StemBase

StemBase is a database (publicly accessible at http://www.stembase.ca) containing data on Affymetrix DNA microarray experiments, and Serial Analysis of Gene Expression, mostly on human and mouse stem cell samples and their derivatives. We currently have more than 180 samples available to public users, with more being added regularly.

The samples were originated by researchers of the Stem Cell Network and processed at the Core Facility of Stemcore Laboratories under the management of Ms. Pearl Campbell 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 and the researchers that submitted the samples.

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 different from GEO in both focus and scope. StemBase is concerned exclusively with stem cell related data. we are focused in Stem Cell research. We have made a significant effort to ensure the quality and consistency of the data included. This allows us to offer more specialized analysis tools related to Stem Cell data. 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.

Reference:
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

If you use StemBase derived data in a publication, please cite this paper.

 

StemBase Citations

  • Ahmad S, Figueiredo F, Lako M. 2006. Corneal epithelial stem cells: characterization, culture and transplantation. Regenerative Medicine 1 (1): 29-44.
  • Arrell K,  Niederländer NJ, et al. 2006, Embryonic stem cell cardiac differentiation: a proteomic perspective. Advances in Molecular Medicine 2(4): 149-156.
  • Assou, S., Le Carrour, et al. 2007. A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas. Stem Cells, 25 (4), pp. 961-973.
  • Balana B, Nicoletti C, Zahanich I, et al. 2006. 5-Azacytidine induces changes in electrophysiological properties of human mesenchymal stem cells. Cell Research16 (12): 949-960.
  • Bernstein BE, Mikkelsen TS, Xie XH, et al. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2): 315-326.
  • Campbell PA, Perez-Iratxeta C, et al 2007, Oct4 Targets Regulatory Nodes to Modulate Stem Cell Function. PLoS ONE 2(6): e553.
  • Deasy BM, Lu AP, Tebbets JC, et al. 2007. A role for cell sex in stem cell-mediated skeletal muscle regeneration: female cells have higher muscle regeneration efficiency. Journal of Cell Biology. 177 (1): 73-86.
  • Glover CH, Marin M, Eaves CJ, et al. 2006. Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set. PLoS Computational Biology. 2 (11): 1463-1474.
  • Hipp J, Atala A. 2006. GeneChips in stem cell research. Methods of Enzymology. 420: 162-224.
  • Ishibashi J, Perry RL, Asakura A, et al., MyoD induces myogenic differentiation through cooperation of its NH2- and COOH-terminal regions. Journal of Cell Biology. 171 (3): 471-48.
  • McCann JA, Muro EM, et al. 2007. ChIP on SNP-chip for genome-wide analysis of human histone H4
    hyperacetylation    . BMC Genomics 8:322.
  • Maurer, MM, Kuchinsky, W 2006, Screening the Brain: Molecular Fingerprints of Neural Stem Cells, Current Stem Cell Research & Therapy, 1: 65-77.
  • Perez-Iratxeta C, Andrade MA. 2005. Inconsistencies over time in 5% of NetAffx probe-to-gene annotations. BMC Bioinformatics. 6: Art. No. 183.
  • Piscaglia AC,  Shupe T, et al. 2007. Microarray RNA/DNA in Different Stem Cell Lines, Current Pharmaceutical Biotechnology, 8: 167-175
  • Puente LG, Borris DJ, Carriere JF, et al. 2006. Identification of candidate regulators of embryonic stem cell differentiation by comparative phosphoprotein affinity profiling. Molecular & Cellular Proteomics. 5 (1): 57-67.
  • Roche E, Jones J, Arribas MI, et al. 2006. Role of small bioorganic molecules in stem cell differentiation to insulin-producing cells. Bioorganic and Medical Chemistry. 14 (19): 6466-6474.
  • Sene KS, Porter CJ, et al. 2007. Gene function in mouse embryonic stem cell differentiation. BMC Genomics  8:85.
  • Stalteri MA, Harrison AP. 2007. Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics. 8: Art. No. 13.
  • Szustakowski JD, Lee JH, Marrese CA, et al. 2006. Identification of novel pathway regulation during myogenic differentiation. Genomics. 87 (1): 129-138.
  • Von Hoof D, Mummery CL, Heck AJR, et al. 2006. Embryonic stem cell proteomics. Expert Review of Proteomics. 3 (4): 427-437.
  • Wang JL, Rao S, Chu JL, et al. 2006. A protein interaction network for pluripotency of embryonic stem cells. Nature 444 (7117): 364-368.
  • Wu JC, Spin JM, Cao F, et al. 2006. Transcriptional profiling of reporter genes used for molecular imaging of embryonic stem cell transplantation. Physiological Genomics. 25 (1): 29-38.
  • Yan H, Zareen N, Levinger L. 2006. Naturally occurring mutations in human mitochondrial pre-tRNA(Ser(UCN)) can affect the transfer ribonuclease Z cleavage site, processing kinetics, and substrate secondary structure. Journal of Biological Chemistry. 281 (7): 3926-3935.
  • Yano K, Subkhankulova T, Livesey FJ, et al. 2006. Electrophysiological and gene expression profiling of neuronal cell types in mammalian neocortex. Journal of Physiology-London. 575 (2): 361-365.