Bait-capture based single molecule footprinting of mouse F1 cell lines

Bait-capture based Single Molecule Footprinting (SMF) data. SMF data is obtained by treating extracted nuclei with a GpC and a CpG methyltransferase, where binding of proteins on DNA, e.g. nucleosomes and transcription factors (TFs), leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from two F1 hybrid embryonic stem cells (ES) obtained by crossing C57BL/6NJ with CAST/EiJ and SPRET/EiJ, respectively. The resulting cell line were underwent triple genetic knockout for the endogenous methyltransferase enzymes (DNMT TKO). Sequencing libraries were prepared using Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for cis-regulatory regions of the mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types.