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Sample GSM931951 Query DataSets for GSM931951
Status Public on Jul 03, 2012
Title BMD DNA 233
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 233
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 0.9796389 0.4835438 0.9918863 -0.2374218
5137 BB 0.9613768 0.9849687 1.069731 0.9959712 -0.01074675
18822 AB 0.8390679 0.602414 1.188594 0.4568392 0.7567146
10277 AB 0.9219033 0.5802327 1.28527 0.4786374 0.04874418
11788 AB 0.7811603 0.7732179 0.4781312 0.6093251 -0.2030759
14336 AB 0.9792573 0.5162989 1.469155 0.4530073 0.3903082
7254 AB 0.8690977 0.7542425 0.5512212 0.5170668 0.02607773
9351 BB 0.4183931 0.9871264 1.256691 0.9930521 -0.06410029
8523 AB 0.9256464 0.5641906 0.9548445 0.4946648 -0.01418366
5138 AB 0.9469349 0.5928832 1.408944 0.5371154 0.2368763
5140 AA 0.9542229 0.004973846 1.128276 0 0.07876656
20166 AA 0.8710682 0.07580842 0.6433264 0.01733374 0.14793
5141 AA 0.8660119 0.000914291 1.057308 0.000274122 0.03003149
5142 AB 0.8143145 0.7621422 1.076131 0.5671614 -0.1871275
7716 AB 0.8319238 0.7037898 1.053282 0.5282163 0.03363539
5143 BB 0.8746183 0.9823071 1.218416 0.9898757 -0.01087937
5144 AB 0.8779246 0.6957152 0.7423798 0.5470554 -0.0919847
5145 AA 0.9658952 0.007351047 0.9107354 0.0041425 -0.04791488
5146 BB 0.6835921 0.978485 1.237789 0.9966215 0.06782715
5147 AA 0.9369485 0.02046569 1.085692 0.0188005 0.05274018

Total number of rows: 22362

Table truncated, full table size 1262 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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