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Sample GSM672894 Query DataSets for GSM672894
Status Public on Feb 17, 2011
Title 3094_Father (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 3094
family member: Father
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 0.007636 AB -0.098011 12.220621
AFFX-2315061 AA 0.007866 AA 0.887816 11.530933
AFFX-2315062 AB 0.128524 AB -0.174228 10.151071
AFFX-2315057 AB 0.476600 AB -0.145661 10.080397
AFFX-2315058 BB 0.013343 BB -0.860020 11.862171
AFFX-2315059 AB 0.027907 AB 0.305431 11.109315
AFFX-2315063 AA 0.044353 AA 0.806802 10.483287
AFFX-2315064 AB 0.430954 AB 0.392675 10.302615
AFFX-2315065 AB 0.466137 AB 0.113037 10.187105
AFFX-2315066 AB 0.017685 AB -0.033570 10.189603
AFFX-2315067 BB 0.096996 BB -0.692653 11.233907
AFFX-2315068 AB 0.011593 AB 0.149343 10.575327
AFFX-2315069 AB 0.096482 AB -0.251602 9.905775
AFFX-2315070 BB 0.060454 BB -0.563623 10.401175
AFFX-2315071 AB 0.014168 AB -0.089489 10.088987
AFFX-2315072 AB 0.149401 AB 0.305885 11.292134
AFFX-2315073 BB 0.025283 BB -0.716316 10.609990
AFFX-2315074 BB 0.115894 BB -0.451336 9.636981
AFFX-2315075 AB 0.147393 AB 0.239546 11.711568
AFFX-2315076 AB 0.014750 AB -0.017534 11.316594

Total number of rows: 238354

Table truncated, full table size 11253 Kbytes.

Supplementary file Size Download File type/resource
GSM672894_3094_Father_Sty.CEL.gz 24.9 Mb (ftp)(http) CEL
GSM672894_3094_Father_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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