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Sample GSM932138 Query DataSets for GSM932138
Status Public on Jul 03, 2012
Title BMD DNA 347
Sample type genomic
 
Source name whole blood, case
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: histiocytic sarcoma (HS)
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 347
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 0.9683244 0.1835467 0.9777305 -1.382152
5137 BB 0.7865571 0.9713197 0.7181872 0.9868866 -0.6096297
18822 BB 0.9032437 0.9980314 0.4703795 1 -0.8040292
10277 BB 0.886975 0.9972106 1.009834 1 0.004589158
11788 BB 0.8554997 0.9436357 0.3185436 0.9413645 -0.8396428
14336 AA 0.9487119 0.03121344 0.7519335 0.01905045 -0.6101589
7254 NC 0 0.2739286 0.1302294 0.1560806 -1.837163
9351 NC 0 0.9941984 0.6830769 1 -0.8978224
8523 AA 0.6495698 0.03261677 0.3330051 0.01146859 -1.566109
5138 BB 0.8012702 0.9865013 0.3780609 0.9907792 -1.32637
5140 NC 0 0.03388233 0.3376755 0.02468511 -1.480626
20166 AA 0.8708363 0.1345756 0.2406977 0.06572124 -1.517751
5141 NC 0 0.005032172 1.01497 0.004322912 -0.1214934
5142 AA 0.7033553 0.01772099 0.2261201 0.005905179 -1.760594
7716 BB 0.8139011 0.9841466 1.673134 0.9915597 0.5701143
5143 NC 0 0.9932708 1.397511 0.999982 0.09763678
5144 BB 0.8749191 0.9853698 1.02377 0.9970636 0.3207577
5145 AA 0.9500132 0.02399581 0.5155994 0.01120532 -0.7498759
5146 NC 0 0.9813095 0.9528514 1 -0.2448167
5147 NC 0 0.02620975 1.235367 0.01498289 0.1722171

Total number of rows: 22362

Table truncated, full table size 1218 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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