Comment[ArrayExpressAccession]	E-GEOD-43691
MAGE-TAB Version	1.1															
Public Release Date	2013-05-01
Investigation Title	Hepatic molecular alterations more than muscle's differentiate obese hyperphagic mice from those prolonged fed with the high-fat diet															
Comment[Submitted Name]	Hepatic molecular alterations more than muscle's differentiate obese hyperphagic mice from those prolonged fed with the high-fat diet
Experiment Description	Although mitochondrial dysfunctions are implicated in the pathogenesis of obesity, the molecular mechanisms underlying obesity-related metabolic abnormalities are still not well established. To acquire a comprehensive picture of mitochondrial molecular changes within metabolically active tissues, we focused on hepatic and muscle whole cellular transcriptome and mitochondrial proteome alterations in 16 and 48 weeks old high fat diet (HFD)-feed wild type C57BL/6J and hyperphagic, genetically modified mice with leptin dysfunction (ob/ob and db/db). On transcriptome level, the most discriminative hepatic alterations distinguished between genetically modified and wild type mice, and between overnight fasted and non-fasted mice, while the muscle transcriptional alterations related mainly to the fasting state. The fractions of uniquely different proteins were consistently higher in hyperphagic than in HFD-fed mice and in fasted than non-fasted mice . The liver samples revealed overall higher number of differentially expressed RNAs and proteins than muscle samples. Differentially expressed genes and proteins in the liver, but not in the muscle, could be assigned to several Gene Ontology terms, including oxidation-reduction and several metabolic processes. Thus, altered expression of genes and proteins accompanied the state of obesity and was quantitatively different in the liver and muscle. Our parallel microarray- and quantitative mitochondrial mass spectrometry-based study performed on hepatic and muscle samples identified a higher number of differentially expressed proteins than any other studies investigating obesity-related proteomes. However, even with our integrated transcriptomic and proteomic approach still many details and dynamics of a chain of metabolic events leading to obesity-related mitochondrial dysfunctions remain unresolved . 48 samples each of liver and muscle (total samples: 96). Samples splitted equally according to 3 criterions: age (24 young/24 old), fasting status (24 fasted/24 non fasted), and strain+diet (12 each: B6.V-Lep ob/J+D12450B, B6.BKS(D)-Lep rdb/J+D12450B, C57BL/6J+D12450B, C57BL/6J+D12492). Overall 3 replicates for each strain+diet/age/fasting_status combination. Low fat diet = D12450B; high fat diet = D12492.															
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	Goryca	Nesteruk	Hennig	Mikula	Karczmarski	Dzwonek	Goryca	Rubel	Paziewska	Woszczynski	Ledwon	Dabrowska	Walewska-Zielecka	Pysniak	Dadlez	Ostrowski
Person First Name	Krzysztof	Monika	Ewa	Michal	Jakub	Artur	Krzysztof	Tymon	Agnieszka	Marek	Joanna	Michalina	Bozena	Kazimiera	Michal	Jerzy
Person Mid Initials			E													
Person Email	geo@ncbi.nlm.nih.gov															
Person Affiliation	Centrum Onkologii Instytut im. Marii Skłodowskiej Curie															
Person Address	Centrum Onkologii Instytut im. Marii Skłodowskiej Curie, Roentgena 5, Warszawa, Poland															
Person Roles	submitter															
Protocol Name	P-GSE43691-1	P-GSE43691-3	P-GSE43691-4	P-GSE43691-6	P-GSE43691-2	P-GSE43691-5										
Protocol Description	The data were quantile normalised using lumi library in R ID_REF =  VALUE = quantile normalized signal Detection Pval = 	Standard Illumina labeling protocol	Standard Illumina hybridization protocol	RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.	RNA was extracted with QIAGEN RNeasy Lipid Tissue mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.	Standard Illumina scanning protocol										
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	array scanning protocol										
Experimental Factor Name	STRAIN OR LINE	DIET	ORGANISM PART	FASTING STATUS	AGE											
Experimental Factor Type	strain or line	diet	organism part	fasting status	age											
Comment[SecondaryAccession]	GSE43691															
Comment[GEOReleaseDate]	2013-05-01															
Comment[ArrayExpressSubmissionDate]	2013-01-23															
Comment[GEOLastUpdateDate]	2013-05-02															
Comment[AEExperimentType]	transcription profiling by array															
Comment[AdditionalFile:Data1]	GSE43691_non-normalized_data_Liver.txt															
Comment[AdditionalFile:Data2]	GSE43691_non-normalized_data_Muscle.txt															
SDRF File	E-GEOD-43691.sdrf.txt