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SuperSAGE as an Analytical Tool for Host and Viral Gene Expression

  • Hideo MatsumuraEmail author
  • Detlev H. Krüger
  • Günter Kahl
  • Ryohei Terauchi
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1236)

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.

Key words

SuperSAGE Next generation sequencing Transcriptome Host-pathogen interaction Gene expression 

Notes

Acknowledgements

HM is supported by the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (BRAIN). This work is also supported by JSPS (Japan Society for the Promotion of Science) grant no. 25450004.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Hideo Matsumura
    • 1
    Email author
  • Detlev H. Krüger
    • 2
  • Günter Kahl
    • 3
  • Ryohei Terauchi
    • 4
  1. 1.Gene Research CenterShinshu UniversityUedaJapan
  2. 2.Institute of Medical VirologyCharité Universitätsmedizin BerlinBerlinGermany
  3. 3.BiocenterUniversity of Frankfurt am MainFrankfurtGermany
  4. 4.Iwate Biotechnology Research CenterKitakamiJapan

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