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High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing

ABSTRACT: We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes permit to enable researchers to analyze digital tags from many transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications were expected and several examples of its applications were introduced in the present study, including analyses of laser-microdissected cells, biological replicates or tag extraction using different anchoring enzymes. 27 different tissue samples from three different life organisms were analyzed. About 2 samples, three different anchoring enzymes were employed.

SUBMITTER: Eiji Kimura Hideo Matsumura Detlev H Krüger Kentaro Yoshida Ryohei Terauchi Shujun Luo Roberto A Barrero Gary P Schroth Takahiro Fujibe Zayed Albertyn Günter Kahl

PROVIDER: E-GEOD-20682 | ArrayExpress | 2010-09-30

SECONDARY ACCESSION(S): GSE20682PRJNA124943

REPOSITORIES: GEO, ArrayExpress

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High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing.

Matsumura Hideo H Yoshida Kentaro K Luo Shujun S Kimura Eiji E Fujibe Takahiro T Albertyn Zayed Z Barrero Roberto A RA Krüger Detlev H DH Kahl Günter G Schroth Gary P GP Terauchi Ryohei R

PloS one 20100806 8

We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined "High-Throughput (HT-) SuperSAGE". SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes allow researchers to analyze digital tags from transcriptomes of many samples in a single sequencing run by ...[more]

PMID: 20700453

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