Title

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

Authors

Andreas Madlung, University of Puget SoundFollow
Hyeon-Se Lee, Department of Soil and Crop Sciences and Intercollegiate Program in Genetics, Texas A&M University, College Station, TX 77843-2474, USA
Jianlin Wang, Department of Soil and Crop Sciences and Intercollegiate Program in Genetics, Texas A&M University, College Station, TX 77843-2474, USA
Lu Tian, Department of Soil and Crop Sciences and Intercollegiate Program in Genetics, Texas A&M University, College Station, TX 77843-2474, USA
Hongmei Jiang, Department of Statistics, 1399 Math Building, Purdue University, West Lafayette, IN 47906, USA; Computational Genomics, 206 Whistler Hall, Purdue University, West Lafayette, IN 47906, USA
Michael A. Black, Department of Statistics, 1399 Math Building, Purdue University, West Lafayette, IN 47906, USA; Computational Genomics, 206 Whistler Hall, Purdue University, West Lafayette, IN 47906, USA
Brian Watson, Department of Biology, Box355325, University of Washington, Seattle, WA 98195-5325, USA
Lewis Lukens, Department of Agronomy, 1575 Linden Drive, University of Wisconsin, Madison, WI 53706, USA
J. Chris Pires, Department of Agronomy, 1575 Linden Drive, University of Wisconsin, Madison, WI 53706, USA
Jiyuan J. Wang, Department of Soil and Crop Sciences and Intercollegiate Program in Genetics, Texas A&M University, College Station, TX 77843-2474, USA
Luca Comai, Department of Biology, Box355325, University of Washington, Seattle, WA 98195-5325, USA
Thomas C. Osborn, Department of Agronomy, 1575 Linden Drive, University of Wisconsin, Madison, WI 53706, USA
R. W. Doerge, Department of Statistics, 1399 Math Building, Purdue University, West Lafayette, IN 47906, USA; Computational Genomics, 206 Whistler Hall, Purdue University, West Lafayette, IN 47906, USA; Department of Agronomy, 1150 Lilly Hall, Purdue University, West Lafayette, IN 47906, USA
Z. Jeffrey Chen, Department of Soil and Crop Sciences and Intercollegiate Program in Genetics, Texas A&M University, College Station, TX 77843-2474, USA

Document Type

Article

Publication Date

1-2004

Publication Title

Plant Biotechnology Journal

Department

Biology

Abstract

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.

ISSN

1467-7644