|
| Status |
Public on May 17, 2012 |
| Title |
tumor 32 |
| 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 |
GPL6801 |
| Series (2) |
| GSE36363 |
Human lung adenocarcinoma DNA copy number profiling |
| GSE36471 |
Human lung adenocarcinoma |
|
