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

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Estefani Gaytan Nunez
5cea8340 1 parent d7b7af1d

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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 -from optparse import OptionParser
3 -import re
4 -import os
5 -import random
6 -
7 -
8 -# Objective
9 -# Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging
10 -# make data sets using only sentences with at least one true-tag
11 -#
12 -# Input parameters
13 -# --inputPath=PATH Path of inputfile
14 -# --outputPath=PATH Path to place output files
15 -# --trainingFile=testFile Output training data set
16 -# --testFile=testFile Output test data set
17 -#
18 -# Output
19 -# training and test data set
20 -#
21 -# Examples
22 -# python label-split_training_test_v2.py
23 -# --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/
24 -# --inputFile sentences.tsv_pakal_.conll
25 -# --trainingFile training-data-set-70.txt
26 -# --testFile test-data-set-30.txt
27 -# --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
28 -#
29 -#
30 -# python label-split_training_test_v2.py --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/ --inputFile raw-metadata-senteneces.txt.conll --trainingFile training-data-set-70_v2.txt --testFile test-data-set-30_v2.txt --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
31 -
32 -
33 -##########################################
34 -# MAIN PROGRAM #
35 -##########################################
36 -
37 -if __name__ == "__main__":
38 - # Defining parameters
39 - parser = OptionParser()
40 - parser.add_option("--inputPath", dest="inputPath",
41 - help="Path of output from CoreNLP", metavar="PATH")
42 - parser.add_option("--outputPath", dest="outputPath",
43 - help="Output path to place output files",
44 - metavar="PATH")
45 - parser.add_option("--inputFile", dest="inputFile",
46 - help="File with CoreNLP-tagging sentences", metavar="FILE")
47 - parser.add_option("--trainingFile", dest="trainingFile",
48 - help="File with training data set", metavar="FILE")
49 - parser.add_option("--testFile", dest="testFile",
50 - help="File with test data set", metavar="FILE")
51 -
52 - (options, args) = parser.parse_args()
53 - if len(args) > 0:
54 - parser.error("Any parameter given.")
55 - sys.exit(1)
56 -
57 - print('-------------------------------- PARAMETERS --------------------------------')
58 - print("Path of CoreNLP output: " + options.inputPath)
59 - print("File with CoreNLP-tagging sentences: " + str(options.inputFile))
60 - print("Path of training data set: " + options.outputPath)
61 - print("File with training data set: " + str(options.trainingFile))
62 - print("Path of test data set: " + options.outputPath)
63 - print("File with test data set: " + str(options.testFile))
64 - print('-------------------------------- PROCESSING --------------------------------')
65 - ## begin of tagging
66 - in_labels = {
67 - '<Gtype>': 'Gtype',
68 - '<Gversion>': 'Gversion',
69 - '<Med>': 'Med',
70 - '<Phase>': 'Phase',
71 - '<Supp>': 'Supp',
72 - '<Technique>': 'Technique',
73 - '<Temp>': 'Temp',
74 - '<OD>': 'OD',
75 - '<Anti>': 'Anti'
76 - }
77 - ## End of tagging
78 - out_labels = {
79 - '<Air>': 'O',
80 - '</Air>': 'O',
81 - '</Gtype>': 'O',
82 - '</Gversion>': 'O',
83 - '</Med>': 'O',
84 - '</Phase>': 'O',
85 - '<Sample>': 'O',
86 - '</Sample>': 'O',
87 - '<Serie>': 'O',
88 - '</Serie>': 'O',
89 - '<Strain>': 'O',
90 - '</Strain>': 'O',
91 - '<Substrain>': 'O',
92 - '</Substrain>': 'O',
93 - '</Supp>': 'O',
94 - '</Technique>': 'O',
95 - '</Temp>': 'O',
96 - '</OD>': 'O',
97 - '<Agit>': 'O',
98 - '</Agit>': 'O',
99 - '<Name>': 'O',
100 - '</Name>': 'O',
101 - '<Orgn>': 'O',
102 - '</Orgn>': 'O',
103 - '</Anti>': 'O',
104 - '<Vess>': 'O',
105 - '</Vess>': 'O'}
106 -
107 - # Other label
108 - flag = 'O'
109 - # sentences counter
110 - lista = []
111 - #First sentence
112 - sentence = ''
113 - with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file:
114 - for line in input_file:
115 - if len(line.split('\t')) > 1:
116 - w = line.split('\t')[1]
117 - if w in in_labels or w in out_labels:
118 - #Tagging
119 - if w in in_labels.keys(): flag = in_labels[w]
120 - if w in out_labels: flag = out_labels[w]
121 - else:
122 - if w == "PGCGROWTHCONDITIONS":
123 - words = sentence.split(' ')
124 - #End of sentence
125 - tags = [tag for tag in words if tag.split('|')[-1] in in_labels.values() ]
126 - #At least one true-tag on sentence
127 - if len(tags)> 0:
128 - lista.append(sentence)
129 - #New setence
130 - sentence = ''
131 - else:
132 - sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ')
133 -
134 - print("Number of sentences: " + str( len(lista) ) )
135 -
136 -
137 - # Split 70 30 training and test sentences
138 - trainingIndex = random.sample(range(len(lista)-1), int(len(lista)*.70))
139 - testIndex = [n for n in range(len(lista)-1) if n not in trainingIndex]
140 -
141 - with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile:
142 - Data = [lista[i] for i in trainingIndex]
143 - oFile.write('\n'.join(Data))
144 -
145 - with open(os.path.join(options.outputPath, options.testFile), "w") as oFile:
146 - Data = [lista[i] for i in testIndex]
147 - oFile.write('\n'.join(Data))
148 -
149 - print("==================================END===================================")
1 -#!/bin/python3
2 from optparse import OptionParser 1 from optparse import OptionParser
3 import re 2 import re
4 import os 3 import os
...@@ -7,7 +6,6 @@ import random ...@@ -7,7 +6,6 @@ import random
7 6
8 # Objective 7 # Objective
9 # Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging 8 # Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging
10 -# make data sets using only sentences with at least one true-tag
11 # 9 #
12 # Input parameters 10 # Input parameters
13 # --inputPath=PATH Path of inputfile 11 # --inputPath=PATH Path of inputfile
...@@ -19,15 +17,15 @@ import random ...@@ -19,15 +17,15 @@ import random
19 # training and test data set 17 # training and test data set
20 # 18 #
21 # Examples 19 # Examples
22 -# python label-split_training_test_v2.py 20 +# python label-split_training_test_v1.py
23 -# --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/ 21 +# --inputPath /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/output/
24 -# --inputFile sentences.tsv_pakal_.conll 22 +# --inputFile raw-metadata-senteneces_v2.txt.conll
25 -# --trainingFile training-data-set-70.txt 23 +# --trainingFile training-data-set-70_v4.txt
26 -# --testFile test-data-set-30.txt 24 +# --testFile test-data-set-30_v4.txt
27 -# --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets 25 +# --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets
28 # 26 #
29 # 27 #
30 -# python label-split_training_test_v2.py --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/ --inputFile raw-metadata-senteneces.txt.conll --trainingFile training-data-set-70_v2.txt --testFile test-data-set-30_v2.txt --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets 28 +# python label-split_training_test_v1.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/output/ --inputFile raw-metadata-senteneces_v2.txt.conll --trainingFile training-data-set-70._v4txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets
31 29
32 30
33 ########################################## 31 ##########################################
...@@ -68,49 +66,46 @@ if __name__ == "__main__": ...@@ -68,49 +66,46 @@ if __name__ == "__main__":
68 '<Gversion>': 'Gversion', 66 '<Gversion>': 'Gversion',
69 '<Med>': 'Med', 67 '<Med>': 'Med',
70 '<Phase>': 'Phase', 68 '<Phase>': 'Phase',
69 + '<Substrain>': 'Substrain',
71 '<Supp>': 'Supp', 70 '<Supp>': 'Supp',
71 + '<Strain>': 'Strain',
72 '<Technique>': 'Technique', 72 '<Technique>': 'Technique',
73 '<Temp>': 'Temp', 73 '<Temp>': 'Temp',
74 '<OD>': 'OD', 74 '<OD>': 'OD',
75 '<Anti>': 'Anti', 75 '<Anti>': 'Anti',
76 '<Agit>': 'Agit', 76 '<Agit>': 'Agit',
77 - '<Vess>': 'Vess' 77 + '<Air>': 'Air',
78 + '<Vess>': 'Vess',
79 + '<pH>': 'pH'
78 } 80 }
79 ## End of tagging 81 ## End of tagging
80 out_labels = { 82 out_labels = {
81 - '<Air>': 'O',
82 - '</Air>': 'O',
83 '</Gtype>': 'O', 83 '</Gtype>': 'O',
84 '</Gversion>': 'O', 84 '</Gversion>': 'O',
85 '</Med>': 'O', 85 '</Med>': 'O',
86 '</Phase>': 'O', 86 '</Phase>': 'O',
87 - '<Sample>': 'O',
88 - '</Sample>': 'O',
89 - '<Serie>': 'O',
90 - '</Serie>': 'O',
91 - '<Strain>': 'O',
92 - '</Strain>': 'O',
93 - '<Substrain>': 'O',
94 '</Substrain>': 'O', 87 '</Substrain>': 'O',
95 '</Supp>': 'O', 88 '</Supp>': 'O',
89 + '</Strain>': 'O',
96 '</Technique>': 'O', 90 '</Technique>': 'O',
97 '</Temp>': 'O', 91 '</Temp>': 'O',
98 '</OD>': 'O', 92 '</OD>': 'O',
99 '</Anti>': 'O', 93 '</Anti>': 'O',
100 '</Agit>': 'O', 94 '</Agit>': 'O',
101 - '<Name>': 'O', 95 + '</Air>': 'O',
102 - '</Name>': 'O', 96 + '</Vess>': 'O',
97 + '</pH>': 'O'}
98 + old_labels = {
103 '<Orgn>': 'O', 99 '<Orgn>': 'O',
104 - '</Orgn>': 'O', 100 + '</Orgn>': 'O'
105 - '</Vess>': 'O'} 101 + }
106 102
107 # Other label 103 # Other label
108 flag = 'O' 104 flag = 'O'
109 - # sentences counter
110 - n=0
111 lista = [] 105 lista = []
112 #First sentence 106 #First sentence
113 sentence = '' 107 sentence = ''
108 + n = 0
114 with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file: 109 with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file:
115 for line in input_file: 110 for line in input_file:
116 if len(line.split('\t')) > 1: 111 if len(line.split('\t')) > 1:
...@@ -121,24 +116,28 @@ if __name__ == "__main__": ...@@ -121,24 +116,28 @@ if __name__ == "__main__":
121 if w in out_labels: flag = out_labels[w] 116 if w in out_labels: flag = out_labels[w]
122 else: 117 else:
123 if w == "PGCGROWTHCONDITIONS": 118 if w == "PGCGROWTHCONDITIONS":
119 + n=n+1
124 words = sentence.split(' ') 120 words = sentence.split(' ')
125 - tags = [tag for tag in words if word.split('|')[-1] in in_labels.values() ] 121 + #End of sentence
122 + tags = [tag for tag in words if tag.split('|')[-1] in in_labels.values() ]
126 #At least one true-tag on sentence 123 #At least one true-tag on sentence
127 if len(tags)> 0: 124 if len(tags)> 0:
128 lista.append(sentence) 125 lista.append(sentence)
129 #New setence 126 #New setence
130 sentence = '' 127 sentence = ''
131 - n=n+1 128 + elif w not in old_labels.keys():
132 - else:
133 #Building and save tagging sentence 129 #Building and save tagging sentence
134 sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ') 130 sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ')
135 131
136 - print("Number of sentences: " + str(n) + str(len(lista)+1)) 132 + print("Number of sentences with at least one tag: " + str(len(lista)))
133 + print("Number of sentences from CoreNLP: " + str(n))
137 134
138 135
139 # Split 70 30 training and test sentences 136 # Split 70 30 training and test sentences
140 - trainingIndex = random.sample(range(len(lista)-1), int(len(lista)*.70)) 137 + trainingIndex = random.sample(range(len(lista)), int(len(lista)*.70))
141 - testIndex = [n for n in range(len(lista)-1) if n not in trainingIndex] 138 + testIndex = [n for n in range(len(lista)) if n not in trainingIndex]
139 + print("Number of sentences for training: " + str(len(trainingIndex)))
140 + print("Number of sentences for test: " + str(len(testIndex)))
142 141
143 with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile: 142 with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile:
144 Data = [lista[i] for i in trainingIndex] 143 Data = [lista[i] for i in trainingIndex]
......
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(['Gtype', 'Gversion', 'Med', 'Phase', 'Supp', 'Technique', 'Temp', 'OD', 'Anti'])
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')
...@@ -32,7 +32,7 @@ from nltk.corpus import stopwords ...@@ -32,7 +32,7 @@ from nltk.corpus import stopwords
32 # --trainingFile File with training data set 32 # --trainingFile File with training data set
33 # --testFile File with test data set 33 # --testFile File with test data set
34 # --outputPath=PATH Output path to place output files 34 # --outputPath=PATH Output path to place output files
35 -# --reportFile Report Fileneme 35 +# --version Version Report
36 36
37 # Output 37 # Output
38 # 1) Best model 38 # 1) Best model
...@@ -43,31 +43,54 @@ from nltk.corpus import stopwords ...@@ -43,31 +43,54 @@ from nltk.corpus import stopwords
43 # --trainingFile training-data-set-70.txt 43 # --trainingFile training-data-set-70.txt
44 # --testFile test-data-set-30.txt 44 # --testFile test-data-set-30.txt
45 # --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/ 45 # --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/
46 -# --reportFile report_1 46 +# --version _v2
47 -# python3.4 training-validation_v5.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/ 47 +# python3 training_validation_v7.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --version _v1
48 48
49 ################################# 49 #################################
50 # FUNCTIONS # 50 # FUNCTIONS #
51 ################################# 51 #################################
52 52
53 def isGreek(word): 53 def isGreek(word):
54 + #al greek letters
54 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', 55 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',
55 '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'] 56 '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']
56 if word in alphabet: 57 if word in alphabet:
57 return True 58 return True
58 else: 59 else:
59 return False 60 return False
61 +
62 +def hNumber(word):
63 + for l in word:
64 + if l.isdigit():
65 + return True
66 + return False
67 +
68 +def symb(word):
69 + n=0
70 + #at least a not alphanumeric character
71 + for l in word:
72 + if l.isdigit(): n = n+1
73 + if l.isalpha(): n = n+1
74 + #Exclude Greek letters
75 + if isGreek(l): n = n+1
76 +
77 + if n<len(word): return True
78 + else: return False
79 +
60 def hUpper(word): 80 def hUpper(word):
81 + #at least an uppers
61 for l in word: 82 for l in word:
62 if l.isupper(): return True 83 if l.isupper(): return True
63 return False 84 return False
64 85
65 def hLower(word): 86 def hLower(word):
87 + #at least a lower
66 for l in word: 88 for l in word:
67 if l.islower(): return True 89 if l.islower(): return True
68 return False 90 return False
69 91
70 def hGreek(word): 92 def hGreek(word):
93 + #at least an greek letter
71 for l in word: 94 for l in word:
72 if isGreek(l): return True 95 if isGreek(l): return True
73 return False 96 return False
...@@ -80,35 +103,20 @@ def word2features(sent, i, S1, S2): ...@@ -80,35 +103,20 @@ def word2features(sent, i, S1, S2):
80 postag = listElem[2] 103 postag = listElem[2]
81 ner = listElem[3] 104 ner = listElem[3]
82 105
106 + #====================== G1 ======================#
107 +
83 features = { 108 features = {
84 #General 109 #General
85 'lemma': lemma, 110 'lemma': lemma,
86 'postag': postag 111 'postag': postag
87 } 112 }
88 113
89 - if S1:
90 - #S1
91 - features['word']: word
92 - features['hUpper']: hUpper(word)
93 - features['hLower']: hUpper(word)
94 - features['hGreek']: hGreek(word)
95 - #features['hAlfNum']: hAlfNum(word)
96 -
97 - if S2:
98 - #S2
99 - features['isUpper']: word.isupper()
100 - features['isLower']: word.isLower()
101 - features['isGreek']: isGreek(word)
102 - features['isNumber']: word.isdigit()
103 -
104 if i > 0: 114 if i > 0:
105 listElem = sent[i - 1].split('|') 115 listElem = sent[i - 1].split('|')
106 - word1 = listElem[0]
107 lemma1 = listElem[1] 116 lemma1 = listElem[1]
108 postag1 = listElem[2] 117 postag1 = listElem[2]
118 +
109 features.update({ 119 features.update({
110 - #Word anterioir
111 - '-1:word': word1,
112 #LemaG posterior 120 #LemaG posterior
113 '-1:lemma': lemma1, 121 '-1:lemma': lemma1,
114 #PostG posterior 122 #PostG posterior
...@@ -117,17 +125,47 @@ def word2features(sent, i, S1, S2): ...@@ -117,17 +125,47 @@ def word2features(sent, i, S1, S2):
117 125
118 if i < len(sent) - 1: 126 if i < len(sent) - 1:
119 listElem = sent[i + 1].split('|') 127 listElem = sent[i + 1].split('|')
120 - word1 = listElem[0]
121 lemma1 = listElem[1] 128 lemma1 = listElem[1]
122 postag1 = listElem[2] 129 postag1 = listElem[2]
130 +
123 features.update({ 131 features.update({
124 - #Word anterioir
125 - '+1:word': word1,
126 #LemaG posterior 132 #LemaG posterior
127 '+1:lemma': lemma1, 133 '+1:lemma': lemma1,
128 #PostG posterior 134 #PostG posterior
129 '+1:postag': postag1, 135 '+1:postag': postag1,
130 }) 136 })
137 +
138 + #====================== S1 ======================#
139 + if S1:
140 + listElem = sent[i - 1].split('|')
141 + lemma1 = listElem[1]
142 + postag1 = listElem[2]
143 +
144 + features['hUpper']: hUpper(word)
145 + features['hLower']: hUpper(word)
146 + features['hGreek']: hGreek(word)
147 + features['symb']: symb(word)
148 + #firstChar
149 + features['lemma1[:1]']: lemma1[:1]
150 + #secondChar
151 + features['postag[:1]']: lemma1[:1]
152 + features['postag[:2]']: lemma1[:2]
153 + features['lemma[:2]']: lemma1[:2]
154 +
155 + #====================== S2 ======================#
156 + if S2:
157 + #S2
158 + features['isUpper']: word.isupper()
159 + features['isLower']: word.isLower()
160 + features['isGreek']: isGreek(word)
161 + features['isNumber']: word.isdigit()
162 +
163 +
164 + '''
165 + #====================== S3 ======================#
166 + if S3:
167 + features['word']: word
168 + '''
131 return features 169 return features
132 170
133 171
...@@ -153,7 +191,7 @@ def print_state_features(state_features, f): ...@@ -153,7 +191,7 @@ def print_state_features(state_features, f):
153 f.write("{:0.6f} {:8} {}\n".format(weight, label, attr.encode("utf-8"))) 191 f.write("{:0.6f} {:8} {}\n".format(weight, label, attr.encode("utf-8")))
154 192
155 193
156 -__author__ = 'CMendezC' 194 +__author__ = 'egaytan'
157 195
158 ########################################## 196 ##########################################
159 # MAIN PROGRAM # 197 # MAIN PROGRAM #
...@@ -177,7 +215,7 @@ if __name__ == "__main__": ...@@ -177,7 +215,7 @@ if __name__ == "__main__":
177 parser.add_option("--excludeSymbols", default=False, 215 parser.add_option("--excludeSymbols", default=False,
178 action="store_true", dest="excludeSymbols", 216 action="store_true", dest="excludeSymbols",
179 help="Exclude punctuation marks") 217 help="Exclude punctuation marks")
180 - parser.add_option("--reportFile", dest="reportFile", 218 + parser.add_option("--version", dest="version",
181 help="Report file", metavar="FILE") 219 help="Report file", metavar="FILE")
182 parser.add_option("--S1", default=False, 220 parser.add_option("--S1", default=False,
183 action="store_true", dest="S1", 221 action="store_true", dest="S1",
...@@ -198,7 +236,7 @@ if __name__ == "__main__": ...@@ -198,7 +236,7 @@ if __name__ == "__main__":
198 print("File with test data set: " + str(options.testFile)) 236 print("File with test data set: " + str(options.testFile))
199 print("Exclude stop words: " + str(options.excludeStopWords)) 237 print("Exclude stop words: " + str(options.excludeStopWords))
200 print("Levels: " + str(options.S1) + " " + str(options.S2)) 238 print("Levels: " + str(options.S1) + " " + str(options.S2))
201 - print("Report file: " + str(options.reportFile)) 239 + print("Report file: " + str(options.version))
202 240
203 241
204 symbols = ['.', ',', ':', ';', '?', '!', '\'', '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{', 242 symbols = ['.', ',', ':', ';', '?', '!', '\'', '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{',
...@@ -254,19 +292,14 @@ if __name__ == "__main__": ...@@ -254,19 +292,14 @@ if __name__ == "__main__":
254 292
255 print("Reading corpus done in: %fs" % (time() - t0)) 293 print("Reading corpus done in: %fs" % (time() - t0))
256 294
257 - if options.S1: S1 = 0 295 + print(sent2features(sentencesTrainingData[0], options.S1, options.S2)[0])
258 - else: S1 = 1 296 + print(sent2features(sentencesTestData[0], options.S1, options.S2)[0])
259 - if options.S2: S2 = 0
260 - else: S2 = 1
261 -
262 - print(sent2features(sentencesTrainingData[0], S1, S2)[0])
263 - print(sent2features(sentencesTestData[0], S1, S2)[0])
264 t0 = time() 297 t0 = time()
265 298
266 - X_train = [sent2features(s, S1, S2) for s in sentencesTrainingData] 299 + X_train = [sent2features(s, options.S1, options.S2) for s in sentencesTrainingData]
267 y_train = [sent2labels(s) for s in sentencesTrainingData] 300 y_train = [sent2labels(s) for s in sentencesTrainingData]
268 301
269 - X_test = [sent2features(s, S1, S2) for s in sentencesTestData] 302 + X_test = [sent2features(s, options.S1, options.S2) for s in sentencesTestData]
270 # print X_test 303 # print X_test
271 y_test = [sent2labels(s) for s in sentencesTestData] 304 y_test = [sent2labels(s) for s in sentencesTestData]
272 305
...@@ -292,7 +325,7 @@ if __name__ == "__main__": ...@@ -292,7 +325,7 @@ if __name__ == "__main__":
292 325
293 # Original: labels = list(crf.classes_) 326 # Original: labels = list(crf.classes_)
294 # Original: labels.remove('O') 327 # Original: labels.remove('O')
295 - labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Supp', 'Technique', 'Temp', 'OD', 'Anti']) 328 + labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Strain', 'Substrain', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Air', 'Vess', 'pH'])
296 329
297 # use the same metric for evaluation 330 # use the same metric for evaluation
298 f1_scorer = make_scorer(metrics.flat_f1_score, 331 f1_scorer = make_scorer(metrics.flat_f1_score,
...@@ -313,7 +346,9 @@ if __name__ == "__main__": ...@@ -313,7 +346,9 @@ if __name__ == "__main__":
313 346
314 # Best hiperparameters 347 # Best hiperparameters
315 # crf = rs.best_estimator_ 348 # crf = rs.best_estimator_
316 - nameReport = options.trainingFile.replace('.txt', str(options.reportFile) + '.txt') 349 +
350 +
351 + nameReport = str(options.S1) + '_S2_' + str(options.S2) + str(options.version) + '.txt'
317 with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="w") as oFile: 352 with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="w") as oFile:
318 oFile.write("********** TRAINING AND TESTING REPORT **********\n") 353 oFile.write("********** TRAINING AND TESTING REPORT **********\n")
319 oFile.write("Training file: " + options.trainingFile + '\n') 354 oFile.write("Training file: " + options.trainingFile + '\n')
...@@ -331,27 +366,13 @@ if __name__ == "__main__": ...@@ -331,27 +366,13 @@ if __name__ == "__main__":
331 # Saving model 366 # Saving model
332 print(" Saving training model...") 367 print(" Saving training model...")
333 t1 = time() 368 t1 = time()
334 - nameModel = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str( 369 + nameModel = 'model_S1_' + str(options.S1) + '_S2_' + str(options.S2) + str(options.version) + '.mod'
335 - options.excludeSymbols) + '.mod')
336 joblib.dump(crf, os.path.join(options.outputPath, "models", nameModel)) 370 joblib.dump(crf, os.path.join(options.outputPath, "models", nameModel))
337 print(" Saving training model done in: %fs" % (time() - t1)) 371 print(" Saving training model done in: %fs" % (time() - t1))
338 372
339 # Evaluation against test data 373 # Evaluation against test data
340 y_pred = crf.predict(X_test) 374 y_pred = crf.predict(X_test)
341 print("*********************************") 375 print("*********************************")
342 - name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
343 - options.excludeSymbols) + '.txt')
344 - with open(os.path.join(options.outputPath, "reports", "y_pred_" + name), "w") as oFile:
345 - for y in y_pred:
346 - oFile.write(str(y) + '\n')
347 -
348 - print("*********************************")
349 - name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
350 - options.excludeSymbols) + '.txt')
351 - with open(os.path.join(options.outputPath, "reports", "y_test_" + name), "w") as oFile:
352 - for y in y_test:
353 - oFile.write(str(y) + '\n')
354 -
355 print("Prediction done in: %fs" % (time() - t0)) 376 print("Prediction done in: %fs" % (time() - t0))
356 377
357 # labels = list(crf.classes_) 378 # labels = list(crf.classes_)
...@@ -387,4 +408,3 @@ if __name__ == "__main__": ...@@ -387,4 +408,3 @@ if __name__ == "__main__":
387 print_state_features(Counter(crf.state_features_).most_common()[-200:], oFile) 408 print_state_features(Counter(crf.state_features_).most_common()[-200:], oFile)
388 oFile.write('\n') 409 oFile.write('\n')
389 410
390 -
......
