|
| Status |
Public on May 02, 2016 |
| Title |
nf_1672 |
| Sample type |
genomic |
| |
|
| Source name |
peripheral blood sample
|
| Organism |
Homo sapiens |
| Characteristics |
sample: UAP016127
population: Newfoundland and Labrador
disease status: Healthy
inferred gender: Male
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from peripheral blood. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to customized Axiom array
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
|
| |
|
| Submission date |
May 02, 2016 |
| Last update date |
May 02, 2016 |
| Contact name |
Guangju Zhai |
| E-mail(s) |
guangju.zhai@med.mun.ca
|
| Phone |
1 709 864 6683
|
| Organization name |
Memorial University of Newfoundland
|
| Department |
Genetics, Medicine
|
| Street address |
300 Prince Philip Drive
|
| City |
St. John's |
| State/province |
NL |
| ZIP/Postal code |
A1B 3V6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21802 |
| Series (1) |
| GSE74392 |
Affymetrix SNP array data for Genetic Structure of the Newfoundland Population samples |
|
