Brief Communication | Published:

Dense transcript profiling in single cells by image correlation decoding

Nature Methods volume 13, pages 657660 (2016) | Download Citation

Abstract

Sequential barcoded fluorescent in situ hybridization (seqFISH) allows large numbers of molecular species to be accurately detected in single cells, but multiplexing is limited by the density of barcoded objects. We present correlation FISH (corrFISH), a method to resolve dense temporal barcodes in sequential hybridization experiments. Using corrFISH, we quantified highly expressed ribosomal protein genes in single cultured cells and mouse thymus sections, revealing cell-type-specific gene expression.

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Acknowledgements

We thank J. Linton from the Elowitz laboratory (Caltech) for providing cell lines and M. Yui from the Rothenberg Laboratory (Caltech) for the intact thymus organ. We appreciate the help of the City of Hope Pathology Core to slice thymus into sections. This work is funded by US National Institute of Health single-cell analysis program award R01HD075605. A.F.C. is supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.

Author information

Affiliations

  1. Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.

    • Ahmet F Coskun
    •  & Long Cai
  2. Program in Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, USA.

    • Ahmet F Coskun
    •  & Long Cai

Authors

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Contributions

A.F.C. and L.C. designed the project and wrote the manuscript. L.C. supervised the project.

Competing interests

L.C. and A.F.C. declare conflict of interests and have filed a patent application.

Corresponding author

Correspondence to Long Cai.

Supplementary information

PDF files

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    Supplementary Text and Figures

    Supplementary Figures 1-22 and Supplementary Note

Zip files

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    Supplementary Software

    Correlation FISH software package v1.0

About this article

Publication history

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DOI

https://doi.org/10.1038/nmeth.3895

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