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Status
Public on Jun 10, 2016
Title
SALU DNA [24003]
Sample type
genomic
Source name
whole blood
Organism
Canis lupus familiaris Characteristics
breed: Saluki
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
24003
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
24003.Score 24003.Theta 24003.R 24003.B Allele Freq 24003.Log R Ratio
Data table ID_REF VALUE 24003.Score 24003.Theta 24003.R 24003.B Allele Freq 24003.Log R Ratio BICF2G630100019
AB
0.8714491
0.5096434
0.764022
0.4436128
-0.5262249
BICF2G630100032
AA
0.9423809
0.02341256
1.13898
0.001072492
0.07861634
BICF2G630100034
BB
0.9264764
0.9843486
1.043143
1
-0.1121275
BICF2G630100043
AA
0.8898949
0.01699481
1.046727
0.00
-0.172619
BICF2G630100054
AB
0.9355912
0.4465182
0.380133
0.4444396
-0.5249881
BICF2G630100063
AB
0.870317
0.5686697
1.587399
0.509877
-0.06790043
BICF2G630100075
AB
0.8513578
0.6040077
0.6956651
0.4631906
-0.2387026
BICF2G63010009
BB
0.8352656
0.9620289
1.402897
0.9875901
0.4943829
BICF2G630100090
AB
0.9588766
0.5098039
1.175932
0.532657
-0.2592479
BICF2G630100094
AB
0.9062778
0.5266989
1.557662
0.4861461
-0.1829172
BICF2G63010010
AB
0.788362
0.6528857
0.9151968
0.5040366
-0.3054133
BICF2G630100114
BB
0.939804
0.9871153
1.423481
1
0.428566
BICF2G630100129
AB
0.8625047
0.5168878
1.571067
0.5162923
0.03694427
BICF2G63010014
NC
0.00
0.578862
0.6921312
0.8877903
-0.1529407
BICF2G630100157
AB
0.9132537
0.4885826
1.383656
0.5022318
-0.1790441
BICF2G63010018
NC
0.00
0.7971805
0.5879202
0.7594107
0.244135
BICF2G63010019
BB
0.7551417
0.9186125
0.383687
0.9625281
-0.8217865
BICF2G630100197
AB
0.4489847
0.5230873
3.631056
0.5146658
0.5031904
BICF2G630100209
AB
0.9577258
0.5630355
1.352562
0.5414619
-0.02803737
BICF2G630100251
AA
0.942551
0.03308546
1.160081
0.0105555
-0.001148355
173662 11281 Kbytes .Supplementary file Size Download File type/resource GSM2195600_3998887021_R06C02_Grn.idat.gz
1.3 Mb
(ftp) (http) IDAT
GSM2195600_3998887021_R06C02_Red.idat.gz
1.3 Mb
(ftp) (http) IDAT
Processed data included within Sample table
