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Sample GSM932038 Query DataSets for GSM932038
Status Public on Jul 03, 2012
Title BMD DNA 320
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 320
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 0.9737642 0.9747798 0.5993593 0.9871126 0.06962933
5137 BB 0.9613768 0.9853637 1.110755 0.9964122 0.04389996
18822 AB 0.8390679 0.6251078 0.9672233 0.4740727 0.4733799
10277 AB 0.9219033 0.5924699 1.364871 0.4889986 0.1299974
11788 BB 0.848551 0.9564987 0.5793538 0.9675528 -0.08698002
14336 AA 0.9792573 0.00170597 1.417199 0 0.1535151
7254 AA 0.8690977 0.04819962 0.3197633 0.01402046 -0.1855082
9351 BB 0.4183931 0.9910359 1.33151 0.9975702 0.01933392
8523 AA 0.9256464 0.02850055 0.964946 0.009478809 0.1975492
5138 BB 0.9469349 0.9870026 1.054824 0.9944519 0.1057573
5140 AA 0.9542229 0.007550056 1.104315 0.001976972 0.04686958
20166 AB 0.8710682 0.5928484 0.5944529 0.5080979 -0.04926639
5141 AA 0.8660119 0.00331188 1.056555 0.002827902 0.02586023
5142 AA 0.8143145 0.001801888 0.7399812 0 -0.04424078
7716 BB 0.8319238 0.9778489 0.8805631 0.9900388 -0.1681696
5143 BB 0.8746183 0.9901888 1.240958 0.9974947 0.02548204
5144 BB 0.8779246 0.9829808 0.8097898 1 0.04827506
5145 AA 0.9658952 0.001116558 0.8354253 0 -0.1656794
5146 BB 0.6835921 0.9783284 1.198434 0.9964364 0.02104511
5147 AA 0.9369485 0.00569392 0.9404597 0.001758387 -0.152728

Total number of rows: 22362

Table truncated, full table size 1251 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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