Fig. 3: A subset of macrophages associated with remyelination after MCAO.

A Experimental design for scRNA-seq of CD45^high immune cells at 14 dpi (up). n = 2 biological replicates for each group. UMAP projection of CD45^high immune cells at 14 dpi (down). B Ridgeline plot summarizing AUCell scores of the myelination and angiogenesis functions of CD45^high infiltrating immune cells at 14 dpi. Involved gene sets were listed in Supplementary Data 1. C UMAP projection of macrophages at 14 dpi (left). Stacked bar plot showing proportions of different macrophage subsets (right). D UMAP plot depicting the functions of macrophages from 14 dpi based on the gene sets listed in Supplementary Data 1. E Scatter plot illustrating upregulated DEGs of MF2 compared to MF1, with the percentage difference (defined as percentage of the expression in MF2 minus that in MF1) along the x-axis and log₂(fold change) along the y-axis. The combined z-score of percentage difference and log₂(fold change) was color-coded. The DEGs of MF2 versus MF1 were listed in Supplementary Data 3. F Violin plots showing expression of Cd63 and Gpnmb in each clusters. G Experimental scheme depicting the PLX5622 diet of mice after MCAO. H Gating strategy for CD45^high CD11b⁺ CD63⁺ GPNMB⁺ cells (left). Quantification of the proportions of CD63⁺ GPNMB⁺ cells in the CD45^high CD11b⁺ cells (right). n = 5 for sham group, n = 3 for control diet group, n = 4 for PLX5622 group. One-way ANOVA and Tukey. Data are presented as mean ± SD. I UMAP projection of blood monocytes (left) and brain macrophages (right) at 5 dpi. J Dot plot illustrating the expression of marker genes of MF2 and MF3 (d14) in macrophages from d5. Abbreviations: MG microglia, MF macrophages, NP neutrophils, cDCs classical dendritic cells, pDCs plasmacytoid dendritic cells, NK natural killer cells, NKT natural killer T cells, Tregs regulatory T cells, γδT gamma delta T cells, ProllifCells proliferating cells. Source data are provided as a Source Data file.