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Sample GSM397834 Query DataSets for GSM397834
Status Public on Jul 31, 2010
Title Blood-Ctrl-2115-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 11 / Mother
twin #: NA
twin info: NA
gender: F
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 BB 0.006222 BB 655.868713 5199.874512
SNP_A-1967418 BB 0.002172 BB 273.661591 819.372375
SNP_A-1969580 BB 0.008080 BB 817.716797 3287.367920
SNP_A-4263484 AB 0.002683 AB 1993.311279 1307.118408
SNP_A-1978185 AA 0.002400 AA 1213.338501 388.933075
SNP_A-4264431 AB 0.002969 AB 1079.629395 980.925598
SNP_A-1980898 BB 0.002711 BB 202.651291 856.991577
SNP_A-1983139 AA 0.001643 AA 4748.586914 1078.752197
SNP_A-4265735 BB 0.000103 BB 744.651184 3030.089844
SNP_A-1995832 AA 0.005042 AA 3453.360352 529.696716
SNP_A-1995893 AA 0.001947 AA 3208.166504 1171.414062
SNP_A-1997689 BB 0.012778 BB 900.392151 4858.566406
SNP_A-1997709 AA 0.003016 AA 2336.407715 257.990326
SNP_A-1997896 AA 0.004939 AA 1513.286011 642.389221
SNP_A-1997922 AA 0.005987 AA 1276.767944 250.180588
SNP_A-2000230 AA 0.000710 AA 2759.119873 1098.405029
SNP_A-2000332 AA 0.002708 AA 4298.137695 891.452332
SNP_A-2000337 AA 0.005414 AA 1454.343994 253.011765
SNP_A-2000342 AA 0.004310 AA 3768.986084 952.395752
SNP_A-4268173 AA 0.001404 AA 1295.471924 260.871460

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.

Supplementary file Size Download File type/resource
GSM397834.CEL.gz 30.3 Mb (ftp)(http) CEL
GSM397834.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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