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Nucleic Acids Research, 2001, Vol. 29, No. 24 4983-4993
© 2001 Oxford University Press

Gene expression in the developing mouse retina by EST sequencing and microarray analysis

Xiuqian Mu, Sheng Zhao1, Rashmi Pershad2, Tzung-Fu Hsieh3, Ann Scarpa, Steven W. Wang, R. Allen White1, Phillip D. Beremand3, Terry L. Thomas3, Lin Gan4 and William H. Klein*

Department of Biochemistry and Molecular Biology, 1Department of Biomathematics and 2Department of Molecular Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA, 3Department of Biology and The Laboratory for Functional Genomics, Texas A&M University, College Station, TX 77843-3258, USA and 4Center for Aging and Development, University of Rochester, Rochester, NY 14642, USA

Retinal development occurs in mice between embryonic day E11.5 and post-natal day P8 as uncommitted neuroblasts assume retinal cell fates. The genetic pathways regulating retinal development are being identified but little is understood about the global networks that link these pathways together or the complexity of the expressed gene set required to form the retina. At E14.5, the retina contains mostly uncommitted neuroblasts and newly differentiated neurons. Here we report a sequence analysis of an E14.5 retinal cDNA library. To date, we have archived 15 268 ESTs and have annotated 9035, which represent 5288 genes. The fraction of singly occurring ESTs as a function of total EST accrual suggests that the total number of expressed genes in the library could approach 27 000. The 9035 ESTs were categorized by their known or putative functions. Representation of the genes involved in eye development was significantly higher in the retinal clone set compared with the NIA mouse 15K cDNA clone set. Screening with a microarray containing 864 cDNA clones using wild-type and brn-3b (–/–) retinal cDNA probes revealed a potential regulatory linkage between the transcription factor Brn-3b and expression of GAP-43, a protein associated with axon growth. The retinal EST database will be a valuable platform for gene expression profiling and a new source for gene discovery.

* To whom correspondence should be addressed at: Department of Biochemistry and Molecular Biology, Box 117, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA. Tel: +1 713 792 3646; Fax: +1 713 790 0329; Email: wklein{at}mdanderson.org +BG799964–BG808997, BI985056–BI991757


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