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Sample GSM672408 Query DataSets for GSM672408
Status Public on Feb 17, 2011
Title 2332_Child_Father (Mapping250_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2332
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
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

Data table
AFFX-2315060 AB 0.209777 AB 0.158424 11.677158
AFFX-2315061 BB 0.010505 BB -0.791127 10.955677
AFFX-2315062 BB 0.016236 BB -0.662313 10.601089
AFFX-2315057 AB 0.110668 AB -0.140295 11.075433
AFFX-2315058 AA 0.015695 AA 0.657098 11.185439
AFFX-2315059 BB 0.005242 BB -0.609778 10.200038
AFFX-2315063 AA 0.010182 AA 0.802046 10.690881
AFFX-2315064 BB 0.007154 BB -0.761548 10.586665
AFFX-2315065 AB 0.016017 AB -0.000189 10.357086
AFFX-2315066 AB 0.001872 AB 0.029792 10.437107
AFFX-2315067 AB 0.007929 AB 0.037632 10.908739
AFFX-2315068 AB 0.007665 AB 0.065488 10.596979
AFFX-2315069 AA 0.001490 AA 0.757726 10.355523
AFFX-2315070 BB 0.009093 BB -0.614823 10.635582
AFFX-2315071 AA 0.007391 AA 0.633921 9.757059
AFFX-2315072 AA 0.044522 AA 0.473262 10.875350
AFFX-2315073 AA 0.002207 AA 0.707987 10.552053
AFFX-2315074 AB 0.002551 AB 0.019929 10.360575
AFFX-2315075 AA 0.080767 AA 0.689568 11.773021
AFFX-2315076 AA 0.013407 AA 0.471539 10.642455

Total number of rows: 262314

Table truncated, full table size 12366 Kbytes.

Supplementary file Size Download File type/resource
GSM672408_2332_Father_Nsp.CEL.gz 25.8 Mb (ftp)(http) CEL
GSM672408_2332_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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