Open AccessHigh-Throughput SuperSAGE for Digital Gene Expression Analysis of Multiple Samples Using Next Generation Sequencing
Author(s) -
Hideo Matsumura,
Kentaro Yoshida,
Shujun Luo,
Eiji Kimura,
Takahiro Fujibe,
Zayed Albertyn,
Roberto A. Barrero,
Detlev H. Krüger,
Günter Kahl,
Gary P. Schroth,
Ryohei Terauchi
Publication year - 2010
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0012010
Subject(s) - barcode , computational biology , dna sequencing , gene expression profiling , pooling , biology , throughput , gene expression , computer science , gene , genetics , artificial intelligence , operating system , telecommunications , wireless
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 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 are foreseen and several examples are provided in the present study, including analyses of laser-microdissected cells, biological replicates and tag extraction using different anchoring enzymes.
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