SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Trimmed adaptor sequences from reads using Flexbar 2.31 PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0 PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq. PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNAsnap followed by RiboZero rRNA removal kit for gram-negative bacteria (Epicentre) PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research). PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter. PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	REL606_glucose-limited minimal medium_48 hr PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	strain: REL606 PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	time point: 48 hours PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	molecule subtype: rRNA-depleted total RNA PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter. PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	REL606_glucose-limited minimal medium_48 hr PGCGROWTHCONDITIONS
SRR1945189SRR1945190	GSE67402	GSM1646289	GPL14548	PMID_26275208	Glucose time course, 48 hour time point, biological replicate 1	Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Jeffrey,E.,Barrick PGCGROWTHCONDITIONS