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Sample GSM931909 Query DataSets for GSM931909
Status Public on Jul 03, 2012
Title BMD DNA 191
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 191
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 0.9827521 0.5497662 0.9949448 -0.05050234
5137 BB 0.9613768 0.9927707 1.069848 1 -0.00358026
18822 BB 0.8390679 0.9904286 0.8791779 0.9930231 -0.03805071
10277 BB 0.9219033 0.9965793 0.9622492 1 -0.1071534
11788 AB 0.848551 0.7088389 0.5513293 0.4937006 0.06161776
14336 AB 0.9792573 0.5080848 1.565377 0.4457504 0.4786873
7254 AB 0.8690977 0.7597429 0.5583748 0.5283938 0.03912625
9351 BB 0.4183931 0.9932721 1.342453 1 0.03114152
8523 AB 0.9256464 0.5706133 1.086903 0.5006414 0.1709481
5138 AB 0.9469349 0.5797576 1.184957 0.5218844 -0.02153139
5140 AA 0.9542229 0.005347208 0.9414259 0 -0.1825687
20166 AA 0.8710682 0.07077375 0.49957 0.01257569 -0.2160742
5141 AA 0.8660119 0.001527261 1.029685 0.000927025 -0.008965946
5142 AB 0.8143145 0.7381812 1.217493 0.5212935 -0.01910115
7716 AB 0.8319238 0.6907208 1.019678 0.5061935 -0.01578628
5143 BB 0.8746183 0.9938908 1.213917 1 -0.001622607
5144 AB 0.8779246 0.6998245 0.8357465 0.5535932 0.07913496
5145 AA 0.9658952 0 0.8565657 0 -0.1284128
5146 BB 0.6835921 0.9830134 1.159402 1 -0.02171753
5147 AA 0.9369485 0 1.142806 0 0.1290736

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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