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

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Kevin Meza Landeros
2d683291 1 parent f0c9555c

extraction

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1 +#!/bin/python3
2 +import os
3 +from itertools import chain
4 +from optparse import OptionParser
5 +from time import time
6 +from collections import Counter
7 +import re
8 +
9 +import nltk
10 +import sklearn
11 +import scipy.stats
12 +import sys
13 +
14 +from sklearn.externals import joblib
15 +from sklearn.metrics import make_scorer
16 +from sklearn.cross_validation import cross_val_score
17 +from sklearn.grid_search import RandomizedSearchCV
18 +
19 +import sklearn_crfsuite
20 +from sklearn_crfsuite import scorers
21 +from sklearn_crfsuite import metrics
22 +
23 +from nltk.corpus import stopwords
24 +import random
25 +
26 +
27 +# Objective
28 +# Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging
29 +#
30 +# Input parameters
31 +# --inputPath=PATH Path of inputfile
32 +# --outputPath=PATH Path to place output files
33 +# --trainingFile=testFile Output training data set
34 +# --testFile=testFile Output test data set
35 +#
36 +# Output
37 +# training and test data set
38 +#
39 +# Examples
40 +# python label-split_training_test_v1.py
41 +# --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/
42 +# --inputFile sentences.tsv_pakal_.conll
43 +# --trainingFile training-data-set-70.txt
44 +# --testFile test-data-set-30.txt
45 +# --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
46 +#
47 +#
48 +# python label-split_training_test_v1.py --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/ --inputFile sentences.tsv_pakal_.conll --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
49 +
50 +
51 +##########################################
52 +# MAIN PROGRAM #
53 +##########################################
54 +
55 +if __name__ == "__main__":
56 + # Defining parameters
57 + parser = OptionParser()
58 + parser.add_option("--inputPath", dest="inputPath",
59 + help="Path of output from CoreNLP", metavar="PATH")
60 + parser.add_option("--outputPath", dest="outputPath",
61 + help="Output path to place output files",
62 + metavar="PATH")
63 + parser.add_option("--inputFile", dest="inputFile",
64 + help="File with CoreNLP-tagging sentences", metavar="FILE")
65 + parser.add_option("--trainingFile", dest="trainingFile",
66 + help="File with training data set", metavar="FILE")
67 + parser.add_option("--testFile", dest="testFile",
68 + help="File with test data set", metavar="FILE")
69 +
70 + (options, args) = parser.parse_args()
71 + if len(args) > 0:
72 + parser.error("Any parameter given.")
73 + sys.exit(1)
74 +
75 + print('-------------------------------- PARAMETERS --------------------------------')
76 + print("Path of CoreNLP output: " + options.inputPath)
77 + print("File with CoreNLP-tagging sentences: " + str(options.inputFile))
78 + print("Path of training data set: " + str(options.outputPath))
79 + print("File with training data set: " + str(options.trainingFile))
80 + print("Path of test data set: " + str(options.outputPath))
81 + print("File with test data set: " + str(options.testFile))
82 + print('-------------------------------- PROCESSING --------------------------------')
83 + ## begin of tagging
84 + in_labels = {
85 + '<Gtype>': 'Gtype',
86 + '<Gversion>': 'Gversion',
87 + '<Med>': 'Med',
88 + '<Phase>': 'Phase',
89 + '<Sample>': 'Sample',
90 + '<Serie>': 'Serie',
91 + '<Substrain>': 'Substrain',
92 + '<Supp>': 'Supp',
93 + '<Technique>': 'Technique',
94 + '<Temp>': 'Temp',
95 + '<OD>': 'OD',
96 + '<Anti>': 'Anti',
97 + '<Agit>': 'Agit',
98 + '<Vess>': 'Vess'
99 + }
100 + ## End of tagging
101 + out_labels = {
102 + '</Air>': 'O',
103 + '</Gtype>': 'O',
104 + '</Gversion>': 'O',
105 + '</Med>': 'O',
106 + '</Phase>': 'O',
107 + '</Sample>': 'O',
108 + '</Serie>': 'O',
109 + '</Strain>': 'O',
110 + '<Strain>': 'O',
111 + '</Substrain>': 'O',
112 + '</Supp>': 'O',
113 + '</Technique>': 'O',
114 + '</Temp>': 'O',
115 + '</OD>': 'O',
116 + '</Anti>': 'O',
117 + '</Agit>': 'O',
118 + '<Name>': 'O',
119 + '</Name>': 'O',
120 + '<Orgn>': 'O',
121 + '</Orgn>': 'O',
122 + '</Vess>': 'O'}
123 +
124 + # Other label
125 + flag = 'O'
126 + # sentences counter
127 + n=0
128 + lista = []
129 + #First sentence
130 + sentence = ''
131 + with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file:
132 + for line in input_file:
133 + if len(line.split('\t')) > 1:
134 + w = line.split('\t')[1]
135 + if w in in_labels or w in out_labels:
136 + #Tagging
137 + if w in in_labels.keys(): flag = in_labels[w]
138 + if w in out_labels: flag = out_labels[w]
139 + else:
140 + if w == "PGCGROWTHCONDITIONS":
141 + #End of sentence
142 + lista.append(sentence)
143 + #New setence
144 + sentence = ''
145 + n=n+1
146 + else:
147 + #Building and save tagging sentence
148 + sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ')
149 +
150 + print("Number of sentences: " + str(n))
151 +
152 + # Split 70 30 training and test sentences
153 + trainingIndex = random.sample(range(len(lista)-1), int(len(lista)*.70))
154 + testIndex = [n for n in range(len(lista)-1) if n not in trainingIndex]
155 + print(len(trainingIndex))
156 + print(len(testIndex))
157 +
158 + with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile:
159 + Data = [lista[i] for i in trainingIndex]
160 + oFile.write('\n'.join(Data))
161 +
162 + with open(os.path.join(options.outputPath, options.testFile), "w") as oFile:
163 + Data = [lista[i] for i in testIndex]
164 + oFile.write('\n'.join(Data))
165 +
166 + print("==================================END===================================")
1 +#!/bin/python3
2 +import os
3 +from itertools import chain
4 +from optparse import OptionParser
5 +from time import time
6 +from collections import Counter
7 +import re
8 +
9 +import nltk
10 +import sklearn
11 +import scipy.stats
12 +import sys
13 +
14 +from sklearn.externals import joblib
15 +from sklearn.metrics import make_scorer
16 +from sklearn.cross_validation import cross_val_score
17 +from sklearn.grid_search import RandomizedSearchCV
18 +
19 +import sklearn_crfsuite
20 +from sklearn_crfsuite import scorers
21 +from sklearn_crfsuite import metrics
22 +
23 +from nltk.corpus import stopwords
24 +
25 +import random
26 +
27 +
28 +# Objective
29 +# Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging
30 +#
31 +# Input parameters
32 +# --inputPath=PATH Path of inputfile
33 +# --outputPath=PATH Path to place output files
34 +# --trainingFile=testFile Output training data set
35 +# --testFile=testFile Output test data set
36 +#
37 +# Output
38 +# training and test data set
39 +#
40 +# Examples
41 +# python label-split_training_test_v1.py
42 +# --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/
43 +# --inputFile sentences.tsv_pakal_.conll
44 +# --trainingFile training-data-set-70.txt
45 +# --testFile test-data-set-30.txt
46 +# --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
47 +#
48 +#
49 +# python label-split_training_test_v1.py --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/ --inputFile sentences.tsv_pakal_.conll --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
50 +
51 +
52 +##########################################
53 +# MAIN PROGRAM #
54 +##########################################
55 +
56 +if __name__ == "__main__":
57 + # Defining parameters
58 + parser = OptionParser()
59 + parser.add_option("--inputPath", dest="inputPath",
60 + help="Path of output from CoreNLP", metavar="PATH")
61 + parser.add_option("--outputPath", dest="outputPath",
62 + help="Output path to place output files",
63 + metavar="PATH")
64 + parser.add_option("--inputFile", dest="inputFile",
65 + help="File with CoreNLP-tagging sentences", metavar="FILE")
66 + parser.add_option("--trainingFile", dest="trainingFile",
67 + help="File with training data set", metavar="FILE")
68 + parser.add_option("--testFile", dest="testFile",
69 + help="File with test data set", metavar="FILE")
70 +
71 + (options, args) = parser.parse_args()
72 + if len(args) > 0:
73 + parser.error("Any parameter given.")
74 + sys.exit(1)
75 +
76 + print('-------------------------------- PARAMETERS --------------------------------')
77 + print("Path of CoreNLP output: " + str(options.inputPath))
78 + print("File with CoreNLP-tagging sentences: " + str(options.inputFile))
79 + print("Path of training data set: " + str(options.outputPath))
80 + print("File with training data set: " + str(options.trainingFile))
81 + print("Path of test data set: " + str(options.outputPath))
82 + print("File with test data set: " + str(options.testFile))
83 + print('-------------------------------- PROCESSING --------------------------------')
84 + ## begin of tagging
85 + in_labels = {
86 + '<Gtype>': 'Gtype',
87 + '<Gversion>': 'Gversion',
88 + '<Med>': 'Med',
89 + '<Phase>': 'Phase',
90 + '<Sample>': 'Sample',
91 + '<Serie>': 'Serie',
92 + '<Substrain>': 'Substrain',
93 + '<Supp>': 'Supp',
94 + '<Technique>': 'Technique',
95 + '<Temp>': 'Temp',
96 + '<OD>': 'OD',
97 + '<Anti>': 'Anti',
98 + '<Agit>': 'Agit',
99 + '<Vess>': 'Vess'
100 + }
101 + ## End of tagging
102 + out_labels = {
103 + '</Air>': 'O',
104 + '</Gtype>': 'O',
105 + '</Gversion>': 'O',
106 + '</Med>': 'O',
107 + '</Phase>': 'O',
108 + '</Sample>': 'O',
109 + '</Serie>': 'O',
110 + '</Strain>': 'O',
111 + '<Strain>': 'O',
112 + '</Substrain>': 'O',
113 + '</Supp>': 'O',
114 + '</Technique>': 'O',
115 + '</Temp>': 'O',
116 + '</OD>': 'O',
117 + '</Anti>': 'O',
118 + '</Agit>': 'O',
119 + '<Name>': 'O',
120 + '</Name>': 'O',
121 + '<Orgn>': 'O',
122 + '</Orgn>': 'O',
123 + '</Vess>': 'O'}
124 +
125 + # Other label
126 + flag = 'O'
127 + # sentences counter
128 + n=0
129 + lista = []
130 + #First sentence
131 + sentence = ''
132 + with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file:
133 + for line in input_file:
134 + if len(line.split('\t')) > 1:
135 + w = line.split('\t')[1]
136 + if w in in_labels or w in out_labels:
137 + #Tagging
138 + if w in in_labels.keys(): flag = in_labels[w]
139 + if w in out_labels: flag = out_labels[w]
140 + else:
141 + if w == "PGCGROWTHCONDITIONS":
142 + #End of sentence
143 + lista.append(sentence)
144 + #New setence
145 + sentence = ''
146 + n=n+1
147 + else:
148 + #Building and save tagging sentence
149 + sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ')
150 +
151 + print("Number of sentences: " + str(n))
152 + print('\n'.join(lista))
153 + # Split 70 30 training and test sentences
154 +# trainingIndex = random.sample(range(len(lista)-1), int(len(lista)*.70))
155 +# testIndex = [n for n in range(len(lista)-1) if n not in trainingIndex]
156 +
157 +# with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile:
158 +# Data = [lista[i] for i in trainingIndex]
159 +# oFile.write('\n'.join(Data))
160 +
161 +# with open(os.path.join(options.outputPath, options.testFile), "w") as oFile:
162 +# Data = [lista[i] for i in testIndex]
163 +# oFile.write('\n'.join(Data))
164 +
165 +# print("==================================END===================================")
166 +
1 +# -*- coding: UTF-8 -*-
2 +
3 +import os
4 +from itertools import chain
5 +from optparse import OptionParser
6 +from time import time
7 +from collections import Counter
8 +import re
9 +
10 +import nltk
11 +import sklearn
12 +import scipy.stats
13 +import sys
14 +
15 +from sklearn.externals import joblib
16 +from sklearn.metrics import make_scorer
17 +from sklearn.cross_validation import cross_val_score
18 +from sklearn.grid_search import RandomizedSearchCV
19 +
20 +import sklearn_crfsuite
21 +from sklearn_crfsuite import scorers
22 +from sklearn_crfsuite import metrics
23 +
24 +from nltk.corpus import stopwords
25 +
26 +
27 +# Objective
28 +# Training and evaluation of CRFs with sklearn-crfsuite.
29 +#
30 +# Input parameters
31 +# --inputPath=PATH Path of training and test data set
32 +# --trainingFile File with training data set
33 +# --testFile File with test data set
34 +# --outputPath=PATH Output path to place output files
35 +
36 +# Output
37 +# 1) Best model
38 +
39 +# Examples
40 +# python training_validation_v3.py
41 +# --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
42 +# --trainingFile training-data-set-70.txt
43 +# --testFile test-data-set-30.txt
44 +# --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/
45 +# python3.4 training-validation_v3.py --inputPatTH /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/
46 +
47 +#################################
48 +# FUNCTIONS #
49 +#################################
50 +
51 +def isGreek(word):
52 + alphabet = ['Α','Β','Γ','Δ','Ε','Ζ','Η','Θ','Ι','Κ','Λ','Μ','Ν','Ξ','Ο','Π','Ρ','Σ','Τ','Υ','Φ','Χ','Ψ','Ω',
53 + 'α','β','γ','δ','ε','ζ','η','θ','ι','κ','λ','μ','ν','ξ','ο','π','ρ','ς','σ','τ','υ','φ','χ','ψ','ω']
54 + if word in alphabet:
55 + return True
56 + else:
57 + return False
58 +
59 +def word2features(sent, i):
60 + listElem = sent[i].split('|')
61 + word = listElem[0]
62 + lemma = listElem[1]
63 + postag = listElem[2]
64 +
65 + features = {
66 + # Suffixes
67 + #'word[-3:]': word[-3:],
68 + #'word[-2:]': word[-2:],
69 + #'word[-1:]': word[-1:],
70 + #'word.isupper()': word.isupper(),
71 + 'word': word,
72 + 'lemma': lemma,
73 + #'postag': postag,
74 + #'lemma[-3:]': lemma[-3:],
75 + #'lemma[-2:]': lemma[-2:],
76 + #'lemma[-1:]': lemma[-1:],
77 + #'lemma[+3:]': lemma[:3],
78 + #'lemma[+2:]': lemma[:2],
79 + #'lemma[+1:]': lemma[:1],
80 + #'word[:3]': word[:3],
81 + #'word[:2]': word[:2],
82 + #'word[:1]': word[:1],
83 + #'endsConLow()={}'.format(endsConLow(word)): endsConLow(word),
84 + 'isNumber()': word.isdigit(),
85 + 'isGreek(){}'.format(isGreek(word)): isGreek(word),
86 + 'isupper()' : word.isupper(),
87 + 'islower()' : word.islower()
88 + }
89 + if i > 0:
90 + listElem = sent[i - 1].split('|')
91 + word1 = listElem[0]
92 + lemma1 = listElem[1]
93 + postag1 = listElem[2]
94 + features.update({
95 + #'-1:word': word1,
96 + '-1:lemma': lemma1,
97 + '-1:postag': postag1,
98 + })
99 +
100 + if i < len(sent) - 1:
101 + listElem = sent[i + 1].split('|')
102 + #word1 = listElem[0]
103 + lemma1 = listElem[1]
104 + postag1 = listElem[2]
105 + features.update({
106 + #'+1:word': word1,
107 + '+1:lemma': lemma1,
108 + '+1:postag': postag1,
109 + })
110 +
111 + '''
112 + if i > 1:
113 + listElem = sent[i - 2].split('|')
114 + word2 = listElem[0]
115 + lemma2 = listElem[1]
116 + postag2 = listElem[2]
117 + features.update({
118 + '-2:word': word2,
119 + '-2:lemma': lemma2,
120 + })
121 +
122 + if i < len(sent) - 2:
123 + listElem = sent[i + 2].split('|')
124 + word2 = listElem[0]
125 + lemma2 = listElem[1]
126 + postag2 = listElem[2]
127 + features.update({
128 + '+2:word': word2,
129 + '+2:lemma': lemma2,
130 + })
131 +
132 + trigrams = False
133 + if trigrams:
134 + if i > 2:
135 + listElem = sent[i - 3].split('|')
136 + word3 = listElem[0]
137 + lemma3 = listElem[1]
138 + postag3 = listElem[2]
139 + features.update({
140 + '-3:word': word3,
141 + '-3:lemma': lemma3,
142 + })
143 +
144 + if i < len(sent) - 3:
145 + listElem = sent[i + 3].split('|')
146 + word3 = listElem[0]
147 + lemma3 = listElem[1]
148 + postag3 = listElem[2]
149 + features.update({
150 + '+3:word': word3,
151 + '+3:lemma': lemma3,
152 + })
153 + '''
154 + return features
155 +
156 +
157 +def sent2features(sent):
158 + return [word2features(sent, i) for i in range(len(sent))]
159 +
160 +
161 +def sent2labels(sent):
162 + return [elem.split('|')[3] for elem in sent]
163 +
164 +
165 +def sent2tokens(sent):
166 + return [token for token, postag, label in sent]
167 +
168 +
169 +def print_transitions(trans_features, f):
170 + for (label_from, label_to), weight in trans_features:
171 + f.write("{:6} -> {:7} {:0.6f}\n".format(label_from, label_to, weight))
172 +
173 +
174 +def print_state_features(state_features, f):
175 + for (attr, label), weight in state_features:
176 + f.write("{:0.6f} {:8} {}\n".format(weight, label, attr.encode("utf-8")))
177 +
178 +
179 +__author__ = 'CMendezC'
180 +
181 +##########################################
182 +# MAIN PROGRAM #
183 +##########################################
184 +
185 +if __name__ == "__main__":
186 + # Defining parameters
187 + parser = OptionParser()
188 + parser.add_option("--inputPath", dest="inputPath",
189 + help="Path of training data set", metavar="PATH")
190 + parser.add_option("--outputPath", dest="outputPath",
191 + help="Output path to place output files",
192 + metavar="PATH")
193 + parser.add_option("--trainingFile", dest="trainingFile",
194 + help="File with training data set", metavar="FILE")
195 + parser.add_option("--testFile", dest="testFile",
196 + help="File with test data set", metavar="FILE")
197 + parser.add_option("--excludeStopWords", default=False,
198 + action="store_true", dest="excludeStopWords",
199 + help="Exclude stop words")
200 + parser.add_option("--excludeSymbols", default=False,
201 + action="store_true", dest="excludeSymbols",
202 + help="Exclude punctuation marks")
203 +
204 + (options, args) = parser.parse_args()
205 + if len(args) > 0:
206 + parser.error("Any parameter given.")
207 + sys.exit(1)
208 +
209 + print('-------------------------------- PARAMETERS --------------------------------')
210 + print("Path of training data set: " + options.inputPath)
211 + print("File with training data set: " + str(options.trainingFile))
212 + print("Path of test data set: " + options.inputPath)
213 + print("File with test data set: " + str(options.testFile))
214 + print("Exclude stop words: " + str(options.excludeStopWords))
215 + symbols = ['.', ',', ':', ';', '?', '!', '\'', '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{',
216 + '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']
217 + #print("Exclude symbols " + str(symbols) + ': ' + str(options.excludeSymbols))
218 + print("Exclude symbols: " + str(options.excludeSymbols))
219 +
220 + print('-------------------------------- PROCESSING --------------------------------')
221 + print('Reading corpus...')
222 + t0 = time()
223 +
224 + sentencesTrainingData = []
225 + sentencesTestData = []
226 +
227 + stopwords = [word for word in stopwords.words('english')]
228 +
229 + with open(os.path.join(options.inputPath, options.trainingFile), "r") as iFile:
230 + for line in iFile.readlines():
231 + listLine = []
232 + line = line.strip('\n')
233 + for token in line.split():
234 + if options.excludeStopWords:
235 + listToken = token.split('|')
236 + lemma = listToken[1]
237 + if lemma in stopwords:
238 + continue
239 + if options.excludeSymbols:
240 + listToken = token.split('|')
241 + lemma = listToken[1]
242 + if lemma in symbols:
243 + continue
244 + listLine.append(token)
245 + sentencesTrainingData.append(listLine)
246 + print(" Sentences training data: " + str(len(sentencesTrainingData)))
247 +
248 + with open(os.path.join(options.inputPath, options.testFile), "r") as iFile:
249 + for line in iFile.readlines():
250 + listLine = []
251 + line = line.strip('\n')
252 + for token in line.split():
253 + if options.excludeStopWords:
254 + listToken = token.split('|')
255 + lemma = listToken[1]
256 + if lemma in stopwords:
257 + continue
258 + if options.excludeSymbols:
259 + listToken = token.split('|')
260 + lemma = listToken[1]
261 + if lemma in symbols:
262 + continue
263 + listLine.append(token)
264 + sentencesTestData.append(listLine)
265 + print(" Sentences test data: " + str(len(sentencesTestData)))
266 +
267 + print("Reading corpus done in: %fs" % (time() - t0))
268 +
269 + print(sent2features(sentencesTrainingData[0])[0])
270 + print(sent2features(sentencesTestData[0])[0])
271 + t0 = time()
272 +
273 + X_train = [sent2features(s) for s in sentencesTrainingData]
274 + y_train = [sent2labels(s) for s in sentencesTrainingData]
275 +
276 + X_test = [sent2features(s) for s in sentencesTestData]
277 + # print X_test
278 + y_test = [sent2labels(s) for s in sentencesTestData]
279 +
280 + # Fixed parameters
281 + # crf = sklearn_crfsuite.CRF(
282 + # algorithm='lbfgs',
283 + # c1=0.1,
284 + # c2=0.1,
285 + # max_iterations=100,
286 + # all_possible_transitions=True
287 + # )
288 +
289 + # Hyperparameter Optimization
290 + crf = sklearn_crfsuite.CRF(
291 + algorithm='lbfgs',
292 + max_iterations=100,
293 + all_possible_transitions=True
294 + )
295 + params_space = {
296 + 'c1': scipy.stats.expon(scale=0.5),
297 + 'c2': scipy.stats.expon(scale=0.05),
298 + }
299 +
300 + # Original: labels = list(crf.classes_)
301 + # Original: labels.remove('O')
302 + labels = list(['Air', 'Gtype', 'Gversion', 'Med', 'Phase', 'Sample', 'Serie', 'Strain', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Vess'])
303 +
304 + # use the same metric for evaluation
305 + f1_scorer = make_scorer(metrics.flat_f1_score,
306 + average='weighted', labels=labels)
307 +
308 + # search
309 + rs = RandomizedSearchCV(crf, params_space,
310 + cv=10,
311 + verbose=3,
312 + n_jobs=-1,
313 + n_iter=20,
314 + # n_iter=50,
315 + scoring=f1_scorer)
316 + rs.fit(X_train, y_train)
317 +
318 + # Fixed parameters
319 + # crf.fit(X_train, y_train)
320 +
321 + # Best hiperparameters
322 + # crf = rs.best_estimator_
323 + nameReport = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
324 + options.excludeSymbols) + '.txt')
325 + with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="w") as oFile:
326 + oFile.write("********** TRAINING AND TESTING REPORT **********\n")
327 + oFile.write("Training file: " + options.trainingFile + '\n')
328 + oFile.write('\n')
329 + oFile.write('best params:' + str(rs.best_params_) + '\n')
330 + oFile.write('best CV score:' + str(rs.best_score_) + '\n')
331 + oFile.write('model size: {:0.2f}M\n'.format(rs.best_estimator_.size_ / 1000000))
332 +
333 + print("Training done in: %fs" % (time() - t0))
334 + t0 = time()
335 +
336 + # Update best crf
337 + crf = rs.best_estimator_
338 +
339 + # Saving model
340 + print(" Saving training model...")
