Extended Data Fig. 1: Microglia induce a sustained brain-resident inflammatory response after MCAO.
a, Double immunostaining for IBA1 (microglial marker) and myelin basic protein (MBP, myelin marker) illustrates sustained myelin loss and microglial accumulation at days 3, 7, 14, 30, 90, and 180 post-MCAO. Dashed lines indicate regions of MBP disruption. Representative images from one of three independent experiments are shown. Scale bar, 500 µm. b, Co-immunostaining of MBP and IBA1 at days 30 and 90 post-MCAO shows spatial association between microglial activation and regions of myelin damage. Representative images from one of three independent experiments are shown. Scale bar, 50 µm. c, Workflow of bulk RNA-seq analysis, detailing the collection and processing of CD11b+ microglia for transcriptomic profiling post-MCAO. d, Quantification of CD11b+ cells reveals increased microglia number during the chronic stage post-MCAO. sham, n = 6 mice/group; MCAO group, n = 4 mice/group. e, Heatmap illustrating changes of toll-like receptor (TLR) signaling and NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome pathways in microglia during the chronic stage post-MCAO. n = 4 mice for the sham group; n = 3 mice per MCAO group. f, Gene set enrichment analysis (GSEA) identifies positive enrichment of inflammatory and immune response pathways. Normalized enrichment scores (NES) and P-value for each gene set are displayed. n = 4 mice for the sham group; n = 3 mice per MCAO group. RES: Running enrichment score; RLM: Ranked list metric. Data are presented as mean ± SD. Statistical significance was assessed by one-way ANOVA (d) followed by Dunnett’s multiple comparisons test, or a one-sided permutation test, and the resulting P-values were adjusted for multiple comparisons(f).
