|
Status |
Public on Jun 01, 2010 |
Title |
YYK015 |
Sample type |
other |
|
|
Source name |
polysomal RNA obtained from WT mouse lung
|
Organism |
Mus musculus |
Characteristics |
mouse genotype: WT replicate set: C
|
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 |
other |
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.
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|
|
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
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|
|
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 |
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