Spatiotemporal analysis of human intestinal development at single-cell resolution(Dataset ID: STDS0000002)

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1,641
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Spots: 9,330
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Genes: 2,893
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PMID: 33406409
Summary
Visualization
Data
Analysis results
Related
Sample
Catalog
Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
Development of the human intestine is not well understood. Here we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including novel epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe new functions for these including as vascular niche cells. We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders.
Overall design:
Colon and terminal ileum tissue sections from 8-22 post-conceptual week fetal intestine samples were subject to single cell RNA-seq analysis.
Technology:
10x Visium,scRNA
Platform:
Illumina MiSeq, Illumina NextSeq 500, Illumina NovaSeq 6000
Species:
Homo sapiens(hg38)
Tissues:
Intestine
Cell types:
epithelial,fibroblast,endothelial (EC),pericytes,neural (ENS),muscularis,mesothelium,myofibroblast,i
Submission date: 2020-09-28Update date: 2020-02-22
Sample number: 31Section number: 8
DOI: To be continue
Contributors
FawknerCorbett D,Antanaviciute A,Parikh K,Jagielowicz M,Sousa Gerós A,Gupta T,Ashley N,Koohy H,Simmo
Contact: alison.simmons@ndm.ox.ac.uk
Accessions
GEO Series Accessions: GSE158704
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] FawknerCorbett D,Antanaviciute A,Parikh K,Jagielowicz M,Sousa Gerós A,Gupta T,Ashley N,Koohy H,Simmo. Spatiotemporal analysis of human intestinal development at single-cell resolution[DS/OL]. STOmicsDB, 2020[2020-09-28]. https://db.cngb.org/stomics/datasets/STDS0000002/. 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: Fawkner-Corbett, David et al. “Spatiotemporal analysis of human intestinal development at single-cell resolution.” Cell vol. 184,3 (2021): 810-826.e23. doi:10.1016/j.cell.2020.12.016