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Sample GSM2515099 Query DataSets for GSM2515099
Status Public on Mar 01, 2017
Title Blood Sample Case 1 [SNP]
Sample type genomic
 
Source name Blood
Organism Homo sapiens
Characteristics gender: Female
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 0.04215484 3.66955 0.00479418 -0.1610286
200610-10 AA 0.3699754 0.03598573 4.168474 6.90E-06 -0.127828
200610-100 BB 0.3076571 0.8998749 1.619763 0.9943938 0.02814636
200610-102 AA 0.3583108 0.03574065 2.705328 0 0.2029624
200610-104 AA 0.3547337 0.03133389 1.455749 0 0.02657139
200610-105 AA 0.3919997 0.03182099 3.230655 0.007151698 -0.1673974
200610-106 AA 0.3332988 0.07333281 2.500813 0.007128083 0.1077204
200610-107 AA 0.3638141 0.07870064 1.260763 0.03825302 -0.3115605
200610-108 AA 0.3546228 0.04370461 3.461057 0 -0.1077159
200610-109 AA 0.3679356 0.03923716 3.413757 0 0.04829961
200610-110 AA 0.3699754 0.03700178 3.203005 0 0.05885335
200610-111 AA 0.3941913 0.01676035 3.610682 0 0.1395279
200610-112 AA 0.379117 0.03142196 2.961051 0.002217228 -0.02041362
200610-113 AA 0.3699754 0.03272076 3.227692 0 -0.002666215
200610-114 AA 0.379117 0.02440407 3.018804 0 0.01683141
200610-115 AA 0.3546228 0.05688242 3.621493 0.001059365 -0.02480293
200610-116 AA 0.3813571 0.09191934 0.7987649 0 0.0452749
200610-117 AA 0.3679356 0.04898569 2.842789 0.005009688 0.03206793
200610-118 AA 0.379117 0.02842895 2.376458 0 0.1013602
200610-119 AA 0.379117 0.03954192 2.738433 0.006805664 -0.02767679

Total number of rows: 1048575

Table truncated, full table size 63008 Kbytes.




Supplementary file Size Download File type/resource
GSM2515099_3999746153_R07C01_Grn.idat.gz 16.1 Mb (ftp)(http) IDAT
GSM2515099_3999746153_R07C01_Red.idat.gz 16.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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