Genome binding/occupancy profiling by high throughput sequencing Other Expression profiling by high throughput sequencing
Crosstalk of androgen signaling induced with dihydrotestosterone (DHT) and proinflammatory signaling induced with tumor necrosis-factor alpha (TNFa) was analyzed in prostate cancer cells (LNCaP) by following chromatin binding of androgen receptor (AR), p65 (activating subunit of nuclear-factor kappa-B [NFkB]), FOXA1 and PIAS1+2 chromatin binding using ChIP-seq and transcriptional changes using GRO-seq.
LNCaP cells that were cultured in charchoal stripped medium were induced with DHT (100mM, 2h), TNFa (1000 U/ml, 2h) or both (DHT+TNFa), while DMSO treatment was used as a control. Chromatin binding of AR, p65, FOXA1, and PIAS (isoforms 1 and 2) were analyzed using ChIP-seq and changes in transcription was analyzed using global run-on sequencing (GRO-seq). All samples were done as biological replicates. Role of FOXA1 in chromatin binding of p65 was analyzed in FOXA1 siRNA silenced and control siRNA transfected cells using ChIP-seq.