Fig. 4: TRAP and IPA analysis of Shp2 loss in rod photoreceptors.

We employed a unique in vivo approach using TRAP. Rod-specific Shp2/Ribo-Tag mice were created by crossing homozygous Shp2 floxed mice with homozygous Ribo-Tag mice, along with rhodopsin-Cre mice. The resulting mice, with one Shp2 allele, homozygous for Ribotag, and carrying the rhodopsin Cre allele, were then bred to generate Cre-positive mice for comparative analysis: heterozygous (^rodShp2^+/-: Control) and homozygous (^rodShp2^−/−: KO). All experimental mice were homozygous for RiboTag (A). Gene Ontologies of Top 500 Rod-Enriched Transcripts (B). Unsupervised hierarchical clustering of TRAP and Retinal Samples (C). Volcano plot of differentially expressed transcripts between rod and retinal fractions (D). Heatmap of differentially expressed transcripts between rod and retinal fractions (E). Volcano plot of differentially expressed transcripts between retinal fractions of ^rodShp2 WT and KO mice (F). Heatmap of significant differentially expressed transcripts between retinal fractions of ^rodShp2 WT and KO mice (G). Volcano plot of differentially expressed transcripts between rod fractions of ^rodShp2 WT and KO mice (H). Heatmap of significant differentially expressed transcripts between rod fractions of ^rodShp2 WT and KO mice (I). Graphical Summary of IPA network analysis showing potential linchpin genes. Orange: Predicted Activation, Blue: Predicted Inhibition (J). Prediction of differentially affected pathways in rods mediated by loss of Shp2. Orange: Predicted Activation (Positive Z-Score), Blue: Predicted Inhibition (Negative Z-Score) (K). Panel (A) was created with BioRender.com.