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Dense transcript profiling in single cells by image correlation decoding


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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Figure 1: Correlation FISH.
Figure 2: corrFISH works accurately in cultured cells.
Figure 3: corrFISH reveals cell-specific ribosomal protein gene expression in tissue sections.


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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.

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

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Correspondence to Long Cai.

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Competing interests

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

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Supplementary Figures 1-22 and Supplementary Note (PDF 4857 kb)

Supplementary Software

Correlation FISH software package v1.0 (ZIP 16177 kb)

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Coskun, A., Cai, L. Dense transcript profiling in single cells by image correlation decoding. Nat Methods 13, 657–660 (2016).

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