|
| Status |
Public on May 14, 2008 |
| Title |
EB, Pool-1, Biological Rep-3 |
| Sample type |
RNA |
| |
|
| Source name |
R-1, Differentiated day-5 Embryoid bodies from mouse ESCs; Fractionated Polysomal RNA
|
| Organism |
Mus musculus |
| Characteristics |
Differentiated day-5 Embryoid Bodies
|
| Treatment protocol |
Cells were incubated with 150 ug/ml of cycloheximide for 15 min to arrest ribosome movement on mRNAs before harvesting the cells.
|
| Growth protocol |
Embryonic stem cells (ESC) maintained in the presence of LIF in an undifferentiated state and its differentiated progeny, grown in the absence of LIF, the day-5 Embryoid bodies (EB) were selected for the experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cytoplasmic lysate was subjected to sucrose-gradient centrifugation followed by fractionation. Fractions were further pooled and RNA was precipitated from each pool and purified using Qiagen RNeasy midi-columns. The quality of RNA was determined using an Agilent Bioanalyzer and quantitated by absorbance at 260 nm.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug of RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix 430_2 mouse expression arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Translation state array analysis
|
| Data processing |
The data were processed from .CEL files with Microarray Suite version 5.0 (MAS 5) algorithm using the affy package of the Bioconductor project with scaling between arrays disabled. In subsequent steps of the analysis data was normalized with the affymetrix spike-in controls.
|
| |
|
| Submission date |
Nov 08, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Charles E Murry |
| Organization name |
University of Washington
|
| Department |
Pathology
|
| Street address |
815 Mercer st., Rm # 454
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE9563 |
Translation state array analysis of Mouse embryonic stem cells and embryoid bodies |
|
| Relations |
| Reanalyzed by |
GSE119085 |
