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Sample GSM397719 Query DataSets for GSM397719
Status Public on Jul 31, 2010
Title Brain-MND-1081-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: 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 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 AB 0.008262 AB 2199.008301 2235.875488
SNP_A-1967418 BB 0.004311 BB 234.964447 813.152954
SNP_A-1969580 BB 0.001781 BB 1228.347534 4047.000000
SNP_A-4263484 AB 0.004143 AB 2309.668701 1584.069214
SNP_A-1978185 AA 0.014418 AA 2078.524658 442.140442
SNP_A-4264431 BB 0.001582 BB 486.598328 1524.927979
SNP_A-1980898 BB 0.000766 BB 219.123688 814.338013
SNP_A-1983139 AA 0.008778 AA 3728.328613 1043.083740
SNP_A-4265735 BB 0.000471 BB 713.348877 2964.139404
SNP_A-1995832 AB 0.003144 AB 1675.910400 1170.149414
SNP_A-1995893 AB 0.002615 AB 1961.518677 2019.858765
SNP_A-1997689 BB 0.007366 BB 515.319519 3975.149414
SNP_A-1997709 AA 0.002219 AA 1900.986450 255.819519
SNP_A-1997896 AB 0.002610 AB 1014.792725 1778.496948
SNP_A-1997922 AA 0.006583 AA 1307.877319 272.997070
SNP_A-2000230 AA 0.001484 AA 2828.136963 1135.389160
SNP_A-2000332 AB 0.004100 AB 3159.140137 2977.070312
SNP_A-2000337 AA 0.002634 AA 1881.507446 237.913895
SNP_A-2000342 AA 0.001013 AA 4256.720215 995.064209
SNP_A-4268173 AA 0.002769 AA 1459.742432 216.197754

Total number of rows: 909622

Table truncated, full table size 46133 Kbytes.

Supplementary file Size Download File type/resource
GSM397719.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM397719.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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