June 2013
Volume 54, Issue 15
Free
ARVO Annual Meeting Abstract  |   June 2013
The Ocular Tissue Database
Author Affiliations & Notes
  • Terry Braun
    Ophthal/Biomed Eng, Univ of Iowa, Iowa City, IA
    Center for Bioinformatics and Computational Biology, Univ of Iowa, Iowa City, IA
  • Alex Wagner
    Genetics, Univ of Iowa, Iowa City, IA
    Center for Bioinformatics and Computational Biology, Univ of Iowa, Iowa City, IA
  • Adam DeLuca
    Biomedical Engineering, Univ of Iowa, Iowa City, IA
    Center for Bioinformatics and Computational Biology, Univ of Iowa, Iowa City, IA
  • Thomas Casavant
    Biomedical Engineering, Univ of Iowa, Iowa City, IA
    Center for Bioinformatics and Computational Biology, Univ of Iowa, Iowa City, IA
  • Todd Scheetz
    Ophthalmology and Visual Sciences, Univ of Iowa, Iowa City, IA
    Institute for Vision Research, Univ of Iowa, Iowa City, IA
  • Abbot Clark
    Department of Cell Biology and Anatomy, Univ North Texas Health Science Center, Fort Worth, TX
    North Texas Eye Research Institute, Univ North Texas Health Science Center, Fort Worth, TX
  • Robert Mullins
    Ophthalmology and Visual Sciences, Univ of Iowa, Iowa City, IA
    Institute for Vision Research, Univ of Iowa, Iowa City, IA
  • Edwin Stone
    Howard Hughes Medical Institute, Univ of Iowa, Iowa City, IA
    Institute for Vision Research, Univ of Iowa, Iowa City, IA
  • Footnotes
    Commercial Relationships Terry Braun, Alcon Research, LTD (F); Alex Wagner, None; Adam DeLuca, None; Thomas Casavant, None; Todd Scheetz, None; Abbot Clark, Alcon Research, Ltd. (F); Robert Mullins, Alcon Research Ltd (F); Edwin Stone, None
  • Footnotes
    Support None
Investigative Ophthalmology & Visual Science June 2013, Vol.54, 3383. doi:https://doi.org/
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    • Get Citation

      Terry Braun, Alex Wagner, Adam DeLuca, Thomas Casavant, Todd Scheetz, Abbot Clark, Robert Mullins, Edwin Stone; The Ocular Tissue Database. Invest. Ophthalmol. Vis. Sci. 2013;54(15):3383. doi: https://doi.org/.

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      © ARVO (1962-2015); The Authors (2016-present)

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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  
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