Single-cell RNA-sequenceing analysis of mouse intestinal organoids cultured in Matriel or type I collagen

Intestinal epithelial regeneration depends on cellular plasticity under inflammatory conditions. Two major forms of plasticity have been described: spatial plasticity, in which mature cells dedifferentiate into crypt base columnar (CBC) stem cells, and fetal reversion, where cells adopt a fetal-like transcriptional state. To investigate the cellular mechanisms underlying these processes, we performed single-cell RNA sequencing on mouse intestinal epithelial organoids cultured in either Matrigel or collagen-based matrices. Combined single-cell transcriptomic and functional analyses revealed bidirectional interconversion between CBCs and revival stem cells (revSCs), as well as the reprogramming of absorptive enterocytes toward revSC-like states. This dataset provides a high-resolution atlas of epithelial stem cell states and plasticity transitions, facilitating further investigation of regenerative hierarchies in the mouse intestine. Overall design: Cells isolated from standard budding organoids cultured in Matrigel and cystic spherical organoids cultured in collagen Type I established WT mouse small intestune were analyzed by scRNA-seq.