Summary of Study ST002189

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 PR001395. The data can be accessed directly via it's Project DOI: 10.21228/M8DB02 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)
Study IDST002189
Study TitleMetabolomic profiling reveals muscle metabolic changes following iliac arteriovenous fistula creation in mice (Aqueous)
Study TypeStudy of the skeletal muscle metabolome in mice with iliac arteriovenous fistula via 1H NMR
Study SummaryIn the present study, we hypothesize that the creation of an iliac AVF would result in significant alterations to the limb muscle metabolome. Recently, our group developed a new murine model to address the pathophysiology of access-related hand dysfunction (ARHD) in mice, where AVF creation is performed in the iliac artery/vein. Because of the anatomical location of the AVF creation, this model produces clinically relevant changes in the mouse hindlimb including hemodynamic alterations, muscle weakness, and mitochondrial function impairment.
Institute
University of Florida
DepartmentApplied Physiology and Kinesiology
LaboratoryRm 42 and Rm 43
Last NameRyan
First NameTerence
Address1864 Stadium Rd, FLG 114, Gainesville, FL, 32611, USA
Emailryant@ufl.edu
Phone352-294-1700
Submit Date2022-02-17
Num Groups4
Total Subjects34
Num MalesAll
Study CommentsMetabolomic study via NMR
PublicationsFrontiers
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2022-08-01
Release Version1
Terence Ryan Terence Ryan
https://dx.doi.org/10.21228/M8DB02
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001395
Project DOI:doi: 10.21228/M8DB02
Project Title:Metabolomic profiling reveals muscle metabolic changes following iliac arteriovenous fistula creation in mice
Project Type:Study of the skeletal muscle metabolome in mice with iliac arteriovenous fistula via 1H NMR
Project Summary:In the present study, we hypothesize that the creation of an iliac AVF would result in significant alterations to the limb muscle metabolome. Recently, our group developed a new murine model to address the pathophysiology of access-related hand dysfunction (ARHD) in mice, where AVF creation is performed in the iliac artery/vein. Because of the anatomical location of the AVF creation, this model produces clinically relevant changes in the mouse hindlimb including hemodynamic alterations, muscle weakness, and mitochondrial function impairment.
Institute:University of Florida
Department:Applied Physiology and Kinesiology
Laboratory:Rm 42 and Rm 43
Last Name:Ryan
First Name:Terence
Address:1864 Stadium Rd, FLG 114, Gainesville, FL, 32611, USA
Email:ryant@ufl.edu
Phone:352-294-1700
Funding Source:National Institutes of Health (NIH) grant R01HL148597 (STS). Additional salary support was provided by NIH grants R01DK119274 (SAB) and R01HL149704 (TER), and a postdoctoral fellowship (POST903198) from the American Heart Association (KK).
Project Comments:Metabolomic study via NMR
Publications:Frontiers
Contributors:Ram B. Khattri, Kyoungrae Kim, Erik M. Anderson, Brian Fazzone, Kenneth C Harland, Qiongyao Hu, Victoria R. Palzkill, Tomas A. Cort, Kerri A. O’Malle, Scott A. Berceli, Terence E. Ryan, Salvatore T. Scali

Subject:

Subject ID:SU002275
Subject Type:Mammal
Subject Species:Mus musculus
Genotype Strain:C57BL/6J
Age Or Age Range:13 weeks
Weight Or Weight Range:(28.4±1.1 g (control SHAM mice) vs 26.4±2.1 g (control AVF mice) vs 23.6±2.1 (CKD SHAM mice) vs 24.7±1.3 (CKD AVF mice), N=8-10/group).
Gender:Male
Animal Animal Supplier:Jackson Labs (Stock # 000664)
Animal Housing:Housed in a temperature of 22 oC
Animal Light Cycle:12-hour light/12-hour dark
Animal Feed:Ad libitum (Casein control diet vs. adenine-supplemented diet to induce CKD)
Animal Water:free access to food and water (3-5 animals per cage).
Animal Inclusion Criteria:(3-5 animals per cage).

Factors:

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

mb_sample_id local_sample_id Factor1***
SA210127Terence_MS37_Quad_AqCKD_AVF
SA210128Terence_MS39_Quad_AqCKD_AVF
SA210129Terence_MS40_Quad_AqCKD_AVF
SA210130Terence_MS36_Quad_AqCKD_AVF
SA210131Terence_MS30_Quad_AqCKD_AVF
SA210132Terence_MS18_Quad_AqCKD_AVF
SA210133Terence_MS26_Quad_AqCKD_AVF
SA210134Terence_MS27_Quad_AqCKD_AVF
SA210135Terence_MS28_Quad_AqCKD_AVF
SA210136Terence_MS29_Quad_AqCKD_AVF
SA210137Terence_MS16_Quad_AqCKD_SHAM
SA210138Terence_MS20_Quad_AqCKD_SHAM
SA210139Terence_MS10_Quad_AqCKD_SHAM
SA210140Terence_MS17_Quad_AqCKD_SHAM
SA210141Terence_MS9_Quad_AqCKD_SHAM
SA210142Terence_MS6_Quad_AqCKD_SHAM
SA210143Terence_MS7_Quad_AqCKD_SHAM
SA210144Terence_MS8_Quad_AqCKD_SHAM
SA210145Terence_MS32_Quad_AqCON_AVF
SA210146Terence_MS35_Quad_AqCON_AVF
SA210147Terence_MS25_Quad_AqCON_AVF
SA210148Terence_MS33_Quad_AqCON_AVF
SA210149Terence_MS24_Quad_AqCON_AVF
SA210150Terence_MS22_Quad_AqCON_AVF
SA210151Terence_MS14_Quad_AqCON_AVF
SA210152Terence_MS23_Quad_AqCON_AVF
SA210153Terence_MS11_Quad_AqCON_SHAM
SA210154Terence_MS12_Quad_AqCON_SHAM
SA210155Terence_MS15_Quad_AqCON_SHAM
SA210156Terence_MS5_Quad_AqCON_SHAM
SA210157Terence_MS3_Quad_AqCON_SHAM
SA210158Terence_MS1_Quad_AqCON_SHAM
SA210159Terence_MS2_Quad_AqCON_SHAM
SA210160Terence_MS4_Quad_AqCON_SHAM
SA210161Sample nameGroup
Showing results 1 to 35 of 35

