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Status |
Public on Dec 31, 2023 |
Title |
Wildtype-comb chicken 13 |
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 F11-3-13
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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 |
GSM4340065_F11-3-13.CEL.gz |
11.5 Mb |
(ftp)(http) |
CEL |
Processed data are available on Series record |
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