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For a long period of time, intestinal mesenchymal stromal cells have been considered as a relatively simple and homogeneous group of cells. With the help of single cell transcriptomics studies, it has now been clear that these cells are quite complex and heterogeneous. However, the detailed cellular and molecular mechanisms that regulate the function of these cells remains poorly understood. Therefore, the ability to perturb and evaluate the function of these stromal cells is critical to the understanding of intestinal stem cell niche and the etiology of the inflammatory bowel diseases and colitis associated colorectal cancer.