SRX2334055 GSM2385549 SRP058848 SRS1787947 GSM2385549 FAIRE-seq GENOMIC other FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen). Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific) Ion Torrent Proton gds 302385549 GEO Accession GSM2385549 SRX2334056 GSM2385550 SRP058848 SRS1787948 GSM2385550 FAIRE-seq GENOMIC other FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen). Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific) Ion Torrent Proton gds 302385550 GEO Accession GSM2385550 SRX2334057 GSM2385551 SRP058848 SRS1787949 GSM2385551 FAIRE-seq GENOMIC other FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen). Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific) Ion Torrent Proton gds 302385551 GEO Accession GSM2385551 SRX2334058 GSM2385552 SRP058848 SRS1787950 GSM2385552 FAIRE-seq GENOMIC other FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen). Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific) Ion Torrent Proton gds 302385552 GEO Accession GSM2385552 SRX2334059 GSM2385553 SRP058848 SRS1787951 GSM2385553 FAIRE-seq GENOMIC other FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen). Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific) Ion Torrent Proton gds 302385553 GEO Accession GSM2385553 SRX2334060 GSM2385554 SRP058848 SRS1787952 GSM2385554 FAIRE-seq GENOMIC other FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen). Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific) Ion Torrent Proton gds 302385554 GEO Accession GSM2385554 SRX2334061 GSM2385555 SRP058848 SRS1787953 GSM2385555 FAIRE-seq GENOMIC other FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen). Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific) Ion Torrent Proton gds 302385555 GEO Accession GSM2385555 SRX2334062 GSM2385556 SRP058848 SRS1787954 GSM2385556 FAIRE-seq GENOMIC other FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen). Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific) Ion Torrent Proton gds 302385556 GEO Accession GSM2385556