Fig. 4: MCAO elicits SAM-foamy microglial clusters during the chronic stage.

a, Workflow showing isolation and scRNA-seq of microglia from sham-operated and MCAO mice at 90 days post MCAO; n = 2 biological replicates per group. b, Uniform manifold approximation and projection (UMAP) of extracted microglia, coloured by inferred cluster identity from sham and MCAO male mice, showing distinct microglial subpopulations. SAM-iron, stroke-associated iron microglia. c, Violin plot illustrating gene signature expression across microglial clusters. d, Bar graphs showing cluster proportion, indicating MCAO-induced shifts in microglial composition. e, UMAP plots highlighting expression of representative genes associated with microglial activation, lipid metabolism and inflammation. f, Heatmap analysis depicting the expression of inflammation-related factors in microglia during the chronic stage post MCAO, revealing upregulated pro-inflammatory pathways. g, Trajectory reconstruction of all microglial cells, revealing four branches of microglial differentiation post MCAO, suggesting dynamic microglial transitions. h, Trajectory analysis highlighting the temporal expression patterns of key genes involved in cholesterol metabolism (for example, Abcg1, Apoe, Lpl, Trem2 and Tspo) and inflammation-related factors (for example, Ccl3, Ccl4, Ccl6, Cxcl14 and Cxcl16) across microglial differentiation states.