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Sample GSM1615920 Query DataSets for GSM1615920
Status Public on Feb 21, 2015
Title 4216L204
Sample type genomic
 
Source name gDNA from ear notch
Organism Sus scrofa
Characteristics tissue: ear notch
breed: Landrace
Sex: male
fertility: high
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using a standard Proteinase K and phenol/chlorophorm method.
Label biotin
Label protocol The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada
 
Hybridization protocol The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada
Scan protocol The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada
Data processing This work analysed DNA copy number variations only. The starting points were the GenomeStudio project files (.bsc) provided by DNAL Landmarks. The LogR data was exported from GenomeStudio using the GoldenHelix SVS exporter. Copy number analysis was done in SNP and Variation Suite ver. 7.7.8. (SVS, GoldenHelix Inc.)
 
Submission date Feb 20, 2015
Last update date Feb 21, 2015
Contact name Tamas Revay
E-mail(s) trevay@uoguelph.ca
Phone 519-824-4120
Organization name University of Guelph
Department Biomedical Sci
Lab RHB
Street address 50 Stone Rd E
City Guelph
State/province ON
ZIP/Postal code N1G2W1
Country Canada
 
Platform ID GPL11379
Series (1)
GSE66170 Using the Porcine SNP60k array to discover copy number variations in high and low fertility boars

Data table header descriptions
ID_REF
VALUE The illumina defined cluster positions were applied to all samples and LogR values were calculated in GenomeStudio (Illumina).
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
ALGA0000009 BB 0.8486087 0.9831924 1.23157 0.9963461 0.03658482
ALGA0000014 BB 0.8145218 0.9805427 0.6912791 1 0.009109594
ALGA0000021 AA 0.9480368 0.02449183 1.193033 0.000684799 0.06084971
ALGA0000022 AA 0.8682662 0.03179589 0.974226 0.005952205 -0.380865
ALGA0000046 BB 0.916555 0.989223 1.167051 1 -0.1418443
ALGA0000047 BB 0.9032862 0.9473752 0.5222259 0.9814095 0.03103038
ALGA0000087 NC 0 0.9713174 0.9677039 0.9838746 -1.471381
ALGA0000112 BB 0.468857 0.9243383 0.88119 1 0.1087385
ALGA0000120 AA 0.8944198 0.04535851 1.256317 0.06174385 -0.03102734
ALGA0000131 AA 0.9518364 0.02031369 1.114043 0 0.1588666
ALGA0000133 BB 0.8528799 0.9844002 1.511144 1 0.04485516
ALGA0000134 BB 0.8617834 0.990086 1.472064 0.9995764 0.08154549
ALGA0000172 AA 0.9490964 0.006543085 1.37849 0 0.2708639
ALGA0000188 AA 0.840633 0.05428889 1.910582 0 0.6023197
ALGA0000195 AA 0.704823 0.02981965 2.342434 0.009864009 0.2097316
ALGA0000218 AB 0.8448049 0.4435162 1.963794 0.4656949 0.02201913
ALGA0000232 AA 0.9600575 0.02310684 1.125922 0.005913536 -0.04514218
ALGA0000251 BB 0.8726248 0.989637 1.162378 0.9986305 0.02589649
ALGA0000269 BB 0.7406444 0.9513479 1.917806 0.9921018 0.02783574
ALGA0000277 BB 0.8527849 0.9842196 1.348034 1 -0.1111892

Total number of rows: 62163

Table truncated, full table size 3790 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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