|
Status |
Public on Feb 16, 2019 |
Title |
semen-BTHO-11 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Sample(semen-BTHO-11)
|
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 |
|