"Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper"	"data_processing.1"
"Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1"	"data_processing.2"
"Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates."	"data_processing.3"
"Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910."	"extract_protocol_ch1.1"
"Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit"	"extract_protocol_ch1.2"
"Aerobic growth at 37°C  in specified media"	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Total RNA from bacterial culture"	"source_name_ch1.1"
"WT_minus_2DG_1"	"title.1"
"Cells treated during mid-exponential growth phase"	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"media: Defined MOPS Minimal + 0.4% Glycerol"	"characteristics_ch1.1"
"genotype: WT"	"characteristics_ch1.2"
"strain: K-12"	"characteristics_ch1.3"
"Aerobic growth at 37°C  in specified media"	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Total RNA from bacterial culture"	"source_name_ch1.1"
"Cells treated during mid-exponential growth phase"	"treatment_protocol_ch1.1"