|
| Status |
Public on Oct 01, 2009 |
| Title |
NSCLC_SCC_65 |
| Sample type |
RNA |
| |
|
| Source name |
human non-small cell lung cancer tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: squamous cell carcinoma
|
| Treatment protocol |
tumor tissue samples from surgically treated patients were collected intraoperatively, snap-frozen and stored at -80 C. All samples underwent a careful analysis of the histopathology, estimation of tumor and stromal content and subsequent macro-dissection of the tumor regions before enrollment into the microarray experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturersÆ instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Affymetrix ROC technical manual 701021 Rev.5).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip« U133 Plus 2.0 in the Affymetrix GeneChip« Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip« Fluidics Station 450.
|
| Scan protocol |
Hybridized microarrays were scanned with the Affymetrix GeneChip« Scanner 3000.
|
| Description |
Gene expression data from human non-small cell lung cancer tumor tissue 65.
|
| Data processing |
Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 1996] were used for pre-processing of the 58 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].
|
| |
|
| Submission date |
Jan 23, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Ruprecht Kuner |
| Organization name |
German Cancer Research Center and National Center of Tumor Diseases
|
| Department |
Molecular Genetics
|
| Lab |
Unit Cancer Genome Research
|
| Street address |
Im Neuenheimer Feld 460
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE10245 |
Gene expression differences between adenocarcinoma and squamous cell carcinoma in human NSCLC |
|
| Relations |
| Reanalyzed by |
GSE60486 |
| Reanalyzed by |
GSE119087 |
