SRX4714451 GSM3395051 SRP162098 SRS3800163 GSM3395051 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395051 GSM3395051 GEO Accession GSM3395051 SRX4714452 GSM3395052 SRP162098 SRS3800162 GSM3395052 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395052 GSM3395052 GEO Accession GSM3395052 SRX4714453 GSM3395053 SRP162098 SRS3800164 GSM3395053 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395053 GSM3395053 GEO Accession GSM3395053 SRX4714454 GSM3395054 SRP162098 SRS3800165 GSM3395054 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395054 GSM3395054 GEO Accession GSM3395054 SRX4714455 GSM3395055 SRP162098 SRS3800166 GSM3395055 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395055 GSM3395055 GEO Accession GSM3395055 SRX4714456 GSM3395056 SRP162098 SRS3800167 GSM3395056 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395056 GSM3395056 GEO Accession GSM3395056 SRX4714457 GSM3395057 SRP162098 SRS3800169 GSM3395057 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395057 GSM3395057 GEO Accession GSM3395057 SRX4714458 GSM3395058 SRP162098 SRS3800168 GSM3395058 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395058 GSM3395058 GEO Accession GSM3395058 SRX4714459 GSM3395059 SRP162098 SRS3800170 GSM3395059 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395059 GSM3395059 GEO Accession GSM3395059 SRX4714460 GSM3395060 SRP162098 SRS3800171 GSM3395060 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395060 GSM3395060 GEO Accession GSM3395060 SRX4714461 GSM3395061 SRP162098 SRS3800172 GSM3395061 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395061 GSM3395061 GEO Accession GSM3395061 SRX4714462 GSM3395062 SRP162098 SRS3800173 GSM3395062 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395062 GSM3395062 GEO Accession GSM3395062 SRX4714463 GSM3395063 SRP162098 SRS3800174 GSM3395063 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395063 GSM3395063 GEO Accession GSM3395063 SRX4714464 GSM3395064 SRP162098 SRS3800175 GSM3395064 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395064 GSM3395064 GEO Accession GSM3395064 SRX4714465 GSM3395065 SRP162098 SRS3800176 GSM3395065 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395065 GSM3395065 GEO Accession GSM3395065 SRX4714466 GSM3395066 SRP162098 SRS3800177 GSM3395066 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395066 GSM3395066 GEO Accession GSM3395066 SRX4714467 GSM3395067 SRP162098 SRS3800178 GSM3395067 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395067 GSM3395067 GEO Accession GSM3395067 SRX4714468 GSM3395068 SRP162098 SRS3800202 GSM3395068 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395068 GSM3395068 GEO Accession GSM3395068 SRX4714469 GSM3395069 SRP162098 SRS3800179 GSM3395069 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395069 GSM3395069 GEO Accession GSM3395069 SRX4714470 GSM3395070 SRP162098 SRS3800180 GSM3395070 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395070 GSM3395070 GEO Accession GSM3395070 SRX4714471 GSM3395071 SRP162098 SRS3800181 GSM3395071 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395071 GSM3395071 GEO Accession GSM3395071 SRX4714472 GSM3395072 SRP162098 SRS3800182 GSM3395072 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395072 GSM3395072 GEO Accession GSM3395072 SRX4714473 GSM3395073 SRP162098 SRS3800183 GSM3395073 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395073 GSM3395073 GEO Accession GSM3395073 SRX4714474 GSM3395074 SRP162098 SRS3800184 GSM3395074 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395074 GSM3395074 GEO Accession GSM3395074 SRX4714475 GSM3395075 SRP162098 SRS3800185 GSM3395075 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395075 GSM3395075 GEO Accession GSM3395075 SRX4714476 GSM3395076 SRP162098 SRS3800186 GSM3395076 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395076 