qPRO-seq of mouse F1 cells

Polymerase Run-On Sequencing (PROseq) performed as previously described (cite original Kwak et al., 2013 and qPRO Judd et al., 2020) with some minor changes. Data is 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 underwent triple genetic knockout for the endogenous methyltransferase enzymes (DNMT TKO). PROseq data was obtained by permeabilizing the cells, performing a 2 biotin run-on reaction using biotin-11-UTP and biotin-11-CTP and subsequent enrichments steps for biotinylated RNA during the library preparation. This results in the enrichment of nascent transcripts, including enhancer RNA.