Fig. 2: Heterogeneous composition and phenotypic changes of microglia after SS2 infection.

A–C t-SNE map, density map and boundaries of clusters of microglia are shown. t-SNE plot shows expression of the indicated marker. The density plot shows the local density of cells and the cluster partition shows the boundaries of the four clusters of microglia. D t-SNE plots of microglia from the CNS samples of five groups are shown. E A heatmap displays the median marker expression value and hierarchical clustering of the markers for nine clusters identified in C. F Vertical bar graph depicting the composition of the microglia compartment in each mouse brain sample at the indicated time points. The colored segment lengths represent the proportion of cells as a percentage of total microglia in each sample. Colors as in E. G Median expression and statistical result of P2RY12 expression on microglia of control and SS2 infected mice (N = 3) at different stages. H Immunohistochemical images of IBa-1⁺ microglia in control and SS2-infected mice (N = 3) at different stages. Scale bar = 50 μm. I Median expression of F4/80, MHCII and TLR2 expression on microglia in healthy and infected SS2 mice at different stages. J The phagocytic ability of three phenotypes microglia (Ki-67^-MHCII^-microglia, Ki-67⁺ MHCII^-microglia and Ki-67^-MHCII⁺microglia) at different stages of SS2 infection was detected by flow cytometry. Four female mouse brains were pooled in one sample, N = 3. K–M The levels of cytokines (TNF-α, IL-6 and IFN-γ) secreted by three types of microglia were detected by flow cytometry. Error bars represent the median ± SEM. A one-way ANOVA or Dunnett’s test was performed for analysis of multiple groups. Student’s t-test was used to compare the two groups. P value < 0.05 (*); p < 0.01 (**); p < 0.001 (***); NS no significant difference.