|
| Status |
Public on Nov 01, 2011 |
| Title |
AB control embryos biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
control embryos, heat-shocked 39 degrees C for 30 mins at 50% epiboly stage
|
| Organism |
Danio rerio |
| Characteristics |
tissue: embryo
genotype/variation: wildtype AB strain
|
| Treatment protocol |
Embryos were heat shocked for 30 minutes at 39 degrees C., then incubated 2 hours at 28.5 degrees C. prior to RNA collection.
|
| Growth protocol |
Wild-type AB strain embryos and Tg(HSP:EWS-FLI1) embryos were derived from crosses under standard conditions and raised until the 50% epiboly stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from groups of 40 embryos using Trizol reagent according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Total RNA (2.5ug) from embryos was reverse-transcribed using a T7-Oligo(dT) Promoter Primer, followed by RNAseH-mediated second-strand cDNA synthesis. Biotinylated cRNA probe was prepared with MessageAmp II (Ambion).
|
| |
|
| Hybridization protocol |
Hybridization was carried out according to Affymetrix protocol 701027 rev 5, using Affymetrix Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned with the Affymetrix GeneChip Scanner 3000 using default parameters
|
| Data processing |
The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7, running in the R statistical environment version 2.2.0 using default parameters.
|
| |
|
| Submission date |
Aug 03, 2011 |
| Last update date |
Nov 01, 2011 |
| Contact name |
James F Amatruda |
| E-mail(s) |
james.amatruda@utsouthwestern.edu
|
| Phone |
214-648-3896
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Department |
Pediatrics and Molecular Biology
|
| Street address |
5323 Harry Hines Boulevard
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8534 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (2) |
| GSE31185 |
The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes developmental defects in zebrafish embryos |
| GSE31217 |
A zebrafish transgenic model of Ewing's Sarcoma reveals conserved mediators of EWS-FLI1 tumorigenesis |
|
