|
| Status |
Public on Nov 04, 2015 |
| Title |
semen-BTHO2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
frozen semen stock
|
| Organism |
Bos taurus |
| Characteristics |
gender: male
breed: Holstein
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from semen using a Qiagen DNEasy tissue and blood kit
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by the third party provider, Nimblegen
|
| |
|
| Channel 2 |
| Source name |
L1 Dominette whole blood DNA extract
|
| Organism |
Bos taurus |
| Characteristics |
gender: female
breed: Hereford
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from semen using a Qiagen DNEasy tissue and blood kit
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed by the third party provider, Nimblegen
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed by the third party provider, Nimblegen. Dye swap experiments with the Dominette reference sample were performed to test probe quality
|
| Scan protocol |
Scanning was performed by the third party provider, Nimblegen
|
| Description |
Processed data files are bed file coordinates for probe locations. Columns 4 and 5 indicate the normalized aCGH copy number value and the rCV value, respectively
|
| Data processing |
Data processing was performed similar to Sudmant et al. 2010 's single channel aCGH methodology. In short, single channel array intensities were transformed into integer copy number estimates by using normalized reference signal intensity derived from all tested array samples.
Median reference signal intensity normalized log2 ratios, and rCV estimates of probe sequence copy number fluctuation.
|
| |
|
| Submission date |
Nov 05, 2014 |
| Last update date |
Nov 13, 2018 |
| Contact name |
Derek Martens Bickhart |
| E-mail(s) |
[email protected]
|
| Phone |
301 504 8592
|
| Organization name |
USDA ARS
|
| Department |
BARC
|
| Lab |
AGIL
|
| Street address |
Building 005, Rm 318, BARC-West 10300 Baltimore Ave
|
| City |
Beltsville |
| State/province |
MD |
| ZIP/Postal code |
20705 |
| Country |
USA |
| |
|
| Platform ID |
GPL11314 |
| Series (1) |
| GSE62990 |
Next generation sequencing reveals the diversity and population-genetic properties of cattle CNVs |
|
| Relations |
| Reanalyzed by |
GSE122478 |
