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Sample GSM672859 Query DataSets for GSM672859
Status Public on Feb 17, 2011
Title 5993_Mother (Mapping250K_Nsp)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 5993
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 AB 0.011041 AB -0.146077 12.109460
AFFX-2315061 AB 0.005682 AB 0.117542 11.132889
AFFX-2315062 BB 0.022737 BB -0.592277 10.613982
AFFX-2315057 AA 0.027066 AA 0.525383 10.540125
AFFX-2315058 AA 0.015712 AA 0.712147 11.693211
AFFX-2315059 AA 0.013521 AA 0.773932 10.588840
AFFX-2315063 AA 0.007719 AA 0.766309 10.674187
AFFX-2315064 AB 0.003203 AB 0.194292 11.112507
AFFX-2315065 AB 0.006753 AB -0.040745 10.639912
AFFX-2315066 BB 0.003277 BB -0.633798 10.650280
AFFX-2315067 AB 0.001565 AB 0.018565 11.211443
AFFX-2315068 BB 0.002436 BB -0.663742 10.724740
AFFX-2315069 AB 0.000850 AB -0.150416 10.791839
AFFX-2315070 AA 0.031040 AA 0.639357 10.492100
AFFX-2315071 BB 0.022575 BB -0.772574 9.910840
AFFX-2315072 AB 0.018231 AB -0.135813 10.892031
AFFX-2315073 AB 0.018474 AB 0.088819 10.650957
AFFX-2315074 AB 0.012948 AB 0.051487 10.364099
AFFX-2315075 AB 0.032031 AB 0.148614 11.509151
AFFX-2315076 AA 0.039541 AA 0.471161 10.754859

Total number of rows: 262314

Table truncated, full table size 12381 Kbytes.




Supplementary file Size Download File type/resource
GSM672859_5993_Mother_Nsp.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM672859_5993_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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