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Sample GSM672838 Query DataSets for GSM672838
Status Public on Feb 17, 2011
Title 1056_Father (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 1056
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 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 AA 0.005017 AA 0.622996 11.973361
AFFX-2315061 BB 0.003143 BB -0.759350 11.070850
AFFX-2315062 AA 0.014591 AA 0.660037 10.707408
AFFX-2315057 AB 0.014066 AB -0.071634 10.970593
AFFX-2315058 AA 0.055989 AA 0.701503 11.346805
AFFX-2315059 AB 0.006902 AB 0.282592 10.514667
AFFX-2315063 AA 0.003739 AA 0.821413 10.856293
AFFX-2315064 AB 0.005579 AB 0.281557 11.075366
AFFX-2315065 AA 0.204412 AA 0.314866 10.448940
AFFX-2315066 BB 0.004793 BB -0.629417 10.706254
AFFX-2315067 BB 0.020121 BB -0.586128 11.182092
AFFX-2315068 AB 0.015922 AB 0.272462 10.888079
AFFX-2315069 AB 0.002811 AB -0.186244 10.691162
AFFX-2315070 AA 0.004655 AA 0.668061 10.827402
AFFX-2315071 BB 0.007129 BB -0.713948 9.826789
AFFX-2315072 AA 0.027704 AA 0.491519 11.054665
AFFX-2315073 AA 0.013796 AA 0.786276 10.869493
AFFX-2315074 BB 0.021741 BB -0.628651 10.700176
AFFX-2315075 AA 0.002706 AA 0.682673 11.836735
AFFX-2315076 AB 0.059516 AB 0.090492 11.157985

Total number of rows: 262314

Table truncated, full table size 12380 Kbytes.

Supplementary file Size Download File type/resource
GSM672838_1056_Father_Nsp.CEL.gz 26.1 Mb (ftp)(http) CEL
GSM672838_1056_Father_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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