|
| Status |
Public on Jun 29, 2015 |
| Title |
R2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ear tissue
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Rongchang pig
gender: male
tissue: ear
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA for each individuals was extracted from the ear tissue using Qiagen DNeasy Tissue kit (Qiagen, Germany).
|
| Label |
Cy5
|
| Label protocol |
Test DNA and reference DNA samples were independently labeled with either Cy3 or Cy5 dyes.
|
| |
|
| Channel 2 |
| Source name |
reference sample
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Duroc
gender: female
tissue: ear
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA for each individuals was extracted from the ear tissue using Qiagen DNeasy Tissue kit (Qiagen, Germany).
|
| Label |
Cy3
|
| Label protocol |
Test DNA and reference DNA samples were independently labeled with either Cy3 or Cy5 dyes.
|
| |
|
| |
| Hybridization protocol |
according to the productor's instruction.
|
| Scan protocol |
according to the productor's instruction.
|
| Description |
1M probes in total
|
| Data processing |
Raw data was normalized (algorithm: LOWESS) using Feature Extraction software 10.7 (Agilent technologies). Then Agilent Genomic Workbench Standard Edition 6.5 software (Agilent Technologies) was used to perform the statistical analysis for CNV interval detection.
The Aberration Detection Method 2 algorithm (ADM2), with threshold of 6, bin of 10, and a centralization threshold of 6, was used to identify genomic variation given the log2 ratio of fluorescent signals between test and reference DNA samples. Additonally, we applied a relatively stringent post-analysis filter: 5 probes, 0.5 log ratio, to ignore small, spurious, or low-quality aberrations.
|
| |
|
| Submission date |
Jul 29, 2013 |
| Last update date |
Jun 29, 2015 |
| Contact name |
Huimin Kang |
| E-mail(s) |
nongdaxiaokang@126.com
|
| Phone |
18810882762
|
| Organization name |
China Agriculture University
|
| Street address |
Beijing
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL17469 |
| Series (1) |
| GSE49299 |
CGH analyses for the Chinese indigenous pig breeds and commercial pig breeds [Agilent] |
|
