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Guidelines for reporting single-cell RNA-seq experiments

Nature Biotechnology volume 38, pages 1384–1386 (2020)Cite this article

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To the Editor — Single-cell RNA-sequencing (scRNA-seq) has undergone major technological advances in recent years, enabling the conception of various organism-level cell atlas projects. With increasing numbers of datasets being deposited in public archives, there is a need to ensure the reproducibility of such datasets. To this end, we describe the minSCe (Minimum Information about a Single-Cell Experiment) guidelines for a minimum set of metadata needed for robust comparative analyses of scRNA-seq.

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Fig. 1: Typical design steps of single-cell transcriptomics experiments with examples for each step.
Fig. 2: Overview of the main components of a minSCe study.

References

  1. Trapnell, C. Genome Res. 25, 1491–1498 (2015).

    CAS  Article  Google Scholar 

  2. Barrett, T. et al. Nucleic Acids Res. 41, D991–D995 (2013).

    CAS  Article  Google Scholar 

  3. Athar, A. et al. Nucleic Acids Res. 47D1, D711–D715 (2019).

    Article  Google Scholar 

  4. Harrison, P. W. et al. Nucleic Acids Res. 47D1, D84–D88 (2019).

    Article  Google Scholar 

  5. Regev, A. et al. Preprint at arXiv https://arxiv.org/abs/1810.05192 (2018).

  6. HuBMAP Consortium. Nature 574, 187–192 (2019).

    CAS  Article  Google Scholar 

  7. Ecker, J. R. et al. Neuron 96, 542–557 (2017).

    CAS  Article  Google Scholar 

  8. Barkas, N. et al. Nat. Methods 16, 695–698 (2019).

    CAS  Article  Google Scholar 

  9. Hie, B., Bryson, B. & Berger, B. Nat. Biotechnol. 37, 685–691 (2019).

    CAS  Article  Google Scholar 

  10. Brazma, A. et al. Nat. Genet. 29, 365–371 (2001).

    CAS  Article  Google Scholar 

  11. Papatheodorou, I. et al. Nucleic Acids Res. 48D1, D77–D83 (2020).

    Google Scholar 

  12. Ziegenhain, C. et al. Mol. Cell 65, 631–643.e634 (2017).

    CAS  Article  Google Scholar 

  13. Picelli, S. et al. Nat. Methods 10, 1096–1098 (2013).

    CAS  Article  Google Scholar 

  14. Federhen, S. Nucleic Acids Res. 40, D136–D143 (2012).

    CAS  Article  Google Scholar 

  15. Anonymous. Nature 419, 323 (2002).

    Google Scholar 

  16. Rung, J. & Brazma, A. Nat. Rev. Genet. 14, 89–99 (2013).

    CAS  Article  Google Scholar 

  17. Stoeckius, M. et al. Nat. Methods 14, 865–868 (2017).

    CAS  Article  Google Scholar 

  18. Davie, K. et al. Cell 174, 982–998.e920 (2018).

    CAS  Article  Google Scholar 

  19. Lein, E., Borm, L. E. & Linnarsson, S. Science 358, 64–69 (2017).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the European Molecular Biology Laboratory; the Wellcome Trust Biomedical Resources grant Single Cell Gene Expression Atlas (108437/Z/15/Z); the California Institute for Regenerative Medicine (GC1R-06673-B); the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation (2018–182730); and the NIH Common Fund, through the Office of Strategic Coordination/Office of the NIH Director (OT2OD026677).

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Author notes

  1. Laura Huerta

    Present address: Dotmatics Limited, Bishop’s Stortford, UK

Authors and Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK

    Anja Füllgrabe, Nancy George, Matthew Green, Silvie Korena Fexova, Mallory Ann Freeberg, Laura Huerta, Norman Morrison, Laura Clarke, John Marioni, Alvis Brazma & Irene Papatheodorou

  2. University of California, Santa Cruz, Santa Cruz, CA, USA

    Parisa Nejad, Clay Fischer & Jim Kent

  3. Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA

    Bruce Aronow

  4. J. Craig Venter Institute, Department of Pathology, University of California, San Diego, La Jolla, CA, USA

    Richard H. Scheuermann

  5. Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Deanne Taylor

  6. Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Deanne Taylor

  7. Oregon Health & Science University, Portland, OR, USA

    Nicole Vasilevsky

  8. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

    Nils Gehlenborg

  9. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK

    Sarah Teichmann

  10. Cavendish Laboratory, University of Cambridge, Cambridge, UK

    Sarah Teichmann

Authors
  1. Anja Füllgrabe
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  2. Nancy George
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  9. Laura Huerta
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  10. Norman Morrison
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  11. Richard H. Scheuermann
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  13. Nicole Vasilevsky
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  14. Laura Clarke
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  15. Nils Gehlenborg
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  17. John Marioni
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  18. Sarah Teichmann
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  19. Alvis Brazma
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  20. Irene Papatheodorou
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Contributions

A.F., N. George, M.G., P.N., B.A., S.K.F., C.F., M.A.F., L.H., D.T., N.V. and N.M. curated data and developed metadata standards; L.C., J.K., N.M., R.H.S., A.B. and I.P. supervised the project and engaged with the larger community; S.T. and J.M. provided support and evaluation of the standards and contributed to the manuscript; A.F., N. George, M.G., P.N., B.A., S.K.F., C.F., M.A.F., L.C., N. Gehlenborg, L.H., R.H.S., D.T., N.V., A.B. and I.P. wrote the manuscript.

Corresponding authors

Correspondence to Anja Füllgrabe or Irene Papatheodorou.

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The authors declare no competing interests.

Additional information

Editorial note: This article has been peer reviewed.

Supplementary information

Supplementary Information

Supplementary Note including Supplementary Tables 1–7 and Supplementary Figs. 1 and 2.

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Füllgrabe, A., George, N., Green, M. et al. Guidelines for reporting single-cell RNA-seq experiments. Nat Biotechnol 38, 1384–1386 (2020). https://doi.org/10.1038/s41587-020-00744-z

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