GSM3395076 GEO Accession GSM3395076 SRX4714477 GSM3395077 SRP162098 SRS3800187 GSM3395077 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395077 GSM3395077 GEO Accession GSM3395077 SRX4714478 GSM3395078 SRP162098 SRS3800188 GSM3395078 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395078 GSM3395078 GEO Accession GSM3395078 SRX4714479 GSM3395079 SRP162098 SRS3800214 GSM3395079 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395079 GSM3395079 GEO Accession GSM3395079 SRX4714480 GSM3395080 SRP162098 SRS3800189 GSM3395080 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395080 GSM3395080 GEO Accession GSM3395080 SRX4714481 GSM3395081 SRP162098 SRS3800190 GSM3395081 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 303395081 GSM3395081 GEO Accession GSM3395081 SRX4714482 GSM3395082 SRP162098 SRS3800191 GSM3395082 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. Illumina HiSeq 2500 gds 303395082 GSM3395082 GEO Accession GSM3395082 SRX4714483 GSM3395083 SRP162098 SRS3800192 GSM3395083 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. Illumina HiSeq 2500 gds 303395083 GSM3395083 GEO Accession GSM3395083 SRX4714484 GSM3395084 SRP162098 SRS3800193 GSM3395084 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. Illumina HiSeq 2500 gds 303395084 GSM3395084 GEO Accession GSM3395084 SRX4714485 GSM3395085 SRP162098 SRS3800194 GSM3395085 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395085 GSM3395085 GEO Accession GSM3395085 SRX4714486 GSM3395086 SRP162098 SRS3800195 GSM3395086 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395086 GSM3395086 GEO Accession GSM3395086 SRX4714487 GSM3395087 SRP162098 SRS3800196 GSM3395087 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395087 GSM3395087 GEO Accession GSM3395087 SRX4714488 GSM3395088 SRP162098 SRS3800197 GSM3395088 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395088 GSM3395088 GEO Accession GSM3395088 SRX4714489 GSM3395089 SRP162098 SRS3800198 GSM3395089 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395089 GSM3395089 GEO Accession GSM3395089 SRX4714490 GSM3395090 SRP162098 SRS3800199 GSM3395090 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395090 GSM3395090 GEO Accession GSM3395090 SRX4714491 GSM3395091 SRP162098 SRS3800200 GSM3395091 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395091 GSM3395091 GEO Accession GSM3395091 SRX4714492 GSM3395092 SRP162098 SRS3800201 GSM3395092 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395092 GSM3395092 GEO Accession GSM3395092 SRX4714493 GSM3395093 SRP162098 SRS3800203 GSM3395093 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395093 GSM3395093 GEO Accession GSM3395093 SRX4714494 GSM3395094 SRP162098 SRS3800204 GSM3395094 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395094 GSM3395094 GEO Accession GSM3395094 SRX4714495 GSM3395095 SRP162098 SRS3800205 GSM3395095 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395095 GSM3395095 GEO Accession GSM3395095 SRX4714496 GSM3395096 SRP162098 SRS3800206 GSM3395096 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395096 GSM3395096 GEO Accession GSM3395096 SRX4714497 GSM3395097 SRP162098 SRS3800207 GSM3395097 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395097 GSM3395097 GEO Accession GSM3395097 SRX4714498 GSM3395098 SRP162098 SRS3800208 GSM3395098 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395098 GSM3395098 GEO Accession GSM3395098 SRX4714499 GSM3395099 SRP162098 SRS3800209 GSM3395099 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395099 GSM3395099 GEO Accession GSM3395099 SRX4714500 GSM3395100 SRP162098 SRS3800210 GSM3395100 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. Illumina HiSeq 2500 gds 303395100 GSM3395100 GEO Accession GSM3395100 SRX4714501 GSM3395101 SRP162098 SRS3800211 GSM3395101 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. Illumina