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Nucleic Acids Research Advance Access originally published online on July 20, 2009
Nucleic Acids Research 2009 37(18):e123; doi:10.1093/nar/gkp596
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Nucleic Acids Research, 2009, Vol. 37, No. 18 e123
© 2009 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

Transcriptome analysis by strand-specific sequencing of complementary DNA

Dmitri Parkhomchuk, Tatiana Borodina, Vyacheslav Amstislavskiy, Maria Banaru, Linda Hallen, Sylvia Krobitsch, Hans Lehrach and Alexey Soldatov*

Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 73, 14195 Berlin, Germany

*To whom correspondence should be addressed. Tel: 49 30 8413 1137; Fax: 49 30 8413 1128; Email: soldatov{at}molgen.mpg.de

Received April 7, 2009. Revised June 4, 2009. Accepted June 30, 2009.

High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript's expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript's direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online.


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