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Sample GSM931914 Query DataSets for GSM931914
Status Public on Jul 03, 2012
Title BMD DNA 196
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 196
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 0.9843046 0.5626711 0.9964701 -0.01615639
5137 BB 0.9613768 0.9954519 1.015122 1 -0.07691681
18822 AB 0.8390679 0.5859869 1.165893 0.4443646 0.7188442
10277 AB 0.9219033 0.5978737 1.3052 0.493574 0.06310765
11788 BB 0.848551 1 0.6545391 1 0.05335439
14336 AA 0.9792573 0 1.214565 0 -0.06966288
7254 AA 0.8690977 0.01482861 0.3744996 0 0.07595964
9351 BB 0.4183931 0.9928308 1.320389 0.9996443 0.007233124
8523 AA 0.9256464 0.01868269 0.8743416 0.000586563 0.05916246
5138 BB 0.9469349 0.9977117 0.999567 1 0.03676724
5140 AA 0.9542229 0 1.045424 0 -0.02947075
20166 AB 0.8710682 0.6290312 0.6261984 0.5545094 0.0341353
5141 AA 0.8660119 0 1.116881 0 0.1103113
5142 AA 0.8143145 0 0.6846307 0 -0.154172
7716 BB 0.8319238 0.991712 0.9691691 1 -0.02692514
5143 BB 0.8746183 0.9941853 1.169211 1 -0.05538439
5144 BB 0.8779246 0.9907504 0.760501 1 -0.04191797
5145 AA 0.9658952 0.000326344 0.9182163 0 -0.02849749
5146 BB 0.6835921 0.9884367 1.140362 1 -0.03978952
5147 AA 0.9369485 0.001167976 0.9346439 0 -0.1611534

Total number of rows: 22362

Table truncated, full table size 1158 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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