GEN	_	_
1189	1	1	CD	_	_	_
1190	_	_	NN	_	_	_
1191	Cy3	cy3	NN	_	_	_
1192	0	0	CD	_	_	_
1193	Cy5	cy5	NN	_	_	_
1194	20	20	CD	_	_	_
1195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1196	Slide	slide	NN	_	_	_
1197	18	18	CD	_	_	_
1198	_	_	SYM	_	_	_
1199	Aerobic	aerobic	JJ	_	_	_
1200	culture	culture	NN	_	_	_
1201	_	_	SYM	_	_	_
1202	CORM-3	corm-3	NN	_	_	_
1203	_	_	NN	_	_	_
1204	biol	biol	NN	_	_	_
1205	rep	rep	NN	GEN	_	_
1206	1	1	CD	_	_	_
1207	_	_	NN	_	_	_
1208	Cy3	cy3	NN	_	_	_
1209	0	0	CD	_	_	_
1210	Cy5	cy5	NN	_	_	_
1211	2.5	2.5	CD	_	_	_
1212	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1213	Slide	Slide	NNP	_	_	_
1214	18	18	CD	_	_	_
1215	_	_	SYM	_	_	_
1216	Aerobic	aerobic	JJ	_	_	_
1217	culture	culture	NN	_	_	_
1218	_	_	SYM	_	_	_
1219	CORM-3	corm-3	NN	_	_	_
1220	_	_	NN	_	_	_
1221	biol	biol	NN	_	_	_
1222	rep	rep	NN	GEN	_	_
1223	1	1	CD	_	_	_
1224	_	_	NN	_	_	_
1225	Cy3	cy3	NN	_	_	_
1226	0	0	CD	_	_	_
1227	Cy5	cy5	NN	_	_	_
1228	40	40	CD	_	_	_
1229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1230	Slide	slide	NN	_	_	_
1231	18	18	CD	_	_	_
1232	_	_	SYM	_	_	_
1233	Aerobic	aerobic	JJ	_	_	_
1234	culture	culture	NN	_	_	_
1235	_	_	SYM	_	_	_
1236	CORM-3	corm-3	NN	_	_	_
1237	_	_	NN	_	_	_
1238	biol	biol	NN	_	_	_
1239	rep	rep	NN	GEN	_	_
1240	1	1	CD	_	_	_
1241	_	_	NN	_	_	_
1242	Cy3	cy3	NN	_	_	_
1243	0	0	CD	_	_	_
1244	Cy5	cy5	NN	_	_	_
1245	5	5	CD	_	_	_
1246	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1247	Slide	Slide	NNP	_	_	_
1248	18	18	CD	_	_	_
1249	_	_	SYM	_	_	_
1250	Aerobic	aerobic	JJ	_	_	_
1251	culture	culture	NN	_	_	_
1252	_	_	SYM	_	_	_
1253	CORM-3	corm-3	NN	_	_	_
1254	_	_	NN	_	_	_
1255	biol	biol	NN	_	_	_
1256	rep	rep	NN	GEN	_	_
1257	1	1	CD	_	_	_
1258	_	_	NN	_	_	_
1259	Cy3	cy3	NN	_	_	_
1260	0	0	CD	_	_	_
1261	Cy5	cy5	NN	_	_	_
1262	80	80	CD	_	_	_
1263	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1264	Slide	Slide	NNP	_	_	_
1265	18	18	CD	_	_	_
1266	_	_	SYM	_	_	_
1267	Aerobic	aerobic	JJ	_	_	_
1268	culture	culture	NN	_	_	_
1269	_	_	SYM	_	_	_
1270	CORM-3	corm-3	NN	_	_	_
1271	_	_	NN	_	_	_
1272	biol	biol	NN	_	_	_
1273	rep	rep	NN	GEN	_	_
1274	1	1	CD	_	_	_
1275	_	_	CD	_	_	_
1276	Cy3	cy3	NN	_	_	_
1277	2.5	2.5	CD	_	_	_
1278	Cy5	cy5	NN	_	_	_
1279	0	0	CD	_	_	_
1280	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1281	Slide	Slide	NNP	_	_	_
1282	18	18	CD	_	_	_
1283	_	_	SYM	_	_	_
1284	Aerobic	aerobic	JJ	_	_	_
1285	culture	culture	NN	_	_	_
1286	_	_	SYM	_	_	_
1287	CORM-3	corm-3	NN	_	_	_
1288	_	_	NN	_	_	_
1289	biol	biol	NN	_	_	_
1290	rep	rep	NN	GEN	_	_
1291	1	1	CD	_	_	_
1292	_	_	CD	_	_	_
1293	Cy3	cy3	NN	_	_	_
1294	5	5	CD	_	_	_
1295	Cy5	cy5	NN	_	_	_
1296	0	0	CD	_	_	_
1297	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1298	Slide	Slide	NNP	_	_	_
1299	19	19	CD	_	_	_
1300	_	_	SYM	_	_	_
1301	Aerobic	aerobic	JJ	_	_	_
1302	culture	culture	NN	_	_	_
1303	_	_	SYM	_	_	_
1304	CORM-3	corm-3	NN	_	_	_
1305	_	_	NN	_	_	_
1306	biol	biol	NN	_	_	_
1307	rep	rep	NN	GEN	_	_
1308	1	1	CD	_	_	_
1309	_	_	CD	_	_	_
1310	Cy3	cy3	NN	_	_	_
1311	10	10	CD	_	_	_
1312	Cy5	cy5	NN	_	_	_
1313	0	0	CD	_	_	_
1314	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1315	Slide	Slide	NNP	_	_	_
1316	19	19	CD	_	_	_
1317	_	_	SYM	_	_	_
1318	Aerobic	aerobic	JJ	_	_	_
1319	culture	culture	NN	_	_	_
1320	_	_	SYM	_	_	_
1321	CORM-3	corm-3	NN	_	_	_
1322	_	_	NN	_	_	_
1323	biol	biol	NN	_	_	_
1324	rep	rep	NN	GEN	_	_
1325	1	1	CD	_	_	_
1326	_	_	CD	_	_	_
1327	Cy3	cy3	NN	_	_	_
1328	20	20	CD	_	_	_
1329	Cy5	cy5	NN	_	_	_
1330	0	0	CD	_	_	_
1331	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1332	Slide	Slide	NNP	_	_	_
1333	19	19	CD	_	_	_
1334	_	_	SYM	_	_	_
1335	Aerobic	aerobic	JJ	_	_	_
1336	culture	culture	NN	_	_	_
1337	_	_	SYM	_	_	_
1338	CORM-3	corm-3	NN	_	_	_
1339	_	_	NN	_	_	_
1340	biol	biol	NN	_	_	_
1341	rep	rep	NN	GEN	_	_
1342	1	1	CD	_	_	_
1343	_	_	CD	_	_	_
1344	Cy3	cy3	NN	_	_	_
1345	40	40	CD	_	_	_
1346	Cy5	cy5	NN	_	_	_
1347	0	0	CD	_	_	_
1348	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1349	Slide	Slide	NNP	_	_	_
1350	19	19	CD	_	_	_
1351	_	_	SYM	_	_	_
1352	Aerobic	aerobic	JJ	_	_	_
1353	culture	culture	NN	_	_	_
1354	_	_	SYM	_	_	_
1355	CORM-3	corm-3	NN	_	_	_
1356	_	_	NN	_	_	_
1357	biol	biol	NN	_	_	_
1358	rep	rep	NN	GEN	_	_
1359	1	1	CD	_	_	_
1360	_	_	CD	_	_	_
1361	Cy3	cy3	NN	_	_	_
1362	80	80	CD	_	_	_
1363	Cy5	cy5	NN	_	_	_
1364	0	0	CD	_	_	_
1365	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1366	Slide	Slide	NNP	_	_	_
1367	19	19	CD	_	_	_
1368	_	_	SYM	_	_	_
1369	Aerobic	aerobic	JJ	_	_	_
1370	culture	culture	NN	_	_	_
1371	_	_	SYM	_	_	_
1372	CORM-3	corm-3	NN	_	_	_
1373	_	_	NN	_	_	_
1374	biol	biol	NN	_	_	_
1375	rep	rep	NN	GEN	_	_
1376	2	2	CD	_	_	_
1377	_	_	CD	_	_	_
1378	Cy3	cy3	NN	_	_	_
1379	0	0	CD	_	_	_
1380	Cy5	cy5	NN	_	_	_
1381	10	10	CD	_	_	_
1382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1383	Slide	slide	NN	_	_	_
1384	19	19	CD	_	_	_
1385	_	_	SYM	_	_	_
1386	Aerobic	aerobic	JJ	_	_	_
1387	culture	culture	NN	_	_	_
1388	_	_	SYM	_	_	_
1389	CORM-3	corm-3	NN	_	_	_
1390	_	_	NN	_	_	_
1391	biol	biol	NN	_	_	_
1392	rep	rep	NN	GEN	_	_
1393	2	2	CD	_	_	_
1394	_	_	CD	_	_	_
1395	Cy3	cy3	NN	_	_	_
1396	0	0	CD	_	_	_
1397	Cy5	cy5	NN	_	_	_
1398	20	20	CD	_	_	_
1399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1400	Slide	slide	NN	_	_	_
1401	19	19	CD	_	_	_
1402	_	_	SYM	_	_	_
1403	Aerobic	aerobic	JJ	_	_	_
1404	culture	culture	NN	_	_	_
1405	_	_	SYM	_	_	_
1406	CORM-3	corm-3	NN	_	_	_
1407	_	_	NN	_	_	_
1408	biol	biol	NN	_	_	_
1409	rep	rep	NN	GEN	_	_
1410	2	2	CD	_	_	_
1411	_	_	CD	_	_	_
1412	Cy3	cy3	NN	_	_	_
1413	0	0	CD	_	_	_
1414	Cy5	cy5	NN	_	_	_
1415	2.5	2.5	CD	_	_	_
1416	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1417	Slide	Slide	NNP	_	_	_
1418	19	19	CD	_	_	_
1419	_	_	SYM	_	_	_
1420	Aerobic	aerobic	JJ	_	_	_
1421	culture	culture	NN	_	_	_
1422	_	_	SYM	_	_	_
1423	CORM-3	corm-3	NN	_	_	_
1424	_	_	NN	_	_	_
1425	biol	biol	NN	_	_	_
1426	rep	rep	NN	GEN	_	_
1427	2	2	CD	_	_	_
1428	_	_	CD	_	_	_
1429	Cy3	cy3	NN	_	_	_
1430	0	0	CD	_	_	_
1431	Cy5	cy5	NN	_	_	_
1432	5	5	CD	_	_	_
1433	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1434	Slide	Slide	NNP	_	_	_
1435	20	20	CD	_	_	_
1436	_	_	SYM	_	_	_
1437	Aerobic	aerobic	JJ	_	_	_
1438	culture	culture	NN	_	_	_
1439	_	_	SYM	_	_	_
1440	CORM-3	corm-3	NN	_	_	_
1441	_	_	NN	_	_	_
1442	biol	biol	NN	_	_	_
1443	rep	rep	NN	GEN	_	_
1444	2	2	CD	_	_	_
1445	_	_	CD	_	_	_
1446	Cy3	cy3	NN	_	_	_
1447	0	0	CD	_	_	_
1448	Cy5	cy5	NN	_	_	_
1449	40	40	CD	_	_	_
1450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1451	Slide	slide	NN	_	_	_
1452	20	20	CD	_	_	_
1453	_	_	SYM	_	_	_
1454	Aerobic	aerobic	JJ	_	_	_
1455	culture	culture	NN	_	_	_
1456	_	_	SYM	_	_	_
1457	CORM-3	corm-3	NN	_	_	_
1458	_	_	NN	_	_	_
1459	biol	biol	NN	_	_	_
1460	rep	rep	NN	GEN	_	_
1461	2	2	CD	_	_	_
1462	_	_	CD	_	_	_
1463	Cy3	cy3	NN	_	_	_
1464	0	0	CD	_	_	_
1465	Cy5	cy5	NN	_	_	_
1466	80	80	CD	_	_	_
1467	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1468	Slide	Slide	NNP	_	_	_
1469	20	20	CD	_	_	_
1470	_	_	SYM	_	_	_
1471	Aerobic	aerobic	JJ	_	_	_
1472	culture	culture	NN	_	_	_
1473	_	_	SYM	_	_	_
1474	CORM-3	corm-3	NN	_	_	_
1475	_	_	NN	_	_	_
1476	biol	biol	NN	_	_	_
1477	rep	rep	NN	GEN	_	_
1478	2	2	CD	_	_	_
1479	_	_	CD	_	_	_
1480	Cy3	cy3	NN	_	_	_
1481	10	10	CD	_	_	_
1482	Cy5	cy5	NN	_	_	_
1483	0	0	CD	_	_	_
1484	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1485	Slide	Slide	NNP	_	_	_
1486	20	20	CD	_	_	_
1487	_	_	SYM	_	_	_
1488	Aerobic	aerobic	JJ	_	_	_
1489	culture	culture	NN	_	_	_
1490	_	_	SYM	_	_	_
1491	CORM-3	corm-3	NN	_	_	_
1492	_	_	NN	_	_	_
1493	biol	biol	NN	_	_	_
1494	rep	rep	NN	GEN	_	_
1495	2	2	CD	_	_	_
1496	_	_	CD	_	_	_
1497	Cy3	cy3	NN	_	_	_
1498	20	20	CD	_	_	_
1499	Cy5	cy5	NN	_	_	_
1500	0	0	CD	_	_	_
1501	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1502	Slide	Slide	NNP	_	_	_
1503	20	20	CD	_	_	_
1504	_	_	SYM	_	_	_
1505	Aerobic	aerobic	JJ	_	_	_
1506	culture	culture	NN	_	_	_
1507	_	_	SYM	_	_	_
1508	CORM-3	corm-3	NN	_	_	_
1509	_	_	NN	_	_	_
1510	biol	biol	NN	_	_	_
1511	rep	rep	NN	GEN	_	_
1512	2	2	CD	_	_	_
1513	_	_	CD	_	_	_
1514	Cy3	cy3	NN	_	_	_
1515	2.5	2.5	CD	_	_	_
1516	Cy5	cy5	NN	_	_	_
1517	0	0	CD	_	_	_
1518	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1519	Slide	Slide	NNP	_	_	_
1520	20	20	CD	_	_	_
1521	_	_	SYM	_	_	_
1522	Aerobic	aerobic	JJ	_	_	_
1523	culture	culture	NN	_	_	_
1524	_	_	SYM	_	_	_
1525	CORM-3	corm-3	NN	_	_	_
1526	_	_	NN	_	_	_
1527	biol	biol	NN	_	_	_
1528	rep	rep	NN	GEN	_	_
1529	2	2	CD	_	_	_
1530	_	_	CD	_	_	_
1531	Cy3	cy3	NN	_	_	_
1532	40	40	CD	_	_	_
1533	Cy5	cy5	NN	_	_	_
1534	0	0	CD	_	_	_
1535	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1536	Slide	Slide	NNP	_	_	_
1537	20	20	CD	_	_	_
1538	_	_	SYM	_	_	_
1539	Aerobic	aerobic	JJ	_	_	_
1540	culture	culture	NN	_	_	_
1541	_	_	SYM	_	_	_
1542	CORM-3	corm-3	NN	_	_	_
1543	_	_	NN	_	_	_
1544	biol	biol	NN	_	_	_
1545	rep	rep	NN	GEN	_	_
1546	2	2	CD	_	_	_
1547	_	_	CD	_	_	_
1548	Cy3	cy3	NN	_	_	_
1549	5	5	CD	_	_	_
1550	Cy5	cy5	NN	_	_	_
1551	0	0	CD	_	_	_
1552	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1553	Slide	Slide	NNP	_	_	_
1554	20	20	CD	_	_	_
1555	_	_	SYM	_	_	_
1556	Aerobic	aerobic	JJ	_	_	_
1557	culture	culture	NN	_	_	_
1558	_	_	SYM	_	_	_
1559	CORM-3	corm-3	NN	_	_	_
1560	_	_	NN	_	_	_
1561	biol	biol	NN	_	_	_
1562	rep	rep	NN	GEN	_	_
1563	2	2	CD	_	_	_
1564	_	_	CD	_	_	_
1565	Cy3	cy3	NN	_	_	_
1566	80	80	CD	_	_	_
1567	Cy5	cy5	NN	_	_	_
1568	0	0	CD	_	_	_
1569	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1570	Slide	Slide	NNP	_	_	_
1571	25	25	CD	_	_	_
1572	_	_	SYM	_	_	_
1573	Aerobic	aerobic	JJ	_	_	_
1574	culture	culture	NN	_	_	_
1575	_	_	SYM	_	_	_
1576	iCORM-3	icorm-3	NN	_	_	_
1577	_	_	NN	_	_	_
1578	biol	biol	NN	_	_	_
1579	rep	rep	NN	GEN	_	_
1580	1	1	CD	_	_	_
1581	_	_	NN	_	_	_
1582	Cy3	cy3	NN	_	_	_
1583	0	0	CD	_	_	_
1584	Cy5	cy5	NN	_	_	_
1585	10	10	CD	_	_	_
1586	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1587	Slide	slide	NN	_	_	_
1588	25	25	CD	_	_	_
1589	_	_	SYM	_	_	_
1590	Aerobic	aerobic	JJ	_	_	_
1591	culture	culture	NN	_	_	_
1592	_	_	SYM	_	_	_
1593	iCORM-3	icorm-3	NN	_	_	_
1594	_	_	NN	_	_	_
1595	biol	biol	NN	_	_	_
1596	rep	rep	NN	GEN	_	_
1597	1	1	CD	_	_	_
1598	_	_	NN	_	_	_
1599	Cy3	cy3	NN	_	_	_
1600	0	0	CD	_	_	_
1601	Cy5	cy5	NN	_	_	_
1602	20	20	CD	_	_	_
1603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1604	Slide	slide	NN	_	_	_
1605	25	25	CD	_	_	_
1606	_	_	SYM	_	_	_
1607	Aerobic	aerobic	JJ	_	_	_
1608	culture	culture	NN	_	_	_
1609	_	_	SYM	_	_	_
1610	iCORM-3	icorm-3	NN	_	_	_
1611	_	_	NN	_	_	_
1612	biol	biol	NN	_	_	_
1613	rep	rep	NN	GEN	_	_
1614	1	1	CD	_	_	_
1615	_	_	NN	_	_	_
1616	Cy3	cy3	NN	_	_	_
1617	0	0	CD	_	_	_
1618	Cy5	cy5	NN	_	_	_
1619	2.5	2.5	CD	_	_	_
1620	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1621	Slide	Slide	NNP	_	_	_
1622	25	25	CD	_	_	_
1623	_	_	SYM	_	_	_
1624	Aerobic	aerobic	JJ	_	_	_
1625	culture	culture	NN	_	_	_
1626	_	_	SYM	_	_	_
1627	iCORM-3	icorm-3	NN	_	_	_
1628	_	_	NN	_	_	_
1629	biol	biol	NN	_	_	_
1630	rep	rep	NN	GEN	_	_
1631	1	1	CD	_	_	_
1632	_	_	NN	_	_	_
1633	Cy3	cy3	NN	_	_	_
1634	0	0	CD	_	_	_
1635	Cy5	cy5	NN	_	_	_
1636	40	40	CD	_	_	_
1637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1638	Slide	slide	NN	_	_	_
1639	25	25	CD	_	_	_
1640	_	_	SYM	_	_	_
1641	Aerobic	aerobic	JJ	_	_	_
1642	culture	culture	NN	_	_	_
1643	_	_	SYM	_	_	_
1644	iCORM-3	icorm-3	NN	_	_	_
1645	_	_	NN	_	_	_
1646	biol	biol	NN	_	_	_
1647	rep	rep	NN	GEN	_	_
1648	1	1	CD	_	_	_
1649	_	_	NN	_	_	_
1650	Cy3	cy3	NN	_	_	_
1651	0	0	CD	_	_	_
1652	Cy5	cy5	NN	_	_	_
1653	5	5	CD	_	_	_
1654	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1655	Slide	Slide	NNP	_	_	_
1656	25	25	CD	_	_	_
1657	_	_	SYM	_	_	_
1658	Aerobic	aerobic	JJ	_	_	_
1659	culture	culture	NN	_	_	_
1660	_	_	SYM	_	_	_
1661	iCORM-3	icorm-3	NN	_	_	_
1662	_	_	NN	_	_	_
1663	biol	biol	NN	_	_	_
1664	rep	rep	NN	GEN	_	_
1665	1	1	CD	_	_	_
1666	_	_	NN	_	_	_
1667	Cy3	cy3	NN	_	_	_
1668	0	0	CD	_	_	_
1669	Cy5	cy5	NN	_	_	_
1670	80	80	CD	_	_	_
1671	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1672	Slide	Slide	NNP	_	_	_
1673	25	25	CD	_	_	_
1674	_	_	SYM	_	_	_
1675	Aerobic	aerobic	JJ	_	_	_
1676	culture	culture	NN	_	_	_
1677	_	_	SYM	_	_	_
1678	iCORM-3	icorm-3	NN	_	_	_
1679	_	_	NN	_	_	_
1680	biol	biol	NN	_	_	_
1681	rep	rep	NN	GEN	_	_
1682	1	1	CD	_	_	_
1683	_	_	CD	_	_	_
1684	Cy3	cy3	NN	_	_	_
1685	2.5	2.5	CD	_	_	_
1686	Cy5	cy5	NN	_	_	_
1687	0	0	CD	_	_	_
1688	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1689	Slide	Slide	NNP	_	_	_
1690	25	25	CD	_	_	_
1691	_	_	SYM	_	_	_
1692	Aerobic	aerobic	JJ	_	_	_
1693	culture	culture	NN	_	_	_
1694	_	_	SYM	_	_	_
1695	iCORM-3	icorm-3	NN	_	_	_
1696	_	_	NN	_	_	_
1697	biol	biol	NN	_	_	_
1698	rep	rep	NN	GEN	_	_
1699	1	1	CD	_	_	_
1700	_	_	CD	_	_	_
1701	Cy3	cy3	NN	_	_	_
1702	5	5	CD	_	_	_
1703	Cy5	cy5	NN	_	_	_
1704	0	0	CD	_	_	_
1705	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1706	Slide	Slide	NNP	_	_	_
1707	26	26	CD	_	_	_
1708	_	_	SYM	_	_	_
1709	Aerobic	aerobic	JJ	_	_	_
1710	culture	culture	NN	_	_	_
1711	_	_	SYM	_	_	_
1712	iCORM-3	icorm-3	NN	_	_	_
1713	_	_	NN	_	_	_
1714	biol	biol	NN	_	_	_
1715	rep	rep	NN	GEN	_	_
1716	1	1	CD	_	_	_
1717	_	_	CD	_	_	_
1718	Cy3	cy3	NN	_	_	_
1719	10	10	CD	_	_	_
1720	Cy5	cy5	NN	_	_	_
1721	0	0	CD	_	_	_
1722	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1723	Slide	Slide	NNP	_	_	_
1724	26	26	CD	_	_	_
1725	_	_	SYM	_	_	_
1726	Aerobic	aerobic	JJ	_	_	_
1727	culture	culture	NN	_	_	_
1728	_	_	SYM	_	_	_
1729	iCORM-3	icorm-3	NN	_	_	_
1730	_	_	NN	_	_	_
1731	biol	biol	NN	_	_	_
1732	rep	rep	NN	GEN	_	_
1733	1	1	CD	_	_	_
1734	_	_	CD	_	_	_
1735	Cy3	cy3	NN	_	_	_
1736	20	20	CD	_	_	_
1737	Cy5	cy5	NN	_	_	_
1738	0	0	CD	_	_	_
1739	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1740	Slide	Slide	NNP	_	_	_
1741	26	26	CD	_	_	_
1742	_	_	SYM	_	_	_
1743	Aerobic	aerobic	JJ	_	_	_
1744	culture	culture	NN	_	_	_
1745	_	_	SYM	_	_	_
1746	iCORM-3	icorm-3	NN	_	_	_
1747	_	_	NN	_	_	_
1748	biol	biol	NN	_	_	_
1749	rep	rep	NN	GEN	_	_
1750	1	1	CD	_	_	_
1751	_	_	CD	_	_	_
1752	Cy3	cy3	NN	_	_	_
1753	40	40	CD	_	_	_
1754	Cy5	cy5	NN	_	_	_
1755	0	0	CD	_	_	_
1756	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1757	Slide	Slide	NNP	_	_	_
1758	26	26	CD	_	_	_
1759	_	_	SYM	_	_	_
1760	Aerobic	aerobic	JJ	_	_	_
1761	culture	culture	NN	_	_	_
1762	_	_	SYM	_	_	_
1763	iCORM-3	icorm-3	NN	_	_	_
1764	_	_	NN	_	_	_
1765	biol	biol	NN	_	_	_
1766	rep	rep	NN	GEN	_	_
1767	1	1	CD	_	_	_
1768	_	_	CD	_	_	_
1769	Cy3	cy3	NN	_	_	_
1770	80	80	CD	_	_	_
1771	Cy5	cy5	NN	_	_	_
1772	0	0	CD	_	_	_
1773	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1774	Slide	Slide	NNP	_	_	_
1775	26	26	CD	_	_	_
1776	_	_	SYM	_	_	_
1777	Aerobic	aerobic	JJ	_	_	_
1778	culture	culture	NN	_	_	_
1779	_	_	SYM	_	_	_
1780	iCORM-3	icorm-3	NN	_	_	_
1781	_	_	NN	_	_	_
1782	biol	biol	NN	_	_	_
1783	rep	rep	NN	GEN	_	_
1784	2	2	CD	_	_	_
1785	_	_	CD	_	_	_
1786	Cy3	cy3	NN	_	_	_
1787	0	0	CD	_	_	_
1788	Cy5	cy5	NN	_	_	_
1789	10	10	CD	_	_	_
1790	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1791	Slide	slide	NN	_	_	_
1792	26	26	CD	_	_	_
1793	_	_	SYM	_	_	_
1794	Aerobic	aerobic	JJ	_	_	_
1795	culture	culture	NN	_	_	_
1796	_	_	SYM	_	_	_
1797	iCORM-3	icorm-3	NN	_	_	_
1798	_	_	NN	_	_	_
1799	biol	biol	NN	_	_	_
1800	rep	rep	NN	GEN	_	_
1801	2	2	CD	_	_	_
1802	_	_	CD	_	_	_
1803	Cy3	cy3	NN	_	_	_
1804	0	0	CD	_	_	_
1805	Cy5	cy5	NN	_	_	_
1806	20	20	CD	_	_	_
1807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1808	Slide	slide	NN	_	_	_
1809	26	26	CD	_	_	_
1810	_	_	SYM	_	_	_
1811	Aerobic	aerobic	JJ	_	_	_
1812	culture	culture	NN	_	_	_
1813	_	_	SYM	_	_	_
1814	iCORM-3	icorm-3	NN	_	_	_
1815	_	_	NN	_	_	_
1816	biol	biol	NN	_	_	_
1817	rep	rep	NN	GEN	_	_
1818	2	2	CD	_	_	_
1819	_	_	CD	_	_	_
1820	Cy3	cy3	NN	_	_	_
1821	0	0	CD	_	_	_
1822	Cy5	cy5	NN	_	_	_
1823	2.5	2.5	CD	_	_	_
1824	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1825	Slide	Slide	NNP	_	_	_
1826	26	26	CD	_	_	_
1827	_	_	SYM	_	_	_
1828	Aerobic	aerobic	JJ	_	_	_
1829	culture	culture	NN	_	_	_
1830	_	_	SYM	_	_	_
1831	iCORM-3	icorm-3	NN	_	_	_
1832	_	_	NN	_	_	_
1833	biol	biol	NN	_	_	_
1834	rep	rep	NN	GEN	_	_
1835	2	2	CD	_	_	_
1836	_	_	CD	_	_	_
1837	Cy3	cy3	NN	_	_	_
1838	0	0	CD	_	_	_
1839	Cy5	cy5	NN	_	_	_
1840	5	5	CD	_	_	_
1841	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1842	Slide	Slide	NNP	_	_	_
1843	27	27	CD	_	_	_
1844	_	_	SYM	_	_	_
1845	Aerobic	aerobic	JJ	_	_	_
1846	culture	culture	NN	_	_	_
1847	_	_	SYM	_	_	_
1848	iCORM-3	icorm-3	NN	_	_	_
1849	_	_	NN	_	_	_
1850	biol	biol	NN	_	_	_
1851	rep	rep	NN	GEN	_	_
1852	2	2	CD	_	_	_
1853	_	_	CD	_	_	_
1854	Cy3	cy3	NN	_	_	_
1855	0	0	CD	_	_	_
1856	Cy5	cy5	NN	_	_	_
1857	40	40	CD	_	_	_
1858	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1859	Slide	slide	NN	_	_	_
1860	27	27	CD	_	_	_
1861	_	_	SYM	_	_	_
1862	Aerobic	aerobic	JJ	_	_	_
1863	culture	culture	NN	_	_	_
1864	_	_	SYM	_	_	_
1865	iCORM-3	icorm-3	NN	_	_	_
1866	_	_	NN	_	_	_
1867	biol	biol	NN	_	_	_
1868	rep	rep	NN	GEN	_	_
1869	2	2	CD	_	_	_
1870	_	_	CD	_	_	_
1871	Cy3	cy3	NN	_	_	_
1872	0	0	CD	_	_	_
1873	Cy5	cy5	NN	_	_	_
1874	80	80	CD	_	_	_
1875	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1876	Slide	Slide	NNP	_	_	_
1877	27	27	CD	_	_	_
1878	_	_	SYM	_	_	_
1879	Aerobic	aerobic	JJ	_	_	_
1880	culture	culture	NN	_	_	_
1881	_	_	SYM	_	_	_
1882	iCORM-3	icorm-3	NN	_	_	_
1883	_	_	NN	_	_	_
1884	biol	biol	NN	_	_	_
1885	rep	rep	NN	GEN	_	_
1886	2	2	CD	_	_	_
1887	_	_	CD	_	_	_
1888	Cy3	cy3	NN	_	_	_
1889	10	10	CD	_	_	_
1890	Cy5	cy5	NN	_	_	_
1891	0	0	CD	_	_	_
1892	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1893	Slide	Slide	NNP	_	_	_
1894	27	27	CD	_	_	_
1895	_	_	SYM	_	_	_
1896	Aerobic	aerobic	JJ	_	_	_
1897	culture	culture	NN	_	_	_
1898	_	_	SYM	_	_	_
1899	iCORM-3	icorm-3	NN	_	_	_
1900	_	_	NN	_	_	_
1901	biol	biol	NN	_	_	_
1902	rep	rep	NN	GEN	_	_
1903	2	2	CD	_	_	_
1904	_	_	CD	_	_	_
1905	Cy3	cy3	NN	_	_	_
1906	20	20	CD	_	_	_
1907	Cy5	cy5	NN	_	_	_
1908	0	0	CD	_	_	_
1909	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1910	Slide	Slide	NNP	_	_	_
1911	27	27	CD	_	_	_
1912	_	_	SYM	_	_	_
1913	Aerobic	aerobic	JJ	_	_	_
1914	culture	culture	NN	_	_	_
1915	_	_	SYM	_	_	_
1916	iCORM-3	icorm-3	NN	_	_	_
1917	_	_	NN	_	_	_
1918	biol	biol	NN	_	_	_
1919	rep	rep	NN	GEN	_	_
1920	2	2	CD	_	_	_
1921	_	_	CD	_	_	_
1922	Cy3	cy3	NN	_	_	_
1923	2.5	2.5	CD	_	_	_
1924	Cy5	cy5	NN	_	_	_
1925	0	0	CD	_	_	_
1926	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1927	Slide	Slide	NNP	_	_	_
1928	27	27	CD	_	_	_
1929	_	_	SYM	_	_	_
1930	Aerobic	aerobic	JJ	_	_	_
1931	culture	culture	NN	_	_	_
1932	_	_	SYM	_	_	_
1933	iCORM-3	icorm-3	NN	_	_	_
1934	_	_	NN	_	_	_
1935	biol	biol	NN	_	_	_
1936	rep	rep	NN	GEN	_	_
1937	2	2	CD	_	_	_
1938	_	_	CD	_	_	_
1939	Cy3	cy3	NN	_	_	_
1940	40	40	CD	_	_	_
1941	Cy5	cy5	NN	_	_	_
1942	0	0	CD	_	_	_
1943	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1944	Slide	Slide	NNP	_	_	_
1945	27	27	CD	_	_	_
1946	_	_	SYM	_	_	_
1947	Aerobic	aerobic	JJ	_	_	_
1948	culture	culture	NN	_	_	_
1949	_	_	SYM	_	_	_
1950	iCORM-3	icorm-3	NN	_	_	_
1951	_	_	NN	_	_	_
1952	biol	biol	NN	_	_	_
1953	rep	rep	NN	GEN	_	_
1954	2	2	CD	_	_	_
1955	_	_	CD	_	_	_
1956	Cy3	cy3	NN	_	_	_
1957	5	5	CD	_	_	_
1958	Cy5	cy5	NN	_	_	_
1959	0	0	CD	_	_	_
1960	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1961	Slide	Slide	NNP	_	_	_
1962	27	27	CD	_	_	_
1963	_	_	SYM	_	_	_
1964	Aerobic	aerobic	JJ	_	_	_
1965	culture	culture	NN	_	_	_
1966	_	_	SYM	_	_	_
1967	iCORM-3	icorm-3	NN	_	_	_
1968	_	_	NN	_	_	_
1969	biol	biol	NN	_	_	_
1970	rep	rep	NN	GEN	_	_
1971	2	2	CD	_	_	_
1972	_	_	CD	_	_	_
1973	Cy3	cy3	NN	_	_	_
1974	80	80	CD	_	_	_
1975	Cy5	cy5	NN	_	_	_
1976	0	0	CD	_	_	_
1977	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1978	Slide	Slide	NNP	_	_	_
1979	28	28	CD	_	_	_
1980	_	_	SYM	_	_	_
1981	Anaerobic	anaerobic	JJ	_	_	_
1982	culture	culture	NN	_	_	_
1983	_	_	SYM	_	_	_
1984	iCORM-3	icorm-3	NN	_	_	_
1985	_	_	NN	_	_	_
1986	biol	biol	NN	_	_	_
1987	rep	rep	NN	GEN	_	_
1988	1	1	CD	_	_	_
1989	_	_	NN	_	_	_
1990	Cy3	cy3	NN	_	_	_
1991	0	0	CD	_	_	_
1992	Cy5	cy5	NN	_	_	_
1993	2.5	2.5	CD	_	_	_
1994	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1995	Slide	Slide	NNP	_	_	_
1996	28	28	CD	_	_	_
1997	_	_	SYM	_	_	_
1998	Anaerobic	anaerobic	JJ	_	_	_
1999	culture	culture	NN	_	_	_
2000	_	_	SYM	_	_	_
2001	iCORM-3	icorm-3	NN	_	_	_
2002	_	_	NN	_	_	_
2003	biol	biol	NN	_	_	_
2004	rep	rep	NN	GEN	_	_
2005	1	1	CD	_	_	_
2006	_	_	NN	_	_	_
2007	Cy3	cy3	NN	_	_	_
2008	0	0	CD	_	_	_
2009	Cy5	cy5	NN	_	_	_
2010	5	5	CD	_	_	_
2011	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2012	Slide	Slide	NNP	_	_	_
2013	28	28	CD	_	_	_
2014	_	_	SYM	_	_	_
2015	Anaerobic	anaerobic	JJ	_	_	_
2016	culture	culture	NN	_	_	_
2017	_	_	SYM	_	_	_
2018	iCORM-3	icorm-3	NN	_	_	_
2019	_	_	NN	_	_	_
2020	biol	biol	NN	_	_	_
2021	rep	rep	NN	GEN	_	_
2022	1	1	CD	_	_	_
2023	_	_	CD	_	_	_
2024	Cy3	cy3	NN	_	_	_
2025	10	10	CD	_	_	_
2026	Cy5	cy5	NN	_	_	_
2027	0	0	CD	_	_	_
2028	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2029	Slide	Slide	NNP	_	_	_
2030	28	28	CD	_	_	_
2031	_	_	SYM	_	_	_
2032	Anaerobic	anaerobic	JJ	_	_	_
2033	culture	culture	NN	_	_	_
2034	_	_	SYM	_	_	_
2035	iCORM-3	icorm-3	NN	_	_	_
2036	_	_	NN	_	_	_
2037	biol	biol	NN	_	_	_
2038	rep	rep	NN	GEN	_	_
2039	1	1	CD	_	_	_
2040	_	_	CD	_	_	_
2041	Cy3	cy3	NN	_	_	_
2042	20	20	CD	_	_	_
2043	Cy5	cy5	NN	_	_	_
2044	0	0	CD	_	_	_
2045	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2046	Slide	Slide	NNP	_	_	_
2047	28	28	CD	_	_	_
2048	_	_	SYM	_	_	_
2049	Anaerobic	anaerobic	JJ	_	_	_
2050	culture	culture	NN	_	_	_
2051	_	_	SYM	_	_	_
2052	iCORM-3	icorm-3	NN	_	_	_
2053	_	_	NN	_	_	_
2054	biol	biol	NN	_	_	_
2055	rep	rep	NN	GEN	_	_
2056	1	1	CD	_	_	_
2057	_	_	CD	_	_	_
2058	Cy3	cy3	NN	_	_	_
2059	2.5	2.5	CD	_	_	_
2060	Cy5	cy5	NN	_	_	_
2061	0	0	CD	_	_	_
2062	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2063	Slide	Slide	NNP	_	_	_
2064	28	28	CD	_	_	_
2065	_	_	SYM	_	_	_
2066	Anaerobic	anaerobic	JJ	_	_	_
2067	culture	culture	NN	_	_	_
2068	_	_	SYM	_	_	_
2069	iCORM-3	icorm-3	NN	_	_	_
2070	_	_	NN	_	_	_
2071	biol	biol	NN	_	_	_
2072	rep	rep	NN	GEN	_	_
2073	1	1	CD	_	_	_
2074	_	_	CD	_	_	_
2075	Cy3	cy3	NN	_	_	_
2076	40	40	CD	_	_	_
2077	Cy5	cy5	NN	_	_	_
2078	0	0	CD	_	_	_
2079	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2080	Slide	Slide	NNP	_	_	_
2081	28	28	CD	_	_	_
2082	_	_	SYM	_	_	_
2083	Anaerobic	anaerobic	JJ	_	_	_
2084	culture	culture	NN	_	_	_
2085	_	_	SYM	_	_	_
2086	iCORM-3	icorm-3	NN	_	_	_
2087	_	_	NN	_	_	_
2088	biol	biol	NN	_	_	_
2089	rep	rep	NN	GEN	_	_
2090	1	1	CD	_	_	_
2091	_	_	CD	_	_	_
2092	Cy3	cy3	NN	_	_	_
2093	5	5	CD	_	_	_
2094	Cy5	cy5	NN	_	_	_
2095	0	0	CD	_	_	_
2096	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2097	Slide	Slide	NNP	_	_	_
2098	28	28	CD	_	_	_
2099	_	_	SYM	_	_	_
2100	Anaerobic	anaerobic	JJ	_	_	_
2101	culture	culture	NN	_	_	_
2102	_	_	SYM	_	_	_
2103	iCORM-3	icorm-3	NN	_	_	_
2104	_	_	NN	_	_	_
2105	biol	biol	NN	_	_	_
2106	rep	rep	NN	GEN	_	_
2107	1	1	CD	_	_	_
2108	_	_	CD	_	_	_
2109	Cy3	cy3	NN	_	_	_
2110	80	80	CD	_	_	_
2111	Cy5	cy5	NN	_	_	_
2112	0	0	CD	_	_	_
2113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2114	Slide	Slide	NNP	_	_	_
2115	29	29	CD	_	_	_
2116	_	_	SYM	_	_	_
2117	Anaerobic	anaerobic	JJ	_	_	_
2118	culture	culture	NN	_	_	_
2119	_	_	SYM	_	_	_
2120	iCORM-3	icorm-3	NN	_	_	_
2121	_	_	NN	_	_	_
2122	biol	biol	NN	_	_	_
2123	rep	rep	NN	GEN	_	_
2124	1	1	CD	_	_	_
2125	_	_	CD	_	_	_
2126	Cy3	cy3	NN	_	_	_
2127	10	10	CD	_	_	_
2128	Cy5	cy5	NN	_	_	_
2129	0	0	CD	_	_	_
2130	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2131	Slide	Slide	NNP	_	_	_
2132	29	29	CD	_	_	_
2133	_	_	SYM	_	_	_
2134	Anaerobic	anaerobic	JJ	_	_	_
2135	culture	culture	NN	_	_	_
2136	_	_	SYM	_	_	_
2137	iCORM-3	icorm-3	NN	_	_	_
2138	_	_	NN	_	_	_
2139	biol	biol	NN	_	_	_
2140	rep	rep	NN	GEN	_	_
2141	1	1	CD	_	_	_
2142	_	_	CD	_	_	_
2143	Cy3	cy3	NN	_	_	_
2144	20	20	CD	_	_	_
2145	Cy5	cy5	NN	_	_	_
2146	0	0	CD	_	_	_
2147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2148	Slide	Slide	NNP	_	_	_
2149	29	29	CD	_	_	_
2150	_	_	SYM	_	_	_
2151	Anaerobic	anaerobic	JJ	_	_	_
2152	culture	culture	NN	_	_	_
2153	_	_	SYM	_	_	_
2154	iCORM-3	icorm-3	NN	_	_	_
2155	_	_	NN	_	_	_
2156	biol	biol	NN	_	_	_
2157	rep	rep	NN	GEN	_	_
2158	1	1	CD	_	_	_
2159	_	_	CD	_	_	_
2160	Cy3	cy3	NN	_	_	_
2161	40	40	CD	_	_	_
2162	Cy5	cy5	NN	_	_	_
2163	0	0	CD	_	_	_
2164	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2165	Slide	Slide	NNP	_	_	_
2166	29	29	CD	_	_	_
2167	_	_	SYM	_	_	_
2168	Anaerobic	anaerobic	JJ	_	_	_
2169	culture	culture	NN	_	_	_
2170	_	_	SYM	_	_	_
2171	iCORM-3	icorm-3	NN	_	_	_
2172	_	_	NN	_	_	_
2173	biol	biol	NN	_	_	_
2174	rep	rep	NN	GEN	_	_
2175	1	1	CD	_	_	_
2176	_	_	CD	_	_	_
2177	Cy3	cy3	NN	_	_	_
2178	80	80	CD	_	_	_
2179	Cy5	cy5	NN	_	_	_
2180	0	0	CD	_	_	_
2181	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2182	Slide	Slide	NNP	_	_	_
2183	29	29	CD	_	_	_
2184	_	_	SYM	_	_	_
2185	Anaerobic	anaerobic	JJ	_	_	_
2186	culture	culture	NN	_	_	_
2187	_	_	SYM	_	_	_
2188	iCORM-3	icorm-3	NN	_	_	_
2189	_	_	NN	_	_	_
2190	biol	biol	NN	_	_	_
2191	rep	rep	NN	GEN	_	_
2192	2	2	CD	_	_	_
2193	_	_	CD	_	_	_
2194	Cy3	cy3	NN	_	_	_
2195	0	0	CD	_	_	_
2196	Cy5	cy5	NN	_	_	_
2197	10	10	CD	_	_	_
2198	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2199	Slide	Slide	NNP	_	_	_
2200	29	29	CD	_	_	_
2201	_	_	SYM	_	_	_
2202	Anaerobic	anaerobic	JJ	_	_	_
2203	culture	culture	NN	_	_	_
2204	_	_	SYM	_	_	_
2205	iCORM-3	icorm-3	NN	_	_	_
2206	_	_	NN	_	_	_
2207	biol	biol	NN	_	_	_
2208	rep	rep	NN	GEN	_	_
2209	2	2	CD	_	_	_
2210	_	_	CD	_	_	_
2211	Cy3	cy3	NN	_	_	_
2212	0	0	CD	_	_	_
2213	Cy5	cy5	NN	_	_	_
2214	20	20	CD	_	_	_
2215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2216	Slide	slide	NN	_	_	_
2217	29	29	CD	_	_	_
2218	_	_	SYM	_	_	_
2219	Anaerobic	anaerobic	JJ	_	_	_
2220	culture	culture	NN	_	_	_
2221	_	_	SYM	_	_	_
2222	iCORM-3	icorm-3	NN	_	_	_
2223	_	_	NN	_	_	_
2224	biol	biol	NN	_	_	_
2225	rep	rep	NN	GEN	_	_
2226	2	2	CD	_	_	_
2227	_	_	CD	_	_	_
2228	Cy3	cy3	NN	_	_	_
2229	0	0	CD	_	_	_
2230	Cy5	cy5	NN	_	_	_
2231	2.5	2.5	CD	_	_	_
2232	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2233	Slide	Slide	NNP	_	_	_
2234	29	29	CD	_	_	_
2235	_	_	SYM	_	_	_
2236	Anaerobic	anaerobic	JJ	_	_	_
2237	culture	culture	NN	_	_	_
2238	_	_	SYM	_	_	_
2239	iCORM-3	icorm-3	NN	_	_	_
2240	_	_	NN	_	_	_
2241	biol	biol	NN	_	_	_
2242	rep	rep	NN	GEN	_	_
2243	2	2	CD	_	_	_
2244	_	_	CD	_	_	_
2245	Cy3	cy3	NN	_	_	_
2246	0	0	CD	_	_	_
2247	Cy5	cy5	NN	_	_	_
2248	5	5	CD	_	_	_
2249	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2250	Slide	Slide	NNP	_	_	_
2251	30	30	CD	_	_	_
2252	_	_	SYM	_	_	_
2253	Anaerobic	anaerobic	JJ	_	_	_
2254	culture	culture	NN	_	_	_
2255	_	_	SYM	_	_	_
2256	iCORM-3	icorm-3	NN	_	_	_
2257	_	_	NN	_	_	_
2258	biol	biol	NN	_	_	_
2259	rep	rep	NN	GEN	_	_
2260	2	2	CD	_	_	_
2261	_	_	CD	_	_	_
2262	Cy3	cy3	NN	_	_	_
2263	0	0	CD	_	_	_
2264	Cy5	cy5	NN	_	_	_
2265	40	40	CD	_	_	_
2266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2267	Slide	slide	NN	_	_	_
2268	30	30	CD	_	_	_
2269	_	_	SYM	_	_	_
2270	Anaerobic	anaerobic	JJ	_	_	_
2271	culture	culture	NN	_	_	_
2272	_	_	SYM	_	_	_
2273	iCORM-3	icorm-3	NN	_	_	_
2274	_	_	NN	_	_	_
2275	biol	biol	NN	_	_	_
2276	rep	rep	NN	GEN	_	_
2277	2	2	CD	_	_	_
2278	_	_	CD	_	_	_
2279	Cy3	cy3	NN	_	_	_
2280	0	0	CD	_	_	_
2281	Cy5	cy5	NN	_	_	_
2282	80	80	CD	_	_	_
2283	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2284	Slide	Slide	NNP	_	_	_
2285	30	30	CD	_	_	_
2286	_	_	SYM	_	_	_
2287	Anaerobic	anaerobic	JJ	_	_	_
2288	culture	culture	NN	_	_	_
2289	_	_	SYM	_	_	_
2290	iCORM-3	icorm-3	NN	_	_	_
2291	_	_	NN	_	_	_
2292	biol	biol	NN	_	_	_
2293	rep	rep	NN	GEN	_	_
2294	2	2	CD	_	_	_
2295	_	_	CD	_	_	_
2296	Cy3	cy3	NN	_	_	_
2297	10	10	CD	_	_	_
2298	Cy5	cy5	NN	_	_	_
2299	0	0	CD	_	_	_
2300	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2301	Slide	Slide	NNP	_	_	_
2302	30	30	CD	_	_	_
2303	_	_	SYM	_	_	_
2304	Anaerobic	anaerobic	JJ	_	_	_
2305	culture	culture	NN	_	_	_
2306	_	_	SYM	_	_	_
2307	iCORM-3	icorm-3	NN	_	_	_
2308	_	_	NN	_	_	_
2309	biol	biol	NN	_	_	_
2310	rep	rep	NN	GEN	_	_
2311	2	2	CD	_	_	_
2312	_	_	CD	_	_	_
2313	Cy3	cy3	NN	_	_	_
2314	20	20	CD	_	_	_
2315	Cy5	cy5	NN	_	_	_
2316	0	0	CD	_	_	_
2317	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2318	Slide	Slide	NNP	_	_	_
2319	30	30	CD	_	_	_
2320	_	_	SYM	_	_	_
2321	Anaerobic	anaerobic	JJ	_	_	_
2322	culture	culture	NN	_	_	_
2323	_	_	SYM	_	_	_
2324	iCORM-3	icorm-3	NN	_	_	_
2325	_	_	NN	_	_	_
2326	biol	biol	NN	_	_	_
2327	rep	rep	NN	GEN	_	_
2328	2	2	CD	_	_	_
2329	_	_	CD	_	_	_
2330	Cy3	cy3	NN	_	_	_
2331	2.5	2.5	CD	_	_	_
2332	Cy5	cy5	NN	_	_	_
2333	0	0	CD	_	_	_
2334	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2335	Slide	Slide	NNP	_	_	_
2336	30	30	CD	_	_	_
2337	_	_	SYM	_	_	_
2338	Anaerobic	anaerobic	JJ	_	_	_
2339	culture	culture	NN	_	_	_
2340	_	_	SYM	_	_	_
2341	iCORM-3	icorm-3	NN	_	_	_
2342	_	_	NN	_	_	_
2343	biol	biol	NN	_	_	_
2344	rep	rep	NN	GEN	_	_
2345	2	2	CD	_	_	_
2346	_	_	CD	_	_	_
2347	Cy3	cy3	NN	_	_	_
2348	40	40	CD	_	_	_
2349	Cy5	cy5	NN	_	_	_
2350	0	0	CD	_	_	_
2351	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2352	Slide	Slide	NNP	_	_	_
2353	30	30	CD	_	_	_
2354	_	_	SYM	_	_	_
2355	Anaerobic	anaerobic	JJ	_	_	_
2356	culture	culture	NN	_	_	_
2357	_	_	SYM	_	_	_
2358	iCORM-3	icorm-3	NN	_	_	_
2359	_	_	NN	_	_	_
2360	biol	biol	NN	_	_	_
2361	rep	rep	NN	GEN	_	_
2362	2	2	CD	_	_	_
2363	_	_	CD	_	_	_
2364	Cy3	cy3	NN	_	_	_
2365	5	5	CD	_	_	_
2366	Cy5	cy5	NN	_	_	_
2367	0	0	CD	_	_	_
2368	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2369	Slide	Slide	NNP	_	_	_
2370	30	30	CD	_	_	_
2371	_	_	SYM	_	_	_
2372	Anaerobic	anaerobic	JJ	_	_	_
2373	culture	culture	NN	_	_	_
2374	_	_	SYM	_	_	_
2375	iCORM-3	icorm-3	NN	_	_	_
2376	_	_	NN	_	_	_
2377	biol	biol	NN	_	_	_
2378	rep	rep	NN	GEN	_	_
2379	2	2	CD	_	_	_
2380	_	_	CD	_	_	_
2381	Cy3	cy3	NN	_	_	_
2382	80	80	CD	_	_	_
2383	Cy5	cy5	NN	_	_	_
2384	0	0	CD	_	_	_
2385	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2386	Slide	Slide	NNP	_	_	_
2387	31	31	CD	_	_	_
2388	_	_	SYM	_	_	_
2389	Aerobic	aerobic	JJ	_	_	_
2390	culture	culture	NN	_	_	_
2391	_	_	CD	_	_	_
2392	CO	CO	NNP	_	_	_
2393	gas	gas	NN	_	_	_
2394	_	_	NN	_	_	_
2395	biol	biol	NN	_	_	_
2396	rep	rep	NN	GEN	_	_
2397	1	1	CD	_	_	_
2398	_	_	NN	_	_	_
2399	Cy3	cy3	NN	_	_	_
2400	0	0	CD	_	_	_
2401	Cy5	cy5	NN	_	_	_
2402	80	80	CD	_	_	_
2403	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2404	Slide	Slide	NNP	_	_	_
2405	31	31	CD	_	_	_
2406	_	_	SYM	_	_	_
2407	Aerobic	aerobic	JJ	_	_	_
2408	culture	culture	NN	_	_	_
2409	_	_	CD	_	_	_
2410	CO	CO	NNP	_	_	_
2411	gas	gas	NN	_	_	_
2412	_	_	NN	_	_	_
2413	biol	biol	NN	_	_	_
2414	rep	rep	NN	GEN	_	_
2415	1	1	CD	_	_	_
2416	_	_	CD	_	_	_
2417	Cy3	cy3	NN	_	_	_
2418	10	10	CD	_	_	_
2419	Cy5	cy5	NN	_	_	_
2420	0	0	CD	_	_	_
2421	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2422	Slide	Slide	NNP	_	_	_
2423	31	31	CD	_	_	_
2424	_	_	SYM	_	_	_
2425	Aerobic	aerobic	JJ	_	_	_
2426	culture	culture	NN	_	_	_
2427	_	_	CD	_	_	_
2428	CO	CO	NNP	_	_	_
2429	gas	gas	NN	_	_	_
2430	_	_	NN	_	_	_
2431	biol	biol	NN	_	_	_
2432	rep	rep	NN	GEN	_	_
2433	1	1	CD	_	_	_
2434	_	_	CD	_	_	_
2435	Cy3	cy3	NN	_	_	_
2436	20	20	CD	_	_	_
2437	Cy5	cy5	NN	_	_	_
2438	0	0	CD	_	_	_
2439	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2440	Slide	Slide	NNP	_	_	_
2441	31	31	CD	_	_	_
2442	_	_	SYM	_	_	_
2443	Aerobic	aerobic	JJ	_	_	_
2444	culture	culture	NN	_	_	_
2445	_	_	CD	_	_	_
2446	CO	CO	NNP	_	_	_
2447	gas	gas	NN	_	_	_
2448	_	_	NN	_	_	_
2449	biol	biol	NN	_	_	_
2450	rep	rep	NN	GEN	_	_
2451	1	1	CD	_	_	_
2452	_	_	CD	_	_	_
2453	Cy3	cy3	NN	_	_	_
2454	40	40	CD	_	_	_
2455	Cy5	cy5	NN	_	_	_
2456	0	0	CD	_	_	_
2457	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2458	Slide	Slide	NNP	_	_	_
2459	31	31	CD	_	_	_
2460	_	_	SYM	_	_	_
2461	Aerobic	aerobic	JJ	_	_	_
2462	culture	culture	NN	_	_	_
2463	_	_	CD	_	_	_
2464	CO	CO	NNP	_	_	_
2465	gas	gas	NN	_	_	_
2466	_	_	NN	_	_	_
2467	biol	biol	NN	_	_	_
2468	rep	rep	NN	GEN	_	_
2469	2	2	CD	_	_	_
2470	_	_	CD	_	_	_
2471	Cy3	cy3	NN	_	_	_
2472	0	0	CD	_	_	_
2473	Cy5	cy5	NN	_	_	_
2474	10	10	CD	_	_	_
2475	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2476	Slide	Slide	NNP	_	_	_
2477	31	31	CD	_	_	_
2478	_	_	SYM	_	_	_
2479	Aerobic	aerobic	JJ	_	_	_
2480	culture	culture	NN	_	_	_
2481	_	_	CD	_	_	_
2482	CO	CO	NNP	_	_	_
2483	gas	gas	NN	_	_	_
2484	_	_	NN	_	_	_
2485	biol	biol	NN	_	_	_
2486	rep	rep	NN	GEN	_	_
2487	2	2	CD	_	_	_
2488	_	_	CD	_	_	_
2489	Cy3	cy3	NN	_	_	_
2490	0	0	CD	_	_	_
2491	Cy5	cy5	NN	_	_	_
2492	20	20	CD	_	_	_
2493	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2494	Slide	Slide	NNP	_	_	_
2495	31	31	CD	_	_	_
2496	_	_	SYM	_	_	_
2497	Aerobic	aerobic	JJ	_	_	_
2498	culture	culture	NN	_	_	_
2499	_	_	CD	_	_	_
2500	CO	CO	NNP	_	_	_
2501	gas	gas	NN	_	_	_
2502	_	_	NN	_	_	_
2503	biol	biol	NN	_	_	_
2504	rep	rep	NN	GEN	_	_
2505	2	2	CD	_	_	_
2506	_	_	CD	_	_	_
2507	Cy3	cy3	NN	_	_	_
2508	0	0	CD	_	_	_
2509	Cy5	cy5	NN	_	_	_
2510	2.5	2.5	CD	_	_	_
2511	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2512	Slide	Slide	NNP	_	_	_
2513	31	31	CD	_	_	_
2514	_	_	SYM	_	_	_
2515	Aerobic	aerobic	JJ	_	_	_
2516	culture	culture	NN	_	_	_
2517	_	_	CD	_	_	_
2518	CO	CO	NNP	_	_	_
2519	gas	gas	NN	_	_	_
2520	_	_	NN	_	_	_
2521	biol	biol	NN	_	_	_
2522	rep	rep	NN	GEN	_	_
2523	2	2	CD	_	_	_
2524	_	_	CD	_	_	_
2525	Cy3	cy3	NN	_	_	_
2526	0	0	CD	_	_	_
2527	Cy5	cy5	NN	_	_	_
2528	5	5	CD	_	_	_
2529	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2530	Slide	Slide	NNP	_	_	_
2531	33	33	CD	_	_	_
2532	_	_	SYM	_	_	_
2533	Aerobic	aerobic	JJ	_	_	_
2534	culture	culture	NN	_	_	_
2535	_	_	CD	_	_	_
2536	CO	CO	NNP	_	_	_
2537	gas	gas	NN	_	_	_
2538	_	_	NN	_	_	_
2539	biol	biol	NN	_	_	_
2540	rep	rep	NN	GEN	_	_
2541	2	2	CD	_	_	_
2542	_	_	CD	_	_	_
2543	Cy3	cy3	NN	_	_	_
2544	0	0	CD	_	_	_
2545	Cy5	cy5	NN	_	_	_
2546	40	40	CD	_	_	_
2547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2548	Slide	slide	NN	_	_	_
2549	33	33	CD	_	_	_
2550	_	_	SYM	_	_	_
2551	Aerobic	aerobic	JJ	_	_	_
2552	culture	culture	NN	_	_	_
2553	_	_	CD	_	_	_
2554	CO	CO	NNP	_	_	_
2555	gas	gas	NN	_	_	_
2556	_	_	NN	_	_	_
2557	biol	biol	NN	_	_	_
2558	rep	rep	NN	GEN	_	_
2559	2	2	CD	_	_	_
2560	_	_	CD	_	_	_
2561	Cy3	cy3	NN	_	_	_
2562	0	0	CD	_	_	_
2563	Cy5	cy5	NN	_	_	_
2564	80	80	CD	_	_	_
2565	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2566	Slide	Slide	NNP	_	_	_
2567	33	33	CD	_	_	_
2568	_	_	SYM	_	_	_
2569	Aerobic	aerobic	JJ	_	_	_
2570	culture	culture	NN	_	_	_
2571	_	_	CD	_	_	_
2572	CO	CO	NNP	_	_	_
2573	gas	gas	NN	_	_	_
2574	_	_	NN	_	_	_
2575	biol	biol	NN	_	_	_
2576	rep	rep	NN	GEN	_	_
2577	2	2	CD	_	_	_
2578	_	_	CD	_	_	_
2579	Cy3	cy3	NN	_	_	_
2580	10	10	CD	_	_	_
2581	Cy5	cy5	NN	_	_	_
2582	0	0	CD	_	_	_
2583	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2584	Slide	Slide	NNP	_	_	_
2585	33	33	CD	_	_	_
2586	_	_	SYM	_	_	_
2587	Aerobic	aerobic	JJ	_	_	_
2588	culture	culture	NN	_	_	_
2589	_	_	CD	_	_	_
2590	CO	CO	NNP	_	_	_
2591	gas	gas	NN	_	_	_
2592	_	_	NN	_	_	_
2593	biol	biol	NN	_	_	_
2594	rep	rep	NN	GEN	_	_
2595	2	2	CD	_	_	_
2596	_	_	CD	_	_	_
2597	Cy3	cy3	NN	_	_	_
2598	20	20	CD	_	_	_
2599	Cy5	cy5	NN	_	_	_
2600	0	0	CD	_	_	_
2601	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2602	Slide	Slide	NNP	_	_	_
2603	33	33	CD	_	_	_
2604	_	_	SYM	_	_	_
2605	Aerobic	aerobic	JJ	_	_	_
2606	culture	culture	NN	_	_	_
2607	_	_	CD	_	_	_
2608	CO	CO	NNP	_	_	_
2609	gas	gas	NN	_	_	_
2610	_	_	NN	_	_	_
2611	biol	biol	NN	_	_	_
2612	rep	rep	NN	GEN	_	_
2613	2	2	CD	_	_	_
2614	_	_	CD	_	_	_
2615	Cy3	cy3	NN	_	_	_
2616	2.5	2.5	CD	_	_	_
2617	Cy5	cy5	NN	_	_	_
2618	0	0	CD	_	_	_
2619	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2620	Slide	Slide	NNP	_	_	_
2621	33	33	CD	_	_	_
2622	_	_	SYM	_	_	_
2623	Aerobic	aerobic	JJ	_	_	_
2624	culture	culture	NN	_	_	_
2625	_	_	CD	_	_	_
2626	CO	CO	NNP	_	_	_
2627	gas	gas	NN	_	_	_
2628	_	_	NN	_	_	_
2629	biol	biol	NN	_	_	_
2630	rep	rep	NN	GEN	_	_
2631	2	2	CD	_	_	_
2632	_	_	CD	_	_	_
2633	Cy3	cy3	NN	_	_	_
2634	40	40	CD	_	_	_
2635	Cy5	cy5	NN	_	_	_
2636	0	0	CD	_	_	_
2637	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2638	Slide	Slide	NNP	_	_	_
2639	33	33	CD	_	_	_
2640	_	_	SYM	_	_	_
2641	Aerobic	aerobic	JJ	_	_	_
2642	culture	culture	NN	_	_	_
2643	_	_	CD	_	_	_
2644	CO	CO	NNP	_	_	_
2645	gas	gas	NN	_	_	_
2646	_	_	NN	_	_	_
2647	biol	biol	NN	_	_	_
2648	rep	rep	NN	GEN	_	_
2649	2	2	CD	_	_	_
2650	_	_	CD	_	_	_
2651	Cy3	cy3	NN	_	_	_
2652	5	5	CD	_	_	_
2653	Cy5	cy5	NN	_	_	_
2654	0	0	CD	_	_	_
2655	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2656	Slide	Slide	NNP	_	_	_
2657	33	33	CD	_	_	_
2658	_	_	SYM	_	_	_
2659	Aerobic	aerobic	JJ	_	_	_
2660	culture	culture	NN	_	_	_
2661	_	_	CD	_	_	_
2662	CO	CO	NNP	_	_	_
2663	gas	gas	NN	_	_	_
2664	_	_	NN	_	_	_
2665	biol	biol	NN	_	_	_
2666	rep	rep	NN	GEN	_	_
2667	2	2	CD	_	_	_
2668	_	_	CD	_	_	_
2669	Cy3	cy3	NN	_	_	_
2670	80	80	CD	_	_	_
2671	Cy5	cy5	NN	_	_	_
2672	0	0	CD	_	_	_
2673	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2674	Slide	Slide	NNP	_	_	_
2675	34	34	CD	_	_	_
2676	_	_	SYM	_	_	_
2677	hemA	hema	NN	GEN	_	_
2678	_	_	CD	_	_	_
2679	iCORM-3	icorm-3	NN	_	_	_
2680	_	_	NN	_	_	_
2681	biol	biol	NN	_	_	_
2682	rep	rep	NN	GEN	_	_
2683	1	1	CD	_	_	_
2684	_	_	NN	_	_	_
2685	Cy3	cy3	NN	_	_	_
2686	0	0	CD	_	_	_
2687	Cy5	cy5	NN	_	_	_
2688	10	10	CD	_	_	_
2689	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2690	Slide	slide	NN	_	_	_
2691	34	34	CD	_	_	_
2692	_	_	NN	_	_	_
2693	hemA	hema	NN	GEN	_	_
2694	_	_	CD	_	_	_
2695	iCORM-3	icorm-3	NN	_	_	_
2696	_	_	NN	_	_	_
2697	biol	biol	NN	_	_	_
2698	rep	rep	NN	GEN	_	_
2699	1	1	CD	_	_	_
2700	_	_	NN	_	_	_
2701	Cy3	cy3	NN	_	_	_
2702	0	0	CD	_	_	_
2703	Cy5	cy5	NN	_	_	_
2704	120	120	CD	_	_	_
2705	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2706	Slide	slide	NN	_	_	_
2707	34	34	CD	_	_	_
2708	_	_	NN	_	_	_
2709	hemA	hema	NN	GEN	_	_
2710	_	_	CD	_	_	_
2711	iCORM-3	icorm-3	NN	_	_	_
2712	_	_	NN	_	_	_
2713	biol	biol	NN	_	_	_
2714	rep	rep	NN	GEN	_	_
2715	1	1	CD	_	_	_
2716	_	_	NN	_	_	_
2717	Cy3	cy3	NN	_	_	_
2718	0	0	CD	_	_	_
2719	Cy5	cy5	NN	_	_	_
2720	20	20	CD	_	_	_
2721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2722	Slide	slide	NN	_	_	_
2723	34	34	CD	_	_	_
2724	_	_	NN	_	_	_
2725	hemA	hema	NN	GEN	_	_
2726	_	_	CD	_	_	_
2727	iCORM-3	icorm-3	NN	_	_	_
2728	_	_	NN	_	_	_
2729	biol	biol	NN	_	_	_
2730	rep	rep	NN	GEN	_	_
2731	1	1	CD	_	_	_
2732	_	_	NN	_	_	_
2733	Cy3	cy3	NN	_	_	_
2734	0	0	CD	_	_	_
2735	Cy5	cy5	NN	_	_	_
2736	40	40	CD	_	_	_
2737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2738	Slide	slide	NN	_	_	_
2739	34	34	CD	_	_	_
2740	_	_	NN	_	_	_
2741	hemA	hema	NN	GEN	_	_
2742	_	_	CD	_	_	_
2743	iCORM-3	icorm-3	NN	_	_	_
2744	_	_	NN	_	_	_
2745	biol	biol	NN	_	_	_
2746	rep	rep	NN	GEN	_	_
2747	1	1	CD	_	_	_
2748	_	_	NN	_	_	_
2749	Cy3	cy3	NN	_	_	_
2750	0	0	CD	_	_	_
2751	Cy5	cy5	NN	_	_	_
2752	60	60	CD	_	_	_
2753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2754	Slide	slide	NN	_	_	_
2755	34	34	CD	_	_	_
2756	_	_	NN	_	_	_
2757	hemA	hema	NN	GEN	_	_
2758	_	_	CD	_	_	_
2759	iCORM-3	icorm-3	NN	_	_	_
2760	_	_	NN	_	_	_
2761	biol	biol	NN	_	_	_
2762	rep	rep	NN	GEN	_	_
2763	1	1	CD	_	_	_
2764	_	_	CD	_	_	_
2765	Cy3	cy3	NN	_	_	_
2766	10	10	CD	_	_	_
2767	Cy5	cy5	NN	_	_	_
2768	0	0	CD	_	_	_
2769	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2770	Slide	Slide	NNP	_	_	_
2771	34	34	CD	_	_	_
2772	_	_	SYM	_	_	_
2773	hemA	hema	NN	GEN	_	_
2774	_	_	CD	_	_	_
2775	iCORM-3	icorm-3	NN	_	_	_
2776	_	_	NN	_	_	_
2777	biol	biol	NN	_	_	_
2778	rep	rep	NN	GEN	_	_
2779	1	1	CD	_	_	_
2780	_	_	CD	_	_	_
2781	Cy3	cy3	NN	_	_	_
2782	20	20	CD	_	_	_
2783	Cy5	cy5	NN	_	_	_
2784	0	0	CD	_	_	_
2785	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2786	Slide	Slide	NNP	_	_	_
2787	34	34	CD	_	_	_
2788	_	_	SYM	_	_	_
2789	hemA	hema	NN	GEN	_	_
2790	_	_	CD	_	_	_
2791	iCORM-3	icorm-3	NN	_	_	_
2792	_	_	NN	_	_	_
2793	biol	biol	NN	_	_	_
2794	rep	rep	NN	GEN	_	_
2795	1	1	CD	_	_	_
2796	_	_	CD	_	_	_
2797	Cy3	cy3	NN	_	_	_
2798	40	40	CD	_	_	_
2799	Cy5	cy5	NN	_	_	_
2800	0	0	CD	_	_	_
2801	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2802	Slide	Slide	NNP	_	_	_
2803	35	35	CD	_	_	_
2804	_	_	SYM	_	_	_
2805	hemA	hema	NN	GEN	_	_
2806	_	_	CD	_	_	_
2807	iCORM-3	icorm-3	NN	_	_	_
2808	_	_	NN	_	_	_
2809	biol	biol	NN	_	_	_
2810	rep	rep	NN	GEN	_	_
2811	1	1	CD	_	_	_
2812	_	_	CD	_	_	_
2813	Cy3	cy3	NN	_	_	_
2814	120	120	CD	_	_	_
2815	Cy5	cy5	NN	_	_	_
2816	0	0	CD	_	_	_
2817	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2818	Slide	Slide	NNP	_	_	_
2819	35	35	CD	_	_	_
2820	_	_	SYM	_	_	_
2821	hemA	hema	NN	GEN	_	_
2822	_	_	CD	_	_	_
2823	iCORM-3	icorm-3	NN	_	_	_
2824	_	_	NN	_	_	_
2825	biol	biol	NN	_	_	_
2826	rep	rep	NN	GEN	_	_
2827	1	1	CD	_	_	_
2828	_	_	CD	_	_	_
2829	Cy3	cy3	NN	_	_	_
2830	60	60	CD	_	_	_
2831	Cy5	cy5	NN	_	_	_
2832	0	0	CD	_	_	_
2833	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2834	Slide	Slide	NNP	_	_	_
2835	35	35	CD	_	_	_
2836	_	_	SYM	_	_	_
2837	hemA	hema	NN	GEN	_	_
2838	_	_	CD	_	_	_
2839	iCORM-3	icorm-3	NN	_	_	_
2840	_	_	NN	_	_	_
2841	biol	biol	NN	_	_	_
2842	rep	rep	NN	GEN	_	_
2843	2	2	CD	_	_	_
2844	_	_	CD	_	_	_
2845	Cy3	cy3	NN	_	_	_
2846	0	0	CD	_	_	_
2847	Cy5	cy5	NN	_	_	_
2848	10	10	CD	_	_	_
2849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2850	Slide	slide	NN	_	_	_
2851	35	35	CD	_	_	_
2852	_	_	NN	_	_	_
2853	hemA	hema	NN	GEN	_	_
2854	_	_	CD	_	_	_
2855	iCORM-3	icorm-3	NN	_	_	_
2856	_	_	NN	_	_	_
2857	biol	biol	NN	_	_	_
2858	rep	rep	NN	GEN	_	_
2859	2	2	CD	_	_	_
2860	_	_	CD	_	_	_
2861	Cy3	cy3	NN	_	_	_
2862	0	0	CD	_	_	_
2863	Cy5	cy5	NN	_	_	_
2864	120	120	CD	_	_	_
2865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2866	Slide	slide	NN	_	_	_
2867	35	35	CD	_	_	_
2868	_	_	NN	_	_	_
2869	hemA	hema	NN	GEN	_	_
2870	_	_	CD	_	_	_
2871	iCORM-3	icorm-3	NN	_	_	_
2872	_	_	NN	_	_	_
2873	biol	biol	NN	_	_	_
2874	rep	rep	NN	GEN	_	_
2875	2	2	CD	_	_	_
2876	_	_	CD	_	_	_
2877	Cy3	cy3	NN	_	_	_
2878	0	0	CD	_	_	_
2879	Cy5	cy5	NN	_	_	_
2880	20	20	CD	_	_	_
2881	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2882	Slide	slide	NN	_	_	_
2883	35	35	CD	_	_	_
2884	_	_	NN	_	_	_
2885	hemA	hema	NN	GEN	_	_
2886	_	_	CD	_	_	_
2887	iCORM-3	icorm-3	NN	_	_	_
2888	_	_	NN	_	_	_
2889	biol	biol	NN	_	_	_
2890	rep	rep	NN	GEN	_	_
2891	2	2	CD	_	_	_
2892	_	_	CD	_	_	_
2893	Cy3	cy3	NN	_	_	_
2894	0	0	CD	_	_	_
2895	Cy5	cy5	NN	_	_	_
2896	40	40	CD	_	_	_
2897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2898	Slide	slide	NN	_	_	_
2899	35	35	CD	_	_	_
2900	_	_	NN	_	_	_
2901	hemA	hema	NN	GEN	_	_
2902	_	_	CD	_	_	_
2903	iCORM-3	icorm-3	NN	_	_	_
2904	_	_	NN	_	_	_
2905	biol	biol	NN	_	_	_
2906	rep	rep	NN	GEN	_	_
2907	2	2	CD	_	_	_
2908	_	_	CD	_	_	_
2909	Cy3	cy3	NN	_	_	_
2910	0	0	CD	_	_	_
2911	Cy5	cy5	NN	_	_	_
2912	60	60	CD	_	_	_
2913	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2914	Slide	slide	NN	_	_	_
2915	35	35	CD	_	_	_
2916	_	_	NN	_	_	_
2917	hemA	hema	NN	GEN	_	_
2918	_	_	CD	_	_	_
2919	iCORM-3	icorm-3	NN	_	_	_
2920	_	_	NN	_	_	_
2921	biol	biol	NN	_	_	_
2922	rep	rep	NN	GEN	_	_
2923	2	2	CD	_	_	_
2924	_	_	CD	_	_	_
2925	Cy3	cy3	NN	_	_	_
2926	10	10	CD	_	_	_
2927	Cy5	cy5	NN	_	_	_
2928	0	0	CD	_	_	_
2929	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2930	Slide	Slide	NNP	_	_	_
2931	36	36	CD	_	_	_
2932	_	_	SYM	_	_	_
2933	hemA	hema	NN	GEN	_	_
2934	_	_	CD	_	_	_
2935	iCORM-3	icorm-3	NN	_	_	_
2936	_	_	NN	_	_	_
2937	biol	biol	NN	_	_	_
2938	rep	rep	NN	GEN	_	_
2939	2	2	CD	_	_	_
2940	_	_	SYM	_	_	_
2941	Cy3	cy3	NN	_	_	_
2942	120	120	CD	_	_	_
2943	Cy5	cy5	NN	_	_	_
2944	0	0	CD	_	_	_
2945	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2946	Slide	Slide	NNP	_	_	_
2947	36	36	CD	_	_	_
2948	_	_	SYM	_	_	_
2949	hemA	hema	NN	GEN	_	_
2950	_	_	CD	_	_	_
2951	iCORM-3	icorm-3	NN	_	_	_
2952	_	_	NN	_	_	_
2953	biol	biol	NN	_	_	_
2954	rep	rep	NN	GEN	_	_
2955	2	2	CD	_	_	_
2956	_	_	CD	_	_	_
2957	Cy3	cy3	NN	_	_	_
2958	20	20	CD	_	_	_
2959	Cy5	cy5	NN	_	_	_
2960	0	0	CD	_	_	_
2961	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2962	Slide	Slide	NNP	_	_	_
2963	36	36	CD	_	_	_
2964	_	_	SYM	_	_	_
2965	hemA	hema	NN	GEN	_	_
2966	_	_	CD	_	_	_
2967	iCORM-3	icorm-3	NN	_	_	_
2968	_	_	NN	_	_	_
2969	biol	biol	NN	_	_	_
2970	rep	rep	NN	GEN	_	_
2971	2	2	CD	_	_	_
2972	_	_	CD	_	_	_
2973	Cy3	cy3	NN	_	_	_
2974	40	40	CD	_	_	_
2975	Cy5	cy5	NN	_	_	_
2976	0	0	CD	_	_	_
2977	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2978	Slide	Slide	NNP	_	_	_
2979	36	36	CD	_	_	_
2980	_	_	SYM	_	_	_
2981	hemA	hema	NN	GEN	_	_
2982	_	_	CD	_	_	_
2983	iCORM-3	icorm-3	NN	_	_	_
2984	_	_	NN	_	_	_
2985	biol	biol	NN	_	_	_
2986	rep	rep	NN	GEN	_	_
2987	2	2	CD	_	_	_
2988	_	_	CD	_	_	_
2989	Cy3	cy3	NN	_	_	_
2990	60	60	CD	_	_	_
2991	Cy5	cy5	NN	_	_	_
2992	0	0	CD	_	_	_
2993	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2994	Slide	Slide	NNP	_	_	_
2995	36	36	CD	_	_	_
2996	_	_	SYM	_	_	_
2997	hemA	hema	NN	GEN	_	_
2998	vs.	vs.	FW	_	_	_
2999	WT	wt	FW	_	_	_
3000	t	t	NN	_	_	_
3001	=	=	JJ	_	_	_
3002	0	0	CD	_	_	_
3003	_	_	NN	_	_	_
3004	biol	biol	NN	_	_	_
3005	rep	rep	NN	GEN	_	_
3006	1	1	CD	_	_	_
3007	_	_	CD	_	_	_
3008	Cy3	cy3	NN	_	_	_
3009	hemA	hema	NN	GEN	_	_
3010	Cy5	cy5	NN	_	_	_
3011	WT	WT	NNP	_	_	_
3012	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3013	Slide	Slide	NNP	_	_	_
3014	36	36	CD	_	_	_
3015	_	_	SYM	_	_	_
3016	hemA	hema	NN	GEN	_	_
3017	vs.	vs.	FW	_	_	_
3018	WT	wt	FW	_	_	_
3019	t	t	NN	_	_	_
3020	=	=	JJ	_	_	_
3021	0	0	CD	_	_	_
3022	_	_	NN	_	_	_
3023	biol	biol	NN	_	_	_
3024	rep	rep	NN	GEN	_	_
3025	2	2	CD	_	_	_
3026	_	_	CD	_	_	_
3027	Cy3	cy3	NN	_	_	_
3028	hemA	hema	NN	GEN	_	_
3029	Cy5	cy5	NN	_	_	_
3030	WT	wt	JJ	_	_	_
3031	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3032	Slide	slide	NN	_	_	_
3033	36	36	CD	_	_	_
3034	_	_	CD	_	_	_
3035	WT	WT	NNP	_	_	_
3036	vs.	vs.	CC	_	_	_
3037	hemA	hemA	NNP	GEN	_	_
3038	t	t	NN	_	_	_
3039	=	=	JJ	_	_	_
3040	0	0	CD	_	_	_
3041	_	_	NN	_	_	_
3042	biol	biol	NN	_	_	_
3043	rep	rep	NN	GEN	_	_
3044	1	1	CD	_	_	_
3045	_	_	CD	_	_	_
3046	Cy3	cy3	NN	_	_	_
3047	WT	WT	NNP	_	_	_
3048	Cy5	Cy5	NNP	_	_	_
3049	hemA	hemA	NNP	GEN	_	_
3050	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3051	Slide	Slide	NNP	_	_	_
3052	36	36	CD	_	_	_
3053	_	_	CD	_	_	_
3054	WT	WT	NNP	_	_	_
3055	vs.	vs.	CC	_	_	_
3056	hemA	hemA	NNP	GEN	_	_
3057	t	t	NN	_	_	_
3058	=	=	JJ	_	_	_
3059	0	0	CD	_	_	_
3060	_	_	NN	_	_	_
3061	biol	biol	NN	_	_	_
3062	rep	rep	NN	GEN	_	_
3063	2	2	CD	_	_	_
3064	_	_	CD	_	_	_
3065	Cy3	cy3	NN	_	_	_
3066	WT	wt	JJ	_	_	_
3067	Cy5	cy5	NN	_	_	_
3068	hemA	hema	NN	GEN	_	_
3069	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3070	Slide	slide	NN	_	_	_
3071	37	37	CD	_	_	_
3072	_	_	SYM	_	_	_
3073	Aerobic	aerobic	JJ	_	_	_
3074	culture	culture	NN	_	_	_
3075	_	_	CD	_	_	_
3076	CO	CO	NNP	_	_	_
3077	gas	gas	NN	_	_	_
3078	_	_	NN	_	_	_
3079	biol	biol	NN	_	_	_
3080	rep	rep	NN	GEN	_	_
3081	1	1	CD	_	_	_
3082	_	_	NN	_	_	_
3083	Cy3	cy3	NN	_	_	_
3084	0	0	CD	_	_	_
3085	Cy5	cy5	NN	_	_	_
3086	10	10	CD	_	_	_
3087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3088	Slide	slide	NN	_	_	_
3089	37	37	CD	_	_	_
3090	_	_	SYM	_	_	_
3091	Aerobic	aerobic	JJ	_	_	_
3092	culture	culture	NN	_	_	_
3093	_	_	CD	_	_	_
3094	CO	CO	NNP	_	_	_
3095	gas	gas	NN	_	_	_
3096	_	_	NN	_	_	_
3097	biol	biol	NN	_	_	_
3098	rep	rep	NN	GEN	_	_
3099	1	1	CD	_	_	_
3100	_	_	NN	_	_	_
3101	Cy3	cy3	NN	_	_	_
3102	0	0	CD	_	_	_
3103	Cy5	cy5	NN	_	_	_
3104	20	20	CD	_	_	_
3105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3106	Slide	slide	NN	_	_	_
3107	37	37	CD	_	_	_
3108	_	_	SYM	_	_	_
3109	Aerobic	aerobic	JJ	_	_	_
3110	culture	culture	NN	_	_	_
3111	_	_	CD	_	_	_
3112	CO	CO	NNP	_	_	_
3113	gas	gas	NN	_	_	_
3114	_	_	NN	_	_	_
3115	biol	biol	NN	_	_	_
3116	rep	rep	NN	GEN	_	_
3117	1	1	CD	_	_	_
3118	_	_	NN	_	_	_
3119	Cy3	cy3	NN	_	_	_
3120	0	0	CD	_	_	_
3121	Cy5	cy5	NN	_	_	_
3122	2.5	2.5	CD	_	_	_
3123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3124	Slide	slide	NN	_	_	_
3125	37	37	CD	_	_	_
3126	_	_	SYM	_	_	_
3127	Aerobic	aerobic	JJ	_	_	_
3128	culture	culture	NN	_	_	_
3129	_	_	CD	_	_	_
3130	CO	CO	NNP	_	_	_
3131	gas	gas	NN	_	_	_
3132	_	_	NN	_	_	_
3133	biol	biol	NN	_	_	_
3134	rep	rep	NN	GEN	_	_
3135	1	1	CD	_	_	_
3136	_	_	NN	_	_	_
3137	Cy3	cy3	NN	_	_	_
3138	0	0	CD	_	_	_
3139	Cy5	cy5	NN	_	_	_
3140	40	40	CD	_	_	_
3141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3142	Slide	slide	NN	_	_	_
3143	37	37	CD	_	_	_
3144	_	_	SYM	_	_	_
3145	Aerobic	aerobic	JJ	_	_	_
3146	culture	culture	NN	_	_	_
3147	_	_	CD	_	_	_
3148	CO	CO	NNP	_	_	_
3149	gas	gas	NN	_	_	_
3150	_	_	NN	_	_	_
3151	biol	biol	NN	_	_	_
3152	rep	rep	NN	GEN	_	_
3153	1	1	CD	_	_	_
3154	_	_	NN	_	_	_
3155	Cy3	cy3	NN	_	_	_
3156	0	0	CD	_	_	_
3157	Cy5	cy5	NN	_	_	_
3158	5	5	CD	_	_	_
3159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3160	Slide	slide	NN	_	_	_
3161	37	37	CD	_	_	_
3162	_	_	SYM	_	_	_
3163	Aerobic	aerobic	JJ	_	_	_
3164	culture	culture	NN	_	_	_
3165	_	_	CD	_	_	_
3166	CO	CO	NNP	_	_	_
3167	gas	gas	NN	_	_	_
3168	_	_	NN	_	_	_
3169	biol	biol	NN	_	_	_
3170	rep	rep	NN	GEN	_	_
3171	1	1	CD	_	_	_
3172	_	_	CD	_	_	_
3173	Cy3	cy3	NN	_	_	_
3174	2.5	2.5	CD	_	_	_
3175	Cy5	cy5	NN	_	_	_
3176	0	0	CD	_	_	_
3177	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3178	Slide	Slide	NNP	_	_	_
3179	37	37	CD	_	_	_
3180	_	_	SYM	_	_	_
3181	Aerobic	aerobic	JJ	_	_	_
3182	culture	culture	NN	_	_	_
3183	_	_	CD	_	_	_
3184	CO	CO	NNP	_	_	_
3185	gas	gas	NN	_	_	_
3186	_	_	NN	_	_	_
3187	biol	biol	NN	_	_	_
3188	rep	rep	NN	GEN	_	_
3189	1	1	CD	_	_	_
3190	_	_	CD	_	_	_
3191	Cy3	cy3	NN	_	_	_
3192	5	5	CD	_	_	_
3193	Cy5	cy5	NN	_	_	_
3194	0	0	CD	_	_	_
3195	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3196	Slide	Slide	NNP	_	_	_
3197	37	37	CD	_	_	_
3198	_	_	SYM	_	_	_
3199	Aerobic	aerobic	JJ	_	_	_
3200	culture	culture	NN	_	_	_
3201	_	_	CD	_	_	_
3202	CO	CO	NNP	_	_	_
3203	gas	gas	NN	_	_	_
3204	_	_	NN	_	_	_
3205	biol	biol	NN	_	_	_
3206	rep	rep	NN	GEN	_	_
3207	1	1	CD	_	_	_
3208	_	_	CD	_	_	_
3209	Cy3	cy3	NN	_	_	_
3210	80	80	CD	_	_	_
3211	Cy5	cy5	NN	_	_	_
3212	0	0	CD	_	_	_
3213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3214	Slide	Slide	NNP	_	_	_
3215	39	39	CD	_	_	_
3216	_	_	SYM	_	_	_
3217	Anaerobic	anaerobic	JJ	_	_	_
3218	culture	culture	NN	_	_	_
3219	_	_	CD	_	_	_
3220	CO	CO	NNP	_	_	_
3221	gas	gas	NN	_	_	_
3222	_	_	NN	_	_	_
3223	biol	biol	NN	_	_	_
3224	rep	rep	NN	GEN	_	_
3225	1	1	CD	_	_	_
3226	_	_	CD	_	_	_
3227	Cy3	cy3	NN	_	_	_
3228	10	10	CD	_	_	_
3229	Cy5	cy5	NN	_	_	_
3230	0	0	CD	_	_	_
3231	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3232	Slide	Slide	NNP	_	_	_
3233	39	39	CD	_	_	_
3234	_	_	SYM	_	_	_
3235	Anaerobic	anaerobic	JJ	_	_	_
3236	culture	culture	NN	_	_	_
3237	_	_	CD	_	_	_
3238	CO	CO	NNP	_	_	_
3239	gas	gas	NN	_	_	_
3240	_	_	NN	_	_	_
3241	biol	biol	NN	_	_	_
3242	rep	rep	NN	GEN	_	_
3243	1	1	CD	_	_	_
3244	_	_	CD	_	_	_
3245	Cy3	cy3	NN	_	_	_
3246	20	20	CD	_	_	_
3247	Cy5	cy5	NN	_	_	_
3248	0	0	CD	_	_	_
3249	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3250	Slide	Slide	NNP	_	_	_
3251	39	39	CD	_	_	_
3252	_	_	SYM	_	_	_
3253	Anaerobic	anaerobic	JJ	_	_	_
3254	culture	culture	NN	_	_	_
3255	_	_	CD	_	_	_
3256	CO	CO	NNP	_	_	_
3257	gas	gas	NN	_	_	_
3258	_	_	NN	_	_	_
3259	biol	biol	NN	_	_	_
3260	rep	rep	NN	GEN	_	_
3261	1	1	CD	_	_	_
3262	_	_	CD	_	_	_
3263	Cy3	cy3	NN	_	_	_
3264	40	40	CD	_	_	_
3265	Cy5	cy5	NN	_	_	_
3266	0	0	CD	_	_	_
3267	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3268	Slide	Slide	NNP	_	_	_
3269	39	39	CD	_	_	_
3270	_	_	SYM	_	_	_
3271	Anaerobic	anaerobic	JJ	_	_	_
3272	culture	culture	NN	_	_	_
3273	_	_	CD	_	_	_
3274	CO	CO	NNP	_	_	_
3275	gas	gas	NN	_	_	_
3276	_	_	NN	_	_	_
3277	biol	biol	NN	_	_	_
3278	rep	rep	NN	GEN	_	_
3279	1	1	CD	_	_	_
3280	_	_	CD	_	_	_
3281	Cy3	cy3	NN	_	_	_
3282	80	80	CD	_	_	_
3283	Cy5	cy5	NN	_	_	_
3284	0	0	CD	_	_	_
3285	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3286	Slide	Slide	NNP	_	_	_
3287	39	39	CD	_	_	_
3288	_	_	SYM	_	_	_
3289	Anaerobic	anaerobic	JJ	_	_	_
3290	culture	culture	NN	_	_	_
3291	_	_	CD	_	_	_
3292	CO	CO	NNP	_	_	_
3293	gas	gas	NN	_	_	_
3294	_	_	NN	_	_	_
3295	biol	biol	NN	_	_	_
3296	rep	rep	NN	GEN	_	_
3297	2	2	CD	_	_	_
3298	_	_	CD	_	_	_
3299	Cy3	cy3	NN	_	_	_
3300	10	10	CD	_	_	_
3301	Cy5	cy5	NN	_	_	_
3302	0	0	CD	_	_	_
3303	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3304	Slide	Slide	NNP	_	_	_
3305	39	39	CD	_	_	_
3306	_	_	SYM	_	_	_
3307	Anaerobic	anaerobic	JJ	_	_	_
3308	culture	culture	NN	_	_	_
3309	_	_	CD	_	_	_
3310	CO	CO	NNP	_	_	_
3311	gas	gas	NN	_	_	_
3312	_	_	NN	_	_	_
3313	biol	biol	NN	_	_	_
3314	rep	rep	NN	GEN	_	_
3315	2	2	CD	_	_	_
3316	_	_	CD	_	_	_
3317	Cy3	cy3	NN	_	_	_
3318	20	20	CD	_	_	_
3319	Cy5	cy5	NN	_	_	_
3320	0	0	CD	_	_	_
3321	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3322	Slide	Slide	NNP	_	_	_
3323	39	39	CD	_	_	_
3324	_	_	SYM	_	_	_
3325	Anaerobic	anaerobic	JJ	_	_	_
3326	culture	culture	NN	_	_	_
3327	_	_	CD	_	_	_
3328	CO	CO	NNP	_	_	_
3329	gas	gas	NN	_	_	_
3330	_	_	NN	_	_	_
3331	biol	biol	NN	_	_	_
3332	rep	rep	NN	GEN	_	_
3333	2	2	CD	_	_	_
3334	_	_	CD	_	_	_
3335	Cy3	cy3	NN	_	_	_
3336	40	40	CD	_	_	_
3337	Cy5	cy5	NN	_	_	_
3338	0	0	CD	_	_	_
3339	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3340	Slide	Slide	NNP	_	_	_
3341	39	39	CD	_	_	_
3342	_	_	SYM	_	_	_
3343	Anaerobic	anaerobic	JJ	_	_	_
3344	culture	culture	NN	_	_	_
3345	_	_	CD	_	_	_
3346	CO	CO	NNP	_	_	_
3347	gas	gas	NN	_	_	_
3348	_	_	NN	_	_	_
3349	biol	biol	NN	_	_	_
3350	rep	rep	NN	GEN	_	_
3351	2	2	CD	_	_	_
3352	_	_	CD	_	_	_
3353	Cy3	cy3	NN	_	_	_
3354	80	80	CD	_	_	_
3355	Cy5	cy5	NN	_	_	_
3356	0	0	CD	_	_	_
3357	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3358	Slide	Slide	NNP	_	_	_
3359	46	46	CD	_	_	_
3360	_	_	SYM	_	_	_
3361	Aerobic	aerobic	JJ	_	_	_
3362	culture	culture	NN	_	_	_
3363	_	_	NN	_	_	_
3364	CORM-401	corm-401	NN	_	_	_
3365	_	_	CD	_	_	_
3366	biol	biol	NN	_	_	_
3367	rep	rep	NN	GEN	_	_
3368	2	2	CD	_	_	_
3369	_	_	CD	_	_	_
3370	Cy3	cy3	NN	_	_	_
3371	0	0	CD	_	_	_
3372	Cy5	cy5	NN	_	_	_
3373	10	10	CD	_	_	_
3374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3375	Slide	slide	NN	_	_	_
3376	46	46	CD	_	_	_
3377	_	_	SYM	_	_	_
3378	Aerobic	aerobic	JJ	_	_	_
3379	culture	culture	NN	_	_	_
3380	_	_	NN	_	_	_
3381	CORM-401	corm-401	NN	_	_	_
3382	_	_	CD	_	_	_
3383	biol	biol	NN	_	_	_
3384	rep	rep	NN	GEN	_	_
3385	2	2	CD	_	_	_
3386	_	_	CD	_	_	_
3387	Cy3	cy3	NN	_	_	_
3388	0	0	CD	_	_	_
3389	Cy5	cy5	NN	_	_	_
3390	20	20	CD	_	_	_
3391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3392	Slide	slide	NN	_	_	_
3393	46	46	CD	_	_	_
3394	_	_	SYM	_	_	_
3395	Aerobic	aerobic	JJ	_	_	_
3396	culture	culture	NN	_	_	_
3397	_	_	NN	_	_	_
3398	CORM-401	corm-401	NN	_	_	_
3399	_	_	CD	_	_	_
3400	biol	biol	NN	_	_	_
3401	rep	rep	NN	GEN	_	_
3402	2	2	CD	_	_	_
3403	_	_	CD	_	_	_
3404	Cy3	cy3	NN	_	_	_
3405	2.5	2.5	CD	_	_	_
3406	Cy5	cy5	NN	_	_	_
3407	0	0	CD	_	_	_
3408	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3409	Slide	Slide	NNP	_	_	_
3410	46	46	CD	_	_	_
3411	_	_	SYM	_	_	_
3412	Aerobic	aerobic	JJ	_	_	_
3413	culture	culture	NN	_	_	_
3414	_	_	NN	_	_	_
3415	CORM-401	corm-401	NN	_	_	_
3416	_	_	CD	_	_	_
3417	biol	biol	NN	_	_	_
3418	rep	rep	NN	GEN	_	_
3419	2	2	CD	_	_	_
3420	_	_	CD	_	_	_
3421	Cy3	cy3	NN	_	_	_
3422	5	5	CD	_	_	_
3423	Cy5	cy5	NN	_	_	_
3424	0	0	CD	_	_	_
3425	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3426	Slide	Slide	NNP	_	_	_
3427	48	48	CD	_	_	_
3428	_	_	SYM	_	_	_
3429	Aerobic	aerobic	JJ	_	_	_
3430	culture	culture	NN	_	_	_
3431	_	_	NN	_	_	_
3432	CORM-401	corm-401	NN	_	_	_
3433	_	_	CD	_	_	_
3434	biol	biol	NN	_	_	_
3435	rep	rep	NN	GEN	_	_
3436	2	2	CD	_	_	_
3437	_	_	CD	_	_	_
3438	Cy3	cy3	NN	_	_	_
3439	0	0	CD	_	_	_
3440	Cy5	cy5	NN	_	_	_
3441	2.5	2.5	CD	_	_	_
3442	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3443	Slide	Slide	NNP	_	_	_
3444	48	48	CD	_	_	_
3445	_	_	SYM	_	_	_
3446	Aerobic	aerobic	JJ	_	_	_
3447	culture	culture	NN	_	_	_
3448	_	_	NN	_	_	_
3449	CORM-401	corm-401	NN	_	_	_
3450	_	_	CD	_	_	_
3451	biol	biol	NN	_	_	_
3452	rep	rep	NN	GEN	_	_
3453	2	2	CD	_	_	_
3454	_	_	CD	_	_	_
3455	Cy3	cy3	NN	_	_	_
3456	0	0	CD	_	_	_
3457	Cy5	cy5	NN	_	_	_
3458	40	40	CD	_	_	_
3459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3460	Slide	slide	NN	_	_	_
3461	48	48	CD	_	_	_
3462	_	_	SYM	_	_	_
3463	Aerobic	aerobic	JJ	_	_	_
3464	culture	culture	NN	_	_	_
3465	_	_	NN	_	_	_
3466	CORM-401	corm-401	NN	_	_	_
3467	_	_	CD	_	_	_
3468	biol	biol	NN	_	_	_
3469	rep	rep	NN	GEN	_	_
3470	2	2	CD	_	_	_
3471	_	_	CD	_	_	_
3472	Cy3	cy3	NN	_	_	_
3473	0	0	CD	_	_	_
3474	Cy5	cy5	NN	_	_	_
3475	5	5	CD	_	_	_
3476	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3477	Slide	Slide	NNP	_	_	_
3478	48	48	CD	_	_	_
3479	_	_	SYM	_	_	_
3480	Aerobic	aerobic	JJ	_	_	_
3481	culture	culture	NN	_	_	_
3482	_	_	NN	_	_	_
3483	CORM-401	corm-401	NN	_	_	_
3484	_	_	CD	_	_	_
3485	biol	biol	NN	_	_	_
3486	rep	rep	NN	GEN	_	_
3487	2	2	CD	_	_	_
3488	_	_	CD	_	_	_
3489	Cy3	cy3	NN	_	_	_
3490	0	0	CD	_	_	_
3491	Cy5	cy5	NN	_	_	_
3492	80	80	CD	_	_	_
3493	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3494	Slide	slide	VBP	_	_	_
3495	48	48	CD	_	_	_
3496	_	_	SYM	_	_	_
3497	Aerobic	aerobic	JJ	_	_	_
3498	culture	culture	NN	_	_	_
3499	_	_	NN	_	_	_
3500	CORM-401	corm-401	NN	_	_	_
3501	_	_	CD	_	_	_
3502	biol	biol	NN	_	_	_
3503	rep	rep	NN	GEN	_	_
3504	2	2	CD	_	_	_
3505	_	_	CD	_	_	_
3506	Cy3	cy3	NN	_	_	_
3507	10	10	CD	_	_	_
3508	Cy5	cy5	NN	_	_	_
3509	0	0	CD	_	_	_
3510	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3511	Slide	Slide	NNP	_	_	_
3512	48	48	CD	_	_	_
3513	_	_	SYM	_	_	_
3514	Aerobic	aerobic	JJ	_	_	_
3515	culture	culture	NN	_	_	_
3516	_	_	NN	_	_	_
3517	CORM-401	corm-401	NN	_	_	_
3518	_	_	CD	_	_	_
3519	biol	biol	NN	_	_	_
3520	rep	rep	NN	GEN	_	_
3521	2	2	CD	_	_	_
3522	_	_	CD	_	_	_
3523	Cy3	cy3	NN	_	_	_
3524	20	20	CD	_	_	_
3525	Cy5	cy5	NN	_	_	_
3526	0	0	CD	_	_	_
3527	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3528	Slide	Slide	NNP	_	_	_
3529	48	48	CD	_	_	_
3530	_	_	SYM	_	_	_
3531	Aerobic	aerobic	JJ	_	_	_
3532	culture	culture	NN	_	_	_
3533	_	_	NN	_	_	_
3534	CORM-401	corm-401	NN	_	_	_
3535	_	_	CD	_	_	_
3536	biol	biol	NN	_	_	_
3537	rep	rep	NN	GEN	_	_
3538	2	2	CD	_	_	_
3539	_	_	CD	_	_	_
3540	Cy3	cy3	NN	_	_	_
3541	40	40	CD	_	_	_
3542	Cy5	cy5	NN	_	_	_
3543	0	0	CD	_	_	_
3544	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3545	Slide	Slide	NNP	_	_	_
3546	48	48	CD	_	_	_
3547	_	_	SYM	_	_	_
3548	Aerobic	aerobic	JJ	_	_	_
3549	culture	culture	NN	_	_	_
3550	_	_	NN	_	_	_
3551	CORM-401	corm-401	NN	_	_	_
3552	_	_	CD	_	_	_
3553	biol	biol	NN	_	_	_
3554	rep	rep	NN	GEN	_	_
3555	2	2	CD	_	_	_
3556	_	_	CD	_	_	_
3557	Cy3	cy3	NN	_	_	_
3558	80	80	CD	_	_	_
3559	Cy5	cy5	NN	_	_	_
3560	0	0	CD	_	_	_
3561	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3562	Slide	Slide	NNP	_	_	_
3563	53	53	CD	_	_	_
3564	_	_	SYM	_	_	_
3565	Aerobic	aerobic	JJ	_	_	_
3566	culture	culture	NN	_	_	_
3567	_	_	NN	_	_	_
3568	CORM-401	corm-401	NN	_	_	_
3569	_	_	CD	_	_	_
3570	biol	biol	NN	_	_	_
3571	rep	rep	NN	GEN	_	_
3572	1	1	CD	_	_	_
3573	_	_	NN	_	_	_
3574	Cy3	cy3	NN	_	_	_
3575	0	0	CD	_	_	_
3576	Cy5	cy5	NN	_	_	_
3577	10	10	CD	_	_	_
3578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3579	Slide	slide	NN	_	_	_
3580	53	53	CD	_	_	_
3581	_	_	SYM	_	_	_
3582	Aerobic	aerobic	JJ	_	_	_
3583	culture	culture	NN	_	_	_
3584	_	_	NN	_	_	_
3585	CORM-401	corm-401	NN	_	_	_
3586	_	_	CD	_	_	_
3587	biol	biol	NN	_	_	_
3588	rep	rep	NN	GEN	_	_
3589	1	1	CD	_	_	_
3590	_	_	NN	_	_	_
3591	Cy3	cy3	NN	_	_	_
3592	0	0	CD	_	_	_
3593	Cy5	cy5	NN	_	_	_
3594	20	20	CD	_	_	_
3595	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3596	Slide	slide	NN	_	_	_
3597	53	53	CD	_	_	_
3598	_	_	SYM	_	_	_
3599	Aerobic	aerobic	JJ	_	_	_
3600	culture	culture	NN	_	_	_
3601	_	_	NN	_	_	_
3602	CORM-401	corm-401	NN	_	_	_
3603	_	_	CD	_	_	_
3604	biol	biol	NN	_	_	_
3605	rep	rep	NN	GEN	_	_
3606	1	1	CD	_	_	_
3607	_	_	NN	_	_	_
3608	Cy3	cy3	NN	_	_	_
3609	0	0	CD	_	_	_
3610	Cy5	cy5	NN	_	_	_
3611	2.5	2.5	CD	_	_	_
3612	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3613	Slide	Slide	NNP	_	_	_
3614	53	53	CD	_	_	_
3615	_	_	SYM	_	_	_
3616	Aerobic	aerobic	JJ	_	_	_
3617	culture	culture	NN	_	_	_
3618	_	_	NN	_	_	_
3619	CORM-401	corm-401	NN	_	_	_
3620	_	_	CD	_	_	_
3621	biol	biol	NN	_	_	_
3622	rep	rep	NN	GEN	_	_
3623	1	1	CD	_	_	_
3624	_	_	NN	_	_	_
3625	Cy3	cy3	NN	_	_	_
3626	0	0	CD	_	_	_
3627	Cy5	cy5	NN	_	_	_
3628	5	5	CD	_	_	_
3629	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3630	Slide	Slide	NNP	_	_	_
3631	53	53	CD	_	_	_
3632	_	_	SYM	_	_	_
3633	Anaerobic	anaerobic	JJ	_	_	_
3634	culture	culture	NN	_	_	_
3635	_	_	CD	_	_	_
3636	CO	CO	NNP	_	_	_
3637	gas	gas	NN	_	_	_
3638	_	_	NN	_	_	_
3639	biol	biol	NN	_	_	_
3640	rep	rep	NN	GEN	_	_
3641	3	3	CD	_	_	_
3642	_	_	NN	_	_	_
3643	Cy3	cy3	NN	_	_	_
3644	0	0	CD	_	_	_
3645	Cy5	cy5	NN	_	_	_
3646	2.5	2.5	CD	_	_	_
3647	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3648	Slide	Slide	NNP	_	_	_
3649	53	53	CD	_	_	_
3650	_	_	SYM	_	_	_
3651	Anaerobic	anaerobic	JJ	_	_	_
3652	culture	culture	NN	_	_	_
3653	_	_	CD	_	_	_
3654	CO	CO	NNP	_	_	_
3655	gas	gas	NN	_	_	_
3656	_	_	NN	_	_	_
3657	biol	biol	NN	_	_	_
3658	rep	rep	NN	GEN	_	_
3659	3	3	CD	_	_	_
3660	_	_	NN	_	_	_
3661	Cy3	cy3	NN	_	_	_
3662	0	0	CD	_	_	_
3663	Cy5	cy5	NN	_	_	_
3664	5	5	CD	_	_	_
3665	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3666	Slide	Slide	NNP	_	_	_
3667	53	53	CD	_	_	_
3668	_	_	SYM	_	_	_
3669	Anaerobic	anaerobic	JJ	_	_	_
3670	culture	culture	NN	_	_	_
3671	_	_	CD	_	_	_
3672	CO	CO	NNP	_	_	_
3673	gas	gas	NN	_	_	_
3674	_	_	NN	_	_	_
3675	biol	biol	NN	_	_	_
3676	rep	rep	NN	GEN	_	_
3677	3	3	CD	_	_	_
3678	_	_	NN	_	_	_
3679	Cy3	cy3	NN	_	_	_
3680	40	40	CD	_	_	_
3681	Cy5	cy5	NN	_	_	_
3682	0	0	CD	_	_	_
3683	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3684	Slide	Slide	NNP	_	_	_
3685	53	53	CD	_	_	_
3686	_	_	SYM	_	_	_
3687	Anaerobic	anaerobic	JJ	_	_	_
3688	culture	culture	NN	_	_	_
3689	_	_	CD	_	_	_
3690	CO	CO	NNP	_	_	_
3691	gas	gas	NN	_	_	_
3692	_	_	NN	_	_	_
3693	biol	biol	NN	_	_	_
3694	rep	rep	NN	GEN	_	_
3695	3	3	CD	_	_	_
3696	_	_	NN	_	_	_
3697	Cy3	cy3	NN	_	_	_
3698	80	80	CD	_	_	_
3699	Cy5	cy5	NN	_	_	_
3700	0	0	CD	_	_	_
3701	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3702	Slide	Slide	NNP	_	_	_
3703	54	54	CD	_	_	_
3704	_	_	SYM	_	_	_
3705	Aerobic	aerobic	JJ	_	_	_
3706	culture	culture	NN	_	_	_
3707	_	_	NN	_	_	_
3708	CORM-401	corm-401	NN	_	_	_
3709	_	_	CD	_	_	_
3710	biol	biol	NN	_	_	_
3711	rep	rep	NN	GEN	_	_
3712	1	1	CD	_	_	_
3713	_	_	NN	_	_	_
3714	Cy3	cy3	NN	_	_	_
3715	0	0	CD	_	_	_
3716	Cy5	cy5	NN	_	_	_
3717	40	40	CD	_	_	_
3718	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3719	Slide	slide	NN	_	_	_
3720	54	54	CD	_	_	_
3721	_	_	SYM	_	_	_
3722	Aerobic	aerobic	JJ	_	_	_
3723	culture	culture	NN	_	_	_
3724	_	_	NN	_	_	_
3725	CORM-401	corm-401	NN	_	_	_
3726	_	_	CD	_	_	_
3727	biol	biol	NN	_	_	_
3728	rep	rep	NN	GEN	_	_
3729	1	1	CD	_	_	_
3730	_	_	NN	_	_	_
3731	Cy3	cy3	NN	_	_	_
3732	0	0	CD	_	_	_
3733	Cy5	cy5	NN	_	_	_
3734	80	80	CD	_	_	_
3735	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3736	Slide	Slide	NNP	_	_	_
3737	54	54	CD	_	_	_
3738	_	_	SYM	_	_	_
3739	Aerobic	aerobic	JJ	_	_	_
3740	culture	culture	NN	_	_	_
3741	_	_	NN	_	_	_
3742	CORM-401	corm-401	NN	_	_	_
3743	_	_	CD	_	_	_
3744	biol	biol	NN	_	_	_
3745	rep	rep	NN	GEN	_	_
3746	1	1	CD	_	_	_
3747	_	_	CD	_	_	_
3748	Cy3	cy3	NN	_	_	_
3749	10	10	CD	_	_	_
3750	Cy5	cy5	NN	_	_	_
3751	0	0	CD	_	_	_
3752	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3753	Slide	Slide	NNP	_	_	_
3754	54	54	CD	_	_	_
3755	_	_	SYM	_	_	_
3756	Aerobic	aerobic	JJ	_	_	_
3757	culture	culture	NN	_	_	_
3758	_	_	NN	_	_	_
3759	CORM-401	corm-401	NN	_	_	_
3760	_	_	CD	_	_	_
3761	biol	biol	NN	_	_	_
3762	rep	rep	NN	GEN	_	_
3763	1	1	CD	_	_	_
3764	_	_	CD	_	_	_
3765	Cy3	cy3	NN	_	_	_
3766	20	20	CD	_	_	_
3767	Cy5	cy5	NN	_	_	_
3768	0	0	CD	_	_	_
3769	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3770	Slide	Slide	NNP	_	_	_
3771	54	54	CD	_	_	_
3772	_	_	SYM	_	_	_
3773	Aerobic	aerobic	JJ	_	_	_
3774	culture	culture	NN	_	_	_
3775	_	_	NN	_	_	_
3776	CORM-401	corm-401	NN	_	_	_
3777	_	_	CD	_	_	_
3778	biol	biol	NN	_	_	_
3779	rep	rep	NN	GEN	_	_
3780	1	1	CD	_	_	_
3781	_	_	CD	_	_	_
3782	Cy3	cy3	NN	_	_	_
3783	2.5	2.5	CD	_	_	_
3784	Cy5	cy5	NN	_	_	_
3785	0	0	CD	_	_	_
3786	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3787	Slide	Slide	NNP	_	_	_
3788	54	54	CD	_	_	_
3789	_	_	SYM	_	_	_
3790	Aerobic	aerobic	JJ	_	_	_
3791	culture	culture	NN	_	_	_
3792	_	_	NN	_	_	_
3793	CORM-401	corm-401	NN	_	_	_
3794	_	_	CD	_	_	_
3795	biol	biol	NN	_	_	_
3796	rep	rep	NN	GEN	_	_
3797	1	1	CD	_	_	_
3798	_	_	CD	_	_	_
3799	Cy3	cy3	NN	_	_	_
3800	40	40	CD	_	_	_
3801	Cy5	cy5	NN	_	_	_
3802	0	0	CD	_	_	_
3803	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3804	Slide	Slide	NNP	_	_	_
3805	54	54	CD	_	_	_
3806	_	_	SYM	_	_	_
3807	Aerobic	aerobic	JJ	_	_	_
3808	culture	culture	NN	_	_	_
3809	_	_	NN	_	_	_
3810	CORM-401	corm-401	NN	_	_	_
3811	_	_	CD	_	_	_
3812	biol	biol	NN	_	_	_
3813	rep	rep	NN	GEN	_	_
3814	1	1	CD	_	_	_
3815	_	_	CD	_	_	_
3816	Cy3	cy3	NN	_	_	_
3817	5	5	CD	_	_	_
3818	Cy5	cy5	NN	_	_	_
3819	0	0	CD	_	_	_
3820	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3821	Slide	Slide	NNP	_	_	_
3822	54	54	CD	_	_	_
3823	_	_	SYM	_	_	_
3824	Aerobic	aerobic	JJ	_	_	_
3825	culture	culture	NN	_	_	_
3826	_	_	NN	_	_	_
3827	CORM-401	corm-401	NN	_	_	_
3828	_	_	CD	_	_	_
3829	biol	biol	NN	_	_	_
3830	rep	rep	NN	GEN	_	_
3831	1	1	CD	_	_	_
3832	_	_	CD	_	_	_
3833	Cy3	cy3	NN	_	_	_
3834	80	80	CD	_	_	_
3835	Cy5	cy5	NN	_	_	_
3836	0	0	CD	_	_	_
3837	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3838	Slide	Slide	NNP	_	_	_
3839	55	55	CD	_	_	_
3840	_	_	SYM	_	_	_
3841	Anaerobic	anaerobic	JJ	_	_	_
3842	culture	culture	NN	_	_	_
3843	_	_	CD	_	_	_
3844	CO	CO	NNP	_	_	_
3845	gas	gas	NN	_	_	_
3846	_	_	NN	_	_	_
3847	biol	biol	NN	_	_	_
3848	rep	rep	NN	GEN	_	_
3849	3	3	CD	_	_	_
3850	_	_	NN	_	_	_
3851	Cy3	cy3	NN	_	_	_
3852	0	0	CD	_	_	_
3853	Cy5	cy5	NN	_	_	_
3854	10	10	CD	_	_	_
3855	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3856	Slide	Slide	NNP	_	_	_
3857	55	55	CD	_	_	_
3858	_	_	SYM	_	_	_
3859	Anaerobic	anaerobic	JJ	_	_	_
3860	culture	culture	NN	_	_	_
3861	_	_	CD	_	_	_
3862	CO	CO	NNP	_	_	_
3863	gas	gas	NN	_	_	_
3864	_	_	NN	_	_	_
3865	biol	biol	NN	_	_	_
3866	rep	rep	NN	GEN	_	_
3867	3	3	CD	_	_	_
3868	_	_	NN	_	_	_
3869	Cy3	cy3	NN	_	_	_
3870	0	0	CD	_	_	_
3871	Cy5	cy5	NN	_	_	_
3872	10	10	CD	_	_	_
3873	2	2	CD	_	_	_
3874	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3875	Slide	Slide	NNP	_	_	_
3876	55	55	CD	_	_	_
3877	_	_	SYM	_	_	_
3878	Anaerobic	anaerobic	JJ	_	_	_
3879	culture	culture	NN	_	_	_
3880	_	_	CD	_	_	_
3881	CO	CO	NNP	_	_	_
3882	gas	gas	NN	_	_	_
3883	_	_	NN	_	_	_
3884	biol	biol	NN	_	_	_
3885	rep	rep	NN	GEN	_	_
3886	3	3	CD	_	_	_
3887	_	_	NN	_	_	_
3888	Cy3	cy3	NN	_	_	_
3889	0	0	CD	_	_	_
3890	Cy5	cy5	NN	_	_	_
3891	20	20	CD	_	_	_
3892	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3893	Slide	Slide	NNP	_	_	_
3894	55	55	CD	_	_	_
3895	_	_	SYM	_	_	_
3896	Anaerobic	anaerobic	JJ	_	_	_
3897	culture	culture	NN	_	_	_
3898	_	_	CD	_	_	_
3899	CO	CO	NNP	_	_	_
3900	gas	gas	NN	_	_	_
3901	_	_	NN	_	_	_
3902	biol	biol	NN	_	_	_
3903	rep	rep	NN	GEN	_	_
3904	3	3	CD	_	_	_
3905	_	_	NN	_	_	_
3906	Cy3	cy3	NN	_	_	_
3907	0	0	CD	_	_	_
3908	Cy5	cy5	NN	_	_	_
3909	2.5	2.5	CD	_	_	_
3910	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3911	Slide	Slide	NNP	_	_	_
3912	55	55	CD	_	_	_
3913	_	_	SYM	_	_	_
3914	Anaerobic	anaerobic	JJ	_	_	_
3915	culture	culture	NN	_	_	_
3916	_	_	CD	_	_	_
3917	CO	CO	NNP	_	_	_
3918	gas	gas	NN	_	_	_
3919	_	_	NN	_	_	_
3920	biol	biol	NN	_	_	_
3921	rep	rep	NN	GEN	_	_
3922	3	3	CD	_	_	_
3923	_	_	NN	_	_	_
3924	Cy3	cy3	NN	_	_	_
3925	0	0	CD	_	_	_
3926	Cy5	cy5	NN	_	_	_
3927	40	40	CD	_	_	_
3928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3929	Slide	slide	NN	_	_	_
3930	55	55	CD	_	_	_
3931	_	_	SYM	_	_	_
3932	Anaerobic	anaerobic	JJ	_	_	_
3933	culture	culture	NN	_	_	_
3934	_	_	CD	_	_	_
3935	CO	CO	NNP	_	_	_
3936	gas	gas	NN	_	_	_
3937	_	_	NN	_	_	_
3938	biol	biol	NN	_	_	_
3939	rep	rep	NN	GEN	_	_
3940	3	3	CD	_	_	_
3941	_	_	NN	_	_	_
3942	Cy3	cy3	NN	_	_	_
3943	0	0	CD	_	_	_
3944	Cy5	cy5	NN	_	_	_
3945	5	5	CD	_	_	_
3946	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3947	Slide	Slide	NNP	_	_	_
3948	55	55	CD	_	_	_
3949	_	_	SYM	_	_	_
3950	Anaerobic	anaerobic	JJ	_	_	_
3951	culture	culture	NN	_	_	_
3952	_	_	CD	_	_	_
3953	CO	CO	NNP	_	_	_
3954	gas	gas	NN	_	_	_
3955	_	_	NN	_	_	_
3956	biol	biol	NN	_	_	_
3957	rep	rep	NN	GEN	_	_
3958	3	3	CD	_	_	_
3959	_	_	NN	_	_	_
3960	Cy3	cy3	NN	_	_	_
3961	2.5	2.5	CD	_	_	_
3962	Cy5	cy5	NN	_	_	_
3963	0	0	CD	_	_	_
3964	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3965	Slide	Slide	NNP	_	_	_
3966	55	55	CD	_	_	_
3967	_	_	SYM	_	_	_
3968	Anaerobic	anaerobic	JJ	_	_	_
3969	culture	culture	NN	_	_	_
3970	_	_	CD	_	_	_
3971	CO	CO	NNP	_	_	_
3972	gas	gas	NN	_	_	_
3973	_	_	NN	_	_	_
3974	biol	biol	NN	_	_	_
3975	rep	rep	NN	GEN	_	_
3976	3	3	CD	_	_	_
3977	_	_	NN	_	_	_
3978	Cy3	cy3	NN	_	_	_
3979	5	5	CD	_	_	_
3980	Cy5	cy5	NN	_	_	_
3981	0	0	CD	_	_	_
3982	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3983	Slide	Slide	NNP	_	_	_
3984	56	56	CD	_	_	_
3985	_	_	SYM	_	_	_
3986	Anaerobic	anaerobic	JJ	_	_	_
3987	culture	culture	NN	_	_	_
3988	_	_	CD	_	_	_
3989	CO	CO	NNP	_	_	_
3990	gas	gas	NN	_	_	_
3991	_	_	NN	_	_	_
3992	biol	biol	NN	_	_	_
3993	rep	rep	NN	GEN	_	_
3994	1	1	CD	_	_	_
3995	_	_	NN	_	_	_
3996	Cy3	cy3	NN	_	_	_
3997	0	0	CD	_	_	_
3998	Cy5	cy5	NN	_	_	_
3999	10	10	CD	_	_	_
4000	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4001	Slide	Slide	NNP	_	_	_
4002	56	56	CD	_	_	_
4003	_	_	SYM	_	_	_
4004	Anaerobic	anaerobic	JJ	_	_	_
4005	culture	culture	NN	_	_	_
4006	_	_	CD	_	_	_
4007	CO	CO	NNP	_	_	_
4008	gas	gas	NN	_	_	_
4009	_	_	NN	_	_	_
4010	biol	biol	NN	_	_	_
4011	rep	rep	NN	GEN	_	_
4012	1	1	CD	_	_	_
4013	_	_	NN	_	_	_
4014	Cy3	cy3	NN	_	_	_
4015	0	0	CD	_	_	_
4016	Cy5	cy5	NN	_	_	_
4017	20	20	CD	_	_	_
4018	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4019	Slide	slide	NN	_	_	_
4020	56	56	CD	_	_	_
4021	_	_	SYM	_	_	_
4022	Anaerobic	anaerobic	JJ	_	_	_
4023	culture	culture	NN	_	_	_
4024	_	_	CD	_	_	_
4025	CO	CO	NNP	_	_	_
4026	gas	gas	NN	_	_	_
4027	_	_	NN	_	_	_
4028	biol	biol	NN	_	_	_
4029	rep	rep	NN	GEN	_	_
4030	1	1	CD	_	_	_
4031	_	_	NN	_	_	_
4032	Cy3	cy3	NN	_	_	_
4033	0	0	CD	_	_	_
4034	Cy5	cy5	NN	_	_	_
4035	2.5	2.5	CD	_	_	_
4036	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4037	Slide	Slide	NNP	_	_	_
4038	56	56	CD	_	_	_
4039	_	_	SYM	_	_	_
4040	Anaerobic	anaerobic	JJ	_	_	_
4041	culture	culture	NN	_	_	_
4042	_	_	CD	_	_	_
4043	CO	CO	NNP	_	_	_
4044	gas	gas	NN	_	_	_
4045	_	_	NN	_	_	_
4046	biol	biol	NN	_	_	_
4047	rep	rep	NN	GEN	_	_
4048	1	1	CD	_	_	_
4049	_	_	NN	_	_	_
4050	Cy3	cy3	NN	_	_	_
4051	0	0	CD	_	_	_
4052	Cy5	cy5	NN	_	_	_
4053	40	40	CD	_	_	_
4054	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4055	Slide	slide	NN	_	_	_
4056	56	56	CD	_	_	_
4057	_	_	SYM	_	_	_
4058	Anaerobic	anaerobic	JJ	_	_	_
4059	culture	culture	NN	_	_	_
4060	_	_	CD	_	_	_
4061	CO	CO	NNP	_	_	_
4062	gas	gas	NN	_	_	_
4063	_	_	NN	_	_	_
4064	biol	biol	NN	_	_	_
4065	rep	rep	NN	GEN	_	_
4066	1	1	CD	_	_	_
4067	_	_	NN	_	_	_
4068	Cy3	cy3	NN	_	_	_
4069	0	0	CD	_	_	_
4070	Cy5	cy5	NN	_	_	_
4071	5	5	CD	_	_	_
4072	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4073	Slide	Slide	NNP	_	_	_
4074	56	56	CD	_	_	_
4075	_	_	SYM	_	_	_
4076	Anaerobic	anaerobic	JJ	_	_	_
4077	culture	culture	NN	_	_	_
4078	_	_	CD	_	_	_
4079	CO	CO	NNP	_	_	_
4080	gas	gas	NN	_	_	_
4081	_	_	NN	_	_	_
4082	biol	biol	NN	_	_	_
4083	rep	rep	NN	GEN	_	_
4084	1	1	CD	_	_	_
4085	_	_	NN	_	_	_
4086	Cy3	cy3	NN	_	_	_
4087	0	0	CD	_	_	_
4088	Cy5	cy5	NN	_	_	_
4089	80	80	CD	_	_	_
4090	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4091	Slide	Slide	NNP	_	_	_
4092	56	56	CD	_	_	_
4093	_	_	SYM	_	_	_
4094	Anaerobic	anaerobic	JJ	_	_	_
4095	culture	culture	NN	_	_	_
4096	_	_	CD	_	_	_
4097	CO	CO	NNP	_	_	_
4098	gas	gas	NN	_	_	_
4099	_	_	NN	_	_	_
4100	biol	biol	NN	_	_	_
4101	rep	rep	NN	GEN	_	_
4102	1	1	CD	_	_	_
4103	_	_	CD	_	_	_
4104	Cy3	cy3	NN	_	_	_
4105	2.5	2.5	CD	_	_	_
4106	Cy5	cy5	NN	_	_	_
4107	0	0	CD	_	_	_
4108	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4109	Slide	Slide	NNP	_	_	_
4110	56	56	CD	_	_	_
4111	_	_	SYM	_	_	_
4112	Anaerobic	anaerobic	JJ	_	_	_
4113	culture	culture	NN	_	_	_
4114	_	_	CD	_	_	_
4115	CO	CO	NNP	_	_	_
4116	gas	gas	NN	_	_	_
4117	_	_	NN	_	_	_
4118	biol	biol	NN	_	_	_
4119	rep	rep	NN	GEN	_	_
4120	1	1	CD	_	_	_
4121	_	_	CD	_	_	_
4122	Cy3	cy3	NN	_	_	_
4123	5	5	CD	_	_	_
4124	Cy5	cy5	NN	_	_	_
4125	0	0	CD	_	_	_
4126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4127	Slide	Slide	NNP	_	_	_
4128	58	58	CD	_	_	_
4129	_	_	SYM	_	_	_
4130	Anaerobic	anaerobic	JJ	_	_	_
4131	culture	culture	NN	_	_	_
4132	_	_	NN	_	_	_
4133	CORM-401	corm-401	NN	_	_	_
4134	_	_	CD	_	_	_
4135	biol	biol	NN	_	_	_
4136	rep	rep	NN	GEN	_	_
4137	1	1	CD	_	_	_
4138	_	_	CD	_	_	_
4139	Cy3	cy3	NN	_	_	_
4140	10	10	CD	_	_	_
4141	Cy5	cy5	NN	_	_	_
4142	0	0	CD	_	_	_
4143	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4144	Slide	Slide	NNP	_	_	_
4145	58	58	CD	_	_	_
4146	_	_	SYM	_	_	_
4147	Anaerobic	anaerobic	JJ	_	_	_
4148	culture	culture	NN	_	_	_
4149	_	_	NN	_	_	_
4150	CORM-401	corm-401	NN	_	_	_
4151	_	_	CD	_	_	_
4152	biol	biol	NN	_	_	_
4153	rep	rep	NN	GEN	_	_
4154	1	1	CD	_	_	_
4155	_	_	CD	_	_	_
4156	Cy3	cy3	NN	_	_	_
4157	20	20	CD	_	_	_
4158	Cy5	cy5	NN	_	_	_
4159	0	0	CD	_	_	_
4160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4161	Slide	Slide	NNP	_	_	_
4162	58	58	CD	_	_	_
4163	_	_	SYM	_	_	_
4164	Anaerobic	anaerobic	JJ	_	_	_
4165	culture	culture	NN	_	_	_
4166	_	_	NN	_	_	_
4167	CORM-401	corm-401	NN	_	_	_
4168	_	_	CD	_	_	_
4169	biol	biol	NN	_	_	_
4170	rep	rep	NN	GEN	_	_
4171	1	1	CD	_	_	_
4172	_	_	CD	_	_	_
4173	Cy3	cy3	NN	_	_	_
4174	40	40	CD	_	_	_
4175	Cy5	cy5	NN	_	_	_
4176	0	0	CD	_	_	_
4177	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4178	Slide	Slide	NNP	_	_	_
4179	58	58	CD	_	_	_
4180	_	_	SYM	_	_	_
4181	Anaerobic	anaerobic	JJ	_	_	_
4182	culture	culture	NN	_	_	_
4183	_	_	NN	_	_	_
4184	CORM-401	corm-401	NN	_	_	_
4185	_	_	CD	_	_	_
4186	biol	biol	NN	_	_	_
4187	rep	rep	NN	GEN	_	_
4188	1	1	CD	_	_	_
4189	_	_	CD	_	_	_
4190	Cy3	cy3	NN	_	_	_
4191	80	80	CD	_	_	_
4192	Cy5	cy5	NN	_	_	_
4193	0	0	CD	_	_	_
4194	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4195	Slide	Slide	NNP	_	_	_
4196	58	58	CD	_	_	_
4197	_	_	SYM	_	_	_
4198	Anaerobic	anaerobic	JJ	_	_	_
4199	culture	culture	NN	_	_	_
4200	_	_	NN	_	_	_
4201	CORM-401	corm-401	NN	_	_	_
4202	_	_	CD	_	_	_
4203	biol	biol	NN	_	_	_
4204	rep	rep	NN	GEN	_	_
4205	2	2	CD	_	_	_
4206	_	_	CD	_	_	_
4207	Cy3	cy3	NN	_	_	_
4208	0	0	CD	_	_	_
4209	Cy5	cy5	NN	_	_	_
4210	10	10	CD	_	_	_
4211	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4212	Slide	Slide	NNP	_	_	_
4213	58	58	CD	_	_	_
4214	_	_	SYM	_	_	_
4215	Anaerobic	anaerobic	JJ	_	_	_
4216	culture	culture	NN	_	_	_
4217	_	_	NN	_	_	_
4218	CORM-401	corm-401	NN	_	_	_
4219	_	_	CD	_	_	_
4220	biol	biol	NN	_	_	_
4221	rep	rep	NN	GEN	_	_
4222	2	2	CD	_	_	_
4223	_	_	CD	_	_	_
4224	Cy3	cy3	NN	_	_	_
4225	0	0	CD	_	_	_
4226	Cy5	cy5	NN	_	_	_
4227	20	20	CD	_	_	_
4228	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4229	Slide	Slide	NNP	_	_	_
4230	58	58	CD	_	_	_
4231	_	_	SYM	_	_	_
4232	Anaerobic	anaerobic	JJ	_	_	_
4233	culture	culture	NN	_	_	_
4234	_	_	NN	_	_	_
4235	CORM-401	corm-401	NN	_	_	_
4236	_	_	CD	_	_	_
4237	biol	biol	NN	_	_	_
4238	rep	rep	NN	GEN	_	_
4239	2	2	CD	_	_	_
4240	_	_	CD	_	_	_
4241	Cy3	cy3	NN	_	_	_
4242	0	0	CD	_	_	_
4243	Cy5	cy5	NN	_	_	_
4244	2.5	2.5	CD	_	_	_
4245	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4246	Slide	Slide	NNP	_	_	_
4247	58	58	CD	_	_	_
4248	_	_	SYM	_	_	_
4249	Anaerobic	anaerobic	JJ	_	_	_
4250	culture	culture	NN	_	_	_
4251	_	_	NN	_	_	_
4252	CORM-401	corm-401	NN	_	_	_
4253	_	_	CD	_	_	_
4254	biol	biol	NN	_	_	_
4255	rep	rep	NN	GEN	_	_
4256	2	2	CD	_	_	_
4257	_	_	CD	_	_	_
4258	Cy3	cy3	NN	_	_	_
4259	0	0	CD	_	_	_
4260	Cy5	cy5	NN	_	_	_
4261	5	5	CD	_	_	_
4262	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4263	Slide	Slide	NNP	_	_	_
4264	59	59	CD	_	_	_
4265	_	_	SYM	_	_	_
4266	Anaerobic	anaerobic	JJ	_	_	_
4267	culture	culture	NN	_	_	_
4268	_	_	NN	_	_	_
4269	CORM-401	corm-401	NN	_	_	_
4270	_	_	CD	_	_	_
4271	biol	biol	NN	_	_	_
4272	rep	rep	NN	GEN	_	_
4273	2	2	CD	_	_	_
4274	_	_	CD	_	_	_
4275	Cy3	cy3	NN	_	_	_
4276	0	0	CD	_	_	_
4277	Cy5	cy5	NN	_	_	_
4278	40	40	CD	_	_	_
4279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4280	Slide	slide	NN	_	_	_
4281	59	59	CD	_	_	_
4282	_	_	SYM	_	_	_
4283	Anaerobic	anaerobic	JJ	_	_	_
4284	culture	culture	NN	_	_	_
4285	_	_	NN	_	_	_
4286	CORM-401	corm-401	NN	_	_	_
4287	_	_	CD	_	_	_
4288	biol	biol	NN	_	_	_
4289	rep	rep	NN	GEN	_	_
4290	2	2	CD	_	_	_
4291	_	_	CD	_	_	_
4292	Cy3	cy3	NN	_	_	_
4293	0	0	CD	_	_	_
4294	Cy5	cy5	NN	_	_	_
4295	80	80	CD	_	_	_
4296	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4297	Slide	Slide	NNP	_	_	_
4298	59	59	CD	_	_	_
4299	_	_	SYM	_	_	_
4300	Anaerobic	anaerobic	JJ	_	_	_
4301	culture	culture	NN	_	_	_
4302	_	_	NN	_	_	_
4303	CORM-401	corm-401	NN	_	_	_
4304	_	_	CD	_	_	_
4305	biol	biol	NN	_	_	_
4306	rep	rep	NN	GEN	_	_
4307	2	2	CD	_	_	_
4308	_	_	CD	_	_	_
4309	Cy3	cy3	NN	_	_	_
4310	10	10	CD	_	_	_
4311	Cy5	cy5	NN	_	_	_
4312	0	0	CD	_	_	_
4313	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4314	Slide	Slide	NNP	_	_	_
4315	59	59	CD	_	_	_
4316	_	_	SYM	_	_	_
4317	Anaerobic	anaerobic	JJ	_	_	_
4318	culture	culture	NN	_	_	_
4319	_	_	NN	_	_	_
4320	CORM-401	corm-401	NN	_	_	_
4321	_	_	CD	_	_	_
4322	biol	biol	NN	_	_	_
4323	rep	rep	NN	GEN	_	_
4324	2	2	CD	_	_	_
4325	_	_	CD	_	_	_
4326	Cy3	cy3	NN	_	_	_
4327	20	20	CD	_	_	_
4328	Cy5	cy5	NN	_	_	_
4329	0	0	CD	_	_	_
4330	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4331	Slide	Slide	NNP	_	_	_
4332	59	59	CD	_	_	_
4333	_	_	SYM	_	_	_
4334	Anaerobic	anaerobic	JJ	_	_	_
4335	culture	culture	NN	_	_	_
4336	_	_	NN	_	_	_
4337	CORM-401	corm-401	NN	_	_	_
4338	_	_	CD	_	_	_
4339	biol	biol	NN	_	_	_
4340	rep	rep	NN	GEN	_	_
4341	2	2	CD	_	_	_
4342	_	_	CD	_	_	_
4343	Cy3	cy3	NN	_	_	_
4344	2.5	2.5	CD	_	_	_
4345	Cy5	cy5	NN	_	_	_
4346	0	0	CD	_	_	_
4347	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4348	Slide	Slide	NNP	_	_	_
4349	59	59	CD	_	_	_
4350	_	_	SYM	_	_	_
4351	Anaerobic	anaerobic	JJ	_	_	_
4352	culture	culture	NN	_	_	_
4353	_	_	NN	_	_	_
4354	CORM-401	corm-401	NN	_	_	_
4355	_	_	CD	_	_	_
4356	biol	biol	NN	_	_	_
4357	rep	rep	NN	GEN	_	_
4358	2	2	CD	_	_	_
4359	_	_	CD	_	_	_
4360	Cy3	cy3	NN	_	_	_
4361	40	40	CD	_	_	_
4362	Cy5	cy5	NN	_	_	_
4363	0	0	CD	_	_	_
4364	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4365	Slide	Slide	NNP	_	_	_
4366	59	59	CD	_	_	_
4367	_	_	SYM	_	_	_
4368	Anaerobic	anaerobic	JJ	_	_	_
4369	culture	culture	NN	_	_	_
4370	_	_	NN	_	_	_
4371	CORM-401	corm-401	NN	_	_	_
4372	_	_	CD	_	_	_
4373	biol	biol	NN	_	_	_
4374	rep	rep	NN	GEN	_	_
4375	2	2	CD	_	_	_
4376	_	_	CD	_	_	_
4377	Cy3	cy3	NN	_	_	_
4378	5	5	CD	_	_	_
4379	Cy5	cy5	NN	_	_	_
4380	0	0	CD	_	_	_
4381	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4382	Slide	Slide	NNP	_	_	_
4383	59	59	CD	_	_	_
4384	_	_	SYM	_	_	_
4385	Anaerobic	anaerobic	JJ	_	_	_
4386	culture	culture	NN	_	_	_
4387	_	_	NN	_	_	_
4388	CORM-401	corm-401	NN	_	_	_
4389	_	_	CD	_	_	_
4390	biol	biol	NN	_	_	_
4391	rep	rep	NN	GEN	_	_
4392	2	2	CD	_	_	_
4393	_	_	CD	_	_	_
4394	Cy3	cy3	NN	_	_	_
4395	80	80	CD	_	_	_
4396	Cy5	cy5	NN	_	_	_
4397	0	0	CD	_	_	_
4398	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4399	Slide	Slide	NNP	_	_	_
4400	70	70	CD	_	_	_
4401	_	_	SYM	_	_	_
4402	Anaerobic	anaerobic	JJ	_	_	_
4403	culture	culture	NN	_	_	_
4404	_	_	NN	_	_	_
4405	CORM-401	corm-401	NN	_	_	_
4406	_	_	CD	_	_	_
4407	biol	biol	NN	_	_	_
4408	rep	rep	NN	GEN	_	_
4409	1	1	CD	_	_	_
4410	_	_	NN	_	_	_
4411	Cy3	cy3	NN	_	_	_
4412	0	0	CD	_	_	_
4413	Cy5	cy5	NN	_	_	_
4414	10	10	CD	_	_	_
4415	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4416	Slide	Slide	NNP	_	_	_
4417	70	70	CD	_	_	_
4418	_	_	SYM	_	_	_
4419	Anaerobic	anaerobic	JJ	_	_	_
4420	culture	culture	NN	_	_	_
4421	_	_	NN	_	_	_
4422	CORM-401	corm-401	NN	_	_	_
4423	_	_	CD	_	_	_
4424	biol	biol	NN	_	_	_
4425	rep	rep	NN	GEN	_	_
4426	1	1	CD	_	_	_
4427	_	_	NN	_	_	_
4428	Cy3	cy3	NN	_	_	_
4429	0	0	CD	_	_	_
4430	Cy5	cy5	NN	_	_	_
4431	20	20	CD	_	_	_
4432	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4433	Slide	Slide	NNP	_	_	_
4434	70	70	CD	_	_	_
4435	_	_	SYM	_	_	_
4436	Anaerobic	anaerobic	JJ	_	_	_
4437	culture	culture	NN	_	_	_
4438	_	_	NN	_	_	_
4439	CORM-401	corm-401	NN	_	_	_
4440	_	_	CD	_	_	_
4441	biol	biol	NN	_	_	_
4442	rep	rep	NN	GEN	_	_
4443	1	1	CD	_	_	_
4444	_	_	NN	_	_	_
4445	Cy3	cy3	NN	_	_	_
4446	0	0	CD	_	_	_
4447	Cy5	cy5	NN	_	_	_
4448	2.5	2.5	CD	_	_	_
4449	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4450	Slide	Slide	NNP	_	_	_
4451	70	70	CD	_	_	_
4452	_	_	SYM	_	_	_
4453	Anaerobic	anaerobic	JJ	_	_	_
4454	culture	culture	NN	_	_	_
4455	_	_	NN	_	_	_
4456	CORM-401	corm-401	NN	_	_	_
4457	_	_	CD	_	_	_
4458	biol	biol	NN	_	_	_
4459	rep	rep	NN	GEN	_	_
4460	1	1	CD	_	_	_
4461	_	_	NN	_	_	_
4462	Cy3	cy3	NN	_	_	_
4463	0	0	CD	_	_	_
4464	Cy5	cy5	NN	_	_	_
4465	40	40	CD	_	_	_
4466	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4467	Slide	slide	NN	_	_	_
4468	70	70	CD	_	_	_
4469	_	_	SYM	_	_	_
4470	Anaerobic	anaerobic	JJ	_	_	_
4471	culture	culture	NN	_	_	_
4472	_	_	NN	_	_	_
4473	CORM-401	corm-401	NN	_	_	_
4474	_	_	CD	_	_	_
4475	biol	biol	NN	_	_	_
4476	rep	rep	NN	GEN	_	_
4477	1	1	CD	_	_	_
4478	_	_	NN	_	_	_
4479	Cy3	cy3	NN	_	_	_
4480	0	0	CD	_	_	_
4481	Cy5	cy5	NN	_	_	_
4482	5	5	CD	_	_	_
4483	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4484	Slide	Slide	NNP	_	_	_
4485	70	70	CD	_	_	_
4486	_	_	SYM	_	_	_
4487	Anaerobic	anaerobic	JJ	_	_	_
4488	culture	culture	NN	_	_	_
4489	_	_	NN	_	_	_
4490	CORM-401	corm-401	NN	_	_	_
4491	_	_	CD	_	_	_
4492	biol	biol	NN	_	_	_
4493	rep	rep	NN	GEN	_	_
4494	1	1	CD	_	_	_
4495	_	_	NN	_	_	_
4496	Cy3	cy3	NN	_	_	_
4497	0	0	CD	_	_	_
4498	Cy5	cy5	NN	_	_	_
4499	80	80	CD	_	_	_
4500	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4501	Slide	Slide	NNP	_	_	_
4502	70	70	CD	_	_	_
4503	_	_	SYM	_	_	_
4504	Anaerobic	anaerobic	JJ	_	_	_
4505	culture	culture	NN	_	_	_
4506	_	_	NN	_	_	_
4507	CORM-401	corm-401	NN	_	_	_
4508	_	_	CD	_	_	_
4509	biol	biol	NN	_	_	_
4510	rep	rep	NN	GEN	_	_
4511	1	1	CD	_	_	_
4512	_	_	CD	_	_	_
4513	Cy3	cy3	NN	_	_	_
4514	2.5	2.5	CD	_	_	_
4515	Cy5	cy5	NN	_	_	_
4516	0	0	CD	_	_	_
4517	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4518	Slide	Slide	NNP	_	_	_
4519	70	70	CD	_	_	_
4520	_	_	SYM	_	_	_
4521	Anaerobic	anaerobic	JJ	_	_	_
4522	culture	culture	NN	_	_	_
4523	_	_	NN	_	_	_
4524	CORM-401	corm-401	NN	_	_	_
4525	_	_	CD	_	_	_
4526	biol	biol	NN	_	_	_
4527	rep	rep	NN	GEN	_	_
4528	1	1	CD	_	_	_
4529	_	_	CD	_	_	_
4530	Cy3	cy3	NN	_	_	_
4531	5	5	CD	_	_	_
4532	Cy5	cy5	NN	_	_	_
4533	0	0	CD	_	_	_
4534	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4535	Sodium	sodium	NN	_	_	_
4536	phosphate	phosphate	NN	_	_	_
4537	-LRB-	-lrb-	-LRB-	_	_	_
4538	1/100	1/100	CD	_	_	_
4539	vol	vol	NN	_	_	_
4540	.	.	.	_	_	_

1	of	of	IN	_	_	_
2	1M	1m	NN	_	_	_
3	,	,	,	_	_	_
4	pH	ph	NN	_	_	_
5	7.6	7.6	CD	_	_	_
6	;	;	:	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	final	final	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	mid-log	mid-log	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	to	to	TO	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	final	final	JJ	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	aerobic	aerobic	JJ	_	_	_
27	or	or	CC	_	_	_
28	anaerobic	anaerobic	JJ	_	_	_
29	sparging	sparging	NN	_	_	_
30	was	be	VBD	_	_	_
31	continued	continue	VBN	_	_	_
32	for	for	IN	_	_	_
33	10	10	CD	_	_	_
34	min	min	NN	_	_	_
35	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	2.5	2.5	CD	_	_	_
3	M	m	NN	_	_	_
4	glycine	glycine	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	100mM	100mm	NN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	aerobic	aerobic	JJ	_	_	_
19	or	or	CC	_	_	_
20	anaerobic	anaerobic	JJ	_	_	_
21	sparging	sparging	NN	_	_	_
22	for	for	IN	_	_	_
23	30	30	CD	_	_	_
24	minutes	minute	NNS	_	_	_
25	to	to	TO	_	_	_
26	stop	stop	VB	_	_	_
27	the	the	DT	_	_	_
28	crosslinking	crosslinking	NN	_	_	_
29	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	spun	spin	VBN	_	_	_
4	at	at	IN	_	_	_
5	3500	3500	CD	_	_	_
6	x	x	CC	_	_	_
7	g	g	NN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	repeatedly	repeatedly	RB	_	_	_
12	with	with	IN	_	_	_
13	phosphate	phosphate	NN	_	_	_
14	buffered	buffer	VBN	_	_	_
15	saline	saline	NN	_	_	_
16	before	before	IN	_	_	_
17	being	be	VBG	_	_	_
18	frozen	freeze	VBN	_	_	_
19	at	at	IN	_	_	_
20	-80	-80	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Sodium	sodium	NN	_	_	_
3	phosphate	phosphate	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	1/100	1/100	CD	_	_	_
6	vol	vol	NN	_	_	_
7	.	.	.	_	_	_

1	of	of	IN	_	_	_
2	1M	1m	NN	_	_	_
3	,	,	,	_	_	_
4	pH	ph	NN	_	_	_
5	7.6	7.6	CD	_	_	_
6	;	;	:	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	final	final	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	mid-log	mid-log	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	formaldehyde	formaldehyde	NN	_	_	_
20	to	to	TO	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	final	final	JJ	_	_	_
24	and	and	CC	_	_	_
25	anaerobic	anaerobic	JJ	_	_	_
26	sparging	sparging	NN	_	_	_
27	was	be	VBD	_	_	_
28	continued	continue	VBN	_	_	_
29	for	for	IN	_	_	_
30	10	10	CD	_	_	_
31	min	min	NN	_	_	_
32	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	2.5	2.5	CD	_	_	_
3	M	m	NN	_	_	_
4	glycine	glycine	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	100mM	100mm	NN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	anaerobic	anaerobic	JJ	_	_	_
19	sparging	sparging	NN	_	_	_
20	for	for	IN	_	_	_
21	30	30	CD	_	_	_
22	minutes	minute	NNS	_	_	_
23	to	to	TO	_	_	_
24	stop	stop	VB	_	_	_
25	the	the	DT	_	_	_
26	crosslinking	crosslinking	NN	_	_	_
27	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	spun	spin	VBN	_	_	_
4	at	at	IN	_	_	_
5	3500	3500	CD	_	_	_
6	x	x	CC	_	_	_
7	g	g	NN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	repeatedly	repeatedly	RB	_	_	_
12	with	with	IN	_	_	_
13	phosphate	phosphate	NN	_	_	_
14	buffered	buffer	VBN	_	_	_
15	saline	saline	NN	_	_	_
16	before	before	IN	_	_	_
17	being	be	VBG	_	_	_
18	frozen	freeze	VBN	_	_	_
19	at	at	IN	_	_	_
20	-80	-80	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	from	from	IN	_	_	_
5	initial	initial	JJ	_	_	_
6	250	250	CD	_	_	_
7	mL	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	culture	culture	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	were	be	VBD	_	_	_
12	thawed	thaw	VBN	_	_	_
13	and	and	CC	_	_	_
14	resuspended	resuspend	VBN	_	_	_
15	in	in	IN	_	_	_
16	250	250	CD	_	_	_
17	μL	μl	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	1	1	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/ml	ng/ml	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	micrococcal	micrococcal	JJ	_	_	_
20	nuclease	nuclease	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	50	50	CD	_	_	_
23	units	unit	NNS	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	20	20	CD	_	_	_
27	μM	μm	NN	_	_	_
28	CaCl2	cacl2	NN	_	_	_
29	,1.2	,1.2	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	KCl	kcl	NN	_	_	_
32	,	,	,	_	_	_
33	0.3	0.3	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	,	,	,	_	_	_
37	6	6	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	sucrose	sucrose	NN	_	_	_
40	,	,	,	_	_	_
41	and	and	CC	_	_	_
42	10	10	CD	_	_	_
43	μM	μm	NN	_	_	_
44	DTT	dtt	NN	_	_	_
45	.	.	.	_	_	_

