Spatial charting of single-cell transcriptomes in tissues
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Dataset information
Summary:
We performed single-cell RNA sequencing and spatial transcriptomics experiments on two ductal carcinoma in situ tissues and applied CellTrek to identify tumor subclones that were restricted to different ducts, and specific T cell states adjacent to the tumor areas. Our data show that CellTrek can accurately map single cells in diverse tissue types to resolve their spatial organization.Overall design:
We developed a computational method called CellTrek that combines single-cell RNA sequencing and spatial transcriptomics datasets to achieve single-cell spatial mapping through coembedding and metric learning approaches.Technology:
10x Visium, scRNA
Platform:
Illumina NovaSeq 6000 (Homo sapiens)
Species:
Homo sapiens(hg38)
Tissues:
Breast
Disease:
Ductal carcinoma in situCitation:
Wei, Runmin et al. “Spatial charting of single-cell transcriptomes in tissues.” Nature biotechnology vol. 40,8 (2022): 1190-1199. doi:10.1038/s41587-022-01233-1Submission date: 2021-07-31Update date: 2022-08-16
Sample number: 4Section number: 4
Contributors
Wei; Runmin; He; Siyuan; Navin; Nicholas
Accessions
GEO Series Accessions:
GSE181254