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

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Kevin Meza Landeros
2d683291 1 parent f0c9555c

extraction

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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
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(['Air', 'Gtype', 'Gversion', 'Med', 'Phase', 'Sample', 'Serie', 'Strain', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Vess'])
# 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')
-------------------------------- PARAMETERS --------------------------------
Path of CoreNLP output: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/
File with CoreNLP-tagging sentences: raw-metadata-senteneces.txt.conll
Path of training data set: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
File with training data set: training-data-set-70.txt
Path of test data set: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
File with test data set: test-data-set-30.txt
-------------------------------- PROCESSING --------------------------------
Number of sentences: 405
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
<Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
<Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|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
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 Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
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
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|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
At|at|IN|O OD450|od450|NN|OD
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
carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
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 <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
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
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 <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
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
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
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
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 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
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
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
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 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
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
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
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
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-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 anti-RpoS|anti-rpos|JJ|Anti -LRB-|-lrb-|-LRB-|O neoclone|neoclone|NN|O ,|,|,|O WP009|wp009|NN|O -RRB-|-rrb-|-RRB-|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
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
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
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
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
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
culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|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
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
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
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.|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
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
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
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
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
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
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
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
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
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
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.|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
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.|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
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
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
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
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
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
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
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
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
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
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 NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
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|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 ArgR-8myc|argr-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|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-gadW|delta-gadw|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|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 fur-8myc|fur-8myc|JJ|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 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 soxR-8myc|soxr-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
genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O anaerobic|anaerobic|JJ|O
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|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 condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
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 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|O phase|phase|NN|O :|:|:|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD
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
ChIP-Seq|chip-seq|NN|Gversion
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
library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
medium|medium|NN|O :|:|:|O M63|m63|NN|Med
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 1|1|CD|O
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 2|2|CD|O
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
Cra|Cra|NNP|O acetate|acetate|NN|O 1|1|CD|O
Cra|Cra|NNP|O acetate|acetate|NN|O 2|2|CD|O
Cra|Cra|NNP|O fructose|fructose|NN|O 1|1|CD|O
Cra|Cra|NNP|O fructose|fructose|NN|O 2|2|CD|O
Cra|cra|NN|O glucose|glucose|NN|O 1|1|CD|O
Cra|cra|NN|O glucose|glucose|NN|O 2|2|CD|O
Crosslink|Crosslink|NNP|O
CsiR|CsiR|NNP|O _|_|VBD|O ChIPSeq|chipseq|NN|O
CsiR|csir|NN|O _|_|CD|O RNASeq|rnaseq|NN|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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|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
Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O C|c|NN|O
∆|∆|CD|O fnr|fnr|SYM|O -|-|:|O Anaeroibc|anaeroibc|NN|O
FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O A|a|NN|O
FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O B|b|NN|O
∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O B|b|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
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O A|A|NNP|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O B|B|NNP|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O C|C|NNP|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O A|A|NNP|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O B|b|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O C|c|NN|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
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
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O B|b|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
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
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
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
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O A|a|NN|O
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O B|b|NN|O
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
Input|input|NN|O ChIP-Seq|chip-seq|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
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
