Summary of Study ST002664
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.
| Study ID | ST002664 |
| Study Title | MoTrPAC: Endurance exercise training study in young adult rats, Tissue:Colon - Untargeted HILIC-Positive |
| Study Summary | The 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 of MIT and Harvard |
| Department | Metabolomics Platform |
| Laboratory | Clish |
| Last Name | Clish |
| First Name | Clary |
| Address | 415 Main St, Cambridge, MA 02142 |
| clary@broadinstitute.org | |
| Phone | (617) 714-7654 |
| Submit Date | 2023-05-02 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | TBD |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-10-06 |
| Release Version | 1 |
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: | SU002766 |
| 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 |
|---|---|---|---|---|
| SA264331 | 90245016103 | Control | 8 weeks of training or control time | Female |
| SA264332 | 90248016103 | Control | 8 weeks of training or control time | Female |
| SA264333 | 90252016103 | Control | 8 weeks of training or control time | Female |
| SA264334 | 90266016103 | Control | 8 weeks of training or control time | Female |
| SA264335 | 90265016103 | Control | 8 weeks of training or control time | Female |
| SA264336 | 90237016103 | Control | 8 weeks of training or control time | Male |
| SA264337 | 90229016103 | Control | 8 weeks of training or control time | Male |
| SA264338 | 90239016103 | Control | 8 weeks of training or control time | Male |
| SA264339 | 90217016103 | Control | 8 weeks of training or control time | Male |
| SA264340 | 90232016103 | Control | 8 weeks of training or control time | Male |
| SA264341 | QC_PREFA03 | QC-DriftCorrection | 0 hour | - |
| SA264342 | QC_PREFA01 | QC-DriftCorrection | 0 hour | - |
| SA264343 | QC_PREFA02 | QC-DriftCorrection | 0 hour | - |
| SA264344 | QC_PREFA04 | QC-DriftCorrection | 0 hour | - |
| SA264345 | QC_PREFB02 | QC-Pooled | 0 hour | - |
| SA264346 | QC_PREFB04 | QC-Pooled | 0 hour | - |
| SA264347 | QC_PREFB01 | QC-Pooled | 0 hour | - |
| SA264348 | QC_PREFB03 | QC-Pooled | 0 hour | - |
| SA264349 | QC_Sed02 | QC-Reference | 0 hour | - |
| SA264350 | QC_IPE01 | QC-Reference | 0 hour | - |
| SA264351 | QC_IPE04 | QC-Reference | 0 hour | - |
| SA264352 | QC_IPE03 | QC-Reference | 0 hour | - |
| SA264353 | QC_Sed01 | QC-Reference | 0 hour | - |
| SA264354 | QC_Sed04 | QC-Reference | 0 hour | - |
| SA264355 | QC_IPE02 | QC-Reference | 0 hour | - |
| SA264356 | QC_Sed03 | QC-Reference | 0 hour | - |
| SA264357 | 90564016103 | Training | 1 week of training or control time | Female |
| SA264358 | 90567016103 | Training | 1 week of training or control time | Female |
| SA264359 | 90559016103 | Training | 1 week of training or control time | Female |
| SA264360 | 90560016103 | Training | 1 week of training or control time | Female |
| SA264361 | 90571016103 | Training | 1 week of training or control time | Female |
| SA264362 | 90423016103 | Training | 1 week of training or control time | Male |
| SA264363 | 90426016103 | Training | 1 week of training or control time | Male |
| SA264364 | 90430016103 | Training | 1 week of training or control time | Male |
| SA264365 | 90421016103 | Training | 1 week of training or control time | Male |
| SA264366 | 90422016103 | Training | 1 week of training or control time | Male |
| SA264367 | 90578016103 | Training | 2 weeks of training | Female |
| SA264368 | 90587016103 | Training | 2 weeks of training | Female |
| SA264369 | 90581016103 | Training | 2 weeks of training | Female |
| SA264370 | 90585016103 | Training | 2 weeks of training | Female |
| SA264371 | 90576016103 | Training | 2 weeks of training | Female |
| SA264372 | 90449016103 | Training | 2 weeks of training | Male |
| SA264373 | 90444016103 | Training | 2 weeks of training | Male |
| SA264374 | 90439016103 | Training | 2 weeks of training | Male |
| SA264375 | 90450016103 | Training | 2 weeks of training | Male |
| SA264376 | 90441016103 | Training | 2 weeks of training | Male |
| SA264377 | 90406016103 | Training | 4 weeks of training | Female |
| SA264378 | 90420016103 | Training | 4 weeks of training | Female |
| SA264379 | 90410016103 | Training | 4 weeks of training | Female |
| SA264380 | 90412016103 | Training | 4 weeks of training | Female |
| SA264381 | 90416016103 | Training | 4 weeks of training | Female |
| SA264382 | 90280016103 | Training | 4 weeks of training | Male |
| SA264383 | 90281016103 | Training | 4 weeks of training | Male |
| SA264384 | 90289016103 | Training | 4 weeks of training | Male |
| SA264385 | 90292016103 | Training | 4 weeks of training | Male |
| SA264386 | 90283016103 | Training | 4 weeks of training | Male |
| SA264387 | 90251016103 | Training | 8 weeks of training or control time | Female |
| SA264388 | 90254016103 | Training | 8 weeks of training or control time | Female |
| SA264389 | 90267016103 | Training | 8 weeks of training or control time | Female |
| SA264390 | 90258016103 | Training | 8 weeks of training or control time | Female |
| SA264391 | 90259016103 | Training | 8 weeks of training or control time | Female |
| SA264392 | 90222016103 | Training | 8 weeks of training or control time | Male |
| SA264393 | 90218016103 | Training | 8 weeks of training or control time | Male |
| SA264394 | 90225016103 | Training | 8 weeks of training or control time | Male |
| SA264395 | 90227016103 | Training | 8 weeks of training or control time | Male |
| SA264396 | 90223016103 | Training | 8 weeks of training or control time | Male |
| Showing results 1 to 66 of 66 |
Collection:
| Collection ID: | CO002759 |
| Collection Summary: | - |
| Sample Type: | Colon |
Treatment:
| Treatment ID: | TR002775 |
| Treatment Summary: | - |
Sample Preparation:
| Sampleprep ID: | SP002772 |
| 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 | AN004336 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Shimadzu Nexera X2 |
| Column | Waters Atlantis HILIC (150 x 2.1mm,3um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH003242 |
| 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 2.1mm,3um) |
| Column Temperature: | - |
| Flow Gradient: | The column was eluted isocratically at a flow rate of 250 µL/min with 5% mobile phase A for 1 minute followed by a linear gradient to 40% mobile phase B over 10 minutes |
| Flow Rate: | 250 µL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004083 |
| Analysis ID: | AN004336 |
| 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 |
