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Visualizing SNVs to quantify allele-specific expression in single cells

Nature Methods volume 10, pages 865–867 (2013)Cite this article

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Abstract

We present a FISH-based method for detecting single-nucleotide variants (SNVs) in exons and introns on individual RNA transcripts with high efficiency. We used this method to quantify allelic expression in cell populations and in single cells, and also to distinguish maternal from paternal chromosomes in single cells.

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Figure 1: Toehold probes enable SNV detection on individual RNA molecules in situ.
Figure 2: Allele-specific expression in GM12878 single cells and populations.

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Change history

  • 14 August 2013

    In the version of this article initially published online, a bar in panel d of Figure 1 was left blank. It should have been filled with the appropriate colors to indicate the number of transcripts derived from wild-type (blue) or mutant (orange) RNA and the number of unclassified transcripts (colorless). The error has been corrected for the print, PDF and HTML versions of the article.

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Acknowledgements

We thank Biosearch technologies for providing many of the reagents used in our assays and G. Nair for many discussions about statistics. We acknowledge the US National Institutes of Health Director's New Innovator Award (1DP2OD008514; M.J.L., P.G., Y.W. and A.R.) and a Burroughs-Wellcome Fund Career Award at the Scientific Interface (A.R.) for supporting our work.

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Authors and Affiliations

  1. Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA

    Marshall J Levesque, Paul Ginart, Yichen Wei & Arjun Raj

  2. Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA

    Paul Ginart

Authors
  1. Marshall J Levesque
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  2. Paul Ginart
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  3. Yichen Wei
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  4. Arjun Raj
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Contributions

M.J.L. conceived of the method with guidance from A.R. M.J.L. performed the image analysis and P.G. performed the statistical analysis. M.J.L., Y.W. and P.G. performed the experiments. M.J.L., P.G. and A.R. wrote the paper.

Corresponding authors

Correspondence to Marshall J Levesque or Arjun Raj.

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Competing interests

A.R. and M.J.L. are inventors on a US provisional patent 61/785,498 on the method described in this paper, and receive royalties related to this and other related patents.

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Supplementary Figures 1–8, Supplementary Tables 1 and 2, and Supplementary Note 1 (PDF 1655 kb)

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Levesque, M., Ginart, P., Wei, Y. et al. Visualizing SNVs to quantify allele-specific expression in single cells. Nat Methods 10, 865–867 (2013). https://doi.org/10.1038/nmeth.2589

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