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
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
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
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
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
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
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 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|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
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
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
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
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
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
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 1|1|CD|O
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 2|2|CD|O
Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 3|3|CD|O
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 3|3|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
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
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
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
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
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
Nac|Nac|NNP|O _|_|NNP|O ChIPSeq|ChIPSeq|NNP|O
Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep1|rep1|NN|O
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep2|rep2|NN|O
NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep3|rep3|NN|O
NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
OmpR|ompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
OmpR|ompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
OxyR|oxyr|NN|O PQ|pq|NN|O 1|1|CD|O
OxyR|oxyr|NN|O PQ|pq|NN|O 2|2|CD|O
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 1|1|CD|O
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
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
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
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
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
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
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
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
PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|SYM|O 1|1|CD|O
PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|NN|O 2|2|CD|O
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 1|1|CD|O
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 2|2|CD|O
RNAP|rnap|NN|O old|old|JJ|O rep1|rep1|NN|O
RNAP|rnap|NN|O old|old|JJ|O rep2|rep2|NN|O
RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 1|1|CD|O
RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 2|2|CD|O
RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 1|1|CD|O
RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 2|2|CD|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
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
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
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
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
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
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
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
RpoB|rpob|NN|O WT|wt|NN|O 1|1|CD|O
RpoB|rpob|NN|O WT|wt|NN|O 2|2|CD|O
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|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
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|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
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O
∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O
SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|O
SeqA|seqa|NN|O new|new|JJ|O rep1|rep1|NN|O
SeqA|seqa|NN|O new|new|JJ|O rep2|rep2|NN|O
SeqA|seqa|NN|O old|old|JJ|O deltaSeqA|deltaseqa|NN|O
SeqA|seqa|NN|O old|old|JJ|O rep1|rep1|NN|O
SeqA|seqa|NN|O old|old|JJ|O rep2|rep2|NN|O
SoxR|soxr|NN|O PQ|pq|NN|O 1|1|CD|O
SoxR|soxr|NN|O PQ|pq|NN|O 2|2|CD|O
SoxS|soxs|NN|O PQ|pq|NN|O 1|1|CD|O
SoxS|soxs|NN|O PQ|pq|NN|O 2|2|CD|O
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O A|a|NN|O
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O B|b|NN|O
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
TrpR|trpr|NN|O _|_|NN|O glucose|glucose|NN|O
TrpR|trpr|NN|O _|_|CD|O Trp|trp|NN|O
Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O A|a|NN|O
Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O B|b|NN|O
Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O A|a|NN|O
Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O B|b|NN|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
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
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
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
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
WT|wt|JJ|O acetate|acetate|NN|O 1|1|CD|O
WT|wt|JJ|O acetate|acetate|NN|O 2|2|CD|O
WT|WT|NNP|O _|_|SYM|O ChIPSeq|ChIPSeq|NNP|O _|_|SYM|O 1|1|CD|O
WT|wt|JJ|O _|_|NN|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
WT|wt|JJ|O fructose|fructose|NN|O 1|1|CD|O
WT|wt|JJ|O fructose|fructose|NN|O 2|2|CD|O
WT|wt|JJ|O glucose|glucose|NN|O 1|1|CD|O
WT|wt|JJ|O glucose|glucose|NN|O 2|2|CD|O
WT|wt|NN|O NaCl|nacl|NN|O 1|1|CD|O
WT|wt|NN|O NaCl|nacl|NN|O 2|2|CD|O
WT|wt|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
WT|wt|JJ|O pH5|ph5|NN|O .5|.5|NN|O 2|2|CD|O
WT|WT|NNP|O PQ|PQ|NNP|O 1|1|CD|O
WT|WT|NNP|O PQ|PQ|NNP|O 2|2|CD|O
WT|WT|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|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 DPD|dpd|NN|O 2|2|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|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
Δcra|δcra|NN|O acetate|acetate|NN|O 1|1|CD|O
Δcra|δcra|NN|O acetate|acetate|NN|O 2|2|CD|O
Δcra|δcra|NN|O fructose|fructose|NN|O 1|1|CD|O
Δcra|δcra|NN|O fructose|fructose|NN|O 2|2|CD|O
Δcra|δcra|NN|O glucose|glucose|NN|O 1|1|CD|O
Δcra|δcra|NN|O glucose|glucose|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
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
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
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
ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ΔompR|δompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
ΔompR|δompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 1|1|CD|O
ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 2|2|CD|O
ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 1|1|CD|O
ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 2|2|CD|O
ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 1|1|CD|O
ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 2|2|CD|O
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep1|rep1|NN|O
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep2|rep2|NN|O
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep1|rep1|NN|O
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep2|rep2|NN|O
σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O control|control|NN|O
σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O heat|heat|NN|O
Escherichia|escherichia|FW|O coli|coli|FW|O K-12|k-12|NN|O
Escherichia|escherichia|FW|O coli|coli|FW|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
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
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
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
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
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 ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
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
strain|strain|NN|O :|:|:|O K-12|k-12|NN|O MG1655|mg1655|NN|O
strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O
strain|strain|NN|O :|:|:|O K-12|k-12|NN|O
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
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
acetate|acetate|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
ChIP-Seq|chip-seq|NN|Technique
RNA-Seq|rna-seq|NN|Technique
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|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
