SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Basecalls performed using CASAVA version 1.7 PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11 PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Labled transcript 5[linebreak] end and 3[linebreak] end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Extracted paired-end reads were mapped to E.coli genome (NC_00913.3) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2. PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data. PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Genome_build: Escherichia coli str. K-12 substr. MG1655, NC_000913.3 PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: wig files PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	For the RNA-seq samples, the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction. For the ChIP-seq samples, the E. coli cells were fixed with 1% formaldehyde with continued shaking at 37 °C for 10 minutes before quenching with glycine (100 mM final concentration). Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment. PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	A new RNA-seq method SEnd-seq was developed and used to prepare the SEnd-seq library, standard RNA-seq library was prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) following the manufacturer’s instructions, ChIP-seq library was prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645)after ChIP DNA enrichment. For SEnd_seq, the RNA was ligated to a RNA adaptor (/5Phos/rNrNrN rNrArArCrCrUrGrCrUrArUrCrArArCrUrG/3ddC/ or /5Phos/rNrNrN rNrGrCrUrUrCrCrUrGrCrUrArUrCrArArCrUrG/3ddC/), both adaptors were used if two different samples were mixed together for library preparation(Log phase samples used the first one and stationary phase samples used the second one). The ligated RNA was converted to cDNA with the same Biotinylated RT primer(5GGGCAG T/iBiodT/GATAGCAGG). For RNA-seq , rRNA was depleted with the Ribo-Zero rRNA Removal Kit. The sequencing library was prepared with the TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions. For ChIP-seq, the enriched ChIP DNA and input DNA sequencing libraries were prepared with NEBNext Ultra II DNA Library Prep Kit. PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	source_name	E.coli cell PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	growth stage: Log phase PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	treatment: 37°C culture PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	strain: wild type PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	source_name	E.coli cell PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	PMID_31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	contact_name	Xiangwu,,Ju PGCGROWTHCONDITIONS