|
| Status |
Public on Sep 01, 2011 |
| Title |
E5_vs_pMSG_4h_rep1 (mRNA) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
pMSG_4h_rep1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: skin keratinocytes
cell line: HaCaT
transfection: vector control
time: 4h
|
| Treatment protocol |
E5 expression was induced by 1 mM dexamethasone treatment for different times.
|
| Growth protocol |
HaCaT-E5 and control cells were grown in D-MEM growth medium with 10% FBS and glutamine and antibiotics, and serum-starved 24h before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from confluent cell cultures using TriPure reagent (Roche Applied Science, Indianapolis, IN, USA)
|
| Label |
Cy5
|
| Label protocol |
Cy5 and Cy3 indirect labelling using (Ambion, Austin, TX) amino allyl messageamp II aRNA amplification kit according to instructions.
|
| |
|
| Channel 2 |
| Source name |
E5_4h_rep1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: skin keratinocytes
cell line: HaCaT
transfection: type 16 E5 oncogene
time: 4h
|
| Treatment protocol |
E5 expression was induced by 1 mM dexamethasone treatment for different times.
|
| Growth protocol |
HaCaT-E5 and control cells were grown in D-MEM growth medium with 10% FBS and glutamine and antibiotics, and serum-starved 24h before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from confluent cell cultures using TriPure reagent (Roche Applied Science, Indianapolis, IN, USA)
|
| Label |
Cy3
|
| Label protocol |
Cy5 and Cy3 indirect labelling using (Ambion, Austin, TX) amino allyl messageamp II aRNA amplification kit according to instructions.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed as described in the Agilent (Agilent Technologies, Rockville, MD) two color microarray-based gene expression analysis manual suggests. Hybridization for 16 h at +65 ºC. Washing was performed by the Agilent protocol 5 minutes in GE wash buffer 1 and one minute in GE wash buffer 2 (+37ºC). Arrays were dried with a 1 minute spin in a Spectrafuge mini (Labnet, Woodbridge, NJ).
|
| Scan protocol |
Default scanning performed with Axon 4200AL for Cy3 and Cy5 using resolution of five micrometer.
|
| Description |
mRNA expression in E5 vs control cells after 4h induction
|
| Data processing |
quantile normalization of the log2 ratios
|
| |
|
| Submission date |
Oct 25, 2010 |
| Last update date |
Sep 01, 2011 |
| Contact name |
Dario Greco |
| E-mail(s) |
dario.greco@tuni.fi
|
| Organization name |
Tampere University
|
| Department |
Faculty of Medicine and Health Technology
|
| Lab |
Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)
|
| Street address |
Arvo ylpön Katu 34
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE24908 |
Human Papillomavirus 16 E5 modulates the expression of host microRNAs |
|
