SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values. PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record. PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	extract_protocol	RNA was purified from lysates by phenol/chloroform method. rRNA was first removed using MICROBExpress following manufacturer’s protocol, except RNA was collected using Zymo’s RNA columns. A second rRNA removal step was performed following the protocol described in Affymetrix Expression Handbook, substituting enzymes MMLV (Ambion), RNase H (NEB), and DnaseI (Amplification grade, Invitrogen). PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	extract_protocol	The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University). PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids. PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	source_name	Escherichia coli PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	treatment_protocol	At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes. PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	strain: DY330 (W3110) PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	treatment group: rifampicin time point 2 PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids. PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	source_name	Escherichia coli PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	treatment_protocol	At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes. PGCGROWTHCONDITIONS
SRR057748	GSE21341	GSM533305	GPL10328	PMID_20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	contact_name	Huiyi,,Chen PGCGROWTHCONDITIONS