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Sample GSM1755127 Query DataSets for GSM1755127
Status Public on Jul 30, 2015
Title HUSK_28926
Sample type genomic
 
Source name whole blood
Organism Canis lupus familiaris
Characteristics origin: North America
breed: Siberian Husky (HUSK)
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 AA 0.8714491 0.009849076 0.7524476 0.001959364 -0.2477935
BICF2G630100032 AA 0.9423809 0.01831296 1.108007 0 0.04188921
BICF2G630100034 BB 0.9264764 0.9812179 1.145784 1 0.02037538
BICF2G630100043 AB 0.8898949 0.6100523 1.641254 0.4797586 0.06781887
BICF2G630100054 BB 0.9355912 0.9654508 0.4263005 0.9917955 -0.06332594
BICF2G630100063 BB 0.870317 0.9673386 1.186472 0.9983424 -0.1434794
BICF2G630100075 AA 0.8513578 0.05020488 0.6394454 0.005390856 -0.009766687
BICF2G63010009 BB 0.8352656 0.9755153 1.207023 1 0.296794
BICF2G630100090 BB 0.9588766 0.9969464 0.9719588 1 -0.09743536
BICF2G630100094 BB 0.9062778 0.997858 1.465919 1 0.1817317
BICF2G63010010 AB 0.788362 0.6193437 1.198597 0.4721193 0.1112331
BICF2G630100114 BB 0.939804 0.9876983 0.9453755 1 -0.1612409
BICF2G630100129 AA 0.8625047 0.0332353 0.958051 0.000637118 -0.4327185
BICF2G63010014 NC 0 0.700404 0.8010334 1 0.05787624
BICF2G630100157 BB 0.9132537 0.9867452 1.088921 1 -0.03873659
BICF2G63010018 NC 0 0.9609884 0.5966411 0.996529 0.3256091
BICF2G63010019 BB 0.7604493 0.9659413 0.7344325 1 0.2012912
BICF2G630100197 BB 0.4489847 0.9454252 1.766948 1 -0.04793056
BICF2G630100209 AB 0.9577258 0.5373853 1.467849 0.5140043 0.06985553
BICF2G630100251 AA 0.942551 0.02276366 1.230335 0 0.09064323

Total number of rows: 173662

Table truncated, full table size 11009 Kbytes.




Supplementary file Size Download File type/resource
GSM1755127_9933510197_R04C02_Grn.idat.gz 1.3 Mb (ftp)(http) IDAT
GSM1755127_9933510197_R04C02_Red.idat.gz 1.3 Mb (ftp)(http) IDAT
Processed data included within Sample table
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