|
| Status |
Public on May 01, 2012 |
| Title |
WG0041906-DNA_E09_RM4172 |
| Sample type |
genomic |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
qc status: Failed QC
cell type: Blood
disease status: AD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
750ng of DNA was denatured and neutralized before amplification. The denatured DNA was isothermally amplified in an overnight step, and the amplified product was them enzymatically fragmented (i.e. End-point fragmentation), precipitated with isopropanol, collected by centrifugation at 4 degrees celciums, and resuspended in hybridization buffer. C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled.
|
| |
|
| Hybridization protocol |
Samples were applied to beadchips and the loaded beadchips were incubated overnight in the Illumina Hybridization oven. Unhybridized and non-specifically hybridized DNA was washed away, and beadchips were prepared for staining and extension.
|
| Scan protocol |
The beadchips were scanned on the Illumina BeadArray Reader using default settings.
|
| Description |
C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled
|
| Data processing |
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.
|
| |
|
| Submission date |
Mar 13, 2012 |
| Last update date |
May 01, 2012 |
| Contact name |
Ekaterina Rogaeva |
| E-mail(s) |
ekaterina.rogaeva@utoronto.ca
|
| Phone |
(416) 946-7927
|
| Fax |
(416)-978-1878
|
| Organization name |
Tanz Centre for Neurodegenerative Diseases
|
| Street address |
6 Queen’s Park Crescent West
|
| City |
Toronto |
| ZIP/Postal code |
M5S 3H2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL14932 |
| Series (1) |
| GSE33528 |
Genome-wide survey of large rare copy number variations in Alzheimer’s disease among Caribbean Hispanics |
|
