Spatial charting of single-cell transcriptomes in tissues

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. 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.