An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes

Kévin Le Brigand, Roslin Russell, Chimène Moreilhon, Jean-Marie Rouillard, Bernard Jost, Franck Amiot, Virginie Magnone, Christine Bole-Feysot, Philippe Rostagno, Virginie Virolle, Virginie Defamie, Philippe Dessen, Gary Williams, Paul Lyons, Géraldine Rios, Bernard Mari, Erdogan Gulari, Philippe Kastner, Xavier Gidrol, Tom C FreemanPascal Barbry

Research output: Contribution to journalArticlepeer-review

Abstract

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 approximately 80% correlation with hybridizations performed on Affymetrix GeneChiptrade mark 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.
Original languageEnglish
Pages (from-to)e87
JournalNucleic Acids Research
Volume34
Issue number12
DOIs
Publication statusPublished - 2006

Keywords

  • Animals
  • Databases, Nucleic Acid
  • Expressed Sequence Tags
  • Gene Expression Profiling
  • Humans
  • Internet
  • Mice
  • Oligonucleotide Array Sequence Analysis
  • Oligonucleotide Probes
  • Transcription, Genetic

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