|
| Status |
Public on Jan 02, 2014 |
| Title |
DS01 |
| Sample type |
genomic |
| |
|
| Source name |
buccal swab genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: M
down synrome status: DS
age: 46.56
brief praxis score: 35
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from buccal swabs using the Isohelix DNA isolation kit following manufacturer's instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
BeadChips were imaged using HiScan with standard recommended Illumina scanner setting
|
| Description |
DS participant
|
| Data processing |
Raw intensities extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B. Then quantile normalization was done to control for chip to chip variation. Finally, average beta is recalculated from normalized intensities: methylated intensity / (methylated + unmethylated intensities). Data points with bad detection P values are removed and then imputed. One CpG site, cg22903370, was removed due to >50% of data points missing.
supplementary matrix contains unmethylated and methylated signal intensities
|
| |
|
| Submission date |
Sep 04, 2013 |
| Last update date |
Jan 02, 2014 |
| Contact name |
Michael S. Kobor |
| Organization name |
Centre for Molecular Medicine and Therapeutics / University of British Columbia
|
| Department |
Medical Genetics
|
| Lab |
Kobor
|
| Street address |
950 West 28th Avenue
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 4H4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE50586 |
Distinct DNA methylation patterns of cognitive impairment and Trisomy 21 in Down Syndrome |
|