HiSeq 2500 gds 303395101 GSM3395101 GEO Accession GSM3395101 SRX4714502 GSM3395102 SRP162098 SRS3800212 GSM3395102 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395102 GSM3395102 GEO Accession GSM3395102 SRX4714503 GSM3395103 SRP162098 SRS3800213 GSM3395103 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. Illumina HiSeq 2500 gds 303395103 GSM3395103 GEO Accession GSM3395103 SRX4714504 GSM3395104 SRP162098 SRS3800215 GSM3395104 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395104 GSM3395104 GEO Accession GSM3395104 SRX4714505 GSM3395105 SRP162098 SRS3800216 GSM3395105 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. Illumina HiSeq 2500 gds 303395105 GSM3395105 GEO Accession GSM3395105 SRX4714506 GSM3395106 SRP162098 SRS3800217 GSM3395106 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. NextSeq 500 gds 303395106 GSM3395106 GEO Accession GSM3395106 SRX4714507 GSM3395107 SRP162098 SRS3800218 GSM3395107 RNA-Seq TRANSCRIPTOMIC cDNA RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads. To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads. Illumina HiSeq 2500 gds 303395107 GSM3395107 GEO Accession GSM3395107 SRX4714508 GSM3395108 SRP162098 SRS3800219 GSM3395108 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395108 GSM3395108 GEO Accession GSM3395108 SRX4714509 GSM3395109 SRP162098 SRS3800220 GSM3395109 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395109 GSM3395109 GEO Accession GSM3395109 SRX4714510 GSM3395110 SRP162098 SRS3800221 GSM3395110 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395110 GSM3395110 GEO Accession GSM3395110 SRX4714511 GSM3395111 SRP162098 SRS3800222 GSM3395111 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395111 GSM3395111 GEO Accession GSM3395111 SRX4714512 GSM3395112 SRP162098 SRS3800224 GSM3395112 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395112 GSM3395112 GEO Accession GSM3395112 SRX4714513 GSM3395113 SRP162098 SRS3800223 GSM3395113 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395113 GSM3395113 GEO Accession GSM3395113 SRX4714514 GSM3395114 SRP162098 SRS3800227 GSM3395114 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395114 GSM3395114 GEO Accession GSM3395114 SRX4714515 GSM3395115 SRP162098 SRS3800225 GSM3395115 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395115 GSM3395115 GEO Accession GSM3395115 SRX4714516 GSM3395116 SRP162098 SRS3800228 GSM3395116 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395116 GSM3395116 GEO Accession GSM3395116 SRX4714517 GSM3395117 SRP162098 SRS3800226 GSM3395117 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395117 GSM3395117 GEO Accession GSM3395117 SRX4714518 GSM3395118 SRP162098 SRS3800229 GSM3395118 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395118 GSM3395118 GEO Accession GSM3395118 SRX4714519 GSM3395119 SRP162098 SRS3800230 GSM3395119 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395119 GSM3395119 GEO Accession GSM3395119 SRX4714520 GSM3395120 SRP162098 SRS3800231 GSM3395120 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395120 GSM3395120 GEO Accession GSM3395120 SRX4714521 GSM3395121 SRP162098 SRS3800232 GSM3395121 Hi-C GENOMIC other In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate. Illumina HiSeq 2500 gds 303395121 GSM3395121 GEO Accession GSM3395121 SRX6639035 GSM4001131 SRP162098 PRJNA491819 SRS5209769 GSM4001131 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 304001131 GSM4001131 SRX6639036 GSM4001132 SRP162098 PRJNA491819 SRS5209770 GSM4001132 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 304001132 GSM4001132 SRX6639037 GSM4001133 SRP162098 PRJNA491819 SRS5209772 GSM4001133 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 304001133 GSM4001133 SRX6639038 GSM4001134 SRP162098 PRJNA491819 SRS5209771 GSM4001134 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 