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Sample GSM932277 Query DataSets for GSM932277
Status Public on Jul 03, 2012
Title BMD DNA 486
Sample type genomic
 
Source name whole blood, case
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: histiocytic sarcoma (HS)
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 486
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 0.9892803 0.4758157 0.9973344 0.004109306
5137 BB 0.7865571 0.9813911 1.071664 0.9983622 -0.02277616
18822 AB 0.9032437 0.5898981 0.9517361 0.4870444 0.07885526
10277 AB 0.886975 0.5862743 1.224934 0.4764601 0.06908622
11788 BB 0.8554997 0.9725722 0.6244082 0.9952214 0.1144017
14336 AA 0.9487119 0.01018335 1.225496 0 0.1030507
7254 AA 0.8376397 0.05230878 0.4886877 0 0.2752905
9351 NC 0 0.9875626 1.297185 0.9975854 0.02744172
8523 AA 0.8726395 0.0175785 0.9390735 0 -0.06796093
5138 BB 0.9007716 0.9989395 1.064669 1 0.1792431
5140 NC 0 0.008726672 1.086491 0 0.2053402
20166 AA 0.8783491 0.06942213 0.7510916 0 0.1261914
5141 NC 0 0.000365753 0.9921169 0 -0.1543489
5142 AA 0.7810274 0.003658982 0.7409645 0 -0.03197512
7716 BB 0.8139011 0.9865869 1.112025 0.9958113 -0.018774
5143 NC 0 0.9936467 1.359162 1 0.05749391
5144 BB 0.8749191 0.9794096 0.7836 0.9887286 -0.06623949
5145 AA 0.9500132 0.01020981 0.90178 0 0.07082948
5146 NC 0 0.9756594 1.260788 0.9939591 0.1591858
5147 NC 0 0.01440712 1.102248 0.001854288 0.007725675

Total number of rows: 22362

Table truncated, full table size 1200 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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