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Sample GSM931961 Query DataSets for GSM931961
Status Public on Jul 03, 2012
Title BMD DNA 243
Sample type genomic
 
Source name whole blood, control
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: unaffected
origin: North America
tissue: whole blood
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from whole blood using either Proteinase K and phenol/chloroform with standard protocols (NIH and University of Utrecht) or the Nucleon BACC Genomic DNA extraction kit (University of Rennes).
Label C-Bio and A-DNP
Label protocol 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.
 
Hybridization protocol Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at 48oC. Single-base extension and allele-specific staining were performed by hand.
Scan protocol After allele-specific staining, BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).
Description 243
Data processing Image data was analyzed using GenomeStudio with GT module (Illumina).
 
Submission date May 16, 2012
Last update date Jul 03, 2012
Contact name Heidi G Parker
E-mail(s) hgparker@mail.nih.gov
Organization name NHGRI
Department CGB
Lab CGS
Street address 50 South Dr. Rm 5347
City Bethesda
State/province MD
ZIP/Postal code 20874
Country USA
 
Platform ID GPL15578
Series (1)
GSE38011 The MTAP-CDKN2A Locus Confers Susceptibility to a Naturally Occurring Canine Cancer

Data table header descriptions
ID_REF
VALUE Genotype: AA, AB, BB, 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
11703 BB 0.9737642 0.9567582 0.6244628 0.9694075 0.1187674
5137 BB 0.9613768 0.9891267 1.063958 1 -0.01482326
18822 AA 0.8390679 0 0.8926518 0 0.01438001
10277 AA 0.9219033 0.01211363 1.249061 0 0.2857346
11788 BB 0.848551 0.9646795 0.5173692 0.9835424 -0.257012
14336 AA 0.9792573 0.004749031 1.267953 0.001069981 -0.005999912
7254 AA 0.8690977 0.05591155 0.3435775 0.01939174 -0.08951136
9351 BB 0.4183931 0.991685 1.385782 0.9983202 0.07697053
8523 AA 0.9256464 0.02287301 0.8984386 0.004381821 0.09673467
5138 BB 0.9469349 0.9803329 1.057975 0.9867123 0.1047071
5140 AA 0.9542229 0.005863086 1.176461 0.000456427 0.1387791
20166 BB 0.8710682 0.979625 0.6597469 1 0.1928835
5141 AA 0.8660119 0.003958947 1.156592 0.003517122 0.1555248
5142 AA 0.8143145 0.000254669 0.7954993 0 0.06204703
7716 BB 0.8319238 0.979368 0.9356116 0.9925986 -0.08036625
5143 BB 0.8746183 0.9855194 1.207676 0.992981 -0.0196201
5144 BB 0.8779246 0.9896585 0.7233296 1 -0.1142717
5145 AA 0.9658952 0.006701722 0.8320916 0.003443345 -0.1775023
5146 BB 0.6835921 0.9764025 1.150579 0.9941593 -0.03979933
5147 AA 0.9369485 0.01001576 1.082406 0.006744477 0.0495753

Total number of rows: 22362

Table truncated, full table size 1254 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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