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

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Estefani Gaytan Nunez
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#!/bin/python3
import os
from itertools import chain
from optparse import OptionParser
from time import time
from collections import Counter
import re
import nltk
import sklearn
import scipy.stats
import sys
from sklearn.externals import joblib
from sklearn.metrics import make_scorer
from sklearn.cross_validation import cross_val_score
from sklearn.grid_search import RandomizedSearchCV
import sklearn_crfsuite
from sklearn_crfsuite import scorers
from sklearn_crfsuite import metrics
from nltk.corpus import stopwords
import random
# Objective
# Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging
#
# Input parameters
# --inputPath=PATH Path of inputfile
# --outputPath=PATH Path to place output files
# --trainingFile=testFile Output training data set
# --testFile=testFile Output test data set
#
# Output
# training and test data set
#
# Examples
# 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
#
#
# 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
##########################################
# MAIN PROGRAM #
##########################################
if __name__ == "__main__":
# Defining parameters
parser = OptionParser()
parser.add_option("--inputPath", dest="inputPath",
help="Path of output from CoreNLP", metavar="PATH")
parser.add_option("--outputPath", dest="outputPath",
help="Output path to place output files",
metavar="PATH")
parser.add_option("--inputFile", dest="inputFile",
help="File with CoreNLP-tagging sentences", metavar="FILE")
parser.add_option("--trainingFile", dest="trainingFile",
help="File with training data set", metavar="FILE")
parser.add_option("--testFile", dest="testFile",
help="File with test data set", metavar="FILE")
(options, args) = parser.parse_args()
if len(args) > 0:
parser.error("Any parameter given.")
sys.exit(1)
print('-------------------------------- PARAMETERS --------------------------------')
print("Path of CoreNLP output: " + options.inputPath)
print("File with CoreNLP-tagging sentences: " + str(options.inputFile))
print("Path of training data set: " + str(options.outputPath))
print("File with training data set: " + str(options.trainingFile))
print("Path of test data set: " + str(options.outputPath))
print("File with test data set: " + str(options.testFile))
print('-------------------------------- PROCESSING --------------------------------')
## begin of tagging
in_labels = {
'<Gtype>': 'Gtype',
'<Gversion>': 'Gversion',
'<Med>': 'Med',
'<Phase>': 'Phase',
'<Sample>': 'Sample',
'<Serie>': 'Serie',
'<Substrain>': 'Substrain',
'<Supp>': 'Supp',
'<Technique>': 'Technique',
'<Temp>': 'Temp',
'<OD>': 'OD',
'<Anti>': 'Anti',
'<Agit>': 'Agit',
'<Vess>': 'Vess'
}
## End of tagging
out_labels = {
'</Air>': 'O',
'</Gtype>': 'O',
'</Gversion>': 'O',
'</Med>': 'O',
'</Phase>': 'O',
'</Sample>': 'O',
'</Serie>': 'O',
'</Strain>': 'O',
'<Strain>': 'O',
'</Substrain>': 'O',
'</Supp>': 'O',
'</Technique>': 'O',
'</Temp>': 'O',
'</OD>': 'O',
'</Anti>': 'O',
'</Agit>': 'O',
'<Name>': 'O',
'</Name>': 'O',
'<Orgn>': 'O',
'</Orgn>': 'O',
'</Vess>': 'O'}
# Other label
flag = 'O'
# sentences counter
n=0
lista = []
#First sentence
sentence = ''
with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file:
for line in input_file:
if len(line.split('\t')) > 1:
w = line.split('\t')[1]
if w in in_labels or w in out_labels:
#Tagging
if w in in_labels.keys(): flag = in_labels[w]
if w in out_labels: flag = out_labels[w]
else:
if w == "PGCGROWTHCONDITIONS":
#End of sentence
lista.append(sentence)
#New setence
sentence = ''
n=n+1
else:
#Building and save tagging sentence
sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ')
print("Number of sentences: " + str(n))
# Split 70 30 training and test sentences
trainingIndex = random.sample(range(len(lista)-1), int(len(lista)*.70))
testIndex = [n for n in range(len(lista)-1) if n not in trainingIndex]
print(len(trainingIndex))
print(len(testIndex))
with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile:
Data = [lista[i] for i in trainingIndex]
oFile.write('\n'.join(Data))
with open(os.path.join(options.outputPath, options.testFile), "w") as oFile:
Data = [lista[i] for i in testIndex]
oFile.write('\n'.join(Data))
print("==================================END===================================")
#!/bin/python3
from optparse import OptionParser
import re
import os
import random
# Objective
# Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging
# make data sets using only sentences with at least one true-tag
#
# Input parameters
# --inputPath=PATH Path of inputfile
# --outputPath=PATH Path to place output files
# --trainingFile=testFile Output training data set
# --testFile=testFile Output test data set
#
# Output
# training and test data set
#
# Examples
# python label-split_training_test_v2.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
#
#
# 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
##########################################
# MAIN PROGRAM #
##########################################
if __name__ == "__main__":
# Defining parameters
parser = OptionParser()
parser.add_option("--inputPath", dest="inputPath",
help="Path of output from CoreNLP", metavar="PATH")
parser.add_option("--outputPath", dest="outputPath",
help="Output path to place output files",
metavar="PATH")
parser.add_option("--inputFile", dest="inputFile",
help="File with CoreNLP-tagging sentences", metavar="FILE")
parser.add_option("--trainingFile", dest="trainingFile",
help="File with training data set", metavar="FILE")
parser.add_option("--testFile", dest="testFile",
help="File with test data set", metavar="FILE")
(options, args) = parser.parse_args()
if len(args) > 0:
parser.error("Any parameter given.")
sys.exit(1)
print('-------------------------------- PARAMETERS --------------------------------')
print("Path of CoreNLP output: " + options.inputPath)
print("File with CoreNLP-tagging sentences: " + str(options.inputFile))
print("Path of training data set: " + options.outputPath)
print("File with training data set: " + str(options.trainingFile))
print("Path of test data set: " + options.outputPath)
print("File with test data set: " + str(options.testFile))
print('-------------------------------- PROCESSING --------------------------------')
## begin of tagging
in_labels = {
'<Gtype>': 'Gtype',
'<Gversion>': 'Gversion',
'<Med>': 'Med',
'<Phase>': 'Phase',
'<Supp>': 'Supp',
'<Technique>': 'Technique',
'<Temp>': 'Temp',
'<OD>': 'OD',
'<Anti>': 'Anti'
}
## End of tagging
out_labels = {
'<Air>': 'O',
'</Air>': 'O',
'</Gtype>': 'O',
'</Gversion>': 'O',
'</Med>': 'O',
'</Phase>': 'O',
'<Sample>': 'O',
'</Sample>': 'O',
'<Serie>': 'O',
'</Serie>': 'O',
'<Strain>': 'O',
'</Strain>': 'O',
'<Substrain>': 'O',
'</Substrain>': 'O',
'</Supp>': 'O',
'</Technique>': 'O',
'</Temp>': 'O',
'</OD>': 'O',
'<Agit>': 'O',
'</Agit>': 'O',
'<Name>': 'O',
'</Name>': 'O',
'<Orgn>': 'O',
'</Orgn>': 'O',
'</Anti>': 'O',
'<Vess>': 'O',
'</Vess>': 'O'}
# Other label
flag = 'O'
# sentences counter
lista = []
#First sentence
sentence = ''
with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file:
for line in input_file:
if len(line.split('\t')) > 1:
w = line.split('\t')[1]
if w in in_labels or w in out_labels:
#Tagging
if w in in_labels.keys(): flag = in_labels[w]
if w in out_labels: flag = out_labels[w]
else:
if w == "PGCGROWTHCONDITIONS":
words = sentence.split(' ')
#End of sentence
tags = [tag for tag in words if tag.split('|')[-1] in in_labels.values() ]
#At least one true-tag on sentence
if len(tags)> 0:
lista.append(sentence)
#New setence
sentence = ''
else:
sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ')
print("Number of sentences: " + str( len(lista) ) )
# Split 70 30 training and test sentences
trainingIndex = random.sample(range(len(lista)-1), int(len(lista)*.70))
testIndex = [n for n in range(len(lista)-1) if n not in trainingIndex]
with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile:
Data = [lista[i] for i in trainingIndex]
oFile.write('\n'.join(Data))
with open(os.path.join(options.outputPath, options.testFile), "w") as oFile:
Data = [lista[i] for i in testIndex]
oFile.write('\n'.join(Data))
print("==================================END===================================")
#!/bin/python3
from optparse import OptionParser
import re
import os
......@@ -7,7 +6,6 @@ import random
# Objective
# Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging
# make data sets using only sentences with at least one true-tag
#
# Input parameters
# --inputPath=PATH Path of inputfile
......@@ -19,15 +17,15 @@ import random
# training and test data set
#
# Examples
# python label-split_training_test_v2.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
# 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_v4.txt
# --testFile test-data-set-30_v4.txt
# --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets
#
#
# 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
# 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
##########################################
......@@ -68,49 +66,46 @@ if __name__ == "__main__":
'<Gversion>': 'Gversion',
'<Med>': 'Med',
'<Phase>': 'Phase',
'<Substrain>': 'Substrain',
'<Supp>': 'Supp',
'<Strain>': 'Strain',
'<Technique>': 'Technique',
'<Temp>': 'Temp',
'<OD>': 'OD',
'<Anti>': 'Anti',
'<Agit>': 'Agit',
'<Vess>': 'Vess'
'<Air>': 'Air',
'<Vess>': 'Vess',
'<pH>': 'pH'
}
## End of tagging
out_labels = {
'<Air>': 'O',
'</Air>': 'O',
'</Gtype>': 'O',
'</Gversion>': 'O',
'</Med>': 'O',
'</Phase>': 'O',
'<Sample>': 'O',
'</Sample>': 'O',
'<Serie>': 'O',
'</Serie>': 'O',
'<Strain>': 'O',
'</Strain>': 'O',
'<Substrain>': 'O',
'</Substrain>': 'O',
'</Supp>': 'O',
'</Strain>': 'O',
'</Technique>': 'O',
'</Temp>': 'O',
'</OD>': 'O',
'</Anti>': 'O',
'</Agit>': 'O',
'<Name>': 'O',
'</Name>': 'O',
'</Air>': 'O',
'</Vess>': 'O',
'</pH>': 'O'}
old_labels = {
'<Orgn>': 'O',
'</Orgn>': 'O',
'</Vess>': 'O'}
'</Orgn>': 'O'
}
# Other label
flag = 'O'
# sentences counter
n=0
lista = []
#First sentence
sentence = ''
n = 0
with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file:
for line in input_file:
if len(line.split('\t')) > 1:
......@@ -121,24 +116,28 @@ if __name__ == "__main__":
if w in out_labels: flag = out_labels[w]
else:
if w == "PGCGROWTHCONDITIONS":
n=n+1
words = sentence.split(' ')
tags = [tag for tag in words if word.split('|')[-1] in in_labels.values() ]
#End of sentence
tags = [tag for tag in words if tag.split('|')[-1] in in_labels.values() ]
#At least one true-tag on sentence
if len(tags)> 0:
lista.append(sentence)
#New setence
sentence = ''
n=n+1
else:
elif w not in old_labels.keys():
#Building and save tagging sentence
sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ')
print("Number of sentences: " + str(n) + str(len(lista)+1))
print("Number of sentences with at least one tag: " + str(len(lista)))
print("Number of sentences from CoreNLP: " + str(n))
# Split 70 30 training and test sentences
trainingIndex = random.sample(range(len(lista)-1), int(len(lista)*.70))
testIndex = [n for n in range(len(lista)-1) if n not in trainingIndex]
trainingIndex = random.sample(range(len(lista)), int(len(lista)*.70))
testIndex = [n for n in range(len(lista)) if n not in trainingIndex]
print("Number of sentences for training: " + str(len(trainingIndex)))
print("Number of sentences for test: " + str(len(testIndex)))
with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile:
Data = [lista[i] for i in trainingIndex]
......
#!/bin/python3
import os
from itertools import chain
from optparse import OptionParser
from time import time
from collections import Counter
import re
import nltk
import sklearn
import scipy.stats
import sys
from sklearn.externals import joblib
from sklearn.metrics import make_scorer
from sklearn.cross_validation import cross_val_score
from sklearn.grid_search import RandomizedSearchCV
import sklearn_crfsuite
from sklearn_crfsuite import scorers
from sklearn_crfsuite import metrics
from nltk.corpus import stopwords
import random
# Objective
# Labaled separated by '|' and split 70/30 sentences on training and tets files from CoreNLP-tagging
#
# Input parameters
# --inputPath=PATH Path of inputfile
# --outputPath=PATH Path to place output files
# --trainingFile=testFile Output training data set
# --testFile=testFile Output test data set
#
# Output
# training and test data set
#
# Examples
# 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
#
#
# 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
##########################################
# MAIN PROGRAM #
##########################################
if __name__ == "__main__":
# Defining parameters
parser = OptionParser()
parser.add_option("--inputPath", dest="inputPath",
help="Path of output from CoreNLP", metavar="PATH")
parser.add_option("--outputPath", dest="outputPath",
help="Output path to place output files",
metavar="PATH")
parser.add_option("--inputFile", dest="inputFile",
help="File with CoreNLP-tagging sentences", metavar="FILE")
parser.add_option("--trainingFile", dest="trainingFile",
help="File with training data set", metavar="FILE")
parser.add_option("--testFile", dest="testFile",
help="File with test data set", metavar="FILE")
(options, args) = parser.parse_args()
if len(args) > 0:
parser.error("Any parameter given.")
sys.exit(1)
print('-------------------------------- PARAMETERS --------------------------------')
print("Path of CoreNLP output: " + str(options.inputPath))
print("File with CoreNLP-tagging sentences: " + str(options.inputFile))
print("Path of training data set: " + str(options.outputPath))
print("File with training data set: " + str(options.trainingFile))
print("Path of test data set: " + str(options.outputPath))
print("File with test data set: " + str(options.testFile))
print('-------------------------------- PROCESSING --------------------------------')
## begin of tagging
in_labels = {
'<Gtype>': 'Gtype',
'<Gversion>': 'Gversion',
'<Med>': 'Med',
'<Phase>': 'Phase',
'<Sample>': 'Sample',
'<Serie>': 'Serie',
'<Substrain>': 'Substrain',
'<Supp>': 'Supp',
'<Technique>': 'Technique',
'<Temp>': 'Temp',
'<OD>': 'OD',
'<Anti>': 'Anti',
'<Agit>': 'Agit',
'<Vess>': 'Vess'
}
## End of tagging
out_labels = {
'</Air>': 'O',
'</Gtype>': 'O',
'</Gversion>': 'O',
'</Med>': 'O',
'</Phase>': 'O',
'</Sample>': 'O',
'</Serie>': 'O',
'</Strain>': 'O',
'<Strain>': 'O',
'</Substrain>': 'O',
'</Supp>': 'O',
'</Technique>': 'O',
'</Temp>': 'O',
'</OD>': 'O',
'</Anti>': 'O',
'</Agit>': 'O',
'<Name>': 'O',
'</Name>': 'O',
'<Orgn>': 'O',
'</Orgn>': 'O',
'</Vess>': 'O'}
# Other label
flag = 'O'
# sentences counter
n=0
lista = []
#First sentence
sentence = ''
with open(os.path.join(options.inputPath, options.inputFile), "r") as input_file:
for line in input_file:
if len(line.split('\t')) > 1:
w = line.split('\t')[1]
if w in in_labels or w in out_labels:
#Tagging
if w in in_labels.keys(): flag = in_labels[w]
if w in out_labels: flag = out_labels[w]
else:
if w == "PGCGROWTHCONDITIONS":
#End of sentence
lista.append(sentence)
#New setence
sentence = ''
n=n+1
else:
#Building and save tagging sentence
sentence = sentence + ' ' + ('|'.join(line.split('\t')[1:4])+'|'+flag+' ')
print("Number of sentences: " + str(n))
print('\n'.join(lista))
# Split 70 30 training and test sentences
# trainingIndex = random.sample(range(len(lista)-1), int(len(lista)*.70))
# testIndex = [n for n in range(len(lista)-1) if n not in trainingIndex]
# with open(os.path.join(options.outputPath, options.trainingFile), "w") as oFile:
# Data = [lista[i] for i in trainingIndex]
# oFile.write('\n'.join(Data))
# with open(os.path.join(options.outputPath, options.testFile), "w") as oFile:
# Data = [lista[i] for i in testIndex]
# oFile.write('\n'.join(Data))
# print("==================================END===================================")
# -*- coding: UTF-8 -*-
import os
from itertools import chain
from optparse import OptionParser
from time import time
from collections import Counter
import re
import nltk
import sklearn
import scipy.stats
import sys
from sklearn.externals import joblib
from sklearn.metrics import make_scorer
from sklearn.cross_validation import cross_val_score
from sklearn.grid_search import RandomizedSearchCV
import sklearn_crfsuite
from sklearn_crfsuite import scorers
from sklearn_crfsuite import metrics
from nltk.corpus import stopwords
# Objective
# Training and evaluation of CRFs with sklearn-crfsuite.
#
# Input parameters
# --inputPath=PATH Path of training and test data set
# --trainingFile File with training data set
# --testFile File with test data set
# --outputPath=PATH Output path to place output files
# Output
# 1) Best model
# Examples
# python training_validation_v3.py
# --inputPath /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/
# 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/
#################################
# FUNCTIONS #
#################################
def isGreek(word):
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',
'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']
if word in alphabet:
return True
else:
return False
def word2features(sent, i):
listElem = sent[i].split('|')
word = listElem[0]
lemma = listElem[1]
postag = listElem[2]
features = {
# Suffixes
#'word[-3:]': word[-3:],
#'word[-2:]': word[-2:],
#'word[-1:]': word[-1:],
#'word.isupper()': word.isupper(),
'word': word,
'lemma': lemma,
#'postag': postag,
#'lemma[-3:]': lemma[-3:],
#'lemma[-2:]': lemma[-2:],
#'lemma[-1:]': lemma[-1:],
#'lemma[+3:]': lemma[:3],
#'lemma[+2:]': lemma[:2],
#'lemma[+1:]': lemma[:1],
#'word[:3]': word[:3],
#'word[:2]': word[:2],
#'word[:1]': word[:1],
#'endsConLow()={}'.format(endsConLow(word)): endsConLow(word),
'isNumber()': word.isdigit(),
'isGreek(){}'.format(isGreek(word)): isGreek(word),
'isupper()' : word.isupper(),
'islower()' : word.islower()
}
if i > 0:
listElem = sent[i - 1].split('|')
word1 = listElem[0]
lemma1 = listElem[1]
postag1 = listElem[2]
features.update({
#'-1:word': word1,
'-1:lemma': lemma1,
'-1:postag': postag1,
})
if i < len(sent) - 1:
listElem = sent[i + 1].split('|')
#word1 = listElem[0]
lemma1 = listElem[1]
postag1 = listElem[2]
features.update({
#'+1:word': word1,
'+1:lemma': lemma1,
'+1:postag': postag1,
})
'''
if i > 1:
listElem = sent[i - 2].split('|')
word2 = listElem[0]
lemma2 = listElem[1]
postag2 = listElem[2]
features.update({
'-2:word': word2,
'-2:lemma': lemma2,
})
if i < len(sent) - 2:
listElem = sent[i + 2].split('|')
word2 = listElem[0]
lemma2 = listElem[1]
postag2 = listElem[2]
features.update({
'+2:word': word2,
'+2:lemma': lemma2,
})
trigrams = False
if trigrams:
if i > 2:
listElem = sent[i - 3].split('|')
word3 = listElem[0]
lemma3 = listElem[1]
postag3 = listElem[2]
features.update({
'-3:word': word3,
'-3:lemma': lemma3,
})
if i < len(sent) - 3:
listElem = sent[i + 3].split('|')
word3 = listElem[0]
lemma3 = listElem[1]
postag3 = listElem[2]
features.update({
'+3:word': word3,
'+3:lemma': lemma3,
})
'''
return features
def sent2features(sent):
return [word2features(sent, i) for i in range(len(sent))]
def sent2labels(sent):
return [elem.split('|')[3] for elem in sent]
def sent2tokens(sent):
return [token for token, postag, label in sent]
def print_transitions(trans_features, f):
for (label_from, label_to), weight in trans_features:
f.write("{:6} -> {:7} {:0.6f}\n".format(label_from, label_to, weight))
def print_state_features(state_features, f):
for (attr, label), weight in state_features:
f.write("{:0.6f} {:8} {}\n".format(weight, label, attr.encode("utf-8")))
__author__ = 'CMendezC'
##########################################
# MAIN PROGRAM #
##########################################
if __name__ == "__main__":
# Defining parameters
parser = OptionParser()
parser.add_option("--inputPath", dest="inputPath",
help="Path of training data set", metavar="PATH")
parser.add_option("--outputPath", dest="outputPath",
help="Output path to place output files",
metavar="PATH")
parser.add_option("--trainingFile", dest="trainingFile",
help="File with training data set", metavar="FILE")
parser.add_option("--testFile", dest="testFile",
help="File with test data set", metavar="FILE")
parser.add_option("--excludeStopWords", default=False,
action="store_true", dest="excludeStopWords",
help="Exclude stop words")
parser.add_option("--excludeSymbols", default=False,
action="store_true", dest="excludeSymbols",
help="Exclude punctuation marks")
(options, args) = parser.parse_args()
if len(args) > 0:
parser.error("Any parameter given.")
sys.exit(1)
print('-------------------------------- PARAMETERS --------------------------------')
print("Path of training data set: " + options.inputPath)
print("File with training data set: " + str(options.trainingFile))
print("Path of test data set: " + options.inputPath)
print("File with test data set: " + str(options.testFile))
print("Exclude stop words: " + str(options.excludeStopWords))
symbols = ['.', ',', ':', ';', '?', '!', '\'', '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{',
'}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']
#print("Exclude symbols " + str(symbols) + ': ' + str(options.excludeSymbols))
print("Exclude symbols: " + str(options.excludeSymbols))
print('-------------------------------- PROCESSING --------------------------------')
print('Reading corpus...')
t0 = time()
sentencesTrainingData = []
sentencesTestData = []
stopwords = [word for word in stopwords.words('english')]
with open(os.path.join(options.inputPath, options.trainingFile), "r") as iFile:
for line in iFile.readlines():
listLine = []
line = line.strip('\n')
for token in line.split():
if options.excludeStopWords:
listToken = token.split('|')
lemma = listToken[1]
if lemma in stopwords:
continue
if options.excludeSymbols:
listToken = token.split('|')
lemma = listToken[1]
if lemma in symbols:
continue
listLine.append(token)
sentencesTrainingData.append(listLine)
print(" Sentences training data: " + str(len(sentencesTrainingData)))
with open(os.path.join(options.inputPath, options.testFile), "r") as iFile:
for line in iFile.readlines():
listLine = []
line = line.strip('\n')
for token in line.split():
if options.excludeStopWords:
listToken = token.split('|')
lemma = listToken[1]
if lemma in stopwords:
continue
if options.excludeSymbols:
listToken = token.split('|')
lemma = listToken[1]
if lemma in symbols:
continue
listLine.append(token)
sentencesTestData.append(listLine)
print(" Sentences test data: " + str(len(sentencesTestData)))
print("Reading corpus done in: %fs" % (time() - t0))
print(sent2features(sentencesTrainingData[0])[0])
print(sent2features(sentencesTestData[0])[0])
t0 = time()
X_train = [sent2features(s) for s in sentencesTrainingData]
y_train = [sent2labels(s) for s in sentencesTrainingData]
X_test = [sent2features(s) for s in sentencesTestData]
# print X_test
y_test = [sent2labels(s) for s in sentencesTestData]
# Fixed parameters
# crf = sklearn_crfsuite.CRF(
# algorithm='lbfgs',
# c1=0.1,
# c2=0.1,
# max_iterations=100,
# all_possible_transitions=True
# )
# Hyperparameter Optimization
crf = sklearn_crfsuite.CRF(
algorithm='lbfgs',
max_iterations=100,
all_possible_transitions=True
)
params_space = {
'c1': scipy.stats.expon(scale=0.5),
'c2': scipy.stats.expon(scale=0.05),
}
# Original: labels = list(crf.classes_)
# Original: labels.remove('O')
labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Supp', 'Technique', 'Temp', 'OD', 'Anti'])
# use the same metric for evaluation
f1_scorer = make_scorer(metrics.flat_f1_score,
average='weighted', labels=labels)
# search
rs = RandomizedSearchCV(crf, params_space,
cv=10,
verbose=3,
n_jobs=-1,
n_iter=20,
# n_iter=50,
scoring=f1_scorer)
rs.fit(X_train, y_train)
# Fixed parameters
# crf.fit(X_train, y_train)
# Best hiperparameters
# crf = rs.best_estimator_
nameReport = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.txt')
with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="w") as oFile:
oFile.write("********** TRAINING AND TESTING REPORT **********\n")
oFile.write("Training file: " + options.trainingFile + '\n')
oFile.write('\n')
oFile.write('best params:' + str(rs.best_params_) + '\n')
oFile.write('best CV score:' + str(rs.best_score_) + '\n')
oFile.write('model size: {:0.2f}M\n'.format(rs.best_estimator_.size_ / 1000000))
print("Training done in: %fs" % (time() - t0))
t0 = time()
# Update best crf
crf = rs.best_estimator_
# Saving model
print(" Saving training model...")
