SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	data_processing	The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5[linebreak]-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	data_processing	Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	data_processing	Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5[linebreak]-end of these uniquely aligned reads were defined as potential TSSs. PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	data_processing	Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build: NC_000913/ASM584v1 PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: counts PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	Total mRNA isolated from each cell culture was treated with Terminator 5[linebreak] Phosphate Dependent Exonuclease (Epicentre) to enrich 5[linebreak] tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5[linebreak]-Polyphosphatase (Epicentre) to generate 5[linebreak]-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp. PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	source_name	Cells at stationary phase (OD600nm 1.5) in M9 glucose media PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	characteristics	strain: MG1655 PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	characteristics	treatment: stationary phase PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	source_name	Cells at stationary phase (OD600nm 1.5) in M9 glucose media PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
SRR847728	GSE46737	GSM1137316	GPL17137	PMID_24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	contact_name	Donghyuk,,Kim PGCGROWTHCONDITIONS