Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

CIC nanoGUNE Seminars

Anna Alemany, Hubrecht Institute
nanoGUNE seminar room, Tolosa Hiribidea 76, Donostia - San Sebastian
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Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids **** **Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids** Anna Alemany (Hubrecht Institute) Gastruloids are three-dimensional aggregates of embryonic stem cells (ESCs) that display key features of mammalian post-implantation development, including germ layer specification and axial organization. So far, the expression pattern of only a small number of genes in gastruloids has been explored with microscopy, but it is still unclear to what extent genome-wide expression patterns mimic those in embryos. In this talk, I will show how mouse gastruloids compare with mouse embryos using single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (tomo-seq). This approach revealed various embryonic cell types that were not known to be present in gastruloids, and showed that key regulators of somitogenesis are expressed similarly between embryos and gastruloids. Using live-imaging I will then show that the somitogenesis clock is active in gastruloids with dynamics resembling those in vivo. Finally, I will demonstrate that Matrigel-embedding induces gastruloids to generate somites with correct rostral-caudal patterning, which appear sequentially in anterior to posterior direction over time. All taken together, I will thus show the power of gastruloids as a model system to explore development and somitogenesis in vitro in a high-throughput manner. **Host:** R. Pérez-Jiménez