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Sample GSM672415 Query DataSets for GSM672415
Status Public on Feb 17, 2011
Title 2569_Child_Mother (Mapping250_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2569
family member: Mother
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 0.076804 AB -0.231310 12.091523
AFFX-2315061 BB 0.010155 BB -0.811629 10.965757
AFFX-2315062 BB 0.008019 BB -0.652845 10.719016
AFFX-2315057 AB 0.106228 AB -0.167649 10.641378
AFFX-2315058 AA 0.023729 AA 0.743286 11.637199
AFFX-2315059 AA 0.192123 AA 0.709246 10.357358
AFFX-2315063 AA 0.002609 AA 0.779916 10.723830
AFFX-2315064 BB 0.007263 BB -0.771522 10.768332
AFFX-2315065 AA 0.014999 AA 0.470142 10.362200
AFFX-2315066 BB 0.011847 BB -0.711800 10.624008
AFFX-2315067 BB 0.094958 BB -0.570810 10.925897
AFFX-2315068 AA 0.017832 AA 0.789437 10.666024
AFFX-2315069 AB 0.069578 AB -0.311614 10.550471
AFFX-2315070 AB 0.102453 AB -0.164596 10.558000
AFFX-2315071 AA 0.130063 AA 0.508587 9.755391
AFFX-2315072 BB 0.173921 BB -0.475245 10.549482
AFFX-2315073 AB 0.015947 AB 0.144820 10.649021
AFFX-2315074 BB 0.118042 BB -0.513087 10.276827
AFFX-2315075 AA 0.038955 AA 0.758956 11.792736
AFFX-2315076 AB 0.023722 AB 0.048137 10.809709

Total number of rows: 262314

Table truncated, full table size 12379 Kbytes.

Supplementary file Size Download File type/resource
GSM672415_2569_Mother_Nsp.CEL.gz 25.2 Mb (ftp)(http) CEL
GSM672415_2569_Mother_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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