SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	bacterial cells PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	treatment_protocol	Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	strain: SK4455 PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	genotype/variation: rnc- deletion mutant PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	time point: time0 PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	bacterial cells PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	treatment_protocol	Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
SRR5282308	GSE95318	GSM2507174	GPL18133	PMID_28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	contact_name	Gina,,Gordon PGCGROWTHCONDITIONS