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Sample GSM397747 Query DataSets for GSM397747
Status Public on Jul 31, 2010
Title Brain-Ctrl-1672-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 0.003348 BB 647.373779 4933.336914
SNP_A-1967418 BB 0.009456 BB 245.712128 537.669922
SNP_A-1969580 BB 0.002002 BB 1203.167114 4369.133789
SNP_A-4263484 BB 0.000858 BB 547.697937 2091.792969
SNP_A-1978185 AA 0.003397 AA 1007.304199 323.287903
SNP_A-4264431 AA 0.001816 AA 1639.622803 300.954956
SNP_A-1980898 AB 0.001352 AB 569.204773 534.901794
SNP_A-1983139 AA 0.004284 AA 4810.567383 974.363708
SNP_A-4265735 AB 0.004488 AB 2159.418457 2319.885254
SNP_A-1995832 BB 0.015984 BB 559.616455 2975.624268
SNP_A-1995893 AB 0.001260 AB 1846.129395 2123.867676
SNP_A-1997689 BB 0.000430 BB 728.784668 4010.629883
SNP_A-1997709 AA 0.005108 AA 2864.740479 305.639587
SNP_A-1997896 AA 0.002163 AA 1169.542725 444.291687
SNP_A-1997922 AB 0.008629 AB 492.831696 454.025909
SNP_A-2000230 AB 0.001967 AB 1807.377808 2273.970703
SNP_A-2000332 AB 0.002922 AB 3116.059326 3244.966064
SNP_A-2000337 AA 0.002966 AA 1936.063965 315.051178
SNP_A-2000342 AA 0.003092 AA 3867.351318 957.249939
SNP_A-4268173 AB 0.003808 AB 830.570557 591.003906

Total number of rows: 909622

Table truncated, full table size 46120 Kbytes.

Supplementary file Size Download File type/resource
GSM397747.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM397747.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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