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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
Study ID | ST001808 |
Study Title | Impact of high intensity and moderate exercise on genomic and metabolic remodeling with age in male mice |
Study 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 |
deCaboRa@grc.nia.nih.gov | |
Phone | +1-410-558-8510 |
Submit Date | 2021-05-27 |
Raw Data Available | Yes |
Raw Data File Type(s) | cdf |
Analysis Type Detail | GC-MS |
Release Date | 2021-09-15 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
---|---|---|
SA167828 | 40 Serum_094 | Old Acute |
SA167829 | 39 Serum_093 | Old Acute |
SA167830 | 38 Serum_092 | Old Acute |
SA167831 | 41 Serum_095 | Old Acute |
SA167832 | 43 Serum_097 | Old Acute |
SA167833 | 45 Serum_099 | Old Acute |
SA167834 | 44 Serum_098 | Old Acute |
SA167835 | 37 Liver_037 | Old Acute |
SA167836 | 42 Serum_096 | Old Acute |
SA167837 | 37 Serum_091 | Old Acute |
SA167838 | 43 Liver_043 | Old Acute |
SA167839 | 44 Liver_044 | Old Acute |
SA167840 | 41 Liver_041 | Old Acute |
SA167841 | 40 Liver_040 | Old Acute |
SA167842 | 38 Liver_038 | Old Acute |
SA167843 | 39 Liver_039 | Old Acute |
SA167844 | 45 Liver_045 | Old Acute |
SA167845 | 42 Liver_042 | Old Acute |
SA167846 | 52 Liver_052 | Old Chronic |
SA167847 | 51 Liver_051 | Old Chronic |
SA167848 | 50 Liver_050 | Old Chronic |
SA167849 | 48 Liver_048 | Old Chronic |
SA167850 | 53 Liver_053 | Old Chronic |
SA167851 | 46 Liver_046 | Old Chronic |
SA167852 | 54 Liver_054 | Old Chronic |
SA167853 | 47 Serum_101 | Old Chronic |
SA167854 | 48 Serum_102 | Old Chronic |
SA167855 | 53 Serum_107 | Old Chronic |
SA167856 | 54 Serum_108 | Old Chronic |
SA167857 | 49 Liver_049 | Old Chronic |
SA167858 | 52 Serum_106 | Old Chronic |
SA167859 | 51 Serum_105 | Old Chronic |
SA167860 | 49 Serum_103 | Old Chronic |
SA167861 | 50 Serum_104 | Old Chronic |
SA167862 | 47 Liver_047 | Old Chronic |
SA167863 | 46 Serum_100 | Old Chronic |
SA167864 | 33 Liver_033 | Old Control |
SA167865 | 32 Liver_032 | Old Control |
SA167866 | 31 Liver_031 | Old Control |
SA167867 | 34 Liver_034 | Old Control |
SA167868 | 35 Liver_035 | Old Control |
SA167869 | 29 Liver_029 | Old Control |
SA167870 | 36 Liver_036 | Old Control |
SA167871 | 29 Serum_083 | Old Control |
SA167872 | 30 Serum_084 | Old Control |
SA167873 | 35 Serum_089 | Old Control |
SA167874 | 36 Serum_090 | Old Control |
SA167875 | 30 Liver_030 | Old Control |
SA167876 | 34 Serum_088 | Old Control |
SA167877 | 33 Serum_087 | Old Control |
SA167878 | 31 Serum_085 | Old Control |
SA167879 | 32 Serum_086 | Old Control |
SA167880 | 28 Liver_028 | Old Control |
SA167881 | 28 Serum_082 | Old Control |
SA167882 | 13 Serum_067 | Young Acute |
SA167883 | 12 Serum_066 | Young Acute |
SA167884 | 11 Serum_065 | Young Acute |
SA167885 | 18 Liver_018 | Young Acute |
SA167886 | 14 Serum_068 | Young Acute |
SA167887 | 15 Serum_069 | Young Acute |
SA167888 | 18 Serum_072 | Young Acute |
SA167889 | 17 Serum_071 | Young Acute |
SA167890 | 16 Serum_070 | Young Acute |
SA167891 | 10 Liver_010 | Young Acute |
SA167892 | 10 Serum_064 | Young Acute |
SA167893 | 13 Liver_013 | Young Acute |
SA167894 | 12 Liver_012 | Young Acute |
SA167895 | 14 Liver_014 | Young Acute |
SA167896 | 15 Liver_015 | Young Acute |
SA167897 | 17 Liver_017 | Young Acute |
SA167898 | 11 Liver_011 | Young Acute |
SA167899 | 16 Liver_016 | Young Acute |
SA167900 | 23 Serum_077 | Young Chronic |
SA167901 | 22 Serum_076 | Young Chronic |
SA167902 | 21 Serum_075 | Young Chronic |
SA167903 | 20 Serum_074 | Young Chronic |
SA167904 | 24 Serum_078 | Young Chronic |
SA167905 | 25 Serum_079 | Young Chronic |
SA167906 | 21 Liver_021 | Young Chronic |
SA167907 | 27 Serum_081 | Young Chronic |
SA167908 | 26 Serum_080 | Young Chronic |
SA167909 | 19 Liver_019 | Young Chronic |
SA167910 | 19 Serum_073 | Young Chronic |
SA167911 | 23 Liver_023 | Young Chronic |
SA167912 | 22 Liver_022 | Young Chronic |
SA167913 | 24 Liver_024 | Young Chronic |
SA167914 | 26 Liver_026 | Young Chronic |
SA167915 | 27 Liver_027 | Young Chronic |
SA167916 | 20 Liver_020 | Young Chronic |
SA167917 | 25 Liver_025 | Young Chronic |
SA167918 | 5 Serum_059 | Young Control |
SA167919 | 4 Serum_058 | Young Control |
SA167920 | 3 Serum_057 | Young Control |
SA167921 | 6 Serum_060 | Young Control |
SA167922 | 7 Serum_061 | Young Control |
SA167923 | 1 Liver_001 | Young Control |
SA167924 | 9 Serum_063 | Young Control |
SA167925 | 8 Serum_062 | Young Control |
SA167926 | 2 Serum_056 | Young Control |
SA167927 | 1 Serum_055 | Young Control |
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 |
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 |
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 |