341 + t1 = time()
342 + nameModel = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
343 + options.excludeSymbols) + '.mod')
344 + joblib.dump(crf, os.path.join(options.outputPath, "models", nameModel))
345 + print(" Saving training model done in: %fs" % (time() - t1))
346 +
347 + # Evaluation against test data
348 + y_pred = crf.predict(X_test)
349 + print("*********************************")
350 + name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
351 + options.excludeSymbols) + '.txt')
352 + with open(os.path.join(options.outputPath, "reports", "y_pred_" + name), "w") as oFile:
353 + for y in y_pred:
354 + oFile.write(str(y) + '\n')
355 +
356 + print("*********************************")
357 + name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
358 + options.excludeSymbols) + '.txt')
359 + with open(os.path.join(options.outputPath, "reports", "y_test_" + name), "w") as oFile:
360 + for y in y_test:
361 + oFile.write(str(y) + '\n')
362 +
363 + print("Prediction done in: %fs" % (time() - t0))
364 +
365 + # labels = list(crf.classes_)
366 + # labels.remove('O')
367 +
368 + with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="a") as oFile:
369 + oFile.write('\n')
370 + oFile.write("Flat F1: " + str(metrics.flat_f1_score(y_test, y_pred, average='weighted', labels=labels)))
371 + oFile.write('\n')
372 + # labels = list(crf.classes_)
373 + sorted_labels = sorted(
374 + labels,
375 + key=lambda name: (name[1:], name[0])
376 + )
377 + oFile.write(metrics.flat_classification_report(
378 + y_test, y_pred, labels=sorted_labels, digits=3
379 + ))
380 + oFile.write('\n')
381 +
382 + oFile.write("\nTop likely transitions:\n")
383 + print_transitions(Counter(crf.transition_features_).most_common(50), oFile)
384 + oFile.write('\n')
385 +
386 + oFile.write("\nTop unlikely transitions:\n")
387 + print_transitions(Counter(crf.transition_features_).most_common()[-50:], oFile)
388 + oFile.write('\n')
389 +
390 + oFile.write("\nTop positive:\n")
391 + print_state_features(Counter(crf.state_features_).most_common(200), oFile)
392 + oFile.write('\n')
393 +
394 + oFile.write("\nTop negative:\n")
395 + print_state_features(Counter(crf.state_features_).most_common()[-200:], oFile)
396 + oFile.write('\n')
1 +-------------------------------- PARAMETERS --------------------------------
2 +Path of CoreNLP output: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/
3 +File with CoreNLP-tagging sentences: raw-metadata-senteneces.txt.conll
4 +Path of training data set: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
5 +File with training data set: training-data-set-70.txt
6 +Path of test data set: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
7 +File with test data set: test-data-set-30.txt
8 +-------------------------------- PROCESSING --------------------------------
9 +Number of sentences: 405
10 + agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
11 + agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
12 + agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
13 + agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
14 + <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
15 + <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
16 + All|all|DT|O sequencing|sequencing|NN|O reads|read|VBZ|O were|be|VBD|O mapped|map|VBN|O to|to|TO|O E.|e.|FW|O coli|coli|FW|O MG1655|mg1655|NN|O reference|reference|NN|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion -RRB-|-rrb-|-RRB-|O using|use|VBG|O CLC|clc|NN|O Genomics|genomic|NNS|O Workbench5|workbench5|NN|O with|with|IN|O the|the|DT|O length|length|NN|O fraction|fraction|NN|O of|of|IN|O 0.9|0.9|CD|O and|and|CC|O the|the|DT|O similarity|similarity|NN|O of|of|IN|O 0.99|0.99|CD|O .|.|.|O
17 + antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
18 + antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
19 + antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
20 + antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
21 + antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti H-NS|h-ns|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
22 + antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
23 + antibody|antibody|NN|O :|:|:|O RNA|rna|NN|Anti Polymerase|polymerase|NN|Anti ß|ß|NN|Anti monoclonal|monoclonal|JJ|Anti antibody|antibody|NN|Anti from|from|IN|O NeoClone|NeoClone|NNP|O -LRB-|-lrb-|-LRB-|O W0002|w0002|NN|O -RRB-|-rrb-|-RRB-|O
24 + At|at|IN|O OD450|od450|NN|OD
25 + A|a|NN|OD total|total|NN|OD of|of|IN|OD six|six|CD|OD samples|sample|NNS|OD were|be|VBD|OD analyzed|analyze|VBN|OD .|.|.|OD oxyR-8myc|oxyr-8myc|NN|OD ,|,|,|OD soxR-8myc|soxr-8myc|NN|OD ,|,|,|OD and|and|CC|OD soxS-8myc|soxs-8myc|NN|OD tagged|tag|VBD|OD cells|cell|NNS|OD were|be|VBD|OD cultured|culture|VBN|OD in|in|IN|OD M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 250|250|CD|O uM|um|NN|O of|of|IN|O paraquat|paraquat|NN|O at|at|IN|O mid-log|mid-log|JJ|O pahse|pahse|NN|O for|for|IN|O 20|20|CD|O min|min|NN|O with|with|IN|O agitation|agitation|NN|O .|.|.|O
26 + A|a|NN|O total|total|NN|O of|of|IN|O two|two|CD|O samples|sample|NNS|O were|be|VBD|O analyzed|analyze|VBN|O .|.|.|O ompR-8myc|ompr-8myc|NN|O tagged|tag|VBD|O cells|cell|NNS|O were|be|VBD|O cultured|culture|VBN|O in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 0.3|0.3|CD|Supp M|m|NN|Supp of|of|IN|Supp NaCl|nacl|NN|Supp at|at|IN|O mid-log|mid-log|NN|Phase pahse|pahse|NN|Phase for|for|IN|O 30|30|CD|Supp min|min|NN|Supp with|with|IN|O agitation|agitation|NN|O .|.|.|O
27 + carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
28 + carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
29 + carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
30 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
31 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O in|in|IN|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp .|.|.|O
32 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
33 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O 70|70|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.35|0.35|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
34 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
35 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O in|in|IN|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp .|.|.|O
36 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
37 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.15|0.15|CD|OD in|in|IN|O 100|100|CD|O ml|ml|NN|O LB|lb|NN|Med -LRB-|-lrb-|-LRB-|O +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp -RRB-|-rrb-|-RRB-|O .|.|.|O
38 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.15|0.15|CD|OD in|in|IN|O 50|50|CD|O ml|ml|NN|O LB|lb|NN|Med -LRB-|-lrb-|-LRB-|O +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp -RRB-|-rrb-|-RRB-|O before|before|IN|O crosslinking|crosslink|VBG|O .|.|.|O
39 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O 65|65|CD|O ml|ml|NN|O LB|lb|NN|O medium|medium|NN|O at|at|IN|O 30|30|CD|O °C|°c|NN|O to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.3|0.3|CD|OD .|.|.|O Subsequently|subsequently|RB|O 30|30|CD|O ml|ml|NN|O of|of|IN|O culture|culture|NN|O were|be|VBD|O transformed|transform|VBN|O to|to|TO|O a|a|DT|O pre|pre|JJ|O warmed|warm|VBN|O flask|flask|NN|Vess at|at|IN|O 43|43|CD|Temp °C|°c|NN|Temp -LRB-|-lrb-|-LRB-|Temp see|see|VB|Temp heat|heat|NN|Temp sample|sample|NN|Temp -RRB-|-rrb-|-RRB-|Temp and|and|CC|O the|the|DT|O remainder|remainder|NN|O kept|keep|VBD|O at|at|IN|O 30|30|CD|Temp °C|°c|NN|Temp .|.|.|O
40 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O 65|65|CD|O ml|ml|NN|O LB|lb|NN|O medium|medium|NN|O at|at|IN|O 30|30|CD|O °C|°c|NN|O to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.3|0.3|CD|OD .|.|.|O Subsequently|subsequently|RB|O 30|30|CD|O ml|ml|NN|O of|of|IN|O culture|culture|NN|O were|be|VBD|O transformed|transform|VBN|O to|to|TO|O a|a|DT|O pre|pre|JJ|O warmed|warm|VBN|O flask|flask|NN|Vess at|at|IN|O 43|43|CD|Temp °C|°c|NN|Temp and|and|CC|O the|the|DT|O remainder|remainder|NN|O kept|keep|VBD|O at|at|IN|O 30|30|CD|Temp °C|°c|NN|Temp -LRB-|-lrb-|-LRB-|Temp see|see|VB|Temp control|control|JJ|Temp sample|sample|NN|Temp -RRB-|-rrb-|-RRB-|Temp .|.|.|O
41 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O LB|LB|NNP|Med media|media|NNS|Med with|with|IN|O 1mM|1mm|NN|Supp IPTG|iptg|NN|Supp at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp with|with|IN|O shaking|shake|VBG|O for|for|IN|O 2|2|CD|Supp hours|hour|NNS|Supp
42 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O with|with|IN|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp and|and|CC|Supp 300|300|CD|Supp µL|µl|NN|Supp Cm20|cm20|NN|Supp <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
43 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O with|with|IN|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp and|and|CC|Supp 300|300|CD|Supp µL|µl|NN|Supp Cm20|cm20|NN|Supp <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
44 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O with|with|IN|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp and|and|CC|Supp 300|300|CD|Supp µL|µl|NN|Supp Cm20|cm20|NN|Supp <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
45 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
46 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
47 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti -LRB-|-lrb-|-LRB-|O Santa|Santa|NNP|O Cruz|Cruz|NNP|O Biotech|Biotech|NNP|O ,|,|,|O sc-28207|sc-28207|NN|O -RRB-|-rrb-|-RRB-|O
48 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-RpoB|anti-rpob|JJ|Anti -LRB-|-lrb-|-LRB-|O Neoclone|Neoclone|NNP|O ,|,|,|O WP002|wp002|NN|O -RRB-|-rrb-|-RRB-|O
49 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-rpoB|anti-rpob|JJ|Anti -LRB-|-lrb-|-LRB-|O Santa|Santa|NNP|O Cruz|Cruz|NNP|O Biotech|Biotech|NNP|O ,|,|,|O sc-56766|sc-56766|NN|O -RRB-|-rrb-|-RRB-|O
50 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-RpoS|anti-rpos|JJ|Anti -LRB-|-lrb-|-LRB-|O neoclone|neoclone|NN|O ,|,|,|O WP009|wp009|NN|O -RRB-|-rrb-|-RRB-|O
51 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
52 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O RNA|rna|NN|Anti polymerase|polymerase|NN|Anti subunit|subunit|NN|Anti β|β|NN|Anti
53 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
54 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
55 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O Custom|Custom|NNP|O anti-Fur|anti-fur|JJ|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
56 + ChIP-exo|chip-exo|NN|O reads|read|VBZ|O were|be|VBD|O aligned|align|VBN|O to|to|TO|O the|the|DT|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion genome|genome|NN|O reference|reference|NN|O sequence|sequence|NN|O using|use|VBG|O using|use|VBG|O bowtie|bowtie|NN|O v1|v1|NN|O .0.0|.0.0|CD|O with|with|IN|O parameters|parameter|NNS|O -|-|:|O S|s|NN|O
57 + ChIP-exo|chip-exo|NN|O reads|read|VBZ|O were|be|VBD|O aligned|align|VBN|O to|to|TO|O the|the|DT|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion genome|genome|NN|O reference|reference|NN|O sequence|sequence|NN|O using|use|VBG|O using|use|VBG|O bowtie|bowtie|NN|O v1|v1|NN|O .0.0|.0.0|CD|O with|with|IN|O parameters|parameter|NNS|O -|-|:|O S|s|NN|O
58 + culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
59 + culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
60 + cultured|culture|VBN|O in|in|IN|O :|:|:|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp acetate|acetate|NN|Supp
61 + cultured|culture|VBN|O in|in|IN|O :|:|:|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp fructose|fructose|NN|Supp
62 + cultured|culture|VBN|O in|in|IN|O :|:|:|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp
63 + Cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp
64 + E.|e.|FW|O coli|coli|FW|O K-12|k-12|NN|O MG1655|mg1655|NN|O cra-8myc|cra-8myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O was|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|O phase|phase|NN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|O minimal|minimal|JJ|O media|media|NNS|O supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|O %|%|NN|O glucose|glucose|NN|O ,|,|,|O fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
65 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Fur-8-myc|fur-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|O mM|mm|NN|O of|of|IN|O FeCl2|fecl2|NN|O were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|Supp mM|mm|NN|Supp of|of|IN|Supp DPD|dpd|NN|Supp were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|Supp .|.|.|O For|for|IN|O the|the|DT|O rifampicin-treated|rifampicin-treated|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O rifampicin|rifampicin|NN|O dissolved|dissolve|VBN|O in|in|IN|O methanol|methanol|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O concentration|concentration|NN|O of|of|IN|O 150|150|CD|O mg/mL|mg/ml|NN|O at|at|IN|O mid-log|mid-log|JJ|O phase|phase|NN|O and|and|CC|O stirred|stir|VBD|O for|for|IN|O 20|20|CD|O min|min|NN|O .|.|.|O
66 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Fur-8-myc|fur-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|O mM|mm|NN|O of|of|IN|O FeCl2|fecl2|NN|O were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|Supp mM|mm|NN|Supp of|of|IN|Supp DPD|dpd|NN|Supp were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|Supp .|.|.|O For|for|IN|O the|the|DT|O rifampicin-treated|rifampicin-treated|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O rifampicin|rifampicin|NN|Supp dissolved|dissolve|VBN|Supp in|in|IN|Supp methanol|methanol|NN|Supp was|be|VBD|O added|add|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O concentration|concentration|NN|O of|of|IN|O 150|150|CD|Supp mg/mL|mg/ml|NN|Supp at|at|IN|O mid-log|mid-log|JJ|O phase|phase|NN|O and|and|CC|O stirred|stir|VBD|O for|for|IN|O 20|20|CD|Supp min|min|NN|Supp .|.|.|O
67 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Fur-8-myc|fur-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|Supp mM|mm|NN|Supp of|of|IN|Supp FeCl2|fecl2|NN|Supp were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|O mM|mm|NN|O of|of|IN|O DPD|dpd|NN|O were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|Supp .|.|.|O For|for|IN|O the|the|DT|O rifampicin-treated|rifampicin-treated|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O rifampicin|rifampicin|NN|O dissolved|dissolve|VBN|O in|in|IN|O methanol|methanol|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O concentration|concentration|NN|O of|of|IN|O 150|150|CD|O mg/mL|mg/ml|NN|O at|at|IN|O mid-log|mid-log|JJ|O phase|phase|NN|O and|and|CC|O stirred|stir|VBD|O for|for|IN|O 20|20|CD|O min|min|NN|O .|.|.|O
68 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Fur-8-myc|fur-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|Supp mM|mm|NN|Supp of|of|IN|Supp FeCl2|fecl2|NN|Supp were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|O mM|mm|NN|O of|of|IN|O DPD|dpd|NN|O were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|Supp .|.|.|O For|for|IN|O the|the|DT|O rifampicin-treated|rifampicin-treated|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O rifampicin|rifampicin|NN|Supp dissolved|dissolve|VBN|Supp in|in|IN|Supp methanol|methanol|NN|Supp was|be|VBD|O added|add|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O concentration|concentration|NN|O of|of|IN|O 150|150|CD|Supp mg/mL|mg/ml|NN|Supp at|at|IN|O mid-log|mid-log|JJ|O phase|phase|NN|O and|and|CC|O stirred|stir|VBD|O for|for|IN|O 20|20|CD|Supp min|min|NN|Supp .|.|.|O
69 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|WT|NNP|O ,|,|,|O and|and|CC|O Δcra|Δcra|NNP|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp ,|,|,|O fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
70 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|WT|NNP|O ,|,|,|O and|and|CC|O Δcra|Δcra|NNP|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|O ,|,|,|O fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
71 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Δfur|δfur|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|O mM|mm|NN|O of|of|IN|O FeCl2|fecl2|NN|O were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|Supp mM|mm|NN|Supp of|of|IN|Supp DPD|dpd|NN|Supp were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|O .|.|.|O
72 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Δfur|δfur|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|Supp mM|mm|NN|Supp of|of|IN|Supp FeCl2|fecl2|NN|Supp were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|O mM|mm|NN|O of|of|IN|O DPD|dpd|NN|O were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|O .|.|.|O
73 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O ΔompR|δompr|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 0.3|0.3|CD|Supp M|m|NN|Supp of|of|IN|Supp NaCl|nacl|NN|Supp at|at|IN|O mid-log|mid-log|JJ|O pahse|pahse|NN|O for|for|IN|O 30|30|CD|Supp min|min|NN|Supp with|with|IN|O agitation|agitation|NN|O .|.|.|O
74 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|WT|NNP|O ,|,|,|O GadE-8-myc|gade-8-myc|NN|O ,|,|,|O GadW-8-myc|gadw-8-myc|NN|O ,|,|,|O and|and|CC|O GadX-8-myc|gadx-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD
75 + E.|e.|FW|OD coli|coli|FW|OD K-12|k-12|NN|OD MG1655|mg1655|NN|OD WT|wt|NN|OD ,|,|,|OD gadE|gade|NN|OD ,|,|,|OD gadW|gadw|NN|OD and|and|CC|OD gadX|gadx|NN|OD mutant|mutant|JJ|OD cells|cell|NNS|OD were|be|VBD|OD grown|grow|VBN|OD to|to|TO|OD mid-log|mid-log|JJ|OD phase|phase|NN|OD -LRB-|-lrb-|-LRB-|OD OD600|od600|NN|OD
76 + E.|e.|FW|OD coli|coli|FW|OD K-12|k-12|NN|OD MG1655|mg1655|NN|OD WT|wt|NN|OD ,|,|,|OD ΔoxyR|δoxyr|NN|OD ,|,|,|OD ΔsoxR|δsoxr|NN|OD ,|,|,|OD and|and|CC|OD ΔsoxS|δsoxs|NN|OD were|be|VBD|OD grown|grow|VBN|OD to|to|TO|OD mid-log|mid-log|JJ|OD phase|phase|NN|OD <Air>|<air>|NN|OD aerobically|aerobically|RB|OD at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 250|250|CD|O uM|um|NN|O of|of|IN|O paraquat|paraquat|NN|O at|at|IN|O mid-log|mid-log|JJ|O pahse|pahse|NN|O for|for|IN|O 20|20|CD|O min|min|NN|O with|with|IN|O agitation|agitation|NN|O .|.|.|O
77 + E.|E.|NNP|O coli|coli|NN|O strains|strain|NNS|O harboring|harbor|VBG|O PurR-8myc|purr-8myc|NN|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O minimal|minimal|JJ|O M9|m9|NN|O medium|medium|NN|O supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|O -LRB-|-lrb-|-LRB-|O 2|2|CD|O g/L|g/l|NN|O -RRB-|-rrb-|-RRB-|O then|then|RB|O inoculated|inoculate|VBN|O into|into|IN|O 100mL|100ml|NN|O of|of|IN|O fresh|fresh|JJ|O M9|m9|NN|Med minimal|minimal|JJ|Med medium|medium|NN|Med .|.|.|O
78 + E.|E.|NNP|O coli|coli|NN|O strains|strain|NNS|O harboring|harbor|VBG|O PurR-8myc|purr-8myc|NN|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O minimal|minimal|JJ|O M9|m9|NN|O medium|medium|NN|O supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|O -LRB-|-lrb-|-LRB-|O 2|2|CD|O g/L|g/l|NN|O -RRB-|-rrb-|-RRB-|O then|then|RB|O inoculated|inoculate|VBN|O into|into|IN|O 100mL|100ml|NN|O of|of|IN|O fresh|fresh|JJ|O M9|m9|NN|Med minimal|minimal|JJ|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 100ug/L|100ug/l|NN|Supp adenine|adenine|NN|Supp .|.|.|O
79 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
80 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
81 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
82 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp and|and|CC|O nitrate|nitrate|VBP|Supp .|.|.|O
83 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp and|and|CC|O nitrate|nitrate|VBP|Supp .|.|.|O
84 + Escherichia|escherichia|FW|O coli|coli|FW|O MG1655|mg1655|NN|O K-12|k-12|NN|O dFNR|dfnr|NN|Gtype -LRB-|-lrb-|-LRB-|Gtype PK4854|pk4854|NN|Gtype -RRB-|-rrb-|-RRB-|Gtype
85 + Escherichia|escherichia|FW|O coli|coli|FW|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|NN|O and|and|CC|O ∆|∆|NN|O fnr|fnr|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O O.D.|o.d.|NN|OD 600nm|600nm|JJ|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O <Air>|<air>|NN|O anerobically|anerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O MOPS|MOPS|NNP|Med +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp media|media|NNS|O -LRB-|-lrb-|-LRB-|O Ref|ref|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O
86 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O Escherichia|escherichia|FW|O coli|coli|FW|O MG1655|mg1655|NN|O K-12|k-12|NN|O genome|genome|NN|O version|version|NN|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion
87 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
88 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
89 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
90 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion -LRB-|-lrb-|-LRB-|O GenBank|genbank|NN|O -RRB-|-rrb-|-RRB-|O
91 + genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
92 + genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
93 + genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
94 + genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
95 + genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
96 + genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
97 + genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
98 + genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
99 + genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
100 + genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
101 + genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
102 + genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
103 + genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
104 + genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
105 + genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
106 + genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
107 + genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
108 + genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
109 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
110 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
111 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
112 + genotype/variation|genotype/variation|NN|O :|:|:|O -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype lacZ|lacz|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype tonB|tonb|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype feoA|feoa|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype zupT|zupt|NN|Gtype K12|k12|NN|Gtype
113 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
114 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
115 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
116 + genotype/variation|genotype/variation|NN|O :|:|:|O -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype tonB|tonb|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype feoA|feoa|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype zupT|zupt|NN|Gtype K12|k12|NN|Gtype
117 + genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
118 + genotype/variation|genotype/variation|NN|O :|:|:|O lacking|lack|VBG|Gtype the|the|DT|Gtype small|small|JJ|Gtype RNA|rna|NN|Gtype RyhB|ryhb|NN|Gtype
119 + genotype/variation|genotype/variation|NN|O :|:|:|O lacking|lack|VBG|Gtype the|the|DT|Gtype transcription|transcription|NN|Gtype factor|factor|NN|Gtype Fur|Fur|NNP|Gtype and|and|CC|Gtype the|the|DT|Gtype small|small|JJ|Gtype RNA|rna|NN|Gtype RyhB|ryhb|NN|Gtype
120 + genotype/variation|genotype/variation|NN|O :|:|:|O lacking|lack|VBG|Gtype the|the|DT|Gtype transcription|transcription|NN|Gtype factor|factor|NN|Gtype Fur|Fur|NNP|Gtype
121 + genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
122 + genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
123 + genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
124 + genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
125 + genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
126 + genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
127 + genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
128 + genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
129 + genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
130 + growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O
