Fig. 3

Single-cell RNA sequencing (scRNA-seq) analysis of microglia in the stroke brains of male and female mice. A Scheme of the experimental design for scRNA-seq analysis. Male and female mice (n = 4/group) were subjected to permanent stroke or sham. Three days later, ipsilateral (stroke) or both (sham) hemispheres were collected for cell sorting and scRNA-seq analysis. B Data table summarizing scRNA-seq analysis. C UMAP plot of aggregated data from all groups. D Split view of UMAP plots of sham and stroke groups. Stacked bar plots (right) depict the proportions of microglia subsets in sham and stroke brains. E Dot plot showing the scaled expression of selected genes for each cluster. Cluster numbers were assigned manually. Dot size indicates proportion of cells within the cluster, and color intensity reflects average expression levels. F Heatmap showing the top 10 upregulated genes in stroke-related microglial clusters 7–13