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| Status |
Public on May 14, 2015 |
| Title |
Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 1) |
| Organism |
Gallus gallus |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.395 to 0.740.
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| Overall design |
The whole blood samples were collected from Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Red Jungle Fowl (RJF), Shouguang (SG), Silkie (SK), Tibetan (TB), Wenchang (WC), and White Plymouth Rock (WR), and genomic DNA was isolated using standard phenol/chloroform extraction methods. Each test sample labeled with Cy3 was mixed with Red Jungle Fowl as reference sample labeled with Cy5. All process and analysis was performed in terms of standard NimbleGen procedure. However, due to some uncontrollable factors, none of results were obtained in three consecutive trials for CS, RIR and WL, so we had to choose a similar Agilent custom-designed 1*1.0 M array.
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| Contributor(s) |
Yi G, Qu L, Liu J, Yan Y, Yang N |
| Citation(s) |
25378104 |
| |
| Submission date |
Jan 15, 2014 |
| Last update date |
May 16, 2015 |
| Contact name |
Guoqiang Yi |
| E-mail(s) |
yiguoqiang20@hotmail.com
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| Phone |
+8662731351
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| Organization name |
Agricultural Genome Institute at Shenzhen
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| Street address |
No 7,Pengfei Road,Dapeng District,Shenzhen
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518120 |
| Country |
China |
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| Platforms (1) |
| GPL18174 |
NimbleGen custom 3*1.4M chicken CGH array |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE54119 |
Validation experiment of copy number variations identified by next-generation sequencing in chickens |
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| Relations |
| BioProject |
PRJNA235206 |
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