Protein-DNA complexes were isolated from sonicated LNCaP cell lysates with indicated antibodies, and the ChIP DNA was extracted using phenol chloroform extraction method. Purified ChIP DNA was dissolved in TE buffer and re-sheared using Covaris sonicator to enable enrichment of fragments with an average size of 300 bp. The re-sheared DNA samples were purified for library preparation using the minElute PCR purification kit (Qiagen). The ChIP-seq libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics; R400427) according to the manufacturer's instructions.