|
| Status |
Public on Dec 30, 2014 |
| Title |
JN2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
blood from Jinnan 2#
|
| Organism |
Bos taurus |
| Characteristics |
breed: Jinnan
gender: male
tissue: blood
|
| Treatment protocol |
Wizard@ Genomic DNA purification Kit
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Blood DNA was extracted from whole blood anticoagulent 0.5 M EDTA. Samples were stored at -80 ℃until DNA isoaltion.500 ul of whole blood were mixed with lysis buffer (10 mmol/LxTris, 0.1 mol/L EDTA, 0.5% SDS), digested with protease K, then extracted twice times with Tris-saturated phenol, phenol /chloroform, once with chloroform. then separate out DNA using frezon absolute ethyl alcohol , finally wash three times with 70% lcohol
|
| Label |
Cy3
|
| Label protocol |
1 ug of test DNA were labeled with Cy3, and 1 ug of reference DNA were labeled with Cy5, using NimbelGen commercial service
|
| |
|
| Channel 2 |
| Source name |
blood from Angus
|
| Organism |
Bos taurus |
| Characteristics |
breed: Angus
gender: female
tissue: blood
|
| Treatment protocol |
Wizard@ Genomic DNA purification Kit
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Blood DNA was extracted from whole blood anticoagulent 0.5 M EDTA. Samples were stored at -80 ℃until DNA isoaltion.500 ul of whole blood were mixed with lysis buffer (10 mmol/LxTris, 0.1 mol/L EDTA, 0.5% SDS), digested with protease K, then extracted twice times with Tris-saturated phenol, phenol /chloroform, once with chloroform. then separate out DNA using frezon absolute ethyl alcohol , finally wash three times with 70% lcohol
|
| Label |
Cy5
|
| Label protocol |
1 ug of test DNA were labeled with Cy3, and 1 ug of reference DNA were labeled with Cy5, using NimbelGen commercial service
|
| |
|
| |
| Hybridization protocol |
Equal amounts of Cy3 labeled test sample and Cy5 labeled reference sample were mixed and hybridized to tiling array, by NimbleGen commercial service
|
| Scan protocol |
performed by NimbleGen
|
| Description |
Hybridization of test sample and reference sample
|
| Data processing |
NimbleScan2.6 was used to analyze the data with qspline normalization . The high confidence calls are filtered and merged according to the following criteria: we merged overlapping CNV coordinates across hybridizations to form unique CNV regions using the 40% overlapping threshold as previously described. For cattle CNV calling, we tested the false discovery rate (FDR) in the self-self control hybridizations.
We selected a set of conservative calling criteria for the final set of high confidence CNVs, requiring that alternations of *0.5* log2 ratios over *5* neighboring probes (0.5_5), under no false positive was found for self-self control hybridizations
|
| |
|
| Submission date |
May 20, 2013 |
| Last update date |
Dec 30, 2014 |
| Contact name |
Liangzhi Zhang |
| E-mail(s) |
qinten306@163.com
|
| Organization name |
Northwest A&F University
|
| Department |
College of Animal Science and Technology
|
| Lab |
Key Laboratory of Molecular Biology for Agriculture
|
| Street address |
No.22 Xinong Road
|
| City |
Yangling |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
| |
|
| Platform ID |
GPL17177 |
| Series (1) |
| GSE47086 |
Analysis of copy number variations among Chinese cattle breeds |
|
