Identify genomic binding sites of Tfcp2l1 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. 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. ChIP-seq is used to identify the genomic bindings sites of Tfcp2l1 in ESCs grown in the 2i medium. Overall design: Two repeats were performed and each repeat includes one input and one ChIP. 50 million of ESCs grown in 2i were subject to ChIP-seq with 10 ug custom-made antibody against mouse Tfcp2l1. To identify genomic peaks of Tfcp2l1, enrichment of ChIP versus input across the genome was calculated.