t1 = time()
nameModel = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.mod')
joblib.dump(crf, os.path.join(options.outputPath, "models", nameModel))
print(" Saving training model done in: %fs" % (time() - t1))
# Evaluation against test data
y_pred = crf.predict(X_test)
print("*********************************")
name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.txt')
with open(os.path.join(options.outputPath, "reports", "y_pred_" + name), "w") as oFile:
for y in y_pred:
oFile.write(str(y) + '\n')
print("*********************************")
name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.txt')
with open(os.path.join(options.outputPath, "reports", "y_test_" + name), "w") as oFile:
for y in y_test:
oFile.write(str(y) + '\n')
print("Prediction done in: %fs" % (time() - t0))
# labels = list(crf.classes_)
# labels.remove('O')
with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="a") as oFile:
oFile.write('\n')
oFile.write("Flat F1: " + str(metrics.flat_f1_score(y_test, y_pred, average='weighted', labels=labels)))
oFile.write('\n')
# labels = list(crf.classes_)
sorted_labels = sorted(
labels,
key=lambda name: (name[1:], name[0])
)
oFile.write(metrics.flat_classification_report(
y_test, y_pred, labels=sorted_labels, digits=3
))
oFile.write('\n')
oFile.write("\nTop likely transitions:\n")
print_transitions(Counter(crf.transition_features_).most_common(50), oFile)
oFile.write('\n')
oFile.write("\nTop unlikely transitions:\n")
print_transitions(Counter(crf.transition_features_).most_common()[-50:], oFile)
oFile.write('\n')
oFile.write("\nTop positive:\n")
print_state_features(Counter(crf.state_features_).most_common(200), oFile)
oFile.write('\n')
oFile.write("\nTop negative:\n")
print_state_features(Counter(crf.state_features_).most_common()[-200:], oFile)
oFile.write('\n')
......@@ -32,7 +32,7 @@ from nltk.corpus import stopwords
# --trainingFile File with training data set
# --testFile File with test data set
# --outputPath=PATH Output path to place output files
# --reportFile Report Fileneme
# --version Version Report
# Output
# 1) Best model
......@@ -43,31 +43,54 @@ from nltk.corpus import stopwords
# --trainingFile training-data-set-70.txt
# --testFile test-data-set-30.txt
# --outputPath /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/
# --reportFile report_1
# 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/
# --version _v2
# 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
#################################
# FUNCTIONS #
#################################
def isGreek(word):
#al greek letters
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',
'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']
if word in alphabet:
return True
else:
return False
def hNumber(word):
for l in word:
if l.isdigit():
return True
return False
def symb(word):
n=0
#at least a not alphanumeric character
for l in word:
if l.isdigit(): n = n+1
if l.isalpha(): n = n+1
#Exclude Greek letters
if isGreek(l): n = n+1
if n<len(word): return True
else: return False
def hUpper(word):
#at least an uppers
for l in word:
if l.isupper(): return True
return False
def hLower(word):
#at least a lower
for l in word:
if l.islower(): return True
return False
def hGreek(word):
#at least an greek letter
for l in word:
if isGreek(l): return True
return False
......@@ -80,35 +103,20 @@ def word2features(sent, i, S1, S2):
postag = listElem[2]
ner = listElem[3]
#====================== G1 ======================#
features = {
#General
'lemma': lemma,
'postag': postag
}
if S1:
#S1
features['word']: word
features['hUpper']: hUpper(word)
features['hLower']: hUpper(word)
features['hGreek']: hGreek(word)
#features['hAlfNum']: hAlfNum(word)
if S2:
#S2
features['isUpper']: word.isupper()
features['isLower']: word.isLower()
features['isGreek']: isGreek(word)
features['isNumber']: word.isdigit()
if i > 0:
listElem = sent[i - 1].split('|')
word1 = listElem[0]
lemma1 = listElem[1]
postag1 = listElem[2]
features.update({
#Word anterioir
'-1:word': word1,
#LemaG posterior
'-1:lemma': lemma1,
#PostG posterior
......@@ -117,17 +125,47 @@ def word2features(sent, i, S1, S2):
if i < len(sent) - 1:
listElem = sent[i + 1].split('|')
word1 = listElem[0]
lemma1 = listElem[1]
postag1 = listElem[2]
features.update({
#Word anterioir
'+1:word': word1,
#LemaG posterior
'+1:lemma': lemma1,
#PostG posterior
'+1:postag': postag1,
})
#====================== S1 ======================#
if S1:
listElem = sent[i - 1].split('|')
lemma1 = listElem[1]
postag1 = listElem[2]
features['hUpper']: hUpper(word)
features['hLower']: hUpper(word)
features['hGreek']: hGreek(word)
features['symb']: symb(word)
#firstChar
features['lemma1[:1]']: lemma1[:1]
#secondChar
features['postag[:1]']: lemma1[:1]
features['postag[:2]']: lemma1[:2]
features['lemma[:2]']: lemma1[:2]
#====================== S2 ======================#
if S2:
#S2
features['isUpper']: word.isupper()
features['isLower']: word.isLower()
features['isGreek']: isGreek(word)
features['isNumber']: word.isdigit()
'''
#====================== S3 ======================#
if S3:
features['word']: word
'''
return features
......@@ -153,7 +191,7 @@ def print_state_features(state_features, f):
f.write("{:0.6f} {:8} {}\n".format(weight, label, attr.encode("utf-8")))
__author__ = 'CMendezC'
__author__ = 'egaytan'
##########################################
# MAIN PROGRAM #
......@@ -177,7 +215,7 @@ if __name__ == "__main__":
parser.add_option("--excludeSymbols", default=False,
action="store_true", dest="excludeSymbols",
help="Exclude punctuation marks")
parser.add_option("--reportFile", dest="reportFile",
parser.add_option("--version", dest="version",
help="Report file", metavar="FILE")
parser.add_option("--S1", default=False,
action="store_true", dest="S1",
......@@ -198,7 +236,7 @@ if __name__ == "__main__":
print("File with test data set: " + str(options.testFile))
print("Exclude stop words: " + str(options.excludeStopWords))
print("Levels: " + str(options.S1) + " " + str(options.S2))
print("Report file: " + str(options.reportFile))
print("Report file: " + str(options.version))
symbols = ['.', ',', ':', ';', '?', '!', '\'', '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{',
......@@ -254,19 +292,14 @@ if __name__ == "__main__":
print("Reading corpus done in: %fs" % (time() - t0))
if options.S1: S1 = 0
else: S1 = 1
if options.S2: S2 = 0
else: S2 = 1
print(sent2features(sentencesTrainingData[0], S1, S2)[0])
print(sent2features(sentencesTestData[0], S1, S2)[0])
print(sent2features(sentencesTrainingData[0], options.S1, options.S2)[0])
print(sent2features(sentencesTestData[0], options.S1, options.S2)[0])
t0 = time()
X_train = [sent2features(s, S1, S2) for s in sentencesTrainingData]
X_train = [sent2features(s, options.S1, options.S2) for s in sentencesTrainingData]
y_train = [sent2labels(s) for s in sentencesTrainingData]
X_test = [sent2features(s, S1, S2) for s in sentencesTestData]
X_test = [sent2features(s, options.S1, options.S2) for s in sentencesTestData]
# print X_test
y_test = [sent2labels(s) for s in sentencesTestData]
......@@ -292,7 +325,7 @@ if __name__ == "__main__":
# Original: labels = list(crf.classes_)
# Original: labels.remove('O')
labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Supp', 'Technique', 'Temp', 'OD', 'Anti'])
labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Strain', 'Substrain', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Air', 'Vess', 'pH'])
# use the same metric for evaluation
f1_scorer = make_scorer(metrics.flat_f1_score,
......@@ -313,7 +346,9 @@ if __name__ == "__main__":
# Best hiperparameters
# crf = rs.best_estimator_
nameReport = options.trainingFile.replace('.txt', str(options.reportFile) + '.txt')
nameReport = str(options.S1) + '_S2_' + str(options.S2) + str(options.version) + '.txt'
with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="w") as oFile:
oFile.write("********** TRAINING AND TESTING REPORT **********\n")
oFile.write("Training file: " + options.trainingFile + '\n')
......@@ -331,27 +366,13 @@ if __name__ == "__main__":
# Saving model
print(" Saving training model...")
t1 = time()
nameModel = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.mod')
nameModel = 'model_S1_' + str(options.S1) + '_S2_' + str(options.S2) + str(options.version) + '.mod'
joblib.dump(crf, os.path.join(options.outputPath, "models", nameModel))
print(" Saving training model done in: %fs" % (time() - t1))
# Evaluation against test data
y_pred = crf.predict(X_test)
print("*********************************")
name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.txt')
with open(os.path.join(options.outputPath, "reports", "y_pred_" + name), "w") as oFile:
for y in y_pred:
oFile.write(str(y) + '\n')
print("*********************************")
name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.txt')
with open(os.path.join(options.outputPath, "reports", "y_test_" + name), "w") as oFile:
for y in y_test:
oFile.write(str(y) + '\n')
print("Prediction done in: %fs" % (time() - t0))
# labels = list(crf.classes_)
......@@ -387,4 +408,3 @@ if __name__ == "__main__":
print_state_features(Counter(crf.state_features_).most_common()[-200:], oFile)
oFile.write('\n')
......
......@@ -32,23 +32,26 @@ from nltk.corpus import stopwords
# --trainingFile File with training data set
# --testFile File with test data set
# --outputPath=PATH Output path to place output files
# --version Version Report
# Output
# 1) Best model
# Examples
# python training_validation_v3.py
# python training_validation_v5.py
# --inputPath /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/
# 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/
# --version _v2
# 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
#################################
# FUNCTIONS #
#################################
def isGreek(word):
#al greek letters
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',
'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']
if word in alphabet:
......@@ -56,106 +59,118 @@ def isGreek(word):
else:
return False
def word2features(sent, i):
def hNumber(word):
for l in word:
if l.isdigit():
return True
return False
def symb(word):
n=0
#at least a not alphanumeric character
for l in word:
if l.isdigit(): n = n+1
if l.isalpha(): n = n+1
#Exclude Greek letters
if isGreek(l): n = n+1
if n<len(word): return True
else: return False
def hUpper(word):
#at least an uppers
for l in word:
if l.isupper(): return True
return False
def hLower(word):
#at least a lower
for l in word:
if l.islower(): return True
return False
def hGreek(word):
#at least an greek letter
for l in word:
if isGreek(l): return True
return False
def word2features(sent, i, S1, S2):
listElem = sent[i].split('|')
word = listElem[0]
lemma = listElem[1]
postag = listElem[2]
ner = listElem[3]
#====================== G1 ======================#
features = {
# Suffixes
#'word[-3:]': word[-3:],
#'word[-2:]': word[-2:],
#'word[-1:]': word[-1:],
#'word.isupper()': word.isupper(),
'word': word,
#General
'lemma': lemma,
#'postag': postag,
#'lemma[-3:]': lemma[-3:],
#'lemma[-2:]': lemma[-2:],
#'lemma[-1:]': lemma[-1:],
#'lemma[+3:]': lemma[:3],
#'lemma[+2:]': lemma[:2],
#'lemma[+1:]': lemma[:1],
#'word[:3]': word[:3],
#'word[:2]': word[:2],
#'word[:1]': word[:1],
#'endsConLow()={}'.format(endsConLow(word)): endsConLow(word),
'isNumber()': word.isdigit(),
'isGreek(){}'.format(isGreek(word)): isGreek(word),
'isupper()' : word.isupper(),
'islower()' : word.islower()
'postag': postag
}
if i > 0:
listElem = sent[i - 1].split('|')
word1 = listElem[0]
lemma1 = listElem[1]
postag1 = listElem[2]
features.update({
#'-1:word': word1,
#LemaG posterior
'-1:lemma': lemma1,
#PostG posterior
'-1:postag': postag1,
})
if i < len(sent) - 1:
listElem = sent[i + 1].split('|')
#word1 = listElem[0]
lemma1 = listElem[1]
postag1 = listElem[2]
features.update({
#'+1:word': word1,
#LemaG posterior
'+1:lemma': lemma1,
#PostG posterior
'+1:postag': postag1,
})
'''
if i > 1:
listElem = sent[i - 2].split('|')
word2 = listElem[0]
lemma2 = listElem[1]
postag2 = listElem[2]
features.update({
'-2:word': word2,
'-2:lemma': lemma2,
})
#====================== S1 ======================#
if S1:
listElem = sent[i - 1].split('|')
lemma1 = listElem[1]
postag1 = listElem[2]
if i < len(sent) - 2:
listElem = sent[i + 2].split('|')
word2 = listElem[0]
lemma2 = listElem[1]
postag2 = listElem[2]
features.update({
'+2:word': word2,
'+2:lemma': lemma2,
})
features['hUpper']: hUpper(word)
features['hLower']: hUpper(word)
features['hGreek']: hGreek(word)
features['symb']: symb(word)
#firstChar
features['lemma1[:1]']: lemma1[:1]
#secondChar
features['postag[:1]']: lemma1[:1]
features['postag[:2]']: lemma1[:2]
features['lemma[:2]']: lemma1[:2]
#====================== S2 ======================#
if S2:
#S2
features['isUpper']: word.isupper()
features['isLower']: word.isLower()
features['isGreek']: isGreek(word)
features['isNumber']: word.isdigit()
trigrams = False
if trigrams:
if i > 2:
listElem = sent[i - 3].split('|')
word3 = listElem[0]
lemma3 = listElem[1]
postag3 = listElem[2]
features.update({
'-3:word': word3,
'-3:lemma': lemma3,
})
if i < len(sent) - 3:
listElem = sent[i + 3].split('|')
word3 = listElem[0]
lemma3 = listElem[1]
postag3 = listElem[2]
features.update({
'+3:word': word3,
'+3:lemma': lemma3,
})
'''
#====================== S3 ======================#
if S3:
features['word']: word
'''
return features
def sent2features(sent):
return [word2features(sent, i) for i in range(len(sent))]
def sent2features(sent, S1, S2):
return [word2features(sent, i, S1, S2) for i in range(len(sent))]
def sent2labels(sent):
......@@ -176,7 +191,7 @@ def print_state_features(state_features, f):
f.write("{:0.6f} {:8} {}\n".format(weight, label, attr.encode("utf-8")))
__author__ = 'CMendezC'
__author__ = 'egaytan'
##########################################
# MAIN PROGRAM #
......@@ -200,8 +215,14 @@ if __name__ == "__main__":
parser.add_option("--excludeSymbols", default=False,
action="store_true", dest="excludeSymbols",
help="Exclude punctuation marks")
parser.add_option("--reportFile", dest="reportFile",
parser.add_option("--version", dest="version",
help="Report file", metavar="FILE")
parser.add_option("--S1", default=False,
action="store_true", dest="S1",
help="Level specificity")
parser.add_option("--S2", default=False,
action="store_true", dest="S2",
help="Level specificity")
(options, args) = parser.parse_args()
if len(args) > 0:
......@@ -214,11 +235,12 @@ if __name__ == "__main__":
print("Path of test data set: " + options.inputPath)
print("File with test data set: " + str(options.testFile))
print("Exclude stop words: " + str(options.excludeStopWords))
print("Report file: " + str(options.reportFile))
print("Levels: " + str(options.S1) + " " + str(options.S2))
print("Report file: " + str(options.version))
symbols = ['.', ',', ':', ';', '?', '!', '\'', '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{',
'}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']
#print("Exclude symbols " + str(symbols) + ': ' + str(options.excludeSymbols))
print("Exclude symbols: " + str(options.excludeSymbols))
print('-------------------------------- PROCESSING --------------------------------')
......@@ -270,14 +292,14 @@ if __name__ == "__main__":
print("Reading corpus done in: %fs" % (time() - t0))
print(sent2features(sentencesTrainingData[0])[0])
print(sent2features(sentencesTestData[0])[0])
print(sent2features(sentencesTrainingData[0], options.S1, options.S2)[0])
print(sent2features(sentencesTestData[0], options.S1, options.S2)[0])
t0 = time()
X_train = [sent2features(s) for s in sentencesTrainingData]
X_train = [sent2features(s, options.S1, options.S2) for s in sentencesTrainingData]
y_train = [sent2labels(s) for s in sentencesTrainingData]
X_test = [sent2features(s) for s in sentencesTestData]
X_test = [sent2features(s, options.S1, options.S2) for s in sentencesTestData]
# print X_test
y_test = [sent2labels(s) for s in sentencesTestData]
......@@ -303,7 +325,7 @@ if __name__ == "__main__":
# Original: labels = list(crf.classes_)
# Original: labels.remove('O')
labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Supp', 'Technique', 'Temp', 'OD', 'Anti'])
labels = list(['Gtype', 'Gversion', 'Med', 'Phase', 'Strain', 'Substrain', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Air', 'Vess', 'pH'])
# use the same metric for evaluation
f1_scorer = make_scorer(metrics.flat_f1_score,
......@@ -324,8 +346,29 @@ if __name__ == "__main__":
# Best hiperparameters
# crf = rs.best_estimator_
#nameReport = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(options.excludeSymbols) + '.txt')
nameReport = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.reportFile))
'''
#ROC curve
# predict probabilities
probs = rs.predict_proba(X_test)
# keep probabilities for the positive outcome only
probs = probs[:, 1]
# calculate AUC
auc = roc_auc_score(y_test, probs)
print('AUC: %.3f' % auc)
# calculate roc curve
print(testy)
print(probs)
fpr, tpr, thresholds = roc_curve(testy, probs)
# plot no skill
pyplot.plot([0, 1], [0, 1], linestyle='--')
# plot the roc curve for the model
pyplot.plot(fpr, tpr, marker='.')
# show the plot
pyplot.show()
'''
nameReport = str(options.S1) + '_S2_' + str(options.S2) + str(options.version) + '.txt'
with open(os.path.join(options.outputPath, "reports", "report_" + nameReport), mode="w") as oFile:
oFile.write("********** TRAINING AND TESTING REPORT **********\n")
oFile.write("Training file: " + options.trainingFile + '\n')
......@@ -343,27 +386,13 @@ if __name__ == "__main__":
# Saving model
print(" Saving training model...")
t1 = time()
nameModel = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.mod')
nameModel = 'model_S1_' + str(options.S1) + '_S2_' + str(options.S2) + str(options.version) + '.mod'
joblib.dump(crf, os.path.join(options.outputPath, "models", nameModel))
print(" Saving training model done in: %fs" % (time() - t1))
# Evaluation against test data
y_pred = crf.predict(X_test)
print("*********************************")
name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.txt')
with open(os.path.join(options.outputPath, "reports", "y_pred_" + name), "w") as oFile:
for y in y_pred:
oFile.write(str(y) + '\n')
print("*********************************")
name = options.trainingFile.replace('.txt', '.fStopWords_' + str(options.excludeStopWords) + '.fSymbols_' + str(
options.excludeSymbols) + '.txt')
with open(os.path.join(options.outputPath, "reports", "y_test_" + name), "w") as oFile:
for y in y_test:
oFile.write(str(y) + '\n')
print("Prediction done in: %fs" % (time() - t0))
# labels = list(crf.classes_)
......
......@@ -3,8 +3,6 @@ Gtype
Gversion
Med
Phase
Sample
Serie
Strain
Supp
Technique
......@@ -13,4 +11,5 @@ OD
Anti
Agit
Vess
Substrain
pH
......
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 2|2|CD|O
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
OmpR|ompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
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
library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|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|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
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O
ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
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
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
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
FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O B|b|NN|O
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O A|a|NN|O
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
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
WT|wt|JJ|O fructose|fructose|NN|O 2|2|CD|O
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
σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O heat|heat|NN|O
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
ΔompR|δompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 1|1|CD|O
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
ΔompR|δompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
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
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
Cra|Cra|NNP|O acetate|acetate|NN|O 1|1|CD|O
Escherichia|escherichia|FW|O coli|coli|FW|O K-12|k-12|NN|O
Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O B|b|NN|O
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
∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
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
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
ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
RpoB|rpob|NN|O WT|wt|NN|O 2|2|CD|O
ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
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
Δcra|δcra|NN|O glucose|glucose|NN|O 1|1|CD|O
∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O A|a|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
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
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
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
WT|wt|NN|O NaCl|nacl|NN|O 2|2|CD|O
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
Cra|Cra|NNP|O acetate|acetate|NN|O 2|2|CD|O
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
Δcra|δcra|NN|O acetate|acetate|NN|O 1|1|CD|O
SoxS|soxs|NN|O PQ|pq|NN|O 2|2|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
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
SeqA|seqa|NN|O old|old|JJ|O rep1|rep1|NN|O
ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 2|2|CD|O
genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
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
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
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
ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 1|1|CD|O
genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
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
ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
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
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
Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
CsiR|CsiR|NNP|O _|_|VBD|O ChIPSeq|chipseq|NN|O
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
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
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
genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
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
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
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
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
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
genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
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
genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
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
SeqA|seqa|NN|O new|new|JJ|O rep2|rep2|NN|O
ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 1|1|CD|O
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
culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
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
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
Input|input|NN|O ChIP-Seq|chip-seq|NN|O
PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|NN|O 2|2|CD|O
Cra|cra|NN|O glucose|glucose|NN|O 1|1|CD|O
RNAP|rnap|NN|O old|old|JJ|O rep1|rep1|NN|O
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
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|NN|O
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
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
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
Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O C|c|NN|O
antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
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
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O B|b|NN|O
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
Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O A|a|NN|O
∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
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
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
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 2|2|CD|O
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
OmpR|ompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
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
library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|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|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
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O
ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
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
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
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
FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O B|b|NN|O
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O A|a|NN|O
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
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
WT|wt|JJ|O fructose|fructose|NN|O 2|2|CD|O
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
σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O heat|heat|NN|O
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
ΔompR|δompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 1|1|CD|O
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
ΔompR|δompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
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
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
Cra|Cra|NNP|O acetate|acetate|NN|O 1|1|CD|O
Escherichia|escherichia|FW|O coli|coli|FW|O K-12|k-12|NN|O
Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O B|b|NN|O
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
∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
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
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
ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
RpoB|rpob|NN|O WT|wt|NN|O 2|2|CD|O
ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
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
Δcra|δcra|NN|O glucose|glucose|NN|O 1|1|CD|O
∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O A|a|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
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
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
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
WT|wt|NN|O NaCl|nacl|NN|O 2|2|CD|O
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
Cra|Cra|NNP|O acetate|acetate|NN|O 2|2|CD|O
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
Δcra|δcra|NN|O acetate|acetate|NN|O 1|1|CD|O
SoxS|soxs|NN|O PQ|pq|NN|O 2|2|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
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
SeqA|seqa|NN|O old|old|JJ|O rep1|rep1|NN|O
ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 2|2|CD|O
genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
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
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
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
ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 1|1|CD|O
genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
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
ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
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
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
Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
CsiR|CsiR|NNP|O _|_|VBD|O ChIPSeq|chipseq|NN|O
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
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
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
genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
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
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
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
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
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
genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
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
genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
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
SeqA|seqa|NN|O new|new|JJ|O rep2|rep2|NN|O
ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 1|1|CD|O
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
culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
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
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
Input|input|NN|O ChIP-Seq|chip-seq|NN|O
PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|NN|O 2|2|CD|O
Cra|cra|NN|O glucose|glucose|NN|O 1|1|CD|O
RNAP|rnap|NN|O old|old|JJ|O rep1|rep1|NN|O
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
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|NN|O
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
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
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
Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O C|c|NN|O
antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
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
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O B|b|NN|O
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
Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O A|a|NN|O
∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
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
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
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
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
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
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
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
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
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
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
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
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
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
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
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
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
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
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
growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
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
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
strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
acetate|acetate|NN|Supp
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
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
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
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
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
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
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
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
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
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
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
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
Anaerobic|anaerobic|JJ|Air cultures|culture|NNS|O
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
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
antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
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
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
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
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
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
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
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
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
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
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
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
CsiR|csir|NN|O _|_|CD|O RNASeq|rnaseq|NN|Technique
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
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
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
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
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
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
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
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
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O A|a|NN|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O C|c|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|Anaerobic|NNP|Air A|A|NNP|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|anaerobic|JJ|Air B|b|NN|O
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
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
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
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
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O harboring|harbor|VBG|O ArcA-8myc|arca-8myc|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O harboring|harbor|VBG|O Fnr-8myc|fnr-8myc|JJ|Gtype
genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
growth|growth|NN|O condition|condition|NN|O :|:|:|O Aerobic|Aerobic|NNP|Air
growth|growth|NN|O condition|condition|NN|O :|:|:|O anaerobic|anaerobic|JJ|Air
growth|growth|NN|O condition|condition|NN|O :|:|:|O Anaerobic|anaerobic|JJ|Air
growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
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
growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
∆|∆|CD|Gtype fnr|fnr|NN|Gtype -|-|:|O Anaeroibc|anaeroibc|NN|Air
∆|∆|CD|Gtype fur|fur|NN|Gtype Anaerobic|anaerobic|JJ|Air A|a|DT|O
∆|∆|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
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
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
∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Anaerobic|anaerobic|JJ|Air
Wild-type|wild-type|JJ|Gtype Aerobic|aerobic|JJ|Air A|a|DT|O
Wild-type|wild-type|JJ|Gtype Anaerobic|anaerobic|JJ|Air A|a|DT|O
Wild-type|wild-type|JJ|Gtype Anaerobic|anaerobic|JJ|Air B|b|NN|O
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
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
WT|wt|JJ|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
WT|wt|JJ|Gtype acetate|acetate|NN|Supp 2|2|CD|O
WT|wt|JJ|Gtype NaCl|nacl|NN|Supp 1|1|CD|O
WT|wt|JJ|Gtype PQ|pq|NN|Supp 1|1|CD|O
WT|wt|JJ|Gtype _|_|NN|O ChIPSeq|chipseq|NN|Technique _|_|NN|O 1|1|CD|O
WT|wt|JJ|Gtype _|_|NN|O ChIPSeq|chipseq|NN|Technique _|_|NN|O 2|2|CD|O
Δcra|δcra|NN|Gtype glucose|glucose|NN|Supp 1|1|CD|O
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
ΔgadE|δgade|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
ΔgadE|δgade|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
ΔgadX|δgadx|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
ΔompR|δompr|NN|Gtype NaCl|nacl|NN|Supp 1|1|CD|O
ΔoxyR|δoxyr|NN|Gtype PQ|pq|NN|Supp 1|1|CD|O
ΔsoxR|δsoxr|NN|Gtype PQ|pq|NN|Supp 2|2|CD|O
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air A|a|DT|O
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air A|a|DT|O
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air B|b|NN|O
medium|medium|NN|O :|:|:|O M63|m63|NN|Med
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
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
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
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
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
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
OmpR|ompr|NN|O NaCl|nacl|NN|Supp 1|1|CD|O
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
RpoB|rpob|NN|O ∆|∆|CD|Gtype cra|cra|NN|Gtype 1|1|CD|O
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
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
SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|Gtype
SoxR|soxr|NN|O PQ|pq|NN|Supp 2|2|CD|O
SoxS|soxs|NN|O PQ|pq|NN|Supp 2|2|CD|O
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O B|b|NN|O
strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
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
ChIP-exo|chip-exo|NN|Technique GadX|gadx|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
ChIP-exo|chip-exo|NN|Technique GadX|gadx|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
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
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
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
TrpR|trpr|NN|O _|_|CD|O glucose|glucose|NN|Supp
TrpR|trpr|NN|O _|_|CD|O Trp|Trp|NNP|Supp
σ32|σ32|NN|O 30|30|CD|Temp °C|°c|NN|Temp rep2|rep2|NN|O
σ32|σ32|NN|O 30|30|CD|Temp °C|°c|NN|Temp short|short|JJ|O RNase|rnase|NN|O
σ32|σ32|NN|O 43|43|CD|Temp °C|°c|NN|Temp rep2|rep2|NN|O
\ No newline at end of file
CsiR|csir|NN|O _|_|CD|O RNASeq|rnaseq|NN|O
genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
RNAP|rnap|NN|O old|old|JJ|O rep2|rep2|NN|O
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
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
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
OxyR|oxyr|NN|O PQ|pq|NN|O 2|2|CD|O
∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O A|a|NN|O
PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|SYM|O 1|1|CD|O
genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
WT|WT|NNP|O _|_|SYM|O ChIPSeq|ChIPSeq|NNP|O _|_|SYM|O 1|1|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
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
genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O A|A|NNP|O
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
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
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
∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
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
genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
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
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
WT|WT|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
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
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
ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O B|B|NNP|O
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
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
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
OmpR|ompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O C|C|NNP|O
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
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
OxyR|oxyr|NN|O PQ|pq|NN|O 1|1|CD|O
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
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O B|b|NN|O
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 3|3|CD|O
At|at|IN|O OD450|od450|NN|OD
Cra|Cra|NNP|O fructose|fructose|NN|O 1|1|CD|O
genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O C|c|NN|O
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
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 3|3|CD|O
WT|wt|JJ|O fructose|fructose|NN|O 1|1|CD|O
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
genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
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
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
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
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
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
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
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
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
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 2|2|CD|O
SeqA|seqa|NN|O old|old|JJ|O deltaSeqA|deltaseqa|NN|O
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
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
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
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
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
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
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 1|1|CD|O
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
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep1|rep1|NN|O
WT|wt|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
TrpR|trpr|NN|O _|_|CD|O Trp|trp|NN|O
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
WT|wt|NN|O NaCl|nacl|NN|O 1|1|CD|O
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
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
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
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
∆|∆|CD|O fnr|fnr|SYM|O -|-|:|O Anaeroibc|anaeroibc|NN|O
Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O B|b|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O A|A|NNP|O
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
strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O
WT|wt|JJ|O acetate|acetate|NN|O 1|1|CD|O
WT|WT|NNP|O PQ|PQ|NNP|O 1|1|CD|O
OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
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
NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 1|1|CD|O
RpoB|rpob|NN|O WT|wt|NN|O 1|1|CD|O
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
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
Nac|Nac|NNP|O _|_|NNP|O ChIPSeq|ChIPSeq|NNP|O
SeqA|seqa|NN|O new|new|JJ|O rep1|rep1|NN|O
carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
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
carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
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
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 2|2|CD|O
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 1|1|CD|O
acetate|acetate|NN|Supp
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
