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Sample GSM397812 Query DataSets for GSM397812
Status Public on Jul 31, 2010
Title Blood-Ctrl-0835-rep1
Sample type genomic
 
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 2 / 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
ID_REF PROBE SET NAME
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
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AB 0.001842 AB 3061.953125 3238.743652
SNP_A-1967418 BB 0.000273 BB 262.413879 727.375427
SNP_A-1969580 BB 0.009090 BB 900.483765 3134.918457
SNP_A-4263484 AB 0.004945 AB 1738.200317 1099.505615
SNP_A-1978185 AA 0.003449 AA 1615.420410 362.468567
SNP_A-4264431 AB 0.004572 AB 1329.374878 832.195740
SNP_A-1980898 BB 0.005172 BB 233.106308 1034.950073
SNP_A-1983139 AA 0.001177 AA 4479.623047 1145.653687
SNP_A-4265735 AA 0.000372 AA 2780.698975 588.488586
SNP_A-1995832 BB 0.002168 BB 609.607727 2528.806885
SNP_A-1995893 BB 0.003841 BB 361.568909 2878.388672
SNP_A-1997689 BB 0.002795 BB 810.169250 4266.953613
SNP_A-1997709 AA 0.003912 AA 1668.577393 257.206940
SNP_A-1997896 AB 0.001551 AB 1055.573975 1705.284058
SNP_A-1997922 AB 0.002383 AB 747.728027 720.819275
SNP_A-2000230 AA 0.001086 AA 2812.560303 1114.013672
SNP_A-2000332 AB 0.002847 AB 3084.819092 2972.432129
SNP_A-2000337 AA 0.001878 AA 1637.250854 265.052979
SNP_A-2000342 AA 0.000802 AA 4160.648438 1071.301880
SNP_A-4268173 AB 0.003135 AB 915.506409 860.735107

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM397812.CEL.gz 31.0 Mb (ftp)(http) CEL
GSM397812.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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