304001134 GSM4001134 SRX6639039 GSM4001135 SRP162098 PRJNA491819 SRS5209773 GSM4001135 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 304001135 GSM4001135 SRX6639040 GSM4001136 SRP162098 PRJNA491819 SRS5209774 GSM4001136 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 304001136 GSM4001136 SRX6639041 GSM4001137 SRP162098 PRJNA491819 SRS5209775 GSM4001137 ChIP-Seq GENOMIC ChIP Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment. NextSeq 500 gds 304001137 GSM4001137 SRX7066599 GSM4142785 SRP162098 PRJNA491819 SRS5583223 GSM4142785 ATAC-seq GENOMIC other For nuclei preparation, 5x10e6 cells were washed with cold phosphate-buffered saline (PBS), harvested in cold PBS supplemented with protease inhibitor cocktail (PIC, Roche), and cell pellets obtained by centrifugation at 900xg for 5 min at 4ºC. The cell pellet was gently resuspended in 50 µl of RBS buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with PIC, and then 1.3 ml of RBS buffer - 0.1% Igepal CA-630 was added, followed by centrifugation at 500xg for 10 min at 4ºC. The supernatant was carefully discarded and 1 ml of RBS buffer was added to resuspend the cell nuclei. For the transposition reaction, 50,000 nuclei were resuspended in 25 µl 2X TD Buffer (Illumina 121-1030), 2.5 µl Tn5 Transposase (Illumina 121-1030) in a final volume of 50 µl. The reaction mix was incubated for 30 min at 37ºC C and DNA purified using the Qiagen Mini-Elute Kit in 10 µl Tris buffer 10mM, pH8.0. Eluate was subjected to PCR amplification in a volume of 50 µl as follow NextSeq 500 gds 304142785 GSM4142785 GEO Accession GSM4142785 SRX7066600 GSM4142786 SRP162098 PRJNA491819 SRS5583224 GSM4142786 ATAC-seq GENOMIC other For nuclei preparation, 5x10e6 cells were washed with cold phosphate-buffered saline (PBS), harvested in cold PBS supplemented with protease inhibitor cocktail (PIC, Roche), and cell pellets obtained by centrifugation at 900xg for 5 min at 4ºC. The cell pellet was gently resuspended in 50 µl of RBS buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with PIC, and then 1.3 ml of RBS buffer - 0.1% Igepal CA-630 was added, followed by centrifugation at 500xg for 10 min at 4ºC. The supernatant was carefully discarded and 1 ml of RBS buffer was added to resuspend the cell nuclei. For the transposition reaction, 50,000 nuclei were resuspended in 25 µl 2X TD Buffer (Illumina 121-1030), 2.5 µl Tn5 Transposase (Illumina 121-1030) in a final volume of 50 µl. The reaction mix was incubated for 30 min at 37ºC C and DNA purified using the Qiagen Mini-Elute Kit in 10 µl Tris buffer 10mM, pH8.0. Eluate was subjected to PCR amplification in a volume of 50 µl as follow NextSeq 500 gds 304142786 GSM4142786 GEO Accession GSM4142786 SRX7066601 GSM4142787 SRP162098 PRJNA491819 SRS5583225 GSM4142787 ATAC-seq GENOMIC other For nuclei preparation, 5x10e6 cells were washed with cold phosphate-buffered saline (PBS), harvested in cold PBS supplemented with protease inhibitor cocktail (PIC, Roche), and cell pellets obtained by centrifugation at 900xg for 5 min at 4ºC. The cell pellet was gently resuspended in 50 µl of RBS buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with PIC, and then 1.3 ml of RBS buffer - 0.1% Igepal CA-630 was added, followed by centrifugation at 500xg for 10 min at 4ºC. The supernatant was carefully discarded and 1 ml of RBS buffer was added to resuspend the cell nuclei. For the transposition reaction, 50,000 nuclei were resuspended in 25 µl 2X TD Buffer (Illumina 121-1030), 2.5 µl Tn5 Transposase (Illumina 121-1030) in a final volume of 50 µl. The reaction mix was incubated for 30 min at 37ºC C and DNA purified using the Qiagen Mini-Elute Kit in 10 µl Tris buffer 10mM, pH8.0. Eluate was subjected to PCR amplification in a volume of 50 µl as follow NextSeq 500 gds 304142787 GSM4142787 GEO Accession GSM4142787