Figure 5. RNA-Seq of 3 individual biological replicates of 1-month-old A/J, BALB/c and B6 mouse eyes reveals differential transcriptome profiles.

(A) Left: Plot of log FPKM from A/J and B6 runs. The most highly expressed transcripts common to both A/J and B6 eyes were the lens crystallin genes (outlined) and rod photoreceptor genes such as Gnat1, Rho, and Sag. Most genes highly differentially expressed in the A/J eye relate to inflammation (red), whereas genes with the lowest differential expression in the A/J eye encode homeostatic proteins (black). Right: Whereas 12,672 genes had similar expression, 332 were differentially expressed by at least 2-fold (P ≤ 0.05) between A/J and B6 eyes. (B) Examination of all 3 mouse eye transcriptomes revealed those genes exclusively more highly expressed in a single mouse strain compared with the other 2 strains, and those sharing increased expression with respect to the third strain. For example, 235 genes are exclusively more highly expressed in the B6 eye; this strain shares 26 genes also highly expressed in the A/J eye and 56 also higher in the BALB/c eye. Importantly, a large cohort of inflammatory genes exhibits increased expression in A/J mice. Interestingly, although both A/J and BALB/c eyes share increased expression of inflammatory genes, only BALB/c exhibits a counteracting increased expression of retinal homeostatic and immune regulatory genes, either exclusively or shared with B6 eyes.