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Sample GSM672486 Query DataSets for GSM672486
Status Public on Feb 17, 2011
Title 8960_Child_Father (Mapping250_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 8960
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
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 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
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 0.002544 AA 0.588220 12.190410
AFFX-2315061 AB 0.009457 AB 0.216727 11.756179
AFFX-2315062 BB 0.030259 BB -0.688589 10.638373
AFFX-2315057 AB 0.035086 AB -0.132364 10.530565
AFFX-2315058 AA 0.003920 AA 0.681495 12.276806
AFFX-2315059 AA 0.006176 AA 0.801022 10.897867
AFFX-2315063 AB 0.009156 AB -0.063412 11.127704
AFFX-2315064 AB 0.248740 AB 0.332583 10.083424
AFFX-2315065 AA 0.032158 AA 0.550985 10.371274
AFFX-2315066 BB 0.008888 BB -0.639826 10.410479
AFFX-2315067 BB 0.043412 BB -0.651948 11.294576
AFFX-2315068 AA 0.000734 AA 0.773897 10.864886
AFFX-2315069 AB 0.014446 AB -0.170693 10.141887
AFFX-2315070 AB 0.007853 AB -0.083382 10.425438
AFFX-2315071 AB 0.000813 AB -0.199315 10.374824
AFFX-2315072 AA 0.051649 AA 0.707913 11.203650
AFFX-2315073 AA 0.010777 AA 0.750689 10.606610
AFFX-2315074 NC 0.804224 AB 0.310447 9.865854
AFFX-2315075 BB 0.056278 BB -0.585714 11.836932
AFFX-2315076 BB 0.006252 BB -0.623675 11.155012

Total number of rows: 238354

Table truncated, full table size 11253 Kbytes.




Supplementary file Size Download File type/resource
GSM672486_8960_Father_Sty.CEL.gz 26.5 Mb (ftp)(http) CEL
GSM672486_8960_Father_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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