Primate gastrulation and early organogenesis at single-cell resolution(Dataset ID: STDS0000294)

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Summary
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Dataset information
Summary:
Our understanding of human early development is severely hampered by limited access to embryonic tissues. Due to their close evolutionary relationship with humans, non-human primates (NHPs) are often used as surrogates to understand human development but currently suffer from a lack of in vivo datasets, especially from gastrulation to early organogenesis during which the major embryonic cell types are dynamically specified. To fill this gap, we have collected six Carnegie stage (CS) 8-CS11 cynomolgus monkey embryos and performed in-depth transcriptome analyses of 56,636 single cells. Our analyses reveal transcriptomic features of major peri-gastrulation cell types, which help shed light on morphogenetic events including primitive streak (PS) development, somitogenesis, gut tube formation, neural tube patterning, and neural crest regionalization in primates. In addition, comparative analyses with mouse embryos and human embryoids uncover conserved and divergent features of peri-gastrulation development across species, e.g. species-specific dependency on Hippo signaling during presomitic mesoderm differentiation, and provide an initial assessment of relevant stem cell models of human early organogenesis. This comprehensive single-cell transcriptome atlas not only fills the knowledge gap in the NHP research field but also serves as an invaluable resource for understanding human embryogenesis and developmental disorders.
Overall design:
single cells from cynomolgus monkey embryo tissues spanning different developmental stages during early pregnancy were used to do single-cell RNA-Seq experiments
Technology:
ST
Platform:
HiSeq X Ten
Species:
Macaca fascicularis
Development stage:
day 20, day 23, day 26, day 29
Submission date: 2022-01-04Update date: 2022-12-30
DOI: To be continue
Contributors
Jiang, Xiangxiang; Zhai, JingLei; Guo, Jing; Wan, Haifeng; Qi, Luqing; Liu, Lizhong; Yan, Long; Xiao, Zhenyu; Xu, Yanhong; Yu, Dainan; Wu, Xulun; Zhao, Wentao; Yu, Kunyuan; Guo, Fan; Wu, Jun; Wang, Hongmei
Contact: contrib1
Accessions
GEO Series Accessions: GSE193007
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] Jiang, Xiangxiang. Primate gastrulation and early organogenesis at single-cell resolution[DS/OL]. STOmicsDB, 2022[2022-01-04]. https://db.cngb.org/stomics/datasets/STDS0000294/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    No results.