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Sample GSM397822 Query DataSets for GSM397822
Status Public on Jul 31, 2010
Title Blood-Ctrl-1687-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 5 / 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 0.005258 BB 734.089294 4071.961914
SNP_A-1967418 AB 0.003203 AB 493.157013 452.283386
SNP_A-1969580 BB 0.001966 BB 1045.794678 4087.908447
SNP_A-4263484 BB 0.013321 BB 479.471588 1663.366577
SNP_A-1978185 AA 0.004000 AA 1232.595825 430.645447
SNP_A-4264431 AA 0.014557 AA 2564.254639 390.817474
SNP_A-1980898 AB 0.008765 AB 759.632629 732.497192
SNP_A-1983139 AA 0.009477 AA 4553.920898 731.308533
SNP_A-4265735 AB 0.004601 AB 1494.166626 1561.845581
SNP_A-1995832 BB 0.007830 BB 517.647339 1789.200195
SNP_A-1995893 BB 0.000662 BB 505.432465 3062.997314
SNP_A-1997689 BB 0.005044 BB 561.312134 3961.418213
SNP_A-1997709 AA 0.004947 AA 1585.875977 200.043533
SNP_A-1997896 AB 0.003839 AB 1095.484131 1863.365845
SNP_A-1997922 AB 0.012017 AB 918.052979 911.891785
SNP_A-2000230 AA 0.003299 AA 2651.716064 1192.501465
SNP_A-2000332 AA 0.017885 AA 3423.066650 1108.977295
SNP_A-2000337 AA 0.003200 AA 1555.861816 283.986633
SNP_A-2000342 AA 0.014761 AA 3493.363281 678.666260
SNP_A-4268173 AB 0.018487 AB 1322.118896 955.449585

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.

Supplementary file Size Download File type/resource
GSM397822.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397822.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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