Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma(Dataset ID: STDS0000001)

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3,429
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Spots: 8,928
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Genes: 33,538
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PMID: 32579974
Summary
Visualization
Data
Analysis results
Related
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Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
To define the cellular composition and spatial architecture of the tumor micoenvironment, we combined single-cell RNA-sequencing, spatial transcriptomics, and multiplexed ion-beam imaging from 10 patient cutaneous squamous cell carcinoma tumors and site-matched normal skin
Overall design:
Patient tumors were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing
Technology:
10x Visium,Spatial Transcriptomics,scRNA
Platform:
Illumina NextSeq 500
Species:
Homo sapiens(hg19)
Tissues:
Skin
Cell types:
fibroblasts,endothelial cells,melanocytes,CLEC9A,CD1C,plasmacytoid,AXL+SIGLEC6+ (AS) dendritic cells
Disease:
Squamous cell carcinoma
Submission date: 2020-01-24Update date: 2020-11-18
Sample number: 6Section number: 19
DOI: To be continue
Contributors
Andrew Ji
Contact: andrewji@stanford.edu
Accessions
GEO Series Accessions: GSE144239
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] Andrew Ji. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma[DS/OL]. STOmicsDB, 2020[2020-01-24]. https://db.cngb.org/stomics/datasets/STDS0000001/. 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: Ji, Andrew L et al. “Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.” Cell vol. 182,2 (2020): 497-514.e22. doi:10.1016/j.cell.2020.05.039