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Sample GSM932222 Query DataSets for GSM932222
Status Public on Jul 03, 2012
Title BMD DNA 431
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 431
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 0.9974495 0.5554466 1 0.232062
5137 BB 0.7865571 0.9791823 1.0116 0.9958455 -0.1080637
18822 AB 0.9032437 0.594619 1.015055 0.490948 0.1696661
10277 AB 0.886975 0.5978821 1.167376 0.486179 -0.005393021
11788 BB 0.8554997 0.9754739 0.5824273 1 0.0123009
14336 AA 0.9487119 0.01480823 1.034669 0.002682249 -0.143024
7254 AA 0.8376397 0.05250631 0.5181577 0 0.3595731
9351 NC 0 0.9869906 1.394729 0.9969195 0.1320426
8523 AA 0.8726395 0.01970455 0.9673789 0 -0.02546526
5138 BB 0.9007716 0.9962023 0.9866644 1 0.06684218
5140 NC 0 0.008950572 1.025859 0 0.1224964
20166 AA 0.8783491 0.05778356 0.8433949 0 0.2937999
5141 NC 0 0.003025295 1.02575 0.002130997 -0.1062521
5142 AA 0.7810274 0.01398792 0.7959615 0.003317109 0.05932513
7716 BB 0.8139011 0.9863955 1.112791 0.9954779 -0.01781781
5143 NC 0 0.9952561 1.241085 1 -0.07362124
5144 BB 0.8749191 0.9892314 0.6781811 1 -0.2725528
5145 AA 0.9500132 0.01947852 0.9137179 0.00661821 0.08025342
5146 NC 0 0.9840304 1.117202 1 -0.01524944
5147 NC 0 0.01786617 1.092836 0.00570195 -0.004646497

Total number of rows: 22362

Table truncated, full table size 1204 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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