Supplementary Figure 14: Comparison of cbMg gene expression patterns with published data sets.

(a) Left: Venn diagrams show overlap between cbMg (orange) and stMg (purple) enriched genes by TRAP with cbMg-enriched genes (red; stMg: p < 0.0001, OR=0.2023, χ2=24.68; cbMg: p < 0.0001, OR=3.752, χ2=77.82) and stMg-enriched genes (blue; stMg: p < 0.0001, 4.206, χ2=154.7; cbMg: p=0.7791, OR=1.095, χ2=0.07869) from Grabert et. al⁴¹. Right: Venn diagrams show overlap between cbMg (orange) and stMg (purple) enriched genes by single nuclei sequencing with cbMg-enriched genes (red; stMg: p < 0.0001, OR=0.5590, χ2=22.71; cbMg: p=0.0852, OR=1.174, χ2=2.963) and stMg-enriched genes (blue; stMg: p < 0.0001, 2.148, χ2=63.39; cbMg: p=0.1205, OR=1.198, χ2=2.410) from Grabert et. al⁴¹. (b) Horizontal bar graphs show log2 (fold change) in the counts of selected cbMg-specific/clearance-related (orange) and stMg-enriched/surveillance-related (purple) transcription factors in (1) expression upon apoptotic cell exposure, (2) enrichment of H3K27me3 in stMg vs cbMg, and (3) expression in Eed-deficient stMg vs control stMg. (c) Venn diagrams show overlap between cbMg (orange) and stMg (purple) enriched genes with genes up-(red; stMg: p=0.906, OR=1.089, χ2=0.01393; cbMg: p < 0.0001, OR=12.63, χ2=71.70) or down-regulated (blue; stMg: p < 0.0001, OR=19.42, χ2=950.8; cbMg: p=0.406, OR=0.558, χ2=0.6903) in microglia upon injection of apoptotic cells from Krasemann et. al¹³. Selected genes are named. (d) Venn diagram shows overlap between 215 genes up-regulated in PRC2-deficient stMg (purple), 144 genes up-regulated in PRC2-deficient cbMg (orange), and 518 genes up-regulated in PRC2-deficient cxMg (blue). Overlapping genes are indicated. p values and odds ratios (underneath each overlap) were calculated using the non-parametric χ2 test from a total 22,706 protein-coding genes analyzed in DESeq2.