|
| Status |
Public on Feb 16, 2019 |
| Title |
semen-BTHO-27 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Sample(semen-BTHO-27)
|
| Organism |
Bos taurus |
| Characteristics |
tissue: semen
gender: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from semen or blood using a Qiagen DNEasy tissue and blood kit (QIAGEN, Valencia, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by the third party provider, Nimblegen
|
| |
|
| Channel 2 |
| Source name |
Reference (L1 Dominette whole blood DNA extract)
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Blood
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from semen or blood using a Qiagen DNEasy tissue and blood kit (QIAGEN, Valencia, CA, USA).
|
| 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 pair file coordinates for probe locations. The initial data analysis (normalization and segmentation) was performed on NimbleScan v2.6 software with segMNT algorithm. log2-transformed (test/control) ratios.
|
| Data processing |
Processed data files are pair file coordinates for probe locations. The initial data analysis (normalization and segmentation) was performed on NimbleScan v2.6 software with segMNT algorithm.
|
| |
|
| Submission date |
Nov 13, 2018 |
| Last update date |
Feb 16, 2019 |
| Contact name |
George E Liu |
| E-mail(s) |
George.Liu@ars.usda.gov
|
| Phone |
13015049843
|
| Organization name |
USDA
|
| Street address |
10300 Baltimore Avenue
|
| City |
Beltsville |
| ZIP/Postal code |
207705 |
| Country |
USA |
| |
|
| Platform ID |
GPL11314 |
| Series (1) |
| GSE122478 |
Genome-Wide Detection of CNVs and Their Association with Complex Traits in Holsteins |
|
