Transcriptomic identification of major cell types that comprise the mouse mid-thoracic spinal cord contusion site at acute time points. (A) UMAP plot of all cells collected from the uninjured spinal cord and injured spinal cord at 1, 3, and 7 dpi (66,178 cells). Cells are colored and annotated by cell type based on a combination of DEGs, canonical marker genes, and previously published spinal cord scRNA-seq datasets (Fig. S2, A and B). Cell counts for each cell type are displayed in parentheses in the legend on the right. (B) UMAP of all cells split by each time point. Cells are colored by neighborhood density in UMAP space to illustrate shifts over time. Darker red colors indicate greater cell density in the UMAP or gray if not from indicated time point. (C) Dot plot of highest DEGs for each major cell type at each time point (right axis). Dot color intensity represents the z-score of expression values, and dot size represents percent of cells with at least one UMI detected per gene. (D) UMAP of expression pattern of the DEG that best identifies each cell type. Values indicated are log-normalized counts per cell. n = 3 biological replicates for uninjured and 1 dpi; n = 2 biological replicates for 3 and 7 dpi. Div, dividing; OPC, oligodendrocyte progenitor cells.