Single-Cell, Single-Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity(Dataset ID: STDS0000103)

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Spots: 2,265
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Genes: 36,601
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PMID: 34792289
Summary
Visualization
Data
Analysis results
Related
Sample
Catalog
Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
Comparison of single cell RNAseq and single nucleus RNAseq on four healthy human liver caudate lobes, with cell-types validated using one slice of a fifth healthy human for VISIUM Spatial Transcriptomics. Raw UMI count tables can be found here: https://figshare.com/projects/Human_Liver_SC_vs_SN_paper/98981 Processed Seurat Objects can be found here: https://www.dropbox.com/sh/sso15ehqmrrh6mk/AACKHOsSlZW0_Zy9cbCkOmMfa?dl=0
Overall design:
Four healthy human liver caudate lobes were removed prior to transplantation into living recipients. A potion of each lobe was frozen then nuclei were extracted and sequenced with 10x Chromium while another portion was dissociated immediately while still fresh and isolated cells were sequenced with 10x Chromium.
Technology:
10x Visium
Platform:
Illumina HiSeq 2500
Species:
Homo sapiens(hg38)
Tissues:
Liver
Submission date: 2021-10-06Update date: 2021-12-02
Sample number: 1
DOI: To be continue
Contributors
Tallulah S Andrews,Jawairia Atif,Jeff C Liu,Sonya MacParland
Contact: tallulandrews@gmail.com
Accessions
GEO Series Accessions: GSE185477
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] Tallulah S Andrews,Jawairia Atif,Jeff C Liu,Sonya MacParland. Single-Cell, Single-Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity[DS/OL]. STOmicsDB, 2021[2021-10-06]. https://db.cngb.org/stomics/datasets/STDS0000103/. 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: Andrews, Tallulah S et al. “Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity.” Hepatology communications vol. 6,4 (2022): 821-840. doi:10.1002/hep4.1854