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Allele-specific detection of single mRNA molecules in situ

Nature Methods volume 10, pages 869–871 (2013)Cite this article

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Abstract

We describe a method for fluorescence in situ identification of individual mRNA molecules, allowing quantitative and accurate measurement, in single cells, of allele-specific transcripts that differ by only a few nucleotides. By using a combination of allele-specific and non–allele-specific probe libraries, we achieve >95% detection accuracy. We investigate the allele-specific stochastic expression of Nanog, which encodes a pluripotency factor, in murine embryonic stem cells.

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Figure 1: Allele-specific in situ detection of single mRNA molecules using SNP-specific probes.
Figure 2: Accurate allele-specific detection using identification probes.

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References

  1. Eldar, A. & Elowitz, M.B. Nature 467, 167–173 (2010).

    Article  CAS  Google Scholar 

  2. Balázsi, G., van Oudenaarden, A. & Collins, J.J. Cell 144, 910–925 (2011).

    Article  Google Scholar 

  3. Femino, A.M., Fay, F.S., Fogarty, K. & Singer, R.H. Science 280, 585–590 (1998).

    Article  CAS  Google Scholar 

  4. Raj, A., van den Bogaard, P., Rifkin, S.A., van Oudenaarden, A. & Tyagi, S. Nat. Methods 5, 877–879 (2008).

    Article  CAS  Google Scholar 

  5. White, A.K. et al. Proc. Natl. Acad. Sci. USA 108, 13999–14004 (2011).

    Article  CAS  Google Scholar 

  6. Larsson, C., Grundberg, I., Söderberg, O. & Nilsson, M. Nat. Methods 7, 395–397 (2010).

    Article  CAS  Google Scholar 

  7. Keane, T.M. et al. Nature 477, 289–294 (2011).

    Article  CAS  Google Scholar 

  8. Panning, B., Dausman, J. & Jaenisch, R. Cell 90, 907–916 (1997).

    Article  CAS  Google Scholar 

  9. Yilmaz, L.S., Parkernar, S. & Noguera, D.R. Appl. Environ. Microbiol. 77, 1118–1122 (2011).

    Article  CAS  Google Scholar 

  10. Ying, Q.L. et al. Nature 453, 519–523 (2008).

    Article  CAS  Google Scholar 

  11. Miyanari, Y. & Torres-Padilla, M.E. Nature 483, 470–473 (2012).

    Article  CAS  Google Scholar 

  12. Levesque, M.J. & Raj, A. Nat. Methods 10, 246–248 (2013).

    Article  CAS  Google Scholar 

  13. Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y. & Tyagi, S. PLoS Biol. 4, e309 (2006).

    Article  Google Scholar 

  14. Zhong, J.F. et al. Lab Chip 8, 68–74 (2008).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank S. Semrau for programming assistance and B. Panning (University of California, San Francisco) for providing the 2-1 embryonic stem cells and helpful discussions and for inspiring the initial idea that led to the development of this method. We thank J.P. Junker, S. Klemm, Y. Lin, D. Mooijman, A. Pawlosky and Y. Zheng for technical assistance, general discussions and/or comments on the manuscript. This work was supported by a grant (U54CA143874) from the US National Institutes of Health (NIH) National Cancer Institute Physical Sciences Oncology Center at Massachusetts Institute of Technology, an NIH Pioneer Award (8 DP1 CA174420-05) and a Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) Vici award to A.v.O.

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Authors and Affiliations

  1. Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, Massachusetts, USA

    Clinton H Hansen

  2. Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Alexander van Oudenaarden

  3. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Alexander van Oudenaarden

  4. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Alexander van Oudenaarden

  5. Hubrecht Institute—Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht, The Netherlands

    Alexander van Oudenaarden

Authors
  1. Clinton H Hansen
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  2. Alexander van Oudenaarden
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Contributions

C.H.H. and A.v.O. conceived the method. C.H.H. performed experiments, analyzed the data and wrote the manuscript. A.v.O. guided experiments and data analysis and wrote the manuscript.

Corresponding author

Correspondence to Alexander van Oudenaarden.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–18, Supplementary Table 2 and Supplementary Note (PDF 1768 kb)

Supplementary Table 1

Probe Sequences (TXT 27 kb)

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Hansen, C., van Oudenaarden, A. Allele-specific detection of single mRNA molecules in situ. Nat Methods 10, 869–871 (2013). https://doi.org/10.1038/nmeth.2601

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