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
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
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
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
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
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
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
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
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
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
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
********** 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:.'
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['O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Phase', 'Phase', 'O', 'O', 'O', 'Temp', 'Temp', 'O', 'Med', 'Med', 'Med', 'O', 'O', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'Supp', 'Supp', 'Supp', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'Supp', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['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', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
['O', '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
echo
echo
echo
echo "==============================Family SOFT files======================================= "
echo
echo "Access to GEO family soft files.."
echo "directory: "$(pwd);
echo
echo
ls -1 ;
echo
echo "Number of files: "$(ls -1 | wc -l);
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 $_" PGCGROWTHCONDITIONS"; }' > /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt
echo
echo "Number of total tag sentences: "$(wc /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt -l);
echo
echo
echo "Saving file: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/input/raw-metadata-senteneces.txt";
echo
echo
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/";
echo "input file: "$input;
echo
echo "output directory: "$output;
echo
echo
corenlp.sh -annotators tokenize,ssplit,pos,lemma -outputFormat conll -file $input -outputDirectory $output;
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 sequencing reads were mapped to E. coli MG1655 reference genome (<Gversion>NC_000913</Gversion>) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99. PGCGROWTHCONDITIONS
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
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>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-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
culture condition: <Air>Aerobic</Air> cultures PGCGROWTHCONDITIONS
culture condition: <Air>Anaerobic</Air> cultures 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
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
