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Sample GSM397733 Query DataSets for GSM397733
Status Public on Jul 31, 2010
Title Blood-MND-1188-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: M
phenotype: MND
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from leukocytes using the phenol chloroform method or Qiamp blood kits (Qiagen Pty Ltd, Doncaster, Vic, Australia), hair using the phenol chloroform method, and from sperm using Pure Sperm 100 kits (Nidacom, Gothenburg, Sweden).
Label biotin
Label protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia), Affymetrix dsDNA terminal label.
Hybridization protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Scan protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Description Affy 6.0 MND Blood
Data processing Data processed using Affymetrix Command Console software and Affymetrix Genotyping Console 3.0.2 software using the Birdseed version 2 algorithm and default settings.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
Submission date Apr 25, 2009
Last update date Jun 26, 2012
Contact name Roger Pamphlett
Organization name University of Sydney
Street address Blackburn Bld
City University of Sydney
ZIP/Postal code 2006
Country Australia
Platform ID GPL6801
Series (1)
GSE15826 Affymetrix 6.0 study of sporadic motor neuron disease patients and controls.

Data table header descriptions
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE A value in the range [0,1] with lower values corresponding to greater confidence
FORCED CALL This value is the genotyping call that would be made if the calling algorithm were tuned to the least stringency. Providing this value allows for determining what the calls would have been at a stringency different to that applied to the calls in the second field, without having to re-run the genotyping algorithm
SIGNAL A Summarized signal A
SIGNAL B Summarized signal B

Data table
SNP_A-2131660 BB 0.001115 BB 742.851562 4773.715820
SNP_A-1967418 BB 0.003612 BB 264.949738 635.729004
SNP_A-1969580 BB 0.009105 BB 894.013062 4235.947754
SNP_A-4263484 BB 0.005176 BB 331.698395 1722.861328
SNP_A-1978185 AA 0.005020 AA 1715.060425 388.031860
SNP_A-4264431 AB 0.005796 AB 1102.585693 737.718079
SNP_A-1980898 BB 0.001563 BB 244.256912 775.356079
SNP_A-1983139 AA 0.003040 AA 5011.437500 1124.296753
SNP_A-4265735 BB 0.003620 BB 516.980469 2755.716309
SNP_A-1995832 BB 0.012097 BB 539.035400 1684.091064
SNP_A-1995893 BB 0.002215 BB 419.425018 2724.377197
SNP_A-1997689 BB 0.004357 BB 576.917175 3953.863525
SNP_A-1997709 AA 0.007454 AA 1300.022705 226.588745
SNP_A-1997896 BB 0.001920 BB 423.707855 2229.375244
SNP_A-1997922 AA 0.001597 AA 1071.711060 291.225372
SNP_A-2000230 AA 0.003513 AA 2936.511719 960.317688
SNP_A-2000332 AA 0.008656 AA 4626.540527 886.840820
SNP_A-2000337 AA 0.002062 AA 1632.864990 288.578827
SNP_A-2000342 AA 0.002146 AA 4275.895996 948.966736
SNP_A-4268173 AA 0.002230 AA 1226.742554 253.286377

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.

Supplementary file Size Download File type/resource
GSM397733.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM397733.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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