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Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation


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

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.

Correspondence to Berthold Göttgens or John C. Marioni.

Supplementary information

Supplementary Information

Supplementary Figures 1–5 and Supplementary References.

Life Sciences Reporting Summary

Supplementary Table 1

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

Supplementary Table 2

Differential expression between the germ layers.

Supplementary Table 3

Differential expression between three foregut subpopulations.

Supplementary Table 4

Transcriptomes of the primordial germ cells.


Supplementary Video 1

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

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Further reading

Fig. 1: scRNA-seq of whole mouse E8.25 embryos identifies 20 major cell types.
Fig. 2: Substructure within the E8.25 mouse foregut.
Fig. 3: Oscillating patterns of gene expression during somitogenesis can be inferred from scRNA-seq data.
Fig. 4: The endothelium can be subdivided based on maturity and location of origin.
Fig. 5: The leukotriene biosynthesis pathway drives blood formation.