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Sample GSM932167 Query DataSets for GSM932167
Status Public on Jul 03, 2012
Title BMD DNA 376
Sample type genomic
 
Source name whole blood, case
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: histiocytic sarcoma (HS)
origin: The Netherlands
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 376
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 0.9987735 0.5543491 1 0.2299728
5137 BB 0.7865571 0.981448 1.055949 0.9984272 -0.044035
18822 AB 0.9032437 0.5766739 0.9827313 0.4761094 0.1310271
10277 AB 0.886975 0.5963331 1.236229 0.4848821 0.07795686
11788 BB 0.8554997 0.977101 0.6529942 1 0.1763468
14336 AA 0.9487119 0.01225484 1.190114 0.000134614 0.05994332
7254 AA 0.8376397 0.06489116 0.4576384 0 0.1681597
9351 NC 0 0.9886116 1.327321 0.9988065 0.0605753
8523 AA 0.8726395 0.0193312 1.050059 0 0.09291364
5138 BB 0.9007716 0.996697 1.007579 1 0.09757809
5140 NC 0 0.01200231 1.060836 0.000422928 0.1708664
20166 AA 0.8783491 0.06358166 0.7435018 0 0.1117339
5141 NC 0 0.004059986 1.098515 0.003261088 -0.007376185
5142 AA 0.7810274 0.01104047 0.7909011 0.001273685 0.05353628
7716 BB 0.8139011 0.9857293 1.090261 0.9943172 -0.04745611
5143 NC 0 0.9964749 1.256408 1 -0.05591768
5144 BB 0.8749191 0.9883348 0.7625965 1 -0.1034983
5145 AA 0.9500132 0.01585671 0.9255273 0.002940424 0.1025041
5146 NC 0 0.9771333 1.187012 0.995707 0.07219432
5147 NC 0 0.01721437 0.9913424 0.004976915 -0.1452674

Total number of rows: 22362

Table truncated, full table size 1182 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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