Fig. 6

Crx mutants lose rod gene expression but up-regulate many phototransduction-unrelated cone gene transcripts. a Classification of genes within groups 1, 2, 3, and 6 as rod-enriched (dark grey), cone-enriched (light grey), or not specific to a particular cell type (N.S., white) in the normal adult retina. Rod and cone-enriched genes are defined based on the comparison of published P21 WT to Nrl−/− RNA-seq data [24]. Rod: FC ≥ 2, FDR ≤ 0.05. Cone: FC ≤ -2, FDR ≤ 0.05. Fishers exact test, *p < 0.05, ***p < 0.0005. b, c Heatmaps depict hierarchical clustering of FC relative to WT for all rod-enriched (b) and cone-enriched (c) genes. Expression data from a published RNA-seq study describing the Crx Rip/+, Rip/Rip, and Crx−/− mice are also separately presented in the order determined by the aforementioned clustering. Regions noted in (b) and (c) with asterisks are presented in larger format in Additional file 14 and represent many down-regulated genes involved in phototransduction in rods and cones. d Immunohistochemical staining for RXRγ, CNGB3, and peanut agglutinin (PNA) in P10 WT and three Crx mutant retina sections. Scale bar = 100 μm. IS inner segment, ONL outer nuclear layer