Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

Susanne C van den Brink, Anna Alemany, Vincent van Batenburg, Naomi Moris, Marloes Blotenburg, Judith Vivié, Peter Baillie-Johnson, Jennifer Nichols, Katharina F Sonnen, Alfonso Martinez Arias, Alexander van Oudenaarden

Research output: Contribution to journal/periodicalArticleScientificpeer-review

216 Citations (Scopus)


Gastruloids are three-dimensional aggregates of embryonic stem cells that display key features of mammalian development after implantation, including germ-layer specification and axial organization1-3. To date, the expression pattern of only a small number of genes in gastruloids has been explored with microscopy, and the extent to which genome-wide expression patterns in gastruloids mimic those in embryos is unclear. Here we compare mouse gastruloids with mouse embryos using single-cell RNA sequencing and spatial transcriptomics. We identify various embryonic cell types that were not previously known to be present in gastruloids, and show that key regulators of somitogenesis are expressed similarly between embryos and gastruloids. Using live imaging, we show that the somitogenesis clock is active in gastruloids and has dynamics that resemble those in vivo. Because gastruloids can be grown in large quantities, we performed a small screen that revealed how reduced FGF signalling induces a short-tail phenotype in embryos. Finally, we demonstrate that embedding in Matrigel induces gastruloids to generate somites with the correct rostral-caudal patterning, which appear sequentially in an anterior-to-posterior direction over time. This study thus shows the power of gastruloids as a model system for exploring development and somitogenesis in vitro in a high-throughput manner.

Original languageEnglish
Pages (from-to)405-409
Number of pages5
Issue number7812
Publication statusPublished - Jun 2020


  • Animals
  • Collagen
  • Drug Combinations
  • Embryo, Mammalian/cytology
  • Embryonic Development
  • Female
  • Gastrula/cytology
  • Gene Expression Regulation, Developmental
  • Laminin
  • Male
  • Mice
  • Mouse Embryonic Stem Cells/cytology
  • Organoids/cytology
  • Proteoglycans
  • RNA-Seq
  • Single-Cell Analysis
  • Somites/cytology
  • Time Factors
  • Transcriptome


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