Total CD45+ cells extracted from the heart of male C57BL6/J mice in the steady state (n=5) and at 5 days after experimental permanent myocardial infarction (n=9) were processed for scRNA-seq and CITE-seq with up to 45 cell surface markers. Cells were obtained from two independent experiments. In each experiment, two scRNA-seq libraries were generated and sequenced. Data from each library was pre-processed in Seurat v3 (Stuart, Cell 2019) for QC filtering, and all libraries were pooled with batch correction using Harmony (Korsunsky, Nature Methods 2019). This dataset contains a few contaminating non-CD45+ cells (endothelial cells, fibroblasts).
Cells corresponding to monocyte and macrophages identified in the total CD45+ fraction were reclustered to identify monocyte/macrophage subpopulations.
Our new datasets were integrated in Harmony with previously published scRNA-seq datasets of cardiac cells at various time points after myocardial infarction: Vafadarnejad et al. Circulation Research 2020, Dick et al. Nature Immunology 2019, and Farbehi et al. eLife 2019.