|
| Status |
Public on Sep 30, 2015 |
| Title |
Holstein breed - Cow No.4 |
| Sample type |
genomic |
| |
|
| Source name |
Bovine blood
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
gender: Female
tissue: blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from blood using the Qiagen DNA Blood Mini Kit. 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 Affymetrix® GeneChip® Command Console® Software (AGCC)
|
| Description |
Hybridized to 648K
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Power Tools APT and PennCNV algorithm.
Primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; LogR Ratio (LRR); B-allele Frequency (BAF).
|
| |
|
| Submission date |
Feb 10, 2014 |
| Last update date |
Sep 30, 2015 |
| Contact name |
RICARDO SALOMON |
| E-mail(s) |
ricardo.salomon@uabc.edu.mx
|
| Organization name |
Autonomous University of Baja California
|
| Department |
Engineering Institute
|
| Lab |
Laboratory of Bioinformatics
|
| Street address |
De la Normal street S/N and Blvd. Benito Juárez Col. Insurgentes Este
|
| City |
Mexicali |
| State/province |
Baja California |
| ZIP/Postal code |
21100 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL18258 |
| Series (1) |
| GSE54813 |
Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays |
|
