Allele-specific detection of single mrna molecules in situ

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. Access through your institution Buy or subscribe This is a preview

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SINGLE-CELL LINEAGE TRACING IN MICE AND HUMANS BASED ON DNA METHYLATION EPIMUTATIONS Article 16 January 2025 SINGLE-MOLECULE IMAGING OF TRANSCRIPTION DYNAMICS IN SOMATIC STEM CELLS Article

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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. AUTHOR

INFORMATION AUTHORS AND AFFILIATIONS * Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, Massachusetts, USA Clinton H Hansen * Department of Physics,

Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Alexander van Oudenaarden * Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

Alexander van Oudenaarden * Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Alexander van Oudenaarden * Hubrecht

Institute—Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht, The Netherlands Alexander van Oudenaarden Authors * Clinton H Hansen View author

publications You can also search for this author inPubMed Google Scholar * Alexander van Oudenaarden View author publications You can also search for this author inPubMed Google Scholar

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. ETHICS DECLARATIONS COMPETING INTERESTS 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) RIGHTS AND

PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE 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 Download citation * Received: 19 April 2013 * Accepted: 19 July 2013 * Published: 11 August 2013 * Issue Date: September 2013 * DOI:

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