|
| Status |
Public on Jul 16, 2010 |
| Title |
D3 EB day 4 biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
D3 cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: D3
|
| Treatment protocol |
For induction of EB formation mES cells were aggregated in 100-mm bacteriological dishes (Greiner) at a specific density (4x106 cells/ 15 ml) in the abscence of LIF. Over the span of four days, embryoid bodies were treated for 12h with DMSO or ATRA (5 mikromol final concentration).
|
| Growth protocol |
mESCs (a clone of D3) were cultured as described in the article. ES medium contained 15% ES qualified FBS (Cat.no.: SH30070.03, HyClone Laboratories, Inc., Utah).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).
|
| Label |
biotin
|
| Label protocol |
Biotinylated ss cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA using WT Expression kit (Ambion).
|
| |
|
| Hybridization protocol |
10 ug of ss cDNA was fragmented and labeled with biotin and were hybridized for 16 hr at 45C on GeneChip 1.0 ST Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
|
| Description |
biological rep1
Gene expression data from four day old embryoid bodies
|
| Data processing |
The data were analyzed with GeneSpring GX11 Software (Agilent). Cel files were imported using RMA16 algorithm and median normalization was performed.
|
| |
|
| Submission date |
Mar 16, 2010 |
| Last update date |
Jul 03, 2010 |
| Contact name |
Zoltan Simandi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Debrecen
|
| Department |
BMBI
|
| Street address |
Egyetem ter 1
|
| City |
Debrecen |
| ZIP/Postal code |
4012 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE20919 |
Short-term (12h) ATRA treatment of embryoid bodies. |
|
