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Sample GSM397795 Query DataSets for GSM397795
Status Public on Jul 31, 2010
Title Blood-Ctrl-1914-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 3
twin info: Monozygotic Control
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 0.012141 AB 3175.909424 4081.437988
SNP_A-1967418 BB 0.011904 BB 205.120529 865.726074
SNP_A-1969580 BB 0.005498 BB 923.480896 4062.266846
SNP_A-4263484 AB 0.002926 AB 1811.859619 1444.143799
SNP_A-1978185 AA 0.000956 AA 1200.104980 330.586914
SNP_A-4264431 AB 0.008341 AB 1474.838867 1161.166504
SNP_A-1980898 AB 0.038616 AB 939.112610 689.031128
SNP_A-1983139 AA 0.001259 AA 4548.193359 1052.514038
SNP_A-4265735 AA 0.002814 AA 2880.136963 510.014221
SNP_A-1995832 AB 0.003815 AB 1706.903320 1539.368042
SNP_A-1995893 AB 0.003672 AB 2278.403809 2383.322021
SNP_A-1997689 BB 0.003473 BB 735.820679 4344.747559
SNP_A-1997709 AA 0.005005 AA 1723.422241 194.275833
SNP_A-1997896 AA 0.005340 AA 1502.447021 387.751740
SNP_A-1997922 AB 0.006347 AB 875.499695 813.127014
SNP_A-2000230 AA 0.000247 AA 2756.475586 1062.840576
SNP_A-2000332 AA 0.004540 AA 4500.799316 1018.556885
SNP_A-2000337 AA 0.007022 AA 1565.539795 347.401947
SNP_A-2000342 AA 0.007603 AA 4673.024414 941.073975
SNP_A-4268173 AB 0.012877 AB 1049.566772 1080.305786

Total number of rows: 909622

Table truncated, full table size 46130 Kbytes.

Supplementary file Size Download File type/resource
GSM397795.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM397795.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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