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Sample GSM672416 Query DataSets for GSM672416
Status Public on Feb 17, 2011
Title 2894_Child (Mapping250_Nsp)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 2894
family member: Child
gender: Male
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 0.028426 AA 0.757052 11.799329
AFFX-2315061 AB 0.002981 AB 0.121393 10.785599
AFFX-2315062 BB 0.120904 BB -0.771488 10.250001
AFFX-2315057 AB 0.441954 AB -0.286890 10.302748
AFFX-2315058 AA 0.094711 AA 0.818527 11.046290
AFFX-2315059 AB 0.289232 AB 0.494123 10.446193
AFFX-2315063 AB 0.036994 AB -0.062156 10.279685
AFFX-2315064 AB 0.020793 AB 0.324868 10.602060
AFFX-2315065 NC 0.602245 AB -0.041483 9.503686
AFFX-2315066 BB 0.119025 BB -0.743524 9.940139
AFFX-2315067 BB 0.048545 BB -0.412548 10.850840
AFFX-2315068 AA 0.053600 AA 0.819616 10.408120
AFFX-2315069 BB 0.019577 BB -0.821786 10.267441
AFFX-2315070 BB 0.144850 BB -0.825640 10.344058
AFFX-2315071 AB 0.290283 AB 0.061283 8.942157
AFFX-2315072 AA 0.227806 AA 0.749362 10.315930
AFFX-2315073 AB 0.038759 AB 0.278775 10.435892
AFFX-2315074 BB 0.191920 BB -0.624097 9.730004
AFFX-2315075 AB 0.001850 AB 0.101285 11.447119
AFFX-2315076 BB 0.203881 BB -0.736575 10.252649

Total number of rows: 262314

Table truncated, full table size 12357 Kbytes.




Supplementary file Size Download File type/resource
GSM672416_2894_Child_Nsp.CEL.gz 24.5 Mb (ftp)(http) CEL
GSM672416_2894_Child_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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