Total RNA-seq of DNMT3a/3b induced double knockouts in mouse embryonic fibroblasts
To test whether DNMT3A/3B are mechanistically responsible for the probabilistic gain of methylation at intermediately methylated CpG sites, we generated four MEF lines (A, B, C, and D) from sibling E13.5 Dnmt3aflox/flox3bflox/flox mouse embryos and used recombinant TAT-CRE protein to induce the double knockout (DKO) in vitro. We subsequently performed RNA-seq with four DKO and four matched control cell lines.