Fig. 4.

RiboTag and scRNA-seq analysis of Muller glia-enriched transcripts in WT and Ndp^KO retinas converge on a common set of differentially expressed genes. (A, Left) CoGAPS sample weights of the Muller glia-RiboTag–enriched pattern for Muller glia-RiboTag and whole-retina samples. (A, Upper Right) Projections of the Muller glia-RiboTag–enriched pattern into WT and Ndp^KO scRNA-seq datasets visualized on UMAP plots. (A, Lower Right) Mean projection scores of the Muller glia-RiboTag–enriched pattern in Ndp^KO and WT Muller glia clusters of the scRNA-seq datasets. Error bars represent the SEM. (B) Expression of Muller glia-enriched transcripts in Muller glia-RiboTag vs. whole-retina RNA-seq (Left) and in scRNA-seq (Right). In B–D, each cell in the scRNA-seq dataset is represented by a point along the horizontal axis, and the regions of the plot corresponding to different cell types and to WT vs. Ndp^KO are color coded across the top. (C) Analysis as in B, except that C shows Muller glia-enriched transcripts that were also up-regulated in Ndp^KO retinas in the Muller glia-RiboTag RNA-seq (Left) and scRNA-seq datasets (Right). (D) Analysis as in B, except that D shows Muller glia-enriched transcripts that were also down-regulated in Ndp^KO retinas in the Muller glia-RiboTag RNA-seq (Left) and scRNA-seq datasets (Right). As seen in B–D, among retinal cells, retinal astrocytes bear the closest resemblance to Muller glia as judged by their patterns of transcript abundances. A, astrocyte; AC, amacrine cell; C, cone; CBC, cone bipolar cell; HC, horizontal cell; M, microglia; MG, Muller glia; PC, perivascular cell; R, rod; RBC, rod bipolar cell; VEC, vascular endothelial cell.