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Sample GSM932290 Query DataSets for GSM932290
Status Public on Jul 03, 2012
Title BMD DNA 499
Sample type genomic
 
Source name whole blood, control
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: unaffected
origin: France
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 499
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 0.5149627 0.9891406 0.5564613 0.9972037 0.2299074
5137 BB 0.7865571 0.9867051 1.190215 1 0.133596
18822 AB 0.9032437 0.6088985 0.990767 0.5042821 0.1309776
10277 AB 0.886975 0.5981513 1.245994 0.4864044 0.08851878
11788 AB 0.8554997 0.7016643 0.4418849 0.4962416 -0.2176732
14336 AB 0.9487119 0.504723 1.218506 0.491492 -0.09335406
7254 AB 0.8376397 0.7309131 0.6100915 0.5191638 0.04223414
9351 NC 0 0.989124 1.278086 0.9994029 0.006042793
8523 AB 0.8726395 0.5081302 1.141495 0.4878042 0.1356677
5138 AB 0.9007716 0.5687699 1.228917 0.5160778 0.02286185
5140 NC 0 0.0102729 1.009593 0 0.09943798
20166 AA 0.8783491 0.06406193 0.6345867 0 -0.1168011
5141 NC 0 0.001541909 1.011589 0.000510839 -0.1263075
5142 AB 0.7810274 0.7009353 1.194613 0.4795663 0.01225052
7716 AB 0.8139011 0.7043631 1.063954 0.5041094 -0.1365242
5143 NC 0 0.9938591 1.328652 1 0.02473956
5144 AB 0.8749191 0.6436558 0.8365328 0.5191991 -0.04303871
5145 AA 0.9500132 0.009344093 0.9558946 0 0.1558007
5146 NC 0 0.9731897 1.246273 0.9910301 0.1424798
5147 NC 0 0.01615435 1.075991 0.003797815 -0.02705691

Total number of rows: 22362

Table truncated, full table size 1175 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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