Skip to main content

Thank you for visiting 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.

Building a high-quality Human Cell Atlas


Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Mission of the Standards and Technology Working Group (STWG).
Fig. 2: Enabling high-quality, cost-effective data generation through systematic benchmarking and decision trees.


  1. 1.

    Regev, A. et al. eLife 6, e27041 (2017).

    Article  Google Scholar 

  2. 2.

    Wilkinson, M. D. et al. Sci. Data 3, 1–9 (2016).

    Article  Google Scholar 

  3. 3.

    Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A. & Teichmann, S. A. Nature 550, 451–453 (2017).

    CAS  Article  Google Scholar 

  4. 4.

    Angermueller, C. et al. Nat. Methods 13, 229–232 (2016).

    CAS  Article  Google Scholar 

  5. 5.

    Macaulay, I. C. et al. Nat. Methods 12, 519–522 (2015).

    CAS  Article  Google Scholar 

  6. 6.

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

    CAS  Article  Google Scholar 

  7. 7.

    Satpathy, A. T. et al. Nat. Biotechnol. 37, 925–936 (2019).

    CAS  Article  Google Scholar 

  8. 8.

    Denisenko, E. et al. Genome Biol. (2020).

  9. 9.

    Mereu, E. et al. Nat. Biotechnol. (2020).

  10. 10.

    Ding, J. et al. Nat. Biotechnol. (2020).

  11. 11.

    Slyper, M. et al. Nat. Med. 26, 792–802 (2020).

    CAS  Article  Google Scholar 

  12. 12.

    Massoni-Badosa, R. et al. Genome Biol. 21, 112 (2020).

    CAS  Article  Google Scholar 

  13. 13.

    Madissoon, E. et al. Genome Biol. 21, 1 (2019).

    CAS  Article  Google Scholar 

  14. 14.

    Rood, J. E. et al. Cell 179, 1455–1467 (2019).

    CAS  Article  Google Scholar 

  15. 15.

    Lambrechts, D. et al. Nat. Med. 24, 1277–1289 (2018).

    CAS  Article  Google Scholar 

  16. 16.

    Habib, N. et al. Science 353, 925–928 (2016).

    CAS  Article  Google Scholar 

  17. 17.

    Bakken, T. E. et al. PLoS One 13, e0209648 (2018).

    Article  Google Scholar 

  18. 18.

    Fleming, S.J., Marioni, J.C. & Babadi, M. Preprint at bioRxiv (2019).

  19. 19.

    Asp, M. et al. Cell 179, 1647–1660.e19 (2019).

    CAS  Article  Google Scholar 

  20. 20.

    Moffitt, J. R. et al. Proc. Natl Acad. Sci. USA 113, 14456–14461 (2016).

    CAS  Article  Google Scholar 

  21. 21.

    Chen, F., Tillberg, P. W. & Boyden, E. S. Science 347, 543–548 (2015).

    CAS  Article  Google Scholar 

  22. 22.

    Elosua, M., Nieto, P., Mereu, E., Gut, I. & Heyn, H. Preprint at bioRxiv (2020).

  23. 23.

    GTEx Consortium. Nat. Genet. 45, 580–585 (2013).

    Article  Google Scholar 

  24. 24.

    Hagemann-Jensen, M. et al. Nat. Biotechnol. (2020).

  25. 25.

    Kang, H. M. et al. Nat. Biotechnol. 36, 89–94 (2018).

    CAS  Article  Google Scholar 

  26. 26.

    McGinnis, C. S. et al. Nat. Methods 16, 619–626 (2019).

    CAS  Article  Google Scholar 

  27. 27.

    Gehring, J., Hwee Park, J., Chen, S., Thomson, M. & Pachter, L. Nat. Biotechnol. 38, 35–38 (2020).

    CAS  Article  Google Scholar 

  28. 28.

    Stoeckius, M. et al. Genome Biol. 19, 224 (2018).

    CAS  Article  Google Scholar 

  29. 29.

    McGinnis, C. S. et al. Preprint at bioRxiv (2020).

Download references


We thank A. K. Shalek for insightful comments on the manuscript. This work has received funding from the Ministerio de Ciencia, Innovación y Universidades of Spain (SAF2017-89109-P; AEI/FEDER, UE). J.W.S. received a research grant for the RIKEN Center for Integrative Medical Sciences from MEXT. This project has been made possible in part by grant number 2018-182827 and HCA-A-1704-01742 from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation. Work was supported by the Manton Foundation, the Klarman Cell Observatory and HHMI (A.R.). This publication is also supported as part of a project (BCLLATLAS and ESPACE) that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement No 810287 and 874710). We acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme / Generalitat de Catalunya. We also acknowledge the support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement, and co-financing by the Spanish Ministry of Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014–2020 Smart Growth Operating Program.

Author information




Corresponding author

Correspondence to Holger Heyn.

Ethics declarations

Competing interests

A.R. is a cofounder and equity holder of Celsius Therapeutics, an equity holder in Immunitas and an SAB member of ThermoFisher Scientific, Syros Pharmaceuticals, Asimov and Neogene Therapeutics. A.R. is a co-inventor on patent applications to advances in single-cell genomics, including droplet-based sequencing technologies, as in PCT/US2015/0949178, and methods for expression and analysis, as in PCT/US2016/059233 and PCT/US2016/059239. O.R.R. is a co-inventor on patent applications filed by the Broad Institute for inventions relating to single-cell genomics, such as in PCT/US2018/060860 and US Provisional Application No. 62/745259.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Rozenblatt-Rosen, O., Shin, J.W., Rood, J.E. et al. Building a high-quality Human Cell Atlas. Nat Biotechnol 39, 149–153 (2021).

Download citation


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