1. DeepSuperSAGE: High-Throughput Transcriptome Sequencing with Now- and Next-Generation Sequencing Technologies

  1. Dr. Matthias Harbers5,6 and
  2. Prof. Dr. Günter Kahl7,8,9
  1. Hideo Matsumura1,
  2. Carlos Molina2,
  3. Detlev H. Krüger3,
  4. Ryohei Terauchi4 and
  5. Prof. Dr. Günter Kahl7,8,9

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch1

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

Matsumura, H., Molina, C., Krüger, D. H., Terauchi, R. and Kahl, G. (2011) DeepSuperSAGE: High-Throughput Transcriptome Sequencing with Now- and Next-Generation Sequencing Technologies, in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch1

Editor Information

  1. 5

    4-2-6 Nishihara, Kashiwa-Shi, Chiba 277-0885, Japan

  2. 6

    DNAFORM Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan

  3. 7

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 8

    University of Frankfurt am Main Biocenter, Max-von-Lauestraße 9, 60439 Frankfurt am Main, Germany

  5. 9

    Frankfurt Biotechnology Innovation Center (FIZ), GenXPro Ltd, Altenhöferallee 3, 60438 Frankfurt am Main, Germany

Author Information

  1. 1

    Shinshu University, Gene Research Center, Tokita 3-15-1, Ueda, Nagano 386-8567, Japan

  2. 2

    INRA-URLEG, Unité de Recherche en Légumineuses, 17 Rue Sully, 21000 Dijon, France

  3. 3

    Charité – Universitätsmedizin Berlin, Institut für Virologie, Schumannstraße 20/21, 10117 Berlin, Germany

  4. 4

    Iwate Biotechnology Research Center, Research Group of Genetics and Genomics, Narita 22-174-4, Kitakami, Iwate 024-0003, Japan

  5. 7

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  6. 8

    University of Frankfurt am Main Biocenter, Max-von-Lauestraße 9, 60439 Frankfurt am Main, Germany

  7. 9

    Frankfurt Biotechnology Innovation Center (FIZ), GenXPro Ltd, Altenhöferallee 3, 60438 Frankfurt am Main, Germany

Publication History

  1. Published Online: 23 JAN 2012
  2. Published Print: 14 DEC 2011

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582

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Keywords:

  • DeepSuperSAGE;
  • transcriptome sequencing;
  • next-generation sequencing;
  • linker preparation;
  • adapter preparation;
  • applications

Summary

SuperSAGE is a variant of the serial analysis of gene expression (SAGE) expression profiling technology, in which 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 by homology searches against genome, transcript, or expressed sequence tag sequences. For organisms without genomic information, the 26-bp tags can be used as polymerase chain reaction primers to recover the full-length cDNA by 5′- and 3′-rapid amplification of cDNA ends. Here, we present the combination of SuperSAGE and high-throughput sequencing technologies (now- or next-generation sequencing (NGS)). We coin this merger deepSuperSAGE. The direct sequencing of millions of tag fragments shortens time and reduces costs for the analysis enormously. Furthermore, the incorporation of an indexing system expands the potential of deepSuperSAGE to analyze multiple samples in a single NGS run. The most recent version of deepSuperSAGE (high-throughput SuperSAGE) at least equals or even outcompetes microarrays in throughput. These improvements allow the application of deepSuperSAGE in transcriptome analysis in any eukaryotic system.