1	EDTA	edta	NN	_	_	_
2	was	be	VBD	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	mM	mm	NN	KWSUPP	_	_
7	to	to	TO	_	_	_
8	stop	stop	VB	_	_	_
9	the	the	DT	_	_	_
10	micrococcal	micrococcal	JJ	_	_	_
11	nuclease	nuclease	NN	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	were	be	VBD	_	_	_
16	spun	spin	VBN	_	_	_
17	down	down	RP	_	_	_
18	to	to	TO	_	_	_
19	remove	remove	VB	_	_	_
20	cell	cell	NN	_	_	_
21	debris	debris	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	precleared	preclear	VBN	_	_	_
6	through	through	IN	_	_	_
7	incubation	incubation	NN	_	_	_
8	with	with	IN	_	_	_
9	a	a	DT	_	_	_
10	50/50	50/50	CD	_	_	_
11	slurry	slurry	NN	_	_	_
12	of	of	IN	_	_	_
13	sepharose	sepharose	NN	_	_	_
14	protein	protein	NN	_	_	_
15	A	a	NN	_	_	_
16	beads	bead	NNS	_	_	_
17	in	in	IN	_	_	_
18	IP	IP	NNP	_	_	_
19	buffer	buffer	NN	_	_	_
20	for	for	IN	_	_	_
21	2-3	2-3	CD	_	_	_
22	hours	hour	NNS	_	_	_
23	at	at	IN	_	_	_
24	4	4	CD	_	_	_
25	°C	°c	NN	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	and	and	CC	_	_	_
8	antibody	antibody	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	pre-cleared	pre-cleared	JJ	_	_	_
14	lysate	lysate	NN	_	_	_
15	for	for	IN	_	_	_
16	an	a	DT	_	_	_
17	overnight	overnight	JJ	_	_	_
18	incubation	incubation	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	next	next	JJ	_	_	_
3	day	day	NN	_	_	_
4	,	,	,	_	_	_
5	30	30	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	50/50	50/50	CD	_	_	_
10	slurry	slurry	NN	_	_	_
11	of	of	IN	_	_	_
12	sepharose	sepharose	NN	_	_	_
13	protein	protein	NN	_	_	_
14	A	a	NN	_	_	_
15	beads	bead	NNS	_	_	_
16	in	in	IN	_	_	_
17	IP	IP	NNP	_	_	_
18	buffer	buffer	NN	_	_	_
19	was	be	VBD	_	_	_
20	added	add	VBN	_	_	_
21	to	to	TO	_	_	_
22	the	the	DT	_	_	_
23	lysate	lysate	NN	_	_	_
24	to	to	TO	_	_	_
25	capture	capture	VB	_	_	_
26	antibody-protein-DNA	antibody-protein-dna	JJ	_	_	_
27	complex	complex	NN	_	_	_
28	for	for	IN	_	_	_
29	one	one	CD	_	_	_
30	hour	hour	NN	_	_	_
31	at	at	IN	_	_	_
32	4	4	CD	_	_	_
33	°C	°c	NN	_	_	_
34	.	.	.	_	_	_

1	Beads	bead	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	washed	wash	VBN	_	_	_
5	once	once	RB	_	_	_
6	with	with	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	LiCl	licl	NN	_	_	_
11	wash	wash	NN	_	_	_
12	buffer	buffer	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	100	100	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	Tris	Tris	NNP	_	_	_
17	pH	ph	NN	_	_	_
18	8	8	CD	_	_	_
19	,	,	,	_	_	_
20	250	250	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	LiCl	licl	NN	_	_	_
23	,	,	,	_	_	_
24	2	2	CD	_	_	_
25	%	%	NN	_	_	_
26	TritonX-100	tritonx-100	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	,	,	,	_	_	_
29	twice	twice	RB	_	_	_
30	with	with	IN	_	_	_
31	600	600	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	NaCl	nacl	NN	_	_	_
34	wash	wash	NN	_	_	_
35	buffer	buffer	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	100	100	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	Tris	Tris	NNP	_	_	_
40	pH	ph	NN	_	_	_
41	8	8	CD	_	_	_
42	,	,	,	_	_	_
43	600	600	CD	_	_	_
44	mM	mm	NN	KWSUPP	_	_
45	NaCl	nacl	NN	_	_	_
46	,	,	,	_	_	_
47	2	2	CD	_	_	_
48	%	%	NN	_	_	_
49	TritonX-100	tritonx-100	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	,	,	,	_	_	_
52	twice	twice	RB	_	_	_
53	with	with	IN	_	_	_
54	300	300	CD	_	_	_
55	mM	mm	NN	KWSUPP	_	_
56	NaCl	nacl	NN	_	_	_
57	wash	wash	NN	_	_	_
58	buffer	buffer	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	100	100	CD	_	_	_
61	mM	mm	NN	KWSUPP	_	_
62	Tris	Tris	NNP	_	_	_
63	pH	ph	NN	_	_	_
64	8	8	CD	_	_	_
65	,	,	,	_	_	_
66	300	300	CD	_	_	_
67	mM	mm	NN	KWSUPP	_	_
68	NaCl	nacl	NN	_	_	_
69	,	,	,	_	_	_
70	2	2	CD	_	_	_
71	%	%	NN	_	_	_
72	TritonX-100	tritonx-100	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	,	,	,	_	_	_
75	and	and	CC	_	_	_
76	twice	twice	RB	_	_	_
77	with	with	IN	_	_	_
78	TE	te	NN	_	_	_
79	.	.	.	_	_	_

1	Elution	elution	NN	_	_	_
2	buffer	buffer	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	50	50	CD	_	_	_
5	mM	mm	NN	KWSUPP	_	_
6	Tris	Tris	NNP	_	_	_
7	pH	ph	NN	_	_	_
8	8	8	CD	_	_	_
9	,	,	,	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	EDTA	edta	NN	_	_	_
13	,	,	,	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	SDS	sds	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	after	after	IN	_	_	_
21	the	the	DT	_	_	_
22	final	final	JJ	_	_	_
23	wash	wash	NN	_	_	_
24	step	step	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	beads	bead	NNS	_	_	_
28	were	be	VBD	_	_	_
29	incubated	incubate	VBN	_	_	_
30	at	at	IN	_	_	_
31	65	65	CD	_	_	_
32	°C	°c	NN	_	_	_
33	for	for	IN	_	_	_
34	30	30	CD	_	_	_
35	minutes	minute	NNS	_	_	_
36	to	to	TO	_	_	_
37	remove	remove	VB	_	_	_
38	the	the	DT	_	_	_
39	crosslinked	crosslink	VBN	_	_	_
40	protein-DNA	protein-dna	JJ	_	_	_
41	complexes	complex	NNS	_	_	_
42	from	from	IN	_	_	_
43	the	the	DT	_	_	_
44	beads	bead	NNS	_	_	_
45	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	to	to	TO	_	_	_
4	remove	remove	VB	_	_	_
5	the	the	DT	_	_	_
6	beads	bead	NNS	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	samples	sample	NNS	_	_	_
10	were	be	VBD	_	_	_
11	incubated	incubate	VBN	_	_	_
12	overnight	overnight	RB	_	_	_
13	at	at	IN	_	_	_
14	65	65	CD	_	_	_
15	°C	°c	NN	_	_	_
16	to	to	TO	_	_	_
17	reverse	reverse	VB	_	_	_
18	the	the	DT	_	_	_
19	protein-DNA	protein-dna	JJ	_	_	_
20	formaldehyde	formaldehyde	NN	_	_	_
21	crosslinks	crosslink	NNS	_	_	_
22	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	's	's	POS	_	_	_
7	PCR	pcr	NN	_	_	_
8	Purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	and	and	CC	_	_	_
11	eluted	elute	VBN	_	_	_
12	to	to	TO	_	_	_
13	a	a	DT	_	_	_
14	final	final	JJ	_	_	_
15	volume	volume	NN	_	_	_
16	of	of	IN	_	_	_
17	50	50	CD	_	_	_
18	μl	μl	NN	_	_	_
19	with	with	IN	_	_	_
20	EB	EB	NNP	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Soil	soil	NN	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	a	a	DT	_	_	_
8	0.5	0.5	CD	_	_	_
9	g	g	NN	_	_	_
10	soil	soil	NN	_	_	_
11	sub-sample	sub-sample	NN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	MoBio	mobio	NN	_	_	_
15	DNA	dna	NN	_	_	_
16	Power	power	NN	_	_	_
17	Soil	soil	NN	_	_	_
18	kit	kit	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	MoBio	mobio	NN	_	_	_
21	Laboratories	Laboratories	NNPS	_	_	_
22	,	,	,	_	_	_
23	Carlsbad	Carlsbad	NNP	_	_	_
24	,	,	,	_	_	_
25	CA	CA	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Solvent	Solvent	NNP	_	_	_
3	control	control	NN	_	_	_
4	,	,	,	_	_	_
5	biological	biological	JJ	_	_	_
6	rep1	rep1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	Solvent	solvent	JJ	_	_	_
9	control	control	NN	_	_	_
10	,	,	,	_	_	_
11	biological	biological	JJ	_	_	_
12	rep2	rep2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	Solvent	solvent	JJ	_	_	_
15	control	control	NN	_	_	_
16	,	,	,	_	_	_
17	biological	biological	JJ	_	_	_
18	rep3	rep3	NN	_	_	_
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	1	1	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	sorted	sort	VBD	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	cells	cell	NNS	_	_	_
32	from	from	IN	_	_	_
33	culture	culture	NN	_	_	_
34	2	2	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	sorted	sort	VBD	_	_	_
37	E.	e.	FW	_	_	_
38	coli	coli	FW	_	_	_
39	cells	cell	NNS	_	_	_
40	from	from	IN	_	_	_
41	dual-species	dual-species	JJ	_	_	_
42	biofilms	biofilm	NNS	_	_	_
43	1	1	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	sorted	sort	VBD	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	cells	cell	NNS	_	_	_
49	from	from	IN	_	_	_
50	dual-species	dual-species	JJ	_	_	_
51	biofilms	biofilm	NNS	_	_	_
52	2	2	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
54	sorted	sort	VBD	_	_	_
55	E.	e.	FW	_	_	_
56	coli	coli	FW	_	_	_
57	cells	cell	NNS	_	_	_
58	from	from	IN	_	_	_
59	dual-species	dual-species	JJ	_	_	_
60	planktonic	planktonic	JJ	_	_	_
61	culture	culture	NN	_	_	_
62	1	1	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	sorted	sort	VBD	_	_	_
65	E.	e.	FW	_	_	_
66	coli	coli	FW	_	_	_
67	cells	cell	NNS	_	_	_
68	from	from	IN	_	_	_
69	dual-species	dual-species	JJ	_	_	_
70	planktonic	planktonic	JJ	_	_	_
71	culture	culture	NN	_	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
74	sorted	sort	VBD	_	_	_
75	E.	e.	FW	_	_	_
76	coli	coli	FW	_	_	_
77	cells	cell	NNS	_	_	_
78	from	from	IN	_	_	_
79	mono-species	mono-species	JJ	_	_	_
80	biofilms	biofilm	NNS	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	sorted	sort	VBD	_	_	_
84	E.	e.	FW	_	_	_
85	coli	coli	FW	_	_	_
86	cells	cell	NNS	_	_	_
87	from	from	IN	_	_	_
88	mono-species	mono-species	JJ	_	_	_
89	biofilms	biofilm	NNS	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
92	sorted	sort	VBD	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	cells	cell	NNS	_	_	_
96	from	from	IN	_	_	_
97	mono-species	mono-species	NNS	_	_	_
98	pure	pure	JJ	_	_	_
99	planktonic	planktonic	JJ	_	_	_
100	culture	culture	NN	_	_	_
101	1	1	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	sorted	sort	VBD	_	_	_
104	E.	e.	FW	_	_	_
105	coli	coli	FW	_	_	_
106	cells	cell	NNS	_	_	_
107	from	from	IN	_	_	_
108	mono-species	mono-species	NNS	_	_	_
109	pure	pure	JJ	_	_	_
110	planktonic	planktonic	JJ	_	_	_
111	culture	culture	NN	_	_	_
112	2	2	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	sorted	sort	VBD	_	_	_
115	vs.	vs.	CC	_	_	_
116	non-sorted	non-sorted	JJ	_	_	_
117	cells	cell	NNS	_	_	_
118	bioreplicate	bioreplicate	VBP	_	_	_
119	1	1	CD	_	_	_
120	technical	technical	JJ	_	_	_
121	replicate	replicate	VBP	_	_	_
122	1	1	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	sorted	sort	VBD	_	_	_
125	vs.	vs.	CC	_	_	_
126	non-sorted	non-sorted	JJ	_	_	_
127	cells	cell	NNS	_	_	_
128	bioreplicate	bioreplicate	VBP	_	_	_
129	1	1	CD	_	_	_
130	technical	technical	JJ	_	_	_
131	replicate	replicate	VB	_	_	_
132	2	2	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
134	sorted	sort	VBD	_	_	_
135	vs.	vs.	CC	_	_	_
136	non-sorted	non-sorted	JJ	_	_	_
137	cells	cell	NNS	_	_	_
138	bioreplicate	bioreplicate	VBP	_	_	_
139	2	2	CD	_	_	_
140	technical	technical	JJ	_	_	_
141	replicate	replicate	VBP	_	_	_
142	1	1	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	sorted	sort	VBD	_	_	_
145	vs.	vs.	CC	_	_	_
146	non-sorted	non-sorted	JJ	_	_	_
147	cells	cell	NNS	_	_	_
148	bioreplicate	bioreplicate	VBP	_	_	_
149	2	2	CD	_	_	_
150	technical	technical	JJ	_	_	_
151	replicate	replicate	VB	_	_	_
152	2	2	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
154	source	source	NN	_	_	_
155	:	:	:	_	_	_
156	Bustamante	Bustamante	NNP	_	_	_
157	et	et	FW	_	_	_
158	al.	al.	FW	_	_	_
159	,	,	,	_	_	_
160	2011	2011	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	source	source	NN	_	_	_
163	:	:	:	_	_	_
164	Peripheral	peripheral	JJ	_	_	_
165	blood	blood	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	soxR-8myc-tagged	soxr-8myc-tagged	JJ	_	_	_
168	_	_	NN	_	_	_
169	PQ	pq	NN	_	_	_
170	treated	treat	VBN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	SoxR	soxr	NN	TF	_	_
173	PQ	pq	NN	_	_	_
174	1	1	CD	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	SoxR	soxr	NN	TF	_	_
177	PQ	pq	NN	_	_	_
178	2	2	CD	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	soxS-8myc-tagged	soxs-8myc-tagged	JJ	_	_	_
181	_	_	NN	_	_	_
182	PQ	pq	NN	_	_	_
183	treated	treat	VBN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	SoxS	soxs	NN	TF	_	_
186	PQ	pq	NN	_	_	_
187	1	1	CD	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	SoxS	soxs	NN	TF	_	_
190	PQ	pq	NN	_	_	_
191	2	2	CD	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	sp1	sp1	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	sp2	sp2	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	Specifically	specifically	RB	_	_	_
198	,	,	,	_	_	_
199	data	datum	NNS	_	_	_
200	were	be	VBD	_	_	_
201	treated	treat	VBN	_	_	_
202	as	as	IN	_	_	_
203	two	two	CD	_	_	_
204	experiments	experiment	NNS	_	_	_
205	constituting	constitute	VBG	_	_	_
206	either	either	CC	_	_	_
207	two	two	CD	_	_	_
208	-LRB-	-lrb-	-LRB-	_	_	_
209	\	\	CD	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	specific	specific	JJ	_	_	_
212	growth	growth	NN	_	_	_
213	rate	rate	NN	_	_	_
214	0.11	0.11	CD	_	_	_
215	1/h	1/h	JJ	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	specific	specific	JJ	_	_	_
218	growth	growth	NN	_	_	_
219	rate	rate	NN	_	_	_
220	0.21	0.21	CD	_	_	_
221	1/h	1/h	JJ	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	specific	specific	JJ	_	_	_
224	growth	growth	NN	_	_	_
225	rate	rate	NN	_	_	_
226	0.26	0.26	CD	_	_	_
227	1/h	1/h	JJ	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	specific	specific	JJ	_	_	_
230	growth	growth	NN	_	_	_
231	rate	rate	NN	_	_	_
232	0.31	0.31	CD	_	_	_
233	1/h	1/h	JJ	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	specific	specific	JJ	_	_	_
236	growth	growth	NN	_	_	_
237	rate	rate	NN	_	_	_
238	0.36	0.36	CD	_	_	_
239	1/h	1/h	JJ	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	specific	specific	JJ	_	_	_
242	growth	growth	NN	_	_	_
243	rate	rate	NN	_	_	_
244	:	:	:	_	_	_
245	0.3	0.3	CD	_	_	_
246	h-1	h-1	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
248	Specific	specific	JJ	_	_	_
249	growth	growth	NN	_	_	_
250	rate	rate	NN	_	_	_
251	0.3	0.3	CD	_	_	_
252	h-1	h-1	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	specific	specific	JJ	_	_	_
255	growth	growth	NN	_	_	_
256	rate	rate	NN	_	_	_
257	0.40	0.40	CD	_	_	_
258	1/h	1/h	JJ	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	specific	specific	JJ	_	_	_
261	growth	growth	NN	_	_	_
262	rate	rate	NN	_	_	_
263	:	:	:	_	_	_
264	0.47	0.47	CD	_	_	_
265	h-1	h-1	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
267	Specific	specific	JJ	_	_	_
268	growth	growth	NN	_	_	_
269	rate	rate	NN	_	_	_
270	0.47	0.47	CD	_	_	_
271	h-1	h-1	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	specific	specific	JJ	_	_	_
274	growth	growth	NN	_	_	_
275	rate	rate	NN	_	_	_
276	0.48	0.48	CD	_	_	_
277	1/h	1/h	JJ	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	specific	specific	JJ	_	_	_
280	growth	growth	NN	_	_	_
281	rate	rate	NN	_	_	_
282	:	:	:	_	_	_
283	0.5h-1	0.5h-1	JJ	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	SPET-seq	spet-seq	NN	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	Ribo	Ribo	NNP	_	_	_
288	-	-	:	_	_	_
289	RNA	rna	NN	_	_	_
290	-RRB-	-rrb-	-RRB-	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	SPET-seq	spet-seq	NN	_	_	_
293	-LRB-	-lrb-	-LRB-	_	_	_
294	Ribo	Ribo	NNP	_	_	_
295	-	-	:	_	_	_
296	RNA	rna	NN	_	_	_
297	-RRB-	-rrb-	-RRB-	_	_	_
298	,	,	,	_	_	_
299	Replicate	replicate	VB	_	_	_
300	#	#	#	_	_	_
301	1	1	CD	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	SPET-seq	spet-seq	NN	_	_	_
304	-LRB-	-lrb-	-LRB-	_	_	_
305	Ribo	Ribo	NNP	_	_	_
306	-	-	:	_	_	_
307	RNA	rna	NN	_	_	_
308	-RRB-	-rrb-	-RRB-	_	_	_
309	,	,	,	_	_	_
310	Replicate	replicate	VB	_	_	_
311	#	#	#	_	_	_
312	2	2	CD	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	SPET-seq	spet-seq	NN	_	_	_
315	-LRB-	-lrb-	-LRB-	_	_	_
316	Total	total	JJ	_	_	_
317	RNA	rna	NN	_	_	_
318	-RRB-	-rrb-	-RRB-	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	Sphingomonas	sphingomonas	FW	_	_	_
321	sp.	sp.	FW	_	_	_
322	.	.	.	_	_	_

1	NM05	nm05	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	S.	S.	NNP	_	_	_
4	pneumoniae	pneumoniae	FW	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	mapped	map	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	D39	d39	NN	_	_	_
11	whole	whole	JJ	_	_	_
12	genome	genome	NN	_	_	_
13	with	with	IN	_	_	_
14	Rockhopper	rockhopper	JJ	_	_	_
15	version	version	NN	_	_	_
16	1.21	1.21	CD	_	_	_
17	,	,	,	_	_	_
18	using	use	VBG	_	_	_
19	default	default	NN	_	_	_
20	parameters	parameter	NNS	_	_	_
21	.	.	.	_	_	_

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	NNP	_	_	_
2	Spot	Spot	NNP	_	_	_
3	intensities	intensity	NNS	_	_	_
4	and	and	CC	_	_	_
5	corresponding	corresponding	JJ	_	_	_
6	background	background	NN	_	_	_
7	signals	signal	NNS	_	_	_
8	were	be	VBD	_	_	_
9	quantified	quantify	VBN	_	_	_
10	with	with	IN	_	_	_
11	Genepix	Genepix	NNP	_	_	_
12	Pro	pro	FW	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	version	version	NN	_	_	_
15	6	6	CD	_	_	_
16	;	;	:	_	_	_
17	Axon	Axon	NNP	_	_	_
18	Instruments	Instruments	NNPS	_	_	_
19	-LSB-	-lsb-	-LRB-	_	_	_
20	http://www.moleculardevices.com/pages/software/gn_genepix_pro.html	http://www.moleculardevices.com/pages/software/gn_genepix_pro.html	NN	_	_	_
21	-RSB-	-rsb-	-RRB-	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	Spots	spot	NNS	_	_	_
2	which	which	WDT	_	_	_
3	had	have	VBD	_	_	_
4	signal-to-noise	signal-to-noise	JJ	_	_	_
5	ratio	ratio	NN	_	_	_
6	less	less	JJR	_	_	_
7	than	than	IN	_	_	_
8	three	three	CD	_	_	_
9	were	be	VBD	_	_	_
10	filtered	filter	VBN	_	_	_
11	.	.	.	_	_	_

1	Further	further	JJ	_	_	_
2	analysis	analysis	NN	_	_	_
3	was	be	VBD	_	_	_
4	carried	carry	VBN	_	_	_
5	out	out	RP	_	_	_
6	in	in	IN	_	_	_
7	R	r	NN	_	_	_
8	environment	environment	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	version	version	NN	_	_	_
11	2.6.1	2.6.1	CD	_	_	_
12	;	;	:	_	_	_
13	-LSB-	-lsb-	-LRB-	_	_	_
14	http://www.r-project.org/	http://www.r-project.org/	NN	_	_	_
15	-RSB-	-rsb-	-RRB-	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	using	use	VBG	_	_	_
18	KTH	kth	NN	_	_	_
19	package	package	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	KTH	kth	NN	_	_	_
22	Microarray	microarray	NN	_	_	_
23	Center	center	NN	_	_	_
24	;	;	:	_	_	_
25	-LSB-	-lsb-	-LRB-	_	_	_
26	http://www.biotech.kth.se/molbio/microarray/dataanalysis/index.html	http://www.biotech.kth.se/molbio/microarray/dataanalysis/index.html	NN	_	_	_
27	-RSB-	-rsb-	-RRB-	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	Flagged	flag	VBN	_	_	_
2	spots	spot	NNS	_	_	_
3	and	and	CC	_	_	_
4	background	background	NN	_	_	_
5	were	be	VBD	_	_	_
6	extracted	extract	VBN	_	_	_
7	before	before	IN	_	_	_
8	``	``	``	_	_	_
9	printTipLoess	printtiploess	NN	_	_	_
10	''	''	''	_	_	_
11	normalization	normalization	NN	_	_	_
12	.	.	.	_	_	_

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	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	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	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/Cy5	cy3/cy5	NN	_	_	_
3	fluorescent	fluorescent	JJ	_	_	_
4	ratios	ratio	NNS	_	_	_
5	were	be	VBD	_	_	_
6	calculated	calculate	VBN	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	normalized	normalize	VBN	_	_	_
10	values	value	NNS	_	_	_
11	.	.	.	_	_	_

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/Cy5	cy3/cy5	NN	_	_	_
3	or	or	CC	_	_	_
4	Cy5/Cy3	cy5/cy3	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	test/reference	test/reference	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	fluorescent	fluorescent	JJ	_	_	_
9	ratios	ratio	NNS	_	_	_
10	were	be	VBD	_	_	_
11	calculated	calculate	VBN	_	_	_
12	from	from	IN	_	_	_
13	the	the	DT	_	_	_
14	normalized	normalize	VBN	_	_	_
15	values	value	NNS	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Spots	spot	NNS	_	_	_
3	with	with	IN	_	_	_
4	reference	reference	NN	_	_	_
5	signal	signal	NN	_	_	_
6	intensities	intensity	NNS	_	_	_
7	lower	lower	JJR	_	_	_
8	than	than	IN	_	_	_
9	the	the	DT	_	_	_
10	local	local	JJ	_	_	_
11	background	background	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	LBG	lbg	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	plus	plus	CC	_	_	_
16	5	5	CD	_	_	_
17	standard	standard	JJ	_	_	_
18	deviations	deviation	NNS	_	_	_
19	or	or	CC	_	_	_
20	with	with	IN	_	_	_
21	some	some	DT	_	_	_
22	spotting	spot	VBG	_	_	_
23	abnormalities	abnormality	NNS	_	_	_
24	were	be	VBD	_	_	_
25	removed	remove	VBN	_	_	_
26	from	from	IN	_	_	_
27	analysis	analysis	NN	_	_	_
28	.	.	.	_	_	_

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	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	ß	ß	SYM	_	_	_
103	-	-	:	_	_	_
104	Aerobic	aerobic	JJ	_	_	_
105	-	-	:	_	_	_
106	A	a	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	ß	ß	SYM	_	_	_
109	-	-	:	_	_	_
110	Aerobic	aerobic	JJ	_	_	_
111	-	-	:	_	_	_
112	B	b	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	ß	ß	SYM	_	_	_
115	-	-	:	_	_	_
116	Anaerobic	anaerobic	JJ	_	_	_
117	-	-	:	_	_	_
118	A	a	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	ß	ß	SYM	_	_	_
121	-	-	:	_	_	_
122	Anaerobic	anaerobic	JJ	_	_	_
123	-	-	:	_	_	_
124	B	b	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	ß	ß	NN	_	_	_
127	ChIP	chip	NN	_	_	_
128	DNA	dna	NN	_	_	_
129	from	from	IN	_	_	_
130	WT	WT	NNP	_	_	_
131	Escherichia	escherichia	FW	Organism	_	_
132	coli	coli	FW	Organism	_	_
133	MG1655	mg1655	NN	_	_	_
134	K-12	k-12	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	ssRNA-seq	ssrna-seq	JJ	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	ssrS	ssrs	NN	GEN	_	_
139	_	_	NN	_	_	_
140	1	1	CD	_	_	_
141	_	_	NN	_	_	_
142	input	input	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	ssrS	ssrs	NN	GEN	_	_
145	_	_	NN	_	_	_
146	1	1	CD	_	_	_
147	_	_	CD	_	_	_
148	IP	IP	NNP	_	_	_
149	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
150	ssrS	ssrs	NN	GEN	_	_
151	_	_	CD	_	_	_
152	EE	ee	NN	_	_	_
153	_	_	NN	_	_	_
154	1	1	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	ssrS	ssrs	NN	GEN	_	_
157	_	_	CD	_	_	_
158	EE	ee	NN	_	_	_
159	_	_	NN	_	_	_
160	2	2	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	ssrS	ssrs	NN	GEN	_	_
163	_	_	NN	_	_	_
164	LS	ls	NN	_	_	_
165	_	_	NN	_	_	_
166	1	1	CD	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	ssrS	ssrs	NN	GEN	_	_
169	_	_	NN	_	_	_
170	LS	ls	NN	_	_	_
171	_	_	NN	_	_	_
172	2	2	CD	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	ssrS	ssrs	NN	GEN	_	_
175	_	_	CD	_	_	_
176	ME	me	NN	_	_	_
177	_	_	NN	_	_	_
178	1	1	CD	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	ssrS	ssrs	NN	GEN	_	_
181	_	_	CD	_	_	_
182	ME	me	NN	_	_	_
183	_	_	NN	_	_	_
184	2	2	CD	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	ssrS	ssrs	NN	GEN	_	_
187	_	_	CD	_	_	_
188	S	s	NN	_	_	_
189	_	_	NN	_	_	_
190	1	1	CD	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	ssrS	ssrs	NN	GEN	_	_
193	_	_	CD	_	_	_
194	S	s	NN	_	_	_
195	_	_	NN	_	_	_
196	2	2	CD	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	ssrS	ssrs	NN	GEN	_	_
199	_	_	CD	_	_	_
200	TS	ts	NN	_	_	_
201	_	_	NN	_	_	_
202	1	1	CD	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	ssrS	ssrs	NN	GEN	_	_
205	_	_	CD	_	_	_
206	TS	ts	NN	_	_	_
207	_	_	NN	_	_	_
208	2	2	CD	_	_	_
209	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
210	Stage	Stage	NNP	_	_	_
211	:	:	:	_	_	_
212	logarithm	logarithm	NN	_	_	_
213	phase	phase	NN	_	_	_
214	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
215	Standard	Standard	NNP	_	_	_
216	Affymetrix	Affymetrix	NNP	_	_	_
217	procedure	procedure	NN	_	_	_
218	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
219	Standard	Standard	NNP	_	_	_
220	hot-phenol	hot-phenol	NN	_	_	_
221	method	method	NN	_	_	_
222	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
223	Standard	Standard	NNP	_	_	_
224	illumina	illumina	NNP	_	_	_
225	library	library	NN	_	_	_
226	construction	construction	NN	_	_	_
227	protocol	protocol	NN	_	_	_
228	for	for	IN	_	_	_
229	ChIP	chip	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	standard	standard	NN	_	_	_
232	in	in	FW	_	_	_
233	vitro	vitro	FW	_	_	_
234	-LRB-	-lrb-	-LRB-	_	_	_
235	Mg2	mg2	NN	_	_	_
236	+	+	CC	_	_	_
237	-RRB-	-rrb-	-RRB-	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
239	standard	standard	NN	_	_	_
240	in	in	FW	_	_	_
241	vitro	vitro	FW	_	_	_
242	MgCl2	mgcl2	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	Standard	standard	JJ	_	_	_
245	library	library	NN	_	_	_
246	construction	construction	NN	_	_	_
247	for	for	IN	_	_	_
248	Illumina	Illumina	NNP	_	_	_
249	Hiseq2500	hiseq2500	NN	_	_	_
250	sequencing	sequencing	NN	_	_	_
251	platform	platform	NN	_	_	_
252	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
253	Standard	Standard	NNP	_	_	_
254	Paired-End	Paired-End	NNP	_	_	_
255	Illumina	Illumina	NNP	_	_	_
256	Library	Library	NNP	_	_	_
257	Construction	Construction	NNP	_	_	_
258	Protocol	Protocol	NNP	_	_	_
259	was	be	VBD	_	_	_
260	used	use	VBN	_	_	_
261	with	with	IN	_	_	_
262	modified	modify	VBN	_	_	_
263	adapters	adapter	NNS	_	_	_
264	containing	contain	VBG	_	_	_
265	optimized	optimize	VBN	_	_	_
266	20	20	CD	_	_	_
267	bp	bp	NN	_	_	_
268	barcode	barcode	NN	_	_	_
269	sequences	sequence	NNS	_	_	_
270	-LRB-	-lrb-	-LRB-	_	_	_
271	see	see	VB	_	_	_
272	original	original	JJ	_	_	_
273	paper	paper	NN	_	_	_
274	-RRB-	-rrb-	-RRB-	_	_	_
275	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Starting	start	VBG	_	_	_
3	from	from	IN	_	_	_
4	single	single	JJ	_	_	_
5	colonies	colony	NNS	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	following	follow	VBG	_	_	_
9	cultures	culture	NNS	_	_	_
10	were	be	VBD	_	_	_
11	set	set	VBN	_	_	_
12	up	up	RP	_	_	_
13	in	in	IN	_	_	_
14	triplicate	triplicate	NN	_	_	_
15	for	for	IN	_	_	_
16	overnight	overnight	JJ	_	_	_
17	incubation	incubation	NN	_	_	_
18	:	:	:	_	_	_
19	GJ13507	gj13507	NN	_	_	_
20	,	,	,	_	_	_
21	GJ13531	gj13531	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	GJ13533	gj13533	NN	_	_	_
25	in	in	IN	_	_	_
26	glucose-minimal	glucose-minimal	JJ	_	_	_
27	A	a	NN	_	_	_
28	;	;	:	_	_	_
29	and	and	CC	_	_	_
30	GJ13519	gj13519	NN	_	_	_
31	also	also	RB	_	_	_
32	in	in	IN	_	_	_
33	0.2	0.2	CD	_	_	_
34	%	%	NN	_	_	_
35	glycerol-minimal	glycerol-minimal	JJ	_	_	_
36	A.	a.	NN	_	_	_
37	All	all	PDT	_	_	_
38	the	the	DT	_	_	_
39	cultures	culture	NNS	_	_	_
40	were	be	VBD	_	_	_
41	supplemented	supplement	VBN	_	_	_
42	with	with	IN	_	_	_
43	200	200	CD	_	_	_
44	μM	μm	NN	_	_	_
45	IPTG	iptg	NN	_	_	_
46	,	,	,	_	_	_
47	with	with	IN	_	_	_
48	the	the	DT	_	_	_
49	exception	exception	NN	_	_	_
50	of	of	IN	_	_	_
51	the	the	DT	_	_	_
52	cultures	culture	NNS	_	_	_
53	of	of	IN	_	_	_
54	GJ13507	gj13507	NN	_	_	_
55	whose	whose	WP$	_	_	_
56	supplementation	supplementation	NN	_	_	_
57	with	with	IN	_	_	_
58	IPTG	iptg	NN	_	_	_
59	was	be	VBD	_	_	_
60	at	at	IN	_	_	_
61	3	3	CD	_	_	_
62	μM	μm	NN	_	_	_
63	.	.	.	_	_	_

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	NN	_	_	_
55	stationary	stationary	JJ	_	_	_
56	culture	culture	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	stationary	stationary	JJ	GrowthPhase	_	_
59	phase	phase	NN	GrowthPhase	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Stationary	stationary	JJ	_	_	_
62	phase	phase	NN	_	_	_
63	culture	culture	NN	_	_	_
64	of	of	IN	_	_	_
65	EDL933	edl933	NN	_	_	_
66	rpoS	rpos	NN	GEN	_	_
67	mutants	mutant	NNS	_	_	_
68	in	in	IN	_	_	_
69	LB	lb	NN	_	_	_
70	at	at	IN	_	_	_
71	OD600	od600	NN	_	_	_
72	of	of	IN	_	_	_
73	1.5	1.5	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
75	Stationary	stationary	JJ	_	_	_
76	phase	phase	NN	_	_	_
77	culture	culture	NN	_	_	_
78	of	of	IN	_	_	_
79	EDL933	edl933	NN	_	_	_
80	wild	wild	JJ	_	_	_
81	type	type	NN	_	_	_
82	in	in	IN	_	_	_
83	LB	lb	NN	_	_	_
84	at	at	IN	_	_	_
85	OD600	od600	NN	_	_	_
86	of	of	IN	_	_	_
87	1.5	1.5	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
89	Stationary	stationary	JJ	_	_	_
90	phase	phase	NN	_	_	_
91	growth	growth	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	24	24	CD	_	_	_
94	hr	hr	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	~	~	NN	_	_	_
97	8	8	CD	_	_	_
98	log	log	NN	_	_	_
99	CFU/ml	cfu/ml	NN	_	_	_
100	was	be	VBD	_	_	_
101	centrifuged	centrifuge	VBN	_	_	_
102	at	at	IN	_	_	_
103	8000xg	8000xg	CD	_	_	_
104	4C	4c	NN	_	_	_
105	and	and	CC	_	_	_
106	resuspended	resuspend	VBN	_	_	_
107	in	in	IN	_	_	_
108	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
109	broth	broth	NN	_	_	_
110	with	with	IN	_	_	_
111	0.5	0.5	CD	_	_	_
112	%	%	NN	_	_	_
113	sodium	sodium	NN	_	_	_
114	benozate	benozate	NN	_	_	_
115	for	for	IN	_	_	_
116	15	15	CD	_	_	_
117	minutes	minute	NNS	_	_	_
118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
119	Stationary	stationary	JJ	_	_	_
120	phase	phase	NN	_	_	_
121	growth	growth	NN	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	24	24	CD	_	_	_
124	hr	hr	NN	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	~	~	NN	_	_	_
127	8	8	CD	_	_	_
128	log	log	NN	_	_	_
129	CFU/ml	cfu/ml	NN	_	_	_
130	was	be	VBD	_	_	_
131	centrifuged	centrifuge	VBN	_	_	_
132	at	at	IN	_	_	_
133	8000xg	8000xg	CD	_	_	_
134	4C	4c	NN	_	_	_
135	and	and	CC	_	_	_
136	resuspended	resuspend	VBN	_	_	_
137	in	in	IN	_	_	_
138	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
139	broth	broth	NN	_	_	_
140	with	with	IN	_	_	_
141	0.5	0.5	CD	_	_	_
142	%	%	NN	_	_	_
143	sodium	sodium	NN	_	_	_
144	benozate	benozate	NN	_	_	_
145	for	for	IN	_	_	_
146	30	30	CD	_	_	_
147	minutes	minute	NNS	_	_	_
148	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
149	Stationary	stationary	JJ	_	_	_
150	phase	phase	NN	_	_	_
151	growth	growth	NN	_	_	_
152	-LRB-	-lrb-	-LRB-	_	_	_
153	24	24	CD	_	_	_
154	hr	hr	NN	_	_	_
155	-RRB-	-rrb-	-RRB-	_	_	_
156	~	~	NN	_	_	_
157	8	8	CD	_	_	_
158	log	log	NN	_	_	_
159	CFU/ml	cfu/ml	NN	_	_	_
160	was	be	VBD	_	_	_
161	centrifuged	centrifuge	VBN	_	_	_
162	at	at	IN	_	_	_
163	8000xg	8000xg	CD	_	_	_
164	4C	4c	NN	_	_	_
165	and	and	CC	_	_	_
166	resuspended	resuspend	VBN	_	_	_
167	in	in	IN	_	_	_
168	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
169	broth	broth	NN	_	_	_
170	with	with	IN	_	_	_
171	0.5	0.5	CD	_	_	_
172	%	%	NN	_	_	_
173	sodium	sodium	NN	_	_	_
174	benozate	benozate	NN	_	_	_
175	for	for	IN	_	_	_
176	5	5	CD	_	_	_
177	minutes	minute	NNS	_	_	_
178	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
179	Stationary	stationary	JJ	_	_	_
180	phase	phase	NN	_	_	_
181	growth	growth	NN	_	_	_
182	-LRB-	-lrb-	-LRB-	_	_	_
183	24	24	CD	_	_	_
184	hr	hr	NN	_	_	_
185	-RRB-	-rrb-	-RRB-	_	_	_
186	~	~	NN	_	_	_
187	8	8	CD	_	_	_
188	log	log	NN	_	_	_
189	CFU/ml	cfu/ml	NN	_	_	_
190	was	be	VBD	_	_	_
191	centrifuged	centrifuge	VBN	_	_	_
192	at	at	IN	_	_	_
193	8000xg	8000xg	CD	_	_	_
194	4C	4c	NN	_	_	_
195	and	and	CC	_	_	_
196	resuspended	resuspend	VBN	_	_	_
197	in	in	IN	_	_	_
198	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
199	broth	broth	NN	_	_	_
200	with	with	IN	_	_	_
201	0.5	0.5	CD	_	_	_
202	%	%	NN	_	_	_
203	sodium	sodium	NN	_	_	_
204	benozate	benozate	NN	_	_	_
205	for	for	IN	_	_	_
206	60	60	CD	_	_	_
207	minutes	minute	NNS	_	_	_
208	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
209	Stationary	stationary	JJ	_	_	_
210	phase	phase	NN	_	_	_
211	growth	growth	NN	_	_	_
212	-LRB-	-lrb-	-LRB-	_	_	_
213	24	24	CD	_	_	_
214	hr	hr	NN	_	_	_
215	-RRB-	-rrb-	-RRB-	_	_	_
216	~	~	NN	_	_	_
217	8	8	CD	_	_	_
218	log	log	NN	_	_	_
219	CFU/ml	cfu/ml	NN	_	_	_
220	was	be	VBD	_	_	_
221	centrifuged	centrifuge	VBN	_	_	_
222	at	at	IN	_	_	_
223	8000xg	8000xg	CD	_	_	_
224	4C	4c	NN	_	_	_
225	and	and	CC	_	_	_
226	resuspended	resuspend	VBN	_	_	_
227	in	in	IN	_	_	_
228	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
229	broth	broth	NN	_	_	_
230	with	with	IN	_	_	_
231	0.5	0.5	CD	_	_	_
232	%	%	NN	_	_	_
233	-LRB-	-lrb-	-LRB-	_	_	_
234	w/v	w/v	NN	_	_	_
235	-RRB-	-rrb-	-RRB-	_	_	_
236	sodium	sodium	NN	_	_	_
237	benozate	benozate	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	Stationary	stationary	JJ	_	_	_
240	phase	phase	NN	_	_	_
241	growth	growth	NN	_	_	_
242	-LRB-	-lrb-	-LRB-	_	_	_
243	24	24	CD	_	_	_
244	hr	hr	NN	_	_	_
245	-RRB-	-rrb-	-RRB-	_	_	_
246	~	~	NN	_	_	_
247	8	8	CD	_	_	_
248	log	log	NN	_	_	_
249	CFU/ml	cfu/ml	NN	_	_	_
250	was	be	VBD	_	_	_
251	centrifuged	centrifuge	VBN	_	_	_
252	at	at	IN	_	_	_
253	8000xg	8000xg	CD	_	_	_
254	4C	4c	NN	_	_	_
255	and	and	CC	_	_	_
256	resuspended	resuspend	VBN	_	_	_
257	in	in	IN	_	_	_
258	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
259	broth	broth	NN	_	_	_
260	with	with	IN	_	_	_
261	0	0	CD	_	_	_
262	%	%	NN	_	_	_
263	sodium	sodium	NN	_	_	_
264	benozate	benozate	NN	_	_	_
265	for	for	IN	_	_	_
266	15	15	CD	_	_	_
267	minutes	minute	NNS	_	_	_
268	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
269	Stationary	stationary	JJ	_	_	_
270	phase	phase	NN	_	_	_
271	growth	growth	NN	_	_	_
272	-LRB-	-lrb-	-LRB-	_	_	_
273	24	24	CD	_	_	_
274	hr	hr	NN	_	_	_
275	-RRB-	-rrb-	-RRB-	_	_	_
276	~	~	NN	_	_	_
277	8	8	CD	_	_	_
278	log	log	NN	_	_	_
279	CFU/ml	cfu/ml	NN	_	_	_
280	was	be	VBD	_	_	_
281	centrifuged	centrifuge	VBN	_	_	_
282	at	at	IN	_	_	_
283	8000xg	8000xg	CD	_	_	_
284	4C	4c	NN	_	_	_
285	and	and	CC	_	_	_
286	resuspended	resuspend	VBN	_	_	_
287	in	in	IN	_	_	_
288	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
289	broth	broth	NN	_	_	_
290	with	with	IN	_	_	_
291	0	0	CD	_	_	_
292	%	%	NN	_	_	_
293	sodium	sodium	NN	_	_	_
294	benozate	benozate	NN	_	_	_
295	for	for	IN	_	_	_
296	30	30	CD	_	_	_
297	minutes	minute	NNS	_	_	_
298	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
299	Stationary	stationary	JJ	_	_	_
300	phase	phase	NN	_	_	_
301	growth	growth	NN	_	_	_
302	-LRB-	-lrb-	-LRB-	_	_	_
303	24	24	CD	_	_	_
304	hr	hr	NN	_	_	_
305	-RRB-	-rrb-	-RRB-	_	_	_
306	~	~	NN	_	_	_
307	8	8	CD	_	_	_
308	log	log	NN	_	_	_
309	CFU/ml	cfu/ml	NN	_	_	_
310	was	be	VBD	_	_	_
311	centrifuged	centrifuge	VBN	_	_	_
312	at	at	IN	_	_	_
313	8000xg	8000xg	CD	_	_	_
314	4C	4c	NN	_	_	_
315	and	and	CC	_	_	_
316	resuspended	resuspend	VBN	_	_	_
317	in	in	IN	_	_	_
318	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
319	broth	broth	NN	_	_	_
320	with	with	IN	_	_	_
321	0	0	CD	_	_	_
322	%	%	NN	_	_	_
323	sodium	sodium	NN	_	_	_
324	benozate	benozate	NN	_	_	_
325	for	for	IN	_	_	_
326	5	5	CD	_	_	_
327	minutes	minute	NNS	_	_	_
328	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
329	Stationary	stationary	JJ	_	_	_
330	phase	phase	NN	_	_	_
331	growth	growth	NN	_	_	_
332	-LRB-	-lrb-	-LRB-	_	_	_
333	24	24	CD	_	_	_
334	hr	hr	NN	_	_	_
335	-RRB-	-rrb-	-RRB-	_	_	_
336	~	~	NN	_	_	_
337	8	8	CD	_	_	_
338	log	log	NN	_	_	_
339	CFU/ml	cfu/ml	NN	_	_	_
340	was	be	VBD	_	_	_
341	centrifuged	centrifuge	VBN	_	_	_
342	at	at	IN	_	_	_
343	8000xg	8000xg	CD	_	_	_
344	4C	4c	NN	_	_	_
345	and	and	CC	_	_	_
346	resuspended	resuspend	VBN	_	_	_
347	in	in	IN	_	_	_
348	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
349	broth	broth	NN	_	_	_
350	with	with	IN	_	_	_
351	0	0	CD	_	_	_
352	%	%	NN	_	_	_
353	sodium	sodium	NN	_	_	_
354	benozate	benozate	NN	_	_	_
355	for	for	IN	_	_	_
356	60	60	CD	_	_	_
357	minutes	minute	NNS	_	_	_
358	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
359	Stationary	stationary	JJ	_	_	_
360	phase	phase	NN	_	_	_
361	growth	growth	NN	_	_	_
362	-LRB-	-lrb-	-LRB-	_	_	_
363	24	24	CD	_	_	_
364	hr	hr	NN	_	_	_
365	-RRB-	-rrb-	-RRB-	_	_	_
366	~	~	NN	_	_	_
367	8	8	CD	_	_	_
368	log	log	NN	_	_	_
369	CFU/ml	cfu/ml	NN	_	_	_
370	was	be	VBD	_	_	_
371	centrifuged	centrifuge	VBN	_	_	_
372	at	at	IN	_	_	_
373	8000xg	8000xg	CD	_	_	_
374	4C	4c	NN	_	_	_
375	and	and	CC	_	_	_
376	resuspended	resuspend	VBN	_	_	_
377	in	in	IN	_	_	_
378	Luria-Bertaini	Luria-Bertaini	NNP	_	_	_
379	broth	broth	NN	_	_	_
380	with	with	IN	_	_	_
381	no	no	DT	_	_	_
382	sodium	sodium	NN	_	_	_
383	benozate	benozate	NN	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	Stationary	stationary	JJ	_	_	_
386	phase	phase	NN	_	_	_
387	t	t	NN	_	_	_
388	=	=	JJ	_	_	_
389	0	0	CD	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
391	Statistical	statistical	JJ	_	_	_
392	analysis	analysis	NN	_	_	_
393	was	be	VBD	_	_	_
394	performed	perform	VBN	_	_	_
395	using	use	VBG	_	_	_
396	R	r	NN	_	_	_
397	Limma	limma	NN	_	_	_
398	package	package	NN	_	_	_
399	-LRB-	-lrb-	-LRB-	_	_	_
400	Linear	linear	JJ	_	_	_
401	Models	model	NNS	_	_	_
402	for	for	IN	_	_	_
403	Microarrays	Microarrays	NNP	_	_	_
404	Data	Data	NNP	_	_	_
405	-RRB-	-rrb-	-RRB-	_	_	_
406	-LRB-	-lrb-	-LRB-	_	_	_
407	Smyth	Smyth	NNP	_	_	_
408	2004	2004	CD	_	_	_
409	-RRB-	-rrb-	-RRB-	_	_	_
410	,	,	,	_	_	_
411	where	where	WRB	_	_	_
412	the	the	DT	_	_	_
413	two	two	CD	_	_	_
414	microarrays	microarray	NNS	_	_	_
415	per	per	IN	_	_	_
416	sample	sample	NN	_	_	_
417	were	be	VBD	_	_	_
418	normalized	normalize	VBN	_	_	_
419	using	use	VBG	_	_	_
420	lowess	lowess	JJ	_	_	_
421	normalization	normalization	NN	_	_	_
422	method	method	NN	_	_	_
423	.	.	.	_	_	_

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://server.molgenrug.nl/	http://server.molgenrug.nl/	NN	_	_	_
22	-	-	:	_	_	_
23	Molecular	molecular	JJ	_	_	_
24	genetics	genetics	NNS	_	_	_
25	,	,	,	_	_	_
26	university	university	NN	_	_	_
27	of	of	IN	_	_	_
28	Groningen	Groningen	NNP	_	_	_
29	,	,	,	_	_	_
30	the	the	DT	_	_	_
31	Netherlands	Netherlands	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Statistical	statistical	JJ	_	_	_
3	comparisons	comparison	NNS	_	_	_
4	were	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	multiple	multiple	JJ	_	_	_
8	testing	testing	NN	_	_	_
9	procedures	procedure	NNS	_	_	_
10	to	to	TO	_	_	_
11	evaluate	evaluate	VB	_	_	_
12	statistical	statistical	JJ	_	_	_
13	significance	significance	NN	_	_	_
14	for	for	IN	_	_	_
15	differentially	differentially	RB	_	_	_
16	expressed	express	VBN	_	_	_
17	genes	gene	NNS	_	_	_
18	.	.	.	_	_	_

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://ecocyc.org/	http://ecocyc.org/	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Statistical	statistical	JJ	_	_	_
3	preprocessing	preprocessing	NN	_	_	_
4	steps	step	NNS	_	_	_
5	were	be	VBD	_	_	_
6	conducted	conduct	VBN	_	_	_
7	with	with	IN	_	_	_
8	ArrayPipe	arraypipe	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	version	version	NN	_	_	_
11	1.7	1.7	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	a	a	DT	_	_	_
15	web-based	web-based	JJ	_	_	_
16	software	software	NN	_	_	_
17	designed	design	VBN	_	_	_
18	for	for	IN	_	_	_
19	processing	processing	NN	_	_	_
20	of	of	IN	_	_	_
21	microarray	microarray	NN	_	_	_
22	data	datum	NNS	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	www.pathogenomics.ca/arraypipe	www.pathogenomics.ca/arraypipe	NN	_	_	_
25	,	,	,	_	_	_
26	Hokamp	Hokamp	NNP	_	_	_
27	et	et	FW	_	_	_
28	al.	al.	FW	_	_	_
29	2004	2004	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	following	follow	VBG	_	_	_
3	pre-processing	pre-processing	JJ	_	_	_
4	steps	step	NNS	_	_	_
5	were	be	VBD	_	_	_
6	applied	apply	VBN	_	_	_
7	:	:	:	_	_	_
8	1	1	LS	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	flagging	flagging	JJ	_	_	_
11	of	of	IN	_	_	_
12	markers	marker	NNS	_	_	_
13	and	and	CC	_	_	_
14	control	control	NN	_	_	_
15	spots	spot	NNS	_	_	_
16	,	,	,	_	_	_
17	2	2	LS	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	subgrid-wise	subgrid-wise	JJ	_	_	_
20	background	background	NN	_	_	_
21	correction	correction	NN	_	_	_
22	,	,	,	_	_	_
23	using	use	VBG	_	_	_
24	the	the	DT	_	_	_
25	median	median	NN	_	_	_
26	of	of	IN	_	_	_
27	the	the	DT	_	_	_
28	lower	lower	JJR	_	_	_
29	10	10	CD	_	_	_
30	%	%	NN	_	_	_
31	foreground	foreground	NN	_	_	_
32	intensity	intensity	NN	_	_	_
33	as	as	IN	_	_	_
34	an	a	DT	_	_	_
35	estimate	estimate	NN	_	_	_
36	for	for	IN	_	_	_
37	the	the	DT	_	_	_
38	background	background	NN	_	_	_
39	noise	noise	NN	_	_	_
40	,	,	,	_	_	_
41	3	3	LS	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	data-shifting	data-shifting	NN	_	_	_
44	,	,	,	_	_	_
45	4	4	LS	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	limma	limma	NN	_	_	_
48	's	's	POS	_	_	_
49	LOESS	loess	JJ	_	_	_
50	normalization	normalization	NN	_	_	_
51	by	by	IN	_	_	_
52	print	print	NN	_	_	_
53	tip	tip	NN	_	_	_
54	,	,	,	_	_	_
55	5	5	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	merging	merge	VBG	_	_	_
58	of	of	IN	_	_	_
59	duplicate	duplicate	VB	_	_	_
60	spots	spot	NNS	_	_	_
61	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Stat-rpoS-rep1	stat-rpos-rep1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Stat-rpoS-Rep1	stat-rpos-rep1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Stat-rpoS-rep2	stat-rpos-rep2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Stat-rpoS-Rep2	stat-rpos-rep2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Stat-rpoS-rep3	stat-rpos-rep3	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Stat-rpoS-Rep3	stat-rpos-rep3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Stat-WT-rep1	stat-wt-rep1	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Stat-WT-Rep1	stat-wt-rep1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Stat-WT-rep2	stat-wt-rep2	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Stat-WT-Rep2	stat-wt-rep2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Stat-WT-rep3	stat-wt-rep3	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Stat-WT-Rep3	stat-wt-rep3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	Steady-state	steady-state	JJ	_	_	_
27	continuously-cultured	continuously-cultured	JJ	_	_	_
28	control	control	NN	_	_	_
29	samples	sample	NNS	_	_	_
30	in	in	IN	_	_	_
31	the	the	DT	_	_	_
32	presence	presence	NN	_	_	_
33	of	of	IN	_	_	_
34	adequate	adequate	JJ	_	_	_
35	Zn	zn	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	Steady-state	steady-state	JJ	_	_	_
38	continuously-cultured	continuously-cultured	JJ	_	_	_
39	experiment	experiment	NN	_	_	_
40	samples	sample	NNS	_	_	_
41	in	in	IN	_	_	_
42	the	the	DT	_	_	_
43	total	total	JJ	_	_	_
44	absence	absence	NN	_	_	_
45	of	of	IN	_	_	_
46	Zn	zn	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	Steady-state	steady-state	JJ	_	_	_
49	continuously-cultured	continuously-cultured	JJ	_	_	_
50	experiment	experiment	NN	_	_	_
51	samples	sample	NNS	_	_	_
52	in	in	IN	_	_	_
53	total	total	JJ	_	_	_
54	absence	absence	NN	_	_	_
55	of	of	IN	_	_	_
56	Zn	zn	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	Steady-state	steady-state	JJ	_	_	_
59	continuously-cultured	continuously-cultured	JJ	_	_	_
60	MG1655	mg1655	NN	_	_	_
61	in	in	IN	_	_	_
62	the	the	DT	_	_	_
63	presence	presence	NN	_	_	_
64	of	of	IN	_	_	_
65	adequate	adequate	JJ	_	_	_
66	Zn	zn	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	Steady-state	steady-state	JJ	_	_	_
69	continuously-cultured	continuously-cultured	JJ	_	_	_
70	MG1655	mg1655	NN	_	_	_
71	in	in	IN	_	_	_
72	the	the	DT	_	_	_
73	total	total	JJ	_	_	_
74	absence	absence	NN	_	_	_
75	of	of	IN	_	_	_
76	Zn	zn	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	STEC	stec	NN	_	_	_
79	EC472/01	ec472/01	NN	_	_	_
80	,	,	,	_	_	_
81	conditioned	conditioned	JJ	_	_	_
82	medium	medium	NN	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	STEC	STEC	NNP	_	_	_
85	EC472/01	ec472/01	NN	_	_	_
86	,	,	,	_	_	_
87	fresh	fresh	JJ	_	_	_
88	medium	medium	NN	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	STEC	STEC	NNP	_	_	_
91	EC472	ec472	NN	_	_	_
92	after	after	IN	_	_	_
93	3	3	CD	_	_	_
94	hrs	hr	NNS	_	_	_
95	incubation	incubation	NN	_	_	_
96	in	in	IN	_	_	_
97	conditioned	conditioned	JJ	_	_	_
98	medium	medium	NN	_	_	_
99	,	,	,	_	_	_
100	replicate	replicate	VB	_	_	_
101	1	1	CD	_	_	_
102	-LSB-	-lsb-	-LRB-	_	_	_
103	COND	cond	NN	_	_	_
104	-RSB-	-rsb-	-RRB-	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	STEC	stec	NN	_	_	_
107	EC472	ec472	NN	_	_	_
108	after	after	IN	_	_	_
109	3	3	CD	_	_	_
110	hrs	hr	NNS	_	_	_
111	incubation	incubation	NN	_	_	_
112	in	in	IN	_	_	_
113	conditioned	conditioned	JJ	_	_	_
114	medium	medium	NN	_	_	_
115	,	,	,	_	_	_
116	replicate	replicate	VB	_	_	_
117	2	2	CD	_	_	_
118	-LSB-	-lsb-	-LRB-	_	_	_
119	COND	cond	NN	_	_	_
120	-RSB-	-rsb-	-RRB-	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	STEC	stec	NN	_	_	_
123	EC472	ec472	NN	_	_	_
124	after	after	IN	_	_	_
125	3	3	CD	_	_	_
126	hrs	hr	NNS	_	_	_
127	incubation	incubation	NN	_	_	_
128	in	in	IN	_	_	_
129	conditioned	conditioned	JJ	_	_	_
130	medium	medium	NN	_	_	_
131	,	,	,	_	_	_
132	replicate	replicate	VB	_	_	_
133	3	3	CD	_	_	_
134	-LSB-	-lsb-	-LRB-	_	_	_
135	COND	cond	NN	_	_	_
136	-RSB-	-rsb-	-RRB-	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	STEC	stec	NN	_	_	_
139	EC472	ec472	NN	_	_	_
140	after	after	IN	_	_	_
141	3	3	CD	_	_	_
142	hrs	hr	NNS	_	_	_
143	incubation	incubation	NN	_	_	_
144	in	in	IN	_	_	_
145	conditioned	conditioned	JJ	_	_	_
146	medium	medium	NN	_	_	_
147	,	,	,	_	_	_
148	replicate	replicate	VB	_	_	_
149	4	4	CD	_	_	_
150	-LSB-	-lsb-	-LRB-	_	_	_
151	COND	cond	NN	_	_	_
152	-RSB-	-rsb-	-RRB-	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	STEC	stec	NN	_	_	_
155	EC472	ec472	NN	_	_	_
156	after	after	IN	_	_	_
157	3	3	CD	_	_	_
158	hrs	hr	NNS	_	_	_
159	incubation	incubation	NN	_	_	_
160	in	in	IN	_	_	_
161	fresh	fresh	JJ	_	_	_
162	medium	medium	NN	_	_	_
163	,	,	,	_	_	_
164	replicate	replicate	VB	_	_	_
165	1	1	CD	_	_	_
166	-LSB-	-lsb-	-LRB-	_	_	_
167	FRESH	fresh	JJ	_	_	_
168	-RSB-	-rsb-	-RRB-	_	_	_
169	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
170	STEC	STEC	NNP	_	_	_
171	EC472	ec472	NN	_	_	_
172	after	after	IN	_	_	_
173	3	3	CD	_	_	_
174	hrs	hr	NNS	_	_	_
175	incubation	incubation	NN	_	_	_
176	in	in	IN	_	_	_
177	fresh	fresh	JJ	_	_	_
178	medium	medium	NN	_	_	_
179	,	,	,	_	_	_
180	replicate	replicate	VB	_	_	_
181	2	2	CD	_	_	_
182	-LSB-	-lsb-	-LRB-	_	_	_
183	FRESH	fresh	JJ	_	_	_
184	-RSB-	-rsb-	-RRB-	_	_	_
185	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
186	STEC	STEC	NNP	_	_	_
187	EC472	ec472	NN	_	_	_
188	after	after	IN	_	_	_
189	3	3	CD	_	_	_
190	hrs	hr	NNS	_	_	_
191	incubation	incubation	NN	_	_	_
192	in	in	IN	_	_	_
193	fresh	fresh	JJ	_	_	_
194	medium	medium	NN	_	_	_
195	,	,	,	_	_	_
196	replicate	replicate	VB	_	_	_
197	3	3	CD	_	_	_
198	-LSB-	-lsb-	-LRB-	_	_	_
199	FRESH	fresh	JJ	_	_	_
200	-RSB-	-rsb-	-RRB-	_	_	_
201	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
202	STEC	STEC	NNP	_	_	_
203	EC472	ec472	NN	_	_	_
204	after	after	IN	_	_	_
205	3	3	CD	_	_	_
206	hrs	hr	NNS	_	_	_
207	incubation	incubation	NN	_	_	_
208	in	in	IN	_	_	_
209	fresh	fresh	JJ	_	_	_
210	medium	medium	NN	_	_	_
211	,	,	,	_	_	_
212	replicate	replicate	VB	_	_	_
213	4	4	CD	_	_	_
214	-LSB-	-lsb-	-LRB-	_	_	_
215	FRESH	fresh	JJ	_	_	_
216	-RSB-	-rsb-	-RRB-	_	_	_
217	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
218	STEC	STEC	NNP	_	_	_
219	EH41	eh41	NN	_	_	_
220	after	after	IN	_	_	_
221	3	3	CD	_	_	_
222	hrs	hr	NNS	_	_	_
223	incubation	incubation	NN	_	_	_
224	in	in	IN	_	_	_
225	conditioned	conditioned	JJ	_	_	_
226	medium	medium	NN	_	_	_
227	,	,	,	_	_	_
228	replicate	replicate	VB	_	_	_
229	1	1	CD	_	_	_
230	-LSB-	-lsb-	-LRB-	_	_	_
231	COND	cond	NN	_	_	_
232	-RSB-	-rsb-	-RRB-	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	STEC	stec	NN	_	_	_
235	EH41	eh41	NN	_	_	_
236	after	after	IN	_	_	_
237	3	3	CD	_	_	_
238	hrs	hr	NNS	_	_	_
239	incubation	incubation	NN	_	_	_
240	in	in	IN	_	_	_
241	conditioned	conditioned	JJ	_	_	_
242	medium	medium	NN	_	_	_
243	,	,	,	_	_	_
244	replicate	replicate	VB	_	_	_
245	2	2	CD	_	_	_
246	-LSB-	-lsb-	-LRB-	_	_	_
247	COND	cond	NN	_	_	_
248	-RSB-	-rsb-	-RRB-	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	STEC	stec	NN	_	_	_
251	EH41	eh41	NN	_	_	_
252	after	after	IN	_	_	_
253	3	3	CD	_	_	_
254	hrs	hr	NNS	_	_	_
255	incubation	incubation	NN	_	_	_
256	in	in	IN	_	_	_
257	conditioned	conditioned	JJ	_	_	_
258	medium	medium	NN	_	_	_
259	,	,	,	_	_	_
260	replicate	replicate	VB	_	_	_
261	3	3	CD	_	_	_
262	-LSB-	-lsb-	-LRB-	_	_	_
263	COND	cond	NN	_	_	_
264	-RSB-	-rsb-	-RRB-	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	STEC	stec	NN	_	_	_
267	EH41	eh41	NN	_	_	_
268	after	after	IN	_	_	_
269	3	3	CD	_	_	_
270	hrs	hr	NNS	_	_	_
271	incubation	incubation	NN	_	_	_
272	in	in	IN	_	_	_
273	conditioned	conditioned	JJ	_	_	_
274	medium	medium	NN	_	_	_
275	,	,	,	_	_	_
276	replicate	replicate	VB	_	_	_
277	4	4	CD	_	_	_
278	-LSB-	-lsb-	-LRB-	_	_	_
279	COND	cond	NN	_	_	_
280	-RSB-	-rsb-	-RRB-	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	STEC	stec	NN	_	_	_
283	EH41	eh41	NN	_	_	_
284	after	after	IN	_	_	_
285	3	3	CD	_	_	_
286	hrs	hr	NNS	_	_	_
287	incubation	incubation	NN	_	_	_
288	in	in	IN	_	_	_
289	fresh	fresh	JJ	_	_	_
290	medium	medium	NN	_	_	_
291	,	,	,	_	_	_
292	replicate	replicate	VB	_	_	_
293	1	1	CD	_	_	_
294	-LSB-	-lsb-	-LRB-	_	_	_
295	FRESH	fresh	JJ	_	_	_
296	-RSB-	-rsb-	-RRB-	_	_	_
297	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
298	STEC	STEC	NNP	_	_	_
299	EH41	eh41	NN	_	_	_
300	after	after	IN	_	_	_
301	3	3	CD	_	_	_
302	hrs	hr	NNS	_	_	_
303	incubation	incubation	NN	_	_	_
304	in	in	IN	_	_	_
305	fresh	fresh	JJ	_	_	_
306	medium	medium	NN	_	_	_
307	,	,	,	_	_	_
308	replicate	replicate	VB	_	_	_
309	2	2	CD	_	_	_
310	-LSB-	-lsb-	-LRB-	_	_	_
311	FRESH	fresh	JJ	_	_	_
312	-RSB-	-rsb-	-RRB-	_	_	_
313	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
314	STEC	STEC	NNP	_	_	_
315	EH41	eh41	NN	_	_	_
316	after	after	IN	_	_	_
317	3	3	CD	_	_	_
318	hrs	hr	NNS	_	_	_
319	incubation	incubation	NN	_	_	_
320	in	in	IN	_	_	_
321	fresh	fresh	JJ	_	_	_
322	medium	medium	NN	_	_	_
323	,	,	,	_	_	_
324	replicate	replicate	VB	_	_	_
325	3	3	CD	_	_	_
326	-LSB-	-lsb-	-LRB-	_	_	_
327	FRESH	fresh	JJ	_	_	_
328	-RSB-	-rsb-	-RRB-	_	_	_
329	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
330	STEC	STEC	NNP	_	_	_
331	EH41	eh41	NN	_	_	_
332	after	after	IN	_	_	_
333	3	3	CD	_	_	_
334	hrs	hr	NNS	_	_	_
335	incubation	incubation	NN	_	_	_
336	in	in	IN	_	_	_
337	fresh	fresh	JJ	_	_	_
338	medium	medium	NN	_	_	_
339	,	,	,	_	_	_
340	replicate	replicate	VB	_	_	_
341	4	4	CD	_	_	_
342	-LSB-	-lsb-	-LRB-	_	_	_
343	FRESH	fresh	JJ	_	_	_
344	-RSB-	-rsb-	-RRB-	_	_	_
345	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
346	STEC	STEC	NNP	_	_	_
347	EH41	eh41	NN	_	_	_
348	,	,	,	_	_	_
349	conditioned	conditioned	JJ	_	_	_
350	medium	medium	NN	_	_	_
351	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
352	STEC	STEC	NNP	_	_	_
353	EH41	eh41	NN	_	_	_
354	,	,	,	_	_	_
355	fresh	fresh	JJ	_	_	_
356	medium	medium	NN	_	_	_
357	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
358	STEC	STEC	NNP	_	_	_
359	strains	strain	NNS	_	_	_
360	were	be	VBD	_	_	_
361	lysate	lysate	NN	_	_	_
362	using	use	VBG	_	_	_
363	lysozyme	lysozyme	NN	_	_	_
364	-LRB-	-lrb-	-LRB-	_	_	_
365	1	1	CD	_	_	_
366	mg/mL	mg/ml	NN	_	_	_
367	-RRB-	-rrb-	-RRB-	_	_	_
368	and	and	CC	_	_	_
369	proteinase	proteinase	NN	_	_	_
370	K	k	NN	_	_	_
371	-LRB-	-lrb-	-LRB-	_	_	_
372	2	2	CD	_	_	_
373	mg/mL	mg/ml	NN	_	_	_
374	-RRB-	-rrb-	-RRB-	_	_	_
375	and	and	CC	_	_	_
376	incubated	incubate	VBN	_	_	_
377	for	for	IN	_	_	_
378	10	10	CD	_	_	_
379	min	min	NN	_	_	_
380	at	at	IN	_	_	_
381	20	20	CD	_	_	_
382	°C	°c	NN	_	_	_
383	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	obtained	obtain	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	NNP	_	_	_
12	cat	cat	NN	_	_	_
13	no.	no.	NN	_	_	_
14	74104	74104	CD	_	_	_
15	,	,	,	_	_	_
16	Valencia	Valencia	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	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	instructions	instruction	NNS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	purity	purity	NN	_	_	_
3	and	and	CC	_	_	_
4	quantification	quantification	NN	_	_	_
5	for	for	IN	_	_	_
6	all	all	DT	_	_	_
7	RNA	rna	NN	_	_	_
8	samples	sample	NNS	_	_	_
9	were	be	VBD	_	_	_
10	done	do	VBN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	NanoVue	NanoVue	NNP	_	_	_
14	spectrophotometer	spectrophotometer	NN	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	RNA	rna	NN	_	_	_
18	quality	quality	NN	_	_	_
19	was	be	VBD	_	_	_
20	assessed	assess	VBN	_	_	_
21	on	on	IN	_	_	_
22	the	the	DT	_	_	_
23	Agilent	Agilent	NNP	_	_	_
24	BioAnalyzer	BioAnalyzer	NNP	_	_	_
25	2100	2100	CD	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Agilent	Agilent	NNP	_	_	_
28	,	,	,	_	_	_
29	Santa	Santa	NNP	_	_	_
30	Clara	Clara	NNP	_	_	_
31	,	,	,	_	_	_
32	CA	CA	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	that	that	WDT	_	_	_
4	present	present	VBP	_	_	_
5	RIN	RIN	NNP	_	_	_
6	>	>	JJR	_	_	_
7	7.0	7.0	CD	_	_	_
8	were	be	VBD	_	_	_
9	stored	store	VBN	_	_	_
10	at	at	IN	_	_	_
11	-80	-80	CD	_	_	_
12	°C	°c	NN	_	_	_
13	until	until	IN	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	hybridization	hybridization	NN	_	_	_
17	experiments	experiment	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	stimulus	stimulus	NN	_	_	_
3	:	:	:	_	_	_
4	1	1	CD	_	_	_
5	MPa	mpa	NN	_	_	_
6	for	for	IN	_	_	_
7	15	15	CD	_	_	_
8	min	min	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	stimulus	stimulus	NN	_	_	_
11	:	:	:	_	_	_
12	Control	Control	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	S	s	NN	_	_	_
15	,	,	,	_	_	_
16	TP1	tp1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	S	s	NN	_	_	_
19	,	,	,	_	_	_
20	TP2	tp2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	S	s	NN	_	_	_
23	,	,	,	_	_	_
24	TP3	tp3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	S	s	NN	_	_	_
27	,	,	,	_	_	_
28	TP4	tp4	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	strain	strain	NN	_	_	_
31	:	:	:	_	_	_
32	173150	173150	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	strain	strain	NN	_	_	_
35	:	:	:	_	_	_
36	174750	174750	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	strain	strain	NN	_	_	_
39	:	:	:	_	_	_
40	174900	174900	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	strain	strain	NN	_	_	_
43	:	:	:	_	_	_
44	178200	178200	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	178850	178850	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	strain	strain	NN	_	_	_
51	:	:	:	_	_	_
52	178900	178900	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	strain	strain	NN	_	_	_
55	:	:	:	_	_	_
56	179100	179100	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	strain	strain	NN	_	_	_
59	:	:	:	_	_	_
60	179550	179550	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	strain	strain	NN	_	_	_
63	:	:	:	_	_	_
64	180050	180050	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	strain	strain	NN	_	_	_
67	:	:	:	_	_	_
68	180200	180200	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	strain	strain	NN	_	_	_
71	:	:	:	_	_	_
72	180600	180600	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	strain	strain	NN	_	_	_
75	:	:	:	_	_	_
76	2-1	2-1	CD	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	strain	strain	NN	_	_	_
79	:	:	:	_	_	_
80	214-4	214-4	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	strain	strain	NN	_	_	_
83	:	:	:	_	_	_
84	2230	2230	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	strain	strain	NN	_	_	_
87	:	:	:	_	_	_
88	229-1	229-1	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	strain	strain	NN	_	_	_
91	:	:	:	_	_	_
92	2429	2429	CD	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	strain	strain	NN	_	_	_
95	:	:	:	_	_	_
96	278485-1	278485-1	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	strain	strain	NN	_	_	_
99	:	:	:	_	_	_
100	292-1	292-1	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	strain	strain	NN	_	_	_
103	:	:	:	_	_	_
104	350C1A	350c1a	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	strain	strain	NN	_	_	_
107	:	:	:	_	_	_
108	3780	3780	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	strain	strain	NN	_	_	_
111	:	:	:	_	_	_
112	42-1	42-1	CD	_	_	_
113	C1	c1	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	strain	strain	NN	_	_	_
116	520	520	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	strain	strain	NN	_	_	_
119	521	521	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	strain	strain	NN	_	_	_
122	:	:	:	_	_	_
123	86-24	86-24	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	strain	strain	NN	_	_	_
126	:	:	:	_	_	_
127	AH28	ah28	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Strain	strain	NN	_	_	_
130	A	a	NN	_	_	_
131	of	of	IN	_	_	_
132	experimental	experimental	JJ	_	_	_
133	evolution	evolution	NN	_	_	_
134	under	under	IN	_	_	_
135	ethanol	ethanol	NN	_	_	_
136	stress	stress	NN	_	_	_
137	in	in	IN	_	_	_
138	1224	1224	CD	_	_	_
139	hours	hour	NNS	_	_	_
140	.	.	.	_	_	_

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	:	:	:	_	_	_
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	ArcA8myc	arca8myc	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	strain	strain	NN	_	_	_
45	:	:	:	_	_	_
46	ARG-2	arg-2	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	strain	strain	NN	_	_	_
49	:	:	:	_	_	_
50	ARG-3	arg-3	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	strain	strain	NN	_	_	_
53	:	:	:	_	_	_
54	ATCC	atcc	NN	_	_	_
55	4157	4157	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	strain	strain	NN	_	_	_
58	:	:	:	_	_	_
59	AW1	aw1	NN	_	_	_
60	.7	.7	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	strain	strain	NN	_	_	_
63	:	:	:	_	_	_
64	B	b	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	strain	strain	NN	_	_	_
67	B02	b02	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	strain	strain	NN	_	_	_
70	B05	b05	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	strain	strain	NN	_	_	_
73	:	:	:	_	_	_
74	B2C	b2c	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	strain	strain	NN	_	_	_
77	:	:	:	_	_	_
78	B7A	b7a	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	strain	strain	NN	_	_	_
81	background	background	NN	_	_	_
82	:	:	:	_	_	_
83	B	b	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	strain	strain	NN	_	_	_
86	background	background	NN	_	_	_
87	:	:	:	_	_	_
88	BW25113	bw25113	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	strain/background	strain/background	NN	_	_	_
91	:	:	:	_	_	_
92	BW25113	bw25113	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	strain	strain	NN	_	_	_
95	background	background	NN	_	_	_
96	:	:	:	_	_	_
97	EDL933	edl933	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	strain	strain	NN	_	_	_
100	background	background	NN	_	_	_
101	:	:	:	_	_	_
102	K-12	k-12	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	strain	strain	NN	_	_	_
105	background	background	NN	_	_	_
106	:	:	:	_	_	_
107	MG1655	mg1655	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	strain/background	strain/background	NN	_	_	_
110	:	:	:	_	_	_
111	MG1655	mg1655	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	strain	strain	NN	_	_	_
114	:	:	:	_	_	_
115	BCE001	bce001	NN	_	_	_
116	,	,	,	_	_	_
117	MS16	ms16	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	strain	strain	NN	_	_	_
120	:	:	:	_	_	_
121	BCE002	bce002	NN	_	_	_
122	,	,	,	_	_	_
123	MS12	ms12	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	strain	strain	NN	_	_	_
126	:	:	:	_	_	_
127	BCE003	bce003	NN	_	_	_
128	,	,	,	_	_	_
129	DS5	ds5	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	strain	strain	NN	_	_	_
132	:	:	:	_	_	_
133	BCE005	bce005	NN	_	_	_
134	,	,	,	_	_	_
135	MS23	ms23	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	strain	strain	NN	_	_	_
138	:	:	:	_	_	_
139	BCE007	bce007	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	strain	strain	NN	_	_	_
142	:	:	:	_	_	_
143	BCE007	bce007	NN	_	_	_
144	,	,	,	_	_	_
145	MS11	ms11	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	strain	strain	NN	_	_	_
148	:	:	:	_	_	_
149	BCE008	bce008	NN	_	_	_
150	_	_	CD	_	_	_
151	MS1	ms1	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	strain	strain	NN	_	_	_
154	:	:	:	_	_	_
155	BCE008	bce008	NN	_	_	_
156	,	,	,	_	_	_
157	MS13	ms13	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	strain	strain	NN	_	_	_
160	:	:	:	_	_	_
161	BCE011	bce011	NN	_	_	_
162	,	,	,	_	_	_
163	DS3	ds3	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	strain	strain	NN	_	_	_
166	:	:	:	_	_	_
167	BCE013	bce013	NN	_	_	_
168	,	,	,	_	_	_
169	DS1	ds1	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	strain	strain	NN	_	_	_
172	:	:	:	_	_	_
173	BCE018	bce018	NN	_	_	_
174	,	,	,	_	_	_
175	DS6	ds6	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	strain	strain	NN	_	_	_
178	:	:	:	_	_	_
179	BCE019	bce019	NN	_	_	_
180	,	,	,	_	_	_
181	MS16	ms16	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	strain	strain	NN	_	_	_
184	:	:	:	_	_	_
185	BCE021	bce021	NN	_	_	_
186	,	,	,	_	_	_
187	DS7	ds7	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	strain	strain	NN	_	_	_
190	:	:	:	_	_	_
191	BCE022DS6	bce022ds6	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	strain	strain	NN	_	_	_
194	:	:	:	_	_	_
195	BCE035	bce035	NN	_	_	_
196	,	,	,	_	_	_
197	DS6	ds6	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	strain	strain	NN	_	_	_
200	:	:	:	_	_	_
201	BCE035	bce035	NN	_	_	_
202	,	,	,	_	_	_
203	MS8	ms8	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	strain	strain	NN	_	_	_
206	:	:	:	_	_	_
207	BCE039	bce039	NN	_	_	_
208	,	,	,	_	_	_
209	DS2	ds2	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	strain	strain	NN	_	_	_
212	:	:	:	_	_	_
213	BCE039	bce039	NN	_	_	_
214	,	,	,	_	_	_
215	MS13	ms13	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	strain	strain	NN	_	_	_
218	:	:	:	_	_	_
219	BCE041	bce041	NN	_	_	_
220	,	,	,	_	_	_
221	MS11	ms11	NN	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	strain	strain	NN	_	_	_
224	:	:	:	_	_	_
225	BCE046	bce046	NN	_	_	_
226	,	,	,	_	_	_
227	DS2	ds2	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	strain	strain	NN	_	_	_
230	:	:	:	_	_	_
231	BCE046	bce046	NN	_	_	_
232	,	,	,	_	_	_
233	DS7	ds7	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	strain	strain	NN	_	_	_
236	:	:	:	_	_	_
237	BCE046	bce046	NN	_	_	_
238	,	,	,	_	_	_
239	MS16	ms16	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	strain	strain	NN	_	_	_
242	:	:	:	_	_	_
243	BCE049	bce049	NN	_	_	_
244	,	,	,	_	_	_
245	DS3	ds3	NN	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	strain	strain	NN	_	_	_
248	:	:	:	_	_	_
249	BCE049	bce049	NN	_	_	_
250	,	,	,	_	_	_
251	MS9	ms9	NN	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	strain	strain	NN	_	_	_
254	:	:	:	_	_	_
255	BCE054	bce054	NN	_	_	_
256	,	,	,	_	_	_
257	DS4	ds4	NN	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	strain	strain	NN	_	_	_
260	:	:	:	_	_	_
261	BCE054	bce054	NN	_	_	_
262	,	,	,	_	_	_
263	MS24	ms24	NN	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	strain	strain	NN	_	_	_
266	:	:	:	_	_	_
267	BCE055	bce055	NN	_	_	_
268	,	,	,	_	_	_
269	DS1	ds1	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	strain	strain	NN	_	_	_
272	:	:	:	_	_	_
273	BCE058	bce058	NN	_	_	_
274	,	,	,	_	_	_
275	MS13	ms13	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	strain	strain	NN	_	_	_
278	:	:	:	_	_	_
279	BCE061	bce061	NN	_	_	_
280	,	,	,	_	_	_
281	DS1	ds1	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	strain	strain	NN	_	_	_
284	:	:	:	_	_	_
285	BCE062	bce062	NN	_	_	_
286	,	,	,	_	_	_
287	DS2	ds2	NN	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	strain	strain	NN	_	_	_
290	:	:	:	_	_	_
291	BCE062	bce062	NN	_	_	_
292	,	,	,	_	_	_
293	MS24	ms24	NN	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	strain	strain	NN	_	_	_
296	:	:	:	_	_	_
297	BCE063	bce063	NN	_	_	_
298	,	,	,	_	_	_
299	DS4	ds4	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	strain	strain	NN	_	_	_
302	:	:	:	_	_	_
303	BCE063	bce063	NN	_	_	_
304	,	,	,	_	_	_
305	MS14	ms14	NN	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	strain	strain	NN	_	_	_
308	:	:	:	_	_	_
309	BCE066	bce066	NN	_	_	_
310	,	,	,	_	_	_
311	DS5	ds5	NN	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	strain	strain	NN	_	_	_
314	:	:	:	_	_	_
315	BCE068	bce068	NN	_	_	_
316	,	,	,	_	_	_
317	MS10	ms10	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	strain	strain	NN	_	_	_
320	:	:	:	_	_	_
321	BCE068	bce068	NN	_	_	_
322	,	,	,	_	_	_
323	MS23	ms23	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	strain	strain	NN	_	_	_
326	:	:	:	_	_	_
327	BCE069	bce069	NN	_	_	_
328	,	,	,	_	_	_
329	DS2	ds2	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	strain	strain	NN	_	_	_
332	:	:	:	_	_	_
333	BCE069	bce069	NN	_	_	_
334	,	,	,	_	_	_
335	MS15	ms15	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	strain	strain	NN	_	_	_
338	:	:	:	_	_	_
339	BCE069	bce069	NN	_	_	_
340	,	,	,	_	_	_
341	MS9	ms9	NN	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	strain	strain	NN	_	_	_
344	:	:	:	_	_	_
345	BCE129	bce129	NN	_	_	_
346	,	,	,	_	_	_
347	DS2	ds2	NN	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	strain	strain	NN	_	_	_
350	:	:	:	_	_	_
351	Bear	Bear	NNP	_	_	_
352	feces	fece	VBZ	_	_	_
353	isolate	isolate	JJ	_	_	_
354	B1	b1	NN	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	strain	strain	NN	_	_	_
357	:	:	:	_	_	_
358	Bear	Bear	NNP	_	_	_
359	feces	fece	VBZ	_	_	_
360	isolate	isolate	JJ	_	_	_
361	B3	b3	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	strain	strain	NN	_	_	_
364	:	:	:	_	_	_
365	Bear	Bear	NNP	_	_	_
366	feces	fece	VBZ	_	_	_
367	isolate	isolate	JJ	_	_	_
368	B5	b5	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	strain	strain	NN	_	_	_
371	:	:	:	_	_	_
372	beta-lactamase	beta-lactamase	NN	_	_	_
373	-LRB-	-lrb-	-LRB-	_	_	_
374	ESBL	esbl	NN	_	_	_
375	-RRB-	-rrb-	-RRB-	_	_	_
376	-	-	:	_	_	_
377	producing	produce	VBG	_	_	_
378	UPEC	upec	NN	_	_	_
379	-LRB-	-lrb-	-LRB-	_	_	_
380	ESBL019	esbl019	NN	_	_	_
381	-RRB-	-rrb-	-RRB-	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	strain	strain	NN	_	_	_
384	:	:	:	_	_	_
385	BJW9	bjw9	NN	_	_	_
386	w	w	NN	_	_	_
387	/	/	:	_	_	_
388	recoded	recode	VBN	_	_	_
389	ompF	ompf	NN	GEN	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	strain	strain	NN	_	_	_
392	:	:	:	_	_	_
393	BL21	bl21	NN	_	_	_
394	-LRB-	-lrb-	-LRB-	_	_	_
395	DE3	de3	NN	_	_	_
396	-RRB-	-rrb-	-RRB-	_	_	_
397	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
398	strain	strain	NN	_	_	_
399	:	:	:	_	_	_
400	BL21	bl21	NN	_	_	_
401	-LRB-	-lrb-	-LRB-	_	_	_
402	DE3	de3	NN	_	_	_
403	-RRB-	-rrb-	-RRB-	_	_	_
404	rne131	rne131	NN	_	_	_
405	DrhlB	drhlb	NN	_	_	_
406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
407	strain	strain	NN	_	_	_
408	B	b	NN	_	_	_
409	of	of	IN	_	_	_
410	experimental	experimental	JJ	_	_	_
411	evolution	evolution	NN	_	_	_
412	under	under	IN	_	_	_
413	ethanol	ethanol	NN	_	_	_
414	stress	stress	NN	_	_	_
415	in	in	IN	_	_	_
416	1224	1224	CD	_	_	_
417	hours	hour	NNS	_	_	_
418	.	.	.	_	_	_

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	BW25113	bw25113	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	strain	strain	NN	_	_	_
6	:	:	:	_	_	_
7	BW25113	bw25113	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Strain	strain	NN	_	_	_
10	BW25113	bw25113	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Strain	strain	NN	_	_	_
13	BW25113	bw25113	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Strain	strain	NN	_	_	_
16	:	:	:	_	_	_
17	BW25113	bw25113	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Strain	strain	NN	_	_	_
20	:	:	:	_	_	_
21	BW25113	bw25113	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Strain	strain	NN	_	_	_
24	:	:	:	_	_	_
25	BW25113/arcA	bw25113/arca	NN	_	_	_
26	-	-	:	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	BW25113/arcA	bw25113/arca	NN	_	_	_
31	-	-	:	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Strain	strain	NN	_	_	_
34	:	:	:	_	_	_
35	BW25113/fur	bw25113/fur	NN	_	_	_
36	-	-	:	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Strain	strain	NN	_	_	_
39	:	:	:	_	_	_
40	BW25113/fur	bw25113/fur	NN	_	_	_
41	-	-	:	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	strain	strain	NN	_	_	_
44	:	:	:	_	_	_
45	BW25113	bw25113	NN	_	_	_
46	hha	hha	NN	GEN	_	_
47	hns	hn	NNS	GEN	_	_
48	/	/	:	_	_	_
49	pCA24N-hns	pca24n-hn	NNS	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	strain	strain	NN	_	_	_
52	:	:	:	_	_	_
53	BW25113	bw25113	NN	_	_	_
54	hha	hha	NN	GEN	_	_
55	hns	hn	NNS	GEN	_	_
56	/	/	:	_	_	_
57	pCA24N-hnsK57N	pca24n-hnsk57n	JJ	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Strain	strain	NN	_	_	_
60	:	:	:	_	_	_
61	BW25113/ihfA	bw25113/ihfa	NN	_	_	_
62	-	-	:	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Strain	strain	NN	_	_	_
65	:	:	:	_	_	_
66	BW25113/ihfA	bw25113/ihfa	NN	_	_	_
67	-	-	:	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Strain	strain	NN	_	_	_
70	:	:	:	_	_	_
71	BW25113/phoB	bw25113/phob	NN	_	_	_
72	-	-	:	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Strain	strain	NN	_	_	_
75	:	:	:	_	_	_
76	BW25113/phoB	bw25113/phob	NN	_	_	_
77	-	-	:	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	strain	strain	NN	_	_	_
80	BW25113	bw25113	NN	_	_	_
81	ppsA	ppsa	NN	GEN	_	_
82	deletion	deletion	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	strain	strain	NN	_	_	_
85	:	:	:	_	_	_
86	BW25113/ubiE	bw25113/ubie	NN	_	_	_
87	-	-	:	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	strain	strain	NN	_	_	_
90	:	:	:	_	_	_
91	BW27786	bw27786	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	K-12	k-12	NN	_	_	_
94	derivative	derivative	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	strain	strain	NN	_	_	_
98	:	:	:	_	_	_
99	BW38028	bw38028	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	strain	strain	NN	_	_	_
102	C01	c01	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	strain	strain	NN	_	_	_
105	C02	c02	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	strain	strain	NN	_	_	_
108	:	:	:	_	_	_
109	C-34666	c-34666	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	strain	strain	NN	_	_	_
112	:	:	:	_	_	_
113	C-35134	c-35134	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	strain	strain	NN	_	_	_
116	:	:	:	_	_	_
117	C-35209	c-35209	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	strain	strain	NN	_	_	_
120	:	:	:	_	_	_
121	C-35213	c-35213	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	strain	strain	NN	_	_	_
124	:	:	:	_	_	_
125	C-35605	c-35605	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	strain	strain	NN	_	_	_
128	:	:	:	_	_	_
129	C-35662	c-35662	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	strain	strain	NN	_	_	_
132	:	:	:	_	_	_
133	C-35776	c-35776	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	strain	strain	NN	_	_	_
136	:	:	:	_	_	_
137	C-35959	c-35959	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	strain	strain	NN	_	_	_
140	:	:	:	_	_	_
141	C-36255	c-36255	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	strain	strain	NN	_	_	_
144	:	:	:	_	_	_
145	CAR005	car005	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	strain	strain	NN	_	_	_
148	:	:	:	_	_	_
149	Cattle	Cattle	NNP	_	_	_
150	feces	fece	NNS	_	_	_
151	isolate	isolate	VBP	_	_	_
152	C1A	c1a	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	strain	strain	NN	_	_	_
155	:	:	:	_	_	_
156	Cattle	Cattle	NNP	_	_	_
157	feces	fece	NNS	_	_	_
158	isolate	isolate	VBP	_	_	_
159	C4A	c4a	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	strain	strain	NN	_	_	_
162	:	:	:	_	_	_
163	Cattle	Cattle	NNP	_	_	_
164	feces	fece	NNS	_	_	_
165	isolate	isolate	VBP	_	_	_
166	C6D	c6d	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	strain	strain	NN	_	_	_
169	:	:	:	_	_	_
170	CFT073	cft073	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	strain	strain	NN	_	_	_
173	CFT073	cft073	NN	_	_	_
174	;	;	:	_	_	_
175	GenBank	genbank	NN	_	_	_
176	accession	accession	NN	_	_	_
177	AE014075	ae014075	NN	_	_	_
178	.1	.1	CD	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	strain	strain	NN	_	_	_
181	:	:	:	_	_	_
182	CFT073	cft073	NN	_	_	_
183	nsrR	nsrr	NN	GEN	_	_
184	:	:	:	_	_	_
185	:	:	:	_	_	_
186	3X-Flag	3x-flag	NN	_	_	_
187	tag	tag	NN	GEN	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	strain	strain	NN	_	_	_
190	:	:	:	_	_	_
191	clinical	clinical	JJ	_	_	_
192	isolate	isolate	JJ	_	_	_
193	LB226692	lb226692	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	strain	strain	NN	_	_	_
196	:	:	:	_	_	_
197	CMA540	cma540	NN	_	_	_
198	-LRB-	-lrb-	-LRB-	_	_	_
199	MG1693	mg1693	NN	_	_	_
200	delta	delta	NN	_	_	_
201	_	_	NN	_	_	_
202	hfq	hfq	NN	GEN	_	_
203	:	:	:	_	_	_
204	:	:	:	_	_	_
205	cat	cat	NN	_	_	_
206	-RRB-	-rrb-	-RRB-	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	strain	strain	NN	_	_	_
209	:	:	:	_	_	_
210	CMCC	cmcc	NN	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	B	b	NN	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	44102	44102	CD	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	strain	strain	NN	_	_	_
217	:	:	:	_	_	_
218	cocar	cocar	NN	_	_	_
219	07-043	07-043	CD	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	strain	strain	NN	_	_	_
222	:	:	:	_	_	_
223	cocar	cocar	NN	_	_	_
224	07-40	07-40	CD	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	strain	strain	NN	_	_	_
227	C	c	NN	_	_	_
228	of	of	IN	_	_	_
229	experimental	experimental	JJ	_	_	_
230	evolution	evolution	NN	_	_	_
231	under	under	IN	_	_	_
232	ethanol	ethanol	NN	_	_	_
233	stress	stress	NN	_	_	_
234	in	in	IN	_	_	_
235	1224	1224	CD	_	_	_
236	hours	hour	NNS	_	_	_
237	.	.	.	_	_	_

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	:	:	:	_	_	_
4	cosin	cosin	NN	_	_	_
5	07-14	07-14	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	cosin	cosin	NN	_	_	_
10	07-36	07-36	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	strain	strain	NN	_	_	_
13	:	:	:	_	_	_
14	cosin	cosin	NN	_	_	_
15	07-61	07-61	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	strain	strain	NN	_	_	_
18	:	:	:	_	_	_
19	cosin	cosin	NN	_	_	_
20	07-88	07-88	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	strain	strain	NN	_	_	_
23	:	:	:	_	_	_
24	cosin	cosin	NN	_	_	_
25	07-92	07-92	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	strain	strain	NN	_	_	_
28	:	:	:	_	_	_
29	Crooks	crook	NNS	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	strain	strain	NN	_	_	_
32	:	:	:	_	_	_
33	Crp	Crp	NNP	_	_	_
34	_	_	SYM	_	_	_
35	delAr1	delar1	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	strain	strain	NN	_	_	_
38	:	:	:	_	_	_
39	Crp	Crp	NNP	_	_	_
40	_	_	SYM	_	_	_
41	delAr1delAr2	delar1delar2	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	strain	strain	NN	_	_	_
44	:	:	:	_	_	_
45	Crp	Crp	NNP	_	_	_
46	_	_	SYM	_	_	_
47	delAr2	delar2	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	strain	strain	NN	_	_	_
50	:	:	:	_	_	_
51	CSH50	csh50	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	strain	strain	NN	_	_	_
54	:	:	:	_	_	_
55	CVCC2943	cvcc2943	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	strain	strain	NN	_	_	_
58	:	:	:	_	_	_
59	D02-2	d02-2	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	strain	strain	NN	_	_	_
62	:	:	:	_	_	_
63	Deer	deer	NNS	_	_	_
64	feces	fece	NNS	_	_	_
65	isolate	isolate	VBP	_	_	_
66	D1	d1	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	strain	strain	NN	_	_	_
69	:	:	:	_	_	_
70	Deer	deer	NNS	_	_	_
71	feces	fece	NNS	_	_	_
72	isolate	isolate	NN	_	_	_
73	D3	d3	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	strain	strain	NN	_	_	_
76	:	:	:	_	_	_
77	Deer	deer	NNS	_	_	_
78	feces	fece	NNS	_	_	_
79	isolate	isolate	VBP	_	_	_
80	W6A	w6a	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	strain	strain	NN	_	_	_
83	:	:	:	_	_	_
84	delta	delta	NN	_	_	_
85	Crp	crp	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	strain	strain	NN	_	_	_
88	description	description	NN	_	_	_
89	:	:	:	_	_	_
90	E.	e.	FW	_	_	_
91	coli	coli	FW	_	_	_
92	BW25113	bw25113	NN	_	_	_
93	with	with	IN	_	_	_
94	an	a	DT	_	_	_
95	integrated	integrate	VBN	_	_	_
96	F	f	NN	_	_	_
97	tra	tra	NN	_	_	_
98	operon	operon	NN	_	_	_
99	at	at	IN	_	_	_
100	the	the	DT	_	_	_
101	trp	trp	NN	_	_	_
102	locus	locus	NN	_	_	_
103	,	,	,	_	_	_
104	plus	plus	CC	_	_	_
105	additional	additional	JJ	_	_	_
106	F	f	NN	_	_	_
107	oriT	orit	NN	_	_	_
108	sequences	sequence	NNS	_	_	_
109	integrated	integrate	VBN	_	_	_
110	at	at	IN	_	_	_
111	mbhA	mbha	NN	_	_	_
112	and	and	CC	_	_	_
113	hyfC	hyfc	NN	GEN	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	strain	strain	NN	_	_	_
116	description	description	NN	_	_	_
117	:	:	:	_	_	_
118	E.	e.	FW	_	_	_
119	coli	coli	FW	_	_	_
120	BW25113	bw25113	NN	_	_	_
121	with	with	IN	_	_	_
122	F	f	NN	_	_	_
123	oriTs	orit	NNS	_	_	_
124	integrated	integrate	VBN	_	_	_
125	at	at	IN	_	_	_
126	mbhA	mbha	NN	_	_	_
127	and	and	CC	_	_	_
128	hyfC	hyfc	NN	GEN	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	strain	strain	NN	_	_	_
131	details	detail	NNS	_	_	_
132	:	:	:	_	_	_
133	lacIq	laciq	NN	_	_	_
134	lacZχ	laczχ	NN	_	_	_
135	-	-	:	_	_	_
136	cynX	cynx	NN	GEN	_	_
137	:	:	:	_	_	_
138	:	:	:	_	_	_
139	GmR	gmr	NN	_	_	_
140	lacZY	laczy	NN	_	_	_
141	:	:	:	_	_	_
142	:	:	:	_	_	_
143	χχχ	χχχ	NN	_	_	_
144	mhpA	mhpa	NN	GEN	_	_
145	:	:	:	_	_	_
146	:	:	:	_	_	_
147	χχχ	χχχ	NN	_	_	_
148	rph	rph	NN	GEN	_	_
149	+	+	CC	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	strain	strain	NN	_	_	_
152	details	detail	NNS	_	_	_
153	:	:	:	_	_	_
154	lacIq	laciq	NN	_	_	_
155	lacZχ	laczχ	NN	_	_	_
156	-	-	:	_	_	_
157	lacZ	lacz	NN	GEN	_	_
158	:	:	:	_	_	_
159	:	:	:	_	_	_
160	246pal	246pal	JJ	_	_	_
161	cynX	cynx	NN	GEN	_	_
162	:	:	:	_	_	_
163	:	:	:	_	_	_
164	GmR	gmr	NN	_	_	_
165	lacZY	laczy	NN	_	_	_
166	:	:	:	_	_	_
167	:	:	:	_	_	_
168	χ	χ	NN	_	_	_
169	mhpA	mhpa	NN	GEN	_	_
170	:	:	:	_	_	_
171	:	:	:	_	_	_
172	χχχ	χχχ	NN	_	_	_
173	codBχ	codbχ	NN	_	_	_
174	-	-	:	_	_	_
175	prpEχ	prpeχ	NN	_	_	_
176	-	-	:	_	_	_
177	mhpCχ	mhpcχ	NN	_	_	_
178	-	-	:	_	_	_
179	cynXχ	cynxχ	NN	_	_	_
180	-	-	:	_	_	_
181	rph	rph	NN	GEN	_	_
182	+	+	CC	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	strain	strain	NN	_	_	_
185	details	detail	NNS	_	_	_
186	:	:	:	_	_	_
187	lacIq	laciq	NN	_	_	_
188	lacZχ	laczχ	NN	_	_	_
189	-	-	:	_	_	_
190	lacZ	lacz	NN	GEN	_	_
191	:	:	:	_	_	_
192	:	:	:	_	_	_
193	246pal	246pal	JJ	_	_	_
194	cynX	cynx	NN	GEN	_	_
195	:	:	:	_	_	_
196	:	:	:	_	_	_
197	GmR	gmr	NN	_	_	_
198	lacZY	laczy	NN	_	_	_
199	:	:	:	_	_	_
200	:	:	:	_	_	_
201	χχ	χχ	NN	_	_	_
202	mhpA	mhpa	NN	GEN	_	_
203	:	:	:	_	_	_
204	:	:	:	_	_	_
205	χχχ	χχχ	NN	_	_	_
206	codBχ	codbχ	NN	_	_	_
207	-	-	:	_	_	_
208	prpEχ	prpeχ	NN	_	_	_
209	-	-	:	_	_	_
210	mhpCχ	mhpcχ	NN	_	_	_
211	-	-	:	_	_	_
212	cynXχ	cynxχ	NN	_	_	_
213	-	-	:	_	_	_
214	rph	rph	NN	GEN	_	_
215	+	+	CC	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	strain	strain	NN	_	_	_
218	details	detail	NNS	_	_	_
219	:	:	:	_	_	_
220	lacIq	laciq	NN	_	_	_
221	lacZχ	laczχ	NN	_	_	_
222	-	-	:	_	_	_
223	lacZ	lacz	NN	GEN	_	_
224	:	:	:	_	_	_
225	:	:	:	_	_	_
226	246pal	246pal	JJ	_	_	_
227	cynX	cynx	NN	GEN	_	_
228	:	:	:	_	_	_
229	:	:	:	_	_	_
230	GmR	gmr	NN	_	_	_
231	lacZY	laczy	NN	_	_	_
232	:	:	:	_	_	_
233	:	:	:	_	_	_
234	χχχ	χχχ	NN	_	_	_
235	mhpA	mhpa	NN	GEN	_	_
236	:	:	:	_	_	_
237	:	:	:	_	_	_
238	χχχ	χχχ	NN	_	_	_
239	codBχ	codbχ	NN	_	_	_
240	-	-	:	_	_	_
241	prpEχ	prpeχ	NN	_	_	_
242	-	-	:	_	_	_
243	mhpCχ	mhpcχ	NN	_	_	_
244	-	-	:	_	_	_
245	cynXχ	cynxχ	NN	_	_	_
246	-	-	:	_	_	_
247	rph	rph	NN	GEN	_	_
248	+	+	CC	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	strain	strain	NN	_	_	_
251	details	detail	NNS	_	_	_
252	:	:	:	_	_	_
253	lacIq	laciq	NN	_	_	_
254	lacZχ	laczχ	NN	_	_	_
255	-	-	:	_	_	_
256	lacZ	lacz	NN	GEN	_	_
257	:	:	:	_	_	_
258	:	:	:	_	_	_
259	246pal	246pal	JJ	_	_	_
260	cynX	cynx	NN	GEN	_	_
261	:	:	:	_	_	_
262	:	:	:	_	_	_
263	GmR	gmr	NN	_	_	_
264	lacZY	laczy	NN	_	_	_
265	:	:	:	_	_	_
266	:	:	:	_	_	_
267	χχχ	χχχ	NN	_	_	_
268	mhpA	mhpa	NN	GEN	_	_
269	:	:	:	_	_	_
270	:	:	:	_	_	_
271	χχχ	χχχ	NN	_	_	_
272	rph	rph	NN	GEN	_	_
273	+	+	CC	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	strain	strain	NN	_	_	_
276	details	detail	NNS	_	_	_
277	:	:	:	_	_	_
278	lacIq	laciq	NN	_	_	_
279	lacZχ	laczχ	NN	_	_	_
280	-	-	:	_	_	_
281	lacZ	lacz	NN	GEN	_	_
282	:	:	:	_	_	_
283	:	:	:	_	_	_
284	246pal	246pal	JJ	_	_	_
285	cynX	cynx	NN	GEN	_	_
286	:	:	:	_	_	_
287	:	:	:	_	_	_
288	GmR	gmr	NN	_	_	_
289	lacZY	laczy	NN	_	_	_
290	:	:	:	_	_	_
291	:	:	:	_	_	_
292	χχχχ	χχχχ	NN	_	_	_
293	mhpA	mhpa	NN	GEN	_	_
294	:	:	:	_	_	_
295	:	:	:	_	_	_
296	χχχ	χχχ	NN	_	_	_
297	codBχ	codbχ	NN	_	_	_
298	-	-	:	_	_	_
299	prpEχ	prpeχ	NN	_	_	_
300	-	-	:	_	_	_
301	mhpCχ	mhpcχ	NN	_	_	_
302	-	-	:	_	_	_
303	cynXχ	cynxχ	NN	_	_	_
304	-	-	:	_	_	_
305	rph	rph	NN	GEN	_	_
306	+	+	CC	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	strain	strain	NN	_	_	_
309	details	detail	NNS	_	_	_
310	:	:	:	_	_	_
311	lacIq	laciq	NN	_	_	_
312	lacZχ	laczχ	NN	_	_	_
313	-	-	:	_	_	_
314	lacZ	lacz	NN	GEN	_	_
315	:	:	:	_	_	_
316	:	:	:	_	_	_
317	246pal	246pal	JJ	_	_	_
318	cynX	cynx	NN	GEN	_	_
319	:	:	:	_	_	_
320	:	:	:	_	_	_
321	GmR	gmr	NN	_	_	_
322	lacZY	laczy	NN	_	_	_
323	:	:	:	_	_	_
324	:	:	:	_	_	_
325	χχχχχ	χχχχχ	NN	_	_	_
326	mhpA	mhpa	NN	GEN	_	_
327	:	:	:	_	_	_
328	:	:	:	_	_	_
329	χχχ	χχχ	NN	_	_	_
330	codBχ	codbχ	NN	_	_	_
331	-	-	:	_	_	_
332	prpEχ	prpeχ	NN	_	_	_
333	-	-	:	_	_	_
334	mhpCχ	mhpcχ	NN	_	_	_
335	-	-	:	_	_	_
336	cynXχ	cynxχ	NN	_	_	_
337	-	-	:	_	_	_
338	rph	rph	NN	GEN	_	_
339	+	+	CC	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	strain	strain	NN	_	_	_
342	details	detail	NNS	_	_	_
343	:	:	:	_	_	_
344	lacIq	laciq	NN	_	_	_
345	lacZχ	laczχ	NN	_	_	_
346	-	-	:	_	_	_
347	lacZ	lacz	NN	GEN	_	_
348	:	:	:	_	_	_
349	:	:	:	_	_	_
350	246pal	246pal	JJ	_	_	_
351	cynX	cynx	NN	GEN	_	_
352	:	:	:	_	_	_
353	:	:	:	_	_	_
354	GmR	gmr	NN	_	_	_
355	lacZY	laczy	NN	_	_	_
356	:	:	:	_	_	_
357	:	:	:	_	_	_
358	χχχχχχ	χχχχχχ	NN	_	_	_
359	mhpA	mhpa	NN	GEN	_	_
360	:	:	:	_	_	_
361	:	:	:	_	_	_
362	χχχ	χχχ	NN	_	_	_
363	codBχ	codbχ	NN	_	_	_
364	-	-	:	_	_	_
365	prpEχ	prpeχ	NN	_	_	_
366	-	-	:	_	_	_
367	mhpCχ	mhpcχ	NN	_	_	_
368	-	-	:	_	_	_
369	cynXχ	cynxχ	NN	_	_	_
370	-	-	:	_	_	_
371	rph	rph	NN	GEN	_	_
372	+	+	CC	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	strain	strain	NN	_	_	_
375	:	:	:	_	_	_
376	DH10BGFP	dh10bgfp	NN	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	strain	strain	NN	_	_	_
379	:	:	:	_	_	_
380	DH1	dh1	NN	_	_	_
381	ΔhisA	δhisa	NN	_	_	_
382	:	:	:	_	_	_
383	:	:	:	_	_	_
384	cat	cat	NN	_	_	_
385	ΔintC	δintc	NN	_	_	_
386	:	:	:	_	_	_
387	:	:	:	_	_	_
388	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
389	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	DH1ΔleuB	dh1δleub	NN	_	_	_
10	:	:	:	_	_	_
11	:	:	:	_	_	_
12	gfpuv5-kmr	gfpuv5-kmr	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	DH5a	dh5a	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	strain	strain	NN	_	_	_
19	:	:	:	_	_	_
20	DH5α	dh5α	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	strain	strain	NN	_	_	_
23	:	:	:	_	_	_
24	DH5α	dh5α	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	pAR060302	par060302	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	strain	strain	NN	_	_	_
30	:	:	:	_	_	_
31	DL4184	dl4184	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	strain	strain	NN	_	_	_
34	:	:	:	_	_	_
35	DL4201	dl4201	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	strain	strain	NN	_	_	_
38	:	:	:	_	_	_
39	DL5966	dl5966	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	strain	strain	NN	_	_	_
42	:	:	:	_	_	_
43	DL6204	dl6204	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	strain	strain	NN	_	_	_
46	:	:	:	_	_	_
47	DMS2545	dms2545	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	K-12	k-12	NN	_	_	_
50	derivative	derivative	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	strain	strain	NN	_	_	_
54	:	:	:	_	_	_
55	DMS2564	dms2564	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	K-12	k-12	NN	_	_	_
58	derivative	derivative	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	strain	strain	NN	_	_	_
62	D	d	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	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	:	:	:	_	_	_
4	DS168-1	ds168-1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	DS26-1	ds26-1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	strain	strain	NN	_	_	_
11	:	:	:	_	_	_
12	DY330	dy330	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	DY330	dy330	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	W3110	w3110	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	strain	strain	NN	_	_	_
22	:	:	:	_	_	_
23	E058	e058	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	strain	strain	NN	_	_	_
26	:	:	:	_	_	_
27	E1392/75	e1392/75	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	strain	strain	NN	_	_	_
30	:	:	:	_	_	_
31	E1777	e1777	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	strain	strain	NN	_	_	_
34	:	:	:	_	_	_
35	E1785	e1785	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	strain	strain	NN	_	_	_
38	:	:	:	_	_	_
39	E1786	e1786	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	strain	strain	NN	_	_	_
42	:	:	:	_	_	_
43	E1787	e1787	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	strain	strain	NN	_	_	_
46	:	:	:	_	_	_
47	E1788	e1788	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	strain	strain	NN	_	_	_
50	:	:	:	_	_	_
51	E1789	e1789	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	strain	strain	NN	_	_	_
54	:	:	:	_	_	_
55	E1790	e1790	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	strain	strain	NN	_	_	_
58	:	:	:	_	_	_
59	E1791	e1791	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	strain	strain	NN	_	_	_
62	:	:	:	_	_	_
63	E1792	e1792	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	strain	strain	NN	_	_	_
66	:	:	:	_	_	_
67	E20738A	e20738a	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	strain	strain	NN	_	_	_
70	:	:	:	_	_	_
71	E24377A	e24377a	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	strain	strain	NN	_	_	_
74	:	:	:	_	_	_
75	E2528C1	e2528c1	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	strain	strain	NN	_	_	_
78	:	:	:	_	_	_
79	E7473/0	e7473/0	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	strain	strain	NN	_	_	_
82	:	:	:	_	_	_
83	E7476A	e7476a	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	strain	strain	NN	_	_	_
86	:	:	:	_	_	_
87	E8775	e8775	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	strain	strain	NN	_	_	_
90	:	:	:	_	_	_
91	E9034A	e9034a	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	strain	strain	NN	_	_	_
94	:	:	:	_	_	_
95	EC472/01	ec472/01	NN	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	isolated	isolate	VBN	_	_	_
98	from	from	IN	_	_	_
99	cattle	cattle	NNS	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	strain	strain	NN	_	_	_
103	:	:	:	_	_	_
104	E.	e.	FW	_	_	_
105	coli	coli	FW	_	_	_
106	ATCC	atcc	NN	_	_	_
107	25922	25922	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	strain	strain	NN	_	_	_
110	:	:	:	_	_	_
111	E.	e.	FW	_	_	_
112	coli	coli	FW	_	_	_
113	DH1	dh1	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	strain	strain	NN	_	_	_
116	:	:	:	_	_	_
117	E.	e.	FW	_	_	_
118	coli	coli	FW	_	_	_
119	imp	imp	FW	_	_	_
120	4231	4231	CD	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	G93V	g93v	NN	_	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	strain	strain	NN	_	_	_
126	:	:	:	_	_	_
127	E.	e.	FW	_	_	_
128	coli	coli	FW	_	_	_
129	imp	imp	FW	_	_	_
130	4231	4231	CD	_	_	_
131	-LRB-	-lrb-	-LRB-	_	_	_
132	G93V	g93v	NN	_	_	_
133	-RRB-	-rrb-	-RRB-	_	_	_
134	,	,	,	_	_	_
135	substitution	substitution	NN	_	_	_
136	of	of	IN	_	_	_
137	the	the	DT	_	_	_
138	93th	93th	JJ	_	_	_
139	codon	codon	NN	_	_	_
140	of	of	IN	_	_	_
141	fabI	fabI	NNP	GEN	_	_
142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
143	strain	strain	NN	_	_	_
144	:	:	:	_	_	_
145	E.	e.	FW	_	_	_
146	coli	coli	FW	_	_	_
147	imp	imp	FW	_	_	_
148	4231	4231	CD	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	G93V	g93v	NN	_	_	_
151	-RRB-	-rrb-	-RRB-	_	_	_
152	,	,	,	_	_	_
153	substitution	substitution	NN	_	_	_
154	of	of	IN	_	_	_
155	the	the	DT	_	_	_
156	94th	94th	JJ	_	_	_
157	codon	codon	NN	_	_	_
158	of	of	IN	_	_	_
159	fabI	fabI	NNP	GEN	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
161	strain	strain	NN	_	_	_
162	:	:	:	_	_	_
163	E.	e.	FW	_	_	_
164	coli	coli	FW	_	_	_
165	K12	k12	NN	_	_	_
166	MG1655	mg1655	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	Strain	strain	NN	_	_	_
169	:	:	:	_	_	_
170	E.coli	e.coli	NNS	_	_	_
171	K-12	k-12	NN	_	_	_
172	MG1655	mg1655	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	Strain	strain	NN	_	_	_
175	:	:	:	_	_	_
176	E.coli	e.coli	NNS	_	_	_
177	K-12	k-12	NN	_	_	_
178	MG1655	mg1655	NN	_	_	_
179	,	,	,	_	_	_
180	Genetic	genetic	JJ	_	_	_
181	background	background	NN	_	_	_
182	:	:	:	_	_	_
183	fnr	fnr	SYM	GEN	_	_
184	-	-	:	_	_	_
185	,	,	,	_	_	_
186	Growth	growth	NN	_	_	_
187	conditions	condition	NNS	_	_	_
188	:	:	:	_	_	_
189	aerobic	aerobic	JJ	_	_	_
190	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
191	Strain	Strain	NNP	_	_	_
192	:	:	:	_	_	_
193	E.coli	e.coli	NNS	_	_	_
194	K-12	k-12	NN	_	_	_
195	MG1655	mg1655	NN	_	_	_
196	,	,	,	_	_	_
197	Genetic	genetic	JJ	_	_	_
198	background	background	NN	_	_	_
199	:	:	:	_	_	_
200	fnr	fnr	SYM	GEN	_	_
201	-	-	:	_	_	_
202	,	,	,	_	_	_
203	Growth	growth	NN	_	_	_
204	conditions	condition	NNS	_	_	_
205	:	:	:	_	_	_
206	anaerobic	anaerobic	JJ	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	Strain	strain	NN	_	_	_
209	:	:	:	_	_	_
210	E.coli	e.coli	NNS	_	_	_
211	K-12	k-12	NN	_	_	_
212	MG1655	mg1655	NN	_	_	_
213	,	,	,	_	_	_
214	Genetic	genetic	JJ	_	_	_
215	background	background	NN	_	_	_
216	:	:	:	_	_	_
217	fnr	fnr	SYM	GEN	_	_
218	-	-	:	_	_	_
219	,	,	,	_	_	_
220	Growth	growth	NN	_	_	_
221	conditions	condition	NNS	_	_	_
222	:	:	:	_	_	_
223	anaerobic	anaerobic	JJ	_	_	_
224	plus	plus	CC	_	_	_
225	NO2	no2	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	Strain	strain	NN	_	_	_
228	:	:	:	_	_	_
229	E.coli	e.coli	NNS	_	_	_
230	K-12	k-12	NN	_	_	_
231	MG1655	mg1655	NN	_	_	_
232	,	,	,	_	_	_
233	Genetic	genetic	JJ	_	_	_
234	background	background	NN	_	_	_
235	:	:	:	_	_	_
236	fnr	fnr	SYM	GEN	_	_
237	-	-	:	_	_	_
238	,	,	,	_	_	_
239	Growth	growth	NN	_	_	_
240	conditions	condition	NNS	_	_	_
241	:	:	:	_	_	_
242	anaerobic	anaerobic	JJ	_	_	_
243	plus	plus	CC	_	_	_
244	NO3	no3	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	Strain	strain	NN	_	_	_
247	:	:	:	_	_	_
248	E.coli	e.coli	NNS	_	_	_
249	K-12	k-12	NN	_	_	_
250	MG1655	mg1655	NN	_	_	_
251	,	,	,	_	_	_
252	Genetic	genetic	JJ	_	_	_
253	background	background	NN	_	_	_
254	:	:	:	_	_	_
255	narXL	narxl	NN	TU	_	_
256	,	,	,	_	_	_
257	Growth	growth	NN	_	_	_
258	conditions	condition	NNS	_	_	_
259	:	:	:	_	_	_
260	anaerobic	anaerobic	JJ	_	_	_
261	plus	plus	CC	_	_	_
262	NO2	no2	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	Strain	strain	NN	_	_	_
265	:	:	:	_	_	_
266	E.coli	e.coli	NNS	_	_	_
267	K-12	k-12	NN	_	_	_
268	MG1655	mg1655	NN	_	_	_
269	,	,	,	_	_	_
270	Genetic	genetic	JJ	_	_	_
271	background	background	NN	_	_	_
272	:	:	:	_	_	_
273	narXLP	narxlp	NN	_	_	_
274	,	,	,	_	_	_
275	Growth	growth	NN	_	_	_
276	conditions	condition	NNS	_	_	_
277	:	:	:	_	_	_
278	anaerobic	anaerobic	JJ	_	_	_
279	plus	plus	CC	_	_	_
280	NO2	no2	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Strain	strain	NN	_	_	_
283	:	:	:	_	_	_
284	E.coli	e.coli	NNS	_	_	_
285	K-12	k-12	NN	_	_	_
286	MG1655	mg1655	NN	_	_	_
287	,	,	,	_	_	_
288	Genetic	genetic	JJ	_	_	_
289	background	background	NN	_	_	_
290	:	:	:	_	_	_
291	wt	wt	JJ	_	_	_
292	,	,	,	_	_	_
293	Growth	growth	NN	_	_	_
294	conditions	condition	NNS	_	_	_
295	:	:	:	_	_	_
296	aerobic	aerobic	JJ	_	_	_
297	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
298	Strain	Strain	NNP	_	_	_
299	:	:	:	_	_	_
300	E.coli	e.coli	NNS	_	_	_
301	K-12	k-12	NN	_	_	_
302	MG1655	mg1655	NN	_	_	_
303	,	,	,	_	_	_
304	Genetic	genetic	JJ	_	_	_
305	background	background	NN	_	_	_
306	:	:	:	_	_	_
307	wt	wt	JJ	_	_	_
308	,	,	,	_	_	_
309	Growth	growth	NN	_	_	_
310	conditions	condition	NNS	_	_	_
311	:	:	:	_	_	_
312	anaerobic	anaerobic	JJ	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	Strain	strain	NN	_	_	_
315	:	:	:	_	_	_
316	E.coli	e.coli	NNS	_	_	_
317	K-12	k-12	NN	_	_	_
318	MG1655	mg1655	NN	_	_	_
319	,	,	,	_	_	_
320	Genetic	genetic	JJ	_	_	_
321	background	background	NN	_	_	_
322	:	:	:	_	_	_
323	wt	wt	JJ	_	_	_
324	,	,	,	_	_	_
325	Growth	growth	NN	_	_	_
326	conditions	condition	NNS	_	_	_
327	:	:	:	_	_	_
328	anaerobic	anaerobic	JJ	_	_	_
329	plus	plus	CC	_	_	_
330	NO2	no2	NN	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	Strain	strain	NN	_	_	_
333	:	:	:	_	_	_
334	E.coli	e.coli	NNS	_	_	_
335	K-12	k-12	NN	_	_	_
336	MG1655	mg1655	NN	_	_	_
337	,	,	,	_	_	_
338	Genetic	genetic	JJ	_	_	_
339	background	background	NN	_	_	_
340	:	:	:	_	_	_
341	wt	wt	JJ	_	_	_
342	,	,	,	_	_	_
343	Growth	growth	NN	_	_	_
344	conditions	condition	NNS	_	_	_
345	:	:	:	_	_	_
346	anaerobic	anaerobic	JJ	_	_	_
347	plus	plus	CC	_	_	_
348	NO3	no3	NN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	strain	strain	NN	_	_	_
351	:	:	:	_	_	_
352	E.coli	e.coli	NNS	_	_	_
353	O157	o157	NN	_	_	_
354	:	:	:	_	_	_
355	H7	h7	NN	_	_	_
356	EDL	edl	NN	_	_	_
357	932	932	CD	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	strain	strain	NN	_	_	_
360	:	:	:	_	_	_
361	e.	e.	FW	_	_	_
362	coli	coli	FW	_	_	_
363	o157	o157	FW	_	_	_
364	H7	h7	NN	_	_	_
365	strain	strain	NN	_	_	_
366	TW10915	tw10915	NN	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	strain	strain	NN	_	_	_
369	:	:	:	_	_	_
370	e.	e.	FW	_	_	_
371	coli	coli	FW	_	_	_
372	o157	o157	FW	_	_	_
373	H7	h7	NN	_	_	_
374	strain	strain	NN	_	_	_
375	TW10916	tw10916	NN	_	_	_
376	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
377	strain	strain	NN	_	_	_
378	:	:	:	_	_	_
379	e.	e.	FW	_	_	_
380	coli	coli	FW	_	_	_
381	o157	o157	FW	_	_	_
382	H7	h7	NN	_	_	_
383	strain	strain	NN	_	_	_
384	TW10917	tw10917	NN	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	strain	strain	NN	_	_	_
387	:	:	:	_	_	_
388	e.	e.	FW	_	_	_
389	coli	coli	FW	_	_	_
390	o157	o157	FW	_	_	_
391	H7	h7	NN	_	_	_
392	strain	strain	NN	_	_	_
393	TW10938	tw10938	NN	_	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
395	strain	strain	NN	_	_	_
396	:	:	:	_	_	_
397	e.	e.	FW	_	_	_
398	coli	coli	FW	_	_	_
399	o157	o157	FW	_	_	_
400	H7	h7	NN	_	_	_
401	strain	strain	NN	_	_	_
402	TW10948	tw10948	NN	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	strain	strain	NN	_	_	_
405	:	:	:	_	_	_
406	e.	e.	FW	_	_	_
407	coli	coli	FW	_	_	_
408	o157	o157	FW	_	_	_
409	H7	h7	NN	_	_	_
410	strain	strain	NN	_	_	_
411	TW10950	tw10950	NN	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	strain	strain	NN	_	_	_
414	:	:	:	_	_	_
415	e.	e.	FW	_	_	_
416	coli	coli	FW	_	_	_
417	o157	o157	FW	_	_	_
418	H7	h7	NN	_	_	_
419	strain	strain	NN	_	_	_
420	TW10957	tw10957	NN	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	strain	strain	NN	_	_	_
423	:	:	:	_	_	_
424	e.	e.	FW	_	_	_
425	coli	coli	FW	_	_	_
426	o157	o157	FW	_	_	_
427	H7	h7	NN	_	_	_
428	strain	strain	NN	_	_	_
429	TW10967	tw10967	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	strain	strain	NN	_	_	_
432	:	:	:	_	_	_
433	E.	e.	FW	_	_	_
434	coli	coli	FW	_	_	_
435	RP437	rp437	NN	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	strain	strain	NN	_	_	_
438	:	:	:	_	_	_
439	ECOM4	ecom4	NN	_	_	_
440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
441	strain	strain	NN	_	_	_
442	:	:	:	_	_	_
443	EDL933	edl933	NN	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	strain	strain	NN	_	_	_
446	:	:	:	_	_	_
447	EDL	edl	NN	_	_	_
448	933	933	CD	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	strain	strain	NN	_	_	_
451	:	:	:	_	_	_
452	EH41	eh41	NN	_	_	_
453	-LRB-	-lrb-	-LRB-	_	_	_
454	isolated	isolate	VBN	_	_	_
455	from	from	IN	_	_	_
456	patient	patient	NN	_	_	_
457	with	with	IN	_	_	_
458	HUS	hus	NN	_	_	_
459	-RRB-	-rrb-	-RRB-	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	strain	strain	NN	_	_	_
462	:	:	:	_	_	_
463	EHEC	ehec	NN	_	_	_
464	strain	strain	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	Strain	strain	NN	_	_	_
467	EM1453	em1453	NN	_	_	_
468	wild-type	wild-type	JJ	_	_	_
469	pBAD-ryhB	pbad-ryhb	NN	_	_	_
470	#	#	#	_	_	_
471	1	1	CD	_	_	_
472	+	+	CC	_	_	_
473	arabinose	arabinose	NN	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	strain	strain	NN	_	_	_
476	E	e	NN	_	_	_
477	of	of	IN	_	_	_
478	experimental	experimental	JJ	_	_	_
479	evolution	evolution	NN	_	_	_
480	under	under	IN	_	_	_
481	ethanol	ethanol	NN	_	_	_
482	stress	stress	NN	_	_	_
483	in	in	IN	_	_	_
484	1224	1224	CD	_	_	_
485	hours	hour	NNS	_	_	_
486	.	.	.	_	_	_

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	:	:	:	_	_	_
4	EP61	ep61	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	EPEC	epec	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	strain	strain	NN	_	_	_
11	:	:	:	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	strain	strain	NN	_	_	_
16	:	:	:	_	_	_
17	Escherichia	escherichia	FW	Organism	_	_
18	coli	coli	FW	Organism	_	_
19	8624	8624	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	strain	strain	NN	_	_	_
22	:	:	:	_	_	_
23	Escherichia	escherichia	FW	Organism	_	_
24	coli	coli	FW	Organism	_	_
25	K12	k12	NN	_	_	_
26	MG1655	mg1655	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	strain	strain	NN	_	_	_
33	8624	8624	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	strain	strain	NN	_	_	_
36	:	:	:	_	_	_
37	Escherichia	escherichia	FW	Organism	_	_
38	coli	coli	FW	Organism	_	_
39	strain	strain	NN	_	_	_
40	8624	8624	CD	_	_	_
41	kdpE	kdpe	NN	GEN	_	_
42	mutant	mutant	JJ	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	strain	strain	NN	_	_	_
45	:	:	:	_	_	_
46	Escherichia	escherichia	FW	Organism	_	_
47	coli	coli	FW	Organism	_	_
48	strain	strain	NN	_	_	_
49	8624	8624	CD	_	_	_
50	qseB	qseb	NN	GEN	_	_
51	mutant	mutant	JJ	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	strain	strain	NN	_	_	_
54	:	:	:	_	_	_
55	Escherichia	escherichia	FW	Organism	_	_
56	coli	coli	FW	Organism	_	_
57	strain	strain	NN	_	_	_
58	8624	8624	CD	_	_	_
59	qseC	qseC	NNP	GEN	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	strain	strain	NN	_	_	_
62	:	:	:	_	_	_
63	Escherichia	escherichia	FW	Organism	_	_
64	coli	coli	FW	Organism	_	_
65	strain	strain	NN	_	_	_
66	8624	8624	CD	_	_	_
67	qseC	qsec	NN	GEN	_	_
68	mutant	mutant	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Strain	strain	NN	_	_	_
71	:	:	:	_	_	_
72	Escherichia	escherichia	FW	Organism	_	_
73	coli	coli	FW	Organism	_	_
74	W3110	w3110	NN	_	_	_
75	-LSB-	-lsb-	-LRB-	_	_	_
76	F	f	NN	_	_	_
77	--	--	:	_	_	_
78	IN	in	IN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	rrnD-rrnE	rrnd-rrne	NN	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	1	1	CD	_	_	_
83	-RSB-	-rsb-	-RRB-	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	strain	strain	NN	_	_	_
86	:	:	:	_	_	_
87	ETEC	ETEC	NNP	_	_	_
88	10/1	10/1	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	strain	strain	NN	_	_	_
91	:	:	:	_	_	_
92	ETEC	etec	NNS	_	_	_
93	18/2	18/2	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	strain	strain	NN	_	_	_
96	:	:	:	_	_	_
97	ETEC	ETEC	NNP	_	_	_
98	20/10	20/10	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	strain	strain	NN	_	_	_
101	:	:	:	_	_	_
102	ETEC	ETEC	NNP	_	_	_
103	8/11	8/11	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	strain	strain	NN	_	_	_
106	:	:	:	_	_	_
107	ETEC	ETEC	NNP	_	_	_
108	Jurua	Jurua	NNP	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	strain	strain	NN	_	_	_
111	:	:	:	_	_	_
112	ETP05-002	etp05-002	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	strain	strain	NN	_	_	_
115	:	:	:	_	_	_
116	ETP05-003	etp05-003	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	strain	strain	NN	_	_	_
119	:	:	:	_	_	_
120	ETP05-007	etp05-007	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	strain	strain	NN	_	_	_
123	:	:	:	_	_	_
124	ETP05-008	etp05-008	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	strain	strain	NN	_	_	_
127	:	:	:	_	_	_
128	ETP05-009	etp05-009	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	strain	strain	NN	_	_	_
131	:	:	:	_	_	_
132	ETP05-010	etp05-010	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	strain	strain	NN	_	_	_
135	:	:	:	_	_	_
136	ETP05-011	etp05-011	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	strain	strain	NN	_	_	_
139	:	:	:	_	_	_
140	ETP05-012	etp05-012	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	strain	strain	NN	_	_	_
143	:	:	:	_	_	_
144	ETP05-015	etp05-015	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	strain	strain	NN	_	_	_
147	:	:	:	_	_	_
148	ETP05-016	etp05-016	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	strain	strain	NN	_	_	_
151	:	:	:	_	_	_
152	ETP05-017	etp05-017	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	strain	strain	NN	_	_	_
155	:	:	:	_	_	_
156	ETP05-019	etp05-019	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	strain	strain	NN	_	_	_
159	:	:	:	_	_	_
160	ETP05-020	etp05-020	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	strain	strain	NN	_	_	_
163	:	:	:	_	_	_
164	ETP05-026	etp05-026	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	strain	strain	NN	_	_	_
167	:	:	:	_	_	_
168	ETP05-035	etp05-035	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	strain	strain	NN	_	_	_
171	:	:	:	_	_	_
172	ETP05-038	etp05-038	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	strain	strain	NN	_	_	_
175	:	:	:	_	_	_
176	ETP05-039	etp05-039	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	strain	strain	NN	_	_	_
179	:	:	:	_	_	_
180	ETP05-044	etp05-044	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	strain	strain	NN	_	_	_
183	:	:	:	_	_	_
184	ETP05-046	etp05-046	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	strain	strain	NN	_	_	_
187	:	:	:	_	_	_
188	ETP05-047	etp05-047	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	strain	strain	NN	_	_	_
191	:	:	:	_	_	_
192	ETP05-050	etp05-050	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	strain	strain	NN	_	_	_
195	:	:	:	_	_	_
196	ETP98004	etp98004	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	strain	strain	NN	_	_	_
199	:	:	:	_	_	_
200	ETP98015	etp98015	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	strain	strain	NN	_	_	_
203	:	:	:	_	_	_
204	ETP98028	etp98028	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	strain	strain	NN	_	_	_
207	:	:	:	_	_	_
208	ETP98038	etp98038	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	strain	strain	NN	_	_	_
211	:	:	:	_	_	_
212	ETP98042	etp98042	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	strain	strain	NN	_	_	_
215	:	:	:	_	_	_
216	ETP98053	etp98053	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	strain	strain	NN	_	_	_
219	:	:	:	_	_	_
220	ETP98056	etp98056	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	strain	strain	NN	_	_	_
223	:	:	:	_	_	_
224	ETP98061	etp98061	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	strain	strain	NN	_	_	_
227	:	:	:	_	_	_
228	ETP98062	etp98062	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	strain	strain	NN	_	_	_
231	:	:	:	_	_	_
232	ETP98066	etp98066	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	strain	strain	NN	_	_	_
235	:	:	:	_	_	_
236	ETP98068	etp98068	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	strain	strain	NN	_	_	_
239	:	:	:	_	_	_
240	ETP98073	etp98073	NN	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	strain	strain	NN	_	_	_
243	:	:	:	_	_	_
244	ETP98097	etp98097	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	strain	strain	NN	_	_	_
247	:	:	:	_	_	_
248	ETP98103	etp98103	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	strain	strain	NN	_	_	_
251	:	:	:	_	_	_
252	ETP98105	etp98105	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	strain	strain	NN	_	_	_
255	:	:	:	_	_	_
256	ETP98109	etp98109	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	strain	strain	NN	_	_	_
259	:	:	:	_	_	_
260	ETP98111	etp98111	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	strain	strain	NN	_	_	_
263	:	:	:	_	_	_
264	ETP98112	etp98112	NN	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	strain	strain	NN	_	_	_
267	:	:	:	_	_	_
268	ETP98114	etp98114	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	strain	strain	NN	_	_	_
271	:	:	:	_	_	_
272	ETP98115	etp98115	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	strain	strain	NN	_	_	_
275	F01	f01	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	strain	strain	NN	_	_	_
278	F02	f02	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	strain	strain	NN	_	_	_
281	:	:	:	_	_	_
282	F5656-C1	f5656-c1	NN	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	strain	strain	NN	_	_	_
285	:	:	:	_	_	_
286	F595C	f595c	NN	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	strain	strain	NN	_	_	_
289	:	:	:	_	_	_
290	FHI12	fhi12	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	strain	strain	NN	_	_	_
293	:	:	:	_	_	_
294	FHI24	fhi24	NN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	strain	strain	NN	_	_	_
297	:	:	:	_	_	_
298	FHI25	fhi25	CD	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	strain	strain	NN	_	_	_
301	:	:	:	_	_	_
302	FHI27	fhi27	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	strain	strain	NN	_	_	_
305	:	:	:	_	_	_
306	FHI36	fhi36	NN	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	strain	strain	NN	_	_	_
309	:	:	:	_	_	_
310	FHI4	fhi4	NN	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	strain	strain	NN	_	_	_
313	:	:	:	_	_	_
314	FHI43	fhi43	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	strain	strain	NN	_	_	_
317	:	:	:	_	_	_
318	FHI48	fhi48	NN	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	strain	strain	NN	_	_	_
321	:	:	:	_	_	_
322	FHI6	fhi6	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	strain	strain	NN	_	_	_
325	:	:	:	_	_	_
326	FHI63	fhi63	NN	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	strain	strain	NN	_	_	_
329	:	:	:	_	_	_
330	FHI66	fhi66	NN	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	strain	strain	NN	_	_	_
333	:	:	:	_	_	_
334	FHI7	fhi7	NN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	strain	strain	NN	_	_	_
337	:	:	:	_	_	_
338	FHI79	fhi79	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	strain	strain	NN	_	_	_
341	:	:	:	_	_	_
342	FHI8	fhi8	NN	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	strain	strain	NN	_	_	_
345	:	:	:	_	_	_
346	FHI83	fhi83	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	strain	strain	NN	_	_	_
349	:	:	:	_	_	_
350	FHI9	fhi9	NN	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	strain	strain	NN	_	_	_
353	:	:	:	_	_	_
354	FHI95	fhi95	NN	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	strain	strain	NN	_	_	_
357	:	:	:	_	_	_
358	Fnr8myc	fnr8myc	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	strain	strain	NN	_	_	_
361	F	f	NN	_	_	_
362	of	of	IN	_	_	_
363	experimental	experimental	JJ	_	_	_
364	evolution	evolution	NN	_	_	_
365	under	under	IN	_	_	_
366	ethanol	ethanol	NN	_	_	_
367	stress	stress	NN	_	_	_
368	in	in	IN	_	_	_
369	1224	1224	CD	_	_	_
370	hours	hour	NNS	_	_	_
371	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	FRIK2000	frik2000	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	FRIK966	frik966	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	strain	strain	NN	_	_	_
11	:	:	:	_	_	_
12	G4H14	g4h14	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	GGG10	ggg10	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	strain	strain	NN	_	_	_
19	:	:	:	_	_	_
20	GLBRCE1	glbrce1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	strain	strain	NN	_	_	_
23	:	:	:	_	_	_
24	GLBRCE1	glbrce1	NN	_	_	_
25	_	_	CD	_	_	_
26	pBBR	pbbr	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	GM11	gm11	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	strain	strain	NN	_	_	_
33	H01	h01	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	strain	strain	NN	_	_	_
36	H02	h02	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	strain	strain	NN	_	_	_
39	H03	h03	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	strain	strain	NN	_	_	_
42	H04	h04	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	strain	strain	NN	_	_	_
45	H05	h05	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	strain	strain	NN	_	_	_
48	H12	h12	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	strain	strain	NN	_	_	_
51	H23	h23	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	strain	strain	NN	_	_	_
54	H27	h27	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	strain	strain	NN	_	_	_
57	:	:	:	_	_	_
58	HB101	hb101	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	strain	strain	NN	_	_	_
61	:	:	:	_	_	_
62	hemA	hema	NN	GEN	_	_
63	strain	strain	NN	_	_	_
64	MG1655	mg1655	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	strain	strain	NN	_	_	_
67	:	:	:	_	_	_
68	∆	∆	CD	_	_	_
69	hns	hn	NNS	GEN	_	_
70	/	/	:	_	_	_
71	∆	∆	SYM	_	_	_
72	stpA	stpa	NN	GEN	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	strain	strain	NN	_	_	_
75	:	:	:	_	_	_
76	HS	hs	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	strain	strain	NN	_	_	_
79	:	:	:	_	_	_
80	HT873	ht873	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	strain	strain	NN	_	_	_
83	:	:	:	_	_	_
84	HT874	ht874	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	strain	strain	NN	_	_	_
87	:	:	:	_	_	_
88	HT875	ht875	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	strain	strain	NN	_	_	_
91	:	:	:	_	_	_
92	Human	human	JJ	_	_	_
93	sewage	sewage	NN	_	_	_
94	isolate	isolate	NN	_	_	_
95	H1	h1	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	strain	strain	NN	_	_	_
98	:	:	:	_	_	_
99	Human	human	JJ	_	_	_
100	sewage	sewage	NN	_	_	_
101	isolate	isolate	NN	_	_	_
102	H2	h2	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	strain	strain	NN	_	_	_
105	:	:	:	_	_	_
106	Human	human	JJ	_	_	_
107	sewage	sewage	NN	_	_	_
108	isolate	isolate	NN	_	_	_
109	H3	h3	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	strain	strain	NN	_	_	_
112	:	:	:	_	_	_
113	IAI1	iai1	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	strain	strain	NN	_	_	_
116	:	:	:	_	_	_
117	ICDDR	icddr	NN	_	_	_
118	,	,	,	_	_	_
119	B	b	NN	_	_	_
120	_	_	NN	_	_	_
121	p1	p1	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	strain	strain	NN	_	_	_
124	:	:	:	_	_	_
125	ICDDR	icddr	NN	_	_	_
126	,	,	,	_	_	_
127	B	b	NN	_	_	_
128	_	_	NN	_	_	_
129	p10	p10	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	strain	strain	NN	_	_	_
132	:	:	:	_	_	_
133	ICDDR	icddr	NN	_	_	_
134	,	,	,	_	_	_
135	B	b	NN	_	_	_
136	_	_	NN	_	_	_
137	p11	p11	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	strain	strain	NN	_	_	_
140	:	:	:	_	_	_
141	ICDDR	icddr	NN	_	_	_
142	,	,	,	_	_	_
143	B	b	NN	_	_	_
144	_	_	NN	_	_	_
145	p12	p12	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	strain	strain	NN	_	_	_
148	:	:	:	_	_	_
149	ICDDR	icddr	NN	_	_	_
150	,	,	,	_	_	_
151	B	b	NN	_	_	_
152	_	_	NN	_	_	_
153	p13	p13	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	strain	strain	NN	_	_	_
156	:	:	:	_	_	_
157	ICDDR	icddr	NN	_	_	_
158	,	,	,	_	_	_
159	B	b	NN	_	_	_
160	_	_	NN	_	_	_
161	p2	p2	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	strain	strain	NN	_	_	_
164	:	:	:	_	_	_
165	ICDDR	icddr	NN	_	_	_
166	,	,	,	_	_	_
167	B	b	NN	_	_	_
168	_	_	NN	_	_	_
169	p4	p4	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	strain	strain	NN	_	_	_
172	:	:	:	_	_	_
173	ICDDR	icddr	NN	_	_	_
174	,	,	,	_	_	_
175	B	b	NN	_	_	_
176	_	_	NN	_	_	_
177	p5	p5	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	strain	strain	NN	_	_	_
180	:	:	:	_	_	_
181	ICDDR	icddr	NN	_	_	_
182	,	,	,	_	_	_
183	B	b	NN	_	_	_
184	_	_	CD	_	_	_
185	p6	p6	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	strain	strain	NN	_	_	_
188	:	:	:	_	_	_
189	ICDDR	icddr	NN	_	_	_
190	,	,	,	_	_	_
191	B	b	NN	_	_	_
192	_	_	NN	_	_	_
193	p7	p7	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	strain	strain	NN	_	_	_
196	:	:	:	_	_	_
197	ICDDR	icddr	NN	_	_	_
198	,	,	,	_	_	_
199	B	b	NN	_	_	_
200	_	_	CD	_	_	_
201	p8	p8	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	strain	strain	NN	_	_	_
204	:	:	:	_	_	_
205	ICDDR	icddr	NN	_	_	_
206	,	,	,	_	_	_
207	B	b	NN	_	_	_
208	_	_	CD	_	_	_
209	p9	p9	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	strain	strain	NN	_	_	_
212	information	information	NN	_	_	_
213	:	:	:	_	_	_
214	E.	e.	FW	_	_	_
215	coli	coli	FW	_	_	_
216	harboring	harboring	NN	_	_	_
217	empty	empty	JJ	_	_	_
218	vector	vector	NN	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	pRADgro	pradgro	NN	_	_	_
221	-RRB-	-rrb-	-RRB-	_	_	_
222	,	,	,	_	_	_
223	used	use	VBN	_	_	_
224	as	as	IN	_	_	_
225	a	a	DT	_	_	_
226	control	control	NN	_	_	_
227	strain	strain	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	strain	strain	NN	_	_	_
230	information	information	NN	_	_	_
231	:	:	:	_	_	_
232	E.	e.	FW	_	_	_
233	coli	coli	FW	_	_	_
234	harboring	harbor	VBG	_	_	_
235	pRADgro	pradgro	NN	_	_	_
236	:	:	:	_	_	_
237	:	:	:	_	_	_
238	dr1558	dr1558	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	strain	strain	NN	_	_	_
241	:	:	:	_	_	_
242	IspG1	ispg1	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	strain	strain	NN	_	_	_
245	:	:	:	_	_	_
246	JM109	jm109	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	strain	strain	NN	_	_	_
249	:	:	:	_	_	_
250	JM83	jm83	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	strain	strain	NN	_	_	_
253	:	:	:	_	_	_
254	JPEP22	jpep22	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	strain	strain	NN	_	_	_
257	:	:	:	_	_	_
258	JW3367	jw3367	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	strain	strain	NN	_	_	_
261	:	:	:	_	_	_
262	K12	k12	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	strain	strain	NN	_	_	_
265	:	:	:	_	_	_
266	K-12	k-12	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	Strain	strain	NN	_	_	_
269	:	:	:	_	_	_
270	K-12	k-12	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	strain	strain	NN	_	_	_
273	:	:	:	_	_	_
274	K-12	k-12	NN	_	_	_
275	MG1655	mg1655	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	strain	strain	NN	_	_	_
278	:	:	:	_	_	_
279	K12	k12	NN	_	_	_
280	MG1655	mg1655	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	strain	strain	NN	_	_	_
283	:	:	:	_	_	_
284	K12	k12	NN	_	_	_
285	-LRB-	-lrb-	-LRB-	_	_	_
286	MG1655	mg1655	NN	_	_	_
287	-RRB-	-rrb-	-RRB-	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	strain	strain	NN	_	_	_
290	:	:	:	_	_	_
291	K12	k12	NN	_	_	_
292	MG1655	mg1655	NN	_	_	_
293	deltaprfC	deltaprfc	NN	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	strain	strain	NN	_	_	_
296	:	:	:	_	_	_
297	K12	k12	NN	_	_	_
298	MG1655	mg1655	NN	_	_	_
299	prfB-Bstrain	prfb-bstrain	JJ	_	_	_
300	allele	allele	NN	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	strain	strain	NN	_	_	_
303	:	:	:	_	_	_
304	K12	k12	NN	_	_	_
305	MG1655	mg1655	NN	_	_	_
306	prfB-Bstrain	prfb-bstrain	JJ	_	_	_
307	allele	allele	NN	_	_	_
308	deltaprfC	deltaprfc	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	strain	strain	NN	_	_	_
311	:	:	:	_	_	_
312	k-12	k-12	NN	_	_	_
313	MG1655	mg1655	NN	_	_	_
314	wild-type	wild-type	JJ	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	strain	strain	NN	_	_	_
317	:	:	:	_	_	_
318	K12-MG1693	k12-mg1693	NN	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	strain	strain	NN	_	_	_
321	:	:	:	_	_	_
322	K-12	k-12	NN	_	_	_
323	PHL644/pMP4655	phl644/pmp4655	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	Strain	strain	NN	_	_	_
326	:	:	:	_	_	_
327	K-12	k-12	NN	_	_	_
328	reduced	reduce	VBD	_	_	_
329	genome	genome	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	strain	strain	NN	_	_	_
332	:	:	:	_	_	_
333	K-12	k-12	NN	_	_	_
334	substrain	substrain	NN	_	_	_
335	MG1655	mg1655	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	strain	strain	NN	_	_	_
338	:	:	:	_	_	_
339	K-12	k-12	NN	_	_	_
340	substr	substr	NN	_	_	_
341	.	.	.	_	_	_

