|
| Status |
Public on Oct 01, 2015 |
| Title |
experiment 2: TAM-treated day 18 replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
C2 iMEFs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iMEFs
genotype/variation: clone C2 18 days after Tamoxifen
|
| Treatment protocol |
Cells were treated with vehicle (EtOH) or Tamoxifen.
|
| Growth protocol |
Sample 1 to 4: mES cells grown in DMEM medium supplemented with 15% FCS, 100 mM non essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM L-Glutamine and 103 U/ul leukemia inhibitory factor (LIF).Sample 5 to 24: iMEF cells grown in DMEM medium supplemented with 10% FCS, 100 mM non essential amino acids, 1 mM L-Glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
100 ng of total RNA was used to prepare biotinilated DNA, according Affymetrix recomandations (http://media.affymetrix.com/support/downloads/manuals/wt_expressionkit_manual.pdf). Whole transcript targets were produced using the Ambion WT kit and the Affymetrix kit (The Affymetrix GeneChip WT Terminal Labeling Kit) to fragment and labelled DNA.
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip Mouse Exon 1.0 ST Array were hybridized with 4,7 µg of labelled DNA according Affymetrix protocols, for 17h at 45°C and 60rpm
|
| Scan protocol |
An Affymetrix GCS3000 7G scanner was used to scan microarrays, following mouse exon array requirements and specifications
|
| Data processing |
Raw data were normalized with the RMA method available in the Bioconductor R package oligo and the pd.mogene.1.1.st.v1 annotation package. For rescue experiments, given the observed batch bias between the first and second replicates, the data were then batch-corrected using a linear model (limma R package).
|
| |
|
| Submission date |
Jul 11, 2014 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Nicolas Servant |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut Curie
|
| Street address |
26 rue d'ulm
|
| City |
Paris Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL11533 |
| Series (2) |
| GSE59346 |
Expression data from Ezh2 conditional C2 iMEFs |
| GSE59427 |
Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis |
|
