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Author Notes:

Correspondence to: Eldon E. Geisert, Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322; Phone: (404) 778-4239; FAX: (404) 778 4111; email: egeiser@emory.edu

We thank XiangDi Wang and Arthur Centeno for their technical assistance in this project.


Research Funding:

This work was supported by DoD CDMRP Grant W81XWH1210255 from the USA Army Medical Research & Materiel Command and the Telemedicine and Advanced Technology (EEG), NIH Grant R01EY017841 (EEG), Vision Core Grant P30EY006360 (P. Michael Iuvone), and Unrestricted Funds from Research to Prevent Blindness (Emory University).

This study was supported in part by the Emory Integrated Genomics Core (EIGC), which is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities.


  • Science & Technology
  • Life Sciences & Biomedicine
  • Biochemistry & Molecular Biology
  • Ophthalmology

Transcriptome networks in the mouse retina: An exon level BXD RI database


Journal Title:

Molecular Vision


Volume 21


, Pages 1235-1251

Type of Work:

Article | Final Publisher PDF


Purpose: Differences in gene expression provide diverse retina phenotypes and may also contribute to susceptibility to injury and disease. The present study defines the transcriptome of the retina in the BXD RI strain set, using the Affymetrix Mouse Gene 2.0 ST array to investigate all exons of traditional protein coding genes, non-coding RNAs, and microRNAs. These data are presented in a highly interactive database on the GeneNetwork website. Methods: In the Normal Retina Database, the mRNA levels of the transcriptome from retinas was quantified using the Affymetrix Mouse Gene 2.0 ST array. This database consists of data from male and female mice. The data set includes a total of 52 BXD RI strains, the parental strains (C57BL/6J and DBA/2J), and a reciprocal cross. Results: In combination with GeneNetwork, the Department of Defense (DoD) Congressionally Directed Medical Research Programs (CDMRP) Normal Retina Database provides a large resource for mapping, graphing, analyzing, and testing complex genetic networks. Protein-coding and non-coding RNAs can be used to map quantitative trait loci (QTLs) that contribute to expression differences among the BXD strains and to establish links between classical ocular phenotypes associated with differences in the genomic sequence. Using this resource, we extracted transcriptome signatures for retinal cells and defined genetic networks associated with the maintenance of the normal retina. Furthermore, we examined differentially expressed exons within a single gene. Conclusions: The high level of variation in mRNA levels found among the BXD RI strains makes it possible to identify expression networks that underline differences in retina structure and function. Ultimately, we will use this database to define changes that occur following blast injury to the retina.

Copyright information:

© 2015 Molecular Vision

This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommerical-NoDerivs 3.0 Unported License (http://creativecommons.org/licenses/by-nc-nd/3.0/).

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