Advertisement

PCR Protocols pp 135-146 | Cite as

High-Throughput SuperSAGE

  • Hideo Matsumura
  • Kentaro Yoshida
  • Shujun Luo
  • Detlev H. Krüger
  • Günter Kahl
  • Gary P. Schroth
  • Ryohei Terauchi
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 687)

Abstract

SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. Combined with the ultrahigh-throughput sequencing technologies, SuperSAGE enables analysis of millions of transcripts with lower cost and reduced effort and time. In this chapter, we present an updated protocol for this High-throughput SuperSAGE method with a special emphasis on the technique of library multiplexing.

Key words

Gene expression profiling Transcriptome analysis Next-generation sequencing Multiplexing 

Notes

Acknowledgments

HM is supported by the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (BRAIN).

References

  1. 1.
    Morozova, O. and Marra, M.A. (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92, 255–64.PubMedCrossRefGoogle Scholar
  2. 2.
    Metzker, M.L. (2010) Sequencing technologies – the next generation. Nat. Rev. Genet. 11, 31–46.PubMedCrossRefGoogle Scholar
  3. 3.
    Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651–6.PubMedCrossRefGoogle Scholar
  4. 4.
    Velculescu, V.E., Zhang, L., Vogelstein, B., and Kinzler, K.W. (1995) Serial analysis of gene expression. Science 270, 484–7.PubMedCrossRefGoogle Scholar
  5. 5.
    Saha, S., Sparks, A.B., Rago, C., Akmaev, V., Wang, C.J., Vogelstein, B., Kinzler, K.W., and Velculescu, V.E. (2002) Using the transcriptome to annotate the genome. Nat. Biotechnol. 20, 508–12.PubMedCrossRefGoogle Scholar
  6. 6.
    Matsumura, H,, Reich, S., Ito, A., Saitoh, H., Kamoun, S., Winter, P., Kahl, G., Reuter, M., Kruger, D.H., and Terauchi, R. (2003) Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc. Natl. Acad. Sci. USA 100, 15718–23.PubMedCrossRefGoogle Scholar
  7. 7.
    Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., Roth, R., George, D., Eletr, S., Albrecht, G., Vermaas, E., Williams, S.R., Moon, K., Burcham, T., Pallas, M., DuBridge, R.B., Kirchner, J., Fearon, K., Mao, J., and Corcoran, K. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630–4.PubMedCrossRefGoogle Scholar
  8. 8.
    Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–8.CrossRefGoogle Scholar
  9. 9.
    Matsumura, H., Ito, A., Saitoh, H., Winter, P., Kahl, G., Reuter, M., Kruger, D.H., and Terauchi, R. (2005) SuperSAGE. Cell. Microbiol. 7, 11–8.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press 2011

Authors and Affiliations

  • Hideo Matsumura
    • 1
  • Kentaro Yoshida
    • 1
  • Shujun Luo
    • 2
  • Detlev H. Krüger
    • 3
  • Günter Kahl
    • 4
  • Gary P. Schroth
    • 2
  • Ryohei Terauchi
    • 1
  1. 1.Iwate Biotechnology Research CenterKitakamiJapan
  2. 2.Illumina, IncHaywardUSA
  3. 3.Institute of Medical VirologyUniversity Hospital CharitéBerlinGermany
  4. 4.Molecular BioSciences, BiocentreUniversity of Frankfurt am MainFrankfurtGermany

Personalised recommendations