10x Visium Spatial transcriptomics of murine colon at d14 (mucosa healing) in B cell sufficient/deficient mice(Dataset ID: STDS0000063)

0
|
287
|
135
|
Spots: 9,984
|
Genes: 31,053
|
PMID: 35149721
Summary
Visualization
Data
Analysis results
Related
Catalog
Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
The limitation of single-cell or bulk transcriptomic profiling is the lack of spatial topographical context. Spatial transcriptomics (ST) allows sequencing of polyadenylated transcripts from a tissue section which can be spatially mapped onto the histological brightfield image using an array of barcoded oligo-dT capturing probes. Using the 10x Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon during mucosal healing upon dextran sodium sulfate (DSS) induced injury in mice in which B cell has been depleted and control.
Overall design:
Female C57BL/6J mice were irradiated and received BM transplants with either CD19cre (ctrl) or CD19cre x iDTR cells. 8 weeks after BM transfer mice were treated with 2%DSS via the drinking water followed by 7 days of recovery. On days 9, 10, 12 and 13 mice received i.p. injections of diphteria toxin (25ng/g BW) in PBS. On day 14 colonic epithelial cells and stromal cells were sorted by flow cytometry and processed according to 10x Genomics protocol for visium and submitted for sequencing.
Technology:
10x Visium
Platform:
Illumina NovaSeq 6000
Species:
Mus musculus
Tissues:
Colon
Sex:
Female
Submission date: 2021-12-09Update date: 2019-12-11
Sample number: 2
DOI: To be continue
Contributors
Das S,Villablanca E,Larsson L
Contact: ludvig.larsson@scilifelab.se
Accessions
GEO Series Accessions: GSE190595
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] Das S,Villablanca E,Larsson L. 10x Visium Spatial transcriptomics of murine colon at d14 (mucosa healing) in B cell sufficient/deficient mice[DS/OL]. STOmicsDB, 2021[2021-12-09]. https://db.cngb.org/stomics/datasets/STDS0000063/. 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: Parigi, Sara M et al. “The spatial transcriptomic landscape of the healing mouse intestine following damage.” Nature communications vol. 13,1 828. 11 Feb. 2022, doi:10.1038/s41467-022-28497-0