Present addresses: Department of Statistics, The University of Auckland, Auckland, New Zealand. ‡Department of Biology, University of Puget Sound, Tacoma, WA 98416. §Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species
Article first published online: 10 NOV 2003
Plant Biotechnology Journal
Volume 2, Issue 1, pages 45–57, January 2004
How to Cite
Lee, H.-S., Wang, J., Tian, L., Jiang, H., Black, M. A., Madlung, A., Watson, B., Lukens, L., Pires, J. C., Wang, J. J., Comai, L., Osborn, T. C., Doerge, R. W. and Chen, Z. J. (2004), Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Plant Biotechnology Journal, 2: 45–57. doi: 10.1046/j.1467-7652.2003.00048.x
- Issue published online: 10 NOV 2003
- Article first published online: 10 NOV 2003
- Received 8 July 2003; revised 26 August 2003; accepted 31 August 2003.
- 70-mer oligo;
- analysis of variance (anova);
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.