Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids(Dataset ID: STDS0000074)

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PMID: 32076263
Summary
Visualization
Data
Analysis results
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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
Submission date: 2018-11-30Update date: 2020-04-15
DOI: To be continue
Contributors
Susanne C van den Brink,Anna Alemany,Vincent van Batenburg,Naomi Moris,Marloes Blotenburg,Judith Viv
Contact: a.alemany@hubrecht.eu
Accessions
GEO Series Accessions: GSE123187
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Susanne C van den Brink,Anna Alemany,Vincent van Batenburg,Naomi Moris,Marloes Blotenburg,Judith Viv. Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids[DS/OL]. STOmicsDB, 2018[2018-11-30]. https://db.cngb.org/stomics/datasets/STDS0000074/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    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