131 + growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O anaerobic|anaerobic|JJ|O
132 + growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O
133 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
134 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
135 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
136 + growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
137 + growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
138 + growth|growth|NN|O medium|medium|NN|O :|:|:|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp
139 + growth|growth|NN|O medium|medium|NN|O :|:|:|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 1|1|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp
140 + growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
141 + growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
142 + growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD
143 + growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
144 + ∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
145 + ChIP-Seq|chip-seq|NN|Gversion
146 + ip|ip|NN|O antibody|antibody|NN|O :|:|:|O affinity|affinity|NN|Anti purified|purify|VBN|Anti anti-Fur|anti-fur|JJ|Anti antibody|antibody|NN|Anti
147 + library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
148 + medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
149 + medium|medium|NN|O :|:|:|O M63|m63|NN|Med
150 + M9|m9|NN|Med minimal|minimal|JJ|Med complete|complete|JJ|Med media|media|NNS|Med ,|,|,|O cultures|culture|NNS|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 30|30|CD|Temp degrees|degree|NNS|Temp C|c|NN|Temp in|in|IN|O a|a|DT|O gyratory|gyratory|JJ|Agit water|water|NN|Agit bath|bath|NN|Agit shaking|shake|VBG|Agit at|at|IN|Agit 240|240|CD|Agit rpm|rpm|NN|Agit
151 + ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 1|1|CD|O
152 + ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 2|2|CD|O
153 + ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
154 + ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
155 + ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
156 + ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
157 + ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
158 + ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
159 + ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
160 + ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
161 + ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
162 + ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
163 + Cra|Cra|NNP|O acetate|acetate|NN|O 1|1|CD|O
164 + Cra|Cra|NNP|O acetate|acetate|NN|O 2|2|CD|O
165 + Cra|Cra|NNP|O fructose|fructose|NN|O 1|1|CD|O
166 + Cra|Cra|NNP|O fructose|fructose|NN|O 2|2|CD|O
167 + Cra|cra|NN|O glucose|glucose|NN|O 1|1|CD|O
168 + Cra|cra|NN|O glucose|glucose|NN|O 2|2|CD|O
169 + Crosslink|Crosslink|NNP|O
170 + CsiR|CsiR|NNP|O _|_|VBD|O ChIPSeq|chipseq|NN|O
171 + CsiR|csir|NN|O _|_|CD|O RNASeq|rnaseq|NN|O
172 + EC18n122|ec18n122|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 4|4|CD|O
173 + EC18n167|ec18n167|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
174 + EC18n168|ec18n168|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
175 + EC18n169|ec18n169|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
176 + EC18n170|ec18n170|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
177 + EC18n171|ec18n171|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
178 + EC18n177|ec18n177|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
179 + EC18n178|ec18n178|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
180 + EC18n179|ec18n179|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
181 + EC18n180|ec18n180|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
182 + EC18n181|ec18n181|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
183 + EC18n182|ec18n182|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
184 + EC18n183|ec18n183|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
185 + EC18n184|ec18n184|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
186 + EC18n185|ec18n185|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
187 + EC18n186|ec18n186|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
188 + Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
189 + Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
190 + Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
191 + Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
192 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|O
193 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|NN|O
194 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
195 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
196 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
197 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O C|c|NN|O
198 + ∆|∆|CD|O fnr|fnr|SYM|O -|-|:|O Anaeroibc|anaeroibc|NN|O
199 + FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O A|a|NN|O
200 + FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O B|b|NN|O
201 + ∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
202 + ∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
203 + ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
204 + ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
205 + ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O -LSB-|-lsb-|-LRB-|O IP|IP|NNP|O vs|vs|CC|O nput|nput|NN|O -RSB-|-rsb-|-RRB-|O
206 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O A|A|NNP|O
207 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O B|B|NNP|O
208 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O C|C|NNP|O
209 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O A|A|NNP|O
210 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O B|b|NN|O
211 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O C|c|NN|O
212 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O ,|,|,|O Iron|Iron|NNP|O Deficient|Deficient|NNP|O A|A|NNP|O
213 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O ,|,|,|O Iron|Iron|NNP|O Deficient|deficient|JJ|O B|b|NN|O
214 + ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
215 + ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
216 + ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
217 + ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
218 + Fur|Fur|NNP|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
219 + Fur|Fur|NNP|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
220 + Fur|Fur|NNP|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
221 + Fur|Fur|NNP|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
222 + HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O A|a|NN|O
223 + HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O B|b|NN|O
224 + HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
225 + HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
226 + IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
227 + IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
228 + Input|input|NN|O ChIP-Seq|chip-seq|NN|O
229 + LB|lb|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
230 + LB|lb|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O GA|ga|NN|O
231 + LB|lb|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS1|hs1|NN|O
232 + LB|lb|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS2|hs2|NN|O
233 + LB|lb|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS1|hs1|NN|O
234 + LB|lb|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS2|hs2|NN|O
235 + LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
236 + LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L2|l2|NN|O HS2|hs2|NN|O
237 + LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O GA|ga|NN|O
238 + LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L2|l2|NN|O HS2|hs2|NN|O
239 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS1|hs1|NN|O
240 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS2|hs2|NN|O
241 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L2|l2|NN|O HS2|hs2|NN|O
242 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS1|hs1|NN|O
243 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS2|hs2|NN|O
244 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L2|l2|NN|O HS2|hs2|NN|O
245 + Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 1|1|CD|O
246 + Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 2|2|CD|O
247 + Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 3|3|CD|O
248 + Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
249 + Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
250 + Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 3|3|CD|O
251 + M63|m63|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
252 + M63|m63|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O GA|ga|NN|O
253 + M63|m63|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS1|hs1|NN|O
254 + M63|m63|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS2|hs2|NN|O
255 + M63|m63|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS1|hs1|NN|O
256 + M63|m63|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS2|hs2|NN|O
257 + Nac|Nac|NNP|O _|_|NNP|O ChIPSeq|ChIPSeq|NNP|O
258 + Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
259 + NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep1|rep1|NN|O
260 + NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep2|rep2|NN|O
261 + NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep3|rep3|NN|O
262 + NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
263 + OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
264 + OmpR|ompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
265 + OmpR|ompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
266 + OxyR|oxyr|NN|O PQ|pq|NN|O 1|1|CD|O
267 + OxyR|oxyr|NN|O PQ|pq|NN|O 2|2|CD|O
268 + pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 1|1|CD|O
269 + pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
270 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
271 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 4|4|CD|O µM|µm|NN|O IPTG|iptg|NN|O
272 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 8|8|CD|O µM|µm|NN|O IPTG|iptg|NN|O
273 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
274 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 4|4|CD|O µM|µm|NN|O IPTG|iptg|NN|O
275 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 8|8|CD|O µM|µm|NN|O IPTG|iptg|NN|O
276 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O C|c|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
277 + PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|SYM|O 1|1|CD|O
278 + PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|NN|O 2|2|CD|O
279 + PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 1|1|CD|O
280 + PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 2|2|CD|O
281 + RNAP|rnap|NN|O old|old|JJ|O rep1|rep1|NN|O
282 + RNAP|rnap|NN|O old|old|JJ|O rep2|rep2|NN|O
283 + RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 1|1|CD|O
284 + RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 2|2|CD|O
285 + RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 1|1|CD|O
286 + RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 2|2|CD|O
287 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
288 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
289 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O and|and|CC|O rifampicin|rifampicin|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
290 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O and|and|CC|O rifampicin|rifampicin|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
291 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
292 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
293 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O and|and|CC|O rifampicin|rifampicin|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
294 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O and|and|CC|O rifampicin|rifampicin|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
295 + RpoB|rpob|NN|O WT|wt|NN|O 1|1|CD|O
296 + RpoB|rpob|NN|O WT|wt|NN|O 2|2|CD|O
297 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
298 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
299 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
300 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 2.5|2.5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
301 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
302 + ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O
303 + ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O
304 + SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|O
305 + SeqA|seqa|NN|O new|new|JJ|O rep1|rep1|NN|O
306 + SeqA|seqa|NN|O new|new|JJ|O rep2|rep2|NN|O
307 + SeqA|seqa|NN|O old|old|JJ|O deltaSeqA|deltaseqa|NN|O
308 + SeqA|seqa|NN|O old|old|JJ|O rep1|rep1|NN|O
309 + SeqA|seqa|NN|O old|old|JJ|O rep2|rep2|NN|O
310 + SoxR|soxr|NN|O PQ|pq|NN|O 1|1|CD|O
311 + SoxR|soxr|NN|O PQ|pq|NN|O 2|2|CD|O
312 + SoxS|soxs|NN|O PQ|pq|NN|O 1|1|CD|O
313 + SoxS|soxs|NN|O PQ|pq|NN|O 2|2|CD|O
314 + ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O A|a|NN|O
315 + ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O B|b|NN|O
316 + ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
317 + ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
318 + TrpR|trpr|NN|O _|_|NN|O glucose|glucose|NN|O
319 + TrpR|trpr|NN|O _|_|CD|O Trp|trp|NN|O
320 + Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O A|a|NN|O
321 + Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O B|b|NN|O
322 + Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O A|a|NN|O
323 + Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O B|b|NN|O
324 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
325 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
326 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
327 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 2.5|2.5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
328 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
329 + WT|wt|JJ|O acetate|acetate|NN|O 1|1|CD|O
330 + WT|wt|JJ|O acetate|acetate|NN|O 2|2|CD|O
331 + WT|WT|NNP|O _|_|SYM|O ChIPSeq|ChIPSeq|NNP|O _|_|SYM|O 1|1|CD|O
332 + WT|wt|JJ|O _|_|NN|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
333 + WT|wt|JJ|O fructose|fructose|NN|O 1|1|CD|O
334 + WT|wt|JJ|O fructose|fructose|NN|O 2|2|CD|O
335 + WT|wt|JJ|O glucose|glucose|NN|O 1|1|CD|O
336 + WT|wt|JJ|O glucose|glucose|NN|O 2|2|CD|O
337 + WT|wt|NN|O NaCl|nacl|NN|O 1|1|CD|O
338 + WT|wt|NN|O NaCl|nacl|NN|O 2|2|CD|O
339 + WT|wt|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
340 + WT|wt|JJ|O pH5|ph5|NN|O .5|.5|NN|O 2|2|CD|O
341 + WT|WT|NNP|O PQ|PQ|NNP|O 1|1|CD|O
342 + WT|WT|NNP|O PQ|PQ|NNP|O 2|2|CD|O
343 + WT|WT|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
344 + WT|wt|NN|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
345 + WT|wt|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
346 + WT|wt|NN|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
347 + WT|wt|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
348 + Δcra|δcra|NN|O acetate|acetate|NN|O 1|1|CD|O
349 + Δcra|δcra|NN|O acetate|acetate|NN|O 2|2|CD|O
350 + Δcra|δcra|NN|O fructose|fructose|NN|O 1|1|CD|O
351 + Δcra|δcra|NN|O fructose|fructose|NN|O 2|2|CD|O
352 + Δcra|δcra|NN|O glucose|glucose|NN|O 1|1|CD|O
353 + Δcra|δcra|NN|O glucose|glucose|NN|O 2|2|CD|O
354 + Δfur|δfur|NN|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
355 + Δfur|δfur|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
356 + Δfur|δfur|NN|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
357 + Δfur|δfur|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
358 + ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
359 + ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
360 + ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
361 + ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
362 + ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
363 + ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
364 + ΔompR|δompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
365 + ΔompR|δompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
366 + ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 1|1|CD|O
367 + ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 2|2|CD|O
368 + ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 1|1|CD|O
369 + ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 2|2|CD|O
370 + ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 1|1|CD|O
371 + ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 2|2|CD|O
372 + σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep1|rep1|NN|O
373 + σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep2|rep2|NN|O
374 + σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
375 + σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep1|rep1|NN|O
376 + σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep2|rep2|NN|O
377 + σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
378 + σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O control|control|NN|O
379 + σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O heat|heat|NN|O
380 + Escherichia|escherichia|FW|O coli|coli|FW|O K-12|k-12|NN|O
381 + Escherichia|escherichia|FW|O coli|coli|FW|O
382 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|NN|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655star|mg1655star|NN|Substrain
383 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|NN|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|Substrain
384 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|O
385 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655star|mg1655star|NN|O
386 + Resulting|result|VBG|O reads|read|VBZ|O were|be|VBD|O aligned|align|VBN|O to|to|TO|O the|the|DT|O published|publish|VBN|O E.|e.|FW|O coli|coli|FW|O K-12|k-12|NN|O MG1655|mg1655|NN|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion -RRB-|-rrb-|-RRB-|O using|use|VBG|O the|the|DT|O software|software|NN|O package|package|NN|O SOAP|soap|NN|O -LRB-|-lrb-|-LRB-|O Li|Li|NNP|O et|et|FW|O al|al|FW|O ,|,|,|O 2009|2009|CD|O -RRB-|-rrb-|-RRB-|O ,|,|,|O allowing|allow|VBG|O no|no|RB|O more|more|JJR|O than|than|IN|O two|two|CD|O mismatches|mismatch|NNS|O -LRB-|-lrb-|-LRB-|O Supplemental|Supplemental|NNP|O File|File|NNP|O -RRB-|-rrb-|-RRB-|O .|.|.|O Reads|read|VBZ|O aligning|align|VBG|O to|to|TO|O repeated|repeated|JJ|O elements|element|NNS|O in|in|IN|O the|the|DT|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O e.g.|e.g.|FW|O rRNA|rrna|NN|O -RRB-|-rrb-|-RRB-|O were|be|VBD|O removed|remove|VBN|O from|from|IN|O analysis|analysis|NN|O .|.|.|O For|for|IN|O reads|read|VBZ|O that|that|IN|O had|have|VBD|O no|no|DT|O mapping|mapping|NN|O locations|location|NNS|O for|for|IN|O the|the|DT|O first|first|JJ|O 36|36|CD|O bp|bp|NN|O ,|,|,|O the|the|DT|O 3-30|3-30|CD|O bp|bp|NN|O subsequences|subsequence|NNS|O were|be|VBD|O used|use|VBN|O in|in|IN|O the|the|DT|O subsequent|subsequent|JJ|O mapping|mapping|NN|O to|to|TO|O the|the|DT|O reference|reference|NN|O genome|genome|NN|O .|.|.|O Reads|read|NNS|O that|that|WDT|O had|have|VBD|O unique|unique|JJ|O mapping|mapping|NN|O locations|location|NNS|O and|and|CC|O did|do|VBD|O not|not|RB|O match|match|VB|O annotated|annotated|JJ|O rRNA|rrna|NN|O genes|gene|NNS|O were|be|VBD|O used|use|VBN|O for|for|IN|O further|further|JJ|O analysis|analysis|NN|O .|.|.|O For|for|IN|O each|each|DT|O gene|gene|NN|O ,|,|,|O the|the|DT|O tag|tag|NN|O density|density|NN|O was|be|VBD|O estimated|estimate|VBN|O as|as|IN|O the|the|DT|O number|number|NN|O of|of|IN|O aligned|align|VBN|O sequencing|sequencing|NN|O tags|tag|NNS|O divided|divide|VBN|O by|by|IN|O gene|gene|NN|O size|size|NN|O in|in|IN|O kb|kb|NN|O .|.|.|O Per-gene|per-gene|JJ|O tag|tag|NN|O density|density|NN|O was|be|VBD|O normalized|normalize|VBN|O using|use|VBG|O quantile|quantile|JJ|O normalization|normalization|NN|O -LRB-|-lrb-|-LRB-|O Supplemental|Supplemental|NNP|O Files|Files|NNP|O -RRB-|-rrb-|-RRB-|O .|.|.|O The|the|DT|O tag|tag|NN|O density|density|NN|O data|datum|NNS|O were|be|VBD|O analyzed|analyze|VBN|O for|for|IN|O statistically|statistically|RB|O significant|significant|JJ|O differential|differential|JJ|O expression|expression|NN|O using|use|VBG|O BaySeq|BaySeq|NNP|O -LRB-|-lrb-|-LRB-|O Hardcastle|Hardcastle|NNP|O &|&|CC|O Kelly|Kelly|NNP|O ,|,|,|O 2010|2010|CD|O -RRB-|-rrb-|-RRB-|O with|with|IN|O a|a|DT|O FDR|FDR|NNP|O of|of|IN|O 0.01|0.01|CD|O ,|,|,|O and|and|CC|O genes|gene|NNS|O were|be|VBD|O organized|organize|VBN|O into|into|IN|O operons|operon|NNS|O using|use|VBG|O data|datum|NNS|O from|from|IN|O EcoCyc|EcoCyc|NNP|O -LRB-|-lrb-|-LRB-|O Keseler|Keseler|NNP|O et|et|FW|O al|al|FW|O ,|,|,|O 2011|2011|CD|O -RRB-|-rrb-|-RRB-|O .|.|.|O
387 + Sequenced|sequence|VBD|O reads|read|VBZ|O were|be|VBD|O mapped|map|VBN|O onto|onto|IN|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion reference|reference|NN|O genome|genome|NN|O sequence|sequence|NN|O using|use|VBG|O bowtie|bowtie|NN|O v1|v1|NN|O .0.0|.0.0|CD|O with|with|IN|O parameters|parameter|NNS|O -|-|:|O X|x|NN|O 1000|1000|CD|O -|-|:|O n|n|NN|O 2|2|CD|O -3|-3|CD|O 3|3|LS|O -|-|:|O S|s|NN|O
388 + Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|NN|Phase cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 3500|3500|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O Cell|cell|NN|O pellets|pellet|NNS|O -LRB-|-lrb-|-LRB-|O from|from|IN|O initial|initial|JJ|O 250|250|CD|O mL|ml|NN|O of|of|IN|O culture|culture|NN|O -RRB-|-rrb-|-RRB-|O were|be|VBD|O thawed|thaw|VBN|O and|and|CC|O resuspended|resuspend|VBN|O in|in|IN|O 250|250|CD|O μL|μl|NN|O of|of|IN|O IP|IP|NNP|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 300|300|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 1|1|CD|O %|%|NN|O TritonX-100|tritonx-100|NN|O -RRB-|-rrb-|-RRB-|O and|and|CC|O sonicated|sonicate|VBN|O using|use|VBG|O a|a|DT|O microtip|microtip|NN|O sonicator|sonicator|NN|O set|set|VBN|O at|at|IN|O 10|10|CD|O %|%|NN|O output|output|NN|O for|for|IN|O 20|20|CD|O second|second|JJ|O intervals|interval|NNS|O with|with|IN|O periods|period|NNS|O of|of|IN|O cooling|cool|VBG|O in|in|IN|O between|between|IN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O then|then|RB|O treated|treat|VBN|O for|for|IN|O one|one|CD|O hour|hour|NN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O RNase|rnase|NN|O A|a|NN|O -LRB-|-lrb-|-LRB-|O 2|2|CD|O ng/ml|ng/ml|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O micrococcal|micrococcal|JJ|O nuclease|nuclease|NN|O -LRB-|-lrb-|-LRB-|O 50|50|CD|O units|unit|NNS|O -RRB-|-rrb-|-RRB-|O ,|,|,|O 20|20|CD|O μM|μm|NN|O CaCl2|cacl2|NN|O ,1.2|,1.2|CD|O mM|mm|NN|O KCl|kcl|NN|O ,|,|,|O 0.3|0.3|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 6|6|CD|O mM|mm|NN|O sucrose|sucrose|NN|O ,|,|,|O and|and|CC|O 10|10|CD|O μM|μm|NN|O DTT|dtt|NN|O .|.|.|O EDTA|edta|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 10|10|CD|O mM|mm|NN|O to|to|TO|O stop|stop|VB|O the|the|DT|O micrococcal|micrococcal|JJ|O nuclease|nuclease|NN|O and|and|CC|O the|the|DT|O samples|sample|NNS|O were|be|VBD|O spun|spin|VBN|O down|down|RP|O to|to|TO|O remove|remove|VB|O cell|cell|NN|O debris|debris|NN|O .|.|.|O The|the|DT|O lysate|lysate|NN|O was|be|VBD|O then|then|RB|O precleared|preclear|VBN|O through|through|IN|O incubation|incubation|NN|O with|with|IN|O a|a|DT|O 50/50|50/50|CD|O slurry|slurry|NN|O of|of|IN|O sepharose|sepharose|NN|O protein|protein|NN|O A|a|NN|O beads|bead|NNS|O in|in|IN|O IP|IP|NNP|O buffer|buffer|NN|O for|for|IN|O 2-3|2-3|CD|O hours|hour|NNS|O at|at|IN|O 4|4|CD|O °C|°c|NN|O .|.|.|O The|the|DT|O beads|bead|NNS|O were|be|VBD|O removed|remove|VBN|O by|by|IN|O centrifugation|centrifugation|NN|O and|and|CC|O antibody|antibody|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O pre-cleared|pre-cleared|JJ|O lysate|lysate|NN|O for|for|IN|O an|a|DT|O overnight|overnight|JJ|O incubation|incubation|NN|O .|.|.|O The|the|DT|O next|next|JJ|O day|day|NN|O ,|,|,|O 30|30|CD|O μl|μl|NN|O of|of|IN|O a|a|DT|O 50/50|50/50|CD|O slurry|slurry|NN|O of|of|IN|O sepharose|sepharose|NN|O protein|protein|NN|O A|a|NN|O beads|bead|NNS|O in|in|IN|O IP|IP|NNP|O buffer|buffer|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O lysate|lysate|NN|O to|to|TO|O capture|capture|VB|O antibody-protein-DNA|antibody-protein-dna|JJ|O complex|complex|NN|O for|for|IN|O one|one|CD|O hour|hour|NN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O .|.|.|O Beads|bead|NNS|O were|be|VBD|O then|then|RB|O washed|wash|VBN|O once|once|RB|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O LiCl|licl|NN|O wash|wash|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 250|250|CD|O mM|mm|NN|O LiCl|licl|NN|O ,|,|,|O 2|2|CD|O %|%|NN|O TritonX-100|tritonx-100|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O twice|twice|RB|O with|with|IN|O 600|600|CD|O mM|mm|NN|O NaCl|nacl|NN|O wash|wash|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 600|600|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 2|2|CD|O %|%|NN|O TritonX-100|tritonx-100|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O twice|twice|RB|O with|with|IN|O 300|300|CD|O mM|mm|NN|O NaCl|nacl|NN|O wash|wash|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 300|300|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 2|2|CD|O %|%|NN|O TritonX-100|tritonx-100|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O and|and|CC|O twice|twice|RB|O with|with|IN|O TE|te|NN|O .|.|.|O Elution|elution|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 50|50|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 10|10|CD|O mM|mm|NN|O EDTA|edta|NN|O ,|,|,|O 1|1|CD|O %|%|NN|O SDS|sds|NN|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O after|after|IN|O the|the|DT|O final|final|JJ|O wash|wash|NN|O step|step|NN|O ,|,|,|O and|and|CC|O beads|bead|NNS|O were|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 65|65|CD|O °C|°c|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O remove|remove|VB|O the|the|DT|O crosslinked|crosslink|VBN|O protein-DNA|protein-dna|JJ|O complexes|complex|NNS|O from|from|IN|O the|the|DT|O beads|bead|NNS|O .|.|.|O After|after|IN|O centrifugation|centrifugation|NN|O to|to|TO|O remove|remove|VB|O the|the|DT|O beads|bead|NNS|O ,|,|,|O the|the|DT|O samples|sample|NNS|O were|be|VBD|O incubated|incubate|VBN|O overnight|overnight|RB|O at|at|IN|O 65|65|CD|O °C|°c|NN|O to|to|TO|O reverse|reverse|VB|O the|the|DT|O protein-DNA|protein-dna|JJ|O formaldehyde|formaldehyde|NN|O crosslinks|crosslink|NNS|O .|.|.|O DNA|dna|NN|O was|be|VBD|O purified|purify|VBN|O using|use|VBG|O Qiagen|Qiagen|NNP|O 's|'s|POS|O PCR|pcr|NN|O Purification|purification|NN|O kit|kit|NN|O and|and|CC|O eluted|elute|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O volume|volume|NN|O of|of|IN|O 50|50|CD|O μl|μl|NN|O with|with|IN|O EB|EB|NNP|O .|.|.|O
