|
| Status |
Public on Jan 15, 2009 |
| Title |
Control GFP RNAi, day 4, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
E14 mouse embryonic stem (ES) cells
|
| Organism |
Mus musculus |
| Characteristics |
Control GFP shRNA (targeting GFP transcript) transfected E14 mouse embryonic stem cells
|
| Treatment protocol |
Transfection of GFP shRNA plasmid was performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s
|
| Growth protocol |
Mouse ES cells were cultured at 37°C with 5% CO2. Mouse ES cells were maintained on gelatin-coated dishes in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen) and purified with RNeasy minikit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 500 ng of total RNA according to the standard protocol (TotalPrep RNA Amplification Kit, Instruction Manual, Catalog #IL1791, Illumina).
|
| |
|
| Hybridization protocol |
1.5 ug of cRNA were hybridized to Illumina Mouse-6 Expression BeadChip v1.1 for 20 hr at 58oC on Ilumina Hybridization Oven.
|
| Scan protocol |
Illumina Mouse-6 Expression BeadChip v1.1 were washed and stained with streptavidin-Cy3 before scanning using the Illumina Bead Reader.
|
| Description |
Gene expression data from Control GFP shRNA treated E14 embryonic stem cells, day 4
|
| Data processing |
The data were analyzed using Bead Array suite software. Rank invariant normalization method was chosen to obtain the signal intensity.
|
| |
|
| Submission date |
Oct 15, 2008 |
| Last update date |
Jan 15, 2009 |
| Contact name |
Vinsensius B Vega |
| E-mail(s) |
vegav@gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL6105 |
| Series (2) |
| GSE13190 |
Global gene-expression analyses of the Esrrb reprogrammed cells and Esrrb knockdown cells |
| GSE13212 |
Global gene-expression analyses of the Esrrb knockdown cells |
|
