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Sample GSM672463 Query DataSets for GSM672463
Status Public on Feb 17, 2011
Title 2894_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2894
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 0.006643 AA 0.720509 11.780086
AFFX-2315061 BB 0.000520 BB -0.820914 10.833967
AFFX-2315062 BB 0.004885 BB -0.652130 10.207011
AFFX-2315057 AB 0.001504 AB -0.074786 10.553993
AFFX-2315058 AA 0.004621 AA 0.768547 11.887120
AFFX-2315059 BB 0.004433 BB -0.773837 10.401986
AFFX-2315063 AB 0.007639 AB -0.085538 10.945048
AFFX-2315064 AA 0.039397 AA 0.719944 10.285606
AFFX-2315065 AA 0.002575 AA 0.500108 10.260990
AFFX-2315066 BB 0.012990 BB -0.705510 10.298289
AFFX-2315067 BB 0.007908 BB -0.634703 11.136174
AFFX-2315068 AA 0.001178 AA 0.848083 10.649771
AFFX-2315069 AB 0.000025 AB -0.103545 9.892478
AFFX-2315070 BB 0.020210 BB -0.557351 10.451462
AFFX-2315071 AA 0.009525 AA 0.728036 10.218328
AFFX-2315072 AA 0.001433 AA 0.763279 11.204299
AFFX-2315073 AB 0.001397 AB 0.116166 10.574102
AFFX-2315074 BB 0.085761 BB -0.397432 9.857044
AFFX-2315075 AA 0.018775 AA 0.811684 11.557893
AFFX-2315076 BB 0.000135 BB -0.694586 11.107490

Total number of rows: 238354

Table truncated, full table size 11214 Kbytes.

Supplementary file Size Download File type/resource
GSM672463_2894_Mother_Sty.CEL.gz 25.6 Mb (ftp)(http) CEL
GSM672463_2894_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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