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Sample GSM932172 Query DataSets for GSM932172
Status Public on Jul 03, 2012
Title BMD DNA 381
Sample type genomic
 
Source name whole blood, control
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: unaffected
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 381
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 0.9946215 0.5681474 1 0.2630475
5137 BB 0.7865571 0.9783182 1.012622 0.9948608 -0.1074172
18822 BB 0.9032437 0.9958617 0.844884 1 0.04008133
10277 BB 0.886975 0.9936684 0.9604191 0.9987724 -0.07005754
11788 AA 0.8554997 0.07745264 0.3596968 0.0108336 -0.09986497
14336 BB 0.9487119 0.9677688 0.954808 0.9949678 -0.0339184
7254 BB 0.8376397 0.9852893 0.6916405 0.9985098 0.04401404
9351 NC 0 0.9898615 1.209205 1 -0.07388316
8523 BB 0.8726395 0.9806355 0.7329379 1 -0.1892452
5138 AA 0.9007716 0.01473967 1.036162 0 0.02213252
5140 NC 0 0.006528784 1.072314 0 0.1863919
20166 AA 0.8783491 0.0751498 0.6125456 0.002839926 -0.1681717
5141 NC 0 0.001515799 1.057124 0.000482321 -0.06278632
5142 BB 0.7810274 0.9823101 1.033417 1 -0.1568566
7716 AA 0.8139011 0.05281527 0.8857684 0.00616892 -0.07411893
5143 NC 0 0.990019 1.208913 0.9962252 -0.1115128
5144 AA 0.8749191 0.01524348 0.653468 0 -0.09339389
5145 AA 0.9500132 0.01687444 0.9410387 0.003973881 0.1254352
5146 NC 0 0.980513 1.042127 0.9997153 -0.1156086
5147 NC 0 0.01765505 1.112174 0.005467106 0.02066006

Total number of rows: 22362

Table truncated, full table size 1210 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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