|
| Status |
Public on Sep 01, 2019 |
| Title |
1-0578-003 whole blood 16p11.2del variant genomic DNA |
| Sample type |
genomic |
| |
|
| Source name |
whole blood genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: M
disease state: ASD
sample type: genomic
tissue: whole blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All genomic DNA were extracted from whole blood using standard procedures. One microgram of genomic DNA was sodium bisulfite modified using the Qiagen EZ DNA Methylation kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Modified genomic DNA was then processed and analyzed on the Infinium HumanMethylation450 BeadChip from Illumina according to the manufacturer’s protocol.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Using an Illumina HiScan
|
| Data processing |
Background subtraction and normalization to internal array controls were performed on raw intensity data using Illumina GenomeStudio v2011.1 Methylation Module 1.9 software. Probes containing single nucleotide polymorphisms (SNPs), cross-reactive probes with sequences aligned to multiple positions with ≥ 90% identity, and non-specific chromosome probes were removed.
|
| |
|
| Submission date |
May 02, 2018 |
| Last update date |
Sep 01, 2019 |
| Contact name |
Rosanna Weksberg |
| Organization name |
The Hospital for Sick Children
|
| Department |
Genetics and Genome Biology
|
| Lab |
Weksberg Lab
|
| Street address |
555 University Ave.
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 2L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE113967 |
Functional DNA methylation signatures for genomic loci that confer an increased risk for autism spectrum disorder: 16p11.2 deletions and CHD8 variants |
|
