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R. Schippert, M. Feldkaemper, F. Schaeffel; Microarray Analysis of Retinal Gene Expression in Egr-1 Knock-Out Mice. Invest. Ophthalmol. Vis. Sci. 2008;49(13):1745. doi: https://doi.org/.
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© ARVO (1962-2015); The Authors (2016-present)
To identify genes that are differentally expressed in the retinae of Egr-1 knock-out mice which have longer eyes than wildtype mice.
The retinae of homozygous and wildtype Egr-1 knock-out mice (Taconic) were prepared at the age of 30 days or 42 days, respectively (n=12each). Three retinae were pooled for RNA isolation (RNeasy Mini Kit, Quiagen) and labelled cRNA was made. The samples were then hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays with more than 39.000 transcripts presented. Hybridization signals were calculated using GC-RMA normalization. Genes were identified as differentially expressed if they showed a fold-change (FC) of at least 1.5 and a p-value < 0.05 (not corrected for multiple testing).
Comparing mRNA expression levels in the wildtype (WT) and the homozygous (HM) Egr-1 mice, we found 73 differentially expressed genes at the age of 30 days and 135 genes at the age of 42 days. Thirteen genes showed up in both lists.Regarding the development related changes, 55 genes were differentially expressed in the WT mice comparing the two age-groups (30 days versus 42 days). Comparing these age-groups in the HM animals, 215 genes were found and only 9 genes showed up in both lists.Noticeable is protocadherin beta 9 (Pcdhb9), which was severely downregulated in the Egr-1 knock-out mice (FC of 14.3 (30 days) and FC of 17.5 (42 days), p<0.0001 in both cases) compared to the WT.
We found earlier that 42 days old Egr-1 knock-out mice had longer eyes compared to the corresponding wildtype mice and were relatively more myopic. The identification of genes which are differentially regulated during development between 30 days (both HM and WT mice have still the same axial length) and 42 days might help understanding the mechanism leading to axial growth and thus to identify potential target genes for pharmacological intervention.
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