Summary of Study ST002695

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 PR001020. The data can be accessed directly via it's Project DOI: 10.21228/M8V97D 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.

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Study IDST002695
Study TitleMoTrPAC: Endurance exercise training study in young adult rats, Rat Vena Cava Powder - Untargeted HILIC-Positive
Study SummaryThe goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
Institute
Broad Institute
DepartmentMetabolomics Platform
LaboratoryClish
Last NameClish
First NameClary
Address415 Main St, Cambridge, MA 02142
Emailclary@broadinstitute.org
Phone(617) 714-7654
Submit Date2023-04-25
Raw Data AvailableYes
Raw Data File Type(s)TBD
Analysis Type DetailLC-MS
Release Date2023-10-06
Release Version1
Clary Clish Clary Clish
https://dx.doi.org/10.21228/M8V97D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001020
Project DOI:doi: 10.21228/M8V97D
Project Title:MoTrPAC
Project Summary:MoTrPAC is a national research consortium designed to discover and perform preliminary characterization of the range of molecular transducers (the "molecular map") that underlie the effects of physical activity in humans. The program's goal is to study the molecular changes that occur during and after exercise and ultimately to advance the understanding of how physical activity improves and preserves health. Preclinical and clinical studies will examine the systemic effects of endurance and resistance exercise across a range of ages and fitness levels by molecular probing of multiple tissues before and after acute and chronic exercise. This program is the largest targeted NIH investment of funds into the mechanisms of how physical activity improves health and prevents disease. The MoTrPAC program is supported by the NIH Common Fund and is managed by a trans-agency working group representing multiple NIH institutes and centers, led by the NIH Office of Strategic Coordination, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute on Aging, and National Institute of Biomedical Imaging and Bioengineering. MoTrPAC Steering Committee: Wendy Kohrt, Chair, Russ Tracy, Co-Chair; NIH Program Manager, Concepcion Nierras. Euan Ashley and Matthew Wheeler are the PIs for the Motrpac Bioinformatics / Data Coordination Center.
Institute:MoTrPAC
Last Name:Ashley
First Name:Euan
Address:Falk Building CV267, 870 Quarry Road, Stanford, California 94305
Email:motrpac-data-deposition@lists.stanford.edu
Phone:(650) 725-1846

Subject:

Subject ID:SU002944
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id Group Timepoint Sex Tissue
SA30719090252016503Control 8 weeks of training or control time Female Rat Vena Cava Powder
SA30719190266016503Control 8 weeks of training or control time Female Rat Vena Cava Powder
SA30719290248016503Control 8 weeks of training or control time Female Rat Vena Cava Powder
SA30719390265016503Control 8 weeks of training or control time Female Rat Vena Cava Powder
SA30719490237016503Control 8 weeks of training or control time Male Rat Vena Cava Powder
SA30719590229016503Control 8 weeks of training or control time Male Rat Vena Cava Powder
SA30719690217016503Control 8 weeks of training or control time Male Rat Vena Cava Powder
SA30719790239016503Control 8 weeks of training or control time Male Rat Vena Cava Powder
SA307198QC_PREFA03QC-DriftCorrection 0 hour - -
SA307199QC_PREFA01QC-DriftCorrection 0 hour - -
SA307200QC_PREFA02QC-DriftCorrection 0 hour - -
SA307201QC_PREFA04QC-DriftCorrection 0 hour - -
SA307202QC_PREFB01QC-Pooled 0 hour - -
SA307203QC_PREFB03QC-Pooled 0 hour - -
SA307204QC_PREFB04QC-Pooled 0 hour - -
SA307205QC_PREFB02QC-Pooled 0 hour - -
SA307206QC_IPE02QC-Reference 0 hour - -
SA307207QC_Sed01QC-Reference 0 hour - -
SA307208QC_Sed03QC-Reference 0 hour - -
SA307209QC_IPE03QC-Reference 0 hour - -
SA307210QC_IPE04QC-Reference 0 hour - -
SA307211QC_IPE01QC-Reference 0 hour - -
SA307212QC_Sed04QC-Reference 0 hour - -
SA307213QC_Sed02QC-Reference 0 hour - -
SA30721490410016503Training 4 weeks of training Female Rat Vena Cava Powder
SA30721590406016503Training 4 weeks of training Female Rat Vena Cava Powder
SA30721690292016503Training 4 weeks of training Male Rat Vena Cava Powder
SA30721790283016503Training 4 weeks of training Male Rat Vena Cava Powder
SA30721890280016503Training 4 weeks of training Male Rat Vena Cava Powder
SA30721990281016503Training 4 weeks of training Male Rat Vena Cava Powder
SA30722090289016503Training 4 weeks of training Male Rat Vena Cava Powder
SA30722190267016503Training 8 weeks of training or control time Female Rat Vena Cava Powder
SA30722290259016503Training 8 weeks of training or control time Female Rat Vena Cava Powder
SA30722390251016503Training 8 weeks of training or control time Female Rat Vena Cava Powder
SA30722490254016503Training 8 weeks of training or control time Female Rat Vena Cava Powder
SA30722590218016503Training 8 weeks of training or control time Male Rat Vena Cava Powder
SA30722690222016503Training 8 weeks of training or control time Male Rat Vena Cava Powder
SA30722790227016503Training 8 weeks of training or control time Male Rat Vena Cava Powder
SA30722890225016503Training 8 weeks of training or control time Male Rat Vena Cava Powder
SA30722990223016503Training 8 weeks of training or control time Male Rat Vena Cava Powder
Showing results 1 to 40 of 40

