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Sample GSM2748035 Query DataSets for GSM2748035
Status Public on Mar 01, 2018
Title CKCS_Saliva_Unaffected_17
Sample type genomic
 
Source name Saliva
Organism Canis lupus familiaris
Characteristics breed: Cavalier King Charles Spaniel
disease state: control
sm: 0
ccd size: 0
vd: 2
f-diam: 44.17
ab: 14.69
bc: 16.79
cd: 12.7
bd: 27.67
ae: 32.44
ID: 29.22
ac: 27.36
ai: 26.52
cj: 12.5
fh: 24.89
fg: 0
bk: 11.01
l1 (hae): 119.99
l2 (fac): 69.54
l3 (dib): 74.89
l4 (fae): 42.56
l5 (aeb): 27.16
l6(dba): 98.97
l7(dbi): 23.81
l8 (ebd): 7.06
l9 (jcb): 43.35
l10 (afg): 0
l11(ebk): 48.16
f-d/cd: 3.477952756
f-d/bc: 2.630732579
l4+l7: 66.37
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from blood or saliva using the ORAGENE Animal kit (DNAgenotek)
Label CY3 and CY5
Label protocol 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MA1, WG-MA2) and primer/neutralization mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
 
Hybridization protocol RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
Scan protocol After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan Autoloader 2X (Illumina).
Description 11404-D0002884-WG3318316-DNA-B05
Data processing Genomic DNA extracted from saliva was genotyped using Infinium CanineHD Genotyping BeadChips (Illumina).
GenomeStudio 2.0 was used to generate processed data using the final report function.
 
Submission date Aug 22, 2017
Last update date Mar 01, 2018
Contact name Philippe Lemay
E-mail(s) lemayph@gmail.com
Organization name Université de Montréal
Street address 3175 Chemin de la Côte-Sainte-Catherine
City Montreal
State/province Quebec
ZIP/Postal code H3T 1C5
Country Canada
 
Platform ID GPL17481
Series (1)
GSE102906 Whole genome QTL study identifies candidate loci associated to syringomyelia

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or 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 0.9546 0.008 0.807 0 -0.098
BICF2G630100032 AA 0.951 0.028 0.835 0.0085 -0.2638
BICF2G630100034 BB 0.9357 0.98 1.026 0.9953 -0.1659
BICF2G630100043 AA 0.8037 0.036 0.793 0.0128 -0.3096
BICF2G630100054 BB 0.9124 0.928 0.424 0.9682 -0.0086
BICF2G630100063 AA 0.8383 0.033 1.356 0.0103 -0.0331
BICF2G630100075 AA 0.9335 0.084 0.486 0.0506 -0.3429
BICF2G63010009 AB 0.8763 0.451 1.35 0.4665 -0.0352
BICF2G630100090 BB 0.9083 0.991 1.114 1 0.0935
BICF2G630100094 BB 0.9 0.994 1.187 0.9949 -0.2105
BICF2G63010010 AB 0.8247 0.69 0.725 0.5262 -0.5003
BICF2G630100114 BB 0.9349 0.963 1.127 0.9826 -0.004
BICF2G630100129 AA 0.8318 0.018 1.402 0 0.0263
BICF2G63010014 NC 0 0.468 0.507 0.3862 -0.3929
BICF2G630100157 AA 0.868 0.018 1.502 0 0.2096
BICF2G63010018 AB 0.7366 0.545 0.543 0.5247 -0.9014
BICF2G63010019 AB 0.8066 0.352 0.694 0.4602 -0.4896
BICF2G630100197 BB 0.5555 0.949 1.915 0.9854 0.0501
BICF2G630100209 AA 0.956 0.02 1.1 0.0045 -0.1277
BICF2G630100251 AA 0.9101 0.022 1.589 0.0034 0.3651

Total number of rows: 173662

Table truncated, full table size 8450 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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