Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids
Dataset ID: STDS0000074
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Dataset information
Summary:
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. Gastruloids have mostly been characterized with microscopy-based approaches, limiting the number of genes that can be explored. It is therefore unclear to what extent gene expression in gastruloids reflects in vivo embryonic expression. Using both single-cell RNA-seq (scRNA-seq) and spatial transcriptomics we systematically compared cell types and spatial expression patterns between mouse gastruloids and mouse embryos.
Overall design:
RNA sequencing data from tissue sections isolated from mouse gastruloids (tomo-seq and scRNA-seq) | For mGst-Lfng-* samples, each processed data was generated from both run1 and run2 samples, and is linked to the corresponding run1 sample records.
Technology:
Tomo-seq
Platform:
Illumina NextSeq 500
Species:
Homo sapiens(Ensembl 93)
Mus musculus(mm10)
Tissues:
Gastrula
Organ parts:
Gastruloid
Citation:
van den Brink, Susanne C et al. “Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids.” Nature vol. 582,7812 (2020): 405-409. doi:10.1038/s41586-020-2024-3
Submission date: 2018-11-30Update date: 2020-04-15

Contributors
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
Contact: a.alemany@hubrecht.eu

Accessions
GEO Series Accessions: GSE123187