Guidelines for reporting single-cell RNA-seq experiments

doi:10.1038/s41587-020-00744-z

. 2020 Dec;38(12):1384-1386.

doi: 10.1038/s41587-020-00744-z.

Guidelines for reporting single-cell RNA-seq experiments

Anja Füllgrabe¹, Nancy George², Matthew Green², Parisa Nejad³, Bruce Aronow⁴, Silvie Korena Fexova², Clay Fischer³, Mallory Ann Freeberg², Laura Huerta^{2

5}, Norman Morrison², Richard H Scheuermann⁶, Deanne Taylor^{7

8}, Nicole Vasilevsky⁹, Laura Clarke², Nils Gehlenborg¹⁰, Jim Kent³, John Marioni², Sarah Teichmann^{11

12}, Alvis Brazma², Irene Papatheodorou¹³

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK. anjaf@ebi.ac.uk.
² European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
³ University of California, Santa Cruz, Santa Cruz, CA, USA.
⁴ Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
⁵ Dotmatics Limited, Bishop's Stortford, UK.
⁶ J. Craig Venter Institute, Department of Pathology, University of California, San Diego, La Jolla, CA, USA.
⁷ Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
⁸ Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁹ Oregon Health & Science University, Portland, OR, USA.
¹⁰ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
¹¹ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
¹² Cavendish Laboratory, University of Cambridge, Cambridge, UK.
¹³ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK. irenep@ebi.ac.uk.

PMID: 33188371
PMCID: PMC9302581
DOI: 10.1038/s41587-020-00744-z

Guidelines for reporting single-cell RNA-seq experiments

Anja Füllgrabe et al. Nat Biotechnol. 2020 Dec.

. 2020 Dec;38(12):1384-1386.

doi: 10.1038/s41587-020-00744-z.

Authors

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK. anjaf@ebi.ac.uk.
² European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
³ University of California, Santa Cruz, Santa Cruz, CA, USA.
⁴ Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
⁵ Dotmatics Limited, Bishop's Stortford, UK.
⁶ J. Craig Venter Institute, Department of Pathology, University of California, San Diego, La Jolla, CA, USA.
⁷ Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
⁸ Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁹ Oregon Health & Science University, Portland, OR, USA.
¹⁰ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
¹¹ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
¹² Cavendish Laboratory, University of Cambridge, Cambridge, UK.
¹³ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK. irenep@ebi.ac.uk.

PMID: 33188371
PMCID: PMC9302581
DOI: 10.1038/s41587-020-00744-z

No abstract available

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Conflict of interest statement

Competing interests

The authors declare no competing interests.

Figures

**Fig. 1 |. Typical design steps of single-cell transcriptomics experiments with examples for each step.**
ERCC, External RNA Controls Consortium; FACS, fluorescence-activated cell sorting; PCR, polymerase chain reaction; UMI, unique molecular identifier.

**Fig. 2 |. Overview of the main components of a minSCe study.**
The new components specific to single-cell experiments are highlighted in yellow (see Supplementary Table 1 for descriptions of the components), with example attributes (see Supplementary Table 2 for the full list of attributes). Asterisks represent placeholders for experiment-specific attributes.

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References

1. Trapnell C Genome Res. 25, 1491–1498 (2015). - PMC - PubMed
1. Barrett T et al. Nucleic Acids Res. 41, D991–D995 (2013). - PMC - PubMed
1. Athar A et al. Nucleic Acids Res. 47D1, D711–D715 (2019). - PMC - PubMed
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1. Regev A et al. Preprint at arXiv https://arxiv.org/abs/1810.05192 (2018).

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[1] Trapnell C Genome Res. 25, 1491–1498 (2015). - PMC - PubMed

[2] Trapnell C Genome Res. 25, 1491–1498 (2015). - PMC - PubMed

[3] Barrett T et al. Nucleic Acids Res. 41, D991–D995 (2013). - PMC - PubMed

[4] Barrett T et al. Nucleic Acids Res. 41, D991–D995 (2013). - PMC - PubMed

[5] Athar A et al. Nucleic Acids Res. 47D1, D711–D715 (2019). - PMC - PubMed

[6] Athar A et al. Nucleic Acids Res. 47D1, D711–D715 (2019). - PMC - PubMed

[7] Harrison PW et al. Nucleic Acids Res. 47D1, D84–D88 (2019). - PMC - PubMed

[8] Harrison PW et al. Nucleic Acids Res. 47D1, D84–D88 (2019). - PMC - PubMed

[9] Regev A et al. Preprint at arXiv https://arxiv.org/abs/1810.05192 (2018).

[10] Regev A et al. Preprint at arXiv https://arxiv.org/abs/1810.05192 (2018).

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Guidelines for reporting single-cell RNA-seq experiments

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Guidelines for reporting single-cell RNA-seq experiments

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Conflict of interest statement

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