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Sample GSM932190 Query DataSets for GSM932190
Status Public on Jul 03, 2012
Title BMD DNA 399
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 399
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 AB 0.5149627 0.4562562 0.5478885 0.4974956 -0.06637981
5137 BB 0.7865571 0.982193 1.04928 0.999276 -0.05247526
18822 AB 0.9032437 0.5691518 1.133236 0.4698894 0.3399938
10277 AB 0.886975 0.5871611 1.199243 0.4772027 0.03812113
11788 AB 0.8554801 0.7525757 0.6115531 0.5857615 0.2185852
14336 AB 0.9487119 0.5118984 1.44518 0.4986513 0.1502245
7254 AB 0.8376397 0.7066342 0.7972268 0.48914 0.4454679
9351 NC 0 0.9865913 1.390232 0.9964547 0.1273837
8523 AB 0.8726395 0.5154123 1.31429 0.4950989 0.3379001
5138 BB 0.9007716 0.9893327 1.093228 0.9939968 0.2082337
5140 NC 0 0.01188069 1.155029 0.000288067 0.2935936
20166 AA 0.8783491 0.0656271 0.9260279 0 0.428385
5141 NC 0 0.00225053 1.334879 0.001284796 0.2737779
5142 AA 0.7810274 0.005431444 0.8567222 0 0.1753826
7716 AB 0.8139011 0.7015126 1.143115 0.4996259 -0.03320989
5143 NC 0 0.9914496 1.434198 0.997878 0.1350206
5144 AB 0.8749191 0.6287892 0.9223274 0.4990722 0.09549842
5145 AA 0.9500132 0.01197234 0.9326039 0 0.1174977
5146 NC 0 0.9656841 1.104873 0.9821287 -0.03125923
5147 NC 0 0.01308953 1.217781 0.000388677 0.1515317

Total number of rows: 22362

Table truncated, full table size 1222 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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