...@@ -32,23 +32,26 @@ from nltk.corpus import stopwords ...@@ -32,23 +32,26 @@ from nltk.corpus import stopwords
32 # --trainingFile File with training data set 32 # --trainingFile File with training data set
33 # --testFile File with test data set 33 # --testFile File with test data set
34 # --outputPath=PATH Output path to place output files 34 # --outputPath=PATH Output path to place output files
35 +# --version Version Report
35 36
36 # Output 37 # Output
37 # 1) Best model 38 # 1) Best model
38 39
39 # Examples 40 # Examples
40 -# python training_validation_v3.py 41 +# python training_validation_v5.py
41 # --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets 42 # --inputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
42 # --trainingFile training-data-set-70.txt 43 # --trainingFile training-data-set-70.txt
43 # --testFile test-data-set-30.txt 44 # --testFile test-data-set-30.txt
44 # --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/ 45 # --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 +# --version _v2
47 +# python3 training_validation_v7.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --version _v1
46 48
47 ################################# 49 #################################
48 # FUNCTIONS # 50 # FUNCTIONS #
49 ################################# 51 #################################
50 52
51 def isGreek(word): 53 def isGreek(word):
54 + #al greek letters
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', 55 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'] 56 '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: 57 if word in alphabet:
...@@ -56,106 +59,118 @@ def isGreek(word): ...@@ -56,106 +59,118 @@ def isGreek(word):
56 else: 59 else:
57 return False 60 return False
58 61
59 -def word2features(sent, i): 62 +def hNumber(word):
63 + for l in word:
64 + if l.isdigit():
65 + return True
66 + return False
67 +
68 +def symb(word):
69 + n=0
70 + #at least a not alphanumeric character
71 + for l in word:
72 + if l.isdigit(): n = n+1
73 + if l.isalpha(): n = n+1
74 + #Exclude Greek letters
75 + if isGreek(l): n = n+1
76 +
77 + if n<len(word): return True
78 + else: return False
79 +
80 +def hUpper(word):
81 + #at least an uppers
82 + for l in word:
83 + if l.isupper(): return True
84 + return False
85 +
86 +def hLower(word):
87 + #at least a lower
88 + for l in word:
89 + if l.islower(): return True
90 + return False
91 +
92 +def hGreek(word):
93 + #at least an greek letter
94 + for l in word:
95 + if isGreek(l): return True
96 + return False
97 +
98 +
99 +def word2features(sent, i, S1, S2):
60 listElem = sent[i].split('|') 100 listElem = sent[i].split('|')
61 word = listElem[0] 101 word = listElem[0]
62 lemma = listElem[1] 102 lemma = listElem[1]
63 postag = listElem[2] 103 postag = listElem[2]
104 + ner = listElem[3]
105 +
106 + #====================== G1 ======================#
64 107
65 features = { 108 features = {
66 - # Suffixes 109 + #General
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, 110 'lemma': lemma,
73 - #'postag': postag, 111 + '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 } 112 }
113 +
89 if i > 0: 114 if i > 0:
90 listElem = sent[i - 1].split('|') 115 listElem = sent[i - 1].split('|')
91 - word1 = listElem[0]
92 lemma1 = listElem[1] 116 lemma1 = listElem[1]
93 postag1 = listElem[2] 117 postag1 = listElem[2]
118 +
94 features.update({ 119 features.update({
95 - #'-1:word': word1, 120 + #LemaG posterior
96 '-1:lemma': lemma1, 121 '-1:lemma': lemma1,
122 + #PostG posterior
97 '-1:postag': postag1, 123 '-1:postag': postag1,
98 }) 124 })
99 125
100 if i < len(sent) - 1: 126 if i < len(sent) - 1:
101 listElem = sent[i + 1].split('|') 127 listElem = sent[i + 1].split('|')
102 - #word1 = listElem[0]
103 lemma1 = listElem[1] 128 lemma1 = listElem[1]
104 postag1 = listElem[2] 129 postag1 = listElem[2]
130 +
105 features.update({ 131 features.update({
106 - #'+1:word': word1, 132 + #LemaG posterior
107 '+1:lemma': lemma1, 133 '+1:lemma': lemma1,
134 + #PostG posterior
108 '+1:postag': postag1, 135 '+1:postag': postag1,
109 }) 136 })
110 137
111 - ''' 138 + #====================== S1 ======================#
112 - if i > 1: 139 + if S1:
113 - listElem = sent[i - 2].split('|') 140 + listElem = sent[i - 1].split('|')
114 - word2 = listElem[0] 141 + lemma1 = listElem[1]
115 - lemma2 = listElem[1] 142 + postag1 = listElem[2]
116 - postag2 = listElem[2]
117 - features.update({
118 - '-2:word': word2,
119 - '-2:lemma': lemma2,
120 - })
121 143
122 - if i < len(sent) - 2: 144 + features['hUpper']: hUpper(word)
123 - listElem = sent[i + 2].split('|') 145 + features['hLower']: hUpper(word)
124 - word2 = listElem[0] 146 + features['hGreek']: hGreek(word)
125 - lemma2 = listElem[1] 147 + features['symb']: symb(word)
126 - postag2 = listElem[2] 148 + #firstChar
127 - features.update({ 149 + features['lemma1[:1]']: lemma1[:1]
128 - '+2:word': word2, 150 + #secondChar
129 - '+2:lemma': lemma2, 151 + features['postag[:1]']: lemma1[:1]
130 - }) 152 + features['postag[:2]']: lemma1[:2]
153 + features['lemma[:2]']: lemma1[:2]
154 +
155 + #====================== S2 ======================#
156 + if S2:
157 + #S2
158 + features['isUpper']: word.isupper()
159 + features['isLower']: word.isLower()
160 + features['isGreek']: isGreek(word)
161 + features['isNumber']: word.isdigit()
131 162
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 - })
143 163
144 - if i < len(sent) - 3: 164 + '''
145 - listElem = sent[i + 3].split('|') 165 + #====================== S3 ======================#
146 - word3 = listElem[0] 166 + if S3:
147 - lemma3 = listElem[1] 167 + features['word']: word
148 - postag3 = listElem[2]
149 - features.update({
150 - '+3:word': word3,
151 - '+3:lemma': lemma3,
152 - })
153 ''' 168 '''
154 return features 169 return features
155 170
156 171
157 -def sent2features(sent): 172 +def sent2features(sent, S1, S2):
158 - return [word2features(sent, i) for i in range(len(sent))] 173 + return [word2features(sent, i, S1, S2) for i in range(len(sent))]
159 174
160 175
161 def sent2labels(sent): 176 def sent2labels(sent):
...@@ -176,7 +191,7 @@ def print_state_features(state_features, f): ...@@ -176,7 +191,7 @@ def print_state_features(state_features, f):
176 f.write("{:0.6f} {:8} {}\n".format(weight, label, attr.encode("utf-8"))) 191 f.write("{:0.6f} {:8} {}\n".format(weight, label, attr.encode("utf-8")))
177 192
178 193
179 -__author__ = 'CMendezC' 194 +__author__ = 'egaytan'
180 195
181 ########################################## 196 ##########################################
182 # MAIN PROGRAM # 197 # MAIN PROGRAM #
...@@ -200,8 +215,14 @@ if __name__ == "__main__": ...@@ -200,8 +215,14 @@ if __name__ == "__main__":
200 parser.add_option("--excludeSymbols", default=False, 215 parser.add_option("--excludeSymbols", default=False,
201 action="store_true", dest="excludeSymbols", 216 action="store_true", dest="excludeSymbols",
202 help="Exclude punctuation marks") 217 help="Exclude punctuation marks")
203 - parser.add_option("--reportFile", dest="reportFile", 218 + parser.add_option("--version", dest="version",
204 help="Report file", metavar="FILE") 219 help="Report file", metavar="FILE")
220 + parser.add_option("--S1", default=False,
221 + action="store_true", dest="S1",
222 + help="Level specificity")
223 + parser.add_option("--S2", default=False,
224 + action="store_true", dest="S2",
225 + help="Level specificity")
205 226
206 (options, args) = parser.parse_args() 227 (options, args) = parser.parse_args()
207 if len(args) > 0: 228 if len(args) > 0:
...@@ -214,11 +235,12 @@ if __name__ == "__main__": ...@@ -214,11 +235,12 @@ if __name__ == "__main__":
214 print("Path of test data set: " + options.inputPath) 235 print("Path of test data set: " + options.inputPath)
215 print("File with test data set: " + str(options.testFile)) 236 print("File with test data set: " + str(options.testFile))
216 print("Exclude stop words: " + str(options.excludeStopWords)) 237 print("Exclude stop words: " + str(options.excludeStopWords))
217 - print("Report file: " + str(options.reportFile)) 238 + print("Levels: " + str(options.S1) + " " + str(options.S2))
239 + print("Report file: " + str(options.version))
240 +
218 241
219 symbols = ['.', ',', ':', ';', '?', '!', '\'', '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{', 242 symbols = ['.', ',', ':', ';', '?', '!', '\'', '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{',
220 '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...'] 243 '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']
221 - #print("Exclude symbols " + str(symbols) + ': ' + str(options.excludeSymbols))
222 print("Exclude symbols: " + str(options.excludeSymbols)) 244 print("Exclude symbols: " + str(options.excludeSymbols))
223 245
224 print('-------------------------------- PROCESSING --------------------------------') 246 print('-------------------------------- PROCESSING --------------------------------')
...@@ -270,14 +292,14 @@ if __name__ == "__main__": ...@@ -270,14 +292,14 @@ if __name__ == "__main__":
270 292
271 print("Reading corpus done in: %fs" % (time() - t0)) 293 print("Reading corpus done in: %fs" % (time() - t0))
272 294
273 - print(sent2features(sentencesTrainingData[0])[0]) 295 + print(sent2features(sentencesTrainingData[0], options.S1, options.S2)[0])
274 - print(sent2features(sentencesTestData[0])[0]) 296 + print(sent2features(sentencesTestData[0], options.S1, options.S2)[0])
275 t0 = time() 297 t0 = time()
276 298
277 - X_train = [sent2features(s) for s in sentencesTrainingData] 299 + X_train = [sent2features(s, options.S1, options.S2) for s in sentencesTrainingData]
278 y_train = [sent2labels(s) for s in sentencesTrainingData] 300 y_train = [sent2labels(s) for s in sentencesTrainingData]
279 301
280 - X_test = [sent2features(s) for s in sentencesTestData] 302 + X_test = [sent2features(s, options.S1, options.S2) for s in sentencesTestData]
281 # print X_test 303 # print X_test
282 y_test = [sent2labels(s) for s in sentencesTestData] 304 y_test = [sent2labels(s) for s in sentencesTestData]
283 305
...@@ -303,7 +325,7 @@ if __name__ == "__main__": ...@@ -303,7 +325,7 @@ if __name__ == "__main__":
303 325
304 # Original: labels = list(crf.classes_) 326 # Original: labels = list(crf.classes_)
305 # Original: labels.remove('O') 327 # Original: labels.remove('O')
306 - labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Supp', 'Technique', 'Temp', 'OD', 'Anti']) 328 + labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Strain', 'Substrain', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Air', 'Vess', 'pH'])
307 329
308 # use the same metric for evaluation 330 # use the same metric for evaluation
309 f1_scorer = make_scorer(metrics.flat_f1_score, 331 f1_scorer = make_scorer(metrics.flat_f1_score,
...@@ -324,8 +346,29 @@ if __name__ == "__main__": ...@@ -324,8 +346,29 @@ if __name__ == "__main__":
324 346
325 # Best hiperparameters 347 # Best hiperparameters
326 # crf = rs.best_estimator_ 348 # crf = rs.best_estimator_
327 - #nameReport = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(options.excludeSymbols) + '.txt') 349 + '''
328 - nameReport = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.reportFile)) 350 + #ROC curve
351 + # predict probabilities
352 + probs = rs.predict_proba(X_test)
353 + # keep probabilities for the positive outcome only
354 + probs = probs[:, 1]
355 + # calculate AUC
356 + auc = roc_auc_score(y_test, probs)
357 +
358 + print('AUC: %.3f' % auc)
359 + # calculate roc curve
360 + print(testy)
361 + print(probs)
362 + fpr, tpr, thresholds = roc_curve(testy, probs)
363 + # plot no skill
364 + pyplot.plot([0, 1], [0, 1], linestyle='--')
365 + # plot the roc curve for the model
366 + pyplot.plot(fpr, tpr, marker='.')
367 + # show the plot
368 + pyplot.show()
369 + '''
370 +
371 + nameReport = str(options.S1) + '_S2_' + str(options.S2) + str(options.version) + '.txt'
329 with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="w") as oFile: 372 with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="w") as oFile:
330 oFile.write("********** TRAINING AND TESTING REPORT **********\n") 373 oFile.write("********** TRAINING AND TESTING REPORT **********\n")
331 oFile.write("Training file: " + options.trainingFile + '\n') 374 oFile.write("Training file: " + options.trainingFile + '\n')
...@@ -343,27 +386,13 @@ if __name__ == "__main__": ...@@ -343,27 +386,13 @@ if __name__ == "__main__":
343 # Saving model 386 # Saving model
344 print(" Saving training model...") 387 print(" Saving training model...")
345 t1 = time() 388 t1 = time()
346 - nameModel = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str( 389 + nameModel = 'model_S1_' + str(options.S1) + '_S2_' + str(options.S2) + str(options.version) + '.mod'
347 - options.excludeSymbols) + '.mod')
348 joblib.dump(crf, os.path.join(options.outputPath, "models", nameModel)) 390 joblib.dump(crf, os.path.join(options.outputPath, "models", nameModel))
349 print(" Saving training model done in: %fs" % (time() - t1)) 391 print(" Saving training model done in: %fs" % (time() - t1))
350 392
351 # Evaluation against test data 393 # Evaluation against test data
352 y_pred = crf.predict(X_test) 394 y_pred = crf.predict(X_test)
353 print("*********************************") 395 print("*********************************")
354 - name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
355 - options.excludeSymbols) + '.txt')
356 - with open(os.path.join(options.outputPath, "reports", "y_pred_" + name), "w") as oFile:
357 - for y in y_pred:
358 - oFile.write(str(y) + '\n')
359 -
360 - print("*********************************")
361 - name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
362 - options.excludeSymbols) + '.txt')
363 - with open(os.path.join(options.outputPath, "reports", "y_test_" + name), "w") as oFile:
364 - for y in y_test:
365 - oFile.write(str(y) + '\n')
366 -
367 print("Prediction done in: %fs" % (time() - t0)) 396 print("Prediction done in: %fs" % (time() - t0))
368 397
369 # labels = list(crf.classes_) 398 # labels = list(crf.classes_)
......
...@@ -3,8 +3,6 @@ Gtype ...@@ -3,8 +3,6 @@ Gtype
3 Gversion 3 Gversion
4 Med 4 Med
5 Phase 5 Phase
6 -Sample
7 -Serie
8 Strain 6 Strain
9 Supp 7 Supp
10 Technique 8 Technique
...@@ -13,4 +11,5 @@ OD ...@@ -13,4 +11,5 @@ OD
13 Anti 11 Anti
14 Agit 12 Agit
15 Vess 13 Vess
16 - 14 +Substrain
15 +pH
......
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 - 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|O water|water|NN|O bath|bath|NN|O shaking|shake|VBG|O at|at|IN|O 240|240|CD|O rpm|rpm|NN|O
1 - agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
2 - antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
3 - antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
4 - carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
5 - 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
6 - 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 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
7 - 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 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
8 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
9 - 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 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
10 - 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 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
11 - 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 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
12 - 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 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
13 - 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 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
14 - 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 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
15 - 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
16 - 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 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
17 - 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 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
18 - genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
19 - genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
20 - genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
21 - genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
22 - genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
23 - genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
24 - genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
25 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
26 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
27 - 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
28 - 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
29 - genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
30 - genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
31 - growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
32 - 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
33 - 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
34 - growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
35 - growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
36 - growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
37 - ∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
38 - 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
39 - 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
40 - strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
41 - acetate|acetate|NN|Supp
42 - 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
43 - 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
44 - 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
45 - 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
46 - 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
47 - 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
...\ No newline at end of file ...\ No newline at end of file
1 + affyexp|affyexp|JJ|O _|_|NN|O delta-fnr|delta-fnr|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 1|1|CD|O .|.|.|O CEL|CEL|NNP|O
2 + affyexp|affyexp|JJ|O _|_|NN|O delta-fnr|delta-fnr|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 2|2|CD|O .|.|.|O CEL|CEL|NNP|O
3 + affyexp|affyexp|JJ|O _|_|NN|O delta-fnr|delta-fnr|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|CD|O 3|3|CD|O .|.|.|O CEL|CEL|NNP|O
4 + affyexp|affyexp|JJ|O _|_|NN|O wt|wt|JJ|Gtype _|_|NN|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 1|1|CD|O .|.|.|O CEL|CEL|NNP|O
5 + affyexp|affyexp|JJ|O _|_|NN|O wt|wt|JJ|Gtype _|_|NN|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|CD|O 3|3|CD|O .|.|.|O CEL|CEL|NNP|O
6 + agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
7 + Anaerobic|anaerobic|JJ|Air cultures|culture|NNS|O
8 + All|all|DT|O strains|strain|NNS|O used|use|VBN|O in|in|IN|O this|this|DT|O study|study|NN|O were|be|VBD|O E.|e.|FW|O coli|coli|FW|O K-12|k-12|NN|O MG1655|mg1655|NN|O and|and|CC|O its|its|PRP$|O derivatives|derivative|NNS|O .|.|.|O The|the|DT|O deletion|deletion|NN|O mutants|mutant|NNS|O -LRB-|-lrb-|-LRB-|O Δfnr|δfnr|NN|O and|and|CC|O ΔarcA|δarca|NN|O -RRB-|-rrb-|-RRB-|O were|be|VBD|O constructed|construct|VBN|O by|by|IN|O a|a|DT|O λ|λ|NN|O red|red|JJ|O and|and|CC|O FLP-mediated|flp-mediated|JJ|O site-specific|site-specific|JJ|O recombination|recombination|NN|O method|method|NN|O .|.|.|O Glycerol|glycerol|NN|O stocks|stock|NNS|O of|of|IN|O E.|e.|FW|O coli|coli|FW|O strains|strain|NNS|O were|be|VBD|O inoculated|inoculate|VBN|O into|into|IN|O M9|m9|NN|O minimal|minimal|JJ|O medium|medium|NN|O containing|contain|VBG|O 0.2|0.2|CD|O %|%|NN|O -LRB-|-lrb-|-LRB-|O w/v|w/v|NN|O -RRB-|-rrb-|-RRB-|O carbon|carbon|NN|O source|source|NN|O -LRB-|-lrb-|-LRB-|O glucose|glucose|NN|O -RRB-|-rrb-|-RRB-|O and|and|CC|O 0.1|0.1|CD|O %|%|NN|O -LRB-|-lrb-|-LRB-|O w/v|w/v|NN|O -RRB-|-rrb-|-RRB-|O nitrogen|nitrogen|NN|O source|source|NN|O -LRB-|-lrb-|-LRB-|O NH4Cl|nh4cl|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O and|and|CC|O cultured|culture|VBN|O overnight|overnight|JJ|O at|at|IN|O 37|37|CD|O °C|°c|NN|O with|with|IN|O constant|constant|JJ|O agitation|agitation|NN|O .|.|.|O The|the|DT|O cultures|culture|NNS|O were|be|VBD|O diluted|dilute|VBN|O 1:100|1:100|CD|O into|into|IN|O fresh|fresh|JJ|O minimal|minimal|JJ|Med medium|medium|NN|Med and|and|CC|O then|then|RB|O cultured|culture|VBN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp to|to|TO|O an|a|DT|O appropriate|appropriate|JJ|O cell|cell|NN|O density|density|NN|O with|with|IN|O constant|constant|JJ|O agitation|agitation|NN|O .|.|.|O For|for|IN|O the|the|DT|O anaerobic|anaerobic|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O minimal|minimal|JJ|O medium|medium|NN|O were|be|VBD|O flushed|flush|VBN|O with|with|IN|O nitrogen|nitrogen|NN|O and|and|CC|O then|then|RB|O continuously|continuously|RB|O monitored|monitor|VBN|O using|use|VBG|O a|a|DT|O polarographic-dissolved|polarographic-dissolved|JJ|O oxygen|oxygen|NN|O probe|probe|NN|O -LRB-|-lrb-|-LRB-|O Cole-Parmer|Cole-Parmer|NNP|O Instruments|Instruments|NNP|O -RRB-|-rrb-|-RRB-|O to|to|TO|O ensure|ensure|VB|O anaerobicity|anaerobicity|NN|O .|.|.|O For|for|IN|O nitrate|nitrate|JJ|O respiration|respiration|NN|O 20|20|CD|Supp mmol|mmol|NN|Supp potassium|potassium|NN|Supp nitrate|nitrate|JJ|Supp was|be|VBD|O added|add|VBN|O .|.|.|O
9 + All|All|NNP|O strains|strain|NNS|O used|use|VBN|O in|in|IN|O this|this|DT|O study|study|NN|O were|be|VBD|O E.|e.|FW|O coli|coli|FW|O K-12|k-12|NN|O MG1655|mg1655|NN|O and|and|CC|O its|its|PRP$|O derivatives|derivative|NNS|O .|.|.|O The|the|DT|O deletion|deletion|NN|O mutants|mutant|NNS|O -LRB-|-lrb-|-LRB-|O Δfnr|δfnr|NN|O and|and|CC|O ΔarcA|δarca|NN|O -RRB-|-rrb-|-RRB-|O were|be|VBD|O constructed|construct|VBN|O by|by|IN|O a|a|DT|O λ|λ|NN|O red|red|JJ|O and|and|CC|O FLP-mediated|flp-mediated|JJ|O site-specific|site-specific|JJ|O recombination|recombination|NN|O method|method|NN|O .|.|.|O Glycerol|glycerol|NN|O stocks|stock|NNS|O of|of|IN|O E.|e.|FW|O coli|coli|FW|O strains|strain|NNS|O were|be|VBD|O inoculated|inoculate|VBN|O into|into|IN|O M9|m9|NN|O minimal|minimal|JJ|O medium|medium|NN|O containing|contain|VBG|O 0.2|0.2|CD|O %|%|NN|O -LRB-|-lrb-|-LRB-|O w/v|w/v|NN|O -RRB-|-rrb-|-RRB-|O carbon|carbon|NN|O source|source|NN|O -LRB-|-lrb-|-LRB-|O glucose|glucose|NN|O -RRB-|-rrb-|-RRB-|O and|and|CC|O 0.1|0.1|CD|O %|%|NN|O -LRB-|-lrb-|-LRB-|O w/v|w/v|NN|O -RRB-|-rrb-|-RRB-|O nitrogen|nitrogen|NN|O source|source|NN|O -LRB-|-lrb-|-LRB-|O NH4Cl|nh4cl|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O and|and|CC|O cultured|culture|VBN|O overnight|overnight|JJ|O at|at|IN|O 37|37|CD|O °C|°c|NN|O with|with|IN|O constant|constant|JJ|O agitation|agitation|NN|O .|.|.|O The|the|DT|O cultures|culture|NNS|O were|be|VBD|O diluted|dilute|VBN|O 1:100|1:100|CD|O into|into|IN|O fresh|fresh|JJ|O minimal|minimal|JJ|Med medium|medium|NN|Med and|and|CC|O then|then|RB|O cultured|culture|VBN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp to|to|TO|O an|a|DT|O appropriate|appropriate|JJ|O cell|cell|NN|O density|density|NN|O with|with|IN|O constant|constant|JJ|O agitation|agitation|NN|O .|.|.|O For|for|IN|O the|the|DT|O anaerobic|anaerobic|JJ|O cultures|culture|NNS|O ,|,|,|O the|the|DT|O minimal|minimal|JJ|O medium|medium|NN|O were|be|VBD|O flushed|flush|VBN|O with|with|IN|O nitrogen|nitrogen|NN|Supp and|and|CC|O then|then|RB|O continuously|continuously|RB|O monitored|monitor|VBN|O using|use|VBG|O a|a|DT|O polarographic-dissolved|polarographic-dissolved|JJ|O oxygen|oxygen|NN|O probe|probe|NN|O -LRB-|-lrb-|-LRB-|O Cole-Parmer|Cole-Parmer|NNP|O Instruments|Instruments|NNP|O -RRB-|-rrb-|-RRB-|O to|to|TO|O ensure|ensure|VB|O anaerobicity|anaerobicity|NN|O .|.|.|O For|for|IN|O nitrate|nitrate|JJ|O respiration|respiration|NN|O 20|20|CD|O mmol|mmol|NN|O potassium|potassium|NN|O nitrate|nitrate|NN|O was|be|VBD|O added|add|VBN|O .|.|.|O
10 + antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
11 + antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
12 + 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
13 + 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
14 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|Air -LRB-|-lrb-|-LRB-|Air 70|70|CD|Air %|%|NN|Air N2|n2|NN|Air ,|,|,|Air 25|25|CD|Air %|%|NN|Air O2|o2|CD|Air ,|,|,|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
15 + 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
16 + 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 anaerobically|anaerobically|RB|Air -LRB-|-lrb-|-LRB-|Air 95|95|CD|Air %|%|NN|Air N2|n2|NN|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
17 + 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 anaerobically|anaerobically|RB|Air -LRB-|-lrb-|-LRB-|Air 95|95|CD|Air %|%|NN|Air N2|n2|NN|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
18 + 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
19 + 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
20 + 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
21 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
22 + chip-ArcA|chip-arca|NN|O _|_|CD|O ArcA8myc|arca8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 3|3|CD|O
23 + chip-Fnr|chip-fnr|JJ|O _|_|NN|O Fnr8myc|fnr8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 2|2|CD|O
24 + CsiR|csir|NN|O _|_|CD|O RNASeq|rnaseq|NN|Technique
25 + 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
26 + 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 aerobically|aerobically|RB|Air 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
27 + 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 aerobically|aerobically|RB|Air 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
28 + 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 aerobically|aerobically|RB|Air 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
29 + 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
30 + 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
31 + 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 anaerobically|anaerobically|RB|Air 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
32 + 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 anaerobically|anaerobically|RB|Air 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
33 + 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
34 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O A|a|NN|O
35 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
36 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O C|c|NN|O
37 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|Anaerobic|NNP|Air A|A|NNP|O
38 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|anaerobic|JJ|Air B|b|NN|O
39 + Fur|Fur|NNP|O with|with|IN|O Fe|Fe|NNP|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
40 + Fur|Fur|NNP|O with|with|IN|O Fe|Fe|NNP|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
41 + genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
42 + genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
43 + genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
44 + genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
45 + genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
46 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
47 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
48 + 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
49 + 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
50 + 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
51 + genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
52 + genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
53 + genotype/variation|genotype/variation|NN|O :|:|:|O harboring|harbor|VBG|O ArcA-8myc|arca-8myc|NN|Gtype
54 + genotype/variation|genotype/variation|NN|O :|:|:|O harboring|harbor|VBG|O Fnr-8myc|fnr-8myc|JJ|Gtype
55 + genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
56 + growth|growth|NN|O condition|condition|NN|O :|:|:|O Aerobic|Aerobic|NNP|Air
57 + growth|growth|NN|O condition|condition|NN|O :|:|:|O anaerobic|anaerobic|JJ|Air
58 + growth|growth|NN|O condition|condition|NN|O :|:|:|O Anaerobic|anaerobic|JJ|Air
59 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
60 + growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
61 + growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
62 + 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
63 + growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
64 + growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
65 + ∆|∆|CD|Gtype fnr|fnr|NN|Gtype -|-|:|O Anaeroibc|anaeroibc|NN|Air
66 + ∆|∆|CD|Gtype fur|fur|NN|Gtype Anaerobic|anaerobic|JJ|Air A|a|DT|O
67 + ∆|∆|CD|Gtype fur|fur|NN|Gtype Anaerobic|anaerobic|JJ|Air -LSB-|-lsb-|-LRB-|O IP|IP|NNP|O vs|vs|CC|O nput|nput|NN|O -RSB-|-rsb-|-RRB-|O
68 + Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O A|a|NN|O -|-|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
69 + Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O A|a|NN|O -|-|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
70 + ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Anaerobic|anaerobic|JJ|Air
71 + Wild-type|wild-type|JJ|Gtype Aerobic|aerobic|JJ|Air A|a|DT|O
72 + Wild-type|wild-type|JJ|Gtype Anaerobic|anaerobic|JJ|Air A|a|DT|O
73 + Wild-type|wild-type|JJ|Gtype Anaerobic|anaerobic|JJ|Air B|b|NN|O
74 + Wild|Wild|NNP|Gtype type|type|NN|Gtype control|control|NN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
75 + Wild|Wild|NNP|Gtype type|type|NN|Gtype control|control|NN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
76 + WT|wt|JJ|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
77 + WT|wt|JJ|Gtype acetate|acetate|NN|Supp 2|2|CD|O
78 + WT|wt|JJ|Gtype NaCl|nacl|NN|Supp 1|1|CD|O
79 + WT|wt|JJ|Gtype PQ|pq|NN|Supp 1|1|CD|O
80 + WT|wt|JJ|Gtype _|_|NN|O ChIPSeq|chipseq|NN|Technique _|_|NN|O 1|1|CD|O
81 + WT|wt|JJ|Gtype _|_|NN|O ChIPSeq|chipseq|NN|Technique _|_|NN|O 2|2|CD|O
82 + Δcra|δcra|NN|Gtype glucose|glucose|NN|Supp 1|1|CD|O
83 + Δfur|δfur|NN|Gtype with|with|IN|O DPD|dpd|NN|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique RNA-seq|rna-seq|NN|Technique -RRB-|-rrb-|-RRB-|Technique
84 + ΔgadE|δgade|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
85 + ΔgadE|δgade|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
86 + ΔgadX|δgadx|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
87 + ΔompR|δompr|NN|Gtype NaCl|nacl|NN|Supp 1|1|CD|O
88 + ΔoxyR|δoxyr|NN|Gtype PQ|pq|NN|Supp 1|1|CD|O
89 + ΔsoxR|δsoxr|NN|Gtype PQ|pq|NN|Supp 2|2|CD|O
90 + HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air A|a|DT|O
91 + HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air A|a|DT|O
92 + IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air B|b|NN|O
93 + medium|medium|NN|O :|:|:|O M63|m63|NN|Med
94 + LB|lb|NN|Med 2.0|2.0|CD|O B1|b1|NN|O TEX|tex|NN|O neg|neg|NN|O L1|l1|NN|O GA|ga|NN|O
95 + LB|lb|NN|Med 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
96 + LB|lb|NN|Med 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
97 + LB|lb|NN|Med 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
98 + M63|m63|NN|Med 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
99 + M63|m63|NN|Med 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
100 + OmpR|ompr|NN|O NaCl|nacl|NN|Supp 1|1|CD|O
101 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|NN|O .|.|.|O K-12|k-12|NN|Strain substr|substr|NN|O .|.|.|O MG1655star|mg1655star|NN|Substrain
102 + RpoB|rpob|NN|O ∆|∆|CD|Gtype cra|cra|NN|Gtype 1|1|CD|O
103 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|Supp and|and|CC|O rifampicin|rifampicin|NN|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
104 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|Supp and|and|CC|O rifampicin|rifampicin|NN|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
105 + SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|Gtype
106 + SoxR|soxr|NN|O PQ|pq|NN|Supp 2|2|CD|O
107 + SoxS|soxs|NN|O PQ|pq|NN|Supp 2|2|CD|O
108 + ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O B|b|NN|O
109 + strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
110 + strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
111 + strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
112 + 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
113 + ChIP-exo|chip-exo|NN|Technique GadX|gadx|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
114 + ChIP-exo|chip-exo|NN|Technique GadX|gadx|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
115 + 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
116 + 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
117 + 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
118 + TrpR|trpr|NN|O _|_|CD|O glucose|glucose|NN|Supp
119 + TrpR|trpr|NN|O _|_|CD|O Trp|Trp|NNP|Supp
120 + σ32|σ32|NN|O 30|30|CD|Temp °C|°c|NN|Temp rep2|rep2|NN|O
121 + σ32|σ32|NN|O 30|30|CD|Temp °C|°c|NN|Temp short|short|JJ|O RNase|rnase|NN|O
122 + σ32|σ32|NN|O 43|43|CD|Temp °C|°c|NN|Temp rep2|rep2|NN|O
...\ No newline at end of file ...\ No newline at end of file
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 - 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|O 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|O 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 - library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
2 - strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
3 - 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
4 - 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
5 - 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 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
6 - 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
7 - genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
8 - 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
9 - 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|O 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
10 - 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|O 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
11 - genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
12 - 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
13 - 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
14 - 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
15 - genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
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 - 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
18 - 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
19 - 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 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
20 - 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
21 - strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
22 - 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
23 - 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
24 - 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
25 - 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 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
26 - Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
27 - genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
28 - Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
29 - genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
30 - genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
31 - genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
32 - genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
33 - genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
34 - growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
35 - 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
36 - strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
37 - carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
38 - 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 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
39 - 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
40 - genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
41 - medium|medium|NN|O :|:|:|O M63|m63|NN|Med
42 - 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
43 - 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
44 - ChIP-Seq|chip-seq|NN|Technique
45 - 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
46 - 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
47 - agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
48 - 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
49 - genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
