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Sample GSM672852 Query DataSets for GSM672852
Status Public on Feb 17, 2011
Title 3519_Child (Mapping250K_Nsp)
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
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

Data table
AFFX-2315060 AB 0.007984 AB -0.129889 11.917088
AFFX-2315061 AB 0.009694 AB 0.196059 10.854461
AFFX-2315062 BB 0.046590 BB -0.571803 10.593387
AFFX-2315057 AB 0.000841 AB -0.116580 10.733267
AFFX-2315058 AA 0.021323 AA 0.746414 11.118328
AFFX-2315059 BB 0.065677 BB -0.497479 10.013055
AFFX-2315063 AB 0.014525 AB -0.107062 10.497899
AFFX-2315064 AB 0.005414 AB 0.271455 10.620030
AFFX-2315065 AB 0.029454 AB 0.008159 10.204409
AFFX-2315066 BB 0.027140 BB -0.589337 10.208532
AFFX-2315067 AB 0.027092 AB 0.032169 10.829628
AFFX-2315068 AA 0.028828 AA 0.733184 10.422379
AFFX-2315069 BB 0.006853 BB -0.806373 10.358997
AFFX-2315070 AB 0.010139 AB -0.128589 10.497861
AFFX-2315071 AB 0.034438 AB -0.113036 9.459053
AFFX-2315072 AA 0.084141 AA 0.435095 10.602283
AFFX-2315073 AB 0.022105 AB 0.115941 10.299433
AFFX-2315074 AB 0.051283 AB 0.203987 10.225093
AFFX-2315075 AB 0.004194 AB 0.017201 11.425875
AFFX-2315076 AA 0.046965 AA 0.501930 10.864935

Total number of rows: 262314

Table truncated, full table size 12354 Kbytes.

Supplementary file Size Download File type/resource
GSM672852_3519_Child_Nsp.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM672852_3519_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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