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Sample GSM672460 Query DataSets for GSM672460
Status Public on Feb 17, 2011
Title 2569_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2569
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 0.001095 AB -0.103854 12.401801
AFFX-2315061 BB 0.013662 BB -0.830895 11.305984
AFFX-2315062 BB 0.073251 BB -0.647553 10.775176
AFFX-2315057 BB 0.050282 BB -0.422711 10.735648
AFFX-2315058 AA 0.026118 AA 0.746894 12.375402
AFFX-2315059 NC 0.633646 AB 0.520069 11.156289
AFFX-2315063 NC 0.919087 AA 0.558077 11.255153
AFFX-2315064 AB 0.043657 AB 0.214573 10.360635
AFFX-2315065 AB 0.023980 AB 0.027913 10.665146
AFFX-2315066 BB 0.183144 BB -0.546419 10.747494
AFFX-2315067 NC 0.554094 BB -0.430578 11.521982
AFFX-2315068 AA 0.119161 AA 0.696445 11.126863
AFFX-2315069 AB 0.020604 AB -0.144730 10.068202
AFFX-2315070 BB 0.395097 BB -0.387387 10.724465
AFFX-2315071 NC 0.669520 AA 0.547993 10.817183
AFFX-2315072 AB 0.202330 AB -0.313331 11.685890
AFFX-2315073 AB 0.379839 AB 0.435193 11.196466
AFFX-2315074 BB 0.033472 BB -0.521907 10.057815
AFFX-2315075 AA 0.063776 AA 0.778347 12.030806
AFFX-2315076 AB 0.109676 AB 0.042546 11.638808

Total number of rows: 238354

Table truncated, full table size 11253 Kbytes.

Supplementary file Size Download File type/resource
GSM672460_2569_Mother_Sty.CEL.gz 26.3 Mb (ftp)(http) CEL
GSM672460_2569_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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