Summary from GEO: "There is limited understanding of how immune-mediated damage impacts intestinal stem cells (ISCs). We found that stem cell compartment injury is a shared feature of both alloreactive and autoreactive intestinal immunopathology, reducing ISCs and impairing their recovery in T-cell-mediated injury models. Modeling with ex vivo epithelial cultures indicated ISC depletion and impaired...

Summary from GEO: "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...

Description from Github: "Palantir is an algorithm to align cells along differentiation trajectories. Palantir models differentiation as a stochastic process where stem cells differentiate to terminally differentiated cells by a series of steps through a low dimensional phenotypic manifold. Palantir effectively captures the continuity in cell states and the stochasticity in cell fate determination....

A jupyter notebook detailing the workflow, including data preprocessing, of running Palantir along with a demonstration of various plots and visualizations