Genome-wide analysis of CHD7 binding sites in cardiac progenitor cells [CUT&RUN]

To identify primary and direct targets of CHD7 during the early stages of cardiac commitment and differentiation, we decided to map the genome-wide binding sites of CHD7. We used an in vitro approach of directed differentiation of mouse embryonic stem cells (ESCs) towards cardiomyocytes (CM). We isolated cells at the cardiac progenitor (CP) stage (Day 5) and used CUT&RUN (“Cleavage Under Targets & Release Using Nuclease”) technique, followed by NGS. The assay was performed in 3 biological replicates using anti-CHD7, and IgG as negative control. Overall design: CUT&RUN was performed using cardiac progenitor (CP) cells at day 5 during cardiomyocyte (CM) differentiation. Three biological replicates were processed for each condition, using antobodies anti-CHD7 and anti IgG (negative control).