|
| Status |
Public on Jun 01, 2010 |
| Title |
YYK_04 |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA obtained from 4ebp1-/-/4ebp2-/- mouse lung
|
| Organism |
Mus musculus |
| Characteristics |
mouse genotype: 4ebp1-/-/4ebp2-/-
replicate set: B
|
| Growth protocol |
Balb/c mice doubly knocked out for Eif4ebp1 and Eif4ebp2 were generously provided by Dr. Nahum Sonenberg. Wild type Balb/c mice were purchased from Charles River Laboratories (Wilmington, MA). At 5 weeks age, mice were started on AIN-93M purified diet (Research Diets, New Brunswick, NJ) until the end of the experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse lungs were removed and processed for total and polyribosome bound RNA as described by Mullany 2007 modified for the lung (J Biol Chem, 282: 21244-21252, 2007). Polyribosome microarray analysis was performed as previously described (Larsson, Cancer Res, 67: 6814-6824, 2007.). The polyribosome stratified RNA was fractionated and ten, 0.5 ml fractions were collected into tubes containing 50 l 10% SDS. RNA in the fractions was purified using Tri-reagent (Sigma) and fractions 7 to10 were combined into the “heavy” fraction (3 or more ribosomes per transcript).
|
| Label |
biotin
|
| Label protocol |
100 ng of sample RNA was labeled utilizing the Affymetrix Two-Cycle Target Labeling and Control Reagent Kit.
|
| |
|
| Hybridization protocol |
Samples were hybridized onto Affymetrix Murine 430A 2.0 arrays using the FS450 Fluidics Work Station
|
| Scan protocol |
Arrays were scanned using the Gene Chip Scanner 3000 by the University of Minnesota Biomedical Genomics Center.
|
| Description |
none
|
| Data processing |
Data was normalized using GCRMA in R
|
| |
|
| Submission date |
Jul 29, 2009 |
| Last update date |
Jul 30, 2009 |
| Contact name |
Ola Larsson |
| E-mail(s) |
ola.larsson@ki.se
|
| Phone |
+46 (0)8 517 73280
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of oncology-pathology
|
| Street address |
CCK, R8:01
|
| City |
Stockholm |
| ZIP/Postal code |
171 76 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL5759 |
| Series (1) |
| GSE17406 |
Eukaryotic Initiation Factor 4E-BP Protien Family: Sentinels at a Translational Checkpoint in Lung Tumor Defense |
|
