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Sample GSM932148 Query DataSets for GSM932148
Status Public on Jul 03, 2012
Title BMD DNA 357
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 357
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 0.9967247 0.5620541 1 0.2487044
5137 BB 0.7865571 0.9778602 1.119662 0.994339 0.03712017
18822 BB 0.9032437 0.9925299 0.87579 0.9972365 0.09065814
10277 BB 0.886975 0.9960023 1.11217 1 0.1430755
11788 AB 0.8554997 0.7070606 0.5071892 0.5010483 -0.02197548
14336 AB 0.9487119 0.5172642 1.285084 0.5043713 -0.0164603
7254 AB 0.8376397 0.7222164 0.5843487 0.5027757 -0.01342326
9351 NC 0 0.9914336 1.273234 1 0.000555807
8523 AB 0.8726395 0.5858018 1.024899 0.5713843 0.01931153
5138 AB 0.9007716 0.5733564 1.192624 0.5212898 -0.01695695
5140 NC 0 0.007730372 1.051389 0 0.1579602
20166 AA 0.8783491 0.07530699 0.7094795 0.003006251 0.04376672
5141 NC 0 0.00160248 1.052774 0.000576995 -0.06873558
5142 AB 0.7810274 0.7164051 1.311677 0.4902913 0.1356281
7716 AB 0.8139011 0.6868671 1.21906 0.4884852 0.06620999
5143 NC 0 0.9929645 1.195336 0.9996282 -0.1278076
5144 AB 0.8749191 0.6207687 0.8503798 0.4925305 -0.01804034
5145 AA 0.9500132 0.01523824 0.9131033 0.002312392 0.08364361
5146 NC 0 0.9781328 1.212515 0.9968925 0.1028627
5147 NC 0 0.008245058 1.109144 0 0.01672352

Total number of rows: 22362

Table truncated, full table size 1204 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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