GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM672849 Query DataSets for GSM672849
Status Public on Feb 17, 2011
Title 3094_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: 3094
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 0.026794 AB -0.184291 12.164511
AFFX-2315061 AB 0.000052 AB 0.105521 11.259453
AFFX-2315062 AB 0.016028 AB -0.130593 10.935490
AFFX-2315057 NC 0.694734 BB -0.409950 10.579671
AFFX-2315058 AB 0.007088 AB 0.078041 11.315152
AFFX-2315059 AA 0.003316 AA 0.754713 10.674699
AFFX-2315063 AA 0.000985 AA 0.800202 10.845153
AFFX-2315064 AB 0.005896 AB 0.247229 11.161577
AFFX-2315065 AB 0.006039 AB -0.012917 10.556154
AFFX-2315066 BB 0.011933 BB -0.655764 10.820618
AFFX-2315067 BB 0.006363 BB -0.521955 11.254722
AFFX-2315068 AB 0.000303 AB 0.192019 10.849175
AFFX-2315069 AB 0.013535 AB -0.201521 10.920435
AFFX-2315070 BB 0.008304 BB -0.665493 10.985286
AFFX-2315071 AB 0.005127 AB -0.065959 10.008710
AFFX-2315072 AB 0.042241 AB -0.180683 10.992426
AFFX-2315073 AB 0.008868 AB 0.203128 11.025387
AFFX-2315074 BB 0.017289 BB -0.646710 10.663382
AFFX-2315075 AB 0.003780 AB 0.144807 11.817157
AFFX-2315076 AA 0.009386 AA 0.529033 11.044574

Total number of rows: 262314

Table truncated, full table size 12376 Kbytes.

Supplementary file Size Download File type/resource
GSM672849_3094_Child_Nsp.CEL.gz 26.8 Mb (ftp)(http) CEL
GSM672849_3094_Child_Nsp.chp.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap