(A) Upregulated and downregulated pseudobulk-derived DEGs per immune subcluster. Numbers over bars indicate DEG count >0. (B) Venn diagram triangulating downregulated DEGs detected in DMAM0, DMAM1, and intermediate subclusters. (C) Apoe average expression per immune subcluster split by genotype. (D) Per immune subcluster Apoe-scaled expression across libraries within the CPZ condition. (E) Representative TEM micrographs of phagocytes. Red circles and red arrowheads mark lipid droplets and crystal clefts, respectively. Nonphagocyte area is shaded blue to ease visualization of phagocyte. Scale bar: 2.0 μm. (F) Lipid droplet–positive cells as fraction of total cells imaged. (G) Lipid droplet count per cell assessed. (H) Crystal-positive cells as a fraction of total cells imaged. (I) Crystal cleft count detected per cell. (J) Representative micrographs for BODIPY and lectin staining within the CPZ condition. Nuclei are stained with propidium iodide dye. Scale bar: 10 μm. (K) BODIPY–positive cell count /mm². (L) BODIPY–positive droplet count per lectin–positive cell. (M) Representative micrographs of dual confocal and reflective microscopy imaging lectin stain and reflective particles (Ref. Par.). Nuclei are stained with propidium iodide. Scale bar: 10 μm. (N) Average area of reflective particle microclusters. (E–N) Representative images were acquired from corpus callosum; cells analyzed and quantitated were imaged from corpus callosum. (F, H, K, and N) Individual data points correspond to biological replicates. (F and H) Square and error bar correspond to mean and SD, respectively. (G, I, and L) Data points represent dataset outliers. Cell number assessed per group are given below each box plot. Statistical analysis for F–I, K, L, and N) involved ANOVA followed by Tukey’s HSD. Adjusted P values are indicated as follows: NS indicates P > 0.05; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. IRM, interferon-responsive microglia; Pos, positive.