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Sample GSM672896 Query DataSets for GSM672896
Status Public on Feb 17, 2011
Title 3519_Child (Mapping250K_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 3519
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 0.008588 AB -0.042321 11.883248
AFFX-2315061 AB 0.003136 AB 0.083728 11.110337
AFFX-2315062 BB 0.024307 BB -0.690719 10.512059
AFFX-2315057 AB 0.007046 AB -0.080829 10.400694
AFFX-2315058 AA 0.010871 AA 0.785021 11.860318
AFFX-2315059 BB 0.002643 BB -0.775307 10.447567
AFFX-2315063 AB 0.006040 AB -0.094170 10.931872
AFFX-2315064 AB 0.118287 AB 0.372296 10.074249
AFFX-2315065 AB 0.192660 AB -0.136095 10.059216
AFFX-2315066 BB 0.047265 BB -0.708051 10.185940
AFFX-2315067 AB 0.003112 AB 0.083805 11.183119
AFFX-2315068 AA 0.001759 AA 0.849342 10.639068
AFFX-2315069 BB 0.045493 BB -0.676036 9.644100
AFFX-2315070 AB 0.037085 AB 0.062088 10.360202
AFFX-2315071 AB 0.004880 AB -0.093003 10.256945
AFFX-2315072 AA 0.007354 AA 0.766726 11.065607
AFFX-2315073 AB 0.002131 AB 0.087574 10.571913
AFFX-2315074 AB 0.006003 AB 0.057175 9.731368
AFFX-2315075 AB 0.001374 AB 0.102195 11.599639
AFFX-2315076 AA 0.046576 AA 0.657295 10.808162

Total number of rows: 238354

Table truncated, full table size 11212 Kbytes.




Supplementary file Size Download File type/resource
GSM672896_3519_Child_Sty.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM672896_3519_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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