Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Guidelines for reporting single-cell RNA-seq experiments

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

Subjects

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.

scRNA-seq experiments have many advantages over so-called bulk RNA-sequencing and microarray experiments, as they allow researchers to study gene expression at an individual-cell rather than at tissue level1. As the scRNA-seq technologies are maturing, these experiments are becoming increasingly high-throughput and widespread. Data from an estimated 3,000 scRNA-seq studies have been submitted to NCBI’s Gene Expression Omnibus (GEO)2, EMBL-EBI’s ArrayExpress3 and the European Nucleotide Archive (ENA)4 in recent years. Large collaborative efforts are taking off, such as the Human Cell Atlas (HCA)5, which aims to uncover the gene expression profiles of all human cell types; the Fly Cell Atlas (http://flycellatlas.org/), which has similar aims for Drosophila, or the Human Biomolecular Atlas Program (HuBMAP)6, as well as organ-specific projects, such as the BRAIN Initiative Cell Census Consortium7.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

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).

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

Author information

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
    View author publications

    Search author on:PubMed Google Scholar

  2. Nancy George
    View author publications

    Search author on:PubMed Google Scholar

  3. Matthew Green
    View author publications

    Search author on:PubMed Google Scholar

  4. Parisa Nejad
    View author publications

    Search author on:PubMed Google Scholar

  5. Bruce Aronow
    View author publications

    Search author on:PubMed Google Scholar

  6. Silvie Korena Fexova
    View author publications

    Search author on:PubMed Google Scholar

  7. Clay Fischer
    View author publications

    Search author on:PubMed Google Scholar

  8. Mallory Ann Freeberg
    View author publications

    Search author on:PubMed Google Scholar

  9. Laura Huerta
    View author publications

    Search author on:PubMed Google Scholar

  10. Norman Morrison
    View author publications

    Search author on:PubMed Google Scholar

  11. Richard H. Scheuermann
    View author publications

    Search author on:PubMed Google Scholar

  12. Deanne Taylor
    View author publications

    Search author on:PubMed Google Scholar

  13. Nicole Vasilevsky
    View author publications

    Search author on:PubMed Google Scholar

  14. Laura Clarke
    View author publications

    Search author on:PubMed Google Scholar

  15. Nils Gehlenborg
    View author publications

    Search author on:PubMed Google Scholar

  16. Jim Kent
    View author publications

    Search author on:PubMed Google Scholar

  17. John Marioni
    View author publications

    Search author on:PubMed Google Scholar

  18. Sarah Teichmann
    View author publications

    Search author on:PubMed Google Scholar

  19. Alvis Brazma
    View author publications

    Search author on:PubMed Google Scholar

  20. Irene Papatheodorou
    View author publications

    Search author on:PubMed Google Scholar

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.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Editorial note: This article has been peer reviewed.

Supplementary information

Supplementary Information (download PDF )

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

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Published:

  • Version of record:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41587-020-00744-z

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing