Single cell RNA-sequencing counts of mucosal biopsies from ulcerative colitis patients

Mucosal biopsy samples were obtained from patients during routine ileocolonoscopy at the Department of Gastroenterology and Hepatology of the Amsterdam UMC between December 2020 and April 2021. Patients were aged ≥16 years with an established diagnosis of ulcerative colitis (UC) determined through endoscopy and histopathology, where disease activity was scored by a trained gastroenterologist using the Mayo Endoscopic Score (MES) and the Ulcerative Colitis Endoscopic Index of Severity (UCEIS). In total, we acquired samples from 10 UC patients: 5 inflamed UC (MES≥1), 5 non-inflamed UC (MES=0). Exclusion criteria were ongoing malignancy, a history of colonic dysplasia, or colonic surgery. Control samples were obtained from resection specimens acquired from 4 patients with no established diagnosis of UC (CD, suspicion of rectum carcinoma, trans-anal total mesorectal excision or hemicolectomy), which were obtained from the biobank of the Amsterdam UMC.Raw reads were aligned to GRCh38 using Cellranger (v7.0.0) (10X Genomics) generating unique molecular identifiers (UMIs) were obtained. Samples were imported separately, processed, and analysed in the R programming environment (v4.2.1) using Seurat (v4.3.0) 43,44. UMI counts were normalized by SCTransform (v) using default parameters.