GSE136830
Expression data and H3K27me3 occupancy profiling by high throughput sequencing from control and SETD2 knockout organoids cells.
To understand the molecular basis how Setd2 loss enhances metastatic traits of PCa, we carried out RNA-seq and H3k27me3 Chip-seq using mice-derived prostatic organoid cells from 3-month-old PtenPC+/- and PtenPC+/-;Setd2PC-/- mice.To further validate Setd2 loss accelerated prostate tumorigenesis is dependent on EZH2 upregulation,we conduct high throughput sequencing of organoid cells derived from PtenPC+/- and PtenPC+/-;Setd2PC-/-  mice with Ezh2 knockout.To understand the molecular basis whether the tumor suppressive function of Setd2 is depends on its methylation of EZH2 at k735, we also carried out RNA-seq using mice-derived prostatic organoid cells from 2-month-old PtenPC-/- and PtenPC-/-;Ezh2K735R mice.We integrated all the RNA-seq and chip-seq data generated from organoid cells. Overall design: The prostatic organoid cells were isolated from 3-month-old PtenPC+/- and PtenPC+/-; Setd2PC-/- mice with or without Ezh2 knockout according to previously reported protocol (Drost et al., 2016). Total RNA was extracted from mouse organoids using TRIzol reagent and then subjected to PE150 Hiseq. Each sample contained pooled RNA from 3 biological replicates and was mixed with equal mass of RNA to minimize variation across samples. Similar approaches were used to generate organoid cells from 2-month-old PtenPC-/- and  PtenPC-/-;Ezh2K735R mice. Each group has two replications.The chromatin from prostatic organoid cells with or without SETD2 deletion was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K27me3 (Active Motif).