1	DH10B	dh10b	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	strain	strain	NN	_	_	_
4	:	:	:	_	_	_
5	K-12	k-12	NN	_	_	_
6	substr	substr	NN	_	_	_
7	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	strain	strain	NN	_	_	_
4	:	:	:	_	_	_
5	K-12	k-12	NN	_	_	_
6	W3110	w3110	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	strain	strain	NN	_	_	_
9	:	:	:	_	_	_
10	K12	k12	NN	_	_	_
11	W3110	w3110	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	strain	strain	NN	_	_	_
14	:	:	:	_	_	_
15	KCTC	KCTC	NNP	_	_	_
16	2571	2571	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	strain	strain	NN	_	_	_
19	:	:	:	_	_	_
20	KMD	KMD	NNP	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
22	strain	strain	NN	_	_	_
23	:	:	:	_	_	_
24	L-form	l-form	JJ	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	strain	strain	NN	_	_	_
27	:	:	:	_	_	_
28	LSN02-012560	lsn02-012560	NN	_	_	_
29	/	/	:	_	_	_
30	A	a	DT	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	strain	strain	NN	_	_	_
33	:	:	:	_	_	_
34	LSN03-016011	lsn03-016011	NN	_	_	_
35	/	/	:	_	_	_
36	A	a	DT	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	strain	strain	NN	_	_	_
39	:	:	:	_	_	_
40	M408C1	m408c1	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	strain	strain	NN	_	_	_
43	:	:	:	_	_	_
44	M424C1	m424c1	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	MC1000	mc1000	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	strain	strain	NN	_	_	_
51	:	:	:	_	_	_
52	MC1061	mc1061	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	strain	strain	NN	_	_	_
55	:	:	:	_	_	_
56	MC4100	mc4100	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	strain	strain	NN	_	_	_
59	:	:	:	_	_	_
60	MC4100	mc4100	NN	_	_	_
61	derivative	derivative	JJ	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	strain	strain	NN	_	_	_
64	:	:	:	_	_	_
65	MC4100	mc4100	NN	_	_	_
66	derivative	derivative	NN	_	_	_
67	,	,	,	_	_	_
68	dcd	dcd	NN	GEN	_	_
69	:	:	:	_	_	_
70	:	:	:	_	_	_
71	kan	kan	FW	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
73	strain	strain	NN	_	_	_
74	:	:	:	_	_	_
75	MC4100	mc4100	NN	_	_	_
76	derivative	derivative	NN	_	_	_
77	,	,	,	_	_	_
78	ndk	ndk	NN	GEN	_	_
79	:	:	:	_	_	_
80	:	:	:	_	_	_
81	cam	cam	FW	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
83	strain	strain	NN	_	_	_
84	:	:	:	_	_	_
85	MC4100	mc4100	NN	_	_	_
86	derivative	derivative	NN	_	_	_
87	,	,	,	_	_	_
88	recA730	reca730	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	strain	strain	NN	_	_	_
91	:	:	:	_	_	_
92	MC4100	mc4100	NN	_	_	_
93	derivative	derivative	NN	_	_	_
94	,	,	,	_	_	_
95	recA730	reca730	NN	_	_	_
96	,	,	,	_	_	_
97	dcd	dcd	NN	GEN	_	_
98	:	:	:	_	_	_
99	:	:	:	_	_	_
100	kan	kan	FW	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
102	strain	strain	NN	_	_	_
103	:	:	:	_	_	_
104	MC4100	mc4100	NN	_	_	_
105	derivative	derivative	NN	_	_	_
106	,	,	,	_	_	_
107	recA730	reca730	NN	_	_	_
108	,	,	,	_	_	_
109	ndk	ndk	NN	GEN	_	_
110	:	:	:	_	_	_
111	:	:	:	_	_	_
112	cam	cam	FW	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
114	strain	strain	NN	_	_	_
115	:	:	:	_	_	_
116	MC4101	mc4101	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	strain	strain	NN	_	_	_
119	:	:	:	_	_	_
120	MC4102	mc4102	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	strain	strain	NN	_	_	_
123	:	:	:	_	_	_
124	MC4103	mc4103	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	strain	strain	NN	_	_	_
127	:	:	:	_	_	_
128	MC4104	mc4104	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	strain	strain	NN	_	_	_
131	:	:	:	_	_	_
132	MC4105	mc4105	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	strain	strain	NN	_	_	_
135	:	:	:	_	_	_
136	MC4106	mc4106	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	strain	strain	NN	_	_	_
139	:	:	:	_	_	_
140	MC4107	mc4107	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	strain	strain	NN	_	_	_
143	:	:	:	_	_	_
144	MDS42	mds42	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	strain	strain	NN	_	_	_
147	:	:	:	_	_	_
148	MDS42	mds42	NN	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	genome	genome	NN	_	_	_
151	reduced	reduce	VBN	_	_	_
152	-RRB-	-rrb-	-RRB-	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	strain	strain	NN	_	_	_
155	:	:	:	_	_	_
156	MDS42	mds42	NN	_	_	_
157	-LRB-	-lrb-	-LRB-	_	_	_
158	RL1961	rl1961	NN	_	_	_
159	-RRB-	-rrb-	-RRB-	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	strain	strain	NN	_	_	_
162	:	:	:	_	_	_
163	MG1655	mg1655	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	strain	strain	NN	_	_	_
166	:	:	:	_	_	_
167	MG	mg	NN	_	_	_
168	1655	1655	CD	_	_	_
169	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
170	Strain	Strain	NNP	_	_	_
171	MG1655	MG1655	NNP	_	_	_
172	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
173	Strain	Strain	NNP	_	_	_
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/resources/protocols/mopsminimal.htm	www.genome.wisc.edu/resources/protocols/mopsminimal.htm	NN	_	_	_
189	-RRB-	-rrb-	-RRB-	_	_	_
190	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	delta	delta	NN	_	_	_
6	lac	lac	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	strain	strain	NN	_	_	_
9	:	:	:	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	delta	delta	NN	_	_	_
12	lac	lac	NN	_	_	_
13	delta	delta	NN	_	_	_
14	dksA	dksa	NN	GEN	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	MG1655	mg1655	NN	_	_	_
19	delta	delta	NN	_	_	_
20	lac	lac	NN	_	_	_
21	+	+	CC	_	_	_
22	MG1655	mg1655	NN	_	_	_
23	delta	delta	NN	_	_	_
24	lac	lac	NN	_	_	_
25	delta	delta	NN	_	_	_
26	dksA	dksa	NN	GEN	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	MG1655	mg1655	NN	_	_	_
31	delta	delta	NN	_	_	_
32	_	_	CD	_	_	_
33	mazF	mazf	NN	GEN	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	strain	strain	NN	_	_	_
36	:	:	:	_	_	_
37	MG1655dnaC2	mg1655dnac2	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	strain	strain	NN	_	_	_
40	:	:	:	_	_	_
41	MG1655GFP	mg1655gfp	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	strain	strain	NN	_	_	_
44	:	:	:	_	_	_
45	MG1655	mg1655	NN	_	_	_
46	K-12	k-12	NN	_	_	_
47	WT	wt	JJ	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Strain	strain	NN	_	_	_
50	MG1655	mg1655	NN	_	_	_
51	or	or	CC	_	_	_
52	isogenic	isogenic	JJ	_	_	_
53	strain	strain	NN	_	_	_
54	MG1655	mg1655	NN	_	_	_
55	HA3	ha3	NN	_	_	_
56	:	:	:	_	_	_
57	:	:	:	_	_	_
58	nusG	nusg	NN	GEN	_	_
59	cells	cell	NNS	_	_	_
60	were	be	VBD	_	_	_
61	grown	grow	VBN	_	_	_
62	in	in	IN	_	_	_
63	MOPS	mop	NNS	MED	_	_
64	minimal	minimal	JJ	_	_	_
65	medium	medium	NN	_	_	_
66	supplemented	supplement	VBN	_	_	_
67	with	with	IN	_	_	_
68	0.2	0.2	CD	_	_	_
69	%	%	NN	_	_	_
70	glucose	glucose	NN	SUPP	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	www.genome.wisc.edu/resources/protocols/mopsminimal.htm	www.genome.wisc.edu/resources/protocols/mopsminimal.htm	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	parent	parent	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	strain	strain	NN	_	_	_
10	:	:	:	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	p-CTRL	p-ctrl	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	MG1655	mg1655	NN	_	_	_
19	-LSB-	-lsb-	-LRB-	_	_	_
20	p-CUA	p-cua	NN	_	_	_
21	-RSB-	-rsb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	strain	strain	NN	_	_	_
24	:	:	:	_	_	_
25	MG1655	mg1655	NN	_	_	_
26	-LSB-	-lsb-	-LRB-	_	_	_
27	p-CUG	p-cug	NN	_	_	_
28	-RSB-	-rsb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Strain	strain	NN	_	_	_
31	:	:	:	_	_	_
32	MG1655	mg1655	NN	_	_	_
33	pGIT1	pgit1	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	carries	carry	VBZ	_	_	_
36	the	the	DT	_	_	_
37	ytfE	ytfe	NN	GEN	_	_
38	promoter	promoter	NN	_	_	_
39	in	in	IN	_	_	_
40	multicopy	multicopy	JJ	_	_	_
41	,	,	,	_	_	_
42	titrates	titrate	VBZ	_	_	_
43	out	out	RP	_	_	_
44	NsrR	nsrr	NN	TF	_	_
45	to	to	TO	_	_	_
46	phenocopy	phenocopy	VB	_	_	_
47	an	a	DT	_	_	_
48	NsrR	nsrr	NN	TF	_	_
49	-	-	:	_	_	_
50	mutation	mutation	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Strain	strain	NN	_	_	_
54	:	:	:	_	_	_
55	MG1655	mg1655	NN	_	_	_
56	pGIT1	pgit1	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	carries	carry	VBZ	_	_	_
59	the	the	DT	_	_	_
60	ytfE	ytfe	NN	GEN	_	_
61	promoter	promoter	NN	_	_	_
62	in	in	IN	_	_	_
63	multicopy	multicopy	JJ	_	_	_
64	,	,	,	_	_	_
65	titrates	titrate	VBZ	_	_	_
66	out	out	RP	_	_	_
67	NsrR	nsrr	NN	TF	_	_
68	to	to	TO	_	_	_
69	phenocopy	phenocopy	VB	_	_	_
70	an	a	DT	_	_	_
71	NsrR	nsrr	NN	TF	_	_
72	-	-	:	_	_	_
73	mutation	mutation	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	Growth	growth	NN	_	_	_
76	:	:	:	_	_	_
77	Anaerobic	anaerobic	JJ	_	_	_
78	to	to	TO	_	_	_
79	early	early	JJ	_	_	_
80	exponential	exponential	JJ	_	_	_
81	growth	growth	NN	_	_	_
82	Media	Media	NNP	_	_	_
83	:	:	:	_	_	_
84	Minimal	minimal	JJ	_	_	_
85	salts	salt	NNS	_	_	_
86	+	+	CC	_	_	_
87	20	20	CD	_	_	_
88	mM	mm	NN	KWSUPP	_	_
89	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	Strain	strain	NN	_	_	_
92	:	:	:	_	_	_
93	MG1655	mg1655	NN	_	_	_
94	pGIT1	pgit1	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	carries	carry	VBZ	_	_	_
97	the	the	DT	_	_	_
98	ytfE	ytfe	NN	GEN	_	_
99	promoter	promoter	NN	_	_	_
100	in	in	IN	_	_	_
101	multicopy	multicopy	JJ	_	_	_
102	,	,	,	_	_	_
103	titrates	titrate	VBZ	_	_	_
104	out	out	RP	_	_	_
105	NsrR	nsrr	NN	TF	_	_
106	to	to	TO	_	_	_
107	phenocopy	phenocopy	VB	_	_	_
108	an	a	DT	_	_	_
109	NsrR	nsrr	NN	TF	_	_
110	-	-	:	_	_	_
111	mutation	mutation	NN	_	_	_
112	-RRB-	-rrb-	-RRB-	_	_	_
113	Growth	growth	NN	_	_	_
114	:	:	:	_	_	_
115	Anaerobic	anaerobic	JJ	_	_	_
116	to	to	TO	_	_	_
117	early	early	JJ	_	_	_
118	exponential	exponential	JJ	_	_	_
119	growth	growth	NN	_	_	_
120	Media	Media	NNP	_	_	_
121	:	:	:	_	_	_
122	Minimal	minimal	JJ	_	_	_
123	salts	salt	NNS	_	_	_
124	+	+	CC	_	_	_
125	20	20	CD	_	_	_
126	mM	mm	NN	KWSUPP	_	_
127	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Strain	strain	NN	_	_	_
130	:	:	:	_	_	_
131	MG1655	mg1655	NN	_	_	_
132	pGIT1	pgit1	NN	_	_	_
133	-LRB-	-lrb-	-LRB-	_	_	_
134	carries	carry	VBZ	_	_	_
135	the	the	DT	_	_	_
136	ytfE	ytfe	NN	GEN	_	_
137	promoter	promoter	NN	_	_	_
138	in	in	IN	_	_	_
139	multicopy	multicopy	JJ	_	_	_
140	,	,	,	_	_	_
141	titrates	titrate	VBZ	_	_	_
142	out	out	RP	_	_	_
143	NsrR	nsrr	NN	TF	_	_
144	to	to	TO	_	_	_
145	phenocopy	phenocopy	VB	_	_	_
146	an	a	DT	_	_	_
147	NsrR	nsrr	NN	TF	_	_
148	-	-	:	_	_	_
149	mutation	mutation	NN	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	Growth	growth	NN	_	_	_
152	:	:	:	_	_	_
153	Anaerobic	anaerobic	JJ	_	_	_
154	to	to	TO	_	_	_
155	early	early	JJ	_	_	_
156	exponential	exponential	JJ	_	_	_
157	growth	growth	NN	_	_	_
158	Media	Media	NNP	_	_	_
159	:	:	:	_	_	_
160	Minimal	minimal	JJ	_	_	_
161	salts	salt	NNS	_	_	_
162	+	+	CC	_	_	_
163	20	20	CD	_	_	_
164	mM	mm	NN	KWSUPP	_	_
165	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
166	+2.5	+2.5	CD	_	_	_
167	mM	mm	NN	KWSUPP	_	_
168	sodium	sodium	NN	_	_	_
169	nitrite	nitrite	JJ	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	Strain	strain	NN	_	_	_
172	:	:	:	_	_	_
173	MG1655	mg1655	NN	_	_	_
174	pGIT8	pgit8	NN	_	_	_
175	-LRB-	-lrb-	-LRB-	_	_	_
176	carries	carry	VBZ	_	_	_
177	1	1	CD	_	_	_
178	base	base	NN	_	_	_
179	pair	pair	NN	_	_	_
180	deletion	deletion	NN	_	_	_
181	in	in	IN	_	_	_
182	the	the	DT	_	_	_
183	NsrR-binding	nsrr-binding	JJ	_	_	_
184	site	site	NN	_	_	_
185	of	of	IN	_	_	_
186	the	the	DT	_	_	_
187	ytfE	ytfe	NN	GEN	_	_
188	promoter	promoter	NN	_	_	_
189	-RRB-	-rrb-	-RRB-	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	Strain	strain	NN	_	_	_
192	:	:	:	_	_	_
193	MG1655	mg1655	NN	_	_	_
194	pGIT8	pgit8	NN	_	_	_
195	-LRB-	-lrb-	-LRB-	_	_	_
196	carries	carry	VBZ	_	_	_
197	1	1	CD	_	_	_
198	base	base	NN	_	_	_
199	pair	pair	NN	_	_	_
200	deletion	deletion	NN	_	_	_
201	in	in	IN	_	_	_
202	the	the	DT	_	_	_
203	NsrR-binding	nsrr-binding	JJ	_	_	_
204	site	site	NN	_	_	_
205	of	of	IN	_	_	_
206	the	the	DT	_	_	_
207	ytfE	ytfe	NN	GEN	_	_
208	promoter	promoter	NN	_	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	Growth	growth	NN	_	_	_
211	:	:	:	_	_	_
212	Anaerobic	anaerobic	JJ	_	_	_
213	to	to	TO	_	_	_
214	early	early	JJ	_	_	_
215	exponential	exponential	JJ	_	_	_
216	growth	growth	NN	_	_	_
217	Media	Media	NNP	_	_	_
218	:	:	:	_	_	_
219	Minimal	minimal	JJ	_	_	_
220	salts	salt	NNS	_	_	_
221	+	+	CC	_	_	_
222	20	20	CD	_	_	_
223	mM	mm	NN	KWSUPP	_	_
224	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
225	+	+	CC	_	_	_
226	2.5	2.5	CD	_	_	_
227	mM	mm	NN	KWSUPP	_	_
228	sodium	sodium	NN	_	_	_
229	nitrite	nitrite	JJ	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	Strain	strain	NN	_	_	_
232	:	:	:	_	_	_
233	MG1655	mg1655	NN	_	_	_
234	pGIT8	pgit8	NN	_	_	_
235	-LRB-	-lrb-	-LRB-	_	_	_
236	carries	carry	VBZ	_	_	_
237	1	1	CD	_	_	_
238	base	base	NN	_	_	_
239	pair	pair	NN	_	_	_
240	deletion	deletion	NN	_	_	_
241	in	in	IN	_	_	_
242	the	the	DT	_	_	_
243	NsrR-binding	nsrr-binding	JJ	_	_	_
244	site	site	NN	_	_	_
245	of	of	IN	_	_	_
246	the	the	DT	_	_	_
247	ytfE	ytfe	NN	GEN	_	_
248	promoter	promoter	NN	_	_	_
249	-RRB-	-rrb-	-RRB-	_	_	_
250	Growth	growth	NN	_	_	_
251	:	:	:	_	_	_
252	Anaerobic	anaerobic	JJ	_	_	_
253	to	to	TO	_	_	_
254	early	early	JJ	_	_	_
255	exponential	exponential	JJ	_	_	_
256	growth	growth	NN	_	_	_
257	Media	Media	NNP	_	_	_
258	:	:	:	_	_	_
259	Minimal	minimal	JJ	_	_	_
260	salts	salt	NNS	_	_	_
261	+	+	CC	_	_	_
262	20	20	CD	_	_	_
263	mM	mm	NN	KWSUPP	_	_
264	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
265	+2.5	+2.5	CD	_	_	_
266	mM	mm	NN	KWSUPP	_	_
267	sodium	sodium	NN	_	_	_
268	nitrite	nitrite	JJ	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	Strain	strain	NN	_	_	_
271	:	:	:	_	_	_
272	MG1655	mg1655	NN	_	_	_
273	pGIT8	pgit8	NN	_	_	_
274	-LRB-	-lrb-	-LRB-	_	_	_
275	carries	carry	VBZ	_	_	_
276	1	1	CD	_	_	_
277	base	base	NN	_	_	_
278	pair	pair	NN	_	_	_
279	deletion	deletion	NN	_	_	_
280	in	in	IN	_	_	_
281	the	the	DT	_	_	_
282	NsrR-binding	nsrr-binding	JJ	_	_	_
283	site	site	NN	_	_	_
284	of	of	IN	_	_	_
285	the	the	DT	_	_	_
286	ytfE	ytfe	NN	GEN	_	_
287	promoter	promoter	NN	_	_	_
288	-RRB-	-rrb-	-RRB-	_	_	_
289	Growth	growth	NN	_	_	_
290	:	:	:	_	_	_
291	Anaerobic	anaerobic	JJ	_	_	_
292	to	to	TO	_	_	_
293	early	early	JJ	_	_	_
294	exponential	exponential	JJ	_	_	_
295	growth	growth	NN	_	_	_
296	Media	Media	NNP	_	_	_
297	:	:	:	_	_	_
298	Minimal	minimal	JJ	_	_	_
299	salts	salt	NNS	_	_	_
300	+	+	CC	_	_	_
301	20	20	CD	_	_	_
302	mM	mm	NN	KWSUPP	_	_
303	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
304	+	+	CC	_	_	_
305	.5	.5	CD	_	_	_
306	mM	mm	NN	KWSUPP	_	_
307	sodium	sodium	NN	_	_	_
308	nitrite	nitrite	JJ	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	Strain	strain	NN	_	_	_
311	:	:	:	_	_	_
312	MG1655	mg1655	NN	_	_	_
313	pGIT8	pgit8	NN	_	_	_
314	-LRB-	-lrb-	-LRB-	_	_	_
315	carries	carry	VBZ	_	_	_
316	1	1	CD	_	_	_
317	base	base	NN	_	_	_
318	pair	pair	NN	_	_	_
319	deletion	deletion	NN	_	_	_
320	in	in	IN	_	_	_
321	the	the	DT	_	_	_
322	NsrR-binding	nsrr-binding	JJ	_	_	_
323	site	site	NN	_	_	_
324	of	of	IN	_	_	_
325	the	the	DT	_	_	_
326	ytfE	ytfe	NN	GEN	_	_
327	promoter	promoter	NN	_	_	_
328	-RRB-	-rrb-	-RRB-	_	_	_
329	Growth	growth	NN	_	_	_
330	:	:	:	_	_	_
331	Anaerobic	anaerobic	JJ	_	_	_
332	to	to	TO	_	_	_
333	early	early	JJ	_	_	_
334	exponential	exponential	JJ	_	_	_
335	growth	growth	NN	_	_	_
336	Media	Media	NNP	_	_	_
337	:	:	:	_	_	_
338	Minimal	minimal	JJ	_	_	_
339	salts	salt	NNS	_	_	_
340	+	+	CC	_	_	_
341	20	20	CD	_	_	_
342	mM	mm	NN	KWSUPP	_	_
343	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
344	Pool	Pool	NNP	_	_	_
345	of	of	IN	_	_	_
346	eight	eight	CD	_	_	_
347	independent	independent	JJ	_	_	_
348	cultures	culture	NNS	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
350	strain	strain	NN	_	_	_
351	:	:	:	_	_	_
352	MG1655	mg1655	NN	_	_	_
353	-LRB-	-lrb-	-LRB-	_	_	_
354	RL1655	rl1655	NN	_	_	_
355	-RRB-	-rrb-	-RRB-	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	strain	strain	NN	_	_	_
358	:	:	:	_	_	_
359	MG1655	mg1655	NN	_	_	_
360	thyA	thya	NN	GEN	_	_
361	-	-	:	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	strain	strain	NN	_	_	_
364	:	:	:	_	_	_
365	MG1655	mg1655	NN	_	_	_
366	ΔseqA	δseqa	NN	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	strain	strain	NN	_	_	_
369	:	:	:	_	_	_
370	MG1693	mg1693	NN	_	_	_
371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
372	strain	strain	NN	_	_	_
373	:	:	:	_	_	_
374	N3431	n3431	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	strain	strain	NN	_	_	_
377	:	:	:	_	_	_
378	N3433	n3433	NN	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	strain	strain	NN	_	_	_
381	:	:	:	_	_	_
382	NEB	NEB	NNP	_	_	_
383	10-beta	10-beta	JJ	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	strain	strain	NN	_	_	_
386	:	:	:	_	_	_
387	NN-34-1-3	nn-34-1-3	NN	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	strain	strain	NN	_	_	_
390	:	:	:	_	_	_
391	no	no	DT	_	_	_
392	tag	tag	NN	GEN	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	strain	strain	NN	_	_	_
395	:	:	:	_	_	_
396	NR-12	nr-12	NN	_	_	_
397	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
398	strain	strain	NN	_	_	_
399	:	:	:	_	_	_
400	NZ-502	nz-502	NN	_	_	_
401	-LRB-	-lrb-	-LRB-	_	_	_
402	RpoB	rpob	NN	_	_	_
403	mutant	mutant	NN	_	_	_
404	-RRB-	-rrb-	-RRB-	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	strain	strain	NN	_	_	_
407	:	:	:	_	_	_
408	O08	o08	NN	_	_	_
409	-LRB-	-lrb-	-LRB-	_	_	_
410	O38	o38	NN	_	_	_
411	:	:	:	_	_	_
412	H10	h10	NN	_	_	_
413	-RRB-	-rrb-	-RRB-	_	_	_
414	obtained	obtain	VBN	_	_	_
415	from	from	IN	_	_	_
416	the	the	DT	_	_	_
417	yolk	yolk	NN	_	_	_
418	of	of	IN	_	_	_
419	the	the	DT	_	_	_
420	abdomen	abdomen	NN	_	_	_
421	of	of	IN	_	_	_
422	a	a	DT	_	_	_
423	diseased	diseased	JJ	_	_	_
424	1-day-old	1-day-old	JJ	_	_	_
425	chick	chick	NN	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	strain	strain	NN	_	_	_
428	:	:	:	_	_	_
429	O157	o157	NN	_	_	_
430	:	:	:	_	_	_
431	h7	h7	NN	_	_	_
432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
433	strain	strain	NN	_	_	_
434	:	:	:	_	_	_
435	O157	o157	NN	_	_	_
436	:	:	:	_	_	_
437	H7	h7	NN	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	Strain	strain	NN	_	_	_
440	:	:	:	_	_	_
441	O157	o157	NN	_	_	_
442	:	:	:	_	_	_
443	H7	h7	NN	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	strain	strain	NN	_	_	_
446	:	:	:	_	_	_
447	O157	o157	NN	_	_	_
448	:	:	:	_	_	_
449	H7	h7	NN	_	_	_
450	EHEC	ehec	NN	_	_	_
451	TUV93-0	tuv93-0	NN	_	_	_
452	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
453	strain	strain	NN	_	_	_
454	:	:	:	_	_	_
455	O157	o157	NN	_	_	_
456	:	:	:	_	_	_
457	H7	h7	NN	_	_	_
458	NCTC	nctc	NN	_	_	_
459	12900	12900	CD	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	strain	strain	NN	_	_	_
462	:	:	:	_	_	_
463	o157	o157	NN	_	_	_
464	:	:	:	_	_	_
465	H7	h7	NN	_	_	_
466	-LRB-	-lrb-	-LRB-	_	_	_
467	Sakai	Sakai	NNP	_	_	_
468	-RRB-	-rrb-	-RRB-	_	_	_
469	wild-type	wild-type	JJ	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	strain	strain	NN	_	_	_
472	:	:	:	_	_	_
473	O2	o2	CD	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	strain	strain	NN	_	_	_
476	:	:	:	_	_	_
477	O63	o63	NN	_	_	_
478	:	:	:	_	_	_
479	nm	nm	NN	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	strain	strain	NN	_	_	_
482	:	:	:	_	_	_
483	O78	o78	NN	_	_	_
484	:	:	:	_	_	_
485	h11	h11	NN	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	strainorline	strainorline	NN	_	_	_
488	:	:	:	_	_	_
489	K-12	k-12	NN	_	_	_
490	substr	substr	NN	_	_	_
491	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Strain	strain	NN	_	_	_
4	P4X	p4x	NN	_	_	_
5	,	,	,	_	_	_
6	grown	grow	VBN	_	_	_
7	on	on	IN	_	_	_
8	minimal	minimal	JJ	_	_	_
9	medium	medium	NN	_	_	_
10	,	,	,	_	_	_
11	reference	reference	NN	_	_	_
12	sample	sample	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	PC1012	pc1012	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	strain	strain	NN	_	_	_
19	:	:	:	_	_	_
20	PE360	pe360	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	strain	strain	NN	_	_	_
23	:	:	:	_	_	_
24	PK4854	pk4854	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	strain	strain	NN	_	_	_
27	:	:	:	_	_	_
28	PK8263	pk8263	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	strain	strain	NN	_	_	_
31	:	:	:	_	_	_
32	PK9416	pk9416	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	strain	strain	NN	_	_	_
35	:	:	:	_	_	_
36	PKH5000	pkh5000	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	strain	strain	NN	_	_	_
39	:	:	:	_	_	_
40	Porcine	porcine	NN	_	_	_
41	EPEC	epec	NN	_	_	_
42	strain	strain	NN	_	_	_
43	O45	o45	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	strain	strain	NN	_	_	_
46	:	:	:	_	_	_
47	Poultry	Poultry	NNP	_	_	_
48	E.	E.	NNP	_	_	_
49	coli	coli	NN	_	_	_
50	Virulent	virulent	JJ	_	_	_
51	and	and	CC	_	_	_
52	multidrug	multidrug	JJ	_	_	_
53	resistant	resistant	JJ	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	strain	strain	NN	_	_	_
56	:	:	:	_	_	_
57	PUTI	puti	NN	_	_	_
58	O26	o26	NN	_	_	_
59	UMN	umn	NN	_	_	_
60	O26	o26	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	strain	strain	NN	_	_	_
63	:	:	:	_	_	_
64	Rabbit	rabbit	NN	_	_	_
65	EPEC	epec	NN	_	_	_
66	strain	strain	NN	_	_	_
67	O103	o103	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	strain	strain	NN	_	_	_
70	:	:	:	_	_	_
71	REL4536	rel4536	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	strain	strain	NN	_	_	_
74	:	:	:	_	_	_
75	REL606	rel606	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	strain	strain	NN	_	_	_
78	:	:	:	_	_	_
79	RL2325	rl2325	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	strain	strain	NN	_	_	_
82	:	:	:	_	_	_
83	RL2673	rl2673	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	strain	strain	NN	_	_	_
86	:	:	:	_	_	_
87	RSW421	rsw421	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	RL1962	rl1962	NN	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	strain	strain	NN	_	_	_
93	:	:	:	_	_	_
94	RSW421	rsw421	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	RL1967	rl1967	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	strain	strain	NN	_	_	_
100	:	:	:	_	_	_
101	RSW422	rsw422	NN	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	RL1963	rl1963	NN	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	strain	strain	NN	_	_	_
107	:	:	:	_	_	_
108	RSW472	rsw472	NN	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	RL1966	rl1966	NN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	strain	strain	NN	_	_	_
114	S04	s04	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	strain	strain	NN	_	_	_
117	S05	s05	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	strain	strain	NN	_	_	_
120	S13	s13	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	strain	strain	NN	_	_	_
123	:	:	:	_	_	_
124	SE15	se15	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	strain	strain	NN	_	_	_
127	:	:	:	_	_	_
128	SH0003	sh0003	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	strain	strain	NN	_	_	_
131	:	:	:	_	_	_
132	SH0012	sh0012	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	strains	strain	NNS	_	_	_
135	:	:	:	_	_	_
136	K-12	k-12	NN	_	_	_
137	BW25113	bw25113	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	strain	strain	NN	_	_	_
140	:	:	:	_	_	_
141	SK4455	sk4455	NNS	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	strain	strain	NN	_	_	_
144	:	:	:	_	_	_
145	sPRH-20	sprh-20	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	strain	strain	NN	_	_	_
148	:	:	:	_	_	_
149	sPRH-21	sprh-21	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	strain	strain	NN	_	_	_
152	:	:	:	_	_	_
153	sPRH-25	sprh-25	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	strain	strain	NN	_	_	_
156	:	:	:	_	_	_
157	sPRH-372	sprh-372	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	strain	strain	NN	_	_	_
160	:	:	:	_	_	_
161	sPRH-403	sprh-403	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	strain	strain	NN	_	_	_
164	:	:	:	_	_	_
165	sPRH-414	sprh-414	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	strain	strain	NN	_	_	_
168	:	:	:	_	_	_
169	sPRH-418	sprh-418	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	strain	strain	NN	_	_	_
172	:	:	:	_	_	_
173	sPRH-420	sprh-420	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	strain	strain	NN	_	_	_
176	:	:	:	_	_	_
177	sPRH-421	sprh-421	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	strain	strain	NN	_	_	_
180	:	:	:	_	_	_
181	sPRH-443	sprh-443	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	strain	strain	NN	_	_	_
184	:	:	:	_	_	_
185	sPRH-445	sprh-445	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	strain	strain	NN	_	_	_
188	:	:	:	_	_	_
189	sPRH-450	sprh-450	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	strain	strain	NN	_	_	_
192	:	:	:	_	_	_
193	sPRH-604	sprh-604	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	strain	strain	NN	_	_	_
196	:	:	:	_	_	_
197	sPRH-605	sprh-605	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	strain	strain	NN	_	_	_
200	:	:	:	_	_	_
201	sPRH-606	sprh-606	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	strain	strain	NN	_	_	_
204	:	:	:	_	_	_
205	sPRH-609	sprh-609	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	strain	strain	NN	_	_	_
208	:	:	:	_	_	_
209	sPRH-610	sprh-610	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	strain	strain	NN	_	_	_
212	:	:	:	_	_	_
213	sPRH-612	sprh-612	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	strain	strain	NN	_	_	_
216	:	:	:	_	_	_
217	sPRH-613	sprh-613	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	strain	strain	NN	_	_	_
220	:	:	:	_	_	_
221	St.	St.	NNP	_	_	_
222	Olav104	Olav104	NNP	_	_	_
223	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
224	strain	strain	NN	_	_	_
225	:	:	:	_	_	_
226	St.	St.	NNP	_	_	_
227	Olav157	Olav157	NNP	_	_	_
228	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
229	strain	strain	NN	_	_	_
230	:	:	:	_	_	_
231	St.	St.	NNP	_	_	_
232	Olav164	Olav164	NNP	_	_	_
233	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
234	strain	strain	NN	_	_	_
235	:	:	:	_	_	_
236	St.	St.	NNP	_	_	_
237	Olav17	Olav17	NNP	_	_	_
238	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
239	strain	strain	NN	_	_	_
240	:	:	:	_	_	_
241	St.	St.	NNP	_	_	_
242	Olav172	Olav172	NNP	_	_	_
243	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
244	strain	strain	NN	_	_	_
245	:	:	:	_	_	_
246	St.	St.	NNP	_	_	_
247	Olav173	Olav173	NNP	_	_	_
248	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
249	strain	strain	NN	_	_	_
250	:	:	:	_	_	_
251	St.	St.	NNP	_	_	_
252	Olav174	Olav174	NNP	_	_	_
253	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
254	strain	strain	NN	_	_	_
255	:	:	:	_	_	_
256	St.	St.	NNP	_	_	_
257	Olav176	Olav176	NNP	_	_	_
258	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
259	strain	strain	NN	_	_	_
260	:	:	:	_	_	_
261	St.	St.	NNP	_	_	_
262	Olav178	Olav178	NNP	_	_	_
263	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
264	strain	strain	NN	_	_	_
265	:	:	:	_	_	_
266	St.	St.	NNP	_	_	_
267	Olav179	Olav179	NNP	_	_	_
268	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
269	strain	strain	NN	_	_	_
270	:	:	:	_	_	_
271	St.	St.	NNP	_	_	_
272	Olav39	Olav39	NNP	_	_	_
273	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
274	strain	strain	NN	_	_	_
275	:	:	:	_	_	_
276	St.	St.	NNP	_	_	_
277	Olav40	Olav40	NNP	_	_	_
278	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
279	strain	strain	NN	_	_	_
280	:	:	:	_	_	_
281	St.	St.	NNP	_	_	_
282	Olav63	Olav63	NNP	_	_	_
283	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
284	strain	strain	NN	_	_	_
285	:	:	:	_	_	_
286	strain	strain	NN	_	_	_
287	K12	k12	NN	_	_	_
288	substrain	substrain	NN	_	_	_
289	MG1655	mg1655	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	strain	strain	NN	_	_	_
292	:	:	:	_	_	_
293	strain	strain	NN	_	_	_
294	O157	o157	NN	_	_	_
295	:	:	:	_	_	_
296	H7	h7	NN	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	strains	strain	NNS	_	_	_
299	TW014359	tw014359	NN	_	_	_
300	vs	vs	CC	_	_	_
301	TW04863	tw04863	NN	_	_	_
302	epithelial	epithelial	JJ	_	_	_
303	exposure	exposure	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	strains	strain	NNS	_	_	_
306	TW014359	tw014359	NN	_	_	_
307	vs	vs	CC	_	_	_
308	TW11037	tw11037	NN	_	_	_
309	epithelial	epithelial	JJ	_	_	_
310	exposure	exposure	NN	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	strains	strain	NNS	_	_	_
313	TW02883	tw02883	NN	_	_	_
314	vs	vs	CC	_	_	_
315	TW11028	tw11028	NN	_	_	_
316	epithelial	epithelial	JJ	_	_	_
317	exposure	exposure	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	strains	strain	NNS	_	_	_
320	TW04863	tw04863	NN	_	_	_
321	vs	vs	CC	_	_	_
322	TW14279	tw14279	NN	_	_	_
323	epithelial	epithelial	JJ	_	_	_
324	exposure	exposure	NN	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	strains	strain	NNS	_	_	_
327	TW07591	tw07591	NN	_	_	_
328	vs	vs	CC	_	_	_
329	TW09098	tw09098	NN	_	_	_
330	epithelial	epithelial	JJ	_	_	_
331	exposure	exposure	NN	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	strains	strain	NNS	_	_	_
334	TW07937	tw07937	NN	_	_	_
335	vs	vs	CC	_	_	_
336	TW11185	tw11185	NN	_	_	_
337	epithelial	epithelial	JJ	_	_	_
338	exposure	exposure	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	strains	strain	NNS	_	_	_
341	TW07961	tw07961	NN	_	_	_
342	vs	vs	CC	_	_	_
343	TW08610	tw08610	NN	_	_	_
344	epithelial	epithelial	JJ	_	_	_
345	exposure	exposure	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	strains	strain	NNS	_	_	_
348	TW07961	tw07961	NN	_	_	_
349	vs	vs	CC	_	_	_
350	TW11029	tw11029	NN	_	_	_
351	epithelial	epithelial	JJ	_	_	_
352	exposure	exposure	NN	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	strains	strain	NNS	_	_	_
355	TW08030	tw08030	NN	_	_	_
356	vs	vs	CC	_	_	_
357	TW10045	tw10045	NN	_	_	_
358	epithelial	epithelial	JJ	_	_	_
359	exposure	exposure	NN	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	strains	strain	NNS	_	_	_
362	TW08609	tw08609	NN	_	_	_
363	vs	vs	CC	_	_	_
364	TW08030	tw08030	NN	_	_	_
365	epithelial	epithelial	JJ	_	_	_
366	exposure	exposure	NN	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	strains	strain	NNS	_	_	_
369	TW08609	tw08609	NN	_	_	_
370	vs	vs	CC	_	_	_
371	TW08623	tw08623	NN	_	_	_
372	epithelial	epithelial	JJ	_	_	_
373	exposure	exposure	NN	_	_	_
374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
375	strains	strain	NNS	_	_	_
376	TW08609	tw08609	NN	_	_	_
377	vs	vs	CC	_	_	_
378	TW11110	tw11110	NN	_	_	_
379	epithelial	epithelial	JJ	_	_	_
380	exposure	exposure	NN	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	strains	strain	NNS	_	_	_
383	TW08610	tw08610	NN	_	_	_
384	vs	vs	CC	_	_	_
385	TW11110	tw11110	NN	_	_	_
386	epithelial	epithelial	JJ	_	_	_
387	exposure	exposure	NN	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	strains	strain	NNS	_	_	_
390	TW08623	tw08623	NN	_	_	_
391	vs	vs	CC	_	_	_
392	TW02883	tw02883	NN	_	_	_
393	epithelial	epithelial	JJ	_	_	_
394	exposure	exposure	NN	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	strains	strain	NNS	_	_	_
397	TW08623	tw08623	NN	_	_	_
398	vs	vs	CC	_	_	_
399	TW08030	tw08030	NN	_	_	_
400	epithelial	epithelial	JJ	_	_	_
401	exposure	exposure	NN	_	_	_
402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
403	strains	strain	NNS	_	_	_
404	TW08635	tw08635	NN	_	_	_
405	vs	vs	CC	_	_	_
406	TW09098	tw09098	NN	_	_	_
407	epithelial	epithelial	JJ	_	_	_
408	exposure	exposure	NN	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	strains	strain	NNS	_	_	_
411	TW09098	tw09098	NN	_	_	_
412	vs	vs	CC	_	_	_
413	TW11308	tw11308	NN	_	_	_
414	epithelial	epithelial	JJ	_	_	_
415	exposure	exposure	NN	_	_	_
416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
417	strains	strain	NNS	_	_	_
418	TW09189	tw09189	NN	_	_	_
419	vs	vs	CC	_	_	_
420	TW11032	tw11032	NN	_	_	_
421	epithelial	epithelial	JJ	_	_	_
422	exposure	exposure	NN	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	strains	strain	NNS	_	_	_
425	TW09189	tw09189	NN	_	_	_
426	vs	vs	CC	_	_	_
427	TW14279	tw14279	NN	_	_	_
428	epithelial	epithelial	JJ	_	_	_
429	exposure	exposure	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	strains	strain	NNS	_	_	_
432	TW10012	tw10012	NN	_	_	_
433	vs	vs	CC	_	_	_
434	TW11037	tw11037	NN	_	_	_
435	epithelial	epithelial	JJ	_	_	_
436	exposure	exposure	NN	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	strains	strain	NNS	_	_	_
439	TW10012	tw10012	NN	_	_	_
440	vs	vs	CC	_	_	_
441	TW14313	tw14313	NN	_	_	_
442	epithelial	epithelial	JJ	_	_	_
443	exposure	exposure	NN	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	strains	strain	NNS	_	_	_
446	TW10045	tw10045	NN	_	_	_
447	vs	vs	CC	_	_	_
448	TW07937	tw07937	NN	_	_	_
449	epithelial	epithelial	JJ	_	_	_
450	exposure	exposure	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	strains	strain	NNS	_	_	_
453	TW11028	tw11028	NN	_	_	_
454	vs	vs	CC	_	_	_
455	TW07937	tw07937	NN	_	_	_
456	epithelial	epithelial	JJ	_	_	_
457	exposure	exposure	NN	_	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	strains	strain	NNS	_	_	_
460	TW11028	tw11028	NN	_	_	_
461	vs	vs	CC	_	_	_
462	TW11308	tw11308	NN	_	_	_
463	epithelial	epithelial	JJ	_	_	_
464	exposure	exposure	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	strains	strain	NNS	_	_	_
467	TW11029	tw11029	NN	_	_	_
468	vs	vs	CC	_	_	_
469	TW02883	tw02883	NN	_	_	_
470	epithelial	epithelial	JJ	_	_	_
471	exposure	exposure	NN	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	strains	strain	NNS	_	_	_
474	TW11029	tw11029	NN	_	_	_
475	vs	vs	CC	_	_	_
476	TW08610	tw08610	NN	_	_	_
477	epithelial	epithelial	JJ	_	_	_
478	exposure	exposure	NN	_	_	_
479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
480	strains	strain	NNS	_	_	_
481	TW11032	tw11032	NN	_	_	_
482	vs	vs	CC	_	_	_
483	TW04863	tw04863	NN	_	_	_
484	epithelial	epithelial	JJ	_	_	_
485	exposure	exposure	NN	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	strains	strain	NNS	_	_	_
488	TW11032	tw11032	NN	_	_	_
489	vs	vs	CC	_	_	_
490	TW09189	tw09189	NN	_	_	_
491	epithelial	epithelial	JJ	_	_	_
492	exposure	exposure	NN	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	strains	strain	NNS	_	_	_
495	TW11037	tw11037	NN	_	_	_
496	vs	vs	CC	_	_	_
497	TW08635	tw08635	NN	_	_	_
498	epithelial	epithelial	JJ	_	_	_
499	exposure	exposure	NN	_	_	_
500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
501	strains	strain	NNS	_	_	_
502	TW11110	tw11110	NN	_	_	_
503	vs	vs	CC	_	_	_
504	TW10012	tw10012	NN	_	_	_
505	epithelial	epithelial	JJ	_	_	_
506	exposure	exposure	NN	_	_	_
507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
508	strains	strain	NNS	_	_	_
509	TW11185	tw11185	NN	_	_	_
510	vs	vs	CC	_	_	_
511	TW014313	tw014313	NN	_	_	_
512	epithelial	epithelial	JJ	_	_	_
513	exposure	exposure	NN	_	_	_
514	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
515	strains	strain	NNS	_	_	_
516	TW11185	tw11185	NN	_	_	_
517	vs	vs	CC	_	_	_
518	TW08635	tw08635	NN	_	_	_
519	epithelial	epithelial	JJ	_	_	_
520	exposure	exposure	NN	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
522	strains	strain	NNS	_	_	_
523	TW11308	tw11308	NN	_	_	_
524	vs	vs	CC	_	_	_
525	TW07591	tw07591	NN	_	_	_
526	epithelial	epithelial	JJ	_	_	_
527	exposure	exposure	NN	_	_	_
528	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
529	strains	strain	NNS	_	_	_
530	TW14279	tw14279	NN	_	_	_
531	vs	vs	CC	_	_	_
532	TW10045	tw10045	NN	_	_	_
533	epithelial	epithelial	JJ	_	_	_
534	exposure	exposure	NN	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	strains	strain	NNS	_	_	_
537	TW14313	tw14313	NN	_	_	_
538	vs	vs	CC	_	_	_
539	TW07591	tw07591	NN	_	_	_
540	epithelial	epithelial	JJ	_	_	_
541	exposure	exposure	NN	_	_	_
542	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
543	strains	strain	NNS	_	_	_
544	TW14359	tw14359	NN	_	_	_
545	vs	vs	CC	_	_	_
546	TW07961	tw07961	NN	_	_	_
547	epithelial	epithelial	JJ	_	_	_
548	exposure	exposure	NN	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	strain	strain	NN	_	_	_
551	:	:	:	_	_	_
552	Suc-T110	suc-t110	NN	_	_	_
553	-LRB-	-lrb-	-LRB-	_	_	_
554	parental	parental	JJ	_	_	_
555	strain	strain	NN	_	_	_
556	-RRB-	-rrb-	-RRB-	_	_	_
557	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
558	Strains	strain	NNS	_	_	_
559	were	be	VBD	_	_	_
560	grown	grow	VBN	_	_	_
561	in	in	IN	_	_	_
562	LB	lb	NN	_	_	_
563	at	at	IN	_	_	_
564	37	37	CD	_	_	_
565	°C	°c	NN	_	_	_
566	with	with	IN	_	_	_
567	shaking	shake	VBG	_	_	_
568	at	at	IN	_	_	_
569	250	250	CD	_	_	_
570	rpm	rpm	NN	_	_	_
571	.	.	.	_	_	_

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	Strains	strain	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	LBCm30	lbcm30	NN	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	with	with	IN	_	_	_
11	shaking	shake	VBG	_	_	_
12	at	at	IN	_	_	_
13	250	250	CD	_	_	_
14	rpm	rpm	NN	_	_	_
15	.	.	.	_	_	_

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	Strains	strain	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	LBCm30	lbcm30	NN	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	with	with	IN	_	_	_
11	shaking	shake	VBG	_	_	_
12	at	at	IN	_	_	_
13	250	250	CD	_	_	_
14	rpm	rpm	NN	_	_	_
15	.	.	.	_	_	_

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	NN	_	_	_
2	Strains	strain	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	LB	lb	NN	MED	_	_
7	medium	medium	NN	MED	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Difco	Difco	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	supplemented	supplement	VBN	_	_	_
12	with	with	IN	_	_	_
13	thymine	thymine	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	50	50	CD	_	_	_
16	µg/ml	µg/ml	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	at	at	IN	_	_	_
19	37ºC	37ºc	NN	_	_	_
20	,	,	,	_	_	_
21	unless	unless	IN	_	_	_
22	otherwise	otherwise	RB	_	_	_
23	stated	state	VBN	_	_	_
24	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	of	of	IN	_	_	_
4	single	single	JJ	_	_	_
5	fresh	fresh	JJ	_	_	_
6	grown	grown	JJ	_	_	_
7	colonies	colony	NNS	_	_	_
8	were	be	VBD	_	_	_
9	diluted	dilute	VBN	_	_	_
10	to	to	TO	_	_	_
11	an	a	DT	_	_	_
12	initial	initial	JJ	_	_	_
13	OD600	od600	NN	_	_	_
14	appr	appr	NN	_	_	_
15	.	.	.	_	_	_

1	0.03	0.03	CD	_	_	_
2	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	at	at	IN	_	_	_
5	exponential	exponential	JJ	GrowthPhase	_	_
6	phase	phase	NN	GrowthPhase	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	OD600	od600	NN	_	_	_
9	appr	appr	NN	_	_	_
10	.	.	.	_	_	_

1	0.5	0.5	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Strains	strain	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	overnight	overnight	RB	_	_	_
6	in	in	IN	_	_	_
7	LB	lb	NN	MED	_	_
8	broth	broth	NN	MED	_	_
9	and	and	CC	_	_	_
10	then	then	RB	_	_	_
11	equalised	equalise	VBD	_	_	_
12	to	to	TO	_	_	_
13	0.15	0.15	CD	_	_	_
14	optical	optical	JJ	_	_	_
15	density	density	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	OD600nm	od600nm	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	units	unit	NNS	_	_	_
20	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	Strains	strain	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	in	in	IN	_	_	_
6	MH	mh	NN	_	_	_
7	broth	broth	NN	_	_	_
8	at	at	IN	_	_	_
9	log	log	NN	_	_	_
10	phase	phase	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	strain	strain	NN	_	_	_
13	:	:	:	_	_	_
14	T175	t175	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	T177	t177	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	strain	strain	NN	_	_	_
21	:	:	:	_	_	_
22	T3	t3	NN	_	_	_
23	5H5	5h5	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	strain	strain	NN	_	_	_
26	:	:	:	_	_	_
27	T3	t3	NN	_	_	_
28	5H5	5h5	NN	_	_	_
29	M	m	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	strain	strain	NN	_	_	_
32	:	:	:	_	_	_
33	T75	t75	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	strain	strain	NN	_	_	_
36	:	:	:	_	_	_
37	TB1	tb1	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	strain	strain	NN	_	_	_
40	:	:	:	_	_	_
41	TB16	tb16	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	strain	strain	NN	_	_	_
44	:	:	:	_	_	_
45	TG-1	tg-1	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	strain	strain	NN	_	_	_
48	:	:	:	_	_	_
49	TG-2	tg-2	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	strain	strain	NN	_	_	_
52	TW02883	tw02883	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	strain	strain	NN	_	_	_
55	TW02883	tw02883	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	strain	strain	NN	_	_	_
58	:	:	:	_	_	_
59	TW03439	tw03439	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	strain	strain	NN	_	_	_
62	:	:	:	_	_	_
63	TW03452	tw03452	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	strain	strain	NN	_	_	_
66	:	:	:	_	_	_
67	TW03574	tw03574	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	strain	strain	NN	_	_	_
70	:	:	:	_	_	_
71	TW03576	tw03576	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	strain	strain	NN	_	_	_
74	:	:	:	_	_	_
75	TW03585	tw03585	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	strain	strain	NN	_	_	_
78	:	:	:	_	_	_
79	TW03741	tw03741	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	strain	strain	NN	_	_	_
82	TW04863	tw04863	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	strain	strain	NN	_	_	_
85	TW07591	tw07591	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	strain	strain	NN	_	_	_
88	TW07937	tw07937	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	strain	strain	NN	_	_	_
91	TW07961	tw07961	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	strain	strain	NN	_	_	_
94	TW07961	tw07961	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	strain	strain	NN	_	_	_
97	TW08030	tw08030	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	strain	strain	NN	_	_	_
100	TW08609	tw08609	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	strain	strain	NN	_	_	_
103	TW08609	tw08609	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	strain	strain	NN	_	_	_
106	TW08610	tw08610	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	strain	strain	NN	_	_	_
109	TW08623	tw08623	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	strain	strain	NN	_	_	_
112	TW08635	tw08635	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	strain	strain	NN	_	_	_
115	TW08635	tw08635	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	strain	strain	NN	_	_	_
118	TW09098	tw09098	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	strain	strain	NN	_	_	_
121	TW09098	tw09098	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	strain	strain	NN	_	_	_
124	TW09189	tw09189	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	strain	strain	NN	_	_	_
127	:	:	:	_	_	_
128	TW09308	tw09308	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	strain	strain	NN	_	_	_
131	TW10012	tw10012	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	strain	strain	NN	_	_	_
134	TW10045	tw10045	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	strain	strain	NN	_	_	_
137	TW10045	tw10045	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	strain	strain	NN	_	_	_
140	TW11028	tw11028	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	strain	strain	NN	_	_	_
143	TW11029	tw11029	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	strain	strain	NN	_	_	_
146	TW11029	tw11029	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	strain	strain	NN	_	_	_
149	TW11032	tw11032	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	strain	strain	NN	_	_	_
152	TW11032	tw11032	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	strain	strain	NN	_	_	_
155	TW11037	tw11037	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	strain	strain	NN	_	_	_
158	TW11110	tw11110	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	strain	strain	NN	_	_	_
161	TW11110	tw11110	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	strain	strain	NN	_	_	_
164	TW11185	tw11185	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	strain	strain	NN	_	_	_
167	TW11185	tw11185	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	strain	strain	NN	_	_	_
170	TW11308	tw11308	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	strain	strain	NN	_	_	_
173	TW11308	tw11308	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	strain	strain	NN	_	_	_
176	:	:	:	_	_	_
177	TW11588	tw11588	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	strain	strain	NN	_	_	_
180	TW14279	tw14279	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	strain	strain	NN	_	_	_
183	TW14279	tw14279	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	strain	strain	NN	_	_	_
186	TW14313	tw14313	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	strain	strain	NN	_	_	_
189	TW14359	tw14359	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	strain	strain	NN	_	_	_
192	:	:	:	_	_	_
193	TWx30	twx30	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	strain	strain	NN	_	_	_
196	:	:	:	_	_	_
197	TWx31	twx31	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	strain	strain	NN	_	_	_
200	:	:	:	_	_	_
201	TWx34	twx34	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	strain	strain	NN	_	_	_
204	:	:	:	_	_	_
205	TWx48	twx48	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	strain	strain	NN	_	_	_
208	:	:	:	_	_	_
209	unevolved	unevolved	JJ	_	_	_
210	parent	parent	NN	_	_	_
211	strain	strain	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	strain	strain	NN	_	_	_
214	:	:	:	_	_	_
215	W3110	w3110	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	Strain	strain	NN	_	_	_
218	W3110	w3110	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	Strain	strain	NN	_	_	_
221	:	:	:	_	_	_
222	W3110	w3110	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	Strain	strain	NN	_	_	_
225	:	:	:	_	_	_
226	W3110	w3110	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	Strain	strain	NN	_	_	_
229	:	:	:	_	_	_
230	W3110	w3110	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	strain	strain	NN	_	_	_
233	:	:	:	_	_	_
234	W3110hns	w3110hn	NNS	_	_	_
235	∆	∆	VBP	_	_	_
236	93-1	93-1	CD	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
238	strain	strain	NN	_	_	_
239	:	:	:	_	_	_
240	wildtype	wildtype	JJ	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	strain	strain	NN	_	_	_
243	:	:	:	_	_	_
244	Wild	Wild	NNP	_	_	_
245	Type	type	NN	_	_	_
246	K-12	k-12	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	strain	strain	NN	_	_	_
249	:	:	:	_	_	_
250	Wild	Wild	NNP	_	_	_
251	type	type	NN	_	_	_
252	strain	strain	NN	_	_	_
253	MG1655	mg1655	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	strain	strain	NN	_	_	_
256	:	:	:	_	_	_
257	WS	ws	NN	_	_	_
258	0115A	0115a	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	strain	strain	NN	_	_	_
261	:	:	:	_	_	_
262	WS1896A	ws1896a	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	strain	strain	NN	_	_	_
265	:	:	:	_	_	_
266	WS1896	ws1896	NN	_	_	_
267	A-1	a-1	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	strain	strain	NN	_	_	_
270	:	:	:	_	_	_
271	WS	ws	NN	_	_	_
272	1933D	1933d	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	strain	strain	NN	_	_	_
275	:	:	:	_	_	_
276	WS2068A	ws2068a	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	strain	strain	NN	_	_	_
279	:	:	:	_	_	_
280	WS	ws	NN	_	_	_
281	2173A	2173a	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	strain	strain	NN	_	_	_
284	:	:	:	_	_	_
285	WS2741	ws2741	NN	_	_	_
286	A-1	a-1	NN	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	strain	strain	NN	_	_	_
289	:	:	:	_	_	_
290	WS3080A	ws3080a	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	strain	strain	NN	_	_	_
293	:	:	:	_	_	_
294	WS	ws	NN	_	_	_
295	3294A	3294a	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	strain	strain	NN	_	_	_
298	:	:	:	_	_	_
299	WS	w	NNS	_	_	_
300	3572	3572	CD	_	_	_
301	A-1	a-1	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	strain	strain	NN	_	_	_
304	:	:	:	_	_	_
305	WS	w	NNS	_	_	_
306	3596	3596	CD	_	_	_
307	A-4	a-4	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	strain	strain	NN	_	_	_
310	:	:	:	_	_	_
311	WS4087	ws4087	NN	_	_	_
312	A-1	a-1	NN	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	strain	strain	NN	_	_	_
315	:	:	:	_	_	_
316	WS4264	ws4264	NN	_	_	_
317	A-1	a-1	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	strain	strain	NN	_	_	_
320	:	:	:	_	_	_
321	WS5874	ws5874	NN	_	_	_
322	A-1	a-1	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	strain	strain	NN	_	_	_
325	:	:	:	_	_	_
326	WS6582	ws6582	NN	_	_	_
327	A-1	a-1	NN	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	strain	strain	NN	_	_	_
330	:	:	:	_	_	_
331	WS	ws	NN	_	_	_
332	6866B-1	6866b-1	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	strain	strain	NN	_	_	_
335	:	:	:	_	_	_
336	WS	w	NNS	_	_	_
337	7162	7162	CD	_	_	_
338	A-1	a-1	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	strain	strain	NN	_	_	_
341	:	:	:	_	_	_
342	WS7179	ws7179	NN	_	_	_
343	A-2	a-2	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	strain	strain	NN	_	_	_
346	:	:	:	_	_	_
347	wt	wt	JJ	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	strain	strain	NN	_	_	_
350	:	:	:	_	_	_
351	wt	wt	JJ	_	_	_
352	3xflag	3xflag	NN	_	_	_
353	strain	strain	NN	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	strain	strain	NN	_	_	_
356	:	:	:	_	_	_
357	Xuzhou21	xuzhou21	NN	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	strain	strain	NN	_	_	_
360	:	:	:	_	_	_
361	Xuzhou21m	xuzhou21m	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	strain	strain	NN	_	_	_
364	:	:	:	_	_	_
365	ZD1	zd1	NN	_	_	_
366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
367	strain	strain	NN	_	_	_
368	:	:	:	_	_	_
369	ZD26	zd26	NN	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	strain	strain	NN	_	_	_
372	:	:	:	_	_	_
373	ZD51	zd51	NN	_	_	_
374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
375	strain	strain	NN	_	_	_
376	:	:	:	_	_	_
377	ZD56	zd56	NN	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	strain	strain	NN	_	_	_
380	:	:	:	_	_	_
381	ZD59	zd59	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	strain	strain	NN	_	_	_
384	:	:	:	_	_	_
385	ZD60	zd60	NN	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	strain	strain	NN	_	_	_
388	:	:	:	_	_	_
389	ZD8	zd8	NN	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	Strand	strand	NN	_	_	_
392	specific	specific	JJ	_	_	_
393	base	base	NN	_	_	_
394	read	read	VBD	_	_	_
395	counts	count	NNS	_	_	_
396	were	be	VBD	_	_	_
397	determined	determine	VBN	_	_	_
398	for	for	IN	_	_	_
399	each	each	DT	_	_	_
400	of	of	IN	_	_	_
401	4091	4091	CD	_	_	_
402	ORFs	orf	NNS	_	_	_
403	for	for	IN	_	_	_
404	the	the	DT	_	_	_
405	15	15	CD	_	_	_
406	samples	sample	NNS	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	Strand-specific	strand-specific	JJ	_	_	_
409	cDNA	cdna	NN	_	_	_
410	libraries	library	NNS	_	_	_
411	were	be	VBD	_	_	_
412	prepared	prepare	VBN	_	_	_
413	from	from	IN	_	_	_
414	50	50	CD	_	_	_
415	ng	ng	NN	_	_	_
416	of	of	IN	_	_	_
417	rRNA-depleted	rrna-depleted	JJ	_	_	_
418	samples	sample	NNS	_	_	_
419	following	follow	VBG	_	_	_
420	the	the	DT	_	_	_
421	TruSeq	TruSeq	NNP	_	_	_
422	RNA	rna	NN	_	_	_
423	protocol	protocol	NN	_	_	_
424	-LRB-	-lrb-	-LRB-	_	_	_
425	Illumina	Illumina	NNP	_	_	_
426	,	,	,	_	_	_
427	San	San	NNP	_	_	_
428	Diego	Diego	NNP	_	_	_
429	,	,	,	_	_	_
430	CA	CA	NNP	_	_	_
431	,	,	,	_	_	_
432	USA	USA	NNP	_	_	_
433	,	,	,	_	_	_
434	without	without	IN	_	_	_
435	purification	purification	NN	_	_	_
436	-RRB-	-rrb-	-RRB-	_	_	_
437	with	with	IN	_	_	_
438	modification	modification	NN	_	_	_
439	of	of	IN	_	_	_
440	the	the	DT	_	_	_
441	2nd	2nd	JJ	_	_	_
442	strand	strand	NN	_	_	_
443	cDNA	cdna	NN	_	_	_
444	synthesis	synthesis	NN	_	_	_
445	as	as	IN	_	_	_
446	previously	previously	RB	_	_	_
447	described	describe	VBN	_	_	_
448	-LRB-	-lrb-	-LRB-	_	_	_
449	Parkhomchuk	Parkhomchuk	NNP	_	_	_
450	et	et	FW	_	_	_
451	al.	al.	FW	_	_	_
452	2009	2009	CD	_	_	_
453	-RRB-	-rrb-	-RRB-	_	_	_
454	.	.	.	_	_	_

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	NN	_	_	_
2	Strand-specific	strand-specific	JJ	_	_	_
3	RNA-Seq	rna-seq	NN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	generated	generate	VBN	_	_	_
7	,	,	,	_	_	_
8	following	follow	VBG	_	_	_
9	rRNA	rrna	NN	_	_	_
10	depletion	depletion	NN	_	_	_
11	with	with	IN	_	_	_
12	a	a	DT	_	_	_
13	Ribo-Zero	Ribo-Zero	NNP	_	_	_
14	kit	kit	NN	_	_	_
15	,	,	,	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	aid	aid	NN	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	di-tagged	di-tagged	JJ	_	_	_
22	cDNA	cdna	NN	_	_	_
23	strategy	strategy	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	ScriptSeq	scriptseq	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	on	on	IN	_	_	_
28	an	a	DT	_	_	_
29	Illumina	Illumina	NNP	_	_	_
30	NextSeq	NextSeq	NNP	_	_	_
31	platform	platform	NN	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Strand	Strand	NNP	_	_	_
34	specific	specific	JJ	_	_	_
35	RNAtag-seq	rnatag-seq	NN	_	_	_
36	libraries	library	NNS	_	_	_
37	were	be	VBD	_	_	_
38	created	create	VBN	_	_	_
39	by	by	IN	_	_	_
40	the	the	DT	_	_	_
41	Broad	Broad	NNP	_	_	_
42	Technology	Technology	NNP	_	_	_
43	Labs	Labs	NNPS	_	_	_
44	specialized	specialized	JJ	_	_	_
45	service	service	NN	_	_	_
46	facility	facility	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	SSF	ssf	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	using	use	VBG	_	_	_
51	the	the	DT	_	_	_
52	standard	standard	JJ	_	_	_
53	protocol	protocol	NN	_	_	_
54	described	describe	VBN	_	_	_
55	in	in	IN	_	_	_
56	Shishkin	Shishkin	NNP	_	_	_
57	et	et	FW	_	_	_
58	al.	al.	FW	_	_	_
59	.	.	.	_	_	_

1	Nature	Nature	NNP	_	_	_
2	Methods	method	NNS	_	_	_
3	2016	2016	CD	_	_	_
4	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	streptomycin	streptomycin	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	Streptomycin	Streptomycin	NNP	_	_	_
6	_	_	NN	_	_	_
7	treatment	treatment	NN	_	_	_
8	_	_	NN	_	_	_
9	plasmidmappedreads	plasmidmappedread	NNS	_	_	_
10	_	_	VBP	_	_	_
11	statistical	statistical	JJ	_	_	_
12	_	_	NN	_	_	_
13	output.txt	output.txt	NN	_	_	_
14	:	:	:	_	_	_
15	NC	nc	NN	_	_	_
16	_	_	SYM	_	_	_
17	012692.1	012692.1	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	Strep	strep	JJ	_	_	_
20	_	_	NN	_	_	_
21	treatment	treatment	NN	_	_	_
22	_	_	NN	_	_	_
23	genomemappedreads	genomemappedread	NNS	_	_	_
24	_	_	VBP	_	_	_
25	statistical	statistical	JJ	_	_	_
26	_	_	NN	_	_	_
27	output.txt	output.txt	NN	_	_	_
28	:	:	:	_	_	_
29	NC	nc	NN	_	_	_
30	_	_	SYM	_	_	_
31	000913.2	000913.2	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	stress	stress	NN	_	_	_
34	:	:	:	_	_	_
35	acidic	acidic	JJ	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	stress	stress	NN	_	_	_
38	:	:	:	_	_	_
39	Adenosine	Adenosine	NNP	_	_	_
40	addition	addition	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	stress	stress	NN	_	_	_
43	:	:	:	_	_	_
44	Alanine	alanine	NN	_	_	_
45	addition	addition	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	stress	stress	NN	_	_	_
48	:	:	:	_	_	_
49	Arginine	arginine	NN	_	_	_
50	addition	addition	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	stress	stress	NN	_	_	_
53	:	:	:	_	_	_
54	Aspartate	Aspartate	NNP	_	_	_
55	addition	addition	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	stress	stress	NN	_	_	_
58	:	:	:	_	_	_
59	control	control	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
61	stress	stress	NN	_	_	_
62	:	:	:	_	_	_
63	control	control	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	before	before	IN	_	_	_
66	perturbation	perturbation	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	stress	stress	NN	_	_	_
70	:	:	:	_	_	_
71	Cysteine	cysteine	NN	_	_	_
72	addition	addition	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	stress	stress	NN	_	_	_
75	:	:	:	_	_	_
76	Cytidine	cytidine	NN	_	_	_
77	addition	addition	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	stress	stress	NN	_	_	_
80	:	:	:	_	_	_
81	Glutamate	glutamate	JJ	_	_	_
82	addition	addition	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	stress	stress	NN	_	_	_
85	:	:	:	_	_	_
86	Glutamine	glutamine	NN	_	_	_
87	addition	addition	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	stress	stress	NN	_	_	_
90	:	:	:	_	_	_
91	Glycine	glycine	NN	_	_	_
92	addition	addition	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	stress	stress	NN	_	_	_
95	:	:	:	_	_	_
96	Guanosine	Guanosine	NNP	_	_	_
97	addition	addition	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	stress	stress	NN	_	_	_
100	:	:	:	_	_	_
101	heptanoic	heptanoic	JJ	_	_	_
102	acid	acid	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	stress	stress	NN	_	_	_
105	:	:	:	_	_	_
106	Histidine	histidine	NN	_	_	_
107	addition	addition	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	stress	stress	NN	_	_	_
110	:	:	:	_	_	_
111	Isoleucine	isoleucine	NN	_	_	_
112	addition	addition	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	stress	stress	NN	_	_	_
115	:	:	:	_	_	_
116	Lysine	lysine	NN	_	_	_
117	addition	addition	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	stress	stress	NN	_	_	_
120	:	:	:	_	_	_
121	Methionine	methionine	NN	_	_	_
122	addition	addition	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	stress	stress	NN	_	_	_
125	:	:	:	_	_	_
126	Minimal	minimal	JJ	_	_	_
127	medium	medium	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	stress	stress	NN	_	_	_
130	:	:	:	_	_	_
131	n-butanol	n-butanol	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	stress	stress	NN	_	_	_
134	:	:	:	_	_	_
135	osmotic	osmotic	JJ	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	stress	stress	NN	_	_	_
138	:	:	:	_	_	_
139	oxidative	oxidative	JJ	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	stress	stress	NN	_	_	_
142	:	:	:	_	_	_
143	Phenylalanine	phenylalanine	NN	_	_	_
144	addition	addition	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	stress	stress	NN	_	_	_
147	:	:	:	_	_	_
148	Proline	Proline	NNP	_	_	_
149	addition	addition	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	stress	stress	NN	_	_	_
152	:	:	:	_	_	_
153	Serine	serine	NN	_	_	_
154	addition	addition	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	stress	stress	NN	_	_	_
157	:	:	:	_	_	_
158	Threonine	threonine	NN	_	_	_
159	addition	addition	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	stress	stress	NN	_	_	_
162	:	:	:	_	_	_
163	Thymidine	Thymidine	NNP	_	_	_
164	addition	addition	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	stress	stress	NN	_	_	_
167	:	:	:	_	_	_
168	Tryptophan	tryptophan	NN	_	_	_
169	addition	addition	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	stress	stress	NN	_	_	_
172	:	:	:	_	_	_
173	Uridine	uridine	NN	_	_	_
174	addition	addition	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	stress	stress	NN	_	_	_
177	:	:	:	_	_	_
178	Valine	Valine	NNP	_	_	_
179	addition	addition	NN	_	_	_
180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
181	Strian	Strian	NNP	_	_	_
182	:	:	:	_	_	_
183	W3110	w3110	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	S.	S.	NNP	_	_	_
186	Typhimurium	Typhimurium	NNP	_	_	_
187	cells	cell	NNS	_	_	_
188	were	be	VBD	_	_	_
189	grown	grow	VBN	_	_	_
190	in	in	IN	_	_	_
191	LB	lb	NN	_	_	_
192	-LRB-	-lrb-	-LRB-	_	_	_
193	supplemented	supplement	VBN	_	_	_
194	with	with	IN	_	_	_
195	10mM	10mm	NN	_	_	_
196	glucose	glucose	NN	SUPP	_	_
197	-RRB-	-rrb-	-RRB-	_	_	_
198	to	to	TO	_	_	_
199	mid-exponential	mid-exponential	JJ	_	_	_
200	phase	phase	NN	_	_	_
201	-LRB-	-lrb-	-LRB-	_	_	_
202	OD600	od600	NN	_	_	_
203	=	=	JJ	_	_	_
204	~	~	NN	_	_	_
205	0.6	0.6	CD	_	_	_
206	-RRB-	-rrb-	-RRB-	_	_	_
207	at	at	IN	_	_	_
208	37C	37c	NN	_	_	_
209	and	and	CC	_	_	_
210	shaking	shake	VBG	_	_	_
211	250rpm	250rpm	JJ	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
213	Subsequent	subsequent	JJ	_	_	_
214	data	datum	NNS	_	_	_
215	visualizations	visualization	NNS	_	_	_
216	were	be	VBD	_	_	_
217	performed	perform	VBN	_	_	_
218	in	in	IN	_	_	_
219	R	r	NN	_	_	_
220	-LRB-	-lrb-	-LRB-	_	_	_
221	version	version	NN	_	_	_
222	3.1.2	3.1.2	CD	_	_	_
223	-RRB-	-rrb-	-RRB-	_	_	_
224	using	use	VBG	_	_	_
225	the	the	DT	_	_	_
226	cummeRbund	cummerbund	NN	_	_	_
227	package	package	NN	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	version	version	NN	_	_	_
230	3.0	3.0	CD	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	substrain	substrain	NN	_	_	_
234	:	:	:	_	_	_
235	ATCC	atcc	NN	_	_	_
236	25922	25922	CD	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	sub	sub	NN	_	_	_
239	strain	strain	NN	_	_	_
240	:	:	:	_	_	_
241	BW38028	bw38028	NN	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	sub	sub	NN	_	_	_
244	strain	strain	NN	_	_	_
245	:	:	:	_	_	_
246	BW39452	bw39452	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	substrain	substrain	NN	_	_	_
249	:	:	:	_	_	_
250	DH1	dh1	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	substrain	substrain	NN	_	_	_
253	:	:	:	_	_	_
254	EC14	ec14	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	substrain	substrain	NN	_	_	_
257	:	:	:	_	_	_
258	EC19	ec19	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	substrain	substrain	NN	_	_	_
261	:	:	:	_	_	_
262	EC24	ec24	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	substrain	substrain	NN	_	_	_
265	:	:	:	_	_	_
266	GJ13507	gj13507	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	substrain	substrain	NN	_	_	_
269	:	:	:	_	_	_
270	GJ13519	gj13519	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	substrain	substrain	NN	_	_	_
273	:	:	:	_	_	_
274	GJ13531	gj13531	NN	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	substrain	substrain	NN	_	_	_
277	:	:	:	_	_	_
278	GJ13533	gj13533	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	substrain	substrain	NN	_	_	_
281	:	:	:	_	_	_
282	MG1655	mg1655	NN	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	substr	substr	NN	_	_	_
285	:	:	:	_	_	_
286	MG1655	mg1655	NN	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	sucrose	sucrose	NN	_	_	_
289	status	status	NN	_	_	_
290	:	:	:	_	_	_
291	no	no	DT	_	_	_
292	sucrose	sucrose	NN	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	sucrose	sucrose	NN	_	_	_
295	status	status	NN	_	_	_
296	:	:	:	_	_	_
297	with	with	IN	_	_	_
298	15	15	CD	_	_	_
299	%	%	NN	_	_	_
300	sucrose	sucrose	NN	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	SucT110	suct110	NN	_	_	_
303	_	_	CD	_	_	_
304	12	12	CD	_	_	_
305	%	%	NN	_	_	_
306	Glu	glu	NN	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	SucT110	suct110	NN	_	_	_
309	_	_	CD	_	_	_
310	5	5	CD	_	_	_
311	%	%	NN	_	_	_
312	Glu	glu	NN	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	sulA	sula	NN	GEN	_	_
315	___	___	CD	_	_	_
316	U	U	NNP	_	_	_
317	_	_	NNP	_	_	_
318	N0025	N0025	NNP	_	_	_
319	_	_	SYM	_	_	_
320	r1	r1	FW	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
322	sulA	sula	NN	GEN	_	_
323	___	___	CD	_	_	_
324	U	U	NNP	_	_	_
325	_	_	NNP	_	_	_
326	N0025	N0025	NNP	_	_	_
327	_	_	SYM	_	_	_
328	r2	r2	FW	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
330	sulA	sula	NN	GEN	_	_
331	___	___	CD	_	_	_
332	U	U	NNP	_	_	_
333	_	_	NNP	_	_	_
334	N0025	N0025	NNP	_	_	_
335	_	_	SYM	_	_	_
336	r3	r3	FW	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
338	sulA	sula	NN	GEN	_	_
339	upregulation	upregulation	NN	_	_	_
340	,	,	,	_	_	_
341	amp	amp	NN	_	_	_
342	50ug/ml	50ug/ml	NN	_	_	_
343	,	,	,	_	_	_
344	0.0125	0.0125	CD	_	_	_
345	%	%	NN	_	_	_
346	arabinose	arabinose	NN	_	_	_
347	,	,	,	_	_	_
348	0.025	0.025	CD	_	_	_
349	ug/ml	ug/ml	NN	_	_	_
350	norfloxacin	norfloxacin	NN	_	_	_
351	OD	od	NN	_	_	_
352	~	~	NN	_	_	_
353	0.3	0.3	CD	_	_	_
354	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
355	Summarize	summarize	VB	_	_	_
356	the	the	DT	_	_	_
357	read	read	NN	_	_	_
358	count	count	NN	_	_	_
359	to	to	TO	_	_	_
360	each	each	DT	_	_	_
361	annotated	annotated	JJ	_	_	_
362	gene	gene	NN	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	Supplementary	supplementary	JJ	_	_	_
365	files	file	NNS	_	_	_
366	contain	contain	VBP	_	_	_
367	the	the	DT	_	_	_
368	following	following	NN	_	_	_
369	:	:	:	_	_	_
370	Raw	raw	NN	_	_	_
371	Signal	signal	NN	_	_	_
372	Values	value	NNS	_	_	_
373	:	:	:	_	_	_
374	The	the	DT	_	_	_
375	term	term	NN	_	_	_
376	``	``	``	_	_	_
377	raw	raw	JJ	_	_	_
378	''	''	''	_	_	_
379	signal	signal	NN	_	_	_
380	values	value	NNS	_	_	_
381	refer	refer	VBP	_	_	_
382	to	to	TO	_	_	_
383	the	the	DT	_	_	_
384	linear	linear	JJ	_	_	_
385	data	datum	NNS	_	_	_
386	after	after	IN	_	_	_
387	thresholding	threshold	VBG	_	_	_
388	and	and	CC	_	_	_
389	summarization	summarization	NN	_	_	_
390	Summarization	summarization	NN	_	_	_
391	is	be	VBZ	_	_	_
392	performed	perform	VBN	_	_	_
393	by	by	IN	_	_	_
394	computing	compute	VBG	_	_	_
395	the	the	DT	_	_	_
396	geometric	geometric	JJ	_	_	_
397	mean	mean	NN	_	_	_
398	.	.	.	_	_	_

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	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	5m_ribozero_counts_cleavage_ratio.csv.gz	5m_ribozero_counts_cleavage_ratio.csv.gz	NN	_	_	_
13	is	be	VBZ	_	_	_
14	a	a	DT	_	_	_
15	log-transformed	log-transformed	JJ	_	_	_
16	list	list	NN	_	_	_
17	of	of	IN	_	_	_
18	sequencing	sequencing	NN	_	_	_
19	depth-normalized	depth-normalized	JJ	_	_	_
20	counts	count	NNS	_	_	_
21	for	for	IN	_	_	_
22	every	every	DT	_	_	_
23	genomic	genomic	JJ	_	_	_
24	position	position	NN	_	_	_
25	at	at	IN	_	_	_
26	both	both	DT	_	_	_
27	strands	strand	NNS	_	_	_
28	for	for	IN	_	_	_
29	each	each	DT	_	_	_
30	ribozero	ribozero	NN	_	_	_
31	treated	treat	VBN	_	_	_
32	sample	sample	NN	_	_	_
33	as	as	RB	_	_	_
34	well	well	RB	_	_	_
35	as	as	IN	_	_	_
36	the	the	DT	_	_	_
37	average	average	JJ	_	_	_
38	cleavage	cleavage	NN	_	_	_
39	ratio	ratio	NN	_	_	_
40	calculated	calculate	VBN	_	_	_
41	from	from	IN	_	_	_
42	all	all	DT	_	_	_
43	samples	sample	NNS	_	_	_
44	.	.	.	_	_	_

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	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	All	all	DT	_	_	_
13	in	in	IN	_	_	_
14	tab-delimited	tab-delimited	JJ	_	_	_
15	ASCII	ASCII	NNP	_	_	_
16	format	format	NN	_	_	_
17	.	.	.	_	_	_

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	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	A	a	DT	_	_	_
40	tab	tab	NN	_	_	_
41	deliminited	deliminit	VBN	_	_	_
42	file	file	NN	_	_	_
43	with	with	IN	_	_	_
44	counts	count	NNS	_	_	_
45	for	for	IN	_	_	_
46	each	each	DT	_	_	_
47	gene	gene	NN	_	_	_
48	.	.	.	_	_	_

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	bed	bed	NN	_	_	_
13	format	format	NN	_	_	_
14	peak	peak	NN	_	_	_
15	file	file	NN	_	_	_
16	generated	generate	VBN	_	_	_
17	from	from	IN	_	_	_
18	MACS2	macs2	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	bedgraph	bedgraph	NN	_	_	_
31	:	:	:	_	_	_
32	Data	datum	NNS	_	_	_
33	presented	present	VBN	_	_	_
34	in	in	IN	_	_	_
35	a	a	DT	_	_	_
36	4	4	CD	_	_	_
37	column	column	NN	_	_	_
38	BED	bed	NN	_	_	_
39	format	format	NN	_	_	_
40	,	,	,	_	_	_
41	of	of	IN	_	_	_
42	which	which	WDT	_	_	_
43	the	the	DT	_	_	_
44	first	first	JJ	_	_	_
45	column	column	NN	_	_	_
46	is	be	VBZ	_	_	_
47	the	the	DT	_	_	_
48	chromosome	chromosome	NN	_	_	_
49	,	,	,	_	_	_
50	the	the	DT	_	_	_
51	second	second	JJ	_	_	_
52	column	column	NN	_	_	_
53	is	be	VBZ	_	_	_
54	the	the	DT	_	_	_
55	start	start	NN	_	_	_
56	position	position	NN	_	_	_
57	of	of	IN	_	_	_
58	the	the	DT	_	_	_
59	chromosome	chromosome	NN	_	_	_
60	,	,	,	_	_	_
61	the	the	DT	_	_	_
62	third	third	JJ	_	_	_
63	column	column	NN	_	_	_
64	is	be	VBZ	_	_	_
65	the	the	DT	_	_	_
66	end	end	NN	_	_	_
67	position	position	NN	_	_	_
68	,	,	,	_	_	_
69	and	and	CC	_	_	_
70	the	the	DT	_	_	_
71	fourth	fourth	JJ	_	_	_
72	column	column	NN	_	_	_
73	is	be	VBZ	_	_	_
74	the	the	DT	_	_	_
75	fragments	fragment	NNS	_	_	_
76	per	per	IN	_	_	_
77	kilobase	kilobase	NN	_	_	_
78	mapped	map	VBN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	FPKM	fpkm	NN	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	for	for	IN	_	_	_
83	that	that	DT	_	_	_
84	sample	sample	NN	_	_	_
85	.	.	.	_	_	_

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	Bedgraphs	bedgraph	NNS	_	_	_
13	files	file	NNS	_	_	_
14	representing	represent	VBG	_	_	_
15	the	the	DT	_	_	_
16	extracted	extract	VBN	_	_	_
17	peak	peak	NN	_	_	_
18	data	datum	NNS	_	_	_
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	BedGraphs	bedgraph	NNS	_	_	_
31	of	of	IN	_	_	_
32	the	the	DT	_	_	_
33	reads	read	VBZ	_	_	_
34	before	before	IN	_	_	_
35	and	and	CC	_	_	_
36	after	after	IN	_	_	_
37	TAP	tap	NN	_	_	_
38	treatment	treatment	NN	_	_	_
39	for	for	IN	_	_	_
40	each	each	DT	_	_	_
41	of	of	IN	_	_	_
42	the	the	DT	_	_	_
43	samples	sample	NNS	_	_	_
44	.	.	.	_	_	_

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	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	Bedgraph	Bedgraph	NNP	_	_	_
13	wiggle	wiggle	NN	_	_	_
14	files	file	NNS	_	_	_
15	were	be	VBD	_	_	_
16	created	create	VBN	_	_	_
17	for	for	IN	_	_	_
18	each	each	DT	_	_	_
19	sample	sample	NN	_	_	_
20	and	and	CC	_	_	_
21	replicate	replicate	VB	_	_	_
22	for	for	IN	_	_	_
23	all	all	DT	_	_	_
24	reads	read	VBZ	_	_	_
25	aligned	align	VBN	_	_	_
26	to	to	TO	_	_	_
27	the	the	DT	_	_	_
28	genome	genome	NN	_	_	_
29	after	after	IN	_	_	_
30	computational	computational	JJ	_	_	_
31	rRNA	rrna	NN	_	_	_
32	and	and	CC	_	_	_
33	tRNA	trna	NN	_	_	_
34	subtraction	subtraction	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Supplementary	supplementary	JJ	_	_	_
37	_	_	NN	_	_	_
38	files	file	NNS	_	_	_
39	_	_	IN	_	_	_
40	format	format	NN	_	_	_
41	_	_	NN	_	_	_
42	and	and	CC	_	_	_
43	_	_	NN	_	_	_
44	content	content	NN	_	_	_
45	:	:	:	_	_	_
46	BIGWIG	bigwig	NN	_	_	_
47	file	file	NN	_	_	_
48	containing	contain	VBG	_	_	_
49	coverage	coverage	NN	_	_	_
50	tracks	track	NNS	_	_	_
51	from	from	IN	_	_	_
52	3	3	CD	_	_	_
53	'	'	''	_	_	_
54	RACE	race	NN	_	_	_
55	data	datum	NNS	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Supplementary	supplementary	JJ	_	_	_
58	_	_	NN	_	_	_
59	files	file	NNS	_	_	_
60	_	_	IN	_	_	_
61	format	format	NN	_	_	_
62	_	_	NN	_	_	_
63	and	and	CC	_	_	_
64	_	_	NN	_	_	_
65	content	content	NN	_	_	_
66	:	:	:	_	_	_
67	BigWIG	bigwig	NN	_	_	_
68	files	file	NNS	_	_	_
69	are	be	VBP	_	_	_
70	provided	provide	VBN	_	_	_
71	showing	show	VBG	_	_	_
72	uniquely	uniquely	RB	_	_	_
73	mapped	map	VBN	_	_	_
74	sequence	sequence	NN	_	_	_
75	reads	read	VBZ	_	_	_
76	.	.	.	_	_	_

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	BigWig	BigWig	NNP	_	_	_
13	files	file	VBZ	_	_	_
14	for	for	IN	_	_	_
15	whole-genome	whole-genome	JJ	_	_	_
16	reads	read	VBZ	_	_	_
17	coverage	coverage	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	including	include	VBG	_	_	_
20	number	number	NN	_	_	_
21	of	of	IN	_	_	_
22	mapped	map	VBN	_	_	_
23	reads	read	VBZ	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	for	for	IN	_	_	_
26	each	each	DT	_	_	_
27	sample	sample	NN	_	_	_
28	.	.	.	_	_	_

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	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	chromosome	chromosome	NN	_	_	_
13	chromosomeStartPosition	chromosomestartposition	NN	_	_	_
14	chromosomeStopPosition	chromosomestopposition	NN	_	_	_
15	readCoverage	readcoverage	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	positive	positive	JJ	_	_	_
18	values	value	NNS	_	_	_
19	on	on	IN	_	_	_
20	+	+	CC	_	_	_
21	strand	strand	NN	_	_	_
22	,	,	,	_	_	_
23	negative	negative	JJ	_	_	_
24	on	on	IN	_	_	_
25	-	-	:	_	_	_
26	strand	strand	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
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	CoK12	cok12	NN	_	_	_
40	_	_	CD	_	_	_
41	LB.xlsx	lb.xlsx	NN	_	_	_
42	:	:	:	_	_	_
43	Average	average	JJ	_	_	_
44	expression	expression	NN	_	_	_
45	values	value	NNS	_	_	_
46	of	of	IN	_	_	_
47	reads	read	VBZ	_	_	_
48	related	related	JJ	_	_	_
49	with	with	IN	_	_	_
50	MG1655	mg1655	NN	_	_	_
51	strain	strain	NN	_	_	_
52	in	in	IN	_	_	_
53	samples	sample	NNS	_	_	_
54	Co-culture	co-culture	NN	_	_	_
55	_	_	CD	_	_	_
56	LB1	lb1	NN	_	_	_
57	and	and	CC	_	_	_
58	LB2	lb2	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
60	Supplementary	supplementary	JJ	_	_	_
61	_	_	NN	_	_	_
62	files	file	NNS	_	_	_
63	_	_	IN	_	_	_
64	format	format	NN	_	_	_
65	_	_	NN	_	_	_
66	and	and	CC	_	_	_
67	_	_	NN	_	_	_
68	content	content	NN	_	_	_
69	:	:	:	_	_	_
70	Column	Column	NNP	_	_	_
71	1	1	CD	_	_	_
72	names	name	NNS	_	_	_
73	the	the	DT	_	_	_
74	nucleotide	nucleotide	NN	_	_	_
75	in	in	IN	_	_	_
76	the	the	DT	_	_	_
77	genome	genome	NN	_	_	_
78	,	,	,	_	_	_
79	column	column	NN	_	_	_
80	2	2	CD	_	_	_
81	gives	give	VBZ	_	_	_
82	counts	count	NNS	_	_	_
83	for	for	IN	_	_	_
84	the	the	DT	_	_	_
85	forward	forward	JJ	_	_	_
86	strand	strand	NN	_	_	_
87	,	,	,	_	_	_
88	column	column	NN	_	_	_
89	3	3	CD	_	_	_
90	for	for	IN	_	_	_
91	the	the	DT	_	_	_
92	reverse	reverse	JJ	_	_	_
93	strand	strand	NN	_	_	_
94	,	,	,	_	_	_
95	columns	column	NNS	_	_	_
96	are	be	VBP	_	_	_
97	tab	tab	NN	_	_	_
98	separated	separated	JJ	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Supplementary	supplementary	JJ	_	_	_
101	_	_	NN	_	_	_
102	files	file	NNS	_	_	_
103	_	_	IN	_	_	_
104	format	format	NN	_	_	_
105	_	_	NN	_	_	_
106	and	and	CC	_	_	_
107	_	_	NN	_	_	_
108	content	content	NN	_	_	_
109	:	:	:	_	_	_
110	Comma-delimited	comma-delimited	JJ	_	_	_
111	text	text	NN	_	_	_
112	file	file	NN	_	_	_
113	includes	include	VBZ	_	_	_
114	RPKM	rpkm	NN	_	_	_
115	values	value	NNS	_	_	_
116	for	for	IN	_	_	_
117	each	each	DT	_	_	_
118	Sample	Sample	NNP	_	_	_
119	.	.	.	_	_	_

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	comma-delimited	comma-delimited	JJ	_	_	_
13	text	text	NN	_	_	_
14	files	file	NNS	_	_	_
15	include	include	VBP	_	_	_
16	FPKM	fpkm	NN	_	_	_
17	values	value	NNS	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	Sample	Sample	NNP	_	_	_
21	.	.	.	_	_	_

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	comma-delimited	comma-delimited	JJ	_	_	_
13	text	text	NN	_	_	_
14	files	file	NNS	_	_	_
15	include	include	VBP	_	_	_
16	RPKM	rpkm	NN	_	_	_
17	values	value	NNS	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	Sample	Sample	NNP	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Supplementary	Supplementary	NNP	_	_	_
23	_	_	VBD	_	_	_
24	files	file	NNS	_	_	_
25	_	_	IN	_	_	_
26	format	format	NN	_	_	_
27	_	_	NN	_	_	_
28	and	and	CC	_	_	_
29	_	_	NN	_	_	_
30	content	content	NN	_	_	_
31	:	:	:	_	_	_
32	Comma	comma	NN	_	_	_
33	separated	separated	JJ	_	_	_
34	value	value	NN	_	_	_
35	files	file	NNS	_	_	_
36	include	include	VBP	_	_	_
37	log-fold	log-fold	JJ	_	_	_
38	changes	change	NNS	_	_	_
39	and	and	CC	_	_	_
40	associated	associate	VBN	_	_	_
41	p-values	p-value	NNS	_	_	_
42	for	for	IN	_	_	_
43	each	each	DT	_	_	_
44	comparison	comparison	NN	_	_	_
45	made	make	VBD	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Supplementary	Supplementary	NNP	_	_	_
48	_	_	VBD	_	_	_
49	files	file	NNS	_	_	_
50	_	_	IN	_	_	_
51	format	format	NN	_	_	_
52	_	_	NN	_	_	_
53	and	and	CC	_	_	_
54	_	_	NN	_	_	_
55	content	content	NN	_	_	_
56	:	:	:	_	_	_
57	contents	contents	NNS	_	_	_
58	:	:	:	_	_	_
59	reference	reference	NN	_	_	_
60	seq,co-ordinate	seq,co-ordinate	JJ	_	_	_
61	start	start	NN	_	_	_
62	position,co-ordinate	position,co-ordinate	JJ	_	_	_
63	end	end	NN	_	_	_
64	position	position	NN	_	_	_
65	,	,	,	_	_	_
66	counts	count	VBZ	_	_	_
67	for	for	IN	_	_	_
68	the	the	DT	_	_	_
69	position	position	NN	_	_	_
70	,	,	,	_	_	_
71	mapping	map	VBG	_	_	_
72	quality	quality	NN	_	_	_
73	,	,	,	_	_	_
74	strand	strand	NN	_	_	_
75	position	position	NN	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Supplementary	Supplementary	NNP	_	_	_
78	_	_	VBD	_	_	_
79	files	file	NNS	_	_	_
80	_	_	IN	_	_	_
81	format	format	NN	_	_	_
82	_	_	NN	_	_	_
83	and	and	CC	_	_	_
84	_	_	NN	_	_	_
85	content	content	NN	_	_	_
86	:	:	:	_	_	_
87	CoT1E	cot1e	NN	_	_	_
88	_	_	CD	_	_	_
89	LB.xlsx	lb.xlsx	NN	_	_	_
90	:	:	:	_	_	_
91	Average	average	JJ	_	_	_
92	expression	expression	NN	_	_	_
93	values	value	NNS	_	_	_
94	of	of	IN	_	_	_
95	reads	read	VBZ	_	_	_
96	related	related	JJ	_	_	_
97	with	with	IN	_	_	_
98	DOT-T1E	dot-t1e	NN	_	_	_
99	strain	strain	NN	_	_	_
100	in	in	IN	_	_	_
101	samples	sample	NNS	_	_	_
102	Co-culture	co-culture	NN	_	_	_
103	_	_	CD	_	_	_
104	LB1	lb1	NN	_	_	_
105	and	and	CC	_	_	_
106	LB2	lb2	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
108	Supplementary	supplementary	JJ	_	_	_
109	_	_	NN	_	_	_
110	files	file	NNS	_	_	_
111	_	_	IN	_	_	_
112	format	format	NN	_	_	_
113	_	_	NN	_	_	_
114	and	and	CC	_	_	_
115	_	_	NN	_	_	_
116	content	content	NN	_	_	_
117	:	:	:	_	_	_
118	counts	count	NNS	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	Supplementary	Supplementary	NNP	_	_	_
121	_	_	VBD	_	_	_
122	files	file	NNS	_	_	_
123	_	_	IN	_	_	_
124	format	format	NN	_	_	_
125	_	_	NN	_	_	_
126	and	and	CC	_	_	_
127	_	_	NN	_	_	_
128	content	content	NN	_	_	_
129	:	:	:	_	_	_
130	CSV	CSV	NNP	_	_	_
131	file	file	NN	_	_	_
132	contains	contain	VBZ	_	_	_
133	counts	count	NNS	_	_	_
134	generated	generate	VBN	_	_	_
135	using	use	VBG	_	_	_
136	RSEM	rsem	NN	_	_	_
137	software	software	NN	_	_	_
138	.	.	.	_	_	_

1	Ribosomal	ribosomal	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	transcripts	transcript	NNS	_	_	_
4	excluded	exclude	VBN	_	_	_
5	.	.	.	_	_	_

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	NN	_	_	_
13	files	file	NNS	_	_	_
14	,	,	,	_	_	_
15	FPKM	fpkm	NN	_	_	_
16	values	value	NNS	_	_	_
17	from	from	IN	_	_	_
18	pairwise	pairwise	JJ	_	_	_
19	comparisons	comparison	NNS	_	_	_
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	CSV	CSV	NNP	_	_	_
32	files	file	NNS	_	_	_
33	of	of	IN	_	_	_
34	raw	raw	JJ	_	_	_
35	read	read	NN	_	_	_
36	counts	count	NNS	_	_	_
37	and	and	CC	_	_	_
38	normalized	normalize	VBN	_	_	_
39	gene	gene	NN	_	_	_
40	expression	expression	NN	_	_	_
41	in	in	IN	_	_	_
42	FPKM	FPKM	NNP	_	_	_
43	units	unit	NNS	_	_	_
44	.	.	.	_	_	_

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	VBZ	_	_	_
14	providing	provide	VBG	_	_	_
15	the	the	DT	_	_	_
16	number	number	NN	_	_	_
17	of	of	IN	_	_	_
18	reads	read	VBZ	_	_	_
19	mapping	map	VBG	_	_	_
20	to	to	TO	_	_	_
21	each	each	DT	_	_	_
22	genomic	genomic	JJ	_	_	_
23	gene	gene	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	DMS-seq	dms-seq	NN	_	_	_
36	data	datum	NNS	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	pooled	pooled	JJ	_	_	_
39	Total	total	JJ	_	_	_
40	and	and	CC	_	_	_
41	Ribo	Ribo	NNP	_	_	_
42	-	-	:	_	_	_
43	RNA	rna	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	is	be	VBZ	_	_	_
46	provided	provide	VBN	_	_	_
47	in	in	IN	_	_	_
48	the	the	DT	_	_	_
49	form	form	NN	_	_	_
50	of	of	IN	_	_	_
51	RNA	rna	NN	_	_	_
52	Framework	framework	NN	_	_	_
53	's	's	POS	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	http://www.rnaframework.com	http://www.rnaframework.com	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	RNA	rna	NN	_	_	_
58	Count	count	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	RC	rc	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	files	file	NNS	_	_	_
63	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	a	a	DT	_	_	_
3	detailed	detailed	JJ	_	_	_
4	description	description	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	RC	rc	NN	_	_	_
8	format	format	NN	_	_	_
9	,	,	,	_	_	_
10	please	please	VB	_	_	_
11	refer	refer	VB	_	_	_
12	to	to	TO	_	_	_
13	:	:	:	_	_	_
14	http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format	http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
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	Each	each	DT	_	_	_
27	wig	wig	NN	_	_	_
28	file	file	NN	_	_	_
29	contains	contain	VBZ	_	_	_
30	the	the	DT	_	_	_
31	alignd	alignd	NN	_	_	_
32	reads	read	VBZ	_	_	_
33	of	of	IN	_	_	_
34	each	each	DT	_	_	_
35	ChIP-exo	ChIP-exo	NNP	_	_	_
36	sample	sample	NN	_	_	_
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	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	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	Enrichement	enrichement	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	IP/input	ip/input	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	wig	wig	NN	_	_	_
17	files	file	NNS	_	_	_
18	were	be	VBD	_	_	_
19	generated	generate	VBN	_	_	_
20	using	use	VBG	_	_	_
21	homemade	homemade	NN	_	_	_
22	matlab	matlab	NN	_	_	_
23	code	code	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	Excel	Excel	NNP	_	_	_
36	file	file	NN	_	_	_
37	include	include	VBP	_	_	_
38	FPKM	fpkm	NN	_	_	_
39	values	value	NNS	_	_	_
40	of	of	IN	_	_	_
41	different	different	JJ	_	_	_
42	genes	gene	NNS	_	_	_
43	for	for	IN	_	_	_
44	each	each	DT	_	_	_
45	sample	sample	NN	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Supplementary	Supplementary	NNP	_	_	_
48	_	_	VBD	_	_	_
49	files	file	NNS	_	_	_
50	_	_	IN	_	_	_
51	format	format	NN	_	_	_
52	_	_	NN	_	_	_
53	and	and	CC	_	_	_
54	_	_	NN	_	_	_
55	content	content	NN	_	_	_
56	:	:	:	_	_	_
57	excel	excel	VB	_	_	_
58	file	file	NN	_	_	_
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	Supplementary	Supplementary	NNP	_	_	_
67	_	_	VBD	_	_	_
68	files	file	NNS	_	_	_
69	_	_	IN	_	_	_
70	format	format	NN	_	_	_
71	_	_	NN	_	_	_
72	and	and	CC	_	_	_
73	_	_	NN	_	_	_
74	content	content	NN	_	_	_
75	:	:	:	_	_	_
76	Excel	Excel	NNP	_	_	_
77	files	file	NNS	_	_	_
78	include	include	VBP	_	_	_
79	FPKM	fpkm	NN	_	_	_
80	values	value	NNS	_	_	_
81	for	for	IN	_	_	_
82	each	each	DT	_	_	_
83	sample	sample	NN	_	_	_
84	.	.	.	_	_	_

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	excel	excel	VB	_	_	_
13	file	file	NN	_	_	_
14	with	with	IN	_	_	_
15	coverage	coverage	NN	_	_	_
16	and	and	CC	_	_	_
17	FPKM	fpkm	NN	_	_	_
18	measurements	measurement	NNS	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Supplementary	Supplementary	NNP	_	_	_
21	_	_	VBD	_	_	_
22	files	file	NNS	_	_	_
23	_	_	IN	_	_	_
24	format	format	NN	_	_	_
25	_	_	NN	_	_	_
26	and	and	CC	_	_	_
27	_	_	NN	_	_	_
28	content	content	NN	_	_	_
29	:	:	:	_	_	_
30	Excel	Excel	NNP	_	_	_
31	formatted	format	VBD	_	_	_
32	matrix	matrix	NN	_	_	_
33	table	table	NN	_	_	_
34	containing	contain	VBG	_	_	_
35	transcript	transcript	NN	_	_	_
36	coordinates	coordinate	VBZ	_	_	_
37	,	,	,	_	_	_
38	normalized	normalize	VBD	_	_	_
39	abundance	abundance	NN	_	_	_
40	estimates	estimate	NNS	_	_	_
41	across	across	IN	_	_	_
42	the	the	DT	_	_	_
43	biological	biological	JJ	_	_	_
44	replicates	replicate	VBZ	_	_	_
45	and	and	CC	_	_	_
46	fold-changes	fold-change	VBZ	_	_	_
47	in	in	IN	_	_	_
48	gene	gene	NN	_	_	_
49	expression	expression	NN	_	_	_
50	between	between	IN	_	_	_
51	cells	cell	NNS	_	_	_
52	expressing	express	VBG	_	_	_
53	Vector	Vector	NNP	_	_	_
54	and	and	CC	_	_	_
55	DicF	dicf	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	expression	expression	NN	_	_	_
13	level	level	NN	_	_	_
14	files	file	NNS	_	_	_
15	are	be	VBP	_	_	_
16	tab-delimited	tab-delimited	JJ	_	_	_
17	text	text	NN	_	_	_
18	with	with	IN	_	_	_
19	columns	column	NNS	_	_	_
20	as	as	IN	_	_	_
21	follows	follow	VBZ	_	_	_
22	:	:	:	_	_	_
23	index	index	NN	_	_	_
24	,	,	,	_	_	_
25	hits	hit	VBZ	_	_	_
26	,	,	,	_	_	_
27	RPKM	rpkm	NN	_	_	_
28	,	,	,	_	_	_
29	RPM	RPM	NNP	_	_	_
30	,	,	,	_	_	_
31	start	start	VB	_	_	_
32	_	_	SYM	_	_	_
33	position	position	NN	_	_	_
34	,	,	,	_	_	_
35	end	end	NN	_	_	_
36	_	_	NN	_	_	_
37	position	position	NN	_	_	_
38	,	,	,	_	_	_
39	strand	strand	NN	_	_	_
40	,	,	,	_	_	_
41	feature	feature	NN	_	_	_
42	_	_	CD	_	_	_
43	type	type	NN	_	_	_
44	,	,	,	_	_	_
45	reference	reference	NN	_	_	_
46	_	_	NN	_	_	_
47	replicon	replicon	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	type	type	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	,	,	,	_	_	_
52	locus	locus	NN	_	_	_
53	_	_	NN	_	_	_
54	tag	tag	NN	GEN	_	_
55	,	,	,	_	_	_
56	gene	gene	NN	_	_	_
57	_	_	NN	_	_	_
58	name	name	NN	_	_	_
59	,	,	,	_	_	_
60	product	product	NN	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Supplementary	Supplementary	NNP	_	_	_
63	_	_	VBD	_	_	_
64	files	file	NNS	_	_	_
65	_	_	IN	_	_	_
66	format	format	NN	_	_	_
67	_	_	NN	_	_	_
68	and	and	CC	_	_	_
69	_	_	NN	_	_	_
70	content	content	NN	_	_	_
71	:	:	:	_	_	_
72	expression	expression	NN	_	_	_
73	of	of	IN	_	_	_
74	genes	gene	NNS	_	_	_
75	in	in	IN	_	_	_
76	time	time	NN	_	_	_
77	,	,	,	_	_	_
78	rows	row	NNS	_	_	_
79	=	=	JJ	_	_	_
80	genes	gene	NNS	_	_	_
81	,	,	,	_	_	_
82	cols	col	NNS	_	_	_
83	=	=	JJ	_	_	_
84	time	time	NN	_	_	_
85	points	point	NNS	_	_	_
86	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
87	Supplementary	Supplementary	NNP	_	_	_
88	_	_	VBD	_	_	_
89	files	file	NNS	_	_	_
90	_	_	IN	_	_	_
91	format	format	NN	_	_	_
92	_	_	NN	_	_	_
93	and	and	CC	_	_	_
94	_	_	NN	_	_	_
95	content	content	NN	_	_	_
96	:	:	:	_	_	_
97	Files	file	NNS	_	_	_
98	ending	end	VBG	_	_	_
99	with	with	IN	_	_	_
100	_	_	CD	_	_	_
101	coverage.txt	coverage.txt	NN	_	_	_
102	:	:	:	_	_	_
103	tab-delimited	tab-delimited	JJ	_	_	_
104	text	text	NN	_	_	_
105	file	file	NN	_	_	_
106	of	of	IN	_	_	_
107	nucleotide-resolution	nucleotide-resolution	JJ	_	_	_
108	coverage	coverage	NN	_	_	_
109	from	from	IN	_	_	_
110	RNA-seq	rna-seq	JJ	_	_	_
111	data	datum	NNS	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	column	column	NN	_	_	_
114	1	1	CD	_	_	_
115	:	:	:	_	_	_
116	genome	genome	NN	_	_	_
117	ID	id	NN	_	_	_
118	,	,	,	_	_	_
119	column	column	NN	_	_	_
120	2	2	CD	_	_	_
121	:	:	:	_	_	_
122	nucleotide	nucleotide	NN	_	_	_
123	position	position	NN	_	_	_
124	,	,	,	_	_	_
125	column	column	NN	_	_	_
126	3	3	CD	_	_	_
127	:	:	:	_	_	_
128	coverage	coverage	NN	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	Supplementary	supplementary	JJ	_	_	_
132	_	_	NN	_	_	_
133	files	file	NNS	_	_	_
134	_	_	IN	_	_	_
135	format	format	NN	_	_	_
136	_	_	NN	_	_	_
137	and	and	CC	_	_	_
138	_	_	NN	_	_	_
139	content	content	NN	_	_	_
140	:	:	:	_	_	_
141	format	format	NN	_	_	_
142	:	:	:	_	_	_
143	bed	bed	NN	_	_	_
144	format	format	NN	_	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	Supplementary	Supplementary	NNP	_	_	_
147	_	_	VBD	_	_	_
148	files	file	NNS	_	_	_
149	_	_	IN	_	_	_
150	format	format	NN	_	_	_
151	_	_	NN	_	_	_
152	and	and	CC	_	_	_
153	_	_	NN	_	_	_
154	content	content	NN	_	_	_
155	:	:	:	_	_	_
156	Gene	Gene	NNP	_	_	_
157	_	_	NNP	_	_	_
158	lists	list	VBZ	_	_	_
159	_	_	SYM	_	_	_
160	GEO.xls	geo.xls	NNS	_	_	_
161	;	;	:	_	_	_
162	The	the	DT	_	_	_
163	supplementary	supplementary	JJ	_	_	_
164	file	file	NN	_	_	_
165	contains	contain	VBZ	_	_	_
166	gene	gene	NN	_	_	_
167	lists	list	NNS	_	_	_
168	used	use	VBN	_	_	_
169	in	in	IN	_	_	_
170	data	data	NN	_	_	_
171	analysis	analysis	NN	_	_	_
172	.	.	.	_	_	_

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	GFF	gff	NN	_	_	_
13	file	file	NN	_	_	_
14	containing	contain	VBG	_	_	_
15	3	3	CD	_	_	_
16	'	'	''	_	_	_
17	end	end	NN	_	_	_
18	annotations	annotation	NNS	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Supplementary	Supplementary	NNP	_	_	_
21	_	_	VBD	_	_	_
22	files	file	NNS	_	_	_
23	_	_	IN	_	_	_
24	format	format	NN	_	_	_
25	_	_	NN	_	_	_
26	and	and	CC	_	_	_
27	_	_	NN	_	_	_
28	content	content	NN	_	_	_
29	:	:	:	_	_	_
30	gff	gff	NN	_	_	_
31	file	file	NN	_	_	_
32	is	be	VBZ	_	_	_
33	generated	generate	VBN	_	_	_
34	by	by	IN	_	_	_
35	in-house	in-house	JJ	_	_	_
36	script	script	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Supplementary	supplementary	JJ	_	_	_
39	_	_	NN	_	_	_
40	files	file	NNS	_	_	_
41	_	_	IN	_	_	_
42	format	format	NN	_	_	_
43	_	_	NN	_	_	_
44	and	and	CC	_	_	_
45	_	_	NN	_	_	_
46	content	content	NN	_	_	_
47	:	:	:	_	_	_
48	htcount	htcount	NN	_	_	_
49	:	:	:	_	_	_
50	expression	expression	NN	_	_	_
51	count	count	NN	_	_	_
52	for	for	IN	_	_	_
53	each	each	DT	_	_	_
54	gene	gene	NN	_	_	_
55	and	and	CC	_	_	_
56	its	its	PRP$	_	_	_
57	name	name	NN	_	_	_
58	.	.	.	_	_	_

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	In	in	IN	_	_	_
13	the	the	DT	_	_	_
14	.	.	.	_	_	_

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	NNP	_	_	_
26	Supplementary	Supplementary	NNP	_	_	_
27	_	_	VBD	_	_	_
28	files	file	NNS	_	_	_
29	_	_	IN	_	_	_
30	format	format	NN	_	_	_
31	_	_	NN	_	_	_
32	and	and	CC	_	_	_
33	_	_	NN	_	_	_
34	content	content	NN	_	_	_
35	:	:	:	_	_	_
36	K12	k12	NN	_	_	_
37	_	_	CD	_	_	_
38	LB.xlsx	lb.xlsx	NN	_	_	_
39	:	:	:	_	_	_
40	Average	average	NN	_	_	_
41	of	of	IN	_	_	_
42	expression	expression	NN	_	_	_
43	values	value	NNS	_	_	_
44	of	of	IN	_	_	_
45	samples	sample	NNS	_	_	_
46	MG1655	mg1655	NN	_	_	_
47	_	_	CD	_	_	_
48	LB1	lb1	NN	_	_	_
49	and	and	CC	_	_	_
50	LB2	lb2	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	Supplementary	supplementary	JJ	_	_	_
53	_	_	NN	_	_	_
54	files	file	NNS	_	_	_
55	_	_	IN	_	_	_
56	format	format	NN	_	_	_
57	_	_	NN	_	_	_
58	and	and	CC	_	_	_
59	_	_	NN	_	_	_
60	content	content	NN	_	_	_
61	:	:	:	_	_	_
62	MACS	macs	NN	_	_	_
63	v2	v2	NN	_	_	_
64	.0.10.20131216	.0.10.20131216	CD	_	_	_
65	peaks	peak	VBZ	_	_	_
66	file	file	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Supplementary	supplementary	JJ	_	_	_
69	_	_	NN	_	_	_
70	files	file	NNS	_	_	_
71	_	_	IN	_	_	_
72	format	format	NN	_	_	_
73	_	_	NN	_	_	_
74	and	and	CC	_	_	_
75	_	_	NN	_	_	_
76	content	content	NN	_	_	_
77	:	:	:	_	_	_
78	Mapped	map	VBN	_	_	_
79	reads	read	VBZ	_	_	_
80	were	be	VBD	_	_	_
81	rescaled	rescale	VBN	_	_	_
82	to	to	TO	_	_	_
83	a	a	DT	_	_	_
84	size	size	NN	_	_	_
85	of	of	IN	_	_	_
86	10	10	CD	_	_	_
87	bp	bp	NN	_	_	_
88	,	,	,	_	_	_
89	and	and	CC	_	_	_
90	BEDGraph	bedgraph	NN	_	_	_
91	files	file	NNS	_	_	_
92	were	be	VBD	_	_	_
93	generated	generate	VBN	_	_	_
94	using	use	VBG	_	_	_
95	the	the	DT	_	_	_
96	genomeCoverageBed	genomecoveragebed	JJ	_	_	_
97	utility	utility	NN	_	_	_
98	of	of	IN	_	_	_
99	the	the	DT	_	_	_
100	BEDTools	bedtool	NNS	_	_	_
101	suite	suite	NN	_	_	_
102	.	.	.	_	_	_

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	Microsoft	Microsoft	NNP	_	_	_
13	Excel	Excel	NNP	_	_	_
14	File	file	VB	_	_	_
15	with	with	IN	_	_	_
16	normalized	normalize	VBN	_	_	_
17	sequencing	sequencing	NN	_	_	_
18	coverage	coverage	NN	_	_	_
19	of	of	IN	_	_	_
20	all	all	DT	_	_	_
21	annotated	annotated	JJ	_	_	_
22	genes	gene	NNS	_	_	_
23	and	and	CC	_	_	_
24	statistical	statistical	JJ	_	_	_
25	comparison	comparison	NN	_	_	_
26	of	of	IN	_	_	_
27	expression	expression	NN	_	_	_
28	in	in	IN	_	_	_
29	antibiotic	antibiotic	JJ	_	_	_
30	treated	treat	VBN	_	_	_
31	to	to	TO	_	_	_
32	untreated	untreated	JJ	_	_	_
33	cells	cell	NNS	_	_	_
34	.	.	.	_	_	_

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	Microsoft	Microsoft	NNP	_	_	_
13	excel	excel	VB	_	_	_
14	spreadsheet	spreadsheet	NN	_	_	_
15	files	file	NNS	_	_	_
16	include	include	VBP	_	_	_
17	RPKM	rpkm	NN	_	_	_
18	values	value	NNS	_	_	_
19	for	for	IN	_	_	_
20	each	each	DT	_	_	_
21	gene	gene	NN	_	_	_
22	of	of	IN	_	_	_
23	sample	sample	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	.	.	.	_	_	_

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	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	peaks.bed	peaks.bed	JJ	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
45	Supplementary	supplementary	JJ	_	_	_
46	_	_	NN	_	_	_
47	files	file	NNS	_	_	_
48	_	_	IN	_	_	_
49	format	format	NN	_	_	_
50	_	_	NN	_	_	_
51	and	and	CC	_	_	_
52	_	_	NN	_	_	_
53	content	content	NN	_	_	_
54	:	:	:	_	_	_
55	Processed	process	VBN	_	_	_
56	data	datum	NNS	_	_	_
57	files	file	NNS	_	_	_
58	are	be	VBP	_	_	_
59	WIG	WIG	NNP	_	_	_
60	files	file	NNS	_	_	_
61	normalized	normalize	VBD	_	_	_
62	to	to	TO	_	_	_
63	reads	read	VBZ	_	_	_
64	per	per	IN	_	_	_
65	million	million	CD	_	_	_
66	per	per	IN	_	_	_
67	position	position	NN	_	_	_
68	.	.	.	_	_	_

1	Those	those	DT	_	_	_
2	designated	designate	VBN	_	_	_
3	\	\	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	Supplementary	supplementary	JJ	_	_	_
6	_	_	NN	_	_	_
7	files	file	NNS	_	_	_
8	_	_	IN	_	_	_
9	format	format	NN	_	_	_
10	_	_	NN	_	_	_
11	and	and	CC	_	_	_
12	_	_	NN	_	_	_
13	content	content	NN	_	_	_
14	:	:	:	_	_	_
15	Processed	process	VBN	_	_	_
16	data	datum	NNS	_	_	_
17	files	file	NNS	_	_	_
18	are	be	VBP	_	_	_
19	WIG	WIG	NNP	_	_	_
20	files	file	NNS	_	_	_
21	with	with	IN	_	_	_
22	non-coding	non-coding	JJ	_	_	_
23	RNAs	rna	NNS	_	_	_
24	removed	remove	VBD	_	_	_
25	,	,	,	_	_	_
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	with	with	IN	_	_	_
3	a	a	DT	_	_	_
4	\	\	JJ	_	_	_
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	Processed	process	VBN	_	_	_
17	data	datum	NNS	_	_	_
18	files	file	NNS	_	_	_
19	contain	contain	VBP	_	_	_
20	raw	raw	JJ	_	_	_
21	counts	count	NNS	_	_	_
22	for	for	IN	_	_	_
23	CDS	cd	NNS	_	_	_
24	genomic	genomic	JJ	_	_	_
25	features	feature	NNS	_	_	_
26	,	,	,	_	_	_
27	locations	location	NNS	_	_	_
28	of	of	IN	_	_	_
29	genomic	genomic	JJ	_	_	_
30	features	feature	NNS	_	_	_
31	are	be	VBP	_	_	_
32	provided	provide	VBN	_	_	_
33	in	in	IN	_	_	_
34	associated	associate	VBN	_	_	_
35	.	.	.	_	_	_

1	gtf	gtf	NN	_	_	_
2	files	file	NNS	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	Supplementary	Supplementary	NNP	_	_	_
5	_	_	VBD	_	_	_
6	files	file	NNS	_	_	_
7	_	_	IN	_	_	_
8	format	format	NN	_	_	_
9	_	_	NN	_	_	_
10	and	and	CC	_	_	_
11	_	_	NN	_	_	_
12	content	content	NN	_	_	_
13	:	:	:	_	_	_
14	Processed	process	VBN	_	_	_
15	data	datum	NNS	_	_	_
16	files	file	NNS	_	_	_
17	contain	contain	VBP	_	_	_
18	the	the	DT	_	_	_
19	number	number	NN	_	_	_
20	of	of	IN	_	_	_
21	reads	read	VBZ	_	_	_
22	mapped	map	VBN	_	_	_
23	to	to	TO	_	_	_
24	each	each	DT	_	_	_
25	base	base	NN	_	_	_
26	pair	pair	NN	_	_	_
27	after	after	IN	_	_	_
28	the	the	DT	_	_	_
29	total	total	JJ	_	_	_
30	number	number	NN	_	_	_
31	of	of	IN	_	_	_
32	reads	read	VBZ	_	_	_
33	were	be	VBD	_	_	_
34	scaled	scale	VBN	_	_	_
35	to	to	TO	_	_	_
36	20	20	CD	_	_	_
37	million	million	CD	_	_	_
38	reads	read	VBZ	_	_	_
39	per	per	IN	_	_	_
40	experiment	experiment	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Supplementary	supplementary	JJ	_	_	_
43	_	_	NN	_	_	_
44	files	file	NNS	_	_	_
45	_	_	IN	_	_	_
46	format	format	NN	_	_	_
47	_	_	NN	_	_	_
48	and	and	CC	_	_	_
49	_	_	NN	_	_	_
50	content	content	NN	_	_	_
51	:	:	:	_	_	_
52	Processed	process	VBN	_	_	_
53	data	datum	NNS	_	_	_
54	include	include	VBP	_	_	_
55	read	read	VBN	_	_	_
56	pileups	pileup	NNS	_	_	_
57	obtained	obtain	VBN	_	_	_
58	in	in	IN	_	_	_
59	two	two	CD	_	_	_
60	ChIP-seq	chip-seq	JJ	_	_	_
61	experiments	experiment	NNS	_	_	_
62	by	by	IN	_	_	_
63	two	two	CD	_	_	_
64	different	different	JJ	_	_	_
65	approaches	approach	NNS	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	files	file	NNS	_	_	_
68	1-4	1-4	CD	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	,	,	,	_	_	_
71	the	the	DT	_	_	_
72	set	set	NN	_	_	_
73	of	of	IN	_	_	_
74	regions	region	NNS	_	_	_
75	bound	bind	VBN	_	_	_
76	by	by	IN	_	_	_
77	Dps	dp	NNS	_	_	_
78	in	in	IN	_	_	_
79	both	both	DT	_	_	_
80	experiments	experiment	NNS	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	file	file	NN	_	_	_
83	5	5	CD	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	and	and	CC	_	_	_
86	the	the	DT	_	_	_
87	set	set	NN	_	_	_
88	of	of	IN	_	_	_
89	regions	region	NNS	_	_	_
90	unbound	unbound	JJ	_	_	_
91	by	by	IN	_	_	_
92	Dps	dp	NNS	_	_	_
93	in	in	IN	_	_	_
94	both	both	DT	_	_	_
95	experiments	experiment	NNS	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	file	file	NN	_	_	_
98	6	6	CD	_	_	_
99	-RRB-	-rrb-	-RRB-	_	_	_
100	.	.	.	_	_	_

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	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	is	be	VBZ	_	_	_
15	presented	present	VBN	_	_	_
16	in	in	IN	_	_	_
17	a	a	DT	_	_	_
18	cuff	cuff	NN	_	_	_
19	diff	diff	NN	_	_	_
20	analysis	analysis	NN	_	_	_
21	format	format	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Supplementary	Supplementary	NNP	_	_	_
24	_	_	VBD	_	_	_
25	files	file	NNS	_	_	_
26	_	_	IN	_	_	_
27	format	format	NN	_	_	_
28	_	_	NN	_	_	_
29	and	and	CC	_	_	_
30	_	_	NN	_	_	_
31	content	content	NN	_	_	_
32	:	:	:	_	_	_
33	Processed	process	VBN	_	_	_
34	data	datum	NNS	_	_	_
35	is	be	VBZ	_	_	_
36	presented	present	VBN	_	_	_
37	in	in	IN	_	_	_
38	gff	gff	NN	_	_	_
39	files	file	NNS	_	_	_
40	containing	contain	VBG	_	_	_
41	a	a	DT	_	_	_
42	pileup	pileup	NN	_	_	_
43	of	of	IN	_	_	_
44	5	5	CD	_	_	_
45	'	'	''	_	_	_
46	tags	tag	NNS	_	_	_
47	.	.	.	_	_	_

1	GFF	gff	NN	_	_	_
2	column	column	NN	_	_	_
3	headers	header	NNS	_	_	_
4	\	\	VBP	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Supplementary	Supplementary	NNP	_	_	_
7	_	_	VBD	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	Processed	process	VBN	_	_	_
17	files	file	NNS	_	_	_
18	are	be	VBP	_	_	_
19	in	in	IN	_	_	_
20	tab	tab	NN	_	_	_
21	delimited	delimit	VBD	_	_	_
22	format	format	NN	_	_	_
23	.	.	.	_	_	_

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	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	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	raw	raw	JJ	_	_	_
37	read	read	NN	_	_	_
38	counts	count	VBZ	_	_	_
39	as	as	RB	_	_	_
40	determined	determine	VBN	_	_	_
41	by	by	IN	_	_	_
42	HTseq-Count	htseq-count	NN	_	_	_
43	,	,	,	_	_	_
44	provided	provide	VBN	_	_	_
45	in	in	IN	_	_	_
46	.	.	.	_	_	_

1	csv	csv	NN	_	_	_
2	format	format	NN	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	Supplementary	Supplementary	NNP	_	_	_
5	_	_	VBD	_	_	_
6	files	file	NNS	_	_	_
7	_	_	IN	_	_	_
8	format	format	NN	_	_	_
9	_	_	NN	_	_	_
10	and	and	CC	_	_	_
11	_	_	NN	_	_	_
12	content	content	NN	_	_	_
13	:	:	:	_	_	_
14	Read	Read	NNP	_	_	_
15	counts	count	VBZ	_	_	_
16	aligned	align	VBN	_	_	_
17	to	to	TO	_	_	_
18	genes	gene	NNS	_	_	_
19	and	and	CC	_	_	_
20	noncoding	noncoding	JJ	_	_	_
21	Rfam	rfam	NN	_	_	_
22	features	feature	NNS	_	_	_
23	in	in	IN	_	_	_
24	CSV	CSV	NNP	_	_	_
25	format	format	NN	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Supplementary	Supplementary	NNP	_	_	_
28	_	_	VBD	_	_	_
29	files	file	NNS	_	_	_
30	_	_	IN	_	_	_
31	format	format	NN	_	_	_
32	_	_	NN	_	_	_
33	and	and	CC	_	_	_
34	_	_	NN	_	_	_
35	content	content	NN	_	_	_
36	:	:	:	_	_	_
37	Read	read	VB	_	_	_
38	counts	count	NNS	_	_	_
39	were	be	VBD	_	_	_
40	normalized	normalize	VBN	_	_	_
41	by	by	IN	_	_	_
42	the	the	DT	_	_	_
43	length	length	NN	_	_	_
44	of	of	IN	_	_	_
45	the	the	DT	_	_	_
46	unique	unique	JJ	_	_	_
47	CDS	cds	NN	_	_	_
48	per	per	IN	_	_	_
49	kilobase	kilobase	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	RPKM	rpkm	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	and	and	CC	_	_	_
54	the	the	DT	_	_	_
55	total	total	JJ	_	_	_
56	mapped	map	VBN	_	_	_
57	reads	read	VBZ	_	_	_
58	per	per	IN	_	_	_
59	million	million	CD	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	RPM	rpm	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
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	Reads	read	NNS	_	_	_
75	,	,	,	_	_	_
76	RPKM	rpkm	NN	_	_	_
77	,	,	,	_	_	_
78	and	and	CC	_	_	_
79	RCV	RCV	NNP	_	_	_
80	mapped	map	VBD	_	_	_
81	to	to	TO	_	_	_
82	NC	NC	NNP	_	_	_
83	_	_	SYM	_	_	_
84	002655	002655	CD	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	RCV	rcv	NN	_	_	_
87	=	=	JJ	_	_	_
88	Ribosomal	ribosomal	JJ	_	_	_
89	Coverage	Coverage	NNP	_	_	_
90	Value	value	NN	_	_	_
91	=	=	JJ	_	_	_
92	RPKM-footprint	rpkm-footprint	NN	_	_	_
93	over	over	IN	_	_	_
94	RPKM-transcription	rpkm-transcription	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
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	rna-seq	rna-seq	NN	_	_	_
108	:	:	:	_	_	_
109	genomic	genomic	JJ	_	_	_
110	position	position	NN	_	_	_
111	-LRB-	-lrb-	-LRB-	_	_	_
112	middle	middle	NN	_	_	_
113	of	of	IN	_	_	_
114	the	the	DT	_	_	_
115	5kb-bin	5kb-bin	NN	_	_	_
116	-RRB-	-rrb-	-RRB-	_	_	_
117	to	to	TO	_	_	_
118	each	each	DT	_	_	_
119	count	count	NN	_	_	_
120	.	.	.	_	_	_

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	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	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	RPKM	RPKM	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Supplementary	Supplementary	NNP	_	_	_
15	_	_	VBD	_	_	_
16	files	file	NNS	_	_	_
17	_	_	IN	_	_	_
18	format	format	NN	_	_	_
19	_	_	NN	_	_	_
20	and	and	CC	_	_	_
21	_	_	NN	_	_	_
22	content	content	NN	_	_	_
23	:	:	:	_	_	_
24	RPKM	rpkm	NN	_	_	_
25	is	be	VBZ	_	_	_
26	generated	generate	VBN	_	_	_
27	by	by	IN	_	_	_
28	in-house	in-house	JJ	_	_	_
29	script	script	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Supplementary	supplementary	JJ	_	_	_
32	_	_	NN	_	_	_
33	files	file	NNS	_	_	_
34	_	_	IN	_	_	_
35	format	format	NN	_	_	_
36	_	_	NN	_	_	_
37	and	and	CC	_	_	_
38	_	_	NN	_	_	_
39	content	content	NN	_	_	_
40	:	:	:	_	_	_
41	sam	sam	NN	_	_	_
42	containing	contain	VBG	_	_	_
43	aligned	align	VBN	_	_	_
44	sequences	sequence	NNS	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Supplementary	Supplementary	NNP	_	_	_
47	_	_	VBD	_	_	_
48	files	file	NNS	_	_	_
49	_	_	IN	_	_	_
50	format	format	NN	_	_	_
51	_	_	NN	_	_	_
52	and	and	CC	_	_	_
53	_	_	NN	_	_	_
54	content	content	NN	_	_	_
55	:	:	:	_	_	_
56	SPET-seq	spet-seq	NN	_	_	_
57	data	datum	NNS	_	_	_
58	is	be	VBZ	_	_	_
59	provided	provide	VBN	_	_	_
60	in	in	IN	_	_	_
61	the	the	DT	_	_	_
62	form	form	NN	_	_	_
63	of	of	IN	_	_	_
64	RNA	rna	NN	_	_	_
65	Framework	framework	NN	_	_	_
66	's	's	POS	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	http://www.rnaframework.com	http://www.rnaframework.com	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	RNA	rna	NN	_	_	_
71	Count	count	NN	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	RC	rc	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	files	file	NNS	_	_	_
76	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	file	file	NN	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	each	each	DT	_	_	_
6	transcription	transcription	NN	_	_	_
7	intermediate	intermediate	NN	_	_	_
8	is	be	VBZ	_	_	_
9	provided	provide	VBN	_	_	_
10	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	a	a	DT	_	_	_
3	detailed	detailed	JJ	_	_	_
4	description	description	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	RC	rc	NN	_	_	_
8	format	format	NN	_	_	_
9	,	,	,	_	_	_
10	please	please	VB	_	_	_
11	refer	refer	VB	_	_	_
12	to	to	TO	_	_	_
13	:	:	:	_	_	_
14	http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format	http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
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	SPET-seq	spet-seq	NN	_	_	_
27	data	datum	NNS	_	_	_
28	is	be	VBZ	_	_	_
29	provided	provide	VBN	_	_	_
30	in	in	IN	_	_	_
31	the	the	DT	_	_	_
32	form	form	NN	_	_	_
33	of	of	IN	_	_	_
34	RNA	rna	NN	_	_	_
35	Framework	framework	NN	_	_	_
36	's	's	POS	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	http://www.rnaframework.com	http://www.rnaframework.com	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	RNA	rna	NN	_	_	_
41	Count	count	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	RC	rc	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	files	file	NNS	_	_	_
46	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	file	file	NN	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	each	each	DT	_	_	_
6	transcription	transcription	NN	_	_	_
7	intermediate	intermediate	NN	_	_	_
8	is	be	VBZ	_	_	_
9	provided	provide	VBN	_	_	_
10	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	a	a	DT	_	_	_
3	detailed	detailed	JJ	_	_	_
4	description	description	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	RC	rc	NN	_	_	_
8	format	format	NN	_	_	_
9	,	,	,	_	_	_
10	please	please	VB	_	_	_
11	refer	refer	VB	_	_	_
12	to	to	TO	_	_	_
13	:	:	:	_	_	_
14	http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format	http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format	NN	_	_	_
15	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	rRNA	rrna	NN	_	_	_
3	23S	23s	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	rrlB	rrlb	NN	GEN	_	_
6	gene	gene	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	,	,	,	_	_	_
9	SPET-seq	spet-seq	JJ	_	_	_
10	data	datum	NNS	_	_	_
11	is	be	VBZ	_	_	_
12	provided	provide	VBN	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	form	form	NN	_	_	_
16	of	of	IN	_	_	_
17	RC	RC	NNP	_	_	_
18	files	file	NNS	_	_	_
19	,	,	,	_	_	_
20	each	each	DT	_	_	_
21	one	one	CD	_	_	_
22	corresponding	correspond	VBG	_	_	_
23	to	to	TO	_	_	_
24	individual	individual	JJ	_	_	_
25	transcription	transcription	NN	_	_	_
26	intermediates	intermediate	NNS	_	_	_
27	.	.	.	_	_	_

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	-LRB-	-lrb-	-LRB-	_	_	_
15	pooled	pooled	JJ	_	_	_
16	Total	total	JJ	_	_	_
17	and	and	CC	_	_	_
18	Ribo	Ribo	NNP	_	_	_
19	-	-	:	_	_	_
20	RNA	rna	NN	_	_	_
21	from	from	IN	_	_	_
22	both	both	DT	_	_	_
23	replicates	replicate	VBZ	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	is	be	VBZ	_	_	_
26	provided	provide	VBN	_	_	_
27	in	in	IN	_	_	_
28	the	the	DT	_	_	_
29	form	form	NN	_	_	_
30	of	of	IN	_	_	_
31	RNA	rna	NN	_	_	_
32	Framework	framework	NN	_	_	_
33	's	's	POS	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	http://www.rnaframework.com	http://www.rnaframework.com	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	RNA	rna	NN	_	_	_
38	Count	count	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	RC	rc	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	files	file	NNS	_	_	_
43	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	analyzed	analyze	VBN	_	_	_
4	transcript	transcript	NN	_	_	_
5	,	,	,	_	_	_
6	10	10	CD	_	_	_
7	files	file	NNS	_	_	_
8	corresponding	correspond	VBG	_	_	_
9	to	to	TO	_	_	_
10	SPET-seq	spet-seq	JJ	_	_	_
11	data	datum	NNS	_	_	_
12	for	for	IN	_	_	_
13	the	the	DT	_	_	_
14	10	10	CD	_	_	_
15	transcription	transcription	NN	_	_	_
16	deciles	decile	NNS	_	_	_
17	are	be	VBP	_	_	_
18	provided	provide	VBN	_	_	_
19	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	a	a	DT	_	_	_
3	detailed	detailed	JJ	_	_	_
4	description	description	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	RC	rc	NN	_	_	_
8	format	format	NN	_	_	_
9	,	,	,	_	_	_
10	please	please	VB	_	_	_
11	refer	refer	VB	_	_	_
12	to	to	TO	_	_	_
13	:	:	:	_	_	_
14	http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format	http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
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	Strain-expression	strain-expression	NN	_	_	_
27	.	.	.	_	_	_

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	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	T1E	t1e	NN	_	_	_
13	_	_	CD	_	_	_
14	LB.xlsx	lb.xlsx	NN	_	_	_
15	:	:	:	_	_	_
16	Average	average	NN	_	_	_
17	of	of	IN	_	_	_
18	expression	expression	NN	_	_	_
19	values	value	NNS	_	_	_
20	of	of	IN	_	_	_
21	samples	sample	NNS	_	_	_
22	DOT-T1E	dot-t1e	NN	_	_	_
23	_	_	CD	_	_	_
24	LB1	lb1	NN	_	_	_
25	and	and	CC	_	_	_
26	LB2	lb2	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	Supplementary	supplementary	JJ	_	_	_
29	_	_	NN	_	_	_
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-delimited	tab-delimited	JJ	_	_	_
39	text	text	NN	_	_	_
40	file	file	NN	_	_	_
41	;	;	:	_	_	_
42	genes	gene	NNS	_	_	_
43	in	in	IN	_	_	_
44	rows	row	NNS	_	_	_
45	and	and	CC	_	_	_
46	samples	sample	NNS	_	_	_
47	in	in	IN	_	_	_
48	columns	column	NNS	_	_	_
49	;	;	:	_	_	_
50	each	each	DT	_	_	_
51	entry	entry	NN	_	_	_
52	corresponds	correspond	VBZ	_	_	_
53	to	to	TO	_	_	_
54	the	the	DT	_	_	_
55	number	number	NN	_	_	_
56	of	of	IN	_	_	_
57	reads	read	VBZ	_	_	_
58	mapping	map	VBG	_	_	_
59	to	to	TO	_	_	_
60	the	the	DT	_	_	_
61	given	give	VBN	_	_	_
62	gene	gene	NN	_	_	_
63	in	in	IN	_	_	_
64	the	the	DT	_	_	_
65	given	give	VBN	_	_	_
66	sample	sample	NN	_	_	_
67	.	.	.	_	_	_

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	tab	NN	_	_	_
13	delimited	delimit	VBN	_	_	_
14	text	text	NN	_	_	_
15	file	file	NN	_	_	_
16	;	;	:	_	_	_
17	includes	include	VBZ	_	_	_
18	:	:	:	_	_	_
19	gene	gene	NN	_	_	_
20	differential	differential	JJ	_	_	_
21	expression	expression	NN	_	_	_
22	levels	level	NNS	_	_	_
23	relative	relative	JJ	_	_	_
24	to	to	TO	_	_	_
25	the	the	DT	_	_	_
26	G500	g500	NN	_	_	_
27	strain	strain	NN	_	_	_
28	with	with	IN	_	_	_
29	corresponding	corresponding	JJ	_	_	_
30	p-values	p-value	NNS	_	_	_
31	and	and	CC	_	_	_
32	processed	process	VBN	_	_	_
33	counts	count	NNS	_	_	_
34	for	for	IN	_	_	_
35	each	each	DT	_	_	_
36	biological	biological	JJ	_	_	_
37	replicate	replicate	VB	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	each	each	DT	_	_	_
40	normolized	normolized	NN	_	_	_
41	and	and	CC	_	_	_
42	averaged	average	VBD	_	_	_
43	between	between	IN	_	_	_
44	2	2	CD	_	_	_
45	technical	technical	JJ	_	_	_
46	replicates	replicate	VBZ	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

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	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	\	\	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
60	Supplementary	supplementary	JJ	_	_	_
61	_	_	NN	_	_	_
62	files	file	NNS	_	_	_
63	_	_	IN	_	_	_
64	format	format	NN	_	_	_
65	_	_	NN	_	_	_
66	and	and	CC	_	_	_
67	_	_	NN	_	_	_
68	content	content	NN	_	_	_
69	:	:	:	_	_	_
70	tab-delimited	tab-delimited	JJ	_	_	_
71	text	text	NN	_	_	_
72	file	file	NN	_	_	_
73	of	of	IN	_	_	_
74	transition	transition	NN	_	_	_
75	error	error	NN	_	_	_
76	rate	rate	NN	_	_	_
77	per	per	IN	_	_	_
78	position	position	NN	_	_	_
79	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
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	Tab	tab	NN	_	_	_
22	delimited	delimit	VBN	_	_	_
23	text	text	NN	_	_	_
24	files	file	NNS	_	_	_
25	containing	contain	VBG	_	_	_
26	transcription	transcription	NN	_	_	_
27	coordinates	coordinate	VBZ	_	_	_
28	and	and	CC	_	_	_
29	abundance	abundance	NN	_	_	_
30	estimates	estimate	NNS	_	_	_
31	.	.	.	_	_	_

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	files	file	NNS	_	_	_
15	include	include	VBP	_	_	_
16	count	count	NN	_	_	_
17	values	value	NNS	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	Sample	Sample	NNP	_	_	_
21	.	.	.	_	_	_

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	files	file	NNS	_	_	_
15	include	include	VBP	_	_	_
16	CPM	CPM	NNP	_	_	_
17	values	value	NNS	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	Sample	Sample	NNP	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Supplementary	Supplementary	NNP	_	_	_
23	_	_	VBD	_	_	_
24	files	file	NNS	_	_	_
25	_	_	IN	_	_	_
26	format	format	NN	_	_	_
27	_	_	NN	_	_	_
28	and	and	CC	_	_	_
29	_	_	NN	_	_	_
30	content	content	NN	_	_	_
31	:	:	:	_	_	_
32	tab-delimited	tab-delimited	JJ	_	_	_
33	text	text	NN	_	_	_
34	files	file	NNS	_	_	_
35	include	include	VBP	_	_	_
36	gene	gene	NN	_	_	_
37	expresion	expresion	NN	_	_	_
38	values	value	NNS	_	_	_
39	for	for	IN	_	_	_
40	each	each	DT	_	_	_
41	Sample	Sample	NNP	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	Supplementary	Supplementary	NNP	_	_	_
44	_	_	VBD	_	_	_
45	files	file	NNS	_	_	_
46	_	_	IN	_	_	_
47	format	format	NN	_	_	_
48	_	_	NN	_	_	_
49	and	and	CC	_	_	_
50	_	_	NN	_	_	_
51	content	content	NN	_	_	_
52	:	:	:	_	_	_
53	tab-delimited	tab-delimited	JJ	_	_	_
54	text	text	NN	_	_	_
55	files	file	NNS	_	_	_
56	include	include	VBP	_	_	_
57	normalized	normalize	VBN	_	_	_
58	FPKM	fpkm	NN	_	_	_
59	values	value	NNS	_	_	_
60	and	and	CC	_	_	_
61	raw	raw	JJ	_	_	_
62	fragment	fragment	NN	_	_	_
63	counts	count	NNS	_	_	_
64	for	for	IN	_	_	_
65	each	each	DT	_	_	_
66	Sample	Sample	NNP	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Supplementary	Supplementary	NNP	_	_	_
69	_	_	VBD	_	_	_
70	files	file	NNS	_	_	_
71	_	_	IN	_	_	_
72	format	format	NN	_	_	_
73	_	_	NN	_	_	_
74	and	and	CC	_	_	_
75	_	_	NN	_	_	_
76	content	content	NN	_	_	_
77	:	:	:	_	_	_
78	tab-delimited	tab-delimited	JJ	_	_	_
79	text	text	NN	_	_	_
80	files	file	NNS	_	_	_
81	include	include	VBP	_	_	_
82	RPKM	rpkm	NN	_	_	_
83	values	value	NNS	_	_	_
84	for	for	IN	_	_	_
85	each	each	DT	_	_	_
86	Sample	Sample	NNP	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Supplementary	Supplementary	NNP	_	_	_
89	_	_	VBD	_	_	_
90	files	file	NNS	_	_	_
91	_	_	IN	_	_	_
92	format	format	NN	_	_	_
93	_	_	NN	_	_	_
94	and	and	CC	_	_	_
95	_	_	NN	_	_	_
96	content	content	NN	_	_	_
97	:	:	:	_	_	_
98	tab-delimited	tab-delimited	JJ	_	_	_
99	text	text	NN	_	_	_
100	files	file	NNS	_	_	_
101	include	include	VBP	_	_	_
102	RPKM	rpkm	NN	_	_	_
103	values	value	NNS	_	_	_
104	for	for	IN	_	_	_
105	each	each	DT	_	_	_
106	Sample	Sample	NNP	_	_	_
107	.	.	.	_	_	_

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	files	file	NNS	_	_	_
15	include	include	VBP	_	_	_
16	RPKM	rpkm	NN	_	_	_
17	values	value	NNS	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	Sample	Sample	NNP	_	_	_
21	...	...	:	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Supplementary	Supplementary	NNP	_	_	_
24	_	_	VBD	_	_	_
25	files	file	NNS	_	_	_
26	_	_	IN	_	_	_
27	format	format	NN	_	_	_
28	_	_	NN	_	_	_
29	and	and	CC	_	_	_
30	_	_	NN	_	_	_
31	content	content	NN	_	_	_
32	:	:	:	_	_	_
33	tab-delimited	tab-delimited	JJ	_	_	_
34	text	text	NN	_	_	_
35	files	file	NNS	_	_	_
36	include	include	VBP	_	_	_
37	RPKM	rpkm	NN	_	_	_
38	values	value	NNS	_	_	_
39	for	for	IN	_	_	_
40	each	each	DT	_	_	_
41	Sample	Sample	NNP	_	_	_
42	.	.	.	_	_	_

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	files	file	NNS	_	_	_
15	include	include	VBP	_	_	_
16	RPKM	rpkm	NN	_	_	_
17	values	value	NNS	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	sample	sample	NN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Supplementary	Supplementary	NNP	_	_	_
23	_	_	VBD	_	_	_
24	files	file	NNS	_	_	_
25	_	_	IN	_	_	_
26	format	format	NN	_	_	_
27	_	_	NN	_	_	_
28	and	and	CC	_	_	_
29	_	_	NN	_	_	_
30	content	content	NN	_	_	_
31	:	:	:	_	_	_
32	Tab-delimited	tab-delimited	JJ	_	_	_
33	text	text	NN	_	_	_
34	files	file	NNS	_	_	_
35	include	include	VBP	_	_	_
36	RPKM	rpkm	NN	_	_	_
37	values	value	NNS	_	_	_
38	for	for	IN	_	_	_
39	each	each	DT	_	_	_
40	sample	sample	NN	_	_	_
41	.	.	.	_	_	_

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	files	file	NNS	_	_	_
15	include	include	VBP	_	_	_
16	the	the	DT	_	_	_
17	average	average	NN	_	_	_
18	of	of	IN	_	_	_
19	the	the	DT	_	_	_
20	expression	expression	NN	_	_	_
21	values	value	NNS	_	_	_
22	obtained	obtain	VBN	_	_	_
23	in	in	IN	_	_	_
24	Rockhopper	Rockhopper	NNP	_	_	_
25	for	for	IN	_	_	_
26	the	the	DT	_	_	_
27	replicates	replicate	VBZ	_	_	_
28	of	of	IN	_	_	_
29	each	each	DT	_	_	_
30	condition	condition	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	tab-delimited	tab-delimited	JJ	_	_	_
43	text	text	NN	_	_	_
44	files	file	NNS	_	_	_
45	include	include	VBP	_	_	_
46	TPM	tpm	NN	_	_	_
47	values	value	NNS	_	_	_
48	for	for	IN	_	_	_
49	each	each	DT	_	_	_
50	Sample	sample	NN	_	_	_
51	;	;	:	_	_	_
52	column1	column1	NN	_	_	_
53	:	:	:	_	_	_
54	transcript	transcript	NN	_	_	_
55	id	id	NN	_	_	_
56	;	;	:	_	_	_
57	column2	column2	NN	_	_	_
58	:	:	:	_	_	_
59	TPM	tpm	NN	_	_	_
60	value	value	NN	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Supplementary	Supplementary	NNP	_	_	_
63	_	_	VBD	_	_	_
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-delimited	tab-delimited	JJ	_	_	_
73	text	text	NN	_	_	_
74	files	file	NNS	_	_	_
75	in	in	IN	_	_	_
76	gff	gff	NN	_	_	_
77	format	format	NN	_	_	_
78	which	which	WDT	_	_	_
79	has	have	VBZ	_	_	_
80	8	8	CD	_	_	_
81	columns	column	NNS	_	_	_
82	:	:	:	_	_	_
83	sequence	sequence	NN	_	_	_
84	id	id	NN	_	_	_
85	,	,	,	_	_	_
86	source	source	NN	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	empty	empty	JJ	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	,	,	,	_	_	_
91	feature	feature	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	+	+	CC	_	_	_
94	/	/	:	_	_	_
95	-	-	:	_	_	_
96	strand	strand	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	,	,	,	_	_	_
99	start	start	VB	_	_	_
100	position	position	NN	_	_	_
101	,	,	,	_	_	_
102	end	end	NN	_	_	_
103	position	position	NN	_	_	_
104	,	,	,	_	_	_
105	intensity	intensity	NN	_	_	_
106	score	score	NN	_	_	_
107	,	,	,	_	_	_
108	strand	strand	NN	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	+	+	CC	_	_	_
111	/	/	:	_	_	_
112	-	-	:	_	_	_
113	-RRB-	-rrb-	-RRB-	_	_	_
114	,	,	,	_	_	_
115	frame	frame	NN	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	.	.	.	_	_	_
118	-RRB-	-rrb-	-RRB-	_	_	_

1	,	,	,	_	_	_
2	attribute	attribute	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	.	.	.	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_

1	.	.	.	_	_	_

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	tab	NN	_	_	_
13	delimited	delimit	VBD	_	_	_
14	text	text	NN	_	_	_
15	files	file	NNS	_	_	_
16	,	,	,	_	_	_
17	with	with	IN	_	_	_
18	feature	feature	NN	_	_	_
19	annotation	annotation	NN	_	_	_
20	,	,	,	_	_	_
21	REC	rec	NN	_	_	_
22	_	_	CD	_	_	_
23	seq	seq	NN	_	_	_
24	score	score	NN	_	_	_
25	,	,	,	_	_	_
26	gene	gene	NN	_	_	_
27	name	name	NN	_	_	_
28	and	and	CC	_	_	_
29	description	description	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Supplementary	supplementary	JJ	_	_	_
32	_	_	NN	_	_	_
33	files	file	NNS	_	_	_
34	_	_	IN	_	_	_
35	format	format	NN	_	_	_
36	_	_	NN	_	_	_
37	and	and	CC	_	_	_
38	_	_	NN	_	_	_
39	content	content	NN	_	_	_
40	:	:	:	_	_	_
41	tab-delimitted	tab-delimitted	JJ	_	_	_
42	text	text	NN	_	_	_
43	files	file	NNS	_	_	_
44	contain	contain	VBP	_	_	_
45	TPM	tpm	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	transcripts	transcript	NNS	_	_	_
48	per	per	IN	_	_	_
49	million	million	CD	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	values	value	NNS	_	_	_
52	for	for	IN	_	_	_
53	each	each	DT	_	_	_
54	sample	sample	NN	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Supplementary	Supplementary	NNP	_	_	_
57	_	_	VBD	_	_	_
58	files	file	NNS	_	_	_
59	_	_	IN	_	_	_
60	format	format	NN	_	_	_
61	_	_	NN	_	_	_
62	and	and	CC	_	_	_
63	_	_	NN	_	_	_
64	content	content	NN	_	_	_
65	:	:	:	_	_	_
66	Table	Table	NNP	_	_	_
67	of	of	IN	_	_	_
68	read	read	VBN	_	_	_
69	counts	count	NNS	_	_	_
70	with	with	IN	_	_	_
71	genes	gene	NNS	_	_	_
72	as	as	IN	_	_	_
73	rows	row	NNS	_	_	_
74	and	and	CC	_	_	_
75	samples	sample	NNS	_	_	_
76	as	as	IN	_	_	_
77	columns	column	NNS	_	_	_
78	.	.	.	_	_	_

