SRX12709509 GSM5643085_r1 SRP342438 GSE186285 SRS10658967 GSM5643085 GSM5643085 OTHER TRANSCRIPTOMIC other Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted. Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR. Illumina HiSeq 2000 SRX12709510 GSM5643086_r1 SRP342438 GSE186285 SRS10658968 GSM5643086 GSM5643086 OTHER TRANSCRIPTOMIC other Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted. Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR. Illumina HiSeq 2000 SRX12709511 GSM5643087_r1 SRP342438 GSE186285 SRS10658969 GSM5643087 GSM5643087 OTHER TRANSCRIPTOMIC other Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted. Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR. Illumina HiSeq 2000 SRX12709512 GSM5643088_r1 SRP342438 GSE186285 SRS10658970 GSM5643088 GSM5643088 OTHER TRANSCRIPTOMIC other Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted. Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR. Illumina HiSeq 2000 SRX12709513 GSM5643089_r1 SRP342438 GSE186285 SRS10658971 GSM5643089 GSM5643089 OTHER TRANSCRIPTOMIC other Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted. Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR. Illumina HiSeq 2000 SRX12709514 GSM5643090_r1 SRP342438 GSE186285 SRS10658972 GSM5643090 GSM5643090 OTHER TRANSCRIPTOMIC other Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted. Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR. Illumina HiSeq 2000 SRX12709515 GSM5643091_r1 SRP342438 GSE186285 SRS10658973 GSM5643091 GSM5643091 OTHER TRANSCRIPTOMIC other Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted. Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR. Illumina HiSeq 2000 SRX12709516 GSM5643092_r1 SRP342438 GSE186285 SRS10658974 GSM5643092 GSM5643092 OTHER TRANSCRIPTOMIC other Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted. Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR. Illumina HiSeq 2000