title: Illumina HiSeq 4000 sequencing; A multi-omics approach to understand and predict therapeutic success of anti-TNF and anti-integrin agents in inflammatory bowel disease
design: A multi-omics approach to understand and predict therapeutic success of anti-TNF and anti-integrin agents in inflammatory bowel disease
library_name: GC049975_s
library_construction_protocol: We collected inflamed colonic and ileal biopsies, as well as blood (of which PBMCs were isolated and sorted through FACS) prior to the initiation of anti-TNF and Vedolizumab therapy. All recruited Crohn's disease patients had endoscopy-proven active disease (SES-CD > 7, and > 4 in patients with pure ileal involvement); all included UC patients had a Mayo endoscopic subscore 2-3.   Total RNA from lysed inflamed biopsies and lysed sorted CD4+ and CD14+ cells was extracted using the AllPrep DNA/RNA Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The integrity and quantity of all RNA was assessed with a 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Waltham, Massachusetts, USA).  Library preparation was performed using the TruSeq Stranded mRNA protocol (Illumina, San Diego, USA) according to the manufacturer's instructions.