Summary of Study ST000607

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000444. The data can be accessed directly via it's Project DOI: 10.21228/M8NW2H This work is supported by NIH grant, U2C- DK119886.


Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST000607
Study Title1D-1H-Nuclear Magnetic Resonance Metabolomics Reveals Age-related Changes in Metabolites Associated with Experimental Venous Thrombosis
Study TypeExperimental venous thrombosis
Study SummarySodium heparin preserved whole blood samples were collected from young and old mice with and without induced VT. Samples were subjected to MeOH:CHCl3 extraction and the MeOH was assayed by 1H-NMR. Chenomx software was used for spectral analysis.
University of Michigan
DepartmentClinical Pharmacy
LaboratoryThe NMR Metabolomics Laboratory (Stringer)
Last NameStringer
First NameKathleen
AddressCollege of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109
Submit Date2016-12-08
Num Groups4
Total Subjects31
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2017-07-10
Release Version1
Kathleen Stringer Kathleen Stringer application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR000444
Project DOI:doi: 10.21228/M8NW2H
Project Title:Metabolomics of Murine Age-related Deep Vein Thrombosis
Project Type:Quantitative 1D-1H-NMR metabolomics
Project Summary:Objective: Age is a significant risk factor for the development of venous thrombosis (VT), but the mechanism(s) that underlie this risk remain(s) undefined and poorly understood. Aging is known to adversely influence inflammation and affect metabolism. Untargeted metabolomics permits an agnostic assessment of the physiological landscape and lends insight into the mechanistic underpinnings of clinical phenotypes. The objective of this exploratory study was to test the feasibility of a metabolomics approach for identifying potential metabolic mechanisms of age-related VT. Methods: We subjected whole blood samples collected from young and old nonthrombosed controls and VT mice 2 days after thrombus induction using the electrolytic inferior vena cava, to a methanol:chloroform extraction and assayed the resulting aqueous fractions using 1D-1H- nuclear magnetic resonance. Normalized mouse metabolite data were compared across groups using analysis of variance (ANOVA) with Holm-Sidak post-testing. In addition, associations between metabolite concentrations and parameters of thrombosis such as thrombus and vein wall weights, and markers of inflammation, vein wall P- and E-selectin levels, were assessed using linear regression. The relatedness of the found significant metabolites was visually assessed using a bioinformatics tool, Metscape, which generates compound-reaction-enzyme-gene networks to aid in the interpretation of metabolomics data. Results: Old mice with VT had a greater mean vein wall weight compared with young mice with VT (P < .05). Clot weight differences between old and young mice followed the same trend as vein wall weight (0.011 % 0.04 g vs 0.008 % 0.003 g; P [ not significant). Glutamine (ANOVA, P < .01), proline (ANOVA, P < .01), and phenylalanine (ANOVA, P <.05) levels were increased in old VT mice compared with age-matched controls and young VT mice. Betaine and/or trimethylamine N-oxide levels were increased in aged mice compared with young animals. Vein wall weight was strongly associated with glutamine (P < .05), and phenylalanine (P <.01) concentrations and there was a trend toward an association with proline (P [ .09) concentration. Vein wall Pselectin, but not E-selectin levels, were increased in old VT mice and were associated with the three found metabolites of age-related VT. Collectively, with the addition of glutamate, these metabolites form a single compound-reaction-enzyme gene network that was generated by Metscape. Conclusions: We used 1D-1H-nuclear magnetic resonance metabolite profiling to identify, for the first time, in an experimental model, three potential metabolites, glutamine, phenylalanine, and proline, associated with age-related VT. These metabolites are metabolically related and their levels are associated with vein wall weight and P-selectin concentrations. In aggregate, these findings provide a “roadmap” of pathways that could be interrogated in future studies, which could include provocation of the glutamine, phenylalanine, and proline pathways in the vein wall. This study introduces metabolomics as a new approach to furthering knowledge about the mechanisms of age-related VT. This study has been published: J Vasc Surg Venous Lymphat Disord. 2016 Apr;4(2):221-30. doi: 10.1016/j.jvsv.2015.09.010. Epub 2015 Nov 24.
Institute:University of Michigan
Department:Department of Surgery
Laboratory:NMR Metabolomics Laboratory, University of Michigan
Last Name:Stringer
First Name:Kathleen
Address:College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109
Funding Source:NIH (DK097153; HL076123), College of Pharmacy Upjohn Award


Subject ID:SU000630
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57Bl6
Age Or Age Range:10 weeks and 12-24 months (young & old)
Weight Or Weight Range:~25 g and ~34 g
Species Group:Mammal


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

mb_sample_id local_sample_id Condition
SA033501CH14WBCntrl young
SA033502CH13WBCntrl young
SA033503CH11WBCntrl young
SA033504CH15WBCntrl young
SA033505CH12WBCntrl young
SA033506CH16WBCntrol old
SA033507CH20WBCntrol old
SA033508CH19WBCntrol old
SA033509CH18WBCntrol old
SA033510CH17WBCntrol old
SA033511CH31WBDVT old
SA033512CH29WBDVT old
SA033513CH28WBDVT old
SA033514CH8WBDVT old
SA033515CH10WBDVT old
SA033516CH7WBDVT old
SA033517CH21WBDVT old
SA033518CH27WBDVT old
SA033519CH5WBDVT young
SA033520CH4WBDVT young
SA033521CH22WBDVT young
SA033522CH25WBDVT young
SA033523CH1WBDVT young
SA033524CH26WBDVT young
SA033525CH24WBDVT young
Showing results 1 to 25 of 25


Collection ID:CO000624
Collection Summary:None
Collection Protocol Filename:SOP_for_whole_blood_collection_exp._animals_v1.3.pdf
Sample Type:Whole blood
Collection Tube Temp:4C
Additives:Sodium heparin
Blood Serum Or Plasma:Whole blood


Treatment ID:TR000644
Treatment Summary:None
Animal Vet Treatments:Electrolytic inferior vena cava (IVC) model (EIM to induce thrombogenesis
Animal Anesthesia:2-5% isoflurane with 100% oxygen
Animal Fasting:No
Animal Endp Euthanasia:Per IUCUCA and 2d following induction of VT
Animal Endp Tissue Coll List:Blood sampling, thrombus and vein wall

Sample Preparation:

Sampleprep ID:SP000637
Sampleprep Summary:Methanol:cholorform extraction
Sampleprep Protocol Filename:Wakefield_Mouse_WB_Extraction_Protocol.pdf
Sampleprep Protocol Comments:Lipid fractions saved, stored at -20°C
Processing Method:Methanol:Chloroform Extraction
Processing Storage Conditions:0-4°C
Extraction Method:Methanol:chloroform extraction
Extract Cleanup:N/A
Extract Storage:-80°C


Analysis ID:AN000928
Laboratory Name:University of Michigan Biochemical NMR Core Laboratory
Analysis Type:NMR
Software Version:VNMRJ 3.2
Operator Name:Michael Finkel
Data Format:.fid
Num Factors:4
Num Metabolites:54


NMR ID:NM000104
Analysis ID:AN000928
Instrument Name:Agilent 500/54 Premium Shielded VNMRS system
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Standard Concentration:10% (~0.5mM)
Spectrometer Frequency:500 MHz
NMR Probe:ONE-Probe
NMR Solvent:D2O
NMR Tube Size:5mm
Shimming Method:Auto shim (gradient shimming)
Pulse Sequence:1D-NOESY
Water Suppression:saturation at 80 Hz induced field strength
Pulse Width:5.5ms
Offset Frequency:around -178Hz
Chemical Shift Ref Cpd:6mM Formate
Number Of Scans:32