389 + strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
390 + strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
391 + strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
392 + strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
393 + strain|strain|NN|O :|:|:|O K-12|k-12|NN|O MG1655|mg1655|NN|O
394 + strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O
395 + strain|strain|NN|O :|:|:|O K-12|k-12|NN|O
396 + MG1655|mg1655|NN|Substrain PhtpG|phtpg|NN|Gtype :|:|:|Gtype :|:|:|Gtype lacZ|lacz|NN|Gtype delta|delta|NN|Gtype lacX74/pTG2|lacx74/ptg2|NN|Gtype -LRB-|-lrb-|-LRB-|Gtype vector|vector|NN|Gtype carrying|carrying|NN|Gtype inducible|inducible|JJ|Gtype Ptrc|ptrc|NN|Gtype :|:|:|Gtype :|:|:|Gtype rpoH|rpoh|NN|Gtype -RRB-|-rrb-|-RRB-|Gtype
397 + MG1655|mg1655|NN|Substrain PhtpG|phtpg|NN|Gtype :|:|:|Gtype :|:|:|Gtype lacZ|lacz|NN|Gtype delta|delta|NN|Gtype lacX74/ptrc99A|lacx74/ptrc99a|NN|Gtype -LRB-|-lrb-|-LRB-|Gtype control|control|NN|Gtype vector|vector|NN|Gtype -RRB-|-rrb-|-RRB-|Gtype
398 + acetate|acetate|NN|Supp
399 + Sodium|sodium|NN|Supp phosphate|phosphate|NN|Supp -LRB-|-lrb-|-LRB-|Supp 1/100|1/100|CD|Supp vol|vol|NN|Supp .|.|.|Supp of|of|IN|Supp 1M|1m|NN|Supp ,|,|,|Supp pH|ph|NN|Supp 7.6|7.6|CD|Supp ;|;|:|Supp 10|10|CD|Supp mM|mm|NN|Supp final|final|JJ|Supp -RRB-|-rrb-|-RRB-|Supp was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|NN|Phase cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O aerobic|aerobic|JJ|O or|or|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O aerobic|aerobic|JJ|O or|or|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 3500|3500|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
400 + ChIP-Seq|chip-seq|NN|Technique
401 + RNA-Seq|rna-seq|NN|Technique
402 + The|the|DT|O cultured|culture|VBN|O cells|cell|NNS|O were|be|VBD|O inoculated|inoculate|VBN|O with|with|IN|O 1:100|1:100|CD|O dilution|dilution|NN|O into|into|IN|O 50|50|CD|O mL|ml|NN|O of|of|IN|O the|the|DT|O fresh|fresh|JJ|O M9|m9|NN|O medium|medium|NN|O containing|contain|VBG|O 2|2|CD|O g/L|g/l|NN|O glucose|glucose|NN|O in|in|IN|O either|either|CC|O the|the|DT|O presence|presence|NN|O or|or|CC|O absence|absence|NN|Supp of|of|IN|Supp 1|1|CD|Supp g/L|g/l|NN|Supp arginine|arginine|NN|Supp and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O at|at|IN|O 37|37|CD|O °C|°c|NN|O until|until|IN|O reaching|reach|VBG|O an|a|DT|O appropriate|appropriate|JJ|O cell|cell|NN|O density|density|NN|O -LRB-|-lrb-|-LRB-|O OD600|od600|NN|O ≈|≈|CD|O 0.5|0.5|CD|O -RRB-|-rrb-|-RRB-|O .|.|.|O
403 + The|the|DT|O cultured|culture|VBN|O cells|cell|NNS|O were|be|VBD|O inoculated|inoculate|VBN|O with|with|IN|O 1:100|1:100|CD|O dilution|dilution|NN|O into|into|IN|O 50|50|CD|O mL|ml|NN|O of|of|IN|O the|the|DT|O fresh|fresh|JJ|O M9|m9|NN|Med medium|medium|NN|Med containing|contain|VBG|O 2|2|CD|Supp g/L|g/l|NN|Supp glucose|glucose|NN|Supp in|in|IN|O either|either|CC|O the|the|DT|O presence|presence|NN|Supp or|or|CC|Supp absence|absence|NN|Supp of|of|IN|Supp 1|1|CD|Supp g/L|g/l|NN|Supp arginine|arginine|NN|Supp and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp until|until|IN|O reaching|reach|VBG|O an|a|DT|O appropriate|appropriate|JJ|O cell|cell|NN|O density|density|NN|O -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD ≈|≈|CD|OD 0.5|0.5|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
404 + To|to|TO|O harvest|harvest|VB|O total|total|JJ|O RNA|rna|NN|O samples|sample|NNS|O ,|,|,|O overnight|overnight|JJ|O cultures|culture|NNS|O of|of|IN|O wild|wild|JJ|Gtype type|type|NN|Gtype MG1655|mg1655|NN|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O at|at|IN|O 37|37|CD|O ˚C|˚c|NN|O were|be|VBD|O diluted|dilute|VBN|O back|back|RB|O 1:500|1:500|CD|O in|in|IN|O either|either|CC|O fresh|fresh|JJ|O LB|lb|NN|O or|or|CC|O M63|m63|NN|O minimal|minimal|JJ|O glucose|glucose|NN|O medium|medium|NN|O and|and|CC|O allowed|allow|VBN|O to|to|TO|O grow|grow|VB|O until|until|IN|O the|the|DT|O cultures|culture|NNS|O reached|reach|VBD|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O and|and|CC|O 2.0|2.0|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O and|and|CC|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O M63|m63|NN|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 25|25|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O Ethanol|ethanol|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O acid|acid|NN|O phenol|phenol|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|OD of|of|IN|OD 2.0|2.0|CD|OD a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O .|.|.|O
405 + To|to|TO|O harvest|harvest|VB|O total|total|JJ|O RNA|rna|NN|O samples|sample|NNS|O ,|,|,|O overnight|overnight|JJ|O cultures|culture|NNS|O of|of|IN|O wild|wild|JJ|Gtype type|type|NN|Gtype MG1655|mg1655|NN|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O at|at|IN|O 37|37|CD|O ˚C|˚c|NN|O were|be|VBD|O diluted|dilute|VBN|O back|back|RB|O 1:500|1:500|CD|O in|in|IN|O either|either|CC|O fresh|fresh|JJ|O LB|lb|NN|O or|or|CC|O M63|m63|NN|O minimal|minimal|JJ|O glucose|glucose|NN|O medium|medium|NN|O and|and|CC|O allowed|allow|VBN|O to|to|TO|O grow|grow|VB|O until|until|IN|O the|the|DT|O cultures|culture|NNS|O reached|reach|VBD|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O and|and|CC|O 2.0|2.0|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O and|and|CC|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O M63|m63|NN|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.4|0.4|CD|OD a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 25|25|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O Ethanol|ethanol|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O acid|acid|NN|O phenol|phenol|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O 2.0|2.0|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O .|.|.|O
406 + To|to|TO|O harvest|harvest|VB|O total|total|JJ|O RNA|rna|NN|O samples|sample|NNS|O ,|,|,|O overnight|overnight|JJ|O cultures|culture|NNS|O of|of|IN|O wild|wild|JJ|Gtype type|type|NN|Gtype MG1655|mg1655|NN|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O at|at|IN|O 37|37|CD|O ˚C|˚c|NN|O were|be|VBD|O diluted|dilute|VBN|O back|back|RB|O 1:500|1:500|CD|O in|in|IN|O either|either|CC|O fresh|fresh|JJ|O LB|lb|NN|O or|or|CC|O M63|m63|NN|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med medium|medium|NN|O and|and|CC|O allowed|allow|VBN|O to|to|TO|O grow|grow|VB|O until|until|IN|O the|the|DT|O cultures|culture|NNS|O reached|reach|VBD|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O and|and|CC|O 2.0|2.0|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O and|and|CC|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.4|0.4|CD|OD for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O M63|m63|NN|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 25|25|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O Ethanol|ethanol|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O acid|acid|NN|O phenol|phenol|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O 2.0|2.0|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O .|.|.|O
407 + treated|treat|VBN|O with|with|IN|O :|:|:|O 250|250|CD|Supp uM|um|NN|Supp of|of|IN|Supp paraquat|paraquat|NN|Supp at|at|IN|O mid-log|mid-log|NN|Phase pahse|pahse|NN|Phase for|for|IN|O 20|20|CD|Supp min|min|NN|Supp
408 + treated|treat|VBN|O with|with|IN|O :|:|:|O 250|250|CD|Supp uM|um|NN|Supp of|of|IN|Supp paraquat|paraquat|NN|Supp at|at|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase for|for|IN|O 20|20|CD|Supp min|min|NN|Supp
409 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med M9|m9|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O without|without|IN|O 10|10|CD|Supp mM|mm|NN|Supp leucine|leucine|NN|Supp .|.|.|O
410 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med M9|m9|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O without|without|IN|O 20|20|CD|Supp mg/L|mg/l|NN|Supp tryptophan|tryptophan|NN|Supp .|.|.|O
411 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med M9|m9|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 10|10|CD|Supp mM|mm|NN|Supp leucine|leucine|NN|Supp .|.|.|O
412 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med M9|m9|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 20|20|CD|Supp mg/L|mg/l|NN|Supp tryptophan|tryptophan|NN|Supp .|.|.|O
413 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med W2|w2|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 1g/L|1g/l|NN|Supp arginine|arginine|NN|Supp .|.|.|O
414 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med W2|w2|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 2g/L|2g/l|NN|Supp glutamine|glutamine|NN|Supp .|.|.|O
1 + ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 2|2|CD|O
2 + Δfur|δfur|NN|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
3 + OmpR|ompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
4 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 2.5|2.5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
5 + library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
6 + ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
7 + Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|NN|Phase cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 3500|3500|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O Cell|cell|NN|O pellets|pellet|NNS|O -LRB-|-lrb-|-LRB-|O from|from|IN|O initial|initial|JJ|O 250|250|CD|O mL|ml|NN|O of|of|IN|O culture|culture|NN|O -RRB-|-rrb-|-RRB-|O were|be|VBD|O thawed|thaw|VBN|O and|and|CC|O resuspended|resuspend|VBN|O in|in|IN|O 250|250|CD|O μL|μl|NN|O of|of|IN|O IP|IP|NNP|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 300|300|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 1|1|CD|O %|%|NN|O TritonX-100|tritonx-100|NN|O -RRB-|-rrb-|-RRB-|O and|and|CC|O sonicated|sonicate|VBN|O using|use|VBG|O a|a|DT|O microtip|microtip|NN|O sonicator|sonicator|NN|O set|set|VBN|O at|at|IN|O 10|10|CD|O %|%|NN|O output|output|NN|O for|for|IN|O 20|20|CD|O second|second|JJ|O intervals|interval|NNS|O with|with|IN|O periods|period|NNS|O of|of|IN|O cooling|cool|VBG|O in|in|IN|O between|between|IN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O then|then|RB|O treated|treat|VBN|O for|for|IN|O one|one|CD|O hour|hour|NN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O RNase|rnase|NN|O A|a|NN|O -LRB-|-lrb-|-LRB-|O 2|2|CD|O ng/ml|ng/ml|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O micrococcal|micrococcal|JJ|O nuclease|nuclease|NN|O -LRB-|-lrb-|-LRB-|O 50|50|CD|O units|unit|NNS|O -RRB-|-rrb-|-RRB-|O ,|,|,|O 20|20|CD|O μM|μm|NN|O CaCl2|cacl2|NN|O ,1.2|,1.2|CD|O mM|mm|NN|O KCl|kcl|NN|O ,|,|,|O 0.3|0.3|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 6|6|CD|O mM|mm|NN|O sucrose|sucrose|NN|O ,|,|,|O and|and|CC|O 10|10|CD|O μM|μm|NN|O DTT|dtt|NN|O .|.|.|O EDTA|edta|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 10|10|CD|O mM|mm|NN|O to|to|TO|O stop|stop|VB|O the|the|DT|O micrococcal|micrococcal|JJ|O nuclease|nuclease|NN|O and|and|CC|O the|the|DT|O samples|sample|NNS|O were|be|VBD|O spun|spin|VBN|O down|down|RP|O to|to|TO|O remove|remove|VB|O cell|cell|NN|O debris|debris|NN|O .|.|.|O The|the|DT|O lysate|lysate|NN|O was|be|VBD|O then|then|RB|O precleared|preclear|VBN|O through|through|IN|O incubation|incubation|NN|O with|with|IN|O a|a|DT|O 50/50|50/50|CD|O slurry|slurry|NN|O of|of|IN|O sepharose|sepharose|NN|O protein|protein|NN|O A|a|NN|O beads|bead|NNS|O in|in|IN|O IP|IP|NNP|O buffer|buffer|NN|O for|for|IN|O 2-3|2-3|CD|O hours|hour|NNS|O at|at|IN|O 4|4|CD|O °C|°c|NN|O .|.|.|O The|the|DT|O beads|bead|NNS|O were|be|VBD|O removed|remove|VBN|O by|by|IN|O centrifugation|centrifugation|NN|O and|and|CC|O antibody|antibody|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O pre-cleared|pre-cleared|JJ|O lysate|lysate|NN|O for|for|IN|O an|a|DT|O overnight|overnight|JJ|O incubation|incubation|NN|O .|.|.|O The|the|DT|O next|next|JJ|O day|day|NN|O ,|,|,|O 30|30|CD|O μl|μl|NN|O of|of|IN|O a|a|DT|O 50/50|50/50|CD|O slurry|slurry|NN|O of|of|IN|O sepharose|sepharose|NN|O protein|protein|NN|O A|a|NN|O beads|bead|NNS|O in|in|IN|O IP|IP|NNP|O buffer|buffer|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O lysate|lysate|NN|O to|to|TO|O capture|capture|VB|O antibody-protein-DNA|antibody-protein-dna|JJ|O complex|complex|NN|O for|for|IN|O one|one|CD|O hour|hour|NN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O .|.|.|O Beads|bead|NNS|O were|be|VBD|O then|then|RB|O washed|wash|VBN|O once|once|RB|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O LiCl|licl|NN|O wash|wash|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 250|250|CD|O mM|mm|NN|O LiCl|licl|NN|O ,|,|,|O 2|2|CD|O %|%|NN|O TritonX-100|tritonx-100|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O twice|twice|RB|O with|with|IN|O 600|600|CD|O mM|mm|NN|O NaCl|nacl|NN|O wash|wash|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 600|600|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 2|2|CD|O %|%|NN|O TritonX-100|tritonx-100|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O twice|twice|RB|O with|with|IN|O 300|300|CD|O mM|mm|NN|O NaCl|nacl|NN|O wash|wash|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 300|300|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 2|2|CD|O %|%|NN|O TritonX-100|tritonx-100|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O and|and|CC|O twice|twice|RB|O with|with|IN|O TE|te|NN|O .|.|.|O Elution|elution|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 50|50|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 10|10|CD|O mM|mm|NN|O EDTA|edta|NN|O ,|,|,|O 1|1|CD|O %|%|NN|O SDS|sds|NN|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O after|after|IN|O the|the|DT|O final|final|JJ|O wash|wash|NN|O step|step|NN|O ,|,|,|O and|and|CC|O beads|bead|NNS|O were|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 65|65|CD|O °C|°c|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O remove|remove|VB|O the|the|DT|O crosslinked|crosslink|VBN|O protein-DNA|protein-dna|JJ|O complexes|complex|NNS|O from|from|IN|O the|the|DT|O beads|bead|NNS|O .|.|.|O After|after|IN|O centrifugation|centrifugation|NN|O to|to|TO|O remove|remove|VB|O the|the|DT|O beads|bead|NNS|O ,|,|,|O the|the|DT|O samples|sample|NNS|O were|be|VBD|O incubated|incubate|VBN|O overnight|overnight|RB|O at|at|IN|O 65|65|CD|O °C|°c|NN|O to|to|TO|O reverse|reverse|VB|O the|the|DT|O protein-DNA|protein-dna|JJ|O formaldehyde|formaldehyde|NN|O crosslinks|crosslink|NNS|O .|.|.|O DNA|dna|NN|O was|be|VBD|O purified|purify|VBN|O using|use|VBG|O Qiagen|Qiagen|NNP|O 's|'s|POS|O PCR|pcr|NN|O Purification|purification|NN|O kit|kit|NN|O and|and|CC|O eluted|elute|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O volume|volume|NN|O of|of|IN|O 50|50|CD|O μl|μl|NN|O with|with|IN|O EB|EB|NNP|O .|.|.|O
8 + growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O
9 + ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
10 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|NN|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|Substrain
11 + Cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp
12 + The|the|DT|O cultured|culture|VBN|O cells|cell|NNS|O were|be|VBD|O inoculated|inoculate|VBN|O with|with|IN|O 1:100|1:100|CD|O dilution|dilution|NN|O into|into|IN|O 50|50|CD|O mL|ml|NN|O of|of|IN|O the|the|DT|O fresh|fresh|JJ|O M9|m9|NN|Med medium|medium|NN|Med containing|contain|VBG|O 2|2|CD|Supp g/L|g/l|NN|Supp glucose|glucose|NN|Supp in|in|IN|O either|either|CC|O the|the|DT|O presence|presence|NN|Supp or|or|CC|Supp absence|absence|NN|Supp of|of|IN|Supp 1|1|CD|Supp g/L|g/l|NN|Supp arginine|arginine|NN|Supp and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp until|until|IN|O reaching|reach|VBG|O an|a|DT|O appropriate|appropriate|JJ|O cell|cell|NN|O density|density|NN|O -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD ≈|≈|CD|OD 0.5|0.5|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
13 + FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O B|b|NN|O
14 + HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O A|a|NN|O
15 + cultured|culture|VBN|O in|in|IN|O :|:|:|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp fructose|fructose|NN|Supp
16 + Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
17 + genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
18 + WT|wt|JJ|O fructose|fructose|NN|O 2|2|CD|O
19 + EC18n178|ec18n178|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
20 + σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O heat|heat|NN|O
21 + ChIP-exo|chip-exo|NN|O reads|read|VBZ|O were|be|VBD|O aligned|align|VBN|O to|to|TO|O the|the|DT|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion genome|genome|NN|O reference|reference|NN|O sequence|sequence|NN|O using|use|VBG|O using|use|VBG|O bowtie|bowtie|NN|O v1|v1|NN|O .0.0|.0.0|CD|O with|with|IN|O parameters|parameter|NNS|O -|-|:|O S|s|NN|O
22 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
23 + genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
24 + ΔompR|δompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
25 + ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 1|1|CD|O
26 + antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
27 + ΔompR|δompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
28 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 4|4|CD|O µM|µm|NN|O IPTG|iptg|NN|O
29 + σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
30 + Cra|Cra|NNP|O acetate|acetate|NN|O 1|1|CD|O
31 + Escherichia|escherichia|FW|O coli|coli|FW|O K-12|k-12|NN|O
32 + Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O B|b|NN|O
33 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
34 + ∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
35 + carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
36 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-RpoS|anti-rpos|JJ|Anti -LRB-|-lrb-|-LRB-|O neoclone|neoclone|NN|O ,|,|,|O WP009|wp009|NN|O -RRB-|-rrb-|-RRB-|O
37 + EC18n168|ec18n168|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
38 + ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
39 + RpoB|rpob|NN|O WT|wt|NN|O 2|2|CD|O
40 + ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
41 + Escherichia|escherichia|FW|O coli|coli|FW|O MG1655|mg1655|NN|O K-12|k-12|NN|O dFNR|dfnr|NN|Gtype -LRB-|-lrb-|-LRB-|Gtype PK4854|pk4854|NN|Gtype -RRB-|-rrb-|-RRB-|Gtype
42 + Δcra|δcra|NN|O glucose|glucose|NN|O 1|1|CD|O
43 + ∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
44 + ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O A|a|NN|O
45 + genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
46 + genotype/variation|genotype/variation|NN|O :|:|:|O lacking|lack|VBG|Gtype the|the|DT|Gtype transcription|transcription|NN|Gtype factor|factor|NN|Gtype Fur|Fur|NNP|Gtype
47 + MG1655|mg1655|NN|Substrain PhtpG|phtpg|NN|Gtype :|:|:|Gtype :|:|:|Gtype lacZ|lacz|NN|Gtype delta|delta|NN|Gtype lacX74/pTG2|lacx74/ptg2|NN|Gtype -LRB-|-lrb-|-LRB-|Gtype vector|vector|NN|Gtype carrying|carrying|NN|Gtype inducible|inducible|JJ|Gtype Ptrc|ptrc|NN|Gtype :|:|:|Gtype :|:|:|Gtype rpoH|rpoh|NN|Gtype -RRB-|-rrb-|-RRB-|Gtype
48 + ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
49 + genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
50 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
51 + WT|wt|NN|O NaCl|nacl|NN|O 2|2|CD|O
52 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O in|in|IN|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp .|.|.|O
53 + Cra|Cra|NNP|O acetate|acetate|NN|O 2|2|CD|O
54 + EC18n171|ec18n171|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
55 + Δcra|δcra|NN|O acetate|acetate|NN|O 1|1|CD|O
56 + SoxS|soxs|NN|O PQ|pq|NN|O 2|2|CD|O
57 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
58 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O with|with|IN|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp and|and|CC|Supp 300|300|CD|Supp µL|µl|NN|Supp Cm20|cm20|NN|Supp <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
59 + SeqA|seqa|NN|O old|old|JJ|O rep1|rep1|NN|O
60 + ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 2|2|CD|O
61 + genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
62 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
63 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Δfur|δfur|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|O mM|mm|NN|O of|of|IN|O FeCl2|fecl2|NN|O were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|Supp mM|mm|NN|Supp of|of|IN|Supp DPD|dpd|NN|Supp were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|O .|.|.|O
64 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
65 + ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 1|1|CD|O
66 + genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
67 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
68 + ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
69 + ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
70 + EC18n180|ec18n180|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
71 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-rpoB|anti-rpob|JJ|Anti -LRB-|-lrb-|-LRB-|O Santa|Santa|NNP|O Cruz|Cruz|NNP|O Biotech|Biotech|NNP|O ,|,|,|O sc-56766|sc-56766|NN|O -RRB-|-rrb-|-RRB-|O
72 + Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
73 + CsiR|CsiR|NNP|O _|_|VBD|O ChIPSeq|chipseq|NN|O
74 + genotype/variation|genotype/variation|NN|O :|:|:|O -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype lacZ|lacz|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype tonB|tonb|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype feoA|feoa|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype zupT|zupt|NN|Gtype K12|k12|NN|Gtype