50 - 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
51 - 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 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
52 - genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
53 - 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
54 - 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
55 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
56 - 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
57 - Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
58 - genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
59 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
60 - 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
61 - 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
62 - antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
63 - genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
64 - growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
65 - At|at|IN|O OD450|od450|NN|OD
66 - 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
67 - 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
68 - 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 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
69 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
70 - ChIP-Seq|chip-seq|NN|Gversion
71 - genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
72 - 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
73 - 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
74 - genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
75 - 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 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
76 - 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
77 - 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
78 - RNA-Seq|rna-seq|NN|Technique
79 - agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
80 - 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
81 - MG1655|mg1655|NN|O 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
82 - growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
83 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
84 - antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
85 - 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
86 - 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
87 - 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
88 - growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
89 - 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 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
90 - genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
91 - 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 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|O water|water|NN|O bath|bath|NN|O shaking|shake|VBG|O at|at|IN|O 240|240|CD|O rpm|rpm|NN|O
92 - 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 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 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
93 - 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
94 - 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
95 - genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
96 - antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
97 - 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
98 - MG1655|mg1655|NN|O 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
99 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
100 - Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|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
101 - 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 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
102 - carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
103 - 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 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
104 - Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|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
105 - agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
106 - 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
107 - 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
108 - genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
109 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
110 - medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
111 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
112 - 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 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
...\ No newline at end of file ...\ No newline at end of file
1 + ΔsoxS|δsoxs|NN|Gtype PQ|pq|NN|Supp 1|1|CD|O
2 + genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
3 + WT|wt|JJ|Gtype with|with|IN|O DPD|dpd|NN|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique RNA-seq|rna-seq|NN|Technique -RRB-|-rrb-|-RRB-|Technique
4 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
5 + antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
6 + 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
7 + 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
8 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
9 + Cra|Cra|NNP|O fructose|fructose|NN|Supp 1|1|CD|O
10 + WT|wt|JJ|Gtype glucose|glucose|NN|Supp 2|2|CD|O
11 + ΔoxyR|δoxyr|NN|Gtype PQ|pq|NN|Supp 2|2|CD|O
12 + 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
13 + σ32|σ32|NN|O 30|30|CD|Temp °C|°c|NN|Temp rep1|rep1|NN|O
14 + 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
15 + Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 2|2|CD|O
16 + chip-Fnr|chip-fnr|JJ|O _|_|NN|O Fnr8myc|fnr8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 1|1|CD|O
17 + ∆|∆|CD|Gtype fur|fur|NN|Gtype ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Anaerobic|anaerobic|JJ|Air A|a|DT|O
18 + LB|lb|NN|Med 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
19 + 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
20 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|Supp and|and|CC|O rifampicin|rifampicin|NN|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
21 + ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Aerobic|aerobic|JJ|Air
22 + IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air A|a|DT|O
23 + PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|Supp _|_|NN|O 1|1|CD|O
24 + 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 aerobically|aerobically|RB|Air 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
25 + ∆|∆|CD|Gtype fur|fur|NN|Gtype Aerobic|aerobic|JJ|Air A|a|DT|O
26 + 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 aerobically|aerobically|RB|Air 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
27 + ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|Supp _|_|NN|O 1|1|CD|O
28 + 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
29 + 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 anaerobically|anaerobically|RB|Air 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
30 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
31 + 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
32 + medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
33 + 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
34 + Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|Gtype _|_|CD|O rep2|rep2|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
35 + affyexp|affyexp|JJ|O _|_|NN|O wt|wt|JJ|Gtype _|_|NN|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 2|2|CD|O .|.|.|O CEL|CEL|NNP|O
36 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|Air -LRB-|-lrb-|-LRB-|Air 70|70|CD|Air %|%|NN|Air N2|n2|NN|Air ,|,|,|Air 25|25|CD|Air %|%|NN|Air O2|o2|CD|Air ,|,|,|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
37 + ChIP-Seq|chip-seq|NN|Gversion
38 + genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
39 + affyexp|affyexp|JJ|O _|_|NN|O wt|wt|JJ|Gtype _|_|NN|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 2|2|CD|O .|.|.|O CEL|CEL|NNP|O
40 + 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 aerobically|aerobically|RB|Air 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
41 + 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 aerobically|aerobically|RB|Air 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
42 + genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
43 + ΔgadW|δgadw|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
44 + 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
45 + WT|wt|JJ|Gtype with|with|IN|O DPD|dpd|NN|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique RNA-seq|rna-seq|NN|Technique -RRB-|-rrb-|-RRB-|Technique
46 + genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
47 + affyexp|affyexp|JJ|O _|_|NN|O delta-arcA|delta-arca|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 3|3|CD|O .|.|.|O CEL|CEL|NNP|O
48 + Wild|Wild|NNP|Gtype type|type|NN|Gtype control|control|NN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
49 + ΔsoxS|δsoxs|NN|Gtype PQ|pq|NN|Supp 2|2|CD|O
50 + pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique _|_|NN|O 1|1|CD|O
51 + Ecoli|ecolus|NNS|O _|_|VBP|O wild-type|wild-type|JJ|Gtype _|_|NN|O rep1|rep1|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
52 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
53 + LB|lb|NN|Med 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
54 + M63|m63|NN|Med 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
55 + genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
56 + Escherichia|escherichia|FW|O coli|coli|FW|O str|str|NN|O .|.|.|O K-12|k-12|NN|Strain substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|Substrain
57 + Sequenced|sequence|VBN|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
58 + Lrp|Lrp|NNP|O _|_|SYM|O Leu|Leu|NNP|Supp _|_|NN|O 2|2|CD|O
59 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Aerobic|Aerobic|NNP|Air B|b|NN|O
60 + Samples|sample|NNS|O for|for|IN|O transcriptome|transcriptome|NN|O analysis|analysis|NN|O were|be|VBD|O taken|take|VBN|O from|from|IN|O exponentially|exponentially|RB|Phase growing|grow|VBG|Phase cells|cell|NNS|Phase .|.|.|O From|from|IN|O the|the|DT|O cells|cell|NNS|O treated|treat|VBN|O by|by|IN|O RNAprotect|rnaprotect|NN|O Bacteria|bacterium|NNS|O Reagent|reagent|NN|O -LRB-|-lrb-|-LRB-|O Qiagen|qiagen|NN|O -RRB-|-rrb-|-RRB-|O ,|,|,|O total|total|JJ|O RNA|rna|NN|O samples|sample|NNS|O were|be|VBD|O isolated|isolate|VBN|O using|use|VBG|O RNeasy|rneasy|JJ|O columns|column|NNS|O -LRB-|-lrb-|-LRB-|O Qiagen|Qiagen|NNP|O -RRB-|-rrb-|-RRB-|O in|in|IN|O accordance|accordance|NN|O with|with|IN|O manufacturer|manufacturer|NN|O 's|'s|POS|O instruction|instruction|NN|O .|.|.|O
61 + Lrp|Lrp|NNP|O _|_|SYM|O Leu|Leu|NNP|Supp _|_|SYM|O 1|1|CD|O
62 + Fur|Fur|NNP|O with|with|IN|O DPD|dpd|NN|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
63 + 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
64 + Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O C|c|NN|O -|-|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
65 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
66 + 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
67 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|Anaerobic|NNP|Air ,|,|,|O Iron|Iron|NNP|Supp Deficient|deficient|JJ|O B|b|NN|O
68 + Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O B|b|NN|O -|-|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
69 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O B|b|NN|O
70 + RNA-Seq|rna-seq|NN|Technique
71 + LB|lb|NN|Med 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
72 + LB|lb|NN|Med 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
73 + strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
74 + 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
75 + σ32|σ32|NN|O 43|43|CD|Temp °C|°c|NN|Temp rep1|rep1|NN|O
76 + chip-Fnr|chip-fnr|JJ|O _|_|NN|O Fnr8myc|fnr8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|CD|O 3|3|CD|O
77 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
78 + Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O B|b|NN|O -|-|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
79 + affyexp|affyexp|JJ|O _|_|NN|O delta-arcA|delta-arca|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|CD|O 3|3|CD|O .|.|.|O CEL|CEL|NNP|O
80 + affyexp|affyexp|JJ|O _|_|NN|O delta-arcA|delta-arca|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 1|1|CD|O .|.|.|O CEL|CEL|NNP|O
81 + Wild|Wild|NNP|Gtype type|type|NN|Gtype control|control|NN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
82 + genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
83 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|Anaerobic|NNP|Air ,|,|,|O Iron|Iron|NNP|Supp Deficient|Deficient|NNP|O A|A|NNP|O
84 + culture|culture|NN|O condition|condition|NN|O :|:|:|O Aerobic|Aerobic|NNP|Air cultures|culture|NNS|O
85 + Wild-type|wild-type|JJ|Gtype Aerobic|aerobic|JJ|Air B|b|NN|O
86 + 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
87 + 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 anaerobically|anaerobically|RB|Air 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
88 + RpoB|rpob|NN|O WT|wt|JJ|Gtype 2|2|CD|O
89 + LB|lb|NN|Med 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
90 + affyexp|affyexp|JJ|O _|_|NN|O delta-fnr|delta-fnr|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 2|2|CD|O .|.|.|O CEL|CEL|NNP|O
91 + 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
92 + LB|lb|NN|Med 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
93 + genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
94 + Cra|Cra|NNP|O glucose|glucose|NN|Supp 2|2|CD|O
95 + Lrp|lrp|NN|O _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O 3|3|CD|O
96 + WT|wt|JJ|Gtype with|with|IN|O Fe|Fe|NNP|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique RNA-seq|rna-seq|NN|Technique -RRB-|-rrb-|-RRB-|Technique
97 + chip-Fnr|chip-fnr|JJ|O _|_|NN|O Fnr8myc|fnr8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 1|1|CD|O
98 + chip-ArcA|chip-arca|NN|O _|_|CD|O ArcA8myc|arca8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 1|1|CD|O
99 + OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique
100 + 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
101 + 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
102 + Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
103 + 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
104 + growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
105 + ChIP-exo|ChIP-exo|NNP|Technique GadW|gadw|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
106 + Δfur|δfur|NN|Gtype with|with|IN|O Fe|Fe|NNP|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique RNA-seq|rna-seq|NN|Technique -RRB-|-rrb-|-RRB-|Technique
107 + PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|Supp _|_|NN|O 2|2|CD|O
108 + Fur|Fur|NNP|O with|with|IN|O DPD|dpd|NN|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
109 + ChIP-exo|ChIP-exo|NNP|Technique RpoS|rpos|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
110 + culture|culture|NN|O condition|condition|NN|O :|:|:|O anaerobic|anaerobic|JJ|Air fermentive|fermentive|JJ|O condition|condition|NN|O
111 + OxyR|oxyr|NN|O PQ|pq|NN|Supp 2|2|CD|O
112 + 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
113 + ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O A|a|NN|O
114 + M63|m63|NN|Med 0.4|0.4|CD|O B1|b1|NN|O TEX|tex|NN|O neg|neg|NN|O L1|l1|NN|O GA|ga|NN|O
115 + affyexp|affyexp|JJ|O _|_|NN|O delta-fnr|delta-fnr|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 3|3|CD|O .|.|.|O CEL|CEL|NNP|O
116 + affyexp|affyexp|JJ|O _|_|NN|O delta-arcA|delta-arca|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 1|1|CD|O .|.|.|O CEL|CEL|NNP|O
117 + ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air -|-|:|O B|b|NN|O
118 + 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
119 + genotype/variation|genotype/variation|NN|O :|:|:|O Δfnr|δfnr|NN|Gtype
120 + PurR|purr|NN|O _|_|SYM|O Adenine|Adenine|NNP|Supp _|_|SYM|O 1|1|CD|O
121 + genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
122 + Lrp|Lrp|NNP|O _|_|SYM|O Leu|Leu|NNP|Supp _|_|SYM|O 3|3|CD|O
123 + FNR|fnr|SYM|O -|-|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype ∆|∆|VBP|Gtype stpA|stpa|NN|Gtype A|a|NN|O
124 + LB|lb|NN|Med 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
125 + ChIP-exo|ChIP-exo|NNP|Technique GadE|gade|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
126 + WT|wt|JJ|Gtype PQ|pq|NN|Supp 2|2|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 with|with|IN|O 10|10|CD|Supp mM|mm|NN|Supp leucine|leucine|NN|Supp .|.|.|O
128 + FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|NN|O
129 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Aerobic|Aerobic|NNP|Air C|C|NNP|O
130 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Aerobic|Aerobic|NNP|Air A|A|NNP|O
131 + antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
132 + NsrR|nsrr|NN|Gtype _|_|CD|Gtype Flagtag|flagtag|NN|Gtype _|_|CD|O rep2|rep2|NN|O
133 + OmpR|ompr|NN|O NaCl|nacl|NN|Supp 2|2|CD|O
134 + genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
135 + ∆|∆|CD|Gtype fur|fur|NN|Gtype ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Aerobic|aerobic|JJ|Air A|a|DT|O
136 + genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
137 + genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
138 + ChIP-Seq|chip-seq|NN|Technique
139 + affyexp|affyexp|JJ|O _|_|NN|O delta-arcA|delta-arca|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 2|2|CD|O .|.|.|O CEL|CEL|NNP|O
140 + 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 aerobically|aerobically|RB|Air 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
141 + RpoB|rpob|NN|O ∆|∆|CD|Gtype crp|crp|NN|Gtype 2|2|CD|O
142 + 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
143 + chip-ArcA|chip-arca|NN|O _|_|CD|O ArcA8myc|arca8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 2|2|CD|O
144 + At|at|IN|O OD450|od450|NN|OD
145 + strain|strain|NN|O :|:|:|O K-12|k-12|NN|Strain
146 + ∆|∆|CD|Gtype fur|fur|NN|Gtype ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Anaerobic|anaerobic|JJ|Air B|b|NN|O
147 + 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
148 + 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 aerobically|aerobically|RB|Air 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
149 + LB|lb|NN|Med 0.4|0.4|CD|O B1|b1|NN|O TEX|tex|NN|O neg|neg|NN|O L1|l1|NN|O GA|ga|NN|O
150 + genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
151 + antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
152 + ΔgadW|δgadw|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
153 + pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique _|_|NN|O 2|2|CD|O
154 + 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 aerobically|aerobically|RB|Air 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
155 + affyexp|affyexp|JJ|O _|_|NN|O wt|wt|JJ|Gtype _|_|NN|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 1|1|CD|O .|.|.|O CEL|CEL|NNP|O
156 + ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|Supp _|_|NN|O 2|2|CD|O
157 + PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|Supp _|_|NN|O 2|2|CD|O
158 + RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
159 + HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air B|b|NN|O
160 + ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 2|2|CD|O
161 + chip-ArcA|chip-arca|NN|O _|_|CD|O ArcA8myc|arca8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 2|2|CD|O
162 + 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 anaerobically|anaerobically|RB|Air 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
163 + ∆|∆|CD|Gtype fur|fur|NN|Gtype Anaerobic|anaerobic|JJ|Air B|b|NN|O
164 + carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
165 + WT|wt|JJ|Gtype fructose|fructose|NN|Supp 1|1|CD|O
166 + LB|lb|NN|Med 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
167 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|Air -LRB-|-lrb-|-LRB-|Air 25|25|CD|Air %|%|NN|Air O2|o2|CD|Air ,|,|,|Air 70|70|CD|Air %|%|NN|Air N2|n2|NN|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
168 + agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
169 + RpoB|rpob|NN|O WT|wt|JJ|Gtype 1|1|CD|O
170 + Input|input|NN|O ChIP-Seq|chip-seq|NN|Technique
171 + 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
172 + WT|wt|JJ|Gtype acetate|acetate|NN|Supp 1|1|CD|O
173 + library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
174 + ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 1|1|CD|O
175 + Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 1|1|CD|O
176 + WT|wt|JJ|Gtype _|_|NN|O RNASeq|rnaseq|NN|Technique
177 + 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
178 + Δcra|δcra|NN|Gtype acetate|acetate|NN|Supp 1|1|CD|O
179 + genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
180 + 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|Air -LRB-|-lrb-|-LRB-|Air 95|95|CD|Air %|%|NN|Air N2|n2|NN|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
181 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
182 + Cra|Cra|NNP|O acetate|acetate|NN|Supp 2|2|CD|O
183 + 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
184 + ΔompR|δompr|NN|Gtype NaCl|nacl|NN|Supp 2|2|CD|O
185 + Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O A|a|NN|O -|-|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
186 + Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|anaerobic|JJ|Air C|c|NN|O
187 + 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
188 + ΔgadX|δgadx|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
189 + 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
190 + chip-Fnr|chip-fnr|JJ|O _|_|NN|O Fnr8myc|fnr8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 3|3|CD|O
191 + CsiR|csir|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique
192 + Δfur|δfur|NN|Gtype with|with|IN|O DPD|dpd|NN|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique RNA-seq|rna-seq|NN|Technique -RRB-|-rrb-|-RRB-|Technique
193 + WT|wt|JJ|Gtype NaCl|nacl|NN|Supp 2|2|CD|O
194 + chip-ArcA|chip-arca|NN|O _|_|CD|O ArcA8myc|arca8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|CD|O 3|3|CD|O
195 + WT|wt|JJ|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
196 + ChIP-exo|ChIP-exo|NNP|Technique RpoS|rpos|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
197 + genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
198 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
199 + genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
200 + NsrR|nsrr|NN|Gtype _|_|CD|Gtype Flagtag|flagtag|NN|Gtype _|_|CD|O rep3|rep3|NN|O
201 + σ32|σ32|NN|O 43|43|CD|Temp °C|°c|NN|Temp short|short|JJ|O RNase|rnase|NN|O
202 + 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
203 + Cra|Cra|NNP|O glucose|glucose|NN|Supp 1|1|CD|O
204 + HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air B|b|NN|O
205 + affyexp|affyexp|JJ|O _|_|NN|O delta-arcA|delta-arca|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 2|2|CD|O .|.|.|O CEL|CEL|NNP|O
206 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
207 + SeqA|seqa|NN|O old|old|JJ|O deltaSeqA|deltaseqa|NN|Gtype
208 + Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O anaerobically|anaerobically|RB|Air -LRB-|-lrb-|-LRB-|Air 95|95|CD|Air %|%|NN|Air N2|n2|NN|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
209 + genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
210 + 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
211 + affyexp|affyexp|JJ|O _|_|NN|O wt|wt|JJ|Gtype _|_|NN|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 3|3|CD|O .|.|.|O CEL|CEL|NNP|O
212 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
213 + Nac|Nac|NNP|O _|_|NNP|O ChIPSeq|ChIPSeq|NNP|Technique
214 + Aerobic|Aerobic|NNP|Air cultures|culture|NNS|O
215 + Δcra|δcra|NN|Gtype glucose|glucose|NN|Supp 2|2|CD|O
216 + WT|wt|JJ|Gtype with|with|IN|O Fe|Fe|NNP|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique RNA-seq|rna-seq|NN|Technique -RRB-|-rrb-|-RRB-|Technique
217 + SoxS|soxs|NN|O PQ|pq|NN|Supp 1|1|CD|O
218 + chip-Fnr|chip-fnr|JJ|O _|_|NN|O Fnr8myc|fnr8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 2|2|CD|O
219 + LB|lb|NN|Med 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
220 + acetate|acetate|NN|Supp
221 + LB|lb|NN|Med 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
222 + WT|wt|JJ|Gtype glucose|glucose|NN|Supp 1|1|CD|O
223 + SoxR|soxr|NN|O PQ|pq|NN|Supp 1|1|CD|O
224 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|Supp and|and|CC|O rifampicin|rifampicin|NN|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
225 + 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
226 + Ecoli|ecolus|NNS|O _|_|VBP|O wild-type|wild-type|JJ|Gtype _|_|NN|O rep2|rep2|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
227 + 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 anaerobically|anaerobically|RB|Air -LRB-|-lrb-|-LRB-|Air 95|95|CD|Air %|%|NN|Air N2|n2|NN|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
228 + 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
229 + Δcra|δcra|NN|Gtype acetate|acetate|NN|Supp 2|2|CD|O
230 + ∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
231 + M63|m63|NN|Med 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
232 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
233 + genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
234 + chip|chip|NN|O antibody|antibody|NN|O :|:|:|O biotin|biotin|NN|Anti conjugated|conjugate|VBN|Anti anti-c-myc|anti-c-myc|JJ|Anti antibody|antibody|NN|Anti
235 + OxyR|oxyr|NN|O PQ|pq|NN|Supp 1|1|CD|O
236 + ΔsoxR|δsoxr|NN|Gtype PQ|pq|NN|Supp 1|1|CD|O
237 + carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
238 + FNR|fnr|SYM|O -|-|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype ∆|∆|VBP|Gtype stpA|stpa|NN|Gtype B|b|NN|O
239 + genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
240 + genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
241 + agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
242 + Cra|Cra|NNP|O fructose|fructose|NN|Supp 2|2|CD|O
243 + Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|Technique
244 + ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air -|-|:|O A|a|NN|O
245 + Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O B|b|NN|O -|-|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
246 + RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|Supp 2|2|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
247 + ∆|∆|CD|Gtype fur|fur|NN|Gtype ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Aerobic|aerobic|JJ|Air B|b|NN|O
248 + LB|lb|NN|Med 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
249 + 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
250 + Δcra|δcra|NN|Gtype fructose|fructose|NN|Supp 2|2|CD|O
251 + Wild|Wild|NNP|Gtype type|type|NN|Gtype control|control|NN|O -LRB-|-lrb-|-LRB-|O 2.5|2.5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
252 + ∆|∆|CD|Gtype fur|fur|NN|Gtype Aerobic|aerobic|JJ|Air B|b|NN|O
253 + RpoB|rpob|NN|O ∆|∆|CD|Gtype crp|crp|NN|Gtype 1|1|CD|O
254 + chip-ArcA|chip-arca|NN|O _|_|CD|O ArcA8myc|arca8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 1|1|CD|O
255 + NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique
256 + WT|wt|JJ|Gtype fructose|fructose|NN|Supp 2|2|CD|O
257 + RpoB|rpob|NN|O ∆|∆|CD|Gtype cra|cra|NN|Gtype 2|2|CD|O
258 + affyexp|affyexp|JJ|O _|_|NN|O delta-fnr|delta-fnr|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 1|1|CD|O .|.|.|O CEL|CEL|NNP|O
259 + 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
260 + 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 anerobically|anerobically|RB|Air -LRB-|-lrb-|-LRB-|Air 95|95|CD|Air %|%|NN|Air N2|n2|NN|Air ,|,|,|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
261 + Δfur|δfur|NN|Gtype with|with|IN|O Fe|Fe|NNP|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique RNA-seq|rna-seq|NN|Technique -RRB-|-rrb-|-RRB-|Technique
262 + Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|Gtype _|_|CD|O rep1|rep1|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
263 + carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
264 + Cra|cra|NN|O acetate|acetate|NN|Supp 1|1|CD|O
265 + culture|culture|NN|O condition|condition|NN|O :|:|:|O nitrate|nitrate|JJ|Supp respiratory|respiratory|JJ|O condition|condition|NN|O
266 + genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
267 + 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
268 + 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
269 + ChIP-exo|ChIP-exo|NNP|Technique GadE|gade|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
270 + M63|m63|NN|Med 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
271 + 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 aerobically|aerobically|RB|Air 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
272 + ChIP-exo|ChIP-exo|NNP|Technique GadW|gadw|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
273 + 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
274 + 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
275 + culture|culture|NN|O condition|condition|NN|O :|:|:|O Anaerobic|anaerobic|JJ|Air cultures|culture|NNS|O
276 + 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|Air -LRB-|-lrb-|-LRB-|Air 95|95|CD|Air %|%|NN|Air N2|n2|NN|Air and|and|CC|Air 5|5|CD|Air %|%|NN|Air CO2|co2|NN|Air -RRB-|-rrb-|-RRB-|Air 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
277 + genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
278 + agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
279 + growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
280 + 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 aerobically|aerobically|RB|Air 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
281 + genotype/variation|genotype/variation|NN|O :|:|:|O ΔarcA|δarca|NN|Gtype
282 + NsrR|nsrr|NN|Gtype _|_|CD|Gtype Flagtag|flagtag|NN|Gtype _|_|CD|O rep1|rep1|NN|O
283 + Δcra|δcra|NN|Gtype fructose|fructose|NN|Supp 1|1|CD|O
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1 +********** TRAINING AND TESTING REPORT **********
2 +Training file: training-data-set-70_v4.txt
3 +
4 +best params:{'c1': 0.0845144703859872, 'c2': 0.0014492583407590665}
5 +best CV score:0.803457407167867
6 +model size: 0.07M
7 +
8 +Flat F1: 0.7886994187596283
9 + precision recall f1-score support
10 +
11 + OD 1.000 0.405 0.577 37
12 + pH 1.000 1.000 1.000 12
13 + Technique 0.952 0.909 0.930 22
14 + Med 0.812 0.912 0.860 57
15 + Temp 0.818 1.000 0.900 18
16 + Vess 0.000 0.000 0.000 0
17 + Agit 0.000 0.000 0.000 0
18 + Phase 1.000 0.947 0.973 19
19 + Air 0.730 0.742 0.736 62
20 + Anti 0.571 0.444 0.500 9
21 + Strain 1.000 1.000 1.000 1
22 + Gtype 0.863 0.774 0.816 106
23 + Substrain 0.000 0.000 0.000 1
24 + Supp 0.815 0.713 0.761 136
25 + Gversion 0.000 0.000 0.000 0
26 +
27 +avg / total 0.841 0.760 0.789 480
28 +
29 +
30 +Top likely transitions:
31 +Agit -> Agit 7.567868
32 +OD -> OD 7.283561
33 +Temp -> Temp 6.525111
34 +Anti -> Anti 6.338173
35 +Med -> Med 6.068203
36 +Air -> Air 5.490227
37 +Gtype -> Gtype 5.364943
38 +O -> O 5.360015
39 +Phase -> Phase 5.088291
40 +Gversion -> Gversion 5.052937
41 +Technique -> Technique 4.734097
42 +Supp -> Supp 4.592596
43 +Gtype -> Supp 1.928700
44 +pH -> pH 1.873562
45 +O -> Supp 1.656908
46 +O -> Technique 1.579934
47 +Substrain -> Gtype 1.367059
48 +O -> Gtype 1.299889
49 +Air -> O 1.168469
50 +O -> Temp 0.796125
51 +O -> Anti 0.464004
52 +OD -> Phase 0.334945
53 +Med -> O 0.323185
54 +O -> Gversion 0.294223
55 +Technique -> Air 0.120065
56 +Temp -> O 0.058292
57 +Gversion -> O 0.017060
58 +Gtype -> pH 0.014023
59 +Anti -> O 0.004741
60 +O -> Med 0.003586
61 +O -> Strain 0.000914
62 +Phase -> O 0.000079
63 +Technique -> O -0.064766
64 +Supp -> Air -0.085487
65 +Air -> OD -0.140828
66 +Supp -> OD -0.140855
67 +OD -> Gtype -0.154848
68 +Gtype -> O -0.178619
69 +Air -> Supp -0.190285
70 +Phase -> Air -0.254683
71 +Supp -> O -0.331239
72 +OD -> Air -0.339236
73 +Supp -> Technique -0.352046
74 +Technique -> OD -0.381551
75 +Gtype -> Anti -0.576175
76 +Agit -> O -0.582420
77 +O -> Air -0.710972
78 +OD -> Med -0.720546
79 +OD -> O -0.754296
80 +Gtype -> OD -0.821534
81 +
82 +
83 +Top unlikely transitions:
84 +Med -> Med 6.068203
85 +Air -> Air 5.490227
86 +Gtype -> Gtype 5.364943
87 +O -> O 5.360015
88 +Phase -> Phase 5.088291
89 +Gversion -> Gversion 5.052937
90 +Technique -> Technique 4.734097
91 +Supp -> Supp 4.592596
92 +Gtype -> Supp 1.928700
93 +pH -> pH 1.873562
94 +O -> Supp 1.656908
95 +O -> Technique 1.579934
96 +Substrain -> Gtype 1.367059
97 +O -> Gtype 1.299889
98 +Air -> O 1.168469
99 +O -> Temp 0.796125
100 +O -> Anti 0.464004
101 +OD -> Phase 0.334945
102 +Med -> O 0.323185
103 +O -> Gversion 0.294223
104 +Technique -> Air 0.120065
105 +Temp -> O 0.058292
106 +Gversion -> O 0.017060
107 +Gtype -> pH 0.014023
108 +Anti -> O 0.004741
109 +O -> Med 0.003586
110 +O -> Strain 0.000914
111 +Phase -> O 0.000079
112 +Technique -> O -0.064766
113 +Supp -> Air -0.085487
114 +Air -> OD -0.140828
115 +Supp -> OD -0.140855
116 +OD -> Gtype -0.154848
117 +Gtype -> O -0.178619
118 +Air -> Supp -0.190285
119 +Phase -> Air -0.254683
120 +Supp -> O -0.331239
121 +OD -> Air -0.339236
122 +Supp -> Technique -0.352046
123 +Technique -> OD -0.381551
124 +Gtype -> Anti -0.576175
125 +Agit -> O -0.582420
126 +O -> Air -0.710972
127 +OD -> Med -0.720546
128 +OD -> O -0.754296
129 +Gtype -> OD -0.821534
130 +Supp -> Med -1.118820
131 +Substrain -> O -1.830467
132 +Phase -> OD -2.403512
133 +Med -> Supp -2.548799
134 +
135 +
136 +Top positive:
137 +12.504936 Supp b'lemma:Iron'
138 +10.792779 O b'lemma:_'
139 +10.427539 Air b'lemma:aerobic'
140 +10.207513 Air b'lemma:anaerobic'
141 +9.451231 Supp b'lemma:nitrate'
142 +9.115772 Phase b'lemma:stationary'
143 +8.575457 O b'lemma:1'
144 +8.408994 Technique b'lemma:ChIP-exo'
145 +8.354108 Air b'-1:lemma:ChIP-Seq'
146 +8.314194 O b'lemma:rpob'
147 +8.264287 Med b'lemma:MOPS'
148 +8.077335 Technique b'lemma:chipseq'
149 +7.675786 O b'-1:lemma:ChIP-exo'
150 +7.432466 Strain b'lemma:k-12'
151 +7.338742 O b'lemma:Custom'
152 +7.132224 O b'-1:lemma:tag'
153 +6.872851 Substrain b'lemma:mg1655'
154 +6.656592 Supp b'lemma:pq'
155 +6.656346 Gtype b'lemma:\xce\xb4cra'
156 +6.631548 O b'lemma:3'
157 +6.608233 O b'lemma:2'
158 +6.514523 Air b'lemma:Aerobic'
159 +6.354650 Technique b'lemma:ChIP-Seq'
160 +6.321273 Gtype b'lemma:flag-tag'
161 +6.321273 Gtype b'-1:lemma:c-terminal'
162 +6.285172 O b'lemma:rep1'
163 +6.282612 O b'lemma:b'
164 +6.260165 Gversion b'lemma:asm584v2'
165 +6.243462 Gversion b'-1:lemma:nc'
166 +6.129172 Gversion b'lemma:nc'
167 +6.117441 O b'lemma:rep2'
168 +6.056865 O b'lemma:rep3'
169 +6.042591 OD b'+1:lemma:stationary'
170 +5.905730 O b'lemma:Cra'
171 +5.761961 Gtype b'lemma:arca8myc'
172 +5.631643 Gtype b'-1:lemma:\xe2\x88\x86'
173 +5.616482 Phase b'lemma:mid-log'
174 +5.599676 Med b'lemma:LB'
175 +5.591086 O b'lemma:a'
176 +5.417363 O b'lemma:chip'
177 +5.415483 O b'lemma:\xcf\x8332'
178 +5.410036 O b'-1:lemma:0.3'
179 +5.383641 Supp b'+1:lemma:\xc2\xb5m'
180 +5.378485 OD b'lemma:od600'
181 +5.357822 O b'postag::'
182 +5.343662 Gtype b'lemma:delta-arca'
183 +5.329601 Supp b'lemma:nh4cl'
184 +5.310595 Gtype b'lemma:fnr8myc'
185 +5.291721 OD b'lemma:od450'
186 +5.278396 Supp b'lemma:Fe'
187 +5.198206 O b'postag:IN'
188 +5.152255 O b'lemma:or'
189 +5.142263 O b'-1:lemma:Aerobic'
190 +5.072815 Med b'lemma:lb'
191 +4.967279 Technique b'lemma:rna-seq'
192 +4.960999 Gtype b'lemma:type'
193 +4.958285 Strain b'+1:lemma:substr'
194 +4.905998 Gtype b'lemma:wt'
195 +4.808130 Supp b'lemma:glucose'
196 +4.806347 Vess b'lemma:flask'
197 +4.806347 Vess b'-1:lemma:warm'
198 +4.772284 O b'lemma:for'
199 +4.744261 Supp b'lemma:arginine'
200 +4.737788 Gtype b'lemma:delta-fnr'
201 +4.691753 O b'-1:lemma:0.3-0.35'
202 +4.668554 Gtype b'+1:lemma:type'
203 +4.631710 Technique b'lemma:rnaseq'
204 +4.584824 Gtype b'lemma:nsrr'
205 +4.584359 O b'-1:lemma:glucose'
206 +4.556168 O b'-1:lemma:anaerobic'
207 +4.539600 Supp b'-1:lemma:Cra'
208 +4.538972 O b'lemma:-'
209 +4.508141 Gtype b'-1:lemma:rpob'
210 +4.499586 Technique b'lemma:chip-seq'
211 +4.488070 Anti b'lemma:none'
212 +4.462302 O b'lemma:ompr'
213 +4.460124 Anti b'lemma:anti-rpos'
214 +4.460049 Supp b'lemma:no3'
215 +4.451202 O b'+1:lemma:od600'
216 +4.424279 Gtype b'lemma:\xce\xb4fur'
217 +4.389978 Supp b'lemma:acetate'
218 +4.387749 Med b'+1:lemma:0.4'
219 +4.335328 O b'lemma:.'
220 +4.335328 O b'postag:.'
221 +4.197130 Temp b'-1:lemma:\xcf\x8332'
222 +4.152430 Anti b'lemma:seqa'
223 +4.141879 O b'lemma:with'
224 +4.081039 Supp b'-1:lemma:+'
225 +4.005391 O b'+1:lemma:o.d.'
