Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects

The study was design to compare transcriptomic profiles of whole biopsies to enteroid/colonoid lines derived from them. In the accompanying publication, we observed substantial overlap of pathways upregulated in Crohn’s disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease. The biopsies were subjected to RNA extraction (Trizol) whole and subsequent library preparation and RNA-seq. To establish enteroids and colonoids, we first isolated crypts from matching biopsies, then seeded these crypts in Matrigel domes. We used complete human IntestiCult OGM to enteroid/colonoid growth. The cultures were passaged once, and then harvested for RNA isolation, library prep and RNA-seq.