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 1|1|CD|O
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
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
ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
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
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep3|rep3|NN|O
strain|strain|NN|O :|:|:|O K-12|k-12|NN|O
∆|∆|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
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 1|1|CD|O
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
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
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
strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
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
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep2|rep2|NN|O
<Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
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
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
strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
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
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
Cra|Cra|NNP|O fructose|fructose|NN|O 2|2|CD|O
SoxR|soxr|NN|O PQ|pq|NN|O 2|2|CD|O
Escherichia|escherichia|FW|O coli|coli|FW|O
SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|O
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
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
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
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
RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 2|2|CD|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
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
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
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
Cra|cra|NN|O glucose|glucose|NN|O 2|2|CD|O
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
RNA-Seq|rna-seq|NN|Technique
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
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
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
growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
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
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
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
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep2|rep2|NN|O
Δcra|δcra|NN|O fructose|fructose|NN|O 2|2|CD|O
growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
Δcra|δcra|NN|O acetate|acetate|NN|O 2|2|CD|O
Δcra|δcra|NN|O glucose|glucose|NN|O 2|2|CD|O
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O anaerobic|anaerobic|JJ|O
antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O
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
culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
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
ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
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
genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 2|2|CD|O
∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O
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
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep1|rep1|NN|O
ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
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
growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep1|rep1|NN|O
Crosslink|Crosslink|NNP|O
genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
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
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
strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
WT|wt|JJ|O glucose|glucose|NN|O 1|1|CD|O
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
Δcra|δcra|NN|O fructose|fructose|NN|O 1|1|CD|O
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
WT|wt|JJ|O acetate|acetate|NN|O 2|2|CD|O
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
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O B|b|NN|O
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
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
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
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
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
WT|WT|NNP|O PQ|PQ|NNP|O 2|2|CD|O
<Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
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
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
ChIP-Seq|chip-seq|NN|Gversion
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
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
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
WT|wt|JJ|O pH5|ph5|NN|O .5|.5|NN|O 2|2|CD|O
strain|strain|NN|O :|:|:|O K-12|k-12|NN|O MG1655|mg1655|NN|O
WT|wt|JJ|O _|_|NN|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
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
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
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
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 1|1|CD|O
ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 2|2|CD|O
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
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
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
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
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
genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
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
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
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
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
RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 2|2|CD|O
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
medium|medium|NN|O :|:|:|O M63|m63|NN|Med
Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O A|a|NN|O
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
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
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
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
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
antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
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
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
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
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep2|rep2|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
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
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
ChIP-Seq|chip-seq|NN|Technique
TrpR|trpr|NN|O _|_|NN|O glucose|glucose|NN|O
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O
ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
SoxR|soxr|NN|O PQ|pq|NN|O 1|1|CD|O
WT|wt|JJ|O glucose|glucose|NN|O 2|2|CD|O
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
SoxS|soxs|NN|O PQ|pq|NN|O 1|1|CD|O
σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O control|control|NN|O
strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
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
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
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
SeqA|seqa|NN|O old|old|JJ|O rep2|rep2|NN|O
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
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
CsiR|csir|NN|O _|_|CD|O RNASeq|rnaseq|NN|O
genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
RNAP|rnap|NN|O old|old|JJ|O rep2|rep2|NN|O
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
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
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
OxyR|oxyr|NN|O PQ|pq|NN|O 2|2|CD|O
∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O A|a|NN|O
PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|SYM|O 1|1|CD|O
genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
WT|WT|NNP|O _|_|SYM|O ChIPSeq|ChIPSeq|NNP|O _|_|SYM|O 1|1|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
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
genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O A|A|NNP|O
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
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
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
∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
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
genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
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
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
WT|WT|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
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
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
ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O B|B|NNP|O
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
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
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
OmpR|ompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O C|C|NNP|O
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
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
OxyR|oxyr|NN|O PQ|pq|NN|O 1|1|CD|O
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
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O B|b|NN|O
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 3|3|CD|O
At|at|IN|O OD450|od450|NN|OD
Cra|Cra|NNP|O fructose|fructose|NN|O 1|1|CD|O
genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O C|c|NN|O
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
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 3|3|CD|O
WT|wt|JJ|O fructose|fructose|NN|O 1|1|CD|O
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
genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
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
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
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
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
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
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
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
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
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 2|2|CD|O
SeqA|seqa|NN|O old|old|JJ|O deltaSeqA|deltaseqa|NN|O
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
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
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
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
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
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
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 1|1|CD|O
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
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep1|rep1|NN|O
WT|wt|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
TrpR|trpr|NN|O _|_|CD|O Trp|trp|NN|O
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
WT|wt|NN|O NaCl|nacl|NN|O 1|1|CD|O
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
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
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
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
∆|∆|CD|O fnr|fnr|SYM|O -|-|:|O Anaeroibc|anaeroibc|NN|O
Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O B|b|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O A|A|NNP|O
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
strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O
WT|wt|JJ|O acetate|acetate|NN|O 1|1|CD|O
WT|WT|NNP|O PQ|PQ|NNP|O 1|1|CD|O
OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
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
NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 1|1|CD|O
RpoB|rpob|NN|O WT|wt|NN|O 1|1|CD|O
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
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
Nac|Nac|NNP|O _|_|NNP|O ChIPSeq|ChIPSeq|NNP|O
SeqA|seqa|NN|O new|new|JJ|O rep1|rep1|NN|O
carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
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
carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
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
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 2|2|CD|O
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 1|1|CD|O
acetate|acetate|NN|Supp
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
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 1|1|CD|O
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
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
ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
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
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep3|rep3|NN|O
strain|strain|NN|O :|:|:|O K-12|k-12|NN|O
∆|∆|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
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 1|1|CD|O
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
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
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
strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
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
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep2|rep2|NN|O
<Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
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
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
strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
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
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
Cra|Cra|NNP|O fructose|fructose|NN|O 2|2|CD|O
SoxR|soxr|NN|O PQ|pq|NN|O 2|2|CD|O
Escherichia|escherichia|FW|O coli|coli|FW|O
SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|O
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
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
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
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
RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 2|2|CD|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
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
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
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
Cra|cra|NN|O glucose|glucose|NN|O 2|2|CD|O
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
RNA-Seq|rna-seq|NN|Technique
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
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
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
growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
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
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
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
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep2|rep2|NN|O
Δcra|δcra|NN|O fructose|fructose|NN|O 2|2|CD|O
growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
Δcra|δcra|NN|O acetate|acetate|NN|O 2|2|CD|O
Δcra|δcra|NN|O glucose|glucose|NN|O 2|2|CD|O
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O anaerobic|anaerobic|JJ|O
antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O
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
culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
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
ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
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
genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 2|2|CD|O
∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O
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
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep1|rep1|NN|O
ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
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
growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep1|rep1|NN|O
Crosslink|Crosslink|NNP|O
genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
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
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
strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
WT|wt|JJ|O glucose|glucose|NN|O 1|1|CD|O
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
Δcra|δcra|NN|O fructose|fructose|NN|O 1|1|CD|O
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
WT|wt|JJ|O acetate|acetate|NN|O 2|2|CD|O
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
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O B|b|NN|O
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
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
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
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
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
WT|WT|NNP|O PQ|PQ|NNP|O 2|2|CD|O
<Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
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
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
ChIP-Seq|chip-seq|NN|Gversion
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
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
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
WT|wt|JJ|O pH5|ph5|NN|O .5|.5|NN|O 2|2|CD|O
strain|strain|NN|O :|:|:|O K-12|k-12|NN|O MG1655|mg1655|NN|O
WT|wt|JJ|O _|_|NN|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
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
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
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
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 1|1|CD|O
ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 2|2|CD|O
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
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
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
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
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
genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
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
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
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
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
RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 2|2|CD|O
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
medium|medium|NN|O :|:|:|O M63|m63|NN|Med
Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O A|a|NN|O
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
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
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
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
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
antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
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
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
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
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep2|rep2|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
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
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
ChIP-Seq|chip-seq|NN|Technique
TrpR|trpr|NN|O _|_|NN|O glucose|glucose|NN|O
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O
ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
SoxR|soxr|NN|O PQ|pq|NN|O 1|1|CD|O
WT|wt|JJ|O glucose|glucose|NN|O 2|2|CD|O
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
SoxS|soxs|NN|O PQ|pq|NN|O 1|1|CD|O
σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O control|control|NN|O
strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
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
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
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
SeqA|seqa|NN|O old|old|JJ|O rep2|rep2|NN|O
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
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
library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
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
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
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
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
genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
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
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
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
genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
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
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
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
genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
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
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
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
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
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
strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
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
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
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
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
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
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
strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
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
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
genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
medium|medium|NN|O :|:|:|O M63|m63|NN|Med
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
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
ChIP-Seq|chip-seq|NN|Technique
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
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
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
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
genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
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
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
genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
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
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
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
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
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
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
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
At|at|IN|O OD450|od450|NN|OD
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
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
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
ChIP-Seq|chip-seq|NN|Gversion
genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
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
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
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
RNA-Seq|rna-seq|NN|Technique
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
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
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
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
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
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
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
genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
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
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
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
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
genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
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
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
carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
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
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
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
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
ΔsoxS|δsoxs|NN|Gtype PQ|pq|NN|Supp 1|1|CD|O
genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
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
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
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
Cra|Cra|NNP|O fructose|fructose|NN|Supp 1|1|CD|O
WT|wt|JJ|Gtype glucose|glucose|NN|Supp 2|2|CD|O
ΔoxyR|δoxyr|NN|Gtype PQ|pq|NN|Supp 2|2|CD|O
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
σ32|σ32|NN|O 30|30|CD|Temp °C|°c|NN|Temp rep1|rep1|NN|O
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
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 2|2|CD|O
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
∆|∆|CD|Gtype fur|fur|NN|Gtype ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Anaerobic|anaerobic|JJ|Air A|a|DT|O
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
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
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
∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Aerobic|aerobic|JJ|Air
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air A|a|DT|O
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|Supp _|_|NN|O 1|1|CD|O
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
∆|∆|CD|Gtype fur|fur|NN|Gtype Aerobic|aerobic|JJ|Air A|a|DT|O
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
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|Supp _|_|NN|O 1|1|CD|O
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
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
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
medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
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
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|Gtype _|_|CD|O rep2|rep2|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
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
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
ChIP-Seq|chip-seq|NN|Gversion
genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
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
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
ΔgadW|δgadw|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
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
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
genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
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
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
ΔsoxS|δsoxs|NN|Gtype PQ|pq|NN|Supp 2|2|CD|O
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique _|_|NN|O 1|1|CD|O
Ecoli|ecolus|NNS|O _|_|VBP|O wild-type|wild-type|JJ|Gtype _|_|NN|O rep1|rep1|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
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
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
Lrp|Lrp|NNP|O _|_|SYM|O Leu|Leu|NNP|Supp _|_|NN|O 2|2|CD|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Aerobic|Aerobic|NNP|Air B|b|NN|O
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
Lrp|Lrp|NNP|O _|_|SYM|O Leu|Leu|NNP|Supp _|_|SYM|O 1|1|CD|O
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
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
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
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
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
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
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O B|b|NN|O
RNA-Seq|rna-seq|NN|Technique
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
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
strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
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
σ32|σ32|NN|O 43|43|CD|Temp °C|°c|NN|Temp rep1|rep1|NN|O
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
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
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
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
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
genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
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
culture|culture|NN|O condition|condition|NN|O :|:|:|O Aerobic|Aerobic|NNP|Air cultures|culture|NNS|O
Wild-type|wild-type|JJ|Gtype Aerobic|aerobic|JJ|Air B|b|NN|O
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
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
RpoB|rpob|NN|O WT|wt|JJ|Gtype 2|2|CD|O
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
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
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
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
genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
Cra|Cra|NNP|O glucose|glucose|NN|Supp 2|2|CD|O
Lrp|lrp|NN|O _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O 3|3|CD|O
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
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
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
OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique
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
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
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
ChIP-exo|ChIP-exo|NNP|Technique GadW|gadw|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
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
PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|Supp _|_|NN|O 2|2|CD|O
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
ChIP-exo|ChIP-exo|NNP|Technique RpoS|rpos|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
culture|culture|NN|O condition|condition|NN|O :|:|:|O anaerobic|anaerobic|JJ|Air fermentive|fermentive|JJ|O condition|condition|NN|O
OxyR|oxyr|NN|O PQ|pq|NN|Supp 2|2|CD|O
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
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O A|a|NN|O
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
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
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
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air -|-|:|O B|b|NN|O
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
genotype/variation|genotype/variation|NN|O :|:|:|O Δfnr|δfnr|NN|Gtype
PurR|purr|NN|O _|_|SYM|O Adenine|Adenine|NNP|Supp _|_|SYM|O 1|1|CD|O
genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
Lrp|Lrp|NNP|O _|_|SYM|O Leu|Leu|NNP|Supp _|_|SYM|O 3|3|CD|O
FNR|fnr|SYM|O -|-|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype ∆|∆|VBP|Gtype stpA|stpa|NN|Gtype A|a|NN|O
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
ChIP-exo|ChIP-exo|NNP|Technique GadE|gade|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
WT|wt|JJ|Gtype PQ|pq|NN|Supp 2|2|CD|O
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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Aerobic|Aerobic|NNP|Air C|C|NNP|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Aerobic|Aerobic|NNP|Air A|A|NNP|O
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
NsrR|nsrr|NN|Gtype _|_|CD|Gtype Flagtag|flagtag|NN|Gtype _|_|CD|O rep2|rep2|NN|O
OmpR|ompr|NN|O NaCl|nacl|NN|Supp 2|2|CD|O
genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
∆|∆|CD|Gtype fur|fur|NN|Gtype ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Aerobic|aerobic|JJ|Air A|a|DT|O
genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
ChIP-Seq|chip-seq|NN|Technique
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
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
RpoB|rpob|NN|O ∆|∆|CD|Gtype crp|crp|NN|Gtype 2|2|CD|O
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
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
At|at|IN|O OD450|od450|NN|OD
strain|strain|NN|O :|:|:|O K-12|k-12|NN|Strain
∆|∆|CD|Gtype fur|fur|NN|Gtype ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Anaerobic|anaerobic|JJ|Air B|b|NN|O
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
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
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
genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
ΔgadW|δgadw|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique _|_|NN|O 2|2|CD|O
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
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
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|Supp _|_|NN|O 2|2|CD|O
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|Supp _|_|NN|O 2|2|CD|O
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
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air B|b|NN|O
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 2|2|CD|O
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
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
∆|∆|CD|Gtype fur|fur|NN|Gtype Anaerobic|anaerobic|JJ|Air B|b|NN|O
carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
WT|wt|JJ|Gtype fructose|fructose|NN|Supp 1|1|CD|O
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
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
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
RpoB|rpob|NN|O WT|wt|JJ|Gtype 1|1|CD|O
Input|input|NN|O ChIP-Seq|chip-seq|NN|Technique
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
WT|wt|JJ|Gtype acetate|acetate|NN|Supp 1|1|CD|O
library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 1|1|CD|O
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 1|1|CD|O
WT|wt|JJ|Gtype _|_|NN|O RNASeq|rnaseq|NN|Technique
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
Δcra|δcra|NN|Gtype acetate|acetate|NN|Supp 1|1|CD|O
genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
Cra|Cra|NNP|O acetate|acetate|NN|Supp 2|2|CD|O
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
ΔompR|δompr|NN|Gtype NaCl|nacl|NN|Supp 2|2|CD|O
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
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|anaerobic|JJ|Air C|c|NN|O
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
ΔgadX|δgadx|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
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
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
CsiR|csir|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique
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
WT|wt|JJ|Gtype NaCl|nacl|NN|Supp 2|2|CD|O
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
WT|wt|JJ|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
ChIP-exo|ChIP-exo|NNP|Technique RpoS|rpos|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
NsrR|nsrr|NN|Gtype _|_|CD|Gtype Flagtag|flagtag|NN|Gtype _|_|CD|O rep3|rep3|NN|O
σ32|σ32|NN|O 43|43|CD|Temp °C|°c|NN|Temp short|short|JJ|O RNase|rnase|NN|O
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
Cra|Cra|NNP|O glucose|glucose|NN|Supp 1|1|CD|O
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air B|b|NN|O
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
SeqA|seqa|NN|O old|old|JJ|O deltaSeqA|deltaseqa|NN|Gtype
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
genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
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
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
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
Nac|Nac|NNP|O _|_|NNP|O ChIPSeq|ChIPSeq|NNP|Technique
Aerobic|Aerobic|NNP|Air cultures|culture|NNS|O
Δcra|δcra|NN|Gtype glucose|glucose|NN|Supp 2|2|CD|O
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
SoxS|soxs|NN|O PQ|pq|NN|Supp 1|1|CD|O
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
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
acetate|acetate|NN|Supp
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
WT|wt|JJ|Gtype glucose|glucose|NN|Supp 1|1|CD|O
SoxR|soxr|NN|O PQ|pq|NN|Supp 1|1|CD|O
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
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
Ecoli|ecolus|NNS|O _|_|VBP|O wild-type|wild-type|JJ|Gtype _|_|NN|O rep2|rep2|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
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
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
Δcra|δcra|NN|Gtype acetate|acetate|NN|Supp 2|2|CD|O
∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
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
OxyR|oxyr|NN|O PQ|pq|NN|Supp 1|1|CD|O
ΔsoxR|δsoxr|NN|Gtype PQ|pq|NN|Supp 1|1|CD|O
carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
FNR|fnr|SYM|O -|-|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype ∆|∆|VBP|Gtype stpA|stpa|NN|Gtype B|b|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
Cra|Cra|NNP|O fructose|fructose|NN|Supp 2|2|CD|O
Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|Technique
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air -|-|:|O A|a|NN|O
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
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
∆|∆|CD|Gtype fur|fur|NN|Gtype ∆|∆|CD|Gtype ryhB|ryhb|NN|Gtype Aerobic|aerobic|JJ|Air B|b|NN|O
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
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
Δcra|δcra|NN|Gtype fructose|fructose|NN|Supp 2|2|CD|O
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
∆|∆|CD|Gtype fur|fur|NN|Gtype Aerobic|aerobic|JJ|Air B|b|NN|O
RpoB|rpob|NN|O ∆|∆|CD|Gtype crp|crp|NN|Gtype 1|1|CD|O
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
NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique
WT|wt|JJ|Gtype fructose|fructose|NN|Supp 2|2|CD|O
RpoB|rpob|NN|O ∆|∆|CD|Gtype cra|cra|NN|Gtype 2|2|CD|O
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
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
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
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
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|Gtype _|_|CD|O rep1|rep1|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
Cra|cra|NN|O acetate|acetate|NN|Supp 1|1|CD|O
culture|culture|NN|O condition|condition|NN|O :|:|:|O nitrate|nitrate|JJ|Supp respiratory|respiratory|JJ|O condition|condition|NN|O
genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
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
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
ChIP-exo|ChIP-exo|NNP|Technique GadE|gade|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
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
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
ChIP-exo|ChIP-exo|NNP|Technique GadW|gadw|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|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|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
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
culture|culture|NN|O condition|condition|NN|O :|:|:|O Anaerobic|anaerobic|JJ|Air cultures|culture|NNS|O
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
genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
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
genotype/variation|genotype/variation|NN|O :|:|:|O ΔarcA|δarca|NN|Gtype
NsrR|nsrr|NN|Gtype _|_|CD|Gtype Flagtag|flagtag|NN|Gtype _|_|CD|O rep1|rep1|NN|O
Δcra|δcra|NN|Gtype fructose|fructose|NN|Supp 1|1|CD|O
\ No newline at end of file
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********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70_v4.txt
best params:{'c1': 0.0845144703859872, 'c2': 0.0014492583407590665}
best CV score:0.803457407167867
model size: 0.07M
Flat F1: 0.7886994187596283
precision recall f1-score support
OD 1.000 0.405 0.577 37
pH 1.000 1.000 1.000 12
Technique 0.952 0.909 0.930 22
Med 0.812 0.912 0.860 57
Temp 0.818 1.000 0.900 18
Vess 0.000 0.000 0.000 0
Agit 0.000 0.000 0.000 0
Phase 1.000 0.947 0.973 19
Air 0.730 0.742 0.736 62
Anti 0.571 0.444 0.500 9
Strain 1.000 1.000 1.000 1
Gtype 0.863 0.774 0.816 106
Substrain 0.000 0.000 0.000 1
Supp 0.815 0.713 0.761 136
Gversion 0.000 0.000 0.000 0
avg / total 0.841 0.760 0.789 480
Top likely transitions:
Agit -> Agit 7.567868
OD -> OD 7.283561
Temp -> Temp 6.525111
Anti -> Anti 6.338173
Med -> Med 6.068203
Air -> Air 5.490227
Gtype -> Gtype 5.364943
O -> O 5.360015
Phase -> Phase 5.088291
Gversion -> Gversion 5.052937
Technique -> Technique 4.734097
Supp -> Supp 4.592596
Gtype -> Supp 1.928700
pH -> pH 1.873562
O -> Supp 1.656908
O -> Technique 1.579934
Substrain -> Gtype 1.367059
O -> Gtype 1.299889
Air -> O 1.168469
O -> Temp 0.796125
O -> Anti 0.464004
OD -> Phase 0.334945
Med -> O 0.323185
O -> Gversion 0.294223
Technique -> Air 0.120065
Temp -> O 0.058292
Gversion -> O 0.017060
Gtype -> pH 0.014023
Anti -> O 0.004741
O -> Med 0.003586
O -> Strain 0.000914
Phase -> O 0.000079
Technique -> O -0.064766
Supp -> Air -0.085487
Air -> OD -0.140828
Supp -> OD -0.140855
OD -> Gtype -0.154848
Gtype -> O -0.178619
Air -> Supp -0.190285
Phase -> Air -0.254683
Supp -> O -0.331239
OD -> Air -0.339236
Supp -> Technique -0.352046
Technique -> OD -0.381551
Gtype -> Anti -0.576175
Agit -> O -0.582420
O -> Air -0.710972
OD -> Med -0.720546
OD -> O -0.754296
Gtype -> OD -0.821534
Top unlikely transitions:
Med -> Med 6.068203
Air -> Air 5.490227
Gtype -> Gtype 5.364943
O -> O 5.360015
Phase -> Phase 5.088291
Gversion -> Gversion 5.052937
Technique -> Technique 4.734097
Supp -> Supp 4.592596
Gtype -> Supp 1.928700
pH -> pH 1.873562
O -> Supp 1.656908
O -> Technique 1.579934
Substrain -> Gtype 1.367059
O -> Gtype 1.299889
Air -> O 1.168469
O -> Temp 0.796125
O -> Anti 0.464004
OD -> Phase 0.334945
Med -> O 0.323185
O -> Gversion 0.294223
Technique -> Air 0.120065
Temp -> O 0.058292
Gversion -> O 0.017060
Gtype -> pH 0.014023
Anti -> O 0.004741
O -> Med 0.003586
O -> Strain 0.000914
Phase -> O 0.000079
Technique -> O -0.064766
Supp -> Air -0.085487
Air -> OD -0.140828
Supp -> OD -0.140855
OD -> Gtype -0.154848
Gtype -> O -0.178619
Air -> Supp -0.190285
Phase -> Air -0.254683
Supp -> O -0.331239
OD -> Air -0.339236
Supp -> Technique -0.352046
Technique -> OD -0.381551
Gtype -> Anti -0.576175
Agit -> O -0.582420
O -> Air -0.710972
OD -> Med -0.720546
OD -> O -0.754296
Gtype -> OD -0.821534
Supp -> Med -1.118820
Substrain -> O -1.830467
Phase -> OD -2.403512
Med -> Supp -2.548799
Top positive:
