scRNA-seq analysis of CD45 ⁺ cells and microglia from 5-mo-old Atg7 ^fl/fl -5xFAD and Atg7 ^ΔMG -5xFAD mice. (A) UMAP showing all CD45⁺ cells captured by scRNA-seq. (B) FeaturePlots showing clusters encompassing T cells, B cells, monocytes, neutrophils, border-associated macrophages (BAMs), and microglia. (C) Quantification of cell type frequency within each sample. Each data point represents one mouse. *, P < 0.05 by two-tailed unpaired t test. Data are presented as mean ± SD. (D) UMAP showing distinct microglia cluster distribution in Atg7^fl/fl, Atg7^fl/fl-5xFAD, Atg7^ΔMG, and Atg7^ΔMG-5xFAD mice. (E) Violin plot displaying the module scores calculated with MIMS-iron gene signatures. ****, P < 0.0001 calculated by stat_compare_means function in ggpubr package. (F–H) GO term analysis for genes upregulated in HM from Atg7^fl/fl mice (F), HM from Atg7^fl/fl-5xFAD mice (G), and TM plus DAM from Atg7^fl/fl-5xFAD mice (H). UMAP: uniform manifold approximation projection.