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| Status |
Public on Dec 31, 2023 |
| Title |
Wildtype-comb chicken 3 |
| Sample type |
genomic |
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| Source name |
120-d chicken, blood
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| Organism |
Gallus gallus |
| Characteristics |
phenotype: Wildtype-comb
Sex: Female
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), following the manufacturer’s instructions. We use Nano Drop (Cat#ND-2000, Thermo Fisher, Waltham, MA, US) and run a 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.
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| Label |
biotin
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| Label protocol |
Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the fragment DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Axiom array kit and reagent kit bundle, (Cat#901835, Affymetrix, Santa Clara, CA,US)followed the manufacturer’s instruction Affymetrix Axiom™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US) to obtain biotin labeled DNA.
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| Hybridization protocol |
Prepare hybridization buffers and perform array hybridization at 49℃ in GeneTitan .After 23.5 hours hybridization, arrays were washed in GeneTitanaccording to Affymetrix Axiom™ Assay User Manual.
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| Scan protocol |
GeneTitan™ Multi-Channel (MC) system was used to scan.
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| Description |
Geno-wide genotyping
F01-3-3
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| Data processing |
Arrays were scanned by GeneTitan and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data passed quality control were further analyzed by Affymetrix® Axiom Analysis Suite (Affymetrix, Santa Clara, CA, US).
36 chickens were genome-wide genotyped in 559,898 position using Affymatrix 600K Axiom® Genome-Wide Chicken Genotyping Array, along with its signal strength given.
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| Submission date |
Feb 26, 2020 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Wei Luo |
| E-mail(s) |
799166371@qq.com
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| Phone |
0086+13926427090
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| Organization name |
South China Agricultural University
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| Department |
The College of Animal Science
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| Lab |
Animal genetics and reproduction
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| Street address |
Wushan Road
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510642 |
| Country |
China |
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| Platform ID |
GPL23815 |
| Series (1) |
| GSE145948 |
Genome-wide association analysis and genome resequencing reveal a genomic duplication possibly concerning a novel chicken comb morphology |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM4340055_F01-3-3.CEL.gz |
11.5 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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