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

摘要: 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 60-70-mer oligos cDNAs detecting gene expression changes. Using 192 pairs Arabidopsis thaliana corresponding 70-mer oligos, we performed three sets dye-swap experiments used variance (anova) compare sources variation sensitivities changes A. thaliana, arenosa Brassica oleracea. Our major findings were: (1) among different RNA preparations from same tissue was small, but large dye-labellings slides indicates need replicate these factors; (2) were similar with all species, suggesting feature types are effective analysing related species; (3) oligo features had they identified common subset significant genes, results quantitative RT-PCR did not support use one over other. These indicate that at least as analyses expression. We using designed approximately 26,000 annotated genes study polyploids.