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	tar	tar	NN	GEN	_	_
13	archives	archive	NNS	_	_	_
14	contain	contain	VBP	_	_	_
15	the	the	DT	_	_	_
16	following	following	NN	_	_	_
17	:	:	:	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	Supplementary	supplementary	JJ	_	_	_
20	_	_	NN	_	_	_
21	files	file	NNS	_	_	_
22	_	_	IN	_	_	_
23	format	format	NN	_	_	_
24	_	_	NN	_	_	_
25	and	and	CC	_	_	_
26	_	_	NN	_	_	_
27	content	content	NN	_	_	_
28	:	:	:	_	_	_
29	text	text	NN	_	_	_
30	files	file	NNS	_	_	_
31	containing	contain	VBG	_	_	_
32	gene	gene	NN	_	_	_
33	counts	count	VBZ	_	_	_
34	output	output	NN	_	_	_
35	by	by	IN	_	_	_
36	htseq-count	htseq-count	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	Supplementary	supplementary	JJ	_	_	_
39	_	_	NN	_	_	_
40	files	file	NNS	_	_	_
41	_	_	IN	_	_	_
42	format	format	NN	_	_	_
43	_	_	NN	_	_	_
44	and	and	CC	_	_	_
45	_	_	NN	_	_	_
46	content	content	NN	_	_	_
47	:	:	:	_	_	_
48	The	the	DT	_	_	_
49	columns	column	NNS	_	_	_
50	in	in	IN	_	_	_
51	the	the	DT	_	_	_
52	processed	process	VBN	_	_	_
53	files	file	NNS	_	_	_
54	are	be	VBP	_	_	_
55	the	the	DT	_	_	_
56	following	follow	VBG	_	_	_
57	in	in	IN	_	_	_
58	order	order	NN	_	_	_
59	:	:	:	_	_	_
60	GeneID	geneid	NN	_	_	_
61	,	,	,	_	_	_
62	Length	length	NN	_	_	_
63	,	,	,	_	_	_
64	ORF1	orf1	NN	_	_	_
65	_	_	NN	_	_	_
66	1	1	CD	_	_	_
67	_	_	NN	_	_	_
68	mapped	map	VBD	_	_	_
69	_	_	CD	_	_	_
70	reads	read	VBZ	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	7655775	7655775	CD	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	,	,	,	_	_	_
75	ORF1	orf1	NN	_	_	_
76	_	_	NN	_	_	_
77	1	1	CD	_	_	_
78	_	_	CD	_	_	_
79	IPTG	iptg	NN	_	_	_
80	_	_	NN	_	_	_
81	mapped	map	VBD	_	_	_
82	_	_	CD	_	_	_
83	reads	read	VBZ	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	7178582	7178582	CD	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	,	,	,	_	_	_
88	ORF1	orf1	NN	_	_	_
89	_	_	NN	_	_	_
90	2	2	CD	_	_	_
91	_	_	NN	_	_	_
92	mapped	map	VBD	_	_	_
93	_	_	CD	_	_	_
94	reads	read	VBZ	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	7706927	7706927	CD	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	,	,	,	_	_	_
99	ORF1	orf1	NN	_	_	_
100	_	_	NN	_	_	_
101	2	2	CD	_	_	_
102	_	_	CD	_	_	_
103	IPTG	iptg	NN	_	_	_
104	_	_	NN	_	_	_
105	mapped	map	VBD	_	_	_
106	_	_	CD	_	_	_
107	reads	read	VBZ	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	7070827	7070827	CD	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	,	,	,	_	_	_
112	Svi3	svi3	NN	_	_	_
113	_	_	NN	_	_	_
114	3	3	CD	_	_	_
115	_	_	NN	_	_	_
116	1	1	CD	_	_	_
117	_	_	NN	_	_	_
118	mapped	map	VBD	_	_	_
119	_	_	CD	_	_	_
120	reads	read	VBZ	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	8018710	8018710	CD	_	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	,	,	,	_	_	_
125	Svi3	svi3	NN	_	_	_
126	_	_	NN	_	_	_
127	3	3	CD	_	_	_
128	_	_	NN	_	_	_
129	1	1	CD	_	_	_
130	_	_	CD	_	_	_
131	IPTG	iptg	NN	_	_	_
132	_	_	NN	_	_	_
133	mapped	map	VBD	_	_	_
134	_	_	CD	_	_	_
135	reads	read	VBZ	_	_	_
136	-LRB-	-lrb-	-LRB-	_	_	_
137	8299205	8299205	CD	_	_	_
138	-RRB-	-rrb-	-RRB-	_	_	_
139	,	,	,	_	_	_
140	Svi3	svi3	NN	_	_	_
141	_	_	NN	_	_	_
142	3	3	CD	_	_	_
143	_	_	NN	_	_	_
144	2	2	CD	_	_	_
145	_	_	NN	_	_	_
146	mapped	map	VBD	_	_	_
147	_	_	CD	_	_	_
148	reads	read	VBZ	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	7313736	7313736	CD	_	_	_
151	-RRB-	-rrb-	-RRB-	_	_	_
152	,	,	,	_	_	_
153	Svi3	svi3	NN	_	_	_
154	_	_	NN	_	_	_
155	3	3	CD	_	_	_
156	_	_	NN	_	_	_
157	2	2	CD	_	_	_
158	_	_	CD	_	_	_
159	IPTG	iptg	NN	_	_	_
160	_	_	NN	_	_	_
161	mapped	map	VBD	_	_	_
162	_	_	CD	_	_	_
163	reads	read	VBZ	_	_	_
164	-LRB-	-lrb-	-LRB-	_	_	_
165	8344539	8344539	CD	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	,	,	,	_	_	_
168	WT1	wt1	NN	_	_	_
169	_	_	CD	_	_	_
170	IPTG	iptg	NN	_	_	_
171	_	_	NN	_	_	_
172	mapped	map	VBD	_	_	_
173	_	_	CD	_	_	_
174	reads	read	VBZ	_	_	_
175	-LRB-	-lrb-	-LRB-	_	_	_
176	8074159	8074159	CD	_	_	_
177	-RRB-	-rrb-	-RRB-	_	_	_
178	,	,	,	_	_	_
179	WT2	wt2	NN	_	_	_
180	_	_	CD	_	_	_
181	IPTG	iptg	NN	_	_	_
182	_	_	NN	_	_	_
183	mapped	map	VBD	_	_	_
184	_	_	CD	_	_	_
185	reads	read	VBZ	_	_	_
186	-LRB-	-lrb-	-LRB-	_	_	_
187	8103887	8103887	CD	_	_	_
188	-RRB-	-rrb-	-RRB-	_	_	_
189	,	,	,	_	_	_
190	ORF1	orf1	NN	_	_	_
191	_	_	NN	_	_	_
192	1	1	CD	_	_	_
193	_	_	NN	_	_	_
194	coverage	coverage	NN	_	_	_
195	,	,	,	_	_	_
196	ORF1	orf1	NN	_	_	_
197	_	_	NN	_	_	_
198	1	1	CD	_	_	_
199	_	_	SYM	_	_	_
200	IPTG	iptg	SYM	_	_	_
201	_	_	SYM	_	_	_
202	coverage	coverage	NN	_	_	_
203	,	,	,	_	_	_
204	ORF1	orf1	NN	_	_	_
205	_	_	NN	_	_	_
206	2	2	CD	_	_	_
207	_	_	CD	_	_	_
208	coverage	coverage	NN	_	_	_
209	,	,	,	_	_	_
210	ORF1	orf1	NN	_	_	_
211	_	_	NN	_	_	_
212	2	2	CD	_	_	_
213	_	_	SYM	_	_	_
214	IPTG	iptg	SYM	_	_	_
215	_	_	SYM	_	_	_
216	coverage	coverage	NN	_	_	_
217	,	,	,	_	_	_
218	Svi3	svi3	NN	_	_	_
219	_	_	NN	_	_	_
220	3	3	CD	_	_	_
221	_	_	NN	_	_	_
222	1	1	CD	_	_	_
223	_	_	NN	_	_	_
224	coverage	coverage	NN	_	_	_
225	,	,	,	_	_	_
226	Svi3	svi3	NN	_	_	_
227	_	_	NN	_	_	_
228	3	3	CD	_	_	_
229	_	_	NN	_	_	_
230	1	1	CD	_	_	_
231	_	_	SYM	_	_	_
232	IPTG	iptg	SYM	_	_	_
233	_	_	SYM	_	_	_
234	coverage	coverage	NN	_	_	_
235	,	,	,	_	_	_
236	Svi3	svi3	NN	_	_	_
237	_	_	NN	_	_	_
238	3	3	CD	_	_	_
239	_	_	NN	_	_	_
240	2	2	CD	_	_	_
241	_	_	CD	_	_	_
242	coverage	coverage	NN	_	_	_
243	,	,	,	_	_	_
244	Svi3	svi3	NN	_	_	_
245	_	_	NN	_	_	_
246	3	3	CD	_	_	_
247	_	_	NN	_	_	_
248	2	2	CD	_	_	_
249	_	_	SYM	_	_	_
250	IPTG	iptg	SYM	_	_	_
251	_	_	SYM	_	_	_
252	coverage	coverage	NN	_	_	_
253	,	,	,	_	_	_
254	WT1	wt1	NN	_	_	_
255	_	_	CD	_	_	_
256	IPTG	IPTG	NNP	_	_	_
257	_	_	CD	_	_	_
258	coverage	coverage	NN	_	_	_
259	,	,	,	_	_	_
260	WT2	wt2	NN	_	_	_
261	_	_	CD	_	_	_
262	IPTG	IPTG	NNP	_	_	_
263	_	_	CD	_	_	_
264	coverage	coverage	NN	_	_	_
265	,	,	,	_	_	_
266	ORF1	orf1	NN	_	_	_
267	_	_	NN	_	_	_
268	1	1	CD	_	_	_
269	_	_	NN	_	_	_
270	rpkm	rpkm	NN	_	_	_
271	,	,	,	_	_	_
272	ORF1	orf1	NN	_	_	_
273	_	_	NN	_	_	_
274	1	1	CD	_	_	_
275	_	_	CD	_	_	_
276	IPTG	iptg	NN	_	_	_
277	_	_	NN	_	_	_
278	rpkm	rpkm	NN	_	_	_
279	,	,	,	_	_	_
280	ORF1	orf1	NN	_	_	_
281	_	_	NN	_	_	_
282	2	2	CD	_	_	_
283	_	_	CD	_	_	_
284	rpkm	rpkm	NN	_	_	_
285	,	,	,	_	_	_
286	ORF1	orf1	NN	_	_	_
287	_	_	NN	_	_	_
288	2	2	CD	_	_	_
289	_	_	CD	_	_	_
290	IPTG	iptg	NN	_	_	_
291	_	_	NN	_	_	_
292	rpkm	rpkm	NN	_	_	_
293	,	,	,	_	_	_
294	Svi3	svi3	NN	_	_	_
295	_	_	NN	_	_	_
296	3	3	CD	_	_	_
297	_	_	NN	_	_	_
298	1	1	CD	_	_	_
299	_	_	NN	_	_	_
300	rpkm	rpkm	NN	_	_	_
301	,	,	,	_	_	_
302	Svi3	svi3	NN	_	_	_
303	_	_	NN	_	_	_
304	3	3	CD	_	_	_
305	_	_	NN	_	_	_
306	1	1	CD	_	_	_
307	_	_	CD	_	_	_
308	IPTG	iptg	NN	_	_	_
309	_	_	NN	_	_	_
310	rpkm	rpkm	NN	_	_	_
311	,	,	,	_	_	_
312	Svi3	svi3	NN	_	_	_
313	_	_	NN	_	_	_
314	3	3	CD	_	_	_
315	_	_	NN	_	_	_
316	2	2	CD	_	_	_
317	_	_	CD	_	_	_
318	rpkm	rpkm	NN	_	_	_
319	,	,	,	_	_	_
320	Svi3	svi3	NN	_	_	_
321	_	_	NN	_	_	_
322	3	3	CD	_	_	_
323	_	_	NN	_	_	_
324	2	2	CD	_	_	_
325	_	_	CD	_	_	_
326	IPTG	iptg	NN	_	_	_
327	_	_	NN	_	_	_
328	rpkm	rpkm	NN	_	_	_
329	,	,	,	_	_	_
330	WT1	wt1	NN	_	_	_
331	_	_	CD	_	_	_
332	IPTG	iptg	NN	_	_	_
333	_	_	NN	_	_	_
334	rpkm	rpkm	NN	_	_	_
335	,	,	,	_	_	_
336	WT2	wt2	NN	_	_	_
337	_	_	CD	_	_	_
338	IPTG	iptg	NN	_	_	_
339	_	_	NN	_	_	_
340	rpkm	rpkm	NN	_	_	_
341	,	,	,	_	_	_
342	Symbol	symbol	NN	_	_	_
343	-LRB-	-lrb-	-LRB-	_	_	_
344	gene	gene	NN	_	_	_
345	name	name	NN	_	_	_
346	-RRB-	-rrb-	-RRB-	_	_	_
347	,	,	,	_	_	_
348	Description	description	NN	_	_	_
349	,	,	,	_	_	_
350	KEGG	KEGG	NNP	_	_	_
351	Orthology	Orthology	NNP	_	_	_
352	,	,	,	_	_	_
353	GO	GO	NNP	_	_	_
354	Component	Component	NNP	_	_	_
355	,	,	,	_	_	_
356	GO	GO	NNP	_	_	_
357	Function	function	NN	_	_	_
358	,	,	,	_	_	_
359	and	and	CC	_	_	_
360	GO	GO	NNP	_	_	_
361	Process	process	VBP	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
363	Supplementary	supplementary	JJ	_	_	_
364	_	_	NN	_	_	_
365	files	file	NNS	_	_	_
366	_	_	IN	_	_	_
367	format	format	NN	_	_	_
368	_	_	NN	_	_	_
369	and	and	CC	_	_	_
370	_	_	NN	_	_	_
371	content	content	NN	_	_	_
372	:	:	:	_	_	_
373	The	the	DT	_	_	_
374	file	file	NN	_	_	_
375	format	format	NN	_	_	_
376	is	be	VBZ	_	_	_
377	.	.	.	_	_	_

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	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	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	text	text	NN	_	_	_
14	file	file	NN	_	_	_
15	contains	contain	VBZ	_	_	_
16	sense	sense	NN	_	_	_
17	and	and	CC	_	_	_
18	antisense	antisense	JJ	_	_	_
19	raw	raw	JJ	_	_	_
20	base	base	NN	_	_	_
21	read	read	VBD	_	_	_
22	counts	count	NNS	_	_	_
23	for	for	IN	_	_	_
24	each	each	DT	_	_	_
25	of	of	IN	_	_	_
26	the	the	DT	_	_	_
27	4091	4091	CD	_	_	_
28	ORFs	orf	NNS	_	_	_
29	for	for	IN	_	_	_
30	all	all	PDT	_	_	_
31	the	the	DT	_	_	_
32	15	15	CD	_	_	_
33	samples	sample	NNS	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	the	the	DT	_	_	_
37	explanation	explanation	NN	_	_	_
38	key	key	NN	_	_	_
39	is	be	VBZ	_	_	_
40	included	include	VBN	_	_	_
41	in	in	IN	_	_	_
42	the	the	DT	_	_	_
43	file	file	NN	_	_	_
44	.	.	.	_	_	_

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	txt	txt	NN	_	_	_
14	file	file	NN	_	_	_
15	includes	include	VBZ	_	_	_
16	the	the	DT	_	_	_
17	gene	gene	NN	_	_	_
18	expression	expression	NN	_	_	_
19	profiles	profile	NNS	_	_	_
20	of	of	IN	_	_	_
21	all	all	PDT	_	_	_
22	the	the	DT	_	_	_
23	samples	sample	NNS	_	_	_
24	.	.	.	_	_	_

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	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	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
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	Txt	txt	NN	_	_	_
23	files	file	NNS	_	_	_
24	are	be	VBP	_	_	_
25	processed	process	VBN	_	_	_
26	data	datum	NNS	_	_	_
27	for	for	IN	_	_	_
28	DMS-MaPseq	dms-mapseq	NN	_	_	_
29	with	with	IN	_	_	_
30	two	two	CD	_	_	_
31	columns	column	NNS	_	_	_
32	:	:	:	_	_	_
33	first	first	JJ	_	_	_
34	column	column	NN	_	_	_
35	containing	contain	VBG	_	_	_
36	chromosome	chromosome	NN	_	_	_
37	positions	position	NNS	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	relative	relative	JJ	_	_	_
40	to	to	TO	_	_	_
41	transcription	transcription	NN	_	_	_
42	start	start	NN	_	_	_
43	site	site	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	1	1	CD	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	of	of	IN	_	_	_
48	cspA	cspa	NN	GEN	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	and	and	CC	_	_	_
51	second	second	JJ	_	_	_
52	column	column	NN	_	_	_
53	containing	contain	VBG	_	_	_
54	the	the	DT	_	_	_
55	mutation	mutation	NN	_	_	_
56	rate	rate	NN	_	_	_
57	.	.	.	_	_	_

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	txt	txt	NN	_	_	_
13	files	file	NNS	_	_	_
14	including	include	VBG	_	_	_
15	count	count	NN	_	_	_
16	data	datum	NNS	_	_	_
17	for	for	IN	_	_	_
18	the	the	DT	_	_	_
19	whole	whole	JJ	_	_	_
20	genome	genome	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Supplementary	supplementary	JJ	_	_	_
23	_	_	NN	_	_	_
24	files	file	NNS	_	_	_
25	_	_	IN	_	_	_
26	format	format	NN	_	_	_
27	_	_	NN	_	_	_
28	and	and	CC	_	_	_
29	_	_	NN	_	_	_
30	content	content	NN	_	_	_
31	:	:	:	_	_	_
32	txt	txt	NN	_	_	_
33	files	file	NNS	_	_	_
34	including	include	VBG	_	_	_
35	count	count	NN	_	_	_
36	numbers	number	NNS	_	_	_
37	of	of	IN	_	_	_
38	RNA	rna	NN	_	_	_
39	's	's	POS	_	_	_
40	and	and	CC	_	_	_
41	quality	quality	NN	_	_	_
42	control	control	NN	_	_	_
43	were	be	VBD	_	_	_
44	generated	generate	VBN	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Supplementary	Supplementary	NNP	_	_	_
47	_	_	VBD	_	_	_
48	files	file	NNS	_	_	_
49	_	_	IN	_	_	_
50	format	format	NN	_	_	_
51	_	_	NN	_	_	_
52	and	and	CC	_	_	_
53	_	_	NN	_	_	_
54	content	content	NN	_	_	_
55	:	:	:	_	_	_
56	txt	txt	NN	_	_	_
57	files	file	NNS	_	_	_
58	of	of	IN	_	_	_
59	a	a	DT	_	_	_
60	matrix	matrix	NN	_	_	_
61	containing	contain	VBG	_	_	_
62	genome	genome	NN	_	_	_
63	position	position	NN	_	_	_
64	in	in	IN	_	_	_
65	column	column	NN	_	_	_
66	1	1	CD	_	_	_
67	and	and	CC	_	_	_
68	number	number	NN	_	_	_
69	of	of	IN	_	_	_
70	depth	depth	NN	_	_	_
71	of	of	IN	_	_	_
72	mapped	map	VBN	_	_	_
73	reads	read	VBZ	_	_	_
74	in	in	IN	_	_	_
75	column	column	NN	_	_	_
76	2	2	CD	_	_	_
77	.	.	.	_	_	_

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	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	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
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	-LSB-	-lsb-	-LRB-	_	_	_
22	.	.	.	_	_	_

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	Supplementary	Supplementary	NNP	_	_	_
11	_	_	VBD	_	_	_
12	files	file	NNS	_	_	_
13	_	_	IN	_	_	_
14	format	format	NN	_	_	_
15	_	_	NN	_	_	_
16	and	and	CC	_	_	_
17	_	_	NN	_	_	_
18	content	content	NN	_	_	_
19	:	:	:	_	_	_
20	txt	txt	NN	_	_	_
21	:	:	:	_	_	_
22	tab-delimited	tab-delimited	JJ	_	_	_
23	text	text	NN	_	_	_
24	files	file	NNS	_	_	_
25	include	include	VBP	_	_	_
26	RPKM	rpkm	NN	_	_	_
27	values	value	NNS	_	_	_
28	for	for	IN	_	_	_
29	each	each	DT	_	_	_
30	Sample	Sample	NNP	_	_	_
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	*	*	SYM	_	_	_
43	txt	txt	NN	_	_	_
44	,	,	,	_	_	_
45	*	*	SYM	_	_	_
46	xml	xml	NN	_	_	_
47	:	:	:	_	_	_
48	These	these	DT	_	_	_
49	files	file	NNS	_	_	_
50	contain	contain	VBP	_	_	_
51	the	the	DT	_	_	_
52	raw	raw	JJ	_	_	_
53	counts	count	NNS	_	_	_
54	,	,	,	_	_	_
55	normalized	normalize	VBD	_	_	_
56	counts	count	NNS	_	_	_
57	,	,	,	_	_	_
58	RPKM	rpkm	NN	_	_	_
59	values	value	NNS	_	_	_
60	,	,	,	_	_	_
61	expression	expression	NN	_	_	_
62	values	value	NNS	_	_	_
63	,	,	,	_	_	_
64	P-values	p-value	NNS	_	_	_
65	and	and	CC	_	_	_
66	Q-values	q-value	NNS	_	_	_
67	.	.	.	_	_	_

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	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	WIG	wig	NN	_	_	_
13	files	file	NNS	_	_	_
14	are	be	VBP	_	_	_
15	provided	provide	VBN	_	_	_
16	showing	show	VBG	_	_	_
17	uniquely	uniquely	RB	_	_	_
18	mapped	map	VBN	_	_	_
19	sequence	sequence	NN	_	_	_
20	reads	read	VBZ	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	normalized	normalize	VBN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

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	wig	wig	NN	_	_	_
13	files	file	NNS	_	_	_
14	representing	represent	VBG	_	_	_
15	the	the	DT	_	_	_
16	normalized	normalize	VBN	_	_	_
17	number	number	NN	_	_	_
18	of	of	IN	_	_	_
19	pAA-associated	paa-associated	JJ	_	_	_
20	mapped	map	VBN	_	_	_
21	reads	read	VBZ	_	_	_
22	per	per	IN	_	_	_
23	nucleotide	nucleotide	NN	_	_	_
24	.	.	.	_	_	_

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	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	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	wiggle	wiggle	NN	_	_	_
25	files	file	NNS	_	_	_
26	with	with	IN	_	_	_
27	two	two	CD	_	_	_
28	columns	column	NNS	_	_	_
29	:	:	:	_	_	_
30	first	first	JJ	_	_	_
31	column	column	NN	_	_	_
32	containing	contain	VBG	_	_	_
33	chromosome	chromosome	NN	_	_	_
34	positions	position	NNS	_	_	_
35	and	and	CC	_	_	_
36	second	second	JJ	_	_	_
37	column	column	NN	_	_	_
38	containing	contain	VBG	_	_	_
39	the	the	DT	_	_	_
40	number	number	NN	_	_	_
41	of	of	IN	_	_	_
42	reads	read	VBZ	_	_	_
43	mapped	map	VBN	_	_	_
44	to	to	TO	_	_	_
45	the	the	DT	_	_	_
46	position	position	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	see	see	VB	_	_	_
49	publication	publication	NN	_	_	_
50	for	for	IN	_	_	_
51	details	detail	NNS	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	.	.	.	_	_	_

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	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	.	.	.	_	_	_

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	Supplementary	supplementary	JJ	_	_	_
23	_	_	NN	_	_	_
24	files	file	NNS	_	_	_
25	_	_	IN	_	_	_
26	format	format	NN	_	_	_
27	_	_	NN	_	_	_
28	and	and	CC	_	_	_
29	_	_	NN	_	_	_
30	content	content	NN	_	_	_
31	:	:	:	_	_	_
32	xls	xl	NNS	_	_	_
33	:	:	:	_	_	_
34	The	the	DT	_	_	_
35	data	datum	NNS	_	_	_
36	are	be	VBP	_	_	_
37	averaged	average	VBN	_	_	_
38	across	across	IN	_	_	_
39	the	the	DT	_	_	_
40	three	three	CD	_	_	_
41	samples	sample	NNS	_	_	_
42	per	per	IN	_	_	_
43	strain	strain	NN	_	_	_
44	.	.	.	_	_	_

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	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	xlsx	xlsx	NN	_	_	_
13	file	file	NN	_	_	_
14	format	format	NN	_	_	_
15	includes	include	VBZ	_	_	_
16	raw	raw	JJ	_	_	_
17	gene	gene	NN	_	_	_
18	counts	count	VBZ	_	_	_
19	for	for	IN	_	_	_
20	each	each	DT	_	_	_
21	sample	sample	NN	_	_	_
22	before	before	IN	_	_	_
23	and	and	CC	_	_	_
24	after	after	IN	_	_	_
25	filtering	filter	VBG	_	_	_
26	for	for	IN	_	_	_
27	low	low	JJ	_	_	_
28	coverage	coverage	NN	_	_	_
29	genes	gene	NNS	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Supplementary	Supplementary	NNP	_	_	_
32	_	_	VBD	_	_	_
33	files	file	NNS	_	_	_
34	_	_	IN	_	_	_
35	format	format	NN	_	_	_
36	_	_	NN	_	_	_
37	and	and	CC	_	_	_
38	_	_	NN	_	_	_
39	content	content	NN	_	_	_
40	:	:	:	_	_	_
41	.	.	.	_	_	_

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	NNP	_	_	_
17	Supplementary	Supplementary	NNP	_	_	_
18	_	_	VBD	_	_	_
19	files	file	NNS	_	_	_
20	_	_	IN	_	_	_
21	format	format	NN	_	_	_
22	_	_	NN	_	_	_
23	and	and	CC	_	_	_
24	_	_	NN	_	_	_
25	content	content	NN	_	_	_
26	:	:	:	_	_	_
27	xlsx	xlsx	NN	_	_	_
28	:	:	:	_	_	_
29	logFC	logfc	NN	_	_	_
30	and	and	CC	_	_	_
31	p-value	p-value	JJ	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	supplementation	supplementation	NN	_	_	_
34	:	:	:	_	_	_
35	adenine	adenine	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	10	10	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	supplementation	supplementation	NN	_	_	_
42	:	:	:	_	_	_
43	L-tryptophan	l-tryptophan	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	20	20	CD	_	_	_
46	mg/L	mg/l	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	supplementation	supplementation	NN	_	_	_
50	:	:	:	_	_	_
51	None	none	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Suspended	suspend	VBN	_	_	_
54	cells	cell	NNS	_	_	_
55	were	be	VBD	_	_	_
56	then	then	RB	_	_	_
57	removed	remove	VBN	_	_	_
58	and	and	CC	_	_	_
59	biofilms	biofilm	NNS	_	_	_
60	were	be	VBD	_	_	_
61	washed	wash	VBN	_	_	_
62	3	3	CD	_	_	_
63	times	time	NNS	_	_	_
64	with	with	IN	_	_	_
65	1	1	CD	_	_	_
66	ml	ml	NN	_	_	_
67	10	10	CD	_	_	_
68	%	%	NN	_	_	_
69	LB	lb	NN	MED	_	_
70	broth	broth	NN	MED	_	_
71	.	.	.	_	_	_

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	Svi3	svi3	NN	_	_	_
3	_	_	CD	_	_	_
4	3	3	CD	_	_	_
5	_	_	NN	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Svi3	svi3	NN	_	_	_
9	_	_	CD	_	_	_
10	3	3	CD	_	_	_
11	_	_	NN	_	_	_
12	1	1	CD	_	_	_
13	_	_	CD	_	_	_
14	IPTG	iptg	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Svi3	svi3	NN	_	_	_
17	_	_	CD	_	_	_
18	3	3	CD	_	_	_
19	_	_	NN	_	_	_
20	2	2	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Svi3	svi3	NN	_	_	_
23	_	_	CD	_	_	_
24	3	3	CD	_	_	_
25	_	_	NN	_	_	_
26	2	2	CD	_	_	_
27	_	_	CD	_	_	_
28	IPTG	iptg	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	symbioflor	symbioflor	NN	_	_	_
31	status	status	NN	_	_	_
32	:	:	:	_	_	_
33	without	without	IN	_	_	_
34	Symbioflor	Symbioflor	NNP	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	symbioflor	symbioflor	NN	_	_	_
37	status	status	NN	_	_	_
38	:	:	:	_	_	_
39	with	with	IN	_	_	_
40	Symbioflor	Symbioflor	NNP	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Synchronization	synchronization	NN	_	_	_
43	was	be	VBD	_	_	_
44	achieved	achieve	VBN	_	_	_
45	by	by	IN	_	_	_
46	passaging	passaging	NN	_	_	_
47	cells	cell	NNS	_	_	_
48	through	through	IN	_	_	_
49	one	one	CD	_	_	_
50	or	or	CC	_	_	_
51	two	two	CD	_	_	_
52	rounds	round	NNS	_	_	_
53	of	of	IN	_	_	_
54	stationary	stationary	JJ	GrowthPhase	_	_
55	phase	phase	NN	GrowthPhase	_	_
56	according	accord	VBG	_	_	_
57	to	to	TO	_	_	_
58	Cutler	Cutler	NNP	_	_	_
59	and	and	CC	_	_	_
60	Evans	Evans	NNP	_	_	_
61	1966	1966	CD	_	_	_
62	.	.	.	_	_	_

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/N	o/n	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	37	37	CD	_	_	_
25	°C	°c	NN	_	_	_
26	,	,	,	_	_	_
27	200	200	CD	_	_	_
28	rpm	rpm	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	M9	m9	NN	_	_	_
2	media	media	NNS	_	_	_
3	was	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	final	final	JJ	_	_	_
8	OD600	od600	NN	_	_	_
9	=	=	JJ	_	_	_
10	0.25	0.25	CD	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	early-logarithmic	early-logarithmic	JJ	_	_	_
13	phase	phase	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	,	,	,	_	_	_
8	200	200	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	and	and	CC	_	_	_
12	maintained	maintain	VBN	_	_	_
13	in	in	IN	_	_	_
14	stationary	stationary	JJ	GrowthPhase	_	_
15	phase	phase	NN	GrowthPhase	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	OD600	od600	NN	_	_	_
18	1.8	1.8	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	for	for	IN	_	_	_
21	approximately	approximately	RB	_	_	_
22	2	2	CD	_	_	_
23	hours	hour	NNS	_	_	_
24	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	appropriate	appropriate	JJ	_	_	_
3	amount	amount	NN	_	_	_
4	of	of	IN	_	_	_
5	each	each	DT	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	used	use	VBN	_	_	_
9	to	to	TO	_	_	_
10	inoculate	inoculate	VB	_	_	_
11	pre-warmed	pre-warmed	JJ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	M9	m9	NN	_	_	_
17	media	media	NNS	_	_	_
18	to	to	TO	_	_	_
19	a	a	DT	_	_	_
20	final	final	JJ	_	_	_
21	OD600	od600	NN	_	_	_
22	=	=	JJ	_	_	_
23	0.25	0.25	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	approximate	approximate	JJ	_	_	_
26	7-fold	7-fold	JJ	_	_	_
27	dilution	dilution	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	Released	release	VBN	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	,	,	,	_	_	_
9	200	200	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	harvested	harvest	VBN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	time	time	NN	_	_	_
16	=	=	JJ	_	_	_
17	0	0	CD	_	_	_
18	,	,	,	_	_	_
19	1	1	CD	_	_	_
20	hr	hr	NN	_	_	_
21	,	,	,	_	_	_
22	or	or	CC	_	_	_
23	2	2	CD	_	_	_
24	hr	hr	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	for	for	IN	_	_	_
27	GCC	gcc	NN	_	_	_
28	and	and	CC	_	_	_
29	RNA	rna	NN	_	_	_
30	isolation	isolation	NN	_	_	_
31	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	1	1	CD	_	_	_
4	mL	ml	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	were	be	VBD	_	_	_
7	also	also	RB	_	_	_
8	taken	take	VBN	_	_	_
9	for	for	IN	_	_	_
10	FACS	facs	NN	_	_	_
11	analysis	analysis	NN	_	_	_
12	and	and	CC	_	_	_
13	fluorescence	fluorescence	NN	_	_	_
14	microscopy	microscopy	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	t	t	NN	_	_	_
17	=	=	JJ	_	_	_
18	0	0	CD	_	_	_
19	,	,	,	_	_	_
20	1	1	CD	_	_	_
21	hr	hr	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	2	2	CD	_	_	_
25	hr	hr	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

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	_	_	SYM	_	_	_
108	CUOB	cuob	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	synthetic	synthetic	JJ	_	_	_
111	circuit	circuit	NN	_	_	_
112	:	:	:	_	_	_
113	H3	h3	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	synthetic	synthetic	JJ	_	_	_
116	circuit	circuit	NN	_	_	_
117	:	:	:	_	_	_
118	LACZ	lacz	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	synthetic	synthetic	JJ	_	_	_
121	circuit	circuit	NN	_	_	_
122	:	:	:	_	_	_
123	Lux	lux	FW	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
125	synthetic	synthetic	JJ	_	_	_
126	circuit	circuit	NN	_	_	_
127	:	:	:	_	_	_
128	M1	m1	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	synthetic	synthetic	JJ	_	_	_
131	circuit	circuit	NN	_	_	_
132	:	:	:	_	_	_
133	None	none	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	T0	t0	NN	_	_	_
136	_	_	SYM	_	_	_
137	N0025	n0025	CD	_	_	_
138	_	_	CD	_	_	_
139	r1	r1	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	T0	t0	NN	_	_	_
142	_	_	SYM	_	_	_
143	N0025	n0025	CD	_	_	_
144	_	_	CD	_	_	_
145	r2	r2	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	T0	t0	NN	_	_	_
148	_	_	SYM	_	_	_
149	N0025	n0025	CD	_	_	_
150	_	_	CD	_	_	_
151	r3	r3	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	T12	t12	NN	_	_	_
154	_	_	SYM	_	_	_
155	N0025	n0025	CD	_	_	_
156	_	_	CD	_	_	_
157	r1	r1	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	T12	t12	NN	_	_	_
160	_	_	SYM	_	_	_
161	N0025	n0025	CD	_	_	_
162	_	_	CD	_	_	_
163	r2	r2	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	T12	t12	NN	_	_	_
166	_	_	SYM	_	_	_
167	N0025	n0025	CD	_	_	_
168	_	_	CD	_	_	_
169	r3	r3	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	T170V	t170v	NN	_	_	_
172	0	0	CD	_	_	_
173	min	min	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	T170V	t170v	NN	_	_	_
176	10	10	CD	_	_	_
177	min	min	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	T18-ParB	t18-parb	NN	_	_	_
180	-LRB-	-lrb-	-LRB-	_	_	_
181	G101S	g101s	NN	_	_	_
182	-RRB-	-rrb-	-RRB-	_	_	_
183	were	be	VBD	_	_	_
184	produced	produce	VBN	_	_	_
185	by	by	IN	_	_	_
186	addition	addition	NN	_	_	_
187	of	of	IN	_	_	_
188	0.5	0.5	CD	_	_	_
189	mM	mm	NN	KWSUPP	_	_
190	IPTG	iptg	NN	_	_	_
191	for	for	IN	_	_	_
192	an	a	DT	_	_	_
193	hour	hour	NN	_	_	_
194	before	before	IN	_	_	_
195	formadehyde	formadehyde	NN	_	_	_
196	to	to	TO	_	_	_
197	1	1	CD	_	_	_
198	%	%	NN	_	_	_
199	-LRB-	-lrb-	-LRB-	_	_	_
200	final	final	JJ	_	_	_
201	concentration	concentration	NN	_	_	_
202	-RRB-	-rrb-	-RRB-	_	_	_
203	was	be	VBD	_	_	_
204	added	add	VBN	_	_	_
205	to	to	TO	_	_	_
206	fix	fix	VB	_	_	_
207	cells	cell	NNS	_	_	_
208	for	for	IN	_	_	_
209	ChIP-seq	ChIP-seq	NNP	_	_	_
210	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
211	T18-ParB	t18-parb	NN	_	_	_
212	-LRB-	-lrb-	-LRB-	_	_	_
213	WT	wt	NN	_	_	_
214	-RRB-	-rrb-	-RRB-	_	_	_
215	were	be	VBD	_	_	_
216	produced	produce	VBN	_	_	_
217	by	by	IN	_	_	_
218	addition	addition	NN	_	_	_
219	of	of	IN	_	_	_
220	0.5	0.5	CD	_	_	_
221	mM	mm	NN	KWSUPP	_	_
222	IPTG	iptg	NN	_	_	_
223	for	for	IN	_	_	_
224	an	a	DT	_	_	_
225	hour	hour	NN	_	_	_
226	before	before	IN	_	_	_
227	formadehyde	formadehyde	NN	_	_	_
228	to	to	TO	_	_	_
229	1	1	CD	_	_	_
230	%	%	NN	_	_	_
231	-LRB-	-lrb-	-LRB-	_	_	_
232	final	final	JJ	_	_	_
233	concentration	concentration	NN	_	_	_
234	-RRB-	-rrb-	-RRB-	_	_	_
235	was	be	VBD	_	_	_
236	added	add	VBN	_	_	_
237	to	to	TO	_	_	_
238	fix	fix	VB	_	_	_
239	cells	cell	NNS	_	_	_
240	for	for	IN	_	_	_
241	ChIP-seq	ChIP-seq	NNP	_	_	_
242	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
243	T24	t24	NN	_	_	_
244	_	_	CD	_	_	_
245	N0000	n0000	NN	_	_	_
246	_	_	CD	_	_	_
247	r1	r1	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	T24	t24	NN	_	_	_
250	_	_	CD	_	_	_
251	N0000	n0000	NN	_	_	_
252	_	_	CD	_	_	_
253	r2	r2	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	T24	t24	NN	_	_	_
256	_	_	CD	_	_	_
257	N0000	n0000	NN	_	_	_
258	_	_	CD	_	_	_
259	r3	r3	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	T24	t24	NN	_	_	_
262	_	_	SYM	_	_	_
263	N0025	n0025	CD	_	_	_
264	_	_	CD	_	_	_
265	r1	r1	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	T24	t24	NN	_	_	_
268	_	_	SYM	_	_	_
269	N0025	n0025	CD	_	_	_
270	_	_	CD	_	_	_
271	r2	r2	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	T24	t24	NN	_	_	_
274	_	_	SYM	_	_	_
275	N0025	n0025	CD	_	_	_
276	_	_	CD	_	_	_
277	r3	r3	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	T24	t24	NN	_	_	_
280	THP-1	thp-1	NN	_	_	_
281	infection	infection	NN	_	_	_
282	,	,	,	_	_	_
283	Microarray	Microarray	NNP	_	_	_
284	#	#	#	_	_	_
285	1	1	CD	_	_	_
286	first	first	JJ	_	_	_
287	replicate	replicate	VB	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	T24	t24	NN	_	_	_
290	THP-1	thp-1	NN	_	_	_
291	infection	infection	NN	_	_	_
292	,	,	,	_	_	_
293	Microarray	Microarray	NNP	_	_	_
294	#	#	#	_	_	_
295	1	1	CD	_	_	_
296	second	second	JJ	_	_	_
297	replicate	replicate	VBP	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	T24	t24	NN	_	_	_
300	THP-1	thp-1	NN	_	_	_
301	infection	infection	NN	_	_	_
302	,	,	,	_	_	_
303	Microarray	Microarray	NNP	_	_	_
304	#	#	#	_	_	_
305	2	2	CD	_	_	_
306	first	first	JJ	_	_	_
307	replicate	replicate	VB	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	T24	t24	NN	_	_	_
310	THP-1	thp-1	NN	_	_	_
311	infection	infection	NN	_	_	_
312	,	,	,	_	_	_
313	Microarray	Microarray	NNP	_	_	_
314	#	#	#	_	_	_
315	2	2	CD	_	_	_
316	second	second	JJ	_	_	_
317	replicate	replicate	VBP	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	T2	t2	NN	_	_	_
320	THP-1	thp-1	NN	_	_	_
321	infection	infection	NN	_	_	_
322	,	,	,	_	_	_
323	Microarray	Microarray	NNP	_	_	_
324	#	#	#	_	_	_
325	1	1	CD	_	_	_
326	first	first	RB	_	_	_
327	replicate	replicate	VB	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	T2	t2	NN	_	_	_
330	THP-1	thp-1	NN	_	_	_
331	infection	infection	NN	_	_	_
332	,	,	,	_	_	_
333	Microarray	Microarray	NNP	_	_	_
334	#	#	#	_	_	_
335	1	1	CD	_	_	_
336	second	second	JJ	_	_	_
337	replicate	replicate	VBP	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	T2	t2	NN	_	_	_
340	THP-1	thp-1	NN	_	_	_
341	infection	infection	NN	_	_	_
342	,	,	,	_	_	_
343	Microarray	Microarray	NNP	_	_	_
344	#	#	#	_	_	_
345	2	2	CD	_	_	_
346	first	first	JJ	_	_	_
347	replicate	replicate	VB	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	T2	t2	NN	_	_	_
350	THP-1	thp-1	NN	_	_	_
351	infection	infection	NN	_	_	_
352	,	,	,	_	_	_
353	Microarray	Microarray	NNP	_	_	_
354	#	#	#	_	_	_
355	2	2	CD	_	_	_
356	second	second	JJ	_	_	_
357	replicate	replicate	VB	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	T36	t36	NN	_	_	_
360	_	_	SYM	_	_	_
361	N0025	n0025	CD	_	_	_
362	_	_	CD	_	_	_
363	r1	r1	NN	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	T36	t36	NN	_	_	_
366	_	_	SYM	_	_	_
367	N0025	n0025	CD	_	_	_
368	_	_	SYM	_	_	_
369	r2	r2	FW	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
371	T36	t36	FW	_	_	_
372	_	_	SYM	_	_	_
373	N0025	n0025	CD	_	_	_
374	_	_	CD	_	_	_
375	r3	r3	NN	_	_	_
376	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
377	T48	t48	NN	_	_	_
378	_	_	SYM	_	_	_
379	N0025	n0025	CD	_	_	_
380	_	_	CD	_	_	_
381	r1	r1	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	T48	t48	NN	_	_	_
384	_	_	SYM	_	_	_
385	N0025	n0025	CD	_	_	_
386	_	_	CD	_	_	_
387	r2	r2	NN	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	T48	t48	NN	_	_	_
390	_	_	SYM	_	_	_
391	N0025	n0025	CD	_	_	_
392	_	_	CD	_	_	_
393	r3	r3	NN	_	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
395	T5	t5	NN	_	_	_
396	_	_	CD	_	_	_
397	1x	1x	NN	_	_	_
398	_	_	NN	_	_	_
399	4	4	CD	_	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	T5	t5	NN	_	_	_
402	_	_	CD	_	_	_
403	27x	27x	CD	_	_	_
404	_	_	NN	_	_	_
405	1	1	CD	_	_	_
406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
407	T60	t60	NN	_	_	_
408	_	_	CD	_	_	_
409	N0000	n0000	NN	_	_	_
410	_	_	CD	_	_	_
411	r1	r1	NN	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	T60	t60	NN	_	_	_
414	_	_	CD	_	_	_
415	N0000	n0000	NN	_	_	_
416	_	_	CD	_	_	_
417	r2	r2	NN	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	T60	t60	NN	_	_	_
420	_	_	CD	_	_	_
421	N0000	n0000	NN	_	_	_
422	_	_	CD	_	_	_
423	r3	r3	NN	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	T60	t60	NN	_	_	_
426	_	_	SYM	_	_	_
427	N0025	n0025	CD	_	_	_
428	_	_	CD	_	_	_
429	r1	r1	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	T60	t60	NN	_	_	_
432	_	_	SYM	_	_	_
433	N0025	n0025	CD	_	_	_
434	_	_	CD	_	_	_
435	r2	r2	NN	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	T60	t60	NN	_	_	_
438	_	_	SYM	_	_	_
439	N0025	n0025	CD	_	_	_
440	_	_	CD	_	_	_
441	r3	r3	NN	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	t7	t7	NN	_	_	_
444	genotype	genotype	NN	_	_	_
445	:	:	:	_	_	_
446	evolved	evolve	VBD	_	_	_
447	,	,	,	_	_	_
448	codon-deoptimized	codon-deoptimized	JJ	_	_	_
449	gene	gene	NN	_	_	_
450	10	10	CD	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	t7	t7	NN	_	_	_
453	genotype	genotype	NN	_	_	_
454	:	:	:	_	_	_
455	wild-type	wild-type	JJ	_	_	_
456	gene	gene	NN	_	_	_
457	10	10	CD	_	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	t7	t7	NN	_	_	_
460	strain	strain	NN	_	_	_
461	:	:	:	_	_	_
462	evolved	evolve	VBD	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	t7	t7	NN	_	_	_
465	strain	strain	NN	_	_	_
466	:	:	:	_	_	_
467	wild	wild	JJ	_	_	_
468	type	type	NN	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
470	T8	t8	NN	_	_	_
471	THP-1	thp-1	NN	_	_	_
472	infection	infection	NN	_	_	_
473	,	,	,	_	_	_
474	Microarray	Microarray	NNP	_	_	_
475	#	#	#	_	_	_
476	1	1	CD	_	_	_
477	first	first	RB	_	_	_
478	replicate	replicate	VB	_	_	_
479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
480	T8	t8	NN	_	_	_
481	THP-1	thp-1	NN	_	_	_
482	infection	infection	NN	_	_	_
483	,	,	,	_	_	_
484	Microarray	Microarray	NNP	_	_	_
485	#	#	#	_	_	_
486	1	1	CD	_	_	_
487	second	second	JJ	_	_	_
488	replicate	replicate	VBP	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	T8	t8	NN	_	_	_
491	THP-1	thp-1	NN	_	_	_
492	infection	infection	NN	_	_	_
493	,	,	,	_	_	_
494	Microarray	Microarray	NNP	_	_	_
495	#	#	#	_	_	_
496	2	2	CD	_	_	_
497	first	first	JJ	_	_	_
498	replicate	replicate	VB	_	_	_
499	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
500	T8	t8	NN	_	_	_
501	THP-1	thp-1	NN	_	_	_
502	infection	infection	NN	_	_	_
503	,	,	,	_	_	_
504	Microarray	Microarray	NNP	_	_	_
505	#	#	#	_	_	_
506	2	2	CD	_	_	_
507	second	second	JJ	_	_	_
508	replicate	replicate	VBP	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	tab-delimited	tab-delimited	JJ	_	_	_
511	text	text	NN	_	_	_
512	files	file	NNS	_	_	_
513	with	with	IN	_	_	_
514	GCSs	gcss	NNS	_	_	_
515	coordinates	coordinate	VBZ	_	_	_
516	,	,	,	_	_	_
517	N3E	n3e	NN	_	_	_
518	values	value	NNS	_	_	_
519	-LRB-	-lrb-	-LRB-	_	_	_
520	\	\	CD	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
522	tagged	tag	VBD	_	_	_
523	gyrase	gyrase	NN	_	_	_
524	subunit	subunit	NN	_	_	_
525	:	:	:	_	_	_
526	GyrA-SPA	gyra-spa	JJ	_	_	_
527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
528	tag	tag	NN	GEN	_	_
529	:	:	:	_	_	_
530	MG1655	mg1655	NN	_	_	_
531	K-12	k-12	NN	_	_	_
532	WT	wt	JJ	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	Tagwise	tagwise	JJ	_	_	_
535	dispersion	dispersion	NN	_	_	_
536	was	be	VBD	_	_	_
537	estimated	estimate	VBN	_	_	_
538	using	use	VBG	_	_	_
539	the	the	DT	_	_	_
540	weighted	weighted	JJ	_	_	_
541	likelihood	likelihood	NN	_	_	_
542	empirical	empirical	JJ	_	_	_
543	Bayes	baye	NNS	_	_	_
544	method	method	NN	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	technical	technical	JJ	_	_	_
547	replicate	replicate	VB	_	_	_
548	:	:	:	_	_	_
549	1	1	CD	_	_	_
550	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
551	technical	technical	JJ	_	_	_
552	replicate	replicate	VB	_	_	_
553	:	:	:	_	_	_
554	2	2	CD	_	_	_
555	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
556	technical	technical	JJ	_	_	_
557	replicates	replicate	VBZ	_	_	_
558	:	:	:	_	_	_
559	2	2	CD	_	_	_
560	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
561	temp	temp	NN	_	_	_
562	:	:	:	_	_	_
563	37ºC	37ºc	NN	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	temperature	temperature	NN	_	_	_
566	:	:	:	_	_	_
567	10	10	CD	_	_	_
568	°C	°c	NN	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	temperature	temperature	NN	_	_	_
571	:	:	:	_	_	_
572	37	37	CD	_	_	_
573	°C	°c	NN	_	_	_
574	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
575	temperature	temperature	NN	_	_	_
576	_	_	CD	_	_	_
577	down	down	IN	_	_	_
578	_	_	CD	_	_	_
579	0	0	CD	_	_	_
580	min	min	NN	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	temperature	temperature	NN	_	_	_
583	_	_	CD	_	_	_
584	down	down	IN	_	_	_
585	_	_	CD	_	_	_
586	12	12	CD	_	_	_
587	min	min	NN	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
589	temperature	temperature	NN	_	_	_
590	_	_	CD	_	_	_
591	down	down	IN	_	_	_
592	_	_	CD	_	_	_
593	20	20	CD	_	_	_
594	min	min	NN	_	_	_
595	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
596	temperature	temperature	NN	_	_	_
597	_	_	CD	_	_	_
598	down	down	IN	_	_	_
599	_	_	CD	_	_	_
600	28	28	CD	_	_	_
601	min	min	NN	_	_	_
602	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
603	temperature	temperature	NN	_	_	_
604	_	_	CD	_	_	_
605	down	down	IN	_	_	_
606	_	_	CD	_	_	_
607	44	44	CD	_	_	_
608	min	min	NN	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	temperature	temperature	NN	_	_	_
611	_	_	CD	_	_	_
612	down	down	IN	_	_	_
613	_	_	CD	_	_	_
614	4	4	CD	_	_	_
615	min	min	NN	_	_	_
616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
617	temperature	temperature	NN	_	_	_
618	_	_	CD	_	_	_
619	down	down	IN	_	_	_
620	_	_	CD	_	_	_
621	8	8	CD	_	_	_
622	min	min	NN	_	_	_
623	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
624	temperature	temperature	NN	_	_	_
625	down	down	IN	_	_	_
626	shift	shift	NN	_	_	_
627	,	,	,	_	_	_
628	0	0	CD	_	_	_
629	min	min	NN	_	_	_
630	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
631	temperature	temperature	NN	_	_	_
632	down	down	IN	_	_	_
633	shift	shift	NN	_	_	_
634	,	,	,	_	_	_
635	12	12	CD	_	_	_
636	min	min	NN	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
638	temperature	temperature	NN	_	_	_
639	down	down	IN	_	_	_
640	shift	shift	NN	_	_	_
641	,	,	,	_	_	_
642	20	20	CD	_	_	_
643	min	min	NN	_	_	_
644	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
645	temperature	temperature	NN	_	_	_
646	down	down	IN	_	_	_
647	shift	shift	NN	_	_	_
648	,	,	,	_	_	_
649	28	28	CD	_	_	_
650	min	min	NN	_	_	_
651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
652	temperature	temperature	NN	_	_	_
653	down	down	IN	_	_	_
654	shift	shift	NN	_	_	_
655	,	,	,	_	_	_
656	44	44	CD	_	_	_
657	min	min	NN	_	_	_
658	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
659	temperature	temperature	NN	_	_	_
660	down	down	IN	_	_	_
661	shift	shift	NN	_	_	_
662	,	,	,	_	_	_
663	4	4	CD	_	_	_
664	min	min	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	temperature	temperature	NN	_	_	_
667	down	down	IN	_	_	_
668	shift	shift	NN	_	_	_
669	,	,	,	_	_	_
670	8	8	CD	_	_	_
671	min	min	NN	_	_	_
672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
673	temperature	temperature	NN	_	_	_
674	_	_	CD	_	_	_
675	Up	up	IN	_	_	_
676	_	_	CD	_	_	_
677	0	0	CD	_	_	_
678	min	min	NN	_	_	_
679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
680	temperature	temperature	NN	_	_	_
681	_	_	VBD	_	_	_
682	Up	up	RP	_	_	_
683	_	_	SYM	_	_	_
684	12	12	CD	_	_	_
685	min	min	NN	_	_	_
686	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
687	temperature	temperature	NN	_	_	_
688	_	_	VBD	_	_	_
689	Up	up	RP	_	_	_
690	_	_	SYM	_	_	_
691	20	20	CD	_	_	_
692	min	min	NN	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	temperature	temperature	NN	_	_	_
695	_	_	VBD	_	_	_
696	Up	up	RP	_	_	_
697	_	_	SYM	_	_	_
698	28	28	CD	_	_	_
699	min	min	NN	_	_	_
700	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
701	temperature	temperature	NN	_	_	_
702	_	_	VBD	_	_	_
703	Up	up	RP	_	_	_
704	_	_	SYM	_	_	_
705	44	44	CD	_	_	_
706	min	min	NN	_	_	_
707	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
708	temperature	temperature	NN	_	_	_
709	_	_	VBD	_	_	_
710	Up	up	RP	_	_	_
711	_	_	SYM	_	_	_
712	4	4	CD	_	_	_
713	min	min	NN	_	_	_
714	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
715	temperature	temperature	NN	_	_	_
716	_	_	VBD	_	_	_
717	Up	up	RP	_	_	_
718	_	_	SYM	_	_	_
719	8	8	CD	_	_	_
720	min	min	NN	_	_	_
721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
722	temperature	temperature	NN	_	_	_
723	up	up	IN	_	_	_
724	shift	shift	NN	_	_	_
725	,	,	,	_	_	_
726	0	0	CD	_	_	_
727	min	min	NN	_	_	_
728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
729	temperature	temperature	NN	_	_	_
730	up	up	IN	_	_	_
731	shift	shift	NN	_	_	_
732	,	,	,	_	_	_
733	12	12	CD	_	_	_
734	min	min	NN	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
736	temperature	temperature	NN	_	_	_
737	up	up	IN	_	_	_
738	shift	shift	NN	_	_	_
739	,	,	,	_	_	_
740	20	20	CD	_	_	_
741	min	min	NN	_	_	_
742	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
743	temperature	temperature	NN	_	_	_
744	up	up	IN	_	_	_
745	shift	shift	NN	_	_	_
746	,	,	,	_	_	_
747	28	28	CD	_	_	_
748	min	min	NN	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
750	temperature	temperature	NN	_	_	_
751	up	up	IN	_	_	_
752	shift	shift	NN	_	_	_
753	,	,	,	_	_	_
754	44	44	CD	_	_	_
755	min	min	NN	_	_	_
756	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
757	temperature	temperature	NN	_	_	_
758	up	up	IN	_	_	_
759	shift	shift	NN	_	_	_
760	,	,	,	_	_	_
761	4	4	CD	_	_	_
762	min	min	NN	_	_	_
763	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
764	temperature	temperature	NN	_	_	_
765	up	up	IN	_	_	_
766	shift	shift	NN	_	_	_
767	,	,	,	_	_	_
768	8	8	CD	_	_	_
769	min	min	NN	_	_	_
770	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
771	test	test	NN	_	_	_
772	:	:	:	_	_	_
773	ChIP	chip	NN	_	_	_
774	DNA	dna	NN	_	_	_
775	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
776	test	test	NN	_	_	_
777	:	:	:	_	_	_
778	E.	e.	FW	_	_	_
779	coli	coli	FW	_	_	_
780	TOP10	top10	NN	_	_	_
781	containing	contain	VBG	_	_	_
782	pBAD18	pbad18	NN	_	_	_
783	vector	vector	NN	_	_	_
784	exposed	expose	VBN	_	_	_
785	to	to	TO	_	_	_
786	arabinose	arabinose	VB	_	_	_
787	inducer	inducer	NN	_	_	_
788	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
789	TEX	tex	SYM	_	_	_
790	-	-	:	_	_	_
791	_	_	SYM	_	_	_
792	E.	e.	FW	_	_	_
793	coli	coli	FW	_	_	_
794	O104	o104	NN	_	_	_
795	:	:	:	_	_	_
796	H4	h4	NN	_	_	_
797	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
798	TEX	tex	NN	_	_	_
799	+	+	CC	_	_	_
800	_	_	SYM	_	_	_
801	E.	e.	FW	_	_	_
802	coli	coli	FW	_	_	_
803	O104	o104	NN	_	_	_
804	:	:	:	_	_	_
805	H4	h4	NN	_	_	_
806	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
807	text	text	NN	_	_	_
808	wig	wig	NN	_	_	_
809	files	file	NNS	_	_	_
810	contain	contain	VBP	_	_	_
811	coverage	coverage	NN	_	_	_
812	depth	depth	NN	_	_	_
813	data	datum	NNS	_	_	_
814	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
815	text	text	NN	_	_	_
816	wig	wig	NN	_	_	_
817	files	file	NNS	_	_	_
818	contain	contain	VBP	_	_	_
819	N3E	n3e	NN	_	_	_
820	values	value	NNS	_	_	_
821	-LRB-	-lrb-	-LRB-	_	_	_
822	number	number	NN	_	_	_
823	of	of	IN	_	_	_
824	DNA	dna	NN	_	_	_
825	fragments	fragment	NNS	_	_	_
826	3	3	CD	_	_	_
827	'	'	''	_	_	_
828	ends	end	VBZ	_	_	_
829	for	for	IN	_	_	_
830	each	each	DT	_	_	_
831	position	position	NN	_	_	_
832	of	of	IN	_	_	_
833	the	the	DT	_	_	_
834	genome	genome	NN	_	_	_
835	-RRB-	-rrb-	-RRB-	_	_	_
836	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
837	TG1/pBS	tg1/pbs	NN	_	_	_
838	-LRB-	-lrb-	-LRB-	_	_	_
839	Kan	Kan	NNP	_	_	_
840	-RRB-	-rrb-	-RRB-	_	_	_
841	/	/	:	_	_	_
842	pMMB277	pmmb277	NN	_	_	_
843	2nd	2nd	JJ	_	_	_
844	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
845	TG1/pBS	tg1/pbs	NN	_	_	_
846	-LRB-	-lrb-	-LRB-	_	_	_
847	Kan	Kan	NNP	_	_	_
848	-RRB-	-rrb-	-RRB-	_	_	_
849	/	/	:	_	_	_
850	pMMB277	pmmb277	NN	_	_	_
851	,	,	,	_	_	_
852	cis-DCE	cis-dce	JJ	_	_	_
853	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
854	TG1/pBS	tg1/pbs	NN	_	_	_
855	-LRB-	-lrb-	-LRB-	_	_	_
856	Kan	Kan	NNP	_	_	_
857	-RRB-	-rrb-	-RRB-	_	_	_
858	-	-	:	_	_	_
859	TOM-Green/pMMB277-IsoILR	tom-green/pmmb277-isoilr	NN	_	_	_
860	1-GSHI	1-gshi	NN	_	_	_
861	2nd	2nd	JJ	_	_	_
862	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
863	TG1/pBS	tg1/pbs	NN	_	_	_
864	-LRB-	-lrb-	-LRB-	_	_	_
865	Kan	Kan	NNP	_	_	_
866	-RRB-	-rrb-	-RRB-	_	_	_
867	-	-	:	_	_	_
868	TOM-Green/pMMB277-IsoILR	tom-green/pmmb277-isoilr	NN	_	_	_
869	1-GSHI	1-gshi	NN	_	_	_
870	,	,	,	_	_	_
871	cis-DCE	cis-dce	JJ	_	_	_
872	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
873	TG1	tg1	NN	_	_	_
874	/	/	:	_	_	_
875	pMMB206-TOM-Green/pBS	pmmb206-tom-green/pbs	NN	_	_	_
876	-LRB-	-lrb-	-LRB-	_	_	_
877	Kan	Kan	NNP	_	_	_
878	-RRB-	-rrb-	-RRB-	_	_	_
879	,	,	,	_	_	_
880	cis-DCE	cis-dce	JJ	_	_	_
881	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
882	TG1/pMMB206-TOM-Green/pBS	tg1/pmmb206-tom-green/pbs	NN	_	_	_
883	-LRB-	-lrb-	-LRB-	_	_	_
884	Kan	Kan	NNP	_	_	_
885	-RRB-	-rrb-	-RRB-	_	_	_
886	-	-	:	_	_	_
887	EchA	echa	NN	_	_	_
888	F108L/I219L/C248I	f108l/i219l/c248i	NN	_	_	_
889	,	,	,	_	_	_
890	cis-DCE	cis-dce	JJ	_	_	_
891	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
892	than	than	IN	_	_	_
893	or	or	CC	_	_	_
894	equal	equal	JJ	_	_	_
895	to	to	TO	_	_	_
896	the	the	DT	_	_	_
897	intensity	intensity	NN	_	_	_
898	of	of	IN	_	_	_
899	the	the	DT	_	_	_
900	foreground	foreground	NN	_	_	_
901	,	,	,	_	_	_
902	the	the	DT	_	_	_
903	resulting	result	VBG	_	_	_
904	log	log	NN	_	_	_
905	ratios	ratio	NNS	_	_	_
906	became	become	VBD	_	_	_
907	complex	complex	JJ	_	_	_
908	or	or	CC	_	_	_
909	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
910	The	the	DT	_	_	_
911	200	200	CD	_	_	_
912	ml	ml	NN	_	_	_
913	eluate	eluate	NN	_	_	_
914	from	from	IN	_	_	_
915	the	the	DT	_	_	_
916	Ni-NTA	ni-nta	NN	_	_	_
917	agarose	agarose	NN	_	_	_
918	was	be	VBD	_	_	_
919	mixed	mix	VBN	_	_	_
920	with	with	IN	_	_	_
921	equal	equal	JJ	_	_	_
922	volume	volume	NN	_	_	_
923	of	of	IN	_	_	_
924	pre-warmed	pre-warmed	JJ	_	_	_
925	PCI	pci	NN	_	_	_
926	and	and	CC	_	_	_
927	incubated	incubate	VBN	_	_	_
928	for	for	IN	_	_	_
929	2	2	CD	_	_	_
930	min	min	NN	_	_	_
931	at	at	IN	_	_	_
932	70	70	CD	_	_	_
933	˚C	˚c	NN	_	_	_
934	.	.	.	_	_	_

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	aligned	align	VBN	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	converted	convert	VBN	_	_	_
7	to	to	TO	_	_	_
8	BAM	BAM	NNP	_	_	_
9	files	file	NNS	_	_	_
10	and	and	CC	_	_	_
11	sorted	sort	VBN	_	_	_
12	and	and	CC	_	_	_
13	indexed	index	VBN	_	_	_
14	using	use	VBG	_	_	_
15	SAMtools	samtool	NNS	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	The	the	DT	_	_	_
18	.	.	.	_	_	_

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	alignment	alignment	NN	_	_	_
4	Bam	bam	UH	_	_	_
5	files	file	NNS	_	_	_
6	were	be	VBD	_	_	_
7	compared	compare	VBN	_	_	_
8	against	against	IN	_	_	_
9	the	the	DT	_	_	_
10	gene	gene	NN	_	_	_
11	annotation	annotation	NN	_	_	_
12	general	general	JJ	_	_	_
13	feature	feature	NN	_	_	_
14	format	format	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	GFF	gff	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	file	file	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	raw	raw	JJ	_	_	_
22	counts	count	NNS	_	_	_
23	for	for	IN	_	_	_
24	each	each	DT	_	_	_
25	gene	gene	NN	_	_	_
26	were	be	VBD	_	_	_
27	generated	generate	VBN	_	_	_
28	using	use	VBG	_	_	_
29	the	the	DT	_	_	_
30	featureCounts	featureCounts	NNPS	_	_	_
31	tool	tool	NN	_	_	_
32	from	from	IN	_	_	_
33	Subread	Subread	NNP	_	_	_
34	.	.	.	_	_	_

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://www.ncbi.nlm.nih.gov/pubmed/20196867	http://www.ncbi.nlm.nih.gov/pubmed/20196867	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	from	from	IN	_	_	_
29	the	the	DT	_	_	_
30	Empirical	empirical	JJ	_	_	_
31	analysis	analysis	NN	_	_	_
32	of	of	IN	_	_	_
33	Digital	Digital	NNP	_	_	_
34	Gene	Gene	NNP	_	_	_
35	Expression	expression	NN	_	_	_
36	Data	datum	NNS	_	_	_
37	in	in	IN	_	_	_
38	R	r	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	EdgeR	edger	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	package	package	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	https://bioconductor.org/packages/release/bioc/html/edgeR.html	https://bioconductor.org/packages/release/bioc/html/edger.html	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	,	,	,	_	_	_
47	then	then	RB	_	_	_
48	transformed	transform	VBN	_	_	_
49	to	to	TO	_	_	_
50	log2CPM	log2cpm	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	counts	count	NNS	_	_	_
53	per	per	IN	_	_	_
54	million	million	CD	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	values	value	NNS	_	_	_
57	using	use	VBG	_	_	_
58	the	the	DT	_	_	_
59	voom	voom	NN	_	_	_
60	method	method	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	http://www.ncbi.nlm.nih.gov/pubmed/24485249	http://www.ncbi.nlm.nih.gov/pubmed/24485249	NN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	from	from	IN	_	_	_
65	the	the	DT	_	_	_
66	R	r	NN	_	_	_
67	LIMMA	limma	NN	_	_	_
68	package	package	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	https://bioconductor.org/packages/release/bioc/html/limma.html	https://bioconductor.org/packages/release/bioc/html/limma.html	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	amplified	amplify	VBN	_	_	_
4	cDNA	cdna	NN	_	_	_
5	libraries	library	NNS	_	_	_
6	from	from	IN	_	_	_
7	two	two	CD	_	_	_
8	biological	biological	JJ	_	_	_
9	replicates	replicate	VBZ	_	_	_
10	for	for	IN	_	_	_
11	each	each	DT	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	were	be	VBD	_	_	_
15	sequenced	sequence	VBN	_	_	_
16	on	on	IN	_	_	_
17	an	a	DT	_	_	_
18	Illumina	Illumina	NNP	_	_	_
19	Genome	Genome	NNP	_	_	_
20	Analyzer	Analyzer	NNP	_	_	_
21	.	.	.	_	_	_

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	analysis	analysis	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	data	datum	NNS	_	_	_
7	is	be	VBZ	_	_	_
8	based	base	VBN	_	_	_
9	on	on	IN	_	_	_
10	cross	cross	NN	_	_	_
11	validation	validation	NN	_	_	_
12	with	with	IN	_	_	_
13	datasets	dataset	NNS	_	_	_
14	generated	generate	VBN	_	_	_
15	by	by	IN	_	_	_
16	Monte-Carlo	Monte-Carlo	NNP	_	_	_
17	simulation	simulation	NN	_	_	_
18	.	.	.	_	_	_

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	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://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/arraytrack_webaccess.htm	http://www.fda.gov/nctr/science/centers/toxicoinformatics/arraytrack/arraytrack_webaccess.htm	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

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	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	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	appropriate	appropriate	JJ	_	_	_
4	protocols	protocol	NNS	_	_	_
5	were	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	standard	standard	JJ	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	procedures	procedure	NNS	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	The	the	DT	_	_	_
13	average	average	JJ	_	_	_
14	fluorescence	fluorescence	NN	_	_	_
15	intensity	intensity	NN	_	_	_
16	for	for	IN	_	_	_
17	each	each	DT	_	_	_
18	spot	spot	NN	_	_	_
19	was	be	VBD	_	_	_
20	calculated	calculate	VBN	_	_	_
21	and	and	CC	_	_	_
22	local	local	JJ	_	_	_
23	background	background	NN	_	_	_
24	was	be	VBD	_	_	_
25	subtracted	subtract	VBN	_	_	_
26	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	average	average	JJ	_	_	_
4	fluorescent	fluorescent	JJ	_	_	_
5	signal	signal	NN	_	_	_
6	intensity	intensity	NN	_	_	_
7	and	and	CC	_	_	_
8	local	local	JJ	_	_	_
9	background	background	NN	_	_	_
10	correction	correction	NN	_	_	_
11	for	for	IN	_	_	_
12	each	each	DT	_	_	_
13	spot	spot	NN	_	_	_
14	were	be	VBD	_	_	_
15	obtained	obtain	VBN	_	_	_
16	using	use	VBG	_	_	_
17	commercially	commercially	RB	_	_	_
18	available	available	JJ	_	_	_
19	software	software	NN	_	_	_
20	from	from	IN	_	_	_
21	Biodiscovery	Biodiscovery	NNP	_	_	_
22	Inc	Inc	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Imagene	Imagene	NNP	_	_	_
25	,	,	,	_	_	_
26	version	version	NN	_	_	_
27	4.0	4.0	CD	_	_	_
28	and	and	CC	_	_	_
29	Genesight	Genesight	NNP	_	_	_
30	,	,	,	_	_	_
31	version	version	NN	_	_	_
32	3.5	3.5	CD	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

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/Cy5	cy3/cy5	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	or	or	CC	_	_	_
5	,	,	,	_	_	_
6	for	for	IN	_	_	_
7	replicates	replicate	VBZ	_	_	_
8	3	3	CD	_	_	_
9	and	and	CC	_	_	_
10	4	4	CD	_	_	_
11	,	,	,	_	_	_
12	Cy3/Cy3	cy3/cy3	NN	_	_	_
13	ratio	ratio	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	fluorescent	fluorescent	JJ	_	_	_
16	ratios	ratio	NNS	_	_	_
17	were	be	VBD	_	_	_
18	calculated	calculated	JJ	_	_	_
19	form	form	NN	_	_	_
20	the	the	DT	_	_	_
21	normalised	normalised	JJ	_	_	_
22	values	value	NNS	_	_	_
23	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	from	from	IN	_	_	_
3	independent	independent	JJ	_	_	_
4	experiments	experiment	NNS	_	_	_
5	were	be	VBD	_	_	_
6	combined	combine	VBN	_	_	_
7	.	.	.	_	_	_

1	Significance	significance	NN	_	_	_
2	analysis	analysis	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	data	datum	NNS	_	_	_
6	used	use	VBD	_	_	_
7	the	the	DT	_	_	_
8	Student	student	NN	_	_	_
9	's	's	POS	_	_	_
10	t	t	NN	_	_	_
11	test	test	NN	_	_	_
12	to	to	TO	_	_	_
13	determine	determine	VB	_	_	_
14	the	the	DT	_	_	_
15	probability	probability	NN	_	_	_
16	that	that	IN	_	_	_
17	the	the	DT	_	_	_
18	average	average	NN	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	experimental	experimental	JJ	_	_	_
22	replicates	replicate	VBZ	_	_	_
23	was	be	VBD	_	_	_
24	significantly	significantly	RB	_	_	_
25	different	different	JJ	_	_	_
26	from	from	IN	_	_	_
27	the	the	DT	_	_	_
28	average	average	NN	_	_	_
29	of	of	IN	_	_	_
30	the	the	DT	_	_	_
31	control	control	NN	_	_	_
32	replicates	replicate	VBZ	_	_	_
33	.	.	.	_	_	_

1	p-values	p-value	NNS	_	_	_
2	for	for	IN	_	_	_
3	the	the	DT	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	calculated	calculate	VBN	_	_	_
7	by	by	IN	_	_	_
8	treating	treat	VBG	_	_	_
9	each	each	DT	_	_	_
10	slide	slide	NN	_	_	_
11	as	as	IN	_	_	_
12	a	a	DT	_	_	_
13	repeat	repeat	NN	_	_	_
14	using	use	VBG	_	_	_
15	Genesight	Genesight	NNP	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	average	average	JJ	_	_	_
4	signal	signal	NN	_	_	_
5	intensity	intensity	NN	_	_	_
6	and	and	CC	_	_	_
7	local	local	JJ	_	_	_
8	background	background	NN	_	_	_
9	correction	correction	NN	_	_	_
10	were	be	VBD	_	_	_
11	obtained	obtain	VBN	_	_	_
12	using	use	VBG	_	_	_
13	a	a	DT	_	_	_
14	commercially	commercially	RB	_	_	_
15	available	available	JJ	_	_	_
16	software	software	NN	_	_	_
17	package	package	NN	_	_	_
18	from	from	IN	_	_	_
19	Biodiscovery	Biodiscovery	NNP	_	_	_
20	,	,	,	_	_	_
21	Inc	Inc	NNP	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Imagene	Imagene	NNP	_	_	_
24	,	,	,	_	_	_
25	version	version	NN	_	_	_
26	4.0	4.0	CD	_	_	_
27	and	and	CC	_	_	_
28	GeneSight	GeneSight	NNP	_	_	_
29	,	,	,	_	_	_
30	version	version	NN	_	_	_
31	3.5	3.5	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

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	bacterial	bacterial	JJ	_	_	_
4	cells	cell	NNS	_	_	_
5	were	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	℃	℃	NN	_	_	_
10	for	for	IN	_	_	_
11	17	17	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	on	on	IN	_	_	_
14	Luria-Bertani	Luria-Bertani	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	LB	LB	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	agar	agar	NN	_	_	_
19	plate	plate	NN	_	_	_
20	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	bacterial	bacterial	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	pellets	pellet	NNS	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	according	accord	VBG	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	instructions	instruction	NNS	_	_	_
12	from	from	IN	_	_	_
13	ATCC	atcc	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	centrifuged	centrifuge	VBN	_	_	_
6	at	at	IN	_	_	_
7	4000	4000	CD	_	_	_
8	×	×	CD	_	_	_
9	g	g	NN	_	_	_
10	at	at	IN	_	_	_
11	4	4	CD	_	_	_
12	°C	°c	NN	_	_	_
13	for	for	IN	_	_	_
14	5	5	CD	_	_	_
15	min	min	NN	_	_	_
16	and	and	CC	_	_	_
17	then	then	RB	_	_	_
18	washed	wash	VBN	_	_	_
19	with	with	IN	_	_	_
20	PBS	PBS	NNP	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	routinely	routinely	RB	_	_	_
6	grown	grow	VBN	_	_	_
7	in	in	IN	_	_	_
8	Luria-Bertani	Luria-Bertani	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	LB	LB	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	broth	broth	NN	_	_	_
13	or	or	CC	_	_	_
14	on	on	IN	_	_	_
15	LB	LB	NNP	_	_	_
16	agar	agar	NN	_	_	_
17	plates	plate	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	pH	ph	NN	_	_	_
20	7.2	7.2	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	bcl2fastq	bcl2fastq	NN	_	_	_
4	Conversion	conversion	NN	_	_	_
5	Software	Software	NNP	_	_	_
6	v.	v.	CC	_	_	_
7	1.8.4	1.8.4	CD	_	_	_
8	from	from	IN	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	http://support.illumina.com/downloads.html	http://support.illumina.com/downloads.html	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	was	be	VBD	_	_	_
14	used	use	VBN	_	_	_
15	to	to	TO	_	_	_
16	translate	translate	VB	_	_	_
17	cluster	cluster	NN	_	_	_
18	intensity	intensity	NN	_	_	_
19	values	value	NNS	_	_	_
20	into	into	IN	_	_	_
21	fastq	fastq	NN	_	_	_
22	files	file	NNS	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	binding	binding	NN	_	_	_
4	regions	region	NNS	_	_	_
5	were	be	VBD	_	_	_
6	considered	consider	VBN	_	_	_
7	by	by	IN	_	_	_
8	taking	take	VBG	_	_	_
9	into	into	IN	_	_	_
10	account	account	NN	_	_	_
11	base	base	NN	_	_	_
12	position	position	NN	_	_	_
13	with	with	IN	_	_	_
14	z-score	z-score	NN	_	_	_
15	greater	greater	JJR	_	_	_
16	than	than	IN	_	_	_
17	threshold	threshold	NN	_	_	_
18	and	and	CC	_	_	_
19	merging	merge	VBG	_	_	_
20	adjacent	adjacent	JJ	_	_	_
21	binding	binding	NN	_	_	_
22	regions	region	NNS	_	_	_
23	seperated	seperate	VBN	_	_	_
24	by	by	IN	_	_	_
25	a	a	DT	_	_	_
26	distance	distance	NN	_	_	_
27	of	of	IN	_	_	_
28	less	less	JJR	_	_	_
29	than	than	IN	_	_	_
30	200bo	200bo	CD	_	_	_
31	into	into	IN	_	_	_
32	the	the	DT	_	_	_
33	single	single	JJ	_	_	_
34	binding	binding	NN	_	_	_
35	regions	region	NNS	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	The	the	DT	_	_	_
38	CEL	cel	NN	_	_	_
39	files	file	VBZ	_	_	_
40	generated	generate	VBN	_	_	_
41	for	for	IN	_	_	_
42	each	each	DT	_	_	_
43	array	array	NN	_	_	_
44	were	be	VBD	_	_	_
45	analyzed	analyze	VBN	_	_	_
46	using	use	VBG	_	_	_
47	Affymetrix	Affymetrix	NNP	_	_	_
48	Expression	expression	NN	_	_	_
49	Console	console	NN	_	_	_
50	software	software	NN	_	_	_
51	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	cultures	culture	NNS	_	_	_
5	were	be	VBD	_	_	_
6	interrupted	interrupt	VBN	_	_	_
7	by	by	IN	_	_	_
8	placing	place	VBG	_	_	_
9	them	they	PRP	_	_	_
10	directly	directly	RB	_	_	_
11	into	into	IN	_	_	_
12	a	a	DT	_	_	_
13	cold	cold	JJ	_	_	_
14	phenol-ethanol	phenol-ethanol	NN	_	_	_
15	solution	solution	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	0.1g-phenol	0.1g-phenol	NN	_	_	_
18	/	/	:	_	_	_
19	mL-ethanol	ml-ethanol	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	using	use	VBG	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	12,000	12,000	CD	_	_	_
9	g	g	NN	_	_	_
10	for	for	IN	_	_	_
11	5	5	CD	_	_	_
12	min	min	NN	_	_	_
13	at	at	IN	_	_	_
14	4C	4c	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	pelleted	pelleted	JJ	_	_	_
19	cells	cell	NNS	_	_	_
20	were	be	VBD	_	_	_
21	once	once	RB	_	_	_
22	stored	store	VBN	_	_	_
23	at	at	IN	_	_	_
24	-80	-80	CD	_	_	_
25	C	c	NN	_	_	_
26	prior	prior	JJ	_	_	_
27	to	to	TO	_	_	_
28	use	use	VB	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	put	put	VBN	_	_	_
7	into	into	IN	_	_	_
8	cold	cold	JJ	_	_	_
9	phenol-ethanol	phenol-ethanol	JJ	_	_	_
10	solution	solution	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	1	1	CD	_	_	_
13	g	g	NN	_	_	_
14	of	of	IN	_	_	_
15	phenol	phenol	NN	_	_	_
16	in	in	IN	_	_	_
17	10	10	CD	_	_	_
18	mL	ml	NN	_	_	_
19	of	of	IN	_	_	_
20	ethanol	ethanol	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	prepared	prepare	VBN	_	_	_
23	in	in	IN	_	_	_
24	advance	advance	NN	_	_	_
25	.	.	.	_	_	_

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	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	put	put	VBN	_	_	_
7	into	into	IN	_	_	_
8	cold	cold	JJ	_	_	_
9	phenol-ethanol	phenol-ethanol	JJ	_	_	_
10	solution	solution	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	1	1	CD	_	_	_
13	g	g	NN	_	_	_
14	of	of	IN	_	_	_
15	phenol	phenol	NN	_	_	_
16	in	in	IN	_	_	_
17	10	10	CD	_	_	_
18	mL	ml	NN	_	_	_
19	of	of	IN	_	_	_
20	ethanol	ethanol	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	prepared	prepare	VBN	_	_	_
23	in	in	IN	_	_	_
24	advance	advance	NN	_	_	_
25	.	.	.	_	_	_

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	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	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	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	cells	cell	NNS	_	_	_
4	for	for	IN	_	_	_
5	RNA	rna	NN	_	_	_
6	extraction	extraction	NN	_	_	_
7	were	be	VBD	_	_	_
8	immediately	immediately	RB	_	_	_
9	mixed	mix	VBN	_	_	_
10	with	with	IN	_	_	_
11	RNA	rna	NN	_	_	_
12	Protect	protect	VB	_	_	_
13	Bacterial	bacterial	JJ	_	_	_
14	reagent	reagent	NN	_	_	_
15	®	®	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	qiagen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	processed	process	VBN	_	_	_
21	by	by	IN	_	_	_
22	the	the	DT	_	_	_
23	RNAeasy	RNAeasy	NNP	_	_	_
24	Mini	Mini	NNP	_	_	_
25	Kit	kit	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Qiagen	qiagen	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	according	accord	VBG	_	_	_
30	to	to	TO	_	_	_
31	the	the	DT	_	_	_
32	manufacturers	manufacturer	NNS	_	_	_
33	instructions	instruction	NNS	_	_	_
34	.	.	.	_	_	_

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	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	centrifuged	centrifuge	VBN	_	_	_
6	at	at	IN	_	_	_
7	8000	8000	CD	_	_	_
8	rpm	rpm	NN	_	_	_
9	for	for	IN	_	_	_
10	5	5	CD	_	_	_
11	min	min	NN	_	_	_
12	at	at	IN	_	_	_
13	4	4	CD	_	_	_
14	°C	°c	NN	_	_	_
15	.	.	.	_	_	_

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	cells	cell	NNS	_	_	_
17	were	be	VBD	_	_	_
18	centrifuged	centrifuge	VBN	_	_	_
19	when	when	WRB	_	_	_
20	they	they	PRP	_	_	_
21	reached	reach	VBD	_	_	_
22	the	the	DT	_	_	_
23	log	log	NN	_	_	_
24	phase	phase	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	then	then	RB	_	_	_
28	rapidly	rapidly	RB	_	_	_
29	chilled	chill	VBD	_	_	_
30	and	and	CC	_	_	_
31	stored	store	VBD	_	_	_
32	in	in	IN	_	_	_
33	liquid	liquid	JJ	_	_	_
34	nitrogen	nitrogen	NN	_	_	_
35	until	until	IN	_	_	_
36	used	use	VBN	_	_	_
37	for	for	IN	_	_	_
38	the	the	DT	_	_	_
39	DNA	dna	NN	_	_	_
40	microarray	microarray	NN	_	_	_
41	assay	assay	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
43	The	the	DT	_	_	_
44	cells	cell	NNS	_	_	_
45	were	be	VBD	_	_	_
46	collected	collect	VBN	_	_	_
47	by	by	IN	_	_	_
48	centrifugation	centrifugation	NN	_	_	_
49	at	at	IN	_	_	_
50	8,000	8,000	CD	_	_	_
51	×	×	CD	_	_	_
52	g	g	NN	_	_	_
53	for	for	IN	_	_	_
54	5	5	CD	_	_	_
55	min	min	NN	_	_	_
56	at	at	IN	_	_	_
57	25	25	CD	_	_	_
58	°C	°c	NN	_	_	_
59	,	,	,	_	_	_
60	and	and	CC	_	_	_
61	the	the	DT	_	_	_
62	pelleted	pelleted	JJ	_	_	_
63	cells	cell	NNS	_	_	_
64	were	be	VBD	_	_	_
65	stored	store	VBN	_	_	_
66	at	at	IN	_	_	_
67	--	--	:	_	_	_
68	80	80	CD	_	_	_
69	°C	°c	NN	_	_	_
70	prior	prior	RB	_	_	_
71	to	to	TO	_	_	_
72	use	use	VB	_	_	_
73	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	cultivated	cultivate	VBN	_	_	_
6	in	in	IN	_	_	_
7	100	100	CD	_	_	_
8	ml	ml	NN	_	_	_
9	LB	lb	NN	MED	_	_
10	broth	broth	NN	MED	_	_
11	containing	contain	VBG	_	_	_
12	2	2	CD	_	_	_
13	mg/L	mg/l	NN	_	_	_
14	Cm	cm	NN	_	_	_
15	with	with	IN	_	_	_
16	50	50	CD	_	_	_
17	mg/L	mg/l	NN	_	_	_
18	triclosan	triclosan	NN	_	_	_
19	and	and	CC	_	_	_
20	harvested	harvest	VBN	_	_	_
21	in	in	IN	_	_	_
22	mid-logarithmic	mid-logarithmic	JJ	_	_	_
23	growth	growth	NN	_	_	_
24	phase	phase	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	OD600	od600	NN	_	_	_
27	=	=	JJ	_	_	_
28	1.1	1.1	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	cultivated	cultivate	VBN	_	_	_
6	in	in	IN	_	_	_
7	100	100	CD	_	_	_
8	ml	ml	NN	_	_	_
9	LB	lb	NN	MED	_	_
10	broth	broth	NN	MED	_	_
11	containing	contain	VBG	_	_	_
12	2	2	CD	_	_	_
13	mg/L	mg/l	NN	_	_	_
14	Cm	cm	NN	_	_	_
15	without	without	IN	_	_	_
16	triclosan	triclosan	NN	_	_	_
17	and	and	CC	_	_	_
18	harvested	harvest	VBN	_	_	_
19	in	in	IN	_	_	_
20	mid-logarithmic	mid-logarithmic	JJ	_	_	_
21	growth	growth	NN	_	_	_
22	phase	phase	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	OD600	od600	NN	_	_	_
25	=	=	JJ	_	_	_
26	1.0	1.0	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
14	kanamycin	kanamycin	NN	_	_	_
15	with	with	IN	_	_	_
16	shaking	shake	VBG	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	˚C	˚c	NN	_	_	_
20	until	until	IN	_	_	_
21	OD600	od600	NN	_	_	_
22	of	of	IN	_	_	_
23	~	~	NN	_	_	_
24	0.5	0.5	CD	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	of	of	IN	_	_	_
4	150	150	CD	_	_	_
5	mg	mg	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	wet	wet	JJ	_	_	_
8	weight	weight	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	were	be	VBD	_	_	_
11	harvested	harvest	VBN	_	_	_
12	by	by	IN	_	_	_
13	centrifugation	centrifugation	NN	_	_	_
14	at	at	IN	_	_	_
15	6,500	6,500	CD	_	_	_
16	×	×	CD	_	_	_
17	g	g	NN	_	_	_
18	for	for	IN	_	_	_
19	4	4	CD	_	_	_
20	min	min	NN	_	_	_
21	at	at	IN	_	_	_
22	4	4	CD	_	_	_
23	˚C	˚c	NN	_	_	_
24	,	,	,	_	_	_
25	aliquoted	aliquote	VBN	_	_	_
26	in	in	IN	_	_	_
27	three	three	CD	_	_	_
28	1.5	1.5	CD	_	_	_
29	ml	ml	NN	_	_	_
30	tubes	tube	NNS	_	_	_
31	,	,	,	_	_	_
32	flash	flash	VBP	_	_	_
33	frozen	freeze	VBN	_	_	_
34	in	in	IN	_	_	_
35	liquid	liquid	JJ	_	_	_
36	nitrogen	nitrogen	NN	_	_	_
37	,	,	,	_	_	_
38	and	and	CC	_	_	_
39	stored	store	VBD	_	_	_
40	at	at	IN	_	_	_
41	-80	-80	CD	_	_	_
42	˚C	˚c	NN	_	_	_
43	.	.	.	_	_	_

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/ml	mg/ml	NN	_	_	_
14	kanamycin	kanamycin	NN	_	_	_
15	with	with	IN	_	_	_
16	shaking	shake	VBG	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	˚C	˚c	NN	_	_	_
20	until	until	IN	_	_	_
21	OD600	od600	NN	_	_	_
22	of	of	IN	_	_	_
23	~	~	NN	_	_	_
24	0.5	0.5	CD	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	of	of	IN	_	_	_
4	150	150	CD	_	_	_
5	mg	mg	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	wet	wet	JJ	_	_	_
8	weight	weight	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	were	be	VBD	_	_	_
11	harvested	harvest	VBN	_	_	_
12	by	by	IN	_	_	_
13	centrifugation	centrifugation	NN	_	_	_
14	at	at	IN	_	_	_
15	6,500	6,500	CD	_	_	_
16	×	×	CD	_	_	_
17	g	g	NN	_	_	_
18	for	for	IN	_	_	_
19	4	4	CD	_	_	_
20	min	min	NN	_	_	_
21	at	at	IN	_	_	_
22	4	4	CD	_	_	_
23	˚C	˚c	NN	_	_	_
24	,	,	,	_	_	_
25	aliquoted	aliquote	VBN	_	_	_
26	in	in	IN	_	_	_
27	three	three	CD	_	_	_
28	1.5	1.5	CD	_	_	_
29	ml	ml	NN	_	_	_
30	tubes	tube	NNS	_	_	_
31	,	,	,	_	_	_
32	flash	flash	VBP	_	_	_
33	frozen	freeze	VBN	_	_	_
34	in	in	IN	_	_	_
35	liquid	liquid	JJ	_	_	_
36	nitrogen	nitrogen	NN	_	_	_
37	,	,	,	_	_	_
38	and	and	CC	_	_	_
39	stored	store	VBD	_	_	_
40	at	at	IN	_	_	_
41	-80	-80	CD	_	_	_
42	˚C	˚c	NN	_	_	_
43	.	.	.	_	_	_

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/mL	100µg/ml	NN	_	_	_
12	Erythromycin	erythromycin	NN	_	_	_
13	or	or	CC	_	_	_
14	50	50	CD	_	_	_
15	µg/mL	µg/ml	NN	_	_	_
16	Clindamycin	clindamycin	NN	_	_	_
17	in	in	IN	_	_	_
18	70	70	CD	_	_	_
19	%	%	NN	_	_	_
20	Ethanol	ethanol	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	10	10	CD	_	_	_
3	minutes	minute	NNS	_	_	_
4	at	at	IN	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	,	,	,	_	_	_
8	1	1	CD	_	_	_
9	mL	ml	NN	_	_	_
10	samples	sample	NNS	_	_	_
11	were	be	VBD	_	_	_
12	subjected	subject	VBN	_	_	_
13	to	to	TO	_	_	_
14	hot	hot	JJ	_	_	_
15	phenol-chloroform	phenol-chloroform	JJ	_	_	_
16	extraction	extraction	NN	_	_	_
17	.	.	.	_	_	_

1	Ref	Ref	NNP	_	_	_
2	:	:	:	_	_	_
3	Chuang	Chuang	NNP	_	_	_
4	SE	se	NN	_	_	_
5	,	,	,	_	_	_
6	Daniels	Daniels	NNP	_	_	_
7	DL	DL	NNP	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	Blattner	Blattner	NNP	_	_	_
11	FR	fr	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	1993	1993	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	Global	global	JJ	_	_	_
16	regulation	regulation	NN	_	_	_
17	of	of	IN	_	_	_
18	gene	gene	NN	_	_	_
19	expression	expression	NN	_	_	_
20	in	in	IN	_	_	_
21	Escherichia	escherichia	FW	Organism	_	_
22	coli	coli	FW	Organism	_	_
23	.	.	.	_	_	_

1	J.	J.	NNP	_	_	_
2	Bacteriol	Bacteriol	NNP	_	_	_
3	.	.	.	_	_	_

1	175:2026-2036	175:2026-2036	CD	_	_	_
2	.	.	.	_	_	_

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	ChIP	chip	NN	_	_	_
4	experiment	experiment	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	essentially	essentially	RB	_	_	_
8	as	as	IN	_	_	_
9	described	describe	VBN	_	_	_
10	previously	previously	RB	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Herring	Herring	NNP	_	_	_
13	,	,	,	_	_	_
14	Raffaelle	Raffaelle	NNP	_	_	_
15	et	et	FW	_	_	_
16	al.	al.	FW	_	_	_
17	2005	2005	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

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	clean	clean	JJ	_	_	_
4	reads	read	VBZ	_	_	_
5	obtained	obtain	VBN	_	_	_
6	were	be	VBD	_	_	_
7	aligned	align	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	genome	genome	NN	_	_	_
11	sequence	sequence	NN	_	_	_
12	of	of	IN	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	O157	o157	NN	_	_	_
16	:	:	:	_	_	_
17	H7	h7	NN	_	_	_
18	EDL933	edl933	NN	_	_	_
19	using	use	VBG	_	_	_
20	SOAP2	soap2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	The	the	DT	_	_	_
23	conditioned	conditioned	JJ	_	_	_
24	medium	medium	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	C	c	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	the	the	DT	_	_	_
30	DMEM	DMEM	NNP	_	_	_
31	medium	medium	NN	_	_	_
32	containing	contain	VBG	_	_	_
33	10	10	CD	_	_	_
34	%	%	NN	_	_	_
35	FBS	fbs	NN	_	_	_
36	without	without	IN	_	_	_
37	antibiotics	antibiotic	NNS	_	_	_
38	recovered	recover	VBN	_	_	_
39	after	after	IN	_	_	_
40	24	24	CD	_	_	_
41	hrs	hr	NNS	_	_	_
42	incubation	incubation	NN	_	_	_
43	with	with	IN	_	_	_
44	differentiated	differentiate	VBN	_	_	_
45	Caco-2	caco-2	NN	_	_	_
46	cells	cell	NNS	_	_	_
47	.	.	.	_	_	_

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	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	cross-linked	cross-linked	JJ	_	_	_
29	DNA-ArgR	dna-argr	NN	_	_	_
30	complexes	complex	NNS	_	_	_
31	in	in	IN	_	_	_
32	the	the	DT	_	_	_
33	supernatant	supernatant	NN	_	_	_
34	were	be	VBD	_	_	_
35	then	then	RB	_	_	_
36	immunoprecipitated	immunoprecipitate	VBN	_	_	_
37	by	by	IN	_	_	_
38	adding	add	VBG	_	_	_
39	10	10	CD	_	_	_
40	µL	µl	NN	_	_	_
41	of	of	IN	_	_	_
42	Anti-myc	anti-myc	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	9E10	9e10	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Santa	Santa	NNP	_	_	_
48	Cruz	Cruz	NNP	_	_	_
49	,	,	,	_	_	_
50	Dallas	Dallas	NNP	_	_	_
51	,	,	,	_	_	_
52	TX	TX	NNP	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	.	.	.	_	_	_

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	cultivations	cultivation	NNS	_	_	_
4	were	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	in	in	IN	_	_	_
7	a	a	DT	_	_	_
8	Biostat	biostat	NN	_	_	_
9	C	c	NN	_	_	_
10	15	15	CD	_	_	_
11	L	l	NN	_	_	_
12	bioreactor	bioreactor	NN	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	DCU-3	dcu-3	NN	_	_	_
16	controlling	control	VBG	_	_	_
17	unit	unit	NN	_	_	_
18	and	and	CC	_	_	_
19	MFCS-win	mfcs-win	NN	_	_	_
20	supervisory	supervisory	JJ	_	_	_
21	system	system	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Sartorius	sartorius	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	with	with	IN	_	_	_
26	an	a	DT	_	_	_
27	initial	initial	JJ	_	_	_
28	working	work	VBG	_	_	_
29	volume	volume	NN	_	_	_
30	of	of	IN	_	_	_
31	8	8	CD	_	_	_
32	L	l	NN	_	_	_
33	.	.	.	_	_	_

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	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/L	g/l	NN	_	_	_
21	glucose	glucose	NN	SUPP	_	_
22	in	in	IN	_	_	_
23	either	either	CC	_	_	_
24	the	the	DT	_	_	_
25	presence	presence	NN	_	_	_
26	or	or	CC	_	_	_
27	absence	absence	NN	_	_	_
28	of	of	IN	_	_	_
29	1	1	CD	_	_	_
30	g/L	g/l	NN	_	_	_
31	arginine	arginine	NN	SUPP	_	_
32	and	and	CC	_	_	_
33	continued	continue	VBD	_	_	_
34	to	to	TO	_	_	_
35	culture	culture	NN	_	_	_
36	at	at	IN	_	_	_
37	37	37	CD	_	_	_
38	°C	°c	NN	_	_	_
39	until	until	IN	_	_	_
40	reaching	reach	VBG	_	_	_
41	an	a	DT	_	_	_
42	appropriate	appropriate	JJ	_	_	_
43	cell	cell	NN	_	_	_
44	density	density	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	OD600	od600	NN	_	_	_
47	≈	≈	CD	_	_	_
48	0.5	0.5	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	centrifuged	centrifuge	VBN	_	_	_
6	at	at	IN	_	_	_
7	8000	8000	CD	_	_	_
8	rpm	rpm	NN	_	_	_
9	for	for	IN	_	_	_
10	10	10	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	pellet	pellet	NN	_	_	_
15	was	be	VBD	_	_	_
16	dissolved	dissolve	VBN	_	_	_
17	in	in	IN	_	_	_
18	15	15	CD	_	_	_
19	mL	ml	NN	_	_	_
20	of	of	IN	_	_	_
21	10	10	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	NaCl	nacl	NN	_	_	_
24	,	,	,	_	_	_
25	20	20	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	Tris-HCl	tris-hcl	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	pH	ph	NN	_	_	_
30	8.0	8.0	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	,	,	,	_	_	_
33	1	1	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	EDTA	edta	NN	_	_	_
36	,	,	,	_	_	_
37	100	100	CD	_	_	_
38	μg/mL	μg/ml	NN	_	_	_
39	proteinase	proteinase	NN	_	_	_
40	K	k	NN	_	_	_
41	and	and	CC	_	_	_
42	0.5	0.5	CD	_	_	_
43	%	%	NN	_	_	_
44	SDS	sds	NN	_	_	_
45	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	suspension	suspension	NN	_	_	_
3	was	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	50oC	50oc	NN	_	_	_
7	for	for	IN	_	_	_
8	2	2	CD	_	_	_
9	h	h	NN	_	_	_
10	and	and	CC	_	_	_
11	DNA	dna	NN	_	_	_
12	extracted	extract	VBN	_	_	_
13	with	with	IN	_	_	_
14	an	a	DT	_	_	_
15	equal	equal	JJ	_	_	_
16	volume	volume	NN	_	_	_
17	of	of	IN	_	_	_
18	phenol	phenol	NN	_	_	_
19	:	:	:	_	_	_
20	chloroform	chloroform	NN	_	_	_
21	:	:	:	_	_	_
22	isoamyl	isoamyl	NN	_	_	_
23	alcohol	alcohol	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	25:24:1	25:24:1	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	for	for	IN	_	_	_
4	10	10	CD	_	_	_
5	min	min	NN	_	_	_
6	at	at	IN	_	_	_
7	8000	8000	CD	_	_	_
8	rpm	rpm	NN	_	_	_
9	,	,	,	_	_	_
10	the	the	DT	_	_	_
11	upper	upper	JJ	_	_	_
12	phase	phase	NN	_	_	_
13	was	be	VBD	_	_	_
14	removed	remove	VBN	_	_	_
15	and	and	CC	_	_	_
16	precipitated	precipitate	VBN	_	_	_
17	by	by	IN	_	_	_
18	adding	add	VBG	_	_	_
19	0.1	0.1	CD	_	_	_
20	volume	volume	NN	_	_	_
21	of	of	IN	_	_	_
22	3	3	CD	_	_	_
23	M	m	NN	_	_	_
24	NaOAc	naoac	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	pH	ph	NN	_	_	_
27	5.2	5.2	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	2	2	CD	_	_	_
31	volumes	volume	NNS	_	_	_
32	of	of	IN	_	_	_
33	99	99	CD	_	_	_
34	%	%	NN	_	_	_
35	ethanol	ethanol	NN	_	_	_
36	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	DNA	dna	NN	_	_	_
3	precipitate	precipitate	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	spooled	spool	VBN	_	_	_
7	out	out	IN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	solution	solution	NN	_	_	_
11	using	use	VBG	_	_	_
12	a	a	DT	_	_	_
13	sterile	sterile	JJ	_	_	_
14	glass	glass	NN	_	_	_
15	rod	rod	NN	_	_	_
16	,	,	,	_	_	_
17	washed	wash	VBN	_	_	_
18	with	with	IN	_	_	_
19	70	70	CD	_	_	_
20	%	%	NN	_	_	_
21	ethanol	ethanol	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	dissolved	dissolve	VBN	_	_	_
25	in	in	IN	_	_	_
26	5	5	CD	_	_	_
27	mL	ml	NN	_	_	_
28	of	of	IN	_	_	_
29	TE	TE	NNP	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	10	10	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	Tris-HCl	tris-hcl	NN	_	_	_
34	,	,	,	_	_	_
35	1	1	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	EDTA	edta	NN	_	_	_
38	,	,	,	_	_	_
39	pH	ph	NN	_	_	_
40	8.0	8.0	CD	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	buffer	buffer	NN	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	by	by	IN	_	_	_
7	inoculating	inoculate	VBG	_	_	_
8	one	one	CD	_	_	_
9	colony	colony	NN	_	_	_
10	from	from	IN	_	_	_
11	tryptone	tryptone	NN	SUPP	_	_
12	soya	soya	NN	_	_	_
13	agar	agar	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	TSA	tsa	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Oxoid	Oxoid	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	overnight	overnight	JJ	_	_	_
22	growth	growth	NN	_	_	_
23	at	at	IN	_	_	_
24	37	37	CD	_	_	_
25	°C	°c	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	to	to	TO	_	_	_
28	5	5	CD	_	_	_
29	ml	ml	NN	_	_	_
30	TSB	tsb	NN	_	_	_
31	and	and	CC	_	_	_
32	incubating	incubate	VBG	_	_	_
33	overnight	overnight	JJ	_	_	_
34	at	at	IN	_	_	_
35	37	37	CD	_	_	_
36	°C	°c	NN	_	_	_
37	,	,	,	_	_	_
38	with	with	IN	_	_	_
39	shaking	shake	VBG	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	200	200	CD	_	_	_
42	rpm	rpm	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	.	.	.	_	_	_

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/ml	cfu/ml	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	1:100	1:100	CD	_	_	_
40	dilution	dilution	NN	_	_	_
41	of	of	IN	_	_	_
42	overnight	overnight	JJ	_	_	_
43	culture	culture	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	cold	cold	JJ	_	_	_
3	stress	stress	NN	_	_	_
4	experiment	experiment	NN	_	_	_
5	the	the	DT	_	_	_
6	medium	medium	NN	_	_	_
7	was	be	VBD	_	_	_
8	chilled	chill	VBN	_	_	_
9	to	to	TO	_	_	_
10	15	15	CD	_	_	_
11	°C	°c	NN	_	_	_
12	prior	prior	RB	_	_	_
13	to	to	TO	_	_	_
14	inoculation	inoculation	NN	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	except	except	IN	_	_	_
10	fpr	fpr	NN	GEN	_	_
11	15	15	CD	_	_	_
12	°C	°c	NN	_	_	_
13	and	and	CC	_	_	_
14	46	46	CD	_	_	_
15	°C	°c	NN	_	_	_
16	conditions	condition	NNS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	shaking	shake	VBG	_	_	_
20	at	at	IN	_	_	_
21	200	200	CD	_	_	_
22	rpm	rpm	NN	_	_	_
23	and	and	CC	_	_	_
24	samples	sample	NNS	_	_	_
25	were	be	VBD	_	_	_
26	collected	collect	VBN	_	_	_
27	during	during	IN	_	_	_
28	exponential	exponential	JJ	_	_	_
29	growth	growth	NN	_	_	_
30	at	at	IN	_	_	_
31	a	a	DT	_	_	_
32	cell	cell	NN	_	_	_
33	density	density	NN	_	_	_
34	of	of	IN	_	_	_
35	approx.	approx.	RB	_	_	_
36	1	1	CD	_	_	_
37	'	'	''	_	_	_
38	108	108	CD	_	_	_
39	CFU/ml	cfu/ml	NN	_	_	_
40	.	.	.	_	_	_

1	All	all	PDT	_	_	_
2	the	the	DT	_	_	_
3	stress	stress	NN	_	_	_
4	conditions	condition	NNS	_	_	_
5	,	,	,	_	_	_
6	including	include	VBG	_	_	_
7	the	the	DT	_	_	_
8	control	control	NN	_	_	_
9	,	,	,	_	_	_
10	were	be	VBD	_	_	_
11	inoculated	inoculate	VBN	_	_	_
12	with	with	IN	_	_	_
13	the	the	DT	_	_	_
14	same	same	JJ	_	_	_
15	overnight	overnight	JJ	_	_	_
16	culture	culture	NN	_	_	_
17	and	and	CC	_	_	_
18	started	start	VBD	_	_	_
19	at	at	IN	_	_	_
20	the	the	DT	_	_	_
21	same	same	JJ	_	_	_
22	time	time	NN	_	_	_
23	point	point	NN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	experiment	experiment	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	3	3	CD	_	_	_
6	times	time	NNS	_	_	_
7	at	at	IN	_	_	_
8	different	different	JJ	_	_	_
9	days	day	NNS	_	_	_
10	and	and	CC	_	_	_
11	with	with	IN	_	_	_
12	freshly	freshly	RB	_	_	_
13	prepared	prepared	JJ	_	_	_
14	solutions	solution	NNS	_	_	_
15	,	,	,	_	_	_
16	resulting	result	VBG	_	_	_
17	in	in	IN	_	_	_
18	3	3	CD	_	_	_
19	biological	biological	JJ	_	_	_
20	replicates	replicate	VBZ	_	_	_
21	.	.	.	_	_	_

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	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/ml	µg/ml	NN	_	_	_
9	of	of	IN	_	_	_
10	chloramphenicol	chloramphenicol	NN	_	_	_
11	for	for	IN	_	_	_
12	2	2	CD	_	_	_
13	min	min	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	harvested	harvest	VBN	_	_	_
17	by	by	IN	_	_	_
18	centrifugation	centrifugation	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	with	with	IN	_	_	_
4	washed	wash	VBN	_	_	_
5	and	and	CC	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	100	100	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	NH4Cl	nh4cl	NN	_	_	_
11	,	,	,	_	_	_
12	10	10	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	MgCl2	mgcl2	NN	_	_	_
15	,	,	,	_	_	_
16	20	20	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	Tris	Tris	NNP	_	_	_
19	Cl	Cl	NNP	_	_	_
20	,	,	,	_	_	_
21	0.4	0.4	CD	_	_	_
22	%	%	NN	_	_	_
23	Triton	Triton	NNP	_	_	_
24	X100	x100	NN	_	_	_
25	,	,	,	_	_	_
26	0.1	0.1	CD	_	_	_
27	%	%	NN	_	_	_
28	NP-40	np-40	NN	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	100	100	CD	_	_	_
32	µl/ml	µl/ml	JJ	_	_	_
33	chloramphenicol	chloramphenicol	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	flash	flash	NN	_	_	_
37	frozen	freeze	VBN	_	_	_
38	over	over	IN	_	_	_
39	liquid	liquid	JJ	_	_	_
40	nitrogen	nitrogen	NN	_	_	_
41	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	frozen	frozen	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	pellets	pellet	NNS	_	_	_
5	were	be	VBD	_	_	_
6	pulverized	pulverize	VBN	_	_	_
7	by	by	IN	_	_	_
8	mixer	mixer	NN	_	_	_
9	milling	milling	NN	_	_	_
10	and	and	CC	_	_	_
11	thawed	thaw	VBN	_	_	_
12	in	in	IN	_	_	_
13	2.5	2.5	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	DSP	DSP	NNP	_	_	_
16	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	did	do	VBD	_	_	_
5	not	not	RB	_	_	_
6	undergo	undergo	VB	_	_	_
7	normalization	normalization	NN	_	_	_
8	across	across	IN	_	_	_
9	samples	sample	NNS	_	_	_
10	.	.	.	_	_	_

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	The	the	DT	_	_	_
17	data	datum	NNS	_	_	_
18	provided	provide	VBN	_	_	_
19	are	be	VBP	_	_	_
20	the	the	DT	_	_	_
21	original	original	JJ	_	_	_
22	data	datum	NNS	_	_	_
23	generated	generate	VBN	_	_	_
24	with	with	IN	_	_	_
25	the	the	DT	_	_	_
26	Jaguar	Jaguar	NNP	_	_	_
27	software	software	NN	_	_	_
28	from	from	IN	_	_	_
29	the	the	DT	_	_	_
30	microarray	microarray	NN	_	_	_
31	images	image	NNS	_	_	_
32	.	.	.	_	_	_

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/Cy3	cy5/cy3	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	ratios	ratio	NNS	_	_	_
10	for	for	IN	_	_	_
11	this	this	DT	_	_	_
12	experiment/sample	experiment/sample	NN	_	_	_
13	.	.	.	_	_	_

1	They	they	PRP	_	_	_
2	were	be	VBD	_	_	_
3	not	not	RB	_	_	_
4	normalized	normalize	VBN	_	_	_
5	across	across	IN	_	_	_
6	all	all	DT	_	_	_
7	samples	sample	NNS	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	study	study	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	provided	provide	VBN	_	_	_
5	are	be	VBP	_	_	_
6	the	the	DT	_	_	_
7	original	original	JJ	_	_	_
8	data	datum	NNS	_	_	_
9	generated	generate	VBN	_	_	_
10	with	with	IN	_	_	_
11	the	the	DT	_	_	_
12	Jaguar	Jaguar	NNP	_	_	_
13	software	software	NN	_	_	_
14	from	from	IN	_	_	_
15	the	the	DT	_	_	_
16	microarray	microarray	NN	_	_	_
17	images	image	NNS	_	_	_
18	.	.	.	_	_	_

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/Cy3	cy5/cy3	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	ratios	ratio	NNS	_	_	_
11	for	for	IN	_	_	_
12	this	this	DT	_	_	_
13	experiment/sample	experiment/sample	NN	_	_	_
14	.	.	.	_	_	_

1	They	they	PRP	_	_	_
2	were	be	VBD	_	_	_
3	not	not	RB	_	_	_
4	normalized	normalize	VBN	_	_	_
5	across	across	IN	_	_	_
6	all	all	DT	_	_	_
7	samples	sample	NNS	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	study	study	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	analyzed	analyze	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Robust	robust	JJ	_	_	_
8	Multi-Array	multi-array	JJ	_	_	_
9	average	average	NN	_	_	_
10	as	as	IN	_	_	_
11	implemented	implement	VBN	_	_	_
12	in	in	IN	_	_	_
13	Bioconductor	Bioconductor	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	The	the	DT	_	_	_
16	data	datum	NNS	_	_	_
17	were	be	VBD	_	_	_
18	analyzed	analyze	VBN	_	_	_
19	with	with	IN	_	_	_
20	ArrayStar	arraystar	NN	_	_	_
21	3	3	CD	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	DNASTAR	dnastar	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	using	use	VBG	_	_	_
26	RMA	RMA	NNP	_	_	_
27	normalization	normalization	NN	_	_	_
28	method	method	NN	_	_	_
29	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	analyzed	analyze	VBN	_	_	_
6	with	with	IN	_	_	_
7	FlexArray	FlexArray	NNP	_	_	_
8	1.4.1	1.4.1	CD	_	_	_
9	software	software	NN	_	_	_
10	program	program	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	http://genomequebec.mcgill.ca/FlexArray/	http://genomequebec.mcgill.ca/flexarray/	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

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	Robust	robust	JJ	_	_	_
8	Multi-Array	Multi-Array	NNP	_	_	_
9	Average	Average	NNP	_	_	_
10	algorithm	algorithm	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	RMA	rma	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	Comparison	comparison	NN	_	_	_
2	between	between	IN	_	_	_
3	the	the	DT	_	_	_
4	two	two	CD	_	_	_
5	data	datum	NNS	_	_	_
6	sets	set	NNS	_	_	_
7	was	be	VBD	_	_	_
8	done	do	VBN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	Randomized	Randomized	NNP	_	_	_
12	Variance	Variance	NNP	_	_	_
13	Model	Model	NNP	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	RVM	RVM	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	with	with	IN	_	_	_
18	a	a	DT	_	_	_
19	cut-off	cut-off	JJ	_	_	_
20	of	of	IN	_	_	_
21	a	a	DT	_	_	_
22	fold	fold	JJ	_	_	_
23	change	change	NN	_	_	_
24	of	of	IN	_	_	_
25	2	2	CD	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	or	or	CC	_	_	_
28	-2	-2	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	a	a	DT	_	_	_
32	P-value	p-value	NN	_	_	_
33	of	of	IN	_	_	_
34	0.05	0.05	CD	_	_	_
35	.	.	.	_	_	_

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	GCOS	gcos	NN	_	_	_
8	1.4	1.4	CD	_	_	_
9	software	software	NN	_	_	_
10	.	.	.	_	_	_

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	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	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	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	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	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	analyzed	analyze	VBN	_	_	_
6	with	with	IN	_	_	_
7	Partek	Partek	NNP	_	_	_
8	Genomics	Genomics	NNP	_	_	_
9	Suite	Suite	NNP	_	_	_
10	using	use	VBG	_	_	_
11	Affymetrix	Affymetrix	NNP	_	_	_
12	default	default	NN	_	_	_
13	analysis	analysis	NN	_	_	_
14	settings	setting	NNS	_	_	_
15	and	and	CC	_	_	_
16	global	global	JJ	_	_	_
17	scaling	scaling	NN	_	_	_
18	as	as	IN	_	_	_
19	normalization	normalization	NN	_	_	_
20	method	method	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	imported	import	VBN	_	_	_
6	into	into	IN	_	_	_
7	FlexArray	FlexArray	NNP	_	_	_
8	using	use	VBG	_	_	_
9	gc-RMA	gc-rma	NN	_	_	_
10	preprocessing	preprocessing	NN	_	_	_
11	for	for	IN	_	_	_
12	analysis	analysis	NN	_	_	_
13	.	.	.	_	_	_

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/gDNA	cdna/gdna	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	ensure	ensure	VB	_	_	_
3	that	that	IN	_	_	_
4	the	the	DT	_	_	_
5	fluorescence	fluorescence	NN	_	_	_
6	measurements	measurement	NNS	_	_	_
7	were	be	VBD	_	_	_
8	independent	independent	JJ	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	overall	overall	JJ	_	_	_
12	signal	signal	NN	_	_	_
13	intensity	intensity	NN	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	spot	spot	NN	_	_	_
17	,	,	,	_	_	_
18	the	the	DT	_	_	_
19	values	value	NNS	_	_	_
20	of	of	IN	_	_	_
21	M	m	NN	_	_	_
22	were	be	VBD	_	_	_
23	made	make	VBN	_	_	_
24	independent	independent	JJ	_	_	_
25	of	of	IN	_	_	_
26	A	a	NN	_	_	_
27	=	=	JJ	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	lncDNA	lncdna	NN	_	_	_
30	+	+	CC	_	_	_
31	lngDNA	lngdna	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	/	/	:	_	_	_
34	2	2	CD	_	_	_
35	with	with	IN	_	_	_
36	a	a	DT	_	_	_
37	linear	linear	JJ	_	_	_
38	shift	shift	NN	_	_	_
39	.	.	.	_	_	_

1	Spots	spot	NNS	_	_	_
2	where	where	WRB	_	_	_
3	the	the	DT	_	_	_
4	A	a	NN	_	_	_
5	values	value	NNS	_	_	_
6	were	be	VBD	_	_	_
7	less	less	JJR	_	_	_
8	than	than	IN	_	_	_
9	5.5	5.5	CD	_	_	_
10	were	be	VBD	_	_	_
11	not	not	RB	_	_	_
12	considered	consider	VBN	_	_	_
13	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	the	the	DT	_	_	_
3	experiments	experiment	NNS	_	_	_
4	were	be	VBD	_	_	_
5	aligned	align	VBN	_	_	_
6	so	so	RB	_	_	_
7	that	that	IN	_	_	_
8	the	the	DT	_	_	_
9	median	median	NN	_	_	_
10	of	of	IN	_	_	_
11	M	m	NN	_	_	_
12	=	=	JJ	_	_	_
13	0	0	CD	_	_	_
14	and	and	CC	_	_	_
15	their	they	PRP$	_	_	_
16	deviation	deviation	NN	_	_	_
17	was	be	VBD	_	_	_
18	normalised	normalised	JJ	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	by	by	IN	_	_	_
7	RMA	rma	NN	_	_	_
8	method	method	NN	_	_	_
9	and	and	CC	_	_	_
10	then	then	RB	_	_	_
11	analyzed	analyze	VBN	_	_	_
12	by	by	IN	_	_	_
13	limma	limma	NN	_	_	_
14	package	package	NN	_	_	_
15	to	to	TO	_	_	_
16	identify	identify	VB	_	_	_
17	differentially	differentially	RB	_	_	_
18	expressed	express	VBN	_	_	_
19	genes	gene	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	bioconductor	bioconductor	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	isolate	isolate	NN	_	_	_
6	ESBL019	esbl019	NN	_	_	_
7	was	be	VBD	_	_	_
8	originally	originally	RB	_	_	_
9	isolated	isolate	VBN	_	_	_
10	from	from	IN	_	_	_
11	a	a	DT	_	_	_
12	patient	patient	NN	_	_	_
13	at	at	IN	_	_	_
14	Örebro	Örebro	NNP	_	_	_
15	University	University	NNP	_	_	_
16	hospital	hospital	NN	_	_	_
17	,	,	,	_	_	_
18	Sweden	Sweden	NNP	_	_	_
19	and	and	CC	_	_	_
20	was	be	VBD	_	_	_
21	maintained	maintain	VBN	_	_	_
22	on	on	IN	_	_	_
23	tryptic	tryptic	JJ	_	_	_
24	soy	soy	NN	_	_	_
25	agar	agar	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	TSA	tsa	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Becton	Becton	NNP	_	_	_
31	Dickinson	Dickinson	NNP	_	_	_
32	,	,	,	_	_	_
33	Le	Le	NNP	_	_	_
34	Pont	Pont	NNP	_	_	_
35	Claix	Claix	NNP	_	_	_
36	,	,	,	_	_	_
37	France	France	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

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/mL	ng/ml	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	K12	k12	NN	_	_	_
6	strain	strain	NN	_	_	_
7	MG1655	mg1655	NN	_	_	_
8	and	and	CC	_	_	_
9	its	its	PRP$	_	_	_
10	isogenic	isogenic	JJ	_	_	_
11	ptsN	ptsn	NN	GEN	_	_
12	mutant	mutant	NN	_	_	_
13	were	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	in	in	IN	_	_	_
16	M9	m9	NN	MED	_	_
17	minimal	minimal	JJ	MED	_	_
18	medium	medium	NN	MED	_	_
19	containing	contain	VBG	_	_	_
20	0.5	0.5	CD	_	_	_
21	%	%	NN	_	_	_
22	glucose	glucose	NN	SUPP	_	_
23	as	as	IN	_	_	_
24	carbon	carbon	NN	_	_	_
25	source	source	NN	_	_	_
26	.	.	.	_	_	_

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	The	the	DT	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	strain	strain	NN	_	_	_
6	BW25113	bw25113	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	2	2	CD	_	_	_
9	x	x	CC	_	_	_
10	10	10	CD	_	_	_
11	^	^	SYM	_	_	_
12	9	9	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	suspended	suspend	VBN	_	_	_
15	with	with	IN	_	_	_
16	insect	insect	JJ	_	_	_
17	saline	saline	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	0.13	0.13	CD	_	_	_
20	M	m	NN	_	_	_
21	NaCl	nacl	NN	_	_	_
22	,	,	,	_	_	_
23	4.7	4.7	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	KCl	kcl	NN	_	_	_
26	,	,	,	_	_	_
27	1.9	1.9	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	CaCl2	cacl2	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	was	be	VBD	_	_	_
33	incubated	incubate	VBN	_	_	_
34	with	with	IN	_	_	_
35	GST	gst	NN	_	_	_
36	or	or	CC	_	_	_
37	GST-fused	gst-fused	JJ	_	_	_
38	Drosophila	drosophila	FW	_	_	_
39	immune	immune	JJ	_	_	_
40	proteins	protein	NNS	_	_	_
41	for	for	IN	_	_	_
42	10	10	CD	_	_	_
43	min	min	NN	_	_	_
44	at	at	IN	_	_	_
45	room	room	NN	_	_	_
46	temperature	temperature	NN	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	strains	strain	NNS	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	for	for	IN	_	_	_
9	six	six	CD	_	_	_
10	hours	hour	NNS	_	_	_
11	under	under	IN	_	_	_
12	anaerobic	anaerobic	JJ	_	_	_
13	growth	growth	NN	_	_	_
14	condition	condition	NN	_	_	_
15	in	in	IN	_	_	_
16	glucose-containing	glucose-containing	JJ	_	_	_
17	complex	complex	JJ	_	_	_
18	medium	medium	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	equivalent	equivalent	NN	_	_	_
4	of	of	IN	_	_	_
5	5	5	CD	_	_	_
6	OD600	od600	NN	_	_	_
7	was	be	VBD	_	_	_
8	saved	save	VBN	_	_	_
9	for	for	IN	_	_	_
10	RNA	rna	NN	_	_	_
11	extraction	extraction	NN	_	_	_
12	with	with	IN	_	_	_
13	TriZOL	trizol	NN	_	_	_
14	before	before	IN	_	_	_
15	adding	add	VBG	_	_	_
16	antibodies	antibody	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	lysate	lysate	NN	_	_	_
19	RNA	rna	NN	_	_	_
20	sample	sample	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

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/µl	pg/µl	NN	_	_	_
17	for	for	IN	_	_	_
18	coIP	coip	NN	_	_	_
19	samples	sample	NNS	_	_	_
20	and	and	CC	_	_	_
21	to	to	TO	_	_	_
22	1.6	1.6	CD	_	_	_
23	ng/µl	ng/µl	NN	_	_	_
24	for	for	IN	_	_	_
25	lysate	lysate	NN	_	_	_
26	samples	sample	NNS	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	exponential	exponential	JJ	GrowthPhase	_	_
4	phase	phase	NN	GrowthPhase	_	_
5	culture	culture	NN	_	_	_
6	was	be	VBD	_	_	_
7	split	split	VBN	_	_	_
8	in	in	IN	_	_	_
9	two	two	CD	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	one	one	CD	_	_	_
13	part	part	NN	_	_	_
14	was	be	VBD	_	_	_
15	induced	induce	VBN	_	_	_
16	with	with	IN	_	_	_
17	mitomycin	mitomycin	NN	_	_	_
18	C	c	NN	_	_	_
19	at	at	IN	_	_	_
20	a	a	DT	_	_	_
21	final	final	JJ	_	_	_
22	concentration	concentration	NN	_	_	_
23	of	of	IN	_	_	_
24	0.25	0.25	CD	_	_	_
25	μg/ml	μg/ml	NN	_	_	_
26	.	.	.	_	_	_

1	Both	both	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	subsequently	subsequently	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	agitation	agitation	NN	_	_	_
11	for	for	IN	_	_	_
12	1.5	1.5	CD	_	_	_
13	hours	hour	NNS	_	_	_
14	.	.	.	_	_	_

1	Bacterial	bacterial	JJ	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	spun	spin	VBN	_	_	_
6	down	down	RP	_	_	_
7	and	and	CC	_	_	_
8	resuspended	resuspend	VBN	_	_	_
9	in	in	IN	_	_	_
10	5-10	5-10	CD	_	_	_
11	volumes	volume	NNS	_	_	_
12	of	of	IN	_	_	_
13	RNA	rna	NN	_	_	_
14	later	later	RB	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	QIAGEN	QIAGEN	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	before	before	IN	_	_	_
19	being	be	VBG	_	_	_
20	frozen	freeze	VBN	_	_	_
21	at	at	IN	_	_	_
22	-20	-20	CD	_	_	_
23	°C	°c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	expression	expression	NN	_	_	_
4	levels	level	NNS	_	_	_
5	were	be	VBD	_	_	_
6	based	base	VBN	_	_	_
7	upon	upon	IN	_	_	_
8	the	the	DT	_	_	_
9	RPKM	RPKM	NNP	_	_	_
10	metric	metric	JJ	_	_	_
11	obtained	obtain	VBN	_	_	_
12	from	from	IN	_	_	_
13	strand-specific	strand-specific	JJ	_	_	_
14	manner	manner	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	fastq	fastq	NN	_	_	_
4	files	file	NNS	_	_	_
5	of	of	IN	_	_	_
6	36-bp	36-bp	JJ	_	_	_
7	sequenced	sequence	VBN	_	_	_
8	reads	read	VBZ	_	_	_
9	were	be	VBD	_	_	_
10	generated	generate	VBN	_	_	_
11	with	with	IN	_	_	_
12	the	the	DT	_	_	_
13	CASAVA	CASAVA	NNP	_	_	_
14	v1	v1	NN	_	_	_
15	.8	.8	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Illumina	Illumina	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

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	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	NN	_	_	_
112	the	the	DT	_	_	_
113	first	first	JJ	_	_	_
114	ten	ten	CD	_	_	_
115	base	base	NN	_	_	_
116	pairs	pair	NNS	_	_	_
117	of	of	IN	_	_	_
118	each	each	DT	_	_	_
119	read	read	NN	_	_	_
120	were	be	VBD	_	_	_
121	trimmed	trim	VBN	_	_	_
122	using	use	VBG	_	_	_
123	FASTXToolkit	fastxtoolkit	NN	_	_	_
124	0.0.13	0.0.13	CD	_	_	_
125	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	five	five	CD	_	_	_
4	bacterial	bacterial	JJ	_	_	_
5	strains	strain	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	JO2057	jo2057	NN	_	_	_
8	,	,	,	_	_	_
9	JO2081	jo2081	NN	_	_	_
10	,	,	,	_	_	_
11	JO2083	jo2083	NN	_	_	_
12	,	,	,	_	_	_
13	JO3020	jo3020	NN	_	_	_
14	and	and	CC	_	_	_
15	MW30	mw30	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	were	be	VBD	_	_	_
18	grown	grow	VBN	_	_	_
19	in	in	IN	_	_	_
20	100	100	CD	_	_	_
21	ml	ml	NN	_	_	_
22	LB	lb	NN	_	_	_
23	0.5	0.5	CD	_	_	_
24	%	%	NN	_	_	_
25	NaCl	nacl	NN	_	_	_
26	,	,	,	_	_	_
27	M9	m9	NN	_	_	_
28	minimal	minimal	JJ	_	_	_
29	glucose	glucose	NN	SUPP	_	_
30	or	or	CC	_	_	_
31	M9	m9	NN	_	_	_
32	minimal	minimal	JJ	_	_	_
33	glycerol	glycerol	NN	SUPP	_	_
34	at	at	IN	_	_	_
35	200	200	CD	_	_	_
36	rpm	rpm	NN	_	_	_
37	in	in	IN	_	_	_
38	New	New	NNP	_	_	_
39	Brunswick	Brunswick	NNP	_	_	_
40	laboratory	laboratory	NN	_	_	_
41	shaker	shaker	NN	_	_	_
42	in	in	IN	_	_	_
43	2liter	2liter	JJ	_	_	_
44	flasks	flask	NNS	_	_	_
45	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	fluorescent	fluorescent	JJ	_	_	_
4	spot	spot	NN	_	_	_
5	intensities	intensity	NNS	_	_	_
6	were	be	VBD	_	_	_
7	quantified	quantify	VBN	_	_	_
8	using	use	VBG	_	_	_
9	ImaGeneÔ	imageneô	NN	_	_	_
10	5.6.1	5.6.1	CD	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	BioDiscovery	BioDiscovery	NNP	_	_	_
13	Inc.	Inc.	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	software	software	NN	_	_	_
16	.	.	.	_	_	_

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	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	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	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	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	genes	gene	NNS	_	_	_
14	were	be	VBD	_	_	_
15	considered	consider	VBN	_	_	_
16	differentially	differentially	RB	_	_	_
17	expressed	express	VBN	_	_	_
18	when	when	WRB	_	_	_
19	the	the	DT	_	_	_
20	logarithmic	logarithmic	JJ	_	_	_
21	gene	gene	NN	_	_	_
22	expression	expression	NN	_	_	_
23	ratios	ratio	NNS	_	_	_
24	had	have	VBD	_	_	_
25	a	a	DT	_	_	_
26	2-fold	2-fold	JJ	_	_	_
27	difference	difference	NN	_	_	_
28	in	in	IN	_	_	_
29	the	the	DT	_	_	_
30	expression	expression	NN	_	_	_
31	level	level	NN	_	_	_
32	.	.	.	_	_	_

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	The	the	DT	_	_	_
3	genomic	genomic	JJ	_	_	_
4	DNA	dna	NN	_	_	_
5	from	from	IN	_	_	_
6	pure	pure	JJ	_	_	_
7	and	and	CC	_	_	_
8	mixed	mixed	JJ	_	_	_
9	bacterial	bacterial	JJ	_	_	_
10	cultures	culture	NNS	_	_	_
11	was	be	VBD	_	_	_
12	isolated	isolate	VBN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	Wizard	Wizard	NNP	_	_	_
16	genomic	genomic	JJ	_	_	_
17	DNA	dna	NN	_	_	_
18	isolation	isolation	NN	_	_	_
19	kit	kit	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Promega	Promega	NNP	_	_	_
22	corporation	corporation	NN	_	_	_
23	,	,	,	_	_	_
24	Madison	Madison	NNP	_	_	_
25	,	,	,	_	_	_
26	USA	USA	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	as	as	IN	_	_	_
29	per	per	IN	_	_	_
30	manufacturer	manufacturer	NN	_	_	_
31	's	's	POS	_	_	_
32	instructions	instruction	NNS	_	_	_
33	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	hybridization	hybridization	NN	_	_	_
4	intensity	intensity	NN	_	_	_
5	data	datum	NNS	_	_	_
6	signals	signal	NNS	_	_	_
7	were	be	VBD	_	_	_
8	analyzed	analyze	VBN	_	_	_
9	,	,	,	_	_	_
10	normalized	normalize	VBD	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	corrected	correct	VBN	_	_	_
14	for	for	IN	_	_	_
15	batch	batch	NN	_	_	_
16	effect	effect	NN	_	_	_
17	using	use	VBG	_	_	_
18	Affymetrix	Affymetrix	NNP	_	_	_
19	GeneChip	GeneChip	NNP	_	_	_
20	®	®	NNP	_	_	_
21	Command	command	NN	_	_	_
22	Console	Console	NNP	_	_	_
23	®	®	NNP	_	_	_
24	Software	Software	NNP	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	AGCC	AGCC	NNP	_	_	_
27	v.	v.	CC	_	_	_
28	3.0	3.0	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	image	image	NN	_	_	_
4	analysis	analysis	NN	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	GenePix	GenePix	NNP	_	_	_
8	Pro	pro	FW	_	_	_
9	6.0	6.0	CD	_	_	_
10	Software	Software	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Molecular	molecular	JJ	_	_	_
13	Devices	Devices	NNPS	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	normalized	normalize	VBN	_	_	_
17	with	with	IN	_	_	_
18	MIDAS	midas	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	LOWESS	lowess	NN	_	_	_
21	method	method	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	with	with	IN	_	_	_
25	clustering	clustering	NN	_	_	_
26	analysis	analysis	NN	_	_	_
27	in	in	IN	_	_	_
28	MeV	mev	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	CAST	cast	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	The	the	DT	_	_	_
34	image	image	NN	_	_	_
35	analysis	analysis	NN	_	_	_
36	was	be	VBD	_	_	_
37	performed	perform	VBN	_	_	_
38	using	use	VBG	_	_	_
39	GenePix	GenePix	NNP	_	_	_
40	Pro	pro	FW	_	_	_
41	6.0	6.0	CD	_	_	_
42	Software	Software	NNP	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	Molecular	molecular	JJ	_	_	_
45	Devices	Devices	NNPS	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

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	The	the	DT	_	_	_
3	intensity	intensity	NN	_	_	_
4	cell	cell	NN	_	_	_
5	files	file	NNS	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	imported	import	VBN	_	_	_
9	,	,	,	_	_	_
10	normalized	normalize	VBN	_	_	_
11	for	for	IN	_	_	_
12	background	background	NN	_	_	_
13	correction	correction	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	used	use	VBN	_	_	_
16	RMA	rma	NN	_	_	_
17	for	for	IN	_	_	_
18	normalization	normalization	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	data	datum	NNS	_	_	_
22	analysed	analyse	VBN	_	_	_
23	using	use	VBG	_	_	_
24	Gene	Gene	NNP	_	_	_
25	Spring	Spring	NNP	_	_	_
26	11.5	11.5	CD	_	_	_
27	software	software	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	intensity	intensity	NN	_	_	_
4	cell	cell	NN	_	_	_
5	files	file	NNS	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	imported	import	VBN	_	_	_
9	,	,	,	_	_	_
10	normalized	normalize	VBN	_	_	_
11	for	for	IN	_	_	_
12	background	background	NN	_	_	_
13	correction	correction	NN	_	_	_
14	using	use	VBG	_	_	_
15	PLIER	plier	NN	_	_	_
16	and	and	CC	_	_	_
17	data	datum	NNS	_	_	_
18	analysed	analyse	VBN	_	_	_
19	using	use	VBG	_	_	_
20	Gene	Gene	NNP	_	_	_
21	Spring	Spring	NNP	_	_	_
22	11.5	11.5	CD	_	_	_
23	software	software	NN	_	_	_
24	.	.	.	_	_	_

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	/	/	:	_	_	_
18	Standard	standard	JJ	_	_	_
19	Deviation	deviation	NN	_	_	_
20	of	of	IN	_	_	_
21	Background	background	NN	_	_	_
22	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	between	between	IN	_	_	_
3	each	each	DT	_	_	_
4	array	array	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	an	a	DT	_	_	_
9	internal	internal	JJ	_	_	_
10	labeling	labeling	NN	_	_	_
11	control	control	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	IC	ic	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	consisting	consist	VBG	_	_	_
16	of	of	IN	_	_	_
17	a	a	DT	_	_	_
18	290	290	CD	_	_	_
19	bp	bp	NN	_	_	_
20	luxA	luxa	NN	_	_	_
21	fragment	fragment	NN	_	_	_
22	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	fragment	fragment	NN	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	each	each	DT	_	_	_
7	labeling	labeling	NN	_	_	_
8	reaction	reaction	NN	_	_	_
9	at	at	IN	_	_	_
10	a	a	DT	_	_	_
11	ratio	ratio	NN	_	_	_
12	of	of	IN	_	_	_
13	0.05	0.05	CD	_	_	_
14	%	%	NN	_	_	_
15	of	of	IN	_	_	_
16	the	the	DT	_	_	_
17	DNA	dna	NN	_	_	_
18	to	to	TO	_	_	_
19	be	be	VB	_	_	_
20	labeled	label	VBN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	intensity	intensity	NN	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	Cy5-sample	cy5-sample	JJ	_	_	_
6	gene	gene	NN	_	_	_
7	spot	spot	NN	_	_	_
8	was	be	VBD	_	_	_
9	corrected	correct	VBN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	average	average	JJ	_	_	_
13	intensity	intensity	NN	_	_	_
14	of	of	IN	_	_	_
15	all	all	DT	_	_	_
16	Cy3-lambda	cy3-lambda	NN	_	_	_
17	signals	signal	NNS	_	_	_
18	.	.	.	_	_	_

1	Corrected	correct	VBN	_	_	_
2	intensity	intensity	NN	_	_	_
3	values	value	NNS	_	_	_
4	were	be	VBD	_	_	_
5	averaged	average	VBN	_	_	_
6	over	over	IN	_	_	_
7	triplicate	triplicate	NN	_	_	_
8	spots	spot	NNS	_	_	_
9	to	to	TO	_	_	_
10	give	give	VB	_	_	_
11	a	a	DT	_	_	_
12	single	single	JJ	_	_	_
13	value	value	NN	_	_	_
14	per	per	IN	_	_	_
15	gene	gene	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	intensity	intensity	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	genes	gene	NNS	_	_	_
6	for	for	IN	_	_	_
7	which	which	WDT	_	_	_
8	hybridization	hybridization	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	probes	probe	NNS	_	_	_
12	could	could	MD	_	_	_
13	not	not	RB	_	_	_
14	be	be	VB	_	_	_
15	visually	visually	RB	_	_	_
16	detected	detect	VBN	_	_	_
17	in	in	IN	_	_	_
18	image	image	NN	_	_	_
19	analysis	analysis	NN	_	_	_
20	was	be	VBD	_	_	_
21	set	set	VBN	_	_	_
22	to	to	TO	_	_	_
23	zero	zero	CD	_	_	_
24	.	.	.	_	_	_

1	Relative	relative	JJ	_	_	_
2	intensity	intensity	NN	_	_	_
3	values	value	NNS	_	_	_
4	were	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	calculated	calculate	VBN	_	_	_
7	by	by	IN	_	_	_
8	dividing	divide	VBG	_	_	_
9	the	the	DT	_	_	_
10	intensity	intensity	NN	_	_	_
11	of	of	IN	_	_	_
12	a	a	DT	_	_	_
13	gene	gene	NN	_	_	_
14	by	by	IN	_	_	_
15	the	the	DT	_	_	_
16	sum	sum	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	intensity	intensity	NN	_	_	_
20	for	for	IN	_	_	_
21	all	all	DT	_	_	_
22	genes	gene	NNS	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	excluding	exclude	VBG	_	_	_
25	controls	control	NNS	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	``	``	``	_	_	_
3	relative	relative	JJ	_	_	_
4	abundance	abundance	NN	_	_	_
5	''	''	''	_	_	_
6	represents	represent	VBZ	_	_	_
7	the	the	DT	_	_	_
8	fraction	fraction	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	total	total	JJ	_	_	_
12	intensity	intensity	NN	_	_	_
13	that	that	WDT	_	_	_
14	is	be	VBZ	_	_	_
15	due	due	JJ	_	_	_
16	to	to	TO	_	_	_
17	a	a	DT	_	_	_
18	particular	particular	JJ	_	_	_
19	gene	gene	NN	_	_	_
20	and	and	CC	_	_	_
21	this	this	DT	_	_	_
22	value	value	NN	_	_	_
23	was	be	VBD	_	_	_
24	subsequently	subsequently	RB	_	_	_
25	used	use	VBN	_	_	_
26	in	in	IN	_	_	_
27	statistical	statistical	JJ	_	_	_
28	analyses	analysis	NNS	_	_	_
29	.	.	.	_	_	_

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	The	the	DT	_	_	_
3	in	in	FW	_	_	_
4	vivo	vivo	FW	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	harvested	harvest	VBN	_	_	_
9	with	with	IN	_	_	_
10	two-step	two-step	JJ	_	_	_
11	centrifugation	centrifugation	NN	_	_	_
12	.	.	.	_	_	_

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	The	the	DT	_	_	_
3	isolated	isolate	VBN	_	_	_
4	persisters	persister	NNS	_	_	_
5	were	be	VBD	_	_	_
6	incubated	incubate	VBN	_	_	_
7	in	in	IN	_	_	_
8	0.85	0.85	CD	_	_	_
9	%	%	NN	_	_	_
10	NaCl	nacl	NN	_	_	_
11	solution	solution	NN	_	_	_
12	for	for	IN	_	_	_
13	1	1	CD	_	_	_
14	h	h	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	200	200	CD	_	_	_
17	rpm	rpm	NN	_	_	_
18	,	,	,	_	_	_
19	37oC	37oc	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	with	with	IN	_	_	_
22	or	or	CC	_	_	_
23	without	without	IN	_	_	_
24	5	5	CD	_	_	_
25	µg/mL	µg/ml	NN	_	_	_
26	BF8	bf8	NN	_	_	_
27	.	.	.	_	_	_

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/L	g/l	NN	_	_	_
38	of	of	IN	_	_	_
39	anhydrous	anhydrous	JJ	_	_	_
40	glucose	glucose	NN	SUPP	_	_
41	,	,	,	_	_	_
42	and	and	CC	_	_	_
43	inoculated	inoculate	VBN	_	_	_
44	at	at	IN	_	_	_
45	108	108	CD	_	_	_
46	CFU/mL	cfu/ml	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	corresponding	correspond	VBG	_	_	_
49	to	to	TO	_	_	_
50	an	a	DT	_	_	_
51	optical	optical	JJ	_	_	_
52	density	density	NN	_	_	_
53	at	at	IN	_	_	_
54	595	595	CD	_	_	_
55	nm	nm	NN	_	_	_
56	-LSB-	-lsb-	-LRB-	_	_	_
57	OD595	od595	CD	_	_	_
58	nm	nm	NN	_	_	_
59	-RSB-	-rsb-	-RRB-	_	_	_
60	of	of	IN	_	_	_
61	0.12	0.12	CD	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	inoculum	inoculum	NN	_	_	_
3	for	for	IN	_	_	_
4	this	this	DT	_	_	_
5	culture	culture	NN	_	_	_
6	was	be	VBD	_	_	_
7	prepared	prepare	VBN	_	_	_
8	in	in	IN	_	_	_
9	40	40	CD	_	_	_
10	mL	ml	NN	_	_	_
11	M9	m9	NN	_	_	_
12	broth	broth	NN	_	_	_
13	inoculated	inoculate	VBN	_	_	_
14	with	with	IN	_	_	_
15	approximately	approximately	RB	_	_	_
16	1.5	1.5	CD	_	_	_
17	x107	x107	CD	_	_	_
18	CFU/mL	cfu/ml	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	corresponding	correspond	VBG	_	_	_
21	to	to	TO	_	_	_
22	an	a	DT	_	_	_
23	OD595	od595	NN	_	_	_
24	nm	nm	NN	_	_	_
25	of	of	IN	_	_	_
26	0.12	0.12	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	incubated	incubate	VBN	_	_	_
30	overnight	overnight	JJ	_	_	_
31	under	under	IN	_	_	_
32	the	the	DT	_	_	_
33	same	same	JJ	_	_	_
34	conditions	condition	NNS	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	37	37	CD	_	_	_
37	°C	°c	NN	_	_	_
38	,	,	,	_	_	_
39	120	120	CD	_	_	_
40	rpm	rpm	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	inoculum	inoculum	NN	_	_	_
3	was	be	VBD	_	_	_
4	obtained	obtain	VBN	_	_	_
5	by	by	IN	_	_	_
6	adding	add	VBG	_	_	_
7	1	1	CD	_	_	_
8	mL	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	stock	stock	NN	_	_	_
11	culture	culture	NN	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	bacterial	bacterial	JJ	_	_	_
15	cells	cell	NNS	_	_	_
16	in	in	IN	_	_	_
17	5	5	CD	_	_	_
18	mL	ml	NN	_	_	_
19	of	of	IN	_	_	_
20	Luria	Luria	NNP	_	_	_
21	Bertani	Bertani	NNP	_	_	_
22	broth	broth	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Biokar	biokar	JJ	_	_	_
25	Diagnotics	diagnotic	NNS	_	_	_
26	,	,	,	_	_	_
27	PRS	prs	NN	_	_	_
28	Panreac	panreac	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	in	in	IN	_	_	_
31	a	a	DT	_	_	_
32	15-mL	15-ml	JJ	_	_	_
33	half-opened	half-opened	JJ	_	_	_
34	BD	bd	NN	_	_	_
35	FalconTM	falcontm	NN	_	_	_
36	tube	tube	NN	_	_	_
37	,	,	,	_	_	_
38	followed	follow	VBN	_	_	_
39	by	by	IN	_	_	_
40	8	8	CD	_	_	_
41	h	h	NN	_	_	_
42	of	of	IN	_	_	_
43	incubation	incubation	NN	_	_	_
44	at	at	IN	_	_	_
45	37	37	CD	_	_	_
46	°C	°c	NN	_	_	_
47	and	and	CC	_	_	_
48	120	120	CD	_	_	_
49	rpm	rpm	NN	_	_	_
50	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	generated	generate	VBN	_	_	_
6	by	by	IN	_	_	_
7	Vertis	Vertis	NNP	_	_	_
8	Biotechnologie	Biotechnologie	NNP	_	_	_
9	AG	AG	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Munich	Munich	NNP	_	_	_
12	,	,	,	_	_	_
13	Germany	Germany	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

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/μl	ng/μl	NN	_	_	_
13	using	use	VBG	_	_	_
14	a	a	DT	_	_	_
15	high	high	JJ	_	_	_
16	fidelity	fidelity	NN	_	_	_
17	DNA	dna	NN	_	_	_
18	polymerase	polymerase	NN	_	_	_
19	.	.	.	_	_	_

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	Agencourt	Agencourt	NNP	_	_	_
8	AMPure	AMPure	NNP	_	_	_
9	XP	xp	NN	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Beckman	Beckman	NNP	_	_	_
13	Coulter	Coulter	NNP	_	_	_
14	Genomics	Genomics	NNPS	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	was	be	VBD	_	_	_
18	analyzed	analyze	VBN	_	_	_
19	by	by	IN	_	_	_
20	capillary	capillary	JJ	_	_	_
21	electrophoresis	electrophoresis	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	primers	primer	NNS	_	_	_
3	used	use	VBN	_	_	_
4	for	for	IN	_	_	_
5	PCR	pcr	NN	_	_	_
6	amplification	amplification	NN	_	_	_
7	were	be	VBD	_	_	_
8	designed	design	VBN	_	_	_
9	for	for	IN	_	_	_
10	TruSeq	TruSeq	NNP	_	_	_
11	sequencing	sequencing	NN	_	_	_
12	according	accord	VBG	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	instructions	instruction	NNS	_	_	_
16	of	of	IN	_	_	_
17	Illumina	Illumina	NNP	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	The	The	NNP	_	_	_
20	log10	log10	NN	_	_	_
21	mRNA	mrna	NN	_	_	_
22	concentration	concentration	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	pM	pm	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	data	datum	NNS	_	_	_
27	are	be	VBP	_	_	_
28	provided	provide	VBN	_	_	_
29	as	as	IN	_	_	_
30	a	a	DT	_	_	_
31	supplementary	supplementary	JJ	_	_	_
32	file	file	NN	_	_	_
33	on	on	IN	_	_	_
34	the	the	DT	_	_	_
35	SERIES	series	NN	_	_	_
36	record	record	NN	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	log2-ratio	log2-ratio	NN	_	_	_
4	is	be	VBZ	_	_	_
5	computed	compute	VBN	_	_	_
6	and	and	CC	_	_	_
7	scaled	scale	VBN	_	_	_
8	to	to	TO	_	_	_
9	center	center	VB	_	_	_
10	the	the	DT	_	_	_
11	ratio	ratio	NN	_	_	_
12	data	datum	NNS	_	_	_
13	around	around	IN	_	_	_
14	zero	zero	CD	_	_	_
15	.	.	.	_	_	_

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	The	the	DT	_	_	_
3	`	`	``	_	_	_
4	LogRatio	LogRatio	NNP	_	_	_
5	'	'	''	_	_	_
6	value	value	NN	_	_	_
7	was	be	VBD	_	_	_
8	used	use	VBN	_	_	_
9	in	in	IN	_	_	_
10	subsequent	subsequent	JJ	_	_	_
11	analyses	analysis	NNS	_	_	_
12	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	lysates	lysate	NNS	_	_	_
4	were	be	VBD	_	_	_
5	applied	apply	VBN	_	_	_
6	to	to	TO	_	_	_
7	gDNA	gdna	NN	_	_	_
8	removal	removal	NN	_	_	_
9	columns	column	NNS	_	_	_
10	and	and	CC	_	_	_
11	rRNA	rrna	NN	_	_	_
12	was	be	VBD	_	_	_
13	removed	remove	VBN	_	_	_
14	from	from	IN	_	_	_
15	total	total	JJ	_	_	_
16	RNA	rna	NN	_	_	_
17	using	use	VBG	_	_	_
18	a	a	DT	_	_	_
19	Ribo-Zero	Ribo-Zero	NNP	_	_	_
20	rRNA	rrna	NN	_	_	_
21	removal	removal	NN	_	_	_
22	kit	kit	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Illumina	Illumina	NNP	_	_	_
25	,	,	,	_	_	_
26	UK	UK	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	following	follow	VBG	_	_	_
29	the	the	DT	_	_	_
30	manufacture	manufacture	NN	_	_	_
31	's	's	POS	_	_	_
32	instruction	instruction	NN	_	_	_
33	for	for	IN	_	_	_
34	Gram-positive	gram-positive	JJ	_	_	_
35	bacteria	bacterium	NNS	_	_	_
36	.	.	.	_	_	_

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	MACS	macs	NN	_	_	_
4	2.1.0	2.1.0	CD	_	_	_
5	software	software	NN	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	to	to	TO	_	_	_
9	call	call	VB	_	_	_
10	peaks	peak	NNS	_	_	_
11	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	mean	mean	JJ	_	_	_
4	signal	signal	NN	_	_	_
5	intensity	intensity	NN	_	_	_
6	values	value	NNS	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	duplicate	duplicate	VB	_	_	_
10	spots	spot	NNS	_	_	_
11	were	be	VBD	_	_	_
12	averaged	average	VBN	_	_	_
13	and	and	CC	_	_	_
14	then	then	RB	_	_	_
15	normalized	normalize	VBN	_	_	_
16	by	by	IN	_	_	_
17	the	the	DT	_	_	_
18	global	global	JJ	_	_	_
19	normalization	normalization	NN	_	_	_
20	method	method	NN	_	_	_
21	.	.	.	_	_	_

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	The	the	DT	_	_	_
3	measured	measure	VBN	_	_	_
4	lifetime	lifetime	NN	_	_	_
5	of	of	IN	_	_	_
6	mRNA	mrna	NN	_	_	_
7	is	be	VBZ	_	_	_
8	available	available	JJ	_	_	_
9	as	as	IN	_	_	_
10	a	a	DT	_	_	_
11	supplementary	supplementary	JJ	_	_	_
12	file	file	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	real_rna_life.txt	real_rna_life.txt	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	Series	Series	NNP	_	_	_
19	record	record	NN	_	_	_
20	.	.	.	_	_	_

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/min	ml/min	NN	_	_	_
18	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	8	8	CD	_	_	_
3	h	h	NN	_	_	_
4	inoculation	inoculation	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	feeding	feeding	NN	_	_	_
8	and	and	CC	_	_	_
9	outlet	outlet	NN	_	_	_
10	pumps	pump	NNS	_	_	_
11	were	be	VBD	_	_	_
12	started	start	VBN	_	_	_
13	at	at	IN	_	_	_
14	flow	flow	NN	_	_	_
15	rate	rate	NN	_	_	_
16	of	of	IN	_	_	_
17	0.166	0.166	CD	_	_	_
18	mL/h	ml/h	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	dilution	dilution	NN	_	_	_
21	rate	rate	NN	_	_	_
22	=	=	JJ	_	_	_
23	0.1	0.1	CD	_	_	_
24	h-1	h-1	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

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/min	ml/min	NN	_	_	_
18	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	8	8	CD	_	_	_
3	h	h	NN	_	_	_
4	inoculation	inoculation	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	feeding	feeding	NN	_	_	_
8	and	and	CC	_	_	_
9	outlet	outlet	NN	_	_	_
10	pumps	pump	NNS	_	_	_
11	were	be	VBD	_	_	_
12	started	start	VBN	_	_	_
13	at	at	IN	_	_	_
14	flow	flow	NN	_	_	_
15	rate	rate	NN	_	_	_
16	of	of	IN	_	_	_
17	0.166	0.166	CD	_	_	_
18	mL/h	ml/h	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	dilution	dilution	NN	_	_	_
21	rate	rate	NN	_	_	_
22	=	=	JJ	_	_	_
23	0.1	0.1	CD	_	_	_
24	h-1	h-1	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

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/L	g/l	NN	_	_	_
64	to	to	TO	_	_	_
65	160	160	CD	_	_	_
66	g/L	g/l	NN	_	_	_
67	during	during	IN	_	_	_
68	9	9	CD	_	_	_
69	months	month	NNS	_	_	_
70	.	.	.	_	_	_

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	8	8	CD	_	_	_
13	.	.	.	_	_	_

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	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/L	g/l	NN	_	_	_
64	to	to	TO	_	_	_
65	160	160	CD	_	_	_
66	g/L	g/l	NN	_	_	_
67	during	during	IN	_	_	_
68	9	9	CD	_	_	_
69	months	month	NNS	_	_	_
70	.	.	.	_	_	_

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	8	8	CD	_	_	_
13	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	microarray	microarray	NN	_	_	_
4	data	datum	NNS	_	_	_
5	files	file	NNS	_	_	_
6	were	be	VBD	_	_	_
7	processed	process	VBN	_	_	_
8	using	use	VBG	_	_	_
9	statistical	statistical	JJ	_	_	_
10	software	software	NN	_	_	_
11	R	r	NN	_	_	_
12	version	version	NN	_	_	_
13	3.0.1	3.0.1	CD	_	_	_
14	and	and	CC	_	_	_
15	Bioconductor	Bioconductor	NNP	_	_	_
16	packages	package	NNS	_	_	_
17	.	.	.	_	_	_

