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Sample GSM672854 Query DataSets for GSM672854
Status Public on Feb 17, 2011
Title 3519_Mother (Mapping250K_Nsp)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 3519
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 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 AB 0.000232 AB -0.079939 11.881561
AFFX-2315061 AB 0.005635 AB 0.097300 11.107437
AFFX-2315062 BB 0.005010 BB -0.659293 10.466344
AFFX-2315057 BB 0.010954 BB -0.652065 10.774240
AFFX-2315058 AA 0.007564 AA 0.669298 11.188049
AFFX-2315059 BB 0.020757 BB -0.518103 10.255460
AFFX-2315063 AA 0.000614 AA 0.752189 10.488775
AFFX-2315064 AB 0.004085 AB 0.273342 10.795831
AFFX-2315065 AB 0.006640 AB -0.020917 10.247808
AFFX-2315066 AB 0.020556 AB 0.119558 10.419686
AFFX-2315067 AB 0.020572 AB 0.092214 10.872901
AFFX-2315068 AB 0.014352 AB 0.246798 10.620256
AFFX-2315069 AB 0.001026 AB -0.107050 10.594087
AFFX-2315070 AB 0.033356 AB -0.165360 10.440576
AFFX-2315071 AA 0.008874 AA 0.578635 9.615614
AFFX-2315072 AA 0.057868 AA 0.489316 10.509554
AFFX-2315073 AB 0.015507 AB 0.051465 10.571971
AFFX-2315074 BB 0.034452 BB -0.511258 10.284723
AFFX-2315075 AB 0.004390 AB 0.065510 11.572601
AFFX-2315076 AA 0.014404 AA 0.496065 10.593451

Total number of rows: 262314

Table truncated, full table size 12358 Kbytes.




Supplementary file Size Download File type/resource
GSM672854_3519_Mother_Nsp.CEL.gz 26.3 Mb (ftp)(http) CEL
GSM672854_3519_Mother_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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