Comment[ArrayExpressAccession]	E-GEOD-21791				
MAGE-TAB Version	1.1				
Public Release Date	2014-05-12				
Investigation Title	Zucker Diabetic Fatty (ZDF) Rat Study - Diaphragm vs. Sternohyoid				
Comment[Submitted Name]	Zucker Diabetic Fatty (ZDF) Rat Study - Diaphragm vs. Sternohyoid				
Experiment Description	Type 2 diabetes differs from type 1 diabetes in its pathogenesis. Type 1 diabetic diaphragm has altered gene expression which includes lipid and carbohydrate metabolism, ubiquitination and oxidoreductase activity. The objectives of the present study were to assess respiratory muscle gene expression changes in type 2 diabetes and to determine whether they are greater for the diaphragm than an upper airway muscle. Diaphragm and sternohyoid muscle from Zucker diabetic fatty (ZDF) rats were analyzed with Affymetrix gene expression arrays. The two muscles had 97 and 102 genes, respectively, with at least ±1.5-fold significantly changed expression with diabetes, and these were assigned to gene ontology groups based on over-representation analysis. Several significantly changed groups were common to both muscles, including lipid metabolism, carbohydrate metabolism, muscle contraction, ion transport and collagen, although the number of genes and the specific genes involved differed considerably for the two muscles. In both muscles there was a shift in metabolism gene expression from carbohydrate metabolism toward lipid metabolism, but the shift was greater and involved more genes in diabetic diaphragm than diabetic sternohyoid muscle. Groups present in only diaphragm were blood circulation and oxidoreductase activity. Groups present in only sternohyoid were immune & inflammation and response to stress & wounding, with complement genes being a prominent component. In conclusion, type 2 diabetes-induced gene expression changes in respiratory muscles has both similarities and differences relative to previous data on type 1 diabetes gene expression. Furthermore, the diabetic alterations in gene expression differ between diaphragm and sternohyoid. 18-week-old Zucker diabetic fatty rats: 6 normal and 5 diabetic diaphragms and sternohyoids.				
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	van Lunteren	van Lunteren	Moyer		
Person First Name	Erik	Erik	Michelle		
Person Mid Initials	--				
Person Email	exv4@cwru.edu				
Person Affiliation	Cleveland VA Medical Center				
Person Phone	216-791-3800				
Person Address	Pulmonary 111J(W), Cleveland VA Medical Center, 10701 East Boulevard, Cleveland, OH, USA				
Person Roles	submitter				
Protocol Name	P-GSE21791-1	P-GSE21791-3	P-GSE21791-4	P-GSE21791-2	P-GSE21791-5
Protocol Description	Affymetrix GCOS version 1.4 software. ID_REF =  VALUE = MAS5.0-calculated signal intensity ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = p-value that indicates the significance level of the detection call	8 ug of RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first strand cDNA. After second strand synthesis, double strand cDNA was used in an in vitro transcription reaction to generate biotinylated cRNA, which was purified and fragmented.	15 ug of biotin-labeled cRNA was used in a 300 ml hybridization cocktail which included spiked transcript controls. 200 ml of cocktail was loaded onto Affymetrix RAE 230A microarrays (Santa Clara, CA) and hybridized for 16 hr at 45oC with agitation. Standard post-hybridization washes and double-stain protocols used an Affymetrix GeneChip Fluidics Station 400.	Total RNA was extracted using Trizol (GibcoBRL, Rockville, MD), and the RNA pellets were resuspended at 1 mg RNA/ml DEPC-treated water. This was followed by a cleanup protocol with a Qiagen (Valencia, CA) RNeasy Total RNA mini kit.	Arrays were scanned using a Hewlett Packard Gene Array scanner.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	disease	organism part			
Experimental Factor Type	disease	organism part			
Comment[SecondaryAccession]	GSE21791				
Comment[GEOReleaseDate]	2014-05-12				
Comment[ArrayExpressSubmissionDate]	2010-05-12				
Comment[GEOLastUpdateDate]	2014-05-12				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-21791.sdrf.txt