Bile acid-dependent transcription factors and chromatin accessibility determine regional heterogeneity of intestinal antimicrobial peptides

The newly generated scRNA-seq data and bulk RNA-seq data are provided here:
1. ScRNA-seq data. To investigate the regional heterogeneity of human intestine, 14 bioptic samples from human duodenum, jejunum and ileum were collected from 10 healthy donors recruited at the time of routine gastroscopy or enteroscopy or colonoscopy for single cell RNA sequencing. Healthy volunteers were individuals without gastrointestinal tumors, polyps or other organic diseases, and who were overall healthy with no underlying diseases such as hypertension and diabetes.
2. Bulk RNA-seq data. To investigate the effect of bile acis on the transcriptome of mouse intestinal organoids, mouse small intestinal organoids cultured for 2 days were incubated with a series of bile acids at 50 mmol/L for 96 hours and lysed for RNA extraction.
3. ScRNA-seq experiments in mouse duodenum organoids stimulated with DCA (50 mmol/L for 96 hours) and DMSO were employed to directly depict the changes in the proportion of epithelial lineages.