12.504936 Supp b'lemma:Iron'
10.792779 O b'lemma:_'
10.427539 Air b'lemma:aerobic'
10.207513 Air b'lemma:anaerobic'
9.451231 Supp b'lemma:nitrate'
9.115772 Phase b'lemma:stationary'
8.575457 O b'lemma:1'
8.408994 Technique b'lemma:ChIP-exo'
8.354108 Air b'-1:lemma:ChIP-Seq'
8.314194 O b'lemma:rpob'
8.264287 Med b'lemma:MOPS'
8.077335 Technique b'lemma:chipseq'
7.675786 O b'-1:lemma:ChIP-exo'
7.432466 Strain b'lemma:k-12'
7.338742 O b'lemma:Custom'
7.132224 O b'-1:lemma:tag'
6.872851 Substrain b'lemma:mg1655'
6.656592 Supp b'lemma:pq'
6.656346 Gtype b'lemma:\xce\xb4cra'
6.631548 O b'lemma:3'
6.608233 O b'lemma:2'
6.514523 Air b'lemma:Aerobic'
6.354650 Technique b'lemma:ChIP-Seq'
6.321273 Gtype b'lemma:flag-tag'
6.321273 Gtype b'-1:lemma:c-terminal'
6.285172 O b'lemma:rep1'
6.282612 O b'lemma:b'
6.260165 Gversion b'lemma:asm584v2'
6.243462 Gversion b'-1:lemma:nc'
6.129172 Gversion b'lemma:nc'
6.117441 O b'lemma:rep2'
6.056865 O b'lemma:rep3'
6.042591 OD b'+1:lemma:stationary'
5.905730 O b'lemma:Cra'
5.761961 Gtype b'lemma:arca8myc'
5.631643 Gtype b'-1:lemma:\xe2\x88\x86'
5.616482 Phase b'lemma:mid-log'
5.599676 Med b'lemma:LB'
5.591086 O b'lemma:a'
5.417363 O b'lemma:chip'
5.415483 O b'lemma:\xcf\x8332'
5.410036 O b'-1:lemma:0.3'
5.383641 Supp b'+1:lemma:\xc2\xb5m'
5.378485 OD b'lemma:od600'
5.357822 O b'postag::'
5.343662 Gtype b'lemma:delta-arca'
5.329601 Supp b'lemma:nh4cl'
5.310595 Gtype b'lemma:fnr8myc'
5.291721 OD b'lemma:od450'
5.278396 Supp b'lemma:Fe'
5.198206 O b'postag:IN'
5.152255 O b'lemma:or'
5.142263 O b'-1:lemma:Aerobic'
5.072815 Med b'lemma:lb'
4.967279 Technique b'lemma:rna-seq'
4.960999 Gtype b'lemma:type'
4.958285 Strain b'+1:lemma:substr'
4.905998 Gtype b'lemma:wt'
4.808130 Supp b'lemma:glucose'
4.806347 Vess b'lemma:flask'
4.806347 Vess b'-1:lemma:warm'
4.772284 O b'lemma:for'
4.744261 Supp b'lemma:arginine'
4.737788 Gtype b'lemma:delta-fnr'
4.691753 O b'-1:lemma:0.3-0.35'
4.668554 Gtype b'+1:lemma:type'
4.631710 Technique b'lemma:rnaseq'
4.584824 Gtype b'lemma:nsrr'
4.584359 O b'-1:lemma:glucose'
4.556168 O b'-1:lemma:anaerobic'
4.539600 Supp b'-1:lemma:Cra'
4.538972 O b'lemma:-'
4.508141 Gtype b'-1:lemma:rpob'
4.499586 Technique b'lemma:chip-seq'
4.488070 Anti b'lemma:none'
4.462302 O b'lemma:ompr'
4.460124 Anti b'lemma:anti-rpos'
4.460049 Supp b'lemma:no3'
4.451202 O b'+1:lemma:od600'
4.424279 Gtype b'lemma:\xce\xb4fur'
4.389978 Supp b'lemma:acetate'
4.387749 Med b'+1:lemma:0.4'
4.335328 O b'lemma:.'
4.335328 O b'postag:.'
4.197130 Temp b'-1:lemma:\xcf\x8332'
4.152430 Anti b'lemma:seqa'
4.141879 O b'lemma:with'
4.081039 Supp b'-1:lemma:+'
4.005391 O b'+1:lemma:o.d.'
3.986966 O b'-1:lemma:type'
3.971115 O b'+1:lemma:sparging'
3.914608 Gversion b'lemma:chip-seq'
3.905122 Supp b'+1:lemma:1'
3.886730 Technique b'-1:lemma:IP'
3.875182 Supp b'+1:lemma:hour'
3.871343 Temp b'-1:lemma:43'
3.798383 pH b'lemma:ph5'
3.798383 pH b'+1:lemma:.5'
3.766343 Supp b'lemma:Leu'
3.758437 Med b'lemma:m63'
3.755680 Supp b'lemma:rifampicin'
3.717291 Gtype b'+1:lemma:ph5'
3.691820 Gtype b'-1:lemma:ptac'
3.686748 Gtype b'lemma:\xe2\x88\x86'
3.655665 Anti b'+1:lemma:antibody'
3.645147 Temp b'-1:lemma:37'
3.584169 O b'lemma:s'
3.582382 Gversion b'lemma:000913'
3.513265 O b'postag:VBN'
3.504182 Temp b'-1:lemma:sample'
3.476410 O b'lemma:CEL'
3.471641 Gtype b'+1:lemma:flagtag'
3.469424 O b'+1:lemma:pq'
3.442038 Med b'+1:lemma:minimal'
3.441203 Gtype b'lemma:\xce\xb4ompr'
3.440050 Supp b'+1:lemma:2'
3.439274 O b'lemma:oxyr'
3.430689 Gtype b'lemma:\xce\xb4soxs'
3.424081 Supp b'lemma:Adenine'
3.394933 O b'-1:lemma:lb'
3.382358 Supp b'lemma:dpd'
3.374432 Anti b'lemma:anti-myc'
3.354369 O b'+1:lemma:chip-seq'
3.325764 O b'-1:lemma:\xc2\xb0c'
3.324069 Air b'lemma:anerobically'
3.306589 Gversion b'lemma:u00096'
3.306589 Gversion b'+1:lemma:.2'
3.290810 Supp b'lemma:fructose'
3.286471 Med b'+1:lemma:2.0'
3.281346 Gversion b'lemma:.2'
3.281346 Gversion b'-1:lemma:u00096'
3.224316 Gtype b'lemma:wild-type'
3.206842 Gtype b'+1:lemma:with'
3.204237 O b'+1:lemma:rifampicin'
3.192028 Gtype b'+1:lemma:aerobic'
3.176568 Supp b'lemma:iptg'
3.174757 Supp b'lemma:nacl'
3.142082 Phase b'-1:lemma:until'
3.138505 Gtype b'lemma:pk4854'
3.102435 Supp b'+1:lemma:_'
3.077765 Technique b'-1:lemma:input'
3.043564 Med b'+1:lemma:contain'
3.043460 O b'lemma:affyexp'
3.030477 O b'+1:postag:NNP'
3.011575 Gtype b'+1:lemma:pq'
3.009802 Technique b'-1:lemma:rna-seq'
3.009086 Phase b'+1:lemma:for'
3.006591 O b'lemma:chip-arca'
2.961198 Technique b'+1:lemma:chip-exo'
2.918766 Gtype b'lemma:deltaseqa'
2.918766 Gtype b'-1:lemma:old'
2.895206 O b'lemma:soxs'
2.895206 O b'lemma:soxr'
2.893483 O b'lemma:argr'
2.883608 Supp b'-1:lemma:\xc2\xb5m'
2.871795 Technique b'-1:lemma:chip-exo'
2.840922 Air b'postag:RB'
2.837804 O b'-1:lemma:l1'
2.834031 O b'lemma:purr'
2.816068 pH b'lemma:.5'
2.816068 pH b'-1:lemma:ph5'
2.793907 O b'+1:postag:RB'
2.787764 Temp b'lemma:43'
2.783505 Gtype b'+1:lemma:knock-out'
2.777516 Med b'-1:lemma:ml'
2.776744 Gtype b'lemma:ptac'
2.754900 Air b'lemma:anaerobically'
2.728375 O b'+1:lemma:acetate'
2.677194 Gtype b'lemma:\xce\xb4oxyr'
2.676114 Gtype b'lemma:WT'
2.664380 O b'-1:lemma:dpd'
2.623289 O b'lemma:at'
2.622409 Air b'+1:lemma:at'
2.621682 O b'lemma:Fur'
2.613642 OD b'lemma:0.3'
2.611845 O b'postag:DT'
2.601745 O b'-1:lemma:stpa'
2.558195 OD b'-1:lemma:about'
2.551265 Gtype b'lemma:\xce\xb4soxr'
2.545283 Gtype b'-1:lemma:from'
2.537660 Med b'lemma:L'
2.537660 Med b'+1:lemma:broth'
2.520762 Temp b'-1:lemma:30'
2.512014 Supp b'+1:lemma:and'
2.485033 Gtype b'lemma:dfnr'
2.478336 Temp b'lemma:\xc2\xb0c'
2.477157 pH b'+1:postag:CD'
2.474581 O b'lemma:2-3'
2.467989 O b'lemma:Lrp'
2.464584 Med b'-1:lemma:LB'
2.446412 O b'+1:postag:VBP'
2.443891 Supp b'lemma:leucine'
2.443008 Air b'-1:lemma:-'
2.331881 Med b'lemma:broth'
2.331881 Med b'-1:lemma:L'
2.324108 Gtype b'+1:lemma:_'
2.320318 O b'-1:lemma:min'
2.319595 O b'+1:lemma:mid-log'
2.316477 Supp b'+1:lemma:iptg'
2.316285 O b'+1:lemma:43'
Top negative:
0.000009 Anti b'+1:lemma:\xce\xb2'
0.000008 Anti b'+1:lemma:subunit'
0.000005 O b'-1:lemma:Deficient'
0.000001 OD b'+1:lemma:0.15'
-0.000001 Temp b'-1:postag:IN'
-0.000007 O b'lemma:medium'
-0.000045 O b'+1:lemma:rep1'
-0.000145 Gtype b'+1:lemma:2'
-0.000168 O b'+1:lemma:culture'
-0.000168 O b'+1:lemma:dissolve'
-0.000355 O b'-1:lemma:1'
-0.000451 OD b'+1:lemma:-lrb-'
-0.000593 O b'+1:lemma:c'
-0.000597 OD b'+1:postag:VBN'
-0.000854 Gtype b'+1:postag:NNS'
-0.001125 O b'lemma:10'
-0.001603 O b'-1:lemma:fresh'
-0.002085 Supp b'-1:lemma:-'
-0.002163 O b'+1:lemma:300'
-0.002264 Air b'-1:postag:NNP'
-0.002713 O b'+1:lemma:min'
-0.003522 Air b'+1:postag:-LRB-'
-0.003594 O b'-1:lemma:iptg'
-0.004379 O b'lemma:cell'
-0.004450 O b'+1:lemma:antibody'
-0.007530 Gtype b'-1:postag:NNP'
-0.011566 Air b'postag:CC'
-0.011603 O b'+1:lemma:a'
-0.011880 O b'+1:lemma:dpd'
-0.013535 OD b'postag:NNS'
-0.013622 Supp b'+1:lemma:glucose'
-0.013806 O b'-1:lemma:the'
-0.014085 O b'+1:lemma:25'
-0.014120 OD b'-1:postag:DT'
-0.016761 OD b'-1:lemma:a'
-0.021729 OD b'+1:postag:-LRB-'
-0.024283 O b'-1:lemma:25'
-0.024519 O b'postag:VBP'
-0.027011 OD b'+1:lemma:0.4'
-0.027020 O b'+1:lemma:co2'
-0.030020 O b'+1:lemma:mm'
-0.030904 Gtype b'postag:NNS'
-0.031338 O b'+1:lemma:grow'
-0.032633 Gtype b'-1:postag:NN'
-0.034461 Med b'-1:lemma:m63'
-0.038347 O b'lemma:coli'
-0.039331 Gtype b'+1:postag:IN'
-0.040098 Air b'+1:postag:NN'
-0.043802 O b'lemma:o2'
-0.044786 Anti b'-1:postag:NN'
-0.050998 Phase b'+1:postag:NN'
-0.053029 Supp b'-1:postag:VBG'
-0.059606 O b'+1:lemma:shake'
-0.060227 O b'lemma:\xc2\xb0c'
-0.061576 O b'+1:lemma:k-12'
-0.068548 O b'lemma:mg/ml'
-0.068548 O b'-1:lemma:150'
-0.071993 O b'-1:lemma:minimal'
-0.075882 OD b'+1:postag:CD'
-0.076224 O b'lemma:glucose'
-0.078957 O b'-1:lemma:at'
-0.082806 O b'lemma:grow'
-0.087424 OD b'-1:postag:NNS'
-0.090506 Supp b'-1:postag:NN'
-0.093124 Temp b'-1:lemma:\xc2\xb0c'
-0.093134 O b'-1:lemma:-lrb-'
-0.093606 O b'lemma:minimal'
-0.094232 O b'+1:lemma:o2'
-0.097879 O b'-1:lemma:mm'
-0.098068 Med b'-1:postag:NN'
-0.107118 O b'-1:lemma:o2'
-0.118175 O b'+1:lemma:phase'
-0.119815 Technique b'-1:lemma::'
-0.130823 Temp b'postag:JJ'
-0.132875 O b'+1:lemma:arginine'
-0.134855 O b'-1:lemma:30'
-0.146776 O b'lemma:aerobically'
-0.147575 O b'-1:lemma:n2'
-0.149484 OD b'postag:IN'
-0.156867 Air b'postag:CD'
-0.156918 O b'-1:lemma:from'
-0.166087 Supp b'+1:postag:IN'
-0.177934 O b'lemma:mg1655'
-0.179064 Anti b'+1:postag:JJ'
-0.179551 Supp b'lemma:and'
-0.188276 O b'-1:lemma:um'
-0.188276 O b'+1:lemma:paraquat'
-0.189403 O b'lemma:n2'
-0.195278 O b'lemma:\xce\xb4fur'
-0.198127 Med b'+1:postag:IN'
-0.214634 O b'+1:lemma:\xc2\xb0c'
-0.215441 O b'lemma:30'
-0.215519 O b'-1:lemma:e.'
-0.226406 O b'-1:postag:IN'
-0.226968 Gtype b'postag:CD'
-0.227233 Phase b'-1:lemma:at'
-0.230930 O b'-1:postag:VBN'
-0.231525 O b'-1:lemma:of'
-0.235093 O b'+1:postag:NNS'
-0.235942 O b'+1:lemma:5'
-0.237587 O b'+1:lemma:_'
-0.253207 Supp b'+1:lemma:rifampicin'
-0.254236 Gversion b'+1:postag:NN'
-0.261414 Med b'postag:CD'
-0.269201 O b'-1:postag:-LRB-'
-0.283772 O b'-1:lemma:od600'
-0.286133 O b'lemma:co2'
-0.286584 O b'+1:lemma:or'
-0.289081 O b'+1:lemma:-rrb-'
-0.293131 O b'+1:lemma:cell'
-0.293510 O b'-1:lemma:0.1'
-0.315643 O b'lemma:phase'
-0.317100 Air b'-1:postag:CC'
-0.328206 Supp b'postag:CC'
-0.328374 O b'-1:lemma:0.2'
-0.342964 Supp b'+1:postag:VBN'
-0.347291 O b'lemma:150'
-0.347291 O b'+1:lemma:mg/ml'
-0.349307 O b'lemma:od600'
-0.351495 OD b'postag:JJ'
-0.353086 Temp b'+1:lemma:to'
-0.353086 Temp b'+1:postag:TO'
-0.374885 O b'-1:lemma:mid-log'
-0.378947 Air b'-1:postag:JJ'
-0.382276 O b'postag:RB'
-0.384726 pH b'postag:NN'
-0.388651 O b'+1:lemma:until'
-0.395876 O b'lemma:e.'
-0.396410 O b'+1:lemma:.'
-0.396410 O b'+1:postag:.'
-0.419403 O b'-1:lemma:ml'
-0.438819 O b'lemma:anaerobic'
-0.441115 Agit b'postag:NN'
-0.458507 Med b'+1:postag:NN'
-0.467746 O b'-1:lemma:grow'
-0.468347 OD b'+1:lemma:and'
-0.477039 Anti b'+1:lemma:anti-fur'
-0.477272 O b'+1:postag:-RRB-'
-0.539475 Phase b'-1:postag:JJ'
-0.544246 O b'-1:lemma:rifampicin'
-0.554986 Technique b'-1:postag::'
-0.557503 O b'-1:lemma:~'
-0.566406 O b'-1:lemma:cra'
-0.585219 O b'-1:lemma:sample'
-0.592872 OD b'lemma:-lrb-'
-0.597579 O b'+1:lemma:0.3'
-0.637939 OD b'+1:postag:CC'
-0.640528 Air b'+1:postag:JJ'
-0.641855 O b'lemma:0.3'
-0.663280 O b'lemma:20'
-0.678531 O b'lemma:media'
-0.679754 O b'+1:postag:IN'
-0.692879 O b'+1:lemma:%'
-0.704594 O b'lemma:of'
-0.746312 O b'-1:lemma:co2'
-0.752462 O b'lemma:dissolve'
-0.774185 O b'+1:lemma:fecl2'
-0.784660 Med b'-1:postag:IN'
-0.813078 O b'-1:lemma:IP'
-0.845987 O b'lemma:dpd'
-0.856881 O b'+1:lemma:+'
-0.917781 O b'-1:postag:VBG'
-0.924251 O b'+1:lemma:g/l'
-0.950062 Temp b'postag:NN'
-0.956490 O b'-1:lemma:dissolve'
-0.956490 O b'+1:lemma:methanol'
-0.973571 OD b'+1:postag:NN'
-0.985083 O b'-1:lemma:rpob'
-1.088717 Supp b'+1:lemma:acetate'
-1.116443 O b'lemma:0.1'
-1.121770 O b'+1:lemma:at'
-1.139282 O b'lemma:fecl2'
-1.139658 O b'lemma:0.2'
-1.143368 O b'lemma:2h'
-1.143368 O b'-1:lemma:additional'
-1.162871 O b'lemma:mid-log'
-1.218300 O b'+1:lemma:in'
-1.230428 OD b'postag:-LRB-'
-1.237811 O b'+1:lemma:supplement'
-1.238950 O b'-1:lemma:37'
-1.269797 O b'+1:postag:VBG'
-1.280950 O b'lemma:anaerobically'
-1.360526 O b'lemma:37'
-1.412947 O b'-1:postag::'
-1.467612 O b'lemma:wt'
-1.469772 O b'+1:lemma:hour'
-1.551225 Supp b'-1:lemma:%'
-1.646983 O b'lemma:methanol'
-1.652478 O b'-1:lemma:nsrr'
-1.705441 Phase b'postag:JJ'
-1.865099 Anti b'postag:NNP'
-2.110303 Supp b'postag:JJ'
-2.251438 Air b'postag:NN'
-2.402454 O b'lemma:rifampicin'
-2.570647 O b'-1:lemma:ompr'
-2.620057 O b'-1:lemma:2'
-2.709520 O b'+1:lemma:2'
-3.092706 O b'+1:lemma:1'
-4.538028 O b'-1:lemma:_'
-4.976237 O b'-1:lemma::'
********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70_v4.txt
best params:{'c1': 0.04733824675634195, 'c2': 0.013567747033585223}
best CV score:0.7954499755233463
model size: 0.08M
Flat F1: 0.8073047538765561
precision recall f1-score support
OD 1.000 0.405 0.577 37
pH 1.000 1.000 1.000 12
Technique 0.952 0.909 0.930 22
Med 0.891 0.860 0.875 57
Temp 0.818 1.000 0.900 18
Vess 0.000 0.000 0.000 0
Agit 0.000 0.000 0.000 0
Phase 1.000 0.947 0.973 19
Air 0.939 0.742 0.829 62
Anti 1.000 0.444 0.615 9
Strain 1.000 1.000 1.000 1
Gtype 0.865 0.783 0.822 106
Substrain 0.000 0.000 0.000 1
Supp 0.869 0.684 0.765 136
Gversion 0.000 0.000 0.000 0
avg / total 0.901 0.748 0.807 480
Top likely transitions:
Agit -> Agit 6.351306
OD -> OD 6.016578
Temp -> Temp 5.927690
Anti -> Anti 5.530188
Med -> Med 5.290933
Air -> Air 4.824974
Gversion -> Gversion 4.795717
Phase -> Phase 4.587222
O -> O 4.562384
Gtype -> Gtype 4.485788
Supp -> Supp 4.175027
Technique -> Technique 3.738966
pH -> pH 2.445982
Substrain -> Gtype 1.983414
O -> Supp 1.704431
Gtype -> Supp 1.702624
Technique -> Air 1.053845
O -> Technique 1.011581
O -> Gtype 0.959004
O -> Temp 0.852096
Air -> O 0.791615
Gtype -> pH 0.696397
O -> Anti 0.684439
O -> Gversion 0.269497
Gtype -> Air 0.261457
O -> Strain 0.143898
Med -> O 0.029331
O -> pH 0.007540
O -> Vess 0.000124
O -> Med 0.000090
Temp -> O 0.000022
Phase -> O -0.002114
Vess -> O -0.020913
O -> Phase -0.027016
Anti -> Gtype -0.034769
Gversion -> Air -0.042314
Phase -> Air -0.063658
O -> Agit -0.107236
OD -> Technique -0.108455
Supp -> pH -0.117168
Gversion -> O -0.140630
Anti -> O -0.151755
Gtype -> Technique -0.152014
Supp -> Phase -0.214979
OD -> Supp -0.232643
O -> OD -0.260286
Supp -> Anti -0.275132
Gtype -> Phase -0.278437
Technique -> O -0.314521
Phase -> Technique -0.315599
Top unlikely transitions:
Phase -> O -0.002114
Vess -> O -0.020913
O -> Phase -0.027016
Anti -> Gtype -0.034769
Gversion -> Air -0.042314
Phase -> Air -0.063658
O -> Agit -0.107236
OD -> Technique -0.108455
Supp -> pH -0.117168
Gversion -> O -0.140630
Anti -> O -0.151755
Gtype -> Technique -0.152014
Supp -> Phase -0.214979
OD -> Supp -0.232643
O -> OD -0.260286
Supp -> Anti -0.275132
Gtype -> Phase -0.278437
Technique -> O -0.314521
Phase -> Technique -0.315599
Supp -> O -0.331781
Med -> Air -0.373175
Supp -> Temp -0.406898
Gtype -> O -0.442607
Temp -> Med -0.464337
Gtype -> Gversion -0.493751
Supp -> Gversion -0.560400
Anti -> OD -0.563611
Supp -> Technique -0.605347
Gtype -> Med -0.614663
Supp -> OD -0.660842
Air -> Supp -0.707856
OD -> Air -0.738038
OD -> Gtype -0.750328
Supp -> Gtype -0.775491
Supp -> Air -0.783032
Gtype -> Anti -0.848608
Air -> Med -0.863324
OD -> Med -0.930579
Agit -> O -0.969044
Air -> OD -0.995424
Technique -> pH -1.068524
OD -> O -1.148371
O -> Air -1.151845
Technique -> OD -1.233856
Gtype -> OD -1.268038
Technique -> Gtype -1.279158
Substrain -> O -1.352003
Supp -> Med -1.440706
Med -> Supp -1.997092
Phase -> OD -2.488972
Top positive:
