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将长链SAGE与Solexa测序相结合非常适合于探究转录组的深度和复杂性。

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

作者信息

Hanriot Lucie, Keime Céline, Gay Nadine, Faure Claudine, Dossat Carole, Wincker Patrick, Scoté-Blachon Céline, Peyron Christelle, Gandrillon Olivier

机构信息

UMR5534 CNRS Université Claude Bernard Lyon1, Université de Lyon, Institut Fédératif des Neurosciences de Lyon, Lyon cedex, France.

出版信息

BMC Genomics. 2008 Sep 16;9:418. doi: 10.1186/1471-2164-9-418.

DOI:10.1186/1471-2164-9-418
PMID:18796152
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2562395/
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.

摘要

背景

“开放”转录组分析方法能够在无需预先了解转录本序列的情况下研究基因表达。截至目前，基因表达序列分析（SAGE）、长片段SAGE和大规模平行信号测序（MPSS）是“开放”转录组分析中最常用的方法。长片段SAGE和MPSS均依赖于从每个转录本中分离出21个碱基对的标签序列。与长片段SAGE不同，MPSS中使用的高通量测序方法能够对包含数百万个标签的非常大的文库进行快速测序，从而实现深度转录组分析。然而，最近发现了MPSS获得的转录组代表性复杂性存在偏差。

结果

为了在避免MPSS所带来的局限性的情况下对小鼠下丘脑转录组进行深度分析，我们将长片段SAGE与Solexa测序技术相结合，获得了一个包含超过1100万个标签的文库。然后我们将其与用桑格法测序的小鼠下丘脑长片段SAGE文库进行了比较。

结论

我们发现Solexa测序技术与长片段SAGE相结合非常适合深度转录组分析。与MPSS不同，它能给出与用桑格法测序的长片段SAGE文库一样可靠的转录组复杂代表性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/4a069b10516c/1471-2164-9-418-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/4cfaabe127c0/1471-2164-9-418-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/be3eeb926e18/1471-2164-9-418-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/cfe54be70b10/1471-2164-9-418-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/d7a004bca5a4/1471-2164-9-418-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/4a069b10516c/1471-2164-9-418-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/4cfaabe127c0/1471-2164-9-418-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/be3eeb926e18/1471-2164-9-418-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/cfe54be70b10/1471-2164-9-418-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/d7a004bca5a4/1471-2164-9-418-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2659/2562395/4a069b10516c/1471-2164-9-418-5.jpg

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