Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model(Dataset ID: STDS0000121)

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596
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993
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Spots: 19,968
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Genes: 32,285
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PMID: 34853151
Summary
Visualization
Data
Analysis results
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Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
We optimized and validated a female bilateral ischemia reperfusion injury model. Using the 10X Genomics Visium Spatial Gene Expression solution, we generated spatial maps of gene expression across the injury and repair time course, and applied two open-source computational tools, Giotto and SPOTlight, to increase resolution and measure cell-cell interaction dynamics. An ischemia time of 34 minutes in a female murine model resulted in comparable injury to males across the time course of injury and repair. We report increased resolution of cell and gene expression with Giotto, a computational toolbox for spatial data analysis. Using a seeded non-negative matrix regression (SPOTlight) to deconvolute the dynamic landscape of cell-cell interactions, we find that injured proximal tubule cells are characterized by increasing macrophage and lymphocyte interactions even at 6 weeks after injury, consistent with a pro-inflammatory role for this cell state. In this transcriptomic atlas, we defined region-specific and injury-induced loss of differentiation markers and their re-expression during repair, as well as region-specific injury and repair transcriptional responses. Lastly, we created a data visualization web application for the scientific community to explore these results (http://humphreyslab.com/SingleCell/).
Overall design:
10X Visium was used to create a transcriptomic atlas of female kidney injury to discover, validate, and define spatial and temporal expression of injury specific genes.
Technology:
10x Visium
Platform:
GPL24247
Species:
Mus musculus(mm10)
Tissues:
Kidney
Sex:
Female
Submission date: 2021-08-27Update date: 2021-11-23
Sample number: 4
DOI: To be continue
Contributors
Dixon, Eryn E,Wu, Haojia,Muto, Yoshiharu,Wilson, Parker C,Humphreys, Benjamin D
Contact: d.eryn@wustl.edu
Accessions
GEO Series Accessions: GSE182939
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] Dixon, Eryn E,Wu, Haojia,Muto, Yoshiharu,Wilson, Parker C,Humphreys, Benjamin D. Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model[DS/OL]. STOmicsDB, 2021[2021-08-27]. https://db.cngb.org/stomics/datasets/STDS0000121/. 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: Dixon, Eryn E et al. “Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model.” Journal of the American Society of Nephrology : JASN vol. 33,2 (2022): 279-289. doi:10.1681/ASN.2021081150