Transcriptomics

Dataset Information

103

Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues


ABSTRACT: A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We describe a set of integrated experiments designed to investigate the effects of common genetic variability on DNA methylation, mRNA expression and microRNA (miRNA) expression in four distinct human brain regions. We show that brain tissues may be readily distinguished based on methylation status or expression profile. We find an abundance of genetic cis regulation mRNA expression and show for the first time abundant quantitative trait loci for DNA CpG methylation. We observe that the largest magnitude effects occur across distinct brain regions. We believe these data, which we have made publicly available, will be useful in understanding the biological effects of genetic variation. Authorized Access data: Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249.v1.p1 Because of our interest in genomic regulation of expression and neurological disorders we embarked upon a series of experiments to provide a brain region-specific contextual framework for genetic and epigenetic regulation of gene expression. We obtained frozen brain tissue from the cerebellum, frontal cortex, pons and temporal cortex from 150 subjects (total 600 tissue samples). We undertook four separate assays across this series; first, genome-wide SNP genotyping; second, assay of >27,000 CpG methylation sites in each of the four brain regions; third, mRNA expression profiling of >22,000 transcripts in all four brain regions; and, fourth, miRNA expression profiling of 735 miRNA transcripts. Here we discuss the results of these experiments, particularly in the context of integrated datasets to define expression and CpG methylation quantitative trait loci (eQTL and methQTL) and detailing differences and similarities across brain regions.

OTHER RELATED OMICS DATASETS IN: phs000249.v1.p1

ORGANISM(S): Homo sapiens  

SUBMITTER: Dena G Hernandez   Jesse R Gibbs  Luigi Ferrucci  Dan L Longo  Sampath Arepalli  Juan Troncoso  Allisa Dillman  Bryan J Traynor  Andrew B Singleton  Mark R Cookson  J Raphael Gibbs  Ian P Rafferty  Marc P van der Brug  Michael A Nalls  Shiao-Lin Lai  H R Zielke  Robert Johnson 

PROVIDER: E-GEOD-15745 | ArrayExpress | 2010-04-20

SECONDARY ACCESSION(S): GSE15745PRJNA116889

REPOSITORIES: GEO, ArrayExpress

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Publications


A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We present a set of integrated experiments that investigate the effects of common genetic variability on DNA methylation and mRNA expression in four human brain regions each from 150 individuals (600 samples total). We find an abundance of genetic cis regulation of mRNA expression and show for the first time abundant quantitative tr  ...[more]

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