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Sample GSM397827 Query DataSets for GSM397827
Status Public on Jul 31, 2010
Title Blood-Ctrl-1931-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 6 / 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 0.010686 BB 717.033081 3682.950195
SNP_A-1967418 AB 0.070623 AB 721.200195 474.527588
SNP_A-1969580 BB 0.009682 BB 1222.663696 4911.441895
SNP_A-4263484 AB 0.004266 AB 1487.346802 1145.299927
SNP_A-1978185 AA 0.002109 AA 1393.098267 281.323883
SNP_A-4264431 AA 0.015009 AA 2473.054199 274.024323
SNP_A-1980898 AB 0.003261 AB 693.813354 629.473022
SNP_A-1983139 AA 0.002378 AA 4325.820312 970.038208
SNP_A-4265735 AB 0.001197 AB 1708.621948 1821.050781
SNP_A-1995832 AB 0.004178 AB 1582.139771 1109.170044
SNP_A-1995893 AB 0.003068 AB 1726.272949 1942.276123
SNP_A-1997689 BB 0.004337 BB 678.437622 3464.555664
SNP_A-1997709 AA 0.000658 AA 2194.227539 298.115692
SNP_A-1997896 AA 0.003199 AA 1465.329590 424.674011
SNP_A-1997922 AB 0.000365 AB 726.320374 630.502197
SNP_A-2000230 AA 0.001996 AA 2940.351562 1063.340454
SNP_A-2000332 AA 0.006649 AA 4217.019043 742.035034
SNP_A-2000337 AA 0.015296 AA 2371.644043 337.785858
SNP_A-2000342 AA 0.002582 AA 4184.669434 913.731995
SNP_A-4268173 AA 0.011856 AA 1922.904785 327.384735

Total number of rows: 909622

Table truncated, full table size 46134 Kbytes.

Supplementary file Size Download File type/resource
GSM397827.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM397827.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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