Comment[ArrayExpressAccession]	E-GEOD-37070
MAGE-TAB Version	1.1						
Public Release Date	2012-12-28
Investigation Title	Microarray analysis of normal and abnormal chick myocardial development						
Comment[Submitted Name]	Microarray analysis of normal and abnormal chick myocardial development
Experiment Description	The goal of this study was to determine developmental differences in gene expression between left and right ventricle, and to assess the differential effect of altered hemodynamic loading on left and right ventricle. Chick ventricles from different developmental stages were isolated for assessment of normal developmental profiles. Conotruncal banding or partial ligation of the left atrial appendage was performed in ovo at embryonic day 4 and ventricles were isolated at embryonic day 5 (banding) or 8 (ligation) for assessment of altered loading effects. Normal heart and ventricle tissues were collected from chicks at embryonic day 4, 5, 6, 8, or 10 (Hamurger-Hamilton stages 29, 34, and 36). Conotruncal banding (CTB) or left atrial ligation (LCL) was performed for experimental groups in ovo at embryonic day 4 and tissues isolated at embryonic day 5 (CTB) or day 8 (LAL). For each sample type, tissues were carefully dissected, collected and stored in RNAlater, and then pooled for RNA isolation. Each sample contained 6 to 12 separate biological specimens. A single pooled RNA sample was generated for each normal and experimental condition.  Following preparation of labeled samples for hybridization, samples were split and hybridized in duplicate to separate microarrays (i.e., technical replicates).						
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	Sedmera	Sedmera	Barth				
Person First Name	David	David	Jeremy				
Person Mid Initials			L				
Person Email	dsedmera@biomed.cas.cz						
Person Affiliation	Charles University						
Person Address	Charles University, U nemocnice 3, Prague, Czech Republic						
Person Roles	submitter						
Protocol Name	P-GSE37070-1	P-GSE37070-5	P-GSE37070-6	P-GSE37070-2	P-GSE37070-3	P-GSE37070-4	P-GSE37070-7
Protocol Description	Gene hybridization intensities were normalized by gcRMA algorithm (Wu et al., 2005) and detection calls generated by MAS5 algorithm, both implemented with the ArrayQuest webtool (Argraves et al., 2005). ID_REF =  VALUE = log2 GC-RMA signal ABS_CALL = MAS5.0 detection call	Total RNA was converted into biotin-labeled cRNA targets using a SuperScript cDNA synthesis kit (Invitrogen) and Bioarray Hi Yield in vitro transcription kit (Enzo).	Targets (4 μg) were hybridized to Affymetrix Chicken Genome arrays according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.	Conotruncal banding (CTB) or partial ligation of the left atrial appendage (LAL) was performed in ovo at embryonic day 4 (Stage 24), as described by Sedmera et al., 1999. Following experimental treatment, eggs were returned to the incubator until the appropriate developemental stage.	Eggs were incubated in a force draft incubator at 37.5 °C and high humidity until the appropriate developmental stage.	Tissues from normal and experimentally treated chicks was collected at the appropriate stage, and tissues were carefully dissected, collected and stored in RNAlater, and then pooled for RNA isolation. RNA was purified using RNeasy Mini columns (Qiagen) and evaluated by Agilent BIoanalyzer.	Microarrays were scanned using an Affymetrix 7G Scanner.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	DEVELOPMENTAL STAGE	EXPERIMENTAL TREATMENT	ORGANISM PART				
Experimental Factor Type	developmental stage	experimental treatment	organism part				
PubMed ID	22827870						
Comment[SecondaryAccession]	GSE37070						
Comment[GEOReleaseDate]	2012-12-28						
Comment[ArrayExpressSubmissionDate]	2012-04-05						
Comment[GEOLastUpdateDate]	2012-12-28						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-37070.sdrf.txt