SRX2875249 GSM2645495 SRP108392 SRS2245326 GSM2645495 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645495 GSM2645495 GEO Accession GSM2645495 SRX2875250 GSM2645496 SRP108392 SRS2245327 GSM2645496 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645496 GSM2645496 GEO Accession GSM2645496 SRX2875251 GSM2645497 SRP108392 SRS2245328 GSM2645497 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645497 GSM2645497 GEO Accession GSM2645497 SRX2875252 GSM2645498 SRP108392 SRS2245329 GSM2645498 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645498 GSM2645498 GEO Accession GSM2645498 SRX2875253 GSM2645499 SRP108392 SRS2245330 GSM2645499 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645499 GSM2645499 GEO Accession GSM2645499 SRX2875254 GSM2645500 SRP108392 SRS2245331 GSM2645500 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645500 GSM2645500 GEO Accession GSM2645500 SRX2875255 GSM2645501 SRP108392 SRS2245332 GSM2645501 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645501 GSM2645501 GEO Accession GSM2645501 SRX2875256 GSM2645502 SRP108392 SRS2245333 GSM2645502 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645502 GSM2645502 GEO Accession GSM2645502 SRX2875257 GSM2645503 SRP108392 SRS2245334 GSM2645503 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645503 GSM2645503 GEO Accession GSM2645503 SRX2875258 GSM2645504 SRP108392 SRS2245335 GSM2645504 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645504 GSM2645504 GEO Accession GSM2645504 SRX2875259 GSM2645505 SRP108392 SRS2245336 GSM2645505 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645505 GSM2645505 GEO Accession GSM2645505 SRX2875260 GSM2645506 SRP108392 SRS2245337 GSM2645506 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645506 GSM2645506 GEO Accession GSM2645506 SRX2875261 GSM2645507 SRP108392 SRS2245338 GSM2645507 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645507 GSM2645507 GEO Accession GSM2645507 SRX2875262 GSM2645508 SRP108392 SRS2245339 GSM2645508 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645508 GSM2645508 GEO Accession GSM2645508 SRX2875263 GSM2645509 SRP108392 SRS2245340 GSM2645509 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645509 GSM2645509 GEO Accession GSM2645509 SRX2875264 GSM2645510 SRP108392 SRS2245341 GSM2645510 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645510 GSM2645510 GEO Accession GSM2645510 SRX2875265 GSM2645511 SRP108392 SRS2245342 GSM2645511 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645511 GSM2645511 GEO Accession GSM2645511 SRX2875266 GSM2645512 SRP108392 SRS2245343 GSM2645512 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645512 GSM2645512 GEO Accession GSM2645512 SRX2875267 GSM2645513 SRP108392 SRS2245344 GSM2645513 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645513 GSM2645513 GEO Accession GSM2645513 SRX2875268 GSM2645514 SRP108392 SRS2245345 GSM2645514 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645514 GSM2645514 GEO Accession GSM2645514 SRX2875269 GSM2645515 SRP108392 SRS2245346 GSM2645515 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645515 GSM2645515 GEO Accession GSM2645515 SRX2875270 GSM2645516 SRP108392 SRS2245347 GSM2645516 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645516 GSM2645516 GEO Accession GSM2645516 SRX2875271 GSM2645517 SRP108392 SRS2245348 GSM2645517 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645517 GSM2645517 GEO Accession GSM2645517 SRX2875272 GSM2645518 SRP108392 SRS2245349 GSM2645518 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645518 GSM2645518 GEO Accession GSM2645518 SRX2875273 GSM2645519 SRP108392 SRS2245350 GSM2645519 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645519 GSM2645519 GEO Accession GSM2645519 SRX2875274 GSM2645520 SRP108392 SRS2245351 GSM2645520 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645520 GSM2645520 GEO Accession GSM2645520 SRX2875275 GSM2645521 SRP108392 SRS2245352 GSM2645521 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645521 GSM2645521 GEO Accession GSM2645521 SRX2875276 GSM2645522 SRP108392 SRS2245353 GSM2645522 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645522 GSM2645522 GEO Accession GSM2645522 SRX2875277 GSM2645523 SRP108392 SRS2245354 GSM2645523 ATAC-seq GENOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645523 GSM2645523 