RNA-seq analysis of SLIRP knockdown with 1nM DHT in LNCaP cells

The purpose of this study was to profile gene expression changes that could occur with the loss of co-repressor SLIRP. In addition, we wanted to investigate how DHT could further alter gene expression. Methods: LNCaP cells were transfected with custom nonsense control siRNA or a pool of SLIRP siRNA (HSS130109, HSS188666, HSS188667 Invitrogen, Carlsbad, CA) at 40nM for 24hrs. Cells were washed once with PBS and replaced with SFM containing EtOH or 1nM/ml DHT for another 24hrs. Two biological replicates were collected from 2 different experiemnts for total of 4 replicates. RNA collected was sequenced using Illumia HiSeq2000 single read 50 bp by the HTSF core at UNC and aligned and normalized by the Bioinformatics core at UNC. Results: We found a differential gene expression pattern between our control and SLIRP knockdown samples. We also identified a 176 AR gene signature with 3 subclasses and a large SLIRP gene signature (~1700). Overall design: Examination of control (NS) vs. SLIRP siRNA treated with 1nM DHT in the prostate cancer cell line LNCaP