ChIP-seq Analysis of AR Genomic Binding

DNA was amplified as previously described^{64 (link)}, and processed for library preparation (Part# 0801-0303, KAPA Biosystems kit). An Illumina HiSeq 2500 Genome Analyzer (65-bp reads) was used for sequencing. Alignment of the sequences was performed on Human Reference Genome (assembly hg19, February 2009) and reads were filtered based on MAPQ quality (>20). Peaks called by both DFilter^{65 (link)} (bs = 100, ks = 50, nonzero) and MACS peak caller (P = 10⁻⁷)^{66 (link)} were used for the analysis. For peaks and motif analysis the Cistrome platform was used (cistrome.org). Also, the cis-regulatory element annotation system (CEAS) was used for analysis of the genomic distributions of binding sites. Integrative Genomic View (IGV) and SeqMINER were used for peaks visualization and IPA (QUIAGEN 2015) was used for analysis of predicted AR-target genes. Binding sites found in the gene body or 20 kb upstream from the transcription start site were considered proximal to the gene.