Time series single cell transcriptomics of cardiac inflammation after myocardial infarction in mice

We performed time-series single-cell RNA-seq analysis of blood CD11b+ cells and of the inflammatory infiltrate in the heart of C57BL/6J male mice in a model of permanent myocardial infarction. Overall design: Cardiac CD45+ total leukocytes (datasets F8, F9, F11, F12, G1), cardiac CD11b+ myeloid cells (dataset H10), or blood and cardiac CD11b+ cells (Sample C11_2) were extracted from the blood or heart of mice in the steady state and at various time points after myocardial infarction or sham surgery in a murine model of permanent myocardial ischemia induced by ligation of the left descendant coronary artery, and analyzed by single-cell RNA-sequencing. In the H10 dataset, CD11b+ cells were sampled at 1, 3, and 5 days after infarction, labeled with CITE-Seq and hashtag antibodies and pooled for multiplexed analysis. In Sample C11_2, blood and cardiac CD11b+ cells from control animals and mice at 1 and 3 days after sham or myocardial infarction surgery were labeled with CITE-seq and hashtag antibodies and pooled for multiplexed analysis.