Fig. 2

Ischemia induces two microglial subclusters. A t-SNE projection of microglia (9396 cells), sub-clustered into four sub-populations (Cluster 1: 4554 cells; Cluster 2: 2362 cells; Cluster 3: 2015 cells; Cluster 4: 465 cells). B Feature plots of selected marker genes enriched in Cluster 1 or Cluster 3. C–D Representative RNAscope images (C) co-stained with Gpr65/Srxn1 and microglial-marker TMEM119 within ischemic penumbra or core in sham and MCAO (3-h, 12-h, 3-day post-ischemic stroke) mice (scale bar: 50 µm; n = 3/group). Data are presented as mean ± SEM (D). **P < 0.01, ***P < 0.001, by Student’s t-test. E 10 × Visium spatial transcriptomics highlighting the presence of Cluster 1 (IPAM) and Cluster 3 (ICAM) in sham (control) and MCAO (3-h, 12-h, 3-day post-ischemic stroke) mouse brain sections, identified by marker genes from scRNA-seq using the AddModuleScore. NeuN was used to define the ischemic lesion