SRX1662134 GSM2098985 SRP072354 SRS1361746 GSM2098985 OTHER GENOMIC other Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight. The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours. The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry. Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. 500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. The product then underwent gel extraction (Qiagen). Illumina HiSeq 2500 gds 302098985 GEO Accession GSM2098985 SRX1662135 GSM2098986 SRP072354 SRS1361745 GSM2098986 OTHER GENOMIC other Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight. The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours. The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry. Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. 500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. The product then underwent gel extraction (Qiagen). Illumina HiSeq 2500 gds 302098986 GEO Accession GSM2098986 SRX1662136 GSM2098987 SRP072354 SRS1361744 GSM2098987 OTHER GENOMIC other Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight. The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours. The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry. Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. 500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. The product then underwent gel extraction (Qiagen). Illumina HiSeq 2500 gds 302098987 GEO Accession GSM2098987 SRX1662137 GSM2098988 SRP072354 SRS1361743 GSM2098988 OTHER GENOMIC other Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight. The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours. The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry. Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. 500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. The product then underwent gel extraction (Qiagen). Illumina HiSeq 2500 gds 302098988 GEO Accession GSM2098988 SRX1662138 GSM2098989 SRP072354 SRS1361742 GSM2098989 OTHER GENOMIC other Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight. The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours. The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry. Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. 500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. The product then underwent gel extraction (Qiagen). Illumina HiSeq 2500 gds 302098989 GEO Accession GSM2098989 SRX1662139 GSM2098990 SRP072354 SRS1361741 GSM2098990 OTHER GENOMIC other Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight. The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours. The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry. Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. 500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. The product then underwent gel extraction (Qiagen). Illumina HiSeq 2500 gds 302098990 GEO Accession GSM2098990 SRX1662140 GSM2098991 SRP072354 SRS1361740 GSM2098991 OTHER GENOMIC other Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight. The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours. The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry. Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. 500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. The product then underwent gel extraction (Qiagen). Illumina HiSeq 2500 gds 302098991 GEO Accession GSM2098991 SRX1662141 GSM2098992 SRP072354 SRS1361739 GSM2098992 OTHER GENOMIC other Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight. The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours. The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry. Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. 500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. The product then underwent gel extraction (Qiagen). Illumina HiSeq 2500 gds 302098992 GEO Accession GSM2098992