Isx-9 induces enteroendocrine cell differentiation in the intestinal organoids

We investigated the cell identity and cell proportion in the intestinal organoids treated by Isoxazole-9 (Isx-9) using single-cell transcriptome analysis. Isx-9 enriches enteroendocrine cells without altering the cell identity of other lineages. To investigate the mechanism of this process, we performed RNA-seq and ATAC-seq of Isx-9 treated intestinal stem cells. Based on the gene expression pattern and differential peaks of open chromatin, we found that Isx-9 upregulated neuroendocrine related genes, and elevated the chromatin accessibility at the promoter region of enteroendocrine related transcription factors. Single-cell transcriptome profiles of 4 samples were generated, including WT intestinal organoids, Chgb-mCherry reporter organoids, and Chgb-mCherry reporter organoids treated by DMSO or Isx-9 for 6 days. In addition, RNA-seq and ATAC-seq of DMSO or Isx-9 treated intestinal stem cells were also performed.