226 +3.986966 O b'-1:lemma:type'
227 +3.971115 O b'+1:lemma:sparging'
228 +3.914608 Gversion b'lemma:chip-seq'
229 +3.905122 Supp b'+1:lemma:1'
230 +3.886730 Technique b'-1:lemma:IP'
231 +3.875182 Supp b'+1:lemma:hour'
232 +3.871343 Temp b'-1:lemma:43'
233 +3.798383 pH b'lemma:ph5'
234 +3.798383 pH b'+1:lemma:.5'
235 +3.766343 Supp b'lemma:Leu'
236 +3.758437 Med b'lemma:m63'
237 +3.755680 Supp b'lemma:rifampicin'
238 +3.717291 Gtype b'+1:lemma:ph5'
239 +3.691820 Gtype b'-1:lemma:ptac'
240 +3.686748 Gtype b'lemma:\xe2\x88\x86'
241 +3.655665 Anti b'+1:lemma:antibody'
242 +3.645147 Temp b'-1:lemma:37'
243 +3.584169 O b'lemma:s'
244 +3.582382 Gversion b'lemma:000913'
245 +3.513265 O b'postag:VBN'
246 +3.504182 Temp b'-1:lemma:sample'
247 +3.476410 O b'lemma:CEL'
248 +3.471641 Gtype b'+1:lemma:flagtag'
249 +3.469424 O b'+1:lemma:pq'
250 +3.442038 Med b'+1:lemma:minimal'
251 +3.441203 Gtype b'lemma:\xce\xb4ompr'
252 +3.440050 Supp b'+1:lemma:2'
253 +3.439274 O b'lemma:oxyr'
254 +3.430689 Gtype b'lemma:\xce\xb4soxs'
255 +3.424081 Supp b'lemma:Adenine'
256 +3.394933 O b'-1:lemma:lb'
257 +3.382358 Supp b'lemma:dpd'
258 +3.374432 Anti b'lemma:anti-myc'
259 +3.354369 O b'+1:lemma:chip-seq'
260 +3.325764 O b'-1:lemma:\xc2\xb0c'
261 +3.324069 Air b'lemma:anerobically'
262 +3.306589 Gversion b'lemma:u00096'
263 +3.306589 Gversion b'+1:lemma:.2'
264 +3.290810 Supp b'lemma:fructose'
265 +3.286471 Med b'+1:lemma:2.0'
266 +3.281346 Gversion b'lemma:.2'
267 +3.281346 Gversion b'-1:lemma:u00096'
268 +3.224316 Gtype b'lemma:wild-type'
269 +3.206842 Gtype b'+1:lemma:with'
270 +3.204237 O b'+1:lemma:rifampicin'
271 +3.192028 Gtype b'+1:lemma:aerobic'
272 +3.176568 Supp b'lemma:iptg'
273 +3.174757 Supp b'lemma:nacl'
274 +3.142082 Phase b'-1:lemma:until'
275 +3.138505 Gtype b'lemma:pk4854'
276 +3.102435 Supp b'+1:lemma:_'
277 +3.077765 Technique b'-1:lemma:input'
278 +3.043564 Med b'+1:lemma:contain'
279 +3.043460 O b'lemma:affyexp'
280 +3.030477 O b'+1:postag:NNP'
281 +3.011575 Gtype b'+1:lemma:pq'
282 +3.009802 Technique b'-1:lemma:rna-seq'
283 +3.009086 Phase b'+1:lemma:for'
284 +3.006591 O b'lemma:chip-arca'
285 +2.961198 Technique b'+1:lemma:chip-exo'
286 +2.918766 Gtype b'lemma:deltaseqa'
287 +2.918766 Gtype b'-1:lemma:old'
288 +2.895206 O b'lemma:soxs'
289 +2.895206 O b'lemma:soxr'
290 +2.893483 O b'lemma:argr'
291 +2.883608 Supp b'-1:lemma:\xc2\xb5m'
292 +2.871795 Technique b'-1:lemma:chip-exo'
293 +2.840922 Air b'postag:RB'
294 +2.837804 O b'-1:lemma:l1'
295 +2.834031 O b'lemma:purr'
296 +2.816068 pH b'lemma:.5'
297 +2.816068 pH b'-1:lemma:ph5'
298 +2.793907 O b'+1:postag:RB'
299 +2.787764 Temp b'lemma:43'
300 +2.783505 Gtype b'+1:lemma:knock-out'
301 +2.777516 Med b'-1:lemma:ml'
302 +2.776744 Gtype b'lemma:ptac'
303 +2.754900 Air b'lemma:anaerobically'
304 +2.728375 O b'+1:lemma:acetate'
305 +2.677194 Gtype b'lemma:\xce\xb4oxyr'
306 +2.676114 Gtype b'lemma:WT'
307 +2.664380 O b'-1:lemma:dpd'
308 +2.623289 O b'lemma:at'
309 +2.622409 Air b'+1:lemma:at'
310 +2.621682 O b'lemma:Fur'
311 +2.613642 OD b'lemma:0.3'
312 +2.611845 O b'postag:DT'
313 +2.601745 O b'-1:lemma:stpa'
314 +2.558195 OD b'-1:lemma:about'
315 +2.551265 Gtype b'lemma:\xce\xb4soxr'
316 +2.545283 Gtype b'-1:lemma:from'
317 +2.537660 Med b'lemma:L'
318 +2.537660 Med b'+1:lemma:broth'
319 +2.520762 Temp b'-1:lemma:30'
320 +2.512014 Supp b'+1:lemma:and'
321 +2.485033 Gtype b'lemma:dfnr'
322 +2.478336 Temp b'lemma:\xc2\xb0c'
323 +2.477157 pH b'+1:postag:CD'
324 +2.474581 O b'lemma:2-3'
325 +2.467989 O b'lemma:Lrp'
326 +2.464584 Med b'-1:lemma:LB'
327 +2.446412 O b'+1:postag:VBP'
328 +2.443891 Supp b'lemma:leucine'
329 +2.443008 Air b'-1:lemma:-'
330 +2.331881 Med b'lemma:broth'
331 +2.331881 Med b'-1:lemma:L'
332 +2.324108 Gtype b'+1:lemma:_'
333 +2.320318 O b'-1:lemma:min'
334 +2.319595 O b'+1:lemma:mid-log'
335 +2.316477 Supp b'+1:lemma:iptg'
336 +2.316285 O b'+1:lemma:43'
337 +
338 +
339 +Top negative:
340 +0.000009 Anti b'+1:lemma:\xce\xb2'
341 +0.000008 Anti b'+1:lemma:subunit'
342 +0.000005 O b'-1:lemma:Deficient'
343 +0.000001 OD b'+1:lemma:0.15'
344 +-0.000001 Temp b'-1:postag:IN'
345 +-0.000007 O b'lemma:medium'
346 +-0.000045 O b'+1:lemma:rep1'
347 +-0.000145 Gtype b'+1:lemma:2'
348 +-0.000168 O b'+1:lemma:culture'
349 +-0.000168 O b'+1:lemma:dissolve'
350 +-0.000355 O b'-1:lemma:1'
351 +-0.000451 OD b'+1:lemma:-lrb-'
352 +-0.000593 O b'+1:lemma:c'
353 +-0.000597 OD b'+1:postag:VBN'
354 +-0.000854 Gtype b'+1:postag:NNS'
355 +-0.001125 O b'lemma:10'
356 +-0.001603 O b'-1:lemma:fresh'
357 +-0.002085 Supp b'-1:lemma:-'
358 +-0.002163 O b'+1:lemma:300'
359 +-0.002264 Air b'-1:postag:NNP'
360 +-0.002713 O b'+1:lemma:min'
361 +-0.003522 Air b'+1:postag:-LRB-'
362 +-0.003594 O b'-1:lemma:iptg'
363 +-0.004379 O b'lemma:cell'
364 +-0.004450 O b'+1:lemma:antibody'
365 +-0.007530 Gtype b'-1:postag:NNP'
366 +-0.011566 Air b'postag:CC'
367 +-0.011603 O b'+1:lemma:a'
368 +-0.011880 O b'+1:lemma:dpd'
369 +-0.013535 OD b'postag:NNS'
370 +-0.013622 Supp b'+1:lemma:glucose'
371 +-0.013806 O b'-1:lemma:the'
372 +-0.014085 O b'+1:lemma:25'
373 +-0.014120 OD b'-1:postag:DT'
374 +-0.016761 OD b'-1:lemma:a'
375 +-0.021729 OD b'+1:postag:-LRB-'
376 +-0.024283 O b'-1:lemma:25'
377 +-0.024519 O b'postag:VBP'
378 +-0.027011 OD b'+1:lemma:0.4'
379 +-0.027020 O b'+1:lemma:co2'
380 +-0.030020 O b'+1:lemma:mm'
381 +-0.030904 Gtype b'postag:NNS'
382 +-0.031338 O b'+1:lemma:grow'
383 +-0.032633 Gtype b'-1:postag:NN'
384 +-0.034461 Med b'-1:lemma:m63'
385 +-0.038347 O b'lemma:coli'
386 +-0.039331 Gtype b'+1:postag:IN'
387 +-0.040098 Air b'+1:postag:NN'
388 +-0.043802 O b'lemma:o2'
389 +-0.044786 Anti b'-1:postag:NN'
390 +-0.050998 Phase b'+1:postag:NN'
391 +-0.053029 Supp b'-1:postag:VBG'
392 +-0.059606 O b'+1:lemma:shake'
393 +-0.060227 O b'lemma:\xc2\xb0c'
394 +-0.061576 O b'+1:lemma:k-12'
395 +-0.068548 O b'lemma:mg/ml'
396 +-0.068548 O b'-1:lemma:150'
397 +-0.071993 O b'-1:lemma:minimal'
398 +-0.075882 OD b'+1:postag:CD'
399 +-0.076224 O b'lemma:glucose'
400 +-0.078957 O b'-1:lemma:at'
401 +-0.082806 O b'lemma:grow'
402 +-0.087424 OD b'-1:postag:NNS'
403 +-0.090506 Supp b'-1:postag:NN'
404 +-0.093124 Temp b'-1:lemma:\xc2\xb0c'
405 +-0.093134 O b'-1:lemma:-lrb-'
406 +-0.093606 O b'lemma:minimal'
407 +-0.094232 O b'+1:lemma:o2'
408 +-0.097879 O b'-1:lemma:mm'
409 +-0.098068 Med b'-1:postag:NN'
410 +-0.107118 O b'-1:lemma:o2'
411 +-0.118175 O b'+1:lemma:phase'
412 +-0.119815 Technique b'-1:lemma::'
413 +-0.130823 Temp b'postag:JJ'
414 +-0.132875 O b'+1:lemma:arginine'
415 +-0.134855 O b'-1:lemma:30'
416 +-0.146776 O b'lemma:aerobically'
417 +-0.147575 O b'-1:lemma:n2'
418 +-0.149484 OD b'postag:IN'
419 +-0.156867 Air b'postag:CD'
420 +-0.156918 O b'-1:lemma:from'
421 +-0.166087 Supp b'+1:postag:IN'
422 +-0.177934 O b'lemma:mg1655'
423 +-0.179064 Anti b'+1:postag:JJ'
424 +-0.179551 Supp b'lemma:and'
425 +-0.188276 O b'-1:lemma:um'
426 +-0.188276 O b'+1:lemma:paraquat'
427 +-0.189403 O b'lemma:n2'
428 +-0.195278 O b'lemma:\xce\xb4fur'
429 +-0.198127 Med b'+1:postag:IN'
430 +-0.214634 O b'+1:lemma:\xc2\xb0c'
431 +-0.215441 O b'lemma:30'
432 +-0.215519 O b'-1:lemma:e.'
433 +-0.226406 O b'-1:postag:IN'
434 +-0.226968 Gtype b'postag:CD'
435 +-0.227233 Phase b'-1:lemma:at'
436 +-0.230930 O b'-1:postag:VBN'
437 +-0.231525 O b'-1:lemma:of'
438 +-0.235093 O b'+1:postag:NNS'
439 +-0.235942 O b'+1:lemma:5'
440 +-0.237587 O b'+1:lemma:_'
441 +-0.253207 Supp b'+1:lemma:rifampicin'
442 +-0.254236 Gversion b'+1:postag:NN'
443 +-0.261414 Med b'postag:CD'
444 +-0.269201 O b'-1:postag:-LRB-'
445 +-0.283772 O b'-1:lemma:od600'
446 +-0.286133 O b'lemma:co2'
447 +-0.286584 O b'+1:lemma:or'
448 +-0.289081 O b'+1:lemma:-rrb-'
449 +-0.293131 O b'+1:lemma:cell'
450 +-0.293510 O b'-1:lemma:0.1'
451 +-0.315643 O b'lemma:phase'
452 +-0.317100 Air b'-1:postag:CC'
453 +-0.328206 Supp b'postag:CC'
454 +-0.328374 O b'-1:lemma:0.2'
455 +-0.342964 Supp b'+1:postag:VBN'
456 +-0.347291 O b'lemma:150'
457 +-0.347291 O b'+1:lemma:mg/ml'
458 +-0.349307 O b'lemma:od600'
459 +-0.351495 OD b'postag:JJ'
460 +-0.353086 Temp b'+1:lemma:to'
461 +-0.353086 Temp b'+1:postag:TO'
462 +-0.374885 O b'-1:lemma:mid-log'
463 +-0.378947 Air b'-1:postag:JJ'
464 +-0.382276 O b'postag:RB'
465 +-0.384726 pH b'postag:NN'
466 +-0.388651 O b'+1:lemma:until'
467 +-0.395876 O b'lemma:e.'
468 +-0.396410 O b'+1:lemma:.'
469 +-0.396410 O b'+1:postag:.'
470 +-0.419403 O b'-1:lemma:ml'
471 +-0.438819 O b'lemma:anaerobic'
472 +-0.441115 Agit b'postag:NN'
473 +-0.458507 Med b'+1:postag:NN'
474 +-0.467746 O b'-1:lemma:grow'
475 +-0.468347 OD b'+1:lemma:and'
476 +-0.477039 Anti b'+1:lemma:anti-fur'
477 +-0.477272 O b'+1:postag:-RRB-'
478 +-0.539475 Phase b'-1:postag:JJ'
479 +-0.544246 O b'-1:lemma:rifampicin'
480 +-0.554986 Technique b'-1:postag::'
481 +-0.557503 O b'-1:lemma:~'
482 +-0.566406 O b'-1:lemma:cra'
483 +-0.585219 O b'-1:lemma:sample'
484 +-0.592872 OD b'lemma:-lrb-'
485 +-0.597579 O b'+1:lemma:0.3'
486 +-0.637939 OD b'+1:postag:CC'
487 +-0.640528 Air b'+1:postag:JJ'
488 +-0.641855 O b'lemma:0.3'
489 +-0.663280 O b'lemma:20'
490 +-0.678531 O b'lemma:media'
491 +-0.679754 O b'+1:postag:IN'
492 +-0.692879 O b'+1:lemma:%'
493 +-0.704594 O b'lemma:of'
494 +-0.746312 O b'-1:lemma:co2'
495 +-0.752462 O b'lemma:dissolve'
496 +-0.774185 O b'+1:lemma:fecl2'
497 +-0.784660 Med b'-1:postag:IN'
498 +-0.813078 O b'-1:lemma:IP'
499 +-0.845987 O b'lemma:dpd'
500 +-0.856881 O b'+1:lemma:+'
501 +-0.917781 O b'-1:postag:VBG'
502 +-0.924251 O b'+1:lemma:g/l'
503 +-0.950062 Temp b'postag:NN'
504 +-0.956490 O b'-1:lemma:dissolve'
505 +-0.956490 O b'+1:lemma:methanol'
506 +-0.973571 OD b'+1:postag:NN'
507 +-0.985083 O b'-1:lemma:rpob'
508 +-1.088717 Supp b'+1:lemma:acetate'
509 +-1.116443 O b'lemma:0.1'
510 +-1.121770 O b'+1:lemma:at'
511 +-1.139282 O b'lemma:fecl2'
512 +-1.139658 O b'lemma:0.2'
513 +-1.143368 O b'lemma:2h'
514 +-1.143368 O b'-1:lemma:additional'
515 +-1.162871 O b'lemma:mid-log'
516 +-1.218300 O b'+1:lemma:in'
517 +-1.230428 OD b'postag:-LRB-'
518 +-1.237811 O b'+1:lemma:supplement'
519 +-1.238950 O b'-1:lemma:37'
520 +-1.269797 O b'+1:postag:VBG'
521 +-1.280950 O b'lemma:anaerobically'
522 +-1.360526 O b'lemma:37'
523 +-1.412947 O b'-1:postag::'
524 +-1.467612 O b'lemma:wt'
525 +-1.469772 O b'+1:lemma:hour'
526 +-1.551225 Supp b'-1:lemma:%'
527 +-1.646983 O b'lemma:methanol'
528 +-1.652478 O b'-1:lemma:nsrr'
529 +-1.705441 Phase b'postag:JJ'
530 +-1.865099 Anti b'postag:NNP'
531 +-2.110303 Supp b'postag:JJ'
532 +-2.251438 Air b'postag:NN'
533 +-2.402454 O b'lemma:rifampicin'
534 +-2.570647 O b'-1:lemma:ompr'
535 +-2.620057 O b'-1:lemma:2'
536 +-2.709520 O b'+1:lemma:2'
537 +-3.092706 O b'+1:lemma:1'
538 +-4.538028 O b'-1:lemma:_'
539 +-4.976237 O b'-1:lemma::'
540 +
1 +********** TRAINING AND TESTING REPORT **********
2 +Training file: training-data-set-70_v4.txt
3 +
4 +best params:{'c1': 0.04733824675634195, 'c2': 0.013567747033585223}
5 +best CV score:0.7954499755233463
6 +model size: 0.08M
7 +
8 +Flat F1: 0.8073047538765561
9 + precision recall f1-score support
10 +
11 + OD 1.000 0.405 0.577 37
12 + pH 1.000 1.000 1.000 12
13 + Technique 0.952 0.909 0.930 22
14 + Med 0.891 0.860 0.875 57
15 + Temp 0.818 1.000 0.900 18
16 + Vess 0.000 0.000 0.000 0
17 + Agit 0.000 0.000 0.000 0
18 + Phase 1.000 0.947 0.973 19
19 + Air 0.939 0.742 0.829 62
20 + Anti 1.000 0.444 0.615 9
21 + Strain 1.000 1.000 1.000 1
22 + Gtype 0.865 0.783 0.822 106
23 + Substrain 0.000 0.000 0.000 1
24 + Supp 0.869 0.684 0.765 136
25 + Gversion 0.000 0.000 0.000 0
26 +
27 +avg / total 0.901 0.748 0.807 480
28 +
29 +
30 +Top likely transitions:
31 +Agit -> Agit 6.351306
32 +OD -> OD 6.016578
33 +Temp -> Temp 5.927690
34 +Anti -> Anti 5.530188
35 +Med -> Med 5.290933
36 +Air -> Air 4.824974
37 +Gversion -> Gversion 4.795717
38 +Phase -> Phase 4.587222
39 +O -> O 4.562384
40 +Gtype -> Gtype 4.485788
41 +Supp -> Supp 4.175027
42 +Technique -> Technique 3.738966
43 +pH -> pH 2.445982
44 +Substrain -> Gtype 1.983414
45 +O -> Supp 1.704431
46 +Gtype -> Supp 1.702624
47 +Technique -> Air 1.053845
48 +O -> Technique 1.011581
49 +O -> Gtype 0.959004
50 +O -> Temp 0.852096
51 +Air -> O 0.791615
52 +Gtype -> pH 0.696397
53 +O -> Anti 0.684439
54 +O -> Gversion 0.269497
55 +Gtype -> Air 0.261457
56 +O -> Strain 0.143898
57 +Med -> O 0.029331
58 +O -> pH 0.007540
59 +O -> Vess 0.000124
60 +O -> Med 0.000090
61 +Temp -> O 0.000022
62 +Phase -> O -0.002114
63 +Vess -> O -0.020913
64 +O -> Phase -0.027016
65 +Anti -> Gtype -0.034769
66 +Gversion -> Air -0.042314
67 +Phase -> Air -0.063658
68 +O -> Agit -0.107236
69 +OD -> Technique -0.108455
70 +Supp -> pH -0.117168
71 +Gversion -> O -0.140630
72 +Anti -> O -0.151755
73 +Gtype -> Technique -0.152014
74 +Supp -> Phase -0.214979
75 +OD -> Supp -0.232643
76 +O -> OD -0.260286
77 +Supp -> Anti -0.275132
78 +Gtype -> Phase -0.278437
79 +Technique -> O -0.314521
80 +Phase -> Technique -0.315599
81 +
82 +
83 +Top unlikely transitions:
84 +Phase -> O -0.002114
85 +Vess -> O -0.020913
86 +O -> Phase -0.027016
87 +Anti -> Gtype -0.034769
88 +Gversion -> Air -0.042314
89 +Phase -> Air -0.063658
90 +O -> Agit -0.107236
91 +OD -> Technique -0.108455
92 +Supp -> pH -0.117168
93 +Gversion -> O -0.140630
94 +Anti -> O -0.151755
95 +Gtype -> Technique -0.152014
96 +Supp -> Phase -0.214979
97 +OD -> Supp -0.232643
98 +O -> OD -0.260286
99 +Supp -> Anti -0.275132
100 +Gtype -> Phase -0.278437
101 +Technique -> O -0.314521
102 +Phase -> Technique -0.315599
103 +Supp -> O -0.331781
104 +Med -> Air -0.373175
105 +Supp -> Temp -0.406898
106 +Gtype -> O -0.442607
107 +Temp -> Med -0.464337
108 +Gtype -> Gversion -0.493751
109 +Supp -> Gversion -0.560400
110 +Anti -> OD -0.563611
111 +Supp -> Technique -0.605347
112 +Gtype -> Med -0.614663
113 +Supp -> OD -0.660842
114 +Air -> Supp -0.707856
115 +OD -> Air -0.738038
116 +OD -> Gtype -0.750328
117 +Supp -> Gtype -0.775491
118 +Supp -> Air -0.783032
119 +Gtype -> Anti -0.848608
120 +Air -> Med -0.863324
121 +OD -> Med -0.930579
122 +Agit -> O -0.969044
123 +Air -> OD -0.995424
124 +Technique -> pH -1.068524
125 +OD -> O -1.148371
126 +O -> Air -1.151845
127 +Technique -> OD -1.233856
128 +Gtype -> OD -1.268038
129 +Technique -> Gtype -1.279158
130 +Substrain -> O -1.352003
131 +Supp -> Med -1.440706
132 +Med -> Supp -1.997092
133 +Phase -> OD -2.488972
134 +
135 +
136 +Top positive:
137 +8.290919 O b'lemma:_'
138 +7.385787 Phase b'lemma:stationary'
139 +7.051234 O b'lemma:1'
140 +6.894708 Supp b'lemma:Iron'
141 +6.675567 Air b'lemma:anaerobic'
142 +6.403841 Air b'lemma:aerobic'
143 +6.381259 Technique b'lemma:ChIP-exo'
144 +6.295199 Strain b'lemma:k-12'
145 +6.076363 O b'lemma:rpob'
146 +6.004917 O b'lemma:2'
147 +5.997376 Technique b'lemma:chipseq'
148 +5.756531 Supp b'lemma:pq'
149 +5.480849 O b'lemma:3'
150 +5.419549 Air b'-1:lemma:ChIP-Seq'
151 +5.377608 O b'-1:lemma:tag'
152 +5.236921 Gversion b'lemma:asm584v2'
153 +5.220500 Supp b'lemma:nitrate'
154 +5.194599 Gtype b'lemma:\xce\xb4cra'
155 +5.105810 O b'lemma:rep1'
156 +5.072402 Phase b'lemma:mid-log'
157 +5.067722 O b'postag:IN'
158 +5.062697 Med b'lemma:MOPS'
159 +5.031333 Supp b'lemma:nh4cl'
160 +5.013490 Gtype b'lemma:arca8myc'
161 +5.000342 Gtype b'lemma:flag-tag'
162 +5.000342 Gtype b'-1:lemma:c-terminal'
163 +4.890613 O b'lemma:rep2'
164 +4.886114 Substrain b'lemma:mg1655'
165 +4.864909 Supp b'lemma:glucose'
166 +4.809146 Supp b'+1:lemma:\xc2\xb5m'
167 +4.725613 Air b'lemma:Aerobic'
168 +4.660445 O b'lemma:rep3'
169 +4.614931 Med b'lemma:LB'
170 +4.549528 O b'lemma:Cra'
171 +4.411392 Gtype b'lemma:wt'
172 +4.409856 Technique b'lemma:rna-seq'
173 +4.384311 Gtype b'-1:lemma:\xe2\x88\x86'
174 +4.354696 O b'lemma:b'
175 +4.328794 Supp b'lemma:acetate'
176 +4.303499 Gtype b'lemma:delta-arca'
177 +4.292242 O b'lemma:Custom'
178 +4.271514 O b'-1:lemma:ChIP-exo'
179 +4.249183 Gtype b'lemma:fnr8myc'
180 +4.166692 O b'postag::'
181 +4.162283 Supp b'lemma:no3'
182 +4.142997 Technique b'lemma:chip-seq'
183 +4.139547 O b'lemma:\xcf\x8332'
184 +4.132690 Supp b'-1:lemma:Cra'
185 +4.123280 Supp b'lemma:Fe'
186 +4.117229 Anti b'lemma:none'
187 +4.089970 O b'-1:lemma:Aerobic'
188 +4.070800 O b'lemma:a'
189 +4.053427 Technique b'lemma:rnaseq'
190 +3.997780 O b'lemma:.'
191 +3.997780 O b'postag:.'
192 +3.955278 OD b'lemma:od450'
193 +3.952430 Med b'lemma:lb'
194 +3.926643 Anti b'lemma:seqa'
195 +3.901600 O b'+1:postag:RB'
196 +3.860379 Supp b'lemma:fructose'
197 +3.843887 O b'+1:lemma:od600'
198 +3.818270 Gversion b'lemma:nc'
199 +3.774402 Gtype b'lemma:type'
200 +3.769802 Gtype b'lemma:delta-fnr'
201 +3.749008 Med b'+1:lemma:0.4'
202 +3.723936 Gtype b'+1:lemma:type'
203 +3.716300 Gtype b'lemma:\xe2\x88\x86'
204 +3.702464 Air b'postag:RB'
205 +3.701643 Supp b'lemma:rifampicin'
206 +3.698023 Gversion b'lemma:chip-seq'
207 +3.685933 O b'lemma:-'
208 +3.684595 O b'-1:lemma:0.3-0.35'
209 +3.676777 Supp b'lemma:dpd'
210 +3.644945 OD b'lemma:od600'
211 +3.635765 Technique b'lemma:ChIP-Seq'
212 +3.623886 O b'lemma:CEL'
213 +3.599273 Supp b'+1:lemma:1'
214 +3.576564 OD b'+1:lemma:stationary'
215 +3.566248 Gtype b'lemma:\xce\xb4fur'
216 +3.461638 O b'-1:lemma:anaerobic'
217 +3.459278 Gtype b'lemma:nsrr'
218 +3.356330 pH b'lemma:ph5'
219 +3.356330 pH b'+1:lemma:.5'
220 +3.352106 O b'-1:lemma:glucose'
221 +3.340294 Supp b'+1:lemma:Deficient'
222 +3.338469 Supp b'lemma:arginine'
223 +3.337805 Gtype b'+1:lemma:with'
224 +3.333928 Strain b'+1:lemma:substr'
225 +3.322235 Anti b'lemma:anti-myc'
226 +3.308233 Gtype b'lemma:wild-type'
227 +3.291619 O b'lemma:with'
228 +3.274998 Vess b'lemma:flask'
229 +3.274998 Vess b'-1:lemma:warm'
230 +3.203208 Supp b'+1:lemma:2'
231 +3.169852 Med b'lemma:m63'
232 +3.132500 Gtype b'lemma:\xce\xb4soxs'
233 +3.105860 Med b'+1:lemma:2.0'
234 +3.077793 Gtype b'lemma:WT'
235 +3.074708 O b'lemma:oxyr'
236 +3.065934 Anti b'+1:lemma:antibody'
237 +3.065570 O b'lemma:s'
238 +3.051751 O b'-1:lemma:type'
239 +3.050447 O b'+1:lemma:o.d.'
240 +3.033846 Technique b'-1:lemma:IP'
241 +3.021636 O b'lemma:chip-arca'
242 +3.007962 Gtype b'lemma:\xce\xb4ompr'
243 +2.993470 O b'-1:lemma:stpa'
244 +2.985907 O b'-1:lemma:lb'
245 +2.982505 O b'lemma:chip'
246 +2.979425 O b'lemma:for'
247 +2.977744 O b'lemma:affyexp'
248 +2.974504 Gversion b'lemma:u00096'
249 +2.974504 Gversion b'+1:lemma:.2'
250 +2.951628 Supp b'lemma:nacl'
251 +2.929411 Supp b'+1:lemma:hour'
252 +2.918651 Med b'-1:lemma:ml'
253 +2.914880 Gversion b'lemma:.2'
254 +2.914880 Gversion b'-1:lemma:u00096'
255 +2.913751 O b'lemma:or'
256 +2.911773 O b'postag:VBN'
257 +2.882260 O b'+1:lemma:anti-fur'
258 +2.876894 O b'+1:lemma:chip-seq'
259 +2.868995 Gtype b'-1:lemma:ptac'
260 +2.866722 Temp b'lemma:\xc2\xb0c'
261 +2.863424 Supp b'+1:lemma:_'
262 +2.862778 O b'lemma:ompr'
263 +2.834787 Air b'lemma:Anaerobic'
264 +2.827994 Gversion b'-1:lemma:nc'
265 +2.824064 Temp b'-1:lemma:43'
266 +2.820717 O b'lemma:argr'
267 +2.820412 Gversion b'lemma:000913'
268 +2.749427 Anti b'lemma:anti-rpos'
269 +2.734729 Gtype b'+1:lemma:flagtag'
270 +2.732480 Supp b'-1:lemma:+'
271 +2.727515 O b'lemma:Lrp'
272 +2.719436 Phase b'+1:lemma:for'
273 +2.711551 Temp b'lemma:43'
274 +2.711404 Gtype b'lemma:deltaseqa'
275 +2.711404 Gtype b'-1:lemma:old'
276 +2.703630 Gtype b'lemma:pk4854'
277 +2.700766 O b'+1:lemma:pq'
278 +2.675879 Air b'lemma:anaerobically'
279 +2.664358 Gtype b'+1:lemma:pq'
280 +2.656000 Technique b'-1:lemma:input'
281 +2.651505 Temp b'-1:lemma:37'
282 +2.648470 O b'lemma:2-3'
283 +2.620313 Temp b'lemma:37'
284 +2.617008 Substrain b'+1:lemma:phtpg'
285 +2.612535 Technique b'-1:lemma:chip-exo'
286 +2.596752 Med b'+1:lemma:minimal'
287 +2.596648 O b'-1:lemma:dpd'
288 +2.596120 O b'lemma:at'
289 +2.593521 O b'postag:SYM'
290 +2.572579 Gtype b'-1:lemma:rpob'
291 +2.572348 O b'postag:CC'
292 +2.562481 O b'lemma:purr'
293 +2.559444 Gtype b'lemma:ptac'
294 +2.547961 O b'postag:DT'
295 +2.528953 Temp b'-1:lemma:sample'
296 +2.519081 Gtype b'+1:lemma:ph5'
297 +2.510093 O b'lemma:soxs'
298 +2.510093 O b'lemma:soxr'
299 +2.489436 pH b'lemma:.5'
300 +2.489436 pH b'-1:lemma:ph5'
301 +2.486692 O b'+1:lemma:sparging'
302 +2.468346 Air b'lemma:anerobically'
303 +2.466200 Gtype b'lemma:\xce\xb4oxyr'
304 +2.460573 O b'-1:lemma:l1'
305 +2.435676 Supp b'lemma:iptg'
306 +2.396322 Air b'-1:lemma:-'
307 +2.381121 Technique b'+1:lemma:chip-exo'
308 +2.375332 Med b'postag:NNP'
309 +2.369739 Supp b'lemma:Leu'
310 +2.367468 Temp b'-1:lemma:\xcf\x8332'
311 +2.358408 O b'lemma:Fur'
312 +2.318420 Supp b'lemma:Adenine'
313 +2.308664 Gtype b'+1:lemma:aerobic'
314 +2.284972 pH b'+1:postag:CD'
315 +2.278223 O b'-1:lemma:0.3'
316 +2.275175 O b'+1:lemma:mid-log'
317 +2.272071 Med b'lemma:L'
318 +2.272071 Med b'+1:lemma:broth'
319 +2.271694 Gversion b'+1:lemma:000913'
320 +2.263241 Temp b'+1:lemma:\xc2\xb0c'
321 +2.251200 Gtype b'lemma:\xce\xb4soxr'
322 +2.250951 Med b'-1:lemma:LB'
323 +2.232437 Phase b'lemma:phase'
324 +2.225558 O b'-1:lemma:\xc2\xb0c'
325 +2.210922 O b'lemma:pt7'
326 +2.195220 Med b'lemma:glucose'
327 +2.189252 Technique b'postag:NNP'
328 +2.171773 O b'lemma:chip-fnr'
329 +2.161995 Gtype b'lemma:dfnr'
330 +2.158766 O b'lemma:genotype/variation'
331 +2.150201 O b'+1:lemma:43'
332 +2.145901 Supp b'-1:lemma:\xc2\xb5m'
333 +2.141092 Supp b'lemma:leucine'
334 +2.114711 Gtype b'-1:lemma:nsrr'
335 +2.112477 O b'lemma:culture'
336 +2.110383 Supp b'+1:lemma:and'
337 +
338 +
339 +Top negative:
340 +-0.004206 Gtype b'-1:lemma:,'
341 +-0.004206 Gtype b'-1:postag:,'
342 +-0.004363 O b'+1:lemma:dissolve'
343 +-0.005226 Air b'-1:lemma:anaerobically'
344 +-0.006081 Med b'postag:-LRB-'
345 +-0.007482 O b'+1:lemma:25'
346 +-0.007505 Air b'+1:postag:-LRB-'
347 +-0.010695 O b'+1:lemma:delta'
348 +-0.010729 Gtype b'lemma:control'
349 +-0.015920 OD b'-1:postag:DT'
350 +-0.016476 Supp b'+1:lemma:glucose'
351 +-0.020393 O b'+1:lemma:o2'
352 +-0.020701 Air b'-1:lemma:-rrb-'
353 +-0.027434 O b'-1:postag:DT'
354 +-0.030363 Air b'postag:CD'
355 +-0.031961 O b'postag:RB'
356 +-0.035995 O b'lemma:aerobically'
357 +-0.040364 O b'lemma:n2'
358 +-0.040535 Med b'-1:postag:CD'
359 +-0.041176 Air b'-1:postag:-RRB-'
360 +-0.042452 OD b'+1:lemma:0.4'
361 +-0.044876 O b'-1:lemma:the'
362 +-0.046558 O b'-1:lemma:25'
363 +-0.047871 O b'+1:lemma:95'
364 +-0.048967 O b'-1:postag:IN'
365 +-0.050524 O b'+1:lemma:strain'
366 +-0.053326 Phase b'+1:postag:NN'
367 +-0.060668 O b'-1:lemma:e.'
