GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM672891 Query DataSets for GSM672891
Status Public on Feb 17, 2011
Title 2714_Father (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2714
family member: Father
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 BB 0.040441 BB -0.731256 11.987752
AFFX-2315061 AB 0.019270 AB 0.024471 11.517492
AFFX-2315062 AA 0.087761 AA 0.697405 10.128446
AFFX-2315057 AB 0.106397 AB 0.026227 10.286762
AFFX-2315058 AA 0.033226 AA 0.712787 12.057425
AFFX-2315059 AB 0.081836 AB 0.264136 10.428802
AFFX-2315063 AA 0.018364 AA 0.782516 10.541539
AFFX-2315064 NC 0.704727 AA 0.402121 9.660020
AFFX-2315065 AB 0.165611 AB -0.060512 10.235754
AFFX-2315066 AA 0.001905 AA 0.681417 10.231598
AFFX-2315067 BB 0.191323 BB -0.654669 10.881902
AFFX-2315068 BB 0.015078 BB -0.749352 10.534008
AFFX-2315069 AB 0.029477 AB -0.110886 9.998369
AFFX-2315070 AB 0.090622 AB -0.094016 10.201830
AFFX-2315071 BB 0.007498 BB -0.799470 10.275359
AFFX-2315072 AA 0.138011 AA 0.714400 10.881616
AFFX-2315073 AA 0.018317 AA 0.746808 10.457996
AFFX-2315074 NC 0.702231 AB 0.130615 9.377793
AFFX-2315075 AB 0.003711 AB 0.005110 11.631682
AFFX-2315076 AB 0.003597 AB -0.027259 11.206893

Total number of rows: 238354

Table truncated, full table size 11252 Kbytes.

Supplementary file Size Download File type/resource
GSM672891_2714_Father_Sty.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM672891_2714_Father_Sty.chp.gz 3.9 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