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Sample GSM672924 Query DataSets for GSM672924
Status Public on Feb 17, 2011
Title 9609_Father (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 9609
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 0.002180 AB -0.107622 12.433184
AFFX-2315061 BB 0.002970 BB -0.785332 11.370701
AFFX-2315062 AA 0.105187 AA 0.727390 10.841491
AFFX-2315057 BB 0.114923 BB -0.597548 10.874837
AFFX-2315058 AA 0.013816 AA 0.719393 12.366780
AFFX-2315059 AB 0.023631 AB 0.252541 11.199161
AFFX-2315063 AA 0.015259 AA 0.801751 10.856700
AFFX-2315064 AB 0.280451 AB 0.373221 10.574012
AFFX-2315065 BB 0.014364 BB -0.483660 10.737854
AFFX-2315066 BB 0.059285 BB -0.671043 10.807833
AFFX-2315067 AB 0.012133 AB 0.049878 11.508971
AFFX-2315068 AA 0.014802 AA 0.811863 11.075877
AFFX-2315069 BB 0.030895 BB -0.722921 10.165684
AFFX-2315070 AA 0.037687 AA 0.589622 10.678398
AFFX-2315071 AA 0.050588 AA 0.810083 10.647403
AFFX-2315072 AB 0.046824 AB 0.006235 11.626238
AFFX-2315073 AB 0.042658 AB 0.065760 11.179853
AFFX-2315074 AB 0.230950 AB -0.078695 10.072590
AFFX-2315075 AA 0.058196 AA 0.720134 11.996092
AFFX-2315076 AB 0.104477 AB 0.042188 11.622279

Total number of rows: 238354

Table truncated, full table size 11253 Kbytes.

Supplementary file Size Download File type/resource
GSM672924_9609_Father_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672924_9609_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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