368 +-0.070033 O b'lemma:e.'
369 +-0.070538 O b'+1:lemma:0.4'
370 +-0.071511 O b'+1:lemma:grow'
371 +-0.072393 Gtype b'+1:lemma:cra'
372 +-0.076483 Med b'postag:CD'
373 +-0.079707 O b'+1:lemma:or'
374 +-0.080785 O b'+1:lemma:5'
375 +-0.081991 OD b'+1:postag:CD'
376 +-0.097802 O b'lemma:glucose'
377 +-0.099284 O b'+1:lemma:b'
378 +-0.100727 Supp b'-1:lemma:and'
379 +-0.107163 Supp b'-1:postag:NN'
380 +-0.121273 O b'lemma:o2'
381 +-0.123375 Anti b'+1:postag:JJ'
382 +-0.128472 Supp b'-1:postag:VBG'
383 +-0.137982 O b'lemma:nacl'
384 +-0.138385 O b'-1:lemma:g/l'
385 +-0.140738 Med b'+1:lemma:media'
386 +-0.143230 O b'+1:lemma:.'
387 +-0.143230 O b'+1:postag:.'
388 +-0.147429 O b'-1:lemma:-lrb-'
389 +-0.150859 O b'+1:lemma:mm'
390 +-0.150867 Gtype b'postag:CD'
391 +-0.155869 O b'-1:lemma:mm'
392 +-0.157092 O b'-1:lemma:of'
393 +-0.160183 O b'+1:postag:IN'
394 +-0.161439 Gtype b'-1:postag:CD'
395 +-0.183365 Gtype b'-1:postag:DT'
396 +-0.184394 Supp b'+1:postag:IN'
397 +-0.185747 O b'+1:lemma:-rrb-'
398 +-0.188736 O b'-1:lemma:20'
399 +-0.189296 O b'-1:postag:-LRB-'
400 +-0.194391 O b'-1:lemma:o2'
401 +-0.196331 O b'lemma:grow'
402 +-0.197265 O b'lemma:m63'
403 +-0.202228 Supp b'lemma:and'
404 +-0.208828 Gtype b'lemma:_'
405 +-0.213147 O b'lemma:co2'
406 +-0.216510 O b'+1:lemma:Aerobic'
407 +-0.219766 O b'-1:lemma:um'
408 +-0.219766 O b'+1:lemma:paraquat'
409 +-0.222760 O b'-1:lemma:n2'
410 +-0.223418 Med b'-1:postag:NN'
411 +-0.226489 O b'-1:lemma:minimal'
412 +-0.229253 O b'-1:postag:VBN'
413 +-0.229413 OD b'+1:lemma:mid-log'
414 +-0.235205 Technique b'-1:lemma::'
415 +-0.245927 O b'+1:lemma:cell'
416 +-0.259152 O b'+1:lemma:shake'
417 +-0.259231 O b'-1:lemma:with'
418 +-0.260969 O b'lemma:lb'
419 +-0.262122 O b'lemma:\xc2\xb0c'
420 +-0.262570 Med b'+1:postag:NNS'
421 +-0.267584 O b'+1:lemma:minimal'
422 +-0.268702 O b'-1:lemma:fresh'
423 +-0.274046 Supp b'-1:postag:NNP'
424 +-0.283215 Temp b'postag:JJ'
425 +-0.289216 O b'+1:postag:-RRB-'
426 +-0.298829 Med b'+1:postag:NN'
427 +-0.300030 O b'lemma:k-12'
428 +-0.303893 Supp b'+1:postag:VBN'
429 +-0.304837 O b'+1:lemma:until'
430 +-0.305487 O b'-1:lemma:mid-log'
431 +-0.314457 O b'lemma:30'
432 +-0.318478 O b'-1:lemma:\xe2\x88\x86'
433 +-0.318630 OD b'postag:JJ'
434 +-0.320224 Gtype b'+1:lemma:\xe2\x88\x86'
435 +-0.328379 O b'lemma:mg1655'
436 +-0.332214 O b'-1:lemma:30'
437 +-0.336273 O b'+1:lemma:phase'
438 +-0.343858 O b'-1:lemma:0.1'
439 +-0.353210 O b'-1:lemma:1'
440 +-0.363425 O b'lemma:minimal'
441 +-0.367846 O b'-1:lemma:from'
442 +-0.393937 Gversion b'+1:postag:NN'
443 +-0.407622 Air b'-1:lemma:or'
444 +-0.419752 Phase b'-1:lemma:at'
445 +-0.419908 Med b'+1:postag:IN'
446 +-0.434159 OD b'+1:postag:NN'
447 +-0.434388 Temp b'-1:lemma:\xc2\xb0c'
448 +-0.437451 OD b'+1:lemma:and'
449 +-0.450338 O b'-1:lemma:rifampicin'
450 +-0.450644 O b'+1:lemma:%'
451 +-0.460508 O b'+1:lemma:_'
452 +-0.468703 O b'-1:lemma:od600'
453 +-0.471110 O b'+1:lemma:c'
454 +-0.473012 OD b'+1:postag:CC'
455 +-0.473111 O b'+1:lemma:rep1'
456 +-0.476279 O b'lemma:purify'
457 +-0.486329 O b'-1:lemma:iptg'
458 +-0.490766 Gtype b'-1:postag:SYM'
459 +-0.492855 O b'+1:lemma:\xc2\xb0c'
460 +-0.520331 Supp b'+1:lemma:rifampicin'
461 +-0.521486 Gtype b'lemma:delta'
462 +-0.544638 O b'lemma:phase'
463 +-0.549770 Supp b'postag:CC'
464 +-0.574118 Technique b'-1:postag::'
465 +-0.588060 O b'lemma:\xe2\x88\x86'
466 +-0.589911 O b'lemma:dissolve'
467 +-0.600471 O b'-1:lemma:until'
468 +-0.605867 OD b'lemma:-lrb-'
469 +-0.606846 O b'-1:lemma:grow'
470 +-0.615232 O b'+1:postag:NNS'
471 +-0.621806 O b'-1:lemma:cra'
472 +-0.628236 O b'+1:lemma:300'
473 +-0.629162 pH b'postag:NN'
474 +-0.647995 O b'+1:lemma:arginine'
475 +-0.663009 O b'lemma:150'
476 +-0.663009 O b'+1:lemma:mg/ml'
477 +-0.668956 O b'lemma:media'
478 +-0.687046 OD b'postag:-LRB-'
479 +-0.688477 Anti b'+1:lemma:anti-fur'
480 +-0.696641 Phase b'-1:postag:JJ'
481 +-0.720714 O b'lemma:od600'
482 +-0.740400 O b'+1:lemma:0.3'
483 +-0.753503 O b'-1:postag:VBG'
484 +-0.798903 O b'lemma:anaerobically'
485 +-0.798945 O b'-1:lemma:0.2'
486 +-0.800846 Med b'-1:postag:IN'
487 +-0.802642 O b'lemma:dpd'
488 +-0.829848 O b'+1:postag:VBG'
489 +-0.837375 O b'lemma:20'
490 +-0.843836 Temp b'+1:lemma:to'
491 +-0.843836 Temp b'+1:postag:TO'
492 +-0.861567 O b'lemma:anaerobic'
493 +-0.895410 O b'-1:lemma:co2'
494 +-0.935654 Supp b'+1:lemma:acetate'
495 +-0.962115 O b'+1:lemma:fecl2'
496 +-0.965287 O b'-1:lemma:ml'
497 +-0.992440 Temp b'postag:NN'
498 +-1.012409 Air b'-1:postag:JJ'
499 +-1.037489 O b'lemma:0.3'
500 +-1.038206 O b'lemma:fecl2'
501 +-1.045928 O b'-1:lemma:~'
502 +-1.050208 O b'lemma:0.1'
503 +-1.059403 O b'postag:VBP'
504 +-1.082188 O b'-1:postag::'
505 +-1.107761 O b'lemma:mid-log'
506 +-1.113185 O b'lemma:\xce\xb4fur'
507 +-1.123078 O b'lemma:0.2'
508 +-1.128103 O b'-1:lemma:sample'
509 +-1.194487 Supp b'-1:lemma:%'
510 +-1.213453 Air b'postag:NN'
511 +-1.229252 O b'lemma:of'
512 +-1.235299 O b'+1:lemma:supplement'
513 +-1.238904 O b'lemma:37'
514 +-1.267382 O b'lemma:2h'
515 +-1.267382 O b'-1:lemma:additional'
516 +-1.275201 O b'-1:lemma:dissolve'
517 +-1.275201 O b'+1:lemma:methanol'
518 +-1.291651 O b'+1:lemma:in'
519 +-1.453841 O b'+1:lemma:at'
520 +-1.495880 Air b'+1:postag:JJ'
521 +-1.522603 Anti b'postag:NNP'
522 +-1.573726 O b'+1:lemma:g/l'
523 +-1.603806 O b'-1:lemma:ompr'
524 +-1.605609 Phase b'postag:JJ'
525 +-1.643331 O b'-1:lemma:rpob'
526 +-1.700527 O b'-1:lemma:37'
527 +-1.724176 O b'-1:lemma:IP'
528 +-1.756223 O b'-1:lemma:nsrr'
529 +-1.790376 O b'+1:lemma:+'
530 +-1.794994 O b'lemma:methanol'
531 +-1.802577 Supp b'postag:JJ'
532 +-1.803599 O b'lemma:wt'
533 +-1.870737 O b'lemma:rifampicin'
534 +-2.105365 O b'-1:lemma:2'
535 +-2.201462 O b'+1:lemma:2'
536 +-2.218990 O b'+1:lemma:hour'
537 +-2.783349 O b'+1:lemma:1'
538 +-3.830507 O b'-1:lemma:_'
539 +-4.238490 O b'-1:lemma::'
540 +
1 +********** TRAINING AND TESTING REPORT **********
2 +Training file: training-data-set-70_v4.txt
3 +
4 +best params:{'c1': 0.28812013544306553, 'c2': 0.007295583222860682}
5 +best CV score:0.7989041592425109
6 +model size: 0.06M
7 +
8 +Flat F1: 0.7893461428977414
9 + precision recall f1-score support
10 +
11 + OD 1.000 0.405 0.577 37
12 + pH 1.000 1.000 1.000 12
13 + Technique 0.952 0.909 0.930 22
14 + Med 1.000 0.842 0.914 57
15 + Temp 0.818 1.000 0.900 18
16 + Vess 0.000 0.000 0.000 0
17 + Agit 0.000 0.000 0.000 0
18 + Phase 1.000 0.895 0.944 19
19 + Air 0.780 0.742 0.760 62
20 + Anti 0.500 0.444 0.471 9
21 + Strain 1.000 1.000 1.000 1
22 + Gtype 0.854 0.774 0.812 106
23 + Substrain 0.000 0.000 0.000 1
24 + Supp 0.802 0.684 0.738 136
25 + Gversion 0.000 0.000 0.000 0
26 +
27 +avg / total 0.863 0.742 0.789 480
28 +
29 +
30 +Top likely transitions:
31 +Agit -> Agit 6.356818
32 +OD -> OD 6.348289
33 +Temp -> Temp 5.553063
34 +Med -> Med 5.370053
35 +Anti -> Anti 5.276075
36 +Air -> Air 5.018155
37 +Gtype -> Gtype 4.515516
38 +Gversion -> Gversion 4.398480
39 +Phase -> Phase 4.359659
40 +O -> O 4.293965
41 +Technique -> Technique 4.237543
42 +Supp -> Supp 4.146423
43 +O -> Supp 1.964836
44 +Gtype -> Supp 1.866470
45 +pH -> pH 1.685265
46 +Air -> O 1.614236
47 +Substrain -> Gtype 1.463550
48 +O -> Technique 1.388918
49 +O -> Gtype 1.222957
50 +O -> Temp 0.798237
51 +Med -> O 0.601567
52 +O -> Anti 0.587178
53 +Technique -> Air 0.378127
54 +O -> Gversion 0.328551
55 +OD -> Phase 0.308573
56 +Temp -> O 0.289779
57 +Supp -> O 0.253243
58 +O -> Med 0.178828
59 +Phase -> O 0.132350
60 +Gtype -> pH 0.097473
61 +O -> Phase 0.003637
62 +Gtype -> Air 0.001121
63 +Supp -> Air -0.008182
64 +Technique -> Gtype -0.085945
65 +Gtype -> Anti -0.165395
66 +Gtype -> O -0.277440
67 +OD -> O -0.365628
68 +Agit -> O -0.521571
69 +Gtype -> OD -0.554390
70 +O -> Air -0.784770
71 +Supp -> Med -0.806802
72 +Substrain -> O -0.835873
73 +Med -> Supp -0.906570
74 +Phase -> OD -0.993184
75 +
76 +
77 +Top unlikely transitions:
78 +Agit -> Agit 6.356818
79 +OD -> OD 6.348289
80 +Temp -> Temp 5.553063
81 +Med -> Med 5.370053
82 +Anti -> Anti 5.276075
83 +Air -> Air 5.018155
84 +Gtype -> Gtype 4.515516
85 +Gversion -> Gversion 4.398480
86 +Phase -> Phase 4.359659
87 +O -> O 4.293965
88 +Technique -> Technique 4.237543
89 +Supp -> Supp 4.146423
90 +O -> Supp 1.964836
91 +Gtype -> Supp 1.866470
92 +pH -> pH 1.685265
93 +Air -> O 1.614236
94 +Substrain -> Gtype 1.463550
95 +O -> Technique 1.388918
96 +O -> Gtype 1.222957
97 +O -> Temp 0.798237
98 +Med -> O 0.601567
99 +O -> Anti 0.587178
100 +Technique -> Air 0.378127
101 +O -> Gversion 0.328551
102 +OD -> Phase 0.308573
103 +Temp -> O 0.289779
104 +Supp -> O 0.253243
105 +O -> Med 0.178828
106 +Phase -> O 0.132350
107 +Gtype -> pH 0.097473
108 +O -> Phase 0.003637
109 +Gtype -> Air 0.001121
110 +Supp -> Air -0.008182
111 +Technique -> Gtype -0.085945
112 +Gtype -> Anti -0.165395
113 +Gtype -> O -0.277440
114 +OD -> O -0.365628
115 +Agit -> O -0.521571
116 +Gtype -> OD -0.554390
117 +O -> Air -0.784770
118 +Supp -> Med -0.806802
119 +Substrain -> O -0.835873
120 +Med -> Supp -0.906570
121 +Phase -> OD -0.993184
122 +
123 +
124 +Top positive:
125 +8.456899 Supp b'lemma:Iron'
126 +7.968467 O b'lemma:_'
127 +7.452197 Air b'lemma:anaerobic'
128 +7.437960 Air b'lemma:aerobic'
129 +7.396388 Technique b'lemma:ChIP-exo'
130 +7.187671 O b'lemma:1'
131 +6.882632 Phase b'lemma:stationary'
132 +6.605608 Supp b'lemma:nitrate'
133 +6.530209 Strain b'lemma:k-12'
134 +6.203118 Air b'-1:lemma:ChIP-Seq'
135 +6.007441 Phase b'lemma:mid-log'
136 +5.856483 O b'lemma:rpob'
137 +5.727633 O b'lemma:2'
138 +5.691995 O b'lemma:3'
139 +5.621467 Technique b'lemma:chipseq'
140 +5.604648 Substrain b'lemma:mg1655'
141 +5.596923 Technique b'lemma:ChIP-Seq'
142 +5.568237 Gtype b'lemma:type'
143 +5.509620 Med b'lemma:MOPS'
144 +5.475086 Gversion b'lemma:asm584v2'
145 +5.234945 O b'lemma:\xcf\x8332'
146 +5.062729 O b'postag:IN'
147 +5.021516 Supp b'lemma:pq'
148 +4.929591 Air b'lemma:Aerobic'
149 +4.874521 O b'lemma:Custom'
150 +4.858511 Gversion b'lemma:nc'
151 +4.830173 Med b'lemma:LB'
152 +4.792027 Gtype b'lemma:\xce\xb4cra'
153 +4.771925 OD b'lemma:od600'
154 +4.722214 O b'lemma:rep1'
155 +4.615430 O b'postag::'
156 +4.604643 Supp b'+1:lemma:\xc2\xb5m'
157 +4.516978 O b'lemma:b'
158 +4.505623 Gtype b'lemma:flag-tag'
159 +4.505623 Gtype b'-1:lemma:c-terminal'
160 +4.503645 Med b'lemma:lb'
161 +4.444381 Supp b'lemma:nh4cl'
162 +4.432940 O b'-1:lemma:tag'
163 +4.401594 O b'lemma:rep2'
164 +4.365296 Gtype b'+1:lemma:type'
165 +4.331532 Gtype b'-1:lemma:\xe2\x88\x86'
166 +4.318893 O b'lemma:rep3'
167 +4.280628 O b'-1:lemma:ChIP-exo'
168 +4.273779 O b'lemma:a'
169 +4.191200 OD b'lemma:od450'
170 +4.187860 Gtype b'lemma:wt'
171 +4.184958 Technique b'lemma:rna-seq'
172 +4.089199 Supp b'lemma:glucose'
173 +4.068712 Temp b'-1:lemma:sample'
174 +4.066149 Gtype b'lemma:arca8myc'
175 +3.877291 O b'lemma:Cra'
176 +3.835115 Gtype b'lemma:nsrr'
177 +3.739614 Supp b'lemma:Fe'
178 +3.722246 Technique b'lemma:chip-seq'
179 +3.715540 O b'+1:lemma:od600'
180 +3.678000 Gtype b'lemma:delta-arca'
181 +3.610668 Gtype b'lemma:\xe2\x88\x86'
182 +3.517468 Med b'+1:lemma:0.4'
183 +3.508191 O b'lemma:.'
184 +3.508191 O b'postag:.'
185 +3.483906 Gtype b'lemma:fnr8myc'
186 +3.468892 Supp b'lemma:acetate'
187 +3.438457 Vess b'lemma:flask'
188 +3.438457 Vess b'-1:lemma:warm'
189 +3.400184 Supp b'lemma:rifampicin'
190 +3.396565 Technique b'lemma:rnaseq'
191 +3.379201 Anti b'lemma:none'
192 +3.369352 O b'-1:lemma:Aerobic'
193 +3.366768 O b'-1:lemma:type'
194 +3.310195 Supp b'lemma:no3'
195 +3.306542 Gtype b'lemma:\xce\xb4fur'
196 +3.289509 O b'-1:lemma:0.3-0.35'
197 +3.240918 Gtype b'lemma:delta-fnr'
198 +3.228917 Supp b'lemma:fructose'
199 +3.199686 Supp b'lemma:dpd'
200 +3.182132 O b'lemma:-'
201 +3.174434 Gversion b'-1:lemma:nc'
202 +3.160676 OD b'+1:lemma:stationary'
203 +3.140034 Supp b'lemma:arginine'
204 +3.107677 O b'postag:VBN'
205 +3.075194 Technique b'-1:lemma:IP'
206 +3.054797 Anti b'+1:lemma:antibody'
207 +2.967185 Supp b'+1:lemma:1'
208 +2.948061 pH b'lemma:ph5'
209 +2.948061 pH b'+1:lemma:.5'
210 +2.919290 Gtype b'-1:lemma:rpob'
211 +2.909319 Anti b'lemma:seqa'
212 +2.876363 O b'lemma:chip'
213 +2.856949 Med b'+1:lemma:minimal'
214 +2.846997 Gtype b'+1:lemma:ph5'
215 +2.846043 Gversion b'lemma:u00096'
216 +2.846043 Gversion b'+1:lemma:.2'
217 +2.842541 Supp b'lemma:20'
218 +2.813149 Gversion b'lemma:chip-seq'
219 +2.799253 Temp b'-1:lemma:\xcf\x8332'
220 +2.787282 O b'-1:lemma:glucose'
221 +2.767972 Anti b'lemma:anti-rpos'
222 +2.763663 Gtype b'lemma:\xce\xb4ompr'
223 +2.762526 O b'postag:DT'
224 +2.753494 O b'postag:CC'
225 +2.734024 Supp b'+1:lemma:2'
226 +2.713273 O b'lemma:CEL'
227 +2.711953 Supp b'-1:lemma:+'
228 +2.708255 Gtype b'+1:lemma:with'
229 +2.662841 Air b'postag:RB'
230 +2.655147 O b'+1:postag:RB'
231 +2.622484 Temp b'-1:lemma:43'
232 +2.621064 Anti b'lemma:anti-myc'
233 +2.585376 O b'lemma:with'
234 +2.579506 Gtype b'+1:lemma:pq'
235 +2.574119 Med b'lemma:m63'
236 +2.560671 Gtype b'-1:lemma:ptac'
237 +2.530970 Supp b'lemma:iptg'
238 +2.522165 Gversion b'lemma:000913'
239 +2.522038 O b'-1:lemma:0.3'
240 +2.518142 O b'lemma:or'
241 +2.510254 pH b'lemma:.5'
242 +2.510254 pH b'-1:lemma:ph5'
243 +2.499838 Gtype b'lemma:wild-type'
244 +2.496012 O b'-1:lemma:anaerobic'
245 +2.493145 O b'+1:postag:NNP'
246 +2.432959 O b'+1:lemma:o.d.'
247 +2.423786 Supp b'lemma:nacl'
248 +2.374439 Gversion b'lemma:.2'
249 +2.374439 Gversion b'-1:lemma:u00096'
250 +2.371897 Supp b'-1:lemma:Cra'
251 +2.333418 Technique b'+1:lemma:chip-exo'
252 +2.330714 Technique b'-1:lemma:chip-exo'
253 +2.318227 Gtype b'+1:lemma:flagtag'
254 +2.299023 Supp b'+1:lemma:_'
255 +2.291540 Supp b'-1:lemma:\xc2\xb5m'
256 +2.270555 Air b'-1:lemma:-'
257 +2.258400 O b'postag:VBG'
258 +2.241112 O b'-1:lemma:l1'
259 +2.239653 Temp b'lemma:\xc2\xb0c'
260 +2.239203 O b'-1:lemma:lb'
261 +2.216105 Med b'lemma:media'
262 +2.215247 Med b'-1:lemma:glucose'
263 +2.198544 O b'lemma:s'
264 +2.181192 Med b'+1:lemma:2.0'
265 +2.180737 Supp b'-1:lemma:with'
266 +2.151013 O b'-1:lemma:\xc2\xb0c'
267 +2.122011 O b'lemma:culture'
268 +2.119623 Gtype b'lemma:\xce\xb4soxs'
269 +2.118038 O b'+1:lemma:pq'
270 +2.107784 Strain b'+1:lemma:substr'
271 +2.084102 Temp b'-1:lemma:37'
272 +2.034197 Med b'lemma:L'
273 +2.034197 Med b'+1:lemma:broth'
274 +2.033322 OD b'-1:lemma:~'
275 +2.031873 Temp b'lemma:37'
276 +2.021465 Air b'lemma:anaerobically'
277 +2.013276 O b'lemma:oxyr'
278 +1.993546 pH b'+1:postag:CD'
279 +1.990912 Temp b'lemma:43'
280 +1.970179 Gtype b'lemma:pk4854'
281 +1.965724 O b'lemma:escherichia'
282 +1.928351 O b'lemma:affyexp'
283 +1.918099 Gtype b'-1:lemma:nsrr'
284 +1.912439 Gversion b'postag:CD'
285 +1.912210 Gtype b'+1:lemma:_'
286 +1.903180 Temp b'+1:lemma:\xc2\xb0c'
287 +1.901831 O b'-1:lemma:media'
288 +1.893202 Supp b'lemma:Leu'
289 +1.888140 O b'+1:lemma:chip-seq'
290 +1.885088 Supp b'lemma:methanol'
291 +1.864512 Med b'+1:lemma:supplement'
292 +1.843743 Gtype b'-1:postag:VBG'
293 +1.840860 Med b'-1:lemma:ml'
294 +1.833228 O b'lemma:genotype/variation'
295 +1.830405 Air b'-1:lemma:co2'
296 +1.824009 OD b'lemma:0.3'
297 +1.823612 O b'-1:lemma:stpa'
298 +1.820300 O b'+1:lemma:sparging'
299 +1.820114 Gtype b'lemma:deltaseqa'
300 +1.820114 Gtype b'-1:lemma:old'
301 +1.808084 O b'lemma:at'
302 +1.804795 Temp b'+1:lemma:and'
303 +1.793786 Gtype b'lemma:ptac'
304 +1.792476 Temp b'lemma:30'
305 +1.780844 Supp b'+1:lemma:hour'
306 +1.749460 Supp b'lemma:of'
307 +1.723530 O b'lemma:condition'
308 +1.717109 Phase b'-1:lemma:mid-log'
309 +1.711480 Med b'+1:lemma:g/l'
310 +1.709245 Gtype b'-1:lemma:_'
311 +1.702188 Gtype b'-1:lemma:phtpg'
312 +1.695199 O b'-1:lemma:dpd'
313 +1.690508 Supp b'lemma:0.2'
314 +1.688329 Air b'-1:postag:CD'
315 +1.682363 Technique b'-1:lemma:_'
316 +1.681577 Phase b'+1:lemma:for'
317 +1.675654 Med b'postag:NNP'
318 +1.654545 O b'lemma:Lrp'
319 +1.636356 Gtype b'+1:postag::'
320 +1.629183 Technique b'-1:lemma:1'
321 +1.628579 Technique b'-1:lemma:input'
322 +1.626463 Med b'lemma:glucose'
323 +1.615682 Temp b'-1:lemma:30'
324 +1.596658 Supp b'lemma:Adenine'
325 +
326 +
327 +Top negative:
328 +0.017267 O b'-1:lemma:phase'
329 +0.015360 O b'-1:lemma:Fur'
330 +0.015015 Gtype b'lemma:-rcb-'
331 +0.014734 Air b'lemma:-lrb-'
332 +0.013480 Phase b'+1:lemma:aerobically'
333 +0.013397 O b'-1:lemma:be'
334 +0.012964 O b'lemma:fresh'
335 +0.012612 Temp b'+1:postag:-RRB-'
336 +0.011601 O b'lemma:2-3'
337 +0.010954 OD b'postag:CC'
338 +0.009883 Med b'+1:postag:VBG'
339 +0.008416 Med b'-1:postag:NNP'
340 +0.007746 Phase b'+1:postag:RB'
341 +0.007283 O b'lemma:acetate'
342 +0.006890 Temp b'-1:postag:NNS'
343 +0.005794 O b'-1:postag:VBD'
344 +0.005770 O b'+1:lemma:n2'
345 +0.005411 Gversion b'-1:postag::'
346 +0.005130 Gtype b'lemma:-lcb-'
347 +0.003653 Med b'-1:lemma:-rrb-'
348 +0.003433 O b'-1:lemma:m63'
349 +0.003399 OD b'postag:CD'
350 +0.003303 Anti b'+1:postag:-LRB-'
351 +0.003264 Gtype b'lemma:cra'
352 +0.003037 Phase b'-1:postag:IN'
353 +0.002641 O b'+1:lemma:ChIP-Seq'
354 +0.001833 O b'-1:lemma:with'
355 +0.001345 O b'-1:postag:VBZ'
356 +0.001191 OD b'-1:lemma:at'
357 +0.001140 Supp b'+1:lemma:of'
358 +0.001083 Med b'-1:postag::'
359 +0.000969 O b'+1:lemma:anerobically'
360 +0.000925 O b'+1:lemma:genbank'
361 +0.000915 O b'-1:lemma:total'
362 +0.000846 O b'postag:VBZ'
363 +0.000778 Air b'+1:lemma:culture'
364 +0.000629 O b'lemma:express'
365 +0.000629 O b'+1:lemma:nsrr'
366 +0.000580 Air b'postag:-RRB-'
367 +0.000523 Supp b'+1:lemma:dissolve'
368 +0.000475 O b'lemma:70'
369 +0.000346 Supp b'-1:postag:VBN'
370 +0.000255 O b'+1:lemma:anaerobically'
371 +0.000233 O b'+1:postag:-LRB-'
372 +0.000229 Air b'lemma:95'
373 +0.000124 Agit b'lemma:bath'
374 +0.000124 Agit b'-1:lemma:water'
375 +0.000123 Agit b'+1:lemma:shake'
376 +0.000098 O b'+1:lemma:_'
377 +0.000070 Gtype b'+1:lemma:control'
378 +0.000049 Anti b'lemma:tag'
379 +0.000044 O b'lemma:glucose'
380 +0.000043 Agit b'+1:lemma:at'
381 +0.000042 Agit b'-1:postag:DT'
382 +0.000033 Air b'-1:lemma:95'
383 +0.000027 Temp b'+1:postag:VB'
384 +0.000027 O b'+1:lemma:wt'
385 +0.000025 O b'lemma:~'
386 +0.000024 Agit b'postag:IN'
387 +0.000018 OD b'-1:lemma:mg1655'
388 +0.000012 OD b'lemma:\xce\xb4soxr'
389 +0.000009 Supp b'lemma:paraquat'
390 +0.000003 Vess b'+1:postag:IN'
391 +0.000001 Med b'+1:lemma:with'
392 +-0.000003 Supp b'+1:postag:VBN'
393 +-0.000004 O b'-1:lemma:sample'
394 +-0.000016 O b'lemma:150'
395 +-0.000016 O b'+1:lemma:mg/ml'
396 +-0.000020 O b'+1:lemma:shake'
397 +-0.000023 OD b'+1:postag:-LRB-'
398 +-0.000033 O b'lemma:anaerobic'
399 +-0.000042 O b'-1:lemma:at'
400 +-0.000051 O b'lemma:e.'
