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Sample GSM672474 Query DataSets for GSM672474
Status Public on Feb 17, 2011
Title 8135_Child_Father (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 8135
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 AA 0.001735 AA 0.657986 11.866220
AFFX-2315061 BB 0.013231 BB -0.812382 11.113362
AFFX-2315062 AB 0.026462 AB 0.001363 10.118693
AFFX-2315057 BB 0.033629 BB -0.489915 10.311913
AFFX-2315058 AA 0.009221 AA 0.744478 11.872382
AFFX-2315059 AB 0.020318 AB 0.297755 10.553017
AFFX-2315063 AB 0.012120 AB -0.167268 10.633126
AFFX-2315064 AB 0.155284 AB 0.282969 9.749003
AFFX-2315065 AA 0.031956 AA 0.526480 10.056705
AFFX-2315066 AA 0.012255 AA 0.736178 10.036181
AFFX-2315067 BB 0.023447 BB -0.567436 10.811731
AFFX-2315068 AA 0.028403 AA 0.829984 10.399135
AFFX-2315069 AA 0.003052 AA 0.717819 9.744580
AFFX-2315070 AA 0.019738 AA 0.534597 10.033269
AFFX-2315071 AB 0.019384 AB -0.119320 9.935132
AFFX-2315072 AA 0.061206 AA 0.709142 10.847237
AFFX-2315073 AA 0.042865 AA 0.767071 10.248083
AFFX-2315074 BB 0.233652 BB -0.329679 9.546687
AFFX-2315075 AB 0.001213 AB 0.053937 11.522269
AFFX-2315076 BB 0.036391 BB -0.684448 10.777344

Total number of rows: 238354

Table truncated, full table size 11216 Kbytes.

Supplementary file Size Download File type/resource
GSM672474_8135_Father_Sty.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM672474_8135_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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