|
| Status |
Public on Jul 13, 2012 |
| Title |
3B4.15_mock_treated_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
3B4.15 T_mock treated
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 3B4.15 T hybridoma cells
treated with: Ethanol (mock)
|
| Treatment protocol |
3B4.15 T hybridoma cells, either mock treated (Ethanol) or treated with 1 μM Dexamethasone (Sigma) for 16 hours.
|
| Growth protocol |
3B4.15 T hybridoma cells grown in 5% CO2 at 37C in RPMI-1640 medium supplemented with 10% fetal calf serum, 100 unit/ml penicillin/streptomycin, 2 mM L-glutamine, 1x MEM vitamins/non-essential amino acids, and 50 μM β−mercaptoethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Tri-Reagent (Sigma), RNA quality was confirmed on an RNA 6000 Nano chip (AGT-5067-1511) in an Agilent Bioanalyzer. Double stranded cDNA was generated using SuperScript cDNA Synthesis Kit (Invitrogen).
|
| Label |
Cy3
|
| Label protocol |
cDNA was labeled with Cy-3, according to the manufacturer’s protocols (Roche-Nimblegen).
|
| |
|
| Hybridization protocol |
Hybridization was performed by Nimblegen systems following their standard operating protocol. See www.nimblegen.com
|
| Scan protocol |
Scanning was performed by the Sabanci University Nanotechnology Research and Application Center (SUNUM http://sunum.sabanciuniv.edu/) following their standard operating protocol and instructions for NimbleGen arrays. See www.nimblegen.com
|
| Description |
This sample is of mock treated 3B4.15 T hybridoma cells It is the first of three mock treated biological replicates used in this experiment, each from separate flasks.
|
| Data processing |
The raw data were processed using the ANAIS software (Simon, A., and Biot, E. (2010) Bioinformatics 26, 2468-2469). Array quality was assessed at the probe level. Values for 3 probes for each gene in each array were combined to summarize gene expression from probe sets. RMA background normalization and quantile normalization were performed for intra- and inter-array normalization respectively. Genes with signal intensities above a 95% random threshold were chosen for further studies. Differentially expressed genes were obtained based on the following criteria: Fold-change ≥ 2.5 and ANOVA p-value ≤ 0.01. Hierarchical clustering was applied to the top 500 differentially expressed genes with Genesis software (Sturn, A., Quackenbush, J., and Trajanoski, Z. (2002) Bioinformatics 18, 207-208).
|
| |
|
| Submission date |
Jul 12, 2012 |
| Last update date |
Jul 13, 2012 |
| Contact name |
Batu Erman |
| E-mail(s) |
batu@sabanciuniv.edu
|
| Phone |
+90 (216) 483 95 30
|
| Organization name |
Sabanci University
|
| Department |
Biological Sciences and Bioengineering Program
|
| Lab |
Faculty of Engineering and Natural Sciences
|
| Street address |
Orhanli, Tuzla
|
| City |
Istanbul |
| ZIP/Postal code |
34956 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL10192 |
| Series (1) |
| GSE39296 |
Dexamethasone treatment of 3B4.15 T hybridoma cells |
|
