Published online 19 July 2006
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes
1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire UMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France 2 University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire UMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France 3 MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SB, UK 4 Department of Chemical Engineering, University of Michigan Ann Arbor, MI 48109, USA 5 Biodiscovery LLC, 3886 Penberton Dr Ann Arbor, MI 48109, USA 6 IGBMC, BP163 F67404 Illkirch Cédex, France 7 CEA—Service de Génomique Fonctionnelle, Genopole d'Evry F91057 Evry Cédex, France 8 Laboratoire de Génétique Oncologique, UMR 1599 CNRS Institut Gustave Roussy, F-94805 Villejuif Cedex, France
*To whom correspondence should be addressed. Tel : +33 4 9395 7793; Fax: +33 4 9395 7794; Email: barbry{at}ipmc.cnrs.fr
*Correspondence may also be addressed to Tom C. Freeman. Tel : +44 131 242 6242; Fax: +44 131 242 6244; Email: drtfreeman{at}ed.ac.uk
Received April 28, 2006. Revised June 5, 2006. Accepted June 23, 2006.
Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148 993 and 121 703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25 342 human and 24 109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity score; (ii) the number of expressed sequence tags matching each probe; (iii) the distance to the 3' end of the target mRNA. Scores were also used to compare in silico the two microarrays with commercial microarrays. The sets described here, called RNG/MRC collections, appear at least as specific and sensitive as those from the commercial platforms. The RNG/MRC collections have now been used by an Anglo-French consortium to distribute more than 3500 microarrays to the academic community. Ad hoc identification of tissue-specific transcripts and a 
80% correlation with hybridizations performed on Affymetrix GeneChipTM suggest that the RNG/MRC microarrays perform well. This work provides a comprehensive open resource for investigators working on human and mouse transcriptomes, as well as a generic method to generate new microarray collections in other organisms. All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE.
Present address: Tom C. Freeman, Scottish Centre for Genomic Technology and Informatics, University of Edinburgh Medical School, The Chancellor's Building, Edinburgh EH16 4SB, UK
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