Single-cell Analysis of Cardiac and Liver Cells

The single-cell dataset of mouse cardiac interstitial cells at 3 and 7 days after sham operation or MI was downloaded from ArrayExpress under accession E-MTAB-7376 and that of mouse liver cells treated with corn oil or CCl₄ was downloaded from GEO under accession GSE171904. The data were processed using the Seurat package. We removed all cells with fewer than 200 genes, and all genes were expressed in fewer than three cells. In addition, cells with more than 10% or 20% mitochondrial genes were filtered out. Subsequently, gene expression measurements were normalized, and 2000 variable genes were selected for dimensionality reduction. The data were then scaled, and linear dimensional reduction was performed. The cells were then clustered and visualized using UMAP. Genes that were differentially expressed between the two groups were identified using the Seurat package, and a heat map was generated using the ggplot2 package. The gene abundance in Dbn1-positive cells (log2 (fold change) > 0.2) was analyzed using DAVID Bioinformatics Resources, version 6.8.