Comment[ArrayExpressAccession] E-GEOD-51541 MAGE-TAB Version 1.1 Public Release Date 2014-03-01 Investigation Title Autophagy is essential for cardiac morphogenesis during vertebrate development Comment[Submitted Name] Autophagy is essential for cardiac morphogenesis during vertebrate development Experiment Description This study examined the effects of genetic knockdown of autophagy genes on vertebrate cardiac development We performed microarray studies comparing the hearts of control zebrafish embryos to the hearts of embryos with decreased expression of the autophagy genes atg5, becn1 or atg7. The results provide insight into the role of autophagy in developmental morphogenesis. Hearts were purified from 3 day-old zebrafish embryos injected with control or autophagy gene-specific morpholino oligonucleotides. RNA was prepared from all samples and hybridized to zebrafish-specific Affymetricx arrays. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Amatruda Lee Ng Xavier Levine Amatruda Person First Name James Eunmyong Aylwin Ramnik Beth James Person Mid Initials F F Person Email james.amatruda@utsouthwestern.edu Person Affiliation University of Texas Southwestern Medical Center Person Phone 214-648-3896 Person Address Pediatrics and Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, USA Person Roles submitter Protocol Name P-GSE51541-1 P-GSE51541-5 P-GSE51541-6 P-GSE51541-2 P-GSE51541-3 P-GSE51541-4 P-GSE51541-7 Protocol Description 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 ID_REF = VALUE = MAS5.0 signal intensity ABS_CALL = 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 was carried out according to Affymetrix protocol 701027 rev 5, using Affymetrix Fluidics Station 450. 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 Embryos were injected at the 1-cell stage and raised under standard conditions Total RNA was extracted from tumors using Trizol reagent according to the manufacturer's instructions. Arrays were scanned with the Affymetrix GeneChip Scanner 3000 using default parameters Protocol Type normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol growth protocol nucleic acid extraction protocol array scanning protocol Comment[SecondaryAccession] GSE51541 Comment[GEOReleaseDate] 2014-03-01 Comment[ArrayExpressSubmissionDate] 2013-10-22 Comment[GEOLastUpdateDate] 2014-03-01 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-51541.sdrf.txt