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Sample GSM932025 Query DataSets for GSM932025
Status Public on Jul 03, 2012
Title BMD DNA 307
Sample type genomic
 
Source name whole blood, control
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: unaffected
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 307
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 0.9641169 0.5817904 0.9766369 0.02074915
5137 BB 0.9613768 0.994424 1.072045 1 0.000868433
18822 AB 0.8349653 0.5728241 0.9836738 0.4343689 0.4656575
10277 AB 0.9219033 0.6107767 1.353384 0.5068111 0.1154313
11788 BB 0.848551 0.9529132 0.5209622 0.9605449 -0.2372638
14336 AA 0.9792573 0.007624809 1.380141 0.003610634 0.1172844
7254 AA 0.8690977 0.06210432 0.3537791 0.02370494 -0.05339925
9351 BB 0.4183931 0.9920304 1.262586 0.9987195 -0.05734774
8523 AA 0.9256464 0.02129028 0.9826413 0.002948308 0.2266029
5138 BB 0.9469349 0.9812302 1.001705 0.9877536 0.02657849
5140 AA 0.9542229 0.01022275 1.018314 0.004385997 -0.07106249
20166 AA 0.8710682 0.0656343 0.5841018 0.007718603 0.0103369
5141 AA 0.8660119 0 1.05341 0 0.02590342
5142 AB 0.8143145 0.7509096 1.223091 0.5456591 -0.007161323
7716 AB 0.8319238 0.6617362 0.9928069 0.4807386 -0.04187437
5143 BB 0.8746183 0.9908037 1.182969 0.998089 -0.04278451
5144 AB 0.8779246 0.6781307 0.663173 0.5190778 -0.2556622
5145 AA 0.9658952 0.004064548 0.8960848 0.000603789 -0.06775366
5146 BB 0.6835921 0.9764887 1.258458 0.9942613 0.08958954
5147 AA 0.9369485 0.00955468 1.041481 0.006212527 -0.005976284

Total number of rows: 22362

Table truncated, full table size 1253 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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