Comment[ArrayExpressAccession]	E-GEOD-58929
MAGE-TAB Version	1.1						
Public Release Date	2014-12-23
Investigation Title	Exercise promotes growth and vascularization of fast skeletal muscle by activating myogenic and angiogenic transcriptional programs in adult zebrafish						
Comment[Submitted Name]	Exercise promotes growth and vascularization of fast skeletal muscle by activating myogenic and angiogenic transcriptional programs in adult zebrafish
Experiment Description	The adult skeletal muscle is a plastic tissue with a remarkable ability to adapt to different levels of activity by altering its excitability, its contractile and metabolic phenotype and its mass. Knowledge on the mechanisms responsible for muscle mass comes primarily from models of muscle inactivity or denervation or from genetic models of muscle diseases. Given that the underlying exercise-induced transcriptional mechanisms regulating muscle mass are not fully understood, here we investigated the cellular and molecular adaptive mechanisms taking place in fast skeletal muscle of adult zebrafish in response to swimming. Fish were trained at low swimming speed (0.1 m/s; non-exercised) or at their optimal swimming speed (0.4 m/s; exercised). A significant increase in fibre cross-sectional area (1,290 M-BM-1 88 vs. 1,665 M-BM-1 106 M-NM-<m2) and vascularization (298 M-BM-1 23 vs. 458 M-BM-1 38 capillaries/mm2) was found in exercised over non-exercised fish. Gene expression profiling evidenced the transcriptional activation of a series of complex networks of extracellular and intracellular signaling molecules and pathways involved in the regulation of muscle mass, myogenesis and angiogenesis, many (e.g. BMP, TGFM-oM-^AM-", FGF, Notch, Wnt, MEF2, Shh, EphrinB2) not previously associated with exercise-induced contractile activity, and that recapitulate in part the transcriptional events occurring during skeletal muscle regeneration. These results demonstrate that fibre hypertrophy is responsible for the growth-promoting effects of exercise accompanied by a switch to a more oxidative capacity of white muscle fibres to fuel the increased energy demands. Importantly, our study identified novel molecular mechanisms regulating muscle mass and function in vertebrates. Adult zebrafish were subjected or not to a swim training regime consisting of swimming at the optimal swimming speed for this species for 6 h/day, 5 days/week for a total of 4 weeks (20 experimental days). Total RNA of fast muscle from individual non-exercised (n = 8) and exercised (n = 8) zebrafish was analyzed.						
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	Planas	Planas					
Person First Name	Josep	Josep					
Person Mid Initials	V	V					
Person Email	jplanas@ub.edu						
Person Affiliation	Universitat de Barcelona						
Person Phone	+34-93-4039384						
Person Address	Fisiologia i Immunologia (Biologia), Universitat de Barcelona, Av. Diagonal 643, Barcelona, Spain						
Person Roles	submitter						
Protocol Name	P-GSE58929-1	P-GSE58929-5	P-GSE58929-6	P-GSE58929-2	P-GSE58929-3	P-GSE58929-4	P-GSE58929-7
Protocol Description	Feature Extraction Software 10.7.3.1 (Agilent Technologies) was used for spot to grid alignment, feature extraction and quantification. Processed data were subsequently imported into GeneSpring GX 11.5 (Agilent Technologies). ID_REF =  VALUE = Normalized signal intensity	RNA was amplified and labeled with Cy3 dye using the single color Low Input Quick Amp Labeling kit (Agilent Technologies) following the manufacturerM-bM-^@M-^Ys indications using 200 ng of RNA in each reaction. Next, 1,65 ng of labeled cRNA were hybridized to the arrays.	Overnight hybridization (17 hrs, 65M-:C and 10 rpm rotation) was performed in a Microrarray Hybridization Oven (Agilent Technologies). After hybridization, microrarrays were washed with Gene Expression Wash Buffers 1 and 2 (Agilent Technologies).	Exercised adult zebrafish swam at Uopt (0.4 m/s) for 6 hours per day during 20 experimental days while non-exercised zebrafish rested at a lower swimming speed of 0.1 m/s.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Experiments complied with the current laws of the Netherlands and were approved by the animal experimental committee (DEC number 09161).	After 20 experimental days, fish were anesthetised with 1 ml clove oil (10% in absolute ethanol) in 1 liter of fresh water and euthanized by decapitation. Dorsal epaxial fast muscle filets were dissected and either immediately stored at -20M-:C in RNA later (Ambion) for microarray analyses. Total RNA from fast skeletal muscle samples of individual adult zebrafish was isolated with TRIzol (Invitrogen, Spain) according to the manufacturerM-bM-^@M-^Ys instructions. The RNA samples were incubated for 20 min at 37M-0 with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).	Microrarrays were scanned using the High-Resolution Scanner G2505C (Agilent Technologies).
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	groups						
Experimental Factor Type	groups						
Publication Title	Swimming-induced exercise promotes hypertrophy and vascularization of fast skeletal muscle fibres and activation of myogenic and angiogenic transcriptional programs in adult zebrafish.						
Publication Author List	Palstra AP, Rovira M, Rizo D, Torrella JR, Spaink HP, Planas JV						
PubMed ID	25518849						
Publication DOI	10.1186/1471-2164-15-1136						
Comment[SecondaryAccession]	GSE58929						
Comment[GEOReleaseDate]	2014-12-23						
Comment[ArrayExpressSubmissionDate]	2014-06-30						
Comment[GEOLastUpdateDate]	2014-12-24						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE58929_differentially-expressed.txt						
SDRF File	E-GEOD-58929.sdrf.txt