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Status
Public on Jun 10, 2016
Title
VPIN DNA [24536]
Sample type
genomic
Source name
whole blood
Organism
Canis lupus familiaris Characteristics
breed: Volpino Italiano
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
24536
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
24536.Score 24536.Theta 24536.R 24536.B Allele Freq 24536.Log R Ratio
Data table ID_REF VALUE 24536.Score 24536.Theta 24536.R 24536.B Allele Freq 24536.Log R Ratio BICF2G630100019
BB
0.8714491
0.9889571
0.9260341
1
5.795699E-05
BICF2G630100032
AA
0.9423809
0.01984704
1.043776
0.00
-0.0451838
BICF2G630100034
BB
0.9264764
0.985555
1.098834
1
-0.03597305
BICF2G630100043
AA
0.8898949
0.02110154
1.149799
0.00
-0.040388
BICF2G630100054
AA
0.9355912
0.02893192
0.4800281
0.009076823
-0.06235544
BICF2G630100063
AA
0.870317
0.02856354
1.325684
0.0005166036
0.03632372
BICF2G630100075
AA
0.8513578
0.03034328
0.6807279
0.00
0.09479017
BICF2G63010009
AA
0.8352656
0.08371209
0.8921359
0.00
-0.2365948
BICF2G630100090
AA
0.9588766
0.01261039
1.267053
0.006729753
0.05447796
BICF2G630100094
AA
0.9062778
0.009540762
1.264511
0.00
0.1104908
BICF2G63010010
AA
0.788362
0.08540936
0.5862734
0.00
-0.2877822
BICF2G630100114
AA
0.939804
0.02768091
1.081693
0.00
-0.1189076
BICF2G630100129
BB
0.8625047
0.9802936
1.18041
0.994393
-0.1321286
BICF2G63010014
NC
0.00
0.6892825
0.8338088
1
0.1157303
BICF2G630100157
AA
0.9132537
0.02593679
1.297167
0.006234091
-0.006117562
BICF2G63010018
NC
0.00
0.9676639
0.4761283
1
0.002604904
BICF2G63010019
BB
0.7604493
0.9707299
0.5360287
1
-0.243994
BICF2G630100197
AA
0.4489847
0.1715521
2.294408
0.00
-0.07109575
BICF2G630100209
BB
0.9577258
0.9948388
1.050781
1
-0.003234403
BICF2G630100251
BB
0.942551
0.9812711
1.129355
0.9978598
0.1060579
173662 11110 Kbytes .Supplementary file Size Download File type/resource GSM2195616_3998887040_R03C02_Grn.idat.gz
1.3 Mb
(ftp) (http) IDAT
GSM2195616_3998887040_R03C02_Red.idat.gz
1.3 Mb
(ftp) (http) IDAT
Processed data included within Sample table
