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Series GSE15745 Query DataSets for GSE15745
Status Public on Apr 20, 2010
Title Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues
Organism Homo sapiens
Experiment type Expression profiling by array
Non-coding RNA profiling by array
Methylation profiling by array
Summary 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
 
Overall design 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.
 
Contributor(s) Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai S, Arepalli S, Dillman A, Rafferty IP, Troncoso J, Johnson R, Zielke HR, Ferrucci L, Longo DL, Cookson MR, Singleton AB
Citation(s) 20485568
Submission date Apr 20, 2009
Last update date Jan 02, 2015
Contact name J Raphael Gibbs
E-mail gibbsr@mail.nih.gov
Organization name National Institutue on Aging, NIH
Department Computational Biology Core
Lab Laboratory of Neurogenetics
Street address 35 Convent Drive, Bldg 35/1A1015, MSC3707
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (3)
GPL6104 Illumina humanRef-8 v2.0 expression beadchip
GPL8178 Illumina Human v1 MicroRNA expression beadchip
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
Samples (1658)
GSM394098 UMARY-1105-CRBLM-miRNA
GSM394099 UMARY-1134-CRBLM-miRNA
GSM394100 UMARY-4549-CRBLM-miRNA
Relations
BioProject PRJNA116889

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
GSE15745_RAW.tar 9.2 Mb (http)(custom) TAR
GSE15745_mRNA_CRBLM_no_normalization.txt.gz 39.3 Mb (ftp)(http) TXT
GSE15745_mRNA_FCTX_no_normalization.txt.gz 39.1 Mb (ftp)(http) TXT
GSE15745_mRNA_PONS_no_normalization.txt.gz 39.1 Mb (ftp)(http) TXT
GSE15745_mRNA_TCTX_no_normalization.txt.gz 39.5 Mb (ftp)(http) TXT
GSE15745_miRNA_CRBLM_no_normalization.txt.gz 1.4 Mb (ftp)(http) TXT
GSE15745_miRNA_FCTX_no_normalization.txt.gz 1.4 Mb (ftp)(http) TXT
GSE15745_miRNA_PONS_no_normalization.txt.gz 1.4 Mb (ftp)(http) TXT
GSE15745_miRNA_TCTX_no_normalization.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Raw data is available on Series record
Raw data included within Sample table

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