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Sample GSM932218 Query DataSets for GSM932218
Status Public on Jul 03, 2012
Title BMD DNA 427
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 427
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 0.9981933 0.5051911 1 0.09567239
5137 BB 0.7865571 0.9893824 1.016256 1 -0.09183665
18822 AA 0.9032437 0 0.8862106 0 0.2678386
10277 AA 0.886975 0.01384921 0.9939271 0 0.04117147
11788 BB 0.8554997 0.9862931 0.635152 1 0.1310439
14336 AA 0.9487119 0.009536273 1.186223 0 0.05632337
7254 AA 0.8376397 0.04906951 0.5530954 0 0.4571226
9351 NC 0 0.991368 1.283916 1 0.01260902
8523 AA 0.8726395 0.0239701 1.039978 0.002806975 0.07823794
5138 BB 0.9007716 0.9959904 1.081913 1 0.1995924
5140 NC 0 0.009876644 1.067337 0 0.1796806
20166 AA 0.8783491 0.06395244 0.7767507 0 0.174837
5141 NC 0 0 1.192306 0 0.1108236
5142 AA 0.7810274 0.00220098 0.6985559 0 -0.1153029
7716 BB 0.8139011 0.9907362 1.091599 1 -0.04471019
5143 NC 0 0.9937846 1.252608 1 -0.06028789
5144 BB 0.8749191 0.9875236 0.8498914 1 0.05268406
5145 AA 0.9500132 0.0138378 0.9127898 0.000890303 0.08459122
5146 NC 0 0.9830129 1.057542 1 -0.09442511
5147 NC 0 0.01482629 1.079274 0.002320558 -0.0226614

Total number of rows: 22362

Table truncated, full table size 1174 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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