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Sample GSM672414 Query DataSets for GSM672414
Status Public on Feb 17, 2011
Title 2569_Child_Father (Mapping250_Nsp)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2569
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 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 0.003241 AB -0.122644 12.149369
AFFX-2315061 BB 0.001319 BB -0.805254 11.081725
AFFX-2315062 AB 0.026114 AB -0.059480 10.643412
AFFX-2315057 BB 0.009421 BB -0.656214 11.095796
AFFX-2315058 AA 0.008178 AA 0.718188 11.557095
AFFX-2315059 BB 0.059373 BB -0.544670 10.157843
AFFX-2315063 AB 0.009521 AB 0.067107 10.936233
AFFX-2315064 AA 0.002876 AA 0.781243 11.059488
AFFX-2315065 BB 0.016335 BB -0.441856 10.619738
AFFX-2315066 AB 0.001589 AB -0.001789 10.671398
AFFX-2315067 NC 0.565395 AB 0.201028 10.825766
AFFX-2315068 AB 0.042637 AB 0.096018 10.570408
AFFX-2315069 AB 0.015763 AB -0.158543 10.518996
AFFX-2315070 BB 0.031898 BB -0.633569 10.703690
AFFX-2315071 AB 0.000187 AB -0.119782 9.867624
AFFX-2315072 AA 0.063703 AA 0.457675 10.826724
AFFX-2315073 AA 0.104675 AA 0.707336 10.555154
AFFX-2315074 BB 0.330265 BB -0.440386 10.172924
AFFX-2315075 AA 0.015766 AA 0.726224 11.851231
AFFX-2315076 AB 0.153488 AB 0.170568 10.842377

Total number of rows: 262314

Table truncated, full table size 12373 Kbytes.




Supplementary file Size Download File type/resource
GSM672414_2569_Father_Nsp.CEL.gz 25.0 Mb (ftp)(http) CEL
GSM672414_2569_Father_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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