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Sample GSM672920 Query DataSets for GSM672920
Status Public on Feb 17, 2011
Title 9390_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: 9390
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 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

Data table
AFFX-2315060 AA 0.005145 AA 0.746568 11.917332
AFFX-2315061 BB 0.000804 BB -0.821558 10.817422
AFFX-2315062 AB 0.001926 AB -0.032420 10.371127
AFFX-2315057 AB 0.009382 AB -0.031966 10.589283
AFFX-2315058 AA 0.000762 AA 0.779509 11.953051
AFFX-2315059 AB 0.001460 AB 0.257822 10.727682
AFFX-2315063 AA 0.003164 AA 0.817083 10.671762
AFFX-2315064 AA 0.003109 AA 0.703233 10.129289
AFFX-2315065 AB 0.002368 AB -0.076386 10.419969
AFFX-2315066 BB 0.010918 BB -0.702751 10.528800
AFFX-2315067 BB 0.002958 BB -0.630352 11.084362
AFFX-2315068 AA 0.004508 AA 0.853299 10.602886
AFFX-2315069 AB 0.001381 AB -0.103358 9.793468
AFFX-2315070 BB 0.028543 BB -0.595371 10.574431
AFFX-2315071 AB 0.000612 AB -0.187231 10.354421
AFFX-2315072 AA 0.008837 AA 0.758449 11.270750
AFFX-2315073 AB 0.007085 AB 0.020320 10.726954
AFFX-2315074 AA 0.012117 AA 0.624389 9.881996
AFFX-2315075 AA 0.008907 AA 0.784969 11.562878
AFFX-2315076 AB 0.005762 AB -0.033434 11.333264

Total number of rows: 238354

Table truncated, full table size 11217 Kbytes.

Supplementary file Size Download File type/resource
GSM672920_9390_Child_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672920_9390_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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