Spatial charting of single-cell transcriptomes in tissues
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.
10x Visium, scRNA
Illumina NovaSeq 6000 (Homo sapiens)
Disease:Ductal carcinoma in situ
Citation:Wei, Runmin et al. “Spatial charting of single-cell transcriptomes in tissues.” Nature biotechnology vol. 40,8 (2022): 1190-1199. doi:10.1038/s41587-022-01233-1
Submission date: 2021-07-31Update date: 2022-08-16
Sample number: 4Section number: 4
Wei; Runmin; He; Siyuan; Navin; Nicholas
AccessionsGEO Series Accessions: GSE181254