8.290919 O b'lemma:_'
7.385787 Phase b'lemma:stationary'
7.051234 O b'lemma:1'
6.894708 Supp b'lemma:Iron'
6.675567 Air b'lemma:anaerobic'
6.403841 Air b'lemma:aerobic'
6.381259 Technique b'lemma:ChIP-exo'
6.295199 Strain b'lemma:k-12'
6.076363 O b'lemma:rpob'
6.004917 O b'lemma:2'
5.997376 Technique b'lemma:chipseq'
5.756531 Supp b'lemma:pq'
5.480849 O b'lemma:3'
5.419549 Air b'-1:lemma:ChIP-Seq'
5.377608 O b'-1:lemma:tag'
5.236921 Gversion b'lemma:asm584v2'
5.220500 Supp b'lemma:nitrate'
5.194599 Gtype b'lemma:\xce\xb4cra'
5.105810 O b'lemma:rep1'
5.072402 Phase b'lemma:mid-log'
5.067722 O b'postag:IN'
5.062697 Med b'lemma:MOPS'
5.031333 Supp b'lemma:nh4cl'
5.013490 Gtype b'lemma:arca8myc'
5.000342 Gtype b'lemma:flag-tag'
5.000342 Gtype b'-1:lemma:c-terminal'
4.890613 O b'lemma:rep2'
4.886114 Substrain b'lemma:mg1655'
4.864909 Supp b'lemma:glucose'
4.809146 Supp b'+1:lemma:\xc2\xb5m'
4.725613 Air b'lemma:Aerobic'
4.660445 O b'lemma:rep3'
4.614931 Med b'lemma:LB'
4.549528 O b'lemma:Cra'
4.411392 Gtype b'lemma:wt'
4.409856 Technique b'lemma:rna-seq'
4.384311 Gtype b'-1:lemma:\xe2\x88\x86'
4.354696 O b'lemma:b'
4.328794 Supp b'lemma:acetate'
4.303499 Gtype b'lemma:delta-arca'
4.292242 O b'lemma:Custom'
4.271514 O b'-1:lemma:ChIP-exo'
4.249183 Gtype b'lemma:fnr8myc'
4.166692 O b'postag::'
4.162283 Supp b'lemma:no3'
4.142997 Technique b'lemma:chip-seq'
4.139547 O b'lemma:\xcf\x8332'
4.132690 Supp b'-1:lemma:Cra'
4.123280 Supp b'lemma:Fe'
4.117229 Anti b'lemma:none'
4.089970 O b'-1:lemma:Aerobic'
4.070800 O b'lemma:a'
4.053427 Technique b'lemma:rnaseq'
3.997780 O b'lemma:.'
3.997780 O b'postag:.'
3.955278 OD b'lemma:od450'
3.952430 Med b'lemma:lb'
3.926643 Anti b'lemma:seqa'
3.901600 O b'+1:postag:RB'
3.860379 Supp b'lemma:fructose'
3.843887 O b'+1:lemma:od600'
3.818270 Gversion b'lemma:nc'
3.774402 Gtype b'lemma:type'
3.769802 Gtype b'lemma:delta-fnr'
3.749008 Med b'+1:lemma:0.4'
3.723936 Gtype b'+1:lemma:type'
3.716300 Gtype b'lemma:\xe2\x88\x86'
3.702464 Air b'postag:RB'
3.701643 Supp b'lemma:rifampicin'
3.698023 Gversion b'lemma:chip-seq'
3.685933 O b'lemma:-'
3.684595 O b'-1:lemma:0.3-0.35'
3.676777 Supp b'lemma:dpd'
3.644945 OD b'lemma:od600'
3.635765 Technique b'lemma:ChIP-Seq'
3.623886 O b'lemma:CEL'
3.599273 Supp b'+1:lemma:1'
3.576564 OD b'+1:lemma:stationary'
3.566248 Gtype b'lemma:\xce\xb4fur'
3.461638 O b'-1:lemma:anaerobic'
3.459278 Gtype b'lemma:nsrr'
3.356330 pH b'lemma:ph5'
3.356330 pH b'+1:lemma:.5'
3.352106 O b'-1:lemma:glucose'
3.340294 Supp b'+1:lemma:Deficient'
3.338469 Supp b'lemma:arginine'
3.337805 Gtype b'+1:lemma:with'
3.333928 Strain b'+1:lemma:substr'
3.322235 Anti b'lemma:anti-myc'
3.308233 Gtype b'lemma:wild-type'
3.291619 O b'lemma:with'
3.274998 Vess b'lemma:flask'
3.274998 Vess b'-1:lemma:warm'
3.203208 Supp b'+1:lemma:2'
3.169852 Med b'lemma:m63'
3.132500 Gtype b'lemma:\xce\xb4soxs'
3.105860 Med b'+1:lemma:2.0'
3.077793 Gtype b'lemma:WT'
3.074708 O b'lemma:oxyr'
3.065934 Anti b'+1:lemma:antibody'
3.065570 O b'lemma:s'
3.051751 O b'-1:lemma:type'
3.050447 O b'+1:lemma:o.d.'
3.033846 Technique b'-1:lemma:IP'
3.021636 O b'lemma:chip-arca'
3.007962 Gtype b'lemma:\xce\xb4ompr'
2.993470 O b'-1:lemma:stpa'
2.985907 O b'-1:lemma:lb'
2.982505 O b'lemma:chip'
2.979425 O b'lemma:for'
2.977744 O b'lemma:affyexp'
2.974504 Gversion b'lemma:u00096'
2.974504 Gversion b'+1:lemma:.2'
2.951628 Supp b'lemma:nacl'
2.929411 Supp b'+1:lemma:hour'
2.918651 Med b'-1:lemma:ml'
2.914880 Gversion b'lemma:.2'
2.914880 Gversion b'-1:lemma:u00096'
2.913751 O b'lemma:or'
2.911773 O b'postag:VBN'
2.882260 O b'+1:lemma:anti-fur'
2.876894 O b'+1:lemma:chip-seq'
2.868995 Gtype b'-1:lemma:ptac'
2.866722 Temp b'lemma:\xc2\xb0c'
2.863424 Supp b'+1:lemma:_'
2.862778 O b'lemma:ompr'
2.834787 Air b'lemma:Anaerobic'
2.827994 Gversion b'-1:lemma:nc'
2.824064 Temp b'-1:lemma:43'
2.820717 O b'lemma:argr'
2.820412 Gversion b'lemma:000913'
2.749427 Anti b'lemma:anti-rpos'
2.734729 Gtype b'+1:lemma:flagtag'
2.732480 Supp b'-1:lemma:+'
2.727515 O b'lemma:Lrp'
2.719436 Phase b'+1:lemma:for'
2.711551 Temp b'lemma:43'
2.711404 Gtype b'lemma:deltaseqa'
2.711404 Gtype b'-1:lemma:old'
2.703630 Gtype b'lemma:pk4854'
2.700766 O b'+1:lemma:pq'
2.675879 Air b'lemma:anaerobically'
2.664358 Gtype b'+1:lemma:pq'
2.656000 Technique b'-1:lemma:input'
2.651505 Temp b'-1:lemma:37'
2.648470 O b'lemma:2-3'
2.620313 Temp b'lemma:37'
2.617008 Substrain b'+1:lemma:phtpg'
2.612535 Technique b'-1:lemma:chip-exo'
2.596752 Med b'+1:lemma:minimal'
2.596648 O b'-1:lemma:dpd'
2.596120 O b'lemma:at'
2.593521 O b'postag:SYM'
2.572579 Gtype b'-1:lemma:rpob'
2.572348 O b'postag:CC'
2.562481 O b'lemma:purr'
2.559444 Gtype b'lemma:ptac'
2.547961 O b'postag:DT'
2.528953 Temp b'-1:lemma:sample'
2.519081 Gtype b'+1:lemma:ph5'
2.510093 O b'lemma:soxs'
2.510093 O b'lemma:soxr'
2.489436 pH b'lemma:.5'
2.489436 pH b'-1:lemma:ph5'
2.486692 O b'+1:lemma:sparging'
2.468346 Air b'lemma:anerobically'
2.466200 Gtype b'lemma:\xce\xb4oxyr'
2.460573 O b'-1:lemma:l1'
2.435676 Supp b'lemma:iptg'
2.396322 Air b'-1:lemma:-'
2.381121 Technique b'+1:lemma:chip-exo'
2.375332 Med b'postag:NNP'
2.369739 Supp b'lemma:Leu'
2.367468 Temp b'-1:lemma:\xcf\x8332'
2.358408 O b'lemma:Fur'
2.318420 Supp b'lemma:Adenine'
2.308664 Gtype b'+1:lemma:aerobic'
2.284972 pH b'+1:postag:CD'
2.278223 O b'-1:lemma:0.3'
2.275175 O b'+1:lemma:mid-log'
2.272071 Med b'lemma:L'
2.272071 Med b'+1:lemma:broth'
2.271694 Gversion b'+1:lemma:000913'
2.263241 Temp b'+1:lemma:\xc2\xb0c'
2.251200 Gtype b'lemma:\xce\xb4soxr'
2.250951 Med b'-1:lemma:LB'
2.232437 Phase b'lemma:phase'
2.225558 O b'-1:lemma:\xc2\xb0c'
2.210922 O b'lemma:pt7'
2.195220 Med b'lemma:glucose'
2.189252 Technique b'postag:NNP'
2.171773 O b'lemma:chip-fnr'
2.161995 Gtype b'lemma:dfnr'
2.158766 O b'lemma:genotype/variation'
2.150201 O b'+1:lemma:43'
2.145901 Supp b'-1:lemma:\xc2\xb5m'
2.141092 Supp b'lemma:leucine'
2.114711 Gtype b'-1:lemma:nsrr'
2.112477 O b'lemma:culture'
2.110383 Supp b'+1:lemma:and'
Top negative:
-0.004206 Gtype b'-1:lemma:,'
-0.004206 Gtype b'-1:postag:,'
-0.004363 O b'+1:lemma:dissolve'
-0.005226 Air b'-1:lemma:anaerobically'
-0.006081 Med b'postag:-LRB-'
-0.007482 O b'+1:lemma:25'
-0.007505 Air b'+1:postag:-LRB-'
-0.010695 O b'+1:lemma:delta'
-0.010729 Gtype b'lemma:control'
-0.015920 OD b'-1:postag:DT'
-0.016476 Supp b'+1:lemma:glucose'
-0.020393 O b'+1:lemma:o2'
-0.020701 Air b'-1:lemma:-rrb-'
-0.027434 O b'-1:postag:DT'
-0.030363 Air b'postag:CD'
-0.031961 O b'postag:RB'
-0.035995 O b'lemma:aerobically'
-0.040364 O b'lemma:n2'
-0.040535 Med b'-1:postag:CD'
-0.041176 Air b'-1:postag:-RRB-'
-0.042452 OD b'+1:lemma:0.4'
-0.044876 O b'-1:lemma:the'
-0.046558 O b'-1:lemma:25'
-0.047871 O b'+1:lemma:95'
-0.048967 O b'-1:postag:IN'
-0.050524 O b'+1:lemma:strain'
-0.053326 Phase b'+1:postag:NN'
-0.060668 O b'-1:lemma:e.'
-0.070033 O b'lemma:e.'
-0.070538 O b'+1:lemma:0.4'
-0.071511 O b'+1:lemma:grow'
-0.072393 Gtype b'+1:lemma:cra'
-0.076483 Med b'postag:CD'
-0.079707 O b'+1:lemma:or'
-0.080785 O b'+1:lemma:5'
-0.081991 OD b'+1:postag:CD'
-0.097802 O b'lemma:glucose'
-0.099284 O b'+1:lemma:b'
-0.100727 Supp b'-1:lemma:and'
-0.107163 Supp b'-1:postag:NN'
-0.121273 O b'lemma:o2'
-0.123375 Anti b'+1:postag:JJ'
-0.128472 Supp b'-1:postag:VBG'
-0.137982 O b'lemma:nacl'
-0.138385 O b'-1:lemma:g/l'
-0.140738 Med b'+1:lemma:media'
-0.143230 O b'+1:lemma:.'
-0.143230 O b'+1:postag:.'
-0.147429 O b'-1:lemma:-lrb-'
-0.150859 O b'+1:lemma:mm'
-0.150867 Gtype b'postag:CD'
-0.155869 O b'-1:lemma:mm'
-0.157092 O b'-1:lemma:of'
-0.160183 O b'+1:postag:IN'
-0.161439 Gtype b'-1:postag:CD'
-0.183365 Gtype b'-1:postag:DT'
-0.184394 Supp b'+1:postag:IN'
-0.185747 O b'+1:lemma:-rrb-'
-0.188736 O b'-1:lemma:20'
-0.189296 O b'-1:postag:-LRB-'
-0.194391 O b'-1:lemma:o2'
-0.196331 O b'lemma:grow'
-0.197265 O b'lemma:m63'
-0.202228 Supp b'lemma:and'
-0.208828 Gtype b'lemma:_'
-0.213147 O b'lemma:co2'
-0.216510 O b'+1:lemma:Aerobic'
-0.219766 O b'-1:lemma:um'
-0.219766 O b'+1:lemma:paraquat'
-0.222760 O b'-1:lemma:n2'
-0.223418 Med b'-1:postag:NN'
-0.226489 O b'-1:lemma:minimal'
-0.229253 O b'-1:postag:VBN'
-0.229413 OD b'+1:lemma:mid-log'
-0.235205 Technique b'-1:lemma::'
-0.245927 O b'+1:lemma:cell'
-0.259152 O b'+1:lemma:shake'
-0.259231 O b'-1:lemma:with'
-0.260969 O b'lemma:lb'
-0.262122 O b'lemma:\xc2\xb0c'
-0.262570 Med b'+1:postag:NNS'
-0.267584 O b'+1:lemma:minimal'
-0.268702 O b'-1:lemma:fresh'
-0.274046 Supp b'-1:postag:NNP'
-0.283215 Temp b'postag:JJ'
-0.289216 O b'+1:postag:-RRB-'
-0.298829 Med b'+1:postag:NN'
-0.300030 O b'lemma:k-12'
-0.303893 Supp b'+1:postag:VBN'
-0.304837 O b'+1:lemma:until'
-0.305487 O b'-1:lemma:mid-log'
-0.314457 O b'lemma:30'
-0.318478 O b'-1:lemma:\xe2\x88\x86'
-0.318630 OD b'postag:JJ'
-0.320224 Gtype b'+1:lemma:\xe2\x88\x86'
-0.328379 O b'lemma:mg1655'
-0.332214 O b'-1:lemma:30'
-0.336273 O b'+1:lemma:phase'
-0.343858 O b'-1:lemma:0.1'
-0.353210 O b'-1:lemma:1'
-0.363425 O b'lemma:minimal'
-0.367846 O b'-1:lemma:from'
-0.393937 Gversion b'+1:postag:NN'
-0.407622 Air b'-1:lemma:or'
-0.419752 Phase b'-1:lemma:at'
-0.419908 Med b'+1:postag:IN'
-0.434159 OD b'+1:postag:NN'
-0.434388 Temp b'-1:lemma:\xc2\xb0c'
-0.437451 OD b'+1:lemma:and'
-0.450338 O b'-1:lemma:rifampicin'
-0.450644 O b'+1:lemma:%'
-0.460508 O b'+1:lemma:_'
-0.468703 O b'-1:lemma:od600'
-0.471110 O b'+1:lemma:c'
-0.473012 OD b'+1:postag:CC'
-0.473111 O b'+1:lemma:rep1'
-0.476279 O b'lemma:purify'
-0.486329 O b'-1:lemma:iptg'
-0.490766 Gtype b'-1:postag:SYM'
-0.492855 O b'+1:lemma:\xc2\xb0c'
-0.520331 Supp b'+1:lemma:rifampicin'
-0.521486 Gtype b'lemma:delta'
-0.544638 O b'lemma:phase'
-0.549770 Supp b'postag:CC'
-0.574118 Technique b'-1:postag::'
-0.588060 O b'lemma:\xe2\x88\x86'
-0.589911 O b'lemma:dissolve'
-0.600471 O b'-1:lemma:until'
-0.605867 OD b'lemma:-lrb-'
-0.606846 O b'-1:lemma:grow'
-0.615232 O b'+1:postag:NNS'
-0.621806 O b'-1:lemma:cra'
-0.628236 O b'+1:lemma:300'
-0.629162 pH b'postag:NN'
-0.647995 O b'+1:lemma:arginine'
-0.663009 O b'lemma:150'
-0.663009 O b'+1:lemma:mg/ml'
-0.668956 O b'lemma:media'
-0.687046 OD b'postag:-LRB-'
-0.688477 Anti b'+1:lemma:anti-fur'
-0.696641 Phase b'-1:postag:JJ'
-0.720714 O b'lemma:od600'
-0.740400 O b'+1:lemma:0.3'
-0.753503 O b'-1:postag:VBG'
-0.798903 O b'lemma:anaerobically'
-0.798945 O b'-1:lemma:0.2'
-0.800846 Med b'-1:postag:IN'
-0.802642 O b'lemma:dpd'
-0.829848 O b'+1:postag:VBG'
-0.837375 O b'lemma:20'
-0.843836 Temp b'+1:lemma:to'
-0.843836 Temp b'+1:postag:TO'
-0.861567 O b'lemma:anaerobic'
-0.895410 O b'-1:lemma:co2'
-0.935654 Supp b'+1:lemma:acetate'
-0.962115 O b'+1:lemma:fecl2'
-0.965287 O b'-1:lemma:ml'
-0.992440 Temp b'postag:NN'
-1.012409 Air b'-1:postag:JJ'
-1.037489 O b'lemma:0.3'
-1.038206 O b'lemma:fecl2'
-1.045928 O b'-1:lemma:~'
-1.050208 O b'lemma:0.1'
-1.059403 O b'postag:VBP'
-1.082188 O b'-1:postag::'
-1.107761 O b'lemma:mid-log'
-1.113185 O b'lemma:\xce\xb4fur'
-1.123078 O b'lemma:0.2'
-1.128103 O b'-1:lemma:sample'
-1.194487 Supp b'-1:lemma:%'
-1.213453 Air b'postag:NN'
-1.229252 O b'lemma:of'
-1.235299 O b'+1:lemma:supplement'
-1.238904 O b'lemma:37'
-1.267382 O b'lemma:2h'
-1.267382 O b'-1:lemma:additional'
-1.275201 O b'-1:lemma:dissolve'
-1.275201 O b'+1:lemma:methanol'
-1.291651 O b'+1:lemma:in'
-1.453841 O b'+1:lemma:at'
-1.495880 Air b'+1:postag:JJ'
-1.522603 Anti b'postag:NNP'
-1.573726 O b'+1:lemma:g/l'
-1.603806 O b'-1:lemma:ompr'
-1.605609 Phase b'postag:JJ'
-1.643331 O b'-1:lemma:rpob'
-1.700527 O b'-1:lemma:37'
-1.724176 O b'-1:lemma:IP'
-1.756223 O b'-1:lemma:nsrr'
-1.790376 O b'+1:lemma:+'
-1.794994 O b'lemma:methanol'
-1.802577 Supp b'postag:JJ'
-1.803599 O b'lemma:wt'
-1.870737 O b'lemma:rifampicin'
-2.105365 O b'-1:lemma:2'
-2.201462 O b'+1:lemma:2'
-2.218990 O b'+1:lemma:hour'
-2.783349 O b'+1:lemma:1'
-3.830507 O b'-1:lemma:_'
-4.238490 O b'-1:lemma::'
********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70_v4.txt
best params:{'c1': 0.28812013544306553, 'c2': 0.007295583222860682}
best CV score:0.7989041592425109
model size: 0.06M
Flat F1: 0.7893461428977414
precision recall f1-score support
OD 1.000 0.405 0.577 37
pH 1.000 1.000 1.000 12
Technique 0.952 0.909 0.930 22
Med 1.000 0.842 0.914 57
Temp 0.818 1.000 0.900 18
Vess 0.000 0.000 0.000 0
Agit 0.000 0.000 0.000 0
Phase 1.000 0.895 0.944 19
Air 0.780 0.742 0.760 62
Anti 0.500 0.444 0.471 9
Strain 1.000 1.000 1.000 1
Gtype 0.854 0.774 0.812 106
Substrain 0.000 0.000 0.000 1
Supp 0.802 0.684 0.738 136
Gversion 0.000 0.000 0.000 0
avg / total 0.863 0.742 0.789 480
Top likely transitions:
Agit -> Agit 6.356818
OD -> OD 6.348289
Temp -> Temp 5.553063
Med -> Med 5.370053
Anti -> Anti 5.276075
Air -> Air 5.018155
Gtype -> Gtype 4.515516
Gversion -> Gversion 4.398480
Phase -> Phase 4.359659
O -> O 4.293965
Technique -> Technique 4.237543
Supp -> Supp 4.146423
O -> Supp 1.964836
Gtype -> Supp 1.866470
pH -> pH 1.685265
Air -> O 1.614236
Substrain -> Gtype 1.463550
O -> Technique 1.388918
O -> Gtype 1.222957
O -> Temp 0.798237
Med -> O 0.601567
O -> Anti 0.587178
Technique -> Air 0.378127
O -> Gversion 0.328551
OD -> Phase 0.308573
Temp -> O 0.289779
Supp -> O 0.253243
O -> Med 0.178828
Phase -> O 0.132350
Gtype -> pH 0.097473
O -> Phase 0.003637
Gtype -> Air 0.001121
Supp -> Air -0.008182
Technique -> Gtype -0.085945
Gtype -> Anti -0.165395
Gtype -> O -0.277440
OD -> O -0.365628
Agit -> O -0.521571
Gtype -> OD -0.554390
O -> Air -0.784770
Supp -> Med -0.806802
Substrain -> O -0.835873
Med -> Supp -0.906570
Phase -> OD -0.993184
Top unlikely transitions:
Agit -> Agit 6.356818
OD -> OD 6.348289
Temp -> Temp 5.553063
Med -> Med 5.370053
Anti -> Anti 5.276075
Air -> Air 5.018155
Gtype -> Gtype 4.515516
Gversion -> Gversion 4.398480
Phase -> Phase 4.359659
O -> O 4.293965
Technique -> Technique 4.237543
Supp -> Supp 4.146423
O -> Supp 1.964836
Gtype -> Supp 1.866470
pH -> pH 1.685265
Air -> O 1.614236
Substrain -> Gtype 1.463550
O -> Technique 1.388918
O -> Gtype 1.222957
O -> Temp 0.798237
Med -> O 0.601567
O -> Anti 0.587178
Technique -> Air 0.378127
O -> Gversion 0.328551
OD -> Phase 0.308573
Temp -> O 0.289779
Supp -> O 0.253243
O -> Med 0.178828
Phase -> O 0.132350
Gtype -> pH 0.097473
O -> Phase 0.003637
Gtype -> Air 0.001121
Supp -> Air -0.008182
Technique -> Gtype -0.085945
Gtype -> Anti -0.165395
Gtype -> O -0.277440
OD -> O -0.365628
Agit -> O -0.521571
Gtype -> OD -0.554390
O -> Air -0.784770
Supp -> Med -0.806802
Substrain -> O -0.835873
Med -> Supp -0.906570
Phase -> OD -0.993184
Top positive:
8.456899 Supp b'lemma:Iron'
7.968467 O b'lemma:_'
7.452197 Air b'lemma:anaerobic'
7.437960 Air b'lemma:aerobic'
7.396388 Technique b'lemma:ChIP-exo'
7.187671 O b'lemma:1'
6.882632 Phase b'lemma:stationary'
6.605608 Supp b'lemma:nitrate'
6.530209 Strain b'lemma:k-12'
6.203118 Air b'-1:lemma:ChIP-Seq'
6.007441 Phase b'lemma:mid-log'
5.856483 O b'lemma:rpob'
5.727633 O b'lemma:2'
5.691995 O b'lemma:3'
5.621467 Technique b'lemma:chipseq'
5.604648 Substrain b'lemma:mg1655'
5.596923 Technique b'lemma:ChIP-Seq'
5.568237 Gtype b'lemma:type'
5.509620 Med b'lemma:MOPS'
5.475086 Gversion b'lemma:asm584v2'
5.234945 O b'lemma:\xcf\x8332'
5.062729 O b'postag:IN'
5.021516 Supp b'lemma:pq'
4.929591 Air b'lemma:Aerobic'
4.874521 O b'lemma:Custom'
4.858511 Gversion b'lemma:nc'
4.830173 Med b'lemma:LB'
4.792027 Gtype b'lemma:\xce\xb4cra'
4.771925 OD b'lemma:od600'
4.722214 O b'lemma:rep1'
4.615430 O b'postag::'
4.604643 Supp b'+1:lemma:\xc2\xb5m'
4.516978 O b'lemma:b'
4.505623 Gtype b'lemma:flag-tag'
4.505623 Gtype b'-1:lemma:c-terminal'
4.503645 Med b'lemma:lb'
4.444381 Supp b'lemma:nh4cl'
4.432940 O b'-1:lemma:tag'
4.401594 O b'lemma:rep2'
4.365296 Gtype b'+1:lemma:type'
4.331532 Gtype b'-1:lemma:\xe2\x88\x86'
4.318893 O b'lemma:rep3'
4.280628 O b'-1:lemma:ChIP-exo'
4.273779 O b'lemma:a'
4.191200 OD b'lemma:od450'
4.187860 Gtype b'lemma:wt'
4.184958 Technique b'lemma:rna-seq'
4.089199 Supp b'lemma:glucose'
4.068712 Temp b'-1:lemma:sample'
4.066149 Gtype b'lemma:arca8myc'
3.877291 O b'lemma:Cra'
3.835115 Gtype b'lemma:nsrr'
3.739614 Supp b'lemma:Fe'
3.722246 Technique b'lemma:chip-seq'
3.715540 O b'+1:lemma:od600'
3.678000 Gtype b'lemma:delta-arca'
3.610668 Gtype b'lemma:\xe2\x88\x86'
3.517468 Med b'+1:lemma:0.4'
3.508191 O b'lemma:.'
3.508191 O b'postag:.'
3.483906 Gtype b'lemma:fnr8myc'
3.468892 Supp b'lemma:acetate'
3.438457 Vess b'lemma:flask'
3.438457 Vess b'-1:lemma:warm'
3.400184 Supp b'lemma:rifampicin'
3.396565 Technique b'lemma:rnaseq'
3.379201 Anti b'lemma:none'
3.369352 O b'-1:lemma:Aerobic'
3.366768 O b'-1:lemma:type'
3.310195 Supp b'lemma:no3'
3.306542 Gtype b'lemma:\xce\xb4fur'
3.289509 O b'-1:lemma:0.3-0.35'
3.240918 Gtype b'lemma:delta-fnr'
3.228917 Supp b'lemma:fructose'
3.199686 Supp b'lemma:dpd'
3.182132 O b'lemma:-'
3.174434 Gversion b'-1:lemma:nc'
3.160676 OD b'+1:lemma:stationary'
3.140034 Supp b'lemma:arginine'
3.107677 O b'postag:VBN'
3.075194 Technique b'-1:lemma:IP'
3.054797 Anti b'+1:lemma:antibody'
2.967185 Supp b'+1:lemma:1'
2.948061 pH b'lemma:ph5'
2.948061 pH b'+1:lemma:.5'
2.919290 Gtype b'-1:lemma:rpob'
2.909319 Anti b'lemma:seqa'
2.876363 O b'lemma:chip'
2.856949 Med b'+1:lemma:minimal'
2.846997 Gtype b'+1:lemma:ph5'
2.846043 Gversion b'lemma:u00096'
2.846043 Gversion b'+1:lemma:.2'
2.842541 Supp b'lemma:20'
2.813149 Gversion b'lemma:chip-seq'
2.799253 Temp b'-1:lemma:\xcf\x8332'
2.787282 O b'-1:lemma:glucose'
2.767972 Anti b'lemma:anti-rpos'
2.763663 Gtype b'lemma:\xce\xb4ompr'
2.762526 O b'postag:DT'
2.753494 O b'postag:CC'
2.734024 Supp b'+1:lemma:2'
2.713273 O b'lemma:CEL'
2.711953 Supp b'-1:lemma:+'
2.708255 Gtype b'+1:lemma:with'
2.662841 Air b'postag:RB'
2.655147 O b'+1:postag:RB'
2.622484 Temp b'-1:lemma:43'
2.621064 Anti b'lemma:anti-myc'
2.585376 O b'lemma:with'
2.579506 Gtype b'+1:lemma:pq'
2.574119 Med b'lemma:m63'
2.560671 Gtype b'-1:lemma:ptac'
2.530970 Supp b'lemma:iptg'
2.522165 Gversion b'lemma:000913'
2.522038 O b'-1:lemma:0.3'
2.518142 O b'lemma:or'
2.510254 pH b'lemma:.5'
2.510254 pH b'-1:lemma:ph5'
