SRX23255250 MEF wt CTCF (rep1) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135339 SAMN28591543 MEF wt CTCF (rep1) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255251 MEF wt CTCF input (rep1) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135339 SAMN28591543 MEF wt CTCF input (rep1) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255252 Melanocytes del30k H3K27ac SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13010007 SAMN28415518 Melanocytes del30k H3K27ac ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255253 Melanocytes del30k H3K27ac input SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13010007 SAMN28415518 Melanocytes del30k H3K27ac input ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255254 MEF del60k CTCF (rep1) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135340 SAMN28591544 MEF del60k CTCF (rep1) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255255 MEF del60k CTCF input (rep1) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135340 SAMN28591544 MEF del60k CTCF input (rep1) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255256 MEF del60k CTCF (rep2) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135340 SAMN28591544 MEF del60k CTCF (rep2) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255257 MEF del60k CTCF input (rep2) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135340 SAMN28591544 MEF del60k CTCF input (rep2) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255258 MEF wt CTCF (rep2) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135339 SAMN28591543 MEF wt CTCF (rep2) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255259 MEF wt CTCF input (rep2) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135339 SAMN28591543 MEF wt CTCF input (rep2) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255260 MEF wt H3K27ac (rep1) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135339 SAMN28591543 MEF wt H3K27ac (rep1) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255261 MEF wt H3K27ac (rep2) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135339 SAMN28591543 MEF wt H3K27ac (rep2) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255262 Mast cells WT CTCF SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046060 SAMN28511996 Mast cells WT CTCF ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255263 MEF wt H3K27ac input (rep2) SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13135339 SAMN28591543 MEF wt H3K27ac input (rep2) ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255264 Melanocytes wt H3K27ac SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13010006 SAMN28415517 Melanocytes wt H3K27ac ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255265 Melanocytes wt H3K27ac input SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13010006 SAMN28415517 Melanocytes wt H3K27ac input ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255266 Mast cells del30k+ H3K27ac SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046061 SAMN28511999 Mast cells del30k+ H3K27ac ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255267 Mast cells del30k+ H3K27ac input SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046061 SAMN28511999 Mast cells del30k+ H3K27ac input ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255268 Mast cells WT CTCF input SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046060 SAMN28511996 Mast cells WT CTCF input ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255269 Mast cells del30k CTCF SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046062 SAMN28511997 Mast cells del30k CTCF ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255270 Mast cells del30k CTCF input SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046062 SAMN28511997 Mast cells del30k CTCF input ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255271 Mast cells del30k+ CTCF SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046061 SAMN28511999 Mast cells del30k+ CTCF ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255272 Mast cells del30k+ CTCF input SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046061 SAMN28511999 Mast cells del30k+ CTCF input ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255273 Mast cells del300k H3K27ac SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046063 SAMN28511998 Mast cells del300k H3K27ac ChIP-Seq GENOMIC ChIP DNBSEQ-T7 SRX23255274 Mast cells del300k H3K27ac input SRP375256 PRJNA838252 1-5 * 106 cells were crosslinked with 1% formaldehyde at RT for 10 min. Cells were lysed on ice in 0.5 ml lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.4-1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, Complete Mini EDTA-free protease inhibitor (Roche)). Lysed chromatin was fragmented using the BANDELIN SONOPULSE until reaching a fragment size of 150500 base pairs . SDS concentration and the number of sonication cycles were adjusted according to a cell type and shearing efficiency. SDS concentration was reduced before the immunoprecipitation step (~0.17% SDS final) by dilution with SDS-free lysis buffer. Chromatin was pre-cleared with Protein A magnetic beads, and 100L of the precleared solution was saved as an input control. During this time, an aliquot of Protein A beads was rotated with the respective antibody at 4 (1.5g or 5g of antibody for CTCF and H3K27ac ChIP reaction, respectively). Protein-DNA complexes were then immunoprecipitated overnight at 4 C with rotation. The beads were washed at 4 in the following buffers: lysis buffer (0.1% SDS, twice), lysis buffer containing 0.5M NaCl (twice), LiCl buffer (0.25 M LiCl, 0.5% IGEPAL-630, 0.5% sodium deoxycholate, twice), TE (pH 8.0) plus 0.2% Triton X-100 (once), and TE (pH 8.0, once). Crosslinks were reversed at 65 overnight and DNA was purified. Sequencing libraries were prepared using the KAPA Hyper Prep kit. SRS13046063 SAMN28511998 Mast cells del300k H3K27ac input ChIP-Seq GENOMIC ChIP DNBSEQ-T7