Brief Communication | Published:

FRT-seq: amplification-free, strand-specific transcriptome sequencing

Nature Methods volume 7, pages 130132 (2010) | Download Citation

Abstract

We report an alternative approach to transcriptome sequencing for the Illumina Genome Analyzer, in which the reverse transcription reaction takes place on the flowcell. No amplification is performed during the library preparation, so PCR biases and duplicates are avoided, and because the template is poly(A)+ RNA rather than cDNA, the resulting sequences are necessarily strand-specific. The method is compatible with paired- or single-end sequencing.

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Acknowledgements

We thank N. Bason and M. Quail for preparing the standard RNA-seq library, J. Burton for coordinating the sequencing of standard RNA-seq libraries, and J. Ule and M. Wollerton for advice on RNA ligation. This work was supported by the Wellcome Trust grant (WT079643).

Author information

Author notes

    • Lira Mamanova
    •  & Robert M Andrews

    These authors contributed equally to this work.

Affiliations

  1. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Lira Mamanova
    • , Robert M Andrews
    • , Keith D James
    • , Elizabeth M Sheridan
    • , Peter D Ellis
    • , Cordelia F Langford
    • , John E Collins
    •  & Daniel J Turner
  2. Illumina Inc., Chesterford Research Park, Little Chesterford, Essex, UK.

    • Tobias W B Ost

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Contributions

D.J.T. and T.W.B.O. devised the project; L.M. and D.J.T. devised the experimental protocols; L.M. and E.M.S. planned and carried out laboratory work; R.M.A. and K.D.J. performed data analysis; P.D.E. performed microarray work; and C.F.L. oversaw analysis and array work. D.J.T., J.E.C. and L.M. wrote the manuscript.

Competing interests

T.W.B.O. is an Illumina employee, shareholder and share option holder.

Corresponding author

Correspondence to Daniel J Turner.

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DOI

https://doi.org/10.1038/nmeth.1417

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