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Status |
Public on Mar 01, 2014 |
Title |
Control Morpholino biological replicate 2 |
Sample type |
RNA |
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Source name |
Zebrafish embryo hearts a 3 days post-fertilization
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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
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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).
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Hybridization protocol |
Hybridization was carried out according to Affymetrix protocol 701027 rev 5, using Affymetrix Fluidics Station 450.
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Scan protocol |
Arrays were scanned with the Affymetrix GeneChip Scanner 3000 using default parameters
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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
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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 |
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|
Platform ID |
GPL1319 |
Series (1) |
GSE51541 |
Autophagy is essential for cardiac morphogenesis during vertebrate development |
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