Figure 7. Global and type-specific gene expression changes in VD RGCs.

A. Pairwise correlation heatmap showing that the average transcriptional profiles of VD RGCs are more similar to the NR RGCs at P56 than they are to NR RGCs at P5. Colors represent Pearson correlation coefficients.

B. Scatter plot comparing average log2-fold changes in the expression of genes (points) between NR RGCs at P56 and NR RGCs at P5 (x-axis) versus between NR and DR RGCs at P56 (y-axis). Dashed red lines denote fold changes of 1.5 along each axis, and the number of genes in each region is indicated. The relative preponderance of dots with |log-fold| > 1.5 along the x-axis compared to the y-axis reflect the fact that maturation-related genes are not substantially impacted during VD.

C. Same as B, for rd1 RGCs.

D. Same as B, for Vsx2-SE^−/− RGCs.

E. Bar-plot showing the number of global vDE genes that are downregulated (red) or upregulated (blue) in a single VD condition compared to controls or shared among conditions. The combination of VD conditions corresponding to each pair of bars is indicated below.

F. Statistical enrichment of maturation modules Mod1–6 (as in Figure 2A) among globally upregulated vDE genes in each VD condition.

G. Same as F for globally downregulated vDE genes in each VD condition.

H. Same as E but for type-specific vDE genes.

I. Same as F but for type-specific upregulated vDE genes.

J. Same as F but for type-specific downregulated vDE genes.

K. Violin plot showing that the proportion of counts associated with mitochondrial transcripts is higher in the VD conditions compared to NR. Note that NR contains both control RGCs used in this study (Tran et al., 2019) and RGCs from (Jacobi et al., 2022) (see Figure S5A).