NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM889681 Query DataSets for GSM889681
Status Public on May 17, 2012
Title tumor 75
Sample type genomic
 
Source name lung adenocarcinoma
Organism Homo sapiens
Characteristics tissue type: lung
cell type: adenocarcinoma
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using Qiagen’s QIAamp DNA minikit.
Label biotin
Label protocol Followed Affymetrix instructions.
 
Hybridization protocol Followed Affymetrix instructions.
Scan protocol Arrays were scanned using the Affmetrix Gene Chip Scanner.
Data processing For SNP6 and 250K_Sty platforms separately, probe intensities were processed using CRMAv2 (Bengtsson, et al. PMID: 19535535), converted to log2 values, sample-wise median centered, and divided by the mean of normal samples to make CN values. CN values were smoothed by circular binary segmentation, sample-wise median centered using autosomes. Finally, CN values were standardized by dividing each sample by its standard deviation. Sex chromosomes were not used in final analysis, so these probesets have NULL for all samples. SNP6 data were subjected to a within-sample outlier removal process (TCGA Research Network, PMID: 21720365), and struck probesets have 'NULL' values.
 
Submission date Mar 08, 2012
Last update date May 17, 2012
Contact name Matthew D Wilkerson
E-mail(s) mwilkers@med.unc.edu
Phone 919-966-3864
Fax 919-966-8212
URL http://cancer.unc.edu/nhayes
Organization name University of North Carolina at Chapel Hill
Department Lineberger Comprehensive Cancer Center
Lab D. Neil Hayes
Street address 450 West Drive
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7295
Country USA
 
Platform ID GPL3720
Series (2)
GSE36363 Human lung adenocarcinoma DNA copy number profiling
GSE36471 Human lung adenocarcinoma

Data table header descriptions
ID_REF
VALUE Values are final normalized CN values.

Data table
ID_REF VALUE
SNP_A-1909444 0.564066685758537
SNP_A-2237149 0.564066685758537
SNP_A-4303947 0.564066685758537
SNP_A-2236359 0.564066685758537
SNP_A-2205441 0.564066685758537
SNP_A-2116190 0.564066685758537
SNP_A-4291020 0.564066685758537
SNP_A-2109914 0.564066685758537
SNP_A-2291997 0.564066685758537
SNP_A-4277872 0.564066685758537
SNP_A-2118217 0.564066685758537
SNP_A-1866065 0.564066685758537
SNP_A-2288244 0.564066685758537
SNP_A-1783407 0.564066685758537
SNP_A-2169457 0.564066685758537
SNP_A-4271011 0.564066685758537
SNP_A-2082515 0.564066685758537
SNP_A-1910751 0.564066685758537
SNP_A-2081399 0.564066685758537
SNP_A-2223642 0.564066685758537

Total number of rows: 238378

Table truncated, full table size 7463 Kbytes.




Supplementary file Size Download File type/resource
GSM889681_EXPID7253.CEL.gz 26.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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