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Sample GSM889673 Query DataSets for GSM889673
Status Public on May 17, 2012
Title tumor 63
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
Phone 919-966-3864
Fax 919-966-8212
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
Affiliated with GSM893481

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

Data table
SNP_A-1909444 0.862036209641496
SNP_A-2237149 0.862036209641496
SNP_A-4303947 0.862036209641496
SNP_A-2236359 0.862036209641496
SNP_A-2205441 0.862036209641496
SNP_A-2116190 0.862036209641496
SNP_A-4291020 0.862036209641496
SNP_A-2109914 0.862036209641496
SNP_A-2291997 0.862036209641496
SNP_A-4277872 0.862036209641496
SNP_A-2118217 0.862036209641496
SNP_A-1866065 0.862036209641496
SNP_A-2288244 0.862036209641496
SNP_A-1783407 0.862036209641496
SNP_A-2169457 0.862036209641496
SNP_A-4271011 0.862036209641496
SNP_A-2082515 0.862036209641496
SNP_A-1910751 0.862036209641496
SNP_A-2081399 0.862036209641496
SNP_A-2223642 0.862036209641496

Total number of rows: 238378

Table truncated, full table size 7349 Kbytes.

Supplementary file Size Download File type/resource
GSM889673_EXPID7201.CEL.gz 28.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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