BASIC SCIENCE Microarray-based gene expression analysis during retinal maturation of albino rats Gil Ben-Shlomo & Ron Ofri & Dikla Bandah & Mordechai Rosner & Dror Sharon Received: 17 October 2007 / Revised: 3 January 2008 / Accepted: 12 January 2008 # Springer-Verlag 2008 Abstract Background In recent years, the rat has become a commonly- used animal model for the study of retinal diseases. Similar to other tissues, the retina undergoes significant functional changes during maturation. Aiming to gain knowledge on additional aspects of retinal maturation, we performed gene expression and histological analyses of the rat retina during maturation. Methods Rat retinas were dissected at three time points. Histological examination of the samples was performed, and the expression levels of retinal genes were evaluated using the rat whole-genome microarray system. Quantita- tive real-time PCR analysis was used to validate selected expression patterns. Various statistical and bioinformatic tools were used to identify differentially expressed genes. Results The microarray analysis revealed a relatively high number of highly expressed non–annotated genes. We identified 603 differentially expressed genes, which were grouped into six clusters based on changes in expression levels during the first 20 weeks of life. A bioinformatic analysis of these clusters revealed sets of genes encoding proteins with functions that are likely to be relevant to retinal maturation (potassium, sodium, calcium, and chloride channels, synaptic vesicle transport, and axonogenesis). The histological analysis revealed a significant reduction of outer nuclear layer thickness and retinal ganglion cell number during maturation. Conclusions These data, taken together with our previously reported electrophysiological data, contribute to our under- standing of the retinal maturation processes of this widely- used animal model. Keywords Dye-swap . Ganglion cells . Gene . Gene expression . Histology . Inner retina . Maturation . Microarray . Rat . Retina . Vision Introduction In recent years, the use of rodents in visual science research has expanded dramatically. In particular, the rat has become a commonly used animal model for the study of both outer retinal diseases [1–3] and inner retinal diseases, mostly glaucoma [4–6]. Similarly to other tissues, the retina undergoes profound developmental, maturation and aging alterations, which could potentially affect the results of retinal studies. Graefes Arch Clin Exp Ophthalmol DOI 10.1007/s00417-008-0772-0 Supported by: The Joseph Alexander Foundation and the Alberto Moscona Foundation. G. Ben-Shlomo : R. Ofri Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot, Israel D. Bandah : D. Sharon (*) Department of Ophthalmology, Hadassah-Hebrew University Medical Center, 91120 Jerusalem, Israel e-mail: dror.sharon1@gmail.com M. Rosner Goldschleger Eye Research Institute, Sackler School of Medicine, Tel-Aviv University, Sheba Medical Center, Tel-Hashomer, Israel