Fig. 3: Changes in the cell type and cell state composition of immune cells were observed across the four different groups.

a Uniform manifold approximation (UMAP) plot of immune cells (n = 16,490). b Proportions of cell types (left panel) among immune cells and cell states (right panel) among microglia or macrophages across the four groups. A chi-square test was conducted to determine p-values. c, d Violin plots showing the interferon response scores (c) and activation scores (d) among the different states of microglia or macrophages. *** indicates an adjusted p-value < 0.001 (one-way ANOVA with Bonferroni’s multiple comparison correction) between two compared groups. e UMAP plot with the trajectories of macrophages, colored based on the pseudotime. f Changes in the expression levels of selected genes within macrophages across the pseudotime axis. Individual dots represent individual cells, which are colored based on the corresponding cell state, and black lines represent trends in the expression levels of selected genes. g Heatmap presenting the identified modules of genes whose expression changed significantly along the trajectory of macrophages. The indicated coloration represents normalized, aggregated, and Z scores for the expression levels of specific modules. h Bar plots present the top 5 significantly enriched Gene Ontology (GO) terms within each module. GO terms with Benjamini‒Hochberg adjusted p-values < 0.05 were considered significant, and the terms were ordered by −log10 (adjusted p-value). i Box plots represent the distribution of the pseudotime of macrophages across four different groups. *** indicates an adjusted p-value < 0.001 (one-way ANOVA with Bonferroni’s multiple comparison correction) between two compared groups.