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1Experiment section 
2domain  ebi.ac.uk
3accession E-NUTR-XX
4name  Expression patterns in liver after resveratrol treatment of mice on a high-calorie diet
5description "GEO Series GSE6089: Resveratrol (3,5,4'-trihydroxystilbene) extends the lifespan of diverse species including yeast, worms, and flies. In these organisms, lifespan extension is dependent on Sir2, a conserved deacetylase proposed to underlie the beneficial effects of caloric restriction (CR). Here we show that resveratrol shifts the physiology of middle-aged mice on a high-calorie diet towards that of mice on a standard diet and significantly increases their survival. Resveratrol produces changes associated with longer lifespan including increased insulin sensitivity, reduced IGF-1, increased AMPK and PGC-1? activity, increased mitochondrial number, and improved motor function. Parametric analysis of gene set enrichment (PAGE) revealed that resveratrol opposed the effects of the high-calorie diet in 144 out of 153 significantly altered pathways. These data show that improving general health in mammals using small molecules is an attainable goal and point to new approaches for treating obesity-related disorders and diseases of ageing."
6experiment_design_type  compound_based_design
7quality_control Biological replicates
8organization  "National Institute on Aging, NIH, Research Resources Branch, Gene Expression and Genomics Unit"
9submitter Kevin G Becker
10publication_title Resveratrol improves health and survival of mice on a high-calorie diet.
11authors "Baur JA, Pearson KJ, Price NL, Jamieson HA, Lerin C, Kalra A, Prabhu VV, Allard JS, Lopez-Lluch G, Lewis K, Pistell PJ, Poosala S, Becker KG, Boss O, Gwinn D, Wang M, Ramaswamy S, Fishbein KW, Spencer RG, Lakatta EG, Le Couteur D, Shaw RJ, Navas P, Puigserver P, Ingram DK, de Cabo R, Sinclair DA"
12journal Nature
13volume  444
14issue   7117
15pages   337-342
16year  2006
17submission_date 15/06/2006
18release_date  05/11/2006
19
20Protocol section
21accession name  text  parameters  type
22P-NUTR-1  treatment   vehicle;route;preservation method; diet availability  grow
23P-NUTR-2  extraction  Total RNA was extracted with the Qiagen RNEasy Columns    extraction
24P-NUTR-3  labeling  Agilent low RNA Input Linear Amplification Kit using Cyanine-5-CTP    labeling
25P-NUTR-4  hybridization "17 hour incubation following Agilent protocols using 750ng of both Cy3 and Cy5 labeled material, In Situ Hybridization Kit reagents and control probes followed by a 10 minute room temperature wash in 6X SSC,0.005% tritonX-102 and 5 minutes at 4 degrees C in 0.1X SSC, 0.005% Triton X-102. The arrays were dried in a Nitrogen stream and scanned."  probe amount;duration hybridization
26P-NUTR-5  scanning  Arrays were scanned using an Agilent Scanner G2565AA .  scanner scanning
27
28Hybridization section
29File[raw] Array[accession]  FactorValue[compound] FactorValue[Dose] FactorValue[Exposure(month)]  FactorValue[diet] BioSource BioMaterialCharacteristics[animal identifier] BioMaterialCharacteristics[Organism]  BioMaterialCharacteristics[StrainOrLine]  BioMaterialCharacteristics[Provider]  BioMaterialCharacteristics[Age] BioMaterialCharacteristics[DevelopmentStage]  BioMaterialCharacteristics[Sex] BioMaterialCharacteristics[OrganismPart]  Sample  Protocol[grow]  Parameter[diet availability]  Parameter[route]  Parameter[vehicle]  Parameter[preservation method]  SampleMaterial  Extract Protocol[extraction]  ExtractMaterial LabeledExtract  Protocol[labeling]  Dye LabeledExtractMaterial  Hybridization Protocol[hybridization] Parameter[duration] Parameter[probe amount] Scan  Protocol[scanning]  Parameter[scanner]
30GSM140954.txt Agilent-012694 Whole Mouse Genome G4122A      18  Standard Diet AIN-93G GSM140954 1 Mus musculus  C57BL/6 NIA 78 weeks  adult male  liver GSM140954 P-NUTR-1  ad libitum  oral    snap frozen in liquid nitrogen  whole_organ GSM140954 P-NUTR-2  total_RNA source1 P-NUTR-3  Cy3 cDNA  GSM140954   P-NUTR-4  17 h  750 ng  GSM140954   P-NUTR-5  Agilent Scanner G2565AA
31GSM140954.txt Agilent-012694 Whole Mouse Genome G4122A      18  Standard Diet AIN-93G GSM140954 pool  Mus musculus  C57BL/6 NIA 78 weeks  adult male  liver GSM140954 P-NUTR-1  ad libitum  oral    snap frozen in liquid nitrogen  whole_organ GSM140954 P-NUTR-2  total_RNA source2 P-NUTR-3  Cy5 cDNA  GSM140954   P-NUTR-4  17 h  750 ng  GSM140954   P-NUTR-5  Agilent Scanner G2565AA
32GSM140955.txt Agilent-012694 Whole Mouse Genome G4122A      18  Standard Diet AIN-93G GSM140955 2 Mus musculus  C57BL/6 NIA 78 weeks  adult male  liver GSM140955 P-NUTR-1  ad libitum  oral    snap frozen in liquid nitrogen  whole_organ GSM140955 P-NUTR-2  total_RNA source3 P-NUTR-3  Cy3 cDNA  GSM140955   P-NUTR-4  17 h  750 ng  GSM140955   P-NUTR-5  Agilent Scanner G2565AA
33GSM140955.txt Agilent-012694 Whole Mouse Genome G4122A      18  Standard Diet AIN-93G GSM140955 pool  Mus musculus  C57BL/6 NIA 78 weeks  adult male  liver GSM140955 P-NUTR-1  ad libitum  oral    snap frozen in liquid nitrogen  whole_organ GSM140955 P-NUTR-2  total_RNA source4 P-NUTR-3  Cy5 cDNA  GSM140955   P-NUTR-4  17 h  750 ng  GSM140955   P-NUTR-5  Agilent Scanner G2565AA
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