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Sample GSM672453 Query DataSets for GSM672453
Status Public on Feb 17, 2011
Title 2332_Child_Father (Mapping250_Sty)
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 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 0.017699 AB -0.074540 12.207815
AFFX-2315061 BB 0.014065 BB -0.828523 11.133778
AFFX-2315062 BB 0.012934 BB -0.723639 10.451514
AFFX-2315057 AB 0.002810 AB -0.101586 10.539494
AFFX-2315058 AA 0.014408 AA 0.757756 12.084739
AFFX-2315059 BB 0.003695 BB -0.801466 10.692398
AFFX-2315063 AA 0.004350 AA 0.823499 10.693300
AFFX-2315064 BB 0.003557 BB -0.457652 9.790588
AFFX-2315065 AB 0.008648 AB -0.096115 10.448768
AFFX-2315066 AB 0.011275 AB -0.007163 10.425889
AFFX-2315067 AB 0.002797 AB 0.026666 11.251476
AFFX-2315068 AB 0.005951 AB 0.196208 10.840193
AFFX-2315069 AA 0.003921 AA 0.714092 9.721778
AFFX-2315070 BB 0.007108 BB -0.634879 10.456748
AFFX-2315071 AA 0.002591 AA 0.813559 10.144839
AFFX-2315072 AA 0.007580 AA 0.751967 11.249529
AFFX-2315073 AA 0.011580 AA 0.821927 10.801136
AFFX-2315074 AB 0.014300 AB 0.160899 9.832219
AFFX-2315075 AA 0.009361 AA 0.766554 11.635099
AFFX-2315076 AA 0.012440 AA 0.637590 11.255392

Total number of rows: 238354

Table truncated, full table size 11216 Kbytes.

Supplementary file Size Download File type/resource
GSM672453_2332_Father_Sty.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM672453_2332_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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