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Sample GSM931992 Query DataSets for GSM931992
Status Public on Jul 03, 2012
Title BMD DNA 274
Sample type genomic
 
Source name whole blood, case
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: histiocytic sarcoma (HS)
origin: North America
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 274
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 0.9737642 0.4282269 0.3818371 0.4451256 -0.8328209
5137 BB 0.9613768 0.9835526 1.285859 0.9943902 0.253469
18822 AB 0.821129 0.5657008 1.110858 0.4289595 0.6367673
10277 AB 0.9219033 0.5824518 1.643267 0.4805163 0.4022516
11788 AB 0.7183334 0.6565387 0.5923887 0.4546869 0.2046701
14336 AB 0.9792573 0.5110424 1.54566 0.4483633 0.4615315
7254 AB 0.7634957 0.681027 0.4513397 0.4547784 -0.2097189
9351 BB 0.4183931 0.9897332 1.331128 0.9960647 0.01891976
8523 AB 0.9256464 0.532563 1.195022 0.4660191 0.3204054
5138 BB 0.9469349 0.975134 0.9185372 0.9806795 -0.1033475
5140 AA 0.9542229 0.004277424 0.9624647 0 -0.1502967
20166 AB 0.8710682 0.5493767 0.4422202 0.4648832 -0.4715204
5141 AA 0.8660119 0.003000416 1.075668 0.002496148 0.05213251
5142 AA 0.8143145 0.004763241 0.9312921 0.001406641 0.2838444
7716 BB 0.8319238 0.9559551 1.077635 0.9531451 0.118597
5143 BB 0.8746183 0.9880596 1.272329 0.9954364 0.05881449
5144 BB 0.8779246 0.9754075 0.8781234 0.9920559 0.1647573
5145 AA 0.9658952 0.001556848 0.7735375 0 -0.2771972
5146 BB 0.6835921 0.975989 1.307711 0.9936705 0.144444
5147 AA 0.9369485 0.01773307 1.140843 0.01564789 0.1245419

Total number of rows: 22362

Table truncated, full table size 1258 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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