EST analysis of mouse retina and RPE/choroid cDNA libraries

Mol Vis. 2004 Jul 6:10:439-44.


Purpose: cDNA libraries from the mouse retina have recently been reported, but no well characterized library from the retinal pigment epithelium (RPE) or choroid of the mouse has yet appeared in the literature. To complement these libraries and to provide the first mouse RPE/choroid library, we used freshly dissected tissue from adult C57BL/6J mice to construct new retina and RPE/choroid libraries.

Methods: Eyes from 100 six to eight week old C57BL/6J mice were dissected in groups of 10. The whole retina and RPE/choroid were isolated individually and then homogenized before RNA isolation. Over 5000 clones each were sequenced from the unamplified and un-normalized retina and RPE/choroid libraries. All sequences were analyzed using GRIST (GRouping and Identification of Sequence Tags), a bioinformatics program for gene identification and clustering.

Results: The RPE/choroid library contained 3145 clusters with 76% of the clusters representing single clones. Nearly 87% of the clusters corresponded to named genes in GenBank, and 8% of the RPE clusters remain unidentified. The retina library contained 3190 clusters of which 78% represented only one clone. Approximately 85% of the clusters matched sequences in GenBank, and 9% of the clusters remain unidentified. The clones most abundant in each library were all well-known sequences and both libraries contained a number of tissue specific or tissue-enhanced genes.

Conclusions: These new libraries should provide a valuable resource for gene discovery and cDNAs for expression analysis and functional studies.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Choroid / metabolism*
  • DNA, Complementary / analysis*
  • Expressed Sequence Tags*
  • Eye Proteins / genetics*
  • Eye Proteins / metabolism
  • Gene Expression Profiling
  • Gene Library*
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Oligonucleotide Array Sequence Analysis
  • Pigment Epithelium of Eye / metabolism*
  • RNA / isolation & purification
  • RNA, Messenger / metabolism
  • Retina / metabolism*


  • DNA, Complementary
  • Eye Proteins
  • RNA, Messenger
  • RNA