Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species

Hyeon Se Lee, Jianlin Wang, Lu Tian, Hongmei Jiang, Michael A. Black, Andreas Madlung, Brian Watson, Lewis Lukens, J. Chris Pires, Jiyuan J. Wang, Luca Comai, Thomas C. Osborn, R. W. Doerge, Z. Jeffrey Chen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


Synthetic oligonucleotides (oligos) represent an attractive alternative to cDNA amplicons for spotted microarray analysis in a number of model organisms, including Arabidopsis, C. elegans, Drosophila, human, mouse and yeast. However, little is known about the relative effectiveness of 60-70-mer oligos and cDNAs for detecting gene expression changes. Using 192 pairs of Arabidopsis thaliana cDNAs and corresponding 70-mer oligos, we performed three sets of dye-swap experiments and used analysis of variance (ANOVA) to compare sources of variation and sensitivities for detecting gene expression changes in A. thaliana, A. arenosa and Brassica oleracea. Our major findings were: (1) variation among different RNA preparations from the same tissue was small, but large variation among dye-labellings and slides indicates the need to replicate these factors; (2) sources of variation were similar for experiments with all three species, suggesting these feature types are effective for analysing gene expression in related species; (3) oligo and cDNA features had similar sensitivities for detecting expression changes and they identified a common subset of significant genes, but results from quantitative RT-PCR did not support the use of one over the other. These findings indicate that spotted oligos are at least as effective as cDNAs for microarray analyses of gene expression. We are using oligos designed from ∼26 000 annotated genes of A. thaliana to study gene expression changes in Arabidopsis and Brassica polyploids.

Original languageEnglish (US)
Pages (from-to)45-57
Number of pages13
JournalPlant Biotechnology Journal
Issue number1
StatePublished - Jan 2004


  • 70-mer oligo
  • Analysis of variance (ANOVA)
  • Arabidopsis
  • Brassica
  • Dye-swap
  • Microarray

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Biotechnology
  • Plant Science


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