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Sample GSM672450 Query DataSets for GSM672450
Status Public on Feb 17, 2011
Title 1511_Child_Father (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 1511
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 BB 0.004450 BB -0.738317 11.960393
AFFX-2315061 AA 0.006293 AA 0.855228 11.096706
AFFX-2315062 AA 0.007831 AA 0.704982 10.299221
AFFX-2315057 AB 0.010458 AB -0.124554 10.464674
AFFX-2315058 AA 0.042032 AA 0.720790 12.097400
AFFX-2315059 AB 0.009965 AB 0.289446 10.837239
AFFX-2315063 AA 0.000172 AA 0.810093 10.538740
AFFX-2315064 BB 0.020772 BB -0.411163 9.980885
AFFX-2315065 BB 0.020966 BB -0.557960 10.393053
AFFX-2315066 BB 0.029364 BB -0.721287 10.626318
AFFX-2315067 AB 0.026097 AB 0.110467 11.375034
AFFX-2315068 AB 0.001486 AB 0.084826 10.765570
AFFX-2315069 AB 0.005804 AB -0.034569 9.797373
AFFX-2315070 BB 0.010019 BB -0.566882 10.410002
AFFX-2315071 AB 0.002446 AB -0.149159 10.447832
AFFX-2315072 AA 0.001978 AA 0.773938 11.183365
AFFX-2315073 AB 0.001417 AB 0.151616 10.681073
AFFX-2315074 BB 0.181371 BB -0.357157 9.835396
AFFX-2315075 BB 0.048189 BB -0.593347 11.775556
AFFX-2315076 AB 0.012660 AB -0.083225 11.342533

Total number of rows: 238354

Table truncated, full table size 11209 Kbytes.

Supplementary file Size Download File type/resource
GSM672450_1511_Father_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672450_1511_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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