Summary of Study ST002697

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 PR001669. The data can be accessed directly via it's Project DOI: 10.21228/M8ZQ5Q 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 IDST002697
Study TitleEmploying Hindlimb Unloading Model for The Identification of Serum Biomarkers Associated with Cardiovascular and Skeletal Muscle Deconditioning.
Study SummaryMicrogravity and prolonged periods of inactivity cause a variety of diseases, including skeletal muscle mass loss and weakening as well as cardiovascular deconditioning. The primary causes of the inadequate preventative measures for these deconditionings are the lack of biomarkers and unknown underlying mechanisms of cardiovascular and skeletal muscle deconditioning in these conditions. Here, we used a hindlimb unloading (HU) mouse model that replicates astronauts in space and bedridden patients to first evaluate cardiovascular and skeletal muscle performance. Serum samples from these mice were used to identify new biomarkers using metabolomic and proteomic approaches. Three weeks of unloading resulted in alterations in cardiovascular system function in C57/Bl6 mice, as measured by changes in mean arterial pressure and heart weight. Unloading for three weeks also altered skeletal muscle function, resulting in a decrease of grip strength in HU mice, as well as skeletal muscle atrophy, as shown by a drop in muscle mass. A two-week recovery time from the unloading condition partially reversed these alterations, stressing the importance of the recovery process.
Institute
Sharjah Institute for Medical Research
Last NameFacility
First NameCore
AddressM32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Emailtims-tof@sharjah.ac.ae
Phone+971 6 5057656
Submit Date2023-05-02
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2023-06-02
Release Version1
Core Facility Core Facility
https://dx.doi.org/10.21228/M8ZQ5Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001669
Project DOI:doi: 10.21228/M8ZQ5Q
Project Title:Employing Hindlimb Unloading Model for The Identification of Serum Biomarkers Associated with Cardiovascular and Skeletal Muscle Deconditioning.
Project Summary:Microgravity and prolonged periods of inactivity cause a variety of diseases, including skeletal muscle mass loss and weakening as well as cardiovascular deconditioning. The primary causes of the inadequate preventative measures for these deconditionings are the lack of biomarkers and unknown underlying mechanisms of cardiovascular and skeletal muscle deconditioning in these conditions. Here, we used a hindlimb unloading (HU) mouse model that replicates astronauts in space and bedridden patients to first evaluate cardiovascular and skeletal muscle performance. Serum samples from these mice were used to identify new biomarkers using metabolomic and proteomic approaches. Three weeks of unloading resulted in alterations in cardiovascular system function in C57/Bl6 mice, as measured by changes in mean arterial pressure and heart weight. Unloading for three weeks also altered skeletal muscle function, resulting in a decrease of grip strength in HU mice, as well as skeletal muscle atrophy, as shown by a drop in muscle mass. A two-week recovery time from the unloading condition partially reversed these alterations, stressing the importance of the recovery process.
Institute:Sharjah Institute for Medical Research
Last Name:Facility
First Name:Core
Address:M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Email:tims-tof@sharjah.ac.ae
Phone:+971 6 5057656

Subject:

Subject ID:SU002800
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:C57/Bl6 mice

Factors:

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

mb_sample_id local_sample_id Group
SA267111CR1-01-8897Control
SA267112CR1-02-8898Control
SA267113C5-02-8896Control
SA267114C4-02-8894Control
SA267115C4-01-8893Control
SA267116CR2-01-8899Control
SA267117CR2-02-8900Control
SA267118CR4-02-8904Control
SA267119CR4-01-8903Control
SA267120CR3-02-8902Control
SA267121CR3-01-8901Control
SA267122C3-02-8892Control
SA267123C5-01-8895Control
SA267124C2-01-8889Control
SA267125C2-02-8890Control
SA267126C3-01-8891Control
SA267127Hu6-01-8908HU
SA267128Hu4-02-8907HU
SA267129Hu6-02-8909HU
SA267130Hu7-02-8911HU
SA267131Hu8-01-8912HU
SA267132Hu8-02-8913HU
SA267133Hu4-01-8906HU
SA267134Hu7-01-8910HU
SA267135HuR2-01-8916HUR
SA267136HuR6-01-8920HUR
SA267137HuR6-02-8921HUR
SA267138HuR3-02-8919HUR
SA267139HuR3-01-8918HUR
SA267140HuR1-02-8915HUR
SA267141HuR2-02-8917HUR
SA267142HuR1-01-8914HUR
Showing results 1 to 32 of 32

