|
| Status |
Public on May 01, 2011 |
| Title |
Quiescent Q3 |
| Sample type |
RNA |
| |
|
| Source name |
Control Without Doxycycline
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c 3T3
clone: Tet-on inducible cell line with a wild-type E1A gene (243 amino-acid)
treatment: none
|
| Treatment protocol |
Treatment with Doxicycline was for 8 hr, and total RNA harvested 1 hour after treatment. Untreated cell cultures were cultivated as for 8 h, and total RNA harvested 1 hour after at the same time as treated cells
|
| Growth protocol |
Maintained in supplemented DMEM with antibiotics, and 10% fetal bovine serum (Tet system approved; Clontech). Shows E1A expression 8h after the addition of 100 ng/ml of doxycycline.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment (DNAfree, Ambion kit in accordance with the prescribed protocol provided with the kit). Quality control was assessed by NanoDrop 1000 (Thermo Scientific, Waltham, MA) and by Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
replicate 3
|
| Data processing |
The data were variance-stabilized and normalized with the help of the 'lumi' R package using Variance-Stabilizing Transformation (VST), a generalized-log(.) transformation ensuring that the variance is approximately independent of the mean intensity, followed by a Robust Spline Normalization (RSN) algorithm.
|
| |
|
| Submission date |
Apr 06, 2011 |
| Last update date |
May 01, 2011 |
| Contact name |
Jean-Eudes Dazard |
| Organization name |
Case Western Reserve University
|
| Department |
Proteomics and Bioinformatics
|
| Lab |
Bioinformatics
|
| Street address |
10900 Euclid Avenue
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL6103 |
| Series (1) |
| GSE28420 |
The dynamics of E1A in regulating networks and canonical pathways in quiescent cells |
|