Collection:

Collection ID:CO002937
Collection Summary:Samples were collected according to consortium protocol (see protocol referenced)
Collection Protocol Filename:pass1b_experimental_design_metabolomics.pdf
Sample Type:Rat Vena Cava Powder

Treatment:

Treatment ID:TR002953
Treatment Summary:Samples were collected according to consortium protocol (see protocol referenced)

Sample Preparation:

Sampleprep ID:SP002950
Sampleprep Summary:Tissue samples (10 mg) were homogenized in 300 µL of 10/67.4/22.4/0.18 (v/v/v/v) water/acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (0.18 ng/µL valine-d8, Isotec; 0.18 ng/µL phenylalanine-d8, Cambridge Isotope Laboratories) using a TissueLyserII bead mill (20 Hz, 2 X 2min; QIAGEN). The samples were place in a -80?C freezer for one hour and then centrifuged for 10 min (9000g, 4?C). 100uL of each supernatent was transferred to a de-activated inserts within an autsampler vial (Waters).
Sampleprep Protocol Filename:pass1b_experimental_design_metabolomics.pdf

Combined analysis:

Analysis ID AN004368
Analysis type MS
Chromatography type HILIC
Chromatography system Shimadzu Nexera X2
Column Waters Atlantis HILIC (150 x 2.1 mm)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH003484
Chromatography Summary:Extracts (10 µL) were injected onto a 150 x 2.1 mm Atlantis HILIC column (Waters). The column was eluted isocratically at a flow rate of 250 µL/min with 5% mobile phase A (10 mM ammonium formate and 0.1% formic acid in water) for 1 minute followed by a linear gradient to 40% mobile phase B (acetonitrile with 0.1% formic acid) over 10 minutes
Methods Filename:pass1b_hilicpos_methods.pdf
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Atlantis HILIC (150 x 2.1 mm)
Flow Gradient:0-0.5 min, isocratic 95% B, 250 uL/min; 0.5-10.5 min, gradient to 40% B, 250 uL/min; 10.5-15 min, isocratic 40% B, 250 uL/min; 15-17 min, gradient to 95% B, 250 uL/min
Flow Rate:0.25 ml/min
Solvent A:100% water;10 mM ammonium formate; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:HILIC

MS:

MS ID:MS004377
Analysis ID:AN004368
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:High resolution, accurate mass data were acquired using a system comprised of a Shimadzu Nexera X2 U-HPLC (Shimadzu Corp.; Marlborough, MA) coupled to a Q Exactive hybrid quadrupole orbitrap mass spectrometer (Thermo Fisher Scientific; Waltham, MA). MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over 70-800 m/z at 70,000 resolution and 3 Hz data acquisition rate. Other MS settings were: sheath gas 40, sweep gas 2, spray voltage 3.5 kV, capillary temperature 350°C, S-lens RF 40, heater temperature 300°C, microscans 1, automatic gain control target 1e6, and maximum ion time 250 ms. Raw data were processed using TraceFinder software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). The identities of 202 profiled metabolites were confirmed using reference standards.
Ion Mode:POSITIVE
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