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Series GSE57481 Query DataSets for GSE57481
Status Public on May 09, 2014
Title Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-array]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915 *cis* methylation QTLs (meQTLs), i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs.
Overall design Bisulfite converted DNA from 64 individuals was hybridized to the Illumina Infinium HumanMethylation450 BeadChip
Contributor(s) Banovich NE, Lan X, van de Geijn B, McVicker G, Degner JF, Blischak JD, Pritchard JK, Gilad Y
Citation(s) 25233095
Submission date May 08, 2014
Last update date Mar 22, 2019
Contact name Nicholas E Banovich
Organization name University of Chicago
Department Human Genetics
Lab Gilad
Street address 920 E. 58th Street, CLSC 317
City Chicago
State/province IL
ZIP/Postal code 60453
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (64)
GSM1383567 GM18498
GSM1383568 GM18499
GSM1383569 GM18501
This SubSeries is part of SuperSeries:
GSE57483 Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels
BioProject PRJNA246536

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
GSE57481_RAW.tar 183.1 Mb (http)(custom) TAR
GSE57481_Unprocessed_matrix.txt.gz 163.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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