SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	library strategy: 3[linebreak]-end RNA-seq PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	FastQ files were examined using the FastQC tool. Reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Escherichia coli str. K-12 substr. MG1655 (GenBank: U00096.2) was used as the reference genome. Reads were mapped to the reference genome using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5). PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Genome_build: U00096.2 PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Mapped reads were rescaled to a size of 10 bp, and BEDGraph files were generated using the genomeCoverageBed utility of the BEDTools suite. PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: DMS-seq data (pooled Total and Ribo- RNA) is provided in the form of RNA Framework[linebreak]s (http://www.rnaframework.com) RNA Count (RC) files. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: SPET-seq data (pooled Total and Ribo- RNA from both replicates) is provided in the form of RNA Framework[linebreak]s (http://www.rnaframework.com) RNA Count (RC) files. For each analyzed transcript, 10 files corresponding to SPET-seq data for the 10 transcription deciles are provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: SPET-seq data is provided in the form of RNA Framework[linebreak]s (http://www.rnaframework.com) RNA Count (RC) files. A file corresponding to each transcription intermediate is provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	Each bacteria pellet from a 25 ml culture (OD600 ~0.3) was homogeneously resuspended in 200 µl of Buffer A [10 mM Tris pH 8.0; 20% Sucrose; 100 mM NaCl] supplemented with 200 U SUPERase• In™ RNase Inhibitor, by pipetting. 50 µl of Buffer B [50 mM EDTA; 120 mM Tris pH 8.0] supplemented with 1 µl Ready-Lyse™ Lysozyme Solution (Epicentre, cat. R1810M) were added dropwise, and the vial was gently tilted 5 times to ensure homogenous mixing. The sample was then incubated 1 minute at room temperature. 250 µl of Buffer C [0.5% Tween-20: 0.4% NaDOC; 2 M NaCl; 10 mM EDTA] were immediately added dropwise. The sample was then incubated 5 minutes at room temperature. At this stage the solution clears considerably without increasing its viscosity, and nucleoid becomes visible. Using a cut P1000 pipette tip, the whole sample was gently layered on the top of a 5-30% w/v sucrose gradient [10 mM Tris pH 8.0; 1 M NaCl; 1 mM EDTA; 1 mM DTT], and centrifuged at 17,000 RPM in a SW55Ti rotor (Beckman Coulter, cat. 342194) for 9 minutes (4°C). After centrifugation, the nucleoid fraction was collected using a syringe with a 18G blunt fill needle, and transferred to a new centrifuge tube. The remaining gradient was assumed to represent the cytosolic fraction. The nucleoid was then resuspended in 2.5 ml Wash & Resuspension buffer [40 mM Tris pH 7.5; 150 mM KCl; 10 mM MgCl2; 1 mM DTT; 0.01% Triton X-100] supplemented with 200 U SUPERase• In™ RNase Inhibitor, pulse vortexed for 5 seconds, and then centrifuged at 28,000 RPM in a SW55Ti rotor for 30 minutes (0°C). After centrifugation the supernatant was decanted, and the nucleoid pellet was washed twice with 2 ml of Wash & Resuspension buffer, taking care not to disturb it. The nucleoid was then resuspended in 500 µl Wash & Resuspension buffer, and solubilized by addition of 0.1 gr acid-washed glass beads (Sigma, cat. G1145), and shaking for 5 minutes in a TissueLyser (QIAGEN). For each 100 µl of purified nucleoids (or cytosolic fraction), 1 ml of TRIzol® Reagent (Invitrogen, cat. 15596-018) was added, and RNA was extracted following manufacturer’s instructions. RNA was analyzed on a 2100 Bioanalyzer (Agilent). In all experiments, RNA from cytosolic fraction (corresponding to mature RNA species) had RIN > 9.5. Total RNA yield from nucleoid fraction was ~6% of the total RNA content. PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	10 pmol of a pre-adenylated (rApp) adapter were ligated to 1 μg of nascent (or mature) RNA in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant (Epicentre, cat. LR2D11310K) in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 20 μl of Fragmentation buffer [65 mM Tris pH 8.3; 100 mM KCl; 5 mM MgCl2]. RNA was fragmented by incubation at 95°C for 8 minutes. Fragmented RNA was purified using RNA Clean & Concentrator™-5 columns, and eluted in 5.5 μl of nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor (Invitrogen, cat. 10777-019), and 100 U SuperScript® III Reverse Transcriptase (Invitrogen, cat. 18080-044), by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments in the range 40-150 nt was cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg/μl), and resuspended in 8.25 μl nuclease-free water. 10 pmol of a 5’-phosphorylated adapter were ligated to the 3’-OH of cDNA fragments in a final reaction volume of 25 μl, in the presence of 0.05 mM ATP, 20% PEG-4000, and 100 U CircLigase™ II ssDNA Ligase (Epicentre, cat. CL9025K), by incubation at 60°C for 4 hours, and 68°C for 2 hours. Adapter-ligated cDNA fragments were purified from excess adapter using 1.8 volumes of Agencourt AMPure XP beads (Beckman Coulter, cat. A63881), following manufacturer’s instructions. cDNA was eluted in 20 μl of nuclease-free water, and indexed sequencing adapters were introduced by 15 cycles of PCR in the presence of 25 pmol of each primer, and 25 μl NEBNext® High-Fidelity 2X PCR Master Mix (NEB, cat. M0541L). PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	source_name	3[linebreak]-end RNA-seq, Nucleoid fraction PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	strain: K-12 PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	substr: MG1655 PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	molecule subtype: Total RNA (Nucleoid fraction) PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	source_name	3[linebreak]-end RNA-seq, Nucleoid fraction PGCGROWTHCONDITIONS
SRR5298763SRR5298765SRR5298766	GSE95567	GSM2516402	GPL16085-GPL21222	PMID_28934475	3'-end RNA-seq, Nucleoid fraction, Replicate #2	In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	contact_name	Danny,,Incarnato PGCGROWTHCONDITIONS