Additional file 1 of Immune stimulation recruits a subset of pro-regenerative macrophages to the retina that promotes axonal regrowth of injured neurons

Additional file 1. scRNA-seq of CD45+CD11b+ cells from naïve or ONC retinas. A UMAP showing all CD11b+ cells profiled from the healthy and ONC retinas. BAM, border associated macrophage, cDC: conventional dendritic cell, migDC: migratory dendritic cell, MDM: monocyte-derived macrophage, Mg: microglia, MO, monocyte, N: neutrophils, NK: natural killer cell. B UMAPs showing the expression of the indicated genes. Red line highlights the putative macrophage-neutrophil doublets. C Volcano plot displaying differential expression between Mg3 and Mg1. Genes with adjusted p-value 1 are shown in red. D Volcano plot displaying differential expression between Mg4 and Mg1. Genes with adjusted p-value 1 are shown in red. E Quantification of the density and activityof microglia in retina at different timepoints after ONC corresponding with images shown in figure 1E. Data are shown as mean ± SEM. Repeated measures one-way ANOVA followed by Tukey’s multiple comparisons test, statistical significance between different timepoints is indicated using different letters: conditions that share the same letter are not significantly different, while conditions with different letters are significantly different from each other. n=3-4 mice per condition. F UMAPs showing the expression of the indicated genes, corresponding to the dataset shown in S1A.