Abstract

High-throughput single-cell RNA sequencing has transformed our understanding of complex cell populations, but it does not provide phenotypic information such as cell-surface protein levels. Here, we describe cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), a method in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout. CITE-seq is compatible with existing single-cell sequencing approaches and scales readily with throughput increases.

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Acknowledgements

We acknowledge S. Jaini and K. Pandit of the NYGC Technology Innovation Lab for critical discussions and support; E. Papalexi for help with CBMCs isolation; M. Coppo, S. Fennessey, B. Baysa and S. Pescatore at NYGC for sequencing support; and C. Kocks for manuscript discussions. Multiparameter flow cytometer instrument time and reagents were generously provided by the Vaccine Research Center of the National Institutes of Health. C.H. was supported by a Deutsche Forschungsgemeinschaft research fellowship. R.S. was supported by an NIH New Innovator Award (DP2-HG-009623). Research reported here was partially supported by the National Human Genome Research Institute under Award Number UM1HG008901.

Author information

Affiliations

  1. New York Genome Center, New York, New York, USA.

    • Marlon Stoeckius
    • , Christoph Hafemeister
    • , William Stephenson
    • , Brian Houck-Loomis
    • , Harold Swerdlow
    • , Rahul Satija
    •  & Peter Smibert
  2. New York University Medical Center, New York, New York, USA.

    • Pratip K Chattopadhyay
  3. New York University Center for Genomics and Systems Biology, New York, New York, USA.

    • Rahul Satija

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Contributions

M.S. conceived and designed the study with input from B.H.-L., R.S., H.S. and P.S. M.S. performed all experiments. C.H. and R.S. designed and contributed the computational analyses. W.S. assisted with Drop-seq experiments. P.K.C provided conceptual input on how to benchmark CITE-seq to flow cytometry and performed multiparameter flow cytometry analysis. M.S., C.H., R.S. and P.S. interpreted the data. M.S. and P.S. wrote the manuscript with input from all authors.

Competing interests

M.S., B.H.-L. and P.S. have filed a patent application based on this work (US provisional patent application 62/515-180).

Corresponding author

Correspondence to Marlon Stoeckius.

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    Supplementary Text and Figures

    Supplementary Figures 1–8 and Supplementary Tables 1 and 2

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    Life Sciences Reporting Summary

  3. 3.

    Supplementary Protocol

    CITE-seq protocol

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DOI

https://doi.org/10.1038/nmeth.4380

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