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Sample GSM672921 Query DataSets for GSM672921
Status Public on Feb 17, 2011
Title 9390_Father (Mapping250K_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 9390
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 0.005453 AA 0.653236 11.955233
AFFX-2315061 BB 0.002199 BB -0.785107 10.893521
AFFX-2315062 AB 0.001889 AB -0.062768 10.269575
AFFX-2315057 BB 0.019138 BB -0.499258 10.377166
AFFX-2315058 AA 0.012469 AA 0.745188 12.048301
AFFX-2315059 AA 0.001819 AA 0.811540 10.892261
AFFX-2315063 AA 0.000063 AA 0.801613 10.530724
AFFX-2315064 AB 0.000032 AB 0.279307 10.068852
AFFX-2315065 AA 0.023543 AA 0.411556 10.344109
AFFX-2315066 BB 0.010777 BB -0.670673 10.415404
AFFX-2315067 BB 0.005536 BB -0.590102 10.911660
AFFX-2315068 AA 0.001726 AA 0.827319 10.640167
AFFX-2315069 AA 0.014731 AA 0.628805 9.686799
AFFX-2315070 BB 0.006614 BB -0.590470 10.470190
AFFX-2315071 AB 0.009141 AB -0.251277 10.310387
AFFX-2315072 AA 0.004514 AA 0.778418 11.138179
AFFX-2315073 AB 0.006829 AB 0.189557 10.575661
AFFX-2315074 AB 0.013257 AB 0.150964 9.755323
AFFX-2315075 AA 0.005012 AA 0.745730 11.599115
AFFX-2315076 BB 0.008652 BB -0.747105 11.152255

Total number of rows: 238354

Table truncated, full table size 11207 Kbytes.




Supplementary file Size Download File type/resource
GSM672921_9390_Father_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672921_9390_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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