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Sample GSM672466 Query DataSets for GSM672466
Status Public on Feb 17, 2011
Title 4821_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 4821
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 0.001600 AA 0.617646 12.328727
AFFX-2315061 AA 0.003017 AA 0.842897 11.539838
AFFX-2315062 AB 0.053944 AB -0.153133 10.280540
AFFX-2315057 AA 0.010547 AA 0.356161 10.540032
AFFX-2315058 AB 0.010171 AB 0.214246 12.304489
AFFX-2315059 AA 0.005837 AA 0.781736 11.056638
AFFX-2315063 AA 0.022454 AA 0.727386 10.441808
AFFX-2315064 BB 0.431072 BB -0.153502 10.142391
AFFX-2315065 AB 0.018092 AB -0.020248 10.704704
AFFX-2315066 BB 0.130530 BB -0.535007 10.596779
AFFX-2315067 AB 0.120671 AB 0.171256 11.227327
AFFX-2315068 AA 0.005502 AA 0.817653 10.866789
AFFX-2315069 AB 0.012683 AB -0.033546 10.434999
AFFX-2315070 BB 0.108094 BB -0.453685 10.741004
AFFX-2315071 BB 0.084904 BB -0.714875 10.129374
AFFX-2315072 AA 0.056872 AA 0.559599 10.918543
AFFX-2315073 AB 0.022167 AB 0.167466 10.220818
AFFX-2315074 BB 0.432821 BB -0.224188 9.918883
AFFX-2315075 AA 0.064425 AA 0.670844 11.248108
AFFX-2315076 AB 0.002060 AB 0.012549 11.157729

Total number of rows: 238354

Table truncated, full table size 11251 Kbytes.

Supplementary file Size Download File type/resource
GSM672466_4821_Mother_Sty.CEL.gz 25.2 Mb (ftp)(http) CEL
GSM672466_4821_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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