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Sample GSM672858 Query DataSets for GSM672858
Status Public on Feb 17, 2011
Title 5993_Father (Mapping250K_Nsp)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 5993
family member: Father
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label Biotin
Label protocol DNA samples were processed according to the instructions provided in the Affymetrix GeneChip® Mapping 500K Assay Manual
 
Hybridization protocol hybridized to GeneChip® Human Mapping 250K Nsp or 250K Sty arrays in an Affymetrix Hybridization Oven 640
Scan protocol images were obtained using an Affymetrix GeneChip® Scanner 3000 7G and GeneChip® Operating Software version 1.4
Data processing CNVs were detected using the Copy Number Analysis Tool (CNAT) (release cn-1.5.6_v3.2), which incorporates a Bayesian Robust Linear Model with the Mahalanobis distance classifier (BRLMM) algorithm to perform quantile normalization, followed by regression to reduce the PCR bias due to GC content and fragment length
An HMM-based algorithm implemented in CNAT4 was used to estimate copy number for each SNP in the context of its surrounding SNPs. The Gaussian bandwidth was set to 0 Kb and a minimum of 5 probes was required to detect a CNV. The findings were visualized using GeneChip Genotyping Analysis Software (GTYPE) from Affymetrix.
 
Submission date Feb 10, 2011
Last update date Feb 17, 2011
Contact name Tracy Tucker
E-mail(s) tbtucker@interchange.ubc.ca
Organization name University of British Columbia
Street address Box 153 4480 Oak Street
City Vancouver
ZIP/Postal code V6H3V4
Country Canada
 
Platform ID GPL3718
Series (2)
GSE27216 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Mapping250K_Nsp and Mapping250K_Sty)
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
AFFX-2315060 AA 0.007983 AA 0.607022 11.955018
AFFX-2315061 BB 0.003382 BB -0.778843 11.024452
AFFX-2315062 BB 0.039138 BB -0.671828 10.584182
AFFX-2315057 AB 0.021636 AB -0.116546 10.790895
AFFX-2315058 AA 0.052566 AA 0.629755 11.605304
AFFX-2315059 AB 0.005656 AB 0.236468 10.669764
AFFX-2315063 AB 0.000894 AB -0.053599 11.067335
AFFX-2315064 AB 0.006311 AB 0.240235 10.939394
AFFX-2315065 AB 0.001082 AB -0.036829 10.571291
AFFX-2315066 AB 0.010742 AB -0.015931 10.569587
AFFX-2315067 BB 0.028532 BB -0.595758 11.161345
AFFX-2315068 AB 0.016624 AB 0.274660 10.877320
AFFX-2315069 AA 0.003766 AA 0.749763 10.621932
AFFX-2315070 AB 0.011846 AB -0.093829 10.772878
AFFX-2315071 BB 0.037145 BB -0.756027 10.110278
AFFX-2315072 AA 0.013582 AA 0.492378 10.891693
AFFX-2315073 AB 0.008867 AB 0.085073 10.783923
AFFX-2315074 BB 0.010686 BB -0.560875 10.498926
AFFX-2315075 AA 0.086575 AA 0.674804 11.547507
AFFX-2315076 AA 0.028491 AA 0.442163 10.878315

Total number of rows: 262314

Table truncated, full table size 12386 Kbytes.




Supplementary file Size Download File type/resource
GSM672858_5993_Father_Nsp.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM672858_5993_Father_Nsp.chp.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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