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Sample GSM672404 Query DataSets for GSM672404
Status Public on Feb 17, 2011
Title 1511_Child (Mapping250_Nsp)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 1511
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 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 0.002144 AB -0.099429 11.902770
AFFX-2315061 AB 0.002466 AB 0.155538 10.948836
AFFX-2315062 AB 0.012522 AB -0.062155 10.412992
AFFX-2315057 AB 0.000786 AB -0.115365 10.705621
AFFX-2315058 AA 0.006684 AA 0.719438 11.135307
AFFX-2315059 AB 0.035727 AB 0.364164 10.436721
AFFX-2315063 AB 0.001744 AB -0.066703 10.839604
AFFX-2315064 AB 0.017106 AB 0.259365 10.953191
AFFX-2315065 BB 0.008135 BB -0.447835 10.369447
AFFX-2315066 AB 0.003137 AB -0.018880 10.330947
AFFX-2315067 AA 0.015093 AA 0.574072 11.081862
AFFX-2315068 AA 0.006261 AA 0.743231 10.528831
AFFX-2315069 AA 0.009118 AA 0.710231 10.467749
AFFX-2315070 BB 0.037653 BB -0.588844 10.706546
AFFX-2315071 AB 0.000868 AB -0.142457 9.721789
AFFX-2315072 AA 0.008653 AA 0.520537 10.636811
AFFX-2315073 AA 0.012718 AA 0.765464 10.523885
AFFX-2315074 BB 0.028692 BB -0.538410 10.360972
AFFX-2315075 BB 0.139241 BB -0.472899 11.300898
AFFX-2315076 AB 0.039427 AB 0.047848 10.865432

Total number of rows: 262314

Table truncated, full table size 12362 Kbytes.




Supplementary file Size Download File type/resource
GSM672404_1511_Child_Nsp.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672404_1511_Child_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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