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Sample GSM397821 Query DataSets for GSM397821
Status Public on Jul 31, 2010
Title Blood-Ctrl-1686-rep1
Sample type genomic
 
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 5 / Father
twin #: NA
twin info: NA
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
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 0.004671 AB 2718.134033 2478.178223
SNP_A-1967418 BB 0.001791 BB 247.860504 669.889771
SNP_A-1969580 BB 0.001746 BB 1254.276978 4231.443359
SNP_A-4263484 AB 0.000464 AB 1955.273193 1385.850586
SNP_A-1978185 AA 0.011368 AA 1954.481445 361.982300
SNP_A-4264431 AA 0.002219 AA 1948.843872 358.007019
SNP_A-1980898 BB 0.001726 BB 224.352371 897.433289
SNP_A-1983139 AA 0.002925 AA 4415.236816 930.881042
SNP_A-4265735 AA 0.003025 AA 2615.516602 413.326477
SNP_A-1995832 BB 0.006299 BB 481.586975 1810.857544
SNP_A-1995893 BB 0.008444 BB 362.608704 2354.015625
SNP_A-1997689 BB 0.006020 BB 535.294189 3627.470703
SNP_A-1997709 AA 0.005033 AA 1720.336792 193.821091
SNP_A-1997896 BB 0.011284 BB 546.698792 2829.845459
SNP_A-1997922 AA 0.003532 AA 1128.371338 331.358398
SNP_A-2000230 AA 0.027267 AA 3747.854004 988.597839
SNP_A-2000332 AB 0.009894 AB 2453.021240 2592.187500
SNP_A-2000337 AA 0.006498 AA 2129.327881 241.129303
SNP_A-2000342 AA 0.000385 AA 4154.944336 1036.981812
SNP_A-4268173 AA 0.001225 AA 1314.215454 262.818604

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.




Supplementary file Size Download File type/resource
GSM397821.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM397821.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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