"Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment"	"data_processing.1"
"FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type"	"data_processing.2"
"Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type"	"data_processing.3"
"Genome_build: NC_000913"	"data_processing.4"
"Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons"	"data_processing.5"
"Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen)."	"extract_protocol_ch1.1"
"Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming."	"extract_protocol_ch1.2"
"E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where."	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"mntR KO"	"source_name_ch1.1"
"Mid log_mntR KO_glc minimal media_aerobic"	"title.1"
"Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"genotype/variation: mntR KO; BW25113 DmntR"	"characteristics_ch1.1"
"growth stage: mid exponetial phase"	"characteristics_ch1.2"
"basal media: M9 + 4 g/L glc (glucose minimal media)"	"characteristics_ch1.3"
"oxygen condition: aerobic"	"characteristics_ch1.4"
"supplementation: None"	"characteristics_ch1.5"
"strain: K-12"	"characteristics_ch1.6"
"E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where."	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"mntR KO"	"source_name_ch1.1"
"Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use."	"treatment_protocol_ch1.1"