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Sample GSM397778 Query DataSets for GSM397778
Status Public on Jul 31, 2010
Title Brain-Ctrl-1913-rep1
Sample type genomic
Source name Ctrl Brain (Brodmann area 46)
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: M
phenotype: Ctrl
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 Ctrl 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 0.006061 BB 720.937012 3974.086426
SNP_A-1967418 BB 0.003202 BB 218.601440 670.109680
SNP_A-1969580 BB 0.021100 BB 1538.873657 3842.519043
SNP_A-4263484 AB 0.002430 AB 1647.980225 1184.460938
SNP_A-1978185 AA 0.003147 AA 1003.276917 283.556610
SNP_A-4264431 AA 0.006042 AA 1403.755005 308.451080
SNP_A-1980898 BB 0.006683 BB 193.776962 546.855896
SNP_A-1983139 AA 0.008385 AA 4179.916016 1334.795044
SNP_A-4265735 AA 0.003600 AA 2528.078857 566.718628
SNP_A-1995832 AB 0.002244 AB 2125.982178 1590.649414
SNP_A-1995893 AB 0.000681 AB 2048.832031 2273.075684
SNP_A-1997689 BB 0.007640 BB 910.759583 4542.078613
SNP_A-1997709 AA 0.002332 AA 2799.576172 378.129150
SNP_A-1997896 AA 0.002514 AA 1155.412476 458.213135
SNP_A-1997922 AB 0.004921 AB 557.706543 520.477112
SNP_A-2000230 AA 0.007306 AA 2361.937988 1199.547363
SNP_A-2000332 AB 0.002326 AB 3062.311768 2990.794678
SNP_A-2000337 AA 0.011574 AA 1750.652832 394.339233
SNP_A-2000342 AA 0.006429 AA 3818.199707 1142.795288
SNP_A-4268173 AB 0.001860 AB 695.851685 628.942078

Total number of rows: 909622

Table truncated, full table size 46123 Kbytes.

Supplementary file Size Download File type/resource
GSM397778.CEL.gz 30.2 Mb (ftp)(http) CEL
GSM397778.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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