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Sample GSM1413589 Query DataSets for GSM1413589
Status Public on May 20, 2015
Title Fat line chicken 43
Sample type genomic
 
Source name chicken in the fat line
Organism Gallus gallus
Characteristics tissue: blood
gender: Male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA samples were extracted from the blood using the standard phenol/chloroform method
Label biotin
Label protocol DNA sample quality was determined by spectrophotometry and agarose gel electrophoresis.
 
Hybridization protocol DNA samples were hybridized onto the Illumina chicken 60k SNPchip containing 57,636 SNPs.
Scan protocol Genotyping data were generated using BeadStudio (Version 3.2.2) and after quality control procedures, a total of 475 birds and 48,034 SNPs on 28 autosomes and the Z sex chromosome were kept for CNV detection.
Description Genomic DNA extracted from blood was genotyped using chicken 60k SNP chip.
Data processing Genomic DNA extracted from the blood was genotyped using the Illumina chicken 60k SNPchip and PennCNV software was used to identify chicken CNVs.
 
Submission date Jun 16, 2014
Last update date May 20, 2015
Contact name Hui Zhang
E-mail(s) 8294zhanghui@gmail.com
Organization name Northeast Agricultural University
Department College of Animal Science and Technology
Street address Mucai street No. 59
City Harbin
State/province Heilongjiang
ZIP/Postal code 150030
Country China
 
Platform ID GPL18807
Series (1)
GSE58551 Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or NC (no call)
GC_SCORE
Theta
R
B_Allele_Freq
Log_R_Ratio

Data table
ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
GGaluGA001820 AA 0.6391591 0.03537162 1.415523 0.000937773 -0.07750344
Gga_rs16686671 BB 0.9056984 0.9693103 0.8567255 1 -0.04196707
GGaluGA001841 AA 0.8607578 0.05815277 0.5650173 0 -0.1891596
Gga_rs15995401 BB 0.6688453 0.9546114 0.774365 1 0.2427211
Gga_rs15995393 AA 0.6886696 0.04236762 1.393348 0 0.05248868
GGaluGA001890 AA 0.8646739 0.01387636 1.29279 0.001800709 -0.02378125
GGaluGA001902 AA 0.7714815 0.1111745 0.3561342 0.009158772 -0.08344457
Gga_rs14688751 BB 0.9282166 0.9829493 1.147154 1 0.009169472
GGaluGA001921 BB 0.7876064 0.9726396 0.7328469 0.9926996 -0.192271
GGaluGA001945 BB 0.832108 0.9508511 0.7281504 0.9930559 -0.02727607
GGaluGA001950 BB 0.6872525 0.9490764 1.348435 0.9934219 -0.0868267
Gga_rs16686356 BB 0.7813052 0.9814869 1.022071 1 0.02532166
Gga_rs14688655 BB 0.5618541 0.8619496 0.7410623 0.9118302 -0.1838223
GGaluGA002014 BB 0.732255 0.8935937 1.135657 0.9654154 -0.1859439
Gga_rs15994854 BB 0.8388187 0.9800209 0.699778 1 -0.03339481
Gga_rs13814482 BB 0.6955354 0.9566783 0.7267445 1 -0.02823789
GGaluGA002069 AB 0.7378266 0.4759288 1.731048 0.5486422 0.005912091
GGaluGA002079 AB 0.7862706 0.6671755 0.6065367 0.4879149 -0.1990784
Gga_rs14096805 BB 0.6736602 0.9802881 1.250897 0.9988045 -0.07342257
Gga_rs16057006 BB 0.8172503 0.9663953 0.9871464 0.9960476 0.03901426

Total number of rows: 48034

Table truncated, full table size 3070 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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