NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM931834 Query DataSets for GSM931834
Status Public on Jul 03, 2012
Title BMD DNA 116
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 116
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 0.9789719 0.5448149 0.991231 -0.06567623
5137 BB 0.9613768 0.991654 1.065334 1 -0.0106862
18822 BB 0.8390679 0.9938566 0.8837961 0.9981263 -0.03406491
10277 BB 0.9219033 0.9976221 1.049287 1 0.01857421
11788 BB 0.848551 0.9723089 0.6105085 0.9984544 -0.02449075
14336 AA 0.9792573 0.006343294 1.293595 0.002478458 0.02342219
7254 AA 0.8690977 0.04956691 0.3518524 0.01497276 -0.04889872
9351 BB 0.4183931 0.9949932 1.245193 1 -0.07736044
8523 AA 0.9256464 0.02173341 0.9352494 0.003349663 0.1551146
5138 BB 0.9469349 0.9926316 1.034825 1 0.0826752
5140 AA 0.9542229 0.004537977 1.018362 0 -0.06894603
20166 AA 0.8710682 0.06797481 0.5344229 0.009930528 -0.118301
5141 AA 0.8660119 0.002410104 1.065021 0.001867381 0.03855616
5142 AA 0.8143145 0 0.795051 0 0.0615495
7716 BB 0.8319238 0.9841084 0.994998 1 0.009416504
5143 BB 0.8746183 0.9938045 1.166656 1 -0.05902207
5144 BB 0.8779246 0.9835932 0.8197091 1 0.06587155
5145 AA 0.9658952 0.003712784 0.9310024 0.00022503 -0.01222282
5146 BB 0.6835921 0.9793142 1.195669 0.9976019 0.01876445
5147 AA 0.9369485 0.002439109 0.9790171 0 -0.09438333

Total number of rows: 22362

Table truncated, full table size 1229 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap