Expression profiling by high throughput sequencing
Summary
We performed RNA sequencing to produce expression quantitative trait loci (eQTL) database of Crohn's disease patients. Using this eQTL data, we tried to determine the most functionally relevant genes at the established Crohn’s disease loci identified in genome-wide association studies (GWAS) involving Asian populations and to find novel disease-associated genes.
Overall design
eQTL analysis was pefromed using whole-blood RNA-sequencing of 101 Korean patients with Crohn’s disease. The Crohn's disease patients were recruited from the IBD Clinic of Asan Medical Center. Whole blood was taken and immediately store in a PAXgene Blood RNA tube at room temperature for > 4h. The total RNA was extracted using the PAXgene Blood RNA kit, following the manufacturer’s instructions. RNA quality and quantity were checked using a 2100 Bioanalyzer (Agilent Technologies, CA, USA) and the samples with an RNA integrity number ≥ 7 were deep-sequenced. Sequencing libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-ZeroTM Globin (Illumina, CA, USA) and paired-end RNA sequencing of 101 bp reads was performed using Illumina HiSeq 2500 platform. FastQTL was used for a pair-wise genome analysis of ~ 6.5 M SNPs and ~ 22 K transcripts.
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