|
| Status |
Public on Aug 27, 2015 |
| Title |
UT_SCC115 |
| Sample type |
RNA |
| |
|
| Source name |
Cutaneous squamous cell carcinoma 115
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Cutaneous SCC
|
| Treatment protocol |
NHEK and cSCC cell lines were serum starved for 24 hours and the cell lysates were harvested.
|
| Growth protocol |
NHEKs and cSCC cell lines were cultured and incubated at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water ( Qiagen Rneasy kit, Qiagen GmbH, Hilden, Germany)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to One-cycle Target Labeling protocol for GeneChip® expression analysis technical manual with specific protocols for using the GeneChip hybridization, wash and stain kit.
|
| |
|
| Hybridization protocol |
Each sample was hybridized to Human Genome Array U133 Plus 2.0 according to Affymetrix GeneChip Analysis Technical Manual.
|
| Scan protocol |
GeneChips were scanned using the GeneChip® Scanner 3000 7G.
|
| Description |
Gene expression data from cutaneous SCC cell lines
|
| Data processing |
Affymetrix GeneChip® Command Console® (AGCC) 3.1 was used to control hybridization process and in summarizing probe cell intensity data. After hybridization, quality was checked with AGCC and Expression ConsoleTM 1.1. The data were normalized to remove variation between samples caused by non-biological reasons. Normalization of the array was performed using GCRMA. Data were subjected to statistical analysis with Chipster (CSC-IT Center for Science, Ltd, Espoo, Finland). R package Limma was used for performing the statistical analysis between the groups.
|
| |
|
| Submission date |
Feb 27, 2015 |
| Last update date |
Aug 27, 2015 |
| Contact name |
Liisa Nissinen |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Turku
|
| Department |
Dermatology
|
| Lab |
Cancer Research Laboratory
|
| Street address |
Medisiina D, 5th floor; Kiinamyllynkatu 10
|
| City |
Turku |
| ZIP/Postal code |
FI-20520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE66359 |
Analysis of the gene expression profile in normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines |
| GSE66368 |
EphB2 promotes progression of cutaneous squamous cell carcinoma |
|
