SOX2 Mediates Metabolic Reprogramming of Prostate Cancer Cells (ChIP-Seq)

To mechanistically define the function of SOX2 in prostate cancer cells and how it contributes to therapeutic resistance, we performed paired SOX2 chromatin immunoprecipitation-sequencing (ChIP-Seq) and RNA-sequencing (RNA-Seq) on a SOX2-positive CRPC cell line, CWR-R1, to determine which genes SOX2 binds and potentially regulates. To identify novel prostate cancer-specific SOX2 gene targets in CRPC cells distinct from known SOX2 stem cell genes, we conducted parallel SOX2 ChIP-Seq and RNA-Seq in the WA01 embryonic stem cell line and compared results to identified SOX2 targets from CWR-R1 cells Overall design: SOX2 immunoprecipitation was performed in CWR-R1 and WA01 cells. Non-immunoprecipitated DNA was used as an input DNA control when calling peaks. Replicates in each condition were pooled using MACS2 to call peaks against the input DNA control.