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Sample GSM672895 Query DataSets for GSM672895
Status Public on Feb 17, 2011
Title 3094_Mother (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 3094
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 AA 0.001259 AA 0.598850 12.209942
AFFX-2315061 BB 0.000319 BB -0.782741 11.565336
AFFX-2315062 AB 0.029216 AB 0.033806 10.616343
AFFX-2315057 NC 0.672323 BB -0.270513 10.399913
AFFX-2315058 AA 0.000629 AA 0.702809 12.228904
AFFX-2315059 AA 0.027513 AA 0.790638 11.183575
AFFX-2315063 AB 0.017337 AB -0.194627 11.086176
AFFX-2315064 BB 0.024628 BB -0.449351 9.987648
AFFX-2315065 AA 0.011551 AA 0.406465 10.489771
AFFX-2315066 BB 0.012437 BB -0.668483 10.599865
AFFX-2315067 BB 0.028692 BB -0.606714 11.443748
AFFX-2315068 AA 0.002874 AA 0.813893 10.934135
AFFX-2315069 AB 0.026714 AB -0.232619 10.197704
AFFX-2315070 BB 0.018673 BB -0.589008 10.719214
AFFX-2315071 AB 0.003103 AB -0.128685 10.551878
AFFX-2315072 AB 0.017624 AB -0.021593 11.370019
AFFX-2315073 AB 0.028352 AB 0.019384 10.878983
AFFX-2315074 BB 0.007540 BB -0.438459 9.951352
AFFX-2315075 AA 0.028077 AA 0.707350 11.822474
AFFX-2315076 AB 0.008734 AB 0.028041 11.212131

Total number of rows: 238354

Table truncated, full table size 11257 Kbytes.

Supplementary file Size Download File type/resource
GSM672895_3094_Mother_Sty.CEL.gz 27.0 Mb (ftp)(http) CEL
GSM672895_3094_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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