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G. Ben–Shlomo, R. Ofri, D. Bandah, D. Sharon; A Temporal Microarray–Based Gene Expression Analysis of the Rat Retina . Invest. Ophthalmol. Vis. Sci. 2006;47(13):4888.
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© ARVO (1962-2015); The Authors (2016-present)
To perform a comprehensive gene expression analysis of the rat retina at 5, 11, and 20 weeks of age, with the aim of identifying differentially expressed genes, and particularly those expressed in retinal ganglion cells (RGCs).
Retinal samples of albino Lewis rats were dissected at 5, 11, and 20 weeks of age. Total RNA was extracted using the RNeasy kit (Qiagen). Retinal samples were labeled with either cy3 or cy5 dyes and hybridized to Agilent rat microarrays. A dye–swap analysis was performed for each microarray hybridization. The data was statistically analyzed with the aim of comparing expression levels for the 3 different age groups. a detailed analysis of a subset of genes was done by collecting gene expression data from previous EST and SAGE analyses of human, mouse, and rat tissues.
The microarray data obtained from the rat retina contain many known retinal genes and are in agreement with previous retinal microarray–based gene expression analyses. However, among the genes showing the highest expression levels in our analysis, a relatively high number (70 out of 118) of non–annotated genes were observed. 841 of the genes showed differential expression levels between at least two of the three time points, and clustered into 7 different groups. The most common cluster contained 484 genes and showed no change in expression level between age 5 and 11 weeks while the expression level at the age of 20 weeks was higher comparing to 5 and 11 weeks. A bioinformatics analysis of the 841 differentially expressed genes revealed that at least 21 of them are expressed in RGCs. Among these genes were Stathmin, known to be involved in axongenesis, with relatively high expression levels in the young retina, and TWIK–2, a potassium channel, with a low expression level in the young retina.
Our analysis revealed many novel and known retinal genes that show differential expression pattern in the rat retina; some of these are already known to be expressed in RGCs. We have recently shown that the pattern electroretinogram (PERG) in rats, which is known to correlate with RGC function, changes with age (peaking at 11 weeks and declining thereafter). We are therefore performing quantitative real–time RT–PCR analysis on a subset of genes that are expressed in ganglion cells and show differential microarray expression that might correlate with RGC function.
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