Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
Summary
In order to dissect the contribution of MYC to prostate cancer development, we overexpressed MYC in RWPE-1 cells and knocked down MYC in LNCaP cells. We performed RNA-seq on those cells. In the LNCaP cells only, we also performed ChIP-seq against MYC, H3K27ac, H3K27me3, and RNAP2.
Overall design
5 RWPE-1 cell lines (two empty vector and 3 MYC overexpression) and 5 LNCaP cell lines (wild-type, scrambled control, and 3 knockdown constructs) were used for RNA-seq. RWPE-1 RNA-seq was performed in duplicate. LNCaP RNA-seq was performed twice with scrambled control and constructs 627 and 637, and three times with wild-type, scrambled control, and the 512, 627 and 637 constructs along with ERCC spike-ins. ChIP-seq was performed on LNCaP wild-type, scrambled control, and MYC knockdown 512, 627 and 637 constructs in duplicate for MYC, H3K27ac and RNAP2, and once for H3K27me3.
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