title: SuperSAGE: powerful serial analysis of gene expression.
abstract: SuperSAGE is a variant of the Serial Analysis of Gene Expression (SAGE) technology, based on counting transcripts by sequencing analysis of short sequence tags. In SuperSAGE, 26 bp tags are extracted from cDNA using the Type III restriction endonuclease EcoP15I. The use of a longer tag size in SuperSAGE allows a secure tag-to-gene annotation in any eukaryotic organism. We have succeeded in combining SuperSAGE and high-throughput sequencing technology (Now- or Next-Generation Sequencing, NGS) in an approach we call High-throughput SuperSAGE (HT-SuperSAGE). This approach allows deep transcriptome analysis and multiplexing, while reducing time, cost, and effort for the analysis. In this chapter, we present the detailed HT-SuperSAGE protocol for both the Illumina Genome Analyzer and also the AppliedBiosystems SOLiD sequencer.
authors.affiliation: Gene Research Center, Shinshu University, Ueda, Nagano, Japan. hideoma@shinshu-u.ac.jp
authors.forename: Hideo
authors.initials: H
authors.lastname: Matsumura
authors.forename: Naoya
authors.initials: N
authors.lastname: Urasaki
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yoshida
authors.forename: Detlev H
authors.initials: DH
authors.lastname: Krüger
authors.forename: Günter
authors.initials: G
authors.lastname: Kahl
authors.forename: Ryohei
authors.initials: R
authors.lastname: Terauchi
mesh_terms: D000818:Animals; D001483:Base Sequence; D002021:Buffers; D017931:DNA Primers / Q000235:genetics; D018076:DNA, Complementary / Q000138:chemical synthesis / Q000302:isolation & purification; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D011119:Polynucleotides / Q000235:genetics; D048348:Reverse Transcription; D017422:Sequence Analysis, DNA / Q000379:methods*; D014158:Transcription, Genetic
chemical_list: D002021:Buffers; D017931:DNA Primers; D018076:DNA, Complementary; D011119:Polynucleotides