Collection:

Collection ID:CO002268
Collection Summary:Two weeks after surgery, mice were anesthetized using isoflurane and the left quadriceps muscle was rapidly dissected and immediately frozen in liquid nitrogen and stored at -80oC for metabolite extraction. Euthanasia was carried out by thoracotomy followed by cervical dislocation.
Sample Type:Muscle
Collection Method:While under isoflurane anesthesia, tissues were rapidly dissected and snap frozen in liquid nitrogen and stored at -80°C until metabolite extraction
Collection Location:University of Florida, Applied Physiology and Kinesiology, 1864 stadium RD, Gainesville, FL 32611
Storage Conditions:-80℃
Storage Vials:cryovials

Treatment:

Treatment ID:TR002287
Treatment Summary:Briefly, mice were acclimated to a standard casein-based chow (Control Diet) for 7 days. Thereafter, the animals were randomly assign to either remain on Control Diet (non-CKD groups) or receive adenine-supplemented diet to induce CKD. Following three weeks of the casein/adenine diet, animals were randomly assigned to receive either an arteriovenous fistula surgery (AVF) or sham surgery (SHAM)
Animal Vet Treatments:none
Animal Anesthesia:isoflurane
Animal Fasting:non-fasted
Animal Endp Euthanasia:Euthanasia was carried out by thoracotomy followed by cervical dislocation.
Animal Endp Tissue Coll List:Skeletal muscle (quadriceps)

Sample Preparation:

Sampleprep ID:SP002281
Sampleprep Summary:Weights of frozen quadriceps specimens were weighed using a microbalance (Mettler-Toledo, Columbus, OH, USA). Next, a slightly modified FOLCH extraction was performed to extract aqueous and lipid phase metabolites. The aqueous phase was lyophilized overnight (Labconco Corporation, Kansas, MO, USA) and the lipid phase was dried by passing inert nitrogen gas. The resulting aqueous and lipid phase dry powders were stored at -80oC until analysis using nuclear magnetic resonance (NMR). The dry powder of aqueous phase samples was dissolved in 50 µL of phosphate buffer system (50 mM, pH 7.2) consisting of 0.5 mM D6-DSS, 2 mM EDTA and 0.2% NaN2. Lipid phase dry powders were dissolved in 70 µL of CDCl3 supplemented with 10 mM of pyrazine (as internal NMR standard). All samples were loaded into 1.5 mm optical density (O.D.) NMR tubes.
Sampleprep Protocol Filename:AVF_NMR_Aqueous_Phase_Procedures.docx
Processing Method:Lyophilization and Homogenization
Processing Storage Conditions:-80℃
Extraction Method:Modified FOLCH extraction
Extract Storage:-80℃
Sample Resuspension:In 50 microliter of 50 mM phosphate buffer (pH 7.2) with 2 mM EDTA, 0.5 mM DSS and 0.2% sodium azide for aqueous phase samples.
Sample Spiking:0.5 mM of DSS for aqueous phase samples

Analysis:

Analysis ID:AN003583
Laboratory Name:Terence lab, UF
Analysis Type:NMR
Acquisition Date:09/14/2021
Software Version:Bruker Topspin
Operator Name:Ram Khattri
Detector Type:Bruker
Data Format:fid, 1r
Num Factors:5
Num Metabolites:37
Units:mM

NMR:

NMR ID:NM000241
Analysis ID:AN003583
Instrument Name:Bruker Avance III Cryo800 MHz 54 mm
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Field Frequency Lock:Deuterium
Standard Concentration:0.5 mM DSS
Spectrometer Frequency:799.9
NMR Probe:CP TXI CryoProbe
NMR Solvent:Phosphate buffer (pH 7.2) + 2 mM EDTA + 0.5 mM DSS + 0.2% of sodium azide in deuterated environment
NMR Tube Size:1.5 mm O.D.
Shimming Method:Topshim
Pulse Sequence:noesypr1d
Water Suppression:presat
Pulse Width:90-degree
Receiver Gain:645
Offset Frequency:2827.31 Hz
Chemical Shift Ref Cpd:DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid)
Temperature:25 o C
Number Of Scans:128 scans
Dummy Scans:8
Acquisition Time:4 s
Relaxation Delay:1 s
Spectral Width:9523.8
Num Data Points Acquired:38094
Real Data Points:65536
Line Broadening:0.22 Hz
Zero Filling:65,536 points
Apodization:Exponential
Baseline Correction Method:Spline
Chemical Shift Ref Std:0 ppm for DSS
Binned Increment:None
Binned Data Excluded Range:None
  logo