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Sample GSM672406 Query DataSets for GSM672406
Status Public on Feb 17, 2011
Title 1511_Child_Mother (Mapping250_Nsp)
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 GPL3718
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 0.007163 AB -0.055527 11.966517
AFFX-2315061 BB 0.003721 BB -0.778814 10.873599
AFFX-2315062 BB 0.034170 BB -0.567906 10.403364
AFFX-2315057 BB 0.010204 BB -0.653356 10.784243
AFFX-2315058 AB 0.005722 AB 0.108771 11.117155
AFFX-2315059 AA 0.011972 AA 0.779401 10.546770
AFFX-2315063 BB 0.004667 BB -0.758125 10.966893
AFFX-2315064 AA 0.051980 AA 0.809125 11.006392
AFFX-2315065 BB 0.001481 BB -0.474728 10.355402
AFFX-2315066 AA 0.023498 AA 0.749710 10.520645
AFFX-2315067 AB 0.013401 AB 0.048277 11.114355
AFFX-2315068 AA 0.012409 AA 0.793149 10.527660
AFFX-2315069 AA 0.003311 AA 0.772350 10.540040
AFFX-2315070 AB 0.003393 AB -0.097815 10.658858
AFFX-2315071 BB 0.018761 BB -0.779267 9.805353
AFFX-2315072 AA 0.006546 AA 0.549007 10.671157
AFFX-2315073 AA 0.006153 AA 0.737064 10.637165
AFFX-2315074 BB 0.007989 BB -0.613675 10.359813
AFFX-2315075 AB 0.110004 AB -0.108905 11.210348
AFFX-2315076 BB 0.017309 BB -0.532638 10.750840

Total number of rows: 262314

Table truncated, full table size 12366 Kbytes.

Supplementary file Size Download File type/resource
GSM672406_1511_Mother_Nsp.CEL.gz 25.4 Mb (ftp)(http) CEL
GSM672406_1511_Mother_Nsp.chp.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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