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>Δfur</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> ChIP DNA from <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS
<Gversion>ChIP-Seq</Gversion> PGCGROWTHCONDITIONS
ip antibody: <Anti>affinity purified anti-Fur antibody</Anti> PGCGROWTHCONDITIONS
library strategy: <Technique>ChIP-exo</Technique> PGCGROWTHCONDITIONS
medium: <Med>LB</Med> PGCGROWTHCONDITIONS
medium: <Med>M63</Med> 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
<Name>ArgR_Arginine_1</Name> PGCGROWTHCONDITIONS
<Name>ArgR_Arginine_2</Name> PGCGROWTHCONDITIONS
<Name>ArgR_NH4Cl_1</Name> PGCGROWTHCONDITIONS
<Name>ArgR_NH4Cl_2</Name> PGCGROWTHCONDITIONS
<Name>ChIP-exo GadE pH5.5 1</Name> PGCGROWTHCONDITIONS
<Name>ChIP-exo GadE pH5.5 2</Name> PGCGROWTHCONDITIONS
<Name>ChIP-exo GadW pH5.5 1</Name> PGCGROWTHCONDITIONS
<Name>ChIP-exo GadW pH5.5 2</Name> PGCGROWTHCONDITIONS
<Name>ChIP-exo GadX pH5.5 1</Name> PGCGROWTHCONDITIONS
<Name>ChIP-exo GadX pH5.5 2</Name> PGCGROWTHCONDITIONS
<Name>ChIP-exo RpoS pH5.5 1</Name> PGCGROWTHCONDITIONS
<Name>ChIP-exo RpoS pH5.5 2</Name> PGCGROWTHCONDITIONS
<Name>Cra acetate 1</Name> PGCGROWTHCONDITIONS
<Name>Cra acetate 2</Name> PGCGROWTHCONDITIONS
<Name>Cra fructose 1</Name> PGCGROWTHCONDITIONS
<Name>Cra fructose 2</Name> PGCGROWTHCONDITIONS
<Name>Cra glucose 1</Name> PGCGROWTHCONDITIONS
<Name>Cra glucose 2</Name> PGCGROWTHCONDITIONS
<Name>Crosslink</Name> PGCGROWTHCONDITIONS
<Name>CsiR_ChIPSeq</Name> PGCGROWTHCONDITIONS
<Name>CsiR_RNASeq</Name> PGCGROWTHCONDITIONS
<Name>EC18n122 RpoH 10 min Time course 4</Name> PGCGROWTHCONDITIONS
<Name>EC18n167 RpoH 0 min Time course 2</Name> PGCGROWTHCONDITIONS
<Name>EC18n168 RpoH 2.5 min Time course 2</Name> PGCGROWTHCONDITIONS
<Name>EC18n169 RpoH 5 min Time course 2</Name> PGCGROWTHCONDITIONS
<Name>EC18n170 RpoH 10 min Time course 2</Name> PGCGROWTHCONDITIONS
<Name>EC18n171 RpoH 20 min Time course 2</Name> PGCGROWTHCONDITIONS
<Name>EC18n177 RpoH 0 min Time course 1</Name> PGCGROWTHCONDITIONS
<Name>EC18n178 RpoH 2.5 min Time course 1</Name> PGCGROWTHCONDITIONS
<Name>EC18n179 RpoH 5 min Time course 1</Name> PGCGROWTHCONDITIONS
<Name>EC18n180 RpoH 10 min Time course 1</Name> PGCGROWTHCONDITIONS
<Name>EC18n181 RpoH 20 min Time course 1</Name> PGCGROWTHCONDITIONS
<Name>EC18n182 RpoH 0 min Time course 3</Name> PGCGROWTHCONDITIONS
<Name>EC18n183 RpoH 2.5 min Time course 3</Name> PGCGROWTHCONDITIONS
<Name>EC18n184 RpoH 5 min Time course 3</Name> PGCGROWTHCONDITIONS
<Name>EC18n185 RpoH 10 min Time course 3</Name> PGCGROWTHCONDITIONS
<Name>EC18n186 RpoH 20 min Time course 3</Name> PGCGROWTHCONDITIONS
<Name>Ecoli_dFNR_rep1_anaerobic</Name> PGCGROWTHCONDITIONS
<Name>Ecoli_dFNR_rep2_anaerobic</Name> PGCGROWTHCONDITIONS
<Name>Ecoli_wild-type_rep1_anaerobic</Name> PGCGROWTHCONDITIONS
