|
Status |
Public on May 01, 2011 |
Title |
Stimulated S2 |
Sample type |
RNA |
|
|
Source name |
Treated with 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: Doxycycline
|
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 2
|
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 |
|