75 + MG1655|mg1655|NN|Substrain PhtpG|phtpg|NN|Gtype :|:|:|Gtype :|:|:|Gtype lacZ|lacz|NN|Gtype delta|delta|NN|Gtype lacX74/ptrc99A|lacx74/ptrc99a|NN|Gtype -LRB-|-lrb-|-LRB-|Gtype control|control|NN|Gtype vector|vector|NN|Gtype -RRB-|-rrb-|-RRB-|Gtype
76 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O and|and|CC|O rifampicin|rifampicin|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
77 + genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
78 + ip|ip|NN|O antibody|antibody|NN|O :|:|:|O affinity|affinity|NN|Anti purified|purify|VBN|Anti anti-Fur|anti-fur|JJ|Anti antibody|antibody|NN|Anti
79 + E.|e.|FW|OD coli|coli|FW|OD K-12|k-12|NN|OD MG1655|mg1655|NN|OD WT|wt|NN|OD ,|,|,|OD ΔoxyR|δoxyr|NN|OD ,|,|,|OD ΔsoxR|δsoxr|NN|OD ,|,|,|OD and|and|CC|OD ΔsoxS|δsoxs|NN|OD were|be|VBD|OD grown|grow|VBN|OD to|to|TO|OD mid-log|mid-log|JJ|OD phase|phase|NN|OD <Air>|<air>|NN|OD aerobically|aerobically|RB|OD at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 250|250|CD|O uM|um|NN|O of|of|IN|O paraquat|paraquat|NN|O at|at|IN|O mid-log|mid-log|JJ|O pahse|pahse|NN|O for|for|IN|O 20|20|CD|O min|min|NN|O with|with|IN|O agitation|agitation|NN|O .|.|.|O
80 + E.|e.|FW|OD coli|coli|FW|OD K-12|k-12|NN|OD MG1655|mg1655|NN|OD WT|wt|NN|OD ,|,|,|OD gadE|gade|NN|OD ,|,|,|OD gadW|gadw|NN|OD and|and|CC|OD gadX|gadx|NN|OD mutant|mutant|JJ|OD cells|cell|NNS|OD were|be|VBD|OD grown|grow|VBN|OD to|to|TO|OD mid-log|mid-log|JJ|OD phase|phase|NN|OD -LRB-|-lrb-|-LRB-|OD OD600|od600|NN|OD
81 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
82 + pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
83 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
84 + Δfur|δfur|NN|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
85 + genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
86 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655star|mg1655star|NN|O
87 + genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
88 + agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
89 + EC18n186|ec18n186|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
90 + SeqA|seqa|NN|O new|new|JJ|O rep2|rep2|NN|O
91 + ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 1|1|CD|O
92 + To|to|TO|O harvest|harvest|VB|O total|total|JJ|O RNA|rna|NN|O samples|sample|NNS|O ,|,|,|O overnight|overnight|JJ|O cultures|culture|NNS|O of|of|IN|O wild|wild|JJ|Gtype type|type|NN|Gtype MG1655|mg1655|NN|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O at|at|IN|O 37|37|CD|O ˚C|˚c|NN|O were|be|VBD|O diluted|dilute|VBN|O back|back|RB|O 1:500|1:500|CD|O in|in|IN|O either|either|CC|O fresh|fresh|JJ|O LB|lb|NN|O or|or|CC|O M63|m63|NN|O minimal|minimal|JJ|O glucose|glucose|NN|O medium|medium|NN|O and|and|CC|O allowed|allow|VBN|O to|to|TO|O grow|grow|VB|O until|until|IN|O the|the|DT|O cultures|culture|NNS|O reached|reach|VBD|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O and|and|CC|O 2.0|2.0|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O and|and|CC|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O M63|m63|NN|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.4|0.4|CD|OD a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 25|25|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O Ethanol|ethanol|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O acid|acid|NN|O phenol|phenol|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O 2.0|2.0|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O .|.|.|O
93 + culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
94 + medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
95 + ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
96 + LB|lb|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS1|hs1|NN|O
97 + agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
98 + Input|input|NN|O ChIP-Seq|chip-seq|NN|O
99 + PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|NN|O 2|2|CD|O
100 + Cra|cra|NN|O glucose|glucose|NN|O 1|1|CD|O
101 + RNAP|rnap|NN|O old|old|JJ|O rep1|rep1|NN|O
102 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
103 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
104 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|NN|O
105 + All|all|DT|O sequencing|sequencing|NN|O reads|read|VBZ|O were|be|VBD|O mapped|map|VBN|O to|to|TO|O E.|e.|FW|O coli|coli|FW|O MG1655|mg1655|NN|O reference|reference|NN|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion -RRB-|-rrb-|-RRB-|O using|use|VBG|O CLC|clc|NN|O Genomics|genomic|NNS|O Workbench5|workbench5|NN|O with|with|IN|O the|the|DT|O length|length|NN|O fraction|fraction|NN|O of|of|IN|O 0.9|0.9|CD|O and|and|CC|O the|the|DT|O similarity|similarity|NN|O of|of|IN|O 0.99|0.99|CD|O .|.|.|O
106 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Δfur|δfur|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|Supp mM|mm|NN|Supp of|of|IN|Supp FeCl2|fecl2|NN|Supp were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|O mM|mm|NN|O of|of|IN|O DPD|dpd|NN|O were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|O .|.|.|O
107 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
108 + Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
109 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 8|8|CD|O µM|µm|NN|O IPTG|iptg|NN|O
110 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Fur-8-myc|fur-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|O mM|mm|NN|O of|of|IN|O FeCl2|fecl2|NN|O were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|Supp mM|mm|NN|Supp of|of|IN|Supp DPD|dpd|NN|Supp were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|Supp .|.|.|O For|for|IN|O the|the|DT|O rifampicin-treated|rifampicin-treated|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O rifampicin|rifampicin|NN|Supp dissolved|dissolve|VBN|Supp in|in|IN|Supp methanol|methanol|NN|Supp was|be|VBD|O added|add|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O concentration|concentration|NN|O of|of|IN|O 150|150|CD|Supp mg/mL|mg/ml|NN|Supp at|at|IN|O mid-log|mid-log|JJ|O phase|phase|NN|O and|and|CC|O stirred|stir|VBD|O for|for|IN|O 20|20|CD|Supp min|min|NN|Supp .|.|.|O
111 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
112 + IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
113 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O C|c|NN|O
114 + antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
115 + EC18n167|ec18n167|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
116 + HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O B|b|NN|O
117 + M63|m63|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS2|hs2|NN|O
118 + Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O A|a|NN|O
119 + ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
120 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS2|hs2|NN|O
121 + M9|m9|NN|Med minimal|minimal|JJ|Med complete|complete|JJ|Med media|media|NNS|Med ,|,|,|O cultures|culture|NNS|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 30|30|CD|Temp degrees|degree|NNS|Temp C|c|NN|Temp in|in|IN|O a|a|DT|O gyratory|gyratory|JJ|Agit water|water|NN|Agit bath|bath|NN|Agit shaking|shake|VBG|Agit at|at|IN|Agit 240|240|CD|Agit rpm|rpm|NN|Agit
1 + CsiR|csir|NN|O _|_|CD|O RNASeq|rnaseq|NN|O
2 + genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
3 + ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
4 + RNAP|rnap|NN|O old|old|JJ|O rep2|rep2|NN|O
5 + Fur|Fur|NNP|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
6 + To|to|TO|O harvest|harvest|VB|O total|total|JJ|O RNA|rna|NN|O samples|sample|NNS|O ,|,|,|O overnight|overnight|JJ|O cultures|culture|NNS|O of|of|IN|O wild|wild|JJ|Gtype type|type|NN|Gtype MG1655|mg1655|NN|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O at|at|IN|O 37|37|CD|O ˚C|˚c|NN|O were|be|VBD|O diluted|dilute|VBN|O back|back|RB|O 1:500|1:500|CD|O in|in|IN|O either|either|CC|O fresh|fresh|JJ|O LB|lb|NN|O or|or|CC|O M63|m63|NN|O minimal|minimal|JJ|O glucose|glucose|NN|O medium|medium|NN|O and|and|CC|O allowed|allow|VBN|O to|to|TO|O grow|grow|VB|O until|until|IN|O the|the|DT|O cultures|culture|NNS|O reached|reach|VBD|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O and|and|CC|O 2.0|2.0|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O and|and|CC|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O M63|m63|NN|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 25|25|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O Ethanol|ethanol|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O acid|acid|NN|O phenol|phenol|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|OD of|of|IN|OD 2.0|2.0|CD|OD a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O .|.|.|O
7 + growth|growth|NN|O medium|medium|NN|O :|:|:|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp
8 + OxyR|oxyr|NN|O PQ|pq|NN|O 2|2|CD|O
9 + ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
10 + FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O A|a|NN|O
11 + PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|SYM|O 1|1|CD|O
12 + genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
13 + WT|WT|NNP|O _|_|SYM|O ChIPSeq|ChIPSeq|NNP|O _|_|SYM|O 1|1|CD|O
14 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
15 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L2|l2|NN|O HS2|hs2|NN|O
16 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
17 + ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
18 + Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
19 + genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
20 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
21 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O and|and|CC|O rifampicin|rifampicin|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
22 + genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
23 + genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
24 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O A|A|NNP|O
25 + genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
26 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O 70|70|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.35|0.35|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
27 + EC18n184|ec18n184|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
28 + ∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
29 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion -LRB-|-lrb-|-LRB-|O GenBank|genbank|NN|O -RRB-|-rrb-|-RRB-|O
30 + genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
31 + WT|wt|NN|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
32 + WT|wt|NN|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
33 + WT|WT|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
34 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 2.5|2.5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
35 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
36 + ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
37 + genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
38 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O B|B|NNP|O
39 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Fur-8-myc|fur-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|Supp mM|mm|NN|Supp of|of|IN|Supp FeCl2|fecl2|NN|Supp were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|O mM|mm|NN|O of|of|IN|O DPD|dpd|NN|O were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|Supp .|.|.|O For|for|IN|O the|the|DT|O rifampicin-treated|rifampicin-treated|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O rifampicin|rifampicin|NN|O dissolved|dissolve|VBN|O in|in|IN|O methanol|methanol|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O concentration|concentration|NN|O of|of|IN|O 150|150|CD|O mg/mL|mg/ml|NN|O at|at|IN|O mid-log|mid-log|JJ|O phase|phase|NN|O and|and|CC|O stirred|stir|VBD|O for|for|IN|O 20|20|CD|O min|min|NN|O .|.|.|O
40 + Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
41 + E.|E.|NNP|O coli|coli|NN|O strains|strain|NNS|O harboring|harbor|VBG|O PurR-8myc|purr-8myc|NN|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O minimal|minimal|JJ|O M9|m9|NN|O medium|medium|NN|O supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|O -LRB-|-lrb-|-LRB-|O 2|2|CD|O g/L|g/l|NN|O -RRB-|-rrb-|-RRB-|O then|then|RB|O inoculated|inoculate|VBN|O into|into|IN|O 100mL|100ml|NN|O of|of|IN|O fresh|fresh|JJ|O M9|m9|NN|Med minimal|minimal|JJ|Med medium|medium|NN|Med .|.|.|O
42 + OmpR|ompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
43 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O C|C|NNP|O
44 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|WT|NNP|O ,|,|,|O and|and|CC|O Δcra|Δcra|NNP|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp ,|,|,|O fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
45 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
46 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|O
47 + OxyR|oxyr|NN|O PQ|pq|NN|O 1|1|CD|O
48 + EC18n179|ec18n179|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
49 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O B|b|NN|O
50 + Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 3|3|CD|O
51 + At|at|IN|O OD450|od450|NN|OD
52 + Cra|Cra|NNP|O fructose|fructose|NN|O 1|1|CD|O
53 + genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
54 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O LB|LB|NNP|Med media|media|NNS|Med with|with|IN|O 1mM|1mm|NN|Supp IPTG|iptg|NN|Supp at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp with|with|IN|O shaking|shake|VBG|O for|for|IN|O 2|2|CD|Supp hours|hour|NNS|Supp
55 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O C|c|NN|O
56 + LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L2|l2|NN|O HS2|hs2|NN|O
57 + Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 3|3|CD|O
58 + WT|wt|JJ|O fructose|fructose|NN|O 1|1|CD|O
59 + Fur|Fur|NNP|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
60 + genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
61 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|WT|NNP|O ,|,|,|O GadE-8-myc|gade-8-myc|NN|O ,|,|,|O GadW-8-myc|gadw-8-myc|NN|O ,|,|,|O and|and|CC|O GadX-8-myc|gadx-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD
62 + E.|E.|NNP|O coli|coli|NN|O strains|strain|NNS|O harboring|harbor|VBG|O PurR-8myc|purr-8myc|NN|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O minimal|minimal|JJ|O M9|m9|NN|O medium|medium|NN|O supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|O -LRB-|-lrb-|-LRB-|O 2|2|CD|O g/L|g/l|NN|O -RRB-|-rrb-|-RRB-|O then|then|RB|O inoculated|inoculate|VBN|O into|into|IN|O 100mL|100ml|NN|O of|of|IN|O fresh|fresh|JJ|O M9|m9|NN|Med minimal|minimal|JJ|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 100ug/L|100ug/l|NN|Supp adenine|adenine|NN|Supp .|.|.|O
63 + ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
64 + EC18n182|ec18n182|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
65 + EC18n183|ec18n183|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
66 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
67 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
68 + cultured|culture|VBN|O in|in|IN|O :|:|:|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp acetate|acetate|NN|Supp
69 + Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 2|2|CD|O
70 + SeqA|seqa|NN|O old|old|JJ|O deltaSeqA|deltaseqa|NN|O
71 + EC18n170|ec18n170|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
72 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O Custom|Custom|NNP|O anti-Fur|anti-fur|JJ|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
73 + genotype/variation|genotype/variation|NN|O :|:|:|O lacking|lack|VBG|Gtype the|the|DT|Gtype transcription|transcription|NN|Gtype factor|factor|NN|Gtype Fur|Fur|NNP|Gtype and|and|CC|Gtype the|the|DT|Gtype small|small|JJ|Gtype RNA|rna|NN|Gtype RyhB|ryhb|NN|Gtype
74 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
75 + WT|wt|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
76 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O ,|,|,|O Iron|Iron|NNP|O Deficient|Deficient|NNP|O A|A|NNP|O
77 + ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
78 + Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 1|1|CD|O
79 + LB|lb|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS2|hs2|NN|O
80 + Sequenced|sequence|VBD|O reads|read|VBZ|O were|be|VBD|O mapped|map|VBN|O onto|onto|IN|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion reference|reference|NN|O genome|genome|NN|O sequence|sequence|NN|O using|use|VBG|O bowtie|bowtie|NN|O v1|v1|NN|O .0.0|.0.0|CD|O with|with|IN|O parameters|parameter|NNS|O -|-|:|O X|x|NN|O 1000|1000|CD|O -|-|:|O n|n|NN|O 2|2|CD|O -3|-3|CD|O 3|3|LS|O -|-|:|O S|s|NN|O
81 + growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
82 + σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep1|rep1|NN|O
83 + WT|wt|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
84 + TrpR|trpr|NN|O _|_|CD|O Trp|trp|NN|O
85 + The|the|DT|O cultured|culture|VBN|O cells|cell|NNS|O were|be|VBD|O inoculated|inoculate|VBN|O with|with|IN|O 1:100|1:100|CD|O dilution|dilution|NN|O into|into|IN|O 50|50|CD|O mL|ml|NN|O of|of|IN|O the|the|DT|O fresh|fresh|JJ|O M9|m9|NN|O medium|medium|NN|O containing|contain|VBG|O 2|2|CD|O g/L|g/l|NN|O glucose|glucose|NN|O in|in|IN|O either|either|CC|O the|the|DT|O presence|presence|NN|O or|or|CC|O absence|absence|NN|Supp of|of|IN|Supp 1|1|CD|Supp g/L|g/l|NN|Supp arginine|arginine|NN|Supp and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O at|at|IN|O 37|37|CD|O °C|°c|NN|O until|until|IN|O reaching|reach|VBG|O an|a|DT|O appropriate|appropriate|JJ|O cell|cell|NN|O density|density|NN|O -LRB-|-lrb-|-LRB-|O OD600|od600|NN|O ≈|≈|CD|O 0.5|0.5|CD|O -RRB-|-rrb-|-RRB-|O .|.|.|O
86 + WT|wt|NN|O NaCl|nacl|NN|O 1|1|CD|O
87 + M63|m63|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
88 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 4|4|CD|O µM|µm|NN|O IPTG|iptg|NN|O
89 + EC18n181|ec18n181|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
90 + Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
91 + ∆|∆|CD|O fnr|fnr|SYM|O -|-|:|O Anaeroibc|anaeroibc|NN|O
92 + Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O B|b|NN|O
93 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O A|A|NNP|O
94 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS1|hs1|NN|O
95 + strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O
96 + WT|wt|JJ|O acetate|acetate|NN|O 1|1|CD|O
97 + WT|WT|NNP|O PQ|PQ|NNP|O 1|1|CD|O
98 + OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
99 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
100 + cultured|culture|VBN|O in|in|IN|O :|:|:|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp
101 + NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
102 + Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
103 + HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
104 + RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 1|1|CD|O
105 + RpoB|rpob|NN|O WT|wt|NN|O 1|1|CD|O
106 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|O
107 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 8|8|CD|O µM|µm|NN|O IPTG|iptg|NN|O
108 + Nac|Nac|NNP|O _|_|NNP|O ChIPSeq|ChIPSeq|NNP|O
109 + SeqA|seqa|NN|O new|new|JJ|O rep1|rep1|NN|O
110 + carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
111 + A|a|NN|O total|total|NN|O of|of|IN|O two|two|CD|O samples|sample|NNS|O were|be|VBD|O analyzed|analyze|VBN|O .|.|.|O ompR-8myc|ompr-8myc|NN|O tagged|tag|VBD|O cells|cell|NNS|O were|be|VBD|O cultured|culture|VBN|O in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 0.3|0.3|CD|Supp M|m|NN|Supp of|of|IN|Supp NaCl|nacl|NN|Supp at|at|IN|O mid-log|mid-log|NN|Phase pahse|pahse|NN|Phase for|for|IN|O 30|30|CD|Supp min|min|NN|Supp with|with|IN|O agitation|agitation|NN|O .|.|.|O
112 + carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
113 + ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
114 + Fur|Fur|NNP|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
115 + PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 2|2|CD|O
116 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
117 + σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
118 + LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
119 + growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
120 + ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 1|1|CD|O
121 + acetate|acetate|NN|Supp
122 + antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti H-NS|h-ns|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
123 + pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 1|1|CD|O
124 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp and|and|CC|O nitrate|nitrate|VBP|Supp .|.|.|O
125 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS1|hs1|NN|O
126 + ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
127 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med M9|m9|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O without|without|IN|O 10|10|CD|Supp mM|mm|NN|Supp leucine|leucine|NN|Supp .|.|.|O
128 + NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep3|rep3|NN|O
129 + strain|strain|NN|O :|:|:|O K-12|k-12|NN|O
130 + ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O -LSB-|-lsb-|-LRB-|O IP|IP|NNP|O vs|vs|CC|O nput|nput|NN|O -RSB-|-rsb-|-RRB-|O
131 + PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 1|1|CD|O
132 + LB|lb|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS1|hs1|NN|O
133 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O 65|65|CD|O ml|ml|NN|O LB|lb|NN|O medium|medium|NN|O at|at|IN|O 30|30|CD|O °C|°c|NN|O to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.3|0.3|CD|OD .|.|.|O Subsequently|subsequently|RB|O 30|30|CD|O ml|ml|NN|O of|of|IN|O culture|culture|NN|O were|be|VBD|O transformed|transform|VBN|O to|to|TO|O a|a|DT|O pre|pre|JJ|O warmed|warm|VBN|O flask|flask|NN|Vess at|at|IN|O 43|43|CD|Temp °C|°c|NN|Temp and|and|CC|O the|the|DT|O remainder|remainder|NN|O kept|keep|VBD|O at|at|IN|O 30|30|CD|Temp °C|°c|NN|Temp -LRB-|-lrb-|-LRB-|Temp see|see|VB|Temp control|control|JJ|Temp sample|sample|NN|Temp -RRB-|-rrb-|-RRB-|Temp .|.|.|O
134 + Sodium|sodium|NN|Supp phosphate|phosphate|NN|Supp -LRB-|-lrb-|-LRB-|Supp 1/100|1/100|CD|Supp vol|vol|NN|Supp .|.|.|Supp of|of|IN|Supp 1M|1m|NN|Supp ,|,|,|Supp pH|ph|NN|Supp 7.6|7.6|CD|Supp ;|;|:|Supp 10|10|CD|Supp mM|mm|NN|Supp final|final|JJ|Supp -RRB-|-rrb-|-RRB-|Supp was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|NN|Phase cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O aerobic|aerobic|JJ|O or|or|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O aerobic|aerobic|JJ|O or|or|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 3500|3500|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
135 + strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
136 + treated|treat|VBN|O with|with|IN|O :|:|:|O 250|250|CD|Supp uM|um|NN|Supp of|of|IN|Supp paraquat|paraquat|NN|Supp at|at|IN|O mid-log|mid-log|NN|Phase pahse|pahse|NN|Phase for|for|IN|O 20|20|CD|Supp min|min|NN|Supp
137 + σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep2|rep2|NN|O
138 + <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
139 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
140 + EC18n177|ec18n177|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
141 + strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
142 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O and|and|CC|O rifampicin|rifampicin|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
143 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-RpoB|anti-rpob|JJ|Anti -LRB-|-lrb-|-LRB-|O Neoclone|Neoclone|NNP|O ,|,|,|O WP002|wp002|NN|O -RRB-|-rrb-|-RRB-|O
144 + Cra|Cra|NNP|O fructose|fructose|NN|O 2|2|CD|O
145 + SoxR|soxr|NN|O PQ|pq|NN|O 2|2|CD|O
146 + Escherichia|escherichia|FW|O coli|coli|FW|O
147 + SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|O
148 + growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD
149 + M63|m63|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS1|hs1|NN|O
150 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
151 + growth|growth|NN|O medium|medium|NN|O :|:|:|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 1|1|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp
