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Status
Public on Jun 10, 2016
Title
CANE DNA [24509]
Sample type
genomic
Source name
whole blood
Organism
Canis lupus familiaris Characteristics
breed: Cane Corso
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
24509
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
24509.Score 24509.Theta 24509.R 24509.B Allele Freq 24509.Log R Ratio
Data table ID_REF VALUE 24509.Score 24509.Theta 24509.R 24509.B Allele Freq 24509.Log R Ratio BICF2G630100019
AB
0.8714491
0.6006793
1.140254
0.5337809
0.03416489
BICF2G630100032
AB
0.9423809
0.4894544
1.291541
0.4656151
0.005436606
BICF2G630100034
AB
0.9264764
0.567739
1.561059
0.5466235
0.127668
BICF2G630100043
AB
0.8898949
0.6141174
1.495534
0.4830736
-0.06875589
BICF2G630100054
AB
0.9355912
0.5847288
0.652604
0.5896887
0.2914351
BICF2G630100063
BB
0.870317
0.9664186
1.194742
0.9972152
-0.1343559
BICF2G630100075
AB
0.8513578
0.6240152
0.8398398
0.4797297
0.02182007
BICF2G63010009
AA
0.8352656
0.07813676
1.047452
0.00
0.001808639
BICF2G630100090
BB
0.9588766
0.9890785
1.046894
0.9972438
0.001500628
BICF2G630100094
BB
0.9062778
0.9921056
1.393516
0.9942311
0.101751
BICF2G63010010
BB
0.788362
0.9671614
0.8266061
1
-0.1675689
BICF2G630100114
BB
0.939804
0.9818625
1.203627
1
0.1806276
BICF2G630100129
AA
0.8625047
0.03373529
1.312811
0.001170781
0.02147327
BICF2G63010014
NC
0.00
0.70816
0.5893323
1
-0.3849049
BICF2G630100157
AB
0.9132537
0.4584013
1.477278
0.4699947
-0.07147647
BICF2G63010018
NC
0.00
0.1180967
0.3141815
0.03903006
-0.2466076
BICF2G63010019
AA
0.7604493
0.06254467
0.8061538
0.00
-0.3301091
BICF2G630100197
AB
0.4489847
0.4637388
2.505351
0.4226839
-0.03119094
BICF2G630100209
BB
0.9577258
0.9926892
1.059698
1
0.006735261
BICF2G630100251
AA
0.942551
0.02201763
1.437781
0.00
0.3159417
173662 11243 Kbytes .Supplementary file Size Download File type/resource GSM2195608_3998887040_R01C01_Grn.idat.gz
1.3 Mb
(ftp) (http) IDAT
GSM2195608_3998887040_R01C01_Red.idat.gz
1.3 Mb
(ftp) (http) IDAT
Processed data included within Sample table
