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Sample GSM397751 Query DataSets for GSM397751
Status Public on Jul 31, 2010
Title Brain-Ctrl-1676-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 AB 0.015796 AB 3736.884277 4136.307129
SNP_A-1967418 BB 0.002058 BB 291.200439 802.863953
SNP_A-1969580 BB 0.012165 BB 1572.356201 4895.919434
SNP_A-4263484 AB 0.000761 AB 1971.899048 1380.069702
SNP_A-1978185 AA 0.001703 AA 1133.348755 282.082672
SNP_A-4264431 AB 0.001375 AB 1144.789307 965.533875
SNP_A-1980898 AB 0.012794 AB 351.413055 321.751617
SNP_A-1983139 AA 0.002244 AA 5124.273438 1331.811401
SNP_A-4265735 AB 0.009470 AB 2338.324951 2551.397217
SNP_A-1995832 BB 0.001387 BB 638.414734 2332.404785
SNP_A-1995893 BB 0.008929 BB 701.322937 3111.654541
SNP_A-1997689 BB 0.003120 BB 856.986328 3998.352783
SNP_A-1997709 AA 0.015633 AA 2052.812500 429.193451
SNP_A-1997896 AA 0.003955 AA 1169.023682 536.878418
SNP_A-1997922 BB 0.036270 BB 373.836060 801.582153
SNP_A-2000230 AA 0.001067 AA 2804.424805 1114.692871
SNP_A-2000332 AA 0.003095 AA 3912.285400 802.174866
SNP_A-2000337 AA 0.016779 AA 2193.993896 396.284302
SNP_A-2000342 AA 0.005819 AA 3741.335205 1068.270508
SNP_A-4268173 AA 0.004275 AA 1049.427002 163.564514

Total number of rows: 909622

Table truncated, full table size 46123 Kbytes.

Supplementary file Size Download File type/resource
GSM397751.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM397751.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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