SRX5246885 GSM3561456 SRP179040 SRS4249120 GSM3561456 ChIP-Seq GENOMIC ChIP Chromatin immunoprecipitation was done as described previously (Ding et al., 2015) using 20 μl of ChIP-grade SMARCA4 (abcam 110641). DNA was fragmented to 200-500bp with a Covaris water-bath sonicator before the IP. DNA was purified and eluted using a PCR purification kit (Qiagen) in 30 μl HPLC-grade water. ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols. Illumina HiSeq 2500 gds 303561456 GSM3561456 GEO Accession GSM3561456 SRX5246886 GSM3561457 SRP179040 SRS4249121 GSM3561457 ChIP-Seq GENOMIC ChIP Total genomic DNA was fragmented to 200-500bp with a Covaris water-bath sonicator. DNA was purified and eluted using a PCR purification kit (Qiagen) in 30 μl HPLC-grade water. ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols. Illumina HiSeq 2500 gds 303561457 GSM3561457 GEO Accession GSM3561457 SRX5246887 GSM3561458 SRP179040 SRS4249122 GSM3561458 RNA-Seq TRANSCRIPTOMIC cDNA For RNA extraction, typically 1-2 million cells were pooled down. Total RNA extraction was performed with the RNeasy Mini kit (Qiagen) according to manufacturer's instructions. To avoid contamination with genomic DNA an on-column DNase I digest was included as part of the RNase Mini kit protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina HiSeq 2500 gds 303561458 GSM3561458 GEO Accession GSM3561458 SRX5246888 GSM3561459 SRP179040 SRS4249123 GSM3561459 RNA-Seq TRANSCRIPTOMIC cDNA For RNA extraction, typically 1-2 million cells were pooled down. Total RNA extraction was performed with the RNeasy Mini kit (Qiagen) according to manufacturer's instructions. To avoid contamination with genomic DNA an on-column DNase I digest was included as part of the RNase Mini kit protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina HiSeq 2500 gds 303561459 GSM3561459 GEO Accession GSM3561459 SRX5246889 GSM3561460 SRP179040 SRS4249124 GSM3561460 RNA-Seq TRANSCRIPTOMIC cDNA For RNA extraction, typically 1-2 million cells were pooled down. Total RNA extraction was performed with the RNeasy Mini kit (Qiagen) according to manufacturer's instructions. To avoid contamination with genomic DNA an on-column DNase I digest was included as part of the RNase Mini kit protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina HiSeq 2500 gds 303561460 GSM3561460 GEO Accession GSM3561460 SRX5246890 GSM3561461 SRP179040 SRS4249125 GSM3561461 RNA-Seq TRANSCRIPTOMIC cDNA For RNA extraction, typically 1-2 million cells were pooled down. Total RNA extraction was performed with the RNeasy Mini kit (Qiagen) according to manufacturer's instructions. To avoid contamination with genomic DNA an on-column DNase I digest was included as part of the RNase Mini kit protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina HiSeq 2500 gds 303561461 GSM3561461 GEO Accession GSM3561461 SRX5246891 GSM3561462 SRP179040 SRS4249126 GSM3561462 OTHER GENOMIC other Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA. Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons. Illumina HiSeq 2500 gds 303561462 GSM3561462 GEO Accession GSM3561462 SRX5246892 GSM3561463 SRP179040 SRS4249127 GSM3561463 OTHER GENOMIC other Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA. Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons. Illumina HiSeq 2500 gds 303561463 GSM3561463 GEO Accession GSM3561463 SRX5246893 GSM3561464 SRP179040 SRS4249128 GSM3561464 OTHER GENOMIC other Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA. Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons. Illumina HiSeq 2500 gds 303561464 GSM3561464 GEO Accession GSM3561464 SRX5246894 GSM3561465 SRP179040 SRS4249129 GSM3561465 OTHER GENOMIC other Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA. Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons. Illumina HiSeq 2500 gds 303561465 GSM3561465 GEO Accession GSM3561465 SRX5246895 GSM3561466 SRP179040 SRS4249130 GSM3561466 OTHER GENOMIC other Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA. Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons. Illumina HiSeq 2500 gds 303561466 GSM3561466 GEO Accession GSM3561466 SRX5246896 GSM3561467 SRP179040 SRS4249131 GSM3561467 OTHER GENOMIC other Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA. Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons. Illumina HiSeq 2500 gds 303561467 GSM3561467 GEO Accession GSM3561467 SRX5246897 GSM3561468 SRP179040 SRS4249132 GSM3561468 OTHER GENOMIC other Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA. Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons. Illumina HiSeq 2500 gds 303561468 GSM3561468 GEO Accession GSM3561468 SRX5246898 GSM3561469 SRP179040 SRS4249133 GSM3561469 OTHER GENOMIC other Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA. Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons. Illumina HiSeq 2500 gds 303561469 GSM3561469 GEO Accession GSM3561469