SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	data_processing	bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	data_processing	Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	data_processing	Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	data_processing	Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	data_processing	Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	data_processing	Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	extract_protocol	At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	extract_protocol	Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	growth_protocol	Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	organism	Escherichia coli K-12 PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	source_name	Bacterial cells PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	library_strategy	ssRNA-seq PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	characteristics	substrain: GJ13507 PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	characteristics	genotype: {delta}nusG PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	growth_protocol	Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	organism	Escherichia coli K-12 PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	source_name	Bacterial cells PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
SRR6048178	GSE103937	GSM2786608	GPL24020	PMID_29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	contact_name	J,,Gowrishankar PGCGROWTHCONDITIONS