During gastrulation, cell types from all three germ layers are specified and the basic body plan is established1. However, molecular analysis of this key developmental stage has been hampered by limited cell numbers and a paucity of markers. Single-cell RNA sequencing circumvents these problems, but has so far been limited to specific organ systems2. Here, we report single-cell transcriptomic characterization of >20,000 cells immediately following gastrulation at E8.25 of mouse development. We identify 20 major cell types, which frequently contain substructure, including three distinct signatures in early foregut cells. Pseudo-space ordering of somitic progenitor cells identifies dynamic waves of transcription and candidate regulators, which are validated by molecular characterization of spatially resolved regions of the embryo. Within the endothelial population, cells that transition from haemogenic endothelial to erythro-myeloid progenitors specifically express Alox5 and its co-factor Alox5ap, which control leukotriene production. Functional assays using mouse embryonic stem cells demonstrate that leukotrienes promote haematopoietic progenitor cell generation. Thus, this comprehensive single-cell map can be exploited to reveal previously unrecognized pathways that contribute to tissue development.

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We thank A. Lun for help with the Cell Ranger tool and the CRUK Cambridge Institute Genomics and Bioinformatics Cores for supporting the DNA sequencing and demultiplexing of the data. Research in the authors’ laboratories is supported by the MRC, CRUK, Bloodwise, the Leukemia and Lymphoma Society, NIH-NIDDK, the Sanger-EBI Single Cell Centre and core support grants by the Wellcome Trust to the Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, and by core funding from Cancer Research UK and the European Molecular Biology Laboratory. W.J. is a Wellcome Trust Clinical Research Fellow. B.P.-S is funded by the Wellcome Trust 4 Year PhD programme in Stem Cell Biology and Medicine and the University of Cambridge. A.S. is supported by the Sanger-EBI Single Cell Centre. L.V. is supported by the ERC starting grant Relieve-IMDs. This work was funded as part of the Wellcome Trust Strategic Award 105031/D/14/Z “Tracing early mammalian lineage decisions by single cell genomics” awarded to W. Reik, S. Teichmann, J.N., B.D.S., T. Voet, S.S., L.V., B.G. and J.C.M.

Author information

Author notes

    • Antonio Scialdone

    Present address: Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany

  1. Ximena Ibarra-Soria and Wajid Jawaid contributed equally to this work.


  1. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK

    • Ximena Ibarra-Soria
    •  & John C. Marioni
  2. Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK

    • Wajid Jawaid
    • , Blanca Pijuan-Sala
    • , Vasileios Ladopoulos
    • , Fernando J. Calero-Nieto
    •  & Berthold Göttgens
  3. Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK

    • Wajid Jawaid
    • , Blanca Pijuan-Sala
    • , Vasileios Ladopoulos
    • , Fernando J. Calero-Nieto
    • , Carla Mulas
    • , Jennifer Nichols
    • , Benjamin D. Simons
    •  & Berthold Göttgens
  4. Department of Paediatric Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK

    • Wajid Jawaid
  5. EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK

    • Antonio Scialdone
    •  & John C. Marioni
  6. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK

    • Antonio Scialdone
    • , Ludovic Vallier
    •  & John C. Marioni
  7. Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK

    • David J. Jörg
    •  & Benjamin D. Simons
  8. The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK

    • David J. Jörg
    •  & Benjamin D. Simons
  9. Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK

    • Richard C. V. Tyser
    •  & Shankar Srinivas
  10. Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK

    • Ludovic Vallier
  11. Department of Surgery, University of Cambridge, Cambridge, UK

    • Ludovic Vallier


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W.J., B.P.-S., V.L., R.T., F.J.C.-N., C.M., J.N. and S.S. performed the experiments. X.I.-S., B.P.-S. and A.S. analysed the data. W.J., D.J.J., L.V. and B.D.S. provided expertise. X.I.-S., W.J., B.P.-S., A.S., D.J.J., L.V., B.G. and J.C.M. interpreted the results. B.G. and J.C.M. conceived the project. X.I.-S., B.P.-S., A.S., B.G. and J.C.M. wrote the manuscript. All authors read and approved the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Berthold Göttgens or John C. Marioni.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1–5 and Supplementary References.

  2. Life Sciences Reporting Summary

  3. Supplementary Table 1

    The different samples contribute equally to each of the 20 identified subpopulations.

  4. Supplementary Table 2

    Differential expression between the germ layers.

  5. Supplementary Table 3

    Differential expression between three foregut subpopulations.

  6. Supplementary Table 4

    Transcriptomes of the primordial germ cells.


  1. Supplementary Video 1

    Dissection strategy used to validate the oscillating genes in the presomitic mesoderm.

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