Effect of depletion of Ctr9, Pcgf6 and Tbx3 on gene expression in embryonic stem cells(ESCs)

For validating the newly defined PAF, PCGF and TBX3 modules, the major transcriptional factor of each module (Ctr9, Pcgf6 and Tbx3) was knocked down individually by RNAi in a Nanog-GFP reporter ESC line. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at one time points. Overall design: Comparative gene expression profiling analysis of RNA-seq data for ESCs and its KD derivatives (shCtr9, shPcgf6, and shTbx3).