22. Helicos Single-Molecule Sequencing for Accurate Tag-Based RNA Quantitation

  1. Dr. Matthias Harbers3,4 and
  2. Prof. Dr. Günter Kahl5,6,7
  1. John F. Thompson1,
  2. Tal Raz1 and
  3. Patrice M. Milos2

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch22

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

Thompson, J. F., Raz, T. and Milos, P. M. (2011) Helicos Single-Molecule Sequencing for Accurate Tag-Based RNA Quantitation, in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch22

Editor Information

  1. 3

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

  2. 4

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

  3. 5

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 6

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

  5. 7

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

Author Information

  1. 1

    Helicos BioSciences Corporation, One Kendall Square, Building 700, Cambridge, MA 02139, USA

  2. 2

    Helicos BioSciences Corporation, One Kendall Square, Building 200, Cambridge, MA 02139, USA

Publication History

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

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582



  • Helicos single-molecule sequencing;
  • tag-based RNA;
  • quantitation;
  • methods;
  • applications


Helicos single-molecule sequencing technology provides the researcher with a comprehensive portfolio of robust sequencing applications for accurate quantitation of nucleic acids. The Helicos digital gene expression assay demonstrates the principles of this single-molecule sequencing technology and provides the researcher with a method for tag-based RNA quantitation. Utilizing total RNA or mRNA, a poly(U) primer is hybridized to the poly(A) region of mRNA and extended with reverse transcriptase, resulting in first-strand cDNA. After digestion of the RNA, the 3′ end of the cDNA is poly(A)-tailed with terminal transferase, which is then hybridized for capture on the Helicos Sequencer Flow Cell oligo(dT) surface. cDNA molecules are then sequenced using the Helicos Genetic Analysis System, generating sequence reads from the 5′ end of the original RNA transcript. One tag is generated from each RNA transcript and each of 50 flow cell channels yields 8–12 million alignable sequence tags or some 400–600 million sequence tags per run. Thus, the researcher is offered the flexibility of sequencing 50 independent samples or using multiple channels of individual samples to allow a deeper view for transcript quantitation. This method provides unique advantages relative to RNA-seq methods for the generation of accurate and reliable gene expression data from biological specimens.