Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

In situ detection and genotyping of individual mRNA molecules

Nature Methods volume 7, pages 395–397 (2010)Cite this article

Subjects

This article has been updated

Abstract

Increasing knowledge about the heterogeneity of mRNA expression within cell populations highlights the need to study transcripts at the level of single cells. We present a method for detection and genotyping of individual transcripts based on padlock probes and in situ target-primed rolling-circle amplification. We detect a somatic point mutation, differentiate between members of a gene family and perform multiplex detection of transcripts in human and mouse cells and tissue.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Detection of individual transcripts in situ with padlock probes and target-primed RCA.
Figure 2: Multiplex in situ detection of cancer-related transcripts in cancer and primary human cell lines.

Accession codes

Accessions

GenBank/EMBL/DDBJ

Change history

  • 30 July 2010

    In the version of this article initially posted online, primer information for detection of mouse α- and β-actin in tissue was incorrect in Online Methods. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Bengtsson, M., Stahlberg, A., Rorsman, P. & Kubista, M. Genome Res. 15, 1388–1392 (2005).

    Article  CAS  Google Scholar 

  2. Levsky, J.M. & Singer, R.H. Trends Cell Biol. 13, 4–6 (2003).

    Article  CAS  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. et al. Nat. Methods 5, 877–879 (2008).

    Article  CAS  Google Scholar 

  5. Emmert-Buck, M.R. et al. Science 274, 998–1001 (1996).

    Article  CAS  Google Scholar 

  6. Espina, V. et al. Nat. Protoc. 1, 586–603 (2006).

    Article  CAS  Google Scholar 

  7. Nilsson, M. et al. Science 265, 2085–2088 (1994).

    Article  CAS  Google Scholar 

  8. Lizardi, P.M. et al. Nat. Genet. 19, 225–232 (1998).

    Article  CAS  Google Scholar 

  9. Larsson, C. et al. Nat. Methods 1, 227–232 (2004).

    Article  CAS  Google Scholar 

  10. Nilsson, M. et al. Nat. Biotechnol. 18, 791–793 (2000).

    Article  CAS  Google Scholar 

  11. Lagunavicius, A. et al. RNA 15, 765–771 (2009).

    Article  CAS  Google Scholar 

  12. Herman, I.M. Curr. Opin. Cell Biol. 5, 48–55 (1993).

    Article  CAS  Google Scholar 

  13. Kranenburg, O. Biochim. Biophys. Acta 1756, 81–82 (2005).

    CAS  PubMed  Google Scholar 

  14. Ge, B. et al. Nat. Genet. 41, 1216–1222 (2009).

    Article  CAS  Google Scholar 

  15. Zhang, K. et al. Nat. Methods 6, 613–618 (2009).

    Article  CAS  Google Scholar 

  16. Pan, Q. et al. Nat. Genet. 40, 1413–1415 (2008).

    Article  CAS  Google Scholar 

  17. Allalou, A. & Wahlby, C. Comput. Methods Programs Biomed. 94, 58–65 (2009).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Botling at the Department of Genetics and Pathology, Uppsala University for selection of the HER2-positive breast tissue from the Uppsala Biobank, K. Kullander and A. Enjin at the Department of Neuroscience, Uppsala University for providing the mouse embryonic tissue and aiding in tissue identification, C. Wählby at the Department of Genetics and Pathology, Uppsala University for providing MatLab scripts for quantification, L. Lindbom for technical aid, J. Göransson and R. Ke for suggesting formamide in the Ampligase protocol and U. Landegren, S. Fredriksson and T. Sjöblom for comments on the manuscript. Funding was provided by the Knut and Alice Wallenberg Foundation, the Swedish Cancer Foundation, the Göran Gustafsson Foundation, the Erik K. Fernström Foundation, the Swedish Research Council, the European Union FP6 project COMICS and the European Union FP7 (FP7/2007-2013) project READNA (grant agreement HEALTH-F4-2008-201418).

Author information

Author notes

  1. Chatarina Larsson and Ida Grundberg: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden

    Chatarina Larsson, Ida Grundberg, Ola Söderberg & Mats Nilsson

Authors
  1. Chatarina Larsson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ida Grundberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ola Söderberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mats Nilsson
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

C.L. and I.G. designed and performed experiments and analyzed data. M.N. supervised. All authors contributed to conceiving the project and writing the manuscript.

Corresponding author

Correspondence to Mats Nilsson.

Ethics declarations

Competing interests

M.N. owns shares in the company Olink AB, Uppsala, Sweden, which holds patents whose value may be affected by publication.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Tables 1–3 and Supplementary Notes 1–8 (PDF 1647 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Larsson, C., Grundberg, I., Söderberg, O. et al. In situ detection and genotyping of individual mRNA molecules. Nat Methods 7, 395–397 (2010). https://doi.org/10.1038/nmeth.1448

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.1448

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing