GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE20682 Query DataSets for GSE20682
Status Public on Oct 01, 2010
Title High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing
Organisms Arabidopsis thaliana; Oryza sativa; Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design 27 different tissue samples from three different life organisms were analyzed. About 2 samples, three different anchoring enzymes were employed.
Contributor(s) Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T, Albertyn Z, Barrero RA, Krüger DH, Kahl G, Schroth GP, Terauchi R
Citation(s) 20700453
Submission date Mar 08, 2010
Last update date Nov 27, 2017
Contact name Hideo Matsumura
Phone 81-268-21-5800
Organization name Shinshu University
Department Gene Research Center
Street address Tokita 3-15-1
City Ueda
State/province Nagano
ZIP/Postal code 3868567
Country Japan
Platforms (3)
GPL9302 Illumina Genome Analyzer II (Arabidopsis thaliana)
GPL9316 Illumina Genome Analyzer II (Oryza sativa)
GPL9319 Illumina Genome Analyzer II (Danio rerio)
Samples (31)
GSM518272 rice mature leaf (3-cyclePCR)
GSM518273 rice leaf (5-cycle PCR)
GSM518274 rice leaf (10-cycle PCR)
BioProject PRJNA124943

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap