Comment[ArrayExpressAccession]	E-GEOD-16595
MAGE-TAB Version	1.1					
Public Release Date	2009-07-31
Investigation Title	RNA profiling of skeletal muscle in RP58 knockout mice					
Comment[Submitted Name]	RNA profiling of skeletal muscle in RP58 knockout mice
Experiment Description	To predict RP58-regulated genes involved in skeletal myogenesis, RNA profiling experiments were performed, comparing RNA derived from skeletal muscle tissue of a RP58+/+ mouse to that from a RP58 knockout (KO) mouse at E18.5. Importantly, well-known dominant-negative inhibitors of muscle differentiation, the Id family of genes (Id1/Id2/Id3), were upregulated in the RP58 KO muscle. On the contrary, a number of muscle differentiation-related genes, such as Ckm, troponin and Myosin, were downregulated in the same sample. These results indicate that the repressor protein RP58 is important for muscle terminal differentiation, possibly suppressing the gene expression of muscle differentiation genes such as the Ids.  Keywords: Knockout tissue Skeletal muscles of WT and RP58 KO mice (E18.5 diaphragm) were dissected under a microscope and RNA was extracted using ISOGEN (Nippongene). After EtOH precipitation, RNA was dissolved into DEPC-DW and its concentration was determined.   Microarray analysis - cRNA was synthesized. 10 ug of cRNA were hybridized to Affymetrix mouse 430A 2.0 arrays. Signal intensities were calculated using the RMA method. MAPPFinder (www.genmapp.org) was used to integrate expression data with known pathways.					
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	Asahara	Yokoyama	Yamashita	Asahara	Ito	
Person First Name	Hiroshi	Shigetoshi	Satoshi	Hiroshi	Yoshiaki	
Person Email	asahara@nch.go.jp					
Person Affiliation	National Research Institute for Child Health and Development					
Person Phone	+81-3-3417-2948					
Person Fax	+81-3-3417-2498					
Person Address	Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, Japan					
Person Roles	submitter					
Protocol Name	P-GSE16595-1	P-GSE16595-5	P-GSE16595-4	P-GSE16595-2	P-GSE16595-3	P-GSE16595-6
Protocol Description	ID_REF =  VALUE = Normalized signal intensity (log2) calculated by the RMA method	GeneChips® were scanned using GeneChip Scanner 3000.	Hybridization of 10 ug cRNA to Affymetrix® GeneChip® Mouse Genome 430 2.0 arrays was carried out following standard Affymetrix® protocols.	RNA of the culture was extracted using ISOGEN (NIPPONGENE).	Biotinylated cRNA were prepared from total RNA following standard Affymetrix® protocols.	Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Command Console using default parameters. We used the Expression Console Version 1.1 software for data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation.
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction
Experimental Factor Name	GENOTYPE					
Experimental Factor Type	genotype					
Comment[SecondaryAccession]	GSE16595					
Comment[GEOReleaseDate]	2009-07-31					
Comment[ArrayExpressSubmissionDate]	2009-06-12					
Comment[GEOLastUpdateDate]	2012-12-20					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-16595.sdrf.txt