title: Illumina HiSeq 4000 sequencing; Transcriptomic profiling predicting response to ustekinumab therapy in patients with Crohn's disease
design: Transcriptomic profiling predicting response to ustekinumab therapy in patients with Crohn's disease
library_name: GC061583_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 ustekinumab therapy. All recruited Crohn's disease patients had endoscopy-proven active disease (SES-CD > 7, and > 4 in patients with pure ileal involvement) and were ustekinumab naÃ¯ve.   Total RNA from inflamed biopsies and 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.