|
| Status |
Public on Mar 01, 2014 |
| Title |
Uninjected control biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Zebrafish embryo hearts a 3 days post-fertilization
|
| Organism |
Danio rerio |
| Characteristics |
tissue: heart
age: 3 days post-fertilization
|
| Treatment protocol |
Hearts were purified from 3 dpf zebrafish as described in Burns CG, MacRae CA. Purification of hearts from zebrafish embryos. Biotechniques 2006; 40:278-81; PMID:16568816. Total RNA was extracted with the Trizol method
|
| Growth protocol |
Embryos were injected at the 1-cell stage and raised under standard conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tumors using Trizol reagent according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 5 ug total RNA using the GeneChip IVT labeling kit, according to the manufacturer's instructions (#702232 rev 2, Afymetrix, Inc., Santa Clara, CA).
|
| |
|
| 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 |
Probeset-level normalization was achieved using the MAS5.0 algorithm. Data analysis and linear modeling were performed in the R programming language, utilizing functions from Linear Models for Microarray Data. For each probe, a moderated t-statistic (with standard errors moderated across genes) was computed using a Bayesian model. For each transcript, signal-to-noise ratios (SNR) were computed for each respective morphant compared to the control group
|
| |
|
| Submission date |
Oct 22, 2013 |
| Last update date |
Mar 01, 2014 |
| 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 (1) |
| GSE51541 |
Autophagy is essential for cardiac morphogenesis during vertebrate development |
|
