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Sample GSM4340059 Query DataSets for GSM4340059
Status Public on Dec 31, 2023
Title Wildtype-comb chicken 7
Sample type genomic
Source name 120-d chicken, blood
Organism Gallus gallus
Characteristics phenotype: Wildtype-comb
Sex: Female
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.
Label biotin
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.
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.
Scan protocol GeneTitan™ Multi-Channel (MC) system was used to scan.
Description Geno-wide genotyping
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.
Submission date Feb 26, 2020
Last update date Dec 31, 2023
Contact name Wei Luo
Phone 0086+13926427090
Organization name South China Agricultural University
Department The College of Animal Science
Lab Animal genetics and reproduction
Street address Wushan Road
City Guangzhou
State/province Guangdong
ZIP/Postal code 510642
Country China
Platform ID GPL23815
Series (1)
GSE145948 Genome-wide association analysis and genome resequencing reveal a genomic duplication possibly concerning a novel chicken comb morphology

Supplementary file Size Download File type/resource
GSM4340059_F05-3-7.CEL.gz 11.4 Mb (ftp)(http) CEL
Processed data are available on Series record

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