|
| Status |
Public on Nov 28, 2007 |
| Title |
Radiosensitive tumor cell line-IFN-treated-rep1 |
| Sample type |
RNA |
| |
|
| Source name |
head&neck tumor cell line
|
| Organism |
Homo sapiens |
| Characteristics |
Squamous cell carcinoma
|
| Treatment protocol |
cell lines were grown to confluence: cells were transferred in 6-well plates with density 10^6/well and left overnight. Next morning, mixture of IFNa, IFNb and IFNg were added in concentrations of 100, 100 and 5 ng/ml respectively and cells were incubated 5 hours. After this, medium was decanted and cells were processed for RNA extraction.
|
| Growth protocol |
nu61 and SCC61 cell lines were maintained in DMEM/F12 (GIBCO, Carlsbad, CA), supplemented with 20% FBS, 1% hydrocortisone and !% penicillin/streptomicin at 37C, 100% humidity and 5% CO2.IFNs alpha, beta and gamma were from R&D Systems, Minneapolis, MN)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized on U133A Human GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Agilent GeneArray Scanner
|
| Description |
Gene expression data from radiosensitive tumor cell line in vitro, treated by IFNalpha, IFNbeta and IFNgamma
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700-800.
|
| |
|
| Submission date |
Nov 28, 2007 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Nikolai N. Khodarev |
| E-mail(s) |
nikolai@rover.uchicago.edu
|
| Phone |
773-834-3282
|
| Fax |
773-702-1968
|
| Organization name |
The University of Chicago
|
| Department |
Radiation and Cellular Oncology
|
| Street address |
5841 South Maryland Avenue
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE9714 |
Interferon response of radioresistant and radiosensitive human head&neck tumor cell lines |
| GSE9716 |
Radioresistant and radiosensitive tumors and cell lines |
|
| Relations |
| Reanalyzed by |
GSE86363 |
