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Sample GSM932268 Query DataSets for GSM932268
Status Public on Jul 03, 2012
Title BMD DNA 477
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 477
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 AB 0.5149627 0.4506211 0.5624912 0.4873532 -0.0145116
5137 BB 0.7865571 0.9791526 1.083688 0.9958116 -0.008781218
18822 BB 0.9032437 0.9944547 0.9057306 0.9997099 0.13988
10277 BB 0.886975 0.9945517 1.04885 0.999934 0.05757884
11788 AB 0.8554997 0.6931529 0.5919791 0.4896229 0.2091253
14336 AB 0.9487119 0.5019854 1.405302 0.4887607 0.1133893
7254 AB 0.8376397 0.7086743 0.700393 0.4907102 0.2572475
9351 NC 0 0.9933641 1.261423 1 -0.0128902
8523 AB 0.8726395 0.4935707 1.237937 0.4732195 0.2549366
5138 AA 0.9007716 0.01816592 1.100328 0 0.1070401
5140 NC 0 0.009412383 0.9655452 0 0.03507999
20166 AB 0.8783491 0.532394 0.7850626 0.4866722 0.1746189
5141 NC 0 0.000256312 1.034535 0 -0.09394827
5142 AB 0.7810274 0.7323622 1.343195 0.5039016 0.1600304
7716 AB 0.8139011 0.6901114 1.076591 0.4909531 -0.1145579
5143 NC 0 0.9938323 1.24252 1 -0.07195377
5144 AA 0.8749191 0.01288394 0.7346218 0 0.07681344
5145 AA 0.9500132 0.0146563 0.9088892 0.001721451 0.07756946
5146 NC 0 0.9827387 1.191533 1 0.07767858
5147 NC 0 0.01565813 1.127005 0.003245846 0.03977093

Total number of rows: 22362

Table truncated, full table size 1215 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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