"Base calling was performed by the DOE Joint Genome Institute using Illumina software."	"data_processing.1"
"Sequenced reads were trimmed, the mapped to the Escherichia coli K-12 MG1655 genome (U00096.2) using SOAP."	"data_processing.2"
"Counts per million unique reads were calculated for each gene."	"data_processing.3"
"Genome_build: U00096.2"	"data_processing.4"
"Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample"	"data_processing.5"
"Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms. 16S and 23S Ribosomal RNA was depleted prior to construction of RNAseq libraries using MICROBExpress reagents."	"extract_protocol_ch1.1"
"RNA-Seq was performed by the DOE Joint Genome Institute using the dUTP method. Briefly, ribosome-depleted RNA was fragmented in a buffered zinc solution, then purified using AMPure SPRI beads. First-strand cDNAs were then synthesized from the fragmented RNA using Superscript II reverse transcriptase, followed by a second bead purification. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand.  Two further bead purification steps using different ratios of beads to cDNA (85/100, then 140/100) selected cDNAs in a range between 150-350 bp. cDNAs were then A-tailed using Exo- Klenow, followed by ligation of sequencing adapter oligos. Following bead purification, dUTP was cleaved from the second strand using AmpErase Uracil N-glycosylase, resulting in adaptor ligated single stranded cDNAs."	"extract_protocol_ch1.2"
"Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4)."	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"MG1655 + 20 ug/ml bicyclomycin"	"source_name_ch1.1"
"MG1655 + 20 ug/ml bicyclomycin 1"	"title.1"
"Cultures were transferred directly into an ice-cold ethanol/phenol stop solution, which immediately inactivated cellular RNases. Cells were collected by centrifugation and stored at -80 oC until RNA extraction."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: MG1655"	"characteristics_ch1.1"
"genotype/variation: wild-type"	"characteristics_ch1.2"
"molecule subtype: ribosome-depeleted RNA"	"characteristics_ch1.3"
"Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4)."	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"MG1655 + 20 ug/ml bicyclomycin"	"source_name_ch1.1"
"Cultures were transferred directly into an ice-cold ethanol/phenol stop solution, which immediately inactivated cellular RNases. Cells were collected by centrifugation and stored at -80 oC until RNA extraction."	"treatment_protocol_ch1.1"