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Single-cell systems biology by super-resolution imaging and combinatorial labeling

Nature Methods volume 9, pages 743748 (2012) | Download Citation

Abstract

Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral overlap between fluorophores. Here we demonstrate a simple but general strategy to drastically increase the capacity for multiplex detection of molecules in single cells by using optical super-resolution microscopy (SRM) and combinatorial labeling. As a proof of principle, we labeled mRNAs with unique combinations of fluorophores using fluorescence in situ hybridization (FISH), and resolved the sequences and combinations of fluorophores with SRM. We measured mRNA levels of 32 genes simultaneously in single Saccharomyces cerevisiae cells. These experiments demonstrate that combinatorial labeling and super-resolution imaging of single cells is a natural approach to bring systems biology into single cells.

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Acknowledgements

We credit B. Wold with discussions that led to this work. We thank M. Elowitz for lending space and equipment in his laboratory, T. Zhiyentayev, H.Q. Li and X. Wang for assistance with experiments, A. Raj for technical assistance with FISH, X.W. Zhuang and her group for STORM, and A. Eldar, S. Fraser, G.W. Li, J. Levine and J. Locke for discussion and reading of the manuscript. This work was supported by a Beckman Institute seed grant and a US National Institutes of Health New Innovator Award 1DP2OD008530.

Author information

Affiliations

  1. Program in Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, USA.

    • Eric Lubeck
    •  & Long Cai
  2. Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.

    • Long Cai

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Contributions

E.L. and L.C. performed the experiments, carried out the analysis and wrote the manuscript. L.C. conceived the idea and designed the experiments.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Long Cai.

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    Supplementary Figures 1–21, Supplementary Tables 1–4, Supplementary Note

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DOI

https://doi.org/10.1038/nmeth.2069

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