Extended Data Fig. 2: Histological validation of microglia marker genes (related to Fig. 1).
a, left: Representative immunofluorescence (IF) image of a whole brain section from a Cx3cr1CreERT2:R26Tdomato mouse subjected to 2 days of MCAo (D02) showing the distribution of Ki67+ cells (white, binary mask) and nuclear DAPI staining (blue); middle and right panels: IF images of magnified areas showing Ki67 expression by Td+(red) Iba1+(green) microglia in the peri-infarct area. Arrowheads indicate Ki67 staining. The border of the ischemic lesion is indicated by yellow dash outline and was traced based on DAPI, Iba1 and Tomato labels. b, top: RNAscope fluorescence in situ hybridization (FISH) validating Cst7 (white) expression in D02 Td+ microglia (red). Left: Representative whole brain section image of Cst7 expression (binary mask) and nuclear DAPI staining; Middle and right panels: FISH-IF images of magnified areas showing upregulation of Cst7 in microglial cells surrounding the ischemic lesion. Bottom: FISH-IF images validating Cst7 (white) expression in D14 mice. Left: Representative whole brain section image of Cst7 expression (binary mask) and nuclear DAPI staining; Middle and right top panels: FISH-IF images of magnified areas showing upregulation of Cst7 in microglia (Iba1+, green) surrounding the ischemic lesion. c, FISH-IF images validating Cxcl10 (white) expression in Cx3cr1-Td+ mice 2 and 14 days after MCAo. Left (D02): Representative whole brain section image of Cxcl10 expression (binary mask) and images of magnified areas showing localization of Cxcl10 in microglial cells (Td+, red) outside of the ischemic lesion. Right (D14): Representative whole brain section image of Cxcl10 expression (binary mask) and images of magnified areas showing localization of Cxcl10 in microglial cells (Td+, red) on the border of the ischemic lesion. d, IF images validating IGF1 (white) expression by Cx3cr1-Td+(red) MHCII–(green) microglia 14 days after MCAo in the ischemic region.
