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Sample GSM672458 Query DataSets for GSM672458
Status Public on Feb 17, 2011
Title 2569_Child (Mapping250_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 2569
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 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 AB 0.016481 AB -0.013260 12.369800
AFFX-2315061 BB 0.002275 BB -0.754635 11.373227
AFFX-2315062 BB 0.084161 BB -0.749025 10.836830
AFFX-2315057 BB 0.086770 BB -0.565093 10.832574
AFFX-2315058 AA 0.049888 AA 0.686671 12.480503
AFFX-2315059 AB 0.026617 AB 0.129043 11.263357
AFFX-2315063 AA 0.093744 AA 0.825301 11.195667
AFFX-2315064 AB 0.028930 AB 0.253132 10.366823
AFFX-2315065 AB 0.037200 AB 0.009651 10.740499
AFFX-2315066 AB 0.098116 AB -0.146236 10.904506
AFFX-2315067 AB 0.036427 AB -0.071230 11.705163
AFFX-2315068 AB 0.025884 AB 0.059275 11.249251
AFFX-2315069 AB 0.010583 AB -0.207284 10.283399
AFFX-2315070 BB 0.075707 BB -0.666729 10.833832
AFFX-2315071 AB 0.034984 AB -0.114940 11.044744
AFFX-2315072 AB 0.067823 AB -0.032032 11.750390
AFFX-2315073 AA 0.136076 AA 0.756927 11.335402
AFFX-2315074 BB 0.043630 BB -0.533022 10.287809
AFFX-2315075 AA 0.071055 AA 0.707586 12.032823
AFFX-2315076 AB 0.069037 AB -0.013293 11.575358

Total number of rows: 238354

Table truncated, full table size 11257 Kbytes.




Supplementary file Size Download File type/resource
GSM672458_2569_Child_Sty.CEL.gz 27.0 Mb (ftp)(http) CEL
GSM672458_2569_Child_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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