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Sample GSM672459 Query DataSets for GSM672459
Status Public on Feb 17, 2011
Title 2569_Child_Father (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2569
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 GPL3720
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 0.006579 AB -0.102559 12.496901
AFFX-2315061 BB 0.000947 BB -0.771607 11.418016
AFFX-2315062 AB 0.062177 AB -0.142198 10.845644
AFFX-2315057 BB 0.135249 BB -0.486002 10.955101
AFFX-2315058 AA 0.022412 AA 0.725402 12.406156
AFFX-2315059 BB 0.015425 BB -0.760634 10.931927
AFFX-2315063 AB 0.034302 AB -0.112246 11.350163
AFFX-2315064 AA 0.111573 AA 0.754786 10.463574
AFFX-2315065 BB 0.017520 BB -0.487717 10.752833
AFFX-2315066 AB 0.019004 AB 0.046018 10.602983
AFFX-2315067 AB 0.027688 AB 0.008403 11.637259
AFFX-2315068 AB 0.015271 AB 0.189848 11.051393
AFFX-2315069 AB 0.023148 AB -0.134316 10.045092
AFFX-2315070 BB 0.062642 BB -0.510470 10.838271
AFFX-2315071 AB 0.017195 AB -0.187421 10.765717
AFFX-2315072 AA 0.148163 AA 0.744795 11.532896
AFFX-2315073 AA 0.076330 AA 0.790925 11.149834
AFFX-2315074 BB 0.019336 BB -0.409000 10.164453
AFFX-2315075 AA 0.064309 AA 0.732098 12.031678
AFFX-2315076 AB 0.058993 AB -0.025694 11.542543

Total number of rows: 238354

Table truncated, full table size 11251 Kbytes.

Supplementary file Size Download File type/resource
GSM672459_2569_Father_Sty.CEL.gz 26.1 Mb (ftp)(http) CEL
GSM672459_2569_Father_Sty.chp.gz 3.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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