401 +-0.000122 O b'-1:lemma:0.1'
402 +-0.000150 O b'-1:lemma:e.'
403 +-0.000237 Gtype b'+1:postag:NNS'
404 +-0.000353 O b'-1:lemma:rifampicin'
405 +-0.000482 Gtype b'+1:lemma:-lrb-'
406 +-0.000998 O b'-1:lemma:ml'
407 +-0.002220 Gtype b'postag:CD'
408 +-0.002782 Gtype b'-1:postag:NN'
409 +-0.002824 Med b'postag:CD'
410 +-0.003203 Air b'postag:-LRB-'
411 +-0.005019 O b'+1:lemma:phase'
412 +-0.008101 Supp b'-1:postag:NN'
413 +-0.008157 Air b'+1:lemma:-lrb-'
414 +-0.009984 Air b'lemma:,'
415 +-0.009984 Air b'postag:,'
416 +-0.009987 Gtype b'-1:postag:CD'
417 +-0.011620 O b'lemma:30'
418 +-0.011986 Supp b'+1:lemma:-rrb-'
419 +-0.012348 Phase b'+1:postag:NN'
420 +-0.012465 Supp b'+1:postag:-RRB-'
421 +-0.016199 O b'+1:lemma:c'
422 +-0.017044 Air b'+1:postag:-RRB-'
423 +-0.018057 Med b'-1:postag:IN'
424 +-0.018532 OD b'+1:postag:CD'
425 +-0.018715 O b'-1:lemma:1'
426 +-0.028572 O b'+1:lemma:arginine'
427 +-0.032917 Anti b'+1:postag:JJ'
428 +-0.033839 Phase b'-1:postag:NN'
429 +-0.035292 O b'-1:lemma:5'
430 +-0.035894 O b'lemma:co2'
431 +-0.037511 O b'-1:lemma:30'
432 +-0.050917 Air b'-1:postag:VBN'
433 +-0.051574 Air b'postag:CD'
434 +-0.052755 Air b'+1:lemma:-rrb-'
435 +-0.053416 Air b'-1:postag:RB'
436 +-0.054843 Air b'-1:lemma:or'
437 +-0.056713 OD b'postag:JJ'
438 +-0.066384 O b'+1:lemma:5'
439 +-0.075993 Air b'-1:lemma:and'
440 +-0.077374 O b'-1:lemma:~'
441 +-0.079056 Air b'-1:lemma:-lrb-'
442 +-0.080674 Supp b'postag:CC'
443 +-0.081179 O b'-1:lemma:,'
444 +-0.081179 O b'-1:postag:,'
445 +-0.091063 Air b'-1:postag:-LRB-'
446 +-0.104880 O b'-1:lemma:-lrb-'
447 +-0.116778 Gversion b'+1:postag:NN'
448 +-0.117338 Med b'+1:postag:IN'
449 +-0.156891 O b'-1:postag:VBN'
450 +-0.158460 O b'+1:lemma:300'
451 +-0.159376 Phase b'-1:lemma:at'
452 +-0.163043 O b'+1:postag:NNS'
453 +-0.185937 O b'-1:lemma:cra'
454 +-0.198845 pH b'postag:NN'
455 +-0.202021 Med b'-1:postag:NN'
456 +-0.206164 O b'-1:postag:IN'
457 +-0.210478 O b'-1:lemma:from'
458 +-0.224002 O b'+1:lemma:hour'
459 +-0.228689 O b'+1:lemma:-rrb-'
460 +-0.230127 Temp b'postag:JJ'
461 +-0.232439 O b'+1:lemma:.'
462 +-0.232439 O b'+1:postag:.'
463 +-0.261795 O b'lemma:0.3'
464 +-0.276668 O b'+1:lemma:%'
465 +-0.283202 O b'+1:postag:IN'
466 +-0.291477 O b'lemma:dissolve'
467 +-0.294314 O b'-1:lemma:of'
468 +-0.332798 O b'-1:postag:-LRB-'
469 +-0.348211 Temp b'postag:NN'
470 +-0.361228 O b'lemma:od600'
471 +-0.373795 O b'lemma:phase'
472 +-0.395276 Med b'+1:postag:NN'
473 +-0.405822 O b'+1:lemma:+'
474 +-0.406990 Supp b'-1:lemma:%'
475 +-0.409533 Temp b'+1:lemma:to'
476 +-0.409533 Temp b'+1:postag:TO'
477 +-0.419386 O b'lemma:anaerobically'
478 +-0.421572 O b'+1:postag:-RRB-'
479 +-0.460490 Air b'-1:postag:JJ'
480 +-0.467245 Technique b'-1:postag::'
481 +-0.476757 Supp b'+1:lemma:rifampicin'
482 +-0.502746 O b'lemma:media'
483 +-0.503360 O b'-1:lemma:od600'
484 +-0.524986 OD b'+1:postag:NN'
485 +-0.543280 O b'-1:lemma:rpob'
486 +-0.557386 O b'-1:lemma:grow'
487 +-0.570906 O b'lemma:fecl2'
488 +-0.574577 O b'+1:lemma:fecl2'
489 +-0.632496 O b'+1:lemma:cell'
490 +-0.640758 O b'+1:lemma:0.3'
491 +-0.696627 O b'-1:lemma:IP'
492 +-0.710065 O b'-1:postag::'
493 +-0.734704 O b'+1:postag:VBG'
494 +-0.735189 OD b'lemma:-lrb-'
495 +-0.753554 O b'lemma:0.1'
496 +-0.763727 O b'lemma:0.2'
497 +-0.785113 O b'-1:lemma:37'
498 +-0.803671 O b'-1:lemma:dissolve'
499 +-0.803671 O b'+1:lemma:methanol'
500 +-0.833476 Supp b'+1:lemma:acetate'
501 +-0.838362 O b'-1:lemma:ompr'
502 +-0.851164 O b'lemma:37'
503 +-0.866382 O b'lemma:2h'
504 +-0.866382 O b'-1:lemma:additional'
505 +-0.882690 O b'-1:postag:VBG'
506 +-0.885831 O b'+1:lemma:g/l'
507 +-0.888919 Phase b'postag:JJ'
508 +-0.905015 O b'lemma:of'
509 +-0.906507 Anti b'postag:NNP'
510 +-1.026494 O b'lemma:mid-log'
511 +-1.028079 O b'lemma:wt'
512 +-1.060908 O b'+1:lemma:supplement'
513 +-1.075926 O b'-1:lemma:co2'
514 +-1.341090 O b'-1:lemma:nsrr'
515 +-1.359406 O b'+1:lemma:at'
516 +-1.375702 Air b'+1:postag:JJ'
517 +-1.442763 O b'lemma:rifampicin'
518 +-1.637602 O b'lemma:methanol'
519 +-1.645866 Air b'postag:NN'
520 +-1.720675 Supp b'postag:JJ'
521 +-1.885525 OD b'postag:-LRB-'
522 +-1.959132 O b'+1:lemma:in'
523 +-2.128110 O b'+1:lemma:2'
524 +-2.307682 O b'-1:lemma:2'
525 +-2.374565 O b'+1:lemma:1'
526 +-4.058703 O b'-1:lemma:_'
527 +-4.145888 O b'-1:lemma::'
528 +
1 +********** TRAINING AND TESTING REPORT **********
2 +Training file: training-data-set-70_v4.txt
3 +
4 +best params:{'c1': 0.03056779653153922, 'c2': 0.04972818685122124}
5 +best CV score:0.7979170694802522
6 +model size: 0.10M
7 +
8 +Flat F1: 0.7933473757323906
9 + precision recall f1-score support
10 +
11 + OD 1.000 0.405 0.577 37
12 + pH 1.000 1.000 1.000 12
13 + Technique 0.952 0.909 0.930 22
14 + Med 0.891 0.860 0.875 57
15 + Temp 0.818 1.000 0.900 18
16 + Vess 0.000 0.000 0.000 0
17 + Agit 0.000 0.000 0.000 0
18 + Phase 1.000 0.947 0.973 19
19 + Air 0.754 0.742 0.748 62
20 + Anti 1.000 0.667 0.800 9
21 + Strain 1.000 1.000 1.000 1
22 + Gtype 0.862 0.764 0.810 106
23 + Substrain 0.000 0.000 0.000 1
24 + Supp 0.865 0.662 0.750 136
25 + Gversion 0.000 0.000 0.000 0
26 +
27 +avg / total 0.876 0.742 0.793 480
28 +
29 +
30 +Top likely transitions:
31 +OD -> OD 5.500349
32 +Temp -> Temp 4.915043
33 +Agit -> Agit 4.909226
34 +Air -> Air 4.785921
35 +Med -> Med 4.785670
36 +Anti -> Anti 4.760878
37 +O -> O 4.531217
38 +Gversion -> Gversion 4.225381
39 +Phase -> Phase 3.928282
40 +Gtype -> Gtype 3.900260
41 +Supp -> Supp 3.589674
42 +Technique -> Technique 2.798353
43 +pH -> pH 2.196128
44 +O -> Supp 1.783329
45 +Substrain -> Gtype 1.742663
46 +Gtype -> Supp 1.431329
47 +Air -> O 1.367539
48 +O -> Gtype 1.348906
49 +O -> Technique 1.109884
50 +Technique -> Air 1.076025
51 +O -> Temp 0.929238
52 +Gtype -> pH 0.717732
53 +O -> Anti 0.700988
54 +Med -> O 0.588191
55 +Gtype -> Air 0.487796
56 +O -> Strain 0.399055
57 +O -> Gversion 0.366108
58 +O -> pH 0.354024
59 +O -> Vess 0.200749
60 +Phase -> O 0.164004
61 +OD -> Phase 0.128366
62 +O -> Med 0.084648
63 +Supp -> O 0.064532
64 +O -> Phase 0.054268
65 +Temp -> O 0.034554
66 +O -> OD 0.002316
67 +pH -> Gversion -0.000024
68 +O -> Substrain -0.000046
69 +Agit -> OD -0.000091
70 +Technique -> Phase -0.002460
71 +Phase -> Air -0.004039
72 +Med -> OD -0.010012
73 +Gversion -> pH -0.019017
74 +Air -> Anti -0.028855
75 +Gtype -> Strain -0.034925
76 +Air -> Gversion -0.046350
77 +Gtype -> Agit -0.051780
78 +pH -> Temp -0.055396
79 +Anti -> pH -0.065064
80 +Substrain -> Supp -0.073862
81 +
82 +
83 +Top unlikely transitions:
84 +OD -> Anti -0.306626
85 +Technique -> Med -0.317775
86 +Technique -> O -0.337656
87 +Technique -> Gversion -0.339632
88 +Anti -> Supp -0.346709
89 +Gversion -> Gtype -0.359654
90 +OD -> Temp -0.364068
91 +Anti -> Gtype -0.374696
92 +Air -> Temp -0.398364
93 +Gversion -> Technique -0.424722
94 +Gversion -> Supp -0.427358
95 +Gtype -> Phase -0.440633
96 +OD -> Technique -0.441830
97 +Gversion -> Air -0.472797
98 +Med -> Air -0.491373
99 +OD -> Supp -0.502001
100 +Anti -> OD -0.541429
101 +Supp -> pH -0.552035
102 +Temp -> Med -0.559365
103 +O -> Air -0.562556
104 +Supp -> Temp -0.563090
105 +Gtype -> Technique -0.587403
106 +Phase -> Technique -0.587965
107 +Supp -> Phase -0.590123
108 +Air -> Supp -0.631042
109 +Air -> Med -0.640889
110 +OD -> Med -0.665368
111 +Technique -> Supp -0.671196
112 +Gtype -> Gversion -0.722812
113 +Supp -> Anti -0.732707
114 +Supp -> OD -0.751148
115 +Air -> OD -0.751415
116 +OD -> Gtype -0.801738
117 +Agit -> O -0.827165
118 +Supp -> Technique -0.836650
119 +Supp -> Gversion -0.836877
120 +Gtype -> Med -0.875397
121 +Supp -> Air -0.884655
122 +Gtype -> Anti -0.943614
123 +Supp -> Gtype -0.974424
124 +OD -> O -1.010665
125 +OD -> Air -1.028154
126 +Substrain -> O -1.046580
127 +Gtype -> OD -1.131529
128 +Technique -> Gtype -1.214725
129 +Technique -> pH -1.220888
130 +Technique -> OD -1.238019
131 +Supp -> Med -1.342545
132 +Med -> Supp -1.444556
133 +Phase -> OD -1.784428
134 +
135 +
136 +Top positive:
137 +6.692463 O b'lemma:_'
138 +5.657865 O b'lemma:1'
139 +4.942948 Phase b'lemma:stationary'
140 +4.925287 O b'lemma:2'
141 +4.843804 Air b'lemma:anaerobic'
142 +4.814975 Strain b'lemma:k-12'
143 +4.647361 Technique b'lemma:ChIP-exo'
144 +4.622048 Supp b'lemma:Iron'
145 +4.599836 Technique b'lemma:chipseq'
146 +4.422488 Air b'lemma:aerobic'
147 +4.412579 O b'lemma:rpob'
148 +4.377913 O b'postag:IN'
149 +4.349481 Supp b'lemma:pq'
150 +4.294520 O b'lemma:3'
151 +4.161278 Supp b'lemma:nh4cl'
152 +4.073955 Supp b'lemma:glucose'
153 +3.969533 O b'lemma:rep1'
154 +3.919806 Gtype b'lemma:arca8myc'
155 +3.916893 Gtype b'lemma:flag-tag'
156 +3.916893 Gtype b'-1:lemma:c-terminal'
157 +3.877994 Gtype b'lemma:\xce\xb4cra'
158 +3.870087 Phase b'lemma:mid-log'
159 +3.844857 Air b'-1:lemma:ChIP-Seq'
160 +3.795026 O b'lemma:rep2'
161 +3.756394 Gtype b'lemma:wt'
162 +3.756244 Gversion b'lemma:asm584v2'
163 +3.735954 Substrain b'lemma:mg1655'
164 +3.630823 Gtype b'-1:lemma:\xe2\x88\x86'
165 +3.587007 Supp b'lemma:nitrate'
166 +3.584699 Supp b'+1:lemma:\xc2\xb5m'
167 +3.571404 O b'lemma:Cra'
168 +3.546169 Supp b'lemma:acetate'
169 +3.518531 O b'lemma:b'
170 +3.492146 O b'postag::'
171 +3.490669 O b'lemma:rep3'
172 +3.441030 O b'lemma:a'
173 +3.439329 O b'-1:lemma:tag'
174 +3.376019 Supp b'lemma:no3'
175 +3.358527 Gtype b'lemma:delta-arca'
176 +3.341462 Med b'lemma:LB'
177 +3.335616 Air b'lemma:Aerobic'
178 +3.304114 OD b'lemma:od600'
179 +3.286213 Supp b'lemma:Fe'
180 +3.283134 Supp b'lemma:dpd'
181 +3.262389 O b'lemma:.'
182 +3.262389 O b'postag:.'
183 +3.262118 Gtype b'lemma:fnr8myc'
184 +3.241225 Technique b'lemma:rna-seq'
185 +3.161606 Med b'lemma:lb'
186 +3.100373 Technique b'lemma:chip-seq'
187 +3.056207 O b'lemma:\xcf\x8332'
188 +3.050606 O b'-1:lemma:Aerobic'
189 +3.038793 Med b'lemma:MOPS'
190 +3.034791 Anti b'lemma:none'
191 +3.020225 O b'postag:VBN'
192 +2.971269 O b'-1:lemma:ChIP-exo'
193 +2.958452 Anti b'lemma:seqa'
194 +2.958367 O b'lemma:CEL'
195 +2.941302 OD b'lemma:od450'
196 +2.935356 O b'+1:lemma:od600'
197 +2.927938 Gtype b'lemma:\xe2\x88\x86'
198 +2.911881 Supp b'+1:lemma:1'
199 +2.911524 Supp b'lemma:fructose'
200 +2.871399 Technique b'lemma:rnaseq'
201 +2.859600 O b'+1:postag:RB'
202 +2.839822 Gtype b'lemma:delta-fnr'
203 +2.810955 O b'lemma:Custom'
204 +2.809182 Supp b'lemma:rifampicin'
205 +2.808831 O b'lemma:-'
206 +2.789937 Gtype b'lemma:type'
207 +2.788256 Supp b'+1:lemma:Deficient'
208 +2.770982 Gtype b'+1:lemma:type'
209 +2.748917 Supp b'+1:lemma:2'
210 +2.743490 Gversion b'lemma:nc'
211 +2.738725 Med b'+1:lemma:0.4'
212 +2.720595 pH b'lemma:ph5'
213 +2.720595 pH b'+1:lemma:.5'
214 +2.676119 Supp b'-1:lemma:Cra'
215 +2.658000 Gtype b'lemma:\xce\xb4fur'
216 +2.652362 Gtype b'+1:lemma:with'
217 +2.618562 Gversion b'lemma:chip-seq'
218 +2.610176 Air b'postag:RB'
219 +2.594937 Gtype b'lemma:nsrr'
220 +2.583087 Technique b'lemma:ChIP-Seq'
221 +2.578250 Vess b'lemma:flask'
222 +2.578250 Vess b'-1:lemma:warm'
223 +2.563672 O b'lemma:affyexp'
224 +2.551761 O b'-1:lemma:glucose'
225 +2.545085 O b'lemma:chip-arca'
226 +2.505127 Supp b'+1:lemma:_'
227 +2.499915 O b'-1:lemma:anaerobic'
228 +2.495203 Supp b'lemma:arginine'
229 +2.492742 O b'lemma:s'
230 +2.486425 Gversion b'lemma:000913'
231 +2.464249 O b'-1:lemma:0.3-0.35'
232 +2.449997 O b'lemma:oxyr'
233 +2.448215 Gversion b'lemma:.2'
234 +2.448215 Gversion b'-1:lemma:u00096'
235 +2.435265 Anti b'lemma:anti-myc'
236 +2.432726 Gtype b'lemma:wild-type'
237 +2.423727 Temp b'lemma:\xc2\xb0c'
238 +2.395174 Technique b'-1:lemma:IP'
239 +2.393484 O b'-1:lemma:stpa'
240 +2.388764 Gversion b'lemma:u00096'
241 +2.388764 Gversion b'+1:lemma:.2'
242 +2.368933 Phase b'-1:lemma:mid-log'
243 +2.366886 Gtype b'lemma:WT'
244 +2.348028 O b'lemma:with'
245 +2.344016 O b'lemma:or'
246 +2.343871 O b'+1:lemma:anti-fur'
247 +2.313839 Gtype b'lemma:\xce\xb4soxs'
248 +2.310686 Strain b'+1:lemma:substr'
249 +2.303744 O b'-1:lemma:lb'
250 +2.288133 O b'lemma:argr'
251 +2.284029 Gtype b'+1:lemma:pq'
252 +2.277137 O b'+1:lemma:pq'
253 +2.253710 O b'lemma:ompr'
254 +2.244848 Gtype b'-1:lemma:ptac'
255 +2.214837 Med b'lemma:m63'
256 +2.208372 Air b'lemma:anaerobically'
257 +2.207760 Gversion b'-1:lemma:nc'
258 +2.185269 Air b'lemma:Anaerobic'
259 +2.177809 Supp b'lemma:nacl'
260 +2.172428 Gtype b'+1:lemma:flagtag'
261 +2.169963 Med b'+1:lemma:2.0'
262 +2.169550 O b'postag:SYM'
263 +2.165014 O b'lemma:purr'
264 +2.160892 pH b'+1:postag:CD'
265 +2.150124 Temp b'-1:lemma:37'
266 +2.150116 O b'lemma:chip'
267 +2.133824 O b'+1:lemma:mid-log'
268 +2.130811 Gtype b'lemma:\xce\xb4ompr'
269 +2.113515 Air b'-1:lemma:-'
270 +2.112847 Gtype b'lemma:ptac'
271 +2.087871 O b'lemma:Lrp'
272 +2.073270 Gtype b'-1:lemma:_'
273 +2.071479 Technique b'-1:lemma:chip-exo'
274 +2.052465 O b'-1:lemma:type'
275 +2.046273 O b'+1:lemma:o.d.'
276 +2.034128 Technique b'postag:NNP'
277 +2.032694 OD b'+1:lemma:stationary'
278 +2.029532 Gtype b'lemma:deltaseqa'
279 +2.029532 Gtype b'-1:lemma:old'
280 +2.029028 Technique b'-1:lemma:input'
281 +2.028724 Temp b'+1:lemma:\xc2\xb0c'
282 +2.028052 Med b'postag:NNP'
283 +2.019887 O b'+1:lemma:chip-seq'
284 +2.016529 Vess b'-1:postag:VBN'
285 +2.014709 Anti b'+1:lemma:antibody'
286 +2.004528 Supp b'+1:lemma:hour'
287 +1.986808 Gtype b'+1:lemma:ph5'
288 +1.982154 Temp b'-1:lemma:43'
289 +1.979758 Gtype b'+1:lemma:aerobic'
290 +1.979385 Supp b'lemma:Leu'
291 +1.977544 Med b'+1:lemma:minimal'
292 +1.972140 Substrain b'+1:lemma:phtpg'
293 +1.966671 O b'lemma:Fur'
294 +1.952996 Technique b'-1:lemma:_'
295 +1.947488 Supp b'lemma:iptg'
296 +1.947369 O b'+1:lemma:43'
297 +1.947148 Temp b'lemma:43'
298 +1.946657 Supp b'-1:lemma:\xc2\xb5m'
299 +1.946349 Med b'+1:lemma:+'
300 +1.946188 Phase b'lemma:phase'
301 +1.940761 Gtype b'lemma:pk4854'
302 +1.924723 O b'lemma:genotype/variation'
303 +1.911694 Gtype b'+1:lemma:_'
304 +1.910805 Temp b'-1:lemma:\xcf\x8332'
305 +1.907106 Supp b'lemma:Adenine'
306 +1.906722 Technique b'+1:lemma:chip-exo'
307 +1.906375 Anti b'lemma:anti-rpos'
308 +1.904230 Air b'+1:lemma:at'
309 +1.903056 Gversion b'+1:lemma:000913'
310 +1.901487 Med b'lemma:glucose'
311 +1.889441 O b'lemma:chip-fnr'
312 +1.887601 Gtype b'-1:lemma:nsrr'
313 +1.878766 O b'postag:DT'
314 +1.873733 pH b'lemma:.5'
315 +1.873733 pH b'-1:lemma:ph5'
316 +1.865998 O b'lemma:culture'
317 +1.855758 O b'lemma:for'
318 +1.853813 Gtype b'-1:lemma:rpob'
319 +1.853644 O b'lemma:soxs'
320 +1.853644 O b'lemma:soxr'
321 +1.846904 Gtype b'-1:lemma::'
322 +1.845474 Temp b'-1:lemma:sample'
323 +1.841250 Air b'lemma:anerobically'
324 +1.838140 Air b'-1:postag:CD'
325 +1.831417 Med b'-1:lemma:ml'
326 +1.825450 Phase b'+1:lemma:for'
327 +1.820952 O b'-1:lemma:0.3'
328 +1.816339 Air b'-1:postag::'
329 +1.812600 O b'postag:CC'
330 +1.810282 Supp b'+1:lemma:respiratory'
331 +1.805085 Supp b'lemma:methanol'
332 +1.803745 Supp b'lemma:20'
333 +1.782276 Med b'lemma:L'
334 +1.782276 Med b'+1:lemma:broth'
335 +1.779488 O b'lemma:pt7'
336 +1.771701 OD b'-1:lemma:~'
337 +
338 +
339 +Top negative:
340 +-0.098597 OD b'+1:lemma:in'
341 +-0.100809 O b'+1:lemma:pahse'
342 +-0.103942 Gtype b'-1:lemma:,'
343 +-0.103942 Gtype b'-1:postag:,'
344 +-0.109064 Supp b'+1:postag:IN'
345 +-0.116184 O b'-1:lemma:the'
346 +-0.120961 Phase b'-1:postag:NN'
347 +-0.125524 Air b'-1:postag:CC'
348 +-0.130098 O b'+1:lemma:sample'
349 +-0.133275 Med b'lemma:-lrb-'
350 +-0.133905 OD b'+1:lemma:0.4'
351 +-0.137686 O b'-1:lemma:minimal'
352 +-0.138574 Air b'-1:postag:-RRB-'
353 +-0.140110 Air b'-1:lemma:-rrb-'
354 +-0.141778 Med b'postag:-LRB-'
355 +-0.148667 Med b'-1:postag:NN'
356 +-0.152662 O b'-1:postag:IN'
357 +-0.152746 O b'lemma:medium'
358 +-0.153545 O b'lemma:n2'
359 +-0.154206 Air b'postag:CC'
360 +-0.163582 O b'-1:postag:VBN'
361 +-0.164052 O b'-1:lemma:n2'
362 +-0.167774 Gtype b'+1:lemma:cra'
363 +-0.171535 O b'-1:lemma:with'
364 +-0.177101 Gtype b'+1:lemma:-lrb-'
365 +-0.181072 Gtype b'postag:CD'
366 +-0.190005 O b'lemma:pahse'
367 +-0.191122 Gtype b'+1:lemma:a'
368 +-0.193246 O b'+1:lemma:_'
369 +-0.200535 OD b'+1:lemma:mid-log'
370 +-0.201151 O b'lemma:co2'
371 +-0.203533 O b'-1:lemma:-lrb-'
372 +-0.203756 O b'+1:lemma:phase'
373 +-0.207632 O b'-1:lemma:e.'
374 +-0.208480 O b'-1:lemma:purify'
375 +-0.211803 O b'lemma:grow'
376 +-0.213447 O b'+1:lemma:delta'
377 +-0.215349 Air b'postag:CD'
378 +-0.217993 O b'+1:lemma:-rrb-'
379 +-0.219170 Supp b'lemma:and'
380 +-0.221278 O b'lemma:10'
381 +-0.224277 O b'+1:lemma:.'
382 +-0.224277 O b'+1:postag:.'
383 +-0.226140 O b'-1:lemma:fresh'
384 +-0.227840 O b'+1:lemma:mg1655'
385 +-0.233692 O b'-1:postag:VBP'
386 +-0.243094 O b'+1:lemma:-lcb-'
387 +-0.244688 O b'lemma:30'
388 +-0.248768 Med b'-1:postag:CD'
389 +-0.248953 O b'lemma:8'
390 +-0.252377 O b'+1:lemma:%'
391 +-0.257481 O b'lemma:minimal'
392 +-0.257830 Technique b'-1:lemma::'
393 +-0.259100 Gversion b'+1:postag:NN'
394 +-0.259164 O b'-1:postag:-LRB-'
395 +-0.259192 Med b'+1:postag:NN'
396 +-0.265097 O b'+1:lemma:strain'
397 +-0.270448 O b'-1:lemma:mm'
398 +-0.271962 O b'+1:lemma:0.4'
399 +-0.272630 O b'-1:lemma:chip-exo'
400 +-0.277009 OD b'+1:postag:CD'
401 +-0.278470 O b'+1:lemma:minimal'
402 +-0.286163 O b'+1:lemma:antibody'
403 +-0.294848 Gtype b'-1:postag:CD'
404 +-0.294973 O b'+1:lemma:from'
405 +-0.303885 O b'-1:lemma:grow'
406 +-0.306933 O b'lemma:e.'
