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Tracking Early Mammalian Organogenesis – Prediction and Validation of Differentiation Trajectories at Whole Organism Scale

Ivan Imaz-Rosshandler1,2,3,*, Christina Rode4,*, Carolina Guibentif5,*, Mai-Linh Ton1,2, Parashar Dhapola10, Daniel Keitley6, Ricard Argelaguet11,12, Fernando J. Calero-Nieto2, Jennifer Nichols2, John C. Marioni7,8,9,**, Marella de Bruijn4,**, Berthold Göttgens1,2,**

Table of Contents

  1. Paper abstract
  2. Data availability
  3. Explore the data
  4. Code availability
  5. Contact
  6. Other links


Early organogenesis represents a key step in animal development, where pluripotent cells divide and diversify to initiate formation of all major organs. Here, we used scRNA-Seq to profile over 300,000 single cell transcriptomes sampled in 6 hour intervals from mouse embryos between E8.5 and E9.5. Combining this dataset with our previous E6.5 to E8.5 atlas resulted in a densely-sampled time course of over 400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction at full organismal scale identified complex waves of blood and endothelial development, including a new molecular programme for somite-derived endothelium. To assess developmental fates across the primitive streak, we dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-Seq and predicted cell fates computationally. We next defined early developmental state/fate relationships experimentally by a combination of orthotopic grafting, microscopic analysis of graft contribution as well as scRNA-Seq to transcriptionally determine cell fates of the grafted primitive streak regions after 24h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with the fates predicted computationally, thus demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in both developmental biology as well as guide the in vitro production of cells for organ regeneration and repair.

Data availability

This data is an extension of a previously reported scRNA-Seq atlas covering mouse gastrulation and the early initiation of organogenesis through a densely sampled time-course of 6h sampling intervals from E6.5 to E8.5 (Pijuan-Sala B., Griffiths J. A., Guibentif C. et al., 2019) with newly sampled time points (E8.75-E9.5) as well as one overlapping time point (E8.5) to facilitate data integration. Combined, the new ‘extended’ atlas, ranging from E6.5 to E9.5 contains 430,339 cells across 13 time points spanning 3 days of mouse development

Various forms of the transcriptomics data such as raw counts, normalised counts, dimensionality reductions and metadata are available here for loading into R and python.

File name Description
embryo_complete.h5ad AnnData object with log normalised UMI counts and raw counts the .raw layer, metadata, batch corrected PCA and other layouts (eg., UMAP). Function, …) is recommended.
embryo_sce.rds Contains a SingleCellExperiment object with counts, metadata and batch corrected layouts for processing in R. Pre-computed library size factors can be accessed to normalise the data.
embryo_counts.tar.gz Counts matrix in sparse format (mtx) with cell and gene metadata files.
metadata_cells.csv Cell metadata.
metadata_genes.csv Gene metadata, ensemble id and gene symbols.
umap_layout.csv UMAP layout.
pca_batch_corrected.csv Batch corrected PCA with MNN.

Raw scRNA-seq files have been deposited in arrayexpress under the accession number E-MTAB-11763. For details of the other, externally generated datasets used in our analysis, see the methods section of the paper.

Note: Smart-Seq2 data generated in this project will be soon made public.

Explore the data

Shiny app

The data can be explored after logging into shiny app.

IMPORTANT: This webpage is currently under development.

UCSC Cell browser

This data can be explored and downloaded from the UCSC cell browser.

Code availability

To be added soon.

Support or Contact

General queries can be directed to Bertie Göttgens , John Marioni. For issues relating to the data or code, you can email Ivan Imaz-Rosshandler at

Göttgens lab website

Marioni lab website

de Bruijn lab website

Shiny application of E6.5-E8.5 atlas of mouse gastrulation and early organogenesis

  1. Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK

  2. Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK

  3. MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK

  4. MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK

  5. Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden

  6. Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK

  7. Wellcome Sanger Institute, Wellcome Genome Campus, Saffron Walden CB10 1SA, UK

  8. European Molecular Biology Laboratory, European Bioinformatics Institute, Saffron Walden CB10 1SA, UK

  9. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK

  10. Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Sweden

  11. Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK

  12. Altos Labs Cambridge Institute, Granta Park, Cambridge, CB21 6GP, UK

* Authors contributed equally ** Corresponding authors