Spatial transcriptomic studies of the small intestine from WT and DDX5△IEC (KO) mice(Dataset ID: STDS0000122)

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167
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178
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Spots: 9,984
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Genes: 32,285
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PMID: 34853057
Summary
Visualization
Data
Analysis results
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Dataset information
Contributors
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Dataset information
Summary:
DDX5, a DEAD box containing RNA binding protein, is involved in multiple aspects of RNA metabolism and is abundantly expressed in all subsets of the intestinal epithelial cells (IEC). Here, we characterized the DDX5-dependent transcriptome in the small intestine. In the DDX5△IEC tissue, we found that secretory IEC lineage progenitor containing spots (Atoh1hi and Sox4hi) had reduced expression of Pou2f3, a master regulator of a subset of IECs called tuft cells. As a result of the loss of Pou2f3 expression in the progenitors, DDX5△IEC tissue harbored lower number of tuft cell containing spots (Dclk1hi) compare to WT tissues.
Overall design:
One intestine tissue from each genotype were obtained from 8wk old cohoused mice. Results of ileum epithelium from DDX5鈻矷EC mutant mice were compared to those from WT mice.
Technology:
10x Visium
Platform:
GPL24247
Species:
Mus musculus(mm10)
Submission date: 2021-09-21Update date: 2021-12-03
Sample number: 2
DOI: To be continue
Contributors
Long, Tianyun,Lemolo, Attilio,Telese, Francesca,Huang, Wendy M
Contact: wjh003@ucsd.edu
Accessions
GEO Series Accessions: GSE184564
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] Long, Tianyun,Lemolo, Attilio,Telese, Francesca,Huang, Wendy M. Spatial transcriptomic studies of the small intestine from WT and DDX5△IEC (KO) mice[DS/OL]. STOmicsDB, 2021[2021-09-21]. https://db.cngb.org/stomics/datasets/STDS0000122/. 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: Long, Tianyun et al. “RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.” Gut vol. 71,9 (2022): 1790-1802. doi:10.1136/gutjnl-2021-324984