<Name>Ecoli_wild-type_rep2_anaerobic</Name> PGCGROWTHCONDITIONS
<Name>Escherichia coli str. K-12 substr. MG1655</Name> PGCGROWTHCONDITIONS
<Name>FNR - Anaerobic - Affinity Purified - A</Name> PGCGROWTHCONDITIONS
<Name>FNR - Anaerobic - Affinity Purified - B</Name> PGCGROWTHCONDITIONS
<Name>FNR - Anaerobic - A</Name> PGCGROWTHCONDITIONS
<Name>FNR - Anaerobic - B</Name> PGCGROWTHCONDITIONS
<Name>FNR - Anaerobic - C</Name> PGCGROWTHCONDITIONS
<Name>∆fnr - Anaeroibc</Name> PGCGROWTHCONDITIONS
<Name>FNR - ∆hns∆stpA A</Name> PGCGROWTHCONDITIONS
<Name>FNR - ∆hns∆stpA B</Name> PGCGROWTHCONDITIONS
<Name>∆fur Aerobic A</Name> PGCGROWTHCONDITIONS
<Name>∆fur Aerobic B</Name> PGCGROWTHCONDITIONS
<Name>∆fur Anaerobic A</Name> PGCGROWTHCONDITIONS
<Name>∆fur Anaerobic B</Name> PGCGROWTHCONDITIONS
<Name>∆fur Anaerobic [IP vs nput]</Name> PGCGROWTHCONDITIONS
<Name>Fur IP ChIP-Seq Aerobic A</Name> PGCGROWTHCONDITIONS
<Name>Fur IP ChIP-Seq Aerobic B</Name> PGCGROWTHCONDITIONS
<Name>Fur IP ChIP-Seq Aerobic C</Name> PGCGROWTHCONDITIONS
<Name>Fur IP ChIP-Seq Anaerobic A</Name> PGCGROWTHCONDITIONS
<Name>Fur IP ChIP-Seq Anaerobic B</Name> PGCGROWTHCONDITIONS
<Name>Fur IP ChIP-Seq Anaerobic C</Name> PGCGROWTHCONDITIONS
<Name>Fur IP ChIP-Seq Anaerobic, Iron Deficient A</Name> PGCGROWTHCONDITIONS
<Name>Fur IP ChIP-Seq Anaerobic, Iron Deficient B</Name> PGCGROWTHCONDITIONS
<Name>∆fur ∆ryhB Aerobic A</Name> PGCGROWTHCONDITIONS
<Name>∆fur ∆ryhB Aerobic B</Name> PGCGROWTHCONDITIONS
<Name>∆fur ∆ryhB Anaerobic A</Name> PGCGROWTHCONDITIONS
<Name>∆fur ∆ryhB Anaerobic B</Name> PGCGROWTHCONDITIONS
<Name>Fur with DPD 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>Fur with DPD 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>Fur with Fe 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>Fur with Fe 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>HNS - Aerobic A</Name> PGCGROWTHCONDITIONS
<Name>HNS - Aerobic B</Name> PGCGROWTHCONDITIONS
<Name>HNS - Anaerobic A</Name> PGCGROWTHCONDITIONS
<Name>HNS - Anaerobic B</Name> PGCGROWTHCONDITIONS
<Name>IHF - Anaerobic A</Name> PGCGROWTHCONDITIONS
<Name>IHF - Anaerobic B</Name> PGCGROWTHCONDITIONS
<Name>Input ChIP-Seq</Name> PGCGROWTHCONDITIONS
<Name>LB 0.4 B1 TEX neg L1 GA</Name> PGCGROWTHCONDITIONS
<Name>LB 0.4 B1 TEX pos L1 GA</Name> PGCGROWTHCONDITIONS
<Name>LB 0.4 B2 TEX neg L1 HS1</Name> PGCGROWTHCONDITIONS
<Name>LB 0.4 B2 TEX neg L1 HS2</Name> PGCGROWTHCONDITIONS
<Name>LB 0.4 B2 TEX pos L1 HS1</Name> PGCGROWTHCONDITIONS
