Summary of Study ST001808

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001142. The data can be accessed directly via it's Project DOI: 10.21228/M8368X This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001808
Study TitleImpact of high intensity and moderate exercise on genomic and metabolic remodeling with age in male mice
Study SummaryHow skeletal muscle adapts to different types of exercise intensity with age is not known. Young and old C57BL/6 male mice were assigned to either a sedentary or two types of exercise regimes consisting of daily high-intensity intermittent (HIIT) or moderate intensity continuous (MICT) training for 4 weeks, compatible with the older group’s exercise capacity. Body composition, fasting blood glucose levels, and muscle strength were improved in exercised old mice compared to sedentary controls, while the exercise benefits were absent in younger animals. Skeletal muscle exhibited structural and functional adaptations in response to exercise, as revealed by electron microscopy, OXPHOS assays, respirometry, and PGC-1 and LC3-II protein levels. Transcriptomics analysis of gastrocnemius muscle combined with liver and serum metabolomics unveiled an age-dependent metabolic remodeling provoked by exercise through mitochondrial biogenesis, energy metabolism, and cellular plasticity. These results are supportive of a tailored exercise prescription approach with the goal of improving health and ameliorating age-associated loss of muscle mass, strength and function in the elderly.
Institute
National Institutes of Health
DepartmentExperimental Gerontology Section and Translational Gerontology Branch, NIA
Last Namede Cabo
First NameRafael
Address251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
EmaildeCaboRa@grc.nia.nih.gov
Phone+1-410-558-8510
Submit Date2021-05-27
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2021-09-15
Release Version1
Rafael de Cabo Rafael de Cabo
https://dx.doi.org/10.21228/M8368X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001142
Project DOI:doi: 10.21228/M8368X
Project Title:Impact of high intensity and moderate exercise on genomic and metabolic remodeling with age in male mice
Project Type:Untargeted metabolomics
Project Summary:How skeletal muscle adapts to different types of exercise intensity with age is not known. Young and old C57BL/6 male mice were assigned to either a sedentary or two types of exercise regimes consisting of daily high-intensity intermittent (HIIT) or moderate intensity continuous (MICT) training for 4 weeks, compatible with the older group’s exercise capacity. Body composition, fasting blood glucose levels, and muscle strength were improved in exercised old mice compared to sedentary controls, while the exercise benefits were absent in younger animals. Skeletal muscle exhibited structural and functional adaptations in response to exercise, as revealed by electron microscopy, OXPHOS assays, respirometry, and PGC-1? and LC3-II protein levels. Transcriptomics analysis of gastrocnemius muscle combined with liver and serum metabolomics unveiled an age-dependent metabolic remodeling provoked by exercise through mitochondrial biogenesis, energy metabolism, and cellular plasticity. These results are supportive of a tailored exercise prescription approach with the goal of improving health and ameliorating age-associated loss of muscle mass, strength and function in the elderly.
Institute:National Institutes of Health
Department:Experimental Gerontology Section and Translational Gerontology Branch, NIA
Last Name:de Cabo
First Name:Rafael
Address:251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
Email:deCaboRa@grc.nia.nih.gov
Phone:+1-410-558-8510
Funding Source:Intramural Research Program of the National Institute on Aging, NIH

Subject:

