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Sample GSM672418 Query DataSets for GSM672418
Status Public on Feb 17, 2011
Title 2894_Child_Mother (Mapping250_Nsp)
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
E-mail(s) tbtucker@interchange.ubc.ca
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
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
AFFX-2315060 AA 0.004877 AA 0.656999 11.623797
AFFX-2315061 BB 0.005638 BB -0.755998 10.647243
AFFX-2315062 BB 0.006905 BB -0.638827 10.409354
AFFX-2315057 AB 0.030019 AB -0.203501 10.662649
AFFX-2315058 AA 0.015525 AA 0.672176 11.062058
AFFX-2315059 BB 0.011507 BB -0.594345 10.145867
AFFX-2315063 AB 0.000096 AB -0.072524 10.719254
AFFX-2315064 AA 0.006198 AA 0.838407 10.777095
AFFX-2315065 AA 0.040625 AA 0.457222 9.992607
AFFX-2315066 BB 0.043777 BB -0.724940 10.189833
AFFX-2315067 BB 0.104254 BB -0.586591 10.674540
AFFX-2315068 AA 0.007002 AA 0.803409 10.627402
AFFX-2315069 AB 0.002752 AB -0.106974 10.666262
AFFX-2315070 BB 0.035957 BB -0.723063 10.493500
AFFX-2315071 AA 0.037961 AA 0.706431 9.404163
AFFX-2315072 AA 0.062636 AA 0.562114 10.472082
AFFX-2315073 AB 0.002228 AB 0.196347 10.585985
AFFX-2315074 BB 0.032635 BB -0.653360 10.170864
AFFX-2315075 AA 0.025678 AA 0.710789 11.503505
AFFX-2315076 BB 0.028899 BB -0.595691 10.649384

Total number of rows: 262314

Table truncated, full table size 12370 Kbytes.




Supplementary file Size Download File type/resource
GSM672418_2894_Mother_Nsp.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM672418_2894_Mother_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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