Cell atlas from human intestinal immune priming and effector sites during homeostasis

This project contains scRNA-seq datasets from the human intestinal lamina propria (LP), submucosa (SM) and gut-associated lymphoid tissues (GALT; i.e. Peyer’s patches (PP), mucosal and submucosal isolated lymphoid follicles (M-ILF and SM-ILF)). The data include CD45- total stromal cells, CD45-CD31- fibroblasts, CD45+ total immune cells and CD45-CD3lowCD19lowHLA-DRhi myeloid cells. Together, the data allows to draw a comprehensive picture of the intestinal immune and stromal cell landscape within the different compartments of the intestine. The cells included in the scRNA-seq datasets were obtained from surgical resection material from untreated donors with colorectal cancer (CRC). Tissues were taken >10 cm distant from the tumor lesion and macroscopically tumor-free. After separation of the intestinal layers (SM, LP, GALT), tissues were digested enzymatically to obtain single cell suspensions as described previously by Jørgensen et al. (PMID: 33619391). Single cell suspensions were stained with immune and stromal markers, and immune and stromal cells enriched using fluorescence-activated cell sorting (FACS).