Figure 6

Summary of immune subpopulations identified by scRNAseq. (a) Comparison of the relative population sizes organized by cloud and cluster number for control (0 hours of light exposure) and degenerating (48 hours of light exposure) tissue. In control retina, almost all of the immune cells were resident microglia, with resting microglia being the dominant type. In denerating tissue, most immune cells were infiltrating monocytes and monocyte-derived macrophages, while only a third were resident microglia, demonstrating that in the degenerating retina, microglia activation occurs concurrently with monocyte infiltration and differentiation into macrophages. The size of each dot corresponds to to the number of cells captured; the percent of cells within each condition is given. (b) Groups based on gene expression profiles for each cluster. The top 10 significantly differentialy expressed genes for each cluster and cloud are given (sorted by adjusted p-value, see Supplemental Tables 1 and 2 for an extended list, see Methods for description of how lists were created). Expression of genes in bold are also shown graphically throughout Figs 3–5.