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Nucleic Acids Research Advance Access originally published online on October 5, 2006
Nucleic Acids Research 2006 34(19):e133; doi:10.1093/nar/gkl714
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Nucleic Acids Research, 2006, Vol. 34, No. 19 e133
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

DeepSAGE—digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples

Kåre L. Nielsen*, Annabeth Laursen Høgh and Jeppe Emmersen

Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University DK-9000 Aalborg, Denmark

*To whom correspondence should be addressed. Tel: +45 9635 8527; Fax: +45 9814 1808; Email: kln{at}bio.aau.dk

Received May 10, 2006. Revised August 23, 2006. Accepted September 15, 2006.

Digital transcriptomics with pyrophosphatase based ultra-high throughput DNA sequencing of di-tags provides high sensitivity and cost-effective gene expression profiling. Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE). We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato. The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest. Importantly, many transcripts were detected that cannot be matched to known genes, but is likely to be part of the abiotic stress-response in potato.


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