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Sample GSM672847 Query DataSets for GSM672847
Status Public on Feb 17, 2011
Title 2714_Father (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2714
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 BB 0.002127 BB -0.666550 12.131129
AFFX-2315061 AB 0.001601 AB 0.126279 11.312484
AFFX-2315062 AA 0.001656 AA 0.591789 10.667129
AFFX-2315057 AB 0.004368 AB -0.164391 10.877769
AFFX-2315058 AA 0.001793 AA 0.684040 11.600875
AFFX-2315059 AB 0.000433 AB 0.219446 10.552350
AFFX-2315063 AA 0.000981 AA 0.783185 10.753776
AFFX-2315064 AB 0.000272 AB 0.219449 11.052797
AFFX-2315065 AB 0.015720 AB 0.008195 10.536367
AFFX-2315066 AA 0.004017 AA 0.700288 10.775048
AFFX-2315067 BB 0.001823 BB -0.544392 11.204162
AFFX-2315068 BB 0.014306 BB -0.660825 10.997224
AFFX-2315069 AB 0.004291 AB -0.121371 10.855847
AFFX-2315070 AB 0.000085 AB -0.108385 10.900482
AFFX-2315071 BB 0.031624 BB -0.705233 10.050735
AFFX-2315072 AA 0.015493 AA 0.576732 10.943876
AFFX-2315073 AA 0.012861 AA 0.751514 11.033464
AFFX-2315074 AB 0.011863 AB -0.062149 10.607253
AFFX-2315075 AB 0.002812 AB 0.156540 11.704348
AFFX-2315076 AB 0.003594 AB 0.028911 11.016579

Total number of rows: 262314

Table truncated, full table size 12379 Kbytes.

Supplementary file Size Download File type/resource
GSM672847_2714_Father_Nsp.CEL.gz 26.5 Mb (ftp)(http) CEL
GSM672847_2714_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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