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A.J. Mears, S. Yoshida, J. Yu, R. Farjo, T. Carter, C. Barlow, A. Swaroop; Identification of Rod or Cone-Enriched Genes through Microarray Analysis of the Nrl Knockout Mouse . Invest. Ophthalmol. Vis. Sci. 2003;44(13):3524.
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© ARVO (1962-2015); The Authors (2016-present)
Purpose: To identify genes that are preferentially expressed in the rod or cone photoreceptors by microarray analysis of the "rod-less" Nrl knockout mouse retina (Mears et al. 2001, Nature Genet 29: 447-452). Methods: Expression profiling was performed using both oligo-based GeneChips (MGU74Av2) from Affymetrix and custom-made eye / retinal cDNA glass slide arrays ("I-gene" arrays). For the GeneChip studies, four replicate experiments were performed for post-natal day 2, 10 and 2 months. Data was analyzed using Mas4 / Mas5 and differentially expressed genes (>1.8 Average Fold Change) were extracted by Bullfrog. Five replicate experiments were performed on custom-made mouse eye cDNA arrays for post-natal day 21. Differentially expressed genes were identified after normalization by an Empirical Bayes method. Quantitative real-time PCR was performed to validate the Affymetrix and cDNA array data. Results: In both types of arrays, genes encoding known rod or cone-specific proteins (e.g. rhodopsin, rod and cone transducin, rod cGMP phosphodiesterase) showed dramatic changes in their expression consistent with the cone only retinal phenotype of the Nrl knockout mouse. This analysis identified over 150 differentially expressed genes of which about half of these genes demonstrated an increase in expression in the knockout (putative cone-enriched) and half a decrease (putative rod-enriched). Approximately 50 are ESTs with an unknown function. Conclusions: Microarray profiling has identified more than 150 differentially expressed genes in the Nrl knockout mouse retina. Of these, there are a number of novel genes that display an apparent rod or cone-enriched expression and these are being further studied as candidates in retinal disease, development or as putative downstream targets of Nrl. More detailed analysis has also identified a number of signaling pathways in which the genes encoding the component proteins are systematically altered in their expression.
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