Bulk RNA-seq of PC3-derived human prostate cancer xenografts and matched mouse blood following treatment with the bivalent BET bromodomain inhibitor MS645 or the monovalent inhibitor JQ1

When tumors reached ~200 mm^3, mice were randomized to one of three treatment arms: vehicle, JQ1 (30 mg/kg), or MS645 (20 mg/kg). Compounds were administered intraperitoneally.

At study end, mice were sacrificed and matched xenograft tumor and whole-blood specimens were collected and snap-frozen for bulk RNA-seq. Tumor RNA-seq reads were aligned to the human reference genome (GRCh38/hg38) and blood RNA-seq reads to the mouse reference genome (GRCm38/mm10). Differential expression analysis (DESeq2) was used to compare MS645 vs vehicle and JQ1 vs vehicle in each compartment.