152 + RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 2|2|CD|O
153 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
154 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O with|with|IN|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp and|and|CC|Supp 300|300|CD|Supp µL|µl|NN|Supp Cm20|cm20|NN|Supp <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
155 + treated|treat|VBN|O with|with|IN|O :|:|:|O 250|250|CD|Supp uM|um|NN|Supp of|of|IN|Supp paraquat|paraquat|NN|Supp at|at|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase for|for|IN|O 20|20|CD|Supp min|min|NN|Supp
156 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
157 + growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
158 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med M9|m9|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O without|without|IN|O 20|20|CD|Supp mg/L|mg/l|NN|Supp tryptophan|tryptophan|NN|Supp .|.|.|O
159 + Cra|cra|NN|O glucose|glucose|NN|O 2|2|CD|O
160 + LB|lb|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O GA|ga|NN|O
161 + EC18n185|ec18n185|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
162 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
163 + RNA-Seq|rna-seq|NN|Technique
164 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O ΔompR|δompr|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 0.3|0.3|CD|Supp M|m|NN|Supp of|of|IN|Supp NaCl|nacl|NN|Supp at|at|IN|O mid-log|mid-log|JJ|O pahse|pahse|NN|O for|for|IN|O 30|30|CD|Supp min|min|NN|Supp with|with|IN|O agitation|agitation|NN|O .|.|.|O
165 + M63|m63|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS1|hs1|NN|O
166 + LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L2|l2|NN|O HS2|hs2|NN|O
167 + growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
168 + A|a|NN|OD total|total|NN|OD of|of|IN|OD six|six|CD|OD samples|sample|NNS|OD were|be|VBD|OD analyzed|analyze|VBN|OD .|.|.|OD oxyR-8myc|oxyr-8myc|NN|OD ,|,|,|OD soxR-8myc|soxr-8myc|NN|OD ,|,|,|OD and|and|CC|OD soxS-8myc|soxs-8myc|NN|OD tagged|tag|VBD|OD cells|cell|NNS|OD were|be|VBD|OD cultured|culture|VBN|OD in|in|IN|OD M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 250|250|CD|O uM|um|NN|O of|of|IN|O paraquat|paraquat|NN|O at|at|IN|O mid-log|mid-log|JJ|O pahse|pahse|NN|O for|for|IN|O 20|20|CD|O min|min|NN|O with|with|IN|O agitation|agitation|NN|O .|.|.|O
169 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O ,|,|,|O Iron|Iron|NNP|O Deficient|deficient|JJ|O B|b|NN|O
170 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
171 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
172 + NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep2|rep2|NN|O
173 + Δcra|δcra|NN|O fructose|fructose|NN|O 2|2|CD|O
174 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
175 + Δcra|δcra|NN|O acetate|acetate|NN|O 2|2|CD|O
176 + Δcra|δcra|NN|O glucose|glucose|NN|O 2|2|CD|O
177 + M63|m63|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS2|hs2|NN|O
178 + growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O anaerobic|anaerobic|JJ|O
179 + antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
180 + ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O
181 + LB|lb|NN|O 0.4|0.4|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS2|hs2|NN|O
182 + culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
183 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
184 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O C|c|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
185 + ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
186 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
187 + genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
188 + genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
189 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O and|and|CC|O rifampicin|rifampicin|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
190 + genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
191 + ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 2|2|CD|O
192 + ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O
193 + EC18n122|ec18n122|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 4|4|CD|O
194 + σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep1|rep1|NN|O
195 + ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
196 + genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
197 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O 65|65|CD|O ml|ml|NN|O LB|lb|NN|O medium|medium|NN|O at|at|IN|O 30|30|CD|O °C|°c|NN|O to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.3|0.3|CD|OD .|.|.|O Subsequently|subsequently|RB|O 30|30|CD|O ml|ml|NN|O of|of|IN|O culture|culture|NN|O were|be|VBD|O transformed|transform|VBN|O to|to|TO|O a|a|DT|O pre|pre|JJ|O warmed|warm|VBN|O flask|flask|NN|Vess at|at|IN|O 43|43|CD|Temp °C|°c|NN|Temp -LRB-|-lrb-|-LRB-|Temp see|see|VB|Temp heat|heat|NN|Temp sample|sample|NN|Temp -RRB-|-rrb-|-RRB-|Temp and|and|CC|O the|the|DT|O remainder|remainder|NN|O kept|keep|VBD|O at|at|IN|O 30|30|CD|Temp °C|°c|NN|Temp .|.|.|O
198 + growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
199 + NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep1|rep1|NN|O
200 + Crosslink|Crosslink|NNP|O
201 + genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
202 + genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
203 + antibody|antibody|NN|O :|:|:|O RNA|rna|NN|Anti Polymerase|polymerase|NN|Anti ß|ß|NN|Anti monoclonal|monoclonal|JJ|Anti antibody|antibody|NN|Anti from|from|IN|O NeoClone|NeoClone|NNP|O -LRB-|-lrb-|-LRB-|O W0002|w0002|NN|O -RRB-|-rrb-|-RRB-|O
204 + To|to|TO|O harvest|harvest|VB|O total|total|JJ|O RNA|rna|NN|O samples|sample|NNS|O ,|,|,|O overnight|overnight|JJ|O cultures|culture|NNS|O of|of|IN|O wild|wild|JJ|Gtype type|type|NN|Gtype MG1655|mg1655|NN|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O at|at|IN|O 37|37|CD|O ˚C|˚c|NN|O were|be|VBD|O diluted|dilute|VBN|O back|back|RB|O 1:500|1:500|CD|O in|in|IN|O either|either|CC|O fresh|fresh|JJ|O LB|lb|NN|O or|or|CC|O M63|m63|NN|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med medium|medium|NN|O and|and|CC|O allowed|allow|VBN|O to|to|TO|O grow|grow|VB|O until|until|IN|O the|the|DT|O cultures|culture|NNS|O reached|reach|VBD|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O and|and|CC|O 2.0|2.0|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O and|and|CC|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.4|0.4|CD|OD for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O M63|m63|NN|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 25|25|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O Ethanol|ethanol|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O acid|acid|NN|O phenol|phenol|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O 2.0|2.0|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O .|.|.|O
205 + strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
206 + WT|wt|JJ|O glucose|glucose|NN|O 1|1|CD|O
207 + Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
208 + Δcra|δcra|NN|O fructose|fructose|NN|O 1|1|CD|O
209 + ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
210 + WT|wt|JJ|O acetate|acetate|NN|O 2|2|CD|O
211 + Δfur|δfur|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
212 + ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O B|b|NN|O
213 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med M9|m9|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 20|20|CD|Supp mg/L|mg/l|NN|Supp tryptophan|tryptophan|NN|Supp .|.|.|O
214 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS2|hs2|NN|O
215 + Δfur|δfur|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
216 + EC18n169|ec18n169|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
217 + agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
218 + WT|WT|NNP|O PQ|PQ|NNP|O 2|2|CD|O
219 + <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
220 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O RNA|rna|NN|Anti polymerase|polymerase|NN|Anti subunit|subunit|NN|Anti β|β|NN|Anti
221 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|WT|NNP|O ,|,|,|O and|and|CC|O Δcra|Δcra|NNP|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|O ,|,|,|O fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
222 + ChIP-Seq|chip-seq|NN|Gversion
223 + LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O GA|ga|NN|O
224 + LB|lb|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
225 + ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
226 + agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
227 + WT|wt|JJ|O pH5|ph5|NN|O .5|.5|NN|O 2|2|CD|O
228 + strain|strain|NN|O :|:|:|O K-12|k-12|NN|O MG1655|mg1655|NN|O
229 + WT|wt|JJ|O _|_|NN|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
230 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Fur-8-myc|fur-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|Supp mM|mm|NN|Supp of|of|IN|Supp FeCl2|fecl2|NN|Supp were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|O mM|mm|NN|O of|of|IN|O DPD|dpd|NN|O were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|Supp .|.|.|O For|for|IN|O the|the|DT|O rifampicin-treated|rifampicin-treated|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O rifampicin|rifampicin|NN|Supp dissolved|dissolve|VBN|Supp in|in|IN|Supp methanol|methanol|NN|Supp was|be|VBD|O added|add|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O concentration|concentration|NN|O of|of|IN|O 150|150|CD|Supp mg/mL|mg/ml|NN|Supp at|at|IN|O mid-log|mid-log|JJ|O phase|phase|NN|O and|and|CC|O stirred|stir|VBD|O for|for|IN|O 20|20|CD|Supp min|min|NN|Supp .|.|.|O
231 + IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
232 + Escherichia|escherichia|FW|O coli|coli|FW|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|NN|O and|and|CC|O ∆|∆|NN|O fnr|fnr|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O O.D.|o.d.|NN|OD 600nm|600nm|JJ|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O <Air>|<air>|NN|O anerobically|anerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O MOPS|MOPS|NNP|Med +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp media|media|NNS|O -LRB-|-lrb-|-LRB-|O Ref|ref|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O
233 + ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
234 + ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
235 + RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 1|1|CD|O
236 + ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 2|2|CD|O
237 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med W2|w2|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 1g/L|1g/l|NN|Supp arginine|arginine|NN|Supp .|.|.|O
238 + LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L2|l2|NN|O HS2|hs2|NN|O
239 + HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
240 + genotype/variation|genotype/variation|NN|O :|:|:|O -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype tonB|tonb|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype feoA|feoa|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype zupT|zupt|NN|Gtype K12|k12|NN|Gtype
241 + Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
242 + genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
243 + genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
244 + E.|e.|FW|O coli|coli|FW|O K-12|k-12|NN|O MG1655|mg1655|NN|O cra-8myc|cra-8myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O was|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|O phase|phase|NN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|O minimal|minimal|JJ|O media|media|NNS|O supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|O %|%|NN|O glucose|glucose|NN|O ,|,|,|O fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
245 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.15|0.15|CD|OD in|in|IN|O 100|100|CD|O ml|ml|NN|O LB|lb|NN|Med -LRB-|-lrb-|-LRB-|O +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp -RRB-|-rrb-|-RRB-|O .|.|.|O
246 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti -LRB-|-lrb-|-LRB-|O Santa|Santa|NNP|O Cruz|Cruz|NNP|O Biotech|Biotech|NNP|O ,|,|,|O sc-28207|sc-28207|NN|O -RRB-|-rrb-|-RRB-|O
247 + E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O Fur-8-myc|fur-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp .|.|.|O For|for|IN|O iron|iron|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.1|0.1|CD|O mM|mm|NN|O of|of|IN|O FeCl2|fecl2|NN|O were|be|VBD|O treated|treat|VBN|O from|from|IN|O the|the|DT|O beginning|beginning|NN|O of|of|IN|O culture|culture|NN|O ,|,|,|O and|and|CC|O for|for|IN|O DPD|dpd|NN|O treated|treat|VBN|O cells|cell|NNS|O ,|,|,|O 0.2|0.2|CD|Supp mM|mm|NN|Supp of|of|IN|Supp DPD|dpd|NN|Supp were|be|VBD|O added|add|VBN|O at|at|IN|O early-log|early-log|JJ|O phase|phase|NN|O and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O for|for|IN|O additional|additional|JJ|O 2h|2h|NN|Supp .|.|.|O For|for|IN|O the|the|DT|O rifampicin-treated|rifampicin-treated|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O rifampicin|rifampicin|NN|O dissolved|dissolve|VBN|O in|in|IN|O methanol|methanol|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O a|a|DT|O final|final|JJ|O concentration|concentration|NN|O of|of|IN|O 150|150|CD|O mg/mL|mg/ml|NN|O at|at|IN|O mid-log|mid-log|JJ|O phase|phase|NN|O and|and|CC|O stirred|stir|VBD|O for|for|IN|O 20|20|CD|O min|min|NN|O .|.|.|O
248 + RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 2|2|CD|O
249 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp and|and|CC|O nitrate|nitrate|VBP|Supp .|.|.|O
250 + medium|medium|NN|O :|:|:|O M63|m63|NN|Med
251 + Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O A|a|NN|O
252 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
253 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O Escherichia|escherichia|FW|O coli|coli|FW|O MG1655|mg1655|NN|O K-12|k-12|NN|O genome|genome|NN|O version|version|NN|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion
254 + RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
255 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
256 + Fur|Fur|NNP|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
257 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O with|with|IN|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp and|and|CC|Supp 300|300|CD|Supp µL|µl|NN|Supp Cm20|cm20|NN|Supp <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O and|and|CC|O treated|treat|VBN|O with|with|IN|O 1|1|CD|O %|%|NN|O final|final|JJ|O volumen|voluman|NNS|O formaldehyde|formaldehyde|NN|O for|for|IN|O ten|ten|CD|O minutes|minute|NNS|O .|.|.|O Sodium|sodium|NN|O phosphate|phosphate|NN|O -LRB-|-lrb-|-LRB-|O 1/100|1/100|CD|O vol|vol|NN|O .|.|.|O of|of|IN|O 1M|1m|NN|O ,|,|,|O pH|ph|NN|O 7.6|7.6|CD|O ;|;|:|O 10|10|CD|O mM|mm|NN|O final|final|JJ|O -RRB-|-rrb-|-RRB-|O was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|JJ|O cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 5000|5000|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
258 + antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
259 + genotype/variation|genotype/variation|NN|O :|:|:|O lacking|lack|VBG|Gtype the|the|DT|Gtype small|small|JJ|Gtype RNA|rna|NN|Gtype RyhB|ryhb|NN|Gtype
260 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O in|in|IN|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp .|.|.|O
261 + treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|Med -LRB-|-lrb-|-LRB-|Med 2|2|CD|Med g/L|g/l|NN|Med -RRB-|-rrb-|-RRB-|Med minimal|minimal|JJ|Med M9|m9|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 10|10|CD|Supp mM|mm|NN|Supp leucine|leucine|NN|Supp .|.|.|O
262 + σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep2|rep2|NN|O
263 + genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
264 + ChIP-exo|chip-exo|NN|O reads|read|VBZ|O were|be|VBD|O aligned|align|VBN|O to|to|TO|O the|the|DT|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion genome|genome|NN|O reference|reference|NN|O sequence|sequence|NN|O using|use|VBG|O using|use|VBG|O bowtie|bowtie|NN|O v1|v1|NN|O .0.0|.0.0|CD|O with|with|IN|O parameters|parameter|NNS|O -|-|:|O S|s|NN|O
265 + antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
266 + ChIP-Seq|chip-seq|NN|Technique
267 + TrpR|trpr|NN|O _|_|NN|O glucose|glucose|NN|O
268 + Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|Gtype with|with|IN|O a|a|DT|O C-terminal|c-terminal|JJ|O Flag-tag|flag-tag|NN|Gtype ,|,|,|O was|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
269 + growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O
270 + ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
271 + SoxR|soxr|NN|O PQ|pq|NN|O 1|1|CD|O
272 + WT|wt|JJ|O glucose|glucose|NN|O 2|2|CD|O
273 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|NN|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655star|mg1655star|NN|Substrain
274 + SoxS|soxs|NN|O PQ|pq|NN|O 1|1|CD|O
275 + σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O control|control|NN|O
276 + strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
277 + M63|m63|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O GA|ga|NN|O
278 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.15|0.15|CD|OD in|in|IN|O 50|50|CD|O ml|ml|NN|O LB|lb|NN|Med -LRB-|-lrb-|-LRB-|O +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp -RRB-|-rrb-|-RRB-|O before|before|IN|O crosslinking|crosslink|VBG|O .|.|.|O
279 + Resulting|result|VBG|O reads|read|VBZ|O were|be|VBD|O aligned|align|VBN|O to|to|TO|O the|the|DT|O published|publish|VBN|O E.|e.|FW|O coli|coli|FW|O K-12|k-12|NN|O MG1655|mg1655|NN|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion -RRB-|-rrb-|-RRB-|O using|use|VBG|O the|the|DT|O software|software|NN|O package|package|NN|O SOAP|soap|NN|O -LRB-|-lrb-|-LRB-|O Li|Li|NNP|O et|et|FW|O al|al|FW|O ,|,|,|O 2009|2009|CD|O -RRB-|-rrb-|-RRB-|O ,|,|,|O allowing|allow|VBG|O no|no|RB|O more|more|JJR|O than|than|IN|O two|two|CD|O mismatches|mismatch|NNS|O -LRB-|-lrb-|-LRB-|O Supplemental|Supplemental|NNP|O File|File|NNP|O -RRB-|-rrb-|-RRB-|O .|.|.|O Reads|read|VBZ|O aligning|align|VBG|O to|to|TO|O repeated|repeated|JJ|O elements|element|NNS|O in|in|IN|O the|the|DT|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O e.g.|e.g.|FW|O rRNA|rrna|NN|O -RRB-|-rrb-|-RRB-|O were|be|VBD|O removed|remove|VBN|O from|from|IN|O analysis|analysis|NN|O .|.|.|O For|for|IN|O reads|read|VBZ|O that|that|IN|O had|have|VBD|O no|no|DT|O mapping|mapping|NN|O locations|location|NNS|O for|for|IN|O the|the|DT|O first|first|JJ|O 36|36|CD|O bp|bp|NN|O ,|,|,|O the|the|DT|O 3-30|3-30|CD|O bp|bp|NN|O subsequences|subsequence|NNS|O were|be|VBD|O used|use|VBN|O in|in|IN|O the|the|DT|O subsequent|subsequent|JJ|O mapping|mapping|NN|O to|to|TO|O the|the|DT|O reference|reference|NN|O genome|genome|NN|O .|.|.|O Reads|read|NNS|O that|that|WDT|O had|have|VBD|O unique|unique|JJ|O mapping|mapping|NN|O locations|location|NNS|O and|and|CC|O did|do|VBD|O not|not|RB|O match|match|VB|O annotated|annotated|JJ|O rRNA|rrna|NN|O genes|gene|NNS|O were|be|VBD|O used|use|VBN|O for|for|IN|O further|further|JJ|O analysis|analysis|NN|O .|.|.|O For|for|IN|O each|each|DT|O gene|gene|NN|O ,|,|,|O the|the|DT|O tag|tag|NN|O density|density|NN|O was|be|VBD|O estimated|estimate|VBN|O as|as|IN|O the|the|DT|O number|number|NN|O of|of|IN|O aligned|align|VBN|O sequencing|sequencing|NN|O tags|tag|NNS|O divided|divide|VBN|O by|by|IN|O gene|gene|NN|O size|size|NN|O in|in|IN|O kb|kb|NN|O .|.|.|O Per-gene|per-gene|JJ|O tag|tag|NN|O density|density|NN|O was|be|VBD|O normalized|normalize|VBN|O using|use|VBG|O quantile|quantile|JJ|O normalization|normalization|NN|O -LRB-|-lrb-|-LRB-|O Supplemental|Supplemental|NNP|O Files|Files|NNP|O -RRB-|-rrb-|-RRB-|O .|.|.|O The|the|DT|O tag|tag|NN|O density|density|NN|O data|datum|NNS|O were|be|VBD|O analyzed|analyze|VBN|O for|for|IN|O statistically|statistically|RB|O significant|significant|JJ|O differential|differential|JJ|O expression|expression|NN|O using|use|VBG|O BaySeq|BaySeq|NNP|O -LRB-|-lrb-|-LRB-|O Hardcastle|Hardcastle|NNP|O &|&|CC|O Kelly|Kelly|NNP|O ,|,|,|O 2010|2010|CD|O -RRB-|-rrb-|-RRB-|O with|with|IN|O a|a|DT|O FDR|FDR|NNP|O of|of|IN|O 0.01|0.01|CD|O ,|,|,|O and|and|CC|O genes|gene|NNS|O were|be|VBD|O organized|organize|VBN|O into|into|IN|O operons|operon|NNS|O using|use|VBG|O data|datum|NNS|O from|from|IN|O EcoCyc|EcoCyc|NNP|O -LRB-|-lrb-|-LRB-|O Keseler|Keseler|NNP|O et|et|FW|O al|al|FW|O ,|,|,|O 2011|2011|CD|O -RRB-|-rrb-|-RRB-|O .|.|.|O
280 + SeqA|seqa|NN|O old|old|JJ|O rep2|rep2|NN|O
281 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
282 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
283 + WT|wt|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
...\ No newline at end of file ...\ No newline at end of file
1 +********** TRAINING AND TESTING REPORT **********
2 +Training file: training-data-set-70.txt
3 +
4 +best params:{'c1': 0.12296384618516742, 'c2': 0.001984598547992556}
5 +best CV score:0.7223961938319273
6 +model size: 0.07M
7 +
8 +Flat F1: 0.6328175528971997
9 + precision recall f1-score support
10 +
11 + OD 1.000 0.211 0.348 57
12 + Sample 0.000 0.000 0.000 0
13 + Technique 0.000 0.000 0.000 1
14 + Med 1.000 0.933 0.966 30
15 + Temp 1.000 0.615 0.762 13
16 + Serie 0.000 0.000 0.000 0
17 + Vess 0.000 0.000 0.000 0
18 + Agit 0.000 0.000 0.000 7
19 + Phase 0.750 0.923 0.828 13
20 + Air 0.000 0.000 0.000 0
21 + Anti 1.000 0.778 0.875 18
22 + Strain 0.000 0.000 0.000 0
23 + Gtype 0.884 0.551 0.679 69
24 + Supp 0.582 0.629 0.605 62
25 + Gversion 0.750 1.000 0.857 6
26 +
27 +avg / total 0.831 0.569 0.633 276
28 +
29 +
30 +Top likely transitions:
31 +OD -> OD 6.108207
32 +Supp -> Supp 5.784131
33 +Gtype -> Gtype 5.685374
34 +Med -> Med 5.675327
35 +Temp -> Temp 5.658789
36 +Anti -> Anti 5.031069
37 +Gversion -> Gversion 4.774936
38 +O -> O 4.746806
39 +Phase -> Phase 3.575687
40 +O -> Gtype 1.949659
41 +OD -> Phase 1.047851
42 +O -> Gversion 0.297969
43 +O -> Supp 0.232142
44 +O -> OD 0.059228
45 +O -> Anti 0.035022
46 +O -> Med 0.022142
47 +Supp -> Phase -0.082451
48 +Supp -> Med -0.113938
49 +Gtype -> Anti -0.177348
50 +Vess -> O -0.195425
51 +Phase -> O -0.308432
52 +Anti -> O -0.319054
53 +Phase -> Supp -0.418345
54 +O -> Technique -0.434100
55 +Temp -> O -0.447292
56 +Gtype -> O -0.546043
57 +Supp -> O -0.756881
58 +OD -> O -0.842201
59 +Technique -> O -0.857966
60 +Med -> O -0.892055
61 +Substrain -> O -0.970661
62 +O -> Phase -1.142533
63 +Temp -> Med -1.246193
64 +O -> Temp -1.298927
65 +Phase -> OD -1.766899
66 +Med -> Supp -2.805768
67 +
68 +
69 +Top unlikely transitions:
70 +OD -> OD 6.108207
71 +Supp -> Supp 5.784131
72 +Gtype -> Gtype 5.685374
73 +Med -> Med 5.675327
74 +Temp -> Temp 5.658789
75 +Anti -> Anti 5.031069
76 +Gversion -> Gversion 4.774936
77 +O -> O 4.746806
78 +Phase -> Phase 3.575687
79 +O -> Gtype 1.949659
80 +OD -> Phase 1.047851
81 +O -> Gversion 0.297969
82 +O -> Supp 0.232142
83 +O -> OD 0.059228
84 +O -> Anti 0.035022
85 +O -> Med 0.022142
86 +Supp -> Phase -0.082451
87 +Supp -> Med -0.113938
88 +Gtype -> Anti -0.177348
89 +Vess -> O -0.195425
90 +Phase -> O -0.308432
91 +Anti -> O -0.319054
92 +Phase -> Supp -0.418345
93 +O -> Technique -0.434100
94 +Temp -> O -0.447292
95 +Gtype -> O -0.546043
96 +Supp -> O -0.756881
97 +OD -> O -0.842201
98 +Technique -> O -0.857966
99 +Med -> O -0.892055
100 +Substrain -> O -0.970661
101 +O -> Phase -1.142533
102 +Temp -> Med -1.246193
103 +O -> Temp -1.298927
104 +Phase -> OD -1.766899
105 +Med -> Supp -2.805768
106 +
107 +
108 +Top positive:
109 +9.769521 OD b'+1:lemma:stationary'
110 +6.573116 Gtype b'-1:lemma:express'
111 +6.473813 O b'lemma:at'
112 +6.401320 Gtype b'+1:lemma:chip'
113 +5.580269 Med b'word:MOPS'
114 +5.580269 Med b'lemma:MOPS'
115 +5.309599 Med b'-1:lemma:ml'
116 +5.105098 Gtype b'+1:lemma:knock-out'
117 +5.053371 Anti b'+1:lemma:antibody'
118 +4.833626 O b'+1:lemma:until'
119 +4.685736 Supp b'word:nitrate'
120 +4.685736 Supp b'lemma:nitrate'
121 +4.578724 Temp b'-1:lemma:sample'
122 +4.338845 O b'+1:postag:VBP'
123 +4.326050 Gversion b'word:NC'
124 +4.326050 Gversion b'lemma:nc'
125 +4.207716 O b'word:.'
126 +4.207716 O b'lemma:.'