Collection:

Collection ID:CO002793
Collection Summary:Blood samples were taken on the day of sacrifice using the cardiac puncture procedure, which was conducted humanely under anesthesia, blood samples were then centrifuged at 2000 RCF for 10 minutes and the serum was transfered into a new tube and stored in -80 freezer. After animal sacrifice and tissue collection, tissues were snap frozen using liquid nitrogen and kept in a -80 freezer.
Sample Type:Blood (serum)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002809
Treatment Summary:Mice in the HU group were unloaded from their tails for three weeks. Mice in the HUR group were unloaded from their tails for three weeks before being reloaded into the ground for two weeks.

Sample Preparation:

Sampleprep ID:SP002806
Sampleprep Summary:100 µL from each plasma sample was transferred to Eppendorf, then a volume of 300 µL of methanol was added to the aliquot. Samples were vortexed, then chilled at -20 °C for 2 hours followed by centrifugation (14000 rpm, 15 minutes, 24°C) to precipitate protein. The metabolite-containing supernatants were collected and transferred to glass vials for drying using the EZ-2 Plus (GeneVac, Ipswich, UK) at 40 ±1°C and the protein pellets that remained were air dried for proteomics (see section 2.4). Dried metabolite samples were resuspended with 200 µl (0.1% formic acid in water), and vortexed for 2 min. The samples were filtered using a hydrophilic nylon syringe filter (0.45 μm pore size) and placed within glass inserts prior to being analyzed by Q-TOF MS.

Combined analysis:

Analysis ID AN004371
Analysis type MS
Chromatography type Reversed phase
Chromatography system Bruker Elute
Column Hamilton Intensity Solo 2 C18 (100 x 2.1 mm, 1.8 um)
MS Type ESI
MS instrument type QTOF
MS instrument name Bruker timsTOF
Ion Mode POSITIVE
Units AU

Chromatography:

Chromatography ID:CH003277
Chromatography Summary:Samples were chromatographically separated by inline reversed-phase chromatography using the Elute HPG 1300 pumps and Elute Autosampler (Bruker, Darmstadt, Germany) with solvent A 0.1% FA in HPLC grade water and solvent B 0.1% FA in ACN. A Hamilton Intensity Solo 2 C18 column (100 mm x 2.1 mm, 1.8µm beads) was maintained at 35C. For metabolomics, 10 µL was injected twice for each sample and eluted using a 30-minute gradient as follows: 1% ACN was held for 2 minutes, ramping to 99% ACN over 15 minutes, held at 99% ACN for 3 minutes before re-equilibrating to 1% ACN for 10 minutes. Flow rates were 250 µL/min for elution and 350 µL/min for re-equilibration.
Instrument Name:Bruker Elute
Column Name:Hamilton Intensity Solo 2 C18 (100 x 2.1 mm, 1.8 um)
Column Temperature:35
Flow Gradient:1%B to 99%B in 15 min
Flow Rate:250 uL/min
Solvent A:Water (0.1% Formic Acid)
Solvent B:ACN (0.1% Formic Acid)
Chromatography Type:Reversed phase

MS:

MS ID:MS004119
Analysis ID:AN004371
Instrument Name:Bruker timsTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The MS analysis was performed using a TimsTOF (Bruker, Darmstadt, Germany) with Apollo II electrospray ionization (ESI) source. The drying gas was set to flow at 10 L/min and the drying temperature to 220C and the nebulizer pressure to 2.2 bar. The capillary voltage was 4500 V and the end plate offset 500V. For metabolomics the scan range was 20-1300 m/z. The collision energy was set to 20 eV, the cycle time to 0.5 seconds with a relative minimum intensity threshold of 400 counts per thousand and target intensity of 20,000. Sodium formate was injected as an external calibrant in the first 0.3 minutes of each LC-MS/MS run. MetaboScape 4.0 software was used for metabolite processing and statistical analysis (Bruker Daltonics). The following parameters for molecular feature identification and "bucketing" were set in the T-ReX 2D/3D workflow: For peak detection, a minimum intensity threshold of 1,000 counts is required, as well as a minimum peak duration of 7 spectra, with feature quantification determine using peak area. The file masses were recalibrated based on the external calibrant injected between 0-0.3 min.
Ion Mode:POSITIVE
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