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Sample GSM672489 Query DataSets for GSM672489
Status Public on Feb 17, 2011
Title 8994_Child_Father (Mapping250_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 8994
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 0.001044 AA 0.601136 12.215318
AFFX-2315061 BB 0.011253 BB -0.799267 11.243869
AFFX-2315062 AB 0.027932 AB -0.058276 10.788454
AFFX-2315057 BB 0.131722 BB -0.620225 10.873230
AFFX-2315058 AA 0.019497 AA 0.746474 12.287993
AFFX-2315059 AA 0.029439 AA 0.821557 11.203712
AFFX-2315063 AA 0.050530 AA 0.811769 11.045633
AFFX-2315064 AA 0.134379 AA 0.723134 10.524481
AFFX-2315065 BB 0.080480 BB -0.416670 10.857449
AFFX-2315066 BB 0.068159 BB -0.685074 10.836423
AFFX-2315067 BB 0.025650 BB -0.632147 11.352962
AFFX-2315068 AA 0.012022 AA 0.844439 10.996963
AFFX-2315069 AA 0.043327 AA 0.565542 9.910587
AFFX-2315070 AB 0.027616 AB -0.067419 10.726161
AFFX-2315071 AA 0.031152 AA 0.791003 10.528761
AFFX-2315072 AA 0.156155 AA 0.739075 11.548908
AFFX-2315073 AB 0.054832 AB 0.185188 11.196925
AFFX-2315074 BB 0.037686 BB -0.472791 10.303363
AFFX-2315075 AA 0.050532 AA 0.736727 11.964741
AFFX-2315076 BB 0.035744 BB -0.680703 11.459672

Total number of rows: 238354

Table truncated, full table size 11252 Kbytes.




Supplementary file Size Download File type/resource
GSM672489_8994_Father_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672489_8994_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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