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Sample GSM931979 Query DataSets for GSM931979
Status Public on Jul 03, 2012
Title BMD DNA 261
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 261
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 0.9693661 0.5562966 0.9817939 -0.04096574
5137 BB 0.9613768 0.9908844 1.047244 1 -0.03608644
18822 AB 0.8390679 0.6693998 0.7115917 0.5151098 0.03804254
10277 AB 0.9219033 0.6496253 1.170483 0.5566093 -0.06906733
11788 BB 0.848551 0.9825176 0.4689088 1 -0.4135763
14336 AA 0.9792573 0.003254895 1.187023 0 -0.1016574
7254 AA 0.8690977 0.04198563 0.2166085 0.009692474 -0.7412419
9351 BB 0.4183931 0.9960604 1.256141 1 -0.06473119
8523 AA 0.9256464 0.01957433 0.8645591 0.00139414 0.04257863
5138 BB 0.9469349 0.9932358 1.050853 1 0.1053361
5140 AA 0.9542229 0.00589567 0.9632677 0.000485796 -0.1496772
20166 AA 0.8687863 0.1079721 0.4230476 0.04773025 -0.4622815
5141 AA 0.8660119 0.000467464 1.034103 0 -0.001397256
5142 AA 0.8143145 0.001423671 0.6496947 0 -0.2314995
7716 BB 0.8319238 0.9640978 1.00398 0.9668664 0.01816932
5143 BB 0.8746183 0.9932513 1.308507 1 0.1058193
5144 BB 0.8779246 0.9869853 0.7839317 1 0.001664027
5145 AA 0.9658952 0.004279786 0.757518 0.000835544 -0.3103421
5146 BB 0.6835921 0.9783081 1.187687 0.9964124 0.008027621
5147 AA 0.9369485 0.001147952 1.058365 0 0.01819698

Total number of rows: 22362

Table truncated, full table size 1227 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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