title: Illumina HiSeq 4000 sequencing; Inflamed colonic biopsies of patients with inflammatory bowel disease
design: Inflamed colonic biopsies of patients with inflammatory bowel disease
library_name: Sample 109_s
library_construction_protocol: Endoscopy-derived inflamed colonic biopsies were obtained cross-sectionally from IBD patients (n = 70 Crohn's disease [CD], n = 60 ulcerative colitis [UC]) with endoscopically proven active disease. Biopsies were taken at the most affected site (expect for the healthy individuals), at the edge of the ulcer, and stored in RNALater buffer (Ambion, Austin, TX, USA) with subsequent preservation at -80°C.  Total RNA from the colonic biopsies was extracted using the AllPrep DNA/RNA Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions, after tissue lysis using the FastPrep Lysing Matrix D tubes (MP Biomedicals, Brussels, Belgium) with RLT lysis buffer (Qiagen, Hilden, Germany). RNA quantity and integrity was assessed with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Extracted RNA was stored at -80°C until further processing.  Library preparation using the TruSeq Stranded mRNA protocol (Illumina, San Diego, USA) according to the manufacturer's instructions