127 +3.987856 O b'lemma:chip'
128 +3.914979 Phase b'-1:lemma:mid-log'
129 +3.836351 O b'+1:postag:NNP'
130 +3.819222 O b'word:-'
131 +3.819222 O b'lemma:-'
132 +3.774330 Gtype b'-1:lemma:wild'
133 +3.733417 Supp b'word:2h'
134 +3.733417 Supp b'lemma:2h'
135 +3.733417 Supp b'-1:lemma:additional'
136 +3.729860 O b'word::'
137 +3.729860 O b'lemma::'
138 +3.704485 O b'-1:lemma:glucose'
139 +3.673897 O b'-1:lemma:-'
140 +3.584033 Phase b'word:mid-log'
141 +3.584033 Phase b'lemma:mid-log'
142 +3.580641 Gtype b'-1:lemma:k-12'
143 +3.329333 Gtype b'word:Flag-tag'
144 +3.329333 Gtype b'lemma:flag-tag'
145 +3.329333 Gtype b'-1:lemma:c-terminal'
146 +3.313956 O b'+1:lemma:coli'
147 +3.198151 Supp b'-1:lemma:vol'
148 +3.190691 O b'-1:lemma:lb'
149 +3.168840 Supp b'-1:lemma:with'
150 +3.134166 Gtype b'word:wild'
151 +3.134166 Gtype b'lemma:wild'
152 +3.092894 O b'word:K-12'
153 +3.092894 O b'lemma:k-12'
154 +3.060219 O b'word:MG1655'
155 +3.060219 O b'lemma:mg1655'
156 +3.020191 Supp b'+1:lemma:\xc2\xb5m'
157 +2.959207 Gversion b'word:ASM584v2'
158 +2.959207 Gversion b'lemma:asm584v2'
159 +2.895464 Gversion b'word:000913'
160 +2.895464 Gversion b'lemma:000913'
161 +2.892382 Vess b'word:flask'
162 +2.892382 Vess b'lemma:flask'
163 +2.892382 Vess b'-1:lemma:warm'
164 +2.889484 Temp b'+1:lemma:and'
165 +2.864457 OD b'word:OD450'
166 +2.864457 OD b'lemma:od450'
167 +2.844361 O b'+1:lemma:od600'
168 +2.760592 O b'word:Custom'
169 +2.760592 O b'lemma:Custom'
170 +2.760592 O b'+1:lemma:anti-fur'
171 +2.749995 Supp b'-1:lemma:without'
172 +2.744252 Phase b'word:exponential'
173 +2.744252 Phase b'lemma:exponential'
174 +2.724404 Phase b'word:stationary'
175 +2.724404 Phase b'lemma:stationary'
176 +2.704170 Supp b'word:glucose'
177 +2.704170 Supp b'lemma:glucose'
178 +2.702637 Med b'-1:lemma:LB'
179 +2.698915 Med b'word:LB'
180 +2.648788 O b'+1:lemma:fructose'
181 +2.522068 Supp b'word:arginine'
182 +2.522068 Supp b'lemma:arginine'
183 +2.521702 O b'+1:lemma:0.2'
184 +2.510135 Gtype b'-1:postag:VBG'
185 +2.500086 Med b'word:L'
186 +2.500086 Med b'lemma:L'
187 +2.500086 Med b'+1:lemma:broth'
188 +2.438147 Gversion b'-1:lemma:nc'
189 +2.435933 O b'word:with'
190 +2.435933 O b'lemma:with'
191 +2.424051 OD b'word:OD600'
192 +2.424051 OD b'lemma:od600'
193 +2.397049 Gversion b'word:U00096'
194 +2.397049 Gversion b'lemma:u00096'
195 +2.397049 Gversion b'+1:lemma:.2'
196 +2.393316 Temp b'-1:lemma:37'
197 +2.384921 Med b'+1:lemma:g/l'
198 +2.343273 O b'lemma:for'
199 +2.287420 O b'-1:lemma:\xc2\xb0c'
200 +2.277217 Supp b'word:acetate'
201 +2.277217 Supp b'lemma:acetate'
202 +2.240391 Gtype b'word:WT'
203 +2.227767 O b'word:Cells'
204 +2.223138 Temp b'+1:lemma:\xc2\xb0c'
205 +2.207530 Gtype b'word:PK4854'
206 +2.207530 Gtype b'lemma:pk4854'
207 +2.204777 Technique b'word:RNA-Seq'
208 +2.200781 Anti b'-1:lemma:polymerase'
209 +2.180743 O b'-1:lemma:phase'
210 +2.168855 Supp b'+1:lemma:at'
211 +2.168107 Supp b'+1:lemma:arginine'
212 +2.152384 O b'word:Crosslink'
213 +2.152384 O b'lemma:Crosslink'
214 +2.151825 O b'word:for'
215 +2.146611 Supp b'+1:lemma:hour'
216 +2.145369 Phase b'+1:lemma:for'
217 +2.130614 Supp b'+1:lemma:and'
218 +2.127595 Temp b'word:\xc2\xb0C'
219 +2.127595 Temp b'lemma:\xc2\xb0c'
220 +2.118493 Med b'word:broth'
221 +2.118493 Med b'lemma:broth'
222 +2.118493 Med b'-1:lemma:L'
223 +2.100174 Supp b'word:Adenine'
224 +2.100174 Supp b'lemma:Adenine'
225 +2.099073 Supp b'word:hours'
226 +2.099073 Supp b'lemma:hour'
227 +2.091461 Technique b'lemma:rna-seq'
228 +2.081270 O b'+1:lemma:0.4'
229 +2.069166 OD b'word:0.3'
230 +2.069166 OD b'lemma:0.3'
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233 +2.016740 Med b'lemma:m63'
234 +1.951269 Supp b'-1:lemma:final'
235 +1.951255 Anti b'+1:lemma:polyclonal'
236 +1.940092 O b'+1:postag:CD'
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238 +1.937643 O b'lemma:supplement'
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240 +1.928437 Gtype b'lemma:oxyr-8myc'
241 +1.925371 Gtype b'word:soxR-8myc'
242 +1.925371 Gtype b'lemma:soxr-8myc'
243 +1.905981 Supp b'-1:lemma:+'
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245 +1.904247 Gversion b'lemma:.2'
246 +1.904247 Gversion b'-1:lemma:u00096'
247 +1.895301 Supp b'-1:lemma::'
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252 +1.887095 Phase b'lemma:phase'
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254 +1.873844 Anti b'lemma:\xcf\x8332'
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257 +1.850543 Supp b'+1:lemma:be'
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261 +1.810937 O b'-1:lemma:_'
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263 +1.808829 Supp b'lemma:fructose'
264 +1.805654 OD b'word:A'
265 +1.799136 Gversion b'lemma:chip-seq'
266 +1.792100 Phase b'-1:lemma:until'
267 +1.787880 Anti b'-1:lemma:monoclonal'
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269 +1.786790 Anti b'lemma:anti-myc'
270 +1.784685 Substrain b'word:MG1655star'
271 +1.784685 Substrain b'lemma:mg1655star'
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275 +1.746035 Supp b'+1:lemma:1/100'
276 +1.733606 Anti b'+1:lemma:from'
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287 +1.646916 Anti b'lemma:anti-rpob'
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310 +
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330 +-0.057967 O b'+1:lemma:mg/ml'
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338 +-0.074848 Supp b'-1:lemma:.'
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511 +-4.411137 Phase b'-1:postag:JJ'
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1 +['O', 'O', 'O', 'O', 'O']
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101 +['O', 'O', 'O']
102 +['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
103 +['O', 'O', 'O', 'O', 'O', 'O', 'O']
104 +['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
105 +['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Gversion', 'Gversion', 'Gversion', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
106 +['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Phase', 'Phase', 'O', 'O', 'O', 'Temp', 'Temp', 'O', 'Med', 'Med', 'Med', 'O', 'O', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'Supp', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
107 +['O', 'O', 'O', 'O', 'O', 'O', 'O']
108 +['O', 'O', 'O', 'O', 'O', 'O', 'O']
109 +['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
110 +['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Phase', 'Phase', 'O', 'O', 'O', 'Temp', 'Temp', 'O', 'Med', 'Med', 'Med', 'O', 'O', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Supp', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Supp', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'Supp', 'Supp', 'O']
111 +['O', 'O', 'Gtype']
112 +['O', 'O', 'O', 'O']
113 +['O', 'O', 'O', 'O', 'O']
114 +['O', 'O', 'Anti', 'Anti', 'Anti', 'Anti']
115 +['O', 'O', 'O', 'O', 'O', 'O', 'O']
116 +['O', 'O', 'O', 'O']
117 +['O', 'O', 'O', 'O', 'O', 'O', 'O']
118 +['O', 'O', 'O']
119 +['O', 'O', 'O', 'O']
120 +['O', 'O', 'O', 'O', 'O', 'O', 'O']
121 +['Med', 'Med', 'Med', 'Med', 'O', 'O', 'O', 'O', 'O', 'O', 'Temp', 'Temp', 'Temp', 'O', 'O', 'Agit', 'Agit', 'Agit', 'Agit', 'Agit', 'Agit', 'Agit']
1 +cd /home/kevinml/automatic-extraction-growth-conditions/data-sets/tagged-xml-data
2 +echo
3 +echo
4 +echo
5 +
6 +echo "==============================Family SOFT files======================================= "
7 +echo
8 +echo "Access to GEO family soft files.."
9 +echo "directory: "$(pwd);
10 +echo
11 +echo
12 +
13 +ls -1 ;
14 +echo
15 +
16 +echo "Number of files: "$(ls -1 | wc -l);
17 +echo
18 +echo
19 +echo "Filter all paragraphs with tags..."
20 +echo "Add sentence-end-tag PGCGROWTHCONDITIONS..."
21 +grep -E "<[^<]*>" * | grep -E '!'| cut -f2 -d'='|sort|uniq|awk '{ print $_" PGCGROWTHCONDITIONS"; }' > /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt
22 +echo
23 +echo "Number of total tag sentences: "$(wc /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt -l);
24 +echo
25 +echo
26 +echo "Saving file: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt";
1 +echo
2 +echo
3 +echo "==============================Run CoreNLP======================================= ";
4 +echo
5 +echo
6 +
7 +input="/home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt";
8 +output="/home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/";
9 +echo "input file: "$input;
10 +echo
11 +echo "output directory: "$output;
12 +echo
13 +echo
14 +
15 +corenlp.sh -annotators tokenize,ssplit,pos,lemma -outputFormat conll -file $input -outputDirectory $output;
16 +
17 +
18 +
1 + agent: <Supp>DPD and rifampicin</Supp> PGCGROWTHCONDITIONS
2 + agent: <Supp>DPD</Supp> PGCGROWTHCONDITIONS
3 + agent: <Supp>Fe and rifampicin</Supp> PGCGROWTHCONDITIONS
4 + agent: <Supp>Fe</Supp> PGCGROWTHCONDITIONS
5 + <Air>Aerobic</Air> cultures PGCGROWTHCONDITIONS
6 + <Air>Anaerobic</Air> cultures PGCGROWTHCONDITIONS
7 + All sequencing reads were mapped to E. coli MG1655 reference genome (<Gversion>NC_000913</Gversion>) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99. PGCGROWTHCONDITIONS
8 + antibody: <Anti>9E10 Myc tag</Anti> antibody PGCGROWTHCONDITIONS
9 + antibody: <Anti>Affinity Purified FNR antibody</Anti> PGCGROWTHCONDITIONS
10 + antibody: <Anti>anti-FLAG mAb</Anti> PGCGROWTHCONDITIONS
11 + antibody: <Anti>Pre-cleared FNR antibody</Anti> PGCGROWTHCONDITIONS
12 + antibody: <Anti>Pre-cleared H-NS polyclonal antibody</Anti> PGCGROWTHCONDITIONS
13 + antibody: <Anti>Pre-cleared IHF polyclonal antibody</Anti> PGCGROWTHCONDITIONS
14 + antibody: <Anti>RNA Polymerase ß monoclonal antibody</Anti> from NeoClone (W0002) PGCGROWTHCONDITIONS
15 + At <OD>OD450 PGCGROWTHCONDITIONS
16 + A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS
17 + A total of two samples were analyzed. ompR-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with <Supp>0.3 M of NaCl</Supp> at <Phase>mid-log pahse</Phase> for <Supp>30 min</Supp> with agitation. PGCGROWTHCONDITIONS
18 + carbon source: <Supp>acetate</Supp> PGCGROWTHCONDITIONS
19 + carbon source: <Supp>fructose</Supp> PGCGROWTHCONDITIONS
20 + carbon source: <Supp>glucose</Supp> PGCGROWTHCONDITIONS
21 + Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>). PGCGROWTHCONDITIONS
22 + Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>. PGCGROWTHCONDITIONS
23 + Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>). PGCGROWTHCONDITIONS
24 + Cells were grown <Air>aerobically (25% O2, 70% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of 0.35</OD>) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. PGCGROWTHCONDITIONS
25 + Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>). PGCGROWTHCONDITIONS
26 + Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>. PGCGROWTHCONDITIONS
27 + Cells were grown <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of 0.3</OD>) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. PGCGROWTHCONDITIONS
28 + Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 100 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>). PGCGROWTHCONDITIONS
29 + Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking. PGCGROWTHCONDITIONS
30 + Cells were grown in 65 ml LB medium at 30 °C to an <OD>OD600 of about 0.3</OD>. Subsequently 30 ml of culture were transformed to a pre warmed <Vess>flask</Vess> at <Temp>43 °C (see heat sample)</Temp> and the remainder kept at <Temp>30 °C</Temp>. PGCGROWTHCONDITIONS
31 + Cells were grown in 65 ml LB medium at 30 °C to an <OD>OD600 of about 0.3</OD>. Subsequently 30 ml of culture were transformed to a pre warmed <Vess>flask</Vess> at <Temp>43 °C</Temp> and the remainder kept at <Temp>30 °C (see control sample)</Temp>. PGCGROWTHCONDITIONS
32 + Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp> PGCGROWTHCONDITIONS
33 + Cells were grown with <Supp>16 µM IPTG and 300 µL Cm20</Supp> <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of 0.3</OD>) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. PGCGROWTHCONDITIONS
34 + Cells were grown with <Supp>4 µM IPTG and 300 µL Cm20</Supp> <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of 0.3</OD>) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. PGCGROWTHCONDITIONS
35 + Cells were grown with <Supp>8 µM IPTG and 300 µL Cm20</Supp> <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of 0.3</OD>) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. PGCGROWTHCONDITIONS
36 + chip antibody: <Anti>9E10 Myc tag</Anti> antibody PGCGROWTHCONDITIONS
37 + chip antibody: <Anti>anti-myc</Anti> PGCGROWTHCONDITIONS
38 + chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207) PGCGROWTHCONDITIONS
39 + chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002) PGCGROWTHCONDITIONS
40 + chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766) PGCGROWTHCONDITIONS
41 + chip antibody: <Anti>anti-RpoS</Anti> (neoclone, WP009) PGCGROWTHCONDITIONS
42 + chip antibody: <Anti>none</Anti> PGCGROWTHCONDITIONS
43 + chip antibody: <Anti>RNA polymerase subunit β</Anti> PGCGROWTHCONDITIONS
44 + chip antibody: <Anti>SeqA</Anti> PGCGROWTHCONDITIONS
45 + chip antibody: <Anti>σ32</Anti> PGCGROWTHCONDITIONS
46 + chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti> PGCGROWTHCONDITIONS
47 + ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters -S PGCGROWTHCONDITIONS
48 + ChIP-exo reads were aligned to the <Gversion>NC_000913 </Gversion>genome reference sequence using using bowtie v1.0.0 with parameters -S PGCGROWTHCONDITIONS
49 + culture condition: <Air>Aerobic</Air> cultures PGCGROWTHCONDITIONS
50 + culture condition: <Air>Anaerobic</Air> cultures PGCGROWTHCONDITIONS
51 + cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% acetate</Supp> PGCGROWTHCONDITIONS
52 + cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% fructose</Supp> PGCGROWTHCONDITIONS
53 + cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp> PGCGROWTHCONDITIONS
54 + Cultures grown in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp> PGCGROWTHCONDITIONS
55 + E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS
56 + E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min. PGCGROWTHCONDITIONS
57 + E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the <Supp>rifampicin dissolved in methanol</Supp> was added to a final concentration of <Supp>150 mg/mL</Supp> at mid-log phase and stirred for <Supp>20 min</Supp>. PGCGROWTHCONDITIONS
58 + E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, <Supp>0.1mM of FeCl2</Supp> were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min. PGCGROWTHCONDITIONS
59 + E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, <Supp>0.1mM of FeCl2</Supp> were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the <Supp>rifampicin dissolved in methanol</Supp> was added to a final concentration of <Supp>150 mg/mL</Supp> at mid-log phase and stirred for <Supp>20 min</Supp>. PGCGROWTHCONDITIONS
60 + E. coli K-12 MG1655 WT, and Δcra were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>, fructose and acetate. PGCGROWTHCONDITIONS
61 + E. coli K-12 MG1655 WT, and Δcra were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2%</Supp> glucose, fructose and acetate. PGCGROWTHCONDITIONS
62 + E. coli K-12 MG1655 WT and Δfur were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS
63 + E. coli K-12 MG1655 WT and Δfur were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, <Supp>0.1mM of FeCl2</Supp> were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS
64 + E. coli K-12 MG1655 WT and ΔompR were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with <Supp>0.3 M of NaCl</Supp> at mid-log pahse for <Supp>30 min</Supp> with agitation. PGCGROWTHCONDITIONS
65 + E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 PGCGROWTHCONDITIONS
66 + E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 PGCGROWTHCONDITIONS
67 + E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS
68 + E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med>. PGCGROWTHCONDITIONS
69 + E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med> supplemented with <Supp>100ug/L adenine</Supp>. PGCGROWTHCONDITIONS
70 + Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp>. PGCGROWTHCONDITIONS
71 + Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp>. PGCGROWTHCONDITIONS
72 + Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp>. PGCGROWTHCONDITIONS
73 + Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>. PGCGROWTHCONDITIONS
74 + Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>. PGCGROWTHCONDITIONS
75 + Escherichia coli MG1655 K-12 <Gtype>dFNR (PK4854)</Gtype> PGCGROWTHCONDITIONS
76 + Escherichia coli MG1655 K-12 WT and ∆fnr were grown to <Phase>mid-log phase </Phase>(<OD>O.D.600nm 0.3</OD>) <Air>anerobically (95% N2, 5% CO2)</Air> at <Temp>37°C </Temp>in <Med>MOPS</Med> +<Supp>0.2% glucose</Supp> media (Ref). PGCGROWTHCONDITIONS
77 + Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion> PGCGROWTHCONDITIONS
78 + Genome_build: <Gversion>ASM584v2</Gversion> PGCGROWTHCONDITIONS
79 + Genome_build: <Gversion>NC_000913.2</Gversion> PGCGROWTHCONDITIONS
80 + Genome_build: <Gversion>NC_000913</Gversion> PGCGROWTHCONDITIONS
81 + Genome_build: <Gversion>U00096.2</Gversion> (GenBank) PGCGROWTHCONDITIONS
82 + genotype: delta-<Gtype>cra Knock-out strain</Gtype> PGCGROWTHCONDITIONS
83 + genotype: delta-<Gtype>crp Knock-out strain</Gtype> PGCGROWTHCONDITIONS
84 + genotype: <Gtype>ArgR-8myc</Gtype> PGCGROWTHCONDITIONS
85 + genotype: <Gtype>gadE-8myc</Gtype> PGCGROWTHCONDITIONS
86 + genotype: <Gtype>gadW-8myc</Gtype> PGCGROWTHCONDITIONS
87 + genotype: <Gtype>gadX-8myc</Gtype> PGCGROWTHCONDITIONS
88 + genotype: <Gtype>Lrp-8myc</Gtype> PGCGROWTHCONDITIONS
89 + genotype: <Gtype>ompR-8myc</Gtype> PGCGROWTHCONDITIONS
90 + genotype: <Gtype>ompR deletion mutant</Gtype> PGCGROWTHCONDITIONS
91 + genotype: <Gtype>PurR-8myc</Gtype> PGCGROWTHCONDITIONS
92 + genotype: <Gtype>TrpR-8myc</Gtype> PGCGROWTHCONDITIONS
93 + genotype: <Gtype>wildtype</Gtype> PGCGROWTHCONDITIONS
94 + genotype: <Gtype>Wildtype</Gtype> PGCGROWTHCONDITIONS
95 + genotype: <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
96 + genotype: <Gtype>ΔseqA</Gtype> PGCGROWTHCONDITIONS
97 + genotype/variation: <Gtype>Combined input</Gtype> PGCGROWTHCONDITIONS
98 + genotype/variation: <Gtype>cra-8myc-tagged</Gtype> PGCGROWTHCONDITIONS
99 + genotype/variation: <Gtype>delta_cra</Gtype> PGCGROWTHCONDITIONS
100 + genotype/variation: <Gtype>delta-gadE</Gtype> PGCGROWTHCONDITIONS
101 + genotype/variation: <Gtype>delta-gadW</Gtype> PGCGROWTHCONDITIONS
102 + genotype/variation: <Gtype>delta-gadX</Gtype> PGCGROWTHCONDITIONS
103 + genotype/variation: <Gtype>{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12</Gtype> PGCGROWTHCONDITIONS
104 + genotype/variation: <Gtype>delta-oxyR</Gtype> PGCGROWTHCONDITIONS
105 + genotype/variation: <Gtype>delta-soxR</Gtype> PGCGROWTHCONDITIONS
106 + genotype/variation: <Gtype>delta-soxS</Gtype> PGCGROWTHCONDITIONS
107 + genotype/variation: <Gtype>{delta}tonB, {delta}feoA, {delta}zupT K12</Gtype> PGCGROWTHCONDITIONS
108 + genotype/variation: <Gtype>fur-8myc</Gtype> PGCGROWTHCONDITIONS
109 + genotype/variation: <Gtype>lacking the small RNA RyhB</Gtype> PGCGROWTHCONDITIONS
110 + genotype/variation: <Gtype>lacking the transcription factor Fur and the small RNA RyhB</Gtype> PGCGROWTHCONDITIONS
111 + genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype> PGCGROWTHCONDITIONS
112 + genotype/variation: <Gtype>oxyR-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
113 + genotype/variation: <Gtype>soxR-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
114 + genotype/variation: <Gtype>soxS-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
115 + genotype/variation: <Gtype>wild type</Gtype> PGCGROWTHCONDITIONS
116 + genotype/variation: <Gtype>Wild-type</Gtype> PGCGROWTHCONDITIONS
117 + genotype/variation: <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
