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Sample GSM931910 Query DataSets for GSM931910
Status Public on Jul 03, 2012
Title BMD DNA 192
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 192
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 0.9853283 0.6514066 0.9974758 0.1956858
5137 BB 0.9613768 0.9940022 1.040949 1 -0.04197725
18822 AB 0.8390679 0.6216734 1.097282 0.4714646 0.6532661
10277 AB 0.9219033 0.61825 1.345574 0.5163907 0.1118523
11788 AB 0.848551 0.7327334 0.5619698 0.5301971 0.0681181
14336 AB 0.9792573 0.5396422 1.48517 0.4736303 0.4149235
7254 AB 0.8690977 0.7546865 0.5593742 0.5179811 0.04681087
9351 BB 0.4183931 0.9933503 1.401839 1 0.09359126
8523 AB 0.9256464 0.5854171 1.072629 0.5184833 0.159268
5138 AB 0.9469349 0.5623353 1.220986 0.5016675 0.0103074
5140 AA 0.9542229 0.005727755 1.022819 0.000334446 -0.06307455
20166 AB 0.8710682 0.6084601 0.6893873 0.528123 0.1680804
5141 AA 0.8660119 0.001156373 1.040328 0.000531975 0.006356941
5142 AB 0.8143145 0.7186678 1.259343 0.4942085 0.03143748
7716 AB 0.8319238 0.6955796 1.038256 0.5143811 0.01124423
5143 BB 0.8746183 0.9928168 1.132916 1 -0.1026104
5144 AB 0.8779246 0.6816215 0.793196 0.5246317 0.002809609
5145 AA 0.9658952 0.006212358 0.9132839 0.002916426 -0.04265163
5146 BB 0.6835921 0.9842606 1.13079 1 -0.0564319
5147 AA 0.9369485 0 1.026743 0 -0.025432

Total number of rows: 22362

Table truncated, full table size 1203 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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