"Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4"	"data_processing.1"
"Read coverage maps and RPKM data was subsequently generated by Geneious."	"data_processing.2"
"BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics"	"data_processing.3"
"Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C."	"extract_protocol_ch1.1"
"RNA libraries were prepared for sequencing using standard Illumina protocols"	"extract_protocol_ch1.2"
"Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"MG1655"	"source_name_ch1.1"
"MFD++_2"	"title.1"
"MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"genotype: Mfd++"	"characteristics_ch1.1"
"Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"MG1655"	"source_name_ch1.1"
"MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour."	"treatment_protocol_ch1.1"