2.499838 Gtype b'lemma:wild-type'
2.496012 O b'-1:lemma:anaerobic'
2.493145 O b'+1:postag:NNP'
2.432959 O b'+1:lemma:o.d.'
2.423786 Supp b'lemma:nacl'
2.374439 Gversion b'lemma:.2'
2.374439 Gversion b'-1:lemma:u00096'
2.371897 Supp b'-1:lemma:Cra'
2.333418 Technique b'+1:lemma:chip-exo'
2.330714 Technique b'-1:lemma:chip-exo'
2.318227 Gtype b'+1:lemma:flagtag'
2.299023 Supp b'+1:lemma:_'
2.291540 Supp b'-1:lemma:\xc2\xb5m'
2.270555 Air b'-1:lemma:-'
2.258400 O b'postag:VBG'
2.241112 O b'-1:lemma:l1'
2.239653 Temp b'lemma:\xc2\xb0c'
2.239203 O b'-1:lemma:lb'
2.216105 Med b'lemma:media'
2.215247 Med b'-1:lemma:glucose'
2.198544 O b'lemma:s'
2.181192 Med b'+1:lemma:2.0'
2.180737 Supp b'-1:lemma:with'
2.151013 O b'-1:lemma:\xc2\xb0c'
2.122011 O b'lemma:culture'
2.119623 Gtype b'lemma:\xce\xb4soxs'
2.118038 O b'+1:lemma:pq'
2.107784 Strain b'+1:lemma:substr'
2.084102 Temp b'-1:lemma:37'
2.034197 Med b'lemma:L'
2.034197 Med b'+1:lemma:broth'
2.033322 OD b'-1:lemma:~'
2.031873 Temp b'lemma:37'
2.021465 Air b'lemma:anaerobically'
2.013276 O b'lemma:oxyr'
1.993546 pH b'+1:postag:CD'
1.990912 Temp b'lemma:43'
1.970179 Gtype b'lemma:pk4854'
1.965724 O b'lemma:escherichia'
1.928351 O b'lemma:affyexp'
1.918099 Gtype b'-1:lemma:nsrr'
1.912439 Gversion b'postag:CD'
1.912210 Gtype b'+1:lemma:_'
1.903180 Temp b'+1:lemma:\xc2\xb0c'
1.901831 O b'-1:lemma:media'
1.893202 Supp b'lemma:Leu'
1.888140 O b'+1:lemma:chip-seq'
1.885088 Supp b'lemma:methanol'
1.864512 Med b'+1:lemma:supplement'
1.843743 Gtype b'-1:postag:VBG'
1.840860 Med b'-1:lemma:ml'
1.833228 O b'lemma:genotype/variation'
1.830405 Air b'-1:lemma:co2'
1.824009 OD b'lemma:0.3'
1.823612 O b'-1:lemma:stpa'
1.820300 O b'+1:lemma:sparging'
1.820114 Gtype b'lemma:deltaseqa'
1.820114 Gtype b'-1:lemma:old'
1.808084 O b'lemma:at'
1.804795 Temp b'+1:lemma:and'
1.793786 Gtype b'lemma:ptac'
1.792476 Temp b'lemma:30'
1.780844 Supp b'+1:lemma:hour'
1.749460 Supp b'lemma:of'
1.723530 O b'lemma:condition'
1.717109 Phase b'-1:lemma:mid-log'
1.711480 Med b'+1:lemma:g/l'
1.709245 Gtype b'-1:lemma:_'
1.702188 Gtype b'-1:lemma:phtpg'
1.695199 O b'-1:lemma:dpd'
1.690508 Supp b'lemma:0.2'
1.688329 Air b'-1:postag:CD'
1.682363 Technique b'-1:lemma:_'
1.681577 Phase b'+1:lemma:for'
1.675654 Med b'postag:NNP'
1.654545 O b'lemma:Lrp'
1.636356 Gtype b'+1:postag::'
1.629183 Technique b'-1:lemma:1'
1.628579 Technique b'-1:lemma:input'
1.626463 Med b'lemma:glucose'
1.615682 Temp b'-1:lemma:30'
1.596658 Supp b'lemma:Adenine'
Top negative:
0.017267 O b'-1:lemma:phase'
0.015360 O b'-1:lemma:Fur'
0.015015 Gtype b'lemma:-rcb-'
0.014734 Air b'lemma:-lrb-'
0.013480 Phase b'+1:lemma:aerobically'
0.013397 O b'-1:lemma:be'
0.012964 O b'lemma:fresh'
0.012612 Temp b'+1:postag:-RRB-'
0.011601 O b'lemma:2-3'
0.010954 OD b'postag:CC'
0.009883 Med b'+1:postag:VBG'
0.008416 Med b'-1:postag:NNP'
0.007746 Phase b'+1:postag:RB'
0.007283 O b'lemma:acetate'
0.006890 Temp b'-1:postag:NNS'
0.005794 O b'-1:postag:VBD'
0.005770 O b'+1:lemma:n2'
0.005411 Gversion b'-1:postag::'
0.005130 Gtype b'lemma:-lcb-'
0.003653 Med b'-1:lemma:-rrb-'
0.003433 O b'-1:lemma:m63'
0.003399 OD b'postag:CD'
0.003303 Anti b'+1:postag:-LRB-'
0.003264 Gtype b'lemma:cra'
0.003037 Phase b'-1:postag:IN'
0.002641 O b'+1:lemma:ChIP-Seq'
0.001833 O b'-1:lemma:with'
0.001345 O b'-1:postag:VBZ'
0.001191 OD b'-1:lemma:at'
0.001140 Supp b'+1:lemma:of'
0.001083 Med b'-1:postag::'
0.000969 O b'+1:lemma:anerobically'
0.000925 O b'+1:lemma:genbank'
0.000915 O b'-1:lemma:total'
0.000846 O b'postag:VBZ'
0.000778 Air b'+1:lemma:culture'
0.000629 O b'lemma:express'
0.000629 O b'+1:lemma:nsrr'
0.000580 Air b'postag:-RRB-'
0.000523 Supp b'+1:lemma:dissolve'
0.000475 O b'lemma:70'
0.000346 Supp b'-1:postag:VBN'
0.000255 O b'+1:lemma:anaerobically'
0.000233 O b'+1:postag:-LRB-'
0.000229 Air b'lemma:95'
0.000124 Agit b'lemma:bath'
0.000124 Agit b'-1:lemma:water'
0.000123 Agit b'+1:lemma:shake'
0.000098 O b'+1:lemma:_'
0.000070 Gtype b'+1:lemma:control'
0.000049 Anti b'lemma:tag'
0.000044 O b'lemma:glucose'
0.000043 Agit b'+1:lemma:at'
0.000042 Agit b'-1:postag:DT'
0.000033 Air b'-1:lemma:95'
0.000027 Temp b'+1:postag:VB'
0.000027 O b'+1:lemma:wt'
0.000025 O b'lemma:~'
0.000024 Agit b'postag:IN'
0.000018 OD b'-1:lemma:mg1655'
0.000012 OD b'lemma:\xce\xb4soxr'
0.000009 Supp b'lemma:paraquat'
0.000003 Vess b'+1:postag:IN'
0.000001 Med b'+1:lemma:with'
-0.000003 Supp b'+1:postag:VBN'
-0.000004 O b'-1:lemma:sample'
-0.000016 O b'lemma:150'
-0.000016 O b'+1:lemma:mg/ml'
-0.000020 O b'+1:lemma:shake'
-0.000023 OD b'+1:postag:-LRB-'
-0.000033 O b'lemma:anaerobic'
-0.000042 O b'-1:lemma:at'
-0.000051 O b'lemma:e.'
-0.000122 O b'-1:lemma:0.1'
-0.000150 O b'-1:lemma:e.'
-0.000237 Gtype b'+1:postag:NNS'
-0.000353 O b'-1:lemma:rifampicin'
-0.000482 Gtype b'+1:lemma:-lrb-'
-0.000998 O b'-1:lemma:ml'
-0.002220 Gtype b'postag:CD'
-0.002782 Gtype b'-1:postag:NN'
-0.002824 Med b'postag:CD'
-0.003203 Air b'postag:-LRB-'
-0.005019 O b'+1:lemma:phase'
-0.008101 Supp b'-1:postag:NN'
-0.008157 Air b'+1:lemma:-lrb-'
-0.009984 Air b'lemma:,'
-0.009984 Air b'postag:,'
-0.009987 Gtype b'-1:postag:CD'
-0.011620 O b'lemma:30'
-0.011986 Supp b'+1:lemma:-rrb-'
-0.012348 Phase b'+1:postag:NN'
-0.012465 Supp b'+1:postag:-RRB-'
-0.016199 O b'+1:lemma:c'
-0.017044 Air b'+1:postag:-RRB-'
-0.018057 Med b'-1:postag:IN'
-0.018532 OD b'+1:postag:CD'
-0.018715 O b'-1:lemma:1'
-0.028572 O b'+1:lemma:arginine'
-0.032917 Anti b'+1:postag:JJ'
-0.033839 Phase b'-1:postag:NN'
-0.035292 O b'-1:lemma:5'
-0.035894 O b'lemma:co2'
-0.037511 O b'-1:lemma:30'
-0.050917 Air b'-1:postag:VBN'
-0.051574 Air b'postag:CD'
-0.052755 Air b'+1:lemma:-rrb-'
-0.053416 Air b'-1:postag:RB'
-0.054843 Air b'-1:lemma:or'
-0.056713 OD b'postag:JJ'
-0.066384 O b'+1:lemma:5'
-0.075993 Air b'-1:lemma:and'
-0.077374 O b'-1:lemma:~'
-0.079056 Air b'-1:lemma:-lrb-'
-0.080674 Supp b'postag:CC'
-0.081179 O b'-1:lemma:,'
-0.081179 O b'-1:postag:,'
-0.091063 Air b'-1:postag:-LRB-'
-0.104880 O b'-1:lemma:-lrb-'
-0.116778 Gversion b'+1:postag:NN'
-0.117338 Med b'+1:postag:IN'
-0.156891 O b'-1:postag:VBN'
-0.158460 O b'+1:lemma:300'
-0.159376 Phase b'-1:lemma:at'
-0.163043 O b'+1:postag:NNS'
-0.185937 O b'-1:lemma:cra'
-0.198845 pH b'postag:NN'
-0.202021 Med b'-1:postag:NN'
-0.206164 O b'-1:postag:IN'
-0.210478 O b'-1:lemma:from'
-0.224002 O b'+1:lemma:hour'
-0.228689 O b'+1:lemma:-rrb-'
-0.230127 Temp b'postag:JJ'
-0.232439 O b'+1:lemma:.'
-0.232439 O b'+1:postag:.'
-0.261795 O b'lemma:0.3'
-0.276668 O b'+1:lemma:%'
-0.283202 O b'+1:postag:IN'
-0.291477 O b'lemma:dissolve'
-0.294314 O b'-1:lemma:of'
-0.332798 O b'-1:postag:-LRB-'
-0.348211 Temp b'postag:NN'
-0.361228 O b'lemma:od600'
-0.373795 O b'lemma:phase'
-0.395276 Med b'+1:postag:NN'
-0.405822 O b'+1:lemma:+'
-0.406990 Supp b'-1:lemma:%'
-0.409533 Temp b'+1:lemma:to'
-0.409533 Temp b'+1:postag:TO'
-0.419386 O b'lemma:anaerobically'
-0.421572 O b'+1:postag:-RRB-'
-0.460490 Air b'-1:postag:JJ'
-0.467245 Technique b'-1:postag::'
-0.476757 Supp b'+1:lemma:rifampicin'
-0.502746 O b'lemma:media'
-0.503360 O b'-1:lemma:od600'
-0.524986 OD b'+1:postag:NN'
-0.543280 O b'-1:lemma:rpob'
-0.557386 O b'-1:lemma:grow'
-0.570906 O b'lemma:fecl2'
-0.574577 O b'+1:lemma:fecl2'
-0.632496 O b'+1:lemma:cell'
-0.640758 O b'+1:lemma:0.3'
-0.696627 O b'-1:lemma:IP'
-0.710065 O b'-1:postag::'
-0.734704 O b'+1:postag:VBG'
-0.735189 OD b'lemma:-lrb-'
-0.753554 O b'lemma:0.1'
-0.763727 O b'lemma:0.2'
-0.785113 O b'-1:lemma:37'
-0.803671 O b'-1:lemma:dissolve'
-0.803671 O b'+1:lemma:methanol'
-0.833476 Supp b'+1:lemma:acetate'
-0.838362 O b'-1:lemma:ompr'
-0.851164 O b'lemma:37'
-0.866382 O b'lemma:2h'
-0.866382 O b'-1:lemma:additional'
-0.882690 O b'-1:postag:VBG'
-0.885831 O b'+1:lemma:g/l'
-0.888919 Phase b'postag:JJ'
-0.905015 O b'lemma:of'
-0.906507 Anti b'postag:NNP'
-1.026494 O b'lemma:mid-log'
-1.028079 O b'lemma:wt'
-1.060908 O b'+1:lemma:supplement'
-1.075926 O b'-1:lemma:co2'
-1.341090 O b'-1:lemma:nsrr'
-1.359406 O b'+1:lemma:at'
-1.375702 Air b'+1:postag:JJ'
-1.442763 O b'lemma:rifampicin'
-1.637602 O b'lemma:methanol'
-1.645866 Air b'postag:NN'
-1.720675 Supp b'postag:JJ'
-1.885525 OD b'postag:-LRB-'
-1.959132 O b'+1:lemma:in'
-2.128110 O b'+1:lemma:2'
-2.307682 O b'-1:lemma:2'
-2.374565 O b'+1:lemma:1'
-4.058703 O b'-1:lemma:_'
-4.145888 O b'-1:lemma::'
********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70_v4.txt
best params:{'c1': 0.03056779653153922, 'c2': 0.04972818685122124}
best CV score:0.7979170694802522
model size: 0.10M
Flat F1: 0.7933473757323906
precision recall f1-score support
OD 1.000 0.405 0.577 37
pH 1.000 1.000 1.000 12
Technique 0.952 0.909 0.930 22
Med 0.891 0.860 0.875 57
Temp 0.818 1.000 0.900 18
Vess 0.000 0.000 0.000 0
Agit 0.000 0.000 0.000 0
Phase 1.000 0.947 0.973 19
Air 0.754 0.742 0.748 62
Anti 1.000 0.667 0.800 9
Strain 1.000 1.000 1.000 1
Gtype 0.862 0.764 0.810 106
Substrain 0.000 0.000 0.000 1
Supp 0.865 0.662 0.750 136
Gversion 0.000 0.000 0.000 0
avg / total 0.876 0.742 0.793 480
Top likely transitions:
OD -> OD 5.500349
Temp -> Temp 4.915043
Agit -> Agit 4.909226
Air -> Air 4.785921
Med -> Med 4.785670
Anti -> Anti 4.760878
O -> O 4.531217
Gversion -> Gversion 4.225381
Phase -> Phase 3.928282
Gtype -> Gtype 3.900260
Supp -> Supp 3.589674
Technique -> Technique 2.798353
pH -> pH 2.196128
O -> Supp 1.783329
Substrain -> Gtype 1.742663
Gtype -> Supp 1.431329
Air -> O 1.367539
O -> Gtype 1.348906
O -> Technique 1.109884
Technique -> Air 1.076025
O -> Temp 0.929238
Gtype -> pH 0.717732
O -> Anti 0.700988
Med -> O 0.588191
Gtype -> Air 0.487796
O -> Strain 0.399055
O -> Gversion 0.366108
O -> pH 0.354024
O -> Vess 0.200749
Phase -> O 0.164004
OD -> Phase 0.128366
O -> Med 0.084648
Supp -> O 0.064532
O -> Phase 0.054268
Temp -> O 0.034554
O -> OD 0.002316
pH -> Gversion -0.000024
O -> Substrain -0.000046
Agit -> OD -0.000091
Technique -> Phase -0.002460
Phase -> Air -0.004039
Med -> OD -0.010012
Gversion -> pH -0.019017
Air -> Anti -0.028855
Gtype -> Strain -0.034925
Air -> Gversion -0.046350
Gtype -> Agit -0.051780
pH -> Temp -0.055396
Anti -> pH -0.065064
Substrain -> Supp -0.073862
Top unlikely transitions:
OD -> Anti -0.306626
Technique -> Med -0.317775
Technique -> O -0.337656
Technique -> Gversion -0.339632
Anti -> Supp -0.346709
Gversion -> Gtype -0.359654
OD -> Temp -0.364068
Anti -> Gtype -0.374696
Air -> Temp -0.398364
Gversion -> Technique -0.424722
Gversion -> Supp -0.427358
Gtype -> Phase -0.440633
OD -> Technique -0.441830
Gversion -> Air -0.472797
Med -> Air -0.491373
OD -> Supp -0.502001
Anti -> OD -0.541429
Supp -> pH -0.552035
Temp -> Med -0.559365
O -> Air -0.562556
Supp -> Temp -0.563090
Gtype -> Technique -0.587403
Phase -> Technique -0.587965
Supp -> Phase -0.590123
Air -> Supp -0.631042
Air -> Med -0.640889
OD -> Med -0.665368
Technique -> Supp -0.671196
Gtype -> Gversion -0.722812
Supp -> Anti -0.732707
Supp -> OD -0.751148
Air -> OD -0.751415
OD -> Gtype -0.801738
Agit -> O -0.827165
Supp -> Technique -0.836650
Supp -> Gversion -0.836877
Gtype -> Med -0.875397
Supp -> Air -0.884655
Gtype -> Anti -0.943614
Supp -> Gtype -0.974424
OD -> O -1.010665
OD -> Air -1.028154
Substrain -> O -1.046580
Gtype -> OD -1.131529
Technique -> Gtype -1.214725
Technique -> pH -1.220888
Technique -> OD -1.238019
Supp -> Med -1.342545
Med -> Supp -1.444556
Phase -> OD -1.784428
Top positive:
6.692463 O b'lemma:_'
5.657865 O b'lemma:1'
4.942948 Phase b'lemma:stationary'
4.925287 O b'lemma:2'
4.843804 Air b'lemma:anaerobic'
4.814975 Strain b'lemma:k-12'
4.647361 Technique b'lemma:ChIP-exo'
4.622048 Supp b'lemma:Iron'
4.599836 Technique b'lemma:chipseq'
4.422488 Air b'lemma:aerobic'
4.412579 O b'lemma:rpob'
4.377913 O b'postag:IN'
4.349481 Supp b'lemma:pq'
4.294520 O b'lemma:3'
4.161278 Supp b'lemma:nh4cl'
4.073955 Supp b'lemma:glucose'
3.969533 O b'lemma:rep1'
3.919806 Gtype b'lemma:arca8myc'
3.916893 Gtype b'lemma:flag-tag'
3.916893 Gtype b'-1:lemma:c-terminal'
3.877994 Gtype b'lemma:\xce\xb4cra'
3.870087 Phase b'lemma:mid-log'
3.844857 Air b'-1:lemma:ChIP-Seq'
3.795026 O b'lemma:rep2'
3.756394 Gtype b'lemma:wt'
3.756244 Gversion b'lemma:asm584v2'
3.735954 Substrain b'lemma:mg1655'
3.630823 Gtype b'-1:lemma:\xe2\x88\x86'
3.587007 Supp b'lemma:nitrate'
3.584699 Supp b'+1:lemma:\xc2\xb5m'
3.571404 O b'lemma:Cra'
3.546169 Supp b'lemma:acetate'
3.518531 O b'lemma:b'
3.492146 O b'postag::'
3.490669 O b'lemma:rep3'
3.441030 O b'lemma:a'
3.439329 O b'-1:lemma:tag'
3.376019 Supp b'lemma:no3'
3.358527 Gtype b'lemma:delta-arca'
3.341462 Med b'lemma:LB'
3.335616 Air b'lemma:Aerobic'
3.304114 OD b'lemma:od600'
3.286213 Supp b'lemma:Fe'
3.283134 Supp b'lemma:dpd'
3.262389 O b'lemma:.'
3.262389 O b'postag:.'
3.262118 Gtype b'lemma:fnr8myc'
3.241225 Technique b'lemma:rna-seq'
3.161606 Med b'lemma:lb'
3.100373 Technique b'lemma:chip-seq'
3.056207 O b'lemma:\xcf\x8332'
3.050606 O b'-1:lemma:Aerobic'
3.038793 Med b'lemma:MOPS'
3.034791 Anti b'lemma:none'
3.020225 O b'postag:VBN'
2.971269 O b'-1:lemma:ChIP-exo'
2.958452 Anti b'lemma:seqa'
2.958367 O b'lemma:CEL'
2.941302 OD b'lemma:od450'
2.935356 O b'+1:lemma:od600'
2.927938 Gtype b'lemma:\xe2\x88\x86'
2.911881 Supp b'+1:lemma:1'
2.911524 Supp b'lemma:fructose'
2.871399 Technique b'lemma:rnaseq'
2.859600 O b'+1:postag:RB'
2.839822 Gtype b'lemma:delta-fnr'
2.810955 O b'lemma:Custom'
2.809182 Supp b'lemma:rifampicin'
2.808831 O b'lemma:-'
2.789937 Gtype b'lemma:type'
2.788256 Supp b'+1:lemma:Deficient'
2.770982 Gtype b'+1:lemma:type'
2.748917 Supp b'+1:lemma:2'
2.743490 Gversion b'lemma:nc'
2.738725 Med b'+1:lemma:0.4'
2.720595 pH b'lemma:ph5'
2.720595 pH b'+1:lemma:.5'
2.676119 Supp b'-1:lemma:Cra'
2.658000 Gtype b'lemma:\xce\xb4fur'
2.652362 Gtype b'+1:lemma:with'
2.618562 Gversion b'lemma:chip-seq'
2.610176 Air b'postag:RB'
2.594937 Gtype b'lemma:nsrr'
2.583087 Technique b'lemma:ChIP-Seq'
2.578250 Vess b'lemma:flask'
2.578250 Vess b'-1:lemma:warm'
2.563672 O b'lemma:affyexp'
2.551761 O b'-1:lemma:glucose'
2.545085 O b'lemma:chip-arca'
2.505127 Supp b'+1:lemma:_'
2.499915 O b'-1:lemma:anaerobic'
2.495203 Supp b'lemma:arginine'
2.492742 O b'lemma:s'
2.486425 Gversion b'lemma:000913'
2.464249 O b'-1:lemma:0.3-0.35'
2.449997 O b'lemma:oxyr'
2.448215 Gversion b'lemma:.2'
2.448215 Gversion b'-1:lemma:u00096'
2.435265 Anti b'lemma:anti-myc'
2.432726 Gtype b'lemma:wild-type'
2.423727 Temp b'lemma:\xc2\xb0c'
2.395174 Technique b'-1:lemma:IP'
2.393484 O b'-1:lemma:stpa'
2.388764 Gversion b'lemma:u00096'
2.388764 Gversion b'+1:lemma:.2'
2.368933 Phase b'-1:lemma:mid-log'
2.366886 Gtype b'lemma:WT'
2.348028 O b'lemma:with'
2.344016 O b'lemma:or'
2.343871 O b'+1:lemma:anti-fur'
2.313839 Gtype b'lemma:\xce\xb4soxs'
2.310686 Strain b'+1:lemma:substr'
2.303744 O b'-1:lemma:lb'
2.288133 O b'lemma:argr'
2.284029 Gtype b'+1:lemma:pq'
2.277137 O b'+1:lemma:pq'
2.253710 O b'lemma:ompr'
2.244848 Gtype b'-1:lemma:ptac'
2.214837 Med b'lemma:m63'
2.208372 Air b'lemma:anaerobically'
2.207760 Gversion b'-1:lemma:nc'
2.185269 Air b'lemma:Anaerobic'
2.177809 Supp b'lemma:nacl'
2.172428 Gtype b'+1:lemma:flagtag'
2.169963 Med b'+1:lemma:2.0'
2.169550 O b'postag:SYM'
2.165014 O b'lemma:purr'
2.160892 pH b'+1:postag:CD'
2.150124 Temp b'-1:lemma:37'
2.150116 O b'lemma:chip'
2.133824 O b'+1:lemma:mid-log'
2.130811 Gtype b'lemma:\xce\xb4ompr'
2.113515 Air b'-1:lemma:-'
2.112847 Gtype b'lemma:ptac'
2.087871 O b'lemma:Lrp'
2.073270 Gtype b'-1:lemma:_'
2.071479 Technique b'-1:lemma:chip-exo'
2.052465 O b'-1:lemma:type'
2.046273 O b'+1:lemma:o.d.'
2.034128 Technique b'postag:NNP'
2.032694 OD b'+1:lemma:stationary'
2.029532 Gtype b'lemma:deltaseqa'
2.029532 Gtype b'-1:lemma:old'
2.029028 Technique b'-1:lemma:input'
2.028724 Temp b'+1:lemma:\xc2\xb0c'
2.028052 Med b'postag:NNP'
2.019887 O b'+1:lemma:chip-seq'
2.016529 Vess b'-1:postag:VBN'
2.014709 Anti b'+1:lemma:antibody'
2.004528 Supp b'+1:lemma:hour'
1.986808 Gtype b'+1:lemma:ph5'
1.982154 Temp b'-1:lemma:43'
1.979758 Gtype b'+1:lemma:aerobic'
1.979385 Supp b'lemma:Leu'
1.977544 Med b'+1:lemma:minimal'
1.972140 Substrain b'+1:lemma:phtpg'
1.966671 O b'lemma:Fur'
1.952996 Technique b'-1:lemma:_'
1.947488 Supp b'lemma:iptg'
1.947369 O b'+1:lemma:43'
1.947148 Temp b'lemma:43'
1.946657 Supp b'-1:lemma:\xc2\xb5m'
1.946349 Med b'+1:lemma:+'
1.946188 Phase b'lemma:phase'
1.940761 Gtype b'lemma:pk4854'
1.924723 O b'lemma:genotype/variation'
1.911694 Gtype b'+1:lemma:_'
1.910805 Temp b'-1:lemma:\xcf\x8332'
1.907106 Supp b'lemma:Adenine'
1.906722 Technique b'+1:lemma:chip-exo'
1.906375 Anti b'lemma:anti-rpos'
1.904230 Air b'+1:lemma:at'
1.903056 Gversion b'+1:lemma:000913'
1.901487 Med b'lemma:glucose'
1.889441 O b'lemma:chip-fnr'
1.887601 Gtype b'-1:lemma:nsrr'
1.878766 O b'postag:DT'
1.873733 pH b'lemma:.5'
1.873733 pH b'-1:lemma:ph5'
1.865998 O b'lemma:culture'
1.855758 O b'lemma:for'
1.853813 Gtype b'-1:lemma:rpob'
1.853644 O b'lemma:soxs'
1.853644 O b'lemma:soxr'
1.846904 Gtype b'-1:lemma::'
1.845474 Temp b'-1:lemma:sample'
1.841250 Air b'lemma:anerobically'
1.838140 Air b'-1:postag:CD'
1.831417 Med b'-1:lemma:ml'
1.825450 Phase b'+1:lemma:for'
1.820952 O b'-1:lemma:0.3'
1.816339 Air b'-1:postag::'
1.812600 O b'postag:CC'
1.810282 Supp b'+1:lemma:respiratory'
1.805085 Supp b'lemma:methanol'
1.803745 Supp b'lemma:20'
1.782276 Med b'lemma:L'
1.782276 Med b'+1:lemma:broth'
1.779488 O b'lemma:pt7'
1.771701 OD b'-1:lemma:~'
Top negative:
-0.098597 OD b'+1:lemma:in'
-0.100809 O b'+1:lemma:pahse'
-0.103942 Gtype b'-1:lemma:,'
-0.103942 Gtype b'-1:postag:,'
-0.109064 Supp b'+1:postag:IN'
-0.116184 O b'-1:lemma:the'
-0.120961 Phase b'-1:postag:NN'
-0.125524 Air b'-1:postag:CC'
-0.130098 O b'+1:lemma:sample'
-0.133275 Med b'lemma:-lrb-'
-0.133905 OD b'+1:lemma:0.4'
-0.137686 O b'-1:lemma:minimal'
-0.138574 Air b'-1:postag:-RRB-'
-0.140110 Air b'-1:lemma:-rrb-'
-0.141778 Med b'postag:-LRB-'
-0.148667 Med b'-1:postag:NN'
-0.152662 O b'-1:postag:IN'
-0.152746 O b'lemma:medium'
-0.153545 O b'lemma:n2'
-0.154206 Air b'postag:CC'
-0.163582 O b'-1:postag:VBN'
-0.164052 O b'-1:lemma:n2'
-0.167774 Gtype b'+1:lemma:cra'
-0.171535 O b'-1:lemma:with'
-0.177101 Gtype b'+1:lemma:-lrb-'
-0.181072 Gtype b'postag:CD'
-0.190005 O b'lemma:pahse'
-0.191122 Gtype b'+1:lemma:a'
-0.193246 O b'+1:lemma:_'
-0.200535 OD b'+1:lemma:mid-log'
-0.201151 O b'lemma:co2'
-0.203533 O b'-1:lemma:-lrb-'
-0.203756 O b'+1:lemma:phase'
-0.207632 O b'-1:lemma:e.'
