Identify Tfcp2l1-regulated genes in mouse embryonic stem cells grown in 2i medium

Mouse embryonic stem cells (ESCs) grown in the 2i (an ERK inhibitor, PD0325901, and a GSK-3b inhibitor, CHIR99021) mimic pluripotent epiblasts in preimplantation blastocysts. ESCs grown in FBS containing medium are more heterogenous in morphology and expression of stem cell factors. Tfcp2l1 is a transcription factor highly expressed in ESCs grown in the 2i medium, suggesting that it plays in important role in ESC biology. To search for the putative role(s) of Tfcp2l1 in ESCs, we plan to use an integrated genomic approach--combing RNA-seq and ChIP-seq--to identify the direct targets of Tfcp2l1 in ESCs. RNA-seq is used to identify the transcripts regulated by Tfcp2l1 in ESCs grown in the 2i medium. Four repeats for each of the three conditions: 1) Wild type ESCs grown in 2i; 2) Tfcp2l1 knockout ESCs grown in 2i; 3) Wild type ESCs grown in FBS. To identify transcripts regulated by Tfcp2l1 in the 2i medium, compared 1) to 2). To perform GSEA of 2i versus FBS, compare 1) to 3).