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

doi:10.1186/1471-2164-9-418

BMC Genomics

Volume 9

Viewing options:

Abstract
Full text
PDF (695KB)

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Hanriot L
Keime C
Gay N
Faure C
Dossat C
Wincker P
Scoté-Blachon C
Peyron C
Gandrillon O

on PubMed

Hanriot L
Keime C
Gay N
Faure C
Dossat C
Wincker P
Scoté-Blachon C
Peyron C
Gandrillon O
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

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 Dossat⁴^,5^,6 , Patrick Wincker⁴^,5^,6 , Céline Scoté-Blachon¹ , Christelle Peyron¹ and Olivier Gandrillon³

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

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

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

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

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

⁶Université d'Evry, 91057 Evry, France

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:418doi: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.