GEO Accession GSM2645523 SRX2875278 GSM2645524 SRP108392 SRS2245355 GSM2645524 ATAC-seq GENOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645524 GSM2645524 GEO Accession GSM2645524 SRX2875279 GSM2645525 SRP108392 SRS2245356 GSM2645525 ATAC-seq GENOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645525 GSM2645525 GEO Accession GSM2645525 SRX2875280 GSM2645526 SRP108392 SRS2245357 GSM2645526 ATAC-seq GENOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645526 GSM2645526 GEO Accession GSM2645526 SRX2875281 GSM2645527 SRP108392 SRS2245358 GSM2645527 ATAC-seq GENOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645527 GSM2645527 GEO Accession GSM2645527 SRX2875282 GSM2645528 SRP108392 SRS2245359 GSM2645528 ATAC-seq GENOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645528 GSM2645528 GEO Accession GSM2645528 SRX2875283 GSM2645529 SRP108392 SRS2245360 GSM2645529 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645529 GSM2645529 GEO Accession GSM2645529 SRX2875284 GSM2645530 SRP108392 SRS2245361 GSM2645530 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645530 GSM2645530 GEO Accession GSM2645530 SRX2875285 GSM2645531 SRP108392 SRS2245362 GSM2645531 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645531 GSM2645531 GEO Accession GSM2645531 SRX2875286 GSM2645532 SRP108392 SRS2245363 GSM2645532 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645532 GSM2645532 GEO Accession GSM2645532 SRX2875287 GSM2645533 SRP108392 SRS2245364 GSM2645533 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645533 GSM2645533 GEO Accession GSM2645533 SRX2875288 GSM2645534 SRP108392 SRS2245365 GSM2645534 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645534 GSM2645534 GEO Accession GSM2645534 SRX2875289 GSM2645535 SRP108392 SRS2245366 GSM2645535 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645535 GSM2645535 GEO Accession GSM2645535 SRX2875290 GSM2645536 SRP108392 SRS2245367 GSM2645536 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645536 GSM2645536 GEO Accession GSM2645536 SRX2875291 GSM2645537 SRP108392 SRS2245368 GSM2645537 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645537 GSM2645537 GEO Accession GSM2645537 SRX2875292 GSM2645538 SRP108392 SRS2245369 GSM2645538 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645538 GSM2645538 GEO Accession GSM2645538 SRX2875293 GSM2645539 SRP108392 SRS2245370 GSM2645539 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645539 GSM2645539 GEO Accession GSM2645539 SRX2875294 GSM2645540 SRP108392 SRS2245371 GSM2645540 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645540 GSM2645540 GEO Accession GSM2645540 SRX2875295 GSM2645541 SRP108392 SRS2245372 GSM2645541 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645541 GSM2645541 GEO Accession GSM2645541 SRX2875296 GSM2645542 SRP108392 SRS2245373 GSM2645542 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645542 GSM2645542 GEO Accession GSM2645542 SRX2875297 GSM2645543 SRP108392 SRS2245374 GSM2645543 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645543 GSM2645543 GEO Accession GSM2645543 SRX2875298 GSM2645544 SRP108392 SRS2245375 GSM2645544 RNA-Seq TRANSCRIPTOMIC cDNA ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). RNAseq: RNA was extracted using RNeasy kit (Qiagen). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302645544 GSM2645544 GEO Accession GSM2645544 SRX3589819 GSM2938885 SRP108392 PRJNA388716 SRS2861424 GSM2938885 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938885 GSM2938885 GEO Accession GSM2938885 SRX3589820 GSM2938886 SRP108392 PRJNA388716 SRS2858052 GSM2938886 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938886 GSM2938886 GEO Accession GSM2938886 SRX3589821 GSM2938887 SRP108392 PRJNA388716 SRS2858053 GSM2938887 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938887 GSM2938887 GEO Accession GSM2938887 SRX3589822 GSM2938888 SRP108392 PRJNA388716 SRS2858054 GSM2938888 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938888 GSM2938888 GEO Accession GSM2938888 SRX3589823 GSM2938889 SRP108392 PRJNA388716 SRS2858055 GSM2938889 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938889 GSM2938889 GEO Accession GSM2938889 SRX3589824 GSM2938890 SRP108392 PRJNA388716 SRS2858056 GSM2938890 ChIP-Seq GENOMIC ChIP ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938890 