Expression data from short hairpin RNA mediated CTCF knockdown in human prostate epithelial cells

Transcriptional profiling of immortalized human prostate epithelial cells after CTCF knockdown by short hairpin RNA. Knockdown by shRNA targeting CTCF was conducted for 5 days by addition of doxycycline to induce shRNA expression. RNA was purified from triplicate biological replicates of induced and uninduced shRNA samples. Gene expression was quantified by hybridization to Affymetrix Human Transciptome 2.0 arrays. Triplicate samples of induced and uninduced shRNA targeting CTCF were used to quantify the effects of CTCF knockdown on genome wide gene expression. Cells were treated with either doxycycline to induce shRNA, or uninduced vehicle only control using DMSO. Raw .CEL files were analyzed using the Affymetrix Transcriptome Analysis Console (v3.0). Triplicate samples were compared using the t-test, followed by False Discovery Rate (FDR) adjustments.