RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: Enhancing the retinal microarray data sets from GeneNetwork

Purpose: The goal of the present study is to provide an independent assessment of the retinal transcriptome signatures of C57BL/6J (B6) and DBA/2J (D2) mice, and to enhance existing microarray data sets for accurately defining the allelic differences in the BXD recombinant inbred strains. Methods: Retinas from B6 and D2 mice (three of each) were used for the RNA sequencing (RNA-seq) analysis. Transcriptome features were examined for both strains. Differentially expressed genes between the two strains were identified, and bioinformatic analysis was performed to analyze the transcriptome differences between the B6 and D2 strains, including Gene Ontology (GO) analysis, Phenotype and Reactome enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The RNA-seq data were then directly compared with one of the microarray data sets (Department of Defense [DoD] Retina Normal Affy MoGene 2.0 ST RMA Gene Level Microarray Database) hosted on GeneNetwork. Results: RNA-seq provided an in-depth analysis of the transcriptome of the B6 and D2 retinas with a total of more than 30,000,000 reads per sample. More than 70% of the reads were uniquely mapped, resulting in a total of 18,100 gene counts for all six samples. A total of 1,665 genes were differentially expressed, with 858 of these more highly expressed in the B6 retinas and 807 more highly expressed in the D2 retinas. Several molecular pathways were differentially active between the two strains, including the retinoic acid metabolic process, endoplasmic reticulum lumen, extracellular matrix (ECM) organization, and the PI3K-Akt signaling pathway. The most enriched KEGG pathways were the pentose and glucuronate interconversions pathway, the cytochrome P450 pathway, the protein digestion and absorption pathway, and the ECM-receptor interaction pathway. Each of these pathways had a more than fourfold enrichment. The DoD Normal Retina Microarray Database provided expression profiling for 26,191 annotated transcripts for B6 mouse, D2 mouse, and 53 BXD strains. A total of 13,793 genes in this microarray data set were comparable to the RNA-seq data set. For the B6 and D2 retinas, the RNA-seq data and the microarray data were highly correlated with each other (Pearson's r= 0.780 for the B6 mice and 0.784 for D2 mice). These results suggest that the microarray data set can reliably detect differentially expressed genes between the B6 and D2 retinas, with an overall accuracy of 91.1%. Examples of true positive and false positive genes are provided. Conclusions: Retinal transcriptome features of B6 and D2 mouse strains provide a useful reference for a better understanding of the mouse retina. Generally, the microarray database presented on GeneNetwork shows good agreement with the RNA-seq data, but we note that any allelic difference between B6 and D2 mice should be verified with the latter.