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. 2023 Jun 15;24(7):1188–1199. doi: 10.1038/s41590-023-01528-8

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 4 — a. MA plot of RNA-seq data from WT versus Het EKO microglia. n = 3/genotype. b. Overlap of differential genes (p-adj. < 0.05 and log₂FC > 1, from DESeq2 analysis (Wald’s test with multiple testing correction using Benjamini–Hochberg method)) identified in EKO microglia vs WT and Sall1 conditional knockout versus control mouse microglia from Buttgereit et al.³. P-values for overlaps were calculated using one-tailed Fisher exact test. c. Metascape GO analysis of pathways significantly changed in EKO vs WT microglia. d. Overlap of differential genes (p-adj. < 0.05 and log₂FC > 1, from DESeq2 analysis (Wald’s test with multiple testing correction using Benjamini–Hochberg method)) identified in EKO vs WT microglia and engrafted vs. endogenous microglia (Shemer et al., 2018)²⁵. P-values for overlaps calculated using one-tailed Fisher exact test. e. Flow cytometry of WT and Het EKO brain nuclei stained for PU1 and SALL1. f. Boxplot of log₂FC of differential genes shared between Het and EKO microglia (n = 3/genotype). Median (center line), whiskers (max, min), box edges (25th - 75th percentile). g. Significance of gene set overlaps from Fig. 2g. P-values were calculated using one-tailed Fisher exact test for the overlap between differentially expressed genes in the Sall1 EKO vs differentially expressed genes in aging²⁹, the SOD model of ALS²⁹, AD risk genes³², upregulated genes in Disease Associated Microglia (DAM)³⁰, genes upregulated in LPS²⁹, genes upregulated in lipid droplet associated microglia (LDAMs)³¹ and microglia homeostatic genes^10,11,40. Dotted line represents p-value = 0.05. h. Expression of Ms4 family genes in EKO and WT microglia.