Isolation of Cardiac Endothelial Cells for Transcriptomic Analysis of the Zebrafish and Mouse Heart

Isolation of high quality cardiac endothelial cells is a prerequisite for successful bulk and single cell sequencing for RNA (scRNA-seq). We describe a protocol using both enzymatic and mechanical dissociation and fluorescence-activated cell sorting (FACS) to isolate endothelial cells from larval and adult zebrafish hearts and from healthy and ischemic adult mouse hearts. Endothelial cells with high viability and purity can be obtained using this method for downstream transcriptional analyses applications.