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Sample GSM397694 Query DataSets for GSM397694
Status Public on Jul 31, 2010
Title Brain-MND-0868-rep1
Sample type genomic
Source name MND Brain (Brodmann area 46)
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 Brain (Brodmann area 46)
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 0.002016 BB 720.740112 4362.976562
SNP_A-1967418 AB 0.001111 AB 546.422668 513.513123
SNP_A-1969580 BB 0.004389 BB 931.816162 3518.169434
SNP_A-4263484 BB 0.001292 BB 428.716583 1996.313965
SNP_A-1978185 AA 0.002023 AA 1093.442993 287.437164
SNP_A-4264431 AB 0.005242 AB 1154.665405 753.185913
SNP_A-1980898 AB 0.001181 AB 583.147461 477.226349
SNP_A-1983139 AA 0.012770 AA 4089.770508 1402.562500
SNP_A-4265735 AB 0.003281 AB 1741.200073 2049.320068
SNP_A-1995832 BB 0.006177 BB 509.318695 2622.327393
SNP_A-1995893 BB 0.000942 BB 510.969269 2943.442383
SNP_A-1997689 BB 0.002487 BB 833.846985 4131.024902
SNP_A-1997709 AA 0.004373 AA 1583.427856 230.150848
SNP_A-1997896 BB 0.002523 BB 619.961243 2305.995117
SNP_A-1997922 AA 0.002376 AA 926.569031 184.973328
SNP_A-2000230 AA 0.006719 AA 2188.385986 976.059814
SNP_A-2000332 AB 0.001975 AB 2986.737061 3239.379395
SNP_A-2000337 AA 0.011041 AA 1298.434326 224.149750
SNP_A-2000342 AA 0.001843 AA 3981.229980 985.367981
SNP_A-4268173 AA 0.002877 AA 1351.473633 301.269348

Total number of rows: 909622

Table truncated, full table size 46124 Kbytes.

Supplementary file Size Download File type/resource
GSM397694.CEL.gz 30.4 Mb (ftp)(http) CEL
GSM397694.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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