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Sample GSM672472 Query DataSets for GSM672472
Status Public on Feb 17, 2011
Title 6942_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 6942
family member: Mother
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 0.021659 AB -0.130742 12.202399
AFFX-2315061 AA 0.000746 AA 0.860907 10.989090
AFFX-2315062 AA 0.004689 AA 0.605477 10.183545
AFFX-2315057 AA 0.018841 AA 0.584879 10.277174
AFFX-2315058 AA 0.012340 AA 0.753210 12.066364
AFFX-2315059 AB 0.002413 AB 0.236582 10.662045
AFFX-2315063 AA 0.007256 AA 0.760771 10.395816
AFFX-2315064 AB 0.072452 AB 0.269087 9.848550
AFFX-2315065 AA 0.049988 AA 0.376553 10.177377
AFFX-2315066 BB 0.012571 BB -0.723446 10.340839
AFFX-2315067 BB 0.020326 BB -0.686507 10.958722
AFFX-2315068 AA 0.002050 AA 0.830827 10.622665
AFFX-2315069 AB 0.027377 AB -0.098253 9.490136
AFFX-2315070 AB 0.018578 AB -0.074083 10.152266
AFFX-2315071 BB 0.005035 BB -0.822428 10.202802
AFFX-2315072 AA 0.001108 AA 0.756063 11.110168
AFFX-2315073 AB 0.053708 AB 0.301377 10.705342
AFFX-2315074 BB 0.197122 BB -0.347860 9.805193
AFFX-2315075 AA 0.026649 AA 0.676973 11.580014
AFFX-2315076 AB 0.008376 AB -0.044020 11.017313

Total number of rows: 238354

Table truncated, full table size 11205 Kbytes.

Supplementary file Size Download File type/resource
GSM672472_6942_Mother_Sty.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM672472_6942_Mother_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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