Intestinal organoids from pediatric Crohns disease patients retain transcriptional differences

Since few therapies for Crohns disease (CD) directly target the epithelium, we used patient-derived organoids (PDOs), which are strict epithelial cell culture models, to study the epithelial-specific signatures of the ileum during CD. RNA sequencing was performed on intestinal organoids prepared from ileal biopsies of CD patients (B1, inflammatory and B2, stricturing disease) and non-IBD controls (16 CD, 13 healthy controls). The read count alignment was performed using reference genome Hg38.