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Sample GSM2515100 Query DataSets for GSM2515100
Status Public on Mar 01, 2017
Title Blood Sample Case 2 [SNP]
Sample type genomic
 
Source name Blood
Organism Homo sapiens
Characteristics gender: Male
tissue: Blood
disease state: Beckwith-Wiedemann Syndrome
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications. Prior to extraction, red cells were lysed by exposure of the sample to 2x Lysis Buffer for 5 minutes in ice. The remaining cells were pelletted by centrifugation at 2300 RPM at 4 degrees celsius.
Label cy3 and cy5
Label protocol Standard Illumina Protocol
 
Hybridization protocol Standard Illumina Protocol
Scan protocol Using an Illumina HiScan
Description Genomic DNA extracted from blood was genotyped using the HumnaOmni2.5M SNP array (Illumina)
Data processing Genomic DNA extracted from blood was genotyped using the Illumina HumanOmni2.5M-8v1-1_B. The processed data file omni2.5M_matrix_processed.txt (available on the series record) contains the GC score, theta, R, B allele frequency, and log R ratios.
 
Submission date Feb 28, 2017
Last update date Mar 01, 2017
Contact name Jack Brzezinski
E-mail(s) jack.brzezinski@mail.utoronto.ca
Organization name University of Toronto
Street address 555 University Avenue
City Toronto
State/province ON
ZIP/Postal code M5G1X8
Country Canada
 
Platform ID GPL20641
Series (2)
GSE95484 Wilms Tumor in Beckwith-Wiedemann Syndrome and Loss of Methylation at Imprinting Centre 2 [HumanOmni2.5M]
GSE95488 Wilms Tumor in Beckwith-Wiedemann Syndrome and Loss of Methylation at Imprinting Centre 2

Data table header descriptions
ID_REF
VALUE genotype calls
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
200610-1 AA 0.3699754 0.03339314 4.466747 0 0.1306436
200610-10 AA 0.3699754 0.03513008 4.881613 0 0.1008104
200610-100 BB 0.3076571 0.9078659 1.550142 1 -0.02566752
200610-102 AA 0.3583108 0.04320911 2.254761 0 -0.06616863
200610-104 AA 0.2610105 0.1077266 0.740761 0.0649159 -1.005615
200610-105 AA 0.3919997 0.02808733 3.635217 0.00322402 0.006119731
200610-106 AA 0.3332988 0.06184746 2.357444 0 0.03234594
200610-107 AA 0.3638141 0.01107502 1.538698 0 0.02772802
200610-108 AA 0.3546228 0.04635941 3.892449 0 0.05931029
200610-109 AA 0.3679356 0.04558743 2.663105 0.003022283 -0.3156009
200610-110 AA 0.3699754 0.04337901 2.959758 0.004511016 -0.06066722
200610-111 AA 0.3941913 0.02050661 3.023907 0.001172608 -0.1195793
200610-112 AA 0.379117 0.02325587 2.773744 0 -0.1076442
200610-113 AA 0.3699754 0.0348486 3.004264 0 -0.1080386
200610-114 AA 0.379117 0.03102279 3.052969 0 0.02731631
200610-115 AA 0.3546228 0.05895714 3.713945 0.003313293 0.009659843
200610-116 AA 0.3813571 0.116323 0.6887878 0.01141209 -0.1857899
200610-117 AA 0.3679356 0.0346598 2.579497 0 -0.09577563
200610-118 AA 0.379117 0.03439714 2.05466 0.004389513 -0.1134126
200610-119 AA 0.379117 0.025159 3.050853 0 0.1404591

Total number of rows: 1048575

Table truncated, full table size 63238 Kbytes.




Supplementary file Size Download File type/resource
GSM2515100_3999746153_R06C01_Grn.idat.gz 16.0 Mb (ftp)(http) IDAT
GSM2515100_3999746153_R06C01_Red.idat.gz 16.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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