The Ocular Tissue Database

Abstract

Purpose: Evaluating gene expression in ocular tissues is useful for identifying genes and pathways involved in normal vision and inherited eye disease. In addition, tissue specific expression and alternative splicing can be observed by profiling multiple ocular tissues. The purpose of our study was to develop a public database of exon expression in ten different human ocular tissues.

Methods: Ten tissues were obtained from each of six human donors: retina, optic nerve head (ONH), optic nerve (ON), ciliary body (CB), trabecular meshwork (TM), sclera, lens, cornea, choroid/RPE and iris. RNA from each tissue was extracted and pooled. Affymetrix human Exon 1.0 ST arrays were used to profile gene expression in these tissues at a resolution of individual exons. The Affymetrix Power Tools (APT) probeset-summarize utility was used for background estimation and expression level quantification.

Results: The estimated values of expression for genes and their exons are now available on a public website at: https://genome.uiowa.edu/otdb/. Expression by tissue, gene or individual probes on the 1.0 ST array are accessible. Probeset-level detection above background estimates and alternate splicing graphs are also accessible. We compared the expression results versus retina RNAseq and other microarray and EST data in various tissues of the eye. We demonstrate the utility of profiling pooled RNA from multiple ocular tissues on a single platform.

Conclusions: We have created a public resource for evaluating normal expression of genes in 10 ocular tissues. Evaluation of genes known to be highly expressed in specific tissues demonstrates the value of this resource. We anticipate that this resource will be valuable for studies of changes in the transcriptome between tissues of the eye and to identify tissue specific alternative splicing.

Keywords: 533 gene/expression • 535 gene microarray • 539 genetics