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Sample GSM672487 Query DataSets for GSM672487
Status Public on Feb 17, 2011
Title 8960_Child_Mother (Mapping250_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 8960
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 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 BB 0.003193 BB -0.705347 12.250278
AFFX-2315061 AB 0.000923 AB 0.157411 11.694668
AFFX-2315062 AB 0.025701 AB -0.118551 10.308639
AFFX-2315057 BB 0.026939 BB -0.475578 10.540459
AFFX-2315058 AA 0.031185 AA 0.671792 12.060065
AFFX-2315059 AB 0.001976 AB 0.260330 10.854452
AFFX-2315063 AB 0.009684 AB -0.181783 11.011977
AFFX-2315064 AA 0.052630 AA 0.696833 10.290085
AFFX-2315065 AB 0.020623 AB 0.004339 10.456642
AFFX-2315066 BB 0.013173 BB -0.637716 10.382952
AFFX-2315067 BB 0.000915 BB -0.573730 11.312854
AFFX-2315068 AB 0.004669 AB 0.154973 10.676752
AFFX-2315069 AB 0.008079 AB -0.148982 10.190096
AFFX-2315070 AB 0.063852 AB -0.170097 10.417841
AFFX-2315071 AA 0.021898 AA 0.683328 10.269537
AFFX-2315072 AA 0.027184 AA 0.682794 11.076906
AFFX-2315073 AA 0.005558 AA 0.737681 10.628836
AFFX-2315074 AB 0.150880 AB 0.210177 9.815859
AFFX-2315075 AA 0.014728 AA 0.688928 11.697373
AFFX-2315076 AB 0.003888 AB 0.023323 11.138080

Total number of rows: 238354

Table truncated, full table size 11254 Kbytes.




Supplementary file Size Download File type/resource
GSM672487_8960_Mother_Sty.CEL.gz 26.5 Mb (ftp)(http) CEL
GSM672487_8960_Mother_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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