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Sample GSM397728 Query DataSets for GSM397728
Status Public on Jul 31, 2010
Title Blood-MND-1140-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 0.012369 BB 829.611816 5847.542480
SNP_A-1967418 BB 0.004573 BB 240.340607 830.497375
SNP_A-1969580 BB 0.002953 BB 1266.205566 4017.504395
SNP_A-4263484 BB 0.006048 BB 606.404663 2444.894531
SNP_A-1978185 AA 0.001015 AA 1345.796265 371.183929
SNP_A-4264431 AB 0.006388 AB 1023.628052 1043.581299
SNP_A-1980898 BB 0.000719 BB 219.196625 799.366577
SNP_A-1983139 AA 0.002342 AA 4731.641113 1340.592285
SNP_A-4265735 AB 0.002911 AB 1557.972046 1737.711426
SNP_A-1995832 AB 0.004846 AB 1654.532227 1536.643555
SNP_A-1995893 AB 0.002291 AB 1830.128174 2212.361816
SNP_A-1997689 BB 0.003445 BB 854.957275 3889.885010
SNP_A-1997709 AA 0.003064 AA 1996.858643 318.246063
SNP_A-1997896 AA 0.002230 AA 1177.220337 406.677155
SNP_A-1997922 AB 0.001674 AB 652.600342 569.448914
SNP_A-2000230 AA 0.013300 AA 2776.125488 1433.844604
SNP_A-2000332 AB 0.010190 AB 3357.382568 3530.770508
SNP_A-2000337 AA 0.004556 AA 2033.505615 319.582703
SNP_A-2000342 AA 0.015403 AA 5030.229492 1369.466431
SNP_A-4268173 AA 0.000593 AA 1336.421753 225.779129

Total number of rows: 909622

Table truncated, full table size 46124 Kbytes.

Supplementary file Size Download File type/resource
GSM397728.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM397728.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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