SRX2765963 GSM2589814 SRP105278 SRS2150050 GSM2589814 ChIP-Seq GENOMIC ChIP For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research). DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. Illumina HiSeq 4000 gds 302589814 GSM2589814 GEO Accession GSM2589814 SRX2765964 GSM2589815 SRP105278 SRS2150051 GSM2589815 ChIP-Seq GENOMIC ChIP For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research). DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. Illumina HiSeq 4000 gds 302589815 GSM2589815 GEO Accession GSM2589815 SRX2765965 GSM2589816 SRP105278 SRS2150052 GSM2589816 ChIP-Seq GENOMIC ChIP For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research). DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. Illumina HiSeq 4000 gds 302589816 GSM2589816 GEO Accession GSM2589816 SRX2765966 GSM2589817 SRP105278 SRS2150053 GSM2589817 ChIP-Seq GENOMIC ChIP For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research). DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. Illumina HiSeq 4000 gds 302589817 GSM2589817 GEO Accession GSM2589817 SRX2765967 GSM2589818 SRP105278 SRS2150054 GSM2589818 ChIP-Seq GENOMIC ChIP For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research). DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. Illumina HiSeq 4000 gds 302589818 GSM2589818 GEO Accession GSM2589818 SRX2765968 GSM2589819 SRP105278 SRS2150055 GSM2589819 ChIP-Seq GENOMIC ChIP For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research). DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. Illumina HiSeq 4000 gds 302589819 GSM2589819 GEO Accession GSM2589819 SRX3585704 GSM2936332 SRP105278 PRJNA384392 SRS2858951 GSM2936332 ChIP-Seq GENOMIC ChIP For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer's instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research). DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. Illumina HiSeq 4000 gds 302936332 GSM2936332 GEO Accession GSM2936332