SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	Basecalling was performed by RTA 1.18. PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	Adaptor and barcode were removed by cutadapt 1.18. PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	For RNET-seq, duplicates were removed by bbmap 38.22. PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	RNET-seq reads were aligned to E. coli MG1655 genome NC_000913.2 using bowtie 1.2.2 with parameters -q -p 10 -v 1 -m 1 --best --strata. RNA-seq reads were mapped to the genome by STAR 2.6.1. PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	For RNET-seq, the counts of all uniquely aligned reads whose the 5’ ends mapped were recorded and counted in each coordinate by bedtools 2.27.1. For RNA-seq, the raw counts of aligned reads in each gene were calculated by HTseq 0.11.2. PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	Genome_build: Escherichia coli str. K-12 substr. MG1655, NC_000913.2 PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped. PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	Supplementary_files_format_and_content: hRpoD_and_hRpoDgreAB-_TPM.csv: Comma-separated text file includes the TMP values for each sample. PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	extract_protocol	Cells were resuspended in TRIzol (Invitrogen) and incubated for 4 min at 95 ºC to disrupt the cells. The total RNA was purified by PCI extraction and chloroform extraction. After centrifugation, equal volume of isopropanol was added to the top water phase to precipitate the total RNA. The genomic DNA was digested by 50 U DNase I for 30 min at room temperature. The RNA was then purified by RNeasy Mini Kit (Qiagen). PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	extract_protocol	Libraries were generated using TruSeq Standard Total RNA Library Prep Kit (Illumina). PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	growth_protocol	The overnight cell cultures were diluted in 100 ml LB medium (OD600 = 0.02) and incubated at 37 ºC to mid-log phase (OD600 = 0.5). PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	organism	Escherichia coli str. K-12 substr. W3110 PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	source_name	hRpoDΔgreAB_RNA-seq PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	characteristics	strain: sigma70 greAB- PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	characteristics	genotype: W3110 6xHis-rpoD greA::tet greB::amp PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	characteristics	growth: OD600 = 0.5 in LB PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	growth_protocol	The overnight cell cultures were diluted in 100 ml LB medium (OD600 = 0.02) and incubated at 37 ºC to mid-log phase (OD600 = 0.5). PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	organism	Escherichia coli str. K-12 substr. W3110 PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	source_name	hRpoDΔgreAB_RNA-seq PGCGROWTHCONDITIONS
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	PMID_33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	contact_name	Zhe,,Sun PGCGROWTHCONDITIONS