Subject ID:SU001885
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id factor
SA16782840 Serum_094Old Acute
SA16782939 Serum_093Old Acute
SA16783038 Serum_092Old Acute
SA16783141 Serum_095Old Acute
SA16783243 Serum_097Old Acute
SA16783345 Serum_099Old Acute
SA16783444 Serum_098Old Acute
SA16783537 Liver_037Old Acute
SA16783642 Serum_096Old Acute
SA16783737 Serum_091Old Acute
SA16783843 Liver_043Old Acute
SA16783944 Liver_044Old Acute
SA16784041 Liver_041Old Acute
SA16784140 Liver_040Old Acute
SA16784238 Liver_038Old Acute
SA16784339 Liver_039Old Acute
SA16784445 Liver_045Old Acute
SA16784542 Liver_042Old Acute
SA16784652 Liver_052Old Chronic
SA16784751 Liver_051Old Chronic
SA16784850 Liver_050Old Chronic
SA16784948 Liver_048Old Chronic
SA16785053 Liver_053Old Chronic
SA16785146 Liver_046Old Chronic
SA16785254 Liver_054Old Chronic
SA16785347 Serum_101Old Chronic
SA16785448 Serum_102Old Chronic
SA16785553 Serum_107Old Chronic
SA16785654 Serum_108Old Chronic
SA16785749 Liver_049Old Chronic
SA16785852 Serum_106Old Chronic
SA16785951 Serum_105Old Chronic
SA16786049 Serum_103Old Chronic
SA16786150 Serum_104Old Chronic
SA16786247 Liver_047Old Chronic
SA16786346 Serum_100Old Chronic
SA16786433 Liver_033Old Control
SA16786532 Liver_032Old Control
SA16786631 Liver_031Old Control
SA16786734 Liver_034Old Control
SA16786835 Liver_035Old Control
SA16786929 Liver_029Old Control
SA16787036 Liver_036Old Control
SA16787129 Serum_083Old Control
SA16787230 Serum_084Old Control
SA16787335 Serum_089Old Control
SA16787436 Serum_090Old Control
SA16787530 Liver_030Old Control
SA16787634 Serum_088Old Control
SA16787733 Serum_087Old Control
SA16787831 Serum_085Old Control
SA16787932 Serum_086Old Control
SA16788028 Liver_028Old Control
SA16788128 Serum_082Old Control
SA16788213 Serum_067Young Acute
SA16788312 Serum_066Young Acute
SA16788411 Serum_065Young Acute
SA16788518 Liver_018Young Acute
SA16788614 Serum_068Young Acute
SA16788715 Serum_069Young Acute
SA16788818 Serum_072Young Acute
SA16788917 Serum_071Young Acute
SA16789016 Serum_070Young Acute
SA16789110 Liver_010Young Acute
SA16789210 Serum_064Young Acute
SA16789313 Liver_013Young Acute
SA16789412 Liver_012Young Acute
SA16789514 Liver_014Young Acute
SA16789615 Liver_015Young Acute
SA16789717 Liver_017Young Acute
SA16789811 Liver_011Young Acute
SA16789916 Liver_016Young Acute
SA16790023 Serum_077Young Chronic
SA16790122 Serum_076Young Chronic
SA16790221 Serum_075Young Chronic
SA16790320 Serum_074Young Chronic
SA16790424 Serum_078Young Chronic
SA16790525 Serum_079Young Chronic
SA16790621 Liver_021Young Chronic
SA16790727 Serum_081Young Chronic
SA16790826 Serum_080Young Chronic
SA16790919 Liver_019Young Chronic
SA16791019 Serum_073Young Chronic
SA16791123 Liver_023Young Chronic
SA16791222 Liver_022Young Chronic
SA16791324 Liver_024Young Chronic
SA16791426 Liver_026Young Chronic
SA16791527 Liver_027Young Chronic
SA16791620 Liver_020Young Chronic
SA16791725 Liver_025Young Chronic
SA1679185 Serum_059Young Control
SA1679194 Serum_058Young Control
SA1679203 Serum_057Young Control
SA1679216 Serum_060Young Control
SA1679227 Serum_061Young Control
SA1679231 Liver_001Young Control
SA1679249 Serum_063Young Control
SA1679258 Serum_062Young Control
SA1679262 Serum_056Young Control
SA1679271 Serum_055Young Control
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Collection:

Collection ID:CO001878
Collection Summary:Mice were euthanized and serum was collected thereafter. Liver was collected and frozen in LN2.
Sample Type:Liver

Treatment:

Treatment ID:TR001898
Treatment Summary:6, 9, Young Control Young Acute Young Chronic Old Control Old Acute Old Chronic

Sample Preparation:

