Fig. 3

Single-cell mRNA sequencing reveals distinct populations of resident immune cells after degeneration. A tSNE plot with cells color-coded by time point (n = 8 retinas (4 mice) per timepoint). B tSNE plot with the same cells color-coded by cluster. C Heatmaps showing the average gene expression in each cluster of genes associated with microglial and monocytic cell lineages (left), and genes associated with microglial and monocyte-derived macrophage activation (right). Disease-associated microglia (DAM) genes were identified previously [11, 31], as were the macrophage activation markers [28]. D tSNE plot from this dataset combined with a previously published dataset of retinal macrophages before (0 days) and relatively early (2 days) during photoreceptor loss [24]. On the left, cells are color-coded using the same cluster identities as in B, with grey indicating cells from the previously published dataset. On the right, cells from the current dataset are indicated in grey, while cells from the previous dataset are color-coded according to clusters identified in [24]. For simplicity, the cluster naming has been collapsed across general cell types