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Related Experiment Videos

Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays.

Jiang Li1, Matthew Pankratz, Jeffrey A Johnson

  • 1School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53706, USA.

Toxicological Sciences : an Official Journal of the Society of Toxicology
|October 16, 2002
PubMed
Summary

Oligonucleotide microarrays (Affymetrix) provide more reliable gene expression data than long cDNA microarrays (IncyteGenomics). This study compared two platforms, finding oligonucleotide arrays better for detecting changes in antioxidant responsive element (ARE)-driven genes.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • DNA microarrays are crucial for global gene expression screening.
  • Two main types exist: oligonucleotide (Affymetrix) and long cDNA (IncyteGenomics).
  • Comparative reliability data between these platforms are limited.

Purpose of the Study:

  • To assess and compare the reliability of datasets generated by Affymetrix oligonucleotide and IncyteGenomics long cDNA microarray platforms.
  • To evaluate platform performance using a model of antioxidant responsive element (ARE)-driven gene upregulation.

Main Methods:

  • Utilized human neuroblastoma cells treated with tert-butylhydroquinone (tBHQ) for 8 and 24 hours.
  • Employed Affymetrix HuGene FL, Affymetrix U95 Av2, and IncyteGenomics UniGem V 2.0 microarray platforms.

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  • Validated findings using Reverse Transcription Polymerase Chain Reaction (RT-PCR).

    • Main Results:

    • Affymetrix U95 Av2 identified 218 upregulated genes after 8h tBHQ treatment, including known ARE-driven genes.
    • IncyteGenomics identified only four upregulated genes, which were also detected by Affymetrix.
    • Significant differences in sensitivity and specificity were observed between platforms, with cross-hybridization contributing to discrepancies.

    Conclusions:

    • Oligonucleotide microarrays (Affymetrix) demonstrate higher reliability for interrogating gene expression changes compared to long cDNA microarrays (IncyteGenomics).
    • The study highlights the importance of platform selection for accurate gene expression profiling.