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Sample GSM932330 Query DataSets for GSM932330
Status Public on Jul 03, 2012
Title BMD DNA 539
Sample type genomic
 
Source name whole blood, case
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: histiocytic sarcoma (HS)
origin: The Netherlands
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 539
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 0.9977566 0.5874768 1 0.3131228
5137 BB 0.7865571 0.9782919 1.109427 0.994831 0.02427639
18822 AB 0.9032437 0.6809283 0.8486913 0.5968382 -0.06746653
10277 AB 0.886975 0.630097 1.323065 0.5206563 0.1766975
11788 BB 0.8554997 0.9651479 0.5692623 0.9814031 -0.01466328
14336 AA 0.9487119 0.01071399 1.185277 0 0.05469428
7254 AA 0.8376397 0.06435907 0.433292 0 0.08981463
9351 NC 0 0.9842643 1.330832 0.993746 0.06438639
8523 AA 0.8726395 0.02647025 1.012028 0.005311446 0.03852685
5138 BB 0.9007716 0.9902115 1.121784 0.9949954 0.2462724
5140 NC 0 0.01206179 0.9748932 0.000488883 0.04898034
20166 AA 0.8783491 0.07575536 0.7092242 0.003480691 0.04323265
5141 NC 0 0.001542431 1.087016 0.000511409 -0.0225578
5142 AA 0.7810274 0.007518451 0.816597 0 0.1037514
7716 BB 0.8139011 0.985571 1.091584 0.9940414 -0.04573723
5143 NC 0 0.9892296 1.183894 0.9953133 -0.1416838
5144 BB 0.8749191 0.9853477 0.8186701 0.9970327 -0.001785123
5145 AA 0.9500132 0.01063237 0.9671718 0 0.1713894
5146 NC 0 0.9804831 1.147903 0.9996798 0.02386083
5147 NC 0 0.02454158 1.119728 0.01312731 0.03042593

Total number of rows: 22362

Table truncated, full table size 1217 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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