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Sample GSM931942 Query DataSets for GSM931942
Status Public on Jul 03, 2012
Title BMD DNA 224
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 224
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 0.9685162 0.5509882 0.9809589 -0.05527359
5137 BB 0.9613768 0.993076 1.047566 1 -0.0336703
18822 BB 0.8390679 0.9932113 0.8606123 0.9971656 -0.07174305
10277 BB 0.9219033 0.9940659 1.099826 0.9981312 0.08370961
11788 AB 0.848551 0.7494745 0.5242421 0.5629179 -0.04802182
14336 AB 0.9792573 0.5235344 1.404325 0.4593996 0.3279735
7254 AB 0.8690977 0.75817 0.5789762 0.5251548 0.0929824
9351 BB 0.4183931 0.9931062 1.388739 0.9999627 0.08004555
8523 AB 0.9256464 0.5689029 0.9884375 0.4989329 0.03408488
5138 AB 0.9469349 0.5745564 1.304157 0.5158489 0.1133473
5140 AA 0.9542229 0.005204642 1.149544 0 0.1056253
20166 AA 0.8710682 0.05836767 0.679896 0.000851225 0.2306738
5141 AA 0.8660119 0.000448404 1.038756 0 0.005104328
5142 AB 0.8143145 0.7455254 1.230748 0.5353523 -0.000411421
7716 AB 0.8319238 0.6904119 1.024976 0.5056729 -0.008372039
5143 BB 0.8746183 0.993476 1.170161 1 -0.05511114
5144 AB 0.8779246 0.6863892 0.7878947 0.5322173 -0.006619427
5145 AA 0.9658952 0.004216387 0.8468617 0.000767281 -0.1494273
5146 BB 0.6835921 0.9878303 1.229292 1 0.06789509
5147 AA 0.9369485 0.000168692 1.036687 0 -0.01154615

Total number of rows: 22362

Table truncated, full table size 1197 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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