Illumina HiSeq 4000 sequencing; RNA-seq of biopsies, crypts and organoids of inflamed and non-inflamed biopsies of ulcerative colitis patients
RNA-seq of biopsies, crypts and organoids of inflamed and non-inflamed biopsies of ulcerative colitis patients
Fresh biopsies from both inflamed and non-inflamed segments were obtained during endoscopy from 8 patients with active UC (endoscopic Mayo subscore of ≥2) and an accessible border of inflammation. Crypts were isolated and cultured as organoids for 4 weeks with weekly mechanical splitting. RNA was extracted from snapfrozen biopsies biopsies, isolated crypts and 1 and 4 week old organoids.  Total RNA was extracted using the RNeasy Mini Kit following the manufacturer instructions (Qiagen, Hilden, Germany). RNA was quantified by Nanodrop and the integrity was evaluated using Agilent Bio-analyzer 2100. The library construction was performed by the Lexogen QuantSeq 3' mRNA-Seq Library Kit FWD (Lexogen, Vienna, Austria)