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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.

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.

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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.

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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

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  1. Anja Füllgrabe
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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.

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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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