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Series GSE20142 Query DataSets for GSE20142
Status Public on Feb 28, 2010
Title Primary human leucocyte RNA expression of unrelated Dutch individuals.
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Multiple common variants for celiac disease influencing immune gene expression
The goal of this study was to study the effect of genetic variation on gene expression of untouched primary leucocytes.
We obtained peripheral blood RNA from unrelated Dutch individuals using PAXgene tubes.
We performed a second-generation genome wide association study of 4,533 celiac disease cases and 10,750 controls. We genotyped 113 selected SNPs with PGWAS<10-4, and 18 SNPs from 14 known loci, in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome wide significance (Pcombined<5x10-8), most contain immune function genes (BACH2, CCR4, CD80, CIITA/SOCS1/CLEC16A, ICOSLG, ZMIZ1) with ETS1, RUNX3, THEMIS and TNFRSF14 playing key roles in thymic T cell selection. A further 13 regions had suggestive association evidence. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P<0.0028, FDR 5%) with cis gene expression.

*** Due to privacy concerns, the SNP data is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access directly from the submitter (contact info below). ***
 
Overall design Gene expression data was determined of untouched primary leucocytes (n=1,240) from unrelated Dutch individuals.
 
Contributor(s) Franke L, Fehrmann R, Wijmenga C, van Heel D, van den Berg L, Ophoff R, Groen H, Weersma R, Veldink J
Citation(s) 20190752, 21829388, 24013639, 22275870, 21425313
Submission date Feb 02, 2010
Last update date Nov 04, 2019
Contact name Lude Franke
E-mail(s) lude@ludesign.nl
Phone +316 41549962
Organization name University Medical Centre Groningen
Department Genetics
Lab Genetics
Street address P.O. Box 30001
City Groningen
State/province Groningen
ZIP/Postal code 9700 RR
Country Netherlands
 
Platforms (1)
GPL6947 Illumina HumanHT-12 V3.0 expression beadchip
Samples (1240)
GSM504016 Peripheral blood RNA from Dutch sample 1
GSM504017 Peripheral blood RNA from Dutch sample 2
GSM504018 Peripheral blood RNA from Dutch sample 3
Relations
BioProject PRJNA125559

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE20142_RAW.tar 307.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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