SRX3029194 GSM2710946 SRP113409 SRS2378111 GSM2710946 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016). Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). NextSeq 500 gds 302710946 GSM2710946 GEO Accession GSM2710946 SRX3029195 GSM2710947 SRP113409 SRS2378112 GSM2710947 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016). Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). NextSeq 500 gds 302710947 GSM2710947 GEO Accession GSM2710947 SRX3029196 GSM2710948 SRP113409 SRS2378113 GSM2710948 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016). Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). NextSeq 500 gds 302710948 GSM2710948 GEO Accession GSM2710948 SRX3029197 GSM2710949 SRP113409 SRS2378114 GSM2710949 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016). Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). NextSeq 500 gds 302710949 GSM2710949 GEO Accession GSM2710949 SRX3029198 GSM2710950 SRP113409 SRS2378115 GSM2710950 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016). Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). NextSeq 500 gds 302710950 GSM2710950 GEO Accession GSM2710950 SRX3029199 GSM2710951 SRP113409 SRS2378116 GSM2710951 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016). Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). NextSeq 500 gds 302710951 GSM2710951 GEO Accession GSM2710951 SRX3029200 GSM2710952 SRP113409 SRS2378117 GSM2710952 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016). Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). NextSeq 500 gds 302710952 GSM2710952 GEO Accession GSM2710952 SRX3029201 GSM2710953 SRP113409 SRS2378118 GSM2710953 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016). Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). NextSeq 500 gds 302710953 GSM2710953 GEO Accession GSM2710953 SRX3029202 GSM2710954 SRP113409 SRS2378119 GSM2710954 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710954 GSM2710954 GEO Accession GSM2710954 SRX3029203 GSM2710955 SRP113409 SRS2378120 GSM2710955 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710955 GSM2710955 GEO Accession GSM2710955 SRX3029204 GSM2710956 SRP113409 SRS2378121 GSM2710956 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710956 GSM2710956 GEO Accession GSM2710956 SRX3029205 GSM2710957 SRP113409 SRS2378122 GSM2710957 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710957 GSM2710957 GEO Accession GSM2710957 SRX3029206 GSM2710958 SRP113409 SRS2378123 GSM2710958 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710958 GSM2710958 GEO Accession GSM2710958 SRX3029207 GSM2710959 SRP113409 SRS2378124 GSM2710959 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710959 GSM2710959 GEO Accession GSM2710959 SRX3029208 GSM2710960 SRP113409 SRS2378125 GSM2710960 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710960 GSM2710960 GEO Accession GSM2710960 SRX3029209 GSM2710961 SRP113409 SRS2378126 GSM2710961 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710961 GSM2710961 GEO Accession GSM2710961 SRX3029210 GSM2710962 SRP113409 SRS2378127 GSM2710962 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710962 GSM2710962 GEO Accession GSM2710962 SRX3029211 GSM2710963 SRP113409 SRS2378128 GSM2710963 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710963 GSM2710963 GEO Accession GSM2710963 SRX3029212 GSM2710964 SRP113409 SRS2378129 GSM2710964 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710964 GSM2710964 GEO Accession GSM2710964 SRX3029213 GSM2710965 SRP113409 SRS2378130 GSM2710965 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710965 GSM2710965 GEO Accession GSM2710965 SRX3029214 GSM2710966 SRP113409 SRS2378131 GSM2710966 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710966 GSM2710966 GEO Accession GSM2710966 SRX3029215 GSM2710967 SRP113409 SRS2378132 GSM2710967 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710967 GSM2710967 GEO Accession GSM2710967 SRX3029216 GSM2710968 SRP113409 SRS2378133 GSM2710968 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710968 GSM2710968 GEO Accession GSM2710968 SRX3029217 GSM2710969 SRP113409 SRS2378134 GSM2710969 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710969 GSM2710969 GEO Accession GSM2710969 SRX3029218 GSM2710970 SRP113409 SRS2378135 GSM2710970 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710970 GSM2710970 GEO Accession GSM2710970 SRX3029219 GSM2710971 SRP113409 SRS2378136 GSM2710971 ChIP-Seq GENOMIC ChIP Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). NextSeq 500 gds 302710971 GSM2710971 GEO Accession GSM2710971 SRX3029220 GSM2710972 SRP113409 SRS2378137 GSM2710972 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710972 GSM2710972 GEO Accession GSM2710972 SRX3029221 GSM2710973 SRP113409 SRS2378138 GSM2710973 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710973 GSM2710973 GEO Accession GSM2710973 SRX3029222 GSM2710974 SRP113409 SRS2378139 GSM2710974 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710974 GSM2710974 GEO Accession GSM2710974 SRX3029223 GSM2710975 SRP113409 SRS2378140 GSM2710975 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710975 GSM2710975 GEO Accession GSM2710975 SRX3029224 GSM2710976 SRP113409 SRS2378141 GSM2710976 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710976 GSM2710976 GEO Accession GSM2710976 SRX3029225 GSM2710977 SRP113409 SRS2378142 GSM2710977 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710977 GSM2710977 GEO Accession GSM2710977 SRX3029226 GSM2710978 SRP113409 SRS2378143 GSM2710978 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710978 GSM2710978 GEO Accession GSM2710978 SRX3029227 GSM2710979 SRP113409 SRS2378144 GSM2710979 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710979 GSM2710979 GEO Accession GSM2710979 SRX3029228 GSM2710980 SRP113409 SRS2378145 GSM2710980 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710980 GSM2710980 GEO Accession GSM2710980 SRX3029229 GSM2710981 SRP113409 SRS2378146 GSM2710981 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710981 GSM2710981 GEO Accession GSM2710981 SRX3029230 GSM2710982 SRP113409 SRS2378147 GSM2710982 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710982 GSM2710982 GEO Accession GSM2710982 SRX3029231 GSM2710983 SRP113409 SRS2378148 GSM2710983 Bisulfite-Seq GENOMIC RANDOM Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN). DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries. Illumina HiSeq 2000 gds 302710983 GSM2710983 GEO Accession GSM2710983