407 +-0.309307 Air b'-1:lemma:or'
408 +-0.312327 O b'postag:RB'
409 +-0.312620 OD b'+1:postag:CC'
410 +-0.316727 Anti b'+1:postag:JJ'
411 +-0.319089 O b'-1:lemma:mid-log'
412 +-0.321702 O b'-1:lemma:um'
413 +-0.321702 O b'+1:lemma:paraquat'
414 +-0.322815 O b'-1:lemma:0.1'
415 +-0.325506 Supp b'+1:postag:VBN'
416 +-0.327089 Med b'+1:postag:NNS'
417 +-0.329088 Supp b'-1:lemma:%'
418 +-0.335665 Med b'postag:CD'
419 +-0.345089 O b'+1:lemma:shake'
420 +-0.346024 O b'lemma:nacl'
421 +-0.346568 Med b'-1:postag:IN'
422 +-0.349877 O b'-1:lemma:iptg'
423 +-0.351934 Supp b'-1:postag:VBG'
424 +-0.361114 Phase b'-1:lemma:at'
425 +-0.363308 Gtype b'+1:lemma:b'
426 +-0.369166 O b'+1:lemma:b'
427 +-0.370353 O b'+1:postag:IN'
428 +-0.375482 O b'+1:lemma:rep1'
429 +-0.382649 OD b'postag:JJ'
430 +-0.389625 O b'-1:lemma:rifampicin'
431 +-0.390229 O b'-1:lemma:20'
432 +-0.392434 O b'+1:lemma:300'
433 +-0.392765 O b'-1:lemma:od600'
434 +-0.396162 O b'lemma:\xc2\xb0c'
435 +-0.397112 Temp b'postag:JJ'
436 +-0.398067 O b'+1:postag:-RRB-'
437 +-0.412750 O b'-1:lemma:affinity'
438 +-0.416189 O b'+1:lemma:dissolve'
439 +-0.417913 O b'+1:lemma:cell'
440 +-0.426120 O b'-1:lemma:from'
441 +-0.472958 O b'-1:lemma:30'
442 +-0.483340 Technique b'-1:postag::'
443 +-0.483753 Temp b'+1:lemma:to'
444 +-0.483753 Temp b'+1:postag:TO'
445 +-0.484495 O b'+1:lemma:c'
446 +-0.487031 Supp b'+1:lemma:glucose'
447 +-0.495206 Gtype b'lemma:_'
448 +-0.505255 Supp b'postag:CC'
449 +-0.505610 O b'-1:lemma:cra'
450 +-0.512805 O b'lemma:dissolve'
451 +-0.519407 O b'lemma:glucose'
452 +-0.530802 O b'+1:lemma:Aerobic'
453 +-0.536055 O b'lemma:mg1655'
454 +-0.538193 O b'+1:lemma:arginine'
455 +-0.540056 O b'lemma:dpd'
456 +-0.543308 O b'+1:lemma:until'
457 +-0.553627 pH b'postag:NN'
458 +-0.557904 O b'-1:lemma:until'
459 +-0.560304 OD b'+1:postag:NN'
460 +-0.577595 O b'-1:lemma:g/l'
461 +-0.579159 OD b'+1:lemma:and'
462 +-0.595749 O b'lemma:phase'
463 +-0.611587 Gtype b'+1:lemma:\xe2\x88\x86'
464 +-0.614217 Gtype b'-1:postag:SYM'
465 +-0.624715 O b'lemma:purify'
466 +-0.636366 O b'lemma:150'
467 +-0.636366 O b'+1:lemma:mg/ml'
468 +-0.638397 Gtype b'-1:postag:DT'
469 +-0.657927 O b'lemma:m63'
470 +-0.664969 Gtype b'lemma:delta'
471 +-0.666049 OD b'lemma:-lrb-'
472 +-0.682691 Supp b'+1:lemma:rifampicin'
473 +-0.692119 Temp b'-1:lemma:\xc2\xb0c'
474 +-0.706829 O b'lemma:lb'
475 +-0.708511 Med b'+1:postag:IN'
476 +-0.711784 O b'-1:lemma:~'
477 +-0.714372 O b'+1:lemma:0.3'
478 +-0.716136 O b'+1:postag:NNS'
479 +-0.736106 O b'+1:lemma:\xc2\xb0c'
480 +-0.738116 Phase b'postag:JJ'
481 +-0.744781 O b'-1:lemma:1'
482 +-0.764657 OD b'postag:-LRB-'
483 +-0.767869 Temp b'postag:NN'
484 +-0.772655 O b'lemma:of'
485 +-0.774528 O b'-1:lemma:\xe2\x88\x86'
486 +-0.806745 O b'+1:lemma:fecl2'
487 +-0.808726 O b'lemma:anaerobically'
488 +-0.817926 O b'-1:lemma:0.2'
489 +-0.828109 O b'lemma:media'
490 +-0.860850 Phase b'-1:postag:JJ'
491 +-0.869705 Air b'-1:postag:JJ'
492 +-0.869779 Anti b'+1:lemma:anti-fur'
493 +-0.913352 O b'lemma:0.3'
494 +-0.926265 O b'lemma:20'
495 +-0.966551 O b'+1:lemma:in'
496 +-0.967999 O b'-1:lemma:co2'
497 +-0.983473 O b'lemma:\xe2\x88\x86'
498 +-1.005883 O b'lemma:0.1'
499 +-1.012563 O b'+1:lemma:supplement'
500 +-1.015961 O b'lemma:2h'
501 +-1.015961 O b'-1:lemma:additional'
502 +-1.030442 O b'lemma:fecl2'
503 +-1.035342 Supp b'+1:lemma:acetate'
504 +-1.055745 O b'+1:lemma:g/l'
505 +-1.058371 O b'+1:lemma:at'
506 +-1.065986 O b'+1:postag:VBG'
507 +-1.108278 O b'lemma:anaerobic'
508 +-1.137604 O b'-1:lemma:ompr'
509 +-1.149433 O b'-1:postag:VBG'
510 +-1.157369 O b'-1:lemma:dissolve'
511 +-1.157369 O b'+1:lemma:methanol'
512 +-1.161744 O b'lemma:0.2'
513 +-1.176749 O b'lemma:mid-log'
514 +-1.210434 O b'lemma:\xce\xb4fur'
515 +-1.224092 O b'-1:lemma:sample'
516 +-1.241862 O b'-1:lemma:ml'
517 +-1.249714 O b'lemma:37'
518 +-1.287855 O b'postag:VBP'
519 +-1.290513 O b'lemma:od600'
520 +-1.322257 O b'lemma:k-12'
521 +-1.332061 O b'-1:lemma:rpob'
522 +-1.387093 Supp b'postag:JJ'
523 +-1.418093 O b'-1:postag::'
524 +-1.520563 Anti b'postag:NNP'
525 +-1.552213 O b'-1:lemma:37'
526 +-1.582655 O b'lemma:methanol'
527 +-1.634214 Air b'+1:postag:JJ'
528 +-1.656961 O b'-1:lemma:2'
529 +-1.660038 O b'-1:lemma:nsrr'
530 +-1.778068 O b'-1:lemma:IP'
531 +-1.782125 O b'lemma:rifampicin'
532 +-1.784846 Air b'postag:NN'
533 +-1.792093 O b'+1:lemma:hour'
534 +-1.833447 O b'+1:lemma:+'
535 +-1.873023 O b'lemma:wt'
536 +-1.948439 O b'+1:lemma:2'
537 +-2.447797 O b'+1:lemma:1'
538 +-2.955767 O b'-1:lemma:_'
539 +-3.288596 O b'-1:lemma::'
540 +
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'
231 -2.025934 O b'-1:lemma:tag'
232 -2.016740 Med b'word:M63'
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'
237 -1.937643 O b'word:supplemented'
238 -1.937643 O b'lemma:supplement'
239 -1.928437 Gtype b'word:oxyR-8myc'
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:+'
244 -1.904247 Gversion b'word:.2'
245 -1.904247 Gversion b'lemma:.2'
246 -1.904247 Gversion b'-1:lemma:u00096'
247 -1.895301 Supp b'-1:lemma::'
248 -1.888517 Med b'+1:lemma:minimal'
249 -1.888285 O b'+1:lemma:nitrate'
250 -1.887992 O b'+1:lemma:anaerobic'
251 -1.887095 Phase b'word:phase'
252 -1.887095 Phase b'lemma:phase'
253 -1.873844 Anti b'word:\xcf\x8332'
254 -1.873844 Anti b'lemma:\xcf\x8332'
255 -1.858813 Med b'lemma:LB'
256 -1.856133 O b'-1:lemma:-80'
257 -1.850543 Supp b'+1:lemma:be'
258 -1.822229 Supp b'word:leucine'
259 -1.822229 Supp b'lemma:leucine'
260 -1.818630 O b'-1:lemma:flag-tag'
261 -1.810937 O b'-1:lemma:_'
262 -1.808829 Supp b'word:fructose'
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'
268 -1.786790 Anti b'word:anti-myc'
269 -1.786790 Anti b'lemma:anti-myc'
270 -1.784685 Substrain b'word:MG1655star'
271 -1.784685 Substrain b'lemma:mg1655star'
272 -1.778678 Technique b'lemma:chip-seq'
273 -1.778353 O b'word:<Air>'
274 -1.751251 Supp b'-1:lemma:1mm'
275 -1.746035 Supp b'+1:lemma:1/100'
276 -1.733606 Anti b'+1:lemma:from'
277 -1.729502 Technique b'word:ChIP-Seq'
278 -1.725373 O b'+1:lemma:mid-log'
279 -1.712485 Gversion b'word:ChIP-Seq'
280 -1.709357 O b'-1:postag:NNS'
281 -1.693666 O b'word:-RRB-'
282 -1.693666 O b'lemma:-rrb-'
283 -1.656579 Supp b'word:rifampicin'
284 -1.656579 Supp b'lemma:rifampicin'
285 -1.654463 O b'lemma:to'
286 -1.646916 Anti b'word:anti-RpoB'
287 -1.646916 Anti b'lemma:anti-rpob'
288 -1.641270 Vess b'-1:postag:VBN'
289 -1.634955 Anti b'word:SeqA'
290 -1.634955 Anti b'lemma:seqa'
291 -1.626876 Med b'+1:lemma:-lrb-'
292 -1.621826 O b'lemma:<air>'
293 -1.616807 Supp b'word:tryptophan'
294 -1.616807 Supp b'lemma:tryptophan'
295 -1.616807 Supp b'-1:lemma:mg/l'
296 -1.584459 O b'lemma:anaerobic'
297 -1.571612 Med b'word:medium'
298 -1.571612 Med b'lemma:medium'
299 -1.550300 Vess b'+1:lemma:at'
300 -1.549343 O b'word:B'
301 -1.547972 Gtype b'-1:lemma:\xe2\x88\x86'
302 -1.546575 OD b'+1:lemma:oxyr-8myc'
303 -1.546406 O b'+1:lemma:aerobic'
304 -1.528557 Supp b'+1:lemma:300'
305 -1.505854 Temp b'-1:lemma:at'
306 -1.482950 Supp b'-1:postag:IN'
307 -1.477298 Med b'-1:lemma:glucose'
308 -1.476212 O b'-1:lemma:media'
309 -
310 -
311 -Top negative:
312 --0.033522 O b'lemma:20'
313 --0.038038 Anti b'isupper()'
314 --0.038347 OD b'isupper()'
315 --0.045438 O b'word:phosphate'
316 --0.045438 O b'lemma:phosphate'
317 --0.046287 O b'word:LB'
318 --0.047486 Gtype b'-1:lemma:,'
319 --0.047486 Gtype b'-1:postag:,'
320 --0.047973 O b'+1:lemma:culture'
321 --0.048635 Med b'-1:postag:NN'
322 --0.048786 Supp b'-1:lemma:,'
323 --0.048786 Supp b'-1:postag:,'
324 --0.049214 Temp b'-1:postag:NN'
325 --0.055607 Supp b'word:vol'
326 --0.055607 Supp b'lemma:vol'
327 --0.055607 Supp b'-1:lemma:1/100'
328 --0.057967 O b'word:150'
329 --0.057967 O b'lemma:150'
330 --0.057967 O b'+1:lemma:mg/ml'
331 --0.065780 Med b'+1:lemma:media'
332 --0.067419 O b'-1:lemma:rifampicin'
333 --0.068390 O b'+1:lemma:medium'
334 --0.069566 Gtype b'+1:postag:JJ'
335 --0.069740 Supp b'word:10'
336 --0.069740 Supp b'lemma:10'
337 --0.072097 Supp b'-1:lemma:;'
338 --0.074848 Supp b'-1:lemma:.'
339 --0.074848 Supp b'-1:postag:.'
340 --0.075753 O b'word:min'
341 --0.075753 O b'lemma:min'
342 --0.076584 Supp b'-1:lemma:-lrb-'
343 --0.079109 Supp b'word:uM'
344 --0.079109 Supp b'lemma:um'
345 --0.079109 Supp b'-1:lemma:250'
346 --0.083627 O b'-1:lemma:m9'
347 --0.084086 Anti b'-1:postag:NN'
348 --0.084792 Supp b'-1:postag:-LRB-'
349 --0.085223 Med b'-1:postag:IN'
350 --0.090978 O b'-1:postag:VBN'
351 --0.091287 Supp b'-1:lemma:10'
352 --0.093086 Gtype b'isupper()'
353 --0.097632 O b'word:1M'
354 --0.097632 O b'lemma:1m'
355 --0.098995 O b'-1:lemma:-lrb-'
356 --0.102411 O b'-1:lemma:Fur'
357 --0.109527 Gtype b'+1:postag:IN'
358 --0.110624 O b'word:7.6'
359 --0.110624 O b'lemma:7.6'
360 --0.110624 O b'-1:lemma:ph'
361 --0.110624 O b'+1:lemma:;'
362 --0.115984 O b'-1:lemma:and'
363 --0.116488 O b'-1:lemma:soxr-8myc'
364 --0.125176 O b'+1:lemma:min'
365 --0.130318 Phase b'-1:lemma:at'
366 --0.132219 O b'word:crp'
367 --0.132219 O b'lemma:crp'
368 --0.135378 Supp b'word:,'
369 --0.135378 Supp b'lemma:,'
370 --0.135758 Supp b'word:250'
371 --0.135758 Supp b'lemma:250'
372 --0.135758 Supp b'+1:lemma:um'
373 --0.145733 Supp b'word:and'
374 --0.145733 Supp b'lemma:and'
375 --0.148126 O b'-1:lemma:.'
376 --0.148126 O b'-1:postag:.'
377 --0.149156 O b'-1:lemma:until'
378 --0.157548 O b'+1:lemma:\xc2\xb5m'
379 --0.160930 O b'+1:lemma:tag'
380 --0.162355 O b'+1:lemma:phase'
381 --0.193262 O b'-1:lemma:2'
382 --0.194523 O b'-1:lemma:43'
383 --0.194585 OD b'+1:lemma:~'
384 --0.205225 O b'-1:postag:CC'
385 --0.217098 Temp b'+1:postag:IN'
386 --0.217465 O b'word:%'
387 --0.217465 O b'lemma:%'
388 --0.221369 Supp b'+1:lemma:acetate'
389 --0.229086 O b'word:43'
390 --0.229086 O b'lemma:43'
391 --0.230011 O b'-1:lemma:delta'
392 --0.230917 O b'+1:postag:NNS'
393 --0.233042 Supp b'+1:postag:VBN'
394 --0.234678 Med b'+1:postag:CC'
395 --0.239379 O b'word:pH'
396 --0.239379 O b'lemma:ph'
397 --0.239379 O b'+1:lemma:7.6'
398 --0.240087 O b'+1:lemma:mg1655'
399 --0.243533 O b'word:0.1'
400 --0.243533 O b'lemma:0.1'
401 --0.247022 Anti b'+1:postag:JJ'
402 --0.254824 O b'-1:lemma:sodium'
403 --0.257080 O b'+1:lemma:dissolve'
404 --0.258767 Supp b'-1:postag:NN'
405 --0.262289 O b'+1:postag:IN'
406 --0.268651 O b'-1:lemma:od600'
407 --0.269420 O b'-1:postag:-LRB-'
408 --0.278544 O b'-1:lemma:0.2'
409 --0.280204 O b'word:of'
410 --0.280204 O b'lemma:of'
411 --0.289904 Gtype b'word:,'
412 --0.289904 Gtype b'lemma:,'
413 --0.293848 O b'+1:lemma:sample'
414 --0.302903 O b'-1:lemma:mid-log'
415 --0.308508 O b'+1:lemma:1m'
416 --0.316766 O b'lemma:sample'
417 --0.317700 O b'-1:lemma:1m'
418 --0.317700 O b'+1:lemma:ph'
419 --0.325320 O b'-1:postag:IN'
420 --0.347306 O b'-1:lemma:contain'
421 --0.353650 O b'word:media'
422 --0.353650 O b'lemma:media'
423 --0.361308 O b'+1:lemma:-rrb-'
424 --0.363822 O b'-1:lemma:mm'
425 --0.370286 O b'-1:lemma:analyze'
426 --0.371370 O b'word:medium'
427 --0.371370 O b'lemma:medium'
428 --0.371526 O b'word:0.2'
429 --0.371526 O b'lemma:0.2'
430 --0.388795 Med b'+1:lemma:m9'
431 --0.389065 O b'-1:lemma:fresh'
432 --0.396824 Phase b'isupper()'
433 --0.407829 O b'word:methanol'
434 --0.407829 O b'lemma:methanol'
435 --0.409652 O b'word:dissolved'
436 --0.409652 O b'lemma:dissolve'
437 --0.420228 Supp b'word:.'
438 --0.420228 Supp b'lemma:.'
439 --0.420585 O b'-1:lemma:final'
440 --0.435371 O b'word:mid-log'
441 --0.435371 O b'lemma:mid-log'
442 --0.449869 Med b'+1:postag:CD'
443 --0.453920 O b'-1:lemma:or'
444 --0.462008 O b'+1:lemma:in'
445 --0.464988 O b'word:rifampicin'
446 --0.464988 O b'lemma:rifampicin'
447 --0.468866 O b'word:30'
448 --0.468866 O b'lemma:30'
449 --0.490303 O b'+1:lemma:-lrb-'
450 --0.521128 O b'-1:lemma:of'
451 --0.549971 O b'+1:postag:-RRB-'
452 --0.552220 O b'-1:lemma:minimal'
453 --0.554112 Supp b'+1:postag:CD'
454 --0.554855 Gtype b'islower()'
455 --0.556777 O b'word:OD600'
456 --0.556777 O b'lemma:od600'
457 --0.558779 O b'+1:lemma:antibody'
458 --0.581083 Med b'islower()'
459 --0.588156 Supp b'+1:postag:JJ'
460 --0.596135 O b'+1:lemma:.'
461 --0.596135 O b'+1:postag:.'
462 --0.603800 O b'word:glucose'
463 --0.603800 O b'lemma:glucose'
464 --0.604194 Temp b'-1:postag:CD'
465 --0.610067 O b'word:minimal'
466 --0.610067 O b'lemma:minimal'
467 --0.613419 Supp b'isupper()'
468 --0.618968 O b'word:phase'
469 --0.618968 O b'lemma:phase'
470 --0.635118 O b'-1:lemma:ml'
471 --0.635236 O b'-1:lemma:dissolve'
472 --0.635236 O b'+1:lemma:methanol'
473 --0.649664 O b'word:37'
474 --0.649664 O b'lemma:37'
475 --0.653888 Med b'+1:postag:NN'
476 --0.672366 Temp b'islower()'
477 --0.679024 O b'word:cra'
478 --0.697555 OD b'+1:postag:NN'
479 --0.726875 Supp b'islower()'
480 --0.736892 O b'-1:lemma:growth'
481 --0.744187 O b'-1:lemma:phosphate'
482 --0.779776 O b'+1:lemma:minimal'
483 --0.789382 O b'-1:lemma:rna'
484 --0.925215 O b'+1:lemma:supplement'
485 --0.938635 O b'+1:lemma:contain'
486 --0.959966 O b'+1:lemma:1/100'
487 --1.005759 Gtype b'isNumber()'
488 --1.020571 O b'+1:postag:-LRB-'
489 --1.023100 O b'+1:lemma:g/l'
490 --1.034129 O b'+1:lemma:chip'
491 --1.057527 O b'+1:lemma:0.3'
492 --1.097957 O b'-1:lemma:37'
493 --1.274500 O b'lemma:tag'
494 --1.286152 O b'-1:postag::'
495 --1.303774 O b'-1:lemma:the'
496 --1.380700 O b'+1:lemma:oxyr-8myc'
497 --1.396643 O b'-1:lemma:k-12'
498 --1.508771 O b'+1:lemma:at'
499 --1.634199 Supp b'+1:lemma:,'
500 --1.634199 Supp b'+1:postag:,'
501 --1.651060 O b'+1:lemma:for'
502 --1.669291 O b'-1:lemma:30'
503 --1.845334 Gversion b'islower()'
504 --1.912631 Supp b'+1:postag:-LRB-'
505 --1.916490 Supp b'+1:lemma:-lrb-'
506 --2.376915 O b'+1:lemma:<air>'
507 --2.666827 O b'-1:lemma:vol'
508 --2.728484 OD b'-1:postag:CD'
509 --3.072458 O b'-1:lemma:sample'
510 --3.939533 O b'-1:lemma::'
511 --4.411137 Phase b'-1:postag:JJ'
512 -
1 -['O', 'O', 'O', 'O', 'O']
2 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
3 -['O', 'O', 'O']
4 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
5 -['O', 'O', 'O', 'Gtype']
6 -['O', 'O', 'O', 'O']
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8 -['O', 'O', 'O', 'O', 'O']
9 -['O', 'O', 'O', 'O', 'O']
10 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
11 -['O', 'O', 'O', 'Med', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp']
12 -['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', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
13 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
14 -['O', 'O', 'O', 'O']
15 -['O', 'O', 'O', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp']
16 -['O', 'O', 'O', 'O', 'O']
17 -['O', 'O', 'Gtype']
18 -['O', 'O', 'O']
19 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
20 -['O', 'O', 'O', 'O', 'O']
21 -['O', 'O', 'O', 'O', 'O', 'O', 'Gversion', 'Gversion', 'Gversion', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
22 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
23 -['O', 'O', 'O', 'O', 'O']
24 -['O', 'O', 'O']
25 -['O', 'O', 'O', 'O', 'O']
26 -['O', 'O', 'Anti', 'Anti', 'Anti']
27 -['O', 'O', 'O']
28 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
29 -['O', 'O', 'O', 'O', 'O']
30 -['O', 'O', 'O']
31 -['O', 'O', 'O']
32 -['O', 'O', 'O']
33 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
34 -['O', 'O', 'O', 'O']
35 -['O', 'O', 'O', 'Supp']
36 -['O', 'O', 'O', 'Gtype', 'O', 'O', 'O', 'O', 'O']
37 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
38 -['O', 'O', 'O', 'O']
39 -['O', 'O', 'O']
40 -['O', 'O', 'O', 'O']
41 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
42 -['O', 'O', 'O']
43 -['O', 'O', 'O', 'O']
44 -['O', 'O', 'O', 'O', 'O']
45 -['O', 'O', 'Gtype']
46 -['O', 'O', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
47 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Gtype', 'Gtype']
48 -['O', 'O', 'O', 'O', 'O', 'O']
49 -['O', 'O', 'O', 'O', 'O']
50 -['O', 'O', 'Gtype']
51 -['O', 'O', 'O']
52 -['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', 'Phase', 'Phase', 'O', 'OD', 'OD', 'OD', 'OD', 'O', 'O', 'Med', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp', 'O']
53 -['O', 'O', 'O']
54 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
55 -['O', 'O', 'O']
56 -['O', 'O', 'O']
57 -['O', 'O', 'O', 'Gtype']
58 -['O', 'O', 'O', 'O', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Phase', 'Phase', 'O', 'OD', 'OD', 'OD', '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', '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', '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', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
59 -['O', 'O', 'O']
60 -['O', 'O', 'O']
61 -['O', 'O', 'Gtype']
62 -['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', 'Phase', 'Phase', 'O', 'OD', 'OD', 'OD', 'OD', 'O', 'O']
63 -['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', 'Supp', 'O']
64 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
65 -['O', 'O', 'O']
66 -['O', 'O', 'Gtype']
67 -['O', 'O', 'O', 'Anti', 'Anti', 'Anti', 'O']
68 -['O', 'O', 'O', 'O']
69 -['O', 'O', 'O', 'O']
70 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
71 -['O', 'O', 'O', 'Anti', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
72 -['O', 'O', 'O']
73 -['O', 'O', 'O']
74 -['O', 'O', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
75 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
76 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
77 -['O', 'O', 'Gtype']
78 -['O', 'O', 'O', 'O', 'O', 'Anti', 'Anti']
79 -['O', 'O', 'O', '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']
80 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Phase', 'Phase', 'O', 'OD']
81 -['O', 'O', 'O', 'O', 'O', 'O']
82 -['O', 'O', 'O', 'O', 'O']
83 -['O', 'O', 'O', 'Anti']
84 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
85 -['O', 'O', 'Gtype']
86 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'Substrain']
87 -['O', 'O', 'Gtype']
88 -['O', 'O', 'Gtype']
89 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
90 -['O', 'O', 'O']
91 -['O', 'O', 'O']
92 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Gtype', 'Gtype', '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', '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', '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', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
93 -['O', 'O', 'O', 'O', 'O', 'O']
94 -['O', 'O', 'Med']
95 -['O', 'O', 'O', 'O', 'O', 'O']
96 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
97 -['O', 'O', 'Gtype']
98 -['Gversion', 'Gversion']
99 -['O', 'O', 'O', 'O', 'O']
100 -['O', 'O', 'O']
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', 'Supp', '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', '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', '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']
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', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
1 -['O', 'O', 'O', 'O', 'O']
2 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
3 -['O', 'O', 'O']
4 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
5 -['O', 'O', 'O', 'Technique']
6 -['O', 'O', 'O', 'O']
7 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Phase', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', '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', 'O', 'O']
8 -['O', 'O', 'O', 'O', 'O']
9 -['O', 'O', 'O', 'O', 'O']
10 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'Substrain']
11 -['O', 'O', 'O', 'Med', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp']
12 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'Temp', 'Temp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'OD', 'OD', 'OD', 'O', 'O']
13 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
14 -['O', 'O', 'O', 'O']
15 -['O', 'O', 'O', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp']
16 -['O', 'O', 'O', 'O', 'O']
17 -['O', 'O', 'Gtype']
18 -['O', 'O', 'O']
19 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
20 -['O', 'O', 'O', 'O', 'O']
21 -['O', 'O', 'O', 'O', 'O', 'O', 'Gversion', 'Gversion', 'Gversion', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
22 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
23 -['O', 'O', 'Gtype', 'Gtype', 'Gtype']
24 -['O', 'O', 'O']
25 -['O', 'O', 'O', 'O', 'O']
26 -['O', 'O', 'Anti', 'Anti', 'Anti']
27 -['O', 'O', 'O']
28 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
29 -['O', 'O', 'O', 'O', 'O']
30 -['O', 'O', 'O']
31 -['O', 'O', 'O']
32 -['O', 'O', 'O']
33 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
34 -['O', 'O', 'O', 'O']
35 -['O', 'O', 'O', 'Supp']
36 -['O', 'O', 'O', 'Anti', 'O', 'O', 'O', 'O', 'O']
37 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
38 -['O', 'O', 'O', 'O']
39 -['O', 'O', 'O']
40 -['O', 'O', 'O', 'O']
41 -['O', 'O', 'O', 'O', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
42 -['O', 'O', 'O']
43 -['O', 'O', 'O', 'O']
44 -['O', 'O', 'O', 'O', 'O']
45 -['O', 'O', 'Gtype']
46 -['O', 'O', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
47 -['Substrain', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
48 -['O', 'O', 'O', 'O', 'O', 'O']
49 -['O', 'O', 'Gtype', 'O', 'O']
50 -['O', 'O', 'Gtype']
51 -['O', 'O', 'O']
52 -['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', 'Phase', 'Phase', 'O', 'OD', 'OD', 'OD', 'OD', 'O', 'O', 'Med', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp', 'O']
53 -['O', 'O', 'O']
54 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
55 -['O', 'O', 'O']
56 -['O', 'O', 'O']
57 -['O', 'O', 'O', 'Anti']
58 -['O', 'O', 'O', 'O', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Phase', 'Phase', 'O', 'OD', 'OD', 'OD', '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', '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', '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', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
59 -['O', 'O', 'O']
60 -['O', 'O', 'O']
61 -['O', 'O', 'Gtype']
62 -['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', 'Phase', 'Phase', 'O', 'OD', 'OD', 'OD', 'OD', 'O', 'O']
63 -['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', 'O', 'O']
64 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
65 -['O', 'O', 'O']
66 -['O', 'O', 'Gtype']
67 -['O', 'O', 'O', 'Anti', 'Anti', 'Anti', 'O']
68 -['O', 'O', 'O', 'O']
69 -['O', 'O', 'O', 'O']
70 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
71 -['O', 'O', 'O', 'Anti', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
72 -['O', 'O', 'O']
73 -['O', 'O', 'O']
74 -['O', 'O', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
75 -['Substrain', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
76 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
77 -['O', 'O', 'Gtype']
78 -['O', 'O', 'O', 'Anti', 'Anti', 'Anti', 'Anti']
79 -['OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', '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']
80 -['OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD']
81 -['O', 'O', 'O', 'O', 'O', 'O']
82 -['O', 'O', 'O', 'O', 'O']
83 -['O', 'O', 'O', 'Anti']
84 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
85 -['O', 'O', 'Gtype']
86 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
87 -['O', 'O', 'Gtype']
88 -['O', 'O', 'Supp']
89 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
90 -['O', 'O', 'O']
91 -['O', 'O', 'O']
92 -['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Gtype', 'Gtype', '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', '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', 'OD', 'OD', 'OD', 'OD', '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', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
93 -['O', 'O', 'O', 'O', 'O', 'O']
94 -['O', 'O', 'Med']
95 -['O', 'O', 'O', 'O', 'O', 'O']
96 -['O', 'O', 'O', 'O', 'O', 'O', 'O']
97 -['O', 'O', 'Supp']
98 -['O', 'O']
99 -['O', 'O', 'O', 'O', 'O']
100 -['O', 'O', 'O']
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 1 +
2 +
3 +# Orgiginal files
4 +#cd /home/egaytan/automatic-extraction-growth-conditions/data-sets/report-manually-tagged-gcs/
5 +
6 +# Re-tagged
7 +cd /home/egaytan/automatic-extraction-growth-conditions/data-sets/tagged-xml-data/
2 echo 8 echo
3 echo 9 echo
4 echo 10 echo
...@@ -18,9 +24,9 @@ echo ...@@ -18,9 +24,9 @@ echo
18 echo 24 echo
19 echo "Filter all paragraphs with tags..." 25 echo "Filter all paragraphs with tags..."
20 echo "Add sentence-end-tag PGCGROWTHCONDITIONS..." 26 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 27 +grep -E "<[^<]*>" * | grep -E '!'| cut -f2 -d'='|sort|uniq|awk '{ print $_" PGCGROWTHCONDITIONS"; }' > /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt
22 echo 28 echo
23 -echo "Number of total tag sentences: "$(wc /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt -l); 29 +echo "Number of total tag sentences: "$(wc /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt -l);
24 echo 30 echo
25 echo 31 echo
26 -echo "Saving file: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt"; 32 +echo "Saving file: /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt";
......
...@@ -4,8 +4,8 @@ echo "==============================Run CoreNLP================================= ...@@ -4,8 +4,8 @@ echo "==============================Run CoreNLP=================================
4 echo 4 echo
5 echo 5 echo
6 6
7 -input="/home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt"; 7 +input="/home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt";
8 -output="/home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/"; 8 +output="/home/egaytan/automatic-extraction-growth-conditions/CoreNLP/output/";
9 echo "input file: "$input; 9 echo "input file: "$input;
10 echo 10 echo
11 echo "output directory: "$output; 11 echo "output directory: "$output;
......
