Extended Data Fig. 6: Dynamics of resident and infiltrating mononuclear phagocytes in the retina, and conserved signature of Gpnmb⁺ macrophages.

a, Changes in frequency of Ms4a7⁺MHC-II^hi, Ms4a7⁺MHC-II^lo and Gpnmb⁺ macrophages across 0, 0.5, 1, 2, 4, 7, and 14dpc. b, Distribution of expression of genes associated with MHC-II^hi and MHC-II^lo BAMs²³ on retinal Ms4a7⁺MHC-II^hi (n = 741) and Ms4a7⁺MHC-II^lo macrophages (n = 1,406). Boxplots denote medians and IQRs; whiskers are the lowest datum still within 1.5 IQR of the lower quartile and the highest datum still within 1.5 IQR of the upper quartile. c, Representative image of smFISH on 7dpc retinal for Gpnmb (blue), Ms4a7 (red) and Ptprc (green) (n = 3 mice). Scale bar, 25 μm. d, Distribution of expression of Gpnmb⁺ macrophage marker gene orthologs in immune cell scRNA-seq data from chronic lesions in human patients with multiple sclerosis⁴⁷. e, Fraction of expressing cells (dot size) and normalized expression level in expressing cells (dot color) of the top 30 differentially expressed genes of Gpnmb⁺ macrophages across the RPE cell clusters. f, Representative IHC on uninjured (0 dpc) retinal whole-mounts showing perivascular and CB-adjacent IA-IE⁺ (green) cells. Blood vessels are labeled with IB4 (red) (representative of five independent experiments with n = 1-3 mice each). The middle panel shows a zoomed-in image of the perivascular macrophage in the inset of the left image. Scale bars, 50 μm g, Force-directed layout view of monocyte and macrophage subsets with optimal transport analysis. Each dot is a cell, color-coded by ancestor probabilities for Ms4a7⁺MHC-II^hi (top row) and Ms4a7⁺MHC-II^lo macrophages (bottom row), as estimated by Waddington-OT⁸⁸.