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Sample GSM672451 Query DataSets for GSM672451
Status Public on Feb 17, 2011
Title 1511_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 1511
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 0.012765 AB -0.168082 11.860952
AFFX-2315061 BB 0.001548 BB -0.787691 10.777668
AFFX-2315062 BB 0.005991 BB -0.704745 10.403410
AFFX-2315057 BB 0.004462 BB -0.539297 10.410466
AFFX-2315058 AB 0.008867 AB 0.132994 11.691924
AFFX-2315059 AA 0.003076 AA 0.804595 10.779457
AFFX-2315063 BB 0.008468 BB -0.762994 10.726127
AFFX-2315064 AA 0.016115 AA 0.714492 9.982784
AFFX-2315065 BB 0.089794 BB -0.586619 10.093411
AFFX-2315066 AA 0.019267 AA 0.724859 9.963844
AFFX-2315067 AB 0.015922 AB 0.096837 11.073581
AFFX-2315068 AA 0.014719 AA 0.798550 10.517569
AFFX-2315069 AA 0.029392 AA 0.623866 9.513560
AFFX-2315070 AB 0.035537 AB -0.165835 10.244527
AFFX-2315071 BB 0.007152 BB -0.789022 10.235039
AFFX-2315072 AA 0.022345 AA 0.774480 11.000982
AFFX-2315073 AA 0.012297 AA 0.783581 10.422462
AFFX-2315074 BB 0.103814 BB -0.425624 9.538732
AFFX-2315075 AB 0.276615 AB -0.167263 11.040056
AFFX-2315076 BB 0.003485 BB -0.681191 10.995192

Total number of rows: 238354

Table truncated, full table size 11203 Kbytes.

Supplementary file Size Download File type/resource
GSM672451_1511_Mother_Sty.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM672451_1511_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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