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Sample GSM672477 Query DataSets for GSM672477
Status Public on Feb 17, 2011
Title 8160_Child_Father (Mapping250_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 8160
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 0.000130 AA 0.693225 11.874096
AFFX-2315061 AB 0.002534 AB 0.139261 11.140018
AFFX-2315062 AA 0.004053 AA 0.684053 10.268084
AFFX-2315057 BB 0.003516 BB -0.582296 10.520099
AFFX-2315058 AA 0.011997 AA 0.734439 12.004509
AFFX-2315059 AB 0.022603 AB 0.322274 10.828468
AFFX-2315063 AB 0.009831 AB -0.227922 10.969781
AFFX-2315064 AB 0.046013 AB 0.342553 10.081385
AFFX-2315065 BB 0.010033 BB -0.533421 10.339852
AFFX-2315066 BB 0.005368 BB -0.708272 10.501918
AFFX-2315067 BB 0.021875 BB -0.687832 10.949683
AFFX-2315068 BB 0.001098 BB -0.812247 10.643981
AFFX-2315069 AB 0.002285 AB -0.065404 9.950001
AFFX-2315070 BB 0.009237 BB -0.642072 10.455153
AFFX-2315071 BB 0.003744 BB -0.832310 10.441036
AFFX-2315072 AA 0.006760 AA 0.782497 11.129850
AFFX-2315073 AA 0.003012 AA 0.782604 10.705106
AFFX-2315074 BB 0.001195 BB -0.514670 9.841565
AFFX-2315075 AB 0.003280 AB 0.031481 11.667611
AFFX-2315076 AB 0.003814 AB -0.060614 11.180226

Total number of rows: 238354

Table truncated, full table size 11214 Kbytes.




Supplementary file Size Download File type/resource
GSM672477_8160_Father_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672477_8160_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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