"bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming)"	"data_processing.1"
"Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool."	"data_processing.2"
"Aligned reads were designated to top and bottom strands using Samtools"	"data_processing.3"
"Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples"	"data_processing.4"
"Genome_build: NC000913.2 MG1655"	"data_processing.5"
"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."	"data_processing.6"
"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."	"extract_protocol_ch1.1"
"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"	"extract_protocol_ch1.2"
"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"	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Bacterial cells"	"source_name_ch1.1"
"∆rho UvsW_replicate3"	"title.1"
"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"	"treatment_protocol_ch1.1"
"ssRNA-seq"	"library_strategy.1"
"substrain: GJ13531"	"characteristics_ch1.1"
"genotype: {delta}rho"	"characteristics_ch1.2"
"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"	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Bacterial cells"	"source_name_ch1.1"
"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"	"treatment_protocol_ch1.1"