5. RNA-PET: Full-Length Transcript Analysis Using 5′- and 3′-Paired-End Tag Next-Generation Sequencing

  1. Dr. Matthias Harbers2,3 and
  2. Prof. Dr. Günter Kahl4,5,6
  1. Xiaoan Ruan and
  2. Yijun Ruan

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch5

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

Ruan, X. and Ruan, Y. (2011) RNA-PET: Full-Length Transcript Analysis Using 5′- and 3′-Paired-End Tag Next-Generation Sequencing, in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch5

Editor Information

  1. 2

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

  2. 3

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

  3. 4

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 5

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

  5. 6

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

Author Information

  1. Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore

Publication History

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

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582



  • RNA-PET;
  • full-length transcript analysis;
  • next-generation sequencing;
  • methods;
  • applications


RNA-PET is a paired-end tag (PET) sequencing method for full-length mRNA analysis using next-generation sequencer platforms such as the Illumina Genome Analyzer and Applied Biosystems SOLiD. Unlike the RNA-seq method that sequences short randomly sheared shotgun RNA fragments, RNA-PET captures and sequences the 5′- and 3′-end tags of full-length cDNA fragments of all expressed genes in a biological sample. When mapped to a reference genome, RNA-PET sequences can demarcate the boundaries of transcription units genome-wide, in addition to its ability to quantify the transcription level of all expressed genes. Furthermore, the unique feature of RNA-PET is to identify fusion transcripts. Therefore, RNA-PET has been regarded as the best PET method for genome annotation. In this chapter, we describe the details of the RNA-PET protocol and discuss the critical issues.