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Sample GSM932307 Query DataSets for GSM932307
Status Public on Jul 03, 2012
Title BMD DNA 516
Sample type genomic
 
Source name whole blood, control
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: unaffected
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 516
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 1 0.533737 1 0.1760156
5137 BB 0.7865571 0.9821837 1.229529 0.9992654 0.176222
18822 AB 0.9032437 0.5954342 0.9824409 0.4916221 0.1221864
10277 AB 0.886975 0.5796372 1.149483 0.4709032 -0.01974013
11788 BB 0.8554997 0.9783217 0.5381433 1 -0.1034425
14336 AA 0.9487119 0.00922326 1.023529 0 -0.1563718
7254 AA 0.8376397 0.0448726 0.481932 0 0.2626021
9351 NC 0 0.9907286 1.30735 1 0.0387034
8523 AA 0.8726395 0.01820989 0.9772584 0 -0.01056209
5138 BB 0.9007716 0.9971918 0.9831263 1 0.06260848
5140 NC 0 0.008400877 1.050293 0 0.1564568
20166 AA 0.8783491 0.05420185 0.7983717 0 0.2147719
5141 NC 0 0 1.20782 0 0.1294746
5142 AA 0.7810274 0.005148998 0.7873456 0 0.05388125
7716 BB 0.8139011 0.9955658 1.147883 1 0.0287638
5143 NC 0 0.9923881 1.332343 0.9989623 0.02874216
5144 BB 0.8749191 0.9904937 0.8074045 1 -0.02065714
5145 AA 0.9500132 0.01080154 0.8737417 0 0.02464925
5146 NC 0 0.9831204 1.124708 1 -0.005589144
5147 NC 0 0.009159526 0.9917468 0 -0.144679

Total number of rows: 22362

Table truncated, full table size 1174 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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