Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses

Heenam Kim, B. Zhao, E. C. Snesrud, B. J. Haas, C. D. Town, John Quackenbush

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

In most microarray assays, labeled cDNA molecules derived from reference and query RNA samples are co-hybridized to probes arrayed on a glass surface. Gene expression profiles are then calculated for each gene based on the relative hybridization intensities measured between the two samples. The most commonly used reference samples are typically isolates from a single representative RNA source (RNA-0) or pooled mixtures of RNA derived from a plurality of sources (RNA-p). Genomic DNA offers an alternative reference nucleic acid with a number of potential advantages, including stability, reproducibility, and a potentially uniform representation of all genes, as each unique gene should have equal representation in a haploid genome. Using hydrogen peroxide-treated Arabidopsis thaliana plants as a model, we evaluated genomic DNA and RNA-p as reference samples and compared expression levels inferred through the reference relative to unexposed plants with expression levels measured directly using an RNA-0 reference. Our analysis demonstrates that while genomic DNA can serve as a reasonable reference source for microarray assays, a much greater correlation with direct measurements can be achieved using an RNA-based reference sample.

Original languageEnglish
Pages (from-to)924-930
Number of pages7
JournalBioTechniques
Volume33
Issue number4
Publication statusPublished - 2002 Oct 1
Externally publishedYes

Fingerprint

Microarray Analysis
Microarrays
Oligonucleotide Array Sequence Analysis
RNA
DNA
Genes
Assays
Haploidy
Transcriptome
Arabidopsis
Gene expression
Nucleic Acids
Hydrogen Peroxide
Glass
Complementary DNA
Genome
Molecules

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Kim, H., Zhao, B., Snesrud, E. C., Haas, B. J., Town, C. D., & Quackenbush, J. (2002). Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. BioTechniques, 33(4), 924-930.

Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. / Kim, Heenam; Zhao, B.; Snesrud, E. C.; Haas, B. J.; Town, C. D.; Quackenbush, John.

In: BioTechniques, Vol. 33, No. 4, 01.10.2002, p. 924-930.

Research output: Contribution to journalArticle

Kim, H, Zhao, B, Snesrud, EC, Haas, BJ, Town, CD & Quackenbush, J 2002, 'Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses', BioTechniques, vol. 33, no. 4, pp. 924-930.
Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J. Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. BioTechniques. 2002 Oct 1;33(4):924-930.
Kim, Heenam ; Zhao, B. ; Snesrud, E. C. ; Haas, B. J. ; Town, C. D. ; Quackenbush, John. / Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. In: BioTechniques. 2002 ; Vol. 33, No. 4. pp. 924-930.
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