Sampleprep ID:SP001891
Sampleprep Summary:Extraction of Mammalian Tissue Samples: Liver 1. References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ (in press) 2.Starting material: Liver sample: weigh 4mg per sample into 2mL Eppendorf tubes. 3. Equipment: Centrifuge (Eppendorf 5415 D) Calibrated pipettes 1-200μl and 100-1000μl Eppendorf tubes 2mL, clear (Cat. No. 022363204) Centrifuge tubes 50mL, polypropylene Eppendorff Tabletop Centrifuge (Proteomics core Lab.) ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer (VWR) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Turex mini homogenizer 4. Chemicals Acetonitrile, LCMS grade (JT Baker; Cat. No.9829-02) Isopropanol, HPLC grade (JT Baker; Cat. No. 9095-02) Methanol Acetone Crushed ice 18 MΩ pure water (Millipore) Nitrogen line with pipette tip pH paper 5-10 (EMD Chem. Inc.) 5. Procedure Preparation of extraction mix and material before experiment: Switch on bath to pre-cool at –20°C (±2°C validity temperature range) Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper Make the extraction solution by mixing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 De-gas the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization. Sample preparation of blood plasma or serum samples for GCTOF analysis Purpose: This SOP describes sample extraction and sample preparation for primary metabolism profiling by gas chromatography/time-of-flight mass spectrometry (GCTOF). References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ. Fiehn, O. Metabolomics by gas chromatography - mass spectrometry: combined targeted and untargeted profiling. 2016. Curr. Protoc. Mol. Biol. 114:30.4.1-30.4.32. doi: 10.1002/0471142727.mb3004s114. Starting material: Plasma/serum: 30 µL sample volume or aliquot Equipment: Centrifuge Eppendorf 5415 D Calibrated pipettes 1-200µL and 100-1000µL Multi-Tube Vortexer (VWR VX-2500) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Nitrogen line with Pasteur pipette Chemicals and consumables: Product Manufacturer & Part Number Eppendorf tubes 1.5 mL, uncolored Eppendorf 022363204 Crushed ice UC Davis Water, LC/MS Grade Fisher Optima W6-4 Acetonitrile, LC/MS Grade Fisher Optima A955-4 Isopropanol, LC/MS Grade Fisher A461-4 pH paper 5-10 Millipore Sigma 1095330001 Bioreclamation human plasma (disodium EDTA) Bioreclamation HMPLEDTA Sample Preparation: Preparation of extraction solvent For 1 L of extraction solvent, combine 375 mL of acetonitrile, 375 mL of isopropanol, and 250 mL water in a 1 L bottle conditioned with the aforementioned chemicals. If a different total volume of extraction solvent is needed, simply mix acetonitrile, isopropanol, and water in volumes in proportion 3:3:2. Purge the extraction solution mix for 5 min with nitrogen with small bubbles. Make sure that the nitrogen line is flushed out of air before using it for degassing the extraction solvent solution. Store at -20°C until use. Note: if solvent freezes, sonicate until thawed and mix before use. Extraction Thaw raw samples at room temperature (or in the refrigerator at 4˚C) and vortex 10 sec at low speed to homogenize. Aliquot 30 μL of plasma sample into a 1.5 mL Eppendorf tube. Keep all samples on ice. Add 1 mL 3:3:2 (v/v/v) ACN:IPA:H2O extraction solvent (prechilled in a -20°C freezer). Vortex the sample for 10 sec. Shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. Continue to keep all extracted samples on ice. Centrifuge samples for 2 min at 14000 rcf. Aliquot two 450 μL portions of the supernatant into 1.5 mL Eppendorf tubes (one for analysis and one as a backup sample). Transfer 100 μL of the remaining supernatant from each sample to a 2, 15, or 50 mL tube for pools, depending on number of samples in the study. Evaporate one 450 μL aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. Proceed with cleanup or store tubes at -20°C until cleanup. Pooling Transfer multiple 475 µL aliquots of pooled samples to 1.5 mL Eppendorf tubes, one aliquot for every 10 samples in the study. If there is still pool remaining, prepare additional aliquots for backup. Centrifuge pool samples for 2 min at 14000 rcf. Remove 450 µL supernatant to new 1.5 mL Eppendorf tube. Evaporate to complete dryness in the Labconco Centrivap cold trap concentrator. Proceed with cleanup or store tubes at -20°C until cleanup. Cleanup Resuspend the dried aliquot with 500 μL 50:50 (v/v) ACN:H2O (degassed as given above) and vortex for about 10 sec. Centrifuge for 2 min at 14000 rcf. Remove 475 μL supernatant to a new 1.5 mL Eppendorf tube. Evaporate the transferred supernatant to complete dryness in the Labconco Centrivap cold trap concentrator. Submit to derivatization (see SOP “Derivatization of GC Samples & Standards”) or store at -20°C until ready for analysis. Quality assurance For every 50 samples, perform one method blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. If no combined pool was made from the extracted samples, use one commercial plasma/serum pool sample per 10 authentic subject samples as control instead.

Combined analysis:

Analysis ID AN002931
Analysis type MS
Chromatography type GC
Chromatography system Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS
Column Rtx-5Sil MS column
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode UNSPECIFIED
Units normalized peak height

Chromatography:

Chromatography ID:CH002172
Chromatography Summary:Gas Chromatography conditions: A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min.
Instrument Name:Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS
Column Name:Rtx-5Sil MS column
Chromatography Type:GC

MS:

MS ID:MS002722
Analysis ID:AN002931
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:Mass spectrometer settings: A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da.
Ion Mode:UNSPECIFIED
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