A lymphatic-stem cell interactome regulates intestinal stem cell activity

Single-cell RNA-sequencing of murine small intestinal organoid cultured with and without lymphatic endothelial cells: Purpose: To identify differences in cell composition in murine organoids upon coculture with lymphatic endothelial cells Results: We recovered 818 cells with a median of 37750 UMIs per cell for the organoid alone and 1233 cells with a median of 79354 UMIs per cells for the cocultured organoid condition. Conclusions: scRNASeq reveals different cell composition in organoids cocultured with lymphatic endothelial cells compared to control Single-cell RNA-Sequencing of murine small and large intestinal tissue: Purpose: To generate a reference dataset of all major cell types present in the small and large intestine of the mouse Results: For the small intestine we recovered 8842 cells with a median of 4088 UMIs per cell compared to 8646 cells with a median of 10009 UMIs per cell for the large intestine. Conclusions: scRNASeq recovers all of the major epithelial, immune and stromal cell types in the intestine. Spatial transcriptomic profiling of murine small and large intestine: Purpose: To spatially map the major cell types in the mouse intestine and infer cell:cell communication from neighboring cells Conclusions: Spatial transcriptomic profiling of the mouse small and large intestine reveals all major cell types and allows for cell:cell signaling analyses upon integration with our matching scRNA-Seq data 16 wells each of organoids alone and cocultured organoids were pooled to sort 100k epithelial cells from each. Ctrl and coculture sample were pooled and submitted for 10X single-cell RNA-Sequencing Bulk intestinal tissue was digested and we sorted 50k alive cells, enriching for LGR5+ intestinal stem cells (50k) and CD31+ PDPN+ LYVE1+ lymphatic endothelial cells (20-25k). Tissue processing and 10X-based single-cell RNA-sequencing was done separately for the small and large intestine. C57BL/6 and Lgr5-eGFP-ires-CreERT2 (C57BL/6 background) mice were used for sorting experiments. 10X-Visium-based spatial transcriptomics was done on mouse small and large intestine (technical duplicates for each). We used the immunofluorescence-based protocol on 10 µm cryosections of small and large intestinal tubes.