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You are here: Home / Teams / Systems Biology of Decision Making - O. Gandrillon / Publications (not up to date) / A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome.

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

Lucie Hanriot, Celine Keime, Nadine Gay, Claudine Faure, Carole Dossat, Patrick Wincker, Celine Scote-Blachon, Christelle Peyron, and Olivier Gandrillon (2008)

BMC Genomics, 9:418.

BACKGROUND: "Open" transcriptome analysis methods allow to study gene expressionwithout 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.

 
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