"The fastq files of 36-bp sequenced reads were generated with the CASAVA v1.8 (Illumina). For the bulk RNET-seq analysis, the specific adapter sequences were trimmed with the Trimmomatic v0.25 to obtain reads ≥ 21-nt from the 5’ end. The reads ≥ 21-nt were mapped to the reference genome of E. coli K-12 strain W3110 (NC_007779.1) using the Bowtie2 v2.1.0 with the default parameter. A gene annotation file of E. coli W3110 was downloaded from the ftp server of Ensembl."	"data_processing.1"
"To analyze RNAP pausing on the E. coli chromosome, we counted the number of reads at every genomic nucleotide position using the mpileup command of SAM tools v0.1.18 with –A –B parameters. Pausing sites were defined P(φ, δ), where φ is the minimal fraction of having 3’ RNA ends in the mapped reads and δ is the minimal read depth for any genomic position. We chose δ to be 100 for WT and 160 for ΔgreAB, which normalized these respective numbers for each strain since there were 1.6-fold more total reads in the ΔgreAB strain. The high φ parameter allowed us to define a reliable pause-inducing element for WT or ΔgreAB cells."	"data_processing.2"
"The processed data file (csv) includes information about genomic position, reference/non-reference bases, read count, the fraction of 3’ RNA end, DNA strand (+/-), gene name, and mapping/base qualities in transcriptional pause sites that are defined by the parameters P(0.9, 160)."	"data_processing.3"
"The 200 ml eluate from the Ni-NTA agarose was mixed with equal volume of pre-warmed PCI and incubated for 2 min at 70˚C. The mixture was centrifuged, and RNA and DNA were precipitated with isopropanol from the supernatant. The pellet was dissolved in 30 ml DNase I buffer with 5 U DNaseI (Takara Bio) and 20 U SUPERase, incubated for 10 min at RT. RNA was separated from the digested DNA by the PCI extraction and RNA was precipitated with isopropanol. The pellet was dissolved in diethylpyrocarbonate-treated water and used for cDNA synthesis."	"extract_protocol_ch1.1"
"cDNA library of the nascent RNA was constructed according to Churchman and Weissman, Nature 2011 (PMID: 21248844)."	"extract_protocol_ch1.2"
"The cells were grown in ~300 ml LB broth +25 mg/ml kanamycin with shaking at 37˚C until OD600 of ~0.5.The cells of 150 mg (wet weight) were harvested by centrifugation at 6,500 × g for 4 min at 4˚C, aliquoted in three 1.5 ml tubes, flash frozen in liquid nitrogen, and stored at -80˚C."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"W3110 rpoC-6xHis::kan greA::tet, greB::amp"	"source_name_ch1.1"
"Pause sites in E. coli ΔgreAB strain identified by RNET-seq"	"title.1"
"Each tube of the cell pellet stored at -80˚C was resuspended in 650 ml TES buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 100 mM NaCl, 0.1% TritonX 100, 0.3 mM PMSF) at room temperature (RT). The cell suspension was mixed with 100 kU Ready-Lyse Lysozyme (Epicentre) and 50 µg RNaseA (Sigma) and incubated for 5 min, allowing rapid cell lysis. To digest the nucleoide, 62.5 U DNaseI (Roche) and 250 µg/ml heparin at the final concentrations as well as 74 ml DNaseI buffer (10 mM MnCl2 10 mM Tris-HCl, pH 7.5) were added to the mixture and incubated for 10 min at RT. To remove cell debris, the mixture was centrifuged at 20,000 x g for 3 min at 4˚C and the supernatant was collected into a new 1.5 ml tube. The supernatant including RNAPs that form ternary complexes with RNA/DNA were immobilized on ~155 