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Status |
Public on May 01, 2012 |
Title |
WG0041907-DNA_C01_RX0294 |
Sample type |
genomic |
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Source name |
Blood
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Organism |
Homo sapiens |
Characteristics |
qc status: Passed QC cell type: Blood disease status: Unaffected
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
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Label |
C-Bio and A-DNP
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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.
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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.
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Scan protocol |
The beadchips were scanned on the Illumina BeadArray Reader using default settings.
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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.
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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
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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 |
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