Bulk RNA sequencing data (raw feature counts and metadata) of pediatric IBD and non-IBD intestinal biopsy samples and the code for the IBrD computations in Siebert et al.

Pediatric patients aged 3-18 years, with suspected or established IBD (CD and UC) were recruited to a mono-centric IBD cohort study (recruitment 2019 – 2022, Dr von Hauner Children’s Hospital, LMU Munich) and followed prospectively. The goal of our study was to collect samples from patients that achieved Endoscopic healing (EH) after active IBD. Biopsies (directly transferred into RNAlater™ Invitrogen) were collected at baseline ileocolonoscopy (timepoint = 1) and follow-up ileocolonoscopy/sigmoidoscopy for evaluation of EH (timepoint > 1). Patients without any evidence of inflammation after complete diagnostic work-up served as non-IBD controls (one timepoint). EH was defined according to STRIDE-II as Mayo endoscopic subscore of 0 and Simple Endoscopic Score for CD (SES-CD) ≤2 and absence of ulcerations. Single biopsy samples from terminal ileum (TI) and sigmoid colon (SC) were sequenced. Biopsies, n = 127; IBD patients, N = 30; non-IBD controls, N = 5; with biopsy classification according to IBD subtype (CD or UC), location (TI or SC) and endoscopic activity (active, non-inflamed (defined as ‘non-inflamed region in an active disease state’), EH and non-IBD controls).