Summary of Study ST002417

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 PR001556. The data can be accessed directly via it's Project DOI: 10.21228/M8K429 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 IDST002417
Study TitleSerum metabolomics and lipidomics profiling in iliac arteriovenous fistula creation in clinical patients: part 1
Study TypeStudy of the serum metabolome in patients with end stage kidney disease before and 6-weeks after iliac arteriovenous fistula creation via 1H NMR
Study SummaryThis project is focused on a longitudinal analysis of the small molecules metabolomes in end stage renal disease patients undergoing iliac arteriovenous fistula creation using solution state NMR spectroscopy. It was hypothesized that after 6-weeks of AVF creation, these patients would present with altered serum metabolite features.
Institute
University of Florida
DepartmentApplied Physiology and Kinesiology
LaboratoryRm 42 and Rm 43
Last NameKhattri
First NameRam
Address1864 Stadium RD, Gainesville, FL, 32611, USA
Emailrbk11@ufl.edu
Phone3307856045
Submit Date2022-12-22
Num Groups2
Total Subjects45 subjects, 2 samples per subject, total of 90 samples
Num Males36
Num Females9
Study CommentsStudy of the serum metabolome in patients with end stage kidney disease before and 6-weeks after iliac arteriovenous fistula creation via 1H NMR
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2023-12-22
Release Version1
Ram Khattri Ram Khattri
https://dx.doi.org/10.21228/M8K429
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001556
Project DOI:doi: 10.21228/M8K429
Project Title:Serum metabolomics and lipidomics profiling in iliac arteriovenous fistula creation in clinical patients: part 1
Project Type:Study of the serum metabolome in patients with end stage kidney disease before and 6-weeks after iliac arteriovenous fistula creation via 1H NMR
Project Summary:This project is focused on a longitudinal analysis of the small molecules metabolomes in end stage renