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Series GSE116193 Query DataSets for GSE116193
Status Public on Jun 25, 2018
Title Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary To fully comprehend how genetic variants influence phenotypes, we must understand the functions of the epigenome. To   assess the degree to which genetic variants influence epigenome activity, we integrate epigenetic and genotypic data from lupus patient lymphoblastoid cell lines to identify variants that induce allelic imbalance in the magnitude of histone post-translational modifications, referred to herein as histone quantitative trait loci (hQTLs). We demonstrate that enhancer hQTLs are enriched on autoimmune disease risk haplotypes and disproportionately influence gene expression variability compared with non-hQTL variants in strong linkage disequilibrium. We show that the epigenome regulates HLA class II genes differently in individuals who carry HLA-DR3 or HLA-DR15 haplotypes, resulting in differential 3D chromatin conformation and gene expression. Finally, we identify significant expression QTL (eQTL) x hQTL interactions that reveal substructure within eQTL gene expression, suggesting potential implications for functional genomic studies that leverage eQTL data for subject selection and stratification.
Overall design H3K27ac ChIP-seq, H3K4me1 ChIP-seq, H3K27ac HiChIP-seq, CTCF HiChIP-seq, and RNA-seq data are generated from 25 lymphoblastoid cell lines (LCLs) from European-American patients with systemic lupus erythematosus
Contributor(s) Pelikan RC, Kelly JA, Glenn SA, Gaffney PM
Citation(s) 30046115
NIH grant(s)
Grant ID Grant title Affiliation Name
U19 AI082714 Mechanisms Regulating TNFAIP3 Gene Expression OKLAHOMA MEDICAL RESEARCH FOUNDATION Patrick M Gaffney
P30 AR053483 Oklahoma Rheumatic Disease Research Cores Center OKLAHOMA MEDICAL RESEARCH FOUNDATION JUDITH A JAMES
R01 AR056360 TNFAIP3 (A20) and Susceptibility to Systemic Lupus Erythematosus OKLAHOMA MEDICAL RESEARCH FOUNDATION Patrick M Gaffney
R01 AR063124 Functional Mechanisms of Causal Variants in Systemic Lupus Erythematosus OKLAHOMA MEDICAL RESEARCH FOUNDATION Patrick M Gaffney
P30 GM110766 Molecular Mechanisms and Genetics of Autoimmunity COBRE OKLAHOMA MEDICAL RESEARCH FOUNDATION Patrick M Gaffney
U54 GM104938 Oklahoma Shared Clinical and Translational Resources University of Oklahoma Health Sciences Center JUDITH A JAMES
Submission date Jun 24, 2018
Last update date Mar 26, 2019
Contact name Patrick M Gaffney
Organization name Oklahoma Medical Research Foundation
Department Genes and Human Disease
Street address 825 NE 13th Street
City Oklahoma City
State/province OK
ZIP/Postal code 73013
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (112)
GSM3212819 lgs101293_H3K27ac ChIP-seq
GSM3212820 lgs301283_H3K27ac ChIP-seq
GSM3212821 lgs301430_H3K27ac ChIP-seq
BioProject PRJNA477708
SRA SRP151215

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
GSE116193_CTCF_HiChIP_connectome.txt.gz 4.3 Mb (ftp)(http) TXT
GSE116193_H3K27ac_HiChIP_connectome.txt.gz 5.9 Mb (ftp)(http) TXT
GSE116193_Kallisto_expression_25cellLines_filtered_PEERnormalized+scaled_lengthScaledTPM.txt.gz 4.3 Mb (ftp)(http) TXT
GSE116193_RAW.tar 396.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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