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Open Access Highly Accessed Methodology article

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome

Lucie Hanriot1, Céline Keime2, Nadine Gay1, Claudine Faure3, Carole Dossat456, Patrick Wincker456, Céline Scoté-Blachon1, Christelle Peyron1 and Olivier Gandrillon3*

Author Affiliations

1 UMR5167 CNRS Université Claude Bernard Lyon1, Université de Lyon, Institut Fédératif des Neurosciences de Lyon, 7 rue Guillaume Paradin, 69372 Lyon cedex 08, France

2 PRABI, Université Claude Bernard Lyon 1, Bâtiment Gregor Mendel, 16 rue Raphaël Dubois, 69622 Villeurbanne Cedex, France

3 UMR5534 CNRS Université Claude Bernard Lyon1, Université de Lyon, Bâtiment Gregor Mendel, 16 rue Raphaël Dubois, 69622 Villeurbanne Cedex, France

4 Genoscope (CEA), 2 rue Gaston Crémieux CP5706, 91057 Evry, France

5 CNRS, UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France

6 Université d'Evry, 91057 Evry, France

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BMC Genomics 2008, 9:418  doi:10.1186/1471-2164-9-418

Published: 16 September 2008

Abstract

Background

"Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression), LongSAGE and MPSS (Massively Parallel Signature Sequencing) are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered.

Results

In order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method.

Conclusion

We found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method.