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Sample GSM672457 Query DataSets for GSM672457
Status Public on Feb 17, 2011
Title 2377_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2377
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 0.029874 AB 0.014360 12.130404
AFFX-2315061 AB 0.007724 AB 0.106806 10.804499
AFFX-2315062 AA 0.001870 AA 0.614431 10.110452
AFFX-2315057 AA 0.068041 AA 0.421908 10.416081
AFFX-2315058 AA 0.020205 AA 0.821532 11.896512
AFFX-2315059 AA 0.006961 AA 0.846146 10.795674
AFFX-2315063 AA 0.014648 AA 0.810488 10.307870
AFFX-2315064 AB 0.002238 AB 0.290282 10.046662
AFFX-2315065 BB 0.361182 BB -0.357595 10.452408
AFFX-2315066 BB 0.003935 BB -0.689350 10.450300
AFFX-2315067 AA 0.032612 AA 0.537090 11.068336
AFFX-2315068 AB 0.004961 AB 0.055674 10.595106
AFFX-2315069 AB 0.013691 AB -0.030771 9.636689
AFFX-2315070 BB 0.010138 BB -0.580594 10.473484
AFFX-2315071 AB 0.013978 AB -0.234320 10.096453
AFFX-2315072 AB 0.003042 AB 0.139551 11.140889
AFFX-2315073 BB 0.005275 BB -0.724259 10.376451
AFFX-2315074 AB 0.051544 AB 0.211016 9.771591
AFFX-2315075 AB 0.002239 AB 0.103523 11.675614
AFFX-2315076 AB 0.001544 AB 0.028370 11.231657

Total number of rows: 238354

Table truncated, full table size 11211 Kbytes.

Supplementary file Size Download File type/resource
GSM672457_2377_Mother_Sty.CEL.gz 25.6 Mb (ftp)(http) CEL
GSM672457_2377_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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