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Sample GSM397692 Query DataSets for GSM397692
Status Public on Jul 31, 2010
Title Brain-MND-0862-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 BB 0.012193 BB 558.999512 3315.719482
SNP_A-1967418 BB 0.007602 BB 292.593658 935.519104
SNP_A-1969580 BB 0.001168 BB 1078.975952 3853.679443
SNP_A-4263484 AB 0.003516 AB 1591.562378 1269.533936
SNP_A-1978185 AA 0.005322 AA 1729.153687 378.348572
SNP_A-4264431 AA 0.002328 AA 2019.576294 299.954651
SNP_A-1980898 BB 0.008136 BB 316.289093 927.433350
SNP_A-1983139 AA 0.006429 AA 4573.533691 1449.844604
SNP_A-4265735 AA 0.003100 AA 2987.748291 741.910828
SNP_A-1995832 AB 0.001000 AB 1780.480469 1425.158325
SNP_A-1995893 AB 0.019172 AB 1196.347778 1408.907593
SNP_A-1997689 BB 0.003894 BB 760.696228 4393.315918
SNP_A-1997709 AA 0.001099 AA 2109.691406 294.093842
SNP_A-1997896 AA 0.004320 AA 1550.151855 612.425354
SNP_A-1997922 AB 0.041922 AB 1280.907227 907.833374
SNP_A-2000230 AA 0.011672 AA 3413.514648 1291.062134
SNP_A-2000332 AA 0.013604 AA 3448.197266 1047.945068
SNP_A-2000337 AA 0.002670 AA 1911.618164 241.887665
SNP_A-2000342 AA 0.014990 AA 4858.566406 1420.253052
SNP_A-4268173 AA 0.001864 AA 1233.828125 247.575668

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.

Supplementary file Size Download File type/resource
GSM397692.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM397692.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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