10x visium spatial transcriptomic spots  (Spatial Transcriptomics Inc)

Journal: bioRxiv

Article Title: Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

doi: 10.1101/2022.06.02.490672

Figure Lengend Snippet: Contextualizing scRNAseq data using SpaceMarkers and transfer learning from matched ST-scRNAseq data in HCC (see also and ). A. CoGAPS factorization reveals spatial patterns associated with tumor annotations of tumor and immune cells. (see ). B. Scatterpie visualization shows the relative pattern activity levels associated with the spatially overlapping tumor (orange) and immune (blue) patterns in each Visium spot using a pie chart (white represents activity from all other patterns). SpaceMarkers are genes exhibiting nonlinear effects in the residual space of the CoGAPS patterns in the region with tumor-immune overlap. C. Transfer learning of Patterns 1, 2, and 8 from ST data to matched scRNAseq data. Scatter plot shows projections of the spatial patterns onto individual cells in the scRNAseq data. Individual cells in the scRNAseq data are associated with the pattern having the highest projection in the cell. D. Expression heatmap of SpaceMarkers in tumor and immune cells from matched single-cell data from the same tumor provide the spatial context of the individual cells.

Article Snippet: In the examples demonstrated here, the spatial data is obtained using the spot-based 10x Visium spatial transcriptomics technology [ ] with 1-10 cells per spot.

Techniques: Activity Assay, Expressing