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T cell fate and clonality inference from single-cell transcriptomes

Nature Methods volume 13, pages 329332 (2016) | Download Citation

Abstract

We developed TraCeR, a computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. We found that T cell clonotypes in a mouse Salmonella infection model span early activated CD4+ T cells as well as mature effector and memory cells.

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Acknowledgements

We thank V. Svensson, T. Hagai, J. Henriksson and other members of the Teichmann laboratory along with G. Lythe for helpful discussions. We thank the Wellcome Trust Sanger Institute Sequencing Facility for performing Illumina sequencing and the Wellcome Trust Sanger Institute Research Support Facility for care of the mice used in these studies. This work was supported by European Research Council (grant ThSWITCH, number 260507, to S.A.T.) and the Lister Institute for Preventative Medicine (S.A.T.).

Author information

Author notes

    • Michael J T Stubbington
    •  & Tapio Lönnberg

    These authors contributed equally to this work.

Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

    • Michael J T Stubbington
    • , Tapio Lönnberg
    • , Valentina Proserpio
    •  & Sarah A Teichmann
  2. Wellcome Trust Sanger Institute, Cambridge, UK.

    • Simon Clare
    • , Anneliese O Speak
    • , Gordon Dougan
    •  & Sarah A Teichmann

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Contributions

M.J.T.S. conceived the project, designed the computational method, wrote the software, designed PCR sequencing primers, analyzed data, generated figures and wrote the manuscript. T.L. and S.C. designed and performed the Salmonella experiments. T.L. performed cell collection and purification, generated scRNA-seq libraries, performed gene expression analyses, analyzed data, generated figures and wrote the manuscript. V.P. performed PCR-based TCR-sequencing experiments. A.O.S. designed the cell-sorting strategy, performed the sorting and generated figures. S.A.T. and G.D. supervised work and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Sarah A Teichmann.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–15, Supplementary Table 1 and Supplementary Notes 1–4

Excel files

  1. 1.

    Supplementary Table 2

    TCR sequences reconstructed from single-cell RNA-sequencing data.

  2. 2.

    Supplementary Table 3

    Comparison between RNA-seq reconstruction and PCR-based detection of TCR sequences.

  3. 3.

    Supplementary Table 4

    Antibodies used in FACS sorting.

  4. 4.

    Supplementary Table 5

    PCR primers used for TCR sequencing.

Zip files

  1. 1.

    Supplementary Software

    Tracer-master Software

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nmeth.3800

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