GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE71443 Query DataSets for GSE71443
Status Public on Jul 29, 2015
Title Affymetrix 6.0 SNP arrays interrogated to detect allele-specific DNA modification in the brain
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Genome variation profiling by SNP array
Methylation profiling by SNP array
Summary It has long been hypothesized that knowledge of allele-specific modification (ASM; "modification" is used to denote various types of epigenetic cytosine marks, not only methylation) can supplement and inform GWAS of complex diseases and traits.
To explore the relationship between GWAS subthreshold SNPs and ASM, we identified brain ASM-SNPs from Caucasian control individuals (n=76) and Caucasian patients affected by schizophrenia (n=65) or bipolar (n=67) using the Affymetrix SNP 6.0 microarray, one of the most common GWAS platforms which has also been thoroughlyt validated for ASM mapping.
Overall design The brain samples (N=230, all ethnicities) were interrogated twice on Affymetrix SNP 6.0 microarrays. First, regular SNP genotyping was performed following the manufacturer's protocol. Second, we investigated allelic differences in DNA methylation by enriching the unmodified DNA fraction using DNA methylation-sensitive restriction enzymes.
Citation(s) 27087318
Submission date Jul 28, 2015
Last update date Oct 04, 2019
Contact name Arturas Petronis
Organization name Centre for Addiction and Mental Health
Street address 250 College Street
City Toronto
ZIP/Postal code M5T 1R8
Country Canada
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (230)
GSM1834553 BD_white_A-2
GSM1834554 SZ_white_A-3
GSM1834555 BD_white_A-4
BioProject PRJNA291241

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 114.1 Mb (ftp)(http) TXT 119.8 Mb (ftp)(http) TXT
GSE71443_RAW.tar 11.0 Gb (http)(custom) TAR (of CEL) 112.3 Mb (ftp)(http) TXT 117.9 Mb (ftp)(http) TXT 348.5 Mb (ftp)(http) TXT 361.2 Mb (ftp)(http) TXT 129.3 Mb (ftp)(http) TXT 135.0 Mb (ftp)(http) TXT
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap