SRX1000234 GSM1661784 SRP057456 SRS914214 GSM1661784 ChIP-Seq GENOMIC ChIP DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script. Illumina HiSeq 2500 GEO Sample GSM1661784 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661784 gds 301661784 GEO Accession GSM1661784 SRX1000235 GSM1661785 SRP057456 SRS914213 GSM1661785 ChIP-Seq GENOMIC ChIP DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script. Illumina HiSeq 2500 GEO Sample GSM1661785 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661785 gds 301661785 GEO Accession GSM1661785 SRX1000236 GSM1661786 SRP057456 SRS914212 GSM1661786 ChIP-Seq GENOMIC ChIP DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script. Illumina HiSeq 2500 GEO Sample GSM1661786 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661786 gds 301661786 GEO Accession GSM1661786 SRX1000237 GSM1661787 SRP057456 SRS914211 GSM1661787 ChIP-Seq GENOMIC ChIP DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script. Illumina HiSeq 2500 GEO Sample GSM1661787 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661787 gds 301661787 GEO Accession GSM1661787 SRX1000238 GSM1661788 SRP057456 SRS914210 GSM1661788 ChIP-Seq GENOMIC ChIP DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script. Illumina HiSeq 2500 GEO Sample GSM1661788 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661788 gds 301661788 GEO Accession GSM1661788 SRX1000239 GSM1661789 SRP057456 SRS914209 GSM1661789 ChIP-Seq GENOMIC ChIP DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script. Illumina HiSeq 2500 GEO Sample GSM1661789 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661789 gds 301661789 GEO Accession GSM1661789 SRX1000240 GSM1661790 SRP057456 SRS914208 GSM1661790 ChIP-Seq GENOMIC ChIP DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script. Illumina HiSeq 2500 GEO Sample GSM1661790 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661790 gds 301661790 GEO Accession GSM1661790 SRX1000241 GSM1661791 SRP057456 SRS914207 GSM1661791 ChIP-Seq GENOMIC ChIP DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script. Illumina HiSeq 2500 GEO Sample GSM1661791 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661791 gds 301661791 GEO Accession GSM1661791