Spatially resolved single-cell RNA-sequencing reveals expression heterogeneity in tumor microenvironment(Dataset ID: STDS0000133)

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PMID: 33883145
Summary
Visualization
Data
Analysis results
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Dataset information
Summary:
To better understand how individual cells function within an anatomical space, we developed XYZeq, a novel scRNA-seq workflow that uses combinatorial indexing in microwells to encode spatial metadata into scRNA-seq libraries. We used XYZeq to profile heterotopic mouse liver and spleen tumor models to capture transcriptomes from tens of thousands of cells across a total of eight tissue slices.
Overall design:
Spatially resolved single-cell RNA-sequencing from eight tissue sections of MC38-injected liver and spleen organs (samples L30C and L30C8 are from the same slice). Additional experiments using cell lines and comparing to droplet-based single-cell RNA-seq.
Technology:
XYZeq
Platform:
GPL21103
Species:
Homo sapiens(hg38)
Mus musculus(mm10)
Cell types:
mouse cell line:3T3,human cell line:HEK293T
Submission date: 2021-01-07Update date: 2021-05-12
Sample number: 12Section number: 12
DOI: To be continue
Contributors
Y Lee,D Bogdanoff,Y Wang,G Hartoularos,A Marson,E D Chow,C J Ye
Contact: george.hartoularos@ucsf.edu
Accessions
GEO Series Accessions: GSE164430
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] Y Lee,D Bogdanoff,Y Wang,G Hartoularos,A Marson,E D Chow,C J Ye. Spatially resolved single-cell RNA-sequencing reveals expression heterogeneity in tumor microenvironment[DS/OL]. STOmicsDB, 2021[2021-01-07]. https://db.cngb.org/stomics/datasets/STDS0000133/. 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: Lee, Youjin et al. “XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.” Science advances vol. 7,17 eabg4755. 21 Apr. 2021, doi:10.1126/sciadv.abg4755