-0.208480 O b'-1:lemma:purify'
-0.211803 O b'lemma:grow'
-0.213447 O b'+1:lemma:delta'
-0.215349 Air b'postag:CD'
-0.217993 O b'+1:lemma:-rrb-'
-0.219170 Supp b'lemma:and'
-0.221278 O b'lemma:10'
-0.224277 O b'+1:lemma:.'
-0.224277 O b'+1:postag:.'
-0.226140 O b'-1:lemma:fresh'
-0.227840 O b'+1:lemma:mg1655'
-0.233692 O b'-1:postag:VBP'
-0.243094 O b'+1:lemma:-lcb-'
-0.244688 O b'lemma:30'
-0.248768 Med b'-1:postag:CD'
-0.248953 O b'lemma:8'
-0.252377 O b'+1:lemma:%'
-0.257481 O b'lemma:minimal'
-0.257830 Technique b'-1:lemma::'
-0.259100 Gversion b'+1:postag:NN'
-0.259164 O b'-1:postag:-LRB-'
-0.259192 Med b'+1:postag:NN'
-0.265097 O b'+1:lemma:strain'
-0.270448 O b'-1:lemma:mm'
-0.271962 O b'+1:lemma:0.4'
-0.272630 O b'-1:lemma:chip-exo'
-0.277009 OD b'+1:postag:CD'
-0.278470 O b'+1:lemma:minimal'
-0.286163 O b'+1:lemma:antibody'
-0.294848 Gtype b'-1:postag:CD'
-0.294973 O b'+1:lemma:from'
-0.303885 O b'-1:lemma:grow'
-0.306933 O b'lemma:e.'
-0.309307 Air b'-1:lemma:or'
-0.312327 O b'postag:RB'
-0.312620 OD b'+1:postag:CC'
-0.316727 Anti b'+1:postag:JJ'
-0.319089 O b'-1:lemma:mid-log'
-0.321702 O b'-1:lemma:um'
-0.321702 O b'+1:lemma:paraquat'
-0.322815 O b'-1:lemma:0.1'
-0.325506 Supp b'+1:postag:VBN'
-0.327089 Med b'+1:postag:NNS'
-0.329088 Supp b'-1:lemma:%'
-0.335665 Med b'postag:CD'
-0.345089 O b'+1:lemma:shake'
-0.346024 O b'lemma:nacl'
-0.346568 Med b'-1:postag:IN'
-0.349877 O b'-1:lemma:iptg'
-0.351934 Supp b'-1:postag:VBG'
-0.361114 Phase b'-1:lemma:at'
-0.363308 Gtype b'+1:lemma:b'
-0.369166 O b'+1:lemma:b'
-0.370353 O b'+1:postag:IN'
-0.375482 O b'+1:lemma:rep1'
-0.382649 OD b'postag:JJ'
-0.389625 O b'-1:lemma:rifampicin'
-0.390229 O b'-1:lemma:20'
-0.392434 O b'+1:lemma:300'
-0.392765 O b'-1:lemma:od600'
-0.396162 O b'lemma:\xc2\xb0c'
-0.397112 Temp b'postag:JJ'
-0.398067 O b'+1:postag:-RRB-'
-0.412750 O b'-1:lemma:affinity'
-0.416189 O b'+1:lemma:dissolve'
-0.417913 O b'+1:lemma:cell'
-0.426120 O b'-1:lemma:from'
-0.472958 O b'-1:lemma:30'
-0.483340 Technique b'-1:postag::'
-0.483753 Temp b'+1:lemma:to'
-0.483753 Temp b'+1:postag:TO'
-0.484495 O b'+1:lemma:c'
-0.487031 Supp b'+1:lemma:glucose'
-0.495206 Gtype b'lemma:_'
-0.505255 Supp b'postag:CC'
-0.505610 O b'-1:lemma:cra'
-0.512805 O b'lemma:dissolve'
-0.519407 O b'lemma:glucose'
-0.530802 O b'+1:lemma:Aerobic'
-0.536055 O b'lemma:mg1655'
-0.538193 O b'+1:lemma:arginine'
-0.540056 O b'lemma:dpd'
-0.543308 O b'+1:lemma:until'
-0.553627 pH b'postag:NN'
-0.557904 O b'-1:lemma:until'
-0.560304 OD b'+1:postag:NN'
-0.577595 O b'-1:lemma:g/l'
-0.579159 OD b'+1:lemma:and'
-0.595749 O b'lemma:phase'
-0.611587 Gtype b'+1:lemma:\xe2\x88\x86'
-0.614217 Gtype b'-1:postag:SYM'
-0.624715 O b'lemma:purify'
-0.636366 O b'lemma:150'
-0.636366 O b'+1:lemma:mg/ml'
-0.638397 Gtype b'-1:postag:DT'
-0.657927 O b'lemma:m63'
-0.664969 Gtype b'lemma:delta'
-0.666049 OD b'lemma:-lrb-'
-0.682691 Supp b'+1:lemma:rifampicin'
-0.692119 Temp b'-1:lemma:\xc2\xb0c'
-0.706829 O b'lemma:lb'
-0.708511 Med b'+1:postag:IN'
-0.711784 O b'-1:lemma:~'
-0.714372 O b'+1:lemma:0.3'
-0.716136 O b'+1:postag:NNS'
-0.736106 O b'+1:lemma:\xc2\xb0c'
-0.738116 Phase b'postag:JJ'
-0.744781 O b'-1:lemma:1'
-0.764657 OD b'postag:-LRB-'
-0.767869 Temp b'postag:NN'
-0.772655 O b'lemma:of'
-0.774528 O b'-1:lemma:\xe2\x88\x86'
-0.806745 O b'+1:lemma:fecl2'
-0.808726 O b'lemma:anaerobically'
-0.817926 O b'-1:lemma:0.2'
-0.828109 O b'lemma:media'
-0.860850 Phase b'-1:postag:JJ'
-0.869705 Air b'-1:postag:JJ'
-0.869779 Anti b'+1:lemma:anti-fur'
-0.913352 O b'lemma:0.3'
-0.926265 O b'lemma:20'
-0.966551 O b'+1:lemma:in'
-0.967999 O b'-1:lemma:co2'
-0.983473 O b'lemma:\xe2\x88\x86'
-1.005883 O b'lemma:0.1'
-1.012563 O b'+1:lemma:supplement'
-1.015961 O b'lemma:2h'
-1.015961 O b'-1:lemma:additional'
-1.030442 O b'lemma:fecl2'
-1.035342 Supp b'+1:lemma:acetate'
-1.055745 O b'+1:lemma:g/l'
-1.058371 O b'+1:lemma:at'
-1.065986 O b'+1:postag:VBG'
-1.108278 O b'lemma:anaerobic'
-1.137604 O b'-1:lemma:ompr'
-1.149433 O b'-1:postag:VBG'
-1.157369 O b'-1:lemma:dissolve'
-1.157369 O b'+1:lemma:methanol'
-1.161744 O b'lemma:0.2'
-1.176749 O b'lemma:mid-log'
-1.210434 O b'lemma:\xce\xb4fur'
-1.224092 O b'-1:lemma:sample'
-1.241862 O b'-1:lemma:ml'
-1.249714 O b'lemma:37'
-1.287855 O b'postag:VBP'
-1.290513 O b'lemma:od600'
-1.322257 O b'lemma:k-12'
-1.332061 O b'-1:lemma:rpob'
-1.387093 Supp b'postag:JJ'
-1.418093 O b'-1:postag::'
-1.520563 Anti b'postag:NNP'
-1.552213 O b'-1:lemma:37'
-1.582655 O b'lemma:methanol'
-1.634214 Air b'+1:postag:JJ'
-1.656961 O b'-1:lemma:2'
-1.660038 O b'-1:lemma:nsrr'
-1.778068 O b'-1:lemma:IP'
-1.782125 O b'lemma:rifampicin'
-1.784846 Air b'postag:NN'
-1.792093 O b'+1:lemma:hour'
-1.833447 O b'+1:lemma:+'
-1.873023 O b'lemma:wt'
-1.948439 O b'+1:lemma:2'
-2.447797 O b'+1:lemma:1'
-2.955767 O b'-1:lemma:_'
-3.288596 O b'-1:lemma::'
********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70.txt
best params:{'c1': 0.12296384618516742, 'c2': 0.001984598547992556}
best CV score:0.7223961938319273
model size: 0.07M
Flat F1: 0.6328175528971997
precision recall f1-score support
OD 1.000 0.211 0.348 57
Sample 0.000 0.000 0.000 0
Technique 0.000 0.000 0.000 1
Med 1.000 0.933 0.966 30
Temp 1.000 0.615 0.762 13
Serie 0.000 0.000 0.000 0
Vess 0.000 0.000 0.000 0
Agit 0.000 0.000 0.000 7
Phase 0.750 0.923 0.828 13
Air 0.000 0.000 0.000 0
Anti 1.000 0.778 0.875 18
Strain 0.000 0.000 0.000 0
Gtype 0.884 0.551 0.679 69
Supp 0.582 0.629 0.605 62
Gversion 0.750 1.000 0.857 6
avg / total 0.831 0.569 0.633 276
Top likely transitions:
OD -> OD 6.108207
Supp -> Supp 5.784131
Gtype -> Gtype 5.685374
Med -> Med 5.675327
Temp -> Temp 5.658789
Anti -> Anti 5.031069
Gversion -> Gversion 4.774936
O -> O 4.746806
Phase -> Phase 3.575687
O -> Gtype 1.949659
OD -> Phase 1.047851
O -> Gversion 0.297969
O -> Supp 0.232142
O -> OD 0.059228
O -> Anti 0.035022
O -> Med 0.022142
Supp -> Phase -0.082451
Supp -> Med -0.113938
Gtype -> Anti -0.177348
Vess -> O -0.195425
Phase -> O -0.308432
Anti -> O -0.319054
Phase -> Supp -0.418345
O -> Technique -0.434100
Temp -> O -0.447292
Gtype -> O -0.546043
Supp -> O -0.756881
OD -> O -0.842201
Technique -> O -0.857966
Med -> O -0.892055
Substrain -> O -0.970661
O -> Phase -1.142533
Temp -> Med -1.246193
O -> Temp -1.298927
Phase -> OD -1.766899
Med -> Supp -2.805768
Top unlikely transitions:
OD -> OD 6.108207
Supp -> Supp 5.784131
Gtype -> Gtype 5.685374
Med -> Med 5.675327
Temp -> Temp 5.658789
Anti -> Anti 5.031069
Gversion -> Gversion 4.774936
O -> O 4.746806
Phase -> Phase 3.575687
O -> Gtype 1.949659
OD -> Phase 1.047851
O -> Gversion 0.297969
O -> Supp 0.232142
O -> OD 0.059228
O -> Anti 0.035022
O -> Med 0.022142
Supp -> Phase -0.082451
Supp -> Med -0.113938
Gtype -> Anti -0.177348
Vess -> O -0.195425
Phase -> O -0.308432
Anti -> O -0.319054
Phase -> Supp -0.418345
O -> Technique -0.434100
Temp -> O -0.447292
Gtype -> O -0.546043
Supp -> O -0.756881
OD -> O -0.842201
Technique -> O -0.857966
Med -> O -0.892055
Substrain -> O -0.970661
O -> Phase -1.142533
Temp -> Med -1.246193
O -> Temp -1.298927
Phase -> OD -1.766899
Med -> Supp -2.805768
Top positive:
9.769521 OD b'+1:lemma:stationary'
6.573116 Gtype b'-1:lemma:express'
6.473813 O b'lemma:at'
6.401320 Gtype b'+1:lemma:chip'
5.580269 Med b'word:MOPS'
5.580269 Med b'lemma:MOPS'
5.309599 Med b'-1:lemma:ml'
5.105098 Gtype b'+1:lemma:knock-out'
5.053371 Anti b'+1:lemma:antibody'
4.833626 O b'+1:lemma:until'
4.685736 Supp b'word:nitrate'
4.685736 Supp b'lemma:nitrate'
4.578724 Temp b'-1:lemma:sample'
4.338845 O b'+1:postag:VBP'
4.326050 Gversion b'word:NC'
4.326050 Gversion b'lemma:nc'
4.207716 O b'word:.'
4.207716 O b'lemma:.'
3.987856 O b'lemma:chip'
3.914979 Phase b'-1:lemma:mid-log'
3.836351 O b'+1:postag:NNP'
3.819222 O b'word:-'
3.819222 O b'lemma:-'
3.774330 Gtype b'-1:lemma:wild'
3.733417 Supp b'word:2h'
3.733417 Supp b'lemma:2h'
3.733417 Supp b'-1:lemma:additional'
3.729860 O b'word::'
3.729860 O b'lemma::'
3.704485 O b'-1:lemma:glucose'
3.673897 O b'-1:lemma:-'
3.584033 Phase b'word:mid-log'
3.584033 Phase b'lemma:mid-log'
3.580641 Gtype b'-1:lemma:k-12'
3.329333 Gtype b'word:Flag-tag'
3.329333 Gtype b'lemma:flag-tag'
3.329333 Gtype b'-1:lemma:c-terminal'
3.313956 O b'+1:lemma:coli'
3.198151 Supp b'-1:lemma:vol'
3.190691 O b'-1:lemma:lb'
3.168840 Supp b'-1:lemma:with'
3.134166 Gtype b'word:wild'
3.134166 Gtype b'lemma:wild'
3.092894 O b'word:K-12'
3.092894 O b'lemma:k-12'
3.060219 O b'word:MG1655'
3.060219 O b'lemma:mg1655'
3.020191 Supp b'+1:lemma:\xc2\xb5m'
2.959207 Gversion b'word:ASM584v2'
2.959207 Gversion b'lemma:asm584v2'
2.895464 Gversion b'word:000913'
2.895464 Gversion b'lemma:000913'
2.892382 Vess b'word:flask'
2.892382 Vess b'lemma:flask'
2.892382 Vess b'-1:lemma:warm'
2.889484 Temp b'+1:lemma:and'
2.864457 OD b'word:OD450'
2.864457 OD b'lemma:od450'
2.844361 O b'+1:lemma:od600'
2.760592 O b'word:Custom'
2.760592 O b'lemma:Custom'
2.760592 O b'+1:lemma:anti-fur'
2.749995 Supp b'-1:lemma:without'
2.744252 Phase b'word:exponential'
2.744252 Phase b'lemma:exponential'
2.724404 Phase b'word:stationary'
2.724404 Phase b'lemma:stationary'
2.704170 Supp b'word:glucose'
2.704170 Supp b'lemma:glucose'
2.702637 Med b'-1:lemma:LB'
2.698915 Med b'word:LB'
2.648788 O b'+1:lemma:fructose'
2.522068 Supp b'word:arginine'
2.522068 Supp b'lemma:arginine'
2.521702 O b'+1:lemma:0.2'
2.510135 Gtype b'-1:postag:VBG'
2.500086 Med b'word:L'
2.500086 Med b'lemma:L'
2.500086 Med b'+1:lemma:broth'
2.438147 Gversion b'-1:lemma:nc'
2.435933 O b'word:with'
2.435933 O b'lemma:with'
2.424051 OD b'word:OD600'
2.424051 OD b'lemma:od600'
2.397049 Gversion b'word:U00096'
2.397049 Gversion b'lemma:u00096'
2.397049 Gversion b'+1:lemma:.2'
2.393316 Temp b'-1:lemma:37'
2.384921 Med b'+1:lemma:g/l'
2.343273 O b'lemma:for'
2.287420 O b'-1:lemma:\xc2\xb0c'
2.277217 Supp b'word:acetate'
2.277217 Supp b'lemma:acetate'
2.240391 Gtype b'word:WT'
2.227767 O b'word:Cells'
2.223138 Temp b'+1:lemma:\xc2\xb0c'
2.207530 Gtype b'word:PK4854'
2.207530 Gtype b'lemma:pk4854'
2.204777 Technique b'word:RNA-Seq'
2.200781 Anti b'-1:lemma:polymerase'
2.180743 O b'-1:lemma:phase'
2.168855 Supp b'+1:lemma:at'
2.168107 Supp b'+1:lemma:arginine'
2.152384 O b'word:Crosslink'
2.152384 O b'lemma:Crosslink'
2.151825 O b'word:for'
2.146611 Supp b'+1:lemma:hour'
2.145369 Phase b'+1:lemma:for'
2.130614 Supp b'+1:lemma:and'
2.127595 Temp b'word:\xc2\xb0C'
2.127595 Temp b'lemma:\xc2\xb0c'
2.118493 Med b'word:broth'
2.118493 Med b'lemma:broth'
2.118493 Med b'-1:lemma:L'
2.100174 Supp b'word:Adenine'
2.100174 Supp b'lemma:Adenine'
2.099073 Supp b'word:hours'
2.099073 Supp b'lemma:hour'
2.091461 Technique b'lemma:rna-seq'
2.081270 O b'+1:lemma:0.4'
2.069166 OD b'word:0.3'
2.069166 OD b'lemma:0.3'
2.025934 O b'-1:lemma:tag'
2.016740 Med b'word:M63'
2.016740 Med b'lemma:m63'
1.951269 Supp b'-1:lemma:final'
1.951255 Anti b'+1:lemma:polyclonal'
1.940092 O b'+1:postag:CD'
1.937643 O b'word:supplemented'
1.937643 O b'lemma:supplement'
1.928437 Gtype b'word:oxyR-8myc'
1.928437 Gtype b'lemma:oxyr-8myc'
1.925371 Gtype b'word:soxR-8myc'
1.925371 Gtype b'lemma:soxr-8myc'
1.905981 Supp b'-1:lemma:+'
1.904247 Gversion b'word:.2'
1.904247 Gversion b'lemma:.2'
1.904247 Gversion b'-1:lemma:u00096'
1.895301 Supp b'-1:lemma::'
1.888517 Med b'+1:lemma:minimal'
1.888285 O b'+1:lemma:nitrate'
1.887992 O b'+1:lemma:anaerobic'
1.887095 Phase b'word:phase'
1.887095 Phase b'lemma:phase'
1.873844 Anti b'word:\xcf\x8332'
1.873844 Anti b'lemma:\xcf\x8332'
1.858813 Med b'lemma:LB'
1.856133 O b'-1:lemma:-80'
1.850543 Supp b'+1:lemma:be'
1.822229 Supp b'word:leucine'
1.822229 Supp b'lemma:leucine'
1.818630 O b'-1:lemma:flag-tag'
1.810937 O b'-1:lemma:_'
1.808829 Supp b'word:fructose'
1.808829 Supp b'lemma:fructose'
1.805654 OD b'word:A'
1.799136 Gversion b'lemma:chip-seq'
1.792100 Phase b'-1:lemma:until'
1.787880 Anti b'-1:lemma:monoclonal'
1.786790 Anti b'word:anti-myc'
1.786790 Anti b'lemma:anti-myc'
1.784685 Substrain b'word:MG1655star'
1.784685 Substrain b'lemma:mg1655star'
1.778678 Technique b'lemma:chip-seq'
1.778353 O b'word:<Air>'
1.751251 Supp b'-1:lemma:1mm'
1.746035 Supp b'+1:lemma:1/100'
1.733606 Anti b'+1:lemma:from'
1.729502 Technique b'word:ChIP-Seq'
1.725373 O b'+1:lemma:mid-log'
1.712485 Gversion b'word:ChIP-Seq'
1.709357 O b'-1:postag:NNS'
1.693666 O b'word:-RRB-'
1.693666 O b'lemma:-rrb-'
1.656579 Supp b'word:rifampicin'
1.656579 Supp b'lemma:rifampicin'
1.654463 O b'lemma:to'
1.646916 Anti b'word:anti-RpoB'
1.646916 Anti b'lemma:anti-rpob'
1.641270 Vess b'-1:postag:VBN'
1.634955 Anti b'word:SeqA'
1.634955 Anti b'lemma:seqa'
1.626876 Med b'+1:lemma:-lrb-'
1.621826 O b'lemma:<air>'
1.616807 Supp b'word:tryptophan'
1.616807 Supp b'lemma:tryptophan'
1.616807 Supp b'-1:lemma:mg/l'
1.584459 O b'lemma:anaerobic'
1.571612 Med b'word:medium'
1.571612 Med b'lemma:medium'
1.550300 Vess b'+1:lemma:at'
1.549343 O b'word:B'
1.547972 Gtype b'-1:lemma:\xe2\x88\x86'
1.546575 OD b'+1:lemma:oxyr-8myc'
1.546406 O b'+1:lemma:aerobic'
1.528557 Supp b'+1:lemma:300'
1.505854 Temp b'-1:lemma:at'
1.482950 Supp b'-1:postag:IN'
1.477298 Med b'-1:lemma:glucose'
1.476212 O b'-1:lemma:media'
Top negative:
-0.033522 O b'lemma:20'
-0.038038 Anti b'isupper()'
-0.038347 OD b'isupper()'
-0.045438 O b'word:phosphate'
-0.045438 O b'lemma:phosphate'
-0.046287 O b'word:LB'
-0.047486 Gtype b'-1:lemma:,'
-0.047486 Gtype b'-1:postag:,'
-0.047973 O b'+1:lemma:culture'
-0.048635 Med b'-1:postag:NN'
-0.048786 Supp b'-1:lemma:,'
-0.048786 Supp b'-1:postag:,'
-0.049214 Temp b'-1:postag:NN'
-0.055607 Supp b'word:vol'
-0.055607 Supp b'lemma:vol'
-0.055607 Supp b'-1:lemma:1/100'
-0.057967 O b'word:150'
-0.057967 O b'lemma:150'
-0.057967 O b'+1:lemma:mg/ml'
-0.065780 Med b'+1:lemma:media'
-0.067419 O b'-1:lemma:rifampicin'
-0.068390 O b'+1:lemma:medium'
-0.069566 Gtype b'+1:postag:JJ'
-0.069740 Supp b'word:10'
-0.069740 Supp b'lemma:10'
-0.072097 Supp b'-1:lemma:;'
-0.074848 Supp b'-1:lemma:.'
-0.074848 Supp b'-1:postag:.'
-0.075753 O b'word:min'
-0.075753 O b'lemma:min'
-0.076584 Supp b'-1:lemma:-lrb-'
-0.079109 Supp b'word:uM'
-0.079109 Supp b'lemma:um'
-0.079109 Supp b'-1:lemma:250'
-0.083627 O b'-1:lemma:m9'
-0.084086 Anti b'-1:postag:NN'
-0.084792 Supp b'-1:postag:-LRB-'
-0.085223 Med b'-1:postag:IN'
-0.090978 O b'-1:postag:VBN'
-0.091287 Supp b'-1:lemma:10'
-0.093086 Gtype b'isupper()'
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['O', 'O', 'Anti', 'Anti', 'Anti', 'Anti']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['Med', 'Med', 'Med', 'Med', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'Technique']
['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', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O', 'Substrain']
['O', 'O', 'O', 'Med', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp']
['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']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp']
['O', 'O', 'O', 'O', 'O']
['O', 'O', 'Gtype']
['O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', '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', 'O', 'O', 'O']
['O', 'O', 'Gtype', 'Gtype', 'Gtype']
['O', 'O', 'O']
['O', 'O', 'O', 'O', 'O']
['O', 'O', 'Anti', 'Anti', 'Anti']
['O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', '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', 'Anti', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
['O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O']
['O', 'O', 'Gtype']
['O', 'O', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
['Substrain', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
['O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'Gtype', 'O', 'O']
['O', 'O', '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', 'Phase', 'Phase', 'O', 'OD', 'OD', 'OD', 'OD', 'O', 'O', 'Med', 'Med', 'Med', 'Med', 'O', 'Supp', 'Supp', 'Supp', 'O']
['O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'O', 'Anti']
['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']
['O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', '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', 'Phase', 'Phase', 'O', 'OD', 'OD', 'OD', 'OD', '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', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'Gtype']
['O', 'O', 'O', 'Anti', 'Anti', 'Anti', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'Anti', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
['Substrain', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype', 'Gtype']
['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'Gtype']
['O', 'O', 'O', 'Anti', 'Anti', 'Anti', 'Anti']
['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']
['OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD', 'OD']
['O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'Anti']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'Gtype']
['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'Gtype']
['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', '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']
['O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'Med']
['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', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['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']
['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']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', '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', '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']
['O', 'O', 'Gtype']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O']
['O', 'O', 'Anti', 'Anti', 'Anti', 'Anti']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', 'O', 'O']
['O', 'O', 'O', 'O']
['O', 'O', 'O', 'O', 'O', 'O', 'O']
['Med', 'Med', 'Med', 'Med', 'O', 'O', 'O', 'O', 'O', 'O', 'Temp', 'Temp', 'Temp', 'O', 'O', 'Agit', 'Agit', 'Agit', 'Agit', 'Agit', 'Agit', 'Agit']
cd /home/kevinml/automatic-extraction-growth-conditions/data-sets/tagged-xml-data
# Orgiginal files
#cd /home/egaytan/automatic-extraction-growth-conditions/data-sets/report-manually-tagged-gcs/
# Re-tagged
cd /home/egaytan/automatic-extraction-growth-conditions/data-sets/tagged-xml-data/
echo
echo
echo
......@@ -18,9 +24,9 @@ echo
echo
echo "Filter all paragraphs with tags..."
echo "Add sentence-end-tag PGCGROWTHCONDITIONS..."
grep -E "<[^<]*>" * | grep -E '!'| cut -f2 -d'='|sort|uniq|awk '{ print $_" PGCGROWTHCONDITIONS"; }' > /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt
grep -E "<[^<]*>" * | grep -E '!'| cut -f2 -d'='|sort|uniq|awk '{ print $_" PGCGROWTHCONDITIONS"; }' > /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt
echo
echo "Number of total tag sentences: "$(wc /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt -l);
echo "Number of total tag sentences: "$(wc /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt -l);
echo
echo
echo "Saving file: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt";
echo "Saving file: /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt";
......
