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Sample GSM932229 Query DataSets for GSM932229
Status Public on Jul 03, 2012
Title BMD DNA 438
Sample type genomic
 
Source name whole blood, case
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: histiocytic sarcoma (HS)
origin: France
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 438
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 0.5149627 0.9968882 0.3779488 1 -0.3237195
5137 BB 0.7865571 0.9864009 1.232346 1 0.1834934
18822 AB 0.9032437 0.6518636 0.9504532 0.559491 0.08582547
10277 AB 0.886975 0.6316137 1.096233 0.522651 -0.09379728
11788 BB 0.8554997 0.9907551 0.5991881 1 0.04436869
14336 AA 0.9487119 0.01235108 1.086707 0.000230634 -0.07123196
7254 AA 0.8376397 0.04729262 0.3923188 0 -0.03661187
9351 NC 0 0.9887285 1.211085 0.9989426 -0.07164197
8523 AA 0.8726395 0.01714966 1.070866 0 0.1215766
5138 BB 0.9007716 0.9974663 0.8715257 1 -0.1109617
5140 NC 0 0.009623215 0.8187857 0 -0.2027778
20166 AA 0.8783491 0.07485989 0.651152 0.00253315 -0.07998485
5141 NC 0 0 1.104417 0 0.000354157
5142 AA 0.7810274 0.005455725 0.7928514 0 0.06357741
7716 BB 0.8139011 0.9936821 1.163097 1 0.04739255
5143 NC 0 0.993683 1.320051 1 0.01537078
5144 BB 0.8749191 0.9862787 0.7646078 0.9983346 -0.1001451
5145 AA 0.9500132 0.0116137 0.7901479 0 -0.1212738
5146 NC 0 0.9818736 1.025252 1 -0.1391618
5147 NC 0 0.01305888 1.091525 0.000354588 -0.00637785

Total number of rows: 22362

Table truncated, full table size 1188 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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