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Sample GSM397839 Query DataSets for GSM397839
Status Public on Jul 31, 2010
Title Blood-Ctrl-2248-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 12 / 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 0.014563 AB 1943.012817 1974.624756
SNP_A-1967418 BB 0.004987 BB 296.639374 665.899963
SNP_A-1969580 BB 0.003306 BB 989.651245 4067.239258
SNP_A-4263484 AB 0.004011 AB 1512.492798 1114.211548
SNP_A-1978185 AA 0.008778 AA 1866.578857 359.923065
SNP_A-4264431 AA 0.002230 AA 1643.647705 320.048981
SNP_A-1980898 AB 0.000953 AB 629.869812 506.152985
SNP_A-1983139 AA 0.005573 AA 4875.802246 951.612549
SNP_A-4265735 AB 0.005880 AB 1505.800903 1892.360107
SNP_A-1995832 AB 0.006955 AB 1343.823242 1077.334351
SNP_A-1995893 BB 0.003295 BB 457.294434 2685.406250
SNP_A-1997689 BB 0.006271 BB 526.069336 3670.512451
SNP_A-1997709 AA 0.005664 AA 1940.992554 194.327026
SNP_A-1997896 AB 0.001180 AB 1065.039795 1580.690308
SNP_A-1997922 AB 0.003255 AB 760.483276 539.681458
SNP_A-2000230 AA 0.027475 AA 3856.520020 1188.517822
SNP_A-2000332 BB 0.003683 BB 1353.657715 4955.728516
SNP_A-2000337 AA 0.006367 AA 2132.085205 244.736374
SNP_A-2000342 AA 0.011032 AA 4602.370605 828.021973
SNP_A-4268173 AA 0.001417 AA 1449.218506 241.563736

Total number of rows: 909622

Table truncated, full table size 46135 Kbytes.

Supplementary file Size Download File type/resource
GSM397839.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM397839.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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