GEO help: Mouse over screen elements for information.
Status
Public on Jun 10, 2016
Title
CIRN DNA [26277]
Sample type
genomic
Source name
whole blood
Organism
Canis lupus familiaris Characteristics
breed: Cirneco dell'Etna
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.
Label
biotin
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
26277
Data processing
Image data was analyzed using GenomeStudio with GT module (Illumina).
Submission date
Jun 09, 2016
Last update date
Jun 10, 2016
Contact name
Dayna Dreger
E-mail(s)
dayna.dreger@nih.gov Organization name
National Institutes of Health
Department
NHGRI
Street address
50 South Drive
City
Bethesda
State/province
MD
ZIP/Postal code
20892
Country
USA
Platform ID
GPL17481 Series (2)
GSE83151 Studies of canine breed development on the island of Sardinia recapitulate genomic features of human population isolates [COO]
GSE83160 Studies of canine breed development on the island of Sardinia recapitulate genomic features of human population isolates
Data table header descriptions ID_REF VALUE genotypes AA, AB, BB, NC=no call
26277.Score 26277.Theta 26277.R 26277.B Allele Freq 26277.Log R Ratio
Data table ID_REF VALUE 26277.Score 26277.Theta 26277.R 26277.B Allele Freq 26277.Log R Ratio BICF2G630100019
BB
0.8714491
0.9806674
0.9177968
1
-0.0190583
BICF2G630100032
AA
0.9423809
0.02148187
1.158527
0.00
0.1043182
BICF2G630100034
BB
0.9264764
0.984992
1.035502
1
-0.1221377
BICF2G630100043
AA
0.8898949
0.0208992
1.170924
0.00
-0.01396225
BICF2G630100054
AB
0.9355912
0.4958958
0.6276327
0.4959191
0.1842295
BICF2G630100063
AB
0.870317
0.5274732
1.816347
0.4688925
0.1407792
BICF2G630100075
AA
0.8513578
0.03697034
0.5446357
0.00
-0.2317836
BICF2G63010009
BB
0.8352656
0.9660003
1.064862
0.9919193
0.1023168
BICF2G630100090
BB
0.9588766
0.991843
1.003335
0.9999237
-0.05693132
BICF2G630100094
BB
0.9062778
0.9960268
1.424314
0.9985278
0.1379925
BICF2G63010010
AB
0.788362
0.6959185
1.080103
0.5740317
-0.03057615
BICF2G630100114
BB
0.939804
0.9784428
1.11827
0.997708
0.07067669
BICF2G630100129
AA
0.8625047
0.03374961
1.474862
0.001186057
0.1893848
BICF2G63010014
NC
0.00
0.6593876
0.8782854
0.981472
0.1907035
BICF2G630100157
BB
0.9132537
0.9770396
1.220986
0.9975573
0.1151986
BICF2G63010018
NC
0.00
0.07512774
0.4378866
0.00
0.2817106
BICF2G63010019
AB
0.7604493
0.3568209
1.000586
0.4610219
-0.1598067
BICF2G630100197
BB
0.4489847
0.9541425
1.801594
1
-0.007880748
BICF2G630100209
BB
0.9577258
0.9915654
1.023659
1
-0.04434131
BICF2G630100251
AB
0.942551
0.4838634
1.457017
0.4840744
0.05217697
173662 11152 Kbytes .Supplementary file Size Download File type/resource GSM2195629_3998887042_R04C02_Grn.idat.gz
1.3 Mb
(ftp) (http) IDAT
GSM2195629_3998887042_R04C02_Red.idat.gz
1.3 Mb
(ftp) (http) IDAT
Processed data included within Sample table
