Transcriptome comparison of RhoP23H/+ mouse retina with wildtype at different age

Rhodopsin P23H mutation is the most comment mutation causing autosomal dominant retinitis pigmentosa in the USA. The goal of this project is to compare the transcriptome changes of the Rhodopsin P23H knock-in mouse model of adRP to the wildtype control at different ages. The transcriptomic profile will help us understand the molecular events along the pathophysiology of reititis pigmentosa in this mouse model. We include the RNA seq data of Rhodopsin P23H heterozygous mouse retinas at 1, 3 and 6 months of age to compare with age-matched wildtype mouse retinas. N=3 and each sample is from an individual animal. Heterozygous Rhodopsin P23H knock-in mice (B6.129S6(Cg)-Rhotm1.1Kpal/J) and wildtype mice were euthanized at 1, 3 and 6 months of age and their retinas were isolated fresh. Total RNA was isolated using the Tryzol kit and RNA integrity was checked by Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq poly(A) selected kit (KAPA Biosystems, Wilmington, MA)using 250 ng total RNAs for each sample. Quality checks with a bioanalyzer were also performed on each library. Paired end sequencing was performed on Illumina HighSeq 4000 (Illumnia Inc., San Diego, CA). The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 [1]and the gene expression level was estimated using RSEM v1.2.15.[2] TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program[3]. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed. Goseq was uesd to perform the GO enrichment analysis and Kobas was used to performed the pathway analysis.