title: SuperSAGE as an analytical tool for host and viral gene expression.
abstract: SuperSAGE is a tag-based transcript profiling method, which allows to analyze the expression of thousands of genes at a time. In SuperSAGE, 26 bp tags are extracted from cDNA using the type III restriction enzyme, EcoP15I. In SuperSAGE, the amount of transcripts was represented by tag counts. Taking advantage of uniqueness of the 26 bp tags, host and virus transcripts can be monitored in virus-infected cells. Combining next generation sequencing technology, we established High-throughput SuperSAGE (Ht-SuperSAGE), which allows the analysis of multiple samples with reduced time and cost. In this chapter, we present the protocol of Ht-SuperSAGE involving a recently available benchtop type next generation sequencer.
authors.affiliation: Gene Research Center, Shinshu University, 3-15-1 Tokita, Ueda, Nagano, 386-8567, Japan, hideoma@shinshu-u.ac.jp.
authors.forename: Hideo
authors.initials: H
authors.lastname: Matsumura
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: D018076:DNA, Complementary / Q000138:chemical synthesis; D020224:Expressed Sequence Tags; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054884:Host-Pathogen Interactions / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods; D014780:Viruses / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D018076:DNA, Complementary