1 + affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1.CEL PGCGROWTHCONDITIONS
2 + affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2.CEL PGCGROWTHCONDITIONS
3 + affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3.CEL PGCGROWTHCONDITIONS
4 + affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_1.CEL PGCGROWTHCONDITIONS
5 + affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_2.CEL PGCGROWTHCONDITIONS
6 + affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_3.CEL PGCGROWTHCONDITIONS
7 + affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1.CEL PGCGROWTHCONDITIONS
8 + affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2.CEL PGCGROWTHCONDITIONS
9 + affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3.CEL PGCGROWTHCONDITIONS
10 + affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_1.CEL PGCGROWTHCONDITIONS
11 + affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_2.CEL PGCGROWTHCONDITIONS
12 + affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_3.CEL PGCGROWTHCONDITIONS
13 + affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1.CEL PGCGROWTHCONDITIONS
14 + affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2.CEL PGCGROWTHCONDITIONS
15 + affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3.CEL PGCGROWTHCONDITIONS
16 + affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_1.CEL PGCGROWTHCONDITIONS
17 + affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_2.CEL PGCGROWTHCONDITIONS
18 + affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_3.CEL PGCGROWTHCONDITIONS
19 + agent: <Supp>DPD and rifampicin</Supp> PGCGROWTHCONDITIONS
20 + agent: <Supp>DPD</Supp> PGCGROWTHCONDITIONS
21 + agent: <Supp>Fe and rifampicin</Supp> PGCGROWTHCONDITIONS
22 + agent: <Supp>Fe</Supp> PGCGROWTHCONDITIONS
23 + <Air>Aerobic</Air> cultures PGCGROWTHCONDITIONS
24 + <Air>Anaerobic</Air> cultures PGCGROWTHCONDITIONS
25 + All strains used in this study were E. coli K-12 MG1655 and its derivatives. The deletion mutants (Δfnr and ΔarcA) were constructed by a λ red and FLP-mediated site-specific recombination method. Glycerol stocks of E. coli strains were inoculated into M9 minimal medium containing 0.2% (w/v) carbon source (glucose) and 0.1% (w/v) nitrogen source (NH4Cl), and cultured overnight at 37 °C with constant agitation. The cultures were diluted 1:100 into fresh <Med>minimal medium</Med> and then cultured at <Temp>37 °C</Temp> to an appropriate cell density with constant agitation. For the anaerobic cultures, the minimal medium were flushed with nitrogen and then continuously monitored using a polarographic-dissolved oxygen probe (Cole-Parmer Instruments) to ensure anaerobicity. For nitrate respiration <Supp>20 mmol potassium nitrate</Supp> was added. PGCGROWTHCONDITIONS
26 + All strains used in this study were E. coli K-12 MG1655 and its derivatives. The deletion mutants (Δfnr and ΔarcA) were constructed by a λ red and FLP-mediated site-specific recombination method. Glycerol stocks of E. coli strains were inoculated into M9 minimal medium containing 0.2% (w/v) carbon source (glucose) and 0.1% (w/v) nitrogen source (NH4Cl), and cultured overnight at 37 °C with constant agitation. The cultures were diluted 1:100 into fresh <Med>minimal medium</Med> and then cultured at <Temp>37 °C</Temp> to an appropriate cell density with constant agitation. For the anaerobic cultures, the minimal medium were flushed with <Supp>nitrogen</Supp> and then continuously monitored using a polarographic-dissolved oxygen probe (Cole-Parmer Instruments) to ensure anaerobicity. For nitrate respiration 20 mmol potassium nitrate was added. PGCGROWTHCONDITIONS
27 + antibody: <Anti>9E10 Myc tag</Anti> antibody PGCGROWTHCONDITIONS
28 + antibody: <Anti>Affinity Purified FNR antibody</Anti> PGCGROWTHCONDITIONS
29 + antibody: <Anti>anti-FLAG mAb</Anti> PGCGROWTHCONDITIONS
30 + antibody: <Anti>Pre-cleared FNR antibody</Anti> PGCGROWTHCONDITIONS
31 + antibody: <Anti>Pre-cleared H-NS polyclonal antibody</Anti> PGCGROWTHCONDITIONS
32 + antibody: <Anti>Pre-cleared IHF polyclonal antibody</Anti> PGCGROWTHCONDITIONS
33 + antibody: <Anti>RNA Polymerase ß monoclonal antibody</Anti> from NeoClone (W0002) PGCGROWTHCONDITIONS
34 + ArgR_<Supp>Arginine</Supp>_1 PGCGROWTHCONDITIONS
35 + ArgR_<Supp>Arginine</Supp>_2 PGCGROWTHCONDITIONS
36 + ArgR_<Supp>NH4Cl</Supp>_1 PGCGROWTHCONDITIONS
37 + ArgR_<Supp>NH4Cl</Supp>_2 PGCGROWTHCONDITIONS
38 + At <OD>OD450 PGCGROWTHCONDITIONS
39 + 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
40 + 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
41 + carbon source: <Supp>acetate</Supp> PGCGROWTHCONDITIONS
42 + carbon source: <Supp>fructose</Supp> PGCGROWTHCONDITIONS
43 + carbon source: <Supp>glucose</Supp> PGCGROWTHCONDITIONS
44 + 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
45 + 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
46 + 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
47 + 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
48 + 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
49 + 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
50 + 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
51 + 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
52 + 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
53 + 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
54 + 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
55 + 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
56 + 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
57 + 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
58 + 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
59 + chip antibody: <Anti>9E10 Myc tag</Anti> antibody PGCGROWTHCONDITIONS
60 + chip antibody: <Anti>anti-myc</Anti> PGCGROWTHCONDITIONS
61 + chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207) PGCGROWTHCONDITIONS
62 + chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002) PGCGROWTHCONDITIONS
63 + chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766) PGCGROWTHCONDITIONS
64 + chip antibody: <Anti>anti-RpoS</Anti> (neoclone, WP009) PGCGROWTHCONDITIONS
65 + chip antibody: <Anti>biotin conjugated anti-c-myc antibody</Anti> PGCGROWTHCONDITIONS
66 + chip antibody: <Anti>none</Anti> PGCGROWTHCONDITIONS
67 + chip antibody: <Anti>RNA polymerase subunit β</Anti> PGCGROWTHCONDITIONS
68 + chip antibody: <Anti>SeqA</Anti> PGCGROWTHCONDITIONS
69 + chip antibody: <Anti>σ32</Anti> PGCGROWTHCONDITIONS
70 + chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti> PGCGROWTHCONDITIONS
71 + chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1 PGCGROWTHCONDITIONS
72 + chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2 PGCGROWTHCONDITIONS
73 + chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3 PGCGROWTHCONDITIONS
74 + chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_1 PGCGROWTHCONDITIONS
75 + chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_2 PGCGROWTHCONDITIONS
76 + chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_3 PGCGROWTHCONDITIONS
77 + ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters -S PGCGROWTHCONDITIONS
78 + ChIP-exo reads were aligned to the <Gversion>NC_000913 </Gversion>genome reference sequence using using bowtie v1.0.0 with parameters -S PGCGROWTHCONDITIONS
79 + chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1 PGCGROWTHCONDITIONS
80 + chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2 PGCGROWTHCONDITIONS
81 + chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3 PGCGROWTHCONDITIONS
82 + chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_1 PGCGROWTHCONDITIONS
83 + chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_2 PGCGROWTHCONDITIONS
84 + chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_3 PGCGROWTHCONDITIONS
85 + Cra <Supp>acetate</Supp> 1 PGCGROWTHCONDITIONS
86 + Cra <Supp>acetate</Supp> 2 PGCGROWTHCONDITIONS
87 + Cra <Supp>fructose</Supp> 1 PGCGROWTHCONDITIONS
88 + Cra <Supp>fructose</Supp> 2 PGCGROWTHCONDITIONS
89 + Cra <Supp>glucose</Supp> 1 PGCGROWTHCONDITIONS
90 + Cra <Supp>glucose</Supp> 2 PGCGROWTHCONDITIONS
91 + CsiR_<Technique>ChIPSeq</Technique> PGCGROWTHCONDITIONS
92 + CsiR_<Technique>RNASeq</Technique> PGCGROWTHCONDITIONS
93 + culture condition: <Air>Aerobic</Air> cultures PGCGROWTHCONDITIONS
94 + culture condition: <Air>Anaerobic</Air> cultures PGCGROWTHCONDITIONS
95 + culture condition: <Air>anaerobic</Air> fermentive condition PGCGROWTHCONDITIONS
96 + culture condition: <Supp>nitrate</Supp> respiratory condition PGCGROWTHCONDITIONS
97 + cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% acetate</Supp> PGCGROWTHCONDITIONS
98 + cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% fructose</Supp> PGCGROWTHCONDITIONS
99 + cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp> PGCGROWTHCONDITIONS
100 + Cultures grown in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp> PGCGROWTHCONDITIONS
101 + Ecoli_<Gtype>dFNR</Gtype>_rep1_<Air>anaerobic</Air> PGCGROWTHCONDITIONS
102 + Ecoli_<Gtype>dFNR</Gtype>_rep2_<Air>anaerobic</Air> PGCGROWTHCONDITIONS
103 + Ecoli_<Gtype>wild-type</Gtype>_rep1_<Air>anaerobic</Air> PGCGROWTHCONDITIONS
104 + Ecoli_<Gtype>wild-type</Gtype>_rep2_<Air>anaerobic</Air> PGCGROWTHCONDITIONS
105 + 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
106 + 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
107 + 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
108 + 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
109 + 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
110 + 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
111 + 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
112 + 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
113 + 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
114 + 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
115 + 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
116 + E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 PGCGROWTHCONDITIONS
117 + 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
118 + 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
119 + 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
120 + 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
121 + 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
122 + 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
123 + 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
124 + 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
125 + Escherichia coli MG1655 K-12 <Gtype>dFNR (PK4854)</Gtype> PGCGROWTHCONDITIONS
126 + 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
127 + FNR - <Air>Anaerobic</Air> - A PGCGROWTHCONDITIONS
128 + FNR - <Air>Anaerobic</Air> - Affinity Purified - A PGCGROWTHCONDITIONS
129 + FNR - <Air>Anaerobic</Air> - Affinity Purified - B PGCGROWTHCONDITIONS
130 + FNR - <Air>Anaerobic</Air> - B PGCGROWTHCONDITIONS
131 + FNR - <Air>Anaerobic</Air> - C PGCGROWTHCONDITIONS
132 + FNR - <Gtype>∆hns∆stpA</Gtype> A PGCGROWTHCONDITIONS
133 + FNR - <Gtype>∆hns∆stpA</Gtype> B PGCGROWTHCONDITIONS
134 + Fur IP <Technique>ChIP-Seq</Technique> <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
135 + Fur IP <Technique>ChIP-Seq</Technique> <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
136 + Fur IP <Technique>ChIP-Seq</Technique> <Air>Aerobic</Air> C PGCGROWTHCONDITIONS
137 + Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
138 + Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
139 + Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air> C PGCGROWTHCONDITIONS
140 + Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air>, <Supp>Iron</Supp> Deficient A PGCGROWTHCONDITIONS
141 + Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air>, <Supp>Iron</Supp> Deficient B PGCGROWTHCONDITIONS
142 + Fur with <Supp>DPD</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
143 + Fur with <Supp>DPD</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
144 + Fur with <Supp>Fe</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
145 + Fur with <Supp>Fe</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
146 + Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion> PGCGROWTHCONDITIONS
147 + Genome_build: <Gversion>ASM584v2</Gversion> PGCGROWTHCONDITIONS
148 + Genome_build: <Gversion>NC_000913.2</Gversion> PGCGROWTHCONDITIONS
149 + Genome_build: <Gversion>NC_000913</Gversion> PGCGROWTHCONDITIONS
150 + Genome_build: <Gversion>U00096.2</Gversion> (GenBank) PGCGROWTHCONDITIONS
151 + genotype: delta-<Gtype>cra Knock-out strain</Gtype> PGCGROWTHCONDITIONS
152 + genotype: delta-<Gtype>crp Knock-out strain</Gtype> PGCGROWTHCONDITIONS
153 + genotype: <Gtype>ArgR-8myc</Gtype> PGCGROWTHCONDITIONS
154 + genotype: <Gtype>gadE-8myc</Gtype> PGCGROWTHCONDITIONS
155 + genotype: <Gtype>gadW-8myc</Gtype> PGCGROWTHCONDITIONS
156 + genotype: <Gtype>gadX-8myc</Gtype> PGCGROWTHCONDITIONS
157 + genotype: <Gtype>Lrp-8myc</Gtype> PGCGROWTHCONDITIONS
158 + genotype: <Gtype>ompR-8myc</Gtype> PGCGROWTHCONDITIONS
159 + genotype: <Gtype>ompR deletion mutant</Gtype> PGCGROWTHCONDITIONS
160 + genotype: <Gtype>PurR-8myc</Gtype> PGCGROWTHCONDITIONS
161 + genotype: <Gtype>TrpR-8myc</Gtype> PGCGROWTHCONDITIONS
162 + genotype: <Gtype>wildtype</Gtype> PGCGROWTHCONDITIONS
163 + genotype: <Gtype>Wildtype</Gtype> PGCGROWTHCONDITIONS
164 + genotype: <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
165 + genotype: <Gtype>ΔseqA</Gtype> PGCGROWTHCONDITIONS
166 + genotype/variation: <Gtype>Combined input</Gtype> PGCGROWTHCONDITIONS
167 + genotype/variation: <Gtype>cra-8myc-tagged</Gtype> PGCGROWTHCONDITIONS
168 + genotype/variation: <Gtype>delta_cra</Gtype> PGCGROWTHCONDITIONS
169 + genotype/variation: <Gtype>delta-gadE</Gtype> PGCGROWTHCONDITIONS
170 + genotype/variation: <Gtype>delta-gadW</Gtype> PGCGROWTHCONDITIONS
171 + genotype/variation: <Gtype>delta-gadX</Gtype> PGCGROWTHCONDITIONS
172 + genotype/variation: <Gtype>{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12</Gtype> PGCGROWTHCONDITIONS
173 + genotype/variation: <Gtype>delta-oxyR</Gtype> PGCGROWTHCONDITIONS
174 + genotype/variation: <Gtype>delta-soxR</Gtype> PGCGROWTHCONDITIONS
175 + genotype/variation: <Gtype>delta-soxS</Gtype> PGCGROWTHCONDITIONS
176 + genotype/variation: <Gtype>{delta}tonB, {delta}feoA, {delta}zupT K12</Gtype> PGCGROWTHCONDITIONS
177 + genotype/variation: <Gtype>fur-8myc</Gtype> PGCGROWTHCONDITIONS
178 + genotype/variation: <Gtype>lacking the small RNA RyhB</Gtype> PGCGROWTHCONDITIONS
179 + genotype/variation: <Gtype>lacking the transcription factor Fur and the small RNA RyhB</Gtype> PGCGROWTHCONDITIONS
180 + genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype> PGCGROWTHCONDITIONS
181 + genotype/variation: <Gtype>oxyR-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
182 + genotype/variation: <Gtype>soxR-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
183 + genotype/variation: <Gtype>soxS-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
184 + genotype/variation: <Gtype>wild type</Gtype> PGCGROWTHCONDITIONS
185 + genotype/variation: <Gtype>Wild-type</Gtype> PGCGROWTHCONDITIONS
186 + genotype/variation: <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
187 + genotype/variation: <Gtype>ΔarcA</Gtype> PGCGROWTHCONDITIONS
188 + genotype/variation: <Gtype>Δfnr</Gtype> PGCGROWTHCONDITIONS
189 + genotype/variation: <Gtype>Δfur</Gtype> PGCGROWTHCONDITIONS
190 + genotype/variation: harboring <Gtype>ArcA-8myc</Gtype> PGCGROWTHCONDITIONS
191 + genotype/variation: harboring <Gtype>Fnr-8myc</Gtype> PGCGROWTHCONDITIONS
192 + genoype: <Gtype>dFNR</Gtype> PGCGROWTHCONDITIONS
193 + genoype: <Gtype>Wild-Type</Gtype> PGCGROWTHCONDITIONS
194 + growth condition: <Air>Aerobic</Air> PGCGROWTHCONDITIONS
195 + growth condition: <Air>anaerobic</Air> PGCGROWTHCONDITIONS
196 + growth condition: <Air>Anaerobic</Air> PGCGROWTHCONDITIONS
197 + growth condition: <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
198 + growth condition: <Supp>4 µM IPTG</Supp> PGCGROWTHCONDITIONS
199 + growth condition: <Supp>8 µM IPTG</Supp> PGCGROWTHCONDITIONS
200 + growth condition: <Supp>Adenine</Supp> PGCGROWTHCONDITIONS
201 + growth condition: <Supp>glucose</Supp> PGCGROWTHCONDITIONS
202 + growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp> PGCGROWTHCONDITIONS
203 + growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>1 µM FeSO4</Supp> PGCGROWTHCONDITIONS
204 + growth phase: <Phase>exponential</Phase> PGCGROWTHCONDITIONS
205 + growth phase: <Phase>mid-log</Phase> PGCGROWTHCONDITIONS
206 + growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 PGCGROWTHCONDITIONS
207 + growth phase: <Phase>stationary</Phase> PGCGROWTHCONDITIONS
208 + <Gtype>∆fnr</Gtype> - <Air>Anaeroibc</Air> PGCGROWTHCONDITIONS
209 + <Gtype>∆fnr</Gtype> ChIP DNA from <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS
210 + <Gtype>∆fur</Gtype> <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
211 + <Gtype>∆fur</Gtype> <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
212 + <Gtype>∆fur</Gtype> <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
213 + <Gtype>∆fur</Gtype> <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
214 + <Gtype>∆fur</Gtype> <Air>Anaerobic</Air> [IP vs nput] PGCGROWTHCONDITIONS
215 + <Gtype>∆fur ∆ryhB</Gtype> <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
216 + <Gtype>∆fur ∆ryhB</Gtype> <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
217 + <Gtype>∆fur ∆ryhB</Gtype> <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
218 + <Gtype>∆fur ∆ryhB</Gtype> <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
219 + <Gtype>NsrR_Flagtag</Gtype>_rep1 PGCGROWTHCONDITIONS
220 + <Gtype>NsrR_Flagtag</Gtype>_rep2 PGCGROWTHCONDITIONS
221 + <Gtype>NsrR_Flagtag</Gtype>_rep3 PGCGROWTHCONDITIONS
222 + <Gtype>Ptac::fnr</Gtype> - A - <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
223 + <Gtype>Ptac::fnr</Gtype> - A - <Supp>4 µM IPTG</Supp> PGCGROWTHCONDITIONS
224 + <Gtype>Ptac::fnr</Gtype> - A - <Supp>8 µM IPTG</Supp> PGCGROWTHCONDITIONS
225 + <Gtype>Ptac::fnr</Gtype> - B - <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
226 + <Gtype>Ptac::fnr</Gtype> - B - <Supp>4 µM IPTG</Supp> PGCGROWTHCONDITIONS
227 + <Gtype>Ptac::fnr</Gtype> - B - <Supp>8 µM IPTG</Supp> PGCGROWTHCONDITIONS
228 + <Gtype>Ptac::fnr</Gtype> - C - <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
229 + <Gtype>∆ryhB</Gtype> <Air>Aerobic</Air> PGCGROWTHCONDITIONS
230 + <Gtype>∆ryhB</Gtype> <Air>Anaerobic</Air> PGCGROWTHCONDITIONS
231 + <Gtype>Wild-type</Gtype> <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
232 + <Gtype>Wild-type</Gtype> <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
233 + <Gtype>Wild-type</Gtype> <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
234 + <Gtype>Wild-type</Gtype> <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
235 + <Gtype>Wild type</Gtype> control (0 min) PGCGROWTHCONDITIONS
236 + <Gtype>Wild type</Gtype> control (10 min) PGCGROWTHCONDITIONS
237 + <Gtype>Wild type</Gtype> control (20 min) PGCGROWTHCONDITIONS
238 + <Gtype>Wild type</Gtype> control (2.5 min) PGCGROWTHCONDITIONS
239 + <Gtype>Wild type</Gtype> control (5 min) PGCGROWTHCONDITIONS
240 + <Gtype>WT</Gtype> <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
241 + <Gtype>WT</Gtype> <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
242 + <Gtype>WT</Gtype> <Supp>acetate</Supp> 1 PGCGROWTHCONDITIONS
243 + <Gtype>WT</Gtype> <Supp>acetate</Supp> 2 PGCGROWTHCONDITIONS
244 + <Gtype>WT</Gtype> <Supp>fructose</Supp> 1 PGCGROWTHCONDITIONS
245 + <Gtype>WT</Gtype> <Supp>fructose</Supp> 2 PGCGROWTHCONDITIONS
246 + <Gtype>WT</Gtype> <Supp>glucose</Supp> 1 PGCGROWTHCONDITIONS
247 + <Gtype>WT</Gtype> <Supp>glucose</Supp> 2 PGCGROWTHCONDITIONS
248 + <Gtype>WT</Gtype> <Supp>NaCl</Supp> 1 PGCGROWTHCONDITIONS
249 + <Gtype>WT</Gtype> <Supp>NaCl</Supp> 2 PGCGROWTHCONDITIONS
250 + <Gtype>WT</Gtype> <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
251 + <Gtype>WT</Gtype> <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
252 + <Gtype>WT</Gtype>_<Technique>ChIPSeq</Technique>_1 PGCGROWTHCONDITIONS
253 + <Gtype>WT</Gtype>_<Technique>ChIPSeq</Technique>_2 PGCGROWTHCONDITIONS
254 + <Gtype>WT</Gtype>_<Technique>RNASeq</Technique> PGCGROWTHCONDITIONS
255 + <Gtype>WT</Gtype> with <Supp>DPD</Supp> 1 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
256 + <Gtype>WT</Gtype> with <Supp>DPD</Supp> 2 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
257 + <Gtype>WT</Gtype> with <Supp>Fe</Supp> 1 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
258 + <Gtype>WT</Gtype> with <Supp>Fe</Supp> 2 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
259 + <Gtype>Δcra</Gtype> <Supp>acetate</Supp> 1 PGCGROWTHCONDITIONS
260 + <Gtype>Δcra</Gtype> <Supp>acetate</Supp> 2 PGCGROWTHCONDITIONS
261 + <Gtype>Δcra</Gtype> <Supp>fructose</Supp> 1 PGCGROWTHCONDITIONS
262 + <Gtype>Δcra</Gtype> <Supp>fructose</Supp> 2 PGCGROWTHCONDITIONS
263 + <Gtype>Δcra</Gtype> <Supp>glucose</Supp> 1 PGCGROWTHCONDITIONS
264 + <Gtype>Δcra</Gtype> <Supp>glucose</Supp> 2 PGCGROWTHCONDITIONS
265 + <Gtype>Δfur</Gtype> with <Supp>DPD</Supp> 1 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
266 + <Gtype>Δfur</Gtype> with <Supp>DPD</Supp> 2 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
267 + <Gtype>Δfur</Gtype> with <Supp>Fe</Supp> 1 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
268 + <Gtype>Δfur</Gtype> with <Supp>Fe</Supp> 2 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
269 + <Gtype>ΔgadE</Gtype> <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
270 + <Gtype>ΔgadE</Gtype> <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
271 + <Gtype>ΔgadW</Gtype> <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
272 + <Gtype>ΔgadW</Gtype> <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
273 + <Gtype>ΔgadX</Gtype> <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
274 + <Gtype>ΔgadX</Gtype> <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
275 + <Gtype>ΔompR</Gtype> <Supp>NaCl</Supp> 1 PGCGROWTHCONDITIONS
276 + <Gtype>ΔompR</Gtype> <Supp>NaCl</Supp> 2 PGCGROWTHCONDITIONS
277 + <Gtype>ΔoxyR</Gtype> <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
278 + <Gtype>ΔoxyR</Gtype> <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
279 + <Gtype>ΔsoxR</Gtype> <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
280 + <Gtype>ΔsoxR</Gtype> <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
281 + <Gtype>ΔsoxS</Gtype> <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
282 + <Gtype>ΔsoxS</Gtype> <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
283 + <Gversion>ChIP-Seq</Gversion> PGCGROWTHCONDITIONS
284 + HNS - <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
285 + HNS - <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
286 + HNS - <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
287 + HNS - <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
288 + IHF - <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
289 + IHF - <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
290 + Input <Technique>ChIP-Seq</Technique> PGCGROWTHCONDITIONS
291 + ip antibody: <Anti>affinity purified anti-Fur antibody</Anti> PGCGROWTHCONDITIONS
292 + library strategy: <Technique>ChIP-exo</Technique> PGCGROWTHCONDITIONS
293 + Lrp_<Supp>Leu</Supp>_1 PGCGROWTHCONDITIONS
294 + Lrp_<Supp>Leu</Supp>_2 PGCGROWTHCONDITIONS
295 + Lrp_<Supp>Leu</Supp>_3 PGCGROWTHCONDITIONS
296 + Lrp_<Supp>NH4Cl</Supp>_1 PGCGROWTHCONDITIONS
297 + Lrp_<Supp>NH4Cl</Supp>_2 PGCGROWTHCONDITIONS
298 + Lrp_<Supp>NH4Cl</Supp>_3 PGCGROWTHCONDITIONS
299 + medium: <Med>LB</Med> PGCGROWTHCONDITIONS
300 + medium: <Med>M63</Med> PGCGROWTHCONDITIONS
301 + <Med>LB</Med> 0.4 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
302 + <Med>LB</Med> 0.4 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
303 + <Med>LB</Med> 0.4 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
304 + <Med>LB</Med> 0.4 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
305 + <Med>LB</Med> 0.4 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
306 + <Med>LB</Med> 0.4 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
307 + <Med>LB</Med> 2.0 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
308 + <Med>LB</Med> 2.0 B1 TEX neg L2 HS2 PGCGROWTHCONDITIONS
309 + <Med>LB</Med> 2.0 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
310 + <Med>LB</Med> 2.0 B1 TEX pos L2 HS2 PGCGROWTHCONDITIONS
311 + <Med>LB</Med> 2.0 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
312 + <Med>LB</Med> 2.0 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
313 + <Med>LB</Med> 2.0 B2 TEX neg L2 HS2 PGCGROWTHCONDITIONS
314 + <Med>LB</Med> 2.0 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
315 + <Med>LB</Med> 2.0 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
316 + <Med>LB</Med> 2.0 B2 TEX pos L2 HS2 PGCGROWTHCONDITIONS
317 + <Med>M63</Med> 0.4 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
318 + <Med>M63</Med> 0.4 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
319 + <Med>M63</Med> 0.4 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
320 + <Med>M63</Med> 0.4 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
321 + <Med>M63</Med> 0.4 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
322 + <Med>M63</Med> 0.4 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
323 + <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
324 + Nac_<Technique>ChIPSeq</Technique> PGCGROWTHCONDITIONS
325 + Nac_<Technique>RNASeq</Technique> PGCGROWTHCONDITIONS
326 + NtrC_<Technique>ChIPSeq</Technique> PGCGROWTHCONDITIONS
327 + OmpR <Supp>NaCl</Supp> 1 PGCGROWTHCONDITIONS
328 + OmpR <Supp>NaCl</Supp> 2 PGCGROWTHCONDITIONS
329 + OmpR_<Technique>ChIPSeq</Technique> PGCGROWTHCONDITIONS
330 + <Orgn>Escherichia coli K-12</Orgn> PGCGROWTHCONDITIONS
331 + <Orgn>Escherichia coli</Orgn> PGCGROWTHCONDITIONS
332 + <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655star</Substrain> PGCGROWTHCONDITIONS
333 + <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain> PGCGROWTHCONDITIONS
334 + <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn> PGCGROWTHCONDITIONS
335 + <Orgn>Escherichia coli str. K-12 substr. MG1655star</Orgn> PGCGROWTHCONDITIONS
336 + OxyR <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
337 + OxyR <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
338 + pT7_<Technique>ChIPSeq</Technique>_1 PGCGROWTHCONDITIONS
339 + pT7_<Technique>ChIPSeq</Technique>_2 PGCGROWTHCONDITIONS
340 + PurR_<Supp>Adenine</Supp>_1 PGCGROWTHCONDITIONS
341 + PurR_<Supp>Adenine</Supp>_2 PGCGROWTHCONDITIONS
342 + PurR_<Supp>glucose</Supp>_1 PGCGROWTHCONDITIONS
343 + PurR_<Supp>glucose</Supp>_2 PGCGROWTHCONDITIONS
344 + 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
345 + RpoB <Gtype>∆cra</Gtype> 1 PGCGROWTHCONDITIONS
346 + RpoB <Gtype>∆cra</Gtype> 2 PGCGROWTHCONDITIONS
347 + RpoB <Gtype>∆crp</Gtype> 1 PGCGROWTHCONDITIONS
348 + RpoB <Gtype>∆crp</Gtype> 2 PGCGROWTHCONDITIONS
349 + RpoB <Gtype>WT</Gtype> 1 PGCGROWTHCONDITIONS
350 + RpoB <Gtype>WT</Gtype> 2 PGCGROWTHCONDITIONS
351 + RpoB with <Supp>DPD</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
352 + RpoB with <Supp>DPD</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
353 + RpoB with <Supp>DPD</Supp> and <Supp>rifampicin</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
354 + RpoB with <Supp>DPD</Supp> and <Supp>rifampicin</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
355 + RpoB with <Supp>Fe</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
356 + RpoB with <Supp>Fe</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
357 + RpoB with <Supp>Fe</Supp> and <Supp>rifampicin</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
358 + RpoB with <Supp>Fe</Supp> and <Supp>rifampicin</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
359 + Samples for transcriptome analysis were taken from <Phase>exponentially growing cells</Phase>. From the cells treated by RNAprotect Bacteria Reagent (Qiagen), total RNA samples were isolated using RNeasy columns (Qiagen) in accordance with manufacturer’s instruction. PGCGROWTHCONDITIONS
360 + SeqA new <Gtype>deltaSeqA</Gtype> PGCGROWTHCONDITIONS
361 + SeqA old <Gtype>deltaSeqA</Gtype> PGCGROWTHCONDITIONS
362 + 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
363 + 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
364 + SoxR <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
365 + SoxR <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
366 + SoxS <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
367 + SoxS <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
368 + ß - <Air>Aerobic</Air> - A PGCGROWTHCONDITIONS
369 + ß - <Air>Aerobic</Air> - B PGCGROWTHCONDITIONS
370 + ß - <Air>Anaerobic</Air> - A PGCGROWTHCONDITIONS
371 + ß - <Air>Anaerobic</Air> - B PGCGROWTHCONDITIONS
372 + strain: <Gtype>∆hns/∆stpA</Gtype> PGCGROWTHCONDITIONS
373 + strain: <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS
374 + strain: <Gtype>PK8263</Gtype> PGCGROWTHCONDITIONS
375 + strain: MG1655 K-12 <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
376 + strain: <Orgn>K-12 MG1655</Orgn> PGCGROWTHCONDITIONS
377 + strain: <Orgn>MG1655</Orgn> PGCGROWTHCONDITIONS
378 + strain: <Strain>K-12</Strain> PGCGROWTHCONDITIONS
379 + <Substrain>MG1655</Substrain> <Gtype>PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)</Gtype> PGCGROWTHCONDITIONS
380 + <Substrain>MG1655</Substrain> <Gtype>PhtpG::lacZ delta lacX74/ptrc99A (control vector)</Gtype> PGCGROWTHCONDITIONS
381 + <Supp>acetate</Supp> PGCGROWTHCONDITIONS
382 + <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
383 + <Technique>ChIP-exo</Technique> GadE <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
384 + <Technique>ChIP-exo</Technique> GadE <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
385 + <Technique>ChIP-exo</Technique> GadW <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
386 + <Technique>ChIP-exo</Technique> GadW <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
387 + <Technique>ChIP-exo</Technique> GadX <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
388 + <Technique>ChIP-exo</Technique> GadX <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
389 + <Technique>ChIP-exo</Technique> RpoS <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
390 + <Technique>ChIP-exo</Technique> RpoS <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
391 + <Technique>ChIP-Seq</Technique> PGCGROWTHCONDITIONS
392 + <Technique>RNA-Seq</Technique> PGCGROWTHCONDITIONS
393 + 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
394 + 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
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 <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
396 + treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp> PGCGROWTHCONDITIONS
397 + treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp> PGCGROWTHCONDITIONS
398 + treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>10 mM leucine</Supp>. PGCGROWTHCONDITIONS
399 + treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>20 mg/L tryptophan</Supp>. PGCGROWTHCONDITIONS
400 + treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>10 mM leucine</Supp>. PGCGROWTHCONDITIONS
401 + treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>20 mg/L tryptophan</Supp>. PGCGROWTHCONDITIONS
402 + treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>1g/L arginine</Supp>. PGCGROWTHCONDITIONS
403 + treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>2g/L glutamine</Supp>. PGCGROWTHCONDITIONS
404 + TrpR_<Supp>glucose</Supp> PGCGROWTHCONDITIONS
405 + TrpR_<Supp>Trp</Supp> PGCGROWTHCONDITIONS
406 + σ32 <Temp>30°C</Temp> rep1 PGCGROWTHCONDITIONS
407 + σ32 <Temp>30°C</Temp> rep2 PGCGROWTHCONDITIONS
408 + σ32 <Temp>30°C</Temp> short RNase PGCGROWTHCONDITIONS
409 + σ32 <Temp>43°C</Temp> rep1 PGCGROWTHCONDITIONS
410 + σ32 <Temp>43°C</Temp> rep2 PGCGROWTHCONDITIONS
411 + σ32 <Temp>43°C</Temp> short RNase PGCGROWTHCONDITIONS
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