Extended Data Fig. 3: NHD microglia signature overlaps with IL-10-induced macrophage signature.

a, UMAP plot of human monocyte-derived macrophages stimulated with cocktails of LPS + IFNγ, IL-4 + IL-13 or IL-10 from GSE199378, designated by treatment. b, Venn diagram showing little overlap among signatures of polarized macrophages. c-e, Violin plot showing gene set scores (by UCell) of the designated macrophage polarization signatures (top 100 genes upregulated under each condition) in the macrophage polarization dataset; c, LPS + IFNγ polarization, n = 8,232 nuclei; d, IL-4 + IL-13 polarization, n = 6,741 nuclei; e, IL-10 polarization, n = 6,890 nuclei. Box center lines, bounds of box, and whiskers indicate median, first and third quartiles, and minima and maxima within 1.5X IQR, respectively. P value by two-sided Wilcoxon Rank Sum test. f-h, GSEA plots showing enrichment of NHD microglia signature in signatures of polarized macrophages stimulated by LPS and IFNγ (f), IL-4 (g) and IL-10 (h) from GSE61298²⁸. P values by permutation. NES, normalized enrichment score. i, Histogram of phospho-STAT3 (pSTAT3) staining of bone marrow derived macrophages (BMDMs) from WT and DAP12 KΔ75 mice, stimulated with 0 ng/ml or 20 ng/ml IL-10 for 15 min after starvation overnight. Data are representative of two independent experiments. j, Quantification of pSTAT3 mean fluorescence intensity (MFI) in i. P value by two-way ANOVA. Data are presented as mean ± s.e.m. n = 3 independent cell culture wells per genotype per experiment; n = two independent experiments. k, Histogram of total STAT3 staining in BMDM from WT and DAP12 KΔ75 mice, treated as in i. Data are representative of two independent experiments. l, Quantification of STAT3 mean fluorescence intensity in k. P value by two-way ANOVA. Data are presented as mean ± s.e.m. n = 3 independent cell culture wells per genotype per experiment; n = two independent experiments. m, Gating strategy for BMDMs from WT and KΔ75 mice. Numbers indicate the percentage of cells within the gate.