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Sample GSM672478 Query DataSets for GSM672478
Status Public on Feb 17, 2011
Title 8160_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 8160
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 0.000758 AB -0.081399 11.957084
AFFX-2315061 AB 0.003249 AB 0.156320 11.142260
AFFX-2315062 AB 0.002994 AB -0.044700 10.442142
AFFX-2315057 AB 0.017010 AB -0.034859 10.362039
AFFX-2315058 AA 0.085438 AA 0.680341 12.041352
AFFX-2315059 AA 0.006008 AA 0.785141 10.797810
AFFX-2315063 BB 0.003031 BB -0.781946 11.017043
AFFX-2315064 AB 0.031133 AB 0.331325 10.108950
AFFX-2315065 AA 0.007784 AA 0.523069 10.256429
AFFX-2315066 BB 0.006157 BB -0.706173 10.338274
AFFX-2315067 BB 0.000167 BB -0.609602 10.991889
AFFX-2315068 AB 0.002725 AB 0.177482 10.785132
AFFX-2315069 AA 0.004467 AA 0.698357 9.899168
AFFX-2315070 BB 0.002820 BB -0.618977 10.360993
AFFX-2315071 AB 0.006748 AB -0.209095 10.505736
AFFX-2315072 AA 0.007171 AA 0.777655 11.101828
AFFX-2315073 AB 0.013315 AB -0.006952 10.789227
AFFX-2315074 AB 0.031413 AB 0.191162 9.823268
AFFX-2315075 AA 0.003164 AA 0.749233 11.576824
AFFX-2315076 BB 0.001341 BB -0.713386 11.147886

Total number of rows: 238354

Table truncated, full table size 11217 Kbytes.

Supplementary file Size Download File type/resource
GSM672478_8160_Mother_Sty.CEL.gz 26.6 Mb (ftp)(http) CEL
GSM672478_8160_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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