Single cell RNA-sequencing studies to examine the heterogeneity of infarct macrophages

Cardiac macrophages exhibit remarkable heterogeneity that is accentuated after myocardial infarction. In order to characterize the transcriptional profile of cardiac macrophage subpopulations after infarction we performed scRNA-seq in FACS-sorted macrophages from normal and infarcted CSF1R-EGFP (macrophage reporter) mouse hearts. CSF1R-EGFP 12-16 week-old mice were subjected to permanent coronary occlusion, and 7 days after surgery macrophage suspensions were harvested from infarcted and control mice. Non-neutrophils (Ly6G-) were gated to identify EGFP+ macrophages, which were sorted with the FACSAria Sorter (BD Biosciences). Subsequently, scRNA-seq was performed. Cardiac Macrophages from CSF1R-EGFP mice were isolated by Fluorescence-activated cell sorting (FACS) based on the presence of EGFP signal after exclusion of Ly6G+ cells. Previous to cell isolation surgery was preformed for the infarct groups (n=3). Seven days after surgery, hearts were harvested for baseline (n=1, 3 control hearts pooled) and infarcted (n=3) mice. Before digestion, the non-infarcted region (remote zone) was excised from the heart and excluded from the digestion. Samples were analyzed using scRNA-seq.