......@@ -4,8 +4,8 @@ echo "==============================Run CoreNLP=================================
echo
echo
input="/home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt";
output="/home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/";
input="/home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt";
output="/home/egaytan/automatic-extraction-growth-conditions/CoreNLP/output/";
echo "input file: "$input;
echo
echo "output directory: "$output;
......
affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_1.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_2.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-arcA</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_3.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_1.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_2.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>delta-fnr</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_3.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_1.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_2.CEL PGCGROWTHCONDITIONS
affyexp_<Gtype>wt</Gtype>_<Supp>glucose</Supp>_<Supp>NH4Cl</Supp>_<Supp>NO3</Supp>_3.CEL PGCGROWTHCONDITIONS
agent: <Supp>DPD and rifampicin</Supp> PGCGROWTHCONDITIONS
agent: <Supp>DPD</Supp> PGCGROWTHCONDITIONS
agent: <Supp>Fe and rifampicin</Supp> PGCGROWTHCONDITIONS
agent: <Supp>Fe</Supp> PGCGROWTHCONDITIONS
<Air>Aerobic</Air> cultures PGCGROWTHCONDITIONS
<Air>Anaerobic</Air> cultures PGCGROWTHCONDITIONS
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
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
antibody: <Anti>9E10 Myc tag</Anti> antibody PGCGROWTHCONDITIONS
antibody: <Anti>Affinity Purified FNR antibody</Anti> PGCGROWTHCONDITIONS
antibody: <Anti>anti-FLAG mAb</Anti> PGCGROWTHCONDITIONS
antibody: <Anti>Pre-cleared FNR antibody</Anti> PGCGROWTHCONDITIONS
antibody: <Anti>Pre-cleared H-NS polyclonal antibody</Anti> PGCGROWTHCONDITIONS
antibody: <Anti>Pre-cleared IHF polyclonal antibody</Anti> PGCGROWTHCONDITIONS
antibody: <Anti>RNA Polymerase ß monoclonal antibody</Anti> from NeoClone (W0002) PGCGROWTHCONDITIONS
ArgR_<Supp>Arginine</Supp>_1 PGCGROWTHCONDITIONS
ArgR_<Supp>Arginine</Supp>_2 PGCGROWTHCONDITIONS
ArgR_<Supp>NH4Cl</Supp>_1 PGCGROWTHCONDITIONS
ArgR_<Supp>NH4Cl</Supp>_2 PGCGROWTHCONDITIONS
At <OD>OD450 PGCGROWTHCONDITIONS
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
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
carbon source: <Supp>acetate</Supp> PGCGROWTHCONDITIONS
carbon source: <Supp>fructose</Supp> PGCGROWTHCONDITIONS
carbon source: <Supp>glucose</Supp> PGCGROWTHCONDITIONS
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
chip antibody: <Anti>9E10 Myc tag</Anti> antibody PGCGROWTHCONDITIONS
chip antibody: <Anti>anti-myc</Anti> PGCGROWTHCONDITIONS
chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207) PGCGROWTHCONDITIONS
chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002) PGCGROWTHCONDITIONS
chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766) PGCGROWTHCONDITIONS
chip antibody: <Anti>anti-RpoS</Anti> (neoclone, WP009) PGCGROWTHCONDITIONS
chip antibody: <Anti>biotin conjugated anti-c-myc antibody</Anti> PGCGROWTHCONDITIONS
chip antibody: <Anti>none</Anti> PGCGROWTHCONDITIONS
chip antibody: <Anti>RNA polymerase subunit β</Anti> PGCGROWTHCONDITIONS
chip antibody: <Anti>SeqA</Anti> PGCGROWTHCONDITIONS
chip antibody: <Anti>σ32</Anti> PGCGROWTHCONDITIONS
chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti> PGCGROWTHCONDITIONS
chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1 PGCGROWTHCONDITIONS
chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2 PGCGROWTHCONDITIONS
chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3 PGCGROWTHCONDITIONS
chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_1 PGCGROWTHCONDITIONS
chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_2 PGCGROWTHCONDITIONS
chip-ArcA_<Gtype>ArcA8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_3 PGCGROWTHCONDITIONS
ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters -S PGCGROWTHCONDITIONS
ChIP-exo reads were aligned to the <Gversion>NC_000913 </Gversion>genome reference sequence using using bowtie v1.0.0 with parameters -S PGCGROWTHCONDITIONS
chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_1 PGCGROWTHCONDITIONS
chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_2 PGCGROWTHCONDITIONS
chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Air>anaerobic</Air>_3 PGCGROWTHCONDITIONS
chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_1 PGCGROWTHCONDITIONS
chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_2 PGCGROWTHCONDITIONS
chip-Fnr_<Gtype>Fnr8myc</Gtype>_<Supp>glucose</Supp>_<Supp>NH4CL</Supp>_<Supp>NO3</Supp>_3 PGCGROWTHCONDITIONS
Cra <Supp>acetate</Supp> 1 PGCGROWTHCONDITIONS
Cra <Supp>acetate</Supp> 2 PGCGROWTHCONDITIONS
Cra <Supp>fructose</Supp> 1 PGCGROWTHCONDITIONS
Cra <Supp>fructose</Supp> 2 PGCGROWTHCONDITIONS
Cra <Supp>glucose</Supp> 1 PGCGROWTHCONDITIONS
Cra <Supp>glucose</Supp> 2 PGCGROWTHCONDITIONS
CsiR_<Technique>ChIPSeq</Technique> PGCGROWTHCONDITIONS
CsiR_<Technique>RNASeq</Technique> PGCGROWTHCONDITIONS
culture condition: <Air>Aerobic</Air> cultures PGCGROWTHCONDITIONS
culture condition: <Air>Anaerobic</Air> cultures PGCGROWTHCONDITIONS
culture condition: <Air>anaerobic</Air> fermentive condition PGCGROWTHCONDITIONS
culture condition: <Supp>nitrate</Supp> respiratory condition PGCGROWTHCONDITIONS
cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% acetate</Supp> PGCGROWTHCONDITIONS
cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% fructose</Supp> PGCGROWTHCONDITIONS
cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp> PGCGROWTHCONDITIONS
Cultures grown in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp> PGCGROWTHCONDITIONS
Ecoli_<Gtype>dFNR</Gtype>_rep1_<Air>anaerobic</Air> PGCGROWTHCONDITIONS
Ecoli_<Gtype>dFNR</Gtype>_rep2_<Air>anaerobic</Air> PGCGROWTHCONDITIONS
Ecoli_<Gtype>wild-type</Gtype>_rep1_<Air>anaerobic</Air> PGCGROWTHCONDITIONS
Ecoli_<Gtype>wild-type</Gtype>_rep2_<Air>anaerobic</Air> PGCGROWTHCONDITIONS
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
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
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
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
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
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
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
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
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
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
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
E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 PGCGROWTHCONDITIONS
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
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
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
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
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
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
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
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
Escherichia coli MG1655 K-12 <Gtype>dFNR (PK4854)</Gtype> PGCGROWTHCONDITIONS
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
FNR - <Air>Anaerobic</Air> - A PGCGROWTHCONDITIONS
FNR - <Air>Anaerobic</Air> - Affinity Purified - A PGCGROWTHCONDITIONS
FNR - <Air>Anaerobic</Air> - Affinity Purified - B PGCGROWTHCONDITIONS
FNR - <Air>Anaerobic</Air> - B PGCGROWTHCONDITIONS
FNR - <Air>Anaerobic</Air> - C PGCGROWTHCONDITIONS
FNR - <Gtype>∆hns∆stpA</Gtype> A PGCGROWTHCONDITIONS
FNR - <Gtype>∆hns∆stpA</Gtype> B PGCGROWTHCONDITIONS
Fur IP <Technique>ChIP-Seq</Technique> <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
Fur IP <Technique>ChIP-Seq</Technique> <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
Fur IP <Technique>ChIP-Seq</Technique> <Air>Aerobic</Air> C PGCGROWTHCONDITIONS
Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air> C PGCGROWTHCONDITIONS
Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air>, <Supp>Iron</Supp> Deficient A PGCGROWTHCONDITIONS
Fur IP <Technique>ChIP-Seq</Technique> <Air>Anaerobic</Air>, <Supp>Iron</Supp> Deficient B PGCGROWTHCONDITIONS
Fur with <Supp>DPD</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
Fur with <Supp>DPD</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
Fur with <Supp>Fe</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
Fur with <Supp>Fe</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion> PGCGROWTHCONDITIONS
Genome_build: <Gversion>ASM584v2</Gversion> PGCGROWTHCONDITIONS
Genome_build: <Gversion>NC_000913.2</Gversion> PGCGROWTHCONDITIONS
Genome_build: <Gversion>NC_000913</Gversion> PGCGROWTHCONDITIONS
Genome_build: <Gversion>U00096.2</Gversion> (GenBank) PGCGROWTHCONDITIONS
genotype: delta-<Gtype>cra Knock-out strain</Gtype> PGCGROWTHCONDITIONS
genotype: delta-<Gtype>crp Knock-out strain</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>ArgR-8myc</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>gadE-8myc</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>gadW-8myc</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>gadX-8myc</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>Lrp-8myc</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>ompR-8myc</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>ompR deletion mutant</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>PurR-8myc</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>TrpR-8myc</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>wildtype</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>Wildtype</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
genotype: <Gtype>ΔseqA</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>Combined input</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>cra-8myc-tagged</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>delta_cra</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>delta-gadE</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>delta-gadW</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>delta-gadX</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>delta-oxyR</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>delta-soxR</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>delta-soxS</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>{delta}tonB, {delta}feoA, {delta}zupT K12</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>fur-8myc</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>lacking the small RNA RyhB</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>lacking the transcription factor Fur and the small RNA RyhB</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>oxyR-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
genotype/variation: <Gtype>soxR-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
genotype/variation: <Gtype>soxS-8myc</Gtype>-tagged PGCGROWTHCONDITIONS
genotype/variation: <Gtype>wild type</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>Wild-type</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>ΔarcA</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>Δfnr</Gtype> PGCGROWTHCONDITIONS
genotype/variation: <Gtype>Δfur</Gtype> PGCGROWTHCONDITIONS
genotype/variation: harboring <Gtype>ArcA-8myc</Gtype> PGCGROWTHCONDITIONS
genotype/variation: harboring <Gtype>Fnr-8myc</Gtype> PGCGROWTHCONDITIONS
genoype: <Gtype>dFNR</Gtype> PGCGROWTHCONDITIONS
genoype: <Gtype>Wild-Type</Gtype> PGCGROWTHCONDITIONS
growth condition: <Air>Aerobic</Air> PGCGROWTHCONDITIONS
growth condition: <Air>anaerobic</Air> PGCGROWTHCONDITIONS
growth condition: <Air>Anaerobic</Air> PGCGROWTHCONDITIONS
growth condition: <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
growth condition: <Supp>4 µM IPTG</Supp> PGCGROWTHCONDITIONS
growth condition: <Supp>8 µM IPTG</Supp> PGCGROWTHCONDITIONS
growth condition: <Supp>Adenine</Supp> PGCGROWTHCONDITIONS
growth condition: <Supp>glucose</Supp> PGCGROWTHCONDITIONS
growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp> PGCGROWTHCONDITIONS
growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>1 µM FeSO4</Supp> PGCGROWTHCONDITIONS
growth phase: <Phase>exponential</Phase> PGCGROWTHCONDITIONS
growth phase: <Phase>mid-log</Phase> PGCGROWTHCONDITIONS
growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 PGCGROWTHCONDITIONS
growth phase: <Phase>stationary</Phase> PGCGROWTHCONDITIONS
<Gtype>∆fnr</Gtype> - <Air>Anaeroibc</Air> PGCGROWTHCONDITIONS
<Gtype>∆fnr</Gtype> ChIP DNA from <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS
<Gtype>∆fur</Gtype> <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
<Gtype>∆fur</Gtype> <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
<Gtype>∆fur</Gtype> <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
<Gtype>∆fur</Gtype> <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
<Gtype>∆fur</Gtype> <Air>Anaerobic</Air> [IP vs nput] PGCGROWTHCONDITIONS
<Gtype>∆fur ∆ryhB</Gtype> <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
<Gtype>∆fur ∆ryhB</Gtype> <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
<Gtype>∆fur ∆ryhB</Gtype> <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
<Gtype>∆fur ∆ryhB</Gtype> <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
<Gtype>NsrR_Flagtag</Gtype>_rep1 PGCGROWTHCONDITIONS
<Gtype>NsrR_Flagtag</Gtype>_rep2 PGCGROWTHCONDITIONS
<Gtype>NsrR_Flagtag</Gtype>_rep3 PGCGROWTHCONDITIONS
<Gtype>Ptac::fnr</Gtype> - A - <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
<Gtype>Ptac::fnr</Gtype> - A - <Supp>4 µM IPTG</Supp> PGCGROWTHCONDITIONS
<Gtype>Ptac::fnr</Gtype> - A - <Supp>8 µM IPTG</Supp> PGCGROWTHCONDITIONS
<Gtype>Ptac::fnr</Gtype> - B - <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
<Gtype>Ptac::fnr</Gtype> - B - <Supp>4 µM IPTG</Supp> PGCGROWTHCONDITIONS
<Gtype>Ptac::fnr</Gtype> - B - <Supp>8 µM IPTG</Supp> PGCGROWTHCONDITIONS
<Gtype>Ptac::fnr</Gtype> - C - <Supp>16 µM IPTG</Supp> PGCGROWTHCONDITIONS
<Gtype>∆ryhB</Gtype> <Air>Aerobic</Air> PGCGROWTHCONDITIONS
<Gtype>∆ryhB</Gtype> <Air>Anaerobic</Air> PGCGROWTHCONDITIONS
<Gtype>Wild-type</Gtype> <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
<Gtype>Wild-type</Gtype> <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
<Gtype>Wild-type</Gtype> <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
<Gtype>Wild-type</Gtype> <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
<Gtype>Wild type</Gtype> control (0 min) PGCGROWTHCONDITIONS
<Gtype>Wild type</Gtype> control (10 min) PGCGROWTHCONDITIONS
<Gtype>Wild type</Gtype> control (20 min) PGCGROWTHCONDITIONS
<Gtype>Wild type</Gtype> control (2.5 min) PGCGROWTHCONDITIONS
<Gtype>Wild type</Gtype> control (5 min) PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>acetate</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>acetate</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>fructose</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>fructose</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>glucose</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>glucose</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>NaCl</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>NaCl</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype>_<Technique>ChIPSeq</Technique>_1 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype>_<Technique>ChIPSeq</Technique>_2 PGCGROWTHCONDITIONS
<Gtype>WT</Gtype>_<Technique>RNASeq</Technique> PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> with <Supp>DPD</Supp> 1 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> with <Supp>DPD</Supp> 2 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> with <Supp>Fe</Supp> 1 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
<Gtype>WT</Gtype> with <Supp>Fe</Supp> 2 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
<Gtype>Δcra</Gtype> <Supp>acetate</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>Δcra</Gtype> <Supp>acetate</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>Δcra</Gtype> <Supp>fructose</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>Δcra</Gtype> <Supp>fructose</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>Δcra</Gtype> <Supp>glucose</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>Δcra</Gtype> <Supp>glucose</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>Δfur</Gtype> with <Supp>DPD</Supp> 1 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
<Gtype>Δfur</Gtype> with <Supp>DPD</Supp> 2 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
<Gtype>Δfur</Gtype> with <Supp>Fe</Supp> 1 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
<Gtype>Δfur</Gtype> with <Supp>Fe</Supp> 2 <Technique>(RNA-seq)</Technique> PGCGROWTHCONDITIONS
<Gtype>ΔgadE</Gtype> <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
<Gtype>ΔgadE</Gtype> <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
<Gtype>ΔgadW</Gtype> <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
<Gtype>ΔgadW</Gtype> <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
<Gtype>ΔgadX</Gtype> <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
<Gtype>ΔgadX</Gtype> <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
<Gtype>ΔompR</Gtype> <Supp>NaCl</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>ΔompR</Gtype> <Supp>NaCl</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>ΔoxyR</Gtype> <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>ΔoxyR</Gtype> <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>ΔsoxR</Gtype> <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>ΔsoxR</Gtype> <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
<Gtype>ΔsoxS</Gtype> <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
<Gtype>ΔsoxS</Gtype> <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
<Gversion>ChIP-Seq</Gversion> PGCGROWTHCONDITIONS
HNS - <Air>Aerobic</Air> A PGCGROWTHCONDITIONS
HNS - <Air>Aerobic</Air> B PGCGROWTHCONDITIONS
HNS - <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
HNS - <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
IHF - <Air>Anaerobic</Air> A PGCGROWTHCONDITIONS
IHF - <Air>Anaerobic</Air> B PGCGROWTHCONDITIONS
Input <Technique>ChIP-Seq</Technique> PGCGROWTHCONDITIONS
ip antibody: <Anti>affinity purified anti-Fur antibody</Anti> PGCGROWTHCONDITIONS
library strategy: <Technique>ChIP-exo</Technique> PGCGROWTHCONDITIONS
Lrp_<Supp>Leu</Supp>_1 PGCGROWTHCONDITIONS
Lrp_<Supp>Leu</Supp>_2 PGCGROWTHCONDITIONS
Lrp_<Supp>Leu</Supp>_3 PGCGROWTHCONDITIONS
Lrp_<Supp>NH4Cl</Supp>_1 PGCGROWTHCONDITIONS
Lrp_<Supp>NH4Cl</Supp>_2 PGCGROWTHCONDITIONS
Lrp_<Supp>NH4Cl</Supp>_3 PGCGROWTHCONDITIONS
medium: <Med>LB</Med> PGCGROWTHCONDITIONS
medium: <Med>M63</Med> PGCGROWTHCONDITIONS
<Med>LB</Med> 0.4 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
<Med>LB</Med> 0.4 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
<Med>LB</Med> 0.4 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
<Med>LB</Med> 0.4 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
<Med>LB</Med> 0.4 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
<Med>LB</Med> 0.4 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B1 TEX neg L2 HS2 PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B1 TEX pos L2 HS2 PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B2 TEX neg L2 HS2 PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
<Med>LB</Med> 2.0 B2 TEX pos L2 HS2 PGCGROWTHCONDITIONS
<Med>M63</Med> 0.4 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
<Med>M63</Med> 0.4 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
<Med>M63</Med> 0.4 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
<Med>M63</Med> 0.4 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
<Med>M63</Med> 0.4 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
<Med>M63</Med> 0.4 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
<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
Nac_<Technique>ChIPSeq</Technique> PGCGROWTHCONDITIONS
Nac_<Technique>RNASeq</Technique> PGCGROWTHCONDITIONS
NtrC_<Technique>ChIPSeq</Technique> PGCGROWTHCONDITIONS
OmpR <Supp>NaCl</Supp> 1 PGCGROWTHCONDITIONS
OmpR <Supp>NaCl</Supp> 2 PGCGROWTHCONDITIONS
OmpR_<Technique>ChIPSeq</Technique> PGCGROWTHCONDITIONS
<Orgn>Escherichia coli K-12</Orgn> PGCGROWTHCONDITIONS
<Orgn>Escherichia coli</Orgn> PGCGROWTHCONDITIONS
<Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655star</Substrain> PGCGROWTHCONDITIONS
<Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain> PGCGROWTHCONDITIONS
<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn> PGCGROWTHCONDITIONS
<Orgn>Escherichia coli str. K-12 substr. MG1655star</Orgn> PGCGROWTHCONDITIONS
OxyR <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
OxyR <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
pT7_<Technique>ChIPSeq</Technique>_1 PGCGROWTHCONDITIONS
pT7_<Technique>ChIPSeq</Technique>_2 PGCGROWTHCONDITIONS
PurR_<Supp>Adenine</Supp>_1 PGCGROWTHCONDITIONS
PurR_<Supp>Adenine</Supp>_2 PGCGROWTHCONDITIONS
PurR_<Supp>glucose</Supp>_1 PGCGROWTHCONDITIONS
PurR_<Supp>glucose</Supp>_2 PGCGROWTHCONDITIONS
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
RpoB <Gtype>∆cra</Gtype> 1 PGCGROWTHCONDITIONS
RpoB <Gtype>∆cra</Gtype> 2 PGCGROWTHCONDITIONS
RpoB <Gtype>∆crp</Gtype> 1 PGCGROWTHCONDITIONS
RpoB <Gtype>∆crp</Gtype> 2 PGCGROWTHCONDITIONS
RpoB <Gtype>WT</Gtype> 1 PGCGROWTHCONDITIONS
RpoB <Gtype>WT</Gtype> 2 PGCGROWTHCONDITIONS
RpoB with <Supp>DPD</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
RpoB with <Supp>DPD</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
RpoB with <Supp>DPD</Supp> and <Supp>rifampicin</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
RpoB with <Supp>DPD</Supp> and <Supp>rifampicin</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
RpoB with <Supp>Fe</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
RpoB with <Supp>Fe</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
RpoB with <Supp>Fe</Supp> and <Supp>rifampicin</Supp> 1 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
RpoB with <Supp>Fe</Supp> and <Supp>rifampicin</Supp> 2 <Technique>(ChIP-exo)</Technique> PGCGROWTHCONDITIONS
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
SeqA new <Gtype>deltaSeqA</Gtype> PGCGROWTHCONDITIONS
SeqA old <Gtype>deltaSeqA</Gtype> PGCGROWTHCONDITIONS
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
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
SoxR <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
SoxR <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
SoxS <Supp>PQ</Supp> 1 PGCGROWTHCONDITIONS
SoxS <Supp>PQ</Supp> 2 PGCGROWTHCONDITIONS
ß - <Air>Aerobic</Air> - A PGCGROWTHCONDITIONS
ß - <Air>Aerobic</Air> - B PGCGROWTHCONDITIONS
ß - <Air>Anaerobic</Air> - A PGCGROWTHCONDITIONS
ß - <Air>Anaerobic</Air> - B PGCGROWTHCONDITIONS
strain: <Gtype>∆hns/∆stpA</Gtype> PGCGROWTHCONDITIONS
strain: <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS
strain: <Gtype>PK8263</Gtype> PGCGROWTHCONDITIONS
strain: MG1655 K-12 <Gtype>WT</Gtype> PGCGROWTHCONDITIONS
strain: <Orgn>K-12 MG1655</Orgn> PGCGROWTHCONDITIONS
strain: <Orgn>MG1655</Orgn> PGCGROWTHCONDITIONS
strain: <Strain>K-12</Strain> PGCGROWTHCONDITIONS
<Substrain>MG1655</Substrain> <Gtype>PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)</Gtype> PGCGROWTHCONDITIONS
<Substrain>MG1655</Substrain> <Gtype>PhtpG::lacZ delta lacX74/ptrc99A (control vector)</Gtype> PGCGROWTHCONDITIONS
<Supp>acetate</Supp> PGCGROWTHCONDITIONS
<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
<Technique>ChIP-exo</Technique> GadE <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
<Technique>ChIP-exo</Technique> GadE <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
<Technique>ChIP-exo</Technique> GadW <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
<Technique>ChIP-exo</Technique> GadW <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
<Technique>ChIP-exo</Technique> GadX <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
<Technique>ChIP-exo</Technique> GadX <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
<Technique>ChIP-exo</Technique> RpoS <pH>pH5.5</pH> 1 PGCGROWTHCONDITIONS
<Technique>ChIP-exo</Technique> RpoS <pH>pH5.5</pH> 2 PGCGROWTHCONDITIONS
<Technique>ChIP-Seq</Technique> PGCGROWTHCONDITIONS
<Technique>RNA-Seq</Technique> PGCGROWTHCONDITIONS
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
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
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
treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp> PGCGROWTHCONDITIONS
treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp> PGCGROWTHCONDITIONS
treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>10 mM leucine</Supp>. PGCGROWTHCONDITIONS
treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>20 mg/L tryptophan</Supp>. PGCGROWTHCONDITIONS
treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>10 mM leucine</Supp>. PGCGROWTHCONDITIONS
treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>20 mg/L tryptophan</Supp>. PGCGROWTHCONDITIONS
treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>1g/L arginine</Supp>. PGCGROWTHCONDITIONS
treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>2g/L glutamine</Supp>. PGCGROWTHCONDITIONS
TrpR_<Supp>glucose</Supp> PGCGROWTHCONDITIONS
TrpR_<Supp>Trp</Supp> PGCGROWTHCONDITIONS
σ32 <Temp>30°C</Temp> rep1 PGCGROWTHCONDITIONS
σ32 <Temp>30°C</Temp> rep2 PGCGROWTHCONDITIONS
σ32 <Temp>30°C</Temp> short RNase PGCGROWTHCONDITIONS
σ32 <Temp>43°C</Temp> rep1 PGCGROWTHCONDITIONS
σ32 <Temp>43°C</Temp> rep2 PGCGROWTHCONDITIONS
σ32 <Temp>43°C</Temp> short RNase PGCGROWTHCONDITIONS
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