For ChIP cells were fixed with 11% formaldehyde in mESC media for 10 minutes on a rotating platform. The fixation was stopped by addition of 125nM of Glycine for 5 minutes on a rotating platform. Cells were scraped, quick-frozen and stored at -80°C. ChIP was done by pulling down the bfTbx3 protein using Dynabeads conjugated to streptavidin (SA) in Tbx3N/N+NBirA+bfTbx3 cells. Pull down in Tbx3N/N+NBirA cells was used as negative control.  For mRNA-Seq sample preparation, the total RNA was isolated using Trizol reagent following the manufacturer’s instructions. Quality and quantity of total RNA was assayed using Nanodrop and Agilent Bioanalyzer. For ChIPSeq, DNA library preparation was done using the Illumina ChIP-seq sample prep kit. The libraries were run on HiSeq 2000 machine. For mRNA-seq, libraries were prepared using the TrueSeq protocol from Illumina. The concentration of the libraries was assayed using Agilent Bioanalyzer and sequenced either using 1*26bp or 1*100bp on an Illumina Genome analyzer II or HiSeq 2000 platform
GEO Accession
GSM1464537