SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	RNA was extracted using TRIzol (Invitrogen), following the manufacturer[linebreak]s protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer[linebreak]s protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer[linebreak]s protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	source_name	Bacterial cells PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: del rpoS PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: Transition to Stationary PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	source_name	Bacterial cells PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
SRR2932665	GSE74809	GSM1933982	GPL15982	PMID_29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	contact_name	Avantika,,Lal PGCGROWTHCONDITIONS