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Sample GSM931868 Query DataSets for GSM931868
Status Public on Jul 03, 2012
Title BMD DNA 150
Sample type genomic
 
Source name whole blood, case
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: histiocytic sarcoma (HS)
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 150
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 0.966219 0.4517801 0.9787021 -0.3429569
5137 BB 0.9613768 0.9884685 1.109424 0.9998783 0.0449551
18822 BB 0.8390679 0.9955017 0.7700304 1 -0.2345744
10277 BB 0.9219033 0.9945681 1.064678 0.9987749 0.0372373
11788 BB 0.848551 0.9794614 0.6150287 1 -0.01972592
14336 AA 0.9792573 0.00344367 1.318758 0 0.0502384
7254 AA 0.8690977 0.0574003 0.2735832 0.02042864 -0.4196364
9351 BB 0.4183931 0.9961797 1.337011 1 0.02528189
8523 AA 0.9256464 0.02094206 1.092063 0.002632922 0.3790595
5138 BB 0.9469349 0.987421 1.026857 0.9949374 0.06732691
5140 AA 0.9542229 0.005037932 0.9656509 0 -0.1458029
20166 AA 0.8710682 0.08685557 0.4487457 0.02777393 -0.3736075
5141 AA 0.8660119 0.002484895 1.115271 0.001947043 0.1049695
5142 AA 0.8143145 0 0.7938966 0 0.05945306
7716 BB 0.8319238 0.9778563 1.099711 0.9900512 0.1524579
5143 BB 0.8746183 0.9959631 1.24587 1 0.03848775
5144 BB 0.8779246 0.9833863 0.8568429 1 0.1297795
5145 AA 0.9658952 0.000552133 0.9511352 0 0.02207346
5146 BB 0.6835921 0.9778329 1.127713 0.9958505 -0.06723471
5147 AA 0.9369485 0.002469966 1.127989 0 0.1099604

Total number of rows: 22362

Table truncated, full table size 1239 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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