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Sample GSM397826 Query DataSets for GSM397826
Status Public on Jul 31, 2010
Title Blood-Ctrl-1912-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 8 / Father
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 Blood
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 0.012171 AB 3656.544434 3441.958252
SNP_A-1967418 BB 0.001470 BB 240.382767 694.568481
SNP_A-1969580 BB 0.007058 BB 958.581482 4297.821777
SNP_A-4263484 AB 0.003663 AB 1561.177124 1237.719482
SNP_A-1978185 AA 0.002661 AA 1044.688599 310.039948
SNP_A-4264431 AB 0.010670 AB 1556.578857 1168.966309
SNP_A-1980898 BB 0.007379 BB 248.071304 1112.505005
SNP_A-1983139 AA 0.002931 AA 5225.846680 1349.315063
SNP_A-4265735 AA 0.002804 AA 2517.324463 526.151794
SNP_A-1995832 AB 0.004251 AB 2250.416504 1581.491211
SNP_A-1995893 AB 0.012164 AB 2443.996338 2890.962158
SNP_A-1997689 BB 0.019761 BB 1110.898071 4594.332031
SNP_A-1997709 AA 0.002650 AA 2394.938232 269.449615
SNP_A-1997896 AA 0.007441 AA 1625.911621 425.284973
SNP_A-1997922 AB 0.006846 AB 897.265686 813.057617
SNP_A-2000230 AA 0.002533 AA 2482.242676 1070.656494
SNP_A-2000332 AA 0.007057 AA 4438.144043 813.082214
SNP_A-2000337 AA 0.000990 AA 1701.352417 269.449615
SNP_A-2000342 AA 0.006845 AA 4765.339355 1221.568604
SNP_A-4268173 AA 0.000635 AA 1413.006104 250.995316

Total number of rows: 909622

Table truncated, full table size 46127 Kbytes.

Supplementary file Size Download File type/resource
GSM397826.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM397826.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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