118 + genotype/variation: <Gtype>Δfur</Gtype> PGCGROWTHCONDITIONS
119 + genoype: <Gtype>dFNR</Gtype> PGCGROWTHCONDITIONS
120 + genoype: <Gtype>Wild-Type</Gtype> PGCGROWTHCONDITIONS
121 + growth condition: <Air>Aerobic</Air> PGCGROWTHCONDITIONS
122 + growth condition: <Air>anaerobic</Air> PGCGROWTHCONDITIONS
123 + growth condition: <Air>Anaerobic</Air> PGCGROWTHCONDITIONS
124 + growth condition: <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
125 + growth condition: <Supp>4 µM IPTG</Supp> PGCGROWTHCONDITIONS
126 + growth condition: <Supp>8 µM IPTG</Supp> PGCGROWTHCONDITIONS
127 + growth condition: <Supp>Adenine</Supp> PGCGROWTHCONDITIONS
128 + growth condition: <Supp>glucose</Supp> PGCGROWTHCONDITIONS
129 + growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp> PGCGROWTHCONDITIONS
130 + growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>1 µM FeSO4</Supp> PGCGROWTHCONDITIONS
131 + growth phase: <Phase>exponential</Phase> PGCGROWTHCONDITIONS
132 + growth phase: <Phase>mid-log</Phase> PGCGROWTHCONDITIONS
133 + growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 PGCGROWTHCONDITIONS
134 + growth phase: <Phase>stationary</Phase> PGCGROWTHCONDITIONS
135 + <Gtype>∆fnr</Gtype> ChIP DNA from <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS
136 + <Gversion>ChIP-Seq</Gversion> PGCGROWTHCONDITIONS
137 + ip antibody: <Anti>affinity purified anti-Fur antibody</Anti> PGCGROWTHCONDITIONS
138 + library strategy: <Technique>ChIP-exo</Technique> PGCGROWTHCONDITIONS
139 + medium: <Med>LB</Med> PGCGROWTHCONDITIONS
140 + medium: <Med>M63</Med> PGCGROWTHCONDITIONS
141 + <Med>M9 minimal complete media</Med>, cultures grown <Air>aerobically</Air> at <Temp>30 degrees C</Temp> in a <Agit>gyratory water bath shaking at 240 rpm</Agit> PGCGROWTHCONDITIONS
142 + <Name>ArgR_Arginine_1</Name> PGCGROWTHCONDITIONS
143 + <Name>ArgR_Arginine_2</Name> PGCGROWTHCONDITIONS
144 + <Name>ArgR_NH4Cl_1</Name> PGCGROWTHCONDITIONS
145 + <Name>ArgR_NH4Cl_2</Name> PGCGROWTHCONDITIONS
146 + <Name>ChIP-exo GadE pH5.5 1</Name> PGCGROWTHCONDITIONS
147 + <Name>ChIP-exo GadE pH5.5 2</Name> PGCGROWTHCONDITIONS
148 + <Name>ChIP-exo GadW pH5.5 1</Name> PGCGROWTHCONDITIONS
149 + <Name>ChIP-exo GadW pH5.5 2</Name> PGCGROWTHCONDITIONS
150 + <Name>ChIP-exo GadX pH5.5 1</Name> PGCGROWTHCONDITIONS
151 + <Name>ChIP-exo GadX pH5.5 2</Name> PGCGROWTHCONDITIONS
152 + <Name>ChIP-exo RpoS pH5.5 1</Name> PGCGROWTHCONDITIONS
153 + <Name>ChIP-exo RpoS pH5.5 2</Name> PGCGROWTHCONDITIONS
154 + <Name>Cra acetate 1</Name> PGCGROWTHCONDITIONS
155 + <Name>Cra acetate 2</Name> PGCGROWTHCONDITIONS
156 + <Name>Cra fructose 1</Name> PGCGROWTHCONDITIONS
157 + <Name>Cra fructose 2</Name> PGCGROWTHCONDITIONS
158 + <Name>Cra glucose 1</Name> PGCGROWTHCONDITIONS
159 + <Name>Cra glucose 2</Name> PGCGROWTHCONDITIONS
160 + <Name>Crosslink</Name> PGCGROWTHCONDITIONS
161 + <Name>CsiR_ChIPSeq</Name> PGCGROWTHCONDITIONS
162 + <Name>CsiR_RNASeq</Name> PGCGROWTHCONDITIONS
163 + <Name>EC18n122 RpoH 10 min Time course 4</Name> PGCGROWTHCONDITIONS
164 + <Name>EC18n167 RpoH 0 min Time course 2</Name> PGCGROWTHCONDITIONS
165 + <Name>EC18n168 RpoH 2.5 min Time course 2</Name> PGCGROWTHCONDITIONS
166 + <Name>EC18n169 RpoH 5 min Time course 2</Name> PGCGROWTHCONDITIONS
167 + <Name>EC18n170 RpoH 10 min Time course 2</Name> PGCGROWTHCONDITIONS
168 + <Name>EC18n171 RpoH 20 min Time course 2</Name> PGCGROWTHCONDITIONS
169 + <Name>EC18n177 RpoH 0 min Time course 1</Name> PGCGROWTHCONDITIONS
170 + <Name>EC18n178 RpoH 2.5 min Time course 1</Name> PGCGROWTHCONDITIONS
171 + <Name>EC18n179 RpoH 5 min Time course 1</Name> PGCGROWTHCONDITIONS
172 + <Name>EC18n180 RpoH 10 min Time course 1</Name> PGCGROWTHCONDITIONS
173 + <Name>EC18n181 RpoH 20 min Time course 1</Name> PGCGROWTHCONDITIONS
174 + <Name>EC18n182 RpoH 0 min Time course 3</Name> PGCGROWTHCONDITIONS
175 + <Name>EC18n183 RpoH 2.5 min Time course 3</Name> PGCGROWTHCONDITIONS
176 + <Name>EC18n184 RpoH 5 min Time course 3</Name> PGCGROWTHCONDITIONS
177 + <Name>EC18n185 RpoH 10 min Time course 3</Name> PGCGROWTHCONDITIONS
178 + <Name>EC18n186 RpoH 20 min Time course 3</Name> PGCGROWTHCONDITIONS
179 + <Name>Ecoli_dFNR_rep1_anaerobic</Name> PGCGROWTHCONDITIONS
180 + <Name>Ecoli_dFNR_rep2_anaerobic</Name> PGCGROWTHCONDITIONS
181 + <Name>Ecoli_wild-type_rep1_anaerobic</Name> PGCGROWTHCONDITIONS
182 + <Name>Ecoli_wild-type_rep2_anaerobic</Name> PGCGROWTHCONDITIONS
183 + <Name>Escherichia coli str. K-12 substr. MG1655</Name> PGCGROWTHCONDITIONS
184 + <Name>FNR - Anaerobic - Affinity Purified - A</Name> PGCGROWTHCONDITIONS
185 + <Name>FNR - Anaerobic - Affinity Purified - B</Name> PGCGROWTHCONDITIONS
186 + <Name>FNR - Anaerobic - A</Name> PGCGROWTHCONDITIONS
187 + <Name>FNR - Anaerobic - B</Name> PGCGROWTHCONDITIONS
188 + <Name>FNR - Anaerobic - C</Name> PGCGROWTHCONDITIONS
189 + <Name>∆fnr - Anaeroibc</Name> PGCGROWTHCONDITIONS
190 + <Name>FNR - ∆hns∆stpA A</Name> PGCGROWTHCONDITIONS
191 + <Name>FNR - ∆hns∆stpA B</Name> PGCGROWTHCONDITIONS
192 + <Name>∆fur Aerobic A</Name> PGCGROWTHCONDITIONS
193 + <Name>∆fur Aerobic B</Name> PGCGROWTHCONDITIONS
194 + <Name>∆fur Anaerobic A</Name> PGCGROWTHCONDITIONS
195 + <Name>∆fur Anaerobic B</Name> PGCGROWTHCONDITIONS
196 + <Name>∆fur Anaerobic [IP vs nput]</Name> PGCGROWTHCONDITIONS
197 + <Name>Fur IP ChIP-Seq Aerobic A</Name> PGCGROWTHCONDITIONS
198 + <Name>Fur IP ChIP-Seq Aerobic B</Name> PGCGROWTHCONDITIONS
199 + <Name>Fur IP ChIP-Seq Aerobic C</Name> PGCGROWTHCONDITIONS
200 + <Name>Fur IP ChIP-Seq Anaerobic A</Name> PGCGROWTHCONDITIONS
201 + <Name>Fur IP ChIP-Seq Anaerobic B</Name> PGCGROWTHCONDITIONS
202 + <Name>Fur IP ChIP-Seq Anaerobic C</Name> PGCGROWTHCONDITIONS
203 + <Name>Fur IP ChIP-Seq Anaerobic, Iron Deficient A</Name> PGCGROWTHCONDITIONS
204 + <Name>Fur IP ChIP-Seq Anaerobic, Iron Deficient B</Name> PGCGROWTHCONDITIONS
205 + <Name>∆fur ∆ryhB Aerobic A</Name> PGCGROWTHCONDITIONS
206 + <Name>∆fur ∆ryhB Aerobic B</Name> PGCGROWTHCONDITIONS
207 + <Name>∆fur ∆ryhB Anaerobic A</Name> PGCGROWTHCONDITIONS
208 + <Name>∆fur ∆ryhB Anaerobic B</Name> PGCGROWTHCONDITIONS
209 + <Name>Fur with DPD 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
210 + <Name>Fur with DPD 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
211 + <Name>Fur with Fe 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
212 + <Name>Fur with Fe 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
213 + <Name>HNS - Aerobic A</Name> PGCGROWTHCONDITIONS
214 + <Name>HNS - Aerobic B</Name> PGCGROWTHCONDITIONS
215 + <Name>HNS - Anaerobic A</Name> PGCGROWTHCONDITIONS
216 + <Name>HNS - Anaerobic B</Name> PGCGROWTHCONDITIONS
217 + <Name>IHF - Anaerobic A</Name> PGCGROWTHCONDITIONS
218 + <Name>IHF - Anaerobic B</Name> PGCGROWTHCONDITIONS
219 + <Name>Input ChIP-Seq</Name> PGCGROWTHCONDITIONS
220 + <Name>LB 0.4 B1 TEX neg L1 GA</Name> PGCGROWTHCONDITIONS
221 + <Name>LB 0.4 B1 TEX pos L1 GA</Name> PGCGROWTHCONDITIONS
222 + <Name>LB 0.4 B2 TEX neg L1 HS1</Name> PGCGROWTHCONDITIONS
223 + <Name>LB 0.4 B2 TEX neg L1 HS2</Name> PGCGROWTHCONDITIONS
224 + <Name>LB 0.4 B2 TEX pos L1 HS1</Name> PGCGROWTHCONDITIONS
225 + <Name>LB 0.4 B2 TEX pos L1 HS2</Name> PGCGROWTHCONDITIONS
226 + <Name>LB 2.0 B1 TEX neg L1 GA</Name> PGCGROWTHCONDITIONS
227 + <Name>LB 2.0 B1 TEX neg L2 HS2</Name> PGCGROWTHCONDITIONS
228 + <Name>LB 2.0 B1 TEX pos L1 GA</Name> PGCGROWTHCONDITIONS
229 + <Name>LB 2.0 B1 TEX pos L2 HS2</Name> PGCGROWTHCONDITIONS
230 + <Name>LB 2.0 B2 TEX neg L1 HS1</Name> PGCGROWTHCONDITIONS
231 + <Name>LB 2.0 B2 TEX neg L1 HS2</Name> PGCGROWTHCONDITIONS
232 + <Name>LB 2.0 B2 TEX neg L2 HS2</Name> PGCGROWTHCONDITIONS
233 + <Name>LB 2.0 B2 TEX pos L1 HS1</Name> PGCGROWTHCONDITIONS
234 + <Name>LB 2.0 B2 TEX pos L1 HS2</Name> PGCGROWTHCONDITIONS
235 + <Name>LB 2.0 B2 TEX pos L2 HS2</Name> PGCGROWTHCONDITIONS
236 + <Name>Lrp_Leu_1</Name> PGCGROWTHCONDITIONS
237 + <Name>Lrp_Leu_2</Name> PGCGROWTHCONDITIONS
238 + <Name>Lrp_Leu_3</Name> PGCGROWTHCONDITIONS
239 + <Name>Lrp_NH4Cl_1</Name> PGCGROWTHCONDITIONS
240 + <Name>Lrp_NH4Cl_2</Name> PGCGROWTHCONDITIONS
241 + <Name>Lrp_NH4Cl_3</Name> PGCGROWTHCONDITIONS
242 + <Name>M63 0.4 B1 TEX neg L1 GA</Name> PGCGROWTHCONDITIONS
243 + <Name>M63 0.4 B1 TEX pos L1 GA</Name> PGCGROWTHCONDITIONS
244 + <Name>M63 0.4 B2 TEX neg L1 HS1</Name> PGCGROWTHCONDITIONS
245 + <Name>M63 0.4 B2 TEX neg L1 HS2</Name> PGCGROWTHCONDITIONS
246 + <Name>M63 0.4 B2 TEX pos L1 HS1</Name> PGCGROWTHCONDITIONS
247 + <Name>M63 0.4 B2 TEX pos L1 HS2</Name> PGCGROWTHCONDITIONS
248 + <Name>Nac_ChIPSeq</Name> PGCGROWTHCONDITIONS
249 + <Name>Nac_RNASeq</Name> PGCGROWTHCONDITIONS
250 + <Name>NsrR_Flagtag_rep1</Name> PGCGROWTHCONDITIONS
251 + <Name>NsrR_Flagtag_rep2</Name> PGCGROWTHCONDITIONS
252 + <Name>NsrR_Flagtag_rep3</Name> PGCGROWTHCONDITIONS
253 + <Name>NtrC_ChIPSeq</Name> PGCGROWTHCONDITIONS
254 + <Name>OmpR_ChIPSeq</Name> PGCGROWTHCONDITIONS
255 + <Name>OmpR NaCl 1</Name> PGCGROWTHCONDITIONS
256 + <Name>OmpR NaCl 2</Name> PGCGROWTHCONDITIONS
257 + <Name>OxyR PQ 1</Name> PGCGROWTHCONDITIONS
258 + <Name>OxyR PQ 2</Name> PGCGROWTHCONDITIONS
259 + <Name>pT7_ChIPSeq_1</Name> PGCGROWTHCONDITIONS
260 + <Name>pT7_ChIPSeq_2</Name> PGCGROWTHCONDITIONS
261 + <Name>Ptac::fnr - A - 16 µM IPTG</Name> PGCGROWTHCONDITIONS
262 + <Name>Ptac::fnr - A - 4 µM IPTG</Name> PGCGROWTHCONDITIONS
263 + <Name>Ptac::fnr - A - 8 µM IPTG</Name> PGCGROWTHCONDITIONS
264 + <Name>Ptac::fnr - B - 16 µM IPTG</Name> PGCGROWTHCONDITIONS
265 + <Name>Ptac::fnr - B - 4 µM IPTG</Name> PGCGROWTHCONDITIONS
266 + <Name>Ptac::fnr - B - 8 µM IPTG</Name> PGCGROWTHCONDITIONS
267 + <Name>Ptac::fnr - C - 16 µM IPTG</Name> PGCGROWTHCONDITIONS
268 + <Name>PurR_Adenine_1</Name> PGCGROWTHCONDITIONS
269 + <Name>PurR_Adenine_2</Name> PGCGROWTHCONDITIONS
270 + <Name>PurR_glucose_1</Name> PGCGROWTHCONDITIONS
271 + <Name>PurR_glucose_2</Name> PGCGROWTHCONDITIONS
272 + <Name>RNAP old rep1</Name> PGCGROWTHCONDITIONS
273 + <Name>RNAP old rep2</Name> PGCGROWTHCONDITIONS
274 + <Name>RpoB ∆cra 1</Name> PGCGROWTHCONDITIONS
275 + <Name>RpoB ∆cra 2</Name> PGCGROWTHCONDITIONS
276 + <Name>RpoB ∆crp 1</Name> PGCGROWTHCONDITIONS
277 + <Name>RpoB ∆crp 2</Name> PGCGROWTHCONDITIONS
278 + <Name>RpoB with DPD 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
279 + <Name>RpoB with DPD 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
280 + <Name>RpoB with DPD and rifampicin 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
281 + <Name>RpoB with DPD and rifampicin 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
282 + <Name>RpoB with Fe 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
283 + <Name>RpoB with Fe 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
284 + <Name>RpoB with Fe and rifampicin 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
285 + <Name>RpoB with Fe and rifampicin 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
286 + <Name>RpoB WT 1</Name> PGCGROWTHCONDITIONS
287 + <Name>RpoB WT 2</Name> PGCGROWTHCONDITIONS
288 + <Name>RpoH induced (0 min)</Name> PGCGROWTHCONDITIONS
289 + <Name>RpoH induced (10 min)</Name> PGCGROWTHCONDITIONS
290 + <Name>RpoH induced (20 min)</Name> PGCGROWTHCONDITIONS
291 + <Name>RpoH induced (2.5 min)</Name> PGCGROWTHCONDITIONS
292 + <Name>RpoH induced (5 min)</Name> PGCGROWTHCONDITIONS
293 + <Name>∆ryhB Aerobic</Name> PGCGROWTHCONDITIONS
294 + <Name>∆ryhB Anaerobic</Name> PGCGROWTHCONDITIONS
295 + <Name>SeqA new deltaSeqA</Name> PGCGROWTHCONDITIONS
296 + <Name>SeqA new rep1</Name> PGCGROWTHCONDITIONS
297 + <Name>SeqA new rep2</Name> PGCGROWTHCONDITIONS
298 + <Name>SeqA old deltaSeqA</Name> PGCGROWTHCONDITIONS
299 + <Name>SeqA old rep1</Name> PGCGROWTHCONDITIONS
300 + <Name>SeqA old rep2</Name> PGCGROWTHCONDITIONS
301 + <Name>SoxR PQ 1</Name> PGCGROWTHCONDITIONS
302 + <Name>SoxR PQ 2</Name> PGCGROWTHCONDITIONS
303 + <Name>SoxS PQ 1</Name> PGCGROWTHCONDITIONS
304 + <Name>SoxS PQ 2</Name> PGCGROWTHCONDITIONS
305 + <Name>ß - Aerobic - A</Name> PGCGROWTHCONDITIONS
306 + <Name>ß - Aerobic - B</Name> PGCGROWTHCONDITIONS
307 + <Name>ß - Anaerobic - A</Name> PGCGROWTHCONDITIONS
308 + <Name>ß - Anaerobic - B</Name> PGCGROWTHCONDITIONS
309 + <Name>TrpR_glucose</Name> PGCGROWTHCONDITIONS
310 + <Name>TrpR_Trp</Name> PGCGROWTHCONDITIONS
311 + <Name>Wild-type Aerobic A</Name> PGCGROWTHCONDITIONS
312 + <Name>Wild-type Aerobic B</Name> PGCGROWTHCONDITIONS
313 + <Name>Wild-type Anaerobic A</Name> PGCGROWTHCONDITIONS
314 + <Name>Wild-type Anaerobic B</Name> PGCGROWTHCONDITIONS
315 + <Name>Wild type control (0 min)</Name> PGCGROWTHCONDITIONS
316 + <Name>Wild type control (10 min)</Name> PGCGROWTHCONDITIONS
317 + <Name>Wild type control (20 min)</Name> PGCGROWTHCONDITIONS
318 + <Name>Wild type control (2.5 min)</Name> PGCGROWTHCONDITIONS
319 + <Name>Wild type control (5 min)</Name> PGCGROWTHCONDITIONS
320 + <Name>WT acetate 1</Name> PGCGROWTHCONDITIONS
321 + <Name>WT acetate 2</Name> PGCGROWTHCONDITIONS
322 + <Name>WT_ChIPSeq_1</Name> PGCGROWTHCONDITIONS
323 + <Name>WT_ChIPSeq_2</Name> PGCGROWTHCONDITIONS
324 + <Name>WT fructose 1</Name> PGCGROWTHCONDITIONS
325 + <Name>WT fructose 2</Name> PGCGROWTHCONDITIONS
326 + <Name>WT glucose 1</Name> PGCGROWTHCONDITIONS
327 + <Name>WT glucose 2</Name> PGCGROWTHCONDITIONS
328 + <Name>WT NaCl 1</Name> PGCGROWTHCONDITIONS
329 + <Name>WT NaCl 2</Name> PGCGROWTHCONDITIONS
330 + <Name>WT pH5.5 1</Name> PGCGROWTHCONDITIONS
331 + <Name>WT pH5.5 2</Name> PGCGROWTHCONDITIONS
332 + <Name>WT PQ 1</Name> PGCGROWTHCONDITIONS
333 + <Name>WT PQ 2</Name> PGCGROWTHCONDITIONS
334 + <Name>WT_RNASeq</Name> PGCGROWTHCONDITIONS
335 + <Name>WT with DPD 1 (RNA-seq)</Name> PGCGROWTHCONDITIONS
336 + <Name>WT with DPD 2 (RNA-seq)</Name> PGCGROWTHCONDITIONS
337 + <Name>WT with Fe 1 (RNA-seq)</Name> PGCGROWTHCONDITIONS
338 + <Name>WT with Fe 2 (RNA-seq)</Name> PGCGROWTHCONDITIONS
339 + <Name>Δcra acetate 1</Name> PGCGROWTHCONDITIONS
340 + <Name>Δcra acetate 2</Name> PGCGROWTHCONDITIONS
341 + <Name>Δcra fructose 1</Name> PGCGROWTHCONDITIONS
342 + <Name>Δcra fructose 2</Name> PGCGROWTHCONDITIONS
343 + <Name>Δcra glucose 1</Name> PGCGROWTHCONDITIONS
344 + <Name>Δcra glucose 2</Name> PGCGROWTHCONDITIONS
345 + <Name>Δfur with DPD 1 (RNA-seq)</Name> PGCGROWTHCONDITIONS
346 + <Name>Δfur with DPD 2 (RNA-seq)</Name> PGCGROWTHCONDITIONS
347 + <Name>Δfur with Fe 1 (RNA-seq)</Name> PGCGROWTHCONDITIONS
348 + <Name>Δfur with Fe 2 (RNA-seq)</Name> PGCGROWTHCONDITIONS
349 + <Name>ΔgadE pH5.5 1</Name> PGCGROWTHCONDITIONS
350 + <Name>ΔgadE pH5.5 2</Name> PGCGROWTHCONDITIONS
351 + <Name>ΔgadW pH5.5 1</Name> PGCGROWTHCONDITIONS
352 + <Name>ΔgadW pH5.5 2</Name> PGCGROWTHCONDITIONS
353 + <Name>ΔgadX pH5.5 1</Name> PGCGROWTHCONDITIONS
354 + <Name>ΔgadX pH5.5 2</Name> PGCGROWTHCONDITIONS
355 + <Name>ΔompR NaCl 1</Name> PGCGROWTHCONDITIONS
356 + <Name>ΔompR NaCl 2</Name> PGCGROWTHCONDITIONS
357 + <Name>ΔoxyR PQ 1</Name> PGCGROWTHCONDITIONS
358 + <Name>ΔoxyR PQ 2</Name> PGCGROWTHCONDITIONS
359 + <Name>ΔsoxR PQ 1</Name> PGCGROWTHCONDITIONS
360 + <Name>ΔsoxR PQ 2</Name> PGCGROWTHCONDITIONS
361 + <Name>ΔsoxS PQ 1</Name> PGCGROWTHCONDITIONS
362 + <Name>ΔsoxS PQ 2</Name> PGCGROWTHCONDITIONS
363 + <Name>σ32 30°C rep1</Name> PGCGROWTHCONDITIONS
364 + <Name>σ32 30°C rep2</Name> PGCGROWTHCONDITIONS
365 + <Name>σ32 30°C short RNase</Name> PGCGROWTHCONDITIONS
366 + <Name>σ32 43°C rep1</Name> PGCGROWTHCONDITIONS
367 + <Name>σ32 43°C rep2</Name> PGCGROWTHCONDITIONS
368 + <Name>σ32 43°C short RNase</Name> PGCGROWTHCONDITIONS
369 + <Name>σ32 ChIP DNA, control</Name> PGCGROWTHCONDITIONS
370 + <Name>σ32 ChIP DNA, heat</Name> PGCGROWTHCONDITIONS
371 + <Orgn>Escherichia coli K-12</Orgn> PGCGROWTHCONDITIONS
372 + <Orgn>Escherichia coli</Orgn> PGCGROWTHCONDITIONS
373 + <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655star</Substrain> PGCGROWTHCONDITIONS
374 + <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain> PGCGROWTHCONDITIONS
375 + <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn> PGCGROWTHCONDITIONS
376 + <Orgn>Escherichia coli str. K-12 substr. MG1655star</Orgn> PGCGROWTHCONDITIONS
377 + Resulting reads were aligned to the published E. coli K-12 MG1655 genome (<Gversion>U00096.2</Gversion>) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File). Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis. For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome. Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis. For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb. Per-gene tag density was normalized using quantile normalization (Supplemental Files). The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle &amp; Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011). PGCGROWTHCONDITIONS
378 + Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S PGCGROWTHCONDITIONS
379 + Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB. PGCGROWTHCONDITIONS
380 + strain: <Gtype>∆hns/∆stpA</Gtype> PGCGROWTHCONDITIONS
381 + strain: <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS
382 + strain: <Gtype>PK8263</Gtype> PGCGROWTHCONDITIONS
383 + strain: MG1655 K-12 <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
384 + strain: <Orgn>K-12 MG1655</Orgn> PGCGROWTHCONDITIONS
385 + strain: <Orgn>MG1655</Orgn> PGCGROWTHCONDITIONS
386 + strain: <Strain>K-12</Strain> PGCGROWTHCONDITIONS
387 + <Substrain>MG1655</Substrain> <Gtype>PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)</Gtype> PGCGROWTHCONDITIONS
388 + <Substrain>MG1655</Substrain> <Gtype>PhtpG::lacZ delta lacX74/ptrc99A (control vector)</Gtype> PGCGROWTHCONDITIONS
389 + <Supp>acetate</Supp> PGCGROWTHCONDITIONS
390 + <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. PGCGROWTHCONDITIONS
391 + <Technique>ChIP-Seq</Technique> PGCGROWTHCONDITIONS
392 + <Technique>RNA-Seq</Technique> PGCGROWTHCONDITIONS
393 + The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh M9 medium containing 2 g/L glucose in either the presence or <Supp>absence of 1 g/L arginine</Supp> and continued to culture at 37°C until reaching an appropriate cell density (OD600 ≈ 0.5). PGCGROWTHCONDITIONS
394 + The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh <Med>M9 medium</Med> containing <Supp>2 g/L glucose</Supp> in either the <Supp>presence or absence of 1 g/L arginine</Supp> and continued to culture at <Temp>37°C</Temp> until reaching an appropriate cell density (<OD>OD600 ≈ 0.5</OD>). PGCGROWTHCONDITIONS
395 + To harvest total RNA samples, overnight cultures of <Gtype>wild type</Gtype> MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to <OD>OD600 of 2.0</OD> a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS
396 + To harvest total RNA samples, overnight cultures of <Gtype>wild type</Gtype> MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to <OD>OD600 of ~0.4</OD> a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS
397 + To harvest total RNA samples, overnight cultures of <Gtype>wild type</Gtype> MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or <Med>M63 minimal glucose</Med> medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an <OD>OD600 of ~0.4</OD> for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS
398 + treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp> PGCGROWTHCONDITIONS
399 + treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp> PGCGROWTHCONDITIONS
400 + treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>10 mM leucine</Supp>. PGCGROWTHCONDITIONS
401 + treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>20 mg/L tryptophan</Supp>. PGCGROWTHCONDITIONS
402 + treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>10 mM leucine</Supp>. PGCGROWTHCONDITIONS
403 + treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>20 mg/L tryptophan</Supp>. PGCGROWTHCONDITIONS
404 + treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>1g/L arginine</Supp>. PGCGROWTHCONDITIONS
405 + treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>2g/L glutamine</Supp>. PGCGROWTHCONDITIONS
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