Figure 3 | Scientific Reports

Figure 3

From: Molecular profiling of resident and infiltrating mononuclear phagocytes during rapid adult retinal degeneration using single-cell RNA sequencing

Figure 3

Identification of immune cells before and during retinal degeneration, displayed in tSNE plot of all cells, collapsed from a k-nearest neighbor comparison of all gene expression comprising the top 10 principal components. (a) Cells color-coded by sample identity, with immune cells from dark-reared control retinas in red and from degenerating retinas in blue. (b) Cells can be broadly grouped into 4 clouds, which correspond to the main 4 cell types: (1) resting microglia, (2) activated microglia, (3) monocytes, and (4) monocyte-derived macrophages. (c) Cells color-coded by cluster, identified by an unsupervised graph-based algorithm, and assigned cell identity using relative abundance of established markers. (d–g) Example marker gene expression of genes associated with resting microglia (d), activated microglia (e), monocytes (f), and monocyte-derived macrophages (g). Scales in (d–g) indicate relative expression (log TPM values), with grey indicating no expression and saturated color indicating highest expression.

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