Brief Communication

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

  • Nature Methods volume 10, pages 122124 (2013)
  • doi:10.1038/nmeth.2306
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Abstract

We developed a cost-effective genome-scale PCR-based method for high-definition DNA FISH (HD-FISH). We visualized gene loci with diffraction-limited resolution, chromosomes as spot clusters and single genes together with transcripts by combining HD-FISH with single-molecule RNA FISH. We provide a database of over 4.3 million primer pairs targeting the human and mouse genomes that is readily usable for rapid and flexible generation of probes.

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Acknowledgements

We thank P. Junker and S. Semrau for helpful discussions. We are grateful to R.A. Weinberg (Massachusetts Institute of Technology) for providing hTERT-HME1 cells. This work was supported by the US National Institutes of Health (NIH)/National Cancer Institute Physical Sciences Oncology Center at Massachusetts Institute of Technology (U54CA143874), an NIH Pioneer award (1DP1OD003936) and a Nederlandse Organisatie voor Wetenschappelijk Onderzoek Vici award to A.v.O. M.B. and S.I. are sponsored by the Human Frontiers Science Program.

Author information

Author notes

    • Magda Bienko
    •  & Nicola Crosetto

    These authors contributed equally to this work.

Affiliations

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

    • Magda Bienko
    • , Nicola Crosetto
    • , Leonid Teytelman
    • , Shalev Itzkovitz
    •  & Alexander van Oudenaarden
  2. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Magda Bienko
    • , Nicola Crosetto
    • , Leonid Teytelman
    • , Shalev Itzkovitz
    •  & Alexander van Oudenaarden
  3. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Magda Bienko
    • , Nicola Crosetto
    • , Leonid Teytelman
    • , Shalev Itzkovitz
    •  & Alexander van Oudenaarden
  4. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Sandy Klemm
  5. Hubrecht Institute–KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands.

    • Alexander van Oudenaarden
  6. University Medical Center Utrecht, Utrecht, The Netherlands.

    • Alexander van Oudenaarden

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Contributions

N.C. and A.v.O. conceived the methods. M.B. and N.C. performed experiments, analyzed the data and wrote the manuscript. L.T. generated the genome-wide primer databases, designed the probes and wrote the manuscript. S.K. and S.I. developed software for image processing, provided suggestions on data analysis and corrected the manuscript. A.v.O. guided experiments and data analysis, and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Alexander van Oudenaarden.

Supplementary information