<Name>LB 0.4 B2 TEX pos L1 HS2</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B1 TEX neg L1 GA</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B1 TEX neg L2 HS2</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B1 TEX pos L1 GA</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B1 TEX pos L2 HS2</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B2 TEX neg L1 HS1</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B2 TEX neg L1 HS2</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B2 TEX neg L2 HS2</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B2 TEX pos L1 HS1</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B2 TEX pos L1 HS2</Name> PGCGROWTHCONDITIONS
<Name>LB 2.0 B2 TEX pos L2 HS2</Name> PGCGROWTHCONDITIONS
<Name>Lrp_Leu_1</Name> PGCGROWTHCONDITIONS
<Name>Lrp_Leu_2</Name> PGCGROWTHCONDITIONS
<Name>Lrp_Leu_3</Name> PGCGROWTHCONDITIONS
<Name>Lrp_NH4Cl_1</Name> PGCGROWTHCONDITIONS
<Name>Lrp_NH4Cl_2</Name> PGCGROWTHCONDITIONS
<Name>Lrp_NH4Cl_3</Name> PGCGROWTHCONDITIONS
<Name>M63 0.4 B1 TEX neg L1 GA</Name> PGCGROWTHCONDITIONS
<Name>M63 0.4 B1 TEX pos L1 GA</Name> PGCGROWTHCONDITIONS
<Name>M63 0.4 B2 TEX neg L1 HS1</Name> PGCGROWTHCONDITIONS
<Name>M63 0.4 B2 TEX neg L1 HS2</Name> PGCGROWTHCONDITIONS
<Name>M63 0.4 B2 TEX pos L1 HS1</Name> PGCGROWTHCONDITIONS
<Name>M63 0.4 B2 TEX pos L1 HS2</Name> PGCGROWTHCONDITIONS
<Name>Nac_ChIPSeq</Name> PGCGROWTHCONDITIONS
<Name>Nac_RNASeq</Name> PGCGROWTHCONDITIONS
<Name>NsrR_Flagtag_rep1</Name> PGCGROWTHCONDITIONS
<Name>NsrR_Flagtag_rep2</Name> PGCGROWTHCONDITIONS
<Name>NsrR_Flagtag_rep3</Name> PGCGROWTHCONDITIONS
<Name>NtrC_ChIPSeq</Name> PGCGROWTHCONDITIONS
<Name>OmpR_ChIPSeq</Name> PGCGROWTHCONDITIONS
<Name>OmpR NaCl 1</Name> PGCGROWTHCONDITIONS
<Name>OmpR NaCl 2</Name> PGCGROWTHCONDITIONS
<Name>OxyR PQ 1</Name> PGCGROWTHCONDITIONS
<Name>OxyR PQ 2</Name> PGCGROWTHCONDITIONS
<Name>pT7_ChIPSeq_1</Name> PGCGROWTHCONDITIONS
<Name>pT7_ChIPSeq_2</Name> PGCGROWTHCONDITIONS
<Name>Ptac::fnr - A - 16 µM IPTG</Name> PGCGROWTHCONDITIONS
<Name>Ptac::fnr - A - 4 µM IPTG</Name> PGCGROWTHCONDITIONS
<Name>Ptac::fnr - A - 8 µM IPTG</Name> PGCGROWTHCONDITIONS
<Name>Ptac::fnr - B - 16 µM IPTG</Name> PGCGROWTHCONDITIONS
<Name>Ptac::fnr - B - 4 µM IPTG</Name> PGCGROWTHCONDITIONS
<Name>Ptac::fnr - B - 8 µM IPTG</Name> PGCGROWTHCONDITIONS
<Name>Ptac::fnr - C - 16 µM IPTG</Name> PGCGROWTHCONDITIONS
<Name>PurR_Adenine_1</Name> PGCGROWTHCONDITIONS
<Name>PurR_Adenine_2</Name> PGCGROWTHCONDITIONS
<Name>PurR_glucose_1</Name> PGCGROWTHCONDITIONS
<Name>PurR_glucose_2</Name> PGCGROWTHCONDITIONS
<Name>RNAP old rep1</Name> PGCGROWTHCONDITIONS
<Name>RNAP old rep2</Name> PGCGROWTHCONDITIONS
<Name>RpoB ∆cra 1</Name> PGCGROWTHCONDITIONS
<Name>RpoB ∆cra 2</Name> PGCGROWTHCONDITIONS
<Name>RpoB ∆crp 1</Name> PGCGROWTHCONDITIONS
<Name>RpoB ∆crp 2</Name> PGCGROWTHCONDITIONS
