StemBase is a database containing data from Affymetrix DNA microarray experiments and Serial Analysis of Gene Expression, of human and mouse stem cell samples and their derivatives. As of July 2009, there were more than 180 samples available to public users and these are updated on a regular basis. The samples were originated by researchers of the Stem Cell Network and processed at the Core Facility of Stemcore Laboratories, a high-throughput genomics facility within the Ottawa Health Research Institute (OHRI), in the frame of the Stem Cell Genomics Project. StemBase is developed and maintained by the Bioinformatics group of the OHRI. The data is curated by the Bioinformatics group in collaboration with Pearl Campbell as well as the researchers that submit the samples to ensure the quality and consistency of the data. Periodically, new expression data is submitted to the Gene Expression Omnibus (GEO) repository at the National Centre for Biotechnological Information, in order to allow researchers to compare the data deposited in StemBase to a large amount of gene expression data sets. StemBase is concerned exclusively with stem cell related data and therefore differs from GEO in both focus and scope. GEO is intended as a large scale public archive. Deposition in a public repository such as GEO is required by most important scientific journals and it is advantageous for a further diffusion of the data since GEO is more broadly used than StemBase. The goal of the Stem Cell Genomics Project (SCGP) is the elucidation of the molecular mechanisms that regulate the formation, self-renewal, and differentiation of stem cells. Affymetrix GeneChip technology, SAGE, and LC MS/MS proteome analysis are being employed to analyze over 1000 preparations of human and mouse embryonic and adult stem cells. A bioinformatics team is facilitating integration and dissemination of this data into StemBase. The data from StemBase is being used to identify probe sets that may act as biomarkers in which samples.

If you use StemBase derived data in a publication, please cite this paper. Perez-Iratxeta, C., G. Palidwor, C.J. Porter, N.A. Sanche, M.R. Huska, B.P. Suomela, E.M. Muro, P.M. Krzyzanowski, E. Hughes, P.A. Campbell, M.A. Rudnicki and M.A. Andrade. 2005. Study of stem cell function using microarray experiments. 2005. FEBS Letters. 579, 1795-1801

Stem cells play an essential role in the human body as they provide the starting material for every organ and tissue. Knowledge of regulatory genes acting in and on stem cells is necessary to exploit their full therapeutic potential. The primary objective of StemBase is to provide a resource that may analyzed to determine gene expression patterns typical of stem cells and changes in gene expression that occur in stem cell differentiation.