GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM672842 Query DataSets for GSM672842
Status Public on Feb 17, 2011
Title 1780_Mother (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 1780
family member: Mother
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 BB 0.006689 BB -0.636940 12.227242
AFFX-2315061 AB 0.003201 AB 0.158212 11.292132
AFFX-2315062 AB 0.003058 AB -0.055460 10.891297
AFFX-2315057 AB 0.003751 AB -0.117365 10.894144
AFFX-2315058 BB 0.001647 BB -0.666933 11.011794
AFFX-2315059 AB 0.000343 AB 0.210282 10.591325
AFFX-2315063 AA 0.000781 AA 0.803818 10.827934
AFFX-2315064 AB 0.002166 AB 0.194559 11.060445
AFFX-2315065 AB 0.019185 AB -0.082431 10.490298
AFFX-2315066 BB 0.003413 BB -0.689139 10.725138
AFFX-2315067 AB 0.011324 AB -0.035489 11.237322
AFFX-2315068 AA 0.000528 AA 0.793599 10.871353
AFFX-2315069 AA 0.005879 AA 0.792869 10.731816
AFFX-2315070 AB 0.003414 AB -0.128725 10.965378
AFFX-2315071 AB 0.001066 AB -0.084528 9.933936
AFFX-2315072 AA 0.030180 AA 0.515604 10.811870
AFFX-2315073 AA 0.003464 AA 0.757759 10.953475
AFFX-2315074 AB 0.003062 AB 0.044698 10.623389
AFFX-2315075 AA 0.002593 AA 0.690398 11.756647
AFFX-2315076 AB 0.008704 AB -0.004819 11.013714

Total number of rows: 262314

Table truncated, full table size 12386 Kbytes.

Supplementary file Size Download File type/resource
GSM672842_1780_Mother_Nsp.CEL.gz 26.6 Mb (ftp)(http) CEL
GSM672842_1780_Mother_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