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Sample GSM397735 Query DataSets for GSM397735
Status Public on Jul 31, 2010
Title Blood-MND-1221-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: F
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 0.001647 BB 605.308167 4238.526855
SNP_A-1967418 BB 0.001091 BB 276.552826 726.514099
SNP_A-1969580 BB 0.002738 BB 977.161865 3904.894531
SNP_A-4263484 AB 0.002481 AB 1641.617065 1260.950562
SNP_A-1978185 AA 0.003483 AA 1519.488281 436.847443
SNP_A-4264431 AA 0.002024 AA 1616.440308 277.730377
SNP_A-1980898 BB 0.001138 BB 215.090164 823.761230
SNP_A-1983139 AA 0.005822 AA 3965.805420 786.177307
SNP_A-4265735 AB 0.008292 AB 1267.005615 1557.287842
SNP_A-1995832 AB 0.005263 AB 1429.703003 1173.128052
SNP_A-1995893 AB 0.020477 AB 1325.738647 2132.095703
SNP_A-1997689 BB 0.005184 BB 665.559570 4374.256348
SNP_A-1997709 AA 0.001477 AA 2378.202637 285.925049
SNP_A-1997896 AB 0.001640 AB 892.996277 1452.168701
SNP_A-1997922 AA 0.003769 AA 847.918640 215.090164
SNP_A-2000230 AA 0.002476 AA 2484.620605 1068.151123
SNP_A-2000332 AA 0.004332 AA 3893.692139 1055.892090
SNP_A-2000337 AA 0.005902 AA 2094.609863 237.771683
SNP_A-2000342 AA 0.003628 AA 4055.416992 868.572144
SNP_A-4268173 AB 0.001524 AB 896.453064 786.177307

Total number of rows: 909622

Table truncated, full table size 46137 Kbytes.

Supplementary file Size Download File type/resource
GSM397735.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397735.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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