A Microarray Dataset of Genes Expressed by the R28 Retinal Precursor Cell Line

The R28 rat retinal progenitor cell line was developed from postnatal day six rat retina immortalized with the 12S E1A gene of adenovirus. R28 cells have been distributed to over 100 laboratories worldwide, with over 60 publications on topics that include in vitro toxicology, cellular physiology, gene expression analysis, and experimental transplantation. In this paper, we present a microarray dataset of R28 cells that describes the presence or absence of 8799 genes and ESTs that may be relevant to current and future studies of R28 retinal precursor cells. 1. Introduction R28 cells were developed over 15 years ago as a growth-stimulated, nontumorigenic retinal cell line immortalized by the 12S E1A gene of adenovirus [1]. Over the years, these cells have been utilized for a wide range of studies that include in vitro toxicology [2], neuroprotection [3, 4], light responses [5], diabetic complications [6], and retinal transplantation [7]. An abbreviated list of genes and ESTs from this R28 cell line dataset with particular relevance to neuroscience was described previously [8]. The presence of a subset of genes (e.g., MAP2, calbindin, nestin, and syntaxin) was validated by immunostaining, while functionality was measured by electrophysiological responses to dopamine, serotonin, and muscarinic receptor agonists [8]. Here, we present the entire 8799 gene/EST microarray dataset in open access format for the benefit of neuroscience investigators with an interest in retinal cell biology. 2. Methodology R28 cells were derived by three rounds of limiting dilution of the parental E1A-NR.3 cell line. Parental E1A-NR.3 cells were originally developed from postnatal day 6 Sprague-Dawley rat retinal tissue immortalized with the 12S E1A gene of adenovirus from a replication-incompetent retroviral vector [1]. Animal sacrifice and tissue harvesting were performed according to institutionally approved animal care and use protocols. R28 cells were grown in Dulbecco’s Modified Eagle’s Medium with 10% calf serum, 0.37% sodium bicarbonate, 0.058% l-glutamine, and 100？μg/mL gentamicin. For this microarray study, R28 cells were trypsinized at passage 48, centrifuged into a pellet, snap-frozen, and stored at ？80°C prior to analysis. Microarray analysis was performed as described previously [8]. Briefly, the RG U34A cDNA microarray (Affymetrix, Inc. Santa Clara, CA, USA), a rat microarray that contains 8799 genes and ESTs, was used for analysis of the R28 rat retinal cell line. Total RNA was extracted from six million R28 cells (passage 48), followed by mRNA extraction with a