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	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	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	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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	MiSeq	MiSeq	NNP	_	_	_
4	Reporter	reporter	NN	_	_	_
5	MiSeq	miseq	NN	_	_	_
6	Reporter	reporter	NN	_	_	_
7	2.4.60.8	2.4.60.8	CD	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	basecalling	basecalling	NN	_	_	_
12	and	and	CC	_	_	_
13	demultiplexing	demultiplex	VBG	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	The	the	DT	_	_	_
16	normalized	normalize	VBN	_	_	_
17	data	datum	NNS	_	_	_
18	can	can	MD	GEN	_	_
19	be	be	VB	_	_	_
20	found	find	VBN	_	_	_
21	on	on	IN	_	_	_
22	the	the	DT	_	_	_
23	series	series	NN	_	_	_
24	record	record	NN	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	file	file	NN	_	_	_
28	\	\	SYM	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
30	The	the	DT	_	_	_
31	number	number	NN	_	_	_
32	of	of	IN	_	_	_
33	R1	r1	NN	_	_	_
34	reads	read	VBZ	_	_	_
35	mapping	map	VBG	_	_	_
36	to	to	TO	_	_	_
37	each	each	DT	_	_	_
38	gene	gene	NN	_	_	_
39	were	be	VBD	_	_	_
40	counted	count	VBN	_	_	_
41	using	use	VBG	_	_	_
42	HTSeq	htseq	NN	_	_	_
43	0.6.0	0.6.0	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
45	The	the	DT	_	_	_
46	number	number	NN	_	_	_
47	of	of	IN	_	_	_
48	reads	read	VBZ	_	_	_
49	at	at	IN	_	_	_
50	each	each	DT	_	_	_
51	position	position	NN	_	_	_
52	in	in	IN	_	_	_
53	the	the	DT	_	_	_
54	genome	genome	NN	_	_	_
55	was	be	VBD	_	_	_
56	counted	count	VBN	_	_	_
57	using	use	VBG	_	_	_
58	in-house	in-house	JJ	_	_	_
59	Python	Python	NNP	_	_	_
60	scripts	script	NNS	_	_	_
61	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	number	number	NN	_	_	_
4	of	of	IN	_	_	_
5	reads	read	VBZ	_	_	_
6	overlapping	overlap	VBG	_	_	_
7	each	each	DT	_	_	_
8	gene	gene	NN	_	_	_
9	was	be	VBD	_	_	_
10	recorded	record	VBN	_	_	_
11	and	and	CC	_	_	_
12	normalized	normalize	VBN	_	_	_
13	based	base	VBN	_	_	_
14	on	on	IN	_	_	_
15	reads	read	VBZ	_	_	_
16	per	per	IN	_	_	_
17	kilobase	kilobase	NN	_	_	_
18	per	per	IN	_	_	_
19	million	million	CD	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	RPKM	rpkm	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	uniquely	uniquely	RB	_	_	_
24	mapped	map	VBD	_	_	_
25	reads	read	VBZ	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	number	number	NN	_	_	_
4	of	of	IN	_	_	_
5	sequence	sequence	NN	_	_	_
6	reads	read	VBZ	_	_	_
7	that	that	IN	_	_	_
8	aligned	align	VBN	_	_	_
9	to	to	TO	_	_	_
10	features	feature	NNS	_	_	_
11	in	in	IN	_	_	_
12	annotation	annotation	NN	_	_	_
13	file	file	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Escherichia	escherichia	FW	_	_	_
16	_	_	FW	_	_	_
17	coli	coli	FW	_	_	_
18	_	_	SYM	_	_	_
19	str	str	FW	_	_	_
20	_	_	FW	_	_	_
21	k	k	NN	_	_	_
22	_	_	SYM	_	_	_
23	12	12	CD	_	_	_
24	_	_	SYM	_	_	_
25	substr	substr	FW	_	_	_
26	_	_	FW	_	_	_
27	mg1655.GCA	mg1655.gca	NN	_	_	_
28	_	_	SYM	_	_	_
29	000005845.2.24	000005845.2.24	CD	_	_	_
30	.	.	.	_	_	_

1	gtf	gtf	NN	_	_	_
2	from	from	IN	_	_	_
3	http://bacteria.ensembl.org	http://bacteria.ensembl.org	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	were	be	VBD	_	_	_
6	tabulated	tabulate	VBN	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	resulting	result	VBG	_	_	_
10	SAM	SAM	NNP	_	_	_
11	alignment	alignment	NN	_	_	_
12	files	file	NNS	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	HTSeq-count	htseq-count	JJ	_	_	_
16	program	program	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Anders	Anders	NNP	_	_	_
19	et	et	FW	_	_	_
20	al.	al.	FW	_	_	_
21	,	,	,	_	_	_
22	2015	2015	CD	_	_	_
23	,	,	,	_	_	_
24	Bioinformatics	bioinformatic	NNS	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	with	with	IN	_	_	_
27	intersection	intersection	NN	_	_	_
28	non-empty	non-empty	JJ	_	_	_
29	mode	mode	NN	_	_	_
30	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
16	The	the	DT	_	_	_
17	numbers	number	NNS	_	_	_
18	of	of	IN	_	_	_
19	4	4	CD	_	_	_
20	bases	basis	NNS	_	_	_
21	A	a	DT	_	_	_
22	,	,	,	_	_	_
23	T	t	NN	_	_	_
24	,	,	,	_	_	_
25	G	g	NN	_	_	_
26	,	,	,	_	_	_
27	C	c	NN	_	_	_
28	,	,	,	_	_	_
29	and	and	CC	_	_	_
30	N	n	NN	_	_	_
31	were	be	VBD	_	_	_
32	counted	count	VBN	_	_	_
33	in	in	IN	_	_	_
34	each	each	DT	_	_	_
35	position	position	NN	_	_	_
36	of	of	IN	_	_	_
37	the	the	DT	_	_	_
38	mapped	map	VBN	_	_	_
39	reads	read	VBZ	_	_	_
40	by	by	IN	_	_	_
41	using	use	VBG	_	_	_
42	the	the	DT	_	_	_
43	program	program	NN	_	_	_
44	SAMtools	samtool	NNS	_	_	_
45	0.1.18	0.1.18	CD	_	_	_
46	with	with	IN	_	_	_
47	supplemental	supplemental	JJ	_	_	_
48	use	use	NN	_	_	_
49	of	of	IN	_	_	_
50	a	a	DT	_	_	_
51	Perl	Perl	NNP	_	_	_
52	script	script	NN	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Theobald	Theobald	NNP	_	_	_
3	,	,	,	_	_	_
4	U.	U.	NNP	_	_	_
5	,	,	,	_	_	_
6	Mailinger	Mailinger	NNP	_	_	_
7	,	,	,	_	_	_
8	W.	W.	NNP	_	_	_
9	,	,	,	_	_	_
10	Baltes	Baltes	NNP	_	_	_
11	,	,	,	_	_	_
12	M.	M.	NNP	_	_	_
13	,	,	,	_	_	_
14	Rizzi	Rizzi	NNP	_	_	_
15	,	,	,	_	_	_
16	M.	M.	NNP	_	_	_
17	,	,	,	_	_	_
18	Reuss	Reuss	NNP	_	_	_
19	,	,	,	_	_	_
20	M.	M.	NNP	_	_	_
21	,	,	,	_	_	_
22	1997	1997	CD	_	_	_
23	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	optical	optical	JJ	_	_	_
4	density	density	NN	_	_	_
5	was	be	VBD	_	_	_
6	measured	measure	VBN	_	_	_
7	every	every	DT	_	_	_
8	30	30	CD	_	_	_
9	min	min	NN	_	_	_
10	and	and	CC	_	_	_
11	expression	expression	NN	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	heterologous	heterologous	JJ	_	_	_
15	sigma	sigma	NN	_	_	_
16	factor	factor	NN	_	_	_
17	was	be	VBD	_	_	_
18	induced	induce	VBN	_	_	_
19	with	with	IN	_	_	_
20	1mM	1mm	NN	_	_	_
21	IPTG	iptg	NN	_	_	_
22	at	at	IN	_	_	_
23	an	a	DT	_	_	_
24	optical	optical	JJ	_	_	_
25	density	density	NN	_	_	_
26	of	of	IN	_	_	_
27	0.1	0.1	CD	_	_	_
28	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	0.25	0.25	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	25	25	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	fresh	fresh	JJ	_	_	_
17	LB	lb	NN	MED	_	_
18	medium	medium	NN	MED	_	_
19	.	.	.	_	_	_

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	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	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/mL	μg/ml	NN	_	_	_
35	ampicillin	ampicillin	NN	_	_	_
36	with	with	IN	_	_	_
37	1	1	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	IPTG	iptg	NN	_	_	_
40	for	for	IN	_	_	_
41	1	1	CD	_	_	_
42	h.	h.	NN	_	_	_
43	Cells	cell	NNS	_	_	_
44	were	be	VBD	_	_	_
45	isolated	isolate	VBN	_	_	_
46	by	by	IN	_	_	_
47	centrifuging	centrifuge	VBG	_	_	_
48	at	at	IN	_	_	_
49	0	0	CD	_	_	_
50	°C	°c	NN	_	_	_
51	,	,	,	_	_	_
52	and	and	CC	_	_	_
53	RNALater	rnalater	NN	_	_	_
54	buffer	buffer	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Ambion	Ambion	NNP	_	_	_
57	,	,	,	_	_	_
58	Cat	Cat	NNP	_	_	_
59	#	#	#	_	_	_
60	AM7021	am7021	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	was	be	VBD	_	_	_
63	added	add	VBN	_	_	_
64	to	to	TO	_	_	_
65	stabilize	stabilize	VB	_	_	_
66	RNA	rna	NN	_	_	_
67	during	during	IN	_	_	_
68	the	the	DT	_	_	_
69	RNA	rna	NN	_	_	_
70	preparation	preparation	NN	_	_	_
71	steps	step	NNS	_	_	_
72	.	.	.	_	_	_

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	the	the	DT	_	_	_
11	total	total	JJ	_	_	_
12	RNA	rna	NN	_	_	_
13	was	be	VBD	_	_	_
14	isolated	isolate	VBN	_	_	_
15	with	with	IN	_	_	_
16	Qiagen	Qiagen	NNP	_	_	_
17	RNeasy	RNeasy	NNP	_	_	_
18	mini	minus	NNS	_	_	_
19	Kit	kit	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Cat	cat	NN	_	_	_
22	#	#	#	_	_	_
23	74104	74104	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	The	the	DT	_	_	_
27	overnight	overnight	JJ	_	_	_
28	culture	culture	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	0.25	0.25	CD	_	_	_
31	mL	ml	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	was	be	VBD	_	_	_
34	used	use	VBN	_	_	_
35	to	to	TO	_	_	_
36	inoculate	inoculate	VB	_	_	_
37	25	25	CD	_	_	_
38	mL	ml	NN	_	_	_
39	of	of	IN	_	_	_
40	fresh	fresh	JJ	_	_	_
41	LB	lb	NN	MED	_	_
42	medium	medium	NN	MED	_	_
43	.	.	.	_	_	_

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/mL	μg/ml	NN	_	_	_
35	ampicillin	ampicillin	NN	_	_	_
36	with	with	IN	_	_	_
37	1	1	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	IPTG	iptg	NN	_	_	_
40	for	for	IN	_	_	_
41	1	1	CD	_	_	_
42	h.	h.	NN	_	_	_
43	Cells	cell	NNS	_	_	_
44	were	be	VBD	_	_	_
45	isolated	isolate	VBN	_	_	_
46	by	by	IN	_	_	_
47	centrifuging	centrifuge	VBG	_	_	_
48	at	at	IN	_	_	_
49	0	0	CD	_	_	_
50	°C	°c	NN	_	_	_
51	,	,	,	_	_	_
52	and	and	CC	_	_	_
53	RNALater	rnalater	NN	_	_	_
54	buffer	buffer	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Ambion	Ambion	NNP	_	_	_
57	,	,	,	_	_	_
58	Cat	Cat	NNP	_	_	_
59	#	#	#	_	_	_
60	AM7021	am7021	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	was	be	VBD	_	_	_
63	added	add	VBN	_	_	_
64	to	to	TO	_	_	_
65	stabilize	stabilize	VB	_	_	_
66	RNA	rna	NN	_	_	_
67	during	during	IN	_	_	_
68	the	the	DT	_	_	_
69	RNA	rna	NN	_	_	_
70	preparation	preparation	NN	_	_	_
71	steps	step	NNS	_	_	_
72	.	.	.	_	_	_

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	the	the	DT	_	_	_
11	total	total	JJ	_	_	_
12	RNA	rna	NN	_	_	_
13	was	be	VBD	_	_	_
14	isolated	isolate	VBN	_	_	_
15	with	with	IN	_	_	_
16	Qiagen	Qiagen	NNP	_	_	_
17	RNeasy	RNeasy	NNP	_	_	_
18	mini	minus	NNS	_	_	_
19	Kit	kit	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Cat	cat	NN	_	_	_
22	#	#	#	_	_	_
23	74104	74104	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

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	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	.	.	.	_	_	_

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	``	``	``	_	_	_
28	The	the	DT	_	_	_
29	overnight	overnight	JJ	_	_	_
30	culture	culture	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	2.5	2.5	CD	_	_	_
33	ml	ml	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	was	be	VBD	_	_	_
36	used	use	VBN	_	_	_
37	to	to	TO	_	_	_
38	inoculate	inoculate	VB	_	_	_
39	250	250	CD	_	_	_
40	ml	ml	NN	_	_	_
41	of	of	IN	_	_	_
42	fresh	fresh	JJ	_	_	_
43	LB	lb	NN	MED	_	_
44	medium	medium	NN	MED	_	_
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	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	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	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	-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	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	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	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	cultures	culture	NNS	_	_	_
5	of	of	IN	_	_	_
6	bacteria	bacterium	NNS	_	_	_
7	in	in	IN	_	_	_
8	LB	lb	NN	MED	_	_
9	broth	broth	NN	MED	_	_
10	were	be	VBD	_	_	_
11	refreshed	refresh	VBN	_	_	_
12	with	with	IN	_	_	_
13	the	the	DT	_	_	_
14	ratio	ratio	NN	_	_	_
15	of	of	IN	_	_	_
16	1:100	1:100	CD	_	_	_
17	into	into	IN	_	_	_
18	fresh	fresh	JJ	_	_	_
19	LB	lb	NN	MED	_	_
20	broth	broth	NN	MED	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	incubated	incubate	VBN	_	_	_
24	at	at	IN	_	_	_
25	30	30	CD	_	_	_
26	℃	℃	NN	_	_	_
27	with	with	IN	_	_	_
28	continuous	continuous	JJ	_	_	_
29	shaking	shake	VBG	_	_	_
30	until	until	IN	_	_	_
31	the	the	DT	_	_	_
32	absorbance	absorbance	NN	_	_	_
33	at	at	IN	_	_	_
34	590	590	CD	_	_	_
35	nm	nm	NN	_	_	_
36	reached	reach	VBD	_	_	_
37	0.5	0.5	CD	_	_	_
38	to	to	TO	_	_	_
39	0.6	0.6	CD	_	_	_
40	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
26	The	the	DT	_	_	_
27	parent	parent	NN	_	_	_
28	strain	strain	NN	_	_	_
29	,	,	,	_	_	_
30	AG102	ag102	NN	_	_	_
31	,	,	,	_	_	_
32	was	be	VBD	_	_	_
33	previously	previously	RB	_	_	_
34	derived	derive	VBN	_	_	_
35	from	from	IN	_	_	_
36	AG100	ag100	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	K-12	k-12	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	pCA24N,-gfp	pca24n,-gfp	NN	_	_	_
4	/	/	:	_	_	_
5	DA4201	da4201	NN	_	_	_
6	cultures	culture	NNS	_	_	_
7	and	and	CC	_	_	_
8	two	two	CD	_	_	_
9	cultures	culture	NNS	_	_	_
10	each	each	DT	_	_	_
11	of	of	IN	_	_	_
12	Svi3-3	svi3-3	NN	_	_	_
13	comp	comp	NN	_	_	_
14	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	recoded	recode	VBN	_	_	_
3	Svi3-3	svi3-3	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	/	/	:	_	_	_
6	DA4201	da4201	NN	_	_	_
7	and	and	CC	_	_	_
8	pORF1/DA4201	porf1/da4201	NN	_	_	_
9	were	be	VBD	_	_	_
10	supplemented	supplement	VBN	_	_	_
11	by	by	IN	_	_	_
12	50	50	CD	_	_	_
13	μM	μm	NN	_	_	_
14	IPTG	iptg	NN	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	OD	od	NN	_	_	_
7	0.15-0.2	0.15-0.2	CD	_	_	_
8	and	and	CC	_	_	_
9	cells	cell	NNS	_	_	_
10	were	be	VBD	_	_	_
11	withdrawn	withdraw	VBN	_	_	_
12	for	for	IN	_	_	_
13	RNA	rna	NN	_	_	_
14	extraction	extraction	NN	_	_	_
15	and	and	CC	_	_	_
16	whole	whole	JJ	_	_	_
17	cell	cell	NN	_	_	_
18	proteomics	proteomic	NNS	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	pre-culture	pre-culture	JJ	_	_	_
4	was	be	VBD	_	_	_
5	the	the	DT	_	_	_
6	overnight	overnight	JJ	_	_	_
7	propagated	propagate	VBN	_	_	_
8	cells	cell	NNS	_	_	_
9	in	in	IN	_	_	_
10	5	5	CD	_	_	_
11	ml	ml	NN	_	_	_
12	of	of	IN	_	_	_
13	LB	lb	NN	MED	_	_
14	medium	medium	NN	MED	_	_
15	at	at	IN	_	_	_
16	37ºC	37ºc	NN	_	_	_
17	and	and	CC	_	_	_
18	180	180	CD	_	_	_
19	rpm	rpm	NN	_	_	_
20	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	probe	probe	NN	_	_	_
4	intensity	intensity	NN	_	_	_
5	data	datum	NNS	_	_	_
6	was	be	VBD	_	_	_
7	analyzed	analyze	VBN	_	_	_
8	using	use	VBG	_	_	_
9	Genetraffic	genetraffic	JJ	_	_	_
10	software	software	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Iobion	Iobion	NNP	_	_	_
13	Informatics	Informatics	NNPS	_	_	_
14	LLC	LLC	NNP	_	_	_
15	,	,	,	_	_	_
16	La	La	NNP	_	_	_
17	Jolla	Jolla	NNP	_	_	_
18	,	,	,	_	_	_
19	CA	CA	NNP	_	_	_
20	,	,	,	_	_	_
21	USA	USA	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

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	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/non-reference	reference/non-reference	NN	_	_	_
16	bases	basis	NNS	_	_	_
17	,	,	,	_	_	_
18	read	read	VBD	_	_	_
19	count	count	NN	_	_	_
20	,	,	,	_	_	_
21	the	the	DT	_	_	_
22	fraction	fraction	NN	_	_	_
23	of	of	IN	_	_	_
24	3	3	CD	_	_	_
25	'	'	''	_	_	_
26	RNA	rna	NN	_	_	_
27	end	end	NN	_	_	_
28	,	,	,	_	_	_
29	DNA	dna	NN	_	_	_
30	strand	strand	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	+	+	CC	_	_	_
33	/	/	:	_	_	_
34	-	-	:	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	gene	gene	NN	_	_	_
38	name	name	NN	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	mapping/base	mapping/base	NN	_	_	_
42	qualities	quality	NNS	_	_	_
43	in	in	IN	_	_	_
44	transcriptional	transcriptional	JJ	_	_	_
45	pause	pause	NN	_	_	_
46	sites	site	NNS	_	_	_
47	that	that	WDT	_	_	_
48	are	be	VBP	_	_	_
49	defined	define	VBN	_	_	_
50	by	by	IN	_	_	_
51	the	the	DT	_	_	_
52	parameters	parameter	NNS	_	_	_
53	P	p	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	0.9,100	0.9,100	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	.	.	.	_	_	_

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/non-reference	reference/non-reference	NN	_	_	_
16	bases	basis	NNS	_	_	_
17	,	,	,	_	_	_
18	read	read	VBD	_	_	_
19	count	count	NN	_	_	_
20	,	,	,	_	_	_
21	the	the	DT	_	_	_
22	fraction	fraction	NN	_	_	_
23	of	of	IN	_	_	_
24	3	3	CD	_	_	_
25	'	'	''	_	_	_
26	RNA	rna	NN	_	_	_
27	end	end	NN	_	_	_
28	,	,	,	_	_	_
29	DNA	dna	NN	_	_	_
30	strand	strand	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	+	+	CC	_	_	_
33	/	/	:	_	_	_
34	-	-	:	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	gene	gene	NN	_	_	_
38	name	name	NN	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	mapping/base	mapping/base	NN	_	_	_
42	qualities	quality	NNS	_	_	_
43	in	in	IN	_	_	_
44	transcriptional	transcriptional	JJ	_	_	_
45	pause	pause	NN	_	_	_
46	sites	site	NNS	_	_	_
47	that	that	WDT	_	_	_
48	are	be	VBP	_	_	_
49	defined	define	VBN	_	_	_
50	by	by	IN	_	_	_
51	the	the	DT	_	_	_
52	parameters	parameter	NNS	_	_	_
53	P	p	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	0.9	0.9	CD	_	_	_
56	,	,	,	_	_	_
57	160	160	CD	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	processed	process	VBN	_	_	_
4	gene	gene	NN	_	_	_
5	expression	expression	NN	_	_	_
6	data	datum	NNS	_	_	_
7	in	in	IN	_	_	_
8	log10	log10	NN	_	_	_
9	scale	scale	NN	_	_	_
10	are	be	VBP	_	_	_
11	provided	provide	VBN	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	supplementary	supplementary	JJ	_	_	_
15	file	file	NN	_	_	_
16	\	\	SYM	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
18	The	the	DT	_	_	_
19	program	program	NN	_	_	_
20	Rockhopper	rockhopper	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	described	describe	VBN	_	_	_
23	in	in	IN	_	_	_
24	Mc	mc	NN	_	_	_
25	Clure	clure	NN	_	_	_
26	,	,	,	_	_	_
27	et	et	FW	_	_	_
28	al.	al.	FW	_	_	_
29	.	.	.	_	_	_

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	/	/	:	_	_	_
9	ASM584v1	asm584v1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
11	The	the	DT	_	_	_
12	program	program	NN	_	_	_
13	used	use	VBN	_	_	_
14	to	to	TO	_	_	_
15	generate	generate	VB	_	_	_
16	the	the	DT	_	_	_
17	bed/bar	bed/bar	JJ	_	_	_
18	files	file	NNS	_	_	_
19	is	be	VBZ	_	_	_
20	``	``	``	_	_	_
21	Affymetrix	Affymetrix	NNP	_	_	_
22	Tiling	Tiling	NNP	_	_	_
23	Analysis	Analysis	NNP	_	_	_
24	Software	Software	NNP	_	_	_
25	.	.	.	_	_	_
26	''	''	''	_	_	_

1	Standardized	standardized	JJ	_	_	_
2	signals	signal	NNS	_	_	_
3	,	,	,	_	_	_
4	for	for	IN	_	_	_
5	each	each	DT	_	_	_
6	probe	probe	NN	_	_	_
7	in	in	IN	_	_	_
8	the	the	DT	_	_	_
9	arrays	array	NNS	_	_	_
10	,	,	,	_	_	_
11	were	be	VBD	_	_	_
12	generated	generate	VBN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	MAT	mat	NN	_	_	_
16	software	software	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Johnson	Johnson	NNP	_	_	_
19	WE	WE	NNP	_	_	_
20	et	et	FW	_	_	_
21	al.	al.	FW	_	_	_
22	2006	2006	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	which	which	WDT	_	_	_
26	provides	provide	VBZ	_	_	_
27	a	a	DT	_	_	_
28	model-based	model-based	JJ	_	_	_
29	,	,	,	_	_	_
30	sequence-specific	sequence-specific	JJ	_	_	_
31	,	,	,	_	_	_
32	background	background	NN	_	_	_
33	correction	correction	NN	_	_	_
34	for	for	IN	_	_	_
35	each	each	DT	_	_	_
36	sample	sample	NN	_	_	_
37	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	gene-specific	gene-specific	JJ	_	_	_
3	score	score	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	calculated	calculate	VBN	_	_	_
7	for	for	IN	_	_	_
8	each	each	DT	_	_	_
9	gene	gene	NN	_	_	_
10	by	by	IN	_	_	_
11	averaging	average	VBG	_	_	_
12	all	all	DT	_	_	_
13	MAT	mat	NN	_	_	_
14	scores	score	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	natural	natural	JJ	_	_	_
17	log	log	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	for	for	IN	_	_	_
20	all	all	DT	_	_	_
21	probes	probe	NNS	_	_	_
22	under	under	IN	_	_	_
23	the	the	DT	_	_	_
24	annotated	annotated	JJ	_	_	_
25	gene	gene	NN	_	_	_
26	coordinates	coordinate	VBZ	_	_	_
27	.	.	.	_	_	_

1	Gene	Gene	NNP	_	_	_
2	annotation	annotation	NN	_	_	_
3	was	be	VBD	_	_	_
4	from	from	IN	_	_	_
5	the	the	DT	_	_	_
6	ASAP	asap	NN	_	_	_
7	database	database	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Glasner	glasner	FW	_	_	_
10	JD	jd	FW	_	_	_
11	et	et	FW	_	_	_
12	al.	al.	FW	_	_	_
13	2003	2003	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	at	at	IN	_	_	_
16	the	the	DT	_	_	_
17	University	University	NNP	_	_	_
18	of	of	IN	_	_	_
19	Wisconsin-Madison	Wisconsin-Madison	NNP	_	_	_
20	,	,	,	_	_	_
21	for	for	IN	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	K-12	k-12	NN	_	_	_
25	MG1655	mg1655	NN	_	_	_
26	version	version	NN	_	_	_
27	m56	m56	NN	_	_	_
28	.	.	.	_	_	_

1	Differences	difference	NNS	_	_	_
2	of	of	IN	_	_	_
3	two	two	CD	_	_	_
4	log	log	NN	_	_	_
5	scale	scale	NN	_	_	_
6	values	value	NNS	_	_	_
7	in	in	IN	_	_	_
8	the	the	DT	_	_	_
9	absence	absence	NN	_	_	_
10	or	or	CC	_	_	_
11	presence	presence	NN	_	_	_
12	of	of	IN	_	_	_
13	D-galactose	d-galactose	NN	_	_	_
14	were	be	VBD	_	_	_
15	calculated	calculate	VBN	_	_	_
16	in	in	IN	_	_	_
17	galT	galT	NNP	GEN	_	_
18	mutant	mutant	JJ	_	_	_
19	cells	cell	NNS	_	_	_
20	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	transcriptome	transcriptome	JJ	_	_	_
5	results	result	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	log	log	NN	_	_	_
8	scale	scale	NN	_	_	_
9	values	value	NNS	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	with	with	IN	_	_	_
12	or	or	CC	_	_	_
13	without	without	IN	_	_	_
14	D-galactose	d-galactose	NN	_	_	_
15	were	be	VBD	_	_	_
16	compared	compare	VBN	_	_	_
17	graphically	graphically	RB	_	_	_
18	-LSB-	-lsb-	-LRB-	_	_	_
19	References	reference	NNS	_	_	_
20	:	:	:	_	_	_
21	Johnson	Johnson	NNP	_	_	_
22	WE	WE	NNP	_	_	_
23	,	,	,	_	_	_
24	et	et	FW	_	_	_
25	al.	al.	FW	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	2006	2006	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	Model-based	model-based	JJ	_	_	_
30	analysis	analysis	NN	_	_	_
31	of	of	IN	_	_	_
32	tiling-arrays	tiling-array	NNS	_	_	_
33	for	for	IN	_	_	_
34	ChIP-chip	ChIP-chip	NNP	_	_	_
35	.	.	.	_	_	_

1	Proc	Proc	NNP	_	_	_
2	Natl	Natl	NNP	_	_	_
3	Acad	Acad	NNP	_	_	_
4	Sci	Sci	NNP	_	_	_
5	USA	USA	NNP	_	_	_
6	103:12457	103:12457	CD	_	_	_
7	--	--	:	_	_	_
8	12462	12462	CD	_	_	_
9	;	;	:	_	_	_
10	Glasner	glasner	FW	_	_	_
11	JD	jd	FW	_	_	_
12	,	,	,	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	2003	2003	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	ASAP	asap	RB	_	_	_
19	,	,	,	_	_	_
20	a	a	DT	_	_	_
21	systematic	systematic	JJ	_	_	_
22	annotation	annotation	NN	_	_	_
23	package	package	NN	_	_	_
24	for	for	IN	_	_	_
25	community	community	NN	_	_	_
26	analysis	analysis	NN	_	_	_
27	of	of	IN	_	_	_
28	genomes	genome	NNS	_	_	_
29	.	.	.	_	_	_

1	Nucleic	nucleic	JJ	_	_	_
2	Acids	acid	NNS	_	_	_
3	Res	Res	NNP	_	_	_
4	31:147	31:147	CD	_	_	_
5	--	--	:	_	_	_
6	151	151	CD	_	_	_
7	-RSB-	-rsb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	The	the	DT	_	_	_
10	quality	quality	NN	_	_	_
11	and	and	CC	_	_	_
12	quantity	quantity	NN	_	_	_
13	of	of	IN	_	_	_
14	rRNA-depleted	rrna-depleted	JJ	_	_	_
15	RNA	rna	NN	_	_	_
16	was	be	VBD	_	_	_
17	assessed	assess	VBN	_	_	_
18	on	on	IN	_	_	_
19	a	a	DT	_	_	_
20	2100	2100	CD	_	_	_
21	Bioanalyzer	Bioanalyzer	NNP	_	_	_
22	RNA	rna	NN	_	_	_
23	pico	pico	NN	_	_	_
24	chip	chip	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Agilent	Agilent	NNP	_	_	_
27	Technologies	Technologies	NNPS	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	using	use	VBG	_	_	_
30	manufacturer	manufacturer	NN	_	_	_
31	's	's	POS	_	_	_
32	recommendations	recommendation	NNS	_	_	_
33	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	quality	quality	NN	_	_	_
4	of	of	IN	_	_	_
5	reads	read	VBZ	_	_	_
6	was	be	VBD	_	_	_
7	assessed	assess	VBN	_	_	_
8	by	by	IN	_	_	_
9	using	use	VBG	_	_	_
10	FastQC	fastqc	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Andrews	Andrews	NNP	_	_	_
13	S	s	NN	_	_	_
14	,	,	,	_	_	_
15	2010	2010	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	any	any	DT	_	_	_
19	reads	read	VBZ	_	_	_
20	with	with	IN	_	_	_
21	a	a	DT	_	_	_
22	quality	quality	NN	_	_	_
23	score	score	NN	_	_	_
24	≤	≤	CD	_	_	_
25	Q28	q28	NN	_	_	_
26	were	be	VBD	_	_	_
27	trimmed	trim	VBN	_	_	_
28	using	use	VBG	_	_	_
29	Trim	Trim	NNP	_	_	_
30	Galore	Galore	NNP	_	_	_
31	!	!	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	Krueger	krueger	NN	_	_	_
3	F	f	NN	_	_	_
4	,	,	,	_	_	_
5	2013	2013	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	.	.	.	_	_	_

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	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	The	the	DT	_	_	_
31	raw	raw	JJ	_	_	_
32	data	data	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	.	.	.	_	_	_

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/mock-IP	ip/mock-ip	JJ	_	_	_
11	ratio	ratio	NN	_	_	_
12	computation	computation	NN	_	_	_
13	and	and	CC	_	_	_
14	enriched	enriched	JJ	_	_	_
15	region	region	NN	_	_	_
16	identification	identification	NN	_	_	_
17	as	as	IN	_	_	_
18	implemented	implement	VBN	_	_	_
19	in	in	IN	_	_	_
20	the	the	DT	_	_	_
21	NimbleScan	NimbleScan	NNP	_	_	_
22	software	software	NN	_	_	_
23	package	package	NN	_	_	_
24	,	,	,	_	_	_
25	version	version	NN	_	_	_
26	2.4.27	2.4.27	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	www.nimblegen.com	www.nimblegen.com	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	raw	raw	JJ	_	_	_
4	data	data	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	raw	raw	JJ	_	_	_
4	data	data	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	raw	raw	JJ	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	normalized	normalize	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	space	space	NN	_	_	_
10	and	and	CC	_	_	_
11	intensity-dependant	intensity-dependant	JJ	_	_	_
12	LOWESS	lowess	NN	_	_	_
13	program	program	NN	_	_	_
14	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	raw	raw	JJ	_	_	_
4	pair	pair	NN	_	_	_
5	data	datum	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	.	.	.	_	_	_

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/mock-IP	ip/mock-ip	JJ	_	_	_
11	ratio	ratio	NN	_	_	_
12	computation	computation	NN	_	_	_
13	and	and	CC	_	_	_
14	enriched	enriched	JJ	_	_	_
15	region	region	NN	_	_	_
16	identification	identification	NN	_	_	_
17	as	as	IN	_	_	_
18	implemented	implement	VBN	_	_	_
19	in	in	IN	_	_	_
20	the	the	DT	_	_	_
21	NimbleScan	NimbleScan	NNP	_	_	_
22	software	software	NN	_	_	_
23	package	package	NN	_	_	_
24	,	,	,	_	_	_
25	version	version	NN	_	_	_
26	2.4.27	2.4.27	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	www.nimblegen.com	www.nimblegen.com	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	raw	raw	JJ	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	filtered	filtered	VBN	_	_	_
7	for	for	IN	_	_	_
8	removing	remove	VBG	_	_	_
9	dirty	dirty	JJ	_	_	_
10	raw	raw	JJ	_	_	_
11	reads	read	VBZ	_	_	_
12	which	which	WDT	_	_	_
13	contain	contain	VBP	_	_	_
14	adapters	adapter	NNS	_	_	_
15	,	,	,	_	_	_
16	unknown	unknown	JJ	_	_	_
17	or	or	CC	_	_	_
18	low	low	JJ	_	_	_
19	quality	quality	NN	_	_	_
20	bases	basis	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	using	use	VBG	_	_	_
7	BWA	BWA	NNP	_	_	_
8	software	software	NN	_	_	_
9	.	.	.	_	_	_

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	to	to	TO	_	_	_
8	genome	genome	NN	_	_	_
9	using	use	VBG	_	_	_
10	Bowtie	Bowtie	NNP	_	_	_
11	v.	v.	CC	_	_	_
12	0.12.0	0.12.0	CD	_	_	_
13	allowing	allow	VBG	_	_	_
14	for	for	IN	_	_	_
15	one	one	CD	_	_	_
16	mismatch	mismatch	NN	_	_	_
17	and	and	CC	_	_	_
18	reads	read	VBZ	_	_	_
19	aligning	align	VBG	_	_	_
20	in	in	IN	_	_	_
21	more	more	JJR	_	_	_
22	than	than	IN	_	_	_
23	one	one	CD	_	_	_
24	position	position	NN	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	genome	genome	NN	_	_	_
28	were	be	VBD	_	_	_
29	discarded	discard	VBN	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	The	the	DT	_	_	_
32	remaining	remain	VBG	_	_	_
33	reads	read	VBZ	_	_	_
34	were	be	VBD	_	_	_
35	aligned	align	VBN	_	_	_
36	using	use	VBG	_	_	_
37	Bowtie	Bowtie	NNP	_	_	_
38	v0	v0	NN	_	_	_
39	.12.7	.12.7	CD	_	_	_
40	against	against	IN	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	MG1655	mg1655	NN	_	_	_
44	genome	genome	NN	_	_	_
45	using	use	VBG	_	_	_
46	parameters	parameter	NNS	_	_	_
47	-	-	:	_	_	_
48	v1	v1	SYM	_	_	_
49	-	-	:	_	_	_
50	m2	m2	SYM	_	_	_
51	-	-	:	_	_	_
52	k1	k1	NN	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	resulting	result	VBG	_	_	_
4	reads	read	VBZ	_	_	_
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	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	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	pgcgrowthcondition	NNS	_	_	_
16	The	the	DT	_	_	_
17	ribosome	ribosome	NN	_	_	_
18	footprints	footprint	NNS	_	_	_
19	and	and	CC	_	_	_
20	fragmented	fragmented	JJ	_	_	_
21	mRNA	mrna	NN	_	_	_
22	were	be	VBD	_	_	_
23	ligated	ligate	VBN	_	_	_
24	to	to	TO	_	_	_
25	miRNA	miRNA	NNP	_	_	_
26	cloning	clone	VBG	_	_	_
27	linker-1	linker-1	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	IDT	idt	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	using	use	VBG	_	_	_
32	truncated	truncate	VBN	_	_	_
33	T4	t4	NN	_	_	_
34	RNA	rna	NN	_	_	_
35	ligase	ligase	NN	_	_	_
36	2	2	CD	_	_	_
37	K227Q	k227q	NN	_	_	_
38	.	.	.	_	_	_

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/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC	5phos/gatcgtcggactgtagaactctgaacctgtcggtggtcgcc	NN	_	_	_
12	GTATCATT/iSp18/CACTCA	gtatcatt/isp18/cactca	NN	_	_	_
13	/	/	:	_	_	_
14	iSp18/CAAGCAGAAGACGGCATACGAATTGATG	isp18/caagcagaagacggcatacgaattgatg	NN	_	_	_
15	GTGCCTACAG	gtgcctacag	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resulting	result	VBG	_	_	_
3	cDNA	cdna	NN	_	_	_
4	was	be	VBD	_	_	_
5	circularized	circularize	VBN	_	_	_
6	with	with	IN	_	_	_
7	CircLigase	circligase	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Epicentre	Epicentre	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	and	and	CC	_	_	_
12	PCR	pcr	NN	_	_	_
13	amplification	amplification	NN	_	_	_
14	was	be	VBD	_	_	_
15	done	do	VBN	_	_	_
16	as	as	IN	_	_	_
17	described	describe	VBN	_	_	_
18	previously	previously	RB	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Ingolia	Ingolia	NNP	_	_	_
21	et	et	FW	_	_	_
22	al.	al.	FW	_	_	_
23	,	,	,	_	_	_
24	2009	2009	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	samples	sample	NNS	_	_	_
8	was	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	by	by	IN	_	_	_
11	Qiagen	Qiagen	NNP	_	_	_
12	RNeasy	RNeasy	NNP	_	_	_
13	Mini	Mini	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	with	with	IN	_	_	_
16	DNAse	dnase	NN	_	_	_
17	treatment	treatment	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Cat.No	cat.no	NN	_	_	_
20	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	chemically	chemically	RB	_	_	_
6	fragmented	fragment	VBN	_	_	_
7	using	use	VBG	_	_	_
8	RNA	rna	NN	_	_	_
9	Fragmentation	fragmentation	NN	_	_	_
10	Reagents	reagent	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Ambion	Ambion	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	size	size	NN	_	_	_
17	range	range	NN	_	_	_
18	of	of	IN	_	_	_
19	200-250	200-250	CD	_	_	_
20	bp	bp	NN	_	_	_
21	using	use	VBG	_	_	_
22	1x	1x	NN	_	_	_
23	fragmentation	fragmentation	NN	_	_	_
24	solution	solution	NN	_	_	_
25	for	for	IN	_	_	_
26	5	5	CD	_	_	_
27	minutes	minute	NNS	_	_	_
28	at	at	IN	_	_	_
29	70	70	CD	_	_	_
30	°C	°c	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Ambion	ambion	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	RNeasy	rneasy	NN	_	_	_
4	Mini	Mini	NNP	_	_	_
5	Kit	kit	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	QIAGEN	qiagen	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	extract	extract	NN	_	_	_
13	RNA	rna	NN	_	_	_
14	.	.	.	_	_	_

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	The	the	DT	_	_	_
24	RNeasy	RNeasy	NNP	_	_	_
25	mini	minus	NNS	_	_	_
26	kit	kit	NN	_	_	_
27	,	,	,	_	_	_
28	with	with	IN	_	_	_
29	on	on	IN	_	_	_
30	column	column	NN	_	_	_
31	RNase-Free	rnase-free	NN	_	_	_
32	DNase	dnase	NN	_	_	_
33	I	i	CD	_	_	_
34	treatment	treatment	NN	_	_	_
35	,	,	,	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	both	both	CC	_	_	_
38	Qiagen	Qiagen	NNP	_	_	_
39	,	,	,	_	_	_
40	Hilden	Hilden	NNP	_	_	_
41	,	,	,	_	_	_
42	Germany	Germany	NNP	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	was	be	VBD	_	_	_
45	used	use	VBN	_	_	_
46	for	for	IN	_	_	_
47	total	total	JJ	_	_	_
48	RNA	rna	NN	_	_	_
49	isolation	isolation	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	RNA	rna	NN	_	_	_
52	≥	≥	NN	_	_	_
53	200	200	CD	_	_	_
54	bases	basis	NNS	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	,	,	,	_	_	_
57	according	accord	VBG	_	_	_
58	to	to	TO	_	_	_
59	the	the	DT	_	_	_
60	manufacturer	manufacturer	NN	_	_	_
61	's	's	POS	_	_	_
62	protocol	protocol	NN	_	_	_
63	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	RNeasy	rneasy	NN	_	_	_
4	Mini	Mini	NNP	_	_	_
5	Purification	purification	NN	_	_	_
6	Kit	kit	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Qiagen	qiagen	NN	_	_	_
9	;	;	:	_	_	_
10	Valencia	Valencia	NNP	_	_	_
11	,	,	,	_	_	_
12	CA	CA	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	was	be	VBD	_	_	_
15	used	use	VBN	_	_	_
16	to	to	TO	_	_	_
17	extract	extract	VB	_	_	_
18	total	total	JJ	_	_	_
19	RNA	rna	NN	_	_	_
20	from	from	IN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	O157	o157	NN	_	_	_
24	:	:	:	_	_	_
25	H7	h7	NN	_	_	_
26	cultures	culture	NNS	_	_	_
27	.	.	.	_	_	_

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	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	R	r	NN	_	_	_
4	package	package	NN	_	_	_
5	,	,	,	_	_	_
6	Ringo	Ringo	NNP	_	_	_
7	,	,	,	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	to	to	TO	_	_	_
11	read	read	VB	_	_	_
12	the	the	DT	_	_	_
13	pair	pair	NN	_	_	_
14	files	file	NNS	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	limma	limma	NN	_	_	_
18	package	package	NN	_	_	_
19	for	for	IN	_	_	_
20	within	within	IN	_	_	_
21	-	-	:	_	_	_
22	and	and	CC	_	_	_
23	between-array	between-array	JJ	_	_	_
24	normalization	normalization	NN	_	_	_
25	.	.	.	_	_	_

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	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	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/G	a/g	NN	_	_	_
17	sepharose	sepharose	NN	_	_	_
18	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	reactions	reaction	NNS	_	_	_
3	are	be	VBP	_	_	_
4	performed	perform	VBN	_	_	_
5	in	in	IN	_	_	_
6	an	a	DT	_	_	_
7	Eppendorf	eppendorf	NN	_	_	_
8	ThermalMixerR	thermalmixerr	NN	_	_	_
9	while	while	IN	_	_	_
10	being	be	VBG	_	_	_
11	mixed	mix	VBN	_	_	_
12	at	at	IN	_	_	_
13	1.4	1.4	CD	_	_	_
14	k	k	NN	_	_	_
15	x	x	NN	_	_	_
16	rpm	rpm	NN	_	_	_
17	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	each	each	DT	_	_	_
3	reaction	reaction	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	sepharose	sepharose	NN	_	_	_
7	was	be	VBD	_	_	_
8	washed	wash	VBN	_	_	_
9	with	with	IN	_	_	_
10	1	1	CD	_	_	_
11	mL	ml	NN	_	_	_
12	of	of	IN	_	_	_
13	each	each	DT	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	following	follow	VBG	_	_	_
17	buffers	buffer	NNS	_	_	_
18	,	,	,	_	_	_
19	leaving	leave	VBG	_	_	_
20	50-100	50-100	CD	_	_	_
21	uL	ul	NN	_	_	_
22	buffer	buffer	NN	_	_	_
23	above	above	IN	_	_	_
24	the	the	DT	_	_	_
25	sepharose	sepharose	NN	_	_	_
26	in-between	in-between	JJ	_	_	_
27	each	each	DT	_	_	_
28	wash	wash	NN	_	_	_
29	:	:	:	_	_	_
30	1x	1x	VB	_	_	_
31	TE	TE	NNP	_	_	_
32	:	:	:	_	_	_
33	10mM	10mm	NN	_	_	_
34	Tris-HCl	tris-hcl	NN	_	_	_
35	,	,	,	_	_	_
36	pH	ph	NN	_	_	_
37	8.0	8.0	CD	_	_	_
38	+	+	CC	_	_	_
39	1	1	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	EDTA	edta	NN	_	_	_
42	;	;	:	_	_	_
43	1	1	CD	_	_	_
44	x	x	CC	_	_	_
45	High	high	JJ	_	_	_
46	Salt	Salt	NNP	_	_	_
47	-	-	:	_	_	_
48	1M	1m	NN	_	_	_
49	NaCl	nacl	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	1	1	CD	_	_	_
52	%	%	NN	_	_	_
53	Triton	Triton	NNP	_	_	_
54	X-100	x-100	NN	_	_	_
55	,	,	,	_	_	_
56	50	50	CD	_	_	_
57	mM	mm	NN	KWSUPP	_	_
58	HEPES	hepes	NN	_	_	_
59	,	,	,	_	_	_
60	pH	ph	NN	_	_	_
61	8.0	8.0	CD	_	_	_
62	,	,	,	_	_	_
63	2	2	CD	_	_	_
64	mM	mm	NN	KWSUPP	_	_
65	EDTA	edta	NN	_	_	_
66	,	,	,	_	_	_
67	0.1	0.1	CD	_	_	_
68	%	%	NN	_	_	_
69	sodium	sodium	NN	_	_	_
70	deoxycholate	deoxycholate	NN	SUPP	_	_
71	and	and	CC	_	_	_
72	1M	1m	NN	_	_	_
73	NaCl	nacl	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	;	;	:	_	_	_
76	1x	1x	CD	_	_	_
77	Wash	Wash	NNP	_	_	_
78	Buffer	Buffer	NNP	_	_	_
79	2	2	CD	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	1	1	CD	_	_	_
82	%	%	NN	_	_	_
83	Triton	Triton	NNP	_	_	_
84	X-100	x-100	NN	_	_	_
85	,	,	,	_	_	_
86	50	50	CD	_	_	_
87	mM	mm	NN	KWSUPP	_	_
88	HEPES	hepes	NN	_	_	_
89	,	,	,	_	_	_
90	pH	ph	NN	_	_	_
91	8.0	8.0	CD	_	_	_
92	,	,	,	_	_	_
93	2	2	CD	_	_	_
94	mM	mm	NN	KWSUPP	_	_
95	EDTA	edta	NN	_	_	_
96	,	,	,	_	_	_
97	0.1	0.1	CD	_	_	_
98	%	%	NN	_	_	_
99	sodium	sodium	NN	_	_	_
100	deoxycholate	deoxycholate	NN	SUPP	_	_
101	and	and	CC	_	_	_
102	0.5	0.5	CD	_	_	_
103	M	m	NN	_	_	_
104	NaCl	nacl	NN	_	_	_
105	-RRB-	-rrb-	-RRB-	_	_	_
106	;	;	:	_	_	_
107	1x	1x	CD	_	_	_
108	Wash	Wash	NNP	_	_	_
109	Buffer	Buffer	NNP	_	_	_
110	3	3	CD	_	_	_
111	-LRB-	-lrb-	-LRB-	_	_	_
112	1	1	CD	_	_	_
113	%	%	NN	_	_	_
114	Triton	Triton	NNP	_	_	_
115	X-100	x-100	NN	_	_	_
116	,	,	,	_	_	_
117	50	50	CD	_	_	_
118	mM	mm	NN	KWSUPP	_	_
119	HEPES	hepes	NN	_	_	_
120	,	,	,	_	_	_
121	pH	ph	NN	_	_	_
122	8.0	8.0	CD	_	_	_
123	,	,	,	_	_	_
124	2	2	CD	_	_	_
125	mM	mm	NN	KWSUPP	_	_
126	EDTA	edta	NN	_	_	_
127	,	,	,	_	_	_
128	1.0	1.0	CD	_	_	_
129	%	%	NN	_	_	_
130	sodium	sodium	NN	_	_	_
131	deoxycholate	deoxycholate	NN	SUPP	_	_
132	,	,	,	_	_	_
133	0.25	0.25	CD	_	_	_
134	M	m	NN	_	_	_
135	LiCl	licl	NN	_	_	_
136	,	,	,	_	_	_
137	1	1	CD	_	_	_
138	%	%	NN	_	_	_
139	NP-40	np-40	NN	_	_	_
140	,	,	,	_	_	_
141	and	and	CC	_	_	_
142	10	10	CD	_	_	_
143	mM	mm	NN	KWSUPP	_	_
144	Tris-HCl	tris-hcl	NN	_	_	_
145	,	,	,	_	_	_
146	pH	ph	NN	_	_	_
147	8.0	8.0	CD	_	_	_
148	-RRB-	-rrb-	-RRB-	_	_	_
149	;	;	:	_	_	_
150	1x	1x	CD	_	_	_
151	TE	TE	NNP	_	_	_
152	:	:	:	_	_	_
153	10mM	10mm	NN	_	_	_
154	Tris-HCl	tris-hcl	NN	_	_	_
155	,	,	,	_	_	_
156	pH	ph	NN	_	_	_
157	8.0	8.0	CD	_	_	_
158	+	+	CC	_	_	_
159	1mM	1mm	NN	_	_	_
160	EDTA	edta	NN	_	_	_
161	.	.	.	_	_	_

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	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Feature	Feature	NNP	_	_	_
10	Extraction	Extraction	NNP	_	_	_
11	Software	Software	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	with	with	IN	_	_	_
16	default	default	NN	_	_	_
17	parameters	parameter	NNS	_	_	_
18	to	to	TO	_	_	_
19	obtain	obtain	VB	_	_	_
20	background	background	NN	_	_	_
21	subtracted	subtract	VBN	_	_	_
22	and	and	CC	_	_	_
23	spatially	spatially	RB	_	_	_
24	detrended	detrend	VBD	_	_	_
25	Processed	processed	JJ	_	_	_
26	Signal	signal	NN	_	_	_
27	intensities	intensity	NNS	_	_	_
28	.	.	.	_	_	_

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	10.5	10.5	CD	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	using	use	VBG	_	_	_
16	default	default	NN	_	_	_
17	parameters	parameter	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	protocol	protocol	NN	_	_	_
20	GE1	ge1	NN	_	_	_
21	_	_	NN	_	_	_
22	105	105	CD	_	_	_
23	_	_	SYM	_	_	_
24	Dec08	dec08	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	scanning	scanning	NN	_	_	_
4	process	process	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	hybridized	hybridize	VBN	_	_	_
8	chips	chip	NNS	_	_	_
9	included	include	VBD	_	_	_
10	a	a	DT	_	_	_
11	fourteen-fold	fourteen-fold	JJ	_	_	_
12	scan	scan	VB	_	_	_
13	of	of	IN	_	_	_
14	each	each	DT	_	_	_
15	chip	chip	NN	_	_	_
16	at	at	IN	_	_	_
17	different	different	JJ	_	_	_
18	settings	setting	NNS	_	_	_
19	,	,	,	_	_	_
20	altering	alter	VBG	_	_	_
21	both	both	CC	_	_	_
22	PMT	PMT	NNP	_	_	_
23	and	and	CC	_	_	_
24	laser	laser	NN	_	_	_
25	power	power	NN	_	_	_
26	settings	setting	NNS	_	_	_
27	.	.	.	_	_	_

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	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	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	/	/	:	_	_	_
23	nmeth	nmeth	JJ	_	_	_
24	.1923	.1923	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	libraries	library	NNS	_	_	_
5	were	be	VBD	_	_	_
6	constructed	construct	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	TruSeq	TruSeq	NNP	_	_	_
10	RNA	rna	NN	_	_	_
11	Sample	sample	NN	_	_	_
12	Preparation	preparation	NN	_	_	_
13	kit	kit	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Illumina	Illumina	NNP	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	,	,	,	_	_	_
18	USA	USA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	signal/noise	signal/noise	NN	_	_	_
4	ratio	ratio	NN	_	_	_
5	for	for	IN	_	_	_
6	each	each	DT	_	_	_
7	array	array	NN	_	_	_
8	was	be	VBD	_	_	_
9	calculated	calculate	VBN	_	_	_
10	,	,	,	_	_	_
11	for	for	IN	_	_	_
12	each	each	DT	_	_	_
13	spot	spot	NN	_	_	_
14	and	and	CC	_	_	_
15	each	each	DT	_	_	_
16	channel	channel	NN	_	_	_
17	,	,	,	_	_	_
18	as	as	IN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	foreground	foreground	NN	_	_	_
21	intensity	intensity	NN	_	_	_
22	minus	minus	CC	_	_	_
23	background	background	NN	_	_	_
24	intensity	intensity	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	/	/	:	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	standard	standard	JJ	_	_	_
29	deviation	deviation	NN	_	_	_
30	of	of	IN	_	_	_
31	the	the	DT	_	_	_
32	background	background	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	raw	raw	JJ	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	space	space	NN	_	_	_
9	and	and	CC	_	_	_
10	intensity-dependant	intensity-dependant	JJ	_	_	_
11	LOWESS	lowess	NN	_	_	_
12	program	program	NN	_	_	_
13	.	.	.	_	_	_

1	Faint	faint	JJ	_	_	_
2	spots	spot	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	data	datum	NNS	_	_	_
8	if	if	IN	_	_	_
9	the	the	DT	_	_	_
10	intensities	intensity	NNS	_	_	_
11	were	be	VBD	_	_	_
12	lower	lower	JJR	_	_	_
13	than	than	IN	_	_	_
14	the	the	DT	_	_	_
15	average	average	JJ	_	_	_
16	intensity	intensity	NN	_	_	_
17	plus	plus	CC	_	_	_
18	2	2	CD	_	_	_
19	standard	standard	JJ	_	_	_
20	deviations	deviation	NNS	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	negative	negative	JJ	_	_	_
24	controls	control	NNS	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	significant	significant	JJ	_	_	_
3	genes	gene	NNS	_	_	_
4	differentiating	differentiate	VBG	_	_	_
5	wild-type	wild-type	JJ	_	_	_
6	and	and	CC	_	_	_
7	deleting	delete	VBG	_	_	_
8	dnaK	dnak	NN	GEN	_	_
9	were	be	VBD	_	_	_
10	selected	select	VBN	_	_	_
11	based	base	VBN	_	_	_
12	on	on	IN	_	_	_
13	q	q	NN	_	_	_
14	<	<	JJR	_	_	_
15	0.05	0.05	CD	_	_	_
16	and	and	CC	_	_	_
17	greater	greater	JJR	_	_	_
18	than	than	IN	_	_	_
19	twofold	twofold	RB	_	_	_
20	as	as	IN	_	_	_
21	criteria	criterion	NNS	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	sigPep.csv	sigpep.csv	NN	_	_	_
4	file	file	NN	_	_	_
5	contains	contain	VBZ	_	_	_
6	the	the	DT	_	_	_
7	counts	count	NNS	_	_	_
8	for	for	IN	_	_	_
9	each	each	DT	_	_	_
10	specific	specific	JJ	_	_	_
11	signal	signal	NN	_	_	_
12	peptide	peptide	NN	_	_	_
13	fusion	fusion	NN	_	_	_
14	to	to	TO	_	_	_
15	each	each	DT	_	_	_
16	specific	specific	JJ	_	_	_
17	test	test	NN	_	_	_
18	gene	gene	NN	_	_	_
19	.	.	.	_	_	_

1	Entries	entry	NNS	_	_	_
2	with	with	IN	_	_	_
3	SP	sp	NN	_	_	_
4	_	_	CD	_	_	_
5	spkA/D/G	spka/d/g	NN	_	_	_
6	/	/	:	_	_	_
7	K	K	NNP	_	_	_
8	represent	represent	VBP	_	_	_
9	spike	spike	NN	_	_	_
10	in	in	IN	_	_	_
11	control	control	NN	_	_	_
12	molecules	molecule	NNS	_	_	_
13	used	use	VBN	_	_	_
14	for	for	IN	_	_	_
15	normalization	normalization	NN	_	_	_
16	.	.	.	_	_	_

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/sludge	soil/sludge	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	collected	collect	VBN	_	_	_
6	in	in	IN	_	_	_
7	air	air	NN	_	_	_
8	tight	tight	JJ	_	_	_
9	vessels	vessel	NNS	_	_	_
10	,	,	,	_	_	_
11	transported	transport	VBN	_	_	_
12	on	on	IN	_	_	_
13	ice	ice	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	4	4	CD	_	_	_
16	○	○	NN	_	_	_
17	C	c	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	to	to	TO	_	_	_
20	the	the	DT	_	_	_
21	laboratory	laboratory	NN	_	_	_
22	and	and	CC	_	_	_
23	processed	process	VBN	_	_	_
24	immediately	immediately	RB	_	_	_
25	for	for	IN	_	_	_
26	DNA	dna	NN	_	_	_
27	isolation	isolation	NN	_	_	_
28	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	each	each	DT	_	_	_
3	sampling	sampling	NN	_	_	_
4	location	location	NN	_	_	_
5	multiple	multiple	JJ	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	collected	collect	VBN	_	_	_
9	from	from	IN	_	_	_
10	close	close	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	100m	100m	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	to	to	TO	_	_	_
15	far	far	RB	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	500m	500m	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	from	from	IN	_	_	_
20	the	the	DT	_	_	_
21	industry	industry	NN	_	_	_
22	,	,	,	_	_	_
23	along	along	IN	_	_	_
24	the	the	DT	_	_	_
25	effluent	effluent	JJ	_	_	_
26	channel	channel	NN	_	_	_
27	and	and	CC	_	_	_
28	at	at	IN	_	_	_
29	the	the	DT	_	_	_
30	place	place	NN	_	_	_
31	where	where	WRB	_	_	_
32	effluent	effluent	JJ	_	_	_
33	channel	channel	NN	_	_	_
34	from	from	IN	_	_	_
35	the	the	DT	_	_	_
36	industrial	industrial	JJ	_	_	_
37	area	area	NN	_	_	_
38	falls	fall	VBZ	_	_	_
39	into	into	IN	_	_	_
40	the	the	DT	_	_	_
41	river	river	NN	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	strain	strain	NN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	CMCC	cmcc	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	B	b	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	44102	44102	CD	_	_	_
11	,	,	,	_	_	_
12	was	be	VBD	_	_	_
13	provided	provide	VBN	_	_	_
14	by	by	IN	_	_	_
15	Institute	Institute	NNP	_	_	_
16	of	of	IN	_	_	_
17	Microbiology	Microbiology	NNP	_	_	_
18	,	,	,	_	_	_
19	Chinese	Chinese	NNP	_	_	_
20	Academy	Academy	NNP	_	_	_
21	of	of	IN	_	_	_
22	Sciences	Sciences	NNPS	_	_	_
23	and	and	CC	_	_	_
24	preserved	preserve	VBN	_	_	_
25	at	at	IN	_	_	_
26	the	the	DT	_	_	_
27	Department	Department	NNP	_	_	_
28	of	of	IN	_	_	_
29	Food	Food	NNP	_	_	_
30	Science	Science	NNP	_	_	_
31	and	and	CC	_	_	_
32	Nutrition	Nutrition	NNP	_	_	_
33	,	,	,	_	_	_
34	Zhejiang	Zhejiang	NNP	_	_	_
35	University	University	NNP	_	_	_
36	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	strain	strain	NN	_	_	_
4	Escherichia	escherichia	FW	Organism	_	_
5	coli	coli	FW	Organism	_	_
6	MG1655	mg1655	NN	_	_	_
7	-LSB-	-lsb-	-LRB-	_	_	_
8	pPROEx-CAT	pproex-cat	NN	_	_	_
9	-RSB-	-rsb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	cultured	culture	VBN	_	_	_
12	in	in	IN	_	_	_
13	a	a	DT	_	_	_
14	fed-batch	fed-batch	JJ	_	_	_
15	fermenter	fermenter	NN	_	_	_
16	in	in	IN	_	_	_
17	LB	LB	NNP	MED	_	_
18	media	media	NNS	MED	_	_
19	w	w	NN	_	_	_
20	/	/	:	_	_	_
21	glucose	glucose	NN	SUPP	_	_
22	and	and	CC	_	_	_
23	a	a	DT	_	_	_
24	glucose/MgS04	glucose/mgs04	NN	_	_	_
25	feed	feed	NN	_	_	_
26	at	at	IN	_	_	_
27	37	37	CD	_	_	_
28	degrees	degree	NNS	_	_	_
29	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	synchronized	synchronize	VBN	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	late	late	JJ	_	_	_
7	log	log	NN	_	_	_
8	phase	phase	NN	_	_	_
9	,	,	,	_	_	_
10	approximately	approximately	RB	_	_	_
11	4.5	4.5	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	of	of	IN	_	_	_
14	fermentation	fermentation	NN	_	_	_
15	time	time	NN	_	_	_
16	.	.	.	_	_	_

1	Serine	serine	NN	_	_	_
2	hydrxamate	hydrxamate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	100mg/L	100mg/l	NN	_	_	_
5	final	final	JJ	_	_	_
6	concentration	concentration	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	added	add	VBN	_	_	_
10	to	to	TO	_	_	_
11	the	the	DT	_	_	_
12	cultures	culture	NNS	_	_	_
13	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	taken	take	VBN	_	_	_
4	1	1	CD	_	_	_
5	hour	hour	NN	_	_	_
6	after	after	IN	_	_	_
7	the	the	DT	_	_	_
8	beginning	begin	VBG	_	_	_
9	the	the	DT	_	_	_
10	serine	serine	NN	_	_	_
11	hydrxamate	hydrxamate	NN	_	_	_
12	addition	addition	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	strain	strain	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	-LSB-	-lsb-	-LRB-	_	_	_
6	pPROEx-CAT	pproex-cat	NN	_	_	_
7	-RSB-	-rsb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	cultured	culture	VBN	_	_	_
10	in	in	IN	_	_	_
11	a	a	DT	_	_	_
12	fed-batch	fed-batch	JJ	_	_	_
13	fermenter	fermenter	NN	_	_	_
14	in	in	IN	_	_	_
15	LB	LB	NNP	MED	_	_
16	media	media	NNS	MED	_	_
17	w	w	NN	_	_	_
18	/	/	:	_	_	_
19	glucose	glucose	NN	SUPP	_	_
20	and	and	CC	_	_	_
21	a	a	DT	_	_	_
22	glucose/MgS04	glucose/mgs04	NN	_	_	_
23	feed	feed	NN	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	degrees	degree	NNS	_	_	_
27	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	synchronized	synchronize	VBN	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	late	late	JJ	_	_	_
7	log	log	NN	_	_	_
8	phase	phase	NN	_	_	_
9	,	,	,	_	_	_
10	approximately	approximately	RB	_	_	_
11	4.5	4.5	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	of	of	IN	_	_	_
14	fermentation	fermentation	NN	_	_	_
15	time	time	NN	_	_	_
16	.	.	.	_	_	_

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

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	strains	strain	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	exponentially	exponentially	RB	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	after	after	IN	_	_	_
9	initiation	initiation	NN	_	_	_
10	by	by	IN	_	_	_
11	a	a	DT	_	_	_
12	1,000-fold	1,000-fold	JJ	_	_	_
13	dilution	dilution	NN	_	_	_
14	from	from	IN	_	_	_
15	overnight	overnight	JJ	_	_	_
16	cultures	culture	NNS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	~	~	NN	_	_	_
20	5	5	CD	_	_	_
21	generations	generation	NNS	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	in	in	IN	_	_	_
26	Vogel-Bonner	Vogel-Bonner	NNP	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	VB	VB	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	minimal	minimal	JJ	_	_	_
31	medium	medium	NN	_	_	_
32	supplemented	supplement	VBN	_	_	_
33	with	with	IN	_	_	_
34	glucose	glucose	NN	SUPP	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	0.4	0.4	CD	_	_	_
37	%	%	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	,	,	,	_	_	_
40	pantothenic	pantothenic	JJ	_	_	_
41	acid	acid	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	5	5	CD	_	_	_
44	µg/ml	µg/ml	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	,	,	,	_	_	_
47	casamino	casamino	NN	SUPP	_	_
48	acids	acid	NNS	SUPP	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	Becton-Dickenson	becton-dickenson	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	1	1	CD	_	_	_
54	%	%	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	,	,	,	_	_	_
57	and	and	CC	_	_	_
58	hypoxanthine	hypoxanthine	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	50	50	CD	_	_	_
61	µg/ml	µg/ml	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	subculture	subculture	NN	_	_	_
4	was	be	VBD	_	_	_
5	split	split	VBN	_	_	_
6	into	into	IN	_	_	_
7	two	two	CD	_	_	_
8	10	10	CD	_	_	_
9	ml	ml	NN	_	_	_
10	portions	portion	NNS	_	_	_
11	,	,	,	_	_	_
12	one	one	CD	_	_	_
13	of	of	IN	_	_	_
14	which	which	WDT	_	_	_
15	was	be	VBD	_	_	_
16	treated	treat	VBN	_	_	_
17	with	with	IN	_	_	_
18	6ug/ml	6ug/ml	JJ	_	_	_
19	triclosan	triclosan	NN	_	_	_
20	and	and	CC	_	_	_
21	the	the	DT	_	_	_
22	other	other	JJ	_	_	_
23	retained	retain	VBN	_	_	_
24	as	as	IN	_	_	_
25	an	a	DT	_	_	_
26	untreated	untreated	JJ	_	_	_
27	control	control	NN	_	_	_
28	.	.	.	_	_	_

1	Treated	treat	VBN	_	_	_
2	and	and	CC	_	_	_
3	untreated	untreated	JJ	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	incubated	incubate	VBN	_	_	_
7	at	at	IN	_	_	_
8	37c	37c	CD	_	_	_
9	for	for	IN	_	_	_
10	30	30	CD	_	_	_
11	min	min	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	TAS	tas	NN	_	_	_
4	software	software	NN	_	_	_
5	provides	provide	VBZ	_	_	_
6	analysis	analysis	NN	_	_	_
7	capabilities	capability	NNS	_	_	_
8	specifically	specifically	RB	_	_	_
9	for	for	IN	_	_	_
10	the	the	DT	_	_	_
11	GeneChip	GeneChip	NNP	_	_	_
12	®	®	NNP	_	_	_
13	Tiling	Tiling	NNP	_	_	_
14	Arrays	Arrays	NNPS	_	_	_
15	.	.	.	_	_	_

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	The	the	DT	_	_	_
8	total	total	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	to	to	TO	_	_	_
11	be	be	VB	_	_	_
12	used	use	VBN	_	_	_
13	as	as	IN	_	_	_
14	target	target	NN	_	_	_
15	for	for	IN	_	_	_
16	microarray	microarray	NN	_	_	_
17	hybridization	hybridization	NN	_	_	_
18	was	be	VBD	_	_	_
19	isolated	isolate	VBN	_	_	_
20	from	from	IN	_	_	_
21	soil	soil	NN	_	_	_
22	/	/	:	_	_	_
23	sediment	sediment	NN	_	_	_
24	samples	sample	NNS	_	_	_
25	using	use	VBG	_	_	_
26	the	the	DT	_	_	_
27	Mo	mo	NN	_	_	_
28	Bio	Bio	NNP	_	_	_
29	Power	Power	NNP	_	_	_
30	soil	soil	NN	_	_	_
31	DNA	dna	NN	_	_	_
32	kit	kit	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Mo	mo	NN	_	_	_
35	Bio	Bio	NNP	_	_	_
36	Inc.	Inc.	NNP	_	_	_
37	,	,	,	_	_	_
38	Carlsbad	Carlsbad	NNP	_	_	_
39	,	,	,	_	_	_
40	CA	CA	NNP	_	_	_
41	,	,	,	_	_	_
42	USA	USA	NNP	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	as	as	IN	_	_	_
45	per	per	IN	_	_	_
46	manufacturer	manufacturer	NN	_	_	_
47	's	's	POS	_	_	_
48	instructions	instruction	NNS	_	_	_
49	.	.	.	_	_	_

1	Before	before	IN	_	_	_
2	processing	processing	NN	_	_	_
3	for	for	IN	_	_	_
4	DNA	dna	NN	_	_	_
5	isolation	isolation	NN	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	soil	soil	NN	_	_	_
9	/	/	:	_	_	_
10	sediments	sediment	NNS	_	_	_
11	were	be	VBD	_	_	_
12	mixed	mixed	JJ	_	_	_
13	thoroughly	thoroughly	RB	_	_	_
14	using	use	VBG	_	_	_
15	a	a	DT	_	_	_
16	mortar-pestle	mortar-pestle	NN	_	_	_
17	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	gm	gm	NN	_	_	_
3	of	of	IN	_	_	_
4	soil/sediment	soil/sediment	NN	_	_	_
5	was	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	for	for	IN	_	_	_
8	DNA	dna	NN	_	_	_
9	isolation	isolation	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	during	during	IN	_	_	_
13	processing	processing	NN	_	_	_
14	with	with	IN	_	_	_
15	the	the	DT	_	_	_
16	kit	kit	NN	_	_	_
17	,	,	,	_	_	_
18	lysozyme	lysozyme	NN	_	_	_
19	was	be	VBD	_	_	_
20	added	add	VBN	_	_	_
21	to	to	TO	_	_	_
22	facilitate	facilitate	VB	_	_	_
23	the	the	DT	_	_	_
24	lysis	lysis	NN	_	_	_
25	of	of	IN	_	_	_
26	bacteria	bacterium	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	from	from	IN	_	_	_
5	pure	pure	JJ	_	_	_
6	bacterial	bacterial	JJ	_	_	_
7	cultures	culture	NNS	_	_	_
8	was	be	VBD	_	_	_
9	isolated	isolate	VBN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	Wizard	Wizard	NNP	_	_	_
13	genomic	genomic	JJ	_	_	_
14	DNA	dna	NN	_	_	_
15	isolation	isolation	NN	_	_	_
16	kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Promega	Promega	NNP	_	_	_
19	corporation	corporation	NN	_	_	_
20	,	,	,	_	_	_
21	Madison	Madison	NNP	_	_	_
22	,	,	,	_	_	_
23	USA	USA	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	as	as	IN	_	_	_
26	per	per	IN	_	_	_
27	manufacturer	manufacturer	NN	_	_	_
28	's	's	POS	_	_	_
29	instructions	instruction	NNS	_	_	_
30	.	.	.	_	_	_

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	total	total	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	Xuzhou21	xuzhou21	NN	_	_	_
8	and	and	CC	_	_	_
9	Xuzhou21m	xuzhou21m	NN	_	_	_
10	were	be	VBD	_	_	_
11	first	first	JJ	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	Ribo-Zero	ribo-zero	NN	_	_	_
15	™	™	CD	_	_	_
16	rRNA	rrna	NN	_	_	_
17	Removal	removal	NN	_	_	_
18	kit	kit	NN	_	_	_
19	to	to	TO	_	_	_
20	remove	remove	VB	_	_	_
21	rRNA	rrna	NN	_	_	_
22	.	.	.	_	_	_

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	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	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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	total	total	JJ	_	_	_
4	sequencing	sequencing	NN	_	_	_
5	base	base	NN	_	_	_
6	pair	pair	NN	_	_	_
7	coverage	coverage	NN	_	_	_
8	for	for	IN	_	_	_
9	all	all	DT	_	_	_
10	annotated	annotated	JJ	_	_	_
11	genes	gene	NNS	_	_	_
12	was	be	VBD	_	_	_
13	summed	sum	VBN	_	_	_
14	for	for	IN	_	_	_
15	each	each	DT	_	_	_
16	sample	sample	NN	_	_	_
17	and	and	CC	_	_	_
18	normalized	normalize	VBD	_	_	_
19	to	to	TO	_	_	_
20	total	total	JJ	_	_	_
21	coverage	coverage	NN	_	_	_
22	using	use	VBG	_	_	_
23	bedtools	bedtool	NNS	_	_	_
24	and	and	CC	_	_	_
25	custom	custom	NN	_	_	_
26	R	r	NN	_	_	_
27	scripts	script	NNS	_	_	_
28	as	as	IN	_	_	_
29	described	describe	VBN	_	_	_
30	in	in	IN	_	_	_
31	Wu	Wu	NNP	_	_	_
32	et	et	FW	_	_	_
33	al.	al.	FW	_	_	_
34	2015	2015	CD	_	_	_
35	PLoS	PLoS	NNP	_	_	_
36	Genetics	Genetics	NNP	_	_	_
37	Nov	Nov	NNP	_	_	_
38	6	6	CD	_	_	_
39	;	;	:	_	_	_
40	11	11	CD	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	11	11	CD	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	:	:	:	_	_	_
45	e1005655	e1005655	NN	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	treatment	treatment	NN	_	_	_
4	condition	condition	NN	_	_	_
5	includes	include	VBZ	_	_	_
6	adding	add	VBG	_	_	_
7	10	10	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	octanoic	octanoic	JJ	_	_	_
10	acid	acid	NN	_	_	_
11	during	during	IN	_	_	_
12	logarithmic	logarithmic	JJ	_	_	_
13	growth	growth	NN	_	_	_
14	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
25	The	the	DT	_	_	_
26	VALUE	VALUE	NNP	_	_	_
27	data	datum	NNS	_	_	_
28	are	be	VBP	_	_	_
29	normalized	normalize	VBN	_	_	_
30	log2	log2	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	test/ref	test/ref	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	ratios	ratio	NNS	_	_	_
35	which	which	WDT	_	_	_
36	were	be	VBD	_	_	_
37	normalized	normalize	VBN	_	_	_
38	`	`	``	_	_	_
39	print-tip-loess	print-tip-loess	NN	_	_	_
40	'	'	''	_	_	_
41	using	use	VBG	_	_	_
42	the	the	DT	_	_	_
43	software	software	NN	_	_	_
44	R	r	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	R	r	NN	_	_	_
47	,	,	,	_	_	_
48	2005	2005	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	and	and	CC	_	_	_
51	the	the	DT	_	_	_
52	Limma	Limma	NNP	_	_	_
53	package	package	NN	_	_	_
54	included	include	VBD	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Smyth	Smyth	NNP	_	_	_
57	,	,	,	_	_	_
58	2005	2005	CD	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	.	.	.	_	_	_

1	Additionally	additionally	RB	_	_	_
2	,	,	,	_	_	_
3	spots	spot	NNS	_	_	_
4	,	,	,	_	_	_
5	which	which	WDT	_	_	_
6	were	be	VBD	_	_	_
7	classified	classify	VBN	_	_	_
8	as	as	IN	_	_	_
9	not	not	RB	_	_	_
10	found	find	VBN	_	_	_
11	by	by	IN	_	_	_
12	the	the	DT	_	_	_
13	image	image	NN	_	_	_
14	analysis	analysis	NN	_	_	_
15	software	software	NN	_	_	_
16	,	,	,	_	_	_
17	were	be	VBD	_	_	_
18	down	down	RB	_	_	_
19	weighted	weight	VBN	_	_	_
20	to	to	TO	_	_	_
21	10	10	CD	_	_	_
22	%	%	NN	_	_	_
23	.	.	.	_	_	_

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	Cy3	cy3	NN	_	_	_
13	and	and	CC	_	_	_
14	Cy5	cy5	NN	_	_	_
15	signals	signal	NNS	_	_	_
16	.	.	.	_	_	_

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	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	The	the	DT	_	_	_
3	web-based	web-based	JJ	_	_	_
4	tool	tool	NN	_	_	_
5	,	,	,	_	_	_
6	DAVID	DAVID	NNP	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	the	the	DT	_	_	_
9	Database	database	NN	_	_	_
10	for	for	IN	_	_	_
11	Annotation	Annotation	NNP	_	_	_
12	,	,	,	_	_	_
13	Visualization	visualization	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	Integrated	Integrated	NNP	_	_	_
17	Discovery	Discovery	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	was	be	VBD	_	_	_
20	used	use	VBN	_	_	_
21	to	to	TO	_	_	_
22	perform	perform	VB	_	_	_
23	the	the	DT	_	_	_
24	biological	biological	JJ	_	_	_
25	interpretation	interpretation	NN	_	_	_
26	of	of	IN	_	_	_
27	differentially	differentially	RB	_	_	_
28	expressed	express	VBN	_	_	_
29	genes	gene	NNS	_	_	_
30	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	wildtype	wildtype	JJ	_	_	_
4	and	and	CC	_	_	_
5	mutant	mutant	JJ	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	O157	o157	NN	_	_	_
9	:	:	:	_	_	_
10	H19	h19	NN	_	_	_
11	strains	strain	NNS	_	_	_
12	were	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	on	on	IN	_	_	_
15	LB	LB	NNP	_	_	_
16	agar	agar	NN	_	_	_
17	incubated	incubate	VBN	_	_	_
18	at	at	IN	_	_	_
19	37c	37c	CD	_	_	_
20	x	x	CC	_	_	_
21	24h	24h	CD	_	_	_
22	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	Zymo	zymo	NN	_	_	_
4	Fungal/Bacterial	fungal/bacterial	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	extraction	extraction	NN	_	_	_
7	kit	kit	NN	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	to	to	TO	_	_	_
11	extract	extract	NN	_	_	_
12	RNA	rna	NN	_	_	_
13	from	from	IN	_	_	_
14	all	all	DT	_	_	_
15	samples	sample	NNS	_	_	_
16	.	.	.	_	_	_

1	In-column	in-column	JJ	_	_	_
2	DNaseI	dnasei	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	was	be	VBD	_	_	_
5	used	use	VBN	_	_	_
6	to	to	TO	_	_	_
7	eliminate	eliminate	VB	_	_	_
8	genomic	genomic	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	carryover	carryover	NN	_	_	_
11	as	as	IN	_	_	_
12	described	describe	VBN	_	_	_
13	by	by	IN	_	_	_
14	the	the	DT	_	_	_
15	manufacturer	manufacturer	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	ΔbolA	δbola	NN	_	_	_
4	and	and	CC	_	_	_
5	wt	wt	JJ	_	_	_
6	3xflag	3xflag	NN	_	_	_
7	strains	strain	NNS	_	_	_
8	were	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	to	to	TO	_	_	_
11	perform	perform	VB	_	_	_
12	ChIP-seq	chip-seq	JJ	_	_	_
13	experiments	experiment	NNS	_	_	_
14	.	.	.	_	_	_

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	MED	_	_
9	medium	medium	NN	MED	_	_
10	and	and	CC	_	_	_
11	grown	grow	VBN	_	_	_
12	until	until	IN	_	_	_
13	OD600	od600	NN	_	_	_
14	0.6	0.6	CD	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Third	Third	NNP	_	_	_
17	biological	biological	JJ	_	_	_
18	repeat	repeat	NN	_	_	_
19	37	37	CD	_	_	_
20	°C	°c	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Third	third	JJ	_	_	_
23	biological	biological	JJ	_	_	_
24	repeat	repeat	NN	_	_	_
25	50	50	CD	_	_	_
26	°C	°c	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Thirty-six	thirty-six	CD	_	_	_
29	dye-swap	dye-swap	JJ	_	_	_
30	hybridizations	hybridization	NNS	_	_	_
31	were	be	VBD	_	_	_
32	performed	perform	VBN	_	_	_
33	between	between	IN	_	_	_
34	four	four	CD	_	_	_
35	groups	group	NNS	_	_	_
36	with	with	IN	_	_	_
37	six	six	CD	_	_	_
38	strains	strain	NNS	_	_	_
39	per	per	IN	_	_	_
40	group	group	NN	_	_	_
41	,	,	,	_	_	_
42	according	accord	VBG	_	_	_
43	to	to	TO	_	_	_
44	a	a	DT	_	_	_
45	balanced	balanced	JJ	_	_	_
46	double	double	JJ	_	_	_
47	loop	loop	NN	_	_	_
48	design	design	NN	_	_	_
49	.	.	.	_	_	_

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	NN	_	_	_
2	three	three	CD	_	_	_
3	different	different	JJ	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	,	,	,	_	_	_
6	without	without	IN	_	_	_
7	H2O2	h2o2	NN	_	_	_
8	,	,	,	_	_	_
9	10	10	CD	_	_	_
10	%	%	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	v/v	v/v	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	or	or	CC	_	_	_
15	30	30	CD	_	_	_
16	%	%	NN	_	_	_
17	H2O2	h2o2	NN	_	_	_
18	were	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	directly	directly	RB	_	_	_
21	to	to	TO	_	_	_
22	the	the	DT	_	_	_
23	cell	cell	NN	_	_	_
24	cultures	culture	NNS	_	_	_
25	of	of	IN	_	_	_
26	wild	wild	JJ	_	_	_
27	type	type	NN	_	_	_
28	or	or	CC	_	_	_
29	luxS	luxs	NN	GEN	_	_
30	mutants	mutant	NNS	_	_	_
31	,	,	,	_	_	_
32	OD	od	NN	_	_	_
33	of	of	IN	_	_	_
34	which	which	WDT	_	_	_
35	is	be	VBZ	_	_	_
36	1.0	1.0	CD	_	_	_
37	.	.	.	_	_	_

1	Treated	treat	VBN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	continuously	continuously	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	at	at	IN	_	_	_
7	30	30	CD	_	_	_
8	degree	degree	NN	_	_	_
9	Celcius	Celcius	NNP	_	_	_
10	for	for	IN	_	_	_
11	30	30	CD	_	_	_
12	min	min	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Threonine	threonine	NN	_	_	_
15	addition	addition	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Thymidine	Thymidine	NNP	_	_	_
18	addition	addition	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	time	time	NN	_	_	_
21	:	:	:	_	_	_
22	0-15h	0-15h	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	time	time	NN	_	_	_
25	:	:	:	_	_	_
26	0-16h	0-16h	JJ	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	time	time	NN	_	_	_
29	:	:	:	_	_	_
30	0-2h	0-2h	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	time	time	NN	_	_	_
33	:	:	:	_	_	_
34	0.5	0.5	CD	_	_	_
35	min	min	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	time	time	NN	_	_	_
38	:	:	:	_	_	_
39	0	0	CD	_	_	_
40	min	min	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	time	time	NN	_	_	_
43	:	:	:	_	_	_
44	0	0	CD	_	_	_
45	mins	min	NNS	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
47	time	time	NN	_	_	_
48	:	:	:	_	_	_
49	10	10	CD	_	_	_
50	min	min	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	time	time	NN	_	_	_
53	:	:	:	_	_	_
54	10	10	CD	_	_	_
55	min	min	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	time	time	NN	_	_	_
58	:	:	:	_	_	_
59	10	10	CD	_	_	_
60	mins	min	NNS	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
62	time	time	NN	_	_	_
63	10	10	CD	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	OD600	od600	NN	_	_	_
66	=	=	JJ	_	_	_
67	4.7	4.7	CD	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	time	time	NN	_	_	_
71	11	11	CD	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	OD600	od600	NN	_	_	_
74	=	=	JJ	_	_	_
75	4.8	4.8	CD	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	time	time	NN	_	_	_
79	:	:	:	_	_	_
80	120	120	CD	_	_	_
81	min	min	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	time	time	NN	_	_	_
84	:	:	:	_	_	_
85	120	120	CD	_	_	_
86	minutes	minute	NNS	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
88	time	time	NN	_	_	_
89	:	:	:	_	_	_
90	12	12	CD	_	_	_
91	h	h	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	time	time	NN	_	_	_
94	:	:	:	_	_	_
95	180	180	CD	_	_	_
96	minutes	minute	NNS	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
98	time	time	NN	_	_	_
99	:	:	:	_	_	_
100	195	195	CD	_	_	_
101	min	min	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	time	time	NN	_	_	_
104	:	:	:	_	_	_
105	1	1	CD	_	_	_
106	h	h	NN	_	_	_
107	with	with	IN	_	_	_
108	20	20	CD	_	_	_
109	μg/mL	μg/ml	NN	_	_	_
110	ampicillin	ampicillin	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	time	time	NN	_	_	_
113	:	:	:	_	_	_
114	1	1	CD	_	_	_
115	min	min	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	time	time	NN	_	_	_
118	:	:	:	_	_	_
119	1	1	CD	_	_	_
120	min	min	NN	_	_	_
121	post-infection	post-infection	JJ	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	time	time	NN	_	_	_
124	1	1	CD	_	_	_
125	-LRB-	-lrb-	-LRB-	_	_	_
126	OD600	od600	NN	_	_	_
127	=	=	JJ	_	_	_
128	0.1	0.1	CD	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	time	time	NN	_	_	_
132	:	:	:	_	_	_
133	20	20	CD	_	_	_
134	min	min	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	time	time	NN	_	_	_
137	:	:	:	_	_	_
138	20	20	CD	_	_	_
139	min	min	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	time	time	NN	_	_	_
142	:	:	:	_	_	_
143	20	20	CD	_	_	_
144	minutes	minute	NNS	_	_	_
145	-LRB-	-lrb-	-LRB-	_	_	_
146	t2	t2	NN	_	_	_
147	-RRB-	-rrb-	-RRB-	_	_	_
148	after	after	IN	_	_	_
149	treatment	treatment	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	time	time	NN	_	_	_
152	:	:	:	_	_	_
153	210	210	CD	_	_	_
154	min	min	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	time	time	NN	_	_	_
157	:	:	:	_	_	_
158	24	24	CD	_	_	_
159	h	h	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	time	time	NN	_	_	_
162	:	:	:	_	_	_
163	25h	25h	JJ	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
165	time	time	NN	_	_	_
166	:	:	:	_	_	_
167	25	25	CD	_	_	_
168	min	min	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	time	time	NN	_	_	_
171	:	:	:	_	_	_
172	2.5	2.5	CD	_	_	_
173	min	min	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	time	time	NN	_	_	_
176	:	:	:	_	_	_
177	2.5	2.5	CD	_	_	_
178	min	min	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	time	time	NN	_	_	_
181	:	:	:	_	_	_
182	2.5	2.5	CD	_	_	_
183	mins	min	NNS	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
185	time	time	NN	_	_	_
186	:	:	:	_	_	_
187	26h	26h	JJ	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
189	time	time	NN	_	_	_
190	:	:	:	_	_	_
191	28h	28h	JJ	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
193	time	time	NN	_	_	_
194	:	:	:	_	_	_
195	2	2	CD	_	_	_
196	min	min	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	time	time	NN	_	_	_
199	2	2	CD	_	_	_
200	-LRB-	-lrb-	-LRB-	_	_	_
201	OD600	od600	NN	_	_	_
202	=	=	JJ	_	_	_
203	0.3	0.3	CD	_	_	_
204	-RRB-	-rrb-	-RRB-	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	time	time	NN	_	_	_
207	:	:	:	_	_	_
208	300	300	CD	_	_	_
209	minutes	minute	NNS	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
211	time	time	NN	_	_	_
212	:	:	:	_	_	_
213	30	30	CD	_	_	_
214	min	min	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	time	time	NN	_	_	_
217	:	:	:	_	_	_
218	30	30	CD	_	_	_
219	mins	min	NNS	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
221	time	time	NN	_	_	_
222	:	:	:	_	_	_
223	330	330	CD	_	_	_
224	min	min	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	time	time	NN	_	_	_
227	3	3	CD	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	OD600	od600	NN	_	_	_
230	=	=	JJ	_	_	_
231	0.4	0.4	CD	_	_	_
232	-RRB-	-rrb-	-RRB-	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	time	time	NN	_	_	_
235	:	:	:	_	_	_
236	40	40	CD	_	_	_
237	min	min	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	time	time	NN	_	_	_
240	:	:	:	_	_	_
241	40	40	CD	_	_	_
242	min	min	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	time	time	NN	_	_	_
245	:	:	:	_	_	_
246	40	40	CD	_	_	_
247	minutes	minute	NNS	_	_	_
248	-LRB-	-lrb-	-LRB-	_	_	_
249	t3	t3	NN	_	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	after	after	IN	_	_	_
252	treatment	treatment	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	time	time	NN	_	_	_
255	:	:	:	_	_	_
256	420	420	CD	_	_	_
257	minutes	minute	NNS	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
259	time	time	NN	_	_	_
260	:	:	:	_	_	_
261	45	45	CD	_	_	_
262	min	min	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	time	time	NN	_	_	_
265	4	4	CD	_	_	_
266	-LRB-	-lrb-	-LRB-	_	_	_
267	OD600	od600	NN	_	_	_
268	=	=	JJ	_	_	_
269	0.6	0.6	CD	_	_	_
270	-RRB-	-rrb-	-RRB-	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	time	time	NN	_	_	_
273	:	:	:	_	_	_
274	5	5	CD	_	_	_
275	min	min	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	time	time	NN	_	_	_
278	:	:	:	_	_	_
279	5	5	CD	_	_	_
280	min	min	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	time	time	NN	_	_	_
283	:	:	:	_	_	_
284	5	5	CD	_	_	_
285	min	min	NN	_	_	_
286	post-infection	post-infection	JJ	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	time	time	NN	_	_	_
289	5	5	CD	_	_	_
290	-LRB-	-lrb-	-LRB-	_	_	_
291	OD600	od600	NN	_	_	_
292	=	=	JJ	_	_	_
293	1.0	1.0	CD	_	_	_
294	-RRB-	-rrb-	-RRB-	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	time	time	NN	_	_	_
297	:	:	:	_	_	_
298	60	60	CD	_	_	_
299	min	min	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	time	time	NN	_	_	_
302	:	:	:	_	_	_
303	60	60	CD	_	_	_
304	minutes	minute	NNS	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
306	time	time	NN	_	_	_
307	:	:	:	_	_	_
308	6	6	CD	_	_	_
309	h	h	NN	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	time	time	NN	_	_	_
312	6	6	CD	_	_	_
313	-LRB-	-lrb-	-LRB-	_	_	_
314	OD600	od600	NN	_	_	_
315	=	=	JJ	_	_	_
316	1.3	1.3	CD	_	_	_
317	-RRB-	-rrb-	-RRB-	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	time	time	NN	_	_	_
320	:	:	:	_	_	_
321	75	75	CD	_	_	_
322	min	min	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	time	time	NN	_	_	_
325	:	:	:	_	_	_
326	7	7	CD	_	_	_
327	hours	hour	NNS	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
329	time	time	NN	_	_	_
330	:	:	:	_	_	_
331	7	7	CD	_	_	_
332	mins	min	NNS	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
334	time	time	NN	_	_	_
335	7	7	CD	_	_	_
336	-LRB-	-lrb-	-LRB-	_	_	_
337	OD	od	NN	_	_	_
338	=	=	JJ	_	_	_
339	1.7	1.7	CD	_	_	_
340	-RRB-	-rrb-	-RRB-	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	time	time	NN	_	_	_
343	7	7	CD	_	_	_
344	-LRB-	-lrb-	-LRB-	_	_	_
345	OD600	od600	NN	_	_	_
346	=	=	JJ	_	_	_
347	1.7	1.7	CD	_	_	_
348	-RRB-	-rrb-	-RRB-	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	time	time	NN	_	_	_
351	:	:	:	_	_	_
352	80	80	CD	_	_	_
353	min	min	NN	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	time	time	NN	_	_	_
356	:	:	:	_	_	_
357	80	80	CD	_	_	_
358	min	min	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	time	time	NN	_	_	_
361	8	8	CD	_	_	_
362	-LRB-	-lrb-	-LRB-	_	_	_
363	OD	od	NN	_	_	_
364	=	=	JJ	_	_	_
365	2.7	2.7	CD	_	_	_
366	-RRB-	-rrb-	-RRB-	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	time	time	NN	_	_	_
369	8	8	CD	_	_	_
370	-LRB-	-lrb-	-LRB-	_	_	_
371	OD600	od600	NN	_	_	_
372	=	=	JJ	_	_	_
373	2.7	2.7	CD	_	_	_
374	-RRB-	-rrb-	-RRB-	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	time	time	NN	_	_	_
377	:	:	:	_	_	_
378	9	9	CD	_	_	_
379	min	min	NN	_	_	_
380	post-infection	post-infection	JJ	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	time	time	NN	_	_	_
383	9	9	CD	_	_	_
384	-LRB-	-lrb-	-LRB-	_	_	_
385	OD600	od600	NN	_	_	_
386	=	=	JJ	_	_	_
387	4.5	4.5	CD	_	_	_
388	-RRB-	-rrb-	-RRB-	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	time	time	NN	_	_	_
391	:	:	:	_	_	_
392	at	at	IN	_	_	_
393	time	time	NN	_	_	_
394	of	of	IN	_	_	_
395	treatment	treatment	NN	_	_	_
396	-LRB-	-lrb-	-LRB-	_	_	_
397	t1	t1	NN	_	_	_
398	-RRB-	-rrb-	-RRB-	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	time	time	NN	_	_	_
401	course	course	NN	_	_	_
402	sample	sample	NN	_	_	_
403	harvested	harvest	VBN	_	_	_
404	after	after	IN	_	_	_
405	15	15	CD	_	_	_
406	min	min	NN	_	_	_
407	of	of	IN	_	_	_
408	glucose	glucose	NN	SUPP	_	_
409	to	to	TO	_	_	_
410	acetate	acetate	NN	SUPP	_	_
411	shift	shift	NN	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	time	time	NN	_	_	_
414	course	course	NN	_	_	_
415	sample	sample	NN	_	_	_
416	harvested	harvest	VBN	_	_	_
417	after	after	IN	_	_	_
418	1	1	CD	_	_	_
419	hour	hour	NN	_	_	_
420	of	of	IN	_	_	_
421	glucose	glucose	NN	SUPP	_	_
422	to	to	TO	_	_	_
423	acetate	acetate	NN	SUPP	_	_
424	shift	shift	NN	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	time	time	NN	_	_	_
427	course	course	NN	_	_	_
428	sample	sample	NN	_	_	_
429	harvested	harvest	VBN	_	_	_
430	after	after	IN	_	_	_
431	2	2	CD	_	_	_
432	hour	hour	NN	_	_	_
433	of	of	IN	_	_	_
434	glucose	glucose	NN	SUPP	_	_
435	to	to	TO	_	_	_
436	acetate	acetate	NN	SUPP	_	_
437	shift	shift	NN	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	time	time	NN	_	_	_
440	course	course	NN	_	_	_
441	sample	sample	NN	_	_	_
442	harvested	harvest	VBN	_	_	_
443	after	after	IN	_	_	_
444	30	30	CD	_	_	_
445	min	min	NN	_	_	_
446	of	of	IN	_	_	_
447	glucose	glucose	NN	SUPP	_	_
448	to	to	TO	_	_	_
449	acetate	acetate	NN	SUPP	_	_
450	shift	shift	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	time	time	NN	_	_	_
453	course	course	NN	_	_	_
454	sample	sample	NN	_	_	_
455	harvested	harvest	VBN	_	_	_
456	after	after	IN	_	_	_
457	3	3	CD	_	_	_
458	hour	hour	NN	_	_	_
459	of	of	IN	_	_	_
460	glucose	glucose	NN	SUPP	_	_
461	to	to	TO	_	_	_
462	acetate	acetate	NN	SUPP	_	_
463	shift	shift	NN	_	_	_
464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
465	time	time	NN	_	_	_
466	course	course	NN	_	_	_
467	sample	sample	NN	_	_	_
468	harvested	harvest	VBN	_	_	_
469	after	after	IN	_	_	_
470	4	4	CD	_	_	_
471	hour	hour	NN	_	_	_
472	of	of	IN	_	_	_
473	glucose	glucose	NN	SUPP	_	_
474	to	to	TO	_	_	_
475	acetate	acetate	NN	SUPP	_	_
476	shift	shift	NN	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	time	time	NN	_	_	_
479	course	course	NN	_	_	_
480	sample	sample	NN	_	_	_
481	harvested	harvest	VBN	_	_	_
482	after	after	IN	_	_	_
483	5	5	CD	_	_	_
484	hour	hour	NN	_	_	_
485	of	of	IN	_	_	_
486	glucose	glucose	NN	SUPP	_	_
487	to	to	TO	_	_	_
488	acetate	acetate	NN	SUPP	_	_
489	shift	shift	NN	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	time	time	NN	_	_	_
492	course	course	NN	_	_	_
493	sample	sample	NN	_	_	_
494	harvested	harvest	VBN	_	_	_
495	after	after	IN	_	_	_
496	5	5	CD	_	_	_
497	min	min	NN	_	_	_
498	of	of	IN	_	_	_
499	glucose	glucose	NN	SUPP	_	_
500	to	to	TO	_	_	_
501	acetate	acetate	NN	SUPP	_	_
502	shift	shift	NN	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	time	time	NN	_	_	_
505	course	course	NN	_	_	_
506	sample	sample	NN	_	_	_
507	harvested	harvest	VBN	_	_	_
508	after	after	IN	_	_	_
509	6	6	CD	_	_	_
510	hour	hour	NN	_	_	_
511	of	of	IN	_	_	_
512	glucose	glucose	NN	SUPP	_	_
513	to	to	TO	_	_	_
514	acetate	acetate	NN	SUPP	_	_
515	shift	shift	NN	_	_	_
516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
517	time	time	NN	_	_	_
518	induction	induction	NN	_	_	_
519	:	:	:	_	_	_
520	30	30	CD	_	_	_
521	minutes	minute	NNS	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
523	time	time	NN	_	_	_
524	induction	induction	NN	_	_	_
525	:	:	:	_	_	_
526	5	5	CD	_	_	_
527	minutes	minute	NNS	_	_	_
528	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
529	time	time	NN	_	_	_
530	induction	induction	NN	_	_	_
531	:	:	:	_	_	_
532	60	60	CD	_	_	_
533	minutes	minute	NNS	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
535	time	time	NN	_	_	_
536	point	point	NN	_	_	_
537	0	0	CD	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
539	time	time	NN	_	_	_
540	point	point	NN	_	_	_
541	:	:	:	_	_	_
542	0	0	CD	_	_	_
543	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
544	time	time	NN	_	_	_
545	point	point	NN	_	_	_
546	:	:	:	_	_	_
547	0	0	CD	_	_	_
548	min	min	NN	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	time	time	NN	_	_	_
551	point	point	NN	_	_	_
552	:	:	:	_	_	_
553	0	0	CD	_	_	_
554	min	min	NN	_	_	_
555	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
556	time	time	NN	_	_	_
557	point	point	NN	_	_	_
558	:	:	:	_	_	_
559	0	0	CD	_	_	_
560	minutes	minute	NNS	_	_	_
561	related	related	JJ	_	_	_
562	to	to	TO	_	_	_
563	point	point	NN	_	_	_
564	of	of	IN	_	_	_
565	BRP	brp	NN	_	_	_
566	induction	induction	NN	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	time	time	NN	_	_	_
569	point	point	NN	_	_	_
570	:	:	:	_	_	_
571	10	10	CD	_	_	_
572	min	min	NN	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	time	time	NN	_	_	_
575	point	point	NN	_	_	_
576	:	:	:	_	_	_
577	-10	-10	CD	_	_	_
578	minutes	minute	NNS	_	_	_
579	related	related	JJ	_	_	_
580	to	to	TO	_	_	_
581	point	point	NN	_	_	_
582	of	of	IN	_	_	_
583	BRP	brp	NN	_	_	_
584	induction	induction	NN	_	_	_
585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
586	time	time	NN	_	_	_
587	point	point	NN	_	_	_
588	:	:	:	_	_	_
589	10	10	CD	_	_	_
590	minutes	minute	NNS	_	_	_
591	related	related	JJ	_	_	_
592	to	to	TO	_	_	_
593	point	point	NN	_	_	_
594	of	of	IN	_	_	_
595	BRP	brp	NN	_	_	_
596	induction	induction	NN	_	_	_
597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
598	time	time	NN	_	_	_
599	point	point	NN	_	_	_
600	:	:	:	_	_	_
601	135	135	CD	_	_	_
602	min	min	NN	_	_	_
603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
604	time	time	NN	_	_	_
605	point	point	NN	_	_	_
606	:	:	:	_	_	_
607	15	15	CD	_	_	_
608	min	min	NN	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	time	time	NN	_	_	_
611	point	point	NN	_	_	_
612	:	:	:	_	_	_
613	168	168	CD	_	_	_
614	hours	hour	NNS	_	_	_
615	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
616	time	time	NN	_	_	_
617	point	point	NN	_	_	_
618	:	:	:	_	_	_
619	180	180	CD	_	_	_
620	min	min	NN	_	_	_
621	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
622	time	time	NN	_	_	_
623	point	point	NN	_	_	_
624	:	:	:	_	_	_
625	1	1	CD	_	_	_
626	min	min	NN	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	time	time	NN	_	_	_
629	point	point	NN	_	_	_
630	2	2	CD	_	_	_
631	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
632	time	time	NN	_	_	_
633	point	point	NN	_	_	_
634	:	:	:	_	_	_
635	20	20	CD	_	_	_
636	min	min	NN	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
638	time	time	NN	_	_	_
639	point	point	NN	_	_	_
640	:	:	:	_	_	_
641	20	20	CD	_	_	_
642	minutes	minute	NNS	_	_	_
643	related	related	JJ	_	_	_
644	to	to	TO	_	_	_
645	point	point	NN	_	_	_
646	of	of	IN	_	_	_
647	BRP	brp	NN	_	_	_
648	induction	induction	NN	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	time	time	NN	_	_	_
651	point	point	NN	_	_	_
652	:	:	:	_	_	_
653	24	24	CD	_	_	_
654	hours	hour	NNS	_	_	_
655	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
656	time	time	NN	_	_	_
657	point	point	NN	_	_	_
658	:	:	:	_	_	_
659	2	2	CD	_	_	_
660	min	min	NN	_	_	_
661	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
662	time	time	NN	_	_	_
663	point	point	NN	_	_	_
664	:	:	:	_	_	_
665	2	2	CD	_	_	_
666	minutes	minute	NNS	_	_	_
667	related	related	JJ	_	_	_
668	to	to	TO	_	_	_
669	point	point	NN	_	_	_
670	of	of	IN	_	_	_
671	BRP	brp	NN	_	_	_
672	induction	induction	NN	_	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
674	time	time	NN	_	_	_
675	point	point	NN	_	_	_
676	:	:	:	_	_	_
677	30	30	CD	_	_	_
678	min	min	NN	_	_	_
679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
680	time	time	NN	_	_	_
681	point	point	NN	_	_	_
682	:	:	:	_	_	_
683	30	30	CD	_	_	_
684	minutes	minute	NNS	_	_	_
685	related	related	JJ	_	_	_
686	to	to	TO	_	_	_
687	point	point	NN	_	_	_
688	of	of	IN	_	_	_
689	BRP	brp	NN	_	_	_
690	induction	induction	NN	_	_	_
691	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
692	time	time	NN	_	_	_
693	point	point	NN	_	_	_
694	:	:	:	_	_	_
695	336	336	CD	_	_	_
696	hours	hour	NNS	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
698	time	time	NN	_	_	_
699	point	point	NN	_	_	_
700	:	:	:	_	_	_
701	3	3	CD	_	_	_
702	hours	hour	NNS	_	_	_
703	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
704	time	time	NN	_	_	_
705	point	point	NN	_	_	_
706	4	4	CD	_	_	_
707	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
708	time	time	NN	_	_	_
709	point	point	NN	_	_	_
710	:	:	:	_	_	_
711	4.5	4.5	CD	_	_	_
712	hrs	hr	NNS	_	_	_
713	after	after	IN	_	_	_
714	induction	induction	NN	_	_	_
715	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
716	time	time	NN	_	_	_
717	point	point	NN	_	_	_
718	:	:	:	_	_	_
719	45	45	CD	_	_	_
720	min	min	NN	_	_	_
721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
722	time	time	NN	_	_	_
723	point	point	NN	_	_	_
724	:	:	:	_	_	_
725	45	45	CD	_	_	_
726	minutes	minute	NNS	_	_	_
727	related	related	JJ	_	_	_
728	to	to	TO	_	_	_
729	point	point	NN	_	_	_
730	of	of	IN	_	_	_
731	BRP	brp	NN	_	_	_
732	induction	induction	NN	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	time	time	NN	_	_	_
735	point	point	NN	_	_	_
736	:	:	:	_	_	_
737	48	48	CD	_	_	_
738	hours	hour	NNS	_	_	_
739	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
740	time	time	NN	_	_	_
741	point	point	NN	_	_	_
742	:	:	:	_	_	_
743	4	4	CD	_	_	_
744	hours	hour	NNS	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
746	time	time	NN	_	_	_
747	point	point	NN	_	_	_
748	:	:	:	_	_	_
749	4	4	CD	_	_	_
750	min	min	NN	_	_	_
751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
752	time	time	NN	_	_	_
753	point	point	NN	_	_	_
754	:	:	:	_	_	_
755	5	5	CD	_	_	_
756	hours	hour	NNS	_	_	_
757	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
758	time	time	NN	_	_	_
759	point	point	NN	_	_	_
760	:	:	:	_	_	_
761	5	5	CD	_	_	_
762	minutes	minute	NNS	_	_	_
763	related	related	JJ	_	_	_
764	to	to	TO	_	_	_
765	point	point	NN	_	_	_
766	of	of	IN	_	_	_
767	BRP	brp	NN	_	_	_
768	induction	induction	NN	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
770	time	time	NN	_	_	_
771	point	point	NN	_	_	_
772	6	6	CD	_	_	_
773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
774	time	time	NN	_	_	_
775	point	point	NN	_	_	_
776	:	:	:	_	_	_
777	60	60	CD	_	_	_
778	minutes	minute	NNS	_	_	_
779	related	related	JJ	_	_	_
780	to	to	TO	_	_	_
781	point	point	NN	_	_	_
782	of	of	IN	_	_	_
783	BRP	brp	NN	_	_	_
784	induction	induction	NN	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	time	time	NN	_	_	_
787	point	point	NN	_	_	_
788	:	:	:	_	_	_
789	6	6	CD	_	_	_
790	hours	hour	NNS	_	_	_
791	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
792	time	time	NN	_	_	_
793	point	point	NN	_	_	_
794	:	:	:	_	_	_
795	6	6	CD	_	_	_
796	hrs	hr	NNS	_	_	_
797	after	after	IN	_	_	_
798	induction	induction	NN	_	_	_
799	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
800	time	time	NN	_	_	_
801	point	point	NN	_	_	_
802	:	:	:	_	_	_
803	6	6	CD	_	_	_
804	min	min	NN	_	_	_
805	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
806	time	time	NN	_	_	_
807	point	point	NN	_	_	_
808	8	8	CD	_	_	_
809	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
810	time	time	NN	_	_	_
811	point	point	NN	_	_	_
812	:	:	:	_	_	_
813	8	8	CD	_	_	_
814	hours	hour	NNS	_	_	_
815	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
816	time	time	NN	_	_	_
817	point	point	NN	_	_	_
818	:	:	:	_	_	_
819	8	8	CD	_	_	_
820	min	min	NN	_	_	_
821	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
822	time	time	NN	_	_	_
823	point	point	NN	_	_	_
824	:	:	:	_	_	_
825	90	90	CD	_	_	_
826	min	min	NN	_	_	_
827	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
828	time	time	NN	_	_	_
829	point	point	NN	_	_	_
830	:	:	:	_	_	_
831	90	90	CD	_	_	_
832	min	min	NN	_	_	_
833	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
834	time	time	NN	_	_	_
835	point	point	NN	_	_	_
836	:	:	:	_	_	_
837	9	9	CD	_	_	_
838	hrs	hr	NNS	_	_	_
839	after	after	IN	_	_	_
840	induction	induction	NN	_	_	_
841	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
842	time	time	NN	_	_	_
843	point	point	NN	_	_	_
844	-LRB-	-lrb-	-LRB-	_	_	_
845	minutes	minute	NNS	_	_	_
846	-RRB-	-rrb-	-RRB-	_	_	_
847	:	:	:	_	_	_
848	0	0	CD	_	_	_
849	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
850	time	time	NN	_	_	_
851	point	point	NN	_	_	_
852	-LRB-	-lrb-	-LRB-	_	_	_
853	minutes	minute	NNS	_	_	_
854	-RRB-	-rrb-	-RRB-	_	_	_
855	:	:	:	_	_	_
856	15	15	CD	_	_	_
857	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
858	time	time	NN	_	_	_
859	point	point	NN	_	_	_
860	-LRB-	-lrb-	-LRB-	_	_	_
861	minutes	minute	NNS	_	_	_
862	-RRB-	-rrb-	-RRB-	_	_	_
863	:	:	:	_	_	_
864	30	30	CD	_	_	_
865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
866	time	time	NN	_	_	_
867	point	point	NN	_	_	_
868	-LRB-	-lrb-	-LRB-	_	_	_
869	minutes	minute	NNS	_	_	_
870	-RRB-	-rrb-	-RRB-	_	_	_
871	:	:	:	_	_	_
872	5	5	CD	_	_	_
873	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
874	Time-point	time-point	NN	_	_	_
875	samples	sample	NNS	_	_	_
876	were	be	VBD	_	_	_
877	taken	take	VBN	_	_	_
878	every	every	DT	_	_	_
879	15-30	15-30	CD	_	_	_
880	minutes	minute	NNS	_	_	_
881	from	from	IN	_	_	_
882	15	15	CD	_	_	_
883	minutes	minute	NNS	_	_	_
884	to	to	TO	_	_	_
885	2	2	CD	_	_	_
886	hours	hour	NNS	_	_	_
887	post	post	NN	_	_	_
888	treatment	treatment	NN	_	_	_
889	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	point	point	NN	_	_	_
4	:	:	:	_	_	_
5	time0	time0	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	time	time	NN	_	_	_
8	point	point	NN	_	_	_
9	:	:	:	_	_	_
10	time10	time10	JJ	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	time	time	NN	_	_	_
13	point	point	NN	_	_	_
14	:	:	:	_	_	_
15	time20	time20	JJ	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	time	time	NN	_	_	_
18	point	point	NN	_	_	_
19	:	:	:	_	_	_
20	time2	time2	CD	_	_	_
21	.5	.5	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	time	time	NN	_	_	_
24	point	point	NN	_	_	_
25	:	:	:	_	_	_
26	time5	time5	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	time	time	NN	_	_	_
29	point	point	NN	_	_	_
30	:	:	:	_	_	_
31	time7	time7	CD	_	_	_
32	.5	.5	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	time	time	NN	_	_	_
35	post-induction	post-induction	JJ	_	_	_
36	:	:	:	_	_	_
37	0h	0h	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	time	time	NN	_	_	_
40	post-induction	post-induction	JJ	_	_	_
41	:	:	:	_	_	_
42	10h	10h	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	time	time	NN	_	_	_
45	post-induction	post-induction	JJ	_	_	_
46	:	:	:	_	_	_
47	16h	16h	JJ	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
49	time	time	NN	_	_	_
50	post-induction	post-induction	JJ	_	_	_
51	:	:	:	_	_	_
52	20h	20h	JJ	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
54	time	time	NN	_	_	_
55	post-induction	post-induction	JJ	_	_	_
56	:	:	:	_	_	_
57	5h	5h	JJ	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
59	time	time	NN	_	_	_
60	post-induction	post-induction	JJ	_	_	_
61	:	:	:	_	_	_
62	6h	6h	JJ	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
64	time	time	NN	_	_	_
65	post-induction	post-induction	JJ	_	_	_
66	:	:	:	_	_	_
67	8h	8h	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	time	time	NN	_	_	_
70	post	post	NN	_	_	_
71	release	release	NN	_	_	_
72	:	:	:	_	_	_
73	E.	e.	FW	_	_	_
74	coli	coli	FW	_	_	_
75	cells	cell	NNS	_	_	_
76	1	1	CD	_	_	_
77	hour	hour	NN	_	_	_
78	following	follow	VBG	_	_	_
79	release	release	NN	_	_	_
80	from	from	IN	_	_	_
81	Stationary	stationary	JJ	_	_	_
82	phase	phase	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	t	t	NN	_	_	_
85	=	=	JJ	_	_	_
86	1	1	CD	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	time	time	NN	_	_	_
90	post	post	NN	_	_	_
91	release	release	NN	_	_	_
92	:	:	:	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	cells	cell	NNS	_	_	_
96	2	2	CD	_	_	_
97	hour2	hour2	NN	_	_	_
98	following	follow	VBG	_	_	_
99	release	release	NN	_	_	_
100	from	from	IN	_	_	_
101	Stationary	stationary	JJ	_	_	_
102	phase	phase	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	t	t	NN	_	_	_
105	=	=	JJ	_	_	_
106	2	2	CD	_	_	_
107	-RRB-	-rrb-	-RRB-	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	time	time	NN	_	_	_
110	post	post	NN	_	_	_
111	release	release	NN	_	_	_
112	:	:	:	_	_	_
113	E.	e.	FW	_	_	_
114	coli	coli	FW	_	_	_
115	cells	cell	NNS	_	_	_
116	immediately	immediately	RB	_	_	_
117	following	follow	VBG	_	_	_
118	release	release	NN	_	_	_
119	from	from	IN	_	_	_
120	Stationary	stationary	JJ	_	_	_
121	phase	phase	NN	_	_	_
122	t	t	NN	_	_	_
123	=	=	JJ	_	_	_
124	0	0	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	time	time	NN	_	_	_
127	:	:	:	_	_	_
128	Sample	sample	NN	_	_	_
129	was	be	VBD	_	_	_
130	taken	take	VBN	_	_	_
131	after	after	IN	_	_	_
132	mouse	mouse	NN	_	_	_
133	was	be	VBD	_	_	_
134	on	on	IN	_	_	_
135	the	the	DT	_	_	_
136	diet	diet	NN	_	_	_
137	for	for	IN	_	_	_
138	14	14	CD	_	_	_
139	days	day	NNS	_	_	_
140	.	.	.	_	_	_

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	tissue	tissue	NN	_	_	_
3	:	:	:	_	_	_
4	bacterial	bacterial	JJ	_	_	_
5	cells	cell	NNS	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	tissue	tissue	NN	_	_	_
8	:	:	:	_	_	_
9	entire	entire	JJ	_	_	_
10	bacterial	bacterial	JJ	_	_	_
11	cell	cell	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	tissue	tissue	NN	_	_	_
14	source	source	NN	_	_	_
15	:	:	:	_	_	_
16	kidney	kidney	NN	_	_	_
17	from	from	IN	_	_	_
18	CD-1	cd-1	JJ	_	_	_
19	mice	mouse	NNS	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	TLD-15-rep1	tld-15-rep1	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	TLD-15-rep2	tld-15-rep2	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	TLD-30-rep1	tld-30-rep1	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	TLD-30-rep2	tld-30-rep2	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	TLD-45-rep1	tld-45-rep1	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	TLD-45-rep2	tld-45-rep2	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	TLD-60-rep1	tld-60-rep1	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	TLD-60-rep2	tld-60-rep2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	TLD-90-rep1	tld-90-rep1	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	TLD-90-rep2	tld-90-rep2	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	TLM-15	tlm-15	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	TLM-30	tlm-30	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	TLM-45	tlm-45	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	TLM-60	tlm-60	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	TLM-90	tlm-90	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	tnaA2trpA46PR9	tnaa2trpa46pr9	NN	_	_	_
52	vs.	vs.	CC	_	_	_
53	tnaA2	tnaa2	NN	_	_	_
54	,	,	,	_	_	_
55	W3110	w3110	NN	_	_	_
56	min	min	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	tnaA2trpA46PR9	tnaa2trpa46pr9	NN	_	_	_
59	,	,	,	_	_	_
60	W3110	w3110	NN	_	_	_
61	min	min	NN	_	_	_
62	,	,	,	_	_	_
63	30	30	CD	_	_	_
64	ug	ug	NN	_	_	_
65	total	total	JJ	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	tnaA2trpR2	tnaa2trpr2	NN	_	_	_
68	vs.	vs.	CC	_	_	_
69	tnaA2	tnaa2	NN	_	_	_
70	,	,	,	_	_	_
71	W3110	w3110	NN	_	_	_
72	min	min	NN	_	_	_
73	+	+	CC	_	_	_
74	Trp	trp	NN	_	_	_
75	50ug/ml	50ug/ml	JJ	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	tnaA2trpR2	tnaa2trpr2	NN	_	_	_
78	,	,	,	_	_	_
79	W3110	w3110	NN	_	_	_
80	min	min	NN	_	_	_
81	+	+	CC	_	_	_
82	Trp	trp	NN	_	_	_
83	50ug/ml	50ug/ml	NN	_	_	_
84	,	,	,	_	_	_
85	30	30	CD	_	_	_
86	ug	ug	NN	_	_	_
87	total	total	JJ	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	tnaA2	tnaa2	NN	_	_	_
90	,	,	,	_	_	_
91	W3110	w3110	NN	_	_	_
92	min	min	NN	_	_	_
93	,30	,30	CD	_	_	_
94	ug	ug	NN	_	_	_
95	total	total	JJ	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	tnaA2	tnaa2	NN	_	_	_
98	,	,	,	_	_	_
99	W3110	w3110	NN	_	_	_
100	minimal	minimal	JJ	_	_	_
101	+	+	CC	_	_	_
102	Trp	trp	NN	_	_	_
103	50ug/ml	50ug/ml	NN	_	_	_
104	,	,	,	_	_	_
105	25	25	CD	_	_	_
106	ug	ug	NN	_	_	_
107	total	total	JJ	_	_	_
108	RNA	rna	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	tnaA2	tnaa2	NN	_	_	_
111	,	,	,	_	_	_
112	W3110	w3110	NN	_	_	_
113	minimal	minimal	JJ	_	_	_
114	+	+	CC	_	_	_
115	Trp	trp	NN	_	_	_
116	50ug/ml	50ug/ml	CD	_	_	_
117	vs.	vs.	CC	_	_	_
118	dnaC	dnaC	NNP	GEN	_	_
119	genomic	genomic	JJ	_	_	_
120	DNA	dna	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	tnaA2	tnaa2	NN	_	_	_
123	,	,	,	_	_	_
124	W3110	w3110	NN	_	_	_
125	min	min	NN	_	_	_
126	+	+	CC	_	_	_
127	Trp	trp	NN	_	_	_
128	50ug/ml	50ug/ml	NN	_	_	_
129	,	,	,	_	_	_
130	30	30	CD	_	_	_
131	ug	ug	NN	_	_	_
132	total	total	JJ	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
134	To	to	TO	_	_	_
135	analyze	analyze	VB	_	_	_
136	RNAP	rnap	NN	_	_	_
137	pausing	pause	VBG	_	_	_
138	on	on	IN	_	_	_
139	the	the	DT	_	_	_
140	E.	e.	FW	_	_	_
141	coli	coli	FW	_	_	_
142	chromosome	chromosome	NN	_	_	_
143	,	,	,	_	_	_
144	we	we	PRP	_	_	_
145	counted	count	VBD	_	_	_
146	the	the	DT	_	_	_
147	number	number	NN	_	_	_
148	of	of	IN	_	_	_
149	reads	read	VBZ	_	_	_
150	at	at	IN	_	_	_
151	every	every	DT	_	_	_
152	genomic	genomic	JJ	_	_	_
153	nucleotide	nucleotide	NN	_	_	_
154	position	position	NN	_	_	_
155	using	use	VBG	_	_	_
156	the	the	DT	_	_	_
157	mpileup	mpileup	NN	_	_	_
158	command	command	NN	_	_	_
159	of	of	IN	_	_	_
160	SAM	SAM	NNP	_	_	_
161	tools	tool	NNS	_	_	_
162	v0	v0	VBP	_	_	_
163	.1.18	.1.18	CD	_	_	_
164	with	with	IN	_	_	_
165	--	--	:	_	_	_
166	A	a	DT	_	_	_
167	--	--	:	_	_	_
168	B	b	NN	_	_	_
169	parameters	parameter	NNS	_	_	_
170	.	.	.	_	_	_

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	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://www.mathcell.ru/DnaRnaTools/Matcher.zip	http://www.mathcell.ru/dnarnatools/matcher.zip	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	software	software	NN	_	_	_
3	maps	map	VBZ	_	_	_
4	only	only	RB	_	_	_
5	5	5	CD	_	_	_
6	'	'	''	_	_	_
7	-	-	:	_	_	_
8	ends	end	VBZ	_	_	_
9	if	if	IN	_	_	_
10	the	the	DT	_	_	_
11	reads	read	VBZ	_	_	_
12	correspond	correspond	VBP	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	top	top	JJ	_	_	_
16	strand	strand	NN	_	_	_
17	of	of	IN	_	_	_
18	genomic	genomic	JJ	_	_	_
19	DNA	dna	NN	_	_	_
20	,	,	,	_	_	_
21	or	or	CC	_	_	_
22	only	only	RB	_	_	_
23	3	3	CD	_	_	_
24	'	'	''	_	_	_
25	-	-	:	_	_	_
26	ends	end	NNS	_	_	_
27	,	,	,	_	_	_
28	if	if	IN	_	_	_
29	they	they	PRP	_	_	_
30	are	be	VBP	_	_	_
31	aligned	align	VBN	_	_	_
32	to	to	TO	_	_	_
33	the	the	DT	_	_	_
34	bottom	bottom	JJ	_	_	_
35	strand	strand	NN	_	_	_
36	.	.	.	_	_	_

1	As	as	IN	_	_	_
2	such	such	JJ	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	signals	signal	NNS	_	_	_
6	from	from	IN	_	_	_
7	fully	fully	RB	_	_	_
8	complementary	complementary	JJ	_	_	_
9	reads	read	VBZ	_	_	_
10	will	will	MD	_	_	_
11	match	match	VB	_	_	_
12	the	the	DT	_	_	_
13	same	same	JJ	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	left	left	JJ	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	position	position	NN	_	_	_
18	.	.	.	_	_	_

1	Reporting	Reporting	NNP	_	_	_
2	the	the	DT	_	_	_
3	distribution	distribution	NN	_	_	_
4	of	of	IN	_	_	_
5	matching	match	VBG	_	_	_
6	reads	read	VBZ	_	_	_
7	across	across	IN	_	_	_
8	the	the	DT	_	_	_
9	genome	genome	NN	_	_	_
10	the	the	DT	_	_	_
11	program	program	NN	_	_	_
12	also	also	RB	_	_	_
13	evaluates	evaluate	VBZ	_	_	_
14	reads	read	VBZ	_	_	_
15	with	with	IN	_	_	_
16	multiple	multiple	JJ	_	_	_
17	occurrence	occurrence	NN	_	_	_
18	and	and	CC	_	_	_
19	their	they	PRP$	_	_	_
20	positions	position	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	capture	capture	VB	_	_	_
4	target	target	NN	_	_	_
5	protein	protein	NN	_	_	_
6	binding	binding	NN	_	_	_
7	sites	site	NNS	_	_	_
8	corresponding	correspond	VBG	_	_	_
9	genomic	genomic	JJ	_	_	_
10	position	position	NN	_	_	_
11	of	of	IN	_	_	_
12	mapped	map	VBN	_	_	_
13	reads	read	VBZ	_	_	_
14	start	start	NN	_	_	_
15	position	position	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	MRSP	mrsp	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	was	be	VBD	_	_	_
20	counted	count	VBN	_	_	_
21	and	and	CC	_	_	_
22	stored	store	VBN	_	_	_
23	for	for	IN	_	_	_
24	visual	visual	JJ	_	_	_
25	inspection	inspection	NN	_	_	_
26	using	use	VBG	_	_	_
27	in-house	in-house	JJ	_	_	_
28	scripts	script	NNS	_	_	_
29	.	.	.	_	_	_

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	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	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	harvest	harvest	VB	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	samples	sample	NNS	_	_	_
7	,	,	,	_	_	_
8	overnight	overnight	JJ	_	_	_
9	cultures	culture	NNS	_	_	_
10	of	of	IN	_	_	_
11	wild	wild	JJ	_	_	_
12	type	type	NN	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	grown	grow	VBN	_	_	_
15	in	in	IN	_	_	_
16	LB	lb	NN	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	˚C	˚c	NN	_	_	_
20	were	be	VBD	_	_	_
21	diluted	dilute	VBN	_	_	_
22	back	back	RB	_	_	_
23	1:500	1:500	CD	_	_	_
24	in	in	IN	_	_	_
25	either	either	CC	_	_	_
26	fresh	fresh	JJ	_	_	_
27	LB	lb	NN	_	_	_
28	or	or	CC	_	_	_
29	M63	m63	NN	_	_	_
30	minimal	minimal	JJ	_	_	_
31	glucose	glucose	NN	SUPP	_	_
32	medium	medium	NN	_	_	_
33	and	and	CC	_	_	_
34	allowed	allow	VBN	_	_	_
35	to	to	TO	_	_	_
36	grow	grow	VB	_	_	_
37	until	until	IN	_	_	_
38	the	the	DT	_	_	_
39	cultures	culture	NNS	_	_	_
40	reached	reach	VBD	_	_	_
41	an	a	DT	_	_	_
42	OD600	od600	NN	_	_	_
43	of	of	IN	_	_	_
44	~	~	NN	_	_	_
45	0.4	0.4	CD	_	_	_
46	and	and	CC	_	_	_
47	2.0	2.0	CD	_	_	_
48	for	for	IN	_	_	_
49	cultures	culture	NNS	_	_	_
50	grown	grow	VBN	_	_	_
51	in	in	IN	_	_	_
52	LB	lb	NN	_	_	_
53	and	and	CC	_	_	_
54	an	a	DT	_	_	_
55	OD600	od600	NN	_	_	_
56	of	of	IN	_	_	_
57	~	~	NN	_	_	_
58	0.4	0.4	CD	_	_	_
59	for	for	IN	_	_	_
60	cultures	culture	NNS	_	_	_
61	grown	grow	VBN	_	_	_
62	in	in	IN	_	_	_
63	M63	m63	NN	_	_	_
64	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	infer	infer	VB	_	_	_
4	the	the	DT	_	_	_
5	tag	tag	NN	GEN	_	_
6	copy	copy	NN	_	_	_
7	numbers	number	NNS	_	_	_
8	in	in	IN	_	_	_
9	each	each	DT	_	_	_
10	Tag-Seq	Tag-Seq	NNP	_	_	_
11	library	library	NN	_	_	_
12	,	,	,	_	_	_
13	all	all	DT	_	_	_
14	sequence	sequence	NN	_	_	_
15	reads	read	VBZ	_	_	_
16	were	be	VBD	_	_	_
17	examined	examine	VBN	_	_	_
18	,	,	,	_	_	_
19	regardless	regardless	RB	_	_	_
20	of	of	IN	_	_	_
21	their	they	PRP$	_	_	_
22	quality	quality	NN	_	_	_
23	scores	score	NNS	_	_	_
24	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	lyse	lyse	VB	_	_	_
4	the	the	DT	_	_	_
5	cells	cell	NNS	_	_	_
6	,	,	,	_	_	_
7	1.0	1.0	CD	_	_	_
8	mL	ml	NN	_	_	_
9	RLT	rlt	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	,	,	,	_	_	_
14	Inc.	Inc.	NNP	_	_	_
15	,	,	,	_	_	_
16	Valencia	Valencia	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	0.2	0.2	CD	_	_	_
22	mL	ml	NN	_	_	_
23	0.1	0.1	CD	_	_	_
24	mm	mm	NN	_	_	_
25	zirconia/silica	zirconia/silica	NN	_	_	_
26	beads	bead	NNS	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Biospec	biospec	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	were	be	VBD	_	_	_
31	added	add	VBN	_	_	_
32	to	to	TO	_	_	_
33	the	the	DT	_	_	_
34	frozen	frozen	JJ	_	_	_
35	bead	bead	NN	_	_	_
36	beater	beater	NN	_	_	_
37	tubes	tube	NNS	_	_	_
38	containing	contain	VBG	_	_	_
39	the	the	DT	_	_	_
40	cell	cell	NN	_	_	_
41	pellets	pellet	NNS	_	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	tubes	tube	NNS	_	_	_
3	were	be	VBD	_	_	_
4	closed	close	VBN	_	_	_
5	tightly	tightly	RB	_	_	_
6	and	and	CC	_	_	_
7	beat	beat	VB	_	_	_
8	for	for	IN	_	_	_
9	50	50	CD	_	_	_
10	seconds	seconds	NNS	_	_	_
11	at	at	IN	_	_	_
12	the	the	DT	_	_	_
13	maximum	maximum	NN	_	_	_
14	speed	speed	NN	_	_	_
15	in	in	IN	_	_	_
16	a	a	DT	_	_	_
17	mini	mini	JJ	_	_	_
18	bead	bead	NN	_	_	_
19	beater	beater	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	cat	cat	NN	_	_	_
22	.	.	.	_	_	_

1	no.	no.	RB	_	_	_
2	3110BX	3110BX	NNP	_	_	_
3	,	,	,	_	_	_
4	Biospec	Biospec	NNP	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	by	by	IN	_	_	_
7	following	follow	VBG	_	_	_
8	the	the	DT	_	_	_
9	protocol	protocol	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	RNeasy	RNeasy	NNP	_	_	_
13	Mini	Mini	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Qiagen	qiagen	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	including	include	VBG	_	_	_
19	an	a	DT	_	_	_
20	on-column	on-column	JJ	_	_	_
21	DNase	dnase	NN	_	_	_
22	digestion	digestion	NN	_	_	_
23	with	with	IN	_	_	_
24	RNase-free	rnase-free	JJ	_	_	_
25	DNase	dnase	NN	_	_	_
26	I	i	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Qiagen	qiagen	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

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	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	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	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	remove	remove	VB	_	_	_
4	contaminating	contaminate	VBG	_	_	_
5	sequences	sequence	NNS	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	reads	read	VBZ	_	_	_
9	were	be	VBD	_	_	_
10	split	split	VBN	_	_	_
11	according	accord	VBG	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	HinfI	hinfi	NN	_	_	_
15	consensus	consensus	NN	_	_	_
16	motif	motif	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	5	5	CD	_	_	_
19	'	'	''	_	_	_
20	-	-	:	_	_	_
21	G	g	NN	_	_	_
22	^	^	SYM	_	_	_
23	ANTC-3	antc-3	NN	_	_	_
24	'	'	''	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	considered	consider	VBN	_	_	_
27	as	as	IN	_	_	_
28	a	a	DT	_	_	_
29	barcode	barcode	NN	_	_	_
30	sequence	sequence	NN	_	_	_
31	using	use	VBG	_	_	_
32	fastx	fastx	NN	_	_	_
33	_	_	NN	_	_	_
34	toolkit	toolkit	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	http://hannonlab.cshl.edu/fastx_toolkit/	http://hannonlab.cshl.edu/fastx_toolkit/	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	fastx_barcode_splitter.pl	fastx_barcode_splitter.pl	NN	_	_	_
40	--	--	:	_	_	_
41	bcfile	bcfile	JJ	_	_	_
42	barcodelist.txt	barcodelist.txt	NN	_	_	_
43	--	--	:	_	_	_
44	bol	bol	NN	_	_	_
45	--	--	:	_	_	_
46	exact	exact	JJ	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	Most	most	JJS	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	reads	read	VBZ	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	more	more	JJR	_	_	_
7	than	than	IN	_	_	_
8	90	90	CD	_	_	_
9	%	%	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	were	be	VBD	_	_	_
12	rejected	reject	VBN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	reads	read	VBZ	_	_	_
17	kept	keep	VBN	_	_	_
18	were	be	VBD	_	_	_
19	remapped	remap	VBN	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	reference	reference	NN	_	_	_
23	genomes	genome	NNS	_	_	_
24	with	with	IN	_	_	_
25	bwa	bwa	NN	_	_	_
26	mem	mem	NN	_	_	_
27	and	and	CC	_	_	_
28	samtools	samtool	NNS	_	_	_
29	to	to	TO	_	_	_
30	generate	generate	VB	_	_	_
31	a	a	DT	_	_	_
32	sorted	sort	VBN	_	_	_
33	bam	bam	NN	_	_	_
34	file	file	NN	_	_	_
35	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bam	bam	NN	_	_	_
3	file	file	NN	_	_	_
4	was	be	VBD	_	_	_
5	further	further	JJ	_	_	_
6	filtered	filter	VBN	_	_	_
7	to	to	TO	_	_	_
8	remove	remove	VB	_	_	_
9	low	low	JJ	_	_	_
10	mapping	mapping	NN	_	_	_
11	quality	quality	NN	_	_	_
12	reads	read	VBZ	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	keeping	keep	VBG	_	_	_
15	AS	as	JJ	_	_	_
16	>	>	JJR	_	_	_
17	=	=	JJ	_	_	_
18	45	45	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	split	split	VBN	_	_	_
22	by	by	IN	_	_	_
23	orientation	orientation	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	alignmentFlag	alignmentflag	NN	_	_	_
26	0	0	CD	_	_	_
27	or	or	CC	_	_	_
28	16	16	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	with	with	IN	_	_	_
31	bamtools	bamtool	NNS	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	reads	read	VBZ	_	_	_
3	were	be	VBD	_	_	_
4	counted	count	VBN	_	_	_
5	at	at	IN	_	_	_
6	5	5	CD	_	_	_
7	'	'	''	_	_	_
8	positions	position	NNS	_	_	_
9	using	use	VBG	_	_	_
10	Bedtools	bedtool	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	bedtools	bedtool	NNS	_	_	_
13	genomecov	genomecov	NN	_	_	_
14	-	-	:	_	_	_
15	d	d	NN	_	_	_
16	-5	-5	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	Both	both	DT	_	_	_
2	orientation	orientation	NN	_	_	_
3	count	count	NN	_	_	_
4	files	file	NNS	_	_	_
5	were	be	VBD	_	_	_
6	combined	combine	VBN	_	_	_
7	into	into	IN	_	_	_
8	a	a	DT	_	_	_
9	bed	bed	NN	_	_	_
10	file	file	NN	_	_	_
11	at	at	IN	_	_	_
12	each	each	DT	_	_	_
13	identified	identify	VBN	_	_	_
14	5	5	CD	_	_	_
15	'	'	''	_	_	_
16	-	-	:	_	_	_
17	GANTC-3	gantc-3	NN	_	_	_
18	'	'	''	_	_	_
19	motif	motif	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	where	where	WRB	_	_	_
22	reverse	reverse	JJ	_	_	_
23	counts	count	NNS	_	_	_
24	>	>	JJR	_	_	_
25	=	=	JJ	_	_	_
26	1	1	CD	_	_	_
27	at	at	IN	_	_	_
28	position	position	NN	_	_	_
29	N	n	NN	_	_	_
30	+1	+1	CD	_	_	_
31	and	and	CC	_	_	_
32	forward	forward	RB	_	_	_
33	counts	count	VBZ	_	_	_
34	>	>	JJR	_	_	_
35	=	=	JJ	_	_	_
36	1	1	CD	_	_	_
37	at	at	IN	_	_	_
38	position	position	NN	_	_	_
39	N-1	n-1	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	using	use	VBG	_	_	_
42	a	a	DT	_	_	_
43	home-made	home-made	JJ	_	_	_
44	PERL	perl	NN	_	_	_
45	script	script	NN	_	_	_
46	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	HinfI	hinfi	NN	_	_	_
3	positions	position	NNS	_	_	_
4	in	in	IN	_	_	_
5	the	the	DT	_	_	_
6	bed	bed	NN	_	_	_
7	file	file	NN	_	_	_
8	were	be	VBD	_	_	_
9	associated	associate	VBN	_	_	_
10	with	with	IN	_	_	_
11	the	the	DT	_	_	_
12	closest	closest	JJS	_	_	_
13	gene	gene	NN	_	_	_
14	using	use	VBG	_	_	_
15	Bedtools	Bedtools	NNP	_	_	_
16	closest	closest	JJS	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	gff3	gff3	NN	_	_	_
20	file	file	NN	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	reference	reference	NN	_	_	_
24	genomes	genome	NNS	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	bed	bed	NN	_	_	_
4	file	file	NN	_	_	_
5	was	be	VBD	_	_	_
6	converted	convert	VBN	_	_	_
7	to	to	TO	_	_	_
8	an	a	DT	_	_	_
9	MS	ms	NN	_	_	_
10	Excel	Excel	NNP	_	_	_
11	sheet	sheet	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	S1	s1	NN	_	_	_
14	and	and	CC	_	_	_
15	S2	s2	NN	_	_	_
16	Tables	table	NNS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	with	with	IN	_	_	_
19	a	a	DT	_	_	_
20	homemade	homemade	NN	_	_	_
21	script	script	NN	_	_	_
22	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	MboI-based	mboi-based	JJ	_	_	_
4	REC-Seq	rec-seq	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	strategy	strategy	NN	_	_	_
8	was	be	VBD	_	_	_
9	identical	identical	JJ	_	_	_
10	except	except	IN	_	_	_
11	that	that	IN	_	_	_
12	a	a	DT	_	_	_
13	different	different	JJ	_	_	_
14	adaptor	adaptor	NN	_	_	_
15	was	be	VBD	_	_	_
16	used	use	VBN	_	_	_
17	for	for	IN	_	_	_
18	ligation	ligation	NN	_	_	_
19	after	after	IN	_	_	_
20	cleavage	cleavage	NN	_	_	_
21	and	and	CC	_	_	_
22	the	the	DT	_	_	_
23	MboI	mboi	NN	_	_	_
24	consensus	consensus	NN	_	_	_
25	motif	motif	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	5	5	CD	_	_	_
28	'	'	''	_	_	_
29	-	-	:	_	_	_
30	^	^	SYM	_	_	_
31	GATC-3	gatc-3	NN	_	_	_
32	'	'	''	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	as	as	IN	_	_	_
37	barcode	barcode	NN	_	_	_
38	for	for	IN	_	_	_
39	filtering	filter	VBG	_	_	_
40	of	of	IN	_	_	_
41	V.	V.	NNP	_	_	_
42	cholerae	cholerae	VBP	_	_	_
43	O1	o1	NN	_	_	_
44	biovar	biovar	JJ	_	_	_
45	El	El	NNP	_	_	_
46	Tor	Tor	NNP	_	_	_
47	and	and	CC	_	_	_
48	E.	e.	FW	_	_	_
49	coli	coli	FW	_	_	_
50	K12	k12	NN	_	_	_
51	Ec100D	ec100d	NN	_	_	_
52	gDNA	gdna	NN	_	_	_
53	mapped	map	VBD	_	_	_
54	onto	onto	IN	_	_	_
55	the	the	DT	_	_	_
56	MG1655	mg1655	NN	_	_	_
57	genome	genome	NN	_	_	_
58	.	.	.	_	_	_

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	v/v	NN	_	_	_
28	glycerol	glycerol	NN	SUPP	_	_
29	.	.	.	_	_	_

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	v/v	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	glycerol	glycerol	NN	SUPP	_	_
24	.	.	.	_	_	_

1	Medium	medium	NN	_	_	_
2	without	without	IN	_	_	_
3	glycerol	glycerol	NN	SUPP	_	_
4	served	serve	VBD	_	_	_
5	as	as	IN	_	_	_
6	a	a	DT	_	_	_
7	control	control	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	cellular	cellular	JJ	_	_	_
4	RNAs	rna	NNS	_	_	_
5	were	be	VBD	_	_	_
6	extracted	extract	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	RNeasy	RNeasy	NNP	_	_	_
10	Mini	Mini	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	according	accord	VBG	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	manufacturers	manufacturer	NNS	_	_	_
19	protocol	protocol	NN	_	_	_
20	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	total	total	VBP	_	_	_
3	DNaseI	dnasei	NN	_	_	_
4	treated	treated	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	depleted	deplete	VBN	_	_	_
8	of	of	IN	_	_	_
9	ribosomal	ribosomal	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	Ribo-Zero	Ribo-Zero	NNP	_	_	_
14	™	™	NN	_	_	_
15	RNA	rna	NN	_	_	_
16	removal	removal	NN	_	_	_
17	kit	kit	NN	_	_	_
18	for	for	IN	_	_	_
19	Gram-negative	gram-negative	JJ	_	_	_
20	bacteria	bacterium	NNS	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Epicentre	Epicentre	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

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/8	polyacrylamide/8	CD	_	_	_
17	M	m	NN	_	_	_
18	urea/TBE	urea/tbe	NN	_	_	_
19	gel	gel	NN	_	_	_
20	.	.	.	_	_	_

1	Gel	gel	NN	_	_	_
2	slices	slice	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	in	in	IN	_	_	_
6	RNA	rna	NN	_	_	_
7	elution	elution	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	10	10	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	Tris-HCl	tris-hcl	NN	_	_	_
13	,	,	,	_	_	_
14	pH	ph	NN	_	_	_
15	7.5	7.5	CD	_	_	_
16	,	,	,	_	_	_
17	2	2	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	EDTA	edta	NN	_	_	_
20	,	,	,	_	_	_
21	0.1	0.1	CD	_	_	_
22	%	%	NN	_	_	_
23	SDS	sds	NN	_	_	_
24	,	,	,	_	_	_
25	0.3	0.3	CD	_	_	_
26	M	m	NN	_	_	_
27	NaOAc	naoac	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	with	with	IN	_	_	_
30	vigorous	vigorous	JJ	_	_	_
31	shaking	shake	VBG	_	_	_
32	at	at	IN	_	_	_
33	4	4	CD	_	_	_
34	°C	°c	NN	_	_	_
35	overnight	overnight	JJ	_	_	_
36	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	subsequently	subsequently	RB	_	_	_
5	ethanol	ethanol	NN	_	_	_
6	precipitated	precipitate	VBD	_	_	_
7	using	use	VBG	_	_	_
8	glycogen	glycogen	NN	_	_	_
9	as	as	IN	_	_	_
10	a	a	DT	_	_	_
11	carrier	carrier	NN	_	_	_
12	molecule	molecule	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	small	small	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	5	5	CD	_	_	_
6	'	'	''	_	_	_
7	adapter	adapter	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	5	5	CD	_	_	_
10	'	'	''	_	_	_
11	-	-	:	_	_	_
12	GUUCAGAGUUCUACAGUCCGACGAUC-3	guucagaguucuacaguccgacgauc-3	NN	_	_	_
13	'	'	''	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	was	be	VBD	_	_	_
16	ligated	ligate	VBN	_	_	_
17	to	to	TO	_	_	_
18	the	the	DT	_	_	_
19	RNA	rna	NN	_	_	_
20	as	as	IN	_	_	_
21	described	describe	VBN	_	_	_
22	before	before	IN	_	_	_
23	except	except	IN	_	_	_
24	the	the	DT	_	_	_
25	concentration	concentration	NN	_	_	_
26	of	of	IN	_	_	_
27	the	the	DT	_	_	_
28	adapter	adapter	NN	_	_	_
29	was	be	VBD	_	_	_
30	52	52	CD	_	_	_
31	mM	mm	NN	KWSUPP	_	_
32	and	and	CC	_	_	_
33	20	20	CD	_	_	_
34	U	u	NN	_	_	_
35	of	of	IN	_	_	_
36	T4	t4	NN	_	_	_
37	RNA	rna	NN	_	_	_
38	ligase	ligase	NN	_	_	_
39	I	I	PRP	_	_	_
40	was	be	VBD	_	_	_
41	used	use	VBN	_	_	_
42	in	in	IN	_	_	_
43	total	total	JJ	_	_	_
44	volume	volume	NN	_	_	_
45	of	of	IN	_	_	_
46	25	25	CD	_	_	_
47	µl	µl	NN	_	_	_
48	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	ligated	ligate	VBN	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	size-selected	size-selected	JJ	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	≈	≈	JJ	_	_	_
8	200-300	200-300	CD	_	_	_
9	nt	nt	NNS	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	and	and	CC	_	_	_
12	gel-purified	gel-purified	JJ	_	_	_
13	over	over	IN	_	_	_
14	a	a	DT	_	_	_
15	denaturing	denature	VBG	_	_	_
16	8	8	CD	_	_	_
17	%	%	NN	_	_	_
18	polyacrylamide/8	polyacrylamide/8	CD	_	_	_
19	M	m	NN	_	_	_
20	urea/TBE	urea/tbe	NN	_	_	_
21	gel	gel	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	as	as	IN	_	_	_
24	described	describe	VBN	_	_	_
25	above	above	IN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	di-tagged	di-tagged	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	libraries	library	NNS	_	_	_
5	were	be	VBD	_	_	_
6	reverse-transcribed	reverse-transcribed	JJ	_	_	_
7	with	with	IN	_	_	_
8	SuperScript	SuperScript	NNP	_	_	_
9	®	®	NNP	_	_	_
10	II	II	NNP	_	_	_
11	reverse	reverse	JJ	_	_	_
12	transcriptase	transcriptase	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Invitrogen	invitrogen	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	using	use	VBG	_	_	_
17	random	random	JJ	_	_	_
18	nonamers	nonamer	NNS	_	_	_
19	per	per	IN	_	_	_
20	the	the	DT	_	_	_
21	manufacturer	manufacturer	NN	_	_	_
22	's	's	POS	_	_	_
23	protocol	protocol	NN	_	_	_
24	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	using	use	VBG	_	_	_
5	RNase	rnase	NN	_	_	_
6	H	h	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Promega	promega	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	per	per	IN	_	_	_
11	the	the	DT	_	_	_
12	manufacturer	manufacturer	NN	_	_	_
13	's	's	POS	_	_	_
14	protocol	protocol	NN	_	_	_
15	and	and	CC	_	_	_
16	cDNA	cdna	NN	_	_	_
17	was	be	VBD	_	_	_
18	amplified	amplify	VBN	_	_	_
19	in	in	IN	_	_	_
20	PCR	pcr	NN	_	_	_
21	carried	carry	VBD	_	_	_
22	out	out	RP	_	_	_
23	using	use	VBG	_	_	_
24	Phusion	Phusion	NNP	_	_	_
25	®	®	SYM	_	_	_
26	High-Fidelity	High-Fidelity	NNP	_	_	_
27	Polymerase	Polymerase	NNP	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	New	New	NNP	_	_	_
30	England	England	NNP	_	_	_
31	Biolabs	Biolabs	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	amplified	amplify	VBN	_	_	_
4	with	with	IN	_	_	_
5	modified	modify	VBN	_	_	_
6	designed	design	VBN	_	_	_
7	Illumina-compatible	illumina-compatible	JJ	_	_	_
8	PCR	pcr	NN	_	_	_
9	primers	primer	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	3	3	CD	_	_	_
12	'	'	''	_	_	_
13	library	library	NN	_	_	_
14	Forward	forward	RB	_	_	_
15	5	5	CD	_	_	_
16	'	'	''	_	_	_
17	-	-	:	_	_	_
18	CAAGCAGAAGACGGCATACGACAGGTTCAGAGTTCTACAGTCCGA-3	caagcagaagacggcatacgacaggttcagagttctacagtccga-3	NN	_	_	_
19	'	'	''	_	_	_
20	;	;	:	_	_	_
21	Reverse	reverse	JJ	_	_	_
22	5	5	CD	_	_	_
23	'	'	''	_	_	_
24	-	-	:	_	_	_
25	AATGATACGGCGACCACCGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3	aatgatacggcgaccaccgagatgtgactggagttcagacgtgtgctcttccgatc-3	NN	_	_	_
26	'	'	''	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	by	by	IN	_	_	_
29	18	18	CD	_	_	_
30	cycles	cycle	NNS	_	_	_
31	of	of	IN	_	_	_
32	PCR	pcr	NN	_	_	_
33	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	products	product	NNS	_	_	_
3	were	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Agencourt	Agencourt	NNP	_	_	_
7	AMPure	AMPure	NNP	_	_	_
8	XP	xp	NN	_	_	_
9	beads	bead	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Beckman	Beckman	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	analyzed	analyze	VBN	_	_	_
15	on	on	IN	_	_	_
16	an	a	DT	_	_	_
17	Agilent	Agilent	NNP	_	_	_
18	2100	2100	CD	_	_	_
19	Bioanalyzer	Bioanalyzer	NNP	_	_	_
20	.	.	.	_	_	_

