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Series GSE143507 Query DataSets for GSE143507
Status Public on Jan 14, 2020
Title RNA sequencing data of peripheral blood isolated from Korean patients with Crohn's disease.
Organism Homo sapiens
Experiment type 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.
Contributor(s) Jung S, Liu W, Baek J, Moon J, Ye B, Lee H, Park S, Yang S, Han B, Liu J, Song K
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Submission date Jan 13, 2020
Last update date Jan 16, 2020
Contact name Seulgi Jung
Organization name University of Ulsan College of Medicine
Department Department of Biochemistry and Molecular Biology
Lab Kyuyoung Song's lab
Street address 88 Olympic-ro 43-gil
City Seoul
ZIP/Postal code 138-040
Country South Korea
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (101)
GSM4260927 Crohn's disease patient 1
GSM4260928 Crohn's disease patient 2
GSM4260929 Crohn's disease patient 3
BioProject PRJNA600846
SRA SRP241695

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Supplementary file Size Download File type/resource
GSE143507_RAW.tar 53.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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