Fig. 3 |. Molecular profiling of microglia from Atg7^cKO mice.

a, UMAP plots of the cells combining Atg7^cKO cells and Atg7^WT cells (combined, left), Atg7^cKO cells (middle) and Atg7^WT cells (right). b, Distribution of Atg7^cKO cells and Atg7^WT cells in each cluster. c, Volcano plot of upregulated genes of cluster 9 (C9 versus other clusters; adjusted P values <0.05, log₂FC >0.5). d, Heat map for enrichment test between upregulated DEGs (adjusted P values <0.05, log₂FC >0.5) in microglial clusters and previously reported dataset. e, The intensity of p21^Cip1 in the nucleus of CD11b⁺ microglia from Atg7^cKO or Atg7^WT brains (two male and one female mice, 65 cells for each genotype) was determined by Imaris software (Methods). P < 0.0001. Scale bar, 20 μm (left) and 10 μm (right). f, Venn diagram of the commonly upregulated genes between cluster 9 (adjusted P values <0.05, log₂FC >0.5) and OA2 cluster. g, S100a4⁺ Iba-1⁺ microglia were examined through RNA scope in situ hybridization assay combined with immunostaining in Atg7^WT and Atg7^cKO brain (two males and one female mice). P = 0.0027. Scale bar, 50 μm and 10 μm (magnified image). h, The number of Cdkn1a⁺ dots was counted in S100a4⁺ or S100a4⁻ microglia in Atg7^cKO brain (two males and one female mice). P < 0.0001. Scale bar, 10 μm. i, Comparison among upregulated marker genes (adjusted P values <0.05, log₂FC >0.5) of each cluster. j, UMAP for trajectory analysis coloured by pseudotime (left) and subclusters (cluster 1, 2, 5 and 9). P values were calculated by unpaired two-tailed Student’s t-test (g), two-tailed Mann–Whitney U test (e and h), Wilcox rank-sum test (c and f) or one-sided Fisher’s exact test (FET; d and i). Values are reported as mean ± s.e.m. Source numerical data are available in source data.