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

Kévin Le Brigand1, Roslin Russell, Chimène Moreilhon

  • 1CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, UMR6097, 660, route des Lucioles, F-06560 Sophia Antipolis, France.

Nucleic Acids Research
|July 21, 2006
PubMed
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Researchers developed new human and mouse microarray oligonucleotide collections (RNG/MRC) that are highly specific and sensitive. These open-access resources, detailed in the MEDIANTE database, support transcriptome research and microarray development.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Microarrays are essential tools for transcriptome analysis.
  • Existing commercial microarrays have limitations in specificity and accessibility.
  • Developing robust and open-access microarray resources is crucial for research.

Purpose of the Study:

  • To design and validate novel oligonucleotide collections for pangenomic human and mouse microarrays.
  • To create a comprehensive, open-access resource for transcriptome research.
  • To establish a generic method for generating new microarray collections.

Main Methods:

  • Designed 148,993 human and 121,703 mouse oligonucleotides against transcripts.
  • Developed quality scores based on BLAST-specificity, EST matches, and 3' end distance.

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  • Performed in silico comparisons with commercial microarrays.
  • Validated performance through tissue-specific transcript identification and correlation with Affymetrix GeneChip hybridizations.

    • Main Results:

    • Selected 25,342 human and 24,109 mouse oligonucleotides for the RNG/MRC collections.
    • RNG/MRC collections demonstrated comparable or superior specificity and sensitivity to commercial platforms.
    • Distributed over 3500 microarrays to the academic community.
    • Achieved approximately 80% correlation with established microarray platforms.

    Conclusions:

    • The RNG/MRC collections represent a valuable, open-access resource for human and mouse transcriptome studies.
    • The developed methodology provides a framework for creating microarray collections in other species.
    • The MEDIANTE database offers comprehensive probe information and facilitates data accessibility.