Comment[ArrayExpressAccession]	E-GEOD-66725
MAGE-TAB Version	1.1					
Public Release Date	2015-07-30
Investigation Title	Genomics of the ovine heart ontogeny during the perinatal period					
Comment[Submitted Name]	Genomics of the ovine heart ontogeny during the perinatal period
Experiment Description	The period of development from the last two weeks of gestation through the first two weeks of life spans a period of great functional and metabolic challenge to the fetal and neonatal lamb heart. Important changes in gene expression occur to meet these challenges. On this study, septa from sheep hearts at 130 days gestation (n=6), term (n=8, gestational lenght is around 145 days) and 14-days-old lambs (n=8) were used to model the changes in gene expression patterns during the perinatal period using Agilent 15k ovine microarrays. Weighted gene co-expression network analysis (WGCNA) determined five major patterns of co-expressed and functionally related genes during this critical period of cardiac transition. Septum samples from the heart were collected from non-treated fetuses at 130 days of gestational age (GA130d, n=6) and term (n=8); and from naturally born 14-days-old lambs (Lamb, n=8). None of the ewes suffered gestational diseases or showed signs of impending labor.					
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	Rabaglino	Richards	Rabaglino	Antolic	Wood	Keller-Wood
Person First Name	Maria	Elaine	Maria	Andrew	Charles	Maureen
Person Mid Initials	Belen	M	B		E	
Person Email	brabaglino@ayv.unrc.edu.ar					
Person Affiliation	Universidad Nacional de Rio Cuarto					
Person Address	Reproducción Animal, Universidad Nacional de Rio Cuarto, Ruta Nac. 36, Km 601, Río Cuarto, Córdoba, Argentina					
Person Roles	submitter					
Protocol Name	P-GSE66725-1	P-GSE66725-4	P-GSE66725-5	P-GSE66725-2	P-GSE66725-3	P-GSE66725-6
Protocol Description	The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal. The limma package was employed to import the raw data into R (http://www.r-project.org), perform background correction and normalize the data by the quantile normalization method. Control probes and low expressed probes were filtered out, retaining for further analysis the probes that were at least 10% brighter than the negative controls on at least four arrays. ID_REF =  VALUE = log2 normalized signal intensity	Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent, Newcastle DE) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.	600 ng of Cy3-labelled cRNA (specific activity >9.7 pmol Cy3/µg cRNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) design 019921 by the ICBR facility at the University of Florida according to Agilent's methodology.	No treatment was given to either ewe or fetus.	RNA was extracted from heart septa with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen RNeasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer.	Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	developmental age					
Experimental Factor Type	developmental age					
Comment[SecondaryAccession]	GSE66725					
Comment[GEOReleaseDate]	2015-07-30					
Comment[ArrayExpressSubmissionDate]	2015-03-10					
Comment[GEOLastUpdateDate]	2015-07-31					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-66725.sdrf.txt