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Sample GSM1755111 Query DataSets for GSM1755111
Status Public on Jul 30, 2015
Title AMAL_29540
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 0.9717102 1.078808 0.9941437 0.2074368
BICF2G630100032 AA 0.9423809 0.0243258 1.043337 0.001982794 -0.04846715
BICF2G630100034 BB 0.9264764 0.978717 1.120821 0.9973927 -0.01371291
BICF2G630100043 BB 0.8898949 0.9634051 1.136361 0.9833627 -0.2276567
BICF2G630100054 AB 0.9355912 0.528451 0.5758708 0.5302498 0.07627656
BICF2G630100063 AB 0.870317 0.5809633 1.61864 0.5249395 -0.03030407
BICF2G630100075 AA 0.8513578 0.07757811 0.7290264 0.02801887 0.1599044
BICF2G63010009 BB 0.8352656 0.9748215 1.06233 1 0.1115708
BICF2G630100090 BB 0.9588766 0.9910586 1.258719 0.9991633 0.2694041
BICF2G630100094 AA 0.9062778 0.06319953 1.149933 0.03924068 -0.1008797
BICF2G63010010 AB 0.788362 0.6060581 1.073774 0.4601937 -0.03462197
BICF2G630100114 BB 0.939804 0.9762248 0.9408986 0.9951968 -0.1809601
BICF2G630100129 BB 0.8625047 0.9870549 1.219277 1 -0.08151769
BICF2G63010014 NC 0 0.4973055 0.9618993 0.7929091 0.3218996
BICF2G630100157 BB 0.9132537 0.9773542 1.080092 0.9978763 -0.06133103
BICF2G63010018 NC 0 0.7014006 0.6125818 0.6207657 0.2693302
BICF2G63010019 BB 0.7604493 0.9683754 0.9254754 1 0.539441
BICF2G630100197 BB 0.4489847 0.9397857 1.543656 0.9951831 -0.2505721
BICF2G630100209 AB 0.9577258 0.5802851 1.421599 0.5599269 0.05746891
BICF2G630100251 AB 0.942551 0.4972981 1.557435 0.4981869 0.1408774

Total number of rows: 173662

Table truncated, full table size 11182 Kbytes.




Supplementary file Size Download File type/resource
GSM1755111_9933510186_R02C01_Grn.idat.gz 1.3 Mb (ftp)(http) IDAT
GSM1755111_9933510186_R02C01_Red.idat.gz 1.3 Mb (ftp)(http) IDAT
Processed data included within Sample table
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