GSM2938890 GEO Accession GSM2938890 SRX3589825 GSM2938891 SRP108392 PRJNA388716 SRS2858057 GSM2938891 OTHER TRANSCRIPTOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938891 GSM2938891 GEO Accession GSM2938891 SRX3589826 GSM2938892 SRP108392 PRJNA388716 SRS2858058 GSM2938892 OTHER TRANSCRIPTOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938892 GSM2938892 GEO Accession GSM2938892 SRX3589827 GSM2938893 SRP108392 PRJNA388716 SRS2858059 GSM2938893 OTHER TRANSCRIPTOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938893 GSM2938893 GEO Accession GSM2938893 SRX3589828 GSM2938894 SRP108392 PRJNA388716 SRS2858060 GSM2938894 OTHER TRANSCRIPTOMIC other ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 302938894 GSM2938894 GEO Accession GSM2938894 SRX3946192 GSM3100846 SRP108392 PRJNA388716 SRS3176576 GSM3100846 ChIP-Seq GENOMIC ChIP ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 303100846 GSM3100846 GEO Accession GSM3100846 SRX3946193 GSM3100847 SRP108392 PRJNA388716 SRS3176578 GSM3100847 ChIP-Seq GENOMIC ChIP ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 303100847 GSM3100847 GEO Accession GSM3100847 SRX3946194 GSM3100848 SRP108392 PRJNA388716 SRS3176577 GSM3100848 ChIP-Seq GENOMIC ChIP ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 303100848 GSM3100848 GEO Accession GSM3100848 SRX3946195 GSM3100849 SRP108392 PRJNA388716 SRS3176582 GSM3100849 ChIP-Seq GENOMIC ChIP ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 303100849 GSM3100849 GEO Accession GSM3100849 SRX3946196 GSM3100850 SRP108392 PRJNA388716 SRS3176580 GSM3100850 ChIP-Seq GENOMIC ChIP ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 303100850 GSM3100850 GEO Accession GSM3100850 SRX3946197 GSM3100851 SRP108392 PRJNA388716 SRS3176581 GSM3100851 ChIP-Seq GENOMIC ChIP ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 303100851 GSM3100851 GEO Accession GSM3100851 SRX3946198 GSM3100852 SRP108392 PRJNA388716 SRS3176579 GSM3100852 ChIP-Seq GENOMIC ChIP ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 303100852 GSM3100852 GEO Accession GSM3100852 SRX3946199 GSM3100853 SRP108392 PRJNA388716 SRS3176583 GSM3100853 ChIP-Seq GENOMIC ChIP ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2000 gds 303100853 GSM3100853 GEO Accession GSM3100853 SRX4374153 GSM3262944 SRP108392 PRJNA388716 SRS3531669 GSM3262944 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262944 GSM3262944 GEO Accession GSM3262944 SRX4374154 GSM3262945 SRP108392 PRJNA388716 SRS3531670 GSM3262945 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262945 GSM3262945 GEO Accession GSM3262945 SRX4374155 GSM3262946 SRP108392 PRJNA388716 SRS3531671 GSM3262946 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262946 GSM3262946 GEO Accession GSM3262946 SRX4374156 GSM3262947 SRP108392 PRJNA388716 SRS3531672 GSM3262947 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262947 GSM3262947 GEO Accession GSM3262947 SRX4374157 GSM3262948 SRP108392 PRJNA388716 SRS3531673 GSM3262948 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262948 GSM3262948 GEO Accession GSM3262948 SRX4374158 GSM3262949 SRP108392 PRJNA388716 SRS3531674 GSM3262949 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262949 GSM3262949 GEO Accession GSM3262949 SRX4374159 GSM3262950 SRP108392 PRJNA388716 SRS3531675 GSM3262950 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262950 GSM3262950 GEO Accession GSM3262950 SRX4374160 GSM3262951 SRP108392 PRJNA388716 SRS3531676 GSM3262951 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262951 GSM3262951 GEO Accession GSM3262951 SRX4374161 GSM3262952 SRP108392 PRJNA388716 SRS3531677 GSM3262952 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262952 GSM3262952 GEO Accession GSM3262952 SRX4374162 GSM3262953 SRP108392 PRJNA388716 SRS3531678 GSM3262953 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262953 GSM3262953 GEO Accession GSM3262953 SRX4374163 GSM3262954 SRP108392 PRJNA388716 SRS3531679 GSM3262954 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262954 GSM3262954 GEO Accession GSM3262954 SRX4374164 GSM3262955 SRP108392 PRJNA388716 SRS3531680 GSM3262955 Hi-C GENOMIC other Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547). Libraries were prepared according to Illumina instructions. Illumina HiSeq 2500 gds 303262955 GSM3262955 GEO Accession GSM3262955