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


CONCLUSIONS
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.
Hanriot
Lucie
L
UMR5534 CNRS Université Claude Bernard Lyon1, Université de Lyon, Institut Fédératif des Neurosciences de Lyon, Lyon cedex, France. lucie.hanriot@hotmail.fr
Keime
Céline
C
Gay
Nadine
N
Faure
Claudine
C
Dossat
Carole
C
Wincker
Patrick
P
Scoté-Blachon
Céline
C
Peyron
Christelle
C
Gandrillon
Olivier
O
D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D007031:Hypothalamus / Q000378:metabolism; D008297:Male; D051379:Mice; D008815:Mice, Inbred Strains; D017422:Sequence Analysis, DNA / Q000379:methods*
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