Molecular and temporal profile of microglia subtype heterogeneity acutely after SCI. (A) Proportion of each microglia subtype among all microglia at each time point. (B) Dot plot of marker genes that differentiate nonhomeostatic microglia subtypes from homeostatic microglia. Color of dots represents z-scored expression level, and size of dots represents percentage of cells with at least one UMI detected per gene. (C) Heatmap of the highest DEGs per microglia subtype. Color represents z-score expression level. Inset stars in B and C indicate statistically significant greater expression compared with all other microglia combined (adjusted P value < 10⁻¹⁰; Wilcoxon rank-sum with Bonferroni correction; see Materials and methods). (D) GO enrichment analysis of the DEGs per subtype. GO biological process terms displayed along y axis, and –log₁₀ (Bonferroni-corrected P values) displayed along x axis. (E) Scatter plot of flow cytometry analysis of microglia in the uninjured spinal cord and injured spinal cord at 1 and 7 dpi. Y axis and x axis display fluorescence intensities of P2RY12 and MSR1, respectively. After removing nonviable cells and gating out Ly6G⁺ cells, CD45^med/CD11b⁺ microglia were selected from other leukocytes for further gating along P2RY12 and MSR1 quadrants (see Materials and methods and Fig. 5 A). (F) Quantification of proportion of microglia subtypes in flow cytometry as gated in E. adj., adjusted; H-microglia, homeostatic microglia; Prop., proportion; Uninj, uninjured; Trans, transition; Lo, low; Hi, high.