|
| Status |
Public on May 15, 2013 |
| Title |
W1_Daweizi pig |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
[test] ear tissue
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Daweizi
gender: female
|
| 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.
|
| |
|
| Channel 2 |
| Source name |
[reference] ear tissue
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Duroc
gender: female
|
| 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.
|
| |
|
| |
| Hybridization protocol |
Standard NimbleGen protocol.
|
| Scan protocol |
Standard NimbleGen protocol.
|
| Data processing |
Spatial correction and Lowess data normalization, segmentation were performed using the DEVA 1.2 software (Roche-NimbleGen).
Two criteria, i.e., mean log2 ratio ≥ |0.5| and at least 5 consecutive probes0.5 log2 shift and 5 neighboring probes, were used to filter CNVs.
|
| |
|
| Submission date |
May 11, 2013 |
| Last update date |
May 15, 2013 |
| 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 |
GPL17150 |
| Series (1) |
| GSE46847 |
CGH analyses for the Chinese indigenous pig breeds and commercial pig breeds |
|
