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| 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.
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| 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.
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| 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 |
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| Samples (230)
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| Relations |
| BioProject |
PRJNA291241 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE71443_BD_Brain_white_crlmm_1.8.11.GEO.methy.tab.txt.gz |
114.1 Mb |
(ftp)(http) |
TXT |
| GSE71443_BD_Brain_white_crlmm_1.8.11.GEO.snp.tab.txt.gz |
119.8 Mb |
(ftp)(http) |
TXT |
| GSE71443_RAW.tar |
11.0 Gb |
(http)(custom) |
TAR (of CEL) |
| GSE71443_SZ_Brain_white_crlmm_1.8.11.GEO.methy.tab.txt.gz |
112.3 Mb |
(ftp)(http) |
TXT |
| GSE71443_SZ_Brain_white_crlmm_1.8.11.GEO.snp.tab.txt.gz |
117.9 Mb |
(ftp)(http) |
TXT |
| GSE71443_control+case_Brain_white_crlmm_1.8.11.GEO.methy.tab.txt.gz |
348.5 Mb |
(ftp)(http) |
TXT |
| GSE71443_control+case_Brain_white_crlmm_1.8.11.GEO.snp.tab.txt.gz |
361.2 Mb |
(ftp)(http) |
TXT |
| GSE71443_control_Brain_white_crlmm_1.8.11.GEO.methy.tab.txt.gz |
129.3 Mb |
(ftp)(http) |
TXT |
| GSE71443_control_Brain_white_crlmm_1.8.11.GEO.snp.tab.txt.gz |
135.0 Mb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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