Single-cell RNA sequencing of small intestinal organoid self-organization [scRNA-Seq]

The self-organization of small intestinal organoids, starting from a single cell (0 h) to a budded crypt-villus structure (96–108 h), recapitulates aspects of such multicellular intestinal morphogenesis. To characterize the cell states and lineage trajectories underlying organoid self-organization, we performed single-cell RNA sequencing of intestinal organoids in a high-resolution time course.

Organoids derived from mouse duodenal epithelium were dissociated to single cells and seeded to initiate organoid formation, followed by sampling for sequencing at 12-hour intervals from 24 to 108 h. This dataset captures dynamic changes in cell state composition during organoid development. Early time points (24–36 h) reveal a population of reprogramming cells characterized by loss of mature lineage markers, followed by the emergence and differentiation of major intestinal lineages, including absorptive, secretory, and stem cell populations.