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Sample GSM1755109 Query DataSets for GSM1755109
Status Public on Jul 30, 2015
Title AMAL_14509
Sample type genomic
 
Source name whole blood
Organism Canis lupus familiaris
Characteristics origin: North America
breed: Alaskan Malamute (AMAL)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.
Label none
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 at 48oC. Single-base extension and allele-specific staining was 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 none
Data processing Image data was analyzed using GenomeStudio with GT module (Illumina).
 
Submission date Jul 01, 2015
Last update date Jul 31, 2015
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 GPL17481
Series (1)
GSE70454 Comparison against 186 canid whole genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor

Data table header descriptions
ID_REF
VALUE genotypes 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
BICF2G630100019 BB 0.8714491 0.9711404 0.9731351 0.9934368 0.05828527
BICF2G630100032 AA 0.9423809 0.021419 1.01804 0 -0.08214156
BICF2G630100034 BB 0.9264764 0.9756774 1.223415 0.9940587 0.109844
BICF2G630100043 BB 0.8898949 0.9750724 1.193086 1 -0.1476656
BICF2G630100054 BB 0.9355912 0.979847 0.455652 1 0.04352982
BICF2G630100063 BB 0.870317 0.9609875 1.289147 0.9905608 -0.0299251
BICF2G630100075 AA 0.8513578 0.04204463 0.6860862 0 0.09766005
BICF2G63010009 BB 0.8352656 0.9749765 0.7698812 1 -0.3527301
BICF2G630100090 BB 0.9588766 0.9854776 1.065567 0.9937533 0.02326316
BICF2G630100094 AA 0.9062778 0.02659682 1.058715 0.003948404 -0.1698229
BICF2G63010010 AA 0.788362 0.120285 0.5860972 0.02414896 -0.3391763
BICF2G630100114 BB 0.939804 0.9756883 0.8346658 0.9945893 -0.3543997
BICF2G630100129 BB 0.8625047 0.9807538 1.206411 0.9948678 -0.1004318
BICF2G63010014 NC 0 0.311574 0.6743538 0.5768331 -0.1904805
BICF2G630100157 BB 0.9132537 0.9783646 1.1695 0.9989009 0.05456987
BICF2G63010018 NC 0 0.9751901 0.5003963 1 0.0771593
BICF2G63010019 BB 0.7604493 0.973344 0.7864637 1 0.3140319
BICF2G630100197 BB 0.4489847 0.9315044 1.44875 0.9856335 -0.3533967
BICF2G630100209 AA 0.9577258 0.02564499 1.150915 0.006796692 -0.01643183
BICF2G630100251 AB 0.942551 0.4983828 1.480402 0.4993263 0.06709359

Total number of rows: 173662

Table truncated, full table size 11243 Kbytes.




Supplementary file Size Download File type/resource
GSM1755109_9933510186_R01C01_Grn.idat.gz 1.3 Mb (ftp)(http) IDAT
GSM1755109_9933510186_R01C01_Red.idat.gz 1.3 Mb (ftp)(http) IDAT
Processed data included within Sample table
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