Fig. 8: Gene expression underlying the retinal ganglion cell (RGC) lineage in the Atoh7-null retina. | Nature Communications

Fig. 8: Gene expression underlying the retinal ganglion cell (RGC) lineage in the Atoh7-null retina.

From: Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas

Fig. 8

a Overlaps of down- and upregulated DEGs (DN and UP, respectively) in Atoh7-null RGCs and RGC-enriched genes (EN) as presented by a Venn-diagram. Source data are provided. b Euclidean distance clustering demonstrating seven different modes of changes in gene expression in Atoh7-null retinal RGCs (C5 and C6, see main text for details). For comparison, expression in C3 and C4 are also presented. The color scale represents relative expression levels which were generated by averaging the normalized gene expression values in each cluster and then centering and scaling the values in each row using R bioconductor package “pheatmap” (see “Methods”). c Example genes with different modes of expression as demonstrated by violin plots, showing their expression levels (heights of plots, representing natural-log transformed normalized gene expression levels as described in “Methods”) across all clusters of wild-type (WT, red) and Atoh7-null (MT, blue) cells. Pou4f2 is from group 1a in (b), Syt4, Pou6f2, Gap43, and Elavl4 are from group 1b, Nhlh2 is from group 2, Kctd8 is from group 3a, and Neurod1 is from group 3b.

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