µl Ni-NTA agarose (Qiagen) pre-equilibrated with the binding buffer (0.5 M NaCl, 5 mM imidazole, 5% glycerol, 20 mM Tris-HCl, pH7.9, 1 mM 2-mercaptoethanol) with shaking for 10 min at 4˚C. The immobilized ternary complexes were washed five times with the wash buffer (1M NaCl, 15 mM imidazole, 5% glycerol, pH7.9, 1 mM 2-mercaptoethanol) at 4˚C, washed twice with the nuclease buffer (40 mM KCl, 15 mM imidazole, 20 mM Tris-HCl, pH 7.9, 0.3 mM MgCl2 5% glycerol, 1 mM 2-mercaptoethanol) at 4˚C. The RNA transcript and DNA unprotected by RNAP were cleaved by the additions of 0.4 U RNase V1 (Invitrogen), 0.7 U RNase T1 (Sigma), and 5 U DNase I (Takara Bio) to the immobilized complexes and incubation for 7 min at RT. The nuclease-treated complexes were washed twice with the wash buffer, twice with the MnCl2-free nuclease buffer at 4˚C, and eluted by increasing the concentration of imidazole to 100 mM followed by shaking for 10 min at 4˚C in the presence of 30 U SUPERase RNase inhibitor (Ambion)."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"genotype/variation: W3110 rpoC-6xHis::kan greA::tet, greB::amp"	"characteristics_ch1.1"
"molecule subtype: nascent 3' RNA"	"characteristics_ch1.2"
"The cells were grown in ~300 ml LB broth +25 mg/ml kanamycin with shaking at 37˚C until OD600 of ~0.5.The cells of 150 mg (wet weight) were harvested by centrifugation at 6,500 × g for 4 min at 4˚C, aliquoted in three 1.5 ml tubes, flash frozen in liquid nitrogen, and stored at -80˚C."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"W3110 rpoC-6xHis::kan greA::tet, greB::amp"	"source_name_ch1.1"
"Each tube of the cell pellet stored at -80˚C was resuspended in 650 ml TES buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 100 mM NaCl, 0.1% TritonX 100, 0.3 mM PMSF) at room temperature (RT). The cell suspension was mixed with 100 kU Ready-Lyse Lysozyme (Epicentre) and 50 µg RNaseA (Sigma) and incubated for 5 min, allowing rapid cell lysis. To digest the nucleoide, 62.5 U DNaseI (Roche) and 250 µg/ml heparin at the final concentrations as well as 74 ml DNaseI buffer (10 mM MnCl2 10 mM Tris-HCl, pH 7.5) were added to the mixture and incubated for 10 min at RT. To remove cell debris, the mixture was centrifuged at 20,000 x g for 3 min at 4˚C and the supernatant was collected into a new 1.5 ml tube. The supernatant including RNAPs that form ternary complexes with RNA/DNA were immobilized on ~155 µl Ni-NTA agarose (Qiagen) pre-equilibrated with the binding buffer (0.5 M NaCl, 5 mM imidazole, 5% glycerol, 20 mM Tris-HCl, pH7.9, 1 mM 2-mercaptoethanol) with shaking for 10 min at 4˚C. The immobilized ternary complexes were washed five times with the wash buffer (1M NaCl, 15 mM imidazole, 5% glycerol, pH7.9, 1 mM 2-mercaptoethanol) at 4˚C, washed twice with the nuclease buffer (40 mM KCl, 15 mM imidazole, 20 mM Tris-HCl, pH 7.9, 0.3 mM MgCl2 5% glycerol, 1 mM 2-mercaptoethanol) at 4˚C. The RNA transcript and DNA unprotected by RNAP were cleaved by the additions of 0.4 U RNase V1 (Invitrogen), 0.7 U RNase T1 (Sigma), and 5 U DNase I (Takara Bio) to the immobilized complexes and incubation for 7 min at RT. The nuclease-treated complexes were washed twice with the wash buffer, twice with the MnCl2-free nuclease buffer at 4˚C, and eluted by increasing the concentration of imidazole to 100 mM followed by shaking for 10 min at 4˚C in the presence of 30 U SUPERase RNase inhibitor (Ambion)."	"treatment_protocol_ch1.1"