Chromatin IP: Chromatin Immuno precipitation performed using Sigma- F1804 [ 1mg/ml ]-Monoclonal ANTI-FLAG M2 antibody produced in mouse. (Lot #: 088K6018) ANTI-FLAG bound chromatin is treated with proteinase K and RNAse followed by clean up using QIAGEN QIAquick PCR Purification Kit (28104) Embryonic tissues were isolated from 129/C57BL/6 (FLAG knock-in) mouse embryos at e11.5. ESCs from the same line were cultured as per standard protocols. Tissue samples and ESCs were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation using an anti-FLAG antibody. ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters. Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the Illumina HiSeq 2000 to generate 50 or 36 bp reads