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Sample GSM2712552 Query DataSets for GSM2712552
Status Public on Jul 21, 2017
Title Beak deformity bird 5
Sample type genomic
 
Source name Beak deformity bird blood 5
Organism Gallus gallus
Characteristics breed: Beijing-You
gender: male
tissue: blood
sample_id: 170
Growth protocol All of the animal procedures were conducted in strict accordance with the guidelines proposed by the China Council on Animal Care and the Ministry of Agriculture of the People’s Republic of China. Animal experiments were approved by the Science Research Department of the IAS, CAAS (Beijing, China).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) was isolated from blood samples using the phenol-chloroform method. The purity and concentration of the gDNA samples was measured using a Nanodrop ND-2000 spectrophotometer (Thermo Scientific, USA). The final concentration was adjusted to 50 ng/μL. gDNA samples with an A260/280 ratio of 1.8-2.0 were submitted for genotyping.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to 600K
Data processing gDNA samples were genotyped using 600K Affymetrix Axiom HD genotyping arrays containing 580,954 SNPs based on the Affymetrix GeneChip platform. The genotypes were identified using Affymetrix Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA). The RM test was performed for the single SNP association analysis in ROADTRIPS (Version 1.2). A SRT program (Version 3, https://sourceforge.net/projects/snpratiotest/) was employed for the pathway-based analysis. PennCNV, downloaded from http://penncnv.openbioinformatics.org/en/latest/user-guide/download/, was used to detect CNVs on autosomes.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
 
Submission date Jul 20, 2017
Last update date Jan 23, 2018
Contact name Hao Bai
E-mail(s) bhowen1027@163.com
Organization name Institute of Animal Science, Chinese Academy of Agricultural Sciences
Street address Yuanmingyuan West Road No. 2, Haidian District
City Beijing
ZIP/Postal code 100193
Country China
 
Platform ID GPL23815
Series (1)
GSE101703 Affymetrix SNP array data for beak deformity and normal Beijing-You Chickens

Supplementary file Size Download File type/resource
GSM2712552_170.CEL.gz 11.7 Mb (ftp)(http) CEL
GSM2712552_170.cnv.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data provided as supplementary file

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