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Nucleic Acids Research 2005 33(16):e136; doi:10.1093/nar/gni136
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Published online 7 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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A novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes

L. Li*, D. Techel1, N. Gretz and A. Hildebrandt2

Centre for Medical Research (ZMF), University of Heidelberg Germany 1Institute for Legal Medicine Bremen, Germany 2Department of Environmental Research and Technology, University of Bremen Germany

*To whom correspondence should be addressed. Tel: +49 621 383 3769; Fax: +49 621 383 2108; Email: li.li{at}gmx.de

Received April 22, 2005. Revised July 4, 2005. Accepted August 19, 2005.

We have designed a novel transcriptome subtraction method for the genome-scale analysis of differential gene expression in highly complex eukaryotes, in which suppression subtractive hybridization (SSH) is performed first to enrich the target and, after exchange of adapters, negative subtraction chain (NSC) is then used to eliminate the remaining background. NSC evolved from differential subtraction chain (DSC). We designed novel adapters which make the subtraction system more robust. SSH and NSC were then combined to successfully detect differentially expressed genes in Solanum. The combined technique improves qualitatively upon SSH, the only commercially available transcriptome subtraction system, by detecting target genes in the middle abundance class, to which most differentially expressed genes in highly complex eukaryotes are expected to belong. The main advantage of the combined technique with SSH/NSC is its ability to isolate differentially expressed genes quickly and cost-efficiently from non-standard models, for those microarrays are unavailable.


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