Fig. 4: Single-cell RNA sequencing of the mouse spinal cord reveals changes in cell composition after SCI and microglia depletion.

a Mice received either vehicle or PLX5622, starting 2 weeks before surgery, until 7 or 28 days post-surgery. At the end point, single-cell RNA sequencing was performed on fresh (un-perfused) mouse spinal cords by dissecting a 1 cm piece of fresh tissue (T4–T13), including the meninges, centered on the laminectomy site. This method optimizes cell viability, allows comparison of leukocyte profiles present in both sham and SCI conditions, and enriches for resident glia and peripheral immune cells. b UMAP plot showing fourteen major cell types pooled from all groups. Each dot represents a single cell. c: Dot Plot showing the top 3 DEGs in each cluster based on adjusted p values. The dot color indicates the average scaled RNA expression of that gene in the cell type, and the dot size represents the percentage of cells in the cluster that express that gene. d–f UMAP plots of vehicle-fed mice split by time point. d’–f’ The percentage of cell types in d–f. g, h Pie chart showing that most of the microglia (g) and MDMs (h) were derived from samples in the vehicle group. Data for each condition were pooled from n = 3–4 mice. Source data are provided as a Source Data file. See also Sup. Fig. 7.