1	3	3	CD	_	_	_
2	'	'	''	_	_	_
3	end	end	NN	_	_	_
4	enriched	enriched	JJ	_	_	_
5	cDNA	cdna	NN	_	_	_
6	libraries	library	NNS	_	_	_
7	were	be	VBD	_	_	_
8	sequenced	sequence	VBN	_	_	_
9	on	on	IN	_	_	_
10	individual	individual	JJ	_	_	_
11	Genome	Genome	NNP	_	_	_
12	Analyzer	Analyzer	NNP	_	_	_
13	IIx	IIx	NNP	_	_	_
14	lanes	lane	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	36	36	CD	_	_	_
17	bp	bp	NN	_	_	_
18	,	,	,	_	_	_
19	single-end	single-end	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	or	or	CC	_	_	_
22	on	on	IN	_	_	_
23	HiSeq	HiSeq	NNP	_	_	_
24	2000	2000	CD	_	_	_
25	lanes	lane	NNS	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	50	50	CD	_	_	_
28	bp	bp	NN	_	_	_
29	,	,	,	_	_	_
30	single-end	single-end	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	using	use	VBG	_	_	_
33	primer	primer	NN	_	_	_
34	based	base	VBN	_	_	_
35	on	on	IN	_	_	_
36	Illumina	Illumina	NNP	_	_	_
37	Multiplexing	Multiplexing	NNP	_	_	_
38	Read	Read	NNP	_	_	_
39	2	2	CD	_	_	_
40	Sequencing	sequencing	NN	_	_	_
41	Primer	primer	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	5	5	CD	_	_	_
44	'	'	''	_	_	_
45	-	-	:	_	_	_
46	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3	gtgactggagttcagacgtgtgctcttccgatc-3	NN	_	_	_
47	'	'	''	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	at	at	IN	_	_	_
50	the	the	DT	_	_	_
51	CSF	csf	NN	_	_	_
52	NGS	ngs	NN	_	_	_
53	unit	unit	NN	_	_	_
54	http://csf.ac.at/	http://csf.ac.at/	NN	_	_	_
55	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	three	three	CD	_	_	_
8	human	human	JJ	_	_	_
9	faecal	faecal	JJ	_	_	_
10	samples	sample	NNS	_	_	_
11	using	use	VBG	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	's	's	POS	_	_	_
14	DNA	dna	NN	_	_	_
15	Stool	Stool	NNP	_	_	_
16	Kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	Qiagen	NNP	_	_	_
19	,	,	,	_	_	_
20	West	West	NNP	_	_	_
21	Sussex	Sussex	NNP	_	_	_
22	,	,	,	_	_	_
23	UK	UK	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

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/v	w/v	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	agarose	agarose	NN	_	_	_
15	gel	gel	NN	_	_	_
16	and	and	CC	_	_	_
17	were	be	VBD	_	_	_
18	purified	purify	VBN	_	_	_
19	using	use	VBG	_	_	_
20	the	the	DT	_	_	_
21	MinElute	MinElute	NNP	_	_	_
22	PCR	pcr	NN	_	_	_
23	Purification	purification	NN	_	_	_
24	Kit	kit	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Qiagen	Qiagen	NNP	_	_	_
27	Ltd.	Ltd.	NNP	_	_	_
28	,	,	,	_	_	_
29	UK	UK	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	following	follow	VBG	_	_	_
32	manufacturer	manufacturer	NN	_	_	_
33	's	's	POS	_	_	_
34	instructions	instruction	NNS	_	_	_
35	and	and	CC	_	_	_
36	stored	store	VBN	_	_	_
37	at	at	IN	_	_	_
38	-20	-20	CD	_	_	_
39	°C	°c	NN	_	_	_
40	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	2ug	2ug	JJ	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	subjected	subject	VBN	_	_	_
9	to	to	TO	_	_	_
10	rRNA	rrna	NN	_	_	_
11	depletion	depletion	NN	_	_	_
12	using	use	VBG	_	_	_
13	Ribozero	Ribozero	NNP	_	_	_
14	rRNA	rrna	NN	_	_	_
15	removal	removal	NN	_	_	_
16	kit	kit	NN	_	_	_
17	--	--	:	_	_	_
18	Bacteria	bacterium	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Epicenter	epicenter	NN	_	_	_
21	,	,	,	_	_	_
22	illumina	illumina	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

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	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	extracted	extract	VBN	_	_	_
21	using	use	VBG	_	_	_
22	Qiagen	Qiagen	NNP	_	_	_
23	RNEASY	RNEASY	NNP	_	_	_
24	kit	kit	NN	_	_	_
25	according	accord	VBG	_	_	_
26	to	to	TO	_	_	_
27	directions	direction	NNS	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Total	Total	NNP	_	_	_
30	RNA	RNA	NNP	_	_	_
31	extracted	extract	VBN	_	_	_
32	using	use	VBG	_	_	_
33	QIAGEN	QIAGEN	NNP	_	_	_
34	RNeasy	RNeasy	NNP	_	_	_
35	kit	kit	NN	_	_	_
36	according	accord	VBG	_	_	_
37	to	to	TO	_	_	_
38	manufacturer	manufacturer	NN	_	_	_
39	's	's	POS	_	_	_
40	instructions	instruction	NNS	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Total	Total	NNP	_	_	_
43	RNA	RNA	NNP	_	_	_
44	extracted	extract	VBN	_	_	_
45	using	use	VBG	_	_	_
46	RiboEX	RiboEX	NNP	_	_	_
47	reagent	reagent	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	GeneAll	GeneAll	NNP	_	_	_
50	,	,	,	_	_	_
51	Korea	Korea	NNP	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	,	,	,	_	_	_
54	treated	treat	VBN	_	_	_
55	with	with	IN	_	_	_
56	Dnase	Dnase	NNP	_	_	_
57	,	,	,	_	_	_
58	and	and	CC	_	_	_
59	purified	purify	VBN	_	_	_
60	using	use	VBG	_	_	_
61	the	the	DT	_	_	_
62	Rneasy	Rneasy	NNP	_	_	_
63	Mini	Mini	NNP	_	_	_
64	kit	kit	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	Qiagen	Qiagen	NNP	_	_	_
67	,	,	,	_	_	_
68	Germany	Germany	NNP	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	according	accord	VBG	_	_	_
71	to	to	TO	_	_	_
72	the	the	DT	_	_	_
73	manufacturer	manufacturer	NN	_	_	_
74	's	's	POS	_	_	_
75	instructions	instruction	NNS	_	_	_
76	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNAprotect	rnaprotect	NN	_	_	_
7	Bacterial	bacterial	JJ	_	_	_
8	Reagent	reagent	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	qiagen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	an	a	DT	_	_	_
14	RNeasy	RNeasy	NNP	_	_	_
15	Mini	Mini	NNP	_	_	_
16	kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	qiagen	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Trizol	Trizol	NNP	_	_	_
7	Extraction	Extraction	NNP	_	_	_
8	Protocol	Protocol	NNP	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Total	Total	NNP	_	_	_
11	RNA	RNA	NNP	_	_	_
12	extracted	extract	VBN	_	_	_
13	using	use	VBG	_	_	_
14	Trizol	Trizol	NNP	_	_	_
15	following	follow	VBG	_	_	_
16	manufacturer	manufacturer	NN	_	_	_
17	's	's	POS	_	_	_
18	instructions	instruction	NNS	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Total	Total	NNP	_	_	_
21	RNA	rna	NN	_	_	_
22	extraction	extraction	NN	_	_	_
23	using	use	VBG	_	_	_
24	Vantage	Vantage	NNP	_	_	_
25	™	™	CD	_	_	_
26	RNA	rna	NN	_	_	_
27	Purification	purification	NN	_	_	_
28	Kit	kit	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Origene	Origene	NNP	_	_	_
31	,	,	,	_	_	_
32	Rockville	Rockville	NNP	_	_	_
33	,	,	,	_	_	_
34	MD	MD	NNP	_	_	_
35	,	,	,	_	_	_
36	USA	USA	NNP	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	was	be	VBD	_	_	_
39	performed	perform	VBN	_	_	_
40	according	accord	VBG	_	_	_
41	with	with	IN	_	_	_
42	the	the	DT	_	_	_
43	manufacter	manufacter	NN	_	_	_
44	instructions	instruction	NNS	_	_	_
45	.	.	.	_	_	_

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	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	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	was	be	VBD	_	_	_
6	done	do	VBN	_	_	_
7	using	use	VBG	_	_	_
8	TRIzol	trizol	NN	_	_	_
9	reagent	reagent	NN	_	_	_
10	and	and	CC	_	_	_
11	DNAse	dnase	NN	_	_	_
12	digested	digest	VBN	_	_	_
13	.	.	.	_	_	_

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	NNP	_	_	_
11	Total	Total	NNP	_	_	_
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	/	/	:	_	_	_
7	280	280	CD	_	_	_
8	nm	nm	NN	_	_	_
9	ratio	ratio	NN	_	_	_
10	of	of	IN	_	_	_
11	1.8	1.8	CD	_	_	_
12	-	-	:	_	_	_
13	2	2	CD	_	_	_
14	as	as	RB	_	_	_
15	well	well	RB	_	_	_
16	as	as	IN	_	_	_
17	260	260	CD	_	_	_
18	nm	nm	NN	_	_	_
19	/	/	:	_	_	_
20	230	230	CD	_	_	_
21	nm	nm	NN	_	_	_
22	ratio	ratio	NN	_	_	_
23	>	>	JJR	_	_	_
24	1.8	1.8	CD	_	_	_
25	was	be	VBD	_	_	_
26	used	use	VBN	_	_	_
27	for	for	IN	_	_	_
28	precipitation	precipitation	NN	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	precipitated	precipitated	JJ	_	_	_
5	and	and	CC	_	_	_
6	resolved	resolve	VBN	_	_	_
7	at	at	IN	_	_	_
8	the	the	DT	_	_	_
9	final	final	JJ	_	_	_
10	concentration	concentration	NN	_	_	_
11	of	of	IN	_	_	_
12	6	6	CD	_	_	_
13	µg	µg	NN	_	_	_
14	/	/	:	_	_	_
15	µl	µl	NN	_	_	_
16	required	require	VBN	_	_	_
17	for	for	IN	_	_	_
18	reverse	reverse	JJ	_	_	_
19	transcription	transcription	NN	_	_	_
20	and	and	CC	_	_	_
21	labeling	labeling	NN	_	_	_
22	with	with	IN	_	_	_
23	fluorescent	fluorescent	JJ	_	_	_
24	dyes	dye	NNS	_	_	_
25	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	isolate	isolate	NN	_	_	_
4	was	be	VBD	_	_	_
5	mixed	mix	VBN	_	_	_
6	with	with	IN	_	_	_
7	1/10	1/10	CD	_	_	_
8	volume	volume	NN	_	_	_
9	of	of	IN	_	_	_
10	NaCl	nacl	NN	_	_	_
11	solution	solution	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	3	3	CD	_	_	_
14	M	m	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	2	2	CD	_	_	_
18	volumes	volume	NNS	_	_	_
19	of	of	IN	_	_	_
20	ethanol	ethanol	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	100	100	CD	_	_	_
23	%	%	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	stored	store	VBN	_	_	_
27	at	at	IN	_	_	_
28	-20	-20	CD	_	_	_
29	°C	°c	NN	_	_	_
30	overnight	overnight	JJ	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	subsequently	subsequently	RB	_	_	_
5	centrifuged	centrifuge	VBN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	14000	14000	CD	_	_	_
8	rpm	rpm	NN	_	_	_
9	;	;	:	_	_	_
10	20800	20800	CD	_	_	_
11	g	g	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	supernatant	supernatant	NN	_	_	_
16	was	be	VBD	_	_	_
17	discarded	discard	VBN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	with	with	IN	_	_	_
6	ethanol	ethanol	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	70	70	CD	_	_	_
9	%	%	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	and	and	CC	_	_	_
12	vacuum	vacuum	NN	_	_	_
13	dried	dry	VBD	_	_	_
14	.	.	.	_	_	_

1	100	100	CD	_	_	_
2	µg	µg	NN	_	_	_
3	of	of	IN	_	_	_
4	RNA	rna	NN	_	_	_
5	were	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	reverse	reverse	JJ	_	_	_
9	transcription	transcription	NN	_	_	_
10	.	.	.	_	_	_

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	NNP	_	_	_
8	Total	Total	NNP	_	_	_
9	RNA	rna	NN	_	_	_
10	from	from	IN	_	_	_
11	both	both	CC	_	_	_
12	the	the	DT	_	_	_
13	in	in	FW	_	_	_
14	vitro	vitro	FW	_	_	_
15	and	and	CC	_	_	_
16	in	in	FW	_	_	_
17	vivo	vivo	FW	_	_	_
18	samples	sample	NNS	_	_	_
19	of	of	IN	_	_	_
20	APEC	APEC	NNP	_	_	_
21	E058	e058	NN	_	_	_
22	was	be	VBD	_	_	_
23	extracted	extract	VBN	_	_	_
24	with	with	IN	_	_	_
25	the	the	DT	_	_	_
26	RNAiso	rnaiso	NN	_	_	_
27	Plus	plus	NN	_	_	_
28	kit	kit	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Takara	Takara	NNP	_	_	_
31	,	,	,	_	_	_
32	Dalian	Dalian	NNP	_	_	_
33	,	,	,	_	_	_
34	China	China	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	and	and	CC	_	_	_
37	further	further	JJ	_	_	_
38	purified	purify	VBN	_	_	_
39	with	with	IN	_	_	_
40	NucleoSpin	nucleospin	NN	_	_	_
41	RNA	rna	NN	_	_	_
42	Clean-up	clean-up	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	Macherey-Nagel	Macherey-Nagel	NNP	_	_	_
45	,	,	,	_	_	_
46	Germany	Germany	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	,	,	,	_	_	_
49	according	accord	VBG	_	_	_
50	to	to	TO	_	_	_
51	the	the	DT	_	_	_
52	manufacturers	manufacturer	NNS	_	_	_
53	'	'	POS	_	_	_
54	instructions	instruction	NNS	_	_	_
55	.	.	.	_	_	_

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	NNP	_	_	_
16	Total	Total	NNP	_	_	_
17	RNA	rna	NN	_	_	_
18	from	from	IN	_	_	_
19	in	in	FW	_	_	_
20	vivo	vivo	FW	_	_	_
21	samples	sample	NNS	_	_	_
22	of	of	IN	_	_	_
23	APEC	APEC	NNP	_	_	_
24	E058	e058	NN	_	_	_
25	and	and	CC	_	_	_
26	E058ΔrstAB	e058δrstab	NN	_	_	_
27	was	be	VBD	_	_	_
28	extracted	extract	VBN	_	_	_
29	and	and	CC	_	_	_
30	purified	purify	VBN	_	_	_
31	using	use	VBG	_	_	_
32	RNeasy	RNeasy	NNP	_	_	_
33	mini	minus	NNS	_	_	_
34	kit	kit	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Cat	cat	NN	_	_	_
37	#	#	#	_	_	_
38	74106	74106	CD	_	_	_
39	,	,	,	_	_	_
40	QIAGEN	QIAGEN	NNP	_	_	_
41	,	,	,	_	_	_
42	GmBH	GmBH	NNP	_	_	_
43	,	,	,	_	_	_
44	Germany	Germany	NNP	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	following	follow	VBG	_	_	_
47	the	the	DT	_	_	_
48	manufacturer	manufacturer	NN	_	_	_
49	's	's	POS	_	_	_
50	instructions	instruction	NNS	_	_	_
51	.	.	.	_	_	_

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	according	accord	VBG	_	_	_
15	to	to	TO	_	_	_
16	Sambrook	Sambrook	NNP	_	_	_
17	et	et	FW	_	_	_
18	al.	al.	FW	_	_	_
19	and	and	CC	_	_	_
20	ethanol	ethanol	NN	_	_	_
21	precipitation	precipitation	NN	_	_	_
22	with	with	IN	_	_	_
23	5M	5m	NN	_	_	_
24	NaCl	nacl	NN	_	_	_
25	.	.	.	_	_	_

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	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	isolation	isolation	NN	_	_	_
12	was	be	VBD	_	_	_
13	performed	perform	VBN	_	_	_
14	using	use	VBG	_	_	_
15	the	the	DT	_	_	_
16	RNeasy	RNeasy	NNP	_	_	_
17	Protect	Protect	NNP	_	_	_
18	Bacteria	bacterium	NNS	_	_	_
19	system	system	NN	_	_	_
20	from	from	IN	_	_	_
21	Qiagen	Qiagen	NNP	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	isolated	isolate	VBN	_	_	_
7	using	use	VBG	_	_	_
8	RNAzol	rnazol	NN	_	_	_
9	RT	rt	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Molecular	molecular	JJ	_	_	_
12	Research	Research	NNP	_	_	_
13	Center	Center	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	by	by	IN	_	_	_
16	following	follow	VBG	_	_	_
17	manufature	manufature	NN	_	_	_
18	's	's	POS	_	_	_
19	instructions	instruction	NNS	_	_	_
20	.	.	.	_	_	_

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	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	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	pgcgrowthcondition	VBZ	_	_	_
153	Total	total	JJ	_	_	_
154	RNAs	rna	NNS	_	_	_
155	from	from	IN	_	_	_
156	two	two	CD	_	_	_
157	biological	biological	JJ	_	_	_
158	replicate	replicate	VB	_	_	_
159	,	,	,	_	_	_
160	each	each	DT	_	_	_
161	with	with	IN	_	_	_
162	two	two	CD	_	_	_
163	technical	technical	JJ	_	_	_
164	replicates	replicate	VBZ	_	_	_
165	were	be	VBD	_	_	_
166	extracted	extract	VBN	_	_	_
167	using	use	VBG	_	_	_
168	the	the	DT	_	_	_
169	Total	total	JJ	_	_	_
170	RNA	rna	NN	_	_	_
171	Purification	purification	NN	_	_	_
172	Kit	kit	NN	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	Norgen	Norgen	NNP	_	_	_
175	Biotek	Biotek	NNP	_	_	_
176	,	,	,	_	_	_
177	UK	UK	NNP	_	_	_
178	-RRB-	-rrb-	-RRB-	_	_	_
179	according	accord	VBG	_	_	_
180	to	to	TO	_	_	_
181	the	the	DT	_	_	_
182	manufacturer	manufacturer	NN	_	_	_
183	's	's	POS	_	_	_
184	protocol	protocol	NN	_	_	_
185	with	with	IN	_	_	_
186	the	the	DT	_	_	_
187	addition	addition	NN	_	_	_
188	of	of	IN	_	_	_
189	1	1	CD	_	_	_
190	mg/ml	mg/ml	NN	_	_	_
191	lysozyme	lysozyme	NN	_	_	_
192	for	for	IN	_	_	_
193	cell	cell	NN	_	_	_
194	lysis	lysis	NN	_	_	_
195	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	bacterial	bacterial	JJ	_	_	_
9	isolates	isolate	NNS	_	_	_
10	using	use	VBG	_	_	_
11	TRIzol	trizol	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	Total	total	JJ	_	_	_
14	RNAs	rna	NNS	_	_	_
15	were	be	VBD	_	_	_
16	extracted	extract	VBN	_	_	_
17	using	use	VBG	_	_	_
18	an	a	DT	_	_	_
19	RNeasy	rneasy	NN	_	_	_
20	mini	minus	NNS	_	_	_
21	kit	kit	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Qiagen	qiagen	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	in	in	IN	_	_	_
26	accordance	accordance	NN	_	_	_
27	with	with	IN	_	_	_
28	the	the	DT	_	_	_
29	manufacturer	manufacturer	NN	_	_	_
30	's	's	POS	_	_	_
31	instructions	instruction	NNS	_	_	_
32	.	.	.	_	_	_

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	RNeasy	RNeasy	NNP	_	_	_
8	mini	minus	NNS	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	Qiagen	NNP	_	_	_
12	,	,	,	_	_	_
13	#	#	#	_	_	_
14	74104	74104	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	following	follow	VBG	_	_	_
17	manufacture	manufacture	NN	_	_	_
18	's	's	POS	_	_	_
19	instruction	instruction	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Total	total	JJ	_	_	_
22	RNAs	rna	NNS	_	_	_
23	were	be	VBD	_	_	_
24	isolated	isolate	VBN	_	_	_
25	using	use	VBG	_	_	_
26	TRIzol	trizol	NN	_	_	_
27	reagent	reagent	NN	_	_	_
28	,	,	,	_	_	_
29	followed	follow	VBN	_	_	_
30	by	by	IN	_	_	_
31	clean-up	clean-up	JJ	_	_	_
32	and	and	CC	_	_	_
33	DNase	dnase	NN	_	_	_
34	I	i	CD	_	_	_
35	treatment	treatment	NN	_	_	_
36	with	with	IN	_	_	_
37	QIAGEN	QIAGEN	NNP	_	_	_
38	RNeasy	RNeasy	NNP	_	_	_
39	mini	minus	NNS	_	_	_
40	kit	kit	NN	_	_	_
41	.	.	.	_	_	_

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	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	kit	kit	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Total	Total	NNP	_	_	_
10	RNA	rna	NN	_	_	_
11	was	be	VBD	_	_	_
12	depleted	deplete	VBN	_	_	_
13	of	of	IN	_	_	_
14	ribosomal	ribosomal	JJ	_	_	_
15	RNAs	rna	NNS	_	_	_
16	using	use	VBG	_	_	_
17	Epicentre	Epicentre	NNP	_	_	_
18	's	's	POS	_	_	_
19	RiboZero	RiboZero	NNP	_	_	_
20	rRNA	rrna	NN	_	_	_
21	removal	removal	NN	_	_	_
22	kit	kit	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	and	and	CC	_	_	_
7	DNase-treated	dnase-treated	JJ	_	_	_
8	according	accord	VBG	_	_	_
9	to	to	TO	_	_	_
10	published	publish	VBN	_	_	_
11	protocols	protocol	NNS	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Khodurksy	khodurksy	NN	_	_	_
14	A	a	NN	_	_	_
15	,	,	,	_	_	_
16	Bernstein	Bernstein	NNP	_	_	_
17	J	J	NNP	_	_	_
18	,	,	,	_	_	_
19	Peter	Peter	NNP	_	_	_
20	B	B	NNP	_	_	_
21	,	,	,	_	_	_
22	Rhodius	Rhodius	NNP	_	_	_
23	V	V	NNP	_	_	_
24	,	,	,	_	_	_
25	Wendisch	Wendisch	NNP	_	_	_
26	V	V	NNP	_	_	_
27	,	,	,	_	_	_
28	Zimmer	Zimmer	NNP	_	_	_
29	D.	D.	NNP	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	Spotted	spot	VBN	_	_	_
33	Double-Strand	Double-Strand	NNP	_	_	_
34	DNA	DNA	NNP	_	_	_
35	Microarrays	Microarrays	NNPS	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Total	total	JJ	_	_	_
39	RNA	rna	NN	_	_	_
40	was	be	VBD	_	_	_
41	extracted	extract	VBN	_	_	_
42	by	by	IN	_	_	_
43	the	the	DT	_	_	_
44	hot	hot	JJ	_	_	_
45	phenol	phenol	NN	_	_	_
46	--	--	:	_	_	_
47	chloroform	chloroform	NN	_	_	_
48	method	method	NN	_	_	_
49	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	5	5	CD	_	_	_
8	ml	ml	NN	_	_	_
9	cell	cell	NN	_	_	_
10	culture	culture	NN	_	_	_
11	after	after	IN	_	_	_
12	30	30	CD	_	_	_
13	min	min	NN	_	_	_
14	incubation	incubation	NN	_	_	_
15	with	with	IN	_	_	_
16	or	or	CC	_	_	_
17	without	without	IN	_	_	_
18	H2O2	h2o2	NN	_	_	_
19	treatment	treatment	NN	_	_	_
20	using	use	VBG	_	_	_
21	RNeasy	RNeasy	NNP	_	_	_
22	Mini	Mini	NNP	_	_	_
23	kit	kit	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Qiagen	Qiagen	NNP	_	_	_
26	,	,	,	_	_	_
27	Inc.	Inc.	NNP	_	_	_
28	,	,	,	_	_	_
29	Valencia	Valencia	NNP	_	_	_
30	,	,	,	_	_	_
31	CA	CA	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	protocol	protocol	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Total	total	JJ	_	_	_
41	RNA	rna	NN	_	_	_
42	was	be	VBD	_	_	_
43	extracted	extract	VBN	_	_	_
44	from	from	IN	_	_	_
45	5	5	CD	_	_	_
46	ml	ml	NN	_	_	_
47	cell	cell	NN	_	_	_
48	culture	culture	NN	_	_	_
49	at	at	IN	_	_	_
50	0	0	CD	_	_	_
51	,	,	,	_	_	_
52	10	10	CD	_	_	_
53	,	,	,	_	_	_
54	30	30	CD	_	_	_
55	and	and	CC	_	_	_
56	60	60	CD	_	_	_
57	min	min	NN	_	_	_
58	incubation	incubation	NN	_	_	_
59	after	after	IN	_	_	_
60	addition	addition	NN	_	_	_
61	of	of	IN	_	_	_
62	5	5	CD	_	_	_
63	%	%	NN	_	_	_
64	isooctane	isooctane	NN	_	_	_
65	using	use	VBG	_	_	_
66	RNeasy	rneasy	NN	_	_	_
67	mini	minus	NNS	_	_	_
68	kit	kit	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	Qiagen	Qiagen	NNP	_	_	_
71	,	,	,	_	_	_
72	Inc.	Inc.	NNP	_	_	_
73	,	,	,	_	_	_
74	Valencia	Valencia	NNP	_	_	_
75	,	,	,	_	_	_
76	CA	CA	NNP	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	according	accord	VBG	_	_	_
79	to	to	TO	_	_	_
80	the	the	DT	_	_	_
81	manufacturer	manufacturer	NN	_	_	_
82	's	's	POS	_	_	_
83	protocol	protocol	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	Total	total	JJ	_	_	_
86	RNA	rna	NN	_	_	_
87	was	be	VBD	_	_	_
88	extracted	extract	VBN	_	_	_
89	from	from	IN	_	_	_
90	5	5	CD	_	_	_
91	ml	ml	NN	_	_	_
92	cell	cell	NN	_	_	_
93	culture	culture	NN	_	_	_
94	at	at	IN	_	_	_
95	10	10	CD	_	_	_
96	min	min	NN	_	_	_
97	incubation	incubation	NN	_	_	_
98	with	with	IN	_	_	_
99	or	or	CC	_	_	_
100	without	without	IN	_	_	_
101	1	1	CD	_	_	_
102	%	%	NN	_	_	_
103	Hydrogen	hydrogen	NN	_	_	_
104	peroxide	peroxide	NN	_	_	_
105	using	use	VBG	_	_	_
106	RNeasy	RNeasy	NNP	_	_	_
107	Mini	Mini	NNP	_	_	_
108	kit	kit	NN	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	Qiagen	Qiagen	NNP	_	_	_
111	,	,	,	_	_	_
112	Inc.	Inc.	NNP	_	_	_
113	,	,	,	_	_	_
114	Valencia	Valencia	NNP	_	_	_
115	,	,	,	_	_	_
116	CA	CA	NNP	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	according	accord	VBG	_	_	_
119	to	to	TO	_	_	_
120	the	the	DT	_	_	_
121	manufacturer	manufacturer	NN	_	_	_
122	's	's	POS	_	_	_
123	protocol	protocol	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Total	total	JJ	_	_	_
126	RNA	rna	NN	_	_	_
127	was	be	VBD	_	_	_
128	extracted	extract	VBN	_	_	_
129	from	from	IN	_	_	_
130	cell	cell	NN	_	_	_
131	pellets	pellet	NNS	_	_	_
132	by	by	IN	_	_	_
133	hot	hot	JJ	_	_	_
134	phenol	phenol	NN	_	_	_
135	extraction	extraction	NN	_	_	_
136	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	cell	cell	NN	_	_	_
8	pellets	pellet	NNS	_	_	_
9	by	by	IN	_	_	_
10	hot	hot	JJ	_	_	_
11	phenol	phenol	NN	_	_	_
12	extraction	extraction	NN	_	_	_
13	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	cell	cell	NN	_	_	_
8	pellets	pellet	NNS	_	_	_
9	with	with	IN	_	_	_
10	TRI	TRI	NNP	_	_	_
11	Reagent	Reagent	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	MRC	MRC	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	cells	cell	NNS	_	_	_
8	with	with	IN	_	_	_
9	the	the	DT	_	_	_
10	UltraClean	UltraClean	NNP	_	_	_
11	Microbial	Microbial	NNP	_	_	_
12	RNA	rna	NN	_	_	_
13	isolation	isolation	NN	_	_	_
14	kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	MO	MO	NNP	_	_	_
17	BIO	BIO	NNP	_	_	_
18	,	,	,	_	_	_
19	CA	CA	NNP	_	_	_
20	,	,	,	_	_	_
21	USA	USA	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

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/chloroform	phenol/chloroform	NN	_	_	_
22	extraction	extraction	NN	_	_	_
23	and	and	CC	_	_	_
24	ethanol	ethanol	NN	_	_	_
25	precipitation	precipitation	NN	_	_	_
26	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	purity	purity	NN	_	_	_
3	and	and	CC	_	_	_
4	quantity	quantity	NN	_	_	_
5	was	be	VBD	_	_	_
6	assess	assess	VB	_	_	_
7	by	by	IN	_	_	_
8	optical	optical	JJ	_	_	_
9	density	density	NN	_	_	_
10	measurements	measurement	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	OD	od	NN	_	_	_
13	260/280	260/280	CD	_	_	_
14	and	and	CC	_	_	_
15	OD	od	NN	_	_	_
16	260/230	260/230	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	RNA	rna	NN	_	_	_
20	integrity	integrity	NN	_	_	_
21	was	be	VBD	_	_	_
22	checked	check	VBN	_	_	_
23	with	with	IN	_	_	_
24	the	the	DT	_	_	_
25	Bioanalyseur	Bioanalyseur	NNP	_	_	_
26	2100	2100	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Agilent	Agilent	NNP	_	_	_
29	,	,	,	_	_	_
30	CA	CA	NNP	_	_	_
31	,	,	,	_	_	_
32	USA	USA	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	Rna	Rna	NNP	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	cultures	culture	NNS	_	_	_
8	using	use	VBG	_	_	_
9	Qiagen	Qiagen	NNP	_	_	_
10	RNeasy	RNeasy	NNP	_	_	_
11	Protect	protect	VB	_	_	_
12	Bacteria	bacterium	NNS	_	_	_
13	Mini	Mini	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	hot	hot	JJ	_	_	_
9	phenol	phenol	NN	_	_	_
10	method	method	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Khodursky	Khodursky	NNP	_	_	_
13	et	et	FW	_	_	_
14	al	al	FW	_	_	_
15	,	,	,	_	_	_
16	Methods	method	NNS	_	_	_
17	in	in	IN	_	_	_
18	Molecular	molecular	JJ	_	_	_
19	Biology	Biology	NNP	_	_	_
20	2003	2003	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

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	a	a	DT	_	_	_
8	Thermo	Thermo	NNP	_	_	_
9	Scientific	Scientific	NNP	_	_	_
10	GeneJET	GeneJET	NNP	_	_	_
11	RNA	rna	NN	_	_	_
12	isolation	isolation	NN	_	_	_
13	kit	kit	NN	_	_	_
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	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	NN	_	_	_
27	Total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	was	be	VBD	_	_	_
30	extracted	extract	VBN	_	_	_
31	using	use	VBG	_	_	_
32	Qiagen	Qiagen	NNP	_	_	_
33	RNeasy	RNeasy	NNP	_	_	_
34	kit	kit	NN	_	_	_
35	.	.	.	_	_	_

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	-LRB-	-lrb-	-LRB-	_	_	_
11	Hilden	hilden	NN	_	_	_
12	,	,	,	_	_	_
13	Germany	Germany	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	following	follow	VBG	_	_	_
16	manufacturer	manufacturer	NN	_	_	_
17	's	's	POS	_	_	_
18	instructions	instruction	NNS	_	_	_
19	and	and	CC	_	_	_
20	checked	check	VBD	_	_	_
21	for	for	IN	_	_	_
22	a	a	DT	_	_	_
23	RIN	rin	NN	_	_	_
24	number	number	NN	_	_	_
25	to	to	TO	_	_	_
26	inspect	inspect	VB	_	_	_
27	RNA	rna	NN	_	_	_
28	integration	integration	NN	_	_	_
29	by	by	IN	_	_	_
30	an	a	DT	_	_	_
31	Agilent	Agilent	NNP	_	_	_
32	Bioanalyzer	Bioanalyzer	NNP	_	_	_
33	2100	2100	CD	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Agilent	agilent	JJ	_	_	_
36	technologies	technology	NNS	_	_	_
37	,	,	,	_	_	_
38	Santa	Santa	NNP	_	_	_
39	Clara	Clara	NNP	_	_	_
40	,	,	,	_	_	_
41	CA	CA	NNP	_	_	_
42	,	,	,	_	_	_
43	US	US	NNP	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

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	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	Mini	Mini	NNP	_	_	_
10	Kit	kit	NN	_	_	_
11	.	.	.	_	_	_

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/OD280	od260/od280	NN	_	_	_
12	ratio	ratio	NN	_	_	_
13	.	.	.	_	_	_

1	Amino-allyl	amino-allyl	JJ	_	_	_
2	dUTP	dutp	NN	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	to	to	TO	_	_	_
6	label	label	VB	_	_	_
7	5µg	5µg	NN	_	_	_
8	of	of	IN	_	_	_
9	RNA	rna	NN	_	_	_
10	during	during	IN	_	_	_
11	reverse	reverse	JJ	_	_	_
12	transcription	transcription	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	reverse	reverse	JJ	_	_	_
3	transcription	transcription	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	at	at	IN	_	_	_
7	42	42	CD	_	_	_
8	°C	°c	NN	_	_	_
9	during	during	IN	_	_	_
10	50	50	CD	_	_	_
11	min	min	NN	_	_	_
12	using	use	VBG	_	_	_
13	600	600	CD	_	_	_
14	units	unit	NNS	_	_	_
15	of	of	IN	_	_	_
16	superscript	superscript	JJ	_	_	_
17	RT	rt	NN	_	_	_
18	II	ii	CD	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Invitrogen	invitrogen	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	3	3	CD	_	_	_
24	µg	µg	NN	_	_	_
25	of	of	IN	_	_	_
26	random	random	JJ	_	_	_
27	hexamers	hexamer	NNS	_	_	_
28	,	,	,	_	_	_
29	0.6	0.6	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	dATP	datp	NN	_	_	_
32	,	,	,	_	_	_
33	dCTP	dctp	NN	_	_	_
34	and	and	CC	_	_	_
35	dGTP	dgtp	NN	_	_	_
36	,	,	,	_	_	_
37	0.2	0.2	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	dTTP	dttp	NN	_	_	_
40	,	,	,	_	_	_
41	and	and	CC	_	_	_
42	0.4	0.4	CD	_	_	_
43	mM	mm	NN	KWSUPP	_	_
44	amino-allyl	amino-allyl	NN	_	_	_
45	dUTP	dutp	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Ambion	ambion	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	degraded	degrade	VBN	_	_	_
5	by	by	IN	_	_	_
6	incubation	incubation	NN	_	_	_
7	at	at	IN	_	_	_
8	65	65	CD	_	_	_
9	°C	°c	NN	_	_	_
10	,	,	,	_	_	_
11	for	for	IN	_	_	_
12	15	15	CD	_	_	_
13	min	min	NN	_	_	_
14	,	,	,	_	_	_
15	after	after	IN	_	_	_
16	adding	add	VBG	_	_	_
17	10µL	10µl	NN	_	_	_
18	of	of	IN	_	_	_
19	0.5	0.5	CD	_	_	_
20	M	m	NN	_	_	_
21	EDTA	edta	NN	_	_	_
22	and	and	CC	_	_	_
23	10µL	10µl	NN	_	_	_
24	of	of	IN	_	_	_
25	1M	1m	NN	_	_	_
26	NaOH	naoh	NN	_	_	_
27	.	.	.	_	_	_

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	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	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	NNP	_	_	_
12	,	,	,	_	_	_
13	Valencia	Valencia	NNP	_	_	_
14	,	,	,	_	_	_
15	CA	CA	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	genomic	genomic	JJ	_	_	_
20	DNA	dna	NN	_	_	_
21	was	be	VBD	_	_	_
22	removed	remove	VBN	_	_	_
23	using	use	VBG	_	_	_
24	RNase-Free	rnase-free	JJ	_	_	_
25	DNase	dnase	NN	_	_	_
26	Set	set	VB	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	QIAGEN	QIAGEN	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

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	commercial	commercial	JJ	_	_	_
9	product	product	NN	_	_	_
10	TRIzol	trizol	NN	_	_	_
11	Reagent	reagent	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Invitrogen	Invitrogen	NNP	_	_	_
14	,	,	,	_	_	_
15	Carlsbad	Carlsbad	NNP	_	_	_
16	,	,	,	_	_	_
17	CA	CA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

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	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	frozen	frozen	JJ	_	_	_
9	acid-phenol	acid-phenol	NN	_	_	_
10	method	method	NN	_	_	_
11	described	describe	VBN	_	_	_
12	by	by	IN	_	_	_
13	Maes	mae	NNS	_	_	_
14	and	and	CC	_	_	_
15	Messens	messen	NNS	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Maes	mae	NNS	_	_	_
18	and	and	CC	_	_	_
19	Messens	messen	NNS	_	_	_
20	,	,	,	_	_	_
21	1992	1992	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	then	then	RB	_	_	_
25	treated	treat	VBN	_	_	_
26	with	with	IN	_	_	_
27	RNase-free	rnase-free	JJ	_	_	_
28	DNaseI	dnasei	NN	_	_	_
29	according	accord	VBG	_	_	_
30	to	to	TO	_	_	_
31	the	the	DT	_	_	_
32	manufacturer	manufacturer	NN	_	_	_
33	's	's	POS	_	_	_
34	recommendations	recommendation	NNS	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Ambion	Ambion	NNP	_	_	_
37	,	,	,	_	_	_
38	USA	USA	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

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	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	,	,	,	_	_	_
14	Hilden	Hilden	NNP	_	_	_
15	,	,	,	_	_	_
16	Germany	Germany	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	according	accord	VBG	_	_	_
19	to	to	TO	_	_	_
20	the	the	DT	_	_	_
21	manufactures	manufacture	VBZ	_	_	_
22	recommendations	recommendation	NNS	_	_	_
23	.	.	.	_	_	_

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	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	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Trizol	Trizol	NNP	_	_	_
9	reagent	reagent	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Thermo	Thermo	NNP	_	_	_
12	Fisher	Fisher	NNP	_	_	_
13	Scientific	Scientific	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	concentration	concentration	NN	_	_	_
18	and	and	CC	_	_	_
19	purity	purity	NN	_	_	_
20	of	of	IN	_	_	_
21	the	the	DT	_	_	_
22	samples	sample	NNS	_	_	_
23	were	be	VBD	_	_	_
24	determined	determine	VBN	_	_	_
25	using	use	VBG	_	_	_
26	Nano	Nano	NNP	_	_	_
27	Drop	Drop	NNP	_	_	_
28	.	.	.	_	_	_

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	/	/	:	_	_	_
18	L	l	NN	_	_	_
19	RiboLock	ribolock	NN	_	_	_
20	RNase	rnase	NN	_	_	_
21	Inhibitor	inhibitor	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Thermo	Thermo	NNP	_	_	_
24	Fisher	Fisher	NNP	_	_	_
25	Scientific	Scientific	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	for	for	IN	_	_	_
28	60	60	CD	_	_	_
29	min	min	NN	_	_	_
30	at	at	IN	_	_	_
31	37	37	CD	_	_	_
32	°C	°c	NN	_	_	_
33	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	organic	organic	JJ	_	_	_
3	extraction	extraction	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	1x	1x	NN	_	_	_
6	25:24:1	25:24:1	CD	_	_	_
7	v/v	v/v	NN	_	_	_
8	phenol/chloroform	phenol/chloroform	NN	_	_	_
9	/	/	:	_	_	_
10	isoamyalcohol	isoamyalcohol	NN	_	_	_
11	,	,	,	_	_	_
12	1x	1x	NN	_	_	_
13	chloroform	chloroform	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	RNA	rna	NN	_	_	_
17	was	be	VBD	_	_	_
18	recovered	recover	VBN	_	_	_
19	by	by	IN	_	_	_
20	overnight	overnight	JJ	_	_	_
21	precipitation	precipitation	NN	_	_	_
22	with	with	IN	_	_	_
23	3	3	CD	_	_	_
24	volumes	volume	NNS	_	_	_
25	of	of	IN	_	_	_
26	30:1	30:1	CD	_	_	_
27	100	100	CD	_	_	_
28	%	%	NN	_	_	_
29	ethanol/3	ethanol/3	CD	_	_	_
30	M	m	NN	_	_	_
31	sodium	sodium	NN	SUPP	_	_
32	acetate	acetate	NN	SUPP	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	pH	ph	NN	_	_	_
35	5.2	5.2	CD	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	Next	next	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	sample	sample	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	TEX	tex	NN	_	_	_
7	+	+	CC	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	depleted	deplete	VBN	_	_	_
11	of	of	IN	_	_	_
12	processed	process	VBN	_	_	_
13	RNAs	rna	NNS	_	_	_
14	using	use	VBG	_	_	_
15	1U	1u	NN	_	_	_
16	per	per	IN	_	_	_
17	1μg	1μg	NN	_	_	_
18	of	of	IN	_	_	_
19	RNA	rna	NN	_	_	_
20	Terminator	Terminator	NNP	_	_	_
21	5	5	CD	_	_	_
22	'	'	''	_	_	_
23	-	-	:	_	_	_
24	Phosphate-Dependent	phosphate-dependent	JJ	_	_	_
25	Exonuclease	exonuclease	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	TEX	tex	NN	_	_	_
28	,	,	,	_	_	_
29	Epicentre	Epicentre	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	in	in	IN	_	_	_
32	the	the	DT	_	_	_
33	presence	presence	NN	_	_	_
34	of	of	IN	_	_	_
35	1U/μL	1u/μl	NN	_	_	_
36	RNase	rnase	NN	_	_	_
37	Inhibitor	inhibitor	NN	_	_	_
38	for	for	IN	_	_	_
39	60	60	CD	_	_	_
40	min	min	NN	_	_	_
41	at	at	IN	_	_	_
42	30	30	CD	_	_	_
43	°	°	CD	_	_	_
44	C	c	NN	_	_	_
45	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	control	control	NN	_	_	_
3	reaction	reaction	NN	_	_	_
4	without	without	IN	_	_	_
5	TEX	TEX	NNP	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	TEX	TEX	NNP	_	_	_
8	-	-	:	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	run	run	VBN	_	_	_
12	in	in	IN	_	_	_
13	parallel	parallel	NN	_	_	_
14	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	organic	organic	JJ	_	_	_
3	extraction	extraction	NN	_	_	_
4	,	,	,	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	recovered	recover	VBN	_	_	_
8	by	by	IN	_	_	_
9	overnight	overnight	JJ	_	_	_
10	precipitation	precipitation	NN	_	_	_
11	and	and	CC	_	_	_
12	resuspended	resuspend	VBN	_	_	_
13	in	in	IN	_	_	_
14	RNase-free	rnase-free	JJ	_	_	_
15	water	water	NN	_	_	_
16	.	.	.	_	_	_

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	TRI	TRI	NNP	_	_	_
8	Reagent	Reagent	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Sigma	Sigma	NNP	_	_	_
11	Aldrich	Aldrich	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	enriched	enrich	VBN	_	_	_
15	by	by	IN	_	_	_
16	depleting	deplete	VBG	_	_	_
17	small	small	JJ	_	_	_
18	RNAs	rna	NNS	_	_	_
19	with	with	IN	_	_	_
20	GeneJET	GeneJET	NNP	_	_	_
21	Purification	purification	NN	_	_	_
22	Kit	kit	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Fermentas	fermentas	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	rRNA	rrna	NN	_	_	_
28	with	with	IN	_	_	_
29	MICROBExpres	microbexpre	NNS	_	_	_
30	Bacterial	bacterial	JJ	_	_	_
31	mRNA	mrna	NN	_	_	_
32	Enrichment	Enrichment	NNP	_	_	_
33	Kit	kit	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Ambion	ambion	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	and	and	CC	_	_	_
38	fragmented	fragmented	JJ	_	_	_
39	in	in	IN	_	_	_
40	alkaline	alkaline	NN	_	_	_
41	solution	solution	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	2	2	CD	_	_	_
44	mM	mm	NN	KWSUPP	_	_
45	EDTA	edta	NN	_	_	_
46	and	and	CC	_	_	_
47	100	100	CD	_	_	_
48	mM	mm	NN	KWSUPP	_	_
49	Na2CO3	na2co3	NN	_	_	_
50	pH	ph	NN	_	_	_
51	9.2	9.2	CD	_	_	_
52	for	for	IN	_	_	_
53	40	40	CD	_	_	_
54	min	min	NN	_	_	_
55	at	at	IN	_	_	_
56	95	95	CD	_	_	_
57	°C	°c	NN	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	to	to	TO	_	_	_
60	fragments	fragment	NNS	_	_	_
61	with	with	IN	_	_	_
62	size	size	NN	_	_	_
63	of	of	IN	_	_	_
64	24-35	24-35	CD	_	_	_
65	nts	nt	NNS	_	_	_
66	.	.	.	_	_	_

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/µl	units/µl	NN	_	_	_
35	micrococcal	micrococcal	JJ	_	_	_
36	nuclease	nuclease	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Fermentas	fermentas	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	for	for	IN	_	_	_
41	10	10	CD	_	_	_
42	min	min	NN	_	_	_
43	at	at	IN	_	_	_
44	room	room	NN	_	_	_
45	temperature	temperature	NN	_	_	_
46	in	in	IN	_	_	_
47	buffer	buffer	NN	_	_	_
48	with	with	IN	_	_	_
49	pH	ph	NN	_	_	_
50	9.2	9.2	CD	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	10	10	CD	_	_	_
53	mM	mm	NN	KWSUPP	_	_
54	Tris	Tris	NNP	_	_	_
55	pH	ph	NN	_	_	_
56	11	11	CD	_	_	_
57	containing	contain	VBG	_	_	_
58	50	50	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	NH4Cl	nh4cl	NN	_	_	_
61	,	,	,	_	_	_
62	10	10	CD	_	_	_
63	mM	mm	NN	KWSUPP	_	_
64	MgCl2	mgcl2	NN	_	_	_
65	,	,	,	_	_	_
66	0.2	0.2	CD	_	_	_
67	%	%	NN	_	_	_
68	triton	triton	NN	_	_	_
69	X-100	x-100	NN	_	_	_
70	,	,	,	_	_	_
71	100	100	CD	_	_	_
72	µg/ml	µg/ml	JJ	_	_	_
73	chloramphenicol	chloramphenicol	NN	_	_	_
74	and	and	CC	_	_	_
75	20	20	CD	_	_	_
76	mM	mm	NN	KWSUPP	_	_
77	CaCl2	cacl2	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	to	to	TO	_	_	_
80	obtain	obtain	VB	_	_	_
81	the	the	DT	_	_	_
82	monosomal	monosomal	JJ	_	_	_
83	fraction	fraction	NN	_	_	_
84	.	.	.	_	_	_

1	Separation	separation	NN	_	_	_
2	was	be	VBD	_	_	_
3	obtained	obtain	VBN	_	_	_
4	by	by	IN	_	_	_
5	sucrose	sucrose	NN	_	_	_
6	density	density	NN	_	_	_
7	gradient	gradient	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	15-50	15-50	CD	_	_	_
10	%	%	NN	_	_	_
11	w/v	w/v	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	20-35-nt	20-35-nt	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	fragments	fragment	NNS	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	monosomal	monosomal	JJ	_	_	_
9	fraction	fraction	NN	_	_	_
10	were	be	VBD	_	_	_
11	size	size	NN	_	_	_
12	selected	select	VBN	_	_	_
13	on	on	IN	_	_	_
14	a	a	DT	_	_	_
15	denaturing	denature	VBG	_	_	_
16	15	15	CD	_	_	_
17	%	%	NN	_	_	_
18	polyacrylamide	polyacrylamide	NN	_	_	_
19	gel	gel	NN	_	_	_
20	.	.	.	_	_	_

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	Total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	extracted	extract	VBN	_	_	_
16	using	use	VBG	_	_	_
17	TRIzol	trizol	NN	_	_	_
18	reagent	reagent	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Invitrogen	invitrogen	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	the	the	DT	_	_	_
24	sample	sample	NN	_	_	_
25	was	be	VBD	_	_	_
26	enriched	enrich	VBN	_	_	_
27	in	in	IN	_	_	_
28	mRNA	mrna	NN	_	_	_
29	,	,	,	_	_	_
30	depleting	deplete	VBG	_	_	_
31	small	small	JJ	_	_	_
32	RNAs	rna	NNS	_	_	_
33	with	with	IN	_	_	_
34	GeneJET	genejet	NN	_	_	_
35	™	™	NN	_	_	_
36	RNA	rna	NN	_	_	_
37	Purification	purification	NN	_	_	_
38	Kit	kit	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Fermentas	fermentas	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	and	and	CC	_	_	_
43	ribosomal	ribosomal	JJ	_	_	_
44	RNA	rna	NN	_	_	_
45	with	with	IN	_	_	_
46	two	two	CD	_	_	_
47	cycle	cycle	NN	_	_	_
48	of	of	IN	_	_	_
49	MICROBExpress	microbexpress	NN	_	_	_
50	™	™	CD	_	_	_
51	Bacterial	bacterial	JJ	_	_	_
52	mRNA	mrna	NN	_	_	_
53	Enrichment	Enrichment	NNP	_	_	_
54	Kit	kit	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Ambion	ambion	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	.	.	.	_	_	_

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/T1-digested	a/t1-digested	JJ	_	_	_
4	sample	sample	NN	_	_	_
5	was	be	VBD	_	_	_
6	phosphorylated	phosphorylate	VBN	_	_	_
7	with	with	IN	_	_	_
8	T4	t4	NN	_	_	_
9	PNK	pnk	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	NEB	neb	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	purified	purify	VBN	_	_	_
15	with	with	IN	_	_	_
16	RNA	rna	NN	_	_	_
17	Clean	Clean	NNP	_	_	_
18	&	&	CC	_	_	_
19	Concentrator	Concentrator	NNP	_	_	_
20	™	™	NNP	_	_	_
21	kit	kit	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Zymo	Zymo	NNP	_	_	_
24	Research	Research	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	Both	both	CC	_	_	_
2	the	the	DT	_	_	_
3	V1	v1	NN	_	_	_
4	and	and	CC	_	_	_
5	A/T1	a/t1	NN	_	_	_
6	digested	digest	VBD	_	_	_
7	samples	sample	NNS	_	_	_
8	were	be	VBD	_	_	_
9	randomly	randomly	RB	_	_	_
10	fragmented	fragmented	JJ	_	_	_
11	in	in	IN	_	_	_
12	buffer	buffer	NN	_	_	_
13	with	with	IN	_	_	_
14	pH	ph	NN	_	_	_
15	9.2	9.2	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	100	100	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	Na2CO3	na2co3	NN	_	_	_
20	,	,	,	_	_	_
21	2	2	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	EDTA	edta	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	for	for	IN	_	_	_
26	12	12	CD	_	_	_
27	min	min	NN	_	_	_
28	at	at	IN	_	_	_
29	95	95	CD	_	_	_
30	°C	°c	NN	_	_	_
31	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	with	with	IN	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	's	's	POS	_	_	_
9	Rneasy	Rneasy	NNP	_	_	_
10	Mini	Mini	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	total	total	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	was	be	VBD	_	_	_
16	extreacted	extreact	VBN	_	_	_
17	using	use	VBG	_	_	_
18	Quagen	quagen	JJ	_	_	_
19	RNA	rna	NN	_	_	_
20	mini	minus	NNS	_	_	_
21	kit	kit	NN	_	_	_
22	.	.	.	_	_	_

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	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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	according	accord	VBG	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	RNeasy	RNeasy	NNP	_	_	_
10	Mini	Mini	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	QIAGEN	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	manufacturer	manufacturer	NN	_	_	_
16	's	's	POS	_	_	_
17	protocol	protocol	NN	_	_	_
18	.	.	.	_	_	_

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	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	as	as	IN	_	_	_
7	described	describe	VBN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Sambrook	Sambrook	NNP	_	_	_
10	et	et	FW	_	_	_
11	al.	al.	FW	_	_	_
12	,	,	,	_	_	_
13	1989	1989	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	as	as	IN	_	_	_
7	desribed	desribe	VBN	_	_	_
8	in	in	IN	_	_	_
9	Kime	Kime	NNP	_	_	_
10	et	et	FW	_	_	_
11	al.	al.	FW	_	_	_
12	,	,	,	_	_	_
13	2008	2008	CD	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Total	Total	NNP	_	_	_
16	RNA	rna	NN	_	_	_
17	was	be	VBD	_	_	_
18	isolated	isolate	VBN	_	_	_
19	by	by	IN	_	_	_
20	the	the	DT	_	_	_
21	Trizol-Phenol-Chloroform	trizol-phenol-chloroform	NN	_	_	_
22	method	method	NN	_	_	_
23	.	.	.	_	_	_

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	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	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	pellets	pellet	NNS	_	_	_
9	using	use	VBG	_	_	_
10	Aurum	Aurum	NNP	_	_	_
11	total	total	JJ	_	_	_
12	RNA	rna	NN	_	_	_
13	mini	minus	NNS	_	_	_
14	kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Bio-Rad	Bio-Rad	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	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	RNA	rna	NN	_	_	_
27	quality	quality	NN	_	_	_
28	was	be	VBD	_	_	_
29	controlled	control	VBN	_	_	_
30	using	use	VBG	_	_	_
31	the	the	DT	_	_	_
32	RNA	rna	NN	_	_	_
33	6000	6000	CD	_	_	_
34	nano	nano	NN	_	_	_
35	kit	kit	NN	_	_	_
36	and	and	CC	_	_	_
37	2100	2100	CD	_	_	_
38	Bioanalyzer	Bioanalyzer	NNP	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Agilent	Agilent	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

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	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	from	from	IN	_	_	_
7	cells	cell	NNS	_	_	_
8	grown	grow	VBN	_	_	_
9	in	in	IN	_	_	_
10	LB	lb	NN	MED	_	_
11	medium	medium	NN	MED	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	Qiagen	Qiagen	NNP	_	_	_
15	RNeasy	RNeasy	NNP	_	_	_
16	column	column	NN	_	_	_
17	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	from	from	IN	_	_	_
7	strains	strain	NNS	_	_	_
8	using	use	VBG	_	_	_
9	NucleoSpin	NucleoSpin	NNP	_	_	_
10	RNAII	RNAII	NNP	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Macherey-Nagel	Macherey-Nagel	NNP	_	_	_
14	Corporation	Corporation	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	following	follow	VBG	_	_	_
17	the	the	DT	_	_	_
18	instruction	instruction	NN	_	_	_
19	.	.	.	_	_	_

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	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	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	cells	cell	NNS	_	_	_
9	stored	store	VBN	_	_	_
10	in	in	IN	_	_	_
11	liquid	liquid	JJ	_	_	_
12	nitrogen	nitrogen	NN	_	_	_
13	using	use	VBG	_	_	_
14	TRIzol	trizol	NN	_	_	_
15	Reagent	reagent	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Invitrogen	Invitrogen	NNP	_	_	_
18	Life	Life	NNP	_	_	_
19	Technologies	Technologies	NNPS	_	_	_
20	,	,	,	_	_	_
21	Carlsbad	Carlsbad	NNP	_	_	_
22	,	,	,	_	_	_
23	CA	CA	NNP	_	_	_
24	,	,	,	_	_	_
25	USA	USA	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	and	and	CC	_	_	_
28	RNeasy	rneasy	NN	_	_	_
29	MinElute	MinElute	NNP	_	_	_
30	Cleanup	Cleanup	NNP	_	_	_
31	Kits	kit	NNS	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Qiagen	Qiagen	NNP	_	_	_
34	,	,	,	_	_	_
35	Valencia	Valencia	NNP	_	_	_
36	,	,	,	_	_	_
37	CA	CA	NNP	_	_	_
38	,	,	,	_	_	_
39	USA	USA	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Total	Total	NNP	_	_	_
43	RNA	rna	NN	_	_	_
44	was	be	VBD	_	_	_
45	isolated	isolate	VBN	_	_	_
46	from	from	IN	_	_	_
47	the	the	DT	_	_	_
48	VBNC	vbnc	NN	_	_	_
49	cells	cell	NNS	_	_	_
50	and	and	CC	_	_	_
51	the	the	DT	_	_	_
52	exponential-phase	exponential-phase	NN	_	_	_
53	cells	cell	NNS	_	_	_
54	using	use	VBG	_	_	_
55	TRIzol	trizol	NN	_	_	_
56	reagent	reagent	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	Invitrogen	invitrogen	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	according	accord	VBG	_	_	_
61	to	to	TO	_	_	_
62	the	the	DT	_	_	_
63	manufacturer	manufacturer	NN	_	_	_
64	's	's	POS	_	_	_
65	instructions	instruction	NNS	_	_	_
66	.	.	.	_	_	_

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	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	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	®	®	NN	_	_	_
10	RNA	rna	NN	_	_	_
11	isolation	isolation	NN	_	_	_
12	kit	kit	NN	_	_	_
13	,	,	,	_	_	_
14	according	accord	VBG	_	_	_
15	to	to	TO	_	_	_
16	the	the	DT	_	_	_
17	manufacturer	manufacturer	NN	_	_	_
18	's	's	POS	_	_	_
19	specifications	specification	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	QIAGEN	QIAGEN	NNP	_	_	_
22	,	,	,	_	_	_
23	Germany	Germany	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	stored	store	VBN	_	_	_
27	in	in	IN	_	_	_
28	RNase-free	rnase-free	JJ	_	_	_
29	water	water	NN	_	_	_
30	at	at	IN	_	_	_
31	--	--	:	_	_	_
32	80	80	CD	_	_	_
33	°C	°c	NN	_	_	_
34	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Mini	Mini	NNP	_	_	_
10	Kit	kit	NN	_	_	_
11	and	and	CC	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	DNase	dnase	NN	_	_	_
15	I	i	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	Total	total	JJ	_	_	_
18	RNA	rna	NN	_	_	_
19	was	be	VBD	_	_	_
20	isolated	isolate	VBN	_	_	_
21	using	use	VBG	_	_	_
22	Ribopure	Ribopure	NNP	_	_	_
23	Bacteria	bacterium	NNS	_	_	_
24	Kit	kit	NN	_	_	_
25	as	as	IN	_	_	_
26	described	describe	VBN	_	_	_
27	by	by	IN	_	_	_
28	the	the	DT	_	_	_
29	manufacturer	manufacturer	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Ambion	Ambion	NNP	_	_	_
32	,	,	,	_	_	_
33	Huntingdon	Huntingdon	NNP	_	_	_
34	,	,	,	_	_	_
35	UK	UK	NNP	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	hot	hot	JJ	_	_	_
9	phenol	phenol	NN	_	_	_
10	method	method	NN	_	_	_
11	as	as	IN	_	_	_
12	described	describe	VBN	_	_	_
13	in	in	IN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Lybecker	Lybecker	NNP	_	_	_
16	et	et	FW	_	_	_
17	al.	al.	FW	_	_	_
18	,	,	,	_	_	_
19	2014	2014	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

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	the	the	DT	_	_	_
8	Rneasy	Rneasy	NNP	_	_	_
9	Mini	Mini	NNP	_	_	_
10	Kit	kit	NN	_	_	_
11	procedure	procedure	NN	_	_	_
12	with	with	IN	_	_	_
13	on	on	IN	_	_	_
14	column	column	NN	_	_	_
15	Dnase	dnase	NN	_	_	_
16	treatment	treatment	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	qiagen	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

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	the	the	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	Mini-Kit	mini-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	`	`	``	_	_	_
18	s	be	VBZ	_	_	_
19	instruction	instruction	NN	_	_	_
20	and	and	CC	_	_	_
21	DNA	dna	NN	_	_	_
22	was	be	VBD	_	_	_
23	removed	remove	VBN	_	_	_
24	by	by	IN	_	_	_
25	using	use	VBG	_	_	_
26	RNAse-Free	rnase-free	JJ	_	_	_
27	DNAse	dnase	NN	_	_	_
28	Set	set	VB	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Qiagen	Qiagen	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	with	with	IN	_	_	_
7	the	the	DT	_	_	_
8	MasterPure	masterpure	NN	_	_	_
9	RNA	rna	NN	_	_	_
10	Isolation	isolation	NN	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Epicentre	Epicentre	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	enriched	enriched	JJ	_	_	_
17	for	for	IN	_	_	_
18	mRNA	mrna	NN	_	_	_
19	using	use	VBG	_	_	_
20	the	the	DT	_	_	_
21	mRNA	mrna	NN	_	_	_
22	Prokaryotic	prokaryotic	JJ	_	_	_
23	mRNA	mrna	NN	_	_	_
24	Isolation	isolation	NN	_	_	_
25	Kit	kit	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Epicentre	Epicentre	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	polyadenylated	polyadenylated	JJ	_	_	_
32	with	with	IN	_	_	_
33	kit	kit	NN	_	_	_
34	all	all	DT	_	_	_
35	based	base	VBN	_	_	_
36	on	on	IN	_	_	_
37	the	the	DT	_	_	_
38	manufacturer	manufacturer	NN	_	_	_
39	's	's	POS	_	_	_
40	instructions	instruction	NNS	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Total	Total	NNP	_	_	_
43	RNA	rna	NN	_	_	_
44	was	be	VBD	_	_	_
45	isolated	isolate	VBN	_	_	_
46	with	with	IN	_	_	_
47	the	the	DT	_	_	_
48	RNeasy	RNeasy	NNP	_	_	_
49	Protect	Protect	NNP	_	_	_
50	Bacteria	bacterium	NNS	_	_	_
51	Mini	Mini	NNP	_	_	_
52	Kit	kit	NN	_	_	_
53	from	from	IN	_	_	_
54	Qiagen	Qiagen	NNP	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Hilden	Hilden	NNP	_	_	_
57	,	,	,	_	_	_
58	Germany	Germany	NNP	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	.	.	.	_	_	_

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	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	on	on	IN	_	_	_
7	a	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	columns	column	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	Qiagen	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	;	;	:	_	_	_
14	ribosomal	ribosomal	JJ	_	_	_
15	RNAs	rna	NNS	_	_	_
16	were	be	VBD	_	_	_
17	removed	remove	VBN	_	_	_
18	with	with	IN	_	_	_
19	the	the	DT	_	_	_
20	MicroExpress	MicroExpress	NNP	_	_	_
21	kit	kit	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Ambion	ambion	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

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	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNAeasy	rnaeasy	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

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	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	NNP	_	_	_
33	Total	Total	NNP	_	_	_
34	RNA	rna	NN	_	_	_
35	were	be	VBD	_	_	_
36	then	then	RB	_	_	_
37	isolated	isolate	VBN	_	_	_
38	according	accord	VBG	_	_	_
39	to	to	TO	_	_	_
40	the	the	DT	_	_	_
41	standard	standard	JJ	_	_	_
42	protocol	protocol	NN	_	_	_
43	using	use	VBG	_	_	_
44	an	a	DT	_	_	_
45	RNeasy	rneasy	NN	_	_	_
46	mini	minus	NNS	_	_	_
47	kit	kit	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	Qiagen	qiagen	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	.	.	.	_	_	_

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	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	TPM	tpm	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	transcripts	transcript	NNS	_	_	_
13	per	per	IN	_	_	_
14	million	million	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	was	be	VBD	_	_	_
17	calculated	calculate	VBN	_	_	_
18	by	by	IN	_	_	_
19	RSEM	rsem	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	version	version	NN	_	_	_
22	1.2.19	1.2.19	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Transcript	Transcript	NNP	_	_	_
26	Abundance	Abundance	NNP	_	_	_
27	in	in	IN	_	_	_
28	LB	LB	NNP	_	_	_
29	at	at	IN	_	_	_
30	30	30	CD	_	_	_
31	degrees	degree	NNS	_	_	_
32	OD600	od600	NN	_	_	_
33	=	=	JJ	_	_	_
34	0.8	0.8	CD	_	_	_
35	Trial	trial	NN	_	_	_
36	A	a	DT	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
38	Transcript	Transcript	NNP	_	_	_
39	Abundance	Abundance	NNP	_	_	_
40	in	in	IN	_	_	_
41	LB	LB	NNP	_	_	_
42	at	at	IN	_	_	_
43	30	30	CD	_	_	_
44	degrees	degree	NNS	_	_	_
45	OD600	od600	NN	_	_	_
46	=	=	JJ	_	_	_
47	0.8	0.8	CD	_	_	_
48	Trial	trial	NN	_	_	_
49	B	b	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Transcript	transcript	NN	_	_	_
52	Abundance	abundance	NN	_	_	_
53	in	in	IN	_	_	_
54	M9	m9	NN	_	_	_
55	at	at	IN	_	_	_
56	30	30	CD	_	_	_
57	degrees	degree	NNS	_	_	_
58	OD600	od600	NN	_	_	_
59	=	=	JJ	_	_	_
60	0.8	0.8	CD	_	_	_
61	Trial	trial	NN	_	_	_
62	A	a	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Transcript	transcript	NN	_	_	_
65	Abundance	abundance	NN	_	_	_
66	in	in	IN	_	_	_
67	M9	m9	NN	_	_	_
68	at	at	IN	_	_	_
69	30	30	CD	_	_	_
70	degrees	degree	NNS	_	_	_
71	OD600	od600	NN	_	_	_
72	=	=	JJ	_	_	_
73	0.8	0.8	CD	_	_	_
74	Trial	trial	NN	_	_	_
75	B	b	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	transcript	transcript	NN	_	_	_
78	abundance	abundance	NN	_	_	_
79	was	be	VBD	_	_	_
80	quantified	quantify	VBN	_	_	_
81	using	use	VBG	_	_	_
82	rockhopper	rockhopper	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Transcript	transcript	NN	_	_	_
85	assembly	assembly	NN	_	_	_
86	an	a	DT	_	_	_
87	quantification	quantification	NN	_	_	_
88	was	be	VBD	_	_	_
89	performed	perform	VBN	_	_	_
90	using	use	VBG	_	_	_
91	a	a	DT	_	_	_
92	protocols	protocol	NNS	_	_	_
93	from	from	IN	_	_	_
94	Trapnell	Trapnell	NNP	_	_	_
95	et	et	FW	_	_	_
96	al.	al.	FW	_	_	_
97	,	,	,	_	_	_
98	and	and	CC	_	_	_
99	Li	Li	NNP	_	_	_
100	et	et	FW	_	_	_
101	al.	al.	FW	_	_	_
102	.	.	.	_	_	_

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	pgcgrowthconditions	NN	_	_	_
2	Transcriptional	transcriptional	JJ	_	_	_
3	profiling	profiling	NN	_	_	_
4	of	of	IN	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	cultured	culture	VBN	_	_	_
8	under	under	IN	_	_	_
9	severe	severe	JJ	_	_	_
10	zinc	zinc	NN	_	_	_
11	limitation	limitation	NN	_	_	_
12	Chemostat	Chemostat	NNP	_	_	_
13	1A	1a	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Transcriptional	transcriptional	JJ	_	_	_
16	profiling	profiling	NN	_	_	_
17	of	of	IN	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	cultured	culture	VBN	_	_	_
21	under	under	IN	_	_	_
22	severe	severe	JJ	_	_	_
23	zinc	zinc	NN	_	_	_
24	limitation	limitation	NN	_	_	_
25	Chemostat	chemostat	NN	_	_	_
26	1B	1b	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Transcriptional	transcriptional	JJ	_	_	_
29	profiling	profiling	NN	_	_	_
30	of	of	IN	_	_	_
31	Escherichia	escherichia	FW	Organism	_	_
32	coli	coli	FW	Organism	_	_
33	cultured	culture	VBN	_	_	_
34	under	under	IN	_	_	_
35	severe	severe	JJ	_	_	_
36	zinc	zinc	NN	_	_	_
37	limitation	limitation	NN	_	_	_
38	Chemostat	Chemostat	NNP	_	_	_
39	2A	2a	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Transcriptional	transcriptional	JJ	_	_	_
42	profiling	profiling	NN	_	_	_
43	of	of	IN	_	_	_
44	Escherichia	escherichia	FW	Organism	_	_
45	coli	coli	FW	Organism	_	_
46	cultured	culture	VBN	_	_	_
47	under	under	IN	_	_	_
48	severe	severe	JJ	_	_	_
49	zinc	zinc	NN	_	_	_
50	limitation	limitation	NN	_	_	_
51	Chemostat	Chemostat	NNP	_	_	_
52	2B	2b	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Transcriptional	transcriptional	JJ	_	_	_
55	profiling	profiling	NN	_	_	_
56	of	of	IN	_	_	_
57	Escherichia	escherichia	FW	Organism	_	_
58	coli	coli	FW	Organism	_	_
59	cultured	culture	VBN	_	_	_
60	under	under	IN	_	_	_
61	severe	severe	JJ	_	_	_
62	zinc	zinc	NN	_	_	_
63	limitation	limitation	NN	_	_	_
64	Chemostat	Chemostat	NNP	_	_	_
65	3A	3a	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Transcriptional	transcriptional	JJ	_	_	_
68	profiling	profiling	NN	_	_	_
69	of	of	IN	_	_	_
70	Escherichia	escherichia	FW	Organism	_	_
71	coli	coli	FW	Organism	_	_
72	cultured	culture	VBN	_	_	_
73	under	under	IN	_	_	_
74	severe	severe	JJ	_	_	_
75	zinc	zinc	NN	_	_	_
76	limitation	limitation	NN	_	_	_
77	Chemostat	Chemostat	NNP	_	_	_
78	3B	3b	NN	_	_	_
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	0A1	0a1	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Transcriptional	transcriptional	JJ	_	_	_
98	profiling	profiling	NN	_	_	_
99	of	of	IN	_	_	_
100	Escherichia	escherichia	FW	Organism	_	_
101	coli	coli	FW	Organism	_	_
102	during	during	IN	_	_	_
103	a	a	DT	_	_	_
104	transition	transition	NN	_	_	_
105	from	from	IN	_	_	_
106	zinc	zinc	NN	_	_	_
107	starvation	starvation	NN	_	_	_
108	to	to	TO	_	_	_
109	surfeit	surfeit	NN	_	_	_
110	-LRB-	-lrb-	-LRB-	_	_	_
111	slide	slide	NN	_	_	_
112	0A2	0a2	NN	_	_	_
113	-RRB-	-rrb-	-RRB-	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	Transcriptional	transcriptional	JJ	_	_	_
116	profiling	profiling	NN	_	_	_
117	of	of	IN	_	_	_
118	Escherichia	escherichia	FW	Organism	_	_
119	coli	coli	FW	Organism	_	_
120	during	during	IN	_	_	_
121	a	a	DT	_	_	_
122	transition	transition	NN	_	_	_
123	from	from	IN	_	_	_
124	zinc	zinc	NN	_	_	_
125	starvation	starvation	NN	_	_	_
126	to	to	TO	_	_	_
127	surfeit	surfeit	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	slide	slide	NN	_	_	_
130	0B1	0b1	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	Transcriptional	transcriptional	JJ	_	_	_
134	profiling	profiling	NN	_	_	_
135	of	of	IN	_	_	_
136	Escherichia	escherichia	FW	Organism	_	_
137	coli	coli	FW	Organism	_	_
138	during	during	IN	_	_	_
139	a	a	DT	_	_	_
140	transition	transition	NN	_	_	_
141	from	from	IN	_	_	_
142	zinc	zinc	NN	_	_	_
143	starvation	starvation	NN	_	_	_
144	to	to	TO	_	_	_
145	surfeit	surfeit	NN	_	_	_
146	-LRB-	-lrb-	-LRB-	_	_	_
147	slide	slide	NN	_	_	_
148	0B2	0b2	NN	_	_	_
149	-RRB-	-rrb-	-RRB-	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	Transcriptional	transcriptional	JJ	_	_	_
152	profiling	profiling	NN	_	_	_
153	of	of	IN	_	_	_
154	Escherichia	escherichia	FW	Organism	_	_
155	coli	coli	FW	Organism	_	_
156	during	during	IN	_	_	_
157	a	a	DT	_	_	_
158	transition	transition	NN	_	_	_
159	from	from	IN	_	_	_
160	zinc	zinc	NN	_	_	_
161	starvation	starvation	NN	_	_	_
162	to	to	TO	_	_	_
163	surfeit	surfeit	NN	_	_	_
164	-LRB-	-lrb-	-LRB-	_	_	_
165	slide	slide	NN	_	_	_
166	10A1	10a1	NN	_	_	_
167	-RRB-	-rrb-	-RRB-	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	Transcriptional	transcriptional	JJ	_	_	_
170	profiling	profiling	NN	_	_	_
171	of	of	IN	_	_	_
172	Escherichia	escherichia	FW	Organism	_	_
173	coli	coli	FW	Organism	_	_
174	during	during	IN	_	_	_
175	a	a	DT	_	_	_
176	transition	transition	NN	_	_	_
177	from	from	IN	_	_	_
178	zinc	zinc	NN	_	_	_
179	starvation	starvation	NN	_	_	_
180	to	to	TO	_	_	_
181	surfeit	surfeit	NN	_	_	_
182	-LRB-	-lrb-	-LRB-	_	_	_
183	slide	slide	NN	_	_	_
184	10A2	10a2	NN	_	_	_
185	-RRB-	-rrb-	-RRB-	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	Transcriptional	transcriptional	JJ	_	_	_
188	profiling	profiling	NN	_	_	_
189	of	of	IN	_	_	_
190	Escherichia	escherichia	FW	Organism	_	_
191	coli	coli	FW	Organism	_	_
192	during	during	IN	_	_	_
193	a	a	DT	_	_	_
194	transition	transition	NN	_	_	_
195	from	from	IN	_	_	_
196	zinc	zinc	NN	_	_	_
197	starvation	starvation	NN	_	_	_
198	to	to	TO	_	_	_
199	surfeit	surfeit	NN	_	_	_
200	-LRB-	-lrb-	-LRB-	_	_	_
201	slide	slide	NN	_	_	_
202	10A3	10a3	NN	_	_	_
203	-RRB-	-rrb-	-RRB-	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	Transcriptional	transcriptional	JJ	_	_	_
206	profiling	profiling	NN	_	_	_
207	of	of	IN	_	_	_
208	Escherichia	escherichia	FW	Organism	_	_
209	coli	coli	FW	Organism	_	_
210	during	during	IN	_	_	_
211	a	a	DT	_	_	_
212	transition	transition	NN	_	_	_
213	from	from	IN	_	_	_
214	zinc	zinc	NN	_	_	_
215	starvation	starvation	NN	_	_	_
216	to	to	TO	_	_	_
217	surfeit	surfeit	NN	_	_	_
218	-LRB-	-lrb-	-LRB-	_	_	_
219	slide	slide	NN	_	_	_
220	10B1	10b1	NN	_	_	_
221	-RRB-	-rrb-	-RRB-	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	Transcriptional	transcriptional	JJ	_	_	_
224	profiling	profiling	NN	_	_	_
225	of	of	IN	_	_	_
226	Escherichia	escherichia	FW	Organism	_	_
227	coli	coli	FW	Organism	_	_
228	during	during	IN	_	_	_
229	a	a	DT	_	_	_
230	transition	transition	NN	_	_	_
231	from	from	IN	_	_	_
232	zinc	zinc	NN	_	_	_
233	starvation	starvation	NN	_	_	_
234	to	to	TO	_	_	_
235	surfeit	surfeit	NN	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	slide	slide	NN	_	_	_
238	10B2	10b2	NN	_	_	_
239	-RRB-	-rrb-	-RRB-	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	Transcriptional	transcriptional	JJ	_	_	_
242	profiling	profiling	NN	_	_	_
243	of	of	IN	_	_	_
244	Escherichia	escherichia	FW	Organism	_	_
245	coli	coli	FW	Organism	_	_
246	during	during	IN	_	_	_
247	a	a	DT	_	_	_
248	transition	transition	NN	_	_	_
249	from	from	IN	_	_	_
250	zinc	zinc	NN	_	_	_
251	starvation	starvation	NN	_	_	_
252	to	to	TO	_	_	_
253	surfeit	surfeit	NN	_	_	_
254	-LRB-	-lrb-	-LRB-	_	_	_
255	slide	slide	NN	_	_	_
256	2.5	2.5	CD	_	_	_
257	A1	a1	NN	_	_	_
258	-RRB-	-rrb-	-RRB-	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	Transcriptional	transcriptional	JJ	_	_	_
261	profiling	profiling	NN	_	_	_
262	of	of	IN	_	_	_
263	Escherichia	escherichia	FW	Organism	_	_
264	coli	coli	FW	Organism	_	_
265	during	during	IN	_	_	_
266	a	a	DT	_	_	_
267	transition	transition	NN	_	_	_
268	from	from	IN	_	_	_
269	zinc	zinc	NN	_	_	_
270	starvation	starvation	NN	_	_	_
271	to	to	TO	_	_	_
272	surfeit	surfeit	NN	_	_	_
273	-LRB-	-lrb-	-LRB-	_	_	_
274	slide	slide	NN	_	_	_
275	2.5	2.5	CD	_	_	_
276	A2	a2	NN	_	_	_
277	-RRB-	-rrb-	-RRB-	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	Transcriptional	transcriptional	JJ	_	_	_
280	profiling	profiling	NN	_	_	_
281	of	of	IN	_	_	_
282	Escherichia	escherichia	FW	Organism	_	_
283	coli	coli	FW	Organism	_	_
284	during	during	IN	_	_	_
285	a	a	DT	_	_	_
286	transition	transition	NN	_	_	_
287	from	from	IN	_	_	_
288	zinc	zinc	NN	_	_	_
289	starvation	starvation	NN	_	_	_
290	to	to	TO	_	_	_
291	surfeit	surfeit	NN	_	_	_
292	-LRB-	-lrb-	-LRB-	_	_	_
293	slide	slide	NN	_	_	_
294	2.5	2.5	CD	_	_	_
295	B1	b1	NN	_	_	_
296	-RRB-	-rrb-	-RRB-	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	Transcriptional	transcriptional	JJ	_	_	_
299	profiling	profiling	NN	_	_	_
300	of	of	IN	_	_	_
301	Escherichia	escherichia	FW	Organism	_	_
302	coli	coli	FW	Organism	_	_
303	during	during	IN	_	_	_
304	a	a	DT	_	_	_
305	transition	transition	NN	_	_	_
306	from	from	IN	_	_	_
307	zinc	zinc	NN	_	_	_
308	starvation	starvation	NN	_	_	_
309	to	to	TO	_	_	_
310	surfeit	surfeit	NN	_	_	_
311	-LRB-	-lrb-	-LRB-	_	_	_
312	slide	slide	NN	_	_	_
313	2.5	2.5	CD	_	_	_
314	B2	b2	NN	_	_	_
315	-RRB-	-rrb-	-RRB-	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	Transcriptional	transcriptional	JJ	_	_	_
318	profiling	profiling	NN	_	_	_
319	of	of	IN	_	_	_
320	Escherichia	escherichia	FW	Organism	_	_
321	coli	coli	FW	Organism	_	_
322	during	during	IN	_	_	_
323	a	a	DT	_	_	_
324	transition	transition	NN	_	_	_
325	from	from	IN	_	_	_
326	zinc	zinc	NN	_	_	_
327	starvation	starvation	NN	_	_	_
328	to	to	TO	_	_	_
329	surfeit	surfeit	NN	_	_	_
330	-LRB-	-lrb-	-LRB-	_	_	_
331	slide	slide	NN	_	_	_
332	30A1	30a1	NN	_	_	_
333	-RRB-	-rrb-	-RRB-	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	Transcriptional	transcriptional	JJ	_	_	_
336	profiling	profiling	NN	_	_	_
337	of	of	IN	_	_	_
338	Escherichia	escherichia	FW	Organism	_	_
339	coli	coli	FW	Organism	_	_
340	during	during	IN	_	_	_
341	a	a	DT	_	_	_
342	transition	transition	NN	_	_	_
343	from	from	IN	_	_	_
344	zinc	zinc	NN	_	_	_
345	starvation	starvation	NN	_	_	_
346	to	to	TO	_	_	_
347	surfeit	surfeit	NN	_	_	_
348	-LRB-	-lrb-	-LRB-	_	_	_
349	slide	slide	NN	_	_	_
350	30A2	30a2	NN	_	_	_
351	-RRB-	-rrb-	-RRB-	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
353	Transcriptional	transcriptional	JJ	_	_	_
354	profiling	profiling	NN	_	_	_
355	of	of	IN	_	_	_
356	Escherichia	escherichia	FW	Organism	_	_
357	coli	coli	FW	Organism	_	_
358	during	during	IN	_	_	_
359	a	a	DT	_	_	_
360	transition	transition	NN	_	_	_
361	from	from	IN	_	_	_
362	zinc	zinc	NN	_	_	_
363	starvation	starvation	NN	_	_	_
364	to	to	TO	_	_	_
365	surfeit	surfeit	NN	_	_	_
366	-LRB-	-lrb-	-LRB-	_	_	_
367	slide	slide	NN	_	_	_
368	30B1	30b1	NN	_	_	_
369	-RRB-	-rrb-	-RRB-	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	Transcriptional	transcriptional	JJ	_	_	_
372	profiling	profiling	NN	_	_	_
373	of	of	IN	_	_	_
374	Escherichia	escherichia	FW	Organism	_	_
375	coli	coli	FW	Organism	_	_
376	during	during	IN	_	_	_
377	a	a	DT	_	_	_
378	transition	transition	NN	_	_	_
379	from	from	IN	_	_	_
380	zinc	zinc	NN	_	_	_
381	starvation	starvation	NN	_	_	_
382	to	to	TO	_	_	_
383	surfeit	surfeit	NN	_	_	_
384	-LRB-	-lrb-	-LRB-	_	_	_
385	slide	slide	NN	_	_	_
386	30B2	30b2	NN	_	_	_
387	-RRB-	-rrb-	-RRB-	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	Transcriptional	transcriptional	JJ	_	_	_
390	profiling	profiling	NN	_	_	_
391	of	of	IN	_	_	_
392	Escherichia	escherichia	FW	Organism	_	_
393	coli	coli	FW	Organism	_	_
394	during	during	IN	_	_	_
395	a	a	DT	_	_	_
396	transition	transition	NN	_	_	_
397	from	from	IN	_	_	_
398	zinc	zinc	NN	_	_	_
399	starvation	starvation	NN	_	_	_
400	to	to	TO	_	_	_
401	surfeit	surfeit	NN	_	_	_
402	-LRB-	-lrb-	-LRB-	_	_	_
403	slide	slide	NN	_	_	_
404	7A1	7a1	NN	_	_	_
405	-RRB-	-rrb-	-RRB-	_	_	_
406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
407	Transcriptional	transcriptional	JJ	_	_	_
408	profiling	profiling	NN	_	_	_
409	of	of	IN	_	_	_
410	Escherichia	escherichia	FW	Organism	_	_
411	coli	coli	FW	Organism	_	_
412	during	during	IN	_	_	_
413	a	a	DT	_	_	_
414	transition	transition	NN	_	_	_
415	from	from	IN	_	_	_
416	zinc	zinc	NN	_	_	_
417	starvation	starvation	NN	_	_	_
418	to	to	TO	_	_	_
419	surfeit	surfeit	NN	_	_	_
420	-LRB-	-lrb-	-LRB-	_	_	_
421	slide	slide	NN	_	_	_
422	7A2	7a2	NN	_	_	_
423	-RRB-	-rrb-	-RRB-	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	Transcriptional	transcriptional	JJ	_	_	_
426	profiling	profiling	NN	_	_	_
427	of	of	IN	_	_	_
428	Escherichia	escherichia	FW	Organism	_	_
429	coli	coli	FW	Organism	_	_
430	during	during	IN	_	_	_
431	a	a	DT	_	_	_
432	transition	transition	NN	_	_	_
433	from	from	IN	_	_	_
434	zinc	zinc	NN	_	_	_
435	starvation	starvation	NN	_	_	_
436	to	to	TO	_	_	_
437	surfeit	surfeit	NN	_	_	_
438	-LRB-	-lrb-	-LRB-	_	_	_
439	slide	slide	NN	_	_	_
440	7B1	7b1	NN	_	_	_
441	-RRB-	-rrb-	-RRB-	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	Transcriptional	transcriptional	JJ	_	_	_
444	profiling	profiling	NN	_	_	_
445	of	of	IN	_	_	_
446	Escherichia	escherichia	FW	Organism	_	_
447	coli	coli	FW	Organism	_	_
448	during	during	IN	_	_	_
449	a	a	DT	_	_	_
450	transition	transition	NN	_	_	_
451	from	from	IN	_	_	_
452	zinc	zinc	NN	_	_	_
453	starvation	starvation	NN	_	_	_
454	to	to	TO	_	_	_
455	surfeit	surfeit	NN	_	_	_
456	-LRB-	-lrb-	-LRB-	_	_	_
457	slide	slide	NN	_	_	_
458	7B2	7b2	NN	_	_	_
459	-RRB-	-rrb-	-RRB-	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	Transcriptional	transcriptional	JJ	_	_	_
462	response	response	NN	_	_	_
463	of	of	IN	_	_	_
464	E.	e.	FW	_	_	_
465	coli	coli	FW	_	_	_
466	to	to	TO	_	_	_
467	TPEN	tpen	NN	_	_	_
468	-LRB-	-lrb-	-LRB-	_	_	_
469	m1	m1	NN	_	_	_
470	-RRB-	-rrb-	-RRB-	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	Transcriptional	transcriptional	JJ	_	_	_
473	response	response	NN	_	_	_
474	of	of	IN	_	_	_
475	E.	e.	FW	_	_	_
476	coli	coli	FW	_	_	_
477	to	to	TO	_	_	_
478	TPEN	tpen	NN	_	_	_
479	-LRB-	-lrb-	-LRB-	_	_	_
480	m2	m2	NN	_	_	_
481	-RRB-	-rrb-	-RRB-	_	_	_
482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
483	Transcriptional	transcriptional	JJ	_	_	_
484	response	response	NN	_	_	_
485	of	of	IN	_	_	_
486	E.	e.	FW	_	_	_
487	coli	coli	FW	_	_	_
488	to	to	TO	_	_	_
489	TPEN	tpen	NN	_	_	_
490	-LRB-	-lrb-	-LRB-	_	_	_
491	m3	m3	NN	_	_	_
492	-RRB-	-rrb-	-RRB-	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	Transcriptional	transcriptional	JJ	_	_	_
495	response	response	NN	_	_	_
496	of	of	IN	_	_	_
497	E.	e.	FW	_	_	_
498	coli	coli	FW	_	_	_
499	to	to	TO	_	_	_
500	TPEN	tpen	NN	_	_	_
501	-LRB-	-lrb-	-LRB-	_	_	_
502	t1	t1	NN	_	_	_
503	-RRB-	-rrb-	-RRB-	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	Transcriptional	transcriptional	JJ	_	_	_
506	response	response	NN	_	_	_
507	of	of	IN	_	_	_
508	E.	e.	FW	_	_	_
509	coli	coli	FW	_	_	_
510	to	to	TO	_	_	_
511	TPEN	tpen	NN	_	_	_
512	-LRB-	-lrb-	-LRB-	_	_	_
513	t2	t2	NN	_	_	_
514	-RRB-	-rrb-	-RRB-	_	_	_
515	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
516	Transcriptional	transcriptional	JJ	_	_	_
517	response	response	NN	_	_	_
518	of	of	IN	_	_	_
519	E.	e.	FW	_	_	_
520	coli	coli	FW	_	_	_
521	to	to	TO	_	_	_
522	TPEN	tpen	NN	_	_	_
523	-LRB-	-lrb-	-LRB-	_	_	_
524	t3	t3	NN	_	_	_
525	-RRB-	-rrb-	-RRB-	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	transcription	transcription	NN	_	_	_
528	factor	factor	NN	_	_	_
529	:	:	:	_	_	_
530	CsiR	csir	NN	TF	_	_
531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
532	transcription	transcription	NN	_	_	_
533	factor	factor	NN	_	_	_
534	:	:	:	_	_	_
535	Nac	Nac	NNP	TF	_	_
536	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
537	transcription	transcription	NN	_	_	_
538	factor	factor	NN	_	_	_
539	:	:	:	_	_	_
540	NtrC	ntrc	NN	TF	_	_
541	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
542	transcription	transcription	NN	_	_	_
543	factor	factor	NN	_	_	_
544	:	:	:	_	_	_
545	OmpR	ompr	NN	TF	_	_
546	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
547	Transcription	transcription	NN	_	_	_
548	profiles	profile	NNS	_	_	_
549	of	of	IN	_	_	_
550	NTG-treated	ntg-treated	JJ	_	_	_
551	E.	e.	FW	_	_	_
552	coli	coli	FW	_	_	_
553	imp	imp	FW	_	_	_
554	fabI	fabi	NN	GEN	_	_
555	-LRB-	-lrb-	-LRB-	_	_	_
556	G93V	g93v	NN	_	_	_
557	-RRB-	-rrb-	-RRB-	_	_	_
558	and	and	CC	_	_	_
559	its	its	PRP$	_	_	_
560	control	control	NN	_	_	_
561	strain	strain	NN	_	_	_
562	in	in	IN	_	_	_
563	the	the	DT	_	_	_
564	absence	absence	NN	_	_	_
565	of	of	IN	_	_	_
566	triclosan	triclosan	NN	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	Transcription	transcription	NN	_	_	_
569	profiles	profile	NNS	_	_	_
570	of	of	IN	_	_	_
571	NTG-treated	ntg-treated	JJ	_	_	_
572	E.	e.	FW	_	_	_
573	coli	coli	FW	_	_	_
574	imp	imp	FW	_	_	_
575	fabI	fabi	NN	GEN	_	_
576	-LRB-	-lrb-	-LRB-	_	_	_
577	G93V	g93v	NN	_	_	_
578	-RRB-	-rrb-	-RRB-	_	_	_
579	and	and	CC	_	_	_
580	its	its	PRP$	_	_	_
581	control	control	NN	_	_	_
582	strain	strain	NN	_	_	_
583	in	in	IN	_	_	_
584	the	the	DT	_	_	_
585	presence	presence	NN	_	_	_
586	of	of	IN	_	_	_
587	triclosan	triclosan	NN	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
589	Transcriptome	transcriptome	NN	_	_	_
590	of	of	IN	_	_	_
591	cells	cell	NNS	_	_	_
592	was	be	VBD	_	_	_
593	prepared	prepare	VBN	_	_	_
594	using	use	VBG	_	_	_
595	a	a	DT	_	_	_
596	RNA	rna	NN	_	_	_
597	extraction	extraction	NN	_	_	_
598	kit	kit	NN	_	_	_
599	-LRB-	-lrb-	-LRB-	_	_	_
600	RNeasy	rneasy	NN	_	_	_
601	mini	minus	NNS	_	_	_
602	kit	kit	NN	_	_	_
603	;	;	:	_	_	_
604	Qiagen	Qiagen	NNP	_	_	_
605	,	,	,	_	_	_
606	Hilden	Hilden	NNP	_	_	_
607	,	,	,	_	_	_
608	Germany	Germany	NNP	_	_	_
609	-RRB-	-rrb-	-RRB-	_	_	_
610	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
611	Transcriptomic	transcriptomic	JJ	_	_	_
612	analyses	analysis	NNS	_	_	_
613	were	be	VBD	_	_	_
614	carried	carry	VBN	_	_	_
615	out	out	RP	_	_	_
616	after	after	IN	_	_	_
617	growing	grow	VBG	_	_	_
618	bacteria	bacterium	NNS	_	_	_
619	in	in	IN	_	_	_
620	minimal	minimal	JJ	_	_	_
621	media	media	NNS	_	_	_
622	supplemented	supplement	VBN	_	_	_
623	with	with	IN	_	_	_
624	glucose	glucose	NN	SUPP	_	_
625	.	.	.	_	_	_

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	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	NNP	_	_	_
10	Transfer	transfer	NN	_	_	_
11	700	700	CD	_	_	_
12	μl	μl	NN	_	_	_
13	lysate	lysate	NN	_	_	_
14	into	into	IN	_	_	_
15	RNeasy	RNeasy	NNP	_	_	_
16	Mini	Mini	NNP	_	_	_
17	column	column	NN	_	_	_
18	place	place	NN	_	_	_
19	in	in	IN	_	_	_
20	a	a	DT	_	_	_
21	2	2	CD	_	_	_
22	ml	ml	NN	_	_	_
23	collection	collection	NN	_	_	_
24	tube	tube	NN	_	_	_
25	and	and	CC	_	_	_
26	centrifuge	centrifuge	NN	_	_	_
27	for	for	IN	_	_	_
28	30	30	CD	_	_	_
29	s	s	NNS	_	_	_
30	at	at	IN	_	_	_
31	highest	highest	JJS	_	_	_
32	speed	speed	NN	_	_	_
33	.	.	.	_	_	_

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	transformation	transformation	NN	_	_	_
3	:	:	:	_	_	_
4	empty	empty	JJ	_	_	_
5	vector	vector	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	transformation	transformation	NN	_	_	_
8	:	:	:	_	_	_
9	pSigma70-LB	psigma70-lb	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	transformation	transformation	NN	_	_	_
12	:	:	:	_	_	_
13	pSigma70-LP	psigma70-lp	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Transform	transform	VB	_	_	_
16	the	the	DT	_	_	_
17	mapped	map	VBN	_	_	_
18	file	file	NN	_	_	_
19	format	format	NN	_	_	_
20	from	from	IN	_	_	_
21	sam	sam	NN	_	_	_
22	to	to	TO	_	_	_
23	sorted	sort	VBN	_	_	_
24	bam	bam	NN	_	_	_
25	which	which	WDT	_	_	_
26	are	be	VBP	_	_	_
27	later	later	RB	_	_	_
28	tranfered	tranfer	VBN	_	_	_
29	to	to	TO	_	_	_
30	bigWig	bigwig	NN	_	_	_
31	,	,	,	_	_	_
32	and	and	CC	_	_	_
33	separated	separate	VBN	_	_	_
34	by	by	IN	_	_	_
35	the	the	DT	_	_	_
36	strand	strand	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	plus	plus	NN	_	_	_
39	and	and	CC	_	_	_
40	minus	minus	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	transition	transition	NN	_	_	_
3	phase	phase	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Transition	transition	NN	_	_	_
6	phase	phase	NN	_	_	_
7	sample	sample	NN	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Transition	transition	NN	_	_	_
11	phase	phase	NN	_	_	_
12	sample	sample	NN	_	_	_
13	2	2	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	Transition	transition	NN	_	_	_
16	phase	phase	NN	_	_	_
17	sample	sample	NN	_	_	_
18	3	3	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Transition	transition	NN	_	_	_
21	phase	phase	NN	_	_	_
22	sample	sample	NN	_	_	_
23	4	4	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Treated	treat	VBN	_	_	_
26	experimental	experimental	JJ	_	_	_
27	sets	set	NNS	_	_	_
28	transformed	transform	VBN	_	_	_
29	with	with	IN	_	_	_
30	plasmids	plasmid	NNS	_	_	_
31	containing	contain	VBG	_	_	_
32	BCM/WT	bcm/wt	NN	_	_	_
33	rho	rho	NN	GEN	_	_
34	.	.	.	_	_	_

1	Rho	rho	NN	_	_	_
2	treated	treated	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	subjected	subject	VBN	_	_	_
5	to	to	TO	_	_	_
6	P1	p1	NN	_	_	_
7	transduction	transduction	NN	_	_	_
8	to	to	TO	_	_	_
9	delete	delete	VB	_	_	_
10	the	the	DT	_	_	_
11	genomic	genomic	JJ	_	_	_
12	counterparts	counterpart	NNS	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	gene	gene	NN	_	_	_
16	.	.	.	_	_	_

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/N340S/G324D	wt/n340s/g324d	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	subjected	subject	VBN	_	_	_
3	to	to	TO	_	_	_
4	P1	p1	NN	_	_	_
5	transduction	transduction	NN	_	_	_
6	to	to	TO	_	_	_
7	delete	delete	VB	_	_	_
8	the	the	DT	_	_	_
9	genomic	genomic	JJ	_	_	_
10	counterparts	counterpart	NNS	_	_	_
11	of	of	IN	_	_	_
12	the	the	DT	_	_	_
13	gene	gene	NN	_	_	_
14	.	.	.	_	_	_

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/G181D/R258C	wt/g181d/r258c	NN	_	_	_
10	NusA	nusa	NN	_	_	_
11	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	subjected	subject	VBN	_	_	_
3	to	to	TO	_	_	_
4	P1	p1	NN	_	_	_
5	transduction	transduction	NN	_	_	_
6	to	to	TO	_	_	_
7	delete	delete	VB	_	_	_
8	the	the	DT	_	_	_
9	genomic	genomic	JJ	_	_	_
10	counterparts	counterpart	NNS	_	_	_
11	of	of	IN	_	_	_
12	the	the	DT	_	_	_
13	respective	respective	JJ	_	_	_
14	gene	gene	NN	_	_	_
15	.	.	.	_	_	_

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	treated	treat	VBN	_	_	_
39	with	with	IN	_	_	_
40	:	:	:	_	_	_
41	0.5	0.5	CD	_	_	_
42	μg/ml	μg/ml	NN	_	_	_
43	trimethoprim	trimethoprim	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	treated	treat	VBN	_	_	_
46	with	with	IN	_	_	_
47	:	:	:	_	_	_
48	100	100	CD	_	_	_
49	µg/ml	µg/ml	JJ	_	_	_
50	BSA	bsa	NN	_	_	_
51	for	for	IN	_	_	_
52	30	30	CD	_	_	_
53	min	min	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	control	control	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	treated	treat	VBN	_	_	_
59	with	with	IN	_	_	_
60	:	:	:	_	_	_
61	100	100	CD	_	_	_
62	µg/ml	µg/ml	JJ	_	_	_
63	PGRP	pgrp	NN	_	_	_
64	for	for	IN	_	_	_
65	30	30	CD	_	_	_
66	min	min	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Treated	treat	VBN	_	_	_
69	with	with	IN	_	_	_
70	100	100	CD	_	_	_
71	uM	um	NN	_	_	_
72	KCN	kcn	NN	_	_	_
73	for	for	IN	_	_	_
74	5	5	CD	_	_	_
75	minutes	minute	NNS	_	_	_
76	before	before	IN	_	_	_
77	harvesting	harvest	VBG	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
79	treated	treat	VBN	_	_	_
80	with	with	IN	_	_	_
81	:	:	:	_	_	_
82	172mM	172mm	NN	_	_	_
83	NaCl	nacl	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	treated	treat	VBN	_	_	_
86	with	with	IN	_	_	_
87	:	:	:	_	_	_
88	172mM	172mm	NN	_	_	_
89	short	short	JJ	_	_	_
90	chain	chain	NN	_	_	_
91	fatty	fatty	JJ	_	_	_
92	acid	acid	NN	_	_	_
93	mix	mix	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Treated	treat	VBN	_	_	_
96	with	with	IN	_	_	_
97	1	1	CD	_	_	_
98	%	%	NN	_	_	_
99	vol/vol	vol/vol	NN	_	_	_
100	butanol	butanol	NN	_	_	_
101	10	10	CD	_	_	_
102	minutes	minute	NNS	_	_	_
103	prior	prior	RB	_	_	_
104	to	to	TO	_	_	_
105	harvest	harvest	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	Treated	treat	VBN	_	_	_
108	with	with	IN	_	_	_
109	1	1	CD	_	_	_
110	%	%	NN	_	_	_
111	vol/vol	vol/vol	NN	_	_	_
112	isobutanol	isobutanol	NN	_	_	_
113	10	10	CD	_	_	_
114	minutes	minute	NNS	_	_	_
115	prior	prior	RB	_	_	_
116	to	to	TO	_	_	_
117	harvest	harvest	VB	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
119	treated	treat	VBN	_	_	_
120	with	with	IN	_	_	_
121	:	:	:	_	_	_
122	20	20	CD	_	_	_
123	ug/ml	ug/ml	NN	_	_	_
124	bicyclomycin	bicyclomycin	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	treated	treat	VBN	_	_	_
127	with	with	IN	_	_	_
128	:	:	:	_	_	_
129	250	250	CD	_	_	_
130	uM	um	NN	_	_	_
131	of	of	IN	_	_	_
132	paraquat	paraquat	NN	SUPP	_	_
133	at	at	IN	_	_	_
134	mid-log	mid-log	JJ	_	_	_
135	pahse	pahse	NN	_	_	_
136	for	for	IN	_	_	_
137	20	20	CD	_	_	_
138	min	min	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	treated	treat	VBN	_	_	_
141	with	with	IN	_	_	_
142	:	:	:	_	_	_
143	250	250	CD	_	_	_
144	uM	um	NN	_	_	_
145	of	of	IN	_	_	_
146	paraquat	paraquat	NN	SUPP	_	_
147	at	at	IN	_	_	_
148	mid-log	mid-log	JJ	_	_	_
149	phase	phase	NN	_	_	_
150	for	for	IN	_	_	_
151	20	20	CD	_	_	_
152	min	min	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	treated	treat	VBN	_	_	_
155	with	with	IN	_	_	_
156	:	:	:	_	_	_
157	30mM	30mm	NN	_	_	_
158	NaCl	nacl	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	treated	treat	VBN	_	_	_
161	with	with	IN	_	_	_
162	:	:	:	_	_	_
163	30mM	30mm	NN	_	_	_
164	short	short	JJ	_	_	_
165	chain	chain	NN	_	_	_
166	fatty	fatty	JJ	_	_	_
167	acid	acid	NN	_	_	_
168	mix	mix	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	Treated	treat	VBN	_	_	_
171	with	with	IN	_	_	_
172	3	3	CD	_	_	_
173	%	%	NN	_	_	_
174	vol/vol	vol/vol	NN	_	_	_
175	ethanol	ethanol	NN	_	_	_
176	10	10	CD	_	_	_
177	minutes	minute	NNS	_	_	_
178	prior	prior	RB	_	_	_
179	to	to	TO	_	_	_
180	harvest	harvest	VB	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
182	treated	treat	VBN	_	_	_
183	with	with	IN	_	_	_
184	:	:	:	_	_	_
185	5	5	CD	_	_	_
186	µg/ml	µg/ml	NN	_	_	_
187	gentamicin	gentamicin	NN	_	_	_
188	for	for	IN	_	_	_
189	30	30	CD	_	_	_
190	min	min	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	treated	treat	VBN	_	_	_
193	with	with	IN	_	_	_
194	:	:	:	_	_	_
195	800	800	CD	_	_	_
196	µM	µm	NN	_	_	_
197	CCCP	cccp	NN	_	_	_
198	for	for	IN	_	_	_
199	15	15	CD	_	_	_
200	min	min	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	treated	treat	VBN	_	_	_
203	with	with	IN	_	_	_
204	:	:	:	_	_	_
205	none	none	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	treated	treat	VBN	_	_	_
208	with	with	IN	_	_	_
209	:	:	:	_	_	_
210	none	none	NN	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	untreated	untreated	JJ	_	_	_
213	control	control	NN	_	_	_
214	-RRB-	-rrb-	-RRB-	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	treated	treat	VBN	_	_	_
217	with	with	IN	_	_	_
218	:	:	:	_	_	_
219	Rifampicin	Rifampicin	NNP	_	_	_
220	for	for	IN	_	_	_
221	20	20	CD	_	_	_
222	minutes	minute	NNS	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	treatment	treatment	NN	_	_	_
225	:	:	:	_	_	_
226	0.025	0.025	CD	_	_	_
227	mM	mm	NN	KWSUPP	_	_
228	CspA	cspa	NN	TF	_	_
229	protein	protein	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	treatment	treatment	NN	_	_	_
232	:	:	:	_	_	_
233	0.05	0.05	CD	_	_	_
234	mM	mm	NN	KWSUPP	_	_
235	CspA	cspa	NN	TF	_	_
236	protein	protein	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	treatment	treatment	NN	_	_	_
239	:	:	:	_	_	_
240	0.1	0.1	CD	_	_	_
241	mM	mm	NN	KWSUPP	_	_
242	CspA	cspa	NN	TF	_	_
243	protein	protein	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	treatment	treatment	NN	_	_	_
246	:	:	:	_	_	_
247	0.3	0.3	CD	_	_	_
248	%	%	NN	_	_	_
249	glucose	glucose	NN	SUPP	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	treatment	treatment	NN	_	_	_
252	:	:	:	_	_	_
253	0.4	0.4	CD	_	_	_
254	%	%	NN	_	_	_
255	glucose	glucose	NN	SUPP	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	treatment	treatment	NN	_	_	_
258	:	:	:	_	_	_
259	0.5	0.5	CD	_	_	_
260	µg/ml	µg/ml	NN	_	_	_
261	Carolacton	carolacton	NN	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	treatment	treatment	NN	_	_	_
264	:	:	:	_	_	_
265	0.5	0.5	CD	_	_	_
266	mg/ml	mg/ml	NN	_	_	_
267	menadione	menadione	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	treatment	treatment	NN	_	_	_
270	:	:	:	_	_	_
271	0.5	0.5	CD	_	_	_
272	mg/ml	mg/ml	NN	_	_	_
273	serine	serine	NN	_	_	_
274	hydroxamate	hydroxamate	NN	_	_	_
275	for	for	IN	_	_	_
276	20	20	CD	_	_	_
277	min	min	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	treatment	treatment	NN	_	_	_
280	:	:	:	_	_	_
281	0.5	0.5	CD	_	_	_
282	mg/ml	mg/ml	NN	_	_	_
283	SHX	shx	NN	_	_	_
284	for	for	IN	_	_	_
285	40	40	CD	_	_	_
286	min	min	NN	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	treatment	treatment	NN	_	_	_
289	:	:	:	_	_	_
290	0.8	0.8	CD	_	_	_
291	%	%	NN	_	_	_
292	n-butanol	n-butanol	NN	_	_	_
293	was	be	VBD	_	_	_
294	added	add	VBN	_	_	_
295	at	at	IN	_	_	_
296	time	time	NN	_	_	_
297	0	0	CD	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	treatment	treatment	NN	_	_	_
300	:	:	:	_	_	_
301	0	0	CD	_	_	_
302	μg/ml	μg/ml	NN	_	_	_
303	nalidixic	nalidixic	JJ	SUPP	_	_
304	acid	acid	NN	SUPP	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	treatment	treatment	NN	_	_	_
307	:	:	:	_	_	_
308	100	100	CD	_	_	_
309	μg/ml	μg/ml	NN	_	_	_
310	nalidixic	nalidixic	JJ	SUPP	_	_
311	acid	acid	NN	SUPP	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	treatment	treatment	NN	_	_	_
314	:	:	:	_	_	_
315	10	10	CD	_	_	_
316	%	%	NN	_	_	_
317	H202	h202	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	treatment	treatment	NN	_	_	_
320	:	:	:	_	_	_
321	10	10	CD	_	_	_
322	μg/ml	μg/ml	NN	_	_	_
323	nalidixic	nalidixic	JJ	SUPP	_	_
324	acid	acid	NN	SUPP	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	treatment	treatment	NN	_	_	_
327	:	:	:	_	_	_
328	15	15	CD	_	_	_
329	min	min	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	treatment	treatment	NN	_	_	_
332	:	:	:	_	_	_
333	15	15	CD	_	_	_
334	min	min	NN	_	_	_
335	after	after	IN	_	_	_
336	induction	induction	NN	_	_	_
337	with	with	IN	_	_	_
338	arabinose	arabinose	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	treatment	treatment	NN	_	_	_
341	:	:	:	_	_	_
342	15	15	CD	_	_	_
343	min	min	NN	_	_	_
344	after	after	IN	_	_	_
345	induction	induction	NN	_	_	_
346	with	with	IN	_	_	_
347	rhamnose	rhamnose	NN	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	treatment	treatment	NN	_	_	_
350	:	:	:	_	_	_
351	1	1	CD	_	_	_
352	%	%	NN	_	_	_
353	H202	h202	NN	_	_	_
354	,	,	,	_	_	_
355	anaerobic	anaerobic	JJ	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	treatment	treatment	NN	_	_	_
358	:	:	:	_	_	_
359	1	1	CD	_	_	_
360	%	%	NN	_	_	_
361	H2O2	h2o2	NN	_	_	_
362	,	,	,	_	_	_
363	anaerobic	anaerobic	JJ	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	treatment	treatment	NN	_	_	_
366	:	:	:	_	_	_
367	1mM	1mm	NN	_	_	_
368	IPTG	iptg	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	Treatment	treatment	NN	_	_	_
371	1	1	CD	_	_	_
372	:	:	:	_	_	_
373	UA30	ua30	NN	_	_	_
374	-LRB-	-lrb-	-LRB-	_	_	_
375	EHEC	ehec	NN	_	_	_
376	86-24	86-24	CD	_	_	_
377	exposed	expose	VBN	_	_	_
378	to	to	TO	_	_	_
379	pH	ph	NN	_	_	_
380	3	3	CD	_	_	_
381	for	for	IN	_	_	_
382	30	30	CD	_	_	_
383	min	min	NN	_	_	_
384	-RRB-	-rrb-	-RRB-	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	treatment	treatment	NN	_	_	_
387	:	:	:	_	_	_
388	200	200	CD	_	_	_
389	mM	mm	NN	KWSUPP	_	_
390	glyphosate	glyphosate	NN	_	_	_
391	shock	shock	NN	_	_	_
392	for	for	IN	_	_	_
393	1	1	CD	_	_	_
394	h	h	NN	_	_	_
395	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
396	Treatment	treatment	NN	_	_	_
397	2	2	CD	_	_	_
398	:	:	:	_	_	_
399	AA30	aa30	NN	_	_	_
400	-LRB-	-lrb-	-LRB-	_	_	_
401	EHEC	ehec	NN	_	_	_
402	86-24	86-24	CD	_	_	_
403	pH	ph	NN	_	_	_
404	5.0	5.0	CD	_	_	_
405	,	,	,	_	_	_
406	followed	follow	VBN	_	_	_
407	by	by	IN	_	_	_
408	30	30	CD	_	_	_
409	min	min	NN	_	_	_
410	pH	ph	NN	_	_	_
411	3.0	3.0	CD	_	_	_
412	-RRB-	-rrb-	-RRB-	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	treatment	treatment	NN	_	_	_
415	:	:	:	_	_	_
416	2	2	CD	_	_	_
417	mM	mm	NN	KWSUPP	_	_
418	NaN3	nan3	NN	_	_	_
419	for	for	IN	_	_	_
420	10	10	CD	_	_	_
421	minutes	minute	NNS	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	treatment	treatment	NN	_	_	_
424	:	:	:	_	_	_
425	2ug/ml	2ug/ml	NN	_	_	_
426	of	of	IN	_	_	_
427	ciprofloxacin	ciprofloxacin	NN	_	_	_
428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
429	treatment	treatment	NN	_	_	_
430	:	:	:	_	_	_
431	30	30	CD	_	_	_
432	C	c	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	treatment	treatment	NN	_	_	_
435	:	:	:	_	_	_
436	30	30	CD	_	_	_
437	%	%	NN	_	_	_
438	H202	h202	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	treatment	treatment	NN	_	_	_
441	:	:	:	_	_	_
442	37	37	CD	_	_	_
443	°C	°c	NN	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	Treatment	treatment	NN	_	_	_
446	3	3	CD	_	_	_
447	:	:	:	_	_	_
448	UA15	ua15	NN	_	_	_
449	-LRB-	-lrb-	-LRB-	_	_	_
450	EHEC	ehec	NN	_	_	_
451	86-24	86-24	CD	_	_	_
452	exposed	expose	VBN	_	_	_
453	to	to	TO	_	_	_
454	pH	ph	NN	_	_	_
455	3	3	CD	_	_	_
456	for	for	IN	_	_	_
457	15	15	CD	_	_	_
458	min	min	NN	_	_	_
459	-RRB-	-rrb-	-RRB-	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	treatment	treatment	NN	_	_	_
462	:	:	:	_	_	_
463	42	42	CD	_	_	_
464	C	c	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	treatment	treatment	NN	_	_	_
467	:	:	:	_	_	_
468	4ug/ml	4ug/ml	NN	_	_	_
469	of	of	IN	_	_	_
470	ciprofloxacin	ciprofloxacin	NN	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	treatment	treatment	NN	_	_	_
473	:	:	:	_	_	_
474	50	50	CD	_	_	_
475	°C	°c	NN	_	_	_
476	heatshock	heatshock	NN	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	treatment	treatment	NN	_	_	_
479	:	:	:	_	_	_
480	5	5	CD	_	_	_
481	percent	percent	NN	_	_	_
482	isooctane	isooctane	NN	_	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
484	treatment	treatment	NN	_	_	_
485	:	:	:	_	_	_
486	60	60	CD	_	_	_
487	min	min	NN	_	_	_
488	after	after	IN	_	_	_
489	induction	induction	NN	_	_	_
490	with	with	IN	_	_	_
491	arabinose	arabinose	NN	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
493	treatment	treatment	NN	_	_	_
494	:	:	:	_	_	_
495	60	60	CD	_	_	_
496	min	min	NN	_	_	_
497	after	after	IN	_	_	_
498	induction	induction	NN	_	_	_
499	with	with	IN	_	_	_
500	rhamnose	rhamnose	NN	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	treatment	treatment	NN	_	_	_
503	:	:	:	_	_	_
504	After	after	IN	_	_	_
505	10	10	CD	_	_	_
506	mg/mL	mg/ml	NN	_	_	_
507	kasugamycin	kasugamycin	NN	_	_	_
508	treatment	treatment	NN	_	_	_
509	for	for	IN	_	_	_
510	40	40	CD	_	_	_
511	min	min	NN	_	_	_
512	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
513	treatment	treatment	NN	_	_	_
514	:	:	:	_	_	_
515	After	after	IN	_	_	_
516	250	250	CD	_	_	_
517	µg/mL	µg/ml	NN	_	_	_
518	rifampicin	rifampicin	NN	SUPP	_	_
519	treatment	treatment	NN	_	_	_
520	for	for	IN	_	_	_
521	2	2	CD	_	_	_
522	hr	hr	NN	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	treatment	treatment	NN	_	_	_
525	:	:	:	_	_	_
526	ampicillin	ampicillin	NN	_	_	_
527	-LRB-	-lrb-	-LRB-	_	_	_
528	50	50	CD	_	_	_
529	µg/mL	µg/ml	NN	_	_	_
530	final	final	JJ	_	_	_
531	concentration	concentration	NN	_	_	_
532	-RRB-	-rrb-	-RRB-	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	Treatment	treatment	NN	_	_	_
535	A	a	NN	_	_	_
536	Population	Population	NNP	_	_	_
537	1	1	CD	_	_	_
538	Colony	Colony	NNP	_	_	_
539	a	a	DT	_	_	_
540	replica	replica	NN	_	_	_
541	1	1	CD	_	_	_
542	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
543	Treatment	treatment	NN	_	_	_
544	A	a	DT	_	_	_
545	Population	Population	NNP	_	_	_
546	1	1	CD	_	_	_
547	Colony	Colony	NNP	_	_	_
548	a	a	DT	_	_	_
549	replica	replica	NN	_	_	_
550	2	2	CD	_	_	_
551	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
552	Treatment	treatment	NN	_	_	_
553	A	a	DT	_	_	_
554	Population	Population	NNP	_	_	_
555	1	1	CD	_	_	_
556	Colony	Colony	NNP	_	_	_
557	b	b	NN	_	_	_
558	replica	replica	NN	_	_	_
559	1	1	CD	_	_	_
560	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
561	Treatment	treatment	NN	_	_	_
562	A	a	DT	_	_	_
563	Population	Population	NNP	_	_	_
564	1	1	CD	_	_	_
565	Colony	Colony	NNP	_	_	_
566	b	b	NN	_	_	_
567	replica	replica	NN	_	_	_
568	2	2	CD	_	_	_
569	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
570	Treatment	treatment	NN	_	_	_
571	A	a	DT	_	_	_
572	Population	Population	NNP	_	_	_
573	1	1	CD	_	_	_
574	Colony	Colony	NNP	_	_	_
575	c	c	NN	_	_	_
576	replica	replica	NN	_	_	_
577	1	1	CD	_	_	_
578	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
579	Treatment	treatment	NN	_	_	_
580	A	a	DT	_	_	_
581	Population	Population	NNP	_	_	_
582	1	1	CD	_	_	_
583	Colony	Colony	NNP	_	_	_
584	c	c	NN	_	_	_
585	replica	replica	NN	_	_	_
586	2	2	CD	_	_	_
587	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
588	Treatment	treatment	NN	_	_	_
589	A	a	DT	_	_	_
590	Population	Population	NNP	_	_	_
591	2	2	CD	_	_	_
592	Colony	Colony	NNP	_	_	_
593	a	a	DT	_	_	_
594	replica	replica	NN	_	_	_
595	1	1	CD	_	_	_
596	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
597	Treatment	treatment	NN	_	_	_
598	A	a	DT	_	_	_
599	Population	Population	NNP	_	_	_
600	2	2	CD	_	_	_
601	Colony	Colony	NNP	_	_	_
602	a	a	DT	_	_	_
603	replica	replica	NN	_	_	_
604	2	2	CD	_	_	_
605	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
606	Treatment	treatment	NN	_	_	_
607	A	a	DT	_	_	_
608	Population	Population	NNP	_	_	_
609	2	2	CD	_	_	_
610	Colony	Colony	NNP	_	_	_
611	b	b	NN	_	_	_
612	replica	replica	NN	_	_	_
613	1	1	CD	_	_	_
614	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
615	Treatment	treatment	NN	_	_	_
616	A	a	DT	_	_	_
617	Population	Population	NNP	_	_	_
618	2	2	CD	_	_	_
619	Colony	Colony	NNP	_	_	_
620	b	b	NN	_	_	_
621	replica	replica	NN	_	_	_
622	2	2	CD	_	_	_
623	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
624	Treatment	treatment	NN	_	_	_
625	A	a	DT	_	_	_
626	Population	Population	NNP	_	_	_
627	2	2	CD	_	_	_
628	Colony	Colony	NNP	_	_	_
629	c	c	NN	_	_	_
630	replica	replica	NN	_	_	_
631	1	1	CD	_	_	_
632	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
633	Treatment	treatment	NN	_	_	_
634	A	a	DT	_	_	_
635	Population	Population	NNP	_	_	_
636	2	2	CD	_	_	_
637	Colony	Colony	NNP	_	_	_
638	c	c	NN	_	_	_
639	replica	replica	NN	_	_	_
640	2	2	CD	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
642	treatment	treatment	NN	_	_	_
643	:	:	:	_	_	_
644	Bacillus	bacillus	NN	_	_	_
645	volatile	volatile	JJ	_	_	_
646	organic	organic	JJ	_	_	_
647	compounds	compound	NNS	_	_	_
648	-LRB-	-lrb-	-LRB-	_	_	_
649	VOCs	voc	NNS	_	_	_
650	-RRB-	-rrb-	-RRB-	_	_	_
651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
652	treatment	treatment	NN	_	_	_
653	:	:	:	_	_	_
654	batch	batch	NN	_	_	_
655	growth	growth	NN	_	_	_
656	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
657	treatment	treatment	NN	_	_	_
658	:	:	:	_	_	_
659	BCM	BCM	NNP	_	_	_
660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
661	treatment	treatment	NN	_	_	_
662	:	:	:	_	_	_
663	Before	before	IN	_	_	_
664	rifampicin	rifampicin	NN	SUPP	_	_
665	treatment	treatment	NN	_	_	_
666	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
667	treatment	treatment	NN	_	_	_
668	:	:	:	_	_	_
669	bicontinious	bicontinious	JJ	_	_	_
670	microemulsion	microemulsion	NN	_	_	_
671	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
672	Treatment	treatment	NN	_	_	_
673	B	b	NN	_	_	_
674	Population	Population	NNP	_	_	_
675	3	3	CD	_	_	_
676	Colony	Colony	NNP	_	_	_
677	a	a	DT	_	_	_
678	replica	replica	NN	_	_	_
679	1	1	CD	_	_	_
680	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
681	Treatment	treatment	NN	_	_	_
682	B	b	NN	_	_	_
683	Population	Population	NNP	_	_	_
684	3	3	CD	_	_	_
685	Colony	Colony	NNP	_	_	_
686	a	a	DT	_	_	_
687	replica	replica	NN	_	_	_
688	2	2	CD	_	_	_
689	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
690	Treatment	treatment	NN	_	_	_
691	B	b	NN	_	_	_
692	Population	Population	NNP	_	_	_
693	3	3	CD	_	_	_
694	Colony	Colony	NNP	_	_	_
695	b	b	NN	_	_	_
696	replica	replica	NN	_	_	_
697	1	1	CD	_	_	_
698	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
699	Treatment	treatment	NN	_	_	_
700	B	b	NN	_	_	_
701	Population	Population	NNP	_	_	_
702	3	3	CD	_	_	_
703	Colony	Colony	NNP	_	_	_
704	b	b	NN	_	_	_
705	replica	replica	NN	_	_	_
706	2	2	CD	_	_	_
707	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
708	Treatment	treatment	NN	_	_	_
709	B	b	NN	_	_	_
710	Population	Population	NNP	_	_	_
711	3	3	CD	_	_	_
712	Colony	Colony	NNP	_	_	_
713	c	c	NN	_	_	_
714	replica	replica	NN	_	_	_
715	1	1	CD	_	_	_
716	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
717	Treatment	treatment	NN	_	_	_
718	B	b	NN	_	_	_
719	Population	Population	NNP	_	_	_
720	3	3	CD	_	_	_
721	Colony	Colony	NNP	_	_	_
722	c	c	NN	_	_	_
723	replica	replica	NN	_	_	_
724	2	2	CD	_	_	_
725	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
726	Treatment	treatment	NN	_	_	_
727	B	b	NN	_	_	_
728	Population	Population	NNP	_	_	_
729	4	4	CD	_	_	_
730	Colony	Colony	NNP	_	_	_
731	a	a	DT	_	_	_
732	replica	replica	NN	_	_	_
733	1	1	CD	_	_	_
734	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
735	Treatment	treatment	NN	_	_	_
736	B	b	NN	_	_	_
737	Population	Population	NNP	_	_	_
738	4	4	CD	_	_	_
739	Colony	Colony	NNP	_	_	_
740	a	a	DT	_	_	_
741	replica	replica	NN	_	_	_
742	2	2	CD	_	_	_
743	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
744	Treatment	treatment	NN	_	_	_
745	B	b	NN	_	_	_
746	Population	Population	NNP	_	_	_
747	4	4	CD	_	_	_
748	Colony	Colony	NNP	_	_	_
749	b	b	NN	_	_	_
750	replica	replica	NN	_	_	_
751	1	1	CD	_	_	_
752	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
753	Treatment	treatment	NN	_	_	_
754	B	b	NN	_	_	_
755	Population	Population	NNP	_	_	_
756	4	4	CD	_	_	_
757	Colony	Colony	NNP	_	_	_
758	b	b	NN	_	_	_
759	replica	replica	NN	_	_	_
760	2	2	CD	_	_	_
761	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
762	Treatment	treatment	NN	_	_	_
763	B	b	NN	_	_	_
764	Population	Population	NNP	_	_	_
765	4	4	CD	_	_	_
766	Colony	Colony	NNP	_	_	_
767	c	c	NN	_	_	_
768	replica	replica	NN	_	_	_
769	1	1	CD	_	_	_
770	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
771	Treatment	treatment	NN	_	_	_
772	B	b	NN	_	_	_
773	Population	Population	NNP	_	_	_
774	4	4	CD	_	_	_
775	Colony	Colony	NNP	_	_	_
776	c	c	NN	_	_	_
777	replica	replica	NN	_	_	_
778	2	2	CD	_	_	_
779	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
780	Treatment	treatment	NN	_	_	_
781	B	b	NN	_	_	_
782	Population	Population	NNP	_	_	_
783	5	5	CD	_	_	_
784	Colony	Colony	NNP	_	_	_
785	a	a	DT	_	_	_
786	replica	replica	NN	_	_	_
787	1	1	CD	_	_	_
788	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
789	Treatment	treatment	NN	_	_	_
790	B	b	NN	_	_	_
791	Population	Population	NNP	_	_	_
792	5	5	CD	_	_	_
793	Colony	Colony	NNP	_	_	_
794	a	a	DT	_	_	_
795	replica	replica	NN	_	_	_
796	2	2	CD	_	_	_
797	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
798	Treatment	treatment	NN	_	_	_
799	B	b	NN	_	_	_
800	Population	Population	NNP	_	_	_
801	5	5	CD	_	_	_
802	Colony	Colony	NNP	_	_	_
803	b	b	NN	_	_	_
804	replica	replica	NN	_	_	_
805	1	1	CD	_	_	_
806	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
807	Treatment	treatment	NN	_	_	_
808	B	b	NN	_	_	_
809	Population	Population	NNP	_	_	_
810	5	5	CD	_	_	_
811	Colony	Colony	NNP	_	_	_
812	b	b	NN	_	_	_
813	replica	replica	NN	_	_	_
814	2	2	CD	_	_	_
815	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
816	Treatment	treatment	NN	_	_	_
817	B	b	NN	_	_	_
818	Population	Population	NNP	_	_	_
819	5	5	CD	_	_	_
820	Colony	Colony	NNP	_	_	_
821	c	c	NN	_	_	_
822	replica	replica	NN	_	_	_
823	1	1	CD	_	_	_
824	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
825	Treatment	treatment	NN	_	_	_
826	B	b	NN	_	_	_
827	Population	Population	NNP	_	_	_
828	5	5	CD	_	_	_
829	Colony	Colony	NNP	_	_	_
830	c	c	NN	_	_	_
831	replica	replica	NN	_	_	_
832	2	2	CD	_	_	_
833	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
834	treatment	treatment	NN	_	_	_
835	:	:	:	_	_	_
836	Carbon	Carbon	NNP	_	_	_
837	starvation	starvation	NN	_	_	_
838	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
839	treatment	treatment	NN	_	_	_
840	:	:	:	_	_	_
841	chemostat	chemostat	NN	_	_	_
842	growth	growth	NN	_	_	_
843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
844	treatment	treatment	NN	_	_	_
845	:	:	:	_	_	_
846	ciprofloxacin	ciprofloxacin	NN	_	_	_
847	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
848	treatment	treatment	NN	_	_	_
849	:	:	:	_	_	_
850	clindamycin	clindamycin	NN	_	_	_
851	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
852	treatment	treatment	NN	_	_	_
853	:	:	:	_	_	_
854	Cold	Cold	NNP	_	_	_
855	Shock	shock	NN	_	_	_
856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
857	treatment	treatment	NN	_	_	_
858	:	:	:	_	_	_
859	Con1	con1	NN	_	_	_
860	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
861	treatment	treatment	NN	_	_	_
862	:	:	:	_	_	_
863	Con2	con2	NN	_	_	_
864	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
865	treatment	treatment	NN	_	_	_
866	:	:	:	_	_	_
867	Con3	con3	NN	_	_	_
868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
869	treatment	treatment	NN	_	_	_
870	:	:	:	_	_	_
871	Continuous	continuous	JJ	_	_	_
872	aerobically	aerobically	RB	_	_	_
873	grown	grow	VBN	_	_	_
874	cultures	culture	NNS	_	_	_
875	in	in	IN	_	_	_
876	Evans	Evans	NNP	_	_	_
877	medium	medium	NN	_	_	_
878	,	,	,	_	_	_
879	exposed	expose	VBN	_	_	_
880	to	to	TO	_	_	_
881	0.1	0.1	CD	_	_	_
882	L/min	l/min	NN	_	_	_
883	CO	co	NN	_	_	_
884	gas	gas	NN	_	_	_
885	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
886	treatment	treatment	NN	_	_	_
887	:	:	:	_	_	_
888	Continuous	continuous	JJ	_	_	_
889	aerobically	aerobically	RB	_	_	_
890	grown	grow	VBN	_	_	_
891	cultures	culture	NNS	_	_	_
892	in	in	IN	_	_	_
893	Evans	Evans	NNP	_	_	_
894	medium	medium	NN	_	_	_
895	,	,	,	_	_	_
896	exposed	expose	VBN	_	_	_
897	to	to	TO	_	_	_
898	40uM	40um	NN	_	_	_
899	CORM-3	corm-3	NN	_	_	_
900	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
901	treatment	treatment	NN	_	_	_
902	:	:	:	_	_	_
903	Continuous	continuous	JJ	_	_	_
904	aerobically	aerobically	RB	_	_	_
905	grown	grow	VBN	_	_	_
906	cultures	culture	NNS	_	_	_
907	in	in	IN	_	_	_
908	Evans	Evans	NNP	_	_	_
909	medium	medium	NN	_	_	_
910	,	,	,	_	_	_
911	exposed	expose	VBN	_	_	_
912	to	to	TO	_	_	_
913	40uM	40um	NN	_	_	_
914	iCORM-3	icorm-3	NN	_	_	_
915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
916	treatment	treatment	NN	_	_	_
917	:	:	:	_	_	_
918	Continuous	continuous	JJ	_	_	_
919	anaerobically	anaerobically	RB	_	_	_
920	grown	grow	VBN	_	_	_
921	cultures	culture	NNS	_	_	_
922	in	in	IN	_	_	_
923	Evans	Evans	NNP	_	_	_
924	medium	medium	NN	_	_	_
925	,	,	,	_	_	_
926	exposed	expose	VBN	_	_	_
927	to	to	TO	_	_	_
928	40uM	40um	NN	_	_	_
929	CORM-3	corm-3	NN	_	_	_
930	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
931	treatment	treatment	NN	_	_	_
932	:	:	:	_	_	_
933	Continuous	continuous	JJ	_	_	_
934	anaerobically	anaerobically	RB	_	_	_
935	grown	grow	VBN	_	_	_
936	cultures	culture	NNS	_	_	_
937	in	in	IN	_	_	_
938	Evans	Evans	NNP	_	_	_
939	medium	medium	NN	_	_	_
940	,	,	,	_	_	_
941	exposed	expose	VBN	_	_	_
942	to	to	TO	_	_	_
943	CO	CO	NNP	_	_	_
944	gas	gas	NN	_	_	_
945	at	at	IN	_	_	_
946	0.1	0.1	CD	_	_	_
947	L/min	l/min	NN	_	_	_
948	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
949	treatment	treatment	NN	_	_	_
950	:	:	:	_	_	_
951	control	control	NN	_	_	_
952	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
953	treatment	treatment	NN	_	_	_
954	:	:	:	_	_	_
955	control	control	NN	_	_	_
956	,	,	,	_	_	_
957	anaerobic	anaerobic	JJ	_	_	_
958	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
959	Treatment	treatment	NN	_	_	_
960	C	c	NN	_	_	_
961	Population	Population	NNP	_	_	_
962	6	6	CD	_	_	_
963	Colony	Colony	NNP	_	_	_
964	b	b	NN	_	_	_
965	replica	replica	NN	_	_	_
966	1	1	CD	_	_	_
967	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
968	Treatment	treatment	NN	_	_	_
969	C	c	NN	_	_	_
970	Population	Population	NNP	_	_	_
971	6	6	CD	_	_	_
972	Colony	Colony	NNP	_	_	_
973	b	b	NN	_	_	_
974	replica	replica	NN	_	_	_
975	2	2	CD	_	_	_
976	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
977	Treatment	treatment	NN	_	_	_
978	C	c	NN	_	_	_
979	Population	Population	NNP	_	_	_
980	6	6	CD	_	_	_
981	Colony	Colony	NNP	_	_	_
982	c	c	NN	_	_	_
983	replica	replica	NN	_	_	_
984	1	1	CD	_	_	_
985	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
986	Treatment	treatment	NN	_	_	_
987	C	c	NN	_	_	_
988	Population	Population	NNP	_	_	_
989	6	6	CD	_	_	_
990	Colony	Colony	NNP	_	_	_
991	c	c	NN	_	_	_
992	replica	replica	NN	_	_	_
993	2	2	CD	_	_	_
994	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
995	Treatment	treatment	NN	_	_	_
996	C	c	NN	_	_	_
997	Population	Population	NNP	_	_	_
998	7	7	CD	_	_	_
999	Colony	Colony	NNP	_	_	_
1000	b	b	NN	_	_	_
1001	replica	replica	NN	_	_	_
1002	1	1	CD	_	_	_
1003	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1004	Treatment	treatment	NN	_	_	_
1005	C	c	NN	_	_	_
1006	Population	Population	NNP	_	_	_
1007	7	7	CD	_	_	_
1008	Colony	Colony	NNP	_	_	_
1009	b	b	NN	_	_	_
1010	replica	replica	NN	_	_	_
1011	2	2	CD	_	_	_
1012	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1013	Treatment	treatment	NN	_	_	_
1014	C	c	NN	_	_	_
1015	Population	Population	NNP	_	_	_
1016	7	7	CD	_	_	_
1017	Colony	Colony	NNP	_	_	_
1018	c	c	NN	_	_	_
1019	replica	replica	NN	_	_	_
1020	1	1	CD	_	_	_
1021	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1022	Treatment	treatment	NN	_	_	_
1023	C	c	NN	_	_	_
1024	Population	Population	NNP	_	_	_
1025	7	7	CD	_	_	_
1026	Colony	Colony	NNP	_	_	_
1027	c	c	NN	_	_	_
1028	replica	replica	NN	_	_	_
1029	2	2	CD	_	_	_
1030	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1031	treatment	treatment	NN	_	_	_
1032	:	:	:	_	_	_
1033	DpnI	dpni	NN	_	_	_
1034	digested	digest	VBD	_	_	_
1035	DNA	dna	NN	_	_	_
1036	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1037	treatment	treatment	NN	_	_	_
1038	duration	duration	NN	_	_	_
1039	:	:	:	_	_	_
1040	10	10	CD	_	_	_
1041	min	min	NN	_	_	_
1042	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1043	treatment	treatment	NN	_	_	_
1044	duration	duration	NN	_	_	_
1045	:	:	:	_	_	_
1046	15	15	CD	_	_	_
1047	h	h	NN	_	_	_
1048	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1049	treatment	treatment	NN	_	_	_
1050	duration	duration	NN	_	_	_
1051	:	:	:	_	_	_
1052	2.5	2.5	CD	_	_	_
1053	h	h	NN	_	_	_
1054	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1055	treatment	treatment	NN	_	_	_
1056	duration	duration	NN	_	_	_
1057	:	:	:	_	_	_
1058	8	8	CD	_	_	_
1059	min	min	NN	_	_	_
1060	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1061	treatment	treatment	NN	_	_	_
1062	duration	duration	NN	_	_	_
1063	:	:	:	_	_	_
1064	none	none	NN	_	_	_
1065	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1066	treatment	treatment	NN	_	_	_
1067	:	:	:	_	_	_
1068	erythromycin	erythromycin	NN	_	_	_
1069	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1070	treatment	treatment	NN	_	_	_
1071	:	:	:	_	_	_
1072	exposed	expose	VBN	_	_	_
1073	to	to	TO	_	_	_
1074	100uM	100um	VB	_	_	_
1075	CORM-3	corm-3	NN	_	_	_
1076	for	for	IN	_	_	_
1077	10	10	CD	_	_	_
1078	min	min	NN	_	_	_
1079	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1080	treatment	treatment	NN	_	_	_
1081	:	:	:	_	_	_
1082	exposed	expose	VBN	_	_	_
1083	to	to	TO	_	_	_
1084	100uM	100um	VB	_	_	_
1085	CORM-3	corm-3	NN	_	_	_
1086	for	for	IN	_	_	_
1087	120	120	CD	_	_	_
1088	min	min	NN	_	_	_
1089	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1090	treatment	treatment	NN	_	_	_
1091	:	:	:	_	_	_
1092	exposed	expose	VBN	_	_	_
1093	to	to	TO	_	_	_
1094	100uM	100um	VB	_	_	_
1095	CORM-3	corm-3	NN	_	_	_
1096	for	for	IN	_	_	_
1097	20	20	CD	_	_	_
1098	min	min	NN	_	_	_
1099	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1100	treatment	treatment	NN	_	_	_
1101	:	:	:	_	_	_
1102	exposed	expose	VBN	_	_	_
1103	to	to	TO	_	_	_
1104	100uM	100um	VB	_	_	_
1105	CORM-3	corm-3	NN	_	_	_
1106	for	for	IN	_	_	_
1107	40	40	CD	_	_	_
1108	min	min	NN	_	_	_
1109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1110	treatment	treatment	NN	_	_	_
1111	:	:	:	_	_	_
1112	exposed	expose	VBN	_	_	_
1113	to	to	TO	_	_	_
1114	100uM	100um	VB	_	_	_
1115	CORM-3	corm-3	NN	_	_	_
1116	for	for	IN	_	_	_
1117	60	60	CD	_	_	_
1118	min	min	NN	_	_	_
1119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1120	treatment	treatment	NN	_	_	_
1121	:	:	:	_	_	_
1122	exposed	expose	VBN	_	_	_
1123	to	to	TO	_	_	_
1124	100uM	100um	VB	_	_	_
1125	iCORM-3	icorm-3	NN	_	_	_
1126	for	for	IN	_	_	_
1127	10	10	CD	_	_	_
1128	min	min	NN	_	_	_
1129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1130	treatment	treatment	NN	_	_	_
1131	:	:	:	_	_	_
1132	exposed	expose	VBN	_	_	_
1133	to	to	TO	_	_	_
1134	100uM	100um	VB	_	_	_
1135	iCORM-3	icorm-3	NN	_	_	_
1136	for	for	IN	_	_	_
1137	120	120	CD	_	_	_
1138	min	min	NN	_	_	_
1139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1140	treatment	treatment	NN	_	_	_
1141	:	:	:	_	_	_
1142	exposed	expose	VBN	_	_	_
1143	to	to	TO	_	_	_
1144	100uM	100um	VB	_	_	_
1145	iCORM-3	icorm-3	NN	_	_	_
1146	for	for	IN	_	_	_
1147	20	20	CD	_	_	_
1148	min	min	NN	_	_	_
1149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1150	treatment	treatment	NN	_	_	_
1151	:	:	:	_	_	_
1152	exposed	expose	VBN	_	_	_
1153	to	to	TO	_	_	_
1154	100uM	100um	VB	_	_	_
1155	iCORM-3	icorm-3	NN	_	_	_
1156	for	for	IN	_	_	_
1157	40	40	CD	_	_	_
1158	min	min	NN	_	_	_
1159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1160	treatment	treatment	NN	_	_	_
1161	:	:	:	_	_	_
1162	exposed	expose	VBN	_	_	_
1163	to	to	TO	_	_	_
1164	100uM	100um	VB	_	_	_
1165	iCORM-3	icorm-3	NN	_	_	_
1166	for	for	IN	_	_	_
1167	60	60	CD	_	_	_
1168	min	min	NN	_	_	_
1169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1170	treatment	treatment	NN	_	_	_
1171	:	:	:	_	_	_
1172	exposed	expose	VBN	_	_	_
1173	to	to	TO	_	_	_
1174	the	the	DT	_	_	_
1175	lettuce	lettuce	NN	_	_	_
1176	rhizosphere	rhizosphere	NN	_	_	_
1177	for	for	IN	_	_	_
1178	3	3	CD	_	_	_
1179	days	day	NNS	_	_	_
1180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1181	treatment	treatment	NN	_	_	_
1182	:	:	:	_	_	_
1183	florfenicol	florfenicol	NN	_	_	_
1184	-LRB-	-lrb-	-LRB-	_	_	_
1185	30	30	CD	_	_	_
1186	µg/mL	µg/ml	NN	_	_	_
1187	final	final	JJ	_	_	_
1188	concentration	concentration	NN	_	_	_
1189	-RRB-	-rrb-	-RRB-	_	_	_
1190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1191	treatment	treatment	NN	_	_	_
1192	:	:	:	_	_	_
1193	glucose	glucose	NN	SUPP	_	_
1194	-LRB-	-lrb-	-LRB-	_	_	_
1195	2	2	CD	_	_	_
1196	g/L	g/l	NN	_	_	_
1197	-RRB-	-rrb-	-RRB-	_	_	_
1198	minimal	minimal	JJ	_	_	_
1199	M9	m9	NN	_	_	_
1200	medium	medium	NN	_	_	_
1201	supplemented	supplement	VBN	_	_	_
1202	with	with	IN	_	_	_
1203	10	10	CD	_	_	_
1204	mM	mm	NN	KWSUPP	_	_
1205	leucine	leucine	NN	SUPP	_	_
1206	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	glucose	glucose	NN	SUPP	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2	2	CD	_	_	_
7	g/L	g/l	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	minimal	minimal	JJ	_	_	_
10	M9	m9	NN	_	_	_
11	medium	medium	NN	_	_	_
12	supplemented	supplement	VBN	_	_	_
13	with	with	IN	_	_	_
14	20	20	CD	_	_	_
15	mg/L	mg/l	NN	_	_	_
16	tryptophan	tryptophan	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	glucose	glucose	NN	SUPP	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2	2	CD	_	_	_
7	g/L	g/l	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	minimal	minimal	JJ	_	_	_
10	M9	m9	NN	_	_	_
11	medium	medium	NN	_	_	_
12	supplemented	supplement	VBN	_	_	_
13	without	without	IN	_	_	_
14	10	10	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	leucine	leucine	NN	SUPP	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	glucose	glucose	NN	SUPP	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2	2	CD	_	_	_
7	g/L	g/l	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	minimal	minimal	JJ	_	_	_
10	M9	m9	NN	_	_	_
11	medium	medium	NN	_	_	_
12	supplemented	supplement	VBN	_	_	_
13	without	without	IN	_	_	_
14	20	20	CD	_	_	_
15	mg/L	mg/l	NN	_	_	_
16	tryptophan	tryptophan	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	glucose	glucose	NN	SUPP	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2	2	CD	_	_	_
7	g/L	g/l	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	minimal	minimal	JJ	_	_	_
10	W2	w2	NN	_	_	_
11	medium	medium	NN	_	_	_
12	supplemented	supplement	VBN	_	_	_
13	with	with	IN	_	_	_
14	1g/L	1g/l	NN	_	_	_
15	arginine	arginine	NN	SUPP	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	glucose	glucose	NN	SUPP	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2	2	CD	_	_	_
7	g/L	g/l	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	minimal	minimal	JJ	_	_	_
10	W2	w2	NN	_	_	_
11	medium	medium	NN	_	_	_
12	supplemented	supplement	VBN	_	_	_
13	with	with	IN	_	_	_
14	2g/L	2g/l	NN	_	_	_
15	glutamine	glutamine	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	glutamine	glutamine	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	group	group	NN	_	_	_
8	:	:	:	_	_	_
9	cold	cold	JJ	_	_	_
10	stress	stress	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	treatment	treatment	NN	_	_	_
13	group	group	NN	_	_	_
14	:	:	:	_	_	_
15	control	control	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	treatment	treatment	NN	_	_	_
18	group	group	NN	_	_	_
19	:	:	:	_	_	_
20	heat	heat	NN	_	_	_
21	stress	stress	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	treatment	treatment	NN	_	_	_
24	group	group	NN	_	_	_
25	:	:	:	_	_	_
26	indole	indole	NN	_	_	_
27	treated	treat	VBN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	treatment	treatment	NN	_	_	_
30	group	group	NN	_	_	_
31	:	:	:	_	_	_
32	lactose	lactose	NN	_	_	_
33	shift	shift	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	treatment	treatment	NN	_	_	_
36	group	group	NN	_	_	_
37	:	:	:	_	_	_
38	oxidative	oxidative	JJ	_	_	_
39	stress	stress	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	treatment	treatment	NN	_	_	_
42	group	group	NN	_	_	_
43	:	:	:	_	_	_
44	rifampicin	rifampicin	NN	SUPP	_	_
45	time	time	NN	_	_	_
46	point	point	NN	_	_	_
47	0	0	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	treatment	treatment	NN	_	_	_
50	group	group	NN	_	_	_
51	:	:	:	_	_	_
52	rifampicin	rifampicin	NN	SUPP	_	_
53	time	time	NN	_	_	_
54	point	point	NN	_	_	_
55	2	2	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	treatment	treatment	NN	_	_	_
58	group	group	NN	_	_	_
59	:	:	:	_	_	_
60	rifampicin	rifampicin	NN	SUPP	_	_
61	time	time	NN	_	_	_
62	point	point	NN	_	_	_
63	4	4	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	treatment	treatment	NN	_	_	_
66	group	group	NN	_	_	_
67	:	:	:	_	_	_
68	rifampicin	rifampicin	NN	SUPP	_	_
69	time	time	NN	_	_	_
70	point	point	NN	_	_	_
71	6	6	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	treatment	treatment	NN	_	_	_
74	group	group	NN	_	_	_
75	:	:	:	_	_	_
76	rifampicin	rifampicin	NN	SUPP	_	_
77	time	time	NN	_	_	_
78	point	point	NN	_	_	_
79	8	8	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	treatment	treatment	NN	_	_	_
82	:	:	:	_	_	_
83	grown	grow	VBN	_	_	_
84	in	in	IN	_	_	_
85	lettuce	lettuce	NN	_	_	_
86	rhizosphere	rhizosphere	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	treatment	treatment	NN	_	_	_
89	:	:	:	_	_	_
90	grown	grow	VBN	_	_	_
91	without	without	IN	_	_	_
92	lettuce	lettuce	NN	_	_	_
93	rhizosphere	rhizosphere	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	treatment	treatment	NN	_	_	_
96	:	:	:	_	_	_
97	heat	heat	NN	_	_	_
98	shock	shock	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	treatment	treatment	NN	_	_	_
101	:	:	:	_	_	_
102	Heat	Heat	NNP	_	_	_
103	Shock	shock	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	treatment	treatment	NN	_	_	_
106	:	:	:	_	_	_
107	induced	induce	VBN	_	_	_
108	DNA	dna	NN	_	_	_
109	double	double	JJ	_	_	_
110	strand	strand	NN	_	_	_
111	break	break	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	treatment	treatment	NN	_	_	_
114	:	:	:	_	_	_
115	log	log	NN	_	_	_
116	phase	phase	NN	_	_	_
117	sample	sample	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	treatment	treatment	NN	_	_	_
120	:	:	:	_	_	_
121	Low	low	JJ	_	_	_
122	pH	ph	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	treatment	treatment	NN	_	_	_
125	:	:	:	_	_	_
126	MG1655	mg1655	NN	_	_	_
127	+	+	CC	_	_	_
128	3µM	3µm	NN	_	_	_
129	HgCl2	hgcl2	NN	_	_	_
130	at	at	IN	_	_	_
131	t10	t10	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	treatment	treatment	NN	_	_	_
134	:	:	:	_	_	_
135	MG1655	mg1655	NN	_	_	_
136	+	+	CC	_	_	_
137	3µM	3µm	NN	_	_	_
138	HgCl2	hgcl2	NN	_	_	_
139	at	at	IN	_	_	_
140	t30	t30	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	treatment	treatment	NN	_	_	_
143	:	:	:	_	_	_
144	MG1655	mg1655	NN	_	_	_
145	+	+	CC	_	_	_
146	3µM	3µm	NN	_	_	_
147	HgCl2	hgcl2	NN	_	_	_
148	at	at	IN	_	_	_
149	t60	t60	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	treatment	treatment	NN	_	_	_
152	:	:	:	_	_	_
153	MG1655	mg1655	NN	_	_	_
154	+	+	CC	_	_	_
155	3µM	3µm	NN	_	_	_
156	PMA	pma	NN	_	_	_
157	at	at	IN	_	_	_
158	t10	t10	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	treatment	treatment	NN	_	_	_
161	:	:	:	_	_	_
162	MG1655	mg1655	NN	_	_	_
163	+	+	CC	_	_	_
164	3µM	3µm	NN	_	_	_
165	PMA	pma	NN	_	_	_
166	at	at	IN	_	_	_
167	t30	t30	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	treatment	treatment	NN	_	_	_
170	:	:	:	_	_	_
171	MG1655	mg1655	NN	_	_	_
172	+	+	CC	_	_	_
173	3µM	3µm	NN	_	_	_
174	PMA	pma	NN	_	_	_
175	at	at	IN	_	_	_
176	t60	t60	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	treatment	treatment	NN	_	_	_
179	:	:	:	_	_	_
180	MG1655	mg1655	SYM	_	_	_
181	-	-	:	_	_	_
182	unexposed	unexposed	JJ	_	_	_
183	at	at	IN	_	_	_
184	t0	t0	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	treatment	treatment	NN	_	_	_
187	:	:	:	_	_	_
188	MG1655	mg1655	SYM	_	_	_
189	-	-	:	_	_	_
190	unexposed	unexposed	JJ	_	_	_
191	at	at	IN	_	_	_
192	t10	t10	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	treatment	treatment	NN	_	_	_
195	:	:	:	_	_	_
196	MG1655	mg1655	SYM	_	_	_
197	-	-	:	_	_	_
198	unexposed	unexposed	JJ	_	_	_
199	at	at	IN	_	_	_
200	t30	t30	CD	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	treatment	treatment	NN	_	_	_
203	:	:	:	_	_	_
204	MG1655	mg1655	SYM	_	_	_
205	-	-	:	_	_	_
206	unexposed	unexposed	JJ	_	_	_
207	at	at	IN	_	_	_
208	t60	t60	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	treatment	treatment	NN	_	_	_
211	:	:	:	_	_	_
212	minimal	minimal	JJ	_	_	_
213	C&N	c&n	NN	_	_	_
214	source	source	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	treatment	treatment	NN	_	_	_
217	:	:	:	_	_	_
218	minimal	minimal	JJ	_	_	_
219	C	c	NN	_	_	_
220	source	source	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	treatment	treatment	NN	_	_	_
223	:	:	:	_	_	_
224	minimal	minimal	JJ	_	_	_
225	N	n	NN	_	_	_
226	source	source	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	treatment	treatment	NN	_	_	_
229	:	:	:	_	_	_
230	NA	NA	NNP	_	_	_
231	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
232	treatment	treatment	NN	_	_	_
233	:	:	:	_	_	_
234	N/A	n/a	NN	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	treatment	treatment	NN	_	_	_
237	:	:	:	_	_	_
238	Nitrogen	nitrogen	NN	_	_	_
239	starvation	starvation	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	treatment	treatment	NN	_	_	_
242	:	:	:	_	_	_
243	none	none	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	treatment	treatment	NN	_	_	_
246	:	:	:	_	_	_
247	None	none	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	treatment	treatment	NN	_	_	_
250	:	:	:	_	_	_
251	non-sorted	non-sorted	JJ	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	treatment	treatment	NN	_	_	_
254	:	:	:	_	_	_
255	No	no	DT	_	_	_
256	treatment	treatment	NN	_	_	_
257	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
258	Treatment	treatment	NN	_	_	_
259	of	of	IN	_	_	_
260	sub-lethal	sub-lethal	JJ	_	_	_
261	triclosan	triclosan	NN	_	_	_
262	;	;	:	_	_	_
263	50	50	CD	_	_	_
264	mg/L	mg/l	NN	_	_	_
265	triclosan	triclosan	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	treatment	treatment	NN	_	_	_
268	:	:	:	_	_	_
269	oil	oil	NN	_	_	_
270	in	in	IN	_	_	_
271	water	water	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	treatment	treatment	NN	_	_	_
274	:	:	:	_	_	_
275	Osmotic	osmotic	JJ	_	_	_
276	stress	stress	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	treatment	treatment	NN	_	_	_
279	:	:	:	_	_	_
280	Oxidative	oxidative	JJ	_	_	_
281	stress	stress	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	treatment	treatment	NN	_	_	_
284	:	:	:	_	_	_
285	PA1	pa1	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	treatment	treatment	NN	_	_	_
288	:	:	:	_	_	_
289	PA2	pa2	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	treatment	treatment	NN	_	_	_
292	:	:	:	_	_	_
293	PA3	pa3	NN	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	treatment	treatment	NN	_	_	_
296	:	:	:	_	_	_
297	Pooled	pool	VBN	_	_	_
298	RNA	rna	NN	_	_	_
299	from	from	IN	_	_	_
300	mixture	mixture	NN	_	_	_
301	of	of	IN	_	_	_
302	the	the	DT	_	_	_
303	same	same	JJ	_	_	_
304	amount	amount	NN	_	_	_
305	of	of	IN	_	_	_
306	wt	wt	JJ	_	_	_
307	,	,	,	_	_	_
308	wt	wt	JJ	_	_	_
309	+	+	CC	_	_	_
310	SHX	shx	NN	_	_	_
311	,	,	,	_	_	_
312	dksA	dksa	NN	GEN	_	_
313	,	,	,	_	_	_
314	dksA	dksa	NN	GEN	_	_
315	+	+	CC	_	_	_
316	SHX	shx	NN	_	_	_
317	RNA	rna	NN	_	_	_
318	samples	sample	NNS	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	treatment	treatment	NN	_	_	_
321	:	:	:	_	_	_
322	prior	prior	RB	_	_	_
323	to	to	TO	_	_	_
324	CORM-3	corm-3	NN	_	_	_
325	addition	addition	NN	_	_	_
326	-LRB-	-lrb-	-LRB-	_	_	_
327	t	t	NN	_	_	_
328	=	=	JJ	_	_	_
329	0	0	CD	_	_	_
330	-RRB-	-rrb-	-RRB-	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	treatment	treatment	NN	_	_	_
333	:	:	:	_	_	_
334	prior	prior	RB	_	_	_
335	to	to	TO	_	_	_
336	iCORM-3	icorm-3	NN	_	_	_
337	addition	addition	NN	_	_	_
338	-LRB-	-lrb-	-LRB-	_	_	_
339	t	t	NN	_	_	_
340	=	=	JJ	_	_	_
341	0	0	CD	_	_	_
342	-RRB-	-rrb-	-RRB-	_	_	_
343	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
344	Treatment	treatment	NN	_	_	_
345	protocol	protocol	NN	_	_	_
346	-	-	:	_	_	_
347	E.coli	e.coli	NN	_	_	_
348	cells	cell	NNS	_	_	_
349	grown	grow	VBN	_	_	_
350	in	in	IN	_	_	_
351	LB	LB	NNP	MED	_	_
352	media	media	NNS	MED	_	_
353	with	with	IN	_	_	_
354	at	at	IN	_	_	_
355	37C	37c	NN	_	_	_
356	until	until	IN	_	_	_
357	early	early	JJ	_	_	_
358	log	log	NN	_	_	_
359	phase	phase	NN	_	_	_
360	-LRB-	-lrb-	-LRB-	_	_	_
361	0.4	0.4	CD	_	_	_
362	-RRB-	-rrb-	-RRB-	_	_	_
363	,	,	,	_	_	_
364	then	then	RB	_	_	_
365	were	be	VBD	_	_	_
366	treated	treat	VBN	_	_	_
367	with	with	IN	_	_	_
368	200	200	CD	_	_	_
369	mM	mm	NN	KWSUPP	_	_
370	glyphosate	glyphosate	NN	_	_	_
371	for	for	IN	_	_	_
372	1	1	CD	_	_	_
373	h	h	NN	_	_	_
374	,	,	,	_	_	_
375	after	after	IN	_	_	_
376	that	that	IN	_	_	_
377	the	the	DT	_	_	_
378	cells	cell	NNS	_	_	_
379	were	be	VBD	_	_	_
380	harvested	harvest	VBN	_	_	_
381	to	to	TO	_	_	_
382	extract	extract	NN	_	_	_
383	RNA	rna	NN	_	_	_
384	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	PS-60min	ps-60min	JJ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	:	:	:	_	_	_
8	Ribosome-protected	ribosome-protected	JJ	_	_	_
9	mRNA	mrna	NN	_	_	_
10	,	,	,	_	_	_
11	Ribosome	ribosome	NN	_	_	_
12	footprint	footprint	NN	_	_	_
13	sample	sample	NN	_	_	_
14	digested	digest	VBN	_	_	_
15	with	with	IN	_	_	_
16	60	60	CD	_	_	_
17	units	unit	NNS	_	_	_
18	of	of	IN	_	_	_
19	micrococcal	micrococcal	JJ	_	_	_
20	nuclease	nuclease	NN	_	_	_
21	per	per	IN	_	_	_
22	A260	a260	NN	_	_	_
23	absorbance	absorbance	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	treatment	treatment	NN	_	_	_
26	:	:	:	_	_	_
27	rifampicin	rifampicin	NN	SUPP	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	treatment	treatment	NN	_	_	_
30	:	:	:	_	_	_
31	saline	saline	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	treatment	treatment	NN	_	_	_
34	:	:	:	_	_	_
35	sham-treated	sham-treated	JJ	_	_	_
36	power	power	NN	_	_	_
37	line	line	NN	_	_	_
38	intermittent	intermittent	JJ	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	2	2	CD	_	_	_
41	min	min	NN	_	_	_
42	on	on	IN	_	_	_
43	,	,	,	_	_	_
44	4	4	CD	_	_	_
45	min	min	NN	_	_	_
46	off	off	IN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	magnetic	magnetic	JJ	_	_	_
49	field	field	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	treatment	treatment	NN	_	_	_
52	:	:	:	_	_	_
53	sham-treated	sham-treated	JJ	_	_	_
54	sinusoidal	sinusoidal	JJ	_	_	_
55	continous	continous	JJ	_	_	_
56	magnetic	magnetic	JJ	_	_	_
57	field	field	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	treatment	treatment	NN	_	_	_
60	:	:	:	_	_	_
61	sham-treated	sham-treated	JJ	_	_	_
62	sinusoidal	sinusoidal	JJ	_	_	_
63	intermittent	intermittent	JJ	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	2	2	CD	_	_	_
66	min	min	NN	_	_	_
67	on	on	IN	_	_	_
68	,	,	,	_	_	_
69	4	4	CD	_	_	_
70	min	min	NN	_	_	_
71	off	off	IN	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	magnetic	magnetic	JJ	_	_	_
74	field	field	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	treatment	treatment	NN	_	_	_
77	:	:	:	_	_	_
78	sorted	sort	VBN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	treatment	treatment	NN	_	_	_
81	:	:	:	_	_	_
82	Standard	Standard	NNP	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	treatment	treatment	NN	_	_	_
85	:	:	:	_	_	_
86	starvation	starvation	NN	_	_	_
87	growth	growth	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	treatment	treatment	NN	_	_	_
90	:	:	:	_	_	_
91	stationary	stationary	JJ	GrowthPhase	_	_
92	phase	phase	NN	GrowthPhase	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	treatment	treatment	NN	_	_	_
95	:	:	:	_	_	_
96	streptomycin	streptomycin	NN	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	50	50	CD	_	_	_
99	µg/mL	µg/ml	NN	_	_	_
100	final	final	JJ	_	_	_
101	concentration	concentration	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	treatment	treatment	NN	_	_	_
105	:	:	:	_	_	_
106	Supernatant	supernatant	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	treatment	treatment	NN	_	_	_
109	temperature	temperature	NN	_	_	_
110	:	:	:	_	_	_
111	30C	30c	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	treatment	treatment	NN	_	_	_
114	temperature	temperature	NN	_	_	_
115	:	:	:	_	_	_
116	42C	42c	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	treatment	treatment	NN	_	_	_
119	time	time	NN	_	_	_
120	:	:	:	_	_	_
121	T10	t10	NN	_	_	_
122	:	:	:	_	_	_
123	210	210	CD	_	_	_
124	min	min	NN	_	_	_
125	after	after	IN	_	_	_
126	stress	stress	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	treatment	treatment	NN	_	_	_
129	time	time	NN	_	_	_
130	:	:	:	_	_	_
131	T11	t11	NN	_	_	_
132	:	:	:	_	_	_
133	235	235	CD	_	_	_
134	min	min	NN	_	_	_
135	after	after	IN	_	_	_
136	stress	stress	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	treatment	treatment	NN	_	_	_
139	time	time	NN	_	_	_
140	:	:	:	_	_	_
141	T12	t12	NN	_	_	_
142	:	:	:	_	_	_
143	260	260	CD	_	_	_
144	min	min	NN	_	_	_
145	after	after	IN	_	_	_
146	stress	stress	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	treatment	treatment	NN	_	_	_
149	time	time	NN	_	_	_
150	:	:	:	_	_	_
151	T1	t1	NN	_	_	_
152	:	:	:	_	_	_
153	OD	od	NN	_	_	_
154	0.3	0.3	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	treatment	treatment	NN	_	_	_
157	time	time	NN	_	_	_
158	:	:	:	_	_	_
159	T1	t1	NN	_	_	_
160	:	:	:	_	_	_
161	OD	od	NN	_	_	_
162	0.5	0.5	CD	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	treatment	treatment	NN	_	_	_
165	time	time	NN	_	_	_
166	:	:	:	_	_	_
167	T2	t2	NN	_	_	_
168	:	:	:	_	_	_
169	OD	od	NN	_	_	_
170	0.5	0.5	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	treatment	treatment	NN	_	_	_
173	time	time	NN	_	_	_
174	:	:	:	_	_	_
175	T2	t2	NN	_	_	_
176	:	:	:	_	_	_
177	OD	od	NN	_	_	_
178	0.6	0.6	CD	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	treatment	treatment	NN	_	_	_
181	time	time	NN	_	_	_
182	:	:	:	_	_	_
183	T3	t3	NN	_	_	_
184	:	:	:	_	_	_
185	10	10	CD	_	_	_
186	min	min	NN	_	_	_
187	after	after	IN	_	_	_
188	reaching	reach	VBG	_	_	_
189	OD	od	NN	_	_	_
190	0.6	0.6	CD	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	treatment	treatment	NN	_	_	_
193	time	time	NN	_	_	_
194	:	:	:	_	_	_
195	T3	t3	NN	_	_	_
196	:	:	:	_	_	_
197	10	10	CD	_	_	_
198	min	min	NN	_	_	_
199	after	after	IN	_	_	_
200	stress	stress	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	treatment	treatment	NN	_	_	_
203	time	time	NN	_	_	_
204	:	:	:	_	_	_
205	T3	t3	NN	_	_	_
206	:	:	:	_	_	_
207	OD	od	NN	_	_	_
208	0.6	0.6	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	treatment	treatment	NN	_	_	_
211	time	time	NN	_	_	_
212	:	:	:	_	_	_
213	T3	t3	NN	_	_	_
214	:	:	:	_	_	_
215	OD	od	NN	_	_	_
216	0.7	0.7	CD	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	treatment	treatment	NN	_	_	_
219	time	time	NN	_	_	_
220	:	:	:	_	_	_
221	T4	t4	NN	_	_	_
222	:	:	:	_	_	_
223	10	10	CD	_	_	_
224	min	min	NN	_	_	_
225	after	after	IN	_	_	_
226	growth	growth	NN	_	_	_
227	lag	lag	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	treatment	treatment	NN	_	_	_
230	time	time	NN	_	_	_
231	:	:	:	_	_	_
232	T4	t4	NN	_	_	_
233	:	:	:	_	_	_
234	10	10	CD	_	_	_
235	min	min	NN	_	_	_
236	after	after	IN	_	_	_
237	stress	stress	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	treatment	treatment	NN	_	_	_
240	time	time	NN	_	_	_
241	:	:	:	_	_	_
242	T4	t4	NN	_	_	_
243	:	:	:	_	_	_
244	20	20	CD	_	_	_
245	min	min	NN	_	_	_
246	after	after	IN	_	_	_
247	reaching	reach	VBG	_	_	_
248	OD	od	NN	_	_	_
249	0.6	0.6	CD	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	treatment	treatment	NN	_	_	_
252	time	time	NN	_	_	_
253	:	:	:	_	_	_
254	T4	t4	NN	_	_	_
255	:	:	:	_	_	_
256	20	20	CD	_	_	_
257	min	min	NN	_	_	_
258	after	after	IN	_	_	_
259	stress	stress	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	treatment	treatment	NN	_	_	_
262	time	time	NN	_	_	_
263	:	:	:	_	_	_
264	T5	t5	NN	_	_	_
265	:	:	:	_	_	_
266	20	20	CD	_	_	_
267	min	min	NN	_	_	_
268	after	after	IN	_	_	_
269	growth	growth	NN	_	_	_
270	lag	lag	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	treatment	treatment	NN	_	_	_
273	time	time	NN	_	_	_
274	:	:	:	_	_	_
275	T5	t5	NN	_	_	_
276	:	:	:	_	_	_
277	20	20	CD	_	_	_
278	min	min	NN	_	_	_
279	after	after	IN	_	_	_
280	stress	stress	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	treatment	treatment	NN	_	_	_
283	time	time	NN	_	_	_
284	:	:	:	_	_	_
285	T5	t5	NN	_	_	_
286	:	:	:	_	_	_
287	30	30	CD	_	_	_
288	min	min	NN	_	_	_
289	after	after	IN	_	_	_
290	reaching	reach	VBG	_	_	_
291	OD	od	NN	_	_	_
292	0.6	0.6	CD	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	treatment	treatment	NN	_	_	_
295	time	time	NN	_	_	_
296	:	:	:	_	_	_
297	T5	t5	NN	_	_	_
298	:	:	:	_	_	_
299	30	30	CD	_	_	_
300	min	min	NN	_	_	_
301	after	after	IN	_	_	_
302	stress	stress	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	treatment	treatment	NN	_	_	_
305	time	time	NN	_	_	_
306	:	:	:	_	_	_
307	T6	t6	NN	_	_	_
308	:	:	:	_	_	_
309	30	30	CD	_	_	_
310	min	min	NN	_	_	_
311	after	after	IN	_	_	_
312	growth	growth	NN	_	_	_
313	lag	lag	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	treatment	treatment	NN	_	_	_
316	time	time	NN	_	_	_
317	:	:	:	_	_	_
318	T6	t6	NN	_	_	_
319	:	:	:	_	_	_
320	30	30	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	T6	t6	NN	_	_	_
329	:	:	:	_	_	_
330	40	40	CD	_	_	_
331	min	min	NN	_	_	_
332	after	after	IN	_	_	_
333	reaching	reach	VBG	_	_	_
334	OD	od	NN	_	_	_
335	0.6	0.6	CD	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	treatment	treatment	NN	_	_	_
338	time	time	NN	_	_	_
339	:	:	:	_	_	_
340	T6	t6	NN	_	_	_
341	:	:	:	_	_	_
342	40	40	CD	_	_	_
343	min	min	NN	_	_	_
344	after	after	IN	_	_	_
345	stress	stress	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	treatment	treatment	NN	_	_	_
348	time	time	NN	_	_	_
349	:	:	:	_	_	_
350	T7	t7	NN	_	_	_
351	:	:	:	_	_	_
352	40	40	CD	_	_	_
353	min	min	NN	_	_	_
354	after	after	IN	_	_	_
355	growth	growth	NN	_	_	_
356	lag	lag	NN	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	treatment	treatment	NN	_	_	_
359	time	time	NN	_	_	_
360	:	:	:	_	_	_
361	T7	t7	NN	_	_	_
362	:	:	:	_	_	_
363	40	40	CD	_	_	_
364	min	min	NN	_	_	_
365	after	after	IN	_	_	_
366	stress	stress	NN	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	treatment	treatment	NN	_	_	_
369	time	time	NN	_	_	_
370	:	:	:	_	_	_
371	T7	t7	NN	_	_	_
372	:	:	:	_	_	_
373	50	50	CD	_	_	_
374	min	min	NN	_	_	_
375	after	after	IN	_	_	_
376	reaching	reach	VBG	_	_	_
377	OD	od	NN	_	_	_
378	0.6	0.6	CD	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	treatment	treatment	NN	_	_	_
381	time	time	NN	_	_	_
382	:	:	:	_	_	_
383	T7	t7	NN	_	_	_
384	:	:	:	_	_	_
385	50	50	CD	_	_	_
386	min	min	NN	_	_	_
387	after	after	IN	_	_	_
388	stress	stress	NN	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	treatment	treatment	NN	_	_	_
391	time	time	NN	_	_	_
392	:	:	:	_	_	_
393	T8	t8	NN	_	_	_
394	:	:	:	_	_	_
395	90	90	CD	_	_	_
396	min	min	NN	_	_	_
397	after	after	IN	_	_	_
398	reaching	reach	VBG	_	_	_
399	OD	od	NN	_	_	_
400	0.6	0.6	CD	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	treatment	treatment	NN	_	_	_
403	time	time	NN	_	_	_
404	:	:	:	_	_	_
405	T8	t8	NN	_	_	_
406	:	:	:	_	_	_
407	90	90	CD	_	_	_
408	min	min	NN	_	_	_
409	after	after	IN	_	_	_
410	stress	stress	NN	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	treatment	treatment	NN	_	_	_
413	time	time	NN	_	_	_
414	:	:	:	_	_	_
415	T9	t9	NN	_	_	_
416	:	:	:	_	_	_
417	150	150	CD	_	_	_
418	min	min	NN	_	_	_
419	after	after	IN	_	_	_
420	stress	stress	NN	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	treatment	treatment	NN	_	_	_
423	:	:	:	_	_	_
424	tobacco	tobacco	NN	_	_	_
425	acid	acid	NN	_	_	_
426	pyrophosphatase	pyrophosphatase	NN	_	_	_
427	-LRB-	-lrb-	-LRB-	_	_	_
428	TAP	tap	NN	_	_	_
429	-RRB-	-rrb-	-RRB-	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	treatment	treatment	NN	_	_	_
432	:	:	:	_	_	_
433	Treated	treat	VBN	_	_	_
434	by	by	IN	_	_	_
435	HPCD	hpcd	NN	_	_	_
436	at	at	IN	_	_	_
437	5	5	CD	_	_	_
438	MPa	mpa	NN	_	_	_
439	and	and	CC	_	_	_
440	25	25	CD	_	_	_
441	℃	℃	NN	_	_	_
442	for	for	IN	_	_	_
443	40	40	CD	_	_	_
444	min	min	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	treatment	treatment	NN	_	_	_
447	:	:	:	_	_	_
448	treated	treated	JJ	_	_	_
449	culture	culture	NN	_	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
451	treatment	treatment	NN	_	_	_
452	:	:	:	_	_	_
453	treated	treat	VBN	_	_	_
454	power	power	NN	_	_	_
455	line	line	NN	_	_	_
456	intermittent	intermittent	JJ	_	_	_
457	-LRB-	-lrb-	-LRB-	_	_	_
458	2	2	CD	_	_	_
459	min	min	NN	_	_	_
460	on	on	IN	_	_	_
461	,	,	,	_	_	_
462	4	4	CD	_	_	_
463	min	min	NN	_	_	_
464	off	off	IN	_	_	_
465	-RRB-	-rrb-	-RRB-	_	_	_
466	magnetic	magnetic	JJ	_	_	_
467	field	field	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	treatment	treatment	NN	_	_	_
470	:	:	:	_	_	_
471	treated	treat	VBN	_	_	_
472	sinusoidal	sinusoidal	JJ	_	_	_
473	continous	continous	JJ	_	_	_
474	magnetic	magnetic	JJ	_	_	_
475	field	field	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	treatment	treatment	NN	_	_	_
478	:	:	:	_	_	_
479	treated	treat	VBN	_	_	_
480	sinusoidal	sinusoidal	JJ	_	_	_
481	intermittent	intermittent	JJ	_	_	_
482	-LRB-	-lrb-	-LRB-	_	_	_
483	2	2	CD	_	_	_
484	min	min	NN	_	_	_
485	on	on	IN	_	_	_
486	,	,	,	_	_	_
487	4	4	CD	_	_	_
488	min	min	NN	_	_	_
489	off	off	IN	_	_	_
490	-RRB-	-rrb-	-RRB-	_	_	_
491	magnetic	magnetic	JJ	_	_	_
492	field	field	NN	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	treatment	treatment	NN	_	_	_
495	:	:	:	_	_	_
496	triclosan	triclosan	NN	_	_	_
497	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
498	treatment	treatment	NN	_	_	_
499	:	:	:	_	_	_
500	unexposed	unexposed	JJ	_	_	_
501	,	,	,	_	_	_
502	left	left	JJ	_	_	_
503	chamber/bioreacator	chamber/bioreacator	NN	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	treatment	treatment	NN	_	_	_
506	:	:	:	_	_	_
507	unexposed	unexposed	JJ	_	_	_
508	,	,	,	_	_	_
509	right	right	JJ	_	_	_
510	chamber/bioreacator	chamber/bioreacator	NN	_	_	_
511	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
512	treatment	treatment	NN	_	_	_
513	:	:	:	_	_	_
514	unexposed	unexposed	JJ	_	_	_
515	,	,	,	_	_	_
516	treated	treat	VBN	_	_	_
517	with	with	IN	_	_	_
518	1mM	1mm	NN	_	_	_
519	H2O2	h2o2	NN	_	_	_
520	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
521	treatment	treatment	NN	_	_	_
522	:	:	:	_	_	_
523	unexposed	unexposed	JJ	_	_	_
524	,	,	,	_	_	_
525	treated	treat	VBN	_	_	_
526	with	with	IN	_	_	_
527	water	water	NN	_	_	_
528	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
529	treatment	treatment	NN	_	_	_
530	:	:	:	_	_	_
531	untreated	untreated	JJ	_	_	_
532	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
533	treatment	treatment	NN	_	_	_
534	:	:	:	_	_	_
535	untreated	untreated	JJ	_	_	_
536	culture	culture	NN	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	treatment	treatment	NN	_	_	_
539	:	:	:	_	_	_
540	UV	uv	NN	_	_	_
541	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
542	treatment	treatment	NN	_	_	_
543	:	:	:	_	_	_
544	vector	vector	NN	_	_	_
545	control	control	NN	_	_	_
546	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
547	treatment	treatment	NN	_	_	_
548	:	:	:	_	_	_
549	water	water	NN	_	_	_
550	in	in	IN	_	_	_
551	oil	oil	NN	_	_	_
552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
553	treatment	treatment	NN	_	_	_
554	:	:	:	_	_	_
555	with	with	IN	_	_	_
556	homogenization	homogenization	NN	_	_	_
557	and	and	CC	_	_	_
558	separation	separation	NN	_	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
560	treatment	treatment	NN	_	_	_
561	:	:	:	_	_	_
562	without	without	IN	_	_	_
563	salt	salt	NN	_	_	_
564	shock	shock	NN	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	treatment	treatment	NN	_	_	_
567	:	:	:	_	_	_
568	WT	WT	NNP	_	_	_
569	Rho	rho	NN	_	_	_
570	plasmid	plasmid	NN	_	_	_
571	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
572	Triclosan	Triclosan	NNP	_	_	_
573	tolerant	tolerant	JJ	_	_	_
574	mutant	mutant	JJ	_	_	_
575	triclosan	triclosan	NN	_	_	_
576	treated	treat	VBN	_	_	_
577	biological	biological	JJ	_	_	_
578	rep	rep	NN	GEN	_	_
579	1	1	CD	_	_	_
580	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
581	Triclosan	Triclosan	NNP	_	_	_
582	tolerant	tolerant	JJ	_	_	_
583	mutant	mutant	JJ	_	_	_
584	triclosan	triclosan	NN	_	_	_
585	treated	treat	VBN	_	_	_
586	biological	biological	JJ	_	_	_
587	rep	rep	NN	GEN	_	_
588	2	2	CD	_	_	_
589	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
590	Triclosan	Triclosan	NNP	_	_	_
591	tolerant	tolerant	JJ	_	_	_
592	mutant	mutant	JJ	_	_	_
593	triclosan	triclosan	NN	_	_	_
594	treated	treat	VBN	_	_	_
595	biological	biological	JJ	_	_	_
596	rep	rep	NN	GEN	_	_
597	3	3	CD	_	_	_
598	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
599	Triclosan	triclosan	NN	_	_	_
600	tolerant	tolerant	JJ	_	_	_
601	mutant	mutant	JJ	_	_	_
602	untreated	untreated	JJ	_	_	_
603	biological	biological	JJ	_	_	_
604	rep	rep	NN	GEN	_	_
605	1	1	CD	_	_	_
606	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
607	Triclosan	Triclosan	NNP	_	_	_
608	tolerant	tolerant	JJ	_	_	_
609	mutant	mutant	JJ	_	_	_
610	untreated	untreated	JJ	_	_	_
611	biological	biological	JJ	_	_	_
612	rep	rep	NN	GEN	_	_
613	2	2	CD	_	_	_
614	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
615	Triclosan	Triclosan	NNP	_	_	_
616	tolerant	tolerant	JJ	_	_	_
617	mutant	mutant	JJ	_	_	_
618	untreated	untreated	JJ	_	_	_
619	biological	biological	JJ	_	_	_
620	rep	rep	NN	GEN	_	_
621	3	3	CD	_	_	_
622	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
623	trim	trim	JJ	_	_	_
624	adaptors	adaptor	NNS	_	_	_
625	on	on	IN	_	_	_
626	raw	raw	JJ	_	_	_
627	reads	read	VBZ	_	_	_
628	and	and	CC	_	_	_
629	moved	move	VBD	_	_	_
630	trimmed	trimmed	RBR	_	_	_
631	reads	read	VBZ	_	_	_
632	to	to	TO	_	_	_
633	trimmed	trimmed	RBR	_	_	_
634	_	_	SYM	_	_	_
635	reads	read	VBZ	_	_	_
636	with	with	IN	_	_	_
637	flexbar	flexbar	JJ	_	_	_
638	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
639	Trimethoprim-treated	trimethoprim-treated	JJ	_	_	_
640	E.	e.	FW	_	_	_
641	coli	coli	FW	_	_	_
642	cells	cell	NNS	_	_	_
643	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
644	Trimmed	trimmed	JJ	_	_	_
645	adaptor	adaptor	NN	_	_	_
646	sequences	sequence	NNS	_	_	_
647	from	from	IN	_	_	_
648	reads	read	VBZ	_	_	_
649	using	use	VBG	_	_	_
650	Flexbar	Flexbar	NNP	_	_	_
651	2.31	2.31	CD	_	_	_
652	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
653	Trimmed	trim	VBD	_	_	_
654	reads	read	VBZ	_	_	_
655	were	be	VBD	_	_	_
656	aligned	align	VBN	_	_	_
657	on	on	IN	_	_	_
658	most	most	JJS	_	_	_
659	recent	recent	JJ	_	_	_
660	reference	reference	NN	_	_	_
661	genome	genome	NN	_	_	_
662	of	of	IN	_	_	_
663	Escherichia	escherichia	FW	Organism	_	_
664	coli	coli	FW	Organism	_	_
665	-LRB-	-lrb-	-LRB-	_	_	_
666	GenBank	genbank	NN	_	_	_
667	U00096	u00096	NN	_	_	_
668	.3	.3	NN	_	_	_
669	-RRB-	-rrb-	-RRB-	_	_	_
670	by	by	IN	_	_	_
671	using	use	VBG	_	_	_
672	TopHat	TopHat	NNP	_	_	_
673	-LRB-	-lrb-	-LRB-	_	_	_
674	v2	v2	NN	_	_	_
675	.0.10	.0.10	CD	_	_	_
676	-RRB-	-rrb-	-RRB-	_	_	_
677	coupled	couple	VBN	_	_	_
678	with	with	IN	_	_	_
679	bowtie	bowtie	NN	_	_	_
680	-LRB-	-lrb-	-LRB-	_	_	_
681	v1	v1	NN	_	_	_
682	.0.0	.0.0	CD	_	_	_
683	-RRB-	-rrb-	-RRB-	_	_	_
684	.	.	.	_	_	_