<Name>RpoB with DPD 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>RpoB with DPD 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>RpoB with DPD and rifampicin 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>RpoB with DPD and rifampicin 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>RpoB with Fe 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>RpoB with Fe 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>RpoB with Fe and rifampicin 1 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>RpoB with Fe and rifampicin 2 (ChIP-exo)</Name> PGCGROWTHCONDITIONS
<Name>RpoB WT 1</Name> PGCGROWTHCONDITIONS
<Name>RpoB WT 2</Name> PGCGROWTHCONDITIONS
<Name>RpoH induced (0 min)</Name> PGCGROWTHCONDITIONS
<Name>RpoH induced (10 min)</Name> PGCGROWTHCONDITIONS
<Name>RpoH induced (20 min)</Name> PGCGROWTHCONDITIONS
<Name>RpoH induced (2.5 min)</Name> PGCGROWTHCONDITIONS
<Name>RpoH induced (5 min)</Name> PGCGROWTHCONDITIONS
<Name>∆ryhB Aerobic</Name> PGCGROWTHCONDITIONS
<Name>∆ryhB Anaerobic</Name> PGCGROWTHCONDITIONS
<Name>SeqA new deltaSeqA</Name> PGCGROWTHCONDITIONS
<Name>SeqA new rep1</Name> PGCGROWTHCONDITIONS
<Name>SeqA new rep2</Name> PGCGROWTHCONDITIONS
<Name>SeqA old deltaSeqA</Name> PGCGROWTHCONDITIONS
<Name>SeqA old rep1</Name> PGCGROWTHCONDITIONS
<Name>SeqA old rep2</Name> PGCGROWTHCONDITIONS
<Name>SoxR PQ 1</Name> PGCGROWTHCONDITIONS
<Name>SoxR PQ 2</Name> PGCGROWTHCONDITIONS
<Name>SoxS PQ 1</Name> PGCGROWTHCONDITIONS
<Name>SoxS PQ 2</Name> PGCGROWTHCONDITIONS
<Name>ß - Aerobic - A</Name> PGCGROWTHCONDITIONS
<Name>ß - Aerobic - B</Name> PGCGROWTHCONDITIONS
<Name>ß - Anaerobic - A</Name> PGCGROWTHCONDITIONS
<Name>ß - Anaerobic - B</Name> PGCGROWTHCONDITIONS
<Name>TrpR_glucose</Name> PGCGROWTHCONDITIONS
<Name>TrpR_Trp</Name> PGCGROWTHCONDITIONS
<Name>Wild-type Aerobic A</Name> PGCGROWTHCONDITIONS
<Name>Wild-type Aerobic B</Name> PGCGROWTHCONDITIONS
<Name>Wild-type Anaerobic A</Name> PGCGROWTHCONDITIONS
<Name>Wild-type Anaerobic B</Name> PGCGROWTHCONDITIONS
<Name>Wild type control (0 min)</Name> PGCGROWTHCONDITIONS
<Name>Wild type control (10 min)</Name> PGCGROWTHCONDITIONS
<Name>Wild type control (20 min)</Name> PGCGROWTHCONDITIONS
<Name>Wild type control (2.5 min)</Name> PGCGROWTHCONDITIONS
<Name>Wild type control (5 min)</Name> PGCGROWTHCONDITIONS
<Name>WT acetate 1</Name> PGCGROWTHCONDITIONS
<Name>WT acetate 2</Name> PGCGROWTHCONDITIONS
<Name>WT_ChIPSeq_1</Name> PGCGROWTHCONDITIONS
<Name>WT_ChIPSeq_2</Name> PGCGROWTHCONDITIONS
<Name>WT fructose 1</Name> PGCGROWTHCONDITIONS
<Name>WT fructose 2</Name> PGCGROWTHCONDITIONS
<Name>WT glucose 1</Name> PGCGROWTHCONDITIONS
<Name>WT glucose 2</Name> PGCGROWTHCONDITIONS
<Name>WT NaCl 1</Name> PGCGROWTHCONDITIONS
<Name>WT NaCl 2</Name> PGCGROWTHCONDITIONS
<Name>WT pH5.5 1</Name> PGCGROWTHCONDITIONS
<Name>WT pH5.5 2</Name> PGCGROWTHCONDITIONS
<Name>WT PQ 1</Name> PGCGROWTHCONDITIONS
<Name>WT PQ 2</Name> PGCGROWTHCONDITIONS
<Name>WT_RNASeq</Name> PGCGROWTHCONDITIONS
