|
| Status |
Public on Jun 06, 2006 |
| Title |
SCC-6 cells transfected with control vector |
| Sample type |
RNA |
| |
|
| Source name |
SCC-6 cells transfected with control vector
|
| Organism |
Homo sapiens |
| Characteristics |
head and neck squamous cell carcinoma
|
| Treatment protocol |
Cells were transfected using Fugene 6 (Roche, Indianapolis, IN). Cells were selected with hygromycin B 48 h after transfection and harvested for mRNA isolation.
|
| Growth protocol |
Cells were grown in DMEM+10% FBS at 37C and harvested for mRNA after selection with Hygromycin
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA isolation was performed as described in Flatt, P. M., Tang, L. J., Scatena, C. D., Szak, S. T., and Pietenpol, J. A. (2000) Mol Cell Biol 20, 4210-4223
|
| Label |
biotin
|
| Label protocol |
300 ng of mRNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
|
| |
|
| Hybridization protocol |
biotinylated cRNA (15µg) was fragmented and hybridized to the Affymetrix GeneChip U133 Plus 2.0. Hybridized cRNAs were washed and detected via streptavidin coupled to phycoerythrin using the Affymetrix 450 Fluidics Station and recommended protocols.
|
| Scan protocol |
Results were visualized by laser scanner (Affymetrix GeneChip Scanner 3000).
|
| Description |
Gene expression data on Affy HG133 Plus 2.0 from SCC-6 cells transfected with control vector
|
| 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 100.
|
| |
|
| Submission date |
Jun 05, 2006 |
| Last update date |
Jun 05, 2006 |
| Contact name |
Jennifer Pietenpol |
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Biochemistry
|
| Lab |
652 PRB
|
| Street address |
23rd Ave South at Pierce
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE4975 |
Expression data from p63 siRNA in squamous cell lines |
|
