NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM931833 Query DataSets for GSM931833
Status Public on Jul 03, 2012
Title BMD DNA 115
Sample type genomic
 
Source name whole blood, control
Organism Canis lupus familiaris
Characteristics breed: Bernese Mountain Dog (BMD)
phenotype: unaffected
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 115
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 0.9789686 0.5658913 0.9912278 -0.01091932
5137 BB 0.9613768 0.9946727 1.153283 1 0.1064744
18822 AA 0.8390679 0 0.8152644 0 -0.1164495
10277 AA 0.9219033 0.01689799 1.109375 0.001663019 0.1120567
11788 BB 0.848551 0.9775126 0.5456253 1 -0.1908699
14336 AA 0.9792573 0.002947939 1.298468 0 0.02770101
7254 AA 0.8690977 0.05219002 0.2802396 0.01679973 -0.3798073
9351 BB 0.4183931 0.9955099 1.268131 1 -0.05102573
8523 AA 0.9256464 0.02253783 0.8847134 0.004078246 0.07465696
5138 BB 0.9469349 0.9874771 0.9516035 0.9950025 -0.04243113
5140 AA 0.9542229 0.004818811 1.086572 0 0.02448567
20166 AB 0.8710682 0.6519741 0.5502745 0.5839382 -0.1470168
5141 AA 0.8660119 0.001842893 0.9840868 0.001263218 -0.07472505
5142 AB 0.8143145 0.7105729 1.299417 0.4886207 0.08284732
7716 AB 0.8319238 0.7229424 1.018717 0.5604907 -0.01062014
5143 BB 0.8746183 0.9958543 1.277263 1 0.07425176
5144 AB 0.8779246 0.7261179 0.8037889 0.5954271 0.02424104
5145 AA 0.9658952 0.003498809 0.940456 0 0.002584734
5146 BB 0.6835921 0.9767616 1.257116 0.994584 0.08834141
5147 AA 0.9369485 0.008575221 1.089043 0.00508253 0.0585613

Total number of rows: 22362

Table truncated, full table size 1231 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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