title: MSTO211H interphase ChIP-seq PolIISer2_5 replicate 2
design: ChIP-seq libraries were prepared using the True MicroChIP-seq Kit (Diagenode, for flow cytometer-sorted mitotic cells) and SimpleChip Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, for BRD4 and SMARCA4 ChIP where PROTAC inhibitors were applied), following the manufacturers instructions. The following antibodies were used: anti-H3K4me3 (Diagenode C15410003), anti-H3K27ac (Epicypher 13-0059), anti-BRD4 (Bethyl Laboratories A301-985A), anti-SMARCA4 (Cell Signaling Technology 49360S for mitotic cells, Abcam 110641 for interphase cells), anti-MED14 (Abcam ab72141), anti-RPB1 (Cell Signaling Technology 2629S), anti-phospho-RPB1 Ser2/5 (Cell Signaling Technology 13546S). For BRD4 and SMARCA4 ChIP where PROTAC inhibitors were applied, spike-in chromatin and antibody (Active Motif) were added to the reaction. ChIP-seq data were aligned to the human hg38. For BRD4 and SMARCA4 ChIP-seq with PROTAC treatments, data were aligned to the dm6 Drosophila reference genome for spike-in normalisation. ecDNA signals were normalised with copy number by the bigwigCompare function (--operation ratio) from deepTools (v3.5.5) software, with the ChIP-seq input serving as a surrogate for whole-genome coverage.