<Name>WT with DPD 1 (RNA-seq)</Name> PGCGROWTHCONDITIONS
<Name>WT with DPD 2 (RNA-seq)</Name> PGCGROWTHCONDITIONS
<Name>WT with Fe 1 (RNA-seq)</Name> PGCGROWTHCONDITIONS
<Name>WT with Fe 2 (RNA-seq)</Name> PGCGROWTHCONDITIONS
<Name>Δcra acetate 1</Name> PGCGROWTHCONDITIONS
<Name>Δcra acetate 2</Name> PGCGROWTHCONDITIONS
<Name>Δcra fructose 1</Name> PGCGROWTHCONDITIONS
<Name>Δcra fructose 2</Name> PGCGROWTHCONDITIONS
<Name>Δcra glucose 1</Name> PGCGROWTHCONDITIONS
<Name>Δcra glucose 2</Name> PGCGROWTHCONDITIONS
<Name>Δfur with DPD 1 (RNA-seq)</Name> PGCGROWTHCONDITIONS
<Name>Δfur with DPD 2 (RNA-seq)</Name> PGCGROWTHCONDITIONS
<Name>Δfur with Fe 1 (RNA-seq)</Name> PGCGROWTHCONDITIONS
<Name>Δfur with Fe 2 (RNA-seq)</Name> PGCGROWTHCONDITIONS
<Name>ΔgadE pH5.5 1</Name> PGCGROWTHCONDITIONS
<Name>ΔgadE pH5.5 2</Name> PGCGROWTHCONDITIONS
<Name>ΔgadW pH5.5 1</Name> PGCGROWTHCONDITIONS
<Name>ΔgadW pH5.5 2</Name> PGCGROWTHCONDITIONS
<Name>ΔgadX pH5.5 1</Name> PGCGROWTHCONDITIONS
<Name>ΔgadX pH5.5 2</Name> PGCGROWTHCONDITIONS
<Name>ΔompR NaCl 1</Name> PGCGROWTHCONDITIONS
<Name>ΔompR NaCl 2</Name> PGCGROWTHCONDITIONS
<Name>ΔoxyR PQ 1</Name> PGCGROWTHCONDITIONS
<Name>ΔoxyR PQ 2</Name> PGCGROWTHCONDITIONS
<Name>ΔsoxR PQ 1</Name> PGCGROWTHCONDITIONS
<Name>ΔsoxR PQ 2</Name> PGCGROWTHCONDITIONS
<Name>ΔsoxS PQ 1</Name> PGCGROWTHCONDITIONS
<Name>ΔsoxS PQ 2</Name> PGCGROWTHCONDITIONS
<Name>σ32 30°C rep1</Name> PGCGROWTHCONDITIONS
<Name>σ32 30°C rep2</Name> PGCGROWTHCONDITIONS
<Name>σ32 30°C short RNase</Name> PGCGROWTHCONDITIONS
<Name>σ32 43°C rep1</Name> PGCGROWTHCONDITIONS
<Name>σ32 43°C rep2</Name> PGCGROWTHCONDITIONS
<Name>σ32 43°C short RNase</Name> PGCGROWTHCONDITIONS
<Name>σ32 ChIP DNA, control</Name> PGCGROWTHCONDITIONS
<Name>σ32 ChIP DNA, heat</Name> 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
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
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
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-Seq</Technique> PGCGROWTHCONDITIONS
<Technique>RNA-Seq</Technique> PGCGROWTHCONDITIONS
The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh M9 medium containing 2 g/L glucose in either the presence or <Supp>absence of 1 g/L arginine</Supp> and continued to culture at 37°C until reaching an appropriate cell density (OD600 ≈ 0.5). PGCGROWTHCONDITIONS
The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh <Med>M9 medium</Med> containing <Supp>2 g/L glucose</Supp> in either the <Supp>presence or absence of 1 g/L arginine</Supp> and continued to culture at <Temp>37°C</Temp> until reaching an appropriate cell density (<OD>OD600 ≈ 0.5</OD>). PGCGROWTHCONDITIONS
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
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