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	NN	_	_	_
25	Trimmed	trim	VBD	_	_	_
26	reads	read	VBZ	_	_	_
27	were	be	VBD	_	_	_
28	sequentially	sequentially	RB	_	_	_
29	aligned	align	VBN	_	_	_
30	using	use	VBG	_	_	_
31	Bowtie	Bowtie	NNP	_	_	_
32	v0	v0	NN	_	_	_
33	.12.7	.12.7	CD	_	_	_
34	to	to	TO	_	_	_
35	E	E	NNP	_	_	_
36	coli	coli	NN	_	_	_
37	genome	genome	NN	_	_	_
38	using	use	VBG	_	_	_
39	parameters	parameter	NNS	_	_	_
40	-	-	:	_	_	_
41	v	v	LS	_	_	_
42	1	1	LS	_	_	_
43	-	-	:	_	_	_
44	m	m	NN	_	_	_
45	1	1	CD	_	_	_
46	--	--	:	_	_	_
47	best	best	JJS	_	_	_
48	.	.	.	_	_	_

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	Trimmed	trim	VBD	_	_	_
20	reads	read	VBZ	_	_	_
21	were	be	VBD	_	_	_
22	sequentially	sequentially	RB	_	_	_
23	aligned	align	VBN	_	_	_
24	using	use	VBG	_	_	_
25	Bowtie	Bowtie	NNP	_	_	_
26	v0	v0	NN	_	_	_
27	.12.7	.12.7	CD	_	_	_
28	to	to	TO	_	_	_
29	E	E	NNP	_	_	_
30	coli	coli	NN	_	_	_
31	rRNA	rrna	NN	_	_	_
32	and	and	CC	_	_	_
33	noncoding	noncoding	JJ	_	_	_
34	RNA	rna	NN	_	_	_
35	allowing	allow	VBG	_	_	_
36	one	one	CD	_	_	_
37	mismatch	mismatch	NN	_	_	_
38	.	.	.	_	_	_

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	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.	FW	_	_	_
13	coli	coli	FW	_	_	_
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	NN	_	_	_
2	triplicate	triplicate	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	by	by	IN	_	_	_
7	combining	combine	VBG	_	_	_
8	cells	cell	NNS	_	_	_
9	from	from	IN	_	_	_
10	5	5	CD	_	_	_
11	tubes	tube	NNS	_	_	_
12	each	each	DT	_	_	_
13	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	TRI	TRI	NNP	_	_	_
6	Reagent	Reagent	NNP	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Sigma	Sigma	NNP	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	or	or	CC	_	_	_
11	Rneasy	rneasy	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	QIAGEN	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	according	accord	VBG	_	_	_
16	to	to	TO	_	_	_
17	manufacturer	manufacturer	NN	_	_	_
18	's	's	POS	_	_	_
19	protocol	protocol	NN	_	_	_
20	.	.	.	_	_	_

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

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	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Trizol	Trizol	NNP	_	_	_
17	extraction	extraction	NN	_	_	_
18	of	of	IN	_	_	_
19	total	total	JJ	_	_	_
20	RNA	rna	NN	_	_	_
21	was	be	VBD	_	_	_
22	performed	perform	VBN	_	_	_
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	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Trizol	trizol	NN	_	_	_
3	for	for	IN	_	_	_
4	RNAseq	rnaseq	NN	_	_	_
5	,	,	,	_	_	_
6	gradient	gradient	NN	_	_	_
7	centrifugation	centrifugation	NN	_	_	_
8	=	=	JJ	_	_	_
9	>	>	JJR	_	_	_
10	RNase	rnase	NN	_	_	_
11	digestions	digestion	NNS	_	_	_
12	=	=	JJ	_	_	_
13	>	>	JJR	_	_	_
14	Trizol	trizol	NN	_	_	_
15	=	=	JJ	_	_	_
16	>	>	JJR	_	_	_
17	gel	gel	NN	_	_	_
18	extraction	extraction	NN	_	_	_
19	for	for	IN	_	_	_
20	RIBOseq	riboseq	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	TRIzol	trizol	NN	_	_	_
23	reagent	reagent	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Gibco	Gibco	NNP	_	_	_
26	BRL	brl	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	used	use	VBN	_	_	_
30	according	accord	VBG	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	manufacturer	manufacturer	NN	_	_	_
34	instruction	instruction	NN	_	_	_
35	.	.	.	_	_	_

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	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	trpEA2trpR2	trpea2trpr2	NN	_	_	_
15	vs.	vs.	CC	_	_	_
16	trpEA2	trpea2	NN	_	_	_
17	,	,	,	_	_	_
18	W3110	w3110	NN	_	_	_
19	min	min	NN	_	_	_
20	+	+	CC	_	_	_
21	Trp	trp	NN	_	_	_
22	50ug/ml	50ug/ml	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	trpEA2trpR2	trpea2trpr2	NN	_	_	_
25	,	,	,	_	_	_
26	W3110	w3110	NN	_	_	_
27	min	min	NN	_	_	_
28	+	+	CC	_	_	_
29	Trp	trp	NN	_	_	_
30	50ug/ml	50ug/ml	NN	_	_	_
31	,	,	,	_	_	_
32	30	30	CD	_	_	_
33	ug	ug	NN	_	_	_
34	total	total	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	trpEA2	trpea2	NN	_	_	_
37	,	,	,	_	_	_
38	W3110	w3110	NN	_	_	_
39	min	min	NN	_	_	_
40	+	+	CC	_	_	_
41	Trp	trp	NN	_	_	_
42	50ug/ml	50ug/ml	NN	_	_	_
43	,	,	,	_	_	_
44	30	30	CD	_	_	_
45	ug	ug	NN	_	_	_
46	total	total	JJ	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	trpR2	trpr2	NN	_	_	_
49	+50	+50	CD	_	_	_
50	ug/ml	ug/ml	JJ	_	_	_
51	Trp	trp	NN	_	_	_
52	,	,	,	_	_	_
53	30	30	CD	_	_	_
54	ug	ug	NN	_	_	_
55	total	total	JJ	_	_	_
56	RNA	rna	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	trpR2	trpr2	NN	_	_	_
59	+50	+50	CD	_	_	_
60	ug/ml	ug/ml	JJ	_	_	_
61	Trp	trp	NN	_	_	_
62	vs.	vs.	CC	_	_	_
63	wt	wt	JJ	_	_	_
64	+50	+50	CD	_	_	_
65	ug/ml	ug/ml	JJ	_	_	_
66	Trp	trp	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	trpR2tnaA2	trpr2tnaa2	NN	_	_	_
69	,	,	,	_	_	_
70	W3110	w3110	NN	_	_	_
71	minimal	minimal	JJ	_	_	_
72	+	+	CC	_	_	_
73	Trp	trp	NN	_	_	_
74	50ug/ml	50ug/ml	CD	_	_	_
75	vs.	vs.	CC	_	_	_
76	dnaC	dnaC	NNP	GEN	_	_
77	genomic	genomic	JJ	_	_	_
78	DNA	dna	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	trpR2tnaA2	trpr2tnaa2	NN	_	_	_
81	,	,	,	_	_	_
82	W3110	w3110	NN	_	_	_
83	min	min	NN	_	_	_
84	+	+	CC	_	_	_
85	Trp	trp	NN	_	_	_
86	50ug/ml	50ug/ml	NN	_	_	_
87	,	,	,	_	_	_
88	25	25	CD	_	_	_
89	ug	ug	NN	_	_	_
90	total	total	JJ	_	_	_
91	RNA	rna	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	trpR2	trpr2	NN	_	_	_
94	+	+	CC	_	_	_
95	trp	trp	NN	_	_	_
96	vs.	vs.	NN	_	_	_
97	-	-	:	_	_	_
98	trp	trp	NN	_	_	_
99	,	,	,	_	_	_
100	min	min	NN	_	_	_
101	+.2	+.2	CD	_	_	_
102	%	%	NN	_	_	_
103	glucose	glucose	NN	SUPP	_	_
104	,	,	,	_	_	_
105	W3110	w3110	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	trpR2	trpr2	NN	_	_	_
108	vs.	vs.	CC	_	_	_
109	wt	wt	JJ	_	_	_
110	,	,	,	_	_	_
111	min	min	NN	_	_	_
112	+.2	+.2	CD	_	_	_
113	%	%	NN	_	_	_
114	glucose	glucose	NN	SUPP	_	_
115	,	,	,	_	_	_
116	W3110	w3110	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	TrpR	trpr	NN	TF	_	_
119	_	_	NN	_	_	_
120	glucose	glucose	NN	SUPP	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	TrpR	trpr	NN	TF	_	_
123	_	_	CD	_	_	_
124	Trp	Trp	NNP	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	TruSeq	TruSeq	NNP	_	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	Truseq	Truseq	NNP	_	_	_
129	ChIP	ChIP	NNP	_	_	_
130	kit	kit	NN	_	_	_
131	was	be	VBD	_	_	_
132	used	use	VBN	_	_	_
133	for	for	IN	_	_	_
134	the	the	DT	_	_	_
135	library	library	NN	_	_	_
136	preparation	preparation	NN	_	_	_
137	.	.	.	_	_	_

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	NN	_	_	_
2	Truseq	truseq	NN	_	_	_
3	Small	small	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Tryptophan	tryptophan	NN	_	_	_
7	addition	addition	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	TTAGGC-D3	ttaggc-d3	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Tube	Tube	NNP	_	_	_
12	state	state	NN	_	_	_
13	1	1	CD	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	IPTG	iptg	SYM	_	_	_
16	-	-	:	_	_	_
17	/	/	:	_	_	_
18	aTc	atc	SYM	_	_	_
19	-	-	:	_	_	_
20	/	/	:	_	_	_
21	Ara	Ara	NNP	_	_	_
22	-	-	:	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Tube	Tube	NNP	_	_	_
26	state	state	NN	_	_	_
27	2	2	CD	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	IPTG	iptg	NN	_	_	_
30	+	+	CC	_	_	_
31	/	/	:	_	_	_
32	aTc	atc	SYM	_	_	_
33	-	-	:	_	_	_
34	/	/	:	_	_	_
35	Ara	Ara	NNP	_	_	_
36	-	-	:	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	Tube	Tube	NNP	_	_	_
40	state	state	NN	_	_	_
41	3	3	CD	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	IPTG	iptg	SYM	_	_	_
44	-	-	:	_	_	_
45	/	/	:	_	_	_
46	aTc	atc	NN	_	_	_
47	+	+	CC	_	_	_
48	/	/	:	_	_	_
49	Ara	Ara	NNP	_	_	_
50	-	-	:	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Tube	Tube	NNP	_	_	_
54	state	state	NN	_	_	_
55	4	4	CD	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	IPTG	iptg	NN	_	_	_
58	+	+	CC	_	_	_
59	/	/	:	_	_	_
60	aTc	atc	NN	_	_	_
61	+	+	CC	_	_	_
62	/	/	:	_	_	_
63	Ara	Ara	NNP	_	_	_
64	-	-	:	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Tube	Tube	NNP	_	_	_
68	state	state	NN	_	_	_
69	5	5	CD	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	IPTG	iptg	SYM	_	_	_
72	-	-	:	_	_	_
73	/	/	:	_	_	_
74	aTc	atc	SYM	_	_	_
75	-	-	:	_	_	_
76	/	/	:	_	_	_
77	Ara	Ara	NNP	_	_	_
78	+	+	CC	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Tube	Tube	NNP	_	_	_
82	state	state	NN	_	_	_
83	6	6	CD	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	IPTG	iptg	NN	_	_	_
86	+	+	CC	_	_	_
87	/	/	:	_	_	_
88	aTc	atc	SYM	_	_	_
89	-	-	:	_	_	_
90	/	/	:	_	_	_
91	Ara	Ara	NNP	_	_	_
92	+	+	CC	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Tube	Tube	NNP	_	_	_
96	state	state	NN	_	_	_
97	7	7	CD	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	IPTG	iptg	SYM	_	_	_
100	-	-	:	_	_	_
101	/	/	:	_	_	_
102	aTc	atc	NN	_	_	_
103	+	+	CC	_	_	_
104	/	/	:	_	_	_
105	Ara	Ara	NNP	_	_	_
106	+	+	CC	_	_	_
107	-RRB-	-rrb-	-RRB-	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Tube	Tube	NNP	_	_	_
110	state	state	NN	_	_	_
111	8	8	CD	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	IPTG	iptg	NN	_	_	_
114	+	+	CC	_	_	_
115	/	/	:	_	_	_
116	aTc	atc	NN	_	_	_
117	+	+	CC	_	_	_
118	/	/	:	_	_	_
119	Ara	Ara	NNP	_	_	_
120	+	+	CC	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	TW09308	tw09308	NN	_	_	_
124	batch	batch	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	TW09308	tw09308	NN	_	_	_
127	chemostat	chemostat	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	TW09308	tw09308	NN	_	_	_
130	starvation	starvation	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	TW09308	tw09308	NN	_	_	_
133	transcriptome	transcriptome	NN	_	_	_
134	from	from	IN	_	_	_
135	batch	batch	NN	_	_	_
136	growth	growth	NN	_	_	_
137	_	_	NN	_	_	_
138	1	1	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	TW09308	tw09308	NN	_	_	_
141	transcriptome	transcriptome	NN	_	_	_
142	from	from	IN	_	_	_
143	batch	batch	NN	_	_	_
144	growth	growth	NN	_	_	_
145	_	_	NN	_	_	_
146	2	2	CD	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	TW09308	tw09308	NN	_	_	_
149	transcriptome	transcriptome	NN	_	_	_
150	from	from	IN	_	_	_
151	chemostat	chemostat	NN	_	_	_
152	growth	growth	NN	_	_	_
153	_	_	NN	_	_	_
154	1	1	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	TW09308	tw09308	NN	_	_	_
157	transcriptome	transcriptome	NN	_	_	_
158	from	from	IN	_	_	_
159	chemostat	chemostat	NN	_	_	_
160	growth	growth	NN	_	_	_
161	_	_	NN	_	_	_
162	2	2	CD	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	TW09308	tw09308	NN	_	_	_
165	transcriptome	transcriptome	NN	_	_	_
166	from	from	IN	_	_	_
167	starvation	starvation	NN	_	_	_
168	growth	growth	NN	_	_	_
169	_	_	NN	_	_	_
170	1	1	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	TW09308	tw09308	NN	_	_	_
173	transcriptome	transcriptome	NN	_	_	_
174	from	from	IN	_	_	_
175	starvation	starvation	NN	_	_	_
176	growth	growth	NN	_	_	_
177	_	_	NN	_	_	_
178	2	2	CD	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	TW10915	tw10915	NN	_	_	_
181	cells	cell	NNS	_	_	_
182	were	be	VBD	_	_	_
183	grown	grow	VBN	_	_	_
184	in	in	IN	_	_	_
185	DMEM	DMEM	NNP	_	_	_
186	medium	medium	NN	_	_	_
187	upto	upto	NN	_	_	_
188	exponential	exponential	JJ	GrowthPhase	_	_
189	phase	phase	NN	GrowthPhase	_	_
190	-LRB-	-lrb-	-LRB-	_	_	_
191	OD600	od600	NN	_	_	_
192	~	~	NN	_	_	_
193	0.5	0.5	CD	_	_	_
194	,	,	,	_	_	_
195	2.5	2.5	CD	_	_	_
196	h	h	NN	_	_	_
197	after	after	IN	_	_	_
198	inoclulation	inoclulation	NN	_	_	_
199	-RRB-	-rrb-	-RRB-	_	_	_
200	at	at	IN	_	_	_
201	37C	37c	NN	_	_	_
202	.	.	.	_	_	_

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	NN	_	_	_
2	TW11588	tw11588	NN	_	_	_
3	batch	batch	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	TW11588	tw11588	NN	_	_	_
6	chemostat	chemostat	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	TW11588	tw11588	NN	_	_	_
9	starvation	starvation	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	TW11588	tw11588	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	TW11588	tw11588	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	TW11588	tw11588	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	TW11588	tw11588	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	TW11588	tw11588	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	TW11588	tw11588	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	Two	two	CD	_	_	_
60	Avian	avian	JJ	_	_	_
61	Pathogenic	pathogenic	JJ	_	_	_
62	Escherichia	escherichia	FW	Organism	_	_
63	coli	coli	FW	Organism	_	_
64	strains	strain	NNS	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	APEC	apec	NNS	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	were	be	VBD	_	_	_
69	grown	grow	VBN	_	_	_
70	at	at	IN	_	_	_
71	37	37	CD	_	_	_
72	°C	°c	NN	_	_	_
73	in	in	IN	_	_	_
74	Dulbecco	Dulbecco	NNP	_	_	_
75	's	's	POS	_	_	_
76	Modified	modify	VBN	_	_	_
77	Eagle	Eagle	NNP	_	_	_
78	's	's	POS	_	_	_
79	Media	Media	NNP	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	DMEM	DMEM	NNP	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	media	media	NNS	_	_	_
84	until	until	IN	_	_	_
85	reach	reach	NN	_	_	_
86	O.D	o.d	NN	_	_	_
87	600	600	CD	_	_	_
88	=	=	JJ	_	_	_
89	0.8	0.8	CD	_	_	_
90	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Two	two	CD	_	_	_
3	biological	biological	JJ	_	_	_
4	replicates	replicate	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	for	for	IN	_	_	_
8	samples	sample	NNS	_	_	_
9	with	with	IN	_	_	_
10	and	and	CC	_	_	_
11	without	without	IN	_	_	_
12	treatment	treatment	NN	_	_	_
13	with	with	IN	_	_	_
14	bicyclomycin	bicyclomycin	NN	_	_	_
15	.	.	.	_	_	_

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	Two	two	CD	_	_	_
13	biological	biological	JJ	_	_	_
14	replicates	replicate	VBZ	_	_	_
15	were	be	VBD	_	_	_
16	processed	process	VBN	_	_	_
17	seperatedly	seperatedly	RB	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	only	only	RB	_	_	_
21	sequence	sequence	NN	_	_	_
22	reads	read	VBZ	_	_	_
23	presented	present	VBN	_	_	_
24	in	in	IN	_	_	_
25	both	both	CC	_	_	_
26	biological	biological	JJ	_	_	_
27	replciates	replciate	NNS	_	_	_
28	were	be	VBD	_	_	_
29	considered	consider	VBN	_	_	_
30	for	for	IN	_	_	_
31	further	further	JJ	_	_	_
32	process	process	NN	_	_	_
33	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	Two	two	CD	_	_	_
3	color	color	NN	_	_	_
4	cDNA	cdna	NN	_	_	_
5	microarray	microarray	NN	_	_	_
6	data	datum	NNS	_	_	_
7	are	be	VBP	_	_	_
8	never	never	RB	_	_	_
9	devoid	devoid	JJ	_	_	_
10	of	of	IN	_	_	_
11	spurious	spurious	JJ	_	_	_
12	technical	technical	JJ	_	_	_
13	contributions	contribution	NNS	_	_	_
14	that	that	WDT	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
16	Two	two	CD	_	_	_
17	color	color	NN	_	_	_
18	cDNA	cdna	NN	_	_	_
19	microarray	microarray	NN	_	_	_
20	data	datum	NNS	_	_	_
21	are	be	VBP	_	_	_
22	never	never	RB	_	_	_
23	devoid	devoid	JJ	_	_	_
24	of	of	IN	_	_	_
25	spurious	spurious	JJ	_	_	_
26	technical	technical	JJ	_	_	_
27	contributions	contribution	NNS	_	_	_
28	that	that	WDT	_	_	_
29	originate	originate	VBP	_	_	_
30	during	during	IN	_	_	_
31	array	array	NN	_	_	_
32	printing	printing	NN	_	_	_
33	,	,	,	_	_	_
34	as	as	RB	_	_	_
35	well	well	RB	_	_	_
36	as	as	IN	_	_	_
37	during	during	IN	_	_	_
38	the	the	DT	_	_	_
39	collection	collection	NN	_	_	_
40	and	and	CC	_	_	_
41	processing	processing	NN	_	_	_
42	of	of	IN	_	_	_
43	samples	sample	NNS	_	_	_
44	,	,	,	_	_	_
45	fluorescent	fluorescent	JJ	_	_	_
46	labeling	labeling	NN	_	_	_
47	and	and	CC	_	_	_
48	hybridization	hybridization	NN	_	_	_
49	and	and	CC	_	_	_
50	scanning	scanning	NN	_	_	_
51	of	of	IN	_	_	_
52	the	the	DT	_	_	_
53	microarray	microarray	NN	_	_	_
54	images	image	NNS	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Balazsi	balazsus	NNS	_	_	_
57	et	et	FW	_	_	_
58	al.	al.	FW	_	_	_
59	2003	2003	CD	_	_	_
60	,	,	,	_	_	_
61	PNAS	PNAS	NNP	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	.	.	.	_	_	_

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	/	/	:	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	F	f	NN	_	_	_
21	_	_	CD	_	_	_
22	g-B	g-b	NN	_	_	_
23	_	_	CD	_	_	_
24	g	g	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	where	where	WRB	_	_	_
28	F	f	NN	_	_	_
29	_	_	NN	_	_	_
30	r	r	NN	_	_	_
31	,	,	,	_	_	_
32	B	b	NN	_	_	_
33	_	_	NN	_	_	_
34	r	r	NN	_	_	_
35	,	,	,	_	_	_
36	F	f	NN	_	_	_
37	_	_	CD	_	_	_
38	g	g	NN	_	_	_
39	and	and	CC	_	_	_
40	B	b	NN	_	_	_
41	_	_	CD	_	_	_
42	g	g	NN	_	_	_
43	represent	represent	VBP	_	_	_
44	the	the	DT	_	_	_
45	median	median	JJ	_	_	_
46	Cy5	cy5	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	red	red	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	foreground	foreground	NN	_	_	_
51	and	and	CC	_	_	_
52	background	background	NN	_	_	_
53	,	,	,	_	_	_
54	and	and	CC	_	_	_
55	the	the	DT	_	_	_
56	median	median	JJ	_	_	_
57	Cy3	cy3	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	green	green	JJ	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	foreground	foreground	NN	_	_	_
62	and	and	CC	_	_	_
63	background	background	NN	_	_	_
64	intensities	intensity	NNS	_	_	_
65	,	,	,	_	_	_
66	respectively	respectively	RB	_	_	_
67	.	.	.	_	_	_

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	than	than	IN	_	_	_
14	or	or	CC	_	_	_
15	equal	equal	JJ	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	intensity	intensity	NN	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	foreground	foreground	NN	_	_	_
22	,	,	,	_	_	_
23	the	the	DT	_	_	_
24	resulting	result	VBG	_	_	_
25	log	log	NN	_	_	_
26	ratios	ratio	NNS	_	_	_
27	became	become	VBD	_	_	_
28	complex	complex	JJ	_	_	_
29	or	or	CC	_	_	_
30	infinity	infinity	NN	_	_	_
31	.	.	.	_	_	_

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	Next	next	RB	_	_	_
2	,	,	,	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	,	,	,	_	_	_
7	by	by	IN	_	_	_
8	averaging	average	VBG	_	_	_
9	the	the	DT	_	_	_
10	log	log	NN	_	_	_
11	ratios	ratio	NNS	_	_	_
12	resulting	result	VBG	_	_	_
13	from	from	IN	_	_	_
14	all	all	DT	_	_	_
15	spots	spot	NNS	_	_	_
16	printed	print	VBN	_	_	_
17	by	by	IN	_	_	_
18	a	a	DT	_	_	_
19	print	print	NN	_	_	_
20	tip	tip	NN	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	subtracting	subtract	VBG	_	_	_
24	the	the	DT	_	_	_
25	resulting	result	VBG	_	_	_
26	average	average	NN	_	_	_
27	from	from	IN	_	_	_
28	all	all	DT	_	_	_
29	the	the	DT	_	_	_
30	individual	individual	JJ	_	_	_
31	log	log	NN	_	_	_
32	ratios	ratio	NNS	_	_	_
33	corresponding	correspond	VBG	_	_	_
34	to	to	TO	_	_	_
35	the	the	DT	_	_	_
36	same	same	JJ	_	_	_
37	tip	tip	NN	_	_	_
38	.	.	.	_	_	_

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	were	be	VBD	_	_	_
15	averaged	average	VBN	_	_	_
16	and	and	CC	_	_	_
17	listed	list	VBN	_	_	_
18	in	in	IN	_	_	_
19	a	a	DT	_	_	_
20	new	new	JJ	_	_	_
21	file	file	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Two	two	CD	_	_	_
3	different	different	JJ	_	_	_
4	approaches	approach	NNS	_	_	_
5	were	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	align	align	VB	_	_	_
9	sequence	sequence	NN	_	_	_
10	reads	read	VBZ	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	genome	genome	NN	_	_	_
14	of	of	IN	_	_	_
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	.	.	.	_	_	_

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	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	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	ug/ml	ug/ml	JJ	_	_	_
18	smx	smx	NN	_	_	_
19	/	/	:	_	_	_
20	ug/ml	ug/ml	JJ	_	_	_
21	tm	tm	NN	_	_	_
22	:	:	:	_	_	_
23	20/4	20/4	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	1x	1x	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	ug/ml	ug/ml	NN	_	_	_
29	smx	smx	NN	_	_	_
30	/	/	:	_	_	_
31	ug/ml	ug/ml	JJ	_	_	_
32	tm	tm	NN	_	_	_
33	:	:	:	_	_	_
34	540/108	540/108	CD	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	27x	27x	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	ugpC	ugpc	NN	GEN	_	_
40	KO	ko	NN	_	_	_
41	rep1	rep1	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	ugpC	ugpc	NN	GEN	_	_
44	KO	ko	NN	_	_	_
45	rep2	rep2	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	ugpC	ugpc	NN	GEN	_	_
48	KO	ko	NN	_	_	_
49	rep3	rep3	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	umuD	umud	NN	GEN	_	_
52	___	___	CD	_	_	_
53	U	U	NNP	_	_	_
54	_	_	NNP	_	_	_
55	N0025	N0025	NNP	_	_	_
56	_	_	VBD	_	_	_
57	r1	r1	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	umuD	umud	NN	GEN	_	_
60	___	___	CD	_	_	_
61	U	U	NNP	_	_	_
62	_	_	NNP	_	_	_
63	N0025	N0025	NNP	_	_	_
64	_	_	VBD	_	_	_
65	r2	r2	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	umuD	umud	NN	GEN	_	_
68	___	___	CD	_	_	_
69	U	U	NNP	_	_	_
70	_	_	NNP	_	_	_
71	N0025	N0025	NNP	_	_	_
72	_	_	VBD	_	_	_
73	r3	r3	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	umuD	umud	NN	GEN	_	_
76	upregulation	upregulation	NN	_	_	_
77	,	,	,	_	_	_
78	amp	amp	NN	_	_	_
79	50ug/ml	50ug/ml	NN	_	_	_
80	,	,	,	_	_	_
81	0.0125	0.0125	CD	_	_	_
82	%	%	NN	_	_	_
83	arabinose	arabinose	NN	_	_	_
84	,	,	,	_	_	_
85	0.025	0.025	CD	_	_	_
86	ug/ml	ug/ml	NN	_	_	_
87	norfloxacin	norfloxacin	NN	_	_	_
88	OD	od	NN	_	_	_
89	~	~	NN	_	_	_
90	0.3	0.3	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Un	un	NN	_	_	_
93	_	_	CD	_	_	_
94	IN	in	IN	_	_	_
95	_	_	CD	_	_	_
96	3	3	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Un	un	NN	_	_	_
99	_	_	CD	_	_	_
100	IN	in	IN	_	_	_
101	_	_	CD	_	_	_
102	Mu	mu	NN	_	_	_
103	_	_	NN	_	_	_
104	1	1	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	Un	un	NN	_	_	_
107	_	_	CD	_	_	_
108	IN	in	IN	_	_	_
109	_	_	CD	_	_	_
110	Mu	mu	NN	_	_	_
111	_	_	NN	_	_	_
112	2	2	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	Un	un	NN	_	_	_
115	_	_	CD	_	_	_
116	IP	IP	NNP	_	_	_
117	_	_	SYM	_	_	_
118	3	3	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Un	un	NN	_	_	_
121	_	_	CD	_	_	_
122	IP	IP	NNP	_	_	_
123	_	_	SYM	_	_	_
124	Mu	mu	FW	_	_	_
125	_	_	FW	_	_	_
126	1	1	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Un	un	NN	_	_	_
129	_	_	CD	_	_	_
130	IP	IP	NNP	_	_	_
131	_	_	SYM	_	_	_
132	Mu	mu	FW	_	_	_
133	_	_	FW	_	_	_
134	2	2	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	untreated	untreated	JJ	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	Untreated	untreated	JJ	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	untreated	untreated	JJ	_	_	_
141	cells	cell	NNS	_	_	_
142	,	,	,	_	_	_
143	25	25	CD	_	_	_
144	ug	ug	NN	_	_	_
145	total	total	JJ	_	_	_
146	RNA	rna	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	untreated	untreated	JJ	_	_	_
149	cells	cell	NNS	_	_	_
150	after	after	IN	_	_	_
151	24	24	CD	_	_	_
152	min	min	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	untreated	untreated	JJ	_	_	_
155	cells	cell	NNS	_	_	_
156	after	after	IN	_	_	_
157	60	60	CD	_	_	_
158	min	min	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	untreated	untreated	JJ	_	_	_
161	control	control	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
163	Untreated	untreated	JJ	_	_	_
164	E.	e.	FW	_	_	_
165	coli	coli	FW	_	_	_
166	cells	cell	NNS	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
168	Untreated	untreated	JJ	_	_	_
169	Rep	Rep	NNP	_	_	_
170	1	1	LS	_	_	_
171	-	-	:	_	_	_
172	A-IP	a-ip	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	Untreated	untreated	JJ	_	_	_
175	Rep	Rep	NNP	_	_	_
176	1	1	LS	_	_	_
177	-	-	:	_	_	_
178	A+IP	a+ip	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	Untreated	untreated	JJ	_	_	_
181	Rep	Rep	NNP	_	_	_
182	2	2	LS	_	_	_
183	-	-	:	_	_	_
184	A-IP	a-ip	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	Untreated	untreated	JJ	_	_	_
187	Rep	Rep	NNP	_	_	_
188	2	2	LS	_	_	_
189	-	-	:	_	_	_
190	A+IP	a+ip	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	Untreated	untreated	JJ	_	_	_
193	Rep	Rep	NNP	_	_	_
194	3	3	LS	_	_	_
195	-	-	:	_	_	_
196	A-IP	a-ip	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	Untreated	untreated	JJ	_	_	_
199	Rep	Rep	NNP	_	_	_
200	3	3	LS	_	_	_
201	-	-	:	_	_	_
202	A+IP	a+ip	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	Untreated	untreated	JJ	_	_	_
205	_	_	NN	_	_	_
206	replicate	replicate	VB	_	_	_
207	_	_	SYM	_	_	_
208	1	1	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	Untreated	untreated	JJ	_	_	_
211	_	_	NN	_	_	_
212	replicate	replicate	VBP	_	_	_
213	_	_	NN	_	_	_
214	2	2	CD	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
216	Untreated	untreated	JJ	_	_	_
217	_	_	NN	_	_	_
218	replicate	replicate	VB	_	_	_
219	_	_	SYM	_	_	_
220	3	3	CD	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	Untreated	untreated	JJ	_	_	_
223	wild	wild	JJ	_	_	_
224	type	type	NN	_	_	_
225	versus	versus	CC	_	_	_
226	untreated	untreated	JJ	_	_	_
227	yajL	yajl	NN	GEN	_	_
228	mutant	mutant	NN	_	_	_
229	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Uridine	uridine	NN	_	_	_
3	addition	addition	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	uropathogenic	uropathogenic	JJ	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	UPEC	upec	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	uropathogenic	uropathogenic	JJ	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	UPEC	upec	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	grown	grow	VBN	_	_	_
19	with	with	IN	_	_	_
20	nitrosative	nitrosative	JJ	_	_	_
21	stress	stress	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	uropathogenic	uropathogenic	JJ	_	_	_
24	Escherichia	escherichia	FW	Organism	_	_
25	coli	coli	FW	Organism	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	UPEC	upec	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	grown	grow	VBN	_	_	_
30	without	without	IN	_	_	_
31	nitrosative	nitrosative	JJ	_	_	_
32	stress	stress	NN	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Used	use	VBD	_	_	_
35	SAMTOOLS	samtools	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Li	Li	NNP	_	_	_
38	,	,	,	_	_	_
39	et	et	FW	_	_	_
40	al.	al.	FW	_	_	_
41	,	,	,	_	_	_
42	PMID	pmid	NN	_	_	_
43	1950593	1950593	CD	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	to	to	TO	_	_	_
46	sort	sort	VB	_	_	_
47	and	and	CC	_	_	_
48	index	index	NN	_	_	_
49	the	the	DT	_	_	_
50	SAM	SAM	NNP	_	_	_
51	files	file	NNS	_	_	_
52	obtained	obtain	VBN	_	_	_
53	from	from	IN	_	_	_
54	Bowtie2	bowtie2	NN	_	_	_
55	and	and	CC	_	_	_
56	convert	convert	VB	_	_	_
57	them	they	PRP	_	_	_
58	to	to	TO	_	_	_
59	BAM	BAM	NNP	_	_	_
60	format	format	NN	_	_	_
61	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Used	use	VBD	_	_	_
3	SAMTOOLS	samtools	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	Li	Li	NNP	_	_	_
6	,	,	,	_	_	_
7	et	et	FW	_	_	_
8	al.	al.	FW	_	_	_
9	,	,	,	_	_	_
10	PMID	pmid	NN	_	_	_
11	1950593	1950593	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	to	to	TO	_	_	_
14	sort	sort	VB	_	_	_
15	and	and	CC	_	_	_
16	index	index	NN	_	_	_
17	the	the	DT	_	_	_
18	SAM	SAM	NNP	_	_	_
19	files	file	NNS	_	_	_
20	obtained	obtain	VBN	_	_	_
21	from	from	IN	_	_	_
22	Bowtie	Bowtie	NNP	_	_	_
23	and	and	CC	_	_	_
24	convert	convert	VB	_	_	_
25	them	they	PRP	_	_	_
26	to	to	TO	_	_	_
27	BAM	BAM	NNP	_	_	_
28	format	format	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Using	use	VBG	_	_	_
3	a	a	DT	_	_	_
4	combination	combination	NN	_	_	_
5	of	of	IN	_	_	_
6	python	python	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	3.2.1	3.2.1	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	and	and	CC	_	_	_
11	bowtie	bowtie	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	0.12.7	0.12.7	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	from	from	IN	_	_	_
17	the	the	DT	_	_	_
18	raw	raw	JJ	_	_	_
19	sequencing	sequencing	NN	_	_	_
20	data	datum	NNS	_	_	_
21	,	,	,	_	_	_
22	we	we	PRP	_	_	_
23	isolated	isolate	VBD	_	_	_
24	reads	read	VBZ	_	_	_
25	which	which	WDT	_	_	_
26	contained	contain	VBD	_	_	_
27	barcode	barcode	NN	_	_	_
28	sequences	sequence	NNS	_	_	_
29	that	that	WDT	_	_	_
30	corresponded	correspond	VBD	_	_	_
31	to	to	TO	_	_	_
32	our	we	PRP$	_	_	_
33	original	original	JJ	_	_	_
34	list	list	NN	_	_	_
35	of	of	IN	_	_	_
36	single	single	JJ	_	_	_
37	molecule	molecule	NN	_	_	_
38	barcodes	barcode	NNS	_	_	_
39	in	in	IN	_	_	_
40	both	both	CC	_	_	_
41	forward	forward	RB	_	_	_
42	and	and	CC	_	_	_
43	reverse	reverse	VB	_	_	_
44	reads	read	VBZ	_	_	_
45	for	for	IN	_	_	_
46	each	each	DT	_	_	_
47	sequence	sequence	NN	_	_	_
48	pair	pair	NN	_	_	_
49	that	that	WDT	_	_	_
50	had	have	VBD	_	_	_
51	at	at	IN	_	_	_
52	most	most	JJS	_	_	_
53	one	one	CD	_	_	_
54	mismatch	mismatch	NN	_	_	_
55	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Using	use	VBG	_	_	_
3	blind	blind	JJ	_	_	_
4	and	and	CC	_	_	_
5	fit-only	fit-only	JJ	_	_	_
6	parameter	parameter	NN	_	_	_
7	in	in	IN	_	_	_
8	DE-Seq	de-seq	NN	_	_	_
9	pakage	pakage	NN	_	_	_
10	,	,	,	_	_	_
11	expressions	expression	NNS	_	_	_
12	of	of	IN	_	_	_
13	genes	gene	NNS	_	_	_
14	in	in	IN	_	_	_
15	all	all	DT	_	_	_
16	samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	changed	change	VBN	_	_	_
19	to	to	TO	_	_	_
20	count	count	VB	_	_	_
21	per	per	IN	_	_	_
22	gene	gene	NN	_	_	_
23	,	,	,	_	_	_
24	using	use	VBG	_	_	_
25	RNA-Seq	rna-seq	NN	_	_	_
26	protocol	protocol	NN	_	_	_
27	on	on	IN	_	_	_
28	Illumina	Illumina	NNP	_	_	_
29	HiSeq2500	HiSeq2500	NNP	_	_	_
30	platform	platform	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Using	use	VBG	_	_	_
33	Bowtie2	bowtie2	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	version	version	NN	_	_	_
36	2.0.2	2.0.2	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	,	,	,	_	_	_
39	sequenced	sequence	VBN	_	_	_
40	reads	read	VBZ	_	_	_
41	were	be	VBD	_	_	_
42	mapped	map	VBN	_	_	_
43	to	to	TO	_	_	_
44	an	a	DT	_	_	_
45	EPEC	epec	NN	_	_	_
46	O127	o127	NN	_	_	_
47	:	:	:	_	_	_
48	H6	h6	NN	_	_	_
49	reference	reference	NN	_	_	_
50	genome	genome	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	EMBL/GenBank	embl/genbank	NN	_	_	_
53	accession	accession	NN	_	_	_
54	codes	code	NNS	_	_	_
55	FM180568	fm180568	NN	_	_	_
56	,	,	,	_	_	_
57	FM180569	fm180569	NN	_	_	_
58	,	,	,	_	_	_
59	and	and	CC	_	_	_
60	FM180570	fm180570	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	.	.	.	_	_	_

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	uspA	uspa	NN	GEN	_	_
8	__	__	CD	_	_	_
9	U	U	NNP	_	_	_
10	_	_	NNP	_	_	_
11	N0075	N0075	NNP	_	_	_
12	_	_	SYM	_	_	_
13	r1	r1	FW	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
15	uspA	uspa	NN	GEN	_	_
16	__	__	CD	_	_	_
17	U	U	NNP	_	_	_
18	_	_	NNP	_	_	_
19	N0075	N0075	NNP	_	_	_
20	_	_	SYM	_	_	_
21	r2	r2	FW	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
23	uspA	uspa	NN	GEN	_	_
24	__	__	CD	_	_	_
25	U	U	NNP	_	_	_
26	_	_	NNP	_	_	_
27	N0075	N0075	NNP	_	_	_
28	_	_	SYM	_	_	_
29	r3	r3	FW	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
31	uspA	uspa	NN	GEN	_	_
32	upregulation	upregulation	NN	_	_	_
33	,	,	,	_	_	_
34	0.075	0.075	CD	_	_	_
35	mg/mL	mg/ml	NN	_	_	_
36	norfloxacin	norfloxacin	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	UVA	uva	NN	_	_	_
39	irradiated	irradiated	JJ	_	_	_
40	chemostat	chemostat	NN	_	_	_
41	for	for	IN	_	_	_
42	1	1	CD	_	_	_
43	h	h	NN	_	_	_
44	,	,	,	_	_	_
45	run	run	VBP	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	UVA	uva	NN	_	_	_
49	irradiated	irradiated	JJ	_	_	_
50	chemostat	chemostat	NN	_	_	_
51	for	for	IN	_	_	_
52	1	1	CD	_	_	_
53	h	h	NN	_	_	_
54	,	,	,	_	_	_
55	run	run	NN	_	_	_
56	2	2	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	UVA	uva	NN	_	_	_
59	irradiated	irradiated	JJ	_	_	_
60	chemostat	chemostat	NN	_	_	_
61	for	for	IN	_	_	_
62	1	1	CD	_	_	_
63	h	h	NN	_	_	_
64	,	,	,	_	_	_
65	run	run	NN	_	_	_
66	2	2	CD	_	_	_
67	dye	dye	VBP	_	_	_
68	swap	swap	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	UVA	uva	NN	_	_	_
71	irradiated	irradiated	JJ	_	_	_
72	chemostat	chemostat	NN	_	_	_
73	for	for	IN	_	_	_
74	1	1	CD	_	_	_
75	h	h	NN	_	_	_
76	,	,	,	_	_	_
77	run	run	VBP	_	_	_
78	3	3	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	UVA	uva	NN	_	_	_
81	irradiated	irradiated	JJ	_	_	_
82	chemostat	chemostat	NN	_	_	_
83	for	for	IN	_	_	_
84	50	50	CD	_	_	_
85	h	h	NN	_	_	_
86	,	,	,	_	_	_
87	run	run	VBP	_	_	_
88	1	1	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	UVA	uva	NN	_	_	_
91	irradiated	irradiated	JJ	_	_	_
92	chemostat	chemostat	NN	_	_	_
93	for	for	IN	_	_	_
94	50	50	CD	_	_	_
95	h	h	NN	_	_	_
96	,	,	,	_	_	_
97	run	run	NN	_	_	_
98	2	2	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	UVA	uva	NN	_	_	_
101	irradiated	irradiated	JJ	_	_	_
102	chemostat	chemostat	NN	_	_	_
103	for	for	IN	_	_	_
104	50	50	CD	_	_	_
105	h	h	NN	_	_	_
106	,	,	,	_	_	_
107	run	run	VBP	_	_	_
108	3	3	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	uvrA	uvra	NN	GEN	_	_
111	___	___	CD	_	_	_
112	U	U	NNP	_	_	_
113	_	_	NNP	_	_	_
114	N0025	N0025	NNP	_	_	_
115	_	_	VBD	_	_	_
116	r1	r1	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	uvrA	uvra	NN	GEN	_	_
119	___	___	CD	_	_	_
120	U	U	NNP	_	_	_
121	_	_	NNP	_	_	_
122	N0025	N0025	NNP	_	_	_
123	_	_	VBD	_	_	_
124	r2	r2	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	uvrA	uvra	NN	GEN	_	_
127	___	___	CD	_	_	_
128	U	U	NNP	_	_	_
129	_	_	NNP	_	_	_
130	N0025	N0025	NNP	_	_	_
131	_	_	SYM	_	_	_
132	r3	r3	FW	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
134	uvrA	uvra	NN	GEN	_	_
135	upregulation	upregulation	NN	_	_	_
136	,	,	,	_	_	_
137	amp	amp	NN	_	_	_
138	50ug/ml	50ug/ml	NN	_	_	_
139	,	,	,	_	_	_
140	0.0125	0.0125	CD	_	_	_
141	%	%	NN	_	_	_
142	arabinose	arabinose	NN	_	_	_
143	,	,	,	_	_	_
144	0.025	0.025	CD	_	_	_
145	ug/ml	ug/ml	NN	_	_	_
146	norfloxacin	norfloxacin	NN	_	_	_
147	OD	od	NN	_	_	_
148	~	~	NN	_	_	_
149	0.3	0.3	CD	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	UvrY	uvry	NN	TF	_	_
152	-	-	:	_	_	_
153	ChIP-exo	ChIP-exo	NNP	_	_	_
154	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
155	UvrY	uvry	NN	TF	_	_
156	-LRB-	-lrb-	-LRB-	_	_	_
157	Response	response	NN	_	_	_
158	regulator	regulator	NN	_	_	_
159	of	of	IN	_	_	_
160	the	the	DT	_	_	_
161	BarA/UvrY	bara/uvry	NN	_	_	_
162	two-component	two-component	JJ	_	_	_
163	system	system	NN	_	_	_
164	-RRB-	-rrb-	-RRB-	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	V1	v1	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	V1	v1	NN	_	_	_
169	biological	biological	JJ	_	_	_
170	replicate	replicate	VB	_	_	_
171	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
172	Valine	Valine	NNP	_	_	_
173	addition	addition	NN	_	_	_
174	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
175	VALUE	VALUE	NNP	_	_	_
176	is	be	VBZ	_	_	_
177	Log	log	NN	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	base	base	NN	_	_	_
180	2	2	CD	_	_	_
181	-RRB-	-rrb-	-RRB-	_	_	_
182	of	of	IN	_	_	_
183	the	the	DT	_	_	_
184	ratio	ratio	NN	_	_	_
185	of	of	IN	_	_	_
186	the	the	DT	_	_	_
187	mean	mean	NN	_	_	_
188	of	of	IN	_	_	_
189	Channel	Channel	NNP	_	_	_
190	2	2	CD	_	_	_
191	-LRB-	-lrb-	-LRB-	_	_	_
192	usually	usually	RB	_	_	_
193	635	635	CD	_	_	_
194	nm	nm	NN	_	_	_
195	-RRB-	-rrb-	-RRB-	_	_	_
196	to	to	TO	_	_	_
197	Channel	Channel	NNP	_	_	_
198	1	1	CD	_	_	_
199	-LRB-	-lrb-	-LRB-	_	_	_
200	usually	usually	RB	_	_	_
201	532	532	CD	_	_	_
202	nm	nm	NN	_	_	_
203	-RRB-	-rrb-	-RRB-	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	VALUE	value	NN	_	_	_
206	is	be	VBZ	_	_	_
207	Log	log	NN	_	_	_
208	-LRB-	-lrb-	-LRB-	_	_	_
209	base	base	NN	_	_	_
210	2	2	CD	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	of	of	IN	_	_	_
213	the	the	DT	_	_	_
214	ratio	ratio	NN	_	_	_
215	of	of	IN	_	_	_
216	the	the	DT	_	_	_
217	median	median	NN	_	_	_
218	of	of	IN	_	_	_
219	Channel	Channel	NNP	_	_	_
220	2	2	CD	_	_	_
221	-LRB-	-lrb-	-LRB-	_	_	_
222	usually	usually	RB	_	_	_
223	635	635	CD	_	_	_
224	nm	nm	NN	_	_	_
225	-RRB-	-rrb-	-RRB-	_	_	_
226	to	to	TO	_	_	_
227	Channel	Channel	NNP	_	_	_
228	1	1	CD	_	_	_
229	-LRB-	-lrb-	-LRB-	_	_	_
230	usually	usually	RB	_	_	_
231	532	532	CD	_	_	_
232	nm	nm	NN	_	_	_
233	-RRB-	-rrb-	-RRB-	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	VALUE	value	NN	_	_	_
236	=	=	JJ	_	_	_
237	log2	log2	NN	_	_	_
238	-LRB-	-lrb-	-LRB-	_	_	_
239	Cy3	cy3	NN	_	_	_
240	_	_	CD	_	_	_
241	signal/Cy5	signal/cy5	NN	_	_	_
242	_	_	NN	_	_	_
243	signal	signal	NN	_	_	_
244	-RRB-	-rrb-	-RRB-	_	_	_
245	=	=	JJ	_	_	_
246	log2	log2	NN	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	SIGNAL	signal	NN	_	_	_
249	_	_	CD	_	_	_
250	GREEN/SIGNAL	green/signal	NN	_	_	_
251	_	_	CD	_	_	_
252	RED	red	NN	_	_	_
253	-RRB-	-rrb-	-RRB-	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	VALUE	value	NN	_	_	_
256	=	=	JJ	_	_	_
257	log2	log2	NN	_	_	_
258	-LRB-	-lrb-	-LRB-	_	_	_
259	Cy5	cy5	NN	_	_	_
260	_	_	CD	_	_	_
261	signal/Cy3	signal/cy3	NN	_	_	_
262	_	_	NN	_	_	_
263	signal	signal	NN	_	_	_
264	-RRB-	-rrb-	-RRB-	_	_	_
265	=	=	JJ	_	_	_
266	log2	log2	NN	_	_	_
267	-LRB-	-lrb-	-LRB-	_	_	_
268	SIGNAL	signal	NN	_	_	_
269	_	_	CD	_	_	_
270	RED/SIGNAL	red/signal	NN	_	_	_
271	_	_	CD	_	_	_
272	GREEN	green	NN	_	_	_
273	-RRB-	-rrb-	-RRB-	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	VALUEs	value	NNS	_	_	_
276	are	be	VBP	_	_	_
277	calculated	calculate	VBN	_	_	_
278	as	as	IN	_	_	_
279	log2-transformed	log2-transformed	JJ	_	_	_
280	-LRB-	-lrb-	-LRB-	_	_	_
281	test/ref	test/ref	NN	_	_	_
282	-RRB-	-rrb-	-RRB-	_	_	_
283	ratios	ratio	NNS	_	_	_
284	after	after	IN	_	_	_
285	background	background	NN	_	_	_
286	correction	correction	NN	_	_	_
287	and	and	CC	_	_	_
288	limma	limma	NN	_	_	_
289	's	's	POS	_	_	_
290	LOESS	loess	JJ	_	_	_
291	normalization	normalization	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	vector	vector	NN	_	_	_
294	:	:	:	_	_	_
295	pET-28a	pet-28a	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	vector	vector	NN	_	_	_
298	:	:	:	_	_	_
299	pET-28a-BnTR1	pet-28a-bntr1	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	Vector	Vector	NNP	_	_	_
302	rep1	rep1	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	Vector	Vector	NNP	_	_	_
305	rep2	rep2	NN	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	Vector	Vector	NNP	_	_	_
308	rep3	rep3	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	Veg	veg	NN	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	verified	verify	VBN	_	_	_
313	with	with	IN	_	_	_
314	in-house	in-house	JJ	_	_	_
315	pipeline	pipeline	NN	_	_	_
316	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
317	Vertis	Vertis	NNP	_	_	_
318	Biotechnologie	Biotechnologie	NNP	_	_	_
319	AG	AG	NNP	_	_	_
320	bioinformatics	bioinformatic	NNS	_	_	_
321	department	department	NN	_	_	_
322	did	do	VBD	_	_	_
323	a	a	DT	_	_	_
324	preliminary	preliminary	JJ	_	_	_
325	analysis	analysis	NN	_	_	_
326	of	of	IN	_	_	_
327	the	the	DT	_	_	_
328	high-throughput	high-throughput	JJ	_	_	_
329	sequencing	sequencing	NN	_	_	_
330	results	result	NNS	_	_	_
331	which	which	WDT	_	_	_
332	included	include	VBD	_	_	_
333	the	the	DT	_	_	_
334	mapping	mapping	NN	_	_	_
335	of	of	IN	_	_	_
336	the	the	DT	_	_	_
337	reads	read	VBZ	_	_	_
338	against	against	IN	_	_	_
339	E.	e.	FW	_	_	_
340	coli	coli	FW	_	_	_
341	genome	genome	NN	_	_	_
342	-LRB-	-lrb-	-LRB-	_	_	_
343	NC	nc	NN	_	_	_
344	_	_	CD	_	_	_
345	000913	000913	CD	_	_	_
346	downloaded	download	VBN	_	_	_
347	from	from	IN	_	_	_
348	NCBI	NCBI	NNP	_	_	_
349	genome	genome	NN	_	_	_
350	database	database	NN	_	_	_
351	-RRB-	-rrb-	-RRB-	_	_	_
352	.	.	.	_	_	_

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/pHYD2411	gj13531/phyd2411	NN	_	_	_
29	and	and	CC	_	_	_
30	GJ13507	gj13507	NN	_	_	_
31	/	/	:	_	_	_
32	pHYD2412	phyd2412	NN	_	_	_
33	on	on	IN	_	_	_
34	glucose-minimal	glucose-minimal	NN	_	_	_
35	A	a	NN	_	_	_
36	plates	plate	VBZ	_	_	_
37	supplemented	supplement	VBN	_	_	_
38	with	with	IN	_	_	_
39	Xgal	xgal	NN	_	_	_
40	and	and	CC	_	_	_
41	IPTG	iptg	NN	_	_	_
42	at	at	IN	_	_	_
43	200	200	CD	_	_	_
44	μM	μm	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	for	for	IN	_	_	_
47	Δrho	δrho	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	or	or	CC	_	_	_
50	3	3	CD	_	_	_
51	μM	μm	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	for	for	IN	_	_	_
54	ΔnusG	δnusg	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	,	,	,	_	_	_
57	as	as	IN	_	_	_
58	previously	previously	RB	_	_	_
59	described	describe	VBN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Visualizations	visualization	NNS	_	_	_
62	for	for	IN	_	_	_
63	assessing	assess	VBG	_	_	_
64	the	the	DT	_	_	_
65	quality	quality	NN	_	_	_
66	of	of	IN	_	_	_
67	the	the	DT	_	_	_
68	array	array	NN	_	_	_
69	data	datum	NNS	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	W3110	w3110	NN	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	KCTC	kctc	NN	_	_	_
74	2223	2223	CD	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	W3110	w3110	NN	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	lacI-deleted	laci-deleted	JJ	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	strain	strain	NN	_	_	_
82	harboring	harbor	VBG	_	_	_
83	pKK223-3	pkk223-3	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	W3110	w3110	NN	_	_	_
86	lsrK	lsrk	NN	GEN	_	_
87	mutants	mutant	NNS	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	W3110	w3110	NN	_	_	_
90	lsrK	lsrk	NN	GEN	_	_
91	mutants	mutant	NNS	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	W3110	w3110	NN	_	_	_
94	lsrK	lsrk	NN	GEN	_	_
95	mutants	mutant	NNS	_	_	_
96	,	,	,	_	_	_
97	biological	biological	JJ	_	_	_
98	rep1	rep1	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	W3110	w3110	NN	_	_	_
101	lsrK	lsrk	NN	GEN	_	_
102	mutants	mutant	NNS	_	_	_
103	,	,	,	_	_	_
104	biological	biological	JJ	_	_	_
105	rep2	rep2	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	W3110	w3110	NN	_	_	_
108	lsrR	lsrr	NN	GEN	_	_
109	mutants	mutant	NNS	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	W3110	w3110	NN	_	_	_
112	lsrR	lsrr	NN	GEN	_	_
113	mutants	mutant	NNS	_	_	_
114	,	,	,	_	_	_
115	biological	biological	JJ	_	_	_
116	rep1	rep1	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	W3110	w3110	NN	_	_	_
119	lsrR	lsrr	NN	GEN	_	_
120	mutants	mutant	NNS	_	_	_
121	,	,	,	_	_	_
122	biological	biological	JJ	_	_	_
123	rep2	rep2	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	W3110	w3110	NN	_	_	_
126	overexpressing	overexpress	VBG	_	_	_
127	pck	pck	NN	GEN	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	W3110	w3110	NN	_	_	_
130	rpoC-6xHis	rpoc-6xhis	NN	_	_	_
131	:	:	:	_	_	_
132	:	:	:	_	_	_
133	kan	kan	FW	_	_	_
134	gal490	gal490	FW	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	W3110	w3110	NN	_	_	_
137	rpoC-6xHis	rpoc-6xhis	NN	_	_	_
138	:	:	:	_	_	_
139	:	:	:	_	_	_
140	kan	kan	NN	_	_	_
141	greA	grea	NN	GEN	_	_
142	:	:	:	_	_	_
143	:	:	:	_	_	_
144	tet	tet	NN	_	_	_
145	,	,	,	_	_	_
146	greB	greb	NN	GEN	_	_
147	:	:	:	_	_	_
148	:	:	:	_	_	_
149	amp	amp	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	W3110	w3110	NN	_	_	_
152	trpR2	trpr2	NN	_	_	_
153	,	,	,	_	_	_
154	min	min	NN	_	_	_
155	+.2	+.2	CD	_	_	_
156	%	%	NN	_	_	_
157	glucose	glucose	NN	SUPP	_	_
158	,	,	,	_	_	_
159	30	30	CD	_	_	_
160	ug	ug	NN	_	_	_
161	RNA	rna	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	W3110	w3110	NN	_	_	_
164	trpR2	trpr2	NN	_	_	_
165	-	-	:	_	_	_
166	trp	trp	NN	_	_	_
167	,	,	,	_	_	_
168	30	30	CD	_	_	_
169	ug	ug	NN	_	_	_
170	total	total	JJ	_	_	_
171	RNA	rna	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	W3110	w3110	NN	_	_	_
174	trpR2	trpr2	NN	_	_	_
175	+	+	CC	_	_	_
176	trp	trp	NN	_	_	_
177	,	,	,	_	_	_
178	30	30	CD	_	_	_
179	ug	ug	NN	_	_	_
180	total	total	JJ	_	_	_
181	RNA	rna	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	W3110	w3110	NN	_	_	_
184	wild	wild	JJ	_	_	_
185	type	type	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	W3110	w3110	NN	_	_	_
188	wild	wild	JJ	_	_	_
189	type	type	NN	_	_	_
190	,	,	,	_	_	_
191	biological	biological	JJ	_	_	_
192	rep1	rep1	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	W3110	w3110	NN	_	_	_
195	wild	wild	JJ	_	_	_
196	type	type	NN	_	_	_
197	,	,	,	_	_	_
198	biological	biological	JJ	_	_	_
199	rep2	rep2	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	W3110	w3110	NN	_	_	_
202	wt	wt	JJ	_	_	_
203	,	,	,	_	_	_
204	min	min	NN	_	_	_
205	+.2	+.2	CD	_	_	_
206	%	%	NN	_	_	_
207	glucose	glucose	NN	SUPP	_	_
208	,	,	,	_	_	_
209	30	30	CD	_	_	_
210	ug	ug	NN	_	_	_
211	RNA	rna	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	W3110	w3110	NN	_	_	_
214	wt-trp	wt-trp	NN	_	_	_
215	,	,	,	_	_	_
216	30	30	CD	_	_	_
217	ug	ug	NN	_	_	_
218	total	total	JJ	_	_	_
219	RNA	rna	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	W3110	w3110	NN	_	_	_
222	wt	wt	JJ	_	_	_
223	+	+	CC	_	_	_
224	trp	trp	NN	_	_	_
225	,	,	,	_	_	_
226	30	30	CD	_	_	_
227	ug	ug	NN	_	_	_
228	total	total	JJ	_	_	_
229	RNA	rna	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	Washed	wash	VBD	_	_	_
232	pellets	pellet	NNS	_	_	_
233	were	be	VBD	_	_	_
234	resuspended	resuspend	VBN	_	_	_
235	in	in	IN	_	_	_
236	1	1	CD	_	_	_
237	ml	ml	NN	_	_	_
238	of	of	IN	_	_	_
239	TESS	TESS	NNP	_	_	_
240	buffer	buffer	NN	_	_	_
241	-LRB-	-lrb-	-LRB-	_	_	_
242	10	10	CD	_	_	_
243	mM	mm	NN	KWSUPP	_	_
244	Tris-Cl	tris-cl	NN	_	_	_
245	pH7	ph7	NN	_	_	_
246	.5	.5	CD	_	_	_
247	,	,	,	_	_	_
248	1	1	CD	_	_	_
249	mM	mm	NN	KWSUPP	_	_
250	EDTA	edta	NN	_	_	_
251	,	,	,	_	_	_
252	250	250	CD	_	_	_
253	mM	mm	NN	KWSUPP	_	_
254	NaCl	nacl	NN	_	_	_
255	,	,	,	_	_	_
256	0.02	0.02	CD	_	_	_
257	%	%	NN	_	_	_
258	SDS	sds	NN	_	_	_
259	,	,	,	_	_	_
260	0.2	0.2	CD	_	_	_
261	%	%	NN	_	_	_
262	Tween-20	tween-20	NN	_	_	_
263	-RRB-	-rrb-	-RRB-	_	_	_
264	with	with	IN	_	_	_
265	addition	addition	NN	_	_	_
266	of	of	IN	_	_	_
267	proteases	protease	NNS	_	_	_
268	inhibitors	inhibitor	NNS	_	_	_
269	cocktail	cocktail	NN	_	_	_
270	-LRB-	-lrb-	-LRB-	_	_	_
271	cOmplete	complete	JJ	_	_	_
272	ultra	ultra	NNS	_	_	_
273	EDTA	edta	NN	_	_	_
274	free	free	JJ	_	_	_
275	,	,	,	_	_	_
276	Roche	Roche	NNP	_	_	_
277	-RRB-	-rrb-	-RRB-	_	_	_
278	and	and	CC	_	_	_
279	RNAse	rnase	NN	_	_	_
280	A	a	NN	_	_	_
281	-LRB-	-lrb-	-LRB-	_	_	_
282	Thermo	Thermo	NNP	_	_	_
283	Scientific	Scientific	NNP	_	_	_
284	-RRB-	-rrb-	-RRB-	_	_	_
285	.	.	.	_	_	_

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	NN	_	_	_
2	was	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	with	with	IN	_	_	_
5	70	70	CD	_	_	_
6	percent	percent	NN	_	_	_
7	ethanol	ethanol	NN	_	_	_
8	,	,	,	_	_	_
9	resuspended	resuspend	VBN	_	_	_
10	in	in	IN	_	_	_
11	30	30	CD	_	_	_
12	ul	ul	NN	_	_	_
13	water	water	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	held	hold	VBN	_	_	_
17	at	at	IN	_	_	_
18	4	4	CD	_	_	_
19	deg	deg	NN	_	_	_
20	.	.	.	_	_	_

1	C	c	NN	_	_	_
2	for	for	IN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	We	we	PRP	_	_	_
5	compared	compare	VBD	_	_	_
6	the	the	DT	_	_	_
7	microarray-determined	microarray-determined	JJ	_	_	_
8	mRNA	mrna	NN	_	_	_
9	profiles	profile	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Affymetrix	Affymetrix	NNP	_	_	_
12	E.	E.	NNP	_	_	_
13	coli	coli	NN	_	_	_
14	Genome	Genome	NNP	_	_	_
15	2.0	2.0	CD	_	_	_
16	Array	array	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	of	of	IN	_	_	_
19	Δfur	δfur	NN	_	_	_
20	and	and	CC	_	_	_
21	WT	wt	JJ	_	_	_
22	genotypes	genotype	NNS	_	_	_
23	in	in	IN	_	_	_
24	response	response	NN	_	_	_
25	to	to	TO	_	_	_
26	ciprofloxacin	ciprofloxacin	NN	_	_	_
27	treatment	treatment	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	100	100	CD	_	_	_
30	ng/ml	ng/ml	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	with	with	IN	_	_	_
33	those	those	DT	_	_	_
34	of	of	IN	_	_	_
35	untreated	untreated	JJ	_	_	_
36	cultures	culture	NNS	_	_	_
37	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	used	use	VBD	_	_	_
3	two	two	CD	_	_	_
4	biological	biological	JJ	_	_	_
5	replicates	replicate	VBZ	_	_	_
6	per	per	IN	_	_	_
7	genotype	genotype	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	We	we	PRP	_	_	_
3	developed	develop	VBD	_	_	_
4	in-house	in-house	JJ	_	_	_
5	computational	computational	JJ	_	_	_
6	and	and	CC	_	_	_
7	statistical	statistical	JJ	_	_	_
8	analysis	analysis	NN	_	_	_
9	tools	tool	NNS	_	_	_
10	for	for	IN	_	_	_
11	use	use	NN	_	_	_
12	with	with	IN	_	_	_
13	the	the	DT	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	tiling	tiling	NN	_	_	_
17	array	array	NN	_	_	_
18	.	.	.	_	_	_

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	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	pgcgrowthconditions	NN	_	_	_
2	We	we	PRP	_	_	_
3	extracted	extract	VBD	_	_	_
4	RNA	rna	NN	_	_	_
5	using	use	VBG	_	_	_
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	and	and	CC	_	_	_
13	RNeasy	RNeasy	NNP	_	_	_
14	Mini	Mini	NNP	_	_	_
15	Kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	qiagen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	combined	combine	VBN	_	_	_
20	with	with	IN	_	_	_
21	RNase-Free	rnase-free	JJ	_	_	_
22	DNase	dnase	NN	_	_	_
23	Set	set	VB	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Qiagen	Qiagen	NNP	_	_	_
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	instructions	instruction	NNS	_	_	_
33	.	.	.	_	_	_

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	were	be	VBD	_	_	_
15	above	above	IN	_	_	_
16	2	2	CD	_	_	_
17	standard	standard	JJ	_	_	_
18	deviations	deviation	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	background	background	NN	_	_	_
22	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
2	were	be	VBD	_	_	_
3	immediately	immediately	RB	_	_	_
4	frozen	freeze	VBN	_	_	_
5	in	in	IN	_	_	_
6	liquid	liquid	JJ	_	_	_
7	nitrogen	nitrogen	NN	_	_	_
8	and	and	CC	_	_	_
9	stored	store	VBD	_	_	_
10	at	at	IN	_	_	_
11	-80	-80	CD	_	_	_
12	deg	deg	NN	_	_	_
13	.	.	.	_	_	_

1	C.	c.	NN	_	_	_
2	For	for	IN	_	_	_
3	RNA	rna	NN	_	_	_
4	isolation	isolation	NN	_	_	_
5	,	,	,	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	We	we	PRP	_	_	_
8	then	then	RB	_	_	_
9	used	use	VBD	_	_	_
10	the	the	DT	_	_	_
11	mapped	map	VBN	_	_	_
12	files	file	NNS	_	_	_
13	to	to	TO	_	_	_
14	run	run	VB	_	_	_
15	Cufflinks	Cufflinks	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	estimates	estimate	VBZ	_	_	_
18	the	the	DT	_	_	_
19	relative	relative	JJ	_	_	_
20	abundance	abundance	NN	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	transcripts	transcript	NNS	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	after	after	IN	_	_	_
27	Cuffdiff	Cuffdiff	NNP	_	_	_
28	to	to	TO	_	_	_
29	find	find	VB	_	_	_
30	significant	significant	JJ	_	_	_
31	changes	change	NNS	_	_	_
32	in	in	IN	_	_	_
33	transcript	transcript	NN	_	_	_
34	expression	expression	NN	_	_	_
35	when	when	WRB	_	_	_
36	comparing	compare	VBG	_	_	_
37	two	two	CD	_	_	_
38	samples	sample	NNS	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Trapnell	Trapnell	NNP	_	_	_
41	,	,	,	_	_	_
42	Williams	Williams	NNP	_	_	_
43	et	et	FW	_	_	_
44	al.	al.	FW	_	_	_
45	2010	2010	CD	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

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	We	we	PRP	_	_	_
3	use	use	VBP	_	_	_
4	Rockhopper	Rockhopper	NNP	_	_	_
5	for	for	IN	_	_	_
6	alignment	alignment	NN	_	_	_
7	and	and	CC	_	_	_
8	the	the	DT	_	_	_
9	complete	complete	JJ	_	_	_
10	analysis	analysis	NN	_	_	_
11	of	of	IN	_	_	_
12	data	datum	NNS	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	When	when	WRB	_	_	_
15	cultures	culture	NNS	_	_	_
16	reached	reach	VBD	_	_	_
17	OD595	od595	NN	_	_	_
18	≈	≈	CD	_	_	_
19	0.470	0.470	CD	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	~	~	NN	_	_	_
22	200	200	CD	_	_	_
23	min	min	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	two	two	CD	_	_	_
27	cultures	culture	NNS	_	_	_
28	were	be	VBD	_	_	_
29	made	make	VBN	_	_	_
30	3	3	CD	_	_	_
31	µM	µm	NN	_	_	_
32	mercuric	mercuric	NN	_	_	_
33	chloride	chloride	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	HgCl2	hgcl2	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	or	or	CC	_	_	_
38	3	3	CD	_	_	_
39	µM	µm	NN	_	_	_
40	phenylmercuric-acetate	phenylmercuric-acetate	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	PMA	pma	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	and	and	CC	_	_	_
45	the	the	DT	_	_	_
46	third	third	JJ	_	_	_
47	was	be	VBD	_	_	_
48	left	leave	VBN	_	_	_
49	as	as	IN	_	_	_
50	an	a	DT	_	_	_
51	unexposed	unexposed	JJ	_	_	_
52	control	control	NN	_	_	_
53	.	.	.	_	_	_

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	PGCGROWTHCONDITIONS	NNP	_	_	_
2	When	when	WRB	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	cultivated	cultivate	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	exponential	exponential	JJ	_	_	_
11	growth	growth	NN	_	_	_
12	phase	phase	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	OD600	od600	NN	_	_	_
15	=	=	JJ	_	_	_
16	0.5	0.5	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	in	in	IN	_	_	_
19	Riesenberg	Riesenberg	NNP	_	_	_
20	medium	medium	NN	_	_	_
21	,	,	,	_	_	_
22	3	3	CD	_	_	_
23	or	or	CC	_	_	_
24	10	10	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	heptanoic	heptanoic	JJ	_	_	_
27	acid	acid	NN	_	_	_
28	was	be	VBD	_	_	_
29	treated	treat	VBN	_	_	_
30	to	to	TO	_	_	_
31	BL21	bl21	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	DE3	de3	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	K-12	k-12	NN	_	_	_
37	MG1655	mg1655	NN	_	_	_
38	,	,	,	_	_	_
39	respectively	respectively	RB	_	_	_
40	.	.	.	_	_	_

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	NNP	_	_	_
16	When	when	WRB	_	_	_
17	OD600	od600	NN	_	_	_
18	of	of	IN	_	_	_
19	the	the	DT	_	_	_
20	culture	culture	NN	_	_	_
21	reached	reach	VBD	_	_	_
22	0.54	0.54	CD	_	_	_
23	±	±	SYM	_	_	_
24	0.06	0.06	CD	_	_	_
25	,	,	,	_	_	_
26	cells	cell	NNS	_	_	_
27	were	be	VBD	_	_	_
28	treated	treat	VBN	_	_	_
29	with	with	IN	_	_	_
30	100	100	CD	_	_	_
31	µg/ml	µg/ml	NN	_	_	_
32	of	of	IN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	-	-	:	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	-	-	:	_	_	_
37	Roemerine	roemerine	NN	_	_	_
38	.	.	.	_	_	_

1	Since	since	IN	_	_	_
2	the	the	DT	_	_	_
3	alkaloid	alkaloid	NN	_	_	_
4	was	be	VBD	_	_	_
5	dissolved	dissolve	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMSO	dmso	NN	_	_	_
8	,	,	,	_	_	_
9	control	control	NN	_	_	_
10	cells	cell	NNS	_	_	_
11	were	be	VBD	_	_	_
12	also	also	RB	_	_	_
13	treated	treat	VBN	_	_	_
14	with	with	IN	_	_	_
15	the	the	DT	_	_	_
16	same	same	JJ	_	_	_
17	amount	amount	NN	_	_	_
18	of	of	IN	_	_	_
19	DMSO	dmso	NN	_	_	_
20	.	.	.	_	_	_

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	When	when	WRB	_	_	_
3	the	the	DT	_	_	_
4	cultures	culture	NNS	_	_	_
5	reached	reach	VBD	_	_	_
6	an	a	DT	_	_	_
7	OD600	od600	NN	_	_	_
8	0.6	0.6	CD	_	_	_
9	they	they	PRP	_	_	_
10	were	be	VBD	_	_	_
11	split	split	VBN	_	_	_
12	into	into	IN	_	_	_
13	two	two	CD	_	_	_
14	flasks	flask	NNS	_	_	_
15	,	,	,	_	_	_
16	each	each	DT	_	_	_
17	containing	contain	VBG	_	_	_
18	20	20	CD	_	_	_
19	ml	ml	NN	_	_	_
20	of	of	IN	_	_	_
21	the	the	DT	_	_	_
22	culture	culture	NN	_	_	_
23	.	.	.	_	_	_

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	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	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	NNP	_	_	_
2	Whole	whole	JJ	_	_	_
3	bacterial	bacterial	JJ	_	_	_
4	cell	cell	NN	_	_	_
5	RNA	rna	NN	_	_	_
6	transcriptome	transcriptome	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Whole	whole	JJ	_	_	_
9	cell	cell	NN	_	_	_
10	,	,	,	_	_	_
11	aspC	aspc	NN	GEN	_	_
12	KO	ko	NN	_	_	_
13	,	,	,	_	_	_
14	M9	m9	NN	_	_	_
15	and	and	CC	_	_	_
16	0.4	0.4	CD	_	_	_
17	%	%	NN	_	_	_
18	glucose	glucose	NN	SUPP	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Whole	whole	JJ	_	_	_
21	cell	cell	NN	_	_	_
22	,	,	,	_	_	_
23	cysA	cysa	NN	GEN	_	_
24	KO	ko	NN	_	_	_
25	,	,	,	_	_	_
26	M9	m9	NN	_	_	_
27	and	and	CC	_	_	_
28	0.4	0.4	CD	_	_	_
29	%	%	NN	_	_	_
30	glucose	glucose	NN	SUPP	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Whole	whole	JJ	_	_	_
33	cell	cell	NN	_	_	_
34	,	,	,	_	_	_
35	cysG	cysg	NN	GEN	_	_
36	KO	ko	NN	_	_	_
37	,	,	,	_	_	_
38	LB	lb	NN	_	_	_
39	and	and	CC	_	_	_
40	0.3	0.3	CD	_	_	_
41	%	%	NN	_	_	_
42	glucose	glucose	NN	SUPP	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Whole	whole	JJ	_	_	_
45	cell	cell	NN	_	_	_
46	,	,	,	_	_	_
47	cysH	cysh	NN	GEN	_	_
48	KO	ko	NN	_	_	_
49	,	,	,	_	_	_
50	LB	lb	NN	_	_	_
51	and	and	CC	_	_	_
52	0.3	0.3	CD	_	_	_
53	%	%	NN	_	_	_
54	glucose	glucose	NN	SUPP	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Whole	whole	JJ	_	_	_
57	cell	cell	NN	_	_	_
58	,	,	,	_	_	_
59	dcd	dcd	NN	GEN	_	_
60	KO	ko	NN	_	_	_
61	,	,	,	_	_	_
62	LB	lb	NN	_	_	_
63	and	and	CC	_	_	_
64	0.3	0.3	CD	_	_	_
65	%	%	NN	_	_	_
66	glucose	glucose	NN	SUPP	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Whole	whole	JJ	_	_	_
69	cell	cell	NN	_	_	_
70	,	,	,	_	_	_
71	dcd	dcd	NN	GEN	_	_
72	KO	ko	NN	_	_	_
73	,	,	,	_	_	_
74	M9	m9	NN	_	_	_
75	and	and	CC	_	_	_
76	0.3	0.3	CD	_	_	_
77	%	%	NN	_	_	_
78	glucose	glucose	NN	SUPP	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Whole	whole	JJ	_	_	_
81	cell	cell	NN	_	_	_
82	,	,	,	_	_	_
83	entF	entf	NN	GEN	_	_
84	KO	ko	NN	_	_	_
85	,	,	,	_	_	_
86	M9	m9	NN	_	_	_
87	and	and	CC	_	_	_
88	0.4	0.4	CD	_	_	_
89	%	%	NN	_	_	_
90	glucose	glucose	NN	SUPP	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Whole	whole	JJ	_	_	_
93	cell	cell	NN	_	_	_
94	,	,	,	_	_	_
95	fadR	fadr	NN	GEN	_	_
96	KO	ko	NN	_	_	_
97	,	,	,	_	_	_
98	LB	lb	NN	_	_	_
99	and	and	CC	_	_	_
100	0.3	0.3	CD	_	_	_
101	%	%	NN	_	_	_
102	glucose	glucose	NN	SUPP	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Whole	whole	JJ	_	_	_
105	cell	cell	NN	_	_	_
106	,	,	,	_	_	_
107	fadR	fadr	NN	GEN	_	_
108	KO	ko	NN	_	_	_
109	,	,	,	_	_	_
110	M9	m9	NN	_	_	_
111	and	and	CC	_	_	_
112	0.3	0.3	CD	_	_	_
113	%	%	NN	_	_	_
114	glucose	glucose	NN	SUPP	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Whole	whole	JJ	_	_	_
117	cell	cell	NN	_	_	_
118	,	,	,	_	_	_
119	fepA	fepa	NN	GEN	_	_
120	KO	ko	NN	_	_	_
121	,	,	,	_	_	_
122	LB	lb	NN	_	_	_
123	and	and	CC	_	_	_
124	0.3	0.3	CD	_	_	_
125	%	%	NN	_	_	_
126	glucose	glucose	NN	SUPP	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Whole	whole	JJ	_	_	_
129	cell	cell	NN	_	_	_
130	,	,	,	_	_	_
131	fepA	fepa	NN	GEN	_	_
132	KO	ko	NN	_	_	_
133	,	,	,	_	_	_
134	M9	m9	NN	_	_	_
135	and	and	CC	_	_	_
136	0.3	0.3	CD	_	_	_
137	%	%	NN	_	_	_
138	glucose	glucose	NN	SUPP	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	Whole	whole	JJ	_	_	_
141	cell	cell	NN	_	_	_
142	,	,	,	_	_	_
143	fliY	fliy	NN	_	_	_
144	KO	ko	NN	_	_	_
145	,	,	,	_	_	_
146	M9	m9	NN	_	_	_
147	and	and	CC	_	_	_
148	0.4	0.4	CD	_	_	_
149	%	%	NN	_	_	_
150	glucose	glucose	NN	SUPP	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	Whole	whole	JJ	_	_	_
153	cell	cell	NN	_	_	_
154	,	,	,	_	_	_
155	gabT	gabt	NN	GEN	_	_
156	KO	ko	NN	_	_	_
157	,	,	,	_	_	_
158	M9	m9	NN	_	_	_
159	and	and	CC	_	_	_
160	0.4	0.4	CD	_	_	_
161	%	%	NN	_	_	_
162	glucose	glucose	NN	SUPP	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	Whole	whole	JJ	_	_	_
165	cell	cell	NN	_	_	_
166	,	,	,	_	_	_
167	galE	gale	NN	GEN	_	_
168	KO	KO	NNP	_	_	_
169	,	,	,	_	_	_
170	M9	m9	NN	_	_	_
171	and	and	CC	_	_	_
172	0.4	0.4	CD	_	_	_
173	%	%	NN	_	_	_
174	glucose	glucose	NN	SUPP	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	Whole	whole	JJ	_	_	_
177	cell	cell	NN	_	_	_
178	,	,	,	_	_	_
179	kefB	kefb	NN	GEN	_	_
180	KO	ko	NN	_	_	_
181	,	,	,	_	_	_
182	M9	m9	NN	_	_	_
183	and	and	CC	_	_	_
184	0.4	0.4	CD	_	_	_
185	%	%	NN	_	_	_
186	glucose	glucose	NN	SUPP	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	Whole	whole	JJ	_	_	_
189	cell	cell	NN	_	_	_
190	,	,	,	_	_	_
191	khc	khc	NN	_	_	_
192	KO	ko	NN	_	_	_
193	,	,	,	_	_	_
194	M9	m9	NN	_	_	_
195	and	and	CC	_	_	_
196	0.4	0.4	CD	_	_	_
197	%	%	NN	_	_	_
198	glucose	glucose	NN	SUPP	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	Whole	whole	JJ	_	_	_
201	cell	cell	NN	_	_	_
202	,	,	,	_	_	_
203	lacA	laca	NN	GEN	_	_
204	KO	ko	NN	_	_	_
205	,	,	,	_	_	_
206	LB	lb	NN	_	_	_
207	and	and	CC	_	_	_
208	0.3	0.3	CD	_	_	_
209	%	%	NN	_	_	_
210	glucose	glucose	NN	SUPP	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	Whole	whole	JJ	_	_	_
213	cell	cell	NN	_	_	_
214	,	,	,	_	_	_
215	lacA	laca	NN	GEN	_	_
216	KO	ko	NN	_	_	_
217	,	,	,	_	_	_
218	M9	m9	NN	_	_	_
219	and	and	CC	_	_	_
220	0.3	0.3	CD	_	_	_
221	%	%	NN	_	_	_
222	glucose	glucose	NN	SUPP	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	Whole	whole	JJ	_	_	_
225	cell	cell	NN	_	_	_
226	,	,	,	_	_	_
227	lplA	lpla	NN	GEN	_	_
228	KO	ko	NN	_	_	_
229	,	,	,	_	_	_
230	M9	m9	NN	_	_	_
231	and	and	CC	_	_	_
232	0.4	0.4	CD	_	_	_
233	%	%	NN	_	_	_
234	glucose	glucose	NN	SUPP	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	whole	whole	JJ	_	_	_
237	cell	cell	NN	_	_	_
238	lysate	lysate	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	Whole	whole	JJ	_	_	_
241	cell	cell	NN	_	_	_
242	lysates	lysate	NNS	_	_	_
243	were	be	VBD	_	_	_
244	clarified	clarify	VBN	_	_	_
245	by	by	IN	_	_	_
246	brief	brief	JJ	_	_	_
247	centrifugation	centrifugation	NN	_	_	_
248	.	.	.	_	_	_

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	Whole	whole	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	,	,	,	_	_	_
5	mgtA	mgta	NN	GEN	_	_
6	KO	ko	NN	_	_	_
7	,	,	,	_	_	_
8	M9	m9	NN	_	_	_
9	and	and	CC	_	_	_
10	0.4	0.4	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Whole	whole	JJ	_	_	_
15	cell	cell	NN	_	_	_
16	,	,	,	_	_	_
17	mhpD	mhpd	NN	GEN	_	_
18	KO	ko	NN	_	_	_
19	,	,	,	_	_	_
20	M9	m9	NN	_	_	_
21	and	and	CC	_	_	_
22	0.4	0.4	CD	_	_	_
23	%	%	NN	_	_	_
24	glucose	glucose	NN	SUPP	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Whole	whole	JJ	_	_	_
27	cell	cell	NN	_	_	_
28	,	,	,	_	_	_
29	ppk	ppk	NN	GEN	_	_
30	KO	ko	NN	_	_	_
31	,	,	,	_	_	_
32	LB	lb	NN	_	_	_
33	and	and	CC	_	_	_
34	0.3	0.3	CD	_	_	_
35	%	%	NN	_	_	_
36	glucose	glucose	NN	SUPP	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Whole	whole	JJ	_	_	_
39	cell	cell	NN	_	_	_
40	,	,	,	_	_	_
41	ppk	ppk	NN	GEN	_	_
42	KO	ko	NN	_	_	_
43	,	,	,	_	_	_
44	M9	m9	NN	_	_	_
45	and	and	CC	_	_	_
46	0.3	0.3	CD	_	_	_
47	%	%	NN	_	_	_
48	glucose	glucose	NN	SUPP	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Whole	whole	JJ	_	_	_
51	cell	cell	NN	_	_	_
52	,	,	,	_	_	_
53	putP	putp	NN	GEN	_	_
54	KO	ko	NN	_	_	_
55	,	,	,	_	_	_
56	M9	m9	NN	_	_	_
57	and	and	CC	_	_	_
58	0.4	0.4	CD	_	_	_
59	%	%	NN	_	_	_
60	glucose	glucose	NN	SUPP	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Whole	whole	JJ	_	_	_
63	cell	cell	NN	_	_	_
64	,	,	,	_	_	_
65	rfbA	rfba	NN	GEN	_	_
66	KO	ko	NN	_	_	_
67	,	,	,	_	_	_
68	M9	m9	NN	_	_	_
69	and	and	CC	_	_	_
70	0.4	0.4	CD	_	_	_
71	%	%	NN	_	_	_
72	glucose	glucose	NN	SUPP	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Whole	whole	JJ	_	_	_
75	cell	cell	NN	_	_	_
76	,	,	,	_	_	_
77	sdhC	sdhc	NN	GEN	_	_
78	KO	ko	NN	_	_	_
79	,	,	,	_	_	_
80	M9	m9	NN	_	_	_
81	and	and	CC	_	_	_
82	0.4	0.4	CD	_	_	_
83	%	%	NN	_	_	_
84	glucose	glucose	NN	SUPP	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Whole	whole	JJ	_	_	_
87	cell	cell	NN	_	_	_
88	,	,	,	_	_	_
89	trpD	trpd	NN	GEN	_	_
90	KO	ko	NN	_	_	_
91	,	,	,	_	_	_
92	M9	m9	NN	_	_	_
93	and	and	CC	_	_	_
94	0.4	0.4	CD	_	_	_
95	%	%	NN	_	_	_
96	glucose	glucose	NN	SUPP	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Whole	whole	JJ	_	_	_
99	cell	cell	NN	_	_	_
100	,	,	,	_	_	_
101	ugpC	ugpc	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	WT	WT	NNP	_	_	_
114	,	,	,	_	_	_
115	LB	LB	NNP	_	_	_
116	and	and	CC	_	_	_
117	0.3	0.3	CD	_	_	_
118	%	%	NN	_	_	_
119	glucose	glucose	NN	SUPP	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Whole	whole	JJ	_	_	_
122	cell	cell	NN	_	_	_
123	,	,	,	_	_	_
124	WT	WT	NNP	_	_	_
125	,	,	,	_	_	_
126	M9	m9	NN	_	_	_
127	and	and	CC	_	_	_
128	0.3	0.3	CD	_	_	_
129	%	%	NN	_	_	_
130	glucose	glucose	NN	SUPP	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	Whole	whole	JJ	_	_	_
133	cell	cell	NN	_	_	_
134	,	,	,	_	_	_
135	WT	WT	NNP	_	_	_
136	,	,	,	_	_	_
137	M9	m9	NN	_	_	_
138	and	and	CC	_	_	_
139	0.4	0.4	CD	_	_	_
140	%	%	NN	_	_	_
141	glucose	glucose	NN	SUPP	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	Whole	whole	JJ	_	_	_
144	cell	cell	NN	_	_	_
145	,	,	,	_	_	_
146	wzc	wzc	NN	GEN	_	_
147	KO	ko	NN	_	_	_
148	,	,	,	_	_	_
149	LB	lb	NN	_	_	_
150	and	and	CC	_	_	_
151	0.3	0.3	CD	_	_	_
152	%	%	NN	_	_	_
153	glucose	glucose	NN	SUPP	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	Whole	whole	JJ	_	_	_
156	cell	cell	NN	_	_	_
157	,	,	,	_	_	_
158	wzc	wzc	NN	GEN	_	_
159	KO	ko	NN	_	_	_
160	,	,	,	_	_	_
161	M9	m9	NN	_	_	_
162	and	and	CC	_	_	_
163	0.3	0.3	CD	_	_	_
164	%	%	NN	_	_	_
165	glucose	glucose	NN	SUPP	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	Whole	whole	JJ	_	_	_
168	cell	cell	NN	_	_	_
169	,	,	,	_	_	_
170	yghD	yghd	NN	GEN	_	_
171	KO	ko	NN	_	_	_
172	,	,	,	_	_	_
173	LB	lb	NN	_	_	_
174	and	and	CC	_	_	_
175	0.3	0.3	CD	_	_	_
176	%	%	NN	_	_	_
177	glucose	glucose	NN	SUPP	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	Whole	whole	JJ	_	_	_
180	cell	cell	NN	_	_	_
181	,	,	,	_	_	_
182	yghD	yghd	NN	GEN	_	_
183	KO	ko	NN	_	_	_
184	,	,	,	_	_	_
185	M9	m9	NN	_	_	_
186	and	and	CC	_	_	_
187	0.3	0.3	CD	_	_	_
188	%	%	NN	_	_	_
189	glucose	glucose	NN	SUPP	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	WIG	wig	NN	_	_	_
192	files	file	NNS	_	_	_
193	were	be	VBD	_	_	_
194	normalized	normalize	VBN	_	_	_
195	by	by	IN	_	_	_
196	using	use	VBG	_	_	_
197	an	a	DT	_	_	_
198	in-house	in-house	JJ	_	_	_
199	script	script	NN	_	_	_
200	that	that	WDT	_	_	_
201	reads	read	VBZ	_	_	_
202	in	in	IN	_	_	_
203	the	the	DT	_	_	_
204	raw	raw	JJ	_	_	_
205	WIG	wig	NN	_	_	_
206	files	file	NNS	_	_	_
207	while	while	IN	_	_	_
208	excluding	exclude	VBG	_	_	_
209	counts	count	NNS	_	_	_
210	from	from	IN	_	_	_
211	all	all	DT	_	_	_
212	22	22	CD	_	_	_
213	rRNA	rrna	NN	_	_	_
214	genes	gene	NNS	_	_	_
215	.	.	.	_	_	_

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	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	wild	wild	JJ	_	_	_
3	type	type	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	wild-type	wild-type	JJ	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	wild	wild	JJ	_	_	_
8	type	type	NN	_	_	_
9	,	,	,	_	_	_
10	10	10	CD	_	_	_
11	%	%	NN	_	_	_
12	H2O2	h2o2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	wild-type	wild-type	JJ	_	_	_
15	1.0	1.0	CD	_	_	_
16	ug/ml	ug/ml	NN	_	_	_
17	norfloxacin	norfloxacin	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	wild-type	wild-type	JJ	_	_	_
20	15	15	CD	_	_	_
21	min	min	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	1	1	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	slide	slide	NN	_	_	_
26	1	1	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	wild-type	wild-type	JJ	_	_	_
29	15	15	CD	_	_	_
30	min	min	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	1	1	CD	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	slide	slide	NN	_	_	_
35	2	2	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	wild-type	wild-type	JJ	_	_	_
38	15	15	CD	_	_	_
39	min	min	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	2	2	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	slide	slide	NN	_	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	wild-type	wild-type	JJ	_	_	_
47	15	15	CD	_	_	_
48	min	min	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	2	2	CD	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	slide	slide	NN	_	_	_
53	2	2	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	wild-type	wild-type	JJ	_	_	_
56	1	1	CD	_	_	_
57	hour	hour	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	1	1	CD	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	slide	slide	NN	_	_	_
62	1	1	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	wild-type	wild-type	JJ	_	_	_
65	1	1	CD	_	_	_
66	hour	hour	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	1	1	CD	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	slide	slide	NN	_	_	_
71	2	2	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	wild-type	wild-type	JJ	_	_	_
74	1	1	CD	_	_	_
75	hour	hour	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	2	2	CD	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	slide	slide	NN	_	_	_
80	2	2	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
82	wild-type	wild-type	JJ	_	_	_
83	1	1	CD	_	_	_
84	hour	hour	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	3	3	CD	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	slide	slide	NN	_	_	_
89	1	1	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	wild-type	wild-type	JJ	_	_	_
92	1	1	CD	_	_	_
93	hour	hour	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	3	3	CD	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	slide	slide	NN	_	_	_
98	2	2	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
100	wild-type	wild-type	JJ	_	_	_
101	2	2	CD	_	_	_
102	hour	hour	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	1	1	CD	_	_	_
105	-RRB-	-rrb-	-RRB-	_	_	_
106	slide	slide	NN	_	_	_
107	1	1	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	wild-type	wild-type	JJ	_	_	_
110	2	2	CD	_	_	_
111	hour	hour	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	1	1	CD	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	slide	slide	NN	_	_	_
116	2	2	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
118	wild-type	wild-type	JJ	_	_	_
119	2	2	CD	_	_	_
120	hour	hour	NN	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	2	2	CD	_	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	slide	slide	NN	_	_	_
125	1	1	CD	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	wild-type	wild-type	JJ	_	_	_
128	2	2	CD	_	_	_
129	hour	hour	NN	_	_	_
130	-LRB-	-lrb-	-LRB-	_	_	_
131	2	2	CD	_	_	_
132	-RRB-	-rrb-	-RRB-	_	_	_
133	slide	slide	NN	_	_	_
134	2	2	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
136	wild-type	wild-type	JJ	_	_	_
137	2	2	CD	_	_	_
138	hour	hour	NN	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	3	3	CD	_	_	_
141	-RRB-	-rrb-	-RRB-	_	_	_
142	slide	slide	NN	_	_	_
143	1	1	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	wild-type	wild-type	JJ	_	_	_
146	2	2	CD	_	_	_
147	hour	hour	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	3	3	CD	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	slide	slide	NN	_	_	_
152	2	2	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
154	wild	wild	JJ	_	_	_
155	type	type	NN	_	_	_
156	,	,	,	_	_	_
157	30	30	CD	_	_	_
158	%	%	NN	_	_	_
159	H2O2	h2o2	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	wild-type	wild-type	JJ	_	_	_
162	30	30	CD	_	_	_
163	min	min	NN	_	_	_
164	-LRB-	-lrb-	-LRB-	_	_	_
165	1	1	CD	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	slide	slide	NN	_	_	_
168	1	1	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	wild-type	wild-type	JJ	_	_	_
171	30	30	CD	_	_	_
172	min	min	NN	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	1	1	CD	_	_	_
175	-RRB-	-rrb-	-RRB-	_	_	_
176	slide	slide	NN	_	_	_
177	2	2	CD	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
179	wild-type	wild-type	JJ	_	_	_
180	30	30	CD	_	_	_
181	min	min	NN	_	_	_
182	-LRB-	-lrb-	-LRB-	_	_	_
183	2	2	CD	_	_	_
184	-RRB-	-rrb-	-RRB-	_	_	_
185	slide	slide	NN	_	_	_
186	1	1	CD	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	wild-type	wild-type	JJ	_	_	_
189	30	30	CD	_	_	_
190	min	min	NN	_	_	_
191	-LRB-	-lrb-	-LRB-	_	_	_
192	2	2	CD	_	_	_
193	-RRB-	-rrb-	-RRB-	_	_	_
194	slide	slide	NN	_	_	_
195	2	2	CD	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
197	wild-type	wild-type	JJ	_	_	_
198	3	3	CD	_	_	_
199	hour	hour	NN	_	_	_
200	-LRB-	-lrb-	-LRB-	_	_	_
201	1	1	CD	_	_	_
202	-RRB-	-rrb-	-RRB-	_	_	_
203	slide	slide	NN	_	_	_
204	1	1	CD	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	wild-type	wild-type	JJ	_	_	_
207	3	3	CD	_	_	_
208	hour	hour	NN	_	_	_
209	-LRB-	-lrb-	-LRB-	_	_	_
210	1	1	CD	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	slide	slide	NN	_	_	_
213	2	2	CD	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
215	wild-type	wild-type	JJ	_	_	_
216	3	3	CD	_	_	_
217	hour	hour	NN	_	_	_
218	-LRB-	-lrb-	-LRB-	_	_	_
219	2	2	CD	_	_	_
220	-RRB-	-rrb-	-RRB-	_	_	_
221	slide	slide	NN	_	_	_
222	1	1	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	wild-type	wild-type	JJ	_	_	_
225	3	3	CD	_	_	_
226	hour	hour	NN	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	2	2	CD	_	_	_
229	-RRB-	-rrb-	-RRB-	_	_	_
230	slide	slide	NN	_	_	_
231	2	2	CD	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
233	wild-type	wild-type	JJ	_	_	_
234	3	3	CD	_	_	_
235	hour	hour	NN	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	3	3	CD	_	_	_
238	-RRB-	-rrb-	-RRB-	_	_	_
239	slide	slide	NN	_	_	_
240	1	1	CD	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	wild-type	wild-type	JJ	_	_	_
243	3	3	CD	_	_	_
244	hour	hour	NN	_	_	_
245	-LRB-	-lrb-	-LRB-	_	_	_
246	3	3	CD	_	_	_
247	-RRB-	-rrb-	-RRB-	_	_	_
248	slide	slide	NN	_	_	_
249	2	2	CD	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
251	wild-type	wild-type	JJ	_	_	_
252	4	4	CD	_	_	_
253	hour	hour	NN	_	_	_
254	-LRB-	-lrb-	-LRB-	_	_	_
255	1	1	CD	_	_	_
256	-RRB-	-rrb-	-RRB-	_	_	_
257	slide	slide	NN	_	_	_
258	1	1	CD	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	wild-type	wild-type	JJ	_	_	_
261	4	4	CD	_	_	_
262	hour	hour	NN	_	_	_
263	-LRB-	-lrb-	-LRB-	_	_	_
264	1	1	CD	_	_	_
265	-RRB-	-rrb-	-RRB-	_	_	_
266	slide	slide	NN	_	_	_
267	2	2	CD	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
269	wild-type	wild-type	JJ	_	_	_
270	4	4	CD	_	_	_
271	hour	hour	NN	_	_	_
272	-LRB-	-lrb-	-LRB-	_	_	_
273	2	2	CD	_	_	_
274	-RRB-	-rrb-	-RRB-	_	_	_
275	slide	slide	NN	_	_	_
276	1	1	CD	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	wild-type	wild-type	JJ	_	_	_
279	4	4	CD	_	_	_
280	hour	hour	NN	_	_	_
281	-LRB-	-lrb-	-LRB-	_	_	_
282	2	2	CD	_	_	_
283	-RRB-	-rrb-	-RRB-	_	_	_
284	slide	slide	NN	_	_	_
285	2	2	CD	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
287	wild-type	wild-type	JJ	_	_	_
288	4	4	CD	_	_	_
289	hour	hour	NN	_	_	_
290	-LRB-	-lrb-	-LRB-	_	_	_
291	3	3	CD	_	_	_
292	-RRB-	-rrb-	-RRB-	_	_	_
293	slide	slide	NN	_	_	_
294	1	1	CD	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	wild-type	wild-type	JJ	_	_	_
297	4	4	CD	_	_	_
298	hour	hour	NN	_	_	_
299	-LRB-	-lrb-	-LRB-	_	_	_
300	3	3	CD	_	_	_
301	-RRB-	-rrb-	-RRB-	_	_	_
302	slide	slide	NN	_	_	_
303	2	2	CD	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
305	wild-type	wild-type	JJ	_	_	_
306	5	5	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	wild-type	wild-type	JJ	_	_	_
315	5	5	CD	_	_	_
316	hour	hour	NN	_	_	_
317	-LRB-	-lrb-	-LRB-	_	_	_
318	1	1	CD	_	_	_
319	-RRB-	-rrb-	-RRB-	_	_	_
320	slide	slide	NN	_	_	_
321	2	2	CD	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
323	wild-type	wild-type	JJ	_	_	_
324	5	5	CD	_	_	_
325	hour	hour	NN	_	_	_
326	-LRB-	-lrb-	-LRB-	_	_	_
327	2	2	CD	_	_	_
328	-RRB-	-rrb-	-RRB-	_	_	_
329	slide	slide	NN	_	_	_
330	1	1	CD	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	wild-type	wild-type	JJ	_	_	_
333	5	5	CD	_	_	_
334	hour	hour	NN	_	_	_
335	-LRB-	-lrb-	-LRB-	_	_	_
336	2	2	CD	_	_	_
337	-RRB-	-rrb-	-RRB-	_	_	_
338	slide	slide	NN	_	_	_
339	2	2	CD	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
341	wild-type	wild-type	JJ	_	_	_
342	5	5	CD	_	_	_
343	min	min	NN	_	_	_
344	-LRB-	-lrb-	-LRB-	_	_	_
345	1	1	CD	_	_	_
346	-RRB-	-rrb-	-RRB-	_	_	_
347	slide	slide	NN	_	_	_
348	1	1	CD	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	wild-type	wild-type	JJ	_	_	_
351	5	5	CD	_	_	_
352	min	min	NN	_	_	_
353	-LRB-	-lrb-	-LRB-	_	_	_
354	1	1	CD	_	_	_
355	-RRB-	-rrb-	-RRB-	_	_	_
356	slide	slide	NN	_	_	_
357	2	2	CD	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
359	wild-type	wild-type	JJ	_	_	_
360	5	5	CD	_	_	_
361	min	min	NN	_	_	_
362	-LRB-	-lrb-	-LRB-	_	_	_
363	2	2	CD	_	_	_
364	-RRB-	-rrb-	-RRB-	_	_	_
365	slide	slide	NN	_	_	_
366	1	1	CD	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	wild-type	wild-type	JJ	_	_	_
369	5	5	CD	_	_	_
370	min	min	NN	_	_	_
371	-LRB-	-lrb-	-LRB-	_	_	_
372	2	2	CD	_	_	_
373	-RRB-	-rrb-	-RRB-	_	_	_
374	slide	slide	NN	_	_	_
375	2	2	CD	_	_	_
376	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
377	wild-type	wild-type	JJ	_	_	_
378	6	6	CD	_	_	_
379	hour	hour	NN	_	_	_
380	-LRB-	-lrb-	-LRB-	_	_	_
381	1	1	CD	_	_	_
382	-RRB-	-rrb-	-RRB-	_	_	_
383	slide	slide	NN	_	_	_
384	1	1	CD	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	wild-type	wild-type	JJ	_	_	_
387	6	6	CD	_	_	_
388	hour	hour	NN	_	_	_
389	-LRB-	-lrb-	-LRB-	_	_	_
390	1	1	CD	_	_	_
391	-RRB-	-rrb-	-RRB-	_	_	_
392	slide	slide	NN	_	_	_
393	2	2	CD	_	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
395	wild-type	wild-type	JJ	_	_	_
396	6	6	CD	_	_	_
397	hour	hour	NN	_	_	_
398	-LRB-	-lrb-	-LRB-	_	_	_
399	2	2	CD	_	_	_
400	-RRB-	-rrb-	-RRB-	_	_	_
401	slide	slide	NN	_	_	_
402	1	1	CD	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	wild-type	wild-type	JJ	_	_	_
405	6	6	CD	_	_	_
406	hour	hour	NN	_	_	_
407	-LRB-	-lrb-	-LRB-	_	_	_
408	2	2	CD	_	_	_
409	-RRB-	-rrb-	-RRB-	_	_	_
410	slide	slide	NN	_	_	_
411	2	2	CD	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
413	Wild-type	wild-type	JJ	_	_	_
414	Aerobic	Aerobic	NNP	_	_	_
415	A	A	NNP	_	_	_
416	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
417	Wild-type	wild-type	JJ	_	_	_
418	Aerobic	aerobic	JJ	_	_	_
419	B	b	NN	_	_	_
420	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
421	Wild-type	wild-type	JJ	_	_	_
422	Anaerobic	anaerobic	JJ	_	_	_
423	A	a	NN	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	Wild-type	wild-type	JJ	_	_	_
426	Anaerobic	anaerobic	JJ	_	_	_
427	B	b	NN	_	_	_
428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
429	Wild	Wild	NNP	_	_	_
430	type	type	NN	_	_	_
431	and	and	CC	_	_	_
432	the	the	DT	_	_	_
433	mutant	mutant	NN	_	_	_
434	were	be	VBD	_	_	_
435	grown	grow	VBN	_	_	_
436	on	on	IN	_	_	_
437	minimal	minimal	JJ	_	_	_
438	M9	m9	NN	_	_	_
439	media	media	NNS	_	_	_
440	with	with	IN	_	_	_
441	4	4	CD	_	_	_
442	g/L	g/l	NN	_	_	_
443	glucose	glucose	NN	SUPP	_	_
444	as	as	IN	_	_	_
445	a	a	DT	_	_	_
446	sole	sole	JJ	_	_	_
447	carbon	carbon	NN	_	_	_
448	source	source	NN	_	_	_
449	at	at	IN	_	_	_
450	37C	37c	NN	_	_	_
451	with	with	IN	_	_	_
452	aeration	aeration	NN	_	_	_
453	-LRB-	-lrb-	-LRB-	_	_	_
454	+	+	CC	_	_	_
455	O2	o2	CD	_	_	_
456	-RRB-	-rrb-	-RRB-	_	_	_
457	or	or	CC	_	_	_
458	nitrogen	nitrogen	NN	_	_	_
459	sparging	sparging	NN	_	_	_
460	-LRB-	-lrb-	-LRB-	_	_	_
461	-	-	:	_	_	_
462	O2	o2	CD	_	_	_
463	-RRB-	-rrb-	-RRB-	_	_	_
464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
465	wild	wild	JJ	_	_	_
466	type	type	NN	_	_	_
467	_	_	CD	_	_	_
468	anoxic	anoxic	JJ	_	_	_
469	-LRB-	-lrb-	-LRB-	_	_	_
470	NO3	no3	NN	_	_	_
471	-RRB-	-rrb-	-RRB-	_	_	_
472	_	_	SYM	_	_	_
473	glycerol	glycerol	NN	SUPP	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	wild	wild	JJ	_	_	_
476	type	type	NN	_	_	_
477	_	_	CD	_	_	_
478	anoxic	anoxic	JJ	_	_	_
479	-LRB-	-lrb-	-LRB-	_	_	_
480	NO3	no3	NN	_	_	_
481	-RRB-	-rrb-	-RRB-	_	_	_
482	_	_	SYM	_	_	_
483	glycerol	glycerol	NN	SUPP	_	_
484	+	+	CC	_	_	_
485	propionate	propionate	NN	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	wildtype	wildtype	JJ	_	_	_
488	,	,	,	_	_	_
489	brain	brain	NN	_	_	_
490	heart	heart	NN	_	_	_
491	infusion	infusion	NN	_	_	_
492	agar	agar	NN	_	_	_
493	,	,	,	_	_	_
494	rep	rep	NN	GEN	_	_
495	1	1	CD	_	_	_
496	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
497	wildtype	wildtype	JJ	_	_	_
498	,	,	,	_	_	_
499	brain	brain	NN	_	_	_
500	heart	heart	NN	_	_	_
501	infusion	infusion	NN	_	_	_
502	agar	agar	NN	_	_	_
503	,	,	,	_	_	_
504	rep	rep	NN	GEN	_	_
505	2	2	CD	_	_	_
506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
507	wildtype	wildtype	JJ	_	_	_
508	,	,	,	_	_	_
509	brain	brain	NN	_	_	_
510	heart	heart	NN	_	_	_
511	infusion	infusion	NN	_	_	_
512	agar	agar	NN	_	_	_
513	,	,	,	_	_	_
514	rep	rep	NN	GEN	_	_
515	3	3	CD	_	_	_
516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
517	wildtype	wildtype	JJ	_	_	_
518	,	,	,	_	_	_
519	brain	brain	NN	_	_	_
520	heart	heart	NN	_	_	_
521	infusion	infusion	NN	_	_	_
522	agar	agar	NN	_	_	_
523	+	+	CC	_	_	_
524	Sucrose	sucrose	NN	_	_	_
525	+	+	CC	_	_	_
526	MgSO4	mgso4	NN	_	_	_
527	,	,	,	_	_	_
528	rep	rep	NN	GEN	_	_
529	1	1	CD	_	_	_
530	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
531	wildtype	wildtype	JJ	_	_	_
532	,	,	,	_	_	_
533	brain	brain	NN	_	_	_
534	heart	heart	NN	_	_	_
535	infusion	infusion	NN	_	_	_
536	agar	agar	NN	_	_	_
537	+	+	CC	_	_	_
538	Sucrose	sucrose	NN	_	_	_
539	+	+	CC	_	_	_
540	MgSO4	mgso4	NN	_	_	_
541	,	,	,	_	_	_
542	rep	rep	NN	GEN	_	_
543	2	2	CD	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	wildtype	wildtype	JJ	_	_	_
546	,	,	,	_	_	_
547	brain	brain	NN	_	_	_
548	heart	heart	NN	_	_	_
549	infusion	infusion	NN	_	_	_
550	agar	agar	NN	_	_	_
551	+	+	CC	_	_	_
552	Sucrose	sucrose	NN	_	_	_
553	+	+	CC	_	_	_
554	MgSO4	mgso4	NN	_	_	_
555	,	,	,	_	_	_
556	rep	rep	NN	GEN	_	_
557	3	3	CD	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
559	Wild-type	wild-type	JJ	_	_	_
560	_	_	NN	_	_	_
561	cDNA	cdna	NN	_	_	_
562	_	_	CD	_	_	_
563	Aerobic	aerobic	JJ	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	Wild-type	wild-type	JJ	_	_	_
566	_	_	NN	_	_	_
567	cDNA	cdna	NN	_	_	_
568	_	_	CD	_	_	_
569	Anaerobic	anaerobic	JJ	_	_	_
570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
571	Wild-type	wild-type	JJ	_	_	_
572	Cells	cell	NNS	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
574	Wild-type	wild-type	JJ	_	_	_
575	Cells	cell	NNS	_	_	_
576	Replicate	replicate	VBP	_	_	_
577	1	1	CD	_	_	_
578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
579	Wild-type	wild-type	JJ	_	_	_
580	Cells	cell	NNS	_	_	_
581	Replicate	replicate	VB	_	_	_
582	2	2	CD	_	_	_
583	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
584	Wild-type	wild-type	JJ	_	_	_
585	Cells	cell	NNS	_	_	_
586	Replicate	replicate	VB	_	_	_
587	3	3	CD	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
589	wild-type	wild-type	JJ	_	_	_
590	cells	cell	NNS	_	_	_
591	with	with	IN	_	_	_
592	0.025	0.025	CD	_	_	_
593	ug/ml	ug/ml	NN	_	_	_
594	norfloxacin	norfloxacin	NN	_	_	_
595	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
596	wild-type	wild-type	JJ	_	_	_
597	cells	cell	NNS	_	_	_
598	with	with	IN	_	_	_
599	0.050	0.050	CD	_	_	_
600	ug/ml	ug/ml	NN	_	_	_
601	norfloxacin	norfloxacin	NN	_	_	_
602	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
603	wild-type	wild-type	JJ	_	_	_
604	cells	cell	NNS	_	_	_
605	with	with	IN	_	_	_
606	0.075	0.075	CD	_	_	_
607	ug/ml	ug/ml	NN	_	_	_
608	norfloxacin	norfloxacin	NN	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	wild-type	wild-type	JJ	_	_	_
611	cells	cell	NNS	_	_	_
612	without	without	IN	_	_	_
613	norfloxacin	norfloxacin	JJ	_	_	_
614	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
615	wildtype	wildtype	JJ	_	_	_
616	colony	colony	NN	_	_	_
617	morphology	morphology	NN	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	Wild	Wild	NNP	_	_	_
620	type	type	NN	_	_	_
621	control	control	NN	_	_	_
622	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
623	Wild	Wild	NNP	_	_	_
624	type	type	NN	_	_	_
625	control	control	NN	_	_	_
626	-LRB-	-lrb-	-LRB-	_	_	_
627	0	0	CD	_	_	_
628	min	min	NN	_	_	_
629	-RRB-	-rrb-	-RRB-	_	_	_
630	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
631	Wild	Wild	NNP	_	_	_
632	type	type	NN	_	_	_
633	control	control	NN	_	_	_
634	-LRB-	-lrb-	-LRB-	_	_	_
635	10	10	CD	_	_	_
636	min	min	NN	_	_	_
637	-RRB-	-rrb-	-RRB-	_	_	_
638	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
639	Wild	Wild	NNP	_	_	_
640	type	type	NN	_	_	_
641	control	control	NN	_	_	_
642	-LRB-	-lrb-	-LRB-	_	_	_
643	15	15	CD	_	_	_
644	min	min	NN	_	_	_
645	-RRB-	-rrb-	-RRB-	_	_	_
646	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
647	Wild	Wild	NNP	_	_	_
648	type	type	NN	_	_	_
649	control	control	NN	_	_	_
650	-LRB-	-lrb-	-LRB-	_	_	_
651	20	20	CD	_	_	_
652	min	min	NN	_	_	_
653	-RRB-	-rrb-	-RRB-	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
655	Wild	Wild	NNP	_	_	_
656	type	type	NN	_	_	_
657	control	control	NN	_	_	_
658	-LRB-	-lrb-	-LRB-	_	_	_
659	2.5	2.5	CD	_	_	_
660	min	min	NN	_	_	_
661	-RRB-	-rrb-	-RRB-	_	_	_
662	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
663	Wild	Wild	NNP	_	_	_
664	type	type	NN	_	_	_
665	control	control	NN	_	_	_
666	-LRB-	-lrb-	-LRB-	_	_	_
667	30	30	CD	_	_	_
668	min	min	NN	_	_	_
669	-RRB-	-rrb-	-RRB-	_	_	_
670	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
671	Wild	Wild	NNP	_	_	_
672	type	type	NN	_	_	_
673	control	control	NN	_	_	_
674	-LRB-	-lrb-	-LRB-	_	_	_
675	5	5	CD	_	_	_
676	min	min	NN	_	_	_
677	-RRB-	-rrb-	-RRB-	_	_	_
678	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
679	Wild	Wild	NNP	_	_	_
680	type	type	NN	_	_	_
681	control	control	NN	_	_	_
682	-LRB-	-lrb-	-LRB-	_	_	_
683	60	60	CD	_	_	_
684	min	min	NN	_	_	_
685	-RRB-	-rrb-	-RRB-	_	_	_
686	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
687	wild	wild	JJ	_	_	_
688	type	type	NN	_	_	_
689	E0	e0	NN	_	_	_
690	,	,	,	_	_	_
691	biological	biological	JJ	_	_	_
692	rep1	rep1	NN	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	wild	wild	JJ	_	_	_
695	type	type	NN	_	_	_
696	E0	e0	NN	_	_	_
697	,	,	,	_	_	_
698	biological	biological	JJ	_	_	_
699	rep2	rep2	NN	_	_	_
700	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
701	wild	wild	JJ	_	_	_
702	type	type	NN	_	_	_
703	E0	e0	NN	_	_	_
704	,	,	,	_	_	_
705	biological	biological	JJ	_	_	_
706	rep3	rep3	NN	_	_	_
707	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
708	Wild-type	wild-type	JJ	_	_	_
709	E.	e.	FW	_	_	_
710	coli	coli	FW	_	_	_
711	ATCC	atcc	NN	_	_	_
712	25922	25922	CD	_	_	_
713	replicate	replicate	VBP	_	_	_
714	1	1	CD	_	_	_
715	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
716	Wild-type	wild-type	JJ	_	_	_
717	E.	e.	FW	_	_	_
718	coli	coli	FW	_	_	_
719	ATCC	atcc	NN	_	_	_
720	25922	25922	CD	_	_	_
721	replicate	replicate	VBP	_	_	_
722	2	2	CD	_	_	_
723	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
724	Wild	Wild	NNP	_	_	_
725	type	type	NN	_	_	_
726	E.	e.	FW	_	_	_
727	coli	coli	FW	_	_	_
728	K-12	k-12	NN	_	_	_
729	-LRB-	-lrb-	-LRB-	_	_	_
730	strain	strain	NN	_	_	_
731	BW38038	bw38038	NN	_	_	_
732	-RRB-	-rrb-	-RRB-	_	_	_
733	and	and	CC	_	_	_
734	BW39452	bw39452	NN	_	_	_
735	-LRB-	-lrb-	-LRB-	_	_	_
736	ΔrpoS	δrpos	NN	_	_	_
737	-RRB-	-rrb-	-RRB-	_	_	_
738	cultures	culture	NNS	_	_	_
739	were	be	VBD	_	_	_
740	grown	grow	VBN	_	_	_
741	on	on	IN	_	_	_
742	MOPS	mop	NNS	MED	_	_
743	glucose	glucose	NN	SUPP	_	_
744	minimal	minimal	JJ	_	_	_
745	medium	medium	NN	_	_	_
746	with	with	IN	_	_	_
747	0.2	0.2	CD	_	_	_
748	%	%	NN	_	_	_
749	glucose	glucose	NN	SUPP	_	_
750	as	as	IN	_	_	_
751	sole	sole	JJ	_	_	_
752	carbon	carbon	NN	_	_	_
753	source	source	NN	_	_	_
754	at	at	IN	_	_	_
755	37	37	CD	_	_	_
756	°C	°c	NN	_	_	_
757	,	,	,	_	_	_
758	pH	ph	NN	_	_	_
759	was	be	VBD	_	_	_
760	initially	initially	RB	_	_	_
761	7.4	7.4	CD	_	_	_
762	,	,	,	_	_	_
763	and	and	CC	_	_	_
764	the	the	DT	_	_	_
765	agitation	agitation	NN	_	_	_
766	speed	speed	NN	_	_	_
767	was	be	VBD	_	_	_
768	500	500	CD	_	_	_
769	rpm	rpm	NN	_	_	_
770	.	.	.	_	_	_

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	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/min	liter/min	JJ	_	_	_
100	air	air	NN	_	_	_
101	flow	flow	NN	_	_	_
102	.	.	.	_	_	_

1	Culture	culture	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	by	by	IN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	homemade	homemade	NN	_	_	_
9	sampling	sampling	NN	_	_	_
10	device	device	NN	_	_	_
11	seven	seven	CD	_	_	_
12	times	time	NNS	_	_	_
13	during	during	IN	_	_	_
14	logarithmic	logarithmic	JJ	_	_	_
15	growth	growth	NN	_	_	_
16	and	and	CC	_	_	_
17	three	three	CD	_	_	_
18	times	time	NNS	_	_	_
19	following	follow	VBG	_	_	_
20	entry	entry	NN	_	_	_
21	into	into	IN	_	_	_
22	stationary	stationary	JJ	GrowthPhase	_	_
23	phase	phase	NN	GrowthPhase	_	_
24	for	for	IN	_	_	_
25	the	the	DT	_	_	_
26	WT	WT	NNP	_	_	_
27	and	and	CC	_	_	_
28	two	two	CD	_	_	_
29	times	time	NNS	_	_	_
30	during	during	IN	_	_	_
31	logarithmic	logarithmic	JJ	_	_	_
32	phase	phase	NN	_	_	_
33	and	and	CC	_	_	_
34	three	three	CD	_	_	_
35	times	time	NNS	_	_	_
36	during	during	IN	_	_	_
37	stationary	stationary	JJ	GrowthPhase	_	_
38	phase	phase	NN	GrowthPhase	_	_
39	for	for	IN	_	_	_
40	the	the	DT	_	_	_
41	rpoS	rpos	NN	GEN	_	_
42	mutant	mutant	NN	_	_	_
43	.	.	.	_	_	_

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	Wildtype	wildtype	NN	_	_	_
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/ml	ug/ml	NN	_	_	_
10	triclosan	triclosan	NN	_	_	_
11	for	for	IN	_	_	_
12	30	30	CD	_	_	_
13	min	min	NN	_	_	_
14	,	,	,	_	_	_
15	biological	biological	JJ	_	_	_
16	rep	rep	NN	GEN	_	_
17	1	1	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Wildtype	wildtype	NN	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	O157	o157	NN	_	_	_
23	treated	treat	VBN	_	_	_
24	with	with	IN	_	_	_
25	6	6	CD	_	_	_
26	ug/ml	ug/ml	NN	_	_	_
27	triclosan	triclosan	NN	_	_	_
28	for	for	IN	_	_	_
29	30	30	CD	_	_	_
30	min	min	NN	_	_	_
31	,	,	,	_	_	_
32	biological	biological	JJ	_	_	_
33	rep	rep	NN	GEN	_	_
34	2	2	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	Wildtype	wildtype	JJ	_	_	_
37	E.	e.	FW	_	_	_
38	coli	coli	FW	_	_	_
39	O157	o157	NN	_	_	_
40	treated	treat	VBN	_	_	_
41	with	with	IN	_	_	_
42	6	6	CD	_	_	_
43	ug/ml	ug/ml	NN	_	_	_
44	triclosan	triclosan	NN	_	_	_
45	for	for	IN	_	_	_
46	30	30	CD	_	_	_
47	min	min	NN	_	_	_
48	,	,	,	_	_	_
49	biological	biological	JJ	_	_	_
50	rep	rep	NN	GEN	_	_
51	3	3	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Wildtype	wildtype	NN	_	_	_
54	E.	e.	FW	_	_	_
55	coli	coli	FW	_	_	_
56	O157	o157	NN	_	_	_
57	untreated	untreated	JJ	_	_	_
58	,	,	,	_	_	_
59	biological	biological	JJ	_	_	_
60	rep	rep	NN	GEN	_	_
61	1	1	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Wildtype	wildtype	NN	_	_	_
64	E.	e.	FW	_	_	_
65	coli	coli	FW	_	_	_
66	O157	o157	NN	_	_	_
67	untreated	untreated	JJ	_	_	_
68	,	,	,	_	_	_
69	biological	biological	JJ	_	_	_
70	rep	rep	NN	GEN	_	_
71	2	2	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	Wildtype	wildtype	JJ	_	_	_
74	E.	e.	FW	_	_	_
75	coli	coli	FW	_	_	_
76	O157	o157	NN	_	_	_
77	untreated	untreated	JJ	_	_	_
78	,	,	,	_	_	_
79	biological	biological	JJ	_	_	_
80	rep	rep	NN	GEN	_	_
81	3	3	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	Wild	Wild	NNP	_	_	_
84	type	type	NN	_	_	_
85	E.coli	e.coli	NN	_	_	_
86	SE15	se15	NN	_	_	_
87	vs.	vs.	CC	_	_	_
88	LuxS	luxs	NN	_	_	_
89	mutant	mutant	JJ	_	_	_
90	E.coli	e.coli	NN	_	_	_
91	SE15	se15	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	wildtype	wildtype	JJ	_	_	_
94	Escherichia	escherichia	FW	Organism	_	_
95	coli	coli	FW	Organism	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	wild	wild	JJ	_	_	_
98	type	type	NN	_	_	_
99	grown	grow	VBN	_	_	_
100	to	to	TO	_	_	_
101	logarithmic	logarithmic	JJ	_	_	_
102	phase	phase	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	wild	wild	JJ	_	_	_
105	type	type	NN	_	_	_
106	grown	grow	VBN	_	_	_
107	to	to	TO	_	_	_
108	transition	transition	NN	_	_	_
109	phase	phase	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	wild-type	wild-type	JJ	_	_	_
112	in	in	IN	_	_	_
113	ala	ala	NN	_	_	_
114	media	media	NNS	_	_	_
115	_	_	NN	_	_	_
116	1	1	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	wild-type	wild-type	JJ	_	_	_
119	in	in	IN	_	_	_
120	ala	ala	NN	_	_	_
121	media	media	NNS	_	_	_
122	_	_	NN	_	_	_
123	2	2	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
125	wild-type	wild-type	JJ	_	_	_
126	in	in	IN	_	_	_
127	gln	gln	NN	_	_	_
128	media	media	NNS	_	_	_
129	_	_	NN	_	_	_
130	1	1	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	wild-type	wild-type	JJ	_	_	_
133	in	in	IN	_	_	_
134	gln	gln	NN	_	_	_
135	media	media	NNS	_	_	_
136	_	_	NN	_	_	_
137	2	2	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
139	Wild-type	wild-type	JJ	_	_	_
140	IrrE	irre	NN	_	_	_
141	,	,	,	_	_	_
142	biological	biological	JJ	_	_	_
143	rep1	rep1	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	Wild-type	wild-type	JJ	_	_	_
146	IrrE	irre	NN	_	_	_
147	,	,	,	_	_	_
148	biological	biological	JJ	_	_	_
149	rep2	rep2	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	Wild-type	wild-type	JJ	_	_	_
152	IrrE	irre	NN	_	_	_
153	,	,	,	_	_	_
154	biological	biological	JJ	_	_	_
155	rep3	rep3	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	Wild	Wild	NNP	_	_	_
158	Type	type	NN	_	_	_
159	-LRB-	-lrb-	-LRB-	_	_	_
160	K10	k10	NN	_	_	_
161	-RRB-	-rrb-	-RRB-	_	_	_
162	M9	m9	NN	_	_	_
163	+	+	CC	_	_	_
164	0.2	0.2	CD	_	_	_
165	%	%	NN	_	_	_
166	Glycerol	glycerol	NN	_	_	_
167	,	,	,	_	_	_
168	0.2	0.2	CD	_	_	_
169	%	%	NN	_	_	_
170	Tryptone	tryptone	NN	_	_	_
171	,	,	,	_	_	_
172	40	40	CD	_	_	_
173	mM	mm	NN	KWSUPP	_	_
174	Suc	suc	NN	_	_	_
175	.	.	.	_	_	_

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	JJ	_	_	_
8	type	type	NN	_	_	_
9	MG1655	mg1655	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
11	wild-type	wild-type	JJ	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	wild-type	wild-type	JJ	_	_	_
15	MG1655	mg1655	NN	_	_	_
16	+	+	CC	_	_	_
17	glycolaldehyde	glycolaldehyde	NN	_	_	_
18	10	10	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Wild-type	wild-type	JJ	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	RNA-seq	rna-seq	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Wild-type	wild-type	JJ	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	T0	t0	NN	_	_	_
32	RNA	rna	NN	_	_	_
33	rep	rep	NN	GEN	_	_
34	2	2	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	Wild-type	wild-type	JJ	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	MG1655	mg1655	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	T0	t0	NN	_	_	_
41	RP	rp	NN	_	_	_
42	rep	rep	NN	GEN	_	_
43	1	1	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Wild-type	wild-type	JJ	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	MG1655	mg1655	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	T0	t0	NN	_	_	_
50	RP	rp	NN	_	_	_
51	rep	rep	NN	GEN	_	_
52	2	2	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
54	Wild-type	wild-type	JJ	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	MG1655	mg1655	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	T1	t1	NN	_	_	_
59	RNA	rna	NN	_	_	_
60	rep	rep	NN	GEN	_	_
61	1	1	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Wild-type	wild-type	JJ	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	MG1655	mg1655	NN	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	T1	t1	NN	_	_	_
68	RNA	rna	NN	_	_	_
69	rep	rep	NN	GEN	_	_
70	2	2	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
72	Wild-type	wild-type	JJ	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	MG1655	mg1655	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	T1	t1	NN	_	_	_
77	RP	rp	NN	_	_	_
78	rep	rep	NN	GEN	_	_
79	1	1	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Wild-type	wild-type	JJ	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	MG1655	mg1655	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	T1	t1	NN	_	_	_
86	RP	rp	NN	_	_	_
87	rep	rep	NN	GEN	_	_
88	2	2	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
90	Wild-type	wild-type	JJ	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	MG1655	mg1655	NN	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	T2	t2	NN	_	_	_
95	RNA	rna	NN	_	_	_
96	rep	rep	NN	GEN	_	_
97	1	1	CD	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	Wild-type	wild-type	JJ	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	MG1655	mg1655	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	T2	t2	NN	_	_	_
104	RNA	rna	NN	_	_	_
105	rep	rep	NN	GEN	_	_
106	2	2	CD	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
108	Wild-type	wild-type	JJ	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	MG1655	mg1655	NN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	T2	t2	NN	_	_	_
113	RP	rp	NN	_	_	_
114	rep	rep	NN	GEN	_	_
115	1	1	CD	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	Wild-type	wild-type	JJ	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	MG1655	mg1655	NN	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	T2	t2	NN	_	_	_
122	RP	rp	NN	_	_	_
123	rep	rep	NN	GEN	_	_
124	2	2	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
126	Wild	Wild	NNP	_	_	_
127	Type	type	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	N3433	n3433	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	in	in	IN	_	_	_
132	M9	m9	NN	_	_	_
133	0.2	0.2	CD	_	_	_
134	%	%	NN	_	_	_
135	Glycerol	glycerol	NN	_	_	_
136	,	,	,	_	_	_
137	0.2	0.2	CD	_	_	_
138	%	%	NN	_	_	_
139	Tryptone	tryptone	NN	_	_	_
140	at	at	IN	_	_	_
141	30	30	CD	_	_	_
142	C	c	NN	_	_	_
143	Mid	Mid	NNP	_	_	_
144	Log	Log	NNP	_	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	Wild	Wild	NNP	_	_	_
147	Type	type	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	N3433	n3433	NN	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	M9	m9	NN	_	_	_
152	0.2	0.2	CD	_	_	_
153	%	%	NN	_	_	_
154	Glycerol	glycerol	NN	_	_	_
155	,	,	,	_	_	_
156	0.2	0.2	CD	_	_	_
157	%	%	NN	_	_	_
158	Tryptone	tryptone	NN	_	_	_
159	at	at	IN	_	_	_
160	30	30	CD	_	_	_
161	C	c	NN	_	_	_
162	Mid	Mid	NNP	_	_	_
163	Log	Log	NNP	_	_	_
164	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
165	Wild	Wild	NNP	_	_	_
166	Type	type	NN	_	_	_
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	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
185	wild	wild	JJ	_	_	_
186	type	type	NN	_	_	_
187	_	_	CD	_	_	_
188	oxic	oxic	JJ	_	_	_
189	_	_	NN	_	_	_
190	glycerol	glycerol	NN	SUPP	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	wild	wild	JJ	_	_	_
193	type	type	NN	_	_	_
194	_	_	CD	_	_	_
195	oxic	oxic	JJ	_	_	_
196	_	_	NN	_	_	_
197	glycerol	glycerol	NN	SUPP	_	_
198	+	+	CC	_	_	_
199	propionate	propionate	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
201	wild-type	wild-type	JJ	_	_	_
202	pBAD-ryhB	pbad-ryhb	NN	_	_	_
203	#	#	#	_	_	_
204	1	1	CD	_	_	_
205	+	+	CC	_	_	_
206	arabinose	arabinose	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
208	wild-type	wild-type	JJ	_	_	_
209	pBAD-ryhB	pbad-ryhb	NN	_	_	_
210	#	#	#	_	_	_
211	1	1	CD	_	_	_
212	+	+	CC	_	_	_
213	FeSO4	feso4	NN	_	_	_
214	+	+	CC	_	_	_
215	arabinose	arabinose	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
217	wild-type	wild-type	JJ	_	_	_
218	pBAD-ryhB	pbad-ryhb	NN	_	_	_
219	#	#	#	_	_	_
220	2	2	CD	_	_	_
221	+	+	CC	_	_	_
222	arabinose	arabinose	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
224	wild-type	wild-type	JJ	_	_	_
225	pBAD-ryhB	pbad-ryhb	NN	_	_	_
226	#	#	#	_	_	_
227	2	2	CD	_	_	_
228	+	+	CC	_	_	_
229	FeSO4	feso4	NN	_	_	_
230	+	+	CC	_	_	_
231	arabinose	arabinose	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
233	wild-type	wild-type	JJ	_	_	_
234	pNM12	pnm12	NN	_	_	_
235	#	#	#	_	_	_
236	1	1	CD	_	_	_
237	+	+	CC	_	_	_
238	arabinose	arabinose	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
240	wild-type	wild-type	JJ	_	_	_
241	pNM12	pnm12	NN	_	_	_
242	#	#	#	_	_	_
243	1	1	CD	_	_	_
244	+	+	CC	_	_	_
245	FeSO4	feso4	NN	_	_	_
246	+	+	CC	_	_	_
247	arabinose	arabinose	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
249	wild-type	wild-type	JJ	_	_	_
250	pNM12	pnm12	NN	_	_	_
251	#	#	#	_	_	_
252	2	2	CD	_	_	_
253	+	+	CC	_	_	_
254	arabinose	arabinose	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
256	wild-type	wild-type	JJ	_	_	_
257	pNM12	pnm12	NN	_	_	_
258	#	#	#	_	_	_
259	2	2	CD	_	_	_
260	+	+	CC	_	_	_
261	FeSO4	feso4	NN	_	_	_
262	+	+	CC	_	_	_
263	arabinose	arabinose	NN	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	wild	wild	JJ	_	_	_
266	type	type	NN	_	_	_
267	rep	rep	NN	GEN	_	_
268	1	1	CD	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	wild	wild	JJ	_	_	_
271	type	type	NN	_	_	_
272	rep	rep	NN	GEN	_	_
273	2	2	CD	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
275	Wild-types	wild-types	JJ	_	_	_
276	cells	cell	NNS	_	_	_
277	were	be	VBD	_	_	_
278	grown	grow	VBN	_	_	_
279	in	in	IN	_	_	_
280	MOPS	MOPS	NNP	MED	_	_
281	medium	medium	NN	_	_	_
282	with	with	IN	_	_	_
283	0.2	0.2	CD	_	_	_
284	%	%	NN	_	_	_
285	glucose	glucose	NN	SUPP	_	_
286	,	,	,	_	_	_
287	leucine	leucine	NN	SUPP	_	_
288	,	,	,	_	_	_
289	isoleucine	isoleucine	NN	_	_	_
290	,	,	,	_	_	_
291	valine	valine	NN	_	_	_
292	,	,	,	_	_	_
293	glycine	glycine	NN	_	_	_
294	,	,	,	_	_	_
295	phenylalanine	phenylalanine	NN	SUPP	_	_
296	,	,	,	_	_	_
297	threonine	threonine	NN	_	_	_
298	-LRB-	-lrb-	-LRB-	_	_	_
299	40	40	CD	_	_	_
300	mg/ml	mg/ml	NN	_	_	_
301	-RRB-	-rrb-	-RRB-	_	_	_
302	and	and	CC	_	_	_
303	uracil	uracil	NN	SUPP	_	_
304	-LRB-	-lrb-	-LRB-	_	_	_
305	50	50	CD	_	_	_
306	mg/ml	mg/ml	NN	_	_	_
307	-RRB-	-rrb-	-RRB-	_	_	_
308	until	until	IN	_	_	_
309	mid-log	mid-log	JJ	_	_	_
310	phase	phase	NN	_	_	_
311	and	and	CC	_	_	_
312	treated	treat	VBN	_	_	_
313	with	with	IN	_	_	_
314	0.5	0.5	CD	_	_	_
315	mg/ml	mg/ml	NN	_	_	_
316	serine	serine	NN	_	_	_
317	hydroxamate	hydroxamate	NN	_	_	_
318	-LRB-	-lrb-	-LRB-	_	_	_
319	SHX	shx	NN	_	_	_
320	-RRB-	-rrb-	-RRB-	_	_	_
321	for	for	IN	_	_	_
322	20	20	CD	_	_	_
323	min	min	NN	_	_	_
324	at	at	IN	_	_	_
325	37	37	CD	_	_	_
326	°C	°c	NN	_	_	_
327	with	with	IN	_	_	_
328	vigorous	vigorous	JJ	_	_	_
329	shaking	shake	VBG	_	_	_
330	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Wild-types	wild-types	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	MOPS	MOPS	NNP	MED	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	,	,	,	_	_	_
14	leucine	leucine	NN	SUPP	_	_
15	,	,	,	_	_	_
16	isoleucine	isoleucine	NN	_	_	_
17	,	,	,	_	_	_
18	valine	valine	NN	_	_	_
19	,	,	,	_	_	_
20	glycine	glycine	NN	_	_	_
21	,	,	,	_	_	_
22	phenylalanine	phenylalanine	NN	SUPP	_	_
23	,	,	,	_	_	_
24	threonine	threonine	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	40	40	CD	_	_	_
27	mg/ml	mg/ml	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	uracil	uracil	NN	SUPP	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	50	50	CD	_	_	_
33	mg/ml	mg/ml	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	until	until	IN	_	_	_
36	mid-log	mid-log	JJ	_	_	_
37	phase	phase	NN	_	_	_
38	at	at	IN	_	_	_
39	37	37	CD	_	_	_
40	°C	°c	NN	_	_	_
41	with	with	IN	_	_	_
42	vigorous	vigorous	JJ	_	_	_
43	shaking	shake	VBG	_	_	_
44	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Wild-types	wild-types	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	MOPS	MOPS	NNP	MED	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	,	,	,	_	_	_
14	leucine	leucine	NN	SUPP	_	_
15	,	,	,	_	_	_
16	isoleucine	isoleucine	NN	_	_	_
17	,	,	,	_	_	_
18	valine	valine	NN	_	_	_
19	,	,	,	_	_	_
20	glycine	glycine	NN	_	_	_
21	,	,	,	_	_	_
22	phenylalanine	phenylalanine	NN	SUPP	_	_
23	,	,	,	_	_	_
24	threonine	threonine	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	40	40	CD	_	_	_
27	mg/ml	mg/ml	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	uracil	uracil	NN	SUPP	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	50	50	CD	_	_	_
33	mg/ml	mg/ml	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	~	~	NN	_	_	_
41	0.4	0.4	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	at	at	IN	_	_	_
44	37	37	CD	_	_	_
45	°C	°c	NN	_	_	_
46	with	with	IN	_	_	_
47	vigorous	vigorous	JJ	_	_	_
48	shaking	shake	VBG	_	_	_
49	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wild	wild	JJ	_	_	_
3	type	type	NN	_	_	_
4	SdiA	sdia	NN	TF	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	wildtype	wildtype	JJ	_	_	_
7	strain	strain	NN	_	_	_
8	;	;	:	_	_	_
9	minimal	minimal	JJ	_	_	_
10	medium	medium	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Wildtype	wildtype	NN	_	_	_
13	strain	strain	NN	_	_	_
14	,	,	,	_	_	_
15	rep1	rep1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	wildtype	wildtype	JJ	_	_	_
18	strain	strain	NN	_	_	_
19	,	,	,	_	_	_
20	rep2	rep2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Wildtype	wildtype	JJ	_	_	_
23	triclosan	triclosan	NN	_	_	_
24	treated	treat	VBN	_	_	_
25	biological	biological	JJ	_	_	_
26	rep	rep	NN	GEN	_	_
27	1	1	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Wildtype	wildtype	JJ	_	_	_
30	triclosan	triclosan	NN	_	_	_
31	treated	treat	VBN	_	_	_
32	biological	biological	JJ	_	_	_
33	rep	rep	NN	GEN	_	_
34	2	2	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Wildtype	wildtype	JJ	_	_	_
37	triclosan	triclosan	NN	_	_	_
38	treated	treat	VBN	_	_	_
39	biological	biological	JJ	_	_	_
40	rep	rep	NN	GEN	_	_
41	3	3	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Wildtype	wildtype	JJ	_	_	_
44	untreated	untreated	JJ	_	_	_
45	biological	biological	JJ	_	_	_
46	rep	rep	NN	GEN	_	_
47	1	1	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Wildtype	wildtype	JJ	_	_	_
50	untreated	untreated	JJ	_	_	_
51	biological	biological	JJ	_	_	_
52	rep	rep	NN	GEN	_	_
53	2	2	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	Wildtype	wildtype	JJ	_	_	_
56	untreated	untreated	JJ	_	_	_
57	biological	biological	JJ	_	_	_
58	rep	rep	NN	GEN	_	_
59	3	3	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	wild	wild	JJ	_	_	_
62	type	type	NN	_	_	_
63	,	,	,	_	_	_
64	without	without	IN	_	_	_
65	H2O2	h2o2	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	with	with	IN	_	_	_
68	D-galactose	d-galactose	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	without	without	IN	_	_	_
71	D-galactose	d-galactose	JJ	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	without	without	IN	_	_	_
74	Symbioflor	Symbioflor	NNP	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	with/without	with/without	NN	_	_	_
77	2.5	2.5	CD	_	_	_
78	mM	mm	NN	KWSUPP	_	_
79	Fumaric	fumaric	JJ	_	_	_
80	acid	acid	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	write.table	write.table	JJ	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	norm.temp	norm.temp	JJ	_	_	_
85	,	,	,	_	_	_
86	file	file	NN	_	_	_
87	=\	=\	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
89	wt	wt	JJ	_	_	_
90	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
91	WT	WT	NNP	_	_	_
92	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
93	WT	WT	NNP	_	_	_
94	_	_	SYM	_	_	_
95	01	01	CD	_	_	_
96	_	_	CD	_	_	_
97	rep1	rep1	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	WT	wt	JJ	_	_	_
100	_	_	NN	_	_	_
101	02	02	CD	_	_	_
102	_	_	NN	_	_	_
103	rep1	rep1	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	WT	wt	JJ	_	_	_
106	_	_	NN	_	_	_
107	03	03	CD	_	_	_
108	_	_	NN	_	_	_
109	rep1	rep1	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	WT	wt	JJ	_	_	_
112	_	_	NN	_	_	_
113	04	04	CD	_	_	_
114	_	_	NN	_	_	_
115	rep1	rep1	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	WT	wt	JJ	_	_	_
118	_	_	NN	_	_	_
119	04	04	CD	_	_	_
120	_	_	NN	_	_	_
121	rep2	rep2	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	WT	wt	JJ	_	_	_
124	_	_	NN	_	_	_
125	04-R	04-r	NN	_	_	_
126	_	_	CD	_	_	_
127	rep1	rep1	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	WT	wt	JJ	_	_	_
130	_	_	NN	_	_	_
131	04	04	CD	_	_	_
132	_	_	SYM	_	_	_
133	TEX	TEX	NNP	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	WT	WT	NNP	_	_	_
136	_	_	SYM	_	_	_
137	08	08	CD	_	_	_
138	_	_	CD	_	_	_
139	rep1	rep1	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	WT	wt	JJ	_	_	_
142	_	_	NN	_	_	_
143	0	0	CD	_	_	_
144	_	_	NN	_	_	_
145	Hx	hx	NN	_	_	_
146	Rep1	rep1	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	WT	wt	JJ	_	_	_
149	_	_	NN	_	_	_
150	0	0	CD	_	_	_
151	_	_	SYM	_	_	_
152	Hx	hx	FW	_	_	_
153	Rep2	rep2	JJ	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	WT	wt	JJ	_	_	_
156	_	_	NN	_	_	_
157	0	0	CD	_	_	_
158	_	_	SYM	_	_	_
159	Hx	hx	FW	_	_	_
160	Rep3	rep3	JJ	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	WT	wt	NN	_	_	_
163	0	0	CD	_	_	_
164	μg/ml	μg/ml	NN	_	_	_
165	NA	na	NN	_	_	_
166	rep1	rep1	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	WT	wt	NN	_	_	_
169	0	0	CD	_	_	_
170	μg/ml	μg/ml	NN	_	_	_
171	NA	na	NN	_	_	_
172	rep2	rep2	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	wt	wt	JJ	_	_	_
175	_	_	NN	_	_	_
176	1	1	CD	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	WT	wt	JJ	_	_	_
179	_	_	NN	_	_	_
180	1	1	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	WT-1	wt-1	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	WT	wt	NN	_	_	_
185	100	100	CD	_	_	_
186	μg/ml	μg/ml	NN	_	_	_
187	NA	na	NN	_	_	_
188	rep1	rep1	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	WT	wt	NN	_	_	_
191	100	100	CD	_	_	_
192	μg/ml	μg/ml	NN	_	_	_
193	NA	na	NN	_	_	_
194	rep2	rep2	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	WT	wt	NN	_	_	_
197	100	100	CD	_	_	_
198	μg/ml	μg/ml	NN	_	_	_
199	NA	na	NN	_	_	_
200	rep3	rep3	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	WT1088	wt1088	NN	_	_	_
203	in	in	IN	_	_	_
204	LB	lb	NN	_	_	_
205	at	at	IN	_	_	_
206	37	37	CD	_	_	_
207	Mid	Mid	NNP	_	_	_
208	Log	Log	NNP	_	_	_
209	Phase	phase	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	WT1088	wt1088	NN	_	_	_
212	vs.	vs.	CC	_	_	_
213	dpiA	dpia	NN	GEN	_	_
214	2x	2x	NN	_	_	_
215	Overexpression	overexpression	NN	_	_	_
216	pHI1429	phi1429	NN	_	_	_
217	in	in	IN	_	_	_
218	LB	lb	NN	_	_	_
219	at	at	IN	_	_	_
220	37	37	CD	_	_	_
221	Mid	Mid	NNP	_	_	_
222	Log	Log	NNP	_	_	_
223	Phase	phase	NN	_	_	_
224	Trial	trial	NN	_	_	_
225	A	a	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	WT1088	wt1088	NN	_	_	_
228	vs.	vs.	CC	_	_	_
229	dpiA	dpia	NN	GEN	_	_
230	2x	2x	NN	_	_	_
231	Overexpression	overexpression	NN	_	_	_
232	pHI1429	phi1429	NN	_	_	_
233	in	in	IN	_	_	_
234	LB	lb	NN	_	_	_
235	at	at	IN	_	_	_
236	37	37	CD	_	_	_
237	Mid	Mid	NNP	_	_	_
238	Log	Log	NNP	_	_	_
239	Phase	phase	NN	_	_	_
240	Trial	trial	NN	_	_	_
241	B	b	NN	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	WT	wt	VBD	_	_	_
244	10	10	CD	_	_	_
245	μg/ml	μg/ml	NN	_	_	_
246	NA	na	NN	_	_	_
247	rep1	rep1	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	WT	wt	VBD	_	_	_
250	10	10	CD	_	_	_
251	μg/ml	μg/ml	NN	_	_	_
252	NA	na	NN	_	_	_
253	rep2	rep2	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	WT	wt	JJ	_	_	_
256	_	_	NN	_	_	_
257	120	120	CD	_	_	_
258	-LRB-	-lrb-	-LRB-	_	_	_
259	Low	low	JJ	_	_	_
260	Dilution	dilution	NN	_	_	_
261	-RRB-	-rrb-	-RRB-	_	_	_
262	Rep1	rep1	JJ	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	WT	wt	JJ	_	_	_
265	_	_	NN	_	_	_
266	120	120	CD	_	_	_
267	-LRB-	-lrb-	-LRB-	_	_	_
268	Low	low	JJ	_	_	_
269	Dilution	dilution	NN	_	_	_
270	-RRB-	-rrb-	-RRB-	_	_	_
271	Rep2	rep2	JJ	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	WT	wt	JJ	_	_	_
274	_	_	NN	_	_	_
275	120	120	CD	_	_	_
276	-LRB-	-lrb-	-LRB-	_	_	_
277	Low	low	JJ	_	_	_
278	Dilution	dilution	NN	_	_	_
279	-RRB-	-rrb-	-RRB-	_	_	_
280	Rep3	rep3	JJ	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Wt	wt	NN	_	_	_
283	--	--	:	_	_	_
284	120	120	CD	_	_	_
285	min	min	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	WT	wt	JJ	_	_	_
288	_	_	NN	_	_	_
289	12h	12h	NN	_	_	_
290	_	_	CD	_	_	_
291	rep1	rep1	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	WT	wt	JJ	_	_	_
294	_	_	NN	_	_	_
295	12h	12h	NN	_	_	_
296	_	_	CD	_	_	_
297	rep2	rep2	NN	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	WT	wt	JJ	_	_	_
300	_	_	NN	_	_	_
301	14	14	CD	_	_	_
302	_	_	NN	_	_	_
303	rep1	rep1	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	wt	wt	JJ	_	_	_
306	150	150	CD	_	_	_
307	minutes	minute	NNS	_	_	_
308	growth	growth	NN	_	_	_
309	rep1	rep1	NN	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	wt	wt	JJ	_	_	_
312	150	150	CD	_	_	_
313	minutes	minute	NNS	_	_	_
314	growth	growth	NN	_	_	_
315	rep2	rep2	NN	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	wt	wt	JJ	_	_	_
318	150	150	CD	_	_	_
319	minutes	minute	NNS	_	_	_
320	growth	growth	NN	_	_	_
321	rep3	rep3	NN	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	WT	wt	JJ	_	_	_
324	_	_	NN	_	_	_
325	15	15	CD	_	_	_
326	-LRB-	-lrb-	-LRB-	_	_	_
327	Low	low	JJ	_	_	_
328	Dilution	dilution	NN	_	_	_
329	-RRB-	-rrb-	-RRB-	_	_	_
330	Rep1	rep1	JJ	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	WT	wt	JJ	_	_	_
333	_	_	NN	_	_	_
334	15	15	CD	_	_	_
335	-LRB-	-lrb-	-LRB-	_	_	_
336	Low	low	JJ	_	_	_
337	Dilution	dilution	NN	_	_	_
338	-RRB-	-rrb-	-RRB-	_	_	_
339	Rep2	rep2	JJ	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	WT	wt	JJ	_	_	_
342	_	_	NN	_	_	_
343	15	15	CD	_	_	_
344	-LRB-	-lrb-	-LRB-	_	_	_
345	Low	low	JJ	_	_	_
346	Dilution	dilution	NN	_	_	_
347	-RRB-	-rrb-	-RRB-	_	_	_
348	Rep3	rep3	JJ	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	WT	wt	JJ	_	_	_
351	_	_	NN	_	_	_
352	15	15	CD	_	_	_
353	min	min	NN	_	_	_
354	_	_	CD	_	_	_
355	rep1	rep1	NN	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	WT	wt	JJ	_	_	_
358	_	_	NN	_	_	_
359	16	16	CD	_	_	_
360	_	_	NN	_	_	_
361	rep1	rep1	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	WT	wt	JJ	_	_	_
364	_	_	NN	_	_	_
365	16-R	16-r	NN	_	_	_
366	_	_	CD	_	_	_
367	rep1	rep1	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	Wt	wt	NN	_	_	_
370	--	--	:	_	_	_
371	180	180	CD	_	_	_
372	min	min	NN	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	WT	wt	JJ	_	_	_
375	_	_	NN	_	_	_
376	180	180	CD	_	_	_
377	min	min	NN	_	_	_
378	_	_	CD	_	_	_
379	rep1	rep1	NN	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
381	wt	wt	JJ	_	_	_
382	_	_	NN	_	_	_
383	1	1	CD	_	_	_
384	_	_	NN	_	_	_
385	input	input	NN	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	wt	wt	JJ	_	_	_
388	_	_	NN	_	_	_
389	1	1	CD	_	_	_
390	_	_	CD	_	_	_
391	IP	IP	NNP	_	_	_
392	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
393	WT1	wt1	NN	_	_	_
394	_	_	CD	_	_	_
395	IPTG	iptg	NN	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
397	WT	wt	NN	_	_	_
398	1	1	CD	_	_	_
399	min	min	NN	_	_	_
400	rep7	rep7	NN	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	wt	wt	JJ	_	_	_
403	_	_	NN	_	_	_
404	2	2	CD	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	WT	wt	JJ	_	_	_
407	_	_	NN	_	_	_
408	2	2	CD	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	WT-2	wt-2	NN	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	WT	wt	NN	_	_	_
413	22	22	CD	_	_	_
414	°C	°c	NN	_	_	_
415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
416	wt	wt	JJ	_	_	_
417	240	240	CD	_	_	_
418	minutes	minute	NNS	_	_	_
419	growth	growth	NN	_	_	_
420	rep1	rep1	NN	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	wt	wt	JJ	_	_	_
423	240	240	CD	_	_	_
424	minutes	minute	NNS	_	_	_
425	growth	growth	NN	_	_	_
426	rep2	rep2	NN	_	_	_
427	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
428	wt	wt	JJ	_	_	_
429	240	240	CD	_	_	_
430	minutes	minute	NNS	_	_	_
431	growth	growth	NN	_	_	_
432	rep3	rep3	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	WT	wt	VBD	_	_	_
435	_	_	CD	_	_	_
436	24h	24h	JJ	_	_	_
437	_	_	NN	_	_	_
438	rep1	rep1	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	WT	wt	VBD	_	_	_
441	_	_	CD	_	_	_
442	24h	24h	JJ	_	_	_
443	_	_	NN	_	_	_
444	rep2	rep2	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	wt	wt	JJ	_	_	_
447	_	_	NN	_	_	_
448	2	2	CD	_	_	_
449	_	_	NN	_	_	_
450	input	input	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	wt	wt	JJ	_	_	_
453	_	_	NN	_	_	_
454	2	2	CD	_	_	_
455	_	_	CD	_	_	_
456	IP	IP	NNP	_	_	_
457	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
458	WT2	wt2	NN	_	_	_
459	_	_	CD	_	_	_
460	IPTG	iptg	NN	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	WT	wt	JJ	_	_	_
463	_	_	NN	_	_	_
464	3	3	CD	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	WT-3	wt-3	NN	_	_	_
467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
468	Wt	wt	NN	_	_	_
469	--	--	:	_	_	_
470	300	300	CD	_	_	_
471	min	min	NN	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	WT	wt	JJ	_	_	_
474	_	_	NN	_	_	_
475	30	30	CD	_	_	_
476	-LRB-	-lrb-	-LRB-	_	_	_
477	Low	low	JJ	_	_	_
478	Dilution	dilution	NN	_	_	_
479	-RRB-	-rrb-	-RRB-	_	_	_
480	Rep1	rep1	JJ	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	WT	wt	JJ	_	_	_
483	_	_	NN	_	_	_
484	30	30	CD	_	_	_
485	-LRB-	-lrb-	-LRB-	_	_	_
486	Low	low	JJ	_	_	_
487	Dilution	dilution	NN	_	_	_
488	-RRB-	-rrb-	-RRB-	_	_	_
489	Rep2	rep2	JJ	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	WT	wt	JJ	_	_	_
492	_	_	NN	_	_	_
493	30	30	CD	_	_	_
494	-LRB-	-lrb-	-LRB-	_	_	_
495	Low	low	JJ	_	_	_
496	Dilution	dilution	NN	_	_	_
497	-RRB-	-rrb-	-RRB-	_	_	_
498	Rep3	rep3	JJ	_	_	_
499	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
500	WT	wt	JJ	_	_	_
501	_	_	NN	_	_	_
502	30	30	CD	_	_	_
503	min	min	NN	_	_	_
504	_	_	CD	_	_	_
505	rep1	rep1	NN	_	_	_
506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
507	WT	wt	JJ	_	_	_
508	_	_	NN	_	_	_
509	30	30	CD	_	_	_
510	min	min	NN	_	_	_
511	_	_	CD	_	_	_
512	rep2	rep2	NN	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	WT	wt	JJ	_	_	_
515	_	_	NN	_	_	_
516	30min-R	30min-r	NN	_	_	_
517	_	_	CD	_	_	_
518	rep1	rep1	NN	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	WT	wt	JJ	_	_	_
521	_	_	NN	_	_	_
522	30	30	CD	_	_	_
523	min	min	NN	_	_	_
524	_	_	CD	_	_	_
525	TEX	TEX	NNP	_	_	_
526	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
527	WT3110	WT3110	NNP	_	_	_
528	_	_	SYM	_	_	_
529	1	1	CD	_	_	_
530	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
531	WT3110	wt3110	NN	_	_	_
532	_	_	NN	_	_	_
533	2	2	CD	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	WT3110	wt3110	NN	_	_	_
536	_	_	CD	_	_	_
537	3	3	CD	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
539	wt	wt	JJ	_	_	_
540	360	360	CD	_	_	_
541	minutes	minute	NNS	_	_	_
542	growth	growth	NN	_	_	_
543	rep1	rep1	NN	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	wt	wt	JJ	_	_	_
546	360	360	CD	_	_	_
547	minutes	minute	NNS	_	_	_
548	growth	growth	NN	_	_	_
549	rep2	rep2	NN	_	_	_
550	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
551	wt	wt	JJ	_	_	_
552	360	360	CD	_	_	_
553	minutes	minute	NNS	_	_	_
554	growth	growth	NN	_	_	_
555	rep3	rep3	NN	_	_	_
556	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
557	WT	wt	NN	_	_	_
558	37	37	CD	_	_	_
559	°C	°c	NN	_	_	_
560	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
561	WT	wt	JJ	_	_	_
562	_	_	NN	_	_	_
563	37C	37c	NN	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	Wt	wt	NN	_	_	_
566	--	--	:	_	_	_
567	420	420	CD	_	_	_
568	min	min	NN	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	WT	wt	JJ	_	_	_
571	_	_	NN	_	_	_
572	45	45	CD	_	_	_
573	-LRB-	-lrb-	-LRB-	_	_	_
574	Low	low	JJ	_	_	_
575	Dilution	dilution	NN	_	_	_
576	-RRB-	-rrb-	-RRB-	_	_	_
577	Rep1	rep1	JJ	_	_	_
578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
579	WT	wt	JJ	_	_	_
580	_	_	NN	_	_	_
581	45	45	CD	_	_	_
582	-LRB-	-lrb-	-LRB-	_	_	_
583	Low	low	JJ	_	_	_
584	Dilution	dilution	NN	_	_	_
585	-RRB-	-rrb-	-RRB-	_	_	_
586	Rep2	rep2	JJ	_	_	_
587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
588	WT	wt	JJ	_	_	_
589	_	_	NN	_	_	_
590	45	45	CD	_	_	_
591	-LRB-	-lrb-	-LRB-	_	_	_
592	Low	low	JJ	_	_	_
593	Dilution	dilution	NN	_	_	_
594	-RRB-	-rrb-	-RRB-	_	_	_
595	Rep3	rep3	JJ	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
597	WT	wt	JJ	_	_	_
598	_	_	NN	_	_	_
599	48h	48h	NN	_	_	_
600	_	_	CD	_	_	_
601	rep1	rep1	NN	_	_	_
602	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
603	WT	wt	JJ	_	_	_
604	_	_	NN	_	_	_
605	48h	48h	NN	_	_	_
606	_	_	CD	_	_	_
607	rep2	rep2	NN	_	_	_
608	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
609	wt	wt	JJ	_	_	_
610	+50	+50	CD	_	_	_
611	ug/ml	ug/ml	JJ	_	_	_
612	Trp	trp	NN	_	_	_
613	,	,	,	_	_	_
614	30	30	CD	_	_	_
615	ug	ug	NN	_	_	_
616	total	total	JJ	_	_	_
617	RNA	rna	NN	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	WT	wt	JJ	_	_	_
620	_	_	NN	_	_	_
621	60	60	CD	_	_	_
622	-LRB-	-lrb-	-LRB-	_	_	_
623	Low	low	JJ	_	_	_
624	Dilution	dilution	NN	_	_	_
625	-RRB-	-rrb-	-RRB-	_	_	_
626	Rep1	rep1	JJ	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	WT	wt	JJ	_	_	_
629	_	_	NN	_	_	_
630	60	60	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	WT	wt	JJ	_	_	_
638	_	_	NN	_	_	_
639	60	60	CD	_	_	_
640	-LRB-	-lrb-	-LRB-	_	_	_
641	Low	low	JJ	_	_	_
642	Dilution	dilution	NN	_	_	_
643	-RRB-	-rrb-	-RRB-	_	_	_
644	Rep3	rep3	JJ	_	_	_
645	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
646	Wt	wt	NN	_	_	_
647	--	--	:	_	_	_
648	60	60	CD	_	_	_
649	min	min	NN	_	_	_
650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
651	WT	wt	VBD	_	_	_
652	_	_	CD	_	_	_
653	6h	6h	JJ	_	_	_
654	_	_	NN	_	_	_
655	rep1	rep1	NN	_	_	_
656	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
657	WT	wt	VBD	_	_	_
658	_	_	CD	_	_	_
659	6h	6h	JJ	_	_	_
660	_	_	NN	_	_	_
661	rep2	rep2	NN	_	_	_
662	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
663	wt	wt	JJ	_	_	_
664	90	90	CD	_	_	_
665	minutes	minute	NNS	_	_	_
666	growth	growth	NN	_	_	_
667	rep1	rep1	NN	_	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
669	wt	wt	JJ	_	_	_
670	90	90	CD	_	_	_
671	minutes	minute	NNS	_	_	_
672	growth	growth	NN	_	_	_
673	rep2	rep2	NN	_	_	_
674	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
675	wt	wt	JJ	_	_	_
676	90	90	CD	_	_	_
677	minutes	minute	NNS	_	_	_
678	growth	growth	NN	_	_	_
679	rep3	rep3	NN	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	WT	wt	VBD	_	_	_
682	9	9	CD	_	_	_
683	min	min	NN	_	_	_
684	rep7	rep7	NN	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
686	WT	wt	VBD	_	_	_
687	9	9	CD	_	_	_
688	min	min	NN	_	_	_
689	rep8	rep8	NN	_	_	_
690	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
691	WTA1	wta1	NN	_	_	_
692	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
693	WT	wt	JJ	_	_	_
694	_	_	NN	_	_	_
695	acetate	acetate	NN	SUPP	_	_
696	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
697	WT	wt	JJ	_	_	_
698	acetate	acetate	NN	SUPP	_	_
699	1	1	CD	_	_	_
700	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
701	WT	wt	JJ	_	_	_
702	acetate	acetate	NN	SUPP	_	_
703	2	2	CD	_	_	_
704	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
705	WT	wt	NN	_	_	_
706	+	+	CC	_	_	_
707	ade	ade	NN	_	_	_
708	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
709	wt	wt	JJ	_	_	_
710	aerobic	aerobic	JJ	_	_	_
711	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
712	wt	wt	JJ	_	_	_
713	aerobic	aerobic	JJ	_	_	_
714	AN	a	DT	_	_	_
715	rep	rep	NN	GEN	_	_
716	1	1	CD	_	_	_
717	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
718	wt	wt	JJ	_	_	_
719	aerobic	aerobic	JJ	_	_	_
720	AN	a	DT	_	_	_
721	rep	rep	NN	GEN	_	_
722	2	2	CD	_	_	_
723	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
724	wt	wt	JJ	_	_	_
725	aerobic	aerobic	JJ	_	_	_
726	AN	a	DT	_	_	_
727	rep	rep	NN	GEN	_	_
728	3	3	CD	_	_	_
729	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
730	wt	wt	JJ	_	_	_
731	aerobic	aerobic	JJ	_	_	_
732	rep	rep	NN	GEN	_	_
733	1	1	CD	_	_	_
734	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
735	wt	wt	JJ	_	_	_
736	aerobic	aerobic	JJ	_	_	_
737	rep	rep	NN	GEN	_	_
738	2	2	CD	_	_	_
739	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
740	wt	wt	JJ	_	_	_
741	aerobic	aerobic	JJ	_	_	_
742	rep	rep	NN	GEN	_	_
743	3	3	CD	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	wt	wt	JJ	_	_	_
746	anaerobic	anaerobic	JJ	_	_	_
747	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
748	wt	wt	JJ	_	_	_
749	anaerobic	anaerobic	JJ	_	_	_
750	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
751	wt	wt	JJ	_	_	_
752	anaerobic	anaerobic	JJ	_	_	_
753	AN	a	DT	_	_	_
754	rep	rep	NN	GEN	_	_
755	1	1	CD	_	_	_
756	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
757	wt	wt	JJ	_	_	_
758	anaerobic	anaerobic	JJ	_	_	_
759	AN	a	DT	_	_	_
760	rep	rep	NN	GEN	_	_
761	2	2	CD	_	_	_
762	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
763	wt	wt	JJ	_	_	_
764	anaerobic	anaerobic	JJ	_	_	_
765	AN	a	DT	_	_	_
766	rep	rep	NN	GEN	_	_
767	3	3	CD	_	_	_
768	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
769	wt	wt	JJ	_	_	_
770	anaerobic	anaerobic	NN	_	_	_
771	plus	plus	CC	_	_	_
772	NO2	no2	NN	_	_	_
773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
774	wt	wt	JJ	_	_	_
775	anaerobic	anaerobic	NN	_	_	_
776	plus	plus	CC	_	_	_
777	NO2	no2	NN	_	_	_
778	AN	a	DT	_	_	_
779	rep	rep	NN	GEN	_	_
780	1	1	CD	_	_	_
781	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
782	wt	wt	JJ	_	_	_
783	anaerobic	anaerobic	NN	_	_	_
784	plus	plus	CC	_	_	_
785	NO2	no2	NN	_	_	_
786	AN	a	DT	_	_	_
787	rep	rep	NN	GEN	_	_
788	2	2	CD	_	_	_
789	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
790	wt	wt	JJ	_	_	_
791	anaerobic	anaerobic	NN	_	_	_
792	plus	plus	CC	_	_	_
793	NO2	no2	NN	_	_	_
794	AN	a	DT	_	_	_
795	rep	rep	NN	GEN	_	_
796	3	3	CD	_	_	_
797	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
798	wt	wt	JJ	_	_	_
799	anaerobic	anaerobic	NN	_	_	_
800	plus	plus	CC	_	_	_
801	NO2	no2	NN	_	_	_
802	rep	rep	NN	GEN	_	_
803	1	1	CD	_	_	_
804	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
805	wt	wt	JJ	_	_	_
806	anaerobic	anaerobic	NN	_	_	_
807	plus	plus	CC	_	_	_
808	NO2	no2	NN	_	_	_
809	rep	rep	NN	GEN	_	_
810	2	2	CD	_	_	_
811	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
812	wt	wt	JJ	_	_	_
813	anaerobic	anaerobic	NN	_	_	_
814	plus	plus	CC	_	_	_
815	NO2	no2	NN	_	_	_
816	rep	rep	NN	GEN	_	_
817	3	3	CD	_	_	_
818	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
819	wt	wt	JJ	_	_	_
820	anaerobic	anaerobic	NN	_	_	_
821	plus	plus	CC	_	_	_
822	NO3	no3	NN	_	_	_
823	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
824	wt	wt	JJ	_	_	_
825	anaerobic	anaerobic	NN	_	_	_
826	plus	plus	CC	_	_	_
827	NO3	no3	NN	_	_	_
828	AN	a	DT	_	_	_
829	rep	rep	NN	GEN	_	_
830	1	1	CD	_	_	_
831	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
832	wt	wt	JJ	_	_	_
833	anaerobic	anaerobic	NN	_	_	_
834	plus	plus	CC	_	_	_
835	NO3	no3	NN	_	_	_
836	AN	a	DT	_	_	_
837	rep	rep	NN	GEN	_	_
838	2	2	CD	_	_	_
839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
840	wt	wt	JJ	_	_	_
841	anaerobic	anaerobic	NN	_	_	_
842	plus	plus	CC	_	_	_
843	NO3	no3	NN	_	_	_
844	AN	a	DT	_	_	_
845	rep	rep	NN	GEN	_	_
846	3	3	CD	_	_	_
847	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
848	wt	wt	JJ	_	_	_
849	anaerobic	anaerobic	NN	_	_	_
850	plus	plus	CC	_	_	_
851	NO3	no3	NN	_	_	_
852	rep	rep	NN	GEN	_	_
853	1	1	CD	_	_	_
854	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
855	wt	wt	JJ	_	_	_
856	anaerobic	anaerobic	NN	_	_	_
857	plus	plus	CC	_	_	_
858	NO3	no3	NN	_	_	_
859	rep	rep	NN	GEN	_	_
860	2	2	CD	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
862	wt	wt	JJ	_	_	_
863	anaerobic	anaerobic	NN	_	_	_
864	plus	plus	CC	_	_	_
865	NO3	no3	NN	_	_	_
866	rep	rep	NN	GEN	_	_
867	3	3	CD	_	_	_
868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
869	wt	wt	JJ	_	_	_
870	anaerobic	anaerobic	JJ	_	_	_
871	rep	rep	NN	GEN	_	_
872	1	1	CD	_	_	_
873	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
874	wt	wt	JJ	_	_	_
875	anaerobic	anaerobic	JJ	_	_	_
876	rep	rep	NN	GEN	_	_
877	2	2	CD	_	_	_
878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
879	wt	wt	JJ	_	_	_
880	anaerobic	anaerobic	JJ	_	_	_
881	rep	rep	NN	GEN	_	_
882	3	3	CD	_	_	_
883	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
884	WT	wt	JJ	_	_	_
885	_	_	CD	_	_	_
886	Anaerobic	anaerobic	JJ	_	_	_
887	_	_	NN	_	_	_
888	RNAseq	rnaseq	NN	_	_	_
889	_	_	CD	_	_	_
890	A	a	DT	_	_	_
891	_	_	NN	_	_	_
892	Tag	tag	NN	_	_	_
893	_	_	CD	_	_	_
894	Count.txt	count.txt	NN	_	_	_
895	:	:	:	_	_	_
896	U00096	u00096	NN	_	_	_
897	.2	.2	NN	_	_	_
898	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
899	WT	wt	VBD	_	_	_
900	_	_	CD	_	_	_
901	Anaerobic	anaerobic	JJ	_	_	_
902	_	_	NN	_	_	_
903	RNAseq	rnaseq	NN	_	_	_
904	_	_	CD	_	_	_
905	A	a	DT	_	_	_
906	_	_	NN	_	_	_
907	WIG.wig	wig.wig	NN	_	_	_
908	:	:	:	_	_	_
909	U00096	u00096	NN	_	_	_
910	.2	.2	NN	_	_	_
911	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
912	WT	wt	VBD	_	_	_
913	_	_	CD	_	_	_
914	Anaerobic	anaerobic	JJ	_	_	_
915	_	_	NN	_	_	_
916	RNAseq	rnaseq	NN	_	_	_
917	_	_	NN	_	_	_
918	B	b	NN	_	_	_
919	_	_	CD	_	_	_
920	Tag	tag	NN	_	_	_
921	_	_	CD	_	_	_
922	Count.txt	count.txt	NN	_	_	_
923	:	:	:	_	_	_
924	U00096	u00096	NN	_	_	_
925	.2	.2	NN	_	_	_
926	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
927	WT	wt	VBD	_	_	_
928	_	_	CD	_	_	_
929	Anaerobic	anaerobic	JJ	_	_	_
930	_	_	NN	_	_	_
931	RNAseq	rnaseq	NN	_	_	_
932	_	_	NN	_	_	_
933	B	b	NN	_	_	_
934	_	_	CD	_	_	_
935	WIG.wig	wig.wig	NN	_	_	_
936	:	:	:	_	_	_
937	U00096	u00096	NN	_	_	_
938	.2	.2	NN	_	_	_
939	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
940	WTA	WTA	NNP	_	_	_
941	_	_	SYM	_	_	_
942	time0	time0	CD	_	_	_
943	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
944	WTA	WTA	NNP	_	_	_
945	_	_	SYM	_	_	_
946	time10	time10	CD	_	_	_
947	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
948	WTA	WTA	NNP	_	_	_
949	_	_	SYM	_	_	_
950	time20	time20	CD	_	_	_
951	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
952	WTA	WTA	NNP	_	_	_
953	_	_	SYM	_	_	_
954	time2	time2	CD	_	_	_
955	.5	.5	CD	_	_	_
956	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
957	WTA	WTA	NNP	_	_	_
958	_	_	SYM	_	_	_
959	time5	time5	CD	_	_	_
960	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
961	WTA	WTA	NNP	_	_	_
962	_	_	SYM	_	_	_
963	time7	time7	CD	_	_	_
964	.5	.5	CD	_	_	_
965	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
966	wt	wt	JJ	_	_	_
967	at	at	IN	_	_	_
968	T0	t0	NN	_	_	_
969	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
970	wt	wt	JJ	_	_	_
971	at	at	IN	_	_	_
972	T1h	t1h	NN	_	_	_
973	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
974	wt	wt	JJ	_	_	_
975	at	at	IN	_	_	_
976	T4h	t4h	NN	_	_	_
977	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
978	WTB1	wtb1	NN	_	_	_
979	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
980	WTB	wtb	NN	_	_	_
981	_	_	CD	_	_	_
982	time0	time0	NN	_	_	_
983	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
984	WTB	wtb	NN	_	_	_
985	_	_	CD	_	_	_
986	time2	time2	NN	_	_	_
987	.5	.5	CD	_	_	_
988	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
989	WTB	wtb	NN	_	_	_
990	_	_	SYM	_	_	_
991	time7	time7	CD	_	_	_
992	.5	.5	CD	_	_	_
993	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
994	WTC3	wtc3	NN	_	_	_
995	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
996	WT	wt	JJ	_	_	_
997	cells	cell	NNS	_	_	_
998	were	be	VBD	_	_	_
999	treated	treat	VBN	_	_	_
1000	with	with	IN	_	_	_
1001	10	10	CD	_	_	_
1002	mM	mm	NN	KWSUPP	_	_
1003	Glycolaldehyde	glycolaldehyde	NN	_	_	_
1004	for	for	IN	_	_	_
1005	30	30	CD	_	_	_
1006	min	min	NN	_	_	_
1007	whenever	whenever	WRB	_	_	_
1008	the	the	DT	_	_	_
1009	culture	culture	NN	_	_	_
1010	OD600nm	od600nm	NN	_	_	_
1011	reached	reach	VBD	_	_	_
1012	~	~	NN	_	_	_
1013	1	1	CD	_	_	_
1014	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	_	_	NNP	_	_	_
4	CPR	CPR	NNP	_	_	_
5	_	_	SYM	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	WT	wt	JJ	_	_	_
9	_	_	NN	_	_	_
10	CPR	CPR	NNP	_	_	_
11	_	_	SYM	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	WT	wt	JJ	_	_	_
15	_	_	NN	_	_	_
16	D	d	NN	_	_	_
17	_	_	CD	_	_	_
18	N1000	n1000	NN	_	_	_
19	_	_	CD	_	_	_
20	r1	r1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	WT	wt	JJ	_	_	_
23	_	_	NN	_	_	_
24	D	d	NN	_	_	_
25	_	_	CD	_	_	_
26	N1000	n1000	NN	_	_	_
27	_	_	CD	_	_	_
28	r2	r2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	wt	wt	JJ	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	,	,	,	_	_	_
34	after	after	IN	_	_	_
35	butanol	butanol	NN	_	_	_
36	treatment	treatment	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	wt	wt	JJ	_	_	_
39	E.	e.	FW	_	_	_
40	coli	coli	FW	_	_	_
41	,	,	,	_	_	_
42	before	before	IN	_	_	_
43	butanol	butanol	NN	_	_	_
44	treatment	treatment	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	wt	wt	JJ	_	_	_
47	_	_	NN	_	_	_
48	EE	ee	NN	_	_	_
49	_	_	NN	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	wt	wt	JJ	_	_	_
53	_	_	NN	_	_	_
54	EE	ee	NN	_	_	_
55	_	_	NN	_	_	_
56	2	2	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	WT	wt	JJ	_	_	_
59	_	_	NN	_	_	_
60	exp1	exp1	NN	_	_	_
61	_	_	NN	_	_	_
62	mRNA	mrna	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	WT	wt	JJ	_	_	_
65	_	_	NN	_	_	_
66	exp1	exp1	NN	_	_	_
67	_	_	NN	_	_	_
68	ribosome	ribosome	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	WT	wt	JJ	_	_	_
71	_	_	NN	_	_	_
72	exp2	exp2	NN	_	_	_
73	_	_	NN	_	_	_
74	mRNA	mrna	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	WT	wt	JJ	_	_	_
77	_	_	NN	_	_	_
78	exp2	exp2	NN	_	_	_
79	_	_	NN	_	_	_
80	ribosome	ribosome	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	WT	wt	JJ	_	_	_
83	_	_	NN	_	_	_
84	exp3	exp3	NN	_	_	_
85	_	_	NN	_	_	_
86	mRNA	mrna	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	WT	wt	JJ	_	_	_
89	_	_	NN	_	_	_
90	exp3	exp3	NN	_	_	_
91	_	_	NN	_	_	_
92	ribosome	ribosome	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	WT	wt	JJ	_	_	_
95	_	_	NN	_	_	_
96	exp4	exp4	NN	_	_	_
97	_	_	NN	_	_	_
98	mRNA	mrna	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	WT	wt	JJ	_	_	_
101	_	_	NN	_	_	_
102	exp4	exp4	NN	_	_	_
103	_	_	CD	_	_	_
104	ribosome	ribosome	NN	_	_	_
105	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
106	WT	WT	NNP	_	_	_
107	exp	exp	NN	_	_	_
108	mRNA	mrna	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	WT	wt	JJ	_	_	_
111	exp	exp	NN	_	_	_
112	RPF	rpf	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	WT	wt	JJ	_	_	_
115	_	_	NN	_	_	_
116	fructose	fructose	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	WT	wt	JJ	_	_	_
119	fructose	fructose	NN	_	_	_
120	1	1	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	WT	wt	JJ	_	_	_
123	fructose	fructose	NN	_	_	_
124	2	2	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	WT	wt	JJ	_	_	_
127	_	_	NN	_	_	_
128	glucose	glucose	NN	SUPP	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	WT	wt	JJ	_	_	_
131	glucose	glucose	NN	SUPP	_	_
132	1	1	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	WT	wt	JJ	_	_	_
135	glucose	glucose	NN	SUPP	_	_
136	2	2	CD	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	WT	wt	JJ	_	_	_
139	_	_	NN	_	_	_
140	glucose	glucose	NN	SUPP	_	_
141	_	_	CD	_	_	_
142	log	log	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	WT	wt	JJ	_	_	_
145	_	_	NN	_	_	_
146	glucose	glucose	NN	SUPP	_	_
147	_	_	CD	_	_	_
148	log	log	NN	_	_	_
149	_	_	CD	_	_	_
150	TEX	TEX	NNP	_	_	_
151	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
152	WT-glucose-Rep1	wt-glucose-rep1	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	WT-glucose-Rep2	wt-glucose-rep2	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	WT	wt	JJ	_	_	_
157	glucose	glucose	NN	SUPP	_	_
158	_	_	NN	_	_	_
159	replicate1	replicate1	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	WT	wt	JJ	_	_	_
162	glucose	glucose	NN	SUPP	_	_
163	_	_	NN	_	_	_
164	replicate2	replicate2	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	WT	wt	JJ	_	_	_
167	glucose	glucose	NN	SUPP	_	_
168	_	_	NN	_	_	_
169	replicate3	replicate3	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	WT	wt	JJ	_	_	_
172	_	_	NN	_	_	_
173	glucose	glucose	NN	SUPP	_	_
174	_	_	CD	_	_	_
175	stat	stat	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	WT	wt	JJ	_	_	_
178	_	_	NN	_	_	_
179	glucose	glucose	NN	SUPP	_	_
180	_	_	CD	_	_	_
181	stat	stat	NN	_	_	_
182	_	_	CD	_	_	_
183	TEX	TEX	NNP	_	_	_
184	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
185	WT	WT	NNP	_	_	_
186	_	_	NNP	_	_	_
187	glycerol	glycerol	NN	SUPP	_	_
188	_	_	CD	_	_	_
189	replicate1	replicate1	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	WT	wt	JJ	_	_	_
192	_	_	NN	_	_	_
193	glycerol	glycerol	NN	SUPP	_	_
194	_	_	CD	_	_	_
195	replicate2	replicate2	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	WT	wt	JJ	_	_	_
198	_	_	NN	_	_	_
199	glycerol	glycerol	NN	SUPP	_	_
200	_	_	CD	_	_	_
201	replicate3	replicate3	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	WT	wt	NN	_	_	_
204	-LRB-	-lrb-	-LRB-	_	_	_
205	K10	k10	NN	_	_	_
206	-RRB-	-rrb-	-RRB-	_	_	_
207	in	in	IN	_	_	_
208	M9	m9	NN	_	_	_
209	0.2	0.2	CD	_	_	_
210	%	%	NN	_	_	_
211	Glycerol	glycerol	NN	_	_	_
212	0.2	0.2	CD	_	_	_
213	%	%	NN	_	_	_
214	Tryptone	tryptone	NN	_	_	_
215	40	40	CD	_	_	_
216	mM	mm	NN	KWSUPP	_	_
217	Suc	suc	NN	_	_	_
218	.	.	.	_	_	_

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	K10	k10	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	vs	vs	CC	_	_	_
32	Eno	eno	NN	_	_	_
33	-	-	:	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	DF261	df261	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	in	in	IN	_	_	_
38	M9	m9	NN	_	_	_
39	+	+	CC	_	_	_
40	0.2	0.2	CD	_	_	_
41	%	%	NN	_	_	_
42	Glycerol	glycerol	NN	_	_	_
43	,	,	,	_	_	_
44	0.2	0.2	CD	_	_	_
45	%	%	NN	_	_	_
46	Tryptone	tryptone	NN	_	_	_
47	,	,	,	_	_	_
48	40	40	CD	_	_	_
49	mM	mm	NN	KWSUPP	_	_
50	Suc	suc	NN	_	_	_
51	.	.	.	_	_	_

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	WTKasRep1	wtkasrep1	NN	_	_	_
10	_	_	NN	_	_	_
11	0	0	CD	_	_	_
12	min	min	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	WTKasRep1	wtkasrep1	NN	_	_	_
15	_	_	CD	_	_	_
16	15	15	CD	_	_	_
17	min	min	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	WTKasRep1	wtkasrep1	NN	_	_	_
20	_	_	CD	_	_	_
21	20	20	CD	_	_	_
22	min	min	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	WTKasRep1	wtkasrep1	NN	_	_	_
25	_	_	NN	_	_	_
26	2	2	CD	_	_	_
27	min	min	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	WTKasRep1	wtkasrep1	NN	_	_	_
30	_	_	CD	_	_	_
31	4	4	CD	_	_	_
32	min	min	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	WTKasRep1	wtkasrep1	NN	_	_	_
35	_	_	CD	_	_	_
36	6	6	CD	_	_	_
37	min	min	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	WTKasRep1	wtkasrep1	NN	_	_	_
40	_	_	CD	_	_	_
41	8	8	CD	_	_	_
42	min	min	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	WTKasRep2	wtkasrep2	NN	_	_	_
45	_	_	NN	_	_	_
46	0	0	CD	_	_	_
47	min	min	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	WTKasRep2	wtkasrep2	NN	_	_	_
50	_	_	CD	_	_	_
51	10	10	CD	_	_	_
52	min	min	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	WTKasRep2	wtkasrep2	NN	_	_	_
55	_	_	CD	_	_	_
56	15	15	CD	_	_	_
57	min	min	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	WTKasRep2	wtkasrep2	NN	_	_	_
60	_	_	CD	_	_	_
61	20	20	CD	_	_	_
62	min	min	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	WTKasRep2	wtkasrep2	NN	_	_	_
65	_	_	NN	_	_	_
66	2	2	CD	_	_	_
67	min	min	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	WTKasRep2	wtkasrep2	NN	_	_	_
70	_	_	CD	_	_	_
71	4	4	CD	_	_	_
72	min	min	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	WTKasRep2	wtkasrep2	NN	_	_	_
75	_	_	CD	_	_	_
76	6	6	CD	_	_	_
77	min	min	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	WTKasRep2	wtkasrep2	NN	_	_	_
80	_	_	CD	_	_	_
81	8	8	CD	_	_	_
82	min	min	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	WT	wt	SYM	_	_	_
85	-	-	:	_	_	_
86	Keio	Keio	NNP	_	_	_
87	Sample	Sample	NNP	_	_	_
88	1	1	CD	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	WT	wt	SYM	_	_	_
91	-	-	:	_	_	_
92	Keio	Keio	NNP	_	_	_
93	Sample	Sample	NNP	_	_	_
94	20	20	CD	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	WT	wt	SYM	_	_	_
97	-	-	:	_	_	_
98	Keio	Keio	NNP	_	_	_
99	Sample	Sample	NNP	_	_	_
100	39	39	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	wt	wt	JJ	_	_	_
103	+	+	CC	_	_	_
104	Leu	leu	NN	_	_	_
105	vs.	vs.	CC	_	_	_
106	wt	wt	JJ	_	_	_
107	-	-	:	_	_	_
108	Leu	leu	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	wt	wt	JJ	_	_	_
111	_	_	NN	_	_	_
112	LS	ls	NN	_	_	_
113	_	_	NN	_	_	_
114	1	1	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	wt	wt	JJ	_	_	_
117	_	_	NN	_	_	_
118	LS	ls	NN	_	_	_
119	_	_	NN	_	_	_
120	2	2	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	WT	wt	NN	_	_	_
123	+	+	CC	_	_	_
124	L-trp	l-trp	JJ	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	WT-mannose	wt-mannose	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	wt	wt	JJ	_	_	_
129	_	_	CD	_	_	_
130	ME	me	NN	_	_	_
131	_	_	NN	_	_	_
132	1	1	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	wt	wt	JJ	_	_	_
135	_	_	CD	_	_	_
136	ME	me	NN	_	_	_
137	_	_	NN	_	_	_
138	2	2	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	WT	wt	JJ	_	_	_
141	_	_	NN	_	_	_
142	minimal	minimal	JJ	_	_	_
143	_	_	NN	_	_	_
144	mRNA	mrna	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	WT	wt	JJ	_	_	_
147	_	_	NN	_	_	_
148	minimal	minimal	JJ	_	_	_
149	_	_	NN	_	_	_
150	ribosome	ribosome	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	WT	wt	JJ	_	_	_
153	_	_	NN	_	_	_
154	minus	minus	CC	_	_	_
155	_	_	SYM	_	_	_
156	2DG	2dg	CD	_	_	_
157	_	_	NN	_	_	_
158	1	1	CD	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	WT	wt	JJ	_	_	_
161	_	_	NN	_	_	_
162	minus	minus	CC	_	_	_
163	_	_	SYM	_	_	_
164	2DG	2dg	CD	_	_	_
165	_	_	NN	_	_	_
166	2	2	CD	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	WT	wt	JJ	_	_	_
169	_	_	NN	_	_	_
170	minus	minus	CC	_	_	_
171	_	_	SYM	_	_	_
172	2DG	2dg	CD	_	_	_
173	_	_	SYM	_	_	_
174	3	3	CD	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	WT-mucus-P1	wt-mucus-p1	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	WT-mucus-P2	wt-mucus-p2	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	WT	wt	JJ	_	_	_
181	_	_	NN	_	_	_
182	N0000	n0000	NN	_	_	_
183	_	_	CD	_	_	_
184	r1	r1	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	WT	wt	JJ	_	_	_
187	_	_	NN	_	_	_
188	N0000	n0000	NN	_	_	_
189	_	_	CD	_	_	_
190	r2	r2	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	WT	wt	JJ	_	_	_
193	_	_	SYM	_	_	_
194	N0025	n0025	CD	_	_	_
195	_	_	SYM	_	_	_
196	r1	r1	FW	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
198	WT	wt	FW	_	_	_
199	_	_	SYM	_	_	_
200	N0025	n0025	CD	_	_	_
201	_	_	CD	_	_	_
202	r2	r2	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	WT	wt	JJ	_	_	_
205	_	_	NN	_	_	_
206	N0050	n0050	NN	_	_	_
207	_	_	CD	_	_	_
208	r1	r1	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	WT	wt	JJ	_	_	_
211	_	_	NN	_	_	_
212	N0050	n0050	NN	_	_	_
213	_	_	CD	_	_	_
214	r2	r2	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	WT	wt	JJ	_	_	_
217	_	_	NN	_	_	_
218	N0075	n0075	NN	_	_	_
219	_	_	CD	_	_	_
220	r1	r1	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	WT	wt	JJ	_	_	_
223	_	_	NN	_	_	_
224	N0075	n0075	NN	_	_	_
225	_	_	CD	_	_	_
226	r2	r2	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	WT	wt	NN	_	_	_
229	-LRB-	-lrb-	-LRB-	_	_	_
230	N3433	n3433	NN	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	in	in	IN	_	_	_
233	M9	m9	NN	_	_	_
234	+	+	CC	_	_	_
235	0.2	0.2	CD	_	_	_
236	%	%	NN	_	_	_
237	Glycerol	glycerol	NN	_	_	_
238	,	,	,	_	_	_
239	0.2	0.2	CD	_	_	_
240	%	%	NN	_	_	_
241	Tryptone	tryptone	NN	_	_	_
242	at	at	IN	_	_	_
243	30	30	CD	_	_	_
244	C	c	NN	_	_	_
245	Mid	Mid	NNP	_	_	_
246	Log	Log	NNP	_	_	_
247	1.5	1.5	CD	_	_	_
248	'	'	''	_	_	_
249	post	post	JJ	_	_	_
250	rif	rif	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	WT	wt	NN	_	_	_
253	-LRB-	-lrb-	-LRB-	_	_	_
254	N3433	n3433	NN	_	_	_
255	-RRB-	-rrb-	-RRB-	_	_	_
256	in	in	IN	_	_	_
257	M9	m9	NN	_	_	_
258	+	+	CC	_	_	_
259	0.2	0.2	CD	_	_	_
260	%	%	NN	_	_	_
261	Glycerol	glycerol	NN	_	_	_
262	,	,	,	_	_	_
263	0.2	0.2	CD	_	_	_
264	%	%	NN	_	_	_
265	Tryptone	tryptone	NN	_	_	_
266	at	at	IN	_	_	_
267	30	30	CD	_	_	_
268	C	c	NN	_	_	_
269	Mid	Mid	NNP	_	_	_
270	Log	Log	NNP	_	_	_
271	3.0	3.0	CD	_	_	_
272	'	'	''	_	_	_
273	post	post	JJ	_	_	_
274	rif	rif	NN	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	WT	wt	NN	_	_	_
277	-LRB-	-lrb-	-LRB-	_	_	_
278	N3433	n3433	NN	_	_	_
279	-RRB-	-rrb-	-RRB-	_	_	_
280	in	in	IN	_	_	_
281	M9	m9	NN	_	_	_
282	+	+	CC	_	_	_
283	0.2	0.2	CD	_	_	_
284	%	%	NN	_	_	_
285	Glycerol	glycerol	NN	_	_	_
286	,	,	,	_	_	_
287	0.2	0.2	CD	_	_	_
288	%	%	NN	_	_	_
289	Tryptone	tryptone	NN	_	_	_
290	at	at	IN	_	_	_
291	30	30	CD	_	_	_
292	C	c	NN	_	_	_
293	Mid	Mid	NNP	_	_	_
294	Log	Log	NNP	_	_	_
295	3	3	CD	_	_	_
296	'	'	''	_	_	_
297	post	post	JJ	_	_	_
298	rif	rif	NN	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	WT	wt	NN	_	_	_
301	-LRB-	-lrb-	-LRB-	_	_	_
302	N3433	n3433	NN	_	_	_
303	-RRB-	-rrb-	-RRB-	_	_	_
304	in	in	IN	_	_	_
305	M9	m9	NN	_	_	_
306	+	+	CC	_	_	_
307	0.2	0.2	CD	_	_	_
308	%	%	NN	_	_	_
309	Glycerol	glycerol	NN	_	_	_
310	,	,	,	_	_	_
311	0.2	0.2	CD	_	_	_
312	%	%	NN	_	_	_
313	Tryptone	tryptone	NN	_	_	_
314	at	at	IN	_	_	_
315	30	30	CD	_	_	_
316	C	c	NN	_	_	_
317	Mid	Mid	NNP	_	_	_
318	Log	Log	NNP	_	_	_
319	4.5	4.5	CD	_	_	_
320	'	'	''	_	_	_
321	post	post	JJ	_	_	_
322	rif	rif	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	WT	wt	NN	_	_	_
325	-LRB-	-lrb-	-LRB-	_	_	_
326	N3433	n3433	NN	_	_	_
327	-RRB-	-rrb-	-RRB-	_	_	_
328	in	in	IN	_	_	_
329	M9	m9	NN	_	_	_
330	+	+	CC	_	_	_
331	0.2	0.2	CD	_	_	_
332	%	%	NN	_	_	_
333	Glycerol	glycerol	NN	_	_	_
334	,	,	,	_	_	_
335	0.2	0.2	CD	_	_	_
336	%	%	NN	_	_	_
337	Tryptone	tryptone	NN	_	_	_
338	at	at	IN	_	_	_
339	30	30	CD	_	_	_
340	C	c	NN	_	_	_
341	Mid	Mid	NNP	_	_	_
342	Log	Log	NNP	_	_	_
343	6	6	CD	_	_	_
344	'	'	''	_	_	_
345	post	post	JJ	_	_	_
346	rif	rif	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	WT	wt	NN	_	_	_
349	-LRB-	-lrb-	-LRB-	_	_	_
350	N3433	n3433	NN	_	_	_
351	-RRB-	-rrb-	-RRB-	_	_	_
352	M9	m9	NN	_	_	_
353	+	+	CC	_	_	_
354	0.2	0.2	CD	_	_	_
355	%	%	NN	_	_	_
356	Glycerol	glycerol	NN	_	_	_
357	,	,	,	_	_	_
358	0.2	0.2	CD	_	_	_
359	%	%	NN	_	_	_
360	Tryptone	tryptone	NN	_	_	_
361	at	at	IN	_	_	_
362	30	30	CD	_	_	_
363	C	c	NN	_	_	_
364	Mid	Mid	NNP	_	_	_
365	Log	Log	NNP	_	_	_
366	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
367	WT	WT	NNP	_	_	_
368	-LRB-	-lrb-	-LRB-	_	_	_
369	N3433	n3433	NN	_	_	_
370	-RRB-	-rrb-	-RRB-	_	_	_
371	M9	m9	NN	_	_	_
372	+	+	CC	_	_	_
373	0.2	0.2	CD	_	_	_
374	%	%	NN	_	_	_
375	Glycerol	glycerol	NN	_	_	_
376	,	,	,	_	_	_
377	0.2	0.2	CD	_	_	_
378	%	%	NN	_	_	_
379	Tryptone	tryptone	NN	_	_	_
380	at	at	IN	_	_	_
381	30	30	CD	_	_	_
382	C	c	NN	_	_	_
383	Mid	Mid	NNP	_	_	_
384	Log	Log	NNP	_	_	_
385	6	6	CD	_	_	_
386	'	'	''	_	_	_
387	post	post	JJ	_	_	_
388	rif	rif	NN	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	WT	wt	NN	_	_	_
391	-LRB-	-lrb-	-LRB-	_	_	_
392	N3433	n3433	NN	_	_	_
393	-RRB-	-rrb-	-RRB-	_	_	_
394	vs	vs	CC	_	_	_
395	Pnp	pnp	NN	_	_	_
396	-	-	:	_	_	_
397	-LRB-	-lrb-	-LRB-	_	_	_
398	YHC012	yhc012	NN	_	_	_
399	-RRB-	-rrb-	-RRB-	_	_	_
400	in	in	IN	_	_	_
401	M9	m9	NN	_	_	_
402	+	+	CC	_	_	_
403	0.2	0.2	CD	_	_	_
404	%	%	NN	_	_	_
405	Glycerol	glycerol	NN	_	_	_
406	,	,	,	_	_	_
407	0.2	0.2	CD	_	_	_
408	%	%	NN	_	_	_
409	Tryptone	tryptone	NN	_	_	_
410	at	at	IN	_	_	_
411	30	30	CD	_	_	_
412	C	c	NN	_	_	_
413	Mid	Mid	NNP	_	_	_
414	Log	Log	NNP	_	_	_
415	Trial	Trial	NNP	_	_	_
416	A2	a2	NN	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	WT	wt	NN	_	_	_
419	-LRB-	-lrb-	-LRB-	_	_	_
420	N3433	n3433	NN	_	_	_
421	-RRB-	-rrb-	-RRB-	_	_	_
422	vs	vs	CC	_	_	_
423	Pnp	pnp	NN	_	_	_
424	-	-	:	_	_	_
425	-LRB-	-lrb-	-LRB-	_	_	_
426	YHC012	yhc012	NN	_	_	_
427	-RRB-	-rrb-	-RRB-	_	_	_
428	in	in	IN	_	_	_
429	M9	m9	NN	_	_	_
430	+	+	CC	_	_	_
431	0.2	0.2	CD	_	_	_
432	%	%	NN	_	_	_
433	Glycerol	glycerol	NN	_	_	_
434	,	,	,	_	_	_
435	0.2	0.2	CD	_	_	_
436	%	%	NN	_	_	_
437	Tryptone	tryptone	NN	_	_	_
438	at	at	IN	_	_	_
439	30	30	CD	_	_	_
440	C	c	NN	_	_	_
441	Mid	Mid	NNP	_	_	_
442	Log	Log	NNP	_	_	_
443	Trial	Trial	NNP	_	_	_
444	B2	b2	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	WT	wt	NN	_	_	_
447	-LRB-	-lrb-	-LRB-	_	_	_
448	N3433	n3433	NN	_	_	_
449	-RRB-	-rrb-	-RRB-	_	_	_
450	vs	vs	CC	_	_	_
451	Pnp	pnp	NN	_	_	_
452	-	-	:	_	_	_
453	-LRB-	-lrb-	-LRB-	_	_	_
454	YHC012	yhc012	NN	_	_	_
455	-RRB-	-rrb-	-RRB-	_	_	_
456	in	in	IN	_	_	_
457	M9	m9	NN	_	_	_
458	+	+	CC	_	_	_
459	0.2	0.2	CD	_	_	_
460	%	%	NN	_	_	_
461	Glycerol	glycerol	NN	_	_	_
462	,	,	,	_	_	_
463	0.2	0.2	CD	_	_	_
464	%	%	NN	_	_	_
465	Tryptone	tryptone	NN	_	_	_
466	at	at	IN	_	_	_
467	30	30	CD	_	_	_
468	C	c	NN	_	_	_
469	Mid	Mid	NNP	_	_	_
470	Log	Log	NNP	_	_	_
471	Trial	Trial	NNP	_	_	_
472	C2	c2	NN	_	_	_
473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
474	WT	wt	NN	_	_	_
475	-LRB-	-lrb-	-LRB-	_	_	_
476	N3433	n3433	NN	_	_	_
477	-RRB-	-rrb-	-RRB-	_	_	_
478	vs	vs	CC	_	_	_
479	RhlB	rhlb	NN	_	_	_
480	-	-	:	_	_	_
481	-LRB-	-lrb-	-LRB-	_	_	_
482	SU02	su02	NN	_	_	_
483	-RRB-	-rrb-	-RRB-	_	_	_
484	in	in	IN	_	_	_
485	M9	m9	NN	_	_	_
486	+	+	CC	_	_	_
487	0.2	0.2	CD	_	_	_
488	%	%	NN	_	_	_
489	Glycerol	glycerol	NN	_	_	_
490	,	,	,	_	_	_
491	0.2	0.2	CD	_	_	_
492	%	%	NN	_	_	_
493	Tryptone	tryptone	NN	_	_	_
494	at	at	IN	_	_	_
495	30	30	CD	_	_	_
496	C	c	NN	_	_	_
497	Mid	Mid	NNP	_	_	_
498	Log	Log	NNP	_	_	_
499	Trial	Trial	NNP	_	_	_
500	A	A	NNP	_	_	_
501	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
502	WT	WT	NNP	_	_	_
503	-LRB-	-lrb-	-LRB-	_	_	_
504	N3433	n3433	NN	_	_	_
505	-RRB-	-rrb-	-RRB-	_	_	_
506	vs	vs	CC	_	_	_
507	RhlB	rhlb	NN	_	_	_
508	-	-	:	_	_	_
509	-LRB-	-lrb-	-LRB-	_	_	_
510	SU02	su02	NN	_	_	_
511	-RRB-	-rrb-	-RRB-	_	_	_
512	in	in	IN	_	_	_
513	M9	m9	NN	_	_	_
514	+	+	CC	_	_	_
515	0.2	0.2	CD	_	_	_
516	%	%	NN	_	_	_
517	Glycerol	glycerol	NN	_	_	_
518	,	,	,	_	_	_
519	0.2	0.2	CD	_	_	_
520	%	%	NN	_	_	_
521	Tryptone	tryptone	NN	_	_	_
522	at	at	IN	_	_	_
523	30	30	CD	_	_	_
524	C	c	NN	_	_	_
525	Mid	Mid	NNP	_	_	_
526	Log	Log	NNP	_	_	_
527	Trial	Trial	NNP	_	_	_
528	A1	a1	NN	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	WT	wt	NN	_	_	_
531	-LRB-	-lrb-	-LRB-	_	_	_
532	N3433	n3433	NN	_	_	_
533	-RRB-	-rrb-	-RRB-	_	_	_
534	vs	vs	CC	_	_	_
535	RhlB	rhlb	NN	_	_	_
536	-	-	:	_	_	_
537	-LRB-	-lrb-	-LRB-	_	_	_
538	SU02	su02	NN	_	_	_
539	-RRB-	-rrb-	-RRB-	_	_	_
540	in	in	IN	_	_	_
541	M9	m9	NN	_	_	_
542	0.2	0.2	CD	_	_	_
543	%	%	NN	_	_	_
544	Glycerol	glycerol	NN	_	_	_
545	,	,	,	_	_	_
546	0.2	0.2	CD	_	_	_
547	%	%	NN	_	_	_
548	Tryptone	tryptone	NN	_	_	_
549	at	at	IN	_	_	_
550	30	30	CD	_	_	_
551	C	c	NN	_	_	_
552	Mid	Mid	NNP	_	_	_
553	Log	Log	NNP	_	_	_
554	Trial	Trial	NNP	_	_	_
555	B	B	NNP	_	_	_
556	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
557	WT	WT	NNP	_	_	_
558	-LRB-	-lrb-	-LRB-	_	_	_
559	N3433	n3433	NN	_	_	_
560	-RRB-	-rrb-	-RRB-	_	_	_
561	vs	vs	CC	_	_	_
562	RhlB	rhlb	NN	_	_	_
563	-	-	:	_	_	_
564	-LRB-	-lrb-	-LRB-	_	_	_
565	SU02	su02	NN	_	_	_
566	-RRB-	-rrb-	-RRB-	_	_	_
567	in	in	IN	_	_	_
568	M9	m9	NN	_	_	_
569	+	+	CC	_	_	_
570	0.2	0.2	CD	_	_	_
571	%	%	NN	_	_	_
572	Glycerol	glycerol	NN	_	_	_
573	,	,	,	_	_	_
574	0.2	0.2	CD	_	_	_
575	%	%	NN	_	_	_
576	Tryptone	tryptone	NN	_	_	_
577	at	at	IN	_	_	_
578	30	30	CD	_	_	_
579	C	c	NN	_	_	_
580	Mid	Mid	NNP	_	_	_
581	Log	Log	NNP	_	_	_
582	Trial	Trial	NNP	_	_	_
583	B1	b1	NN	_	_	_
584	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
585	WT	wt	NN	_	_	_
586	-LRB-	-lrb-	-LRB-	_	_	_
587	N3433	n3433	NN	_	_	_
588	-RRB-	-rrb-	-RRB-	_	_	_
589	vs	vs	CC	_	_	_
590	RhlB	rhlb	NN	_	_	_
591	-	-	:	_	_	_
592	-LRB-	-lrb-	-LRB-	_	_	_
593	SU02	su02	NN	_	_	_
594	-RRB-	-rrb-	-RRB-	_	_	_
595	in	in	IN	_	_	_
596	M9	m9	NN	_	_	_
597	0.2	0.2	CD	_	_	_
598	%	%	NN	_	_	_
599	Glycerol	glycerol	NN	_	_	_
600	,	,	,	_	_	_
601	0.2	0.2	CD	_	_	_
602	%	%	NN	_	_	_
603	Tryptone	tryptone	NN	_	_	_
604	at	at	IN	_	_	_
605	30	30	CD	_	_	_
606	C	c	NN	_	_	_
607	Mid	Mid	NNP	_	_	_
608	Log	Log	NNP	_	_	_
609	Trial	Trial	NNP	_	_	_
610	C	C	NNP	_	_	_
611	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
612	WT	WT	NNP	_	_	_
613	-LRB-	-lrb-	-LRB-	_	_	_
614	N3433	n3433	NN	_	_	_
615	-RRB-	-rrb-	-RRB-	_	_	_
616	vs	vs	CC	_	_	_
617	RhlB	rhlb	NN	_	_	_
618	-	-	:	_	_	_
619	-LRB-	-lrb-	-LRB-	_	_	_
620	SU02	su02	NN	_	_	_
621	-RRB-	-rrb-	-RRB-	_	_	_
622	in	in	IN	_	_	_
623	M9	m9	NN	_	_	_
624	+	+	CC	_	_	_
625	0.2	0.2	CD	_	_	_
626	%	%	NN	_	_	_
627	Glycerol	glycerol	NN	_	_	_
628	,	,	,	_	_	_
629	0.2	0.2	CD	_	_	_
630	%	%	NN	_	_	_
631	Tryptone	tryptone	NN	_	_	_
632	at	at	IN	_	_	_
633	30	30	CD	_	_	_
634	C	c	NN	_	_	_
635	Mid	Mid	NNP	_	_	_
636	Log	Log	NNP	_	_	_
637	Trial	Trial	NNP	_	_	_
638	C1	c1	NN	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	WT	wt	JJ	_	_	_
641	NaCl	nacl	NN	_	_	_
642	1	1	CD	_	_	_
643	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
644	WT	wt	JJ	_	_	_
645	NaCl	nacl	NN	_	_	_
646	2	2	CD	_	_	_
647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
648	WT	wt	JJ	_	_	_
649	NO3	no3	NN	_	_	_
650	1	1	CD	_	_	_
651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
652	WT	wt	JJ	_	_	_
653	NO3	no3	NN	_	_	_
654	2	2	CD	_	_	_
655	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
656	WT	wt	JJ	_	_	_
657	NO3	no3	NN	_	_	_
658	w/propionate	w/propionate	NN	_	_	_
659	1	1	CD	_	_	_
660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
661	WT	wt	JJ	_	_	_
662	NO3	no3	NN	_	_	_
663	w/propionate	w/propionate	NN	_	_	_
664	2	2	CD	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	WT	wt	JJ	_	_	_
667	_	_	NN	_	_	_
668	noCPR	nocpr	NN	_	_	_
669	_	_	NN	_	_	_
670	1	1	CD	_	_	_
671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
672	WT	wt	JJ	_	_	_
673	_	_	NN	_	_	_
674	noCPR	nocpr	NN	_	_	_
675	_	_	NN	_	_	_
676	2	2	CD	_	_	_
677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
678	WT	wt	JJ	_	_	_
679	_	_	NN	_	_	_
680	N	n	NN	_	_	_
681	_	_	CD	_	_	_
682	strv	strv	NN	_	_	_
683	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
684	WT	wt	JJ	_	_	_
685	_	_	NN	_	_	_
686	N	n	NN	_	_	_
687	_	_	CD	_	_	_
688	strv	strv	NN	_	_	_
689	_	_	CD	_	_	_
690	TEX	TEX	NNP	_	_	_
691	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
692	WT	wt	SYM	_	_	_
693	-	-	:	_	_	_
694	O2	o2	CD	_	_	_
695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
696	WT	wt	SYM	_	_	_
697	-	-	:	_	_	_
698	O2	o2	CD	_	_	_
699	1	1	CD	_	_	_
700	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
701	WT	wt	NN	_	_	_
702	+	+	CC	_	_	_
703	O2	o2	CD	_	_	_
704	1	1	CD	_	_	_
705	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
706	WT	wt	NN	_	_	_
707	O2	o2	CD	_	_	_
708	1	1	CD	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	WT	wt	SYM	_	_	_
711	-	-	:	_	_	_
712	O2	o2	CD	_	_	_
713	2	2	CD	_	_	_
714	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
715	WT	wt	NN	_	_	_
716	+	+	CC	_	_	_
717	O2	o2	CD	_	_	_
718	2	2	CD	_	_	_
719	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
720	WT	WT	NNP	_	_	_
721	O2	o2	CD	_	_	_
722	2	2	CD	_	_	_
723	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
724	WT	wt	SYM	_	_	_
725	-	-	:	_	_	_
726	O2	o2	CD	_	_	_
727	3	3	CD	_	_	_
728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
729	WT	wt	NN	_	_	_
730	+	+	CC	_	_	_
731	O2	o2	CD	_	_	_
732	3	3	CD	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	WT	wt	NN	_	_	_
735	O2	o2	CD	_	_	_
736	w/propionate	w/propionate	NN	_	_	_
737	1	1	CD	_	_	_
738	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
739	WT	wt	NN	_	_	_
740	O2	o2	CD	_	_	_
741	w/propionate	w/propionate	NN	_	_	_
742	2	2	CD	_	_	_
743	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
744	wt	wt	JJ	_	_	_
745	or	or	CC	_	_	_
746	mutant	mutant	JJ	_	_	_
747	:	:	:	_	_	_
748	P2-08	p2-08	NN	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
750	wt	wt	JJ	_	_	_
751	or	or	CC	_	_	_
752	mutant	mutant	JJ	_	_	_
753	:	:	:	_	_	_
754	P2-51	p2-51	NN	_	_	_
755	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
756	wt	wt	JJ	_	_	_
757	or	or	CC	_	_	_
758	mutant	mutant	JJ	_	_	_
759	:	:	:	_	_	_
760	P2-58	p2-58	NN	_	_	_
761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
762	wt	wt	JJ	_	_	_
763	or	or	CC	_	_	_
764	mutant	mutant	JJ	_	_	_
765	:	:	:	_	_	_
766	P2-66	p2-66	NN	_	_	_
767	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
768	wt	wt	JJ	_	_	_
769	or	or	CC	_	_	_
770	mutant	mutant	JJ	_	_	_
771	:	:	:	_	_	_
772	P2-77	p2-77	NN	_	_	_
773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
774	wt	wt	JJ	_	_	_
775	or	or	CC	_	_	_
776	mutant	mutant	JJ	_	_	_
777	:	:	:	_	_	_
778	PF2-04	pf2-04	NN	_	_	_
779	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
780	wt	wt	JJ	_	_	_
781	or	or	CC	_	_	_
782	mutant	mutant	JJ	_	_	_
783	:	:	:	_	_	_
784	PF2-08	pf2-08	NN	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	wt	wt	JJ	_	_	_
787	or	or	CC	_	_	_
788	mutant	mutant	JJ	_	_	_
789	:	:	:	_	_	_
790	PF2-12	pf2-12	NN	_	_	_
791	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
792	wt	wt	JJ	_	_	_
793	or	or	CC	_	_	_
794	mutant	mutant	JJ	_	_	_
795	:	:	:	_	_	_
796	WT	WT	NNP	_	_	_
797	@	@	SYM	_	_	_
798	0.8	0.8	CD	_	_	_
799	%	%	NN	_	_	_
800	But	but	CC	_	_	_
801	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
802	WT	WT	NNP	_	_	_
803	pH5	ph5	NN	_	_	_
804	.5	.5	CD	_	_	_
805	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
806	WT	wt	JJ	_	_	_
807	pH5	ph5	NN	_	_	_
808	.5	.5	CD	_	_	_
809	1	1	CD	_	_	_
810	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
811	WT	wt	JJ	_	_	_
812	pH5	ph5	NN	_	_	_
813	.5	.5	NN	_	_	_
814	2	2	CD	_	_	_
815	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
816	WT	WT	NNP	_	_	_
817	pH	ph	NN	_	_	_
818	5.6	5.6	CD	_	_	_
819	A	a	DT	_	_	_
820	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
821	WT	wt	NN	_	_	_
822	pH	ph	NN	_	_	_
823	5.6	5.6	CD	_	_	_
824	B	b	NN	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	WT	wt	NN	_	_	_
827	pH	ph	NN	_	_	_
828	5.6	5.6	CD	_	_	_
829	C	c	NN	_	_	_
830	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
831	WT	wt	JJ	_	_	_
832	pH	ph	NN	_	_	_
833	7.2	7.2	CD	_	_	_
834	+15	+15	CD	_	_	_
835	%	%	NN	_	_	_
836	sucrose	sucrose	NN	_	_	_
837	A	a	NN	_	_	_
838	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
839	WT	wt	JJ	_	_	_
840	pH	ph	NN	_	_	_
841	7.2	7.2	CD	_	_	_
842	+15	+15	CD	_	_	_
843	%	%	NN	_	_	_
844	sucrose	sucrose	NN	_	_	_
845	B	b	NN	_	_	_
846	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
847	WT	wt	JJ	_	_	_
848	pH	ph	NN	_	_	_
849	7.2	7.2	CD	_	_	_
850	+15	+15	CD	_	_	_
851	%	%	NN	_	_	_
852	sucrose	sucrose	NN	_	_	_
853	C	c	NN	_	_	_
854	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
855	WT	wt	JJ	_	_	_
856	_	_	NN	_	_	_
857	plus	plus	CC	_	_	_
858	_	_	SYM	_	_	_
859	2DG	2dg	CD	_	_	_
860	_	_	NN	_	_	_
861	1	1	CD	_	_	_
862	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
863	WT	wt	JJ	_	_	_
864	_	_	NN	_	_	_
865	plus	plus	CC	_	_	_
866	_	_	SYM	_	_	_
867	2DG	2dg	CD	_	_	_
868	_	_	NN	_	_	_
869	2	2	CD	_	_	_
870	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
871	WT	wt	JJ	_	_	_
872	_	_	NN	_	_	_
873	plus	plus	CC	_	_	_
874	_	_	SYM	_	_	_
875	2DG	2dg	CD	_	_	_
876	_	_	SYM	_	_	_
877	3	3	CD	_	_	_
878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
879	WT	WT	NNP	_	_	_
880	PQ	PQ	NNP	_	_	_
881	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
882	WT	WT	NNP	_	_	_
883	PQ	PQ	NNP	_	_	_
884	1	1	CD	_	_	_
885	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
886	WT	WT	NNP	_	_	_
887	PQ	PQ	NNP	_	_	_
888	2	2	CD	_	_	_
889	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
890	WT	WT	NNP	_	_	_
891	rep1	rep1	NN	_	_	_
892	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
893	WT	wt	JJ	_	_	_
894	rep	rep	NN	GEN	_	_
895	1	1	CD	_	_	_
896	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
897	WTRep1	wtrep1	NN	_	_	_
898	_	_	NN	_	_	_
899	0	0	CD	_	_	_
900	min	min	NN	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	WTRep1	wtrep1	NN	_	_	_
903	_	_	CD	_	_	_
904	10	10	CD	_	_	_
905	min	min	NN	_	_	_
906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
907	WTRep1	wtrep1	NN	_	_	_
908	_	_	CD	_	_	_
909	15	15	CD	_	_	_
910	min	min	NN	_	_	_
911	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
912	WTRep1	wtrep1	NN	_	_	_
913	_	_	CD	_	_	_
914	20	20	CD	_	_	_
915	min	min	NN	_	_	_
916	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
917	WTRep1	wtrep1	NN	_	_	_
918	_	_	NN	_	_	_
919	2	2	CD	_	_	_
920	min	min	NN	_	_	_
921	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
922	WTRep1	wtrep1	NN	_	_	_
923	_	_	CD	_	_	_
924	4	4	CD	_	_	_
925	min	min	NN	_	_	_
926	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
927	WTRep1	wtrep1	NN	_	_	_
928	_	_	CD	_	_	_
929	6	6	CD	_	_	_
930	min	min	NN	_	_	_
931	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
932	WTRep1	wtrep1	NN	_	_	_
933	_	_	CD	_	_	_
934	8	8	CD	_	_	_
935	min	min	NN	_	_	_
936	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
937	wt.rep1.ee	wt.rep1.ee	NN	_	_	_
938	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
939	wt.rep1.me	wt.rep1.me	NN	_	_	_
940	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
941	WT	wt	JJ	_	_	_
942	rep2	rep2	NN	_	_	_
943	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
944	WT	wt	JJ	_	_	_
945	rep	rep	NN	GEN	_	_
946	2	2	CD	_	_	_
947	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
948	WTRep2	wtrep2	NN	_	_	_
949	_	_	NN	_	_	_
950	0	0	CD	_	_	_
951	min	min	NN	_	_	_
952	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
953	WTRep2	wtrep2	NN	_	_	_
954	_	_	CD	_	_	_
955	10	10	CD	_	_	_
956	min	min	NN	_	_	_
957	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
958	WTRep2	wtrep2	NN	_	_	_
959	_	_	CD	_	_	_
960	15	15	CD	_	_	_
961	min	min	NN	_	_	_
962	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
963	WTRep2	wtrep2	NN	_	_	_
964	_	_	CD	_	_	_
965	20	20	CD	_	_	_
966	min	min	NN	_	_	_
967	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
968	WTRep2	wtrep2	NN	_	_	_
969	_	_	NN	_	_	_
970	2	2	CD	_	_	_
971	min	min	NN	_	_	_
972	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
973	WTRep2	wtrep2	NN	_	_	_
974	_	_	CD	_	_	_
975	4	4	CD	_	_	_
976	min	min	NN	_	_	_
977	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
978	WTRep2	wtrep2	NN	_	_	_
979	_	_	CD	_	_	_
980	6	6	CD	_	_	_
981	min	min	NN	_	_	_
982	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
983	WTRep2	wtrep2	NN	_	_	_
984	_	_	CD	_	_	_
985	8	8	CD	_	_	_
986	min	min	NN	_	_	_
987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
988	wt.rep2.ee	wt.rep2.ee	NN	_	_	_
989	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
990	wt.rep2.me	wt.rep2.me	NN	_	_	_
991	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
992	WT	wt	JJ	_	_	_
993	rep3	rep3	NN	_	_	_
994	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
995	WT	wt	JJ	_	_	_
996	rep	rep	NN	GEN	_	_
997	3	3	CD	_	_	_
998	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
999	WT	wt	JJ	_	_	_
1000	_	_	NN	_	_	_
1001	RNA-Seq	rna-seq	NN	_	_	_
1002	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1003	wt	wt	JJ	_	_	_
1004	_	_	NN	_	_	_
1005	S	s	NN	_	_	_
1006	_	_	NN	_	_	_
1007	1	1	CD	_	_	_
1008	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1009	wt	wt	JJ	_	_	_
1010	_	_	NN	_	_	_
1011	S	s	NN	_	_	_
1012	_	_	NN	_	_	_
1013	2	2	CD	_	_	_
1014	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1015	WT	wt	NN	_	_	_
1016	-LRB-	-lrb-	-LRB-	_	_	_
1017	SH3208	sh3208	NN	_	_	_
1018	-RRB-	-rrb-	-RRB-	_	_	_
1019	in	in	IN	_	_	_
1020	M9	m9	NN	_	_	_
1021	+	+	CC	_	_	_
1022	0.2	0.2	CD	_	_	_
1023	%	%	NN	_	_	_
1024	Glycerol	glycerol	NN	_	_	_
1025	,	,	,	_	_	_
1026	0.2	0.2	CD	_	_	_
1027	%	%	NN	_	_	_
1028	Tryptone	tryptone	NN	_	_	_
1029	at	at	IN	_	_	_
1030	30	30	CD	_	_	_
1031	C	c	NN	_	_	_
1032	Mid	Mid	NNP	_	_	_
1033	Log	Log	NNP	_	_	_
1034	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1035	WT	WT	NNP	_	_	_
1036	-LRB-	-lrb-	-LRB-	_	_	_
1037	SH3208	sh3208	NN	_	_	_
1038	-RRB-	-rrb-	-RRB-	_	_	_
1039	in	in	IN	_	_	_
1040	M9	m9	NN	_	_	_
1041	+	+	CC	_	_	_
1042	0.2	0.2	CD	_	_	_
1043	%	%	NN	_	_	_
1044	Glycerol	glycerol	NN	_	_	_
1045	,	,	,	_	_	_
1046	0.2	0.2	CD	_	_	_
1047	%	%	NN	_	_	_
1048	Tryptone	tryptone	NN	_	_	_
1049	at	at	IN	_	_	_
1050	30	30	CD	_	_	_
1051	C	c	NN	_	_	_
1052	Mid	Mid	NNP	_	_	_
1053	Log	Log	NNP	_	_	_
1054	1.5	1.5	CD	_	_	_
1055	'	'	''	_	_	_
1056	post	post	JJ	_	_	_
1057	rif	rif	NN	_	_	_
1058	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1059	WT	wt	NN	_	_	_
1060	-LRB-	-lrb-	-LRB-	_	_	_
1061	SH3208	sh3208	NN	_	_	_
1062	-RRB-	-rrb-	-RRB-	_	_	_
1063	in	in	IN	_	_	_
1064	M9	m9	NN	_	_	_
1065	+	+	CC	_	_	_
1066	0.2	0.2	CD	_	_	_
1067	%	%	NN	_	_	_
1068	Glycerol	glycerol	NN	_	_	_
1069	,	,	,	_	_	_
1070	0.2	0.2	CD	_	_	_
1071	%	%	NN	_	_	_
1072	Tryptone	tryptone	NN	_	_	_
1073	at	at	IN	_	_	_
1074	30	30	CD	_	_	_
1075	C	c	NN	_	_	_
1076	Mid	Mid	NNP	_	_	_
1077	Log	Log	NNP	_	_	_
1078	3	3	CD	_	_	_
1079	'	'	''	_	_	_
1080	post	post	JJ	_	_	_
1081	rif	rif	NN	_	_	_
1082	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1083	WT	wt	NN	_	_	_
1084	-LRB-	-lrb-	-LRB-	_	_	_
1085	SH3208	sh3208	NN	_	_	_
1086	-RRB-	-rrb-	-RRB-	_	_	_
1087	in	in	IN	_	_	_
1088	M9	m9	NN	_	_	_
1089	+	+	CC	_	_	_
1090	0.2	0.2	CD	_	_	_
1091	%	%	NN	_	_	_
1092	Glycerol	glycerol	NN	_	_	_
1093	,	,	,	_	_	_
1094	0.2	0.2	CD	_	_	_
1095	%	%	NN	_	_	_
1096	Tryptone	tryptone	NN	_	_	_
1097	at	at	IN	_	_	_
1098	30	30	CD	_	_	_
1099	C	c	NN	_	_	_
1100	Mid	Mid	NNP	_	_	_
1101	Log	Log	NNP	_	_	_
1102	4.5	4.5	CD	_	_	_
1103	'	'	''	_	_	_
1104	post	post	JJ	_	_	_
1105	rif	rif	NN	_	_	_
1106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1107	WT	wt	NN	_	_	_
1108	-LRB-	-lrb-	-LRB-	_	_	_
1109	SH3208	sh3208	NN	_	_	_
1110	-RRB-	-rrb-	-RRB-	_	_	_
1111	in	in	IN	_	_	_
1112	M9	m9	NN	_	_	_
1113	+	+	CC	_	_	_
1114	0.2	0.2	CD	_	_	_
1115	%	%	NN	_	_	_
1116	Glycerol	glycerol	NN	_	_	_
1117	,	,	,	_	_	_
1118	0.2	0.2	CD	_	_	_
1119	%	%	NN	_	_	_
1120	Tryptone	tryptone	NN	_	_	_
1121	at	at	IN	_	_	_
1122	30	30	CD	_	_	_
1123	C	c	NN	_	_	_
1124	Mid	Mid	NNP	_	_	_
1125	Log	Log	NNP	_	_	_
1126	6	6	CD	_	_	_
1127	'	'	''	_	_	_
1128	post	post	JJ	_	_	_
1129	rif	rif	NN	_	_	_
1130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1131	WT	wt	NN	_	_	_
1132	-LRB-	-lrb-	-LRB-	_	_	_
1133	SH3208	sh3208	NN	_	_	_
1134	-RRB-	-rrb-	-RRB-	_	_	_
1135	M9	m9	NN	_	_	_
1136	+	+	CC	_	_	_
1137	0.2	0.2	CD	_	_	_
1138	%	%	NN	_	_	_
1139	Glycerol	glycerol	NN	_	_	_
1140	,	,	,	_	_	_
1141	0.2	0.2	CD	_	_	_
1142	%	%	NN	_	_	_
1143	Tryptone	tryptone	NN	_	_	_
1144	at	at	IN	_	_	_
1145	30	30	CD	_	_	_
1146	C	c	NN	_	_	_
1147	Mid	Mid	NNP	_	_	_
1148	Log	Log	NNP	_	_	_
1149	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1150	WT	WT	NNP	_	_	_
1151	-LRB-	-lrb-	-LRB-	_	_	_
1152	SH3208	sh3208	NN	_	_	_
1153	-RRB-	-rrb-	-RRB-	_	_	_
1154	vs	vs	CC	_	_	_
1155	N-RNaseE	n-rnasee	NN	_	_	_
1156	-LRB-	-lrb-	-LRB-	_	_	_
1157	BZ453	bz453	NN	_	_	_
1158	-RRB-	-rrb-	-RRB-	_	_	_
1159	in	in	IN	_	_	_
1160	M9	m9	NN	_	_	_
1161	+	+	CC	_	_	_
1162	0.2	0.2	CD	_	_	_
1163	%	%	NN	_	_	_
1164	Glycerol	glycerol	NN	_	_	_
1165	,	,	,	_	_	_
1166	0.2	0.2	CD	_	_	_
1167	%	%	NN	_	_	_
1168	Tryptone	tryptone	NN	_	_	_
1169	at	at	IN	_	_	_
1170	30	30	CD	_	_	_
1171	C	c	NN	_	_	_
1172	Mid	Mid	NNP	_	_	_
1173	Log	Log	NNP	_	_	_
1174	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1175	WT	WT	NNP	_	_	_
1176	-LRB-	-lrb-	-LRB-	_	_	_
1177	SH3208	sh3208	NN	_	_	_
1178	-RRB-	-rrb-	-RRB-	_	_	_
1179	vs	vs	CC	_	_	_
1180	N-RNaseE	n-rnasee	NN	_	_	_
1181	-LRB-	-lrb-	-LRB-	_	_	_
1182	BZ453	bz453	NN	_	_	_
1183	-RRB-	-rrb-	-RRB-	_	_	_
1184	in	in	IN	_	_	_
1185	M9	m9	NN	_	_	_
1186	+	+	CC	_	_	_
1187	0.2	0.2	CD	_	_	_
1188	%	%	NN	_	_	_
1189	Glycerol	glycerol	NN	_	_	_
1190	,	,	,	_	_	_
1191	0.2	0.2	CD	_	_	_
1192	%	%	NN	_	_	_
1193	Tryptone	tryptone	NN	_	_	_
1194	at	at	IN	_	_	_
1195	30	30	CD	_	_	_
1196	C	c	NN	_	_	_
1197	Mid	Mid	NNP	_	_	_
1198	Log	Log	NNP	_	_	_
1199	Trial	Trial	NNP	_	_	_
1200	A	A	NNP	_	_	_
1201	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1202	WT	WT	NNP	_	_	_
1203	-LRB-	-lrb-	-LRB-	_	_	_
1204	SH3208	sh3208	NN	_	_	_
1205	-RRB-	-rrb-	-RRB-	_	_	_
1206	vs	vs	CC	_	_	_
1207	N-RNaseE	n-rnasee	NN	_	_	_
1208	-LRB-	-lrb-	-LRB-	_	_	_
1209	BZ453	bz453	NN	_	_	_
1210	-RRB-	-rrb-	-RRB-	_	_	_
1211	in	in	IN	_	_	_
1212	M9	m9	NN	_	_	_
1213	+	+	CC	_	_	_
1214	0.2	0.2	CD	_	_	_
1215	%	%	NN	_	_	_
1216	Glycerol	glycerol	NN	_	_	_
1217	,	,	,	_	_	_
1218	0.2	0.2	CD	_	_	_
1219	%	%	NN	_	_	_
1220	Tryptone	tryptone	NN	_	_	_
1221	at	at	IN	_	_	_
1222	30	30	CD	_	_	_
1223	C	c	NN	_	_	_
1224	Mid	Mid	NNP	_	_	_
1225	Log	Log	NNP	_	_	_
1226	Trial	trial	NN	_	_	_
1227	B	b	NN	_	_	_
1228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1229	WT	wt	NN	_	_	_
1230	-LRB-	-lrb-	-LRB-	_	_	_
1231	SH3208	sh3208	NN	_	_	_
1232	-RRB-	-rrb-	-RRB-	_	_	_
1233	vs	vs	CC	_	_	_
1234	N-RNaseE	n-rnasee	NN	_	_	_
1235	-LRB-	-lrb-	-LRB-	_	_	_
1236	BZ453	bz453	NN	_	_	_
1237	-RRB-	-rrb-	-RRB-	_	_	_
1238	in	in	IN	_	_	_
1239	M9	m9	NN	_	_	_
1240	+	+	CC	_	_	_
1241	0.2	0.2	CD	_	_	_
1242	%	%	NN	_	_	_
1243	Glycerol	glycerol	NN	_	_	_
1244	,	,	,	_	_	_
1245	0.2	0.2	CD	_	_	_
1246	%	%	NN	_	_	_
1247	Tryptone	tryptone	NN	_	_	_
1248	at	at	IN	_	_	_
1249	30	30	CD	_	_	_
1250	C	c	NN	_	_	_
1251	Mid	Mid	NNP	_	_	_
1252	Log	Log	NNP	_	_	_
1253	Trial	Trial	NNP	_	_	_
1254	C	C	NNP	_	_	_
1255	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1256	WT	WT	NNP	_	_	_
1257	strain	strain	NN	_	_	_
1258	treated	treat	VBN	_	_	_
1259	with	with	IN	_	_	_
1260	glycolaldehyde	glycolaldehyde	NN	_	_	_
1261	first	first	JJ	_	_	_
1262	repetition	repetition	NN	_	_	_
1263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1264	WT	wt	JJ	_	_	_
1265	strain	strain	NN	_	_	_
1266	treated	treat	VBN	_	_	_
1267	with	with	IN	_	_	_
1268	glycolaldehyde	glycolaldehyde	NN	_	_	_
1269	second	second	JJ	_	_	_
1270	repetition	repetition	NN	_	_	_
1271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1272	WT	wt	JJ	_	_	_
1273	strain	strain	NN	_	_	_
1274	treated	treat	VBN	_	_	_
1275	with	with	IN	_	_	_
1276	glycolaldehyde	glycolaldehyde	NN	_	_	_
1277	third	third	JJ	_	_	_
1278	repetition	repetition	NN	_	_	_
1279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1280	WT	wt	JJ	_	_	_
1281	strain	strain	NN	_	_	_
1282	without	without	IN	_	_	_
1283	glycolaldehyde	glycolaldehyde	NN	_	_	_
1284	first	first	JJ	_	_	_
1285	repetition	repetition	NN	_	_	_
1286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1287	WT	wt	JJ	_	_	_
1288	strain	strain	NN	_	_	_
1289	without	without	IN	_	_	_
1290	glycolaldehyde	glycolaldehyde	NN	_	_	_
1291	second	second	JJ	_	_	_
1292	repetition	repetition	NN	_	_	_
1293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1294	WT	wt	JJ	_	_	_
1295	strain	strain	NN	_	_	_
1296	without	without	IN	_	_	_
1297	glycolaldehyde	glycolaldehyde	NN	_	_	_
1298	third	third	JJ	_	_	_
1299	repetition	repetition	NN	_	_	_
1300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1301	wt	wt	JJ	_	_	_
1302	_	_	NN	_	_	_
1303	T	t	NN	_	_	_
1304	_	_	NN	_	_	_
1305	1	1	CD	_	_	_
1306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1307	wt	wt	JJ	_	_	_
1308	_	_	NN	_	_	_
1309	T	t	NN	_	_	_
1310	_	_	NN	_	_	_
1311	2	2	CD	_	_	_
1312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1313	wt	wt	JJ	_	_	_
1314	_	_	NN	_	_	_
1315	T	t	NN	_	_	_
1316	_	_	CD	_	_	_
1317	3	3	CD	_	_	_
1318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1319	wt	wt	JJ	_	_	_
1320	+	+	CC	_	_	_
1321	trp	trp	NN	_	_	_
1322	vs.	vs.	NN	_	_	_
1323	-	-	:	_	_	_
1324	trp	trp	NN	_	_	_
1325	,	,	,	_	_	_
1326	min	min	NN	_	_	_
1327	+.2	+.2	CD	_	_	_
1328	%	%	NN	_	_	_
1329	glucose	glucose	NN	SUPP	_	_
1330	,	,	,	_	_	_
1331	W3110	w3110	NN	_	_	_
1332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1333	wt	wt	JJ	_	_	_
1334	_	_	NN	_	_	_
1335	TS	ts	NN	_	_	_
1336	_	_	NN	_	_	_
1337	1	1	CD	_	_	_
1338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1339	wt	wt	JJ	_	_	_
1340	_	_	NN	_	_	_
1341	TS	ts	NN	_	_	_
1342	_	_	NN	_	_	_
1343	2	2	CD	_	_	_
1344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1345	wt	wt	JJ	_	_	_
1346	_	_	NN	_	_	_
1347	un	un	NN	_	_	_
1348	_	_	NN	_	_	_
1349	1	1	CD	_	_	_
1350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1351	wt	wt	JJ	_	_	_
1352	_	_	NN	_	_	_
1353	un	un	NN	_	_	_
1354	_	_	NN	_	_	_
1355	2	2	CD	_	_	_
1356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1357	wt	wt	JJ	_	_	_
1358	_	_	NN	_	_	_
1359	un	un	NN	_	_	_
1360	_	_	NN	_	_	_
1361	3	3	CD	_	_	_
1362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1363	WT	wt	JJ	_	_	_
1364	UvsW	uvsw	NN	_	_	_
1365	_	_	NN	_	_	_
1366	replicate1	replicate1	NN	_	_	_
1367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1368	WT	wt	JJ	_	_	_
1369	UvsW	uvsw	NN	_	_	_
1370	_	_	NN	_	_	_
1371	replicate2	replicate2	NN	_	_	_
1372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1373	WT	wt	JJ	_	_	_
1374	UvsW	uvsw	NN	_	_	_
1375	_	_	NN	_	_	_
1376	replicate3	replicate3	NN	_	_	_
1377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1378	WT	wt	VBD	_	_	_
1379	_	_	CD	_	_	_
1380	vs	vs	CC	_	_	_
1381	_	_	CD	_	_	_
1382	dcd	dcd	NN	GEN	_	_
1383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1384	WT	wt	VBD	_	_	_
1385	_	_	CD	_	_	_
1386	vs	vs	CC	_	_	_
1387	_	_	CD	_	_	_
1388	ndk	ndk	NN	GEN	_	_
1389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1390	WT	wt	VBD	_	_	_
1391	_	_	CD	_	_	_
1392	vs	vs	CC	_	_	_
1393	_	_	CD	_	_	_
1394	recA730	reca730	NN	_	_	_
1395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1396	WT	wt	NN	_	_	_
1397	with	with	IN	_	_	_
1398	DPD	dpd	NN	_	_	_
1399	1	1	CD	_	_	_
1400	-LRB-	-lrb-	-LRB-	_	_	_
1401	RNA-seq	rna-seq	NN	_	_	_
1402	-RRB-	-rrb-	-RRB-	_	_	_
1403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1404	WT	wt	NN	_	_	_
1405	with	with	IN	_	_	_
1406	DPD	dpd	NN	_	_	_
1407	2	2	CD	_	_	_
1408	-LRB-	-lrb-	-LRB-	_	_	_
1409	RNA-seq	rna-seq	NN	_	_	_
1410	-RRB-	-rrb-	-RRB-	_	_	_
1411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1412	WT	wt	NN	_	_	_
1413	with	with	IN	_	_	_
1414	Fe	Fe	NNP	_	_	_
1415	1	1	CD	_	_	_
1416	-LRB-	-lrb-	-LRB-	_	_	_
1417	RNA-seq	rna-seq	NN	_	_	_
1418	-RRB-	-rrb-	-RRB-	_	_	_
1419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1420	WT	wt	NN	_	_	_
1421	with	with	IN	_	_	_
1422	Fe	Fe	NNP	_	_	_
1423	2	2	CD	_	_	_
1424	-LRB-	-lrb-	-LRB-	_	_	_
1425	RNA-seq	rna-seq	NN	_	_	_
1426	-RRB-	-rrb-	-RRB-	_	_	_
1427	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1428	wzc	wzc	NN	GEN	_	_
1429	KO	ko	NN	_	_	_
1430	LB	lb	NN	_	_	_
1431	rep1	rep1	NN	_	_	_
1432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1433	wzc	wzc	NN	GEN	_	_
1434	KO	ko	NN	_	_	_
1435	LB	lb	NN	_	_	_
1436	rep2	rep2	NN	_	_	_
1437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1438	wzc	wzc	NN	GEN	_	_
1439	KO	ko	NN	_	_	_
1440	M9	m9	NN	_	_	_
1441	rep1	rep1	NN	_	_	_
1442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1443	wzc	wzc	NN	GEN	_	_
1444	KO	ko	NN	_	_	_
1445	M9	m9	NN	_	_	_
1446	rep2	rep2	NN	_	_	_
1447	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1448	X515	x515	NN	_	_	_
1449	_	_	CD	_	_	_
1450	V1	v1	NN	_	_	_
1451	_	_	CD	_	_	_
1452	T4	t4	NN	_	_	_
1453	_	_	CD	_	_	_
1454	424287A03	424287a03	NN	_	_	_
1455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1456	X515	x515	NN	_	_	_
1457	_	_	CD	_	_	_
1458	V1	v1	NN	_	_	_
1459	_	_	CD	_	_	_
1460	T4	t4	NN	_	_	_
1461	_	_	CD	_	_	_
1462	475655A02	475655a02	NN	_	_	_
1463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1464	X515	x515	NN	_	_	_
1465	_	_	CD	_	_	_
1466	V1	v1	NN	_	_	_
1467	_	_	CD	_	_	_
1468	T6	t6	NN	_	_	_
1469	_	_	CD	_	_	_
1470	475649A04s	475649a04	NNS	_	_	_
1471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1472	X515	x515	NN	_	_	_
1473	_	_	CD	_	_	_
1474	V1	v1	NN	_	_	_
1475	_	_	CD	_	_	_
1476	T7	t7	NN	_	_	_
1477	_	_	CD	_	_	_
1478	475654A02	475654a02	NN	_	_	_
1479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1480	X515	x515	NN	_	_	_
1481	_	_	CD	_	_	_
1482	V1	v1	NN	_	_	_
1483	_	_	CD	_	_	_
1484	T8	t8	NN	_	_	_
1485	_	_	CD	_	_	_
1486	475585A04	475585a04	NN	_	_	_
1487	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1488	X515	x515	NN	_	_	_
1489	_	_	CD	_	_	_
1490	V2	v2	NN	_	_	_
1491	_	_	CD	_	_	_
1492	T4	t4	NN	_	_	_
1493	_	_	CD	_	_	_
1494	424219A04	424219a04	NN	_	_	_
1495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1496	X515	x515	NN	_	_	_
1497	_	_	CD	_	_	_
1498	V2	v2	NN	_	_	_
1499	_	_	CD	_	_	_
1500	T4	t4	NN	_	_	_
1501	_	_	CD	_	_	_
1502	475655A03	475655a03	NN	_	_	_
1503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1504	X515	x515	NN	_	_	_
1505	_	_	CD	_	_	_
1506	V2	v2	NN	_	_	_
1507	_	_	CD	_	_	_
1508	T6	t6	NN	_	_	_
1509	_	_	CD	_	_	_
1510	475644A04	475644a04	NN	_	_	_
1511	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1512	X515	x515	NN	_	_	_
1513	_	_	CD	_	_	_
1514	V2	v2	NN	_	_	_
1515	_	_	CD	_	_	_
1516	T7	t7	NN	_	_	_
1517	_	_	CD	_	_	_
1518	475649A01	475649a01	NN	_	_	_
1519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1520	X515	x515	NN	_	_	_
1521	_	_	CD	_	_	_
1522	V2	v2	NN	_	_	_
1523	_	_	CD	_	_	_
1524	T8	t8	NN	_	_	_
1525	_	_	CD	_	_	_
1526	424219A01s	424219a01	NNS	_	_	_
1527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1528	X515	x515	NN	_	_	_
1529	_	_	CD	_	_	_
1530	V3	v3	NN	_	_	_
1531	_	_	CD	_	_	_
1532	T4	t4	NN	_	_	_
1533	_	_	CD	_	_	_
1534	475585A02s	475585a02	NNS	_	_	_
1535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1536	X515	x515	NN	_	_	_
1537	_	_	CD	_	_	_
1538	V3	v3	NN	_	_	_
1539	_	_	CD	_	_	_
1540	T6	t6	NN	_	_	_
1541	_	_	CD	_	_	_
1542	424221A04	424221a04	NN	_	_	_
1543	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1544	X515	x515	NN	_	_	_
1545	_	_	CD	_	_	_
1546	V3	v3	NN	_	_	_
1547	_	_	CD	_	_	_
1548	T7	t7	NN	_	_	_
1549	_	_	CD	_	_	_
1550	475649A02	475649a02	NN	_	_	_
1551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1552	X515	x515	NN	_	_	_
1553	_	_	CD	_	_	_
1554	V3	v3	NN	_	_	_
1555	_	_	CD	_	_	_
1556	T8	t8	NN	_	_	_
1557	_	_	CD	_	_	_
1558	475641A04	475641a04	NN	_	_	_
1559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1560	X515	x515	NN	_	_	_
1561	_	_	CD	_	_	_
1562	V4	v4	NN	_	_	_
1563	_	_	CD	_	_	_
1564	T4	t4	NN	_	_	_
1565	_	_	CD	_	_	_
1566	475585A03	475585a03	NN	_	_	_
1567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1568	X515	x515	NN	_	_	_
1569	_	_	CD	_	_	_
1570	V4	v4	NN	_	_	_
1571	_	_	CD	_	_	_
1572	T4	t4	NN	_	_	_
1573	_	_	CD	_	_	_
1574	475644A01	475644a01	NN	_	_	_
1575	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1576	X515	x515	NN	_	_	_
1577	_	_	CD	_	_	_
1578	V4	v4	NN	_	_	_
1579	_	_	CD	_	_	_
1580	T6	t6	NN	_	_	_
1581	_	_	CD	_	_	_
1582	424221A03	424221a03	NN	_	_	_
1583	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1584	X515	x515	NN	_	_	_
1585	_	_	CD	_	_	_
1586	V4	v4	NN	_	_	_
1587	_	_	CD	_	_	_
1588	T7	t7	NN	_	_	_
1589	_	_	CD	_	_	_
1590	424287A04	424287a04	NN	_	_	_
1591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1592	X515	x515	NN	_	_	_
1593	_	_	CD	_	_	_
1594	V4	v4	NN	_	_	_
1595	_	_	CD	_	_	_
1596	T8	t8	NN	_	_	_
1597	_	_	CD	_	_	_
1598	475655A04	475655a04	NN	_	_	_
1599	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1600	X520	x520	NN	_	_	_
1601	_	_	CD	_	_	_
1602	V1	v1	NN	_	_	_
1603	_	_	CD	_	_	_
1604	T4	t4	NN	_	_	_
1605	_	_	CD	_	_	_
1606	424221A01	424221a01	NN	_	_	_
1607	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1608	X520	x520	NN	_	_	_
1609	_	_	CD	_	_	_
1610	V1	v1	NN	_	_	_
1611	_	_	CD	_	_	_
1612	T6	t6	NN	_	_	_
1613	_	_	CD	_	_	_
1614	475649A03	475649a03	NN	_	_	_
1615	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1616	X520	x520	NN	_	_	_
1617	_	_	CD	_	_	_
1618	V1	v1	NN	_	_	_
1619	_	_	CD	_	_	_
1620	T7	t7	NN	_	_	_
1621	_	_	CD	_	_	_
1622	475655A01	475655a01	NN	_	_	_
1623	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1624	X520	x520	NN	_	_	_
1625	_	_	CD	_	_	_
1626	V1	v1	NN	_	_	_
1627	_	_	CD	_	_	_
1628	T8	t8	NN	_	_	_
1629	_	_	CD	_	_	_
1630	475641A01	475641a01	NN	_	_	_
1631	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1632	X520	x520	NN	_	_	_
1633	_	_	CD	_	_	_
1634	V2	v2	NN	_	_	_
1635	_	_	CD	_	_	_
1636	T3	t3	NN	_	_	_
1637	_	_	CD	_	_	_
1638	424221A02	424221a02	NN	_	_	_
1639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1640	X520	x520	NN	_	_	_
1641	_	_	CD	_	_	_
1642	V2	v2	NN	_	_	_
1643	_	_	CD	_	_	_
1644	T4	t4	NN	_	_	_
1645	_	_	CD	_	_	_
1646	475641A03	475641a03	NN	_	_	_
1647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1648	X520	x520	NN	_	_	_
1649	_	_	CD	_	_	_
1650	V2	v2	NN	_	_	_
1651	_	_	CD	_	_	_
1652	T6	t6	NN	_	_	_
1653	_	_	CD	_	_	_
1654	424287A02	424287a02	NN	_	_	_
1655	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1656	X520	x520	NN	_	_	_
1657	_	_	CD	_	_	_
1658	V2	v2	NN	_	_	_
1659	_	_	CD	_	_	_
1660	T7	t7	NN	_	_	_
1661	_	_	CD	_	_	_
1662	475654A01	475654a01	NN	_	_	_
1663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1664	X520	x520	NN	_	_	_
1665	_	_	CD	_	_	_
1666	V2	v2	NN	_	_	_
1667	_	_	CD	_	_	_
1668	T8	t8	NN	_	_	_
1669	_	_	CD	_	_	_
1670	424219A02	424219a02	NN	_	_	_
1671	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1672	X520	x520	NN	_	_	_
1673	_	_	CD	_	_	_
1674	V3	v3	NN	_	_	_
1675	_	_	CD	_	_	_
1676	T4	t4	NN	_	_	_
1677	_	_	CD	_	_	_
1678	475654A04	475654a04	NN	_	_	_
1679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1680	X520	x520	NN	_	_	_
1681	_	_	CD	_	_	_
1682	V3	v3	NN	_	_	_
1683	_	_	CD	_	_	_
1684	T6	t6	NN	_	_	_
1685	_	_	CD	_	_	_
1686	475641A02	475641a02	NN	_	_	_
1687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1688	X520	x520	NN	_	_	_
1689	_	_	CD	_	_	_
1690	V3	v3	NN	_	_	_
1691	_	_	CD	_	_	_
1692	T7	t7	NN	_	_	_
1693	_	_	CD	_	_	_
1694	475644A02s	475644a02	NNS	_	_	_
1695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1696	X520	x520	NN	_	_	_
1697	_	_	CD	_	_	_
1698	V3	v3	NN	_	_	_
1699	_	_	CD	_	_	_
1700	T8	t8	NN	_	_	_
1701	_	_	CD	_	_	_
1702	424219A03	424219a03	NN	_	_	_
1703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1704	X520	x520	NN	_	_	_
1705	_	_	CD	_	_	_
1706	V4	v4	NN	_	_	_
1707	_	_	CD	_	_	_
1708	T4	t4	NN	_	_	_
1709	_	_	CD	_	_	_
1710	475654A03	475654a03	NN	_	_	_
1711	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1712	X520	x520	NN	_	_	_
1713	_	_	CD	_	_	_
1714	V4	v4	NN	_	_	_
1715	_	_	CD	_	_	_
1716	T6	t6	NN	_	_	_
1717	_	_	CD	_	_	_
1718	424287A01	424287a01	NN	_	_	_
1719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1720	X520	x520	NN	_	_	_
1721	_	_	CD	_	_	_
1722	V4	v4	NN	_	_	_
1723	_	_	CD	_	_	_
1724	T7	t7	NN	_	_	_
1725	_	_	CD	_	_	_
1726	475644A03	475644a03	NN	_	_	_
1727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1728	X520	x520	NN	_	_	_
1729	_	_	CD	_	_	_
1730	V4	v4	NN	_	_	_
1731	_	_	CD	_	_	_
1732	T8	t8	NN	_	_	_
1733	_	_	CD	_	_	_
1734	475585A01	475585a01	NN	_	_	_
1735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1736	Xpression	xpression	NN	_	_	_
1737	-LRB-	-lrb-	-LRB-	_	_	_
1738	https://depts.washington.edu/cshlab/html/rnaseq.html	https://depts.washington.edu/cshlab/html/rnaseq.html	NN	_	_	_
1739	-RRB-	-rrb-	-RRB-	_	_	_
1740	was	be	VBD	_	_	_
1741	used	use	VBN	_	_	_
1742	for	for	IN	_	_	_
1743	RNA-Seq	rna-seq	NN	_	_	_
1744	data	datum	NNS	_	_	_
1745	processing	processing	NN	_	_	_
1746	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Xpression	xpression	NN	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	for	for	IN	_	_	_
6	filtering	filter	VBG	_	_	_
7	and	and	CC	_	_	_
8	trimming	trim	VBG	_	_	_
9	reads	read	VBZ	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Xuzhou21	xuzhou21	NN	_	_	_
3	cured	cure	VBD	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	pO157	po157	NN	_	_	_
7	_	_	NN	_	_	_
8	Sal	sal	NN	_	_	_
9	plasmid	plasmid	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	yajL	yajl	NN	GEN	_	_
12	mutant	mutant	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	genetic	genetic	JJ	_	_	_
15	background	background	NN	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	year	year	NN	_	_	_
20	:	:	:	_	_	_
21	2000	2000	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	year	year	NN	_	_	_
24	:	:	:	_	_	_
25	2001	2001	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	year	year	NN	_	_	_
28	:	:	:	_	_	_
29	2003	2003	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	year	year	NN	_	_	_
32	:	:	:	_	_	_
33	2004	2004	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	year	year	NN	_	_	_
36	:	:	:	_	_	_
37	2005	2005	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	year	year	NN	_	_	_
40	:	:	:	_	_	_
41	2006	2006	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	year	year	NN	_	_	_
44	:	:	:	_	_	_
45	2007	2007	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	year	year	NN	_	_	_
48	:	:	:	_	_	_
49	2008	2008	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	yebF	yebf	NN	GEN	_	_
52	__	__	CD	_	_	_
53	U	U	NNP	_	_	_
54	_	_	NNP	_	_	_
55	N0075	N0075	NNP	_	_	_
56	_	_	VBD	_	_	_
57	r1	r1	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	yebF	yebf	NN	GEN	_	_
60	__	__	CD	_	_	_
61	U	U	NNP	_	_	_
62	_	_	NNP	_	_	_
63	N0075	N0075	NNP	_	_	_
64	_	_	VBD	_	_	_
65	r2	r2	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	yebF	yebf	NN	GEN	_	_
68	__	__	CD	_	_	_
69	U	U	NNP	_	_	_
70	_	_	NNP	_	_	_
71	N0075	N0075	NNP	_	_	_
72	_	_	SYM	_	_	_
73	r3	r3	FW	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
75	yebF	yebf	NN	GEN	_	_
76	upregulation	upregulation	NN	_	_	_
77	,	,	,	_	_	_
78	0.075	0.075	CD	_	_	_
79	ug/ml	ug/ml	NN	_	_	_
80	norfloxacin	norfloxacin	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	yghD	yghd	NN	GEN	_	_
83	KO	ko	NN	_	_	_
84	LB	lb	NN	_	_	_
85	rep1	rep1	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	yghD	yghd	NN	GEN	_	_
88	KO	ko	NN	_	_	_
89	LB	lb	NN	_	_	_
90	rep2	rep2	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	yghD	yghd	NN	GEN	_	_
93	KO	ko	NN	_	_	_
94	M9	m9	NN	_	_	_
95	rep1	rep1	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	yghD	yghd	NN	GEN	_	_
98	KO	ko	NN	_	_	_
99	M9	m9	NN	_	_	_
100	rep2	rep2	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	yoeB	yoeb	NN	GEN	_	_
103	__	__	CD	_	_	_
104	U	U	NNP	_	_	_
105	_	_	NNP	_	_	_
106	N0075	N0075	NNP	_	_	_
107	_	_	VBD	_	_	_
108	r1	r1	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	yoeB	yoeb	NN	GEN	_	_
111	__	__	CD	_	_	_
112	U	U	NNP	_	_	_
113	_	_	NNP	_	_	_
114	N0075	N0075	NNP	_	_	_
115	_	_	VBD	_	_	_
116	r2	r2	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	yoeB	yoeb	NN	GEN	_	_
119	__	__	CD	_	_	_
120	U	U	NNP	_	_	_
121	_	_	NNP	_	_	_
122	N0075	N0075	NNP	_	_	_
123	_	_	SYM	_	_	_
124	r3	r3	FW	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
126	yoeB	yoeb	NN	GEN	_	_
127	upregulation	upregulation	NN	_	_	_
128	,	,	,	_	_	_
129	0.075	0.075	CD	_	_	_
130	mg/mL	mg/ml	NN	_	_	_
131	norfloxacin	norfloxacin	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	yPileup	ypileup	NN	_	_	_
134	was	be	VBD	_	_	_
135	used	use	VBN	_	_	_
136	to	to	TO	_	_	_
137	generate	generate	VB	_	_	_
138	count	count	NN	_	_	_
139	data	datum	NNS	_	_	_
140	for	for	IN	_	_	_
141	the	the	DT	_	_	_
142	whole	whole	JJ	_	_	_
143	genome	genome	NN	_	_	_
144	-	-	:	_	_	_
145	Example	example	NN	_	_	_
146	:	:	:	_	_	_
147	pyPileup.py	pypileup.py	NN	_	_	_
148	--	--	:	_	_	_
149	file	file	NN	_	_	_
150	_	_	NN	_	_	_
151	type	type	NN	_	_	_
152	=	=	JJ	_	_	_
153	novo	novo	FW	_	_	_
154	-	-	:	_	_	_
155	f	f	LS	_	_	_
156	DL4184.novo	dl4184.novo	NN	_	_	_
157	--	--	:	_	_	_
158	tab	tab	NN	_	_	_
159	=	=	JJ	_	_	_
160	NC000913	nc000913	NN	_	_	_
161	.3	.3	NN	_	_	_
162	.	.	.	_	_	_

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	yPileup	ypileup	NN	_	_	_
10	was	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	to	to	TO	_	_	_
13	generate	generate	VB	_	_	_
14	count	count	NN	_	_	_
15	data	datum	NNS	_	_	_
16	for	for	IN	_	_	_
17	the	the	DT	_	_	_
18	whole	whole	JJ	_	_	_
19	genome	genome	NN	_	_	_
20	-	-	:	_	_	_
21	Example	example	NN	_	_	_
22	:	:	:	_	_	_
23	pyPileup.py	pypileup.py	NN	_	_	_
24	--	--	:	_	_	_
25	file	file	NN	_	_	_
26	_	_	NN	_	_	_
27	type	type	NN	_	_	_
28	=	=	JJ	_	_	_
29	novo	novo	FW	_	_	_
30	-	-	:	_	_	_
31	f	f	LS	_	_	_
32	DL4900.novo	dl4900.novo	NN	_	_	_
33	--	--	:	_	_	_
34	tab	tab	NN	_	_	_
35	=	=	JJ	_	_	_
36	NC000913	nc000913	NN	_	_	_
37	.3	.3	NN	_	_	_
38	.	.	.	_	_	_

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	pgcgrowthcondition	NNS	_	_	_
9	zipA	zipa	NN	GEN	_	_
10	__	__	CD	_	_	_
11	U	U	NNP	_	_	_
12	_	_	NNP	_	_	_
13	N0075	N0075	NNP	_	_	_
14	_	_	VBD	_	_	_
15	r1	r1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	zipA	zipa	NN	GEN	_	_
18	__	__	CD	_	_	_
19	U	U	NNP	_	_	_
20	_	_	NNP	_	_	_
21	N0075	N0075	NNP	_	_	_
22	_	_	SYM	_	_	_
23	r2	r2	FW	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
25	zipA	zipa	NN	GEN	_	_
26	__	__	CD	_	_	_
27	U	U	NNP	_	_	_
28	_	_	NNP	_	_	_
29	N0075	N0075	NNP	_	_	_
30	_	_	SYM	_	_	_
31	r3	r3	FW	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
33	zipA	zipa	NN	GEN	_	_
34	upregulation	upregulation	NN	_	_	_
35	,	,	,	_	_	_
36	0.075	0.075	CD	_	_	_
37	ug/ml	ug/ml	NN	_	_	_
38	norfloxacin	norfloxacin	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	zi	zi	NN	_	_	_
41	=	=	JJ	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	Ri	Ri	NNP	_	_	_
44	--	--	:	_	_	_
45	mean	mean	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	R	r	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	/	/	:	_	_	_
51	sd	sd	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	R	r	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	,	,	,	_	_	_
56	where	where	WRB	_	_	_
57	zi	zi	NN	_	_	_
58	is	be	VBZ	_	_	_
59	the	the	DT	_	_	_
60	z-score	z-score	NN	_	_	_
61	for	for	IN	_	_	_
62	each	each	DT	_	_	_
63	element	element	NN	_	_	_
64	,	,	,	_	_	_
65	Ri	Ri	NNP	_	_	_
66	is	be	VBZ	_	_	_
67	the	the	DT	_	_	_
68	log-ratio	log-ratio	NN	_	_	_
69	for	for	IN	_	_	_
70	each	each	DT	_	_	_
71	element	element	NN	_	_	_
72	,	,	,	_	_	_
73	and	and	CC	_	_	_
74	sd	sd	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	R	r	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	is	be	VBZ	_	_	_
79	the	the	DT	_	_	_
80	standard	standard	JJ	_	_	_
81	deviation	deviation	NN	_	_	_
82	of	of	IN	_	_	_
83	the	the	DT	_	_	_
84	log-ratio	log-ratio	NN	_	_	_
85	.	.	.	_	_	_

1	With	with	IN	_	_	_
2	this	this	DT	_	_	_
3	criterion	criterion	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	elements	element	NNS	_	_	_
7	with	with	IN	_	_	_
8	a	a	DT	_	_	_
9	z-score	z-score	NN	_	_	_
10	>	>	RBR	_	_	_
11	2	2	CD	_	_	_
12	standard	standard	JJ	_	_	_
13	deviations	deviation	NNS	_	_	_
14	would	would	MD	_	_	_
15	be	be	VB	_	_	_
16	the	the	DT	_	_	_
17	significantly	significantly	RB	_	_	_
18	differentially	differentially	RB	_	_	_
19	expressed	express	VBN	_	_	_
20	genes	gene	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Zn-depleted	zn-depleted	JJ	_	_	_
3	custom-built	custom-built	JJ	_	_	_
4	chemostats	chemostat	NNS	_	_	_
5	were	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	for	for	IN	_	_	_
8	50	50	CD	_	_	_
9	h	h	NN	_	_	_
10	.	.	.	_	_	_

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	NN	_	_	_
2	∆	∆	SYM	_	_	_
3	zwf	zwf	FW	GEN	_	_
4	parent	parent	NN	_	_	_
5	Sample	sample	NN	_	_	_
6	2	2	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	∆	∆	CD	_	_	_
9	zwf	zwf	NN	GEN	_	_
10	parent	parent	NN	_	_	_
11	Sample	sample	NN	_	_	_
12	21	21	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	∆	∆	CD	_	_	_
15	zwf	zwf	NN	GEN	_	_
16	parent	parent	NN	_	_	_
17	Sample	Sample	NNP	_	_	_
18	40	40	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	zwf	zwf	NN	GEN	_	_
21	suppressor	suppressor	NN	_	_	_
22	1-1	1-1	CD	_	_	_
23	Sample	sample	NN	_	_	_
24	22	22	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	zwf	zwf	NN	GEN	_	_
27	suppressor	suppressor	NN	_	_	_
28	1-1	1-1	CD	_	_	_
29	Sample	sample	NN	_	_	_
30	3	3	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	zwf	zwf	NN	GEN	_	_
33	suppressor	suppressor	NN	_	_	_
34	1-1	1-1	CD	_	_	_
35	Sample	sample	NN	_	_	_
36	41	41	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	zwf	zwf	NN	GEN	_	_
39	suppressor	suppressor	NN	_	_	_
40	1-2	1-2	CD	_	_	_
41	Sample	sample	NN	_	_	_
42	23	23	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	zwf	zwf	NN	GEN	_	_
45	suppressor	suppressor	NN	_	_	_
46	1-2	1-2	CD	_	_	_
47	Sample	sample	NN	_	_	_
48	4	4	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	zwf	zwf	NN	GEN	_	_
51	suppressor	suppressor	NN	_	_	_
52	1-2	1-2	CD	_	_	_
53	Sample	sample	NN	_	_	_
54	42	42	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	ΔbolA	δbola	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Δcra	δcra	NN	_	_	_
59	_	_	NN	_	_	_
60	acetate	acetate	NN	SUPP	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Δcra	δcra	NN	_	_	_
63	acetate	acetate	NN	SUPP	_	_
64	1	1	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Δcra	δcra	NN	_	_	_
67	acetate	acetate	NN	SUPP	_	_
68	2	2	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Δcra	δcra	NN	_	_	_
71	_	_	NN	_	_	_
72	fructose	fructose	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Δcra	δcra	NN	_	_	_
75	fructose	fructose	NN	_	_	_
76	1	1	CD	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	Δcra	δcra	NN	_	_	_
79	fructose	fructose	NN	_	_	_
80	2	2	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Δcra	δcra	NN	_	_	_
83	_	_	NN	_	_	_
84	glucose	glucose	NN	SUPP	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Δcra	δcra	NN	_	_	_
87	glucose	glucose	NN	SUPP	_	_
88	1	1	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Δcra	δcra	NN	_	_	_
91	glucose	glucose	NN	SUPP	_	_
92	2	2	CD	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Δfur	δfur	NN	_	_	_
95	with	with	IN	_	_	_
96	DPD	dpd	NN	_	_	_
97	1	1	CD	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	RNA-seq	rna-seq	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	Δfur	δfur	NN	_	_	_
103	with	with	IN	_	_	_
104	DPD	dpd	NN	_	_	_
105	2	2	CD	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	RNA-seq	rna-seq	NN	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	Δfur	δfur	NN	_	_	_
111	with	with	IN	_	_	_
112	Fe	Fe	NNP	_	_	_
113	1	1	CD	_	_	_
114	-LRB-	-lrb-	-LRB-	_	_	_
115	RNA-seq	rna-seq	NN	_	_	_
116	-RRB-	-rrb-	-RRB-	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	Δfur	δfur	NN	_	_	_
119	with	with	IN	_	_	_
120	Fe	Fe	NNP	_	_	_
121	2	2	CD	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	RNA-seq	rna-seq	NN	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	ΔgadE	δgade	NN	_	_	_
127	pH5	ph5	NN	_	_	_
128	.5	.5	CD	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	ΔgadE	δgade	NN	_	_	_
131	pH5	ph5	NN	_	_	_
132	.5	.5	CD	_	_	_
133	1	1	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	ΔgadE	δgade	NN	_	_	_
136	pH5	ph5	NN	_	_	_
137	.5	.5	CD	_	_	_
138	2	2	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	ΔgadW	δgadw	NN	_	_	_
141	pH5	ph5	NN	_	_	_
142	.5	.5	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	ΔgadW	δgadw	NN	_	_	_
145	pH5	ph5	NN	_	_	_
146	.5	.5	CD	_	_	_
147	1	1	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	ΔgadW	δgadw	NN	_	_	_
150	pH5	ph5	NN	_	_	_
151	.5	.5	CD	_	_	_
152	2	2	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	ΔgadX	δgadx	NN	_	_	_
155	pH5	ph5	NN	_	_	_
156	.5	.5	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	ΔgadX	δgadx	NN	_	_	_
159	pH5	ph5	NN	_	_	_
160	.5	.5	CD	_	_	_
161	1	1	CD	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	ΔgadX	δgadx	NN	_	_	_
164	pH5	ph5	NN	_	_	_
165	.5	.5	CD	_	_	_
166	2	2	CD	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	ΔompR	δompr	NN	_	_	_
169	NaCl	nacl	NN	_	_	_
170	1	1	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	ΔompR	δompr	NN	_	_	_
173	NaCl	nacl	NN	_	_	_
174	2	2	CD	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	ΔoxyR	δoxyr	NN	_	_	_
177	PQ	pq	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	ΔoxyR	δoxyr	NN	_	_	_
180	PQ	pq	NN	_	_	_
181	1	1	CD	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	ΔoxyR	δoxyr	NN	_	_	_
184	PQ	pq	NN	_	_	_
185	2	2	CD	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	Δrac	δrac	JJ	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	Δrac	δrac	NN	_	_	_
190	1	1	CD	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	Δrac	δrac	NN	_	_	_
193	2	2	CD	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	Δrac	δrac	NN	_	_	_
196	+	+	CC	_	_	_
197	20	20	CD	_	_	_
198	ug/ml	ug/ml	NN	_	_	_
199	bicyclomycin	bicyclomycin	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	Δrac	δrac	NN	_	_	_
202	+	+	CC	_	_	_
203	20	20	CD	_	_	_
204	ug/ml	ug/ml	NN	_	_	_
205	bicyclomycin	bicyclomycin	NN	_	_	_
206	1	1	CD	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	Δrac	δrac	NN	_	_	_
209	+	+	CC	_	_	_
210	20	20	CD	_	_	_
211	ug/ml	ug/ml	NN	_	_	_
212	bicyclomycin	bicyclomycin	NN	_	_	_
213	2	2	CD	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	Δrac	δrac	NN	_	_	_
216	ΔnusG	δnusg	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	Δrac	δrac	NN	_	_	_
219	ΔnusG	δnusg	NN	_	_	_
220	1	1	CD	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	Δrac	δrac	NN	_	_	_
223	ΔnusG	δnusg	NN	_	_	_
224	2	2	CD	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	ΔsoxR	δsoxr	NN	_	_	_
227	PQ	pq	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	ΔsoxR	δsoxr	NN	_	_	_
230	PQ	pq	NN	_	_	_
231	1	1	CD	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	ΔsoxR	δsoxr	NN	_	_	_
234	PQ	pq	NN	_	_	_
235	2	2	CD	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	ΔsoxS	δsoxs	NN	_	_	_
238	PQ	pq	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	ΔsoxS	δsoxs	VBZ	_	_	_
241	PQ	pq	NN	_	_	_
242	1	1	CD	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	ΔsoxS	δsoxs	NN	_	_	_
245	PQ	pq	NN	_	_	_
246	2	2	CD	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	σ32	σ32	NN	_	_	_
249	30	30	CD	_	_	_
250	°C	°c	NN	_	_	_
251	rep1	rep1	NN	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	σ32	σ32	NN	_	_	_
254	30	30	CD	_	_	_
255	°C	°c	NN	_	_	_
256	rep2	rep2	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	σ32	σ32	NN	_	_	_
259	30	30	CD	_	_	_
260	°C	°c	NN	_	_	_
261	short	short	JJ	_	_	_
262	RNase	rnase	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	σ32	σ32	NN	_	_	_
265	43	43	CD	_	_	_
266	°C	°c	NN	_	_	_
267	rep1	rep1	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	σ32	σ32	NN	_	_	_
270	43	43	CD	_	_	_
271	°C	°c	NN	_	_	_
272	rep2	rep2	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	σ32	σ32	NN	_	_	_
275	43	43	CD	_	_	_
276	°C	°c	NN	_	_	_
277	short	short	JJ	_	_	_
278	RNase	rnase	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	σ32	σ32	NN	_	_	_
281	ChIP	chip	NN	_	_	_
282	DNA	dna	NN	_	_	_
283	,	,	,	_	_	_
284	control	control	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	σ32	σ32	NN	_	_	_
287	ChIP	chip	NN	_	_	_
288	DNA	dna	NN	_	_	_
289	,	,	,	_	_	_
290	heat	heat	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	σ32	σ32	NN	_	_	_
293	ChIP	chip	NN	_	_	_
294	DNA	dna	NN	_	_	_
295	,	,	,	_	_	_
296	short	short	JJ	_	_	_
297	RNase	rnase	NN	_	_	_
298	digestion	digestion	NN	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	σ70	σ70	NN	_	_	_
301	IP	IP	NNP	_	_	_
302	ChIP-seq	ChIP-seq	NNP	_	_	_
303	Aerobic	Aerobic	NNP	_	_	_
304	A	A	NNP	_	_	_
305	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
306	σ70	σ70	NN	_	_	_
307	IP	IP	NNP	_	_	_
308	ChIP-seq	ChIP-seq	NNP	_	_	_
309	Aerobic	Aerobic	NNP	_	_	_
310	B	B	NNP	_	_	_
311	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
312	σ70	σ70	NN	_	_	_
313	IP	IP	NNP	_	_	_
314	ChIP-seq	ChIP-seq	NNP	_	_	_
315	Anaerobic	Anaerobic	NNP	_	_	_
316	A	A	NNP	_	_	_
317	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
318	σ70	σ70	NN	_	_	_
319	IP	IP	NNP	_	_	_
320	ChIP-seq	ChIP-seq	NNP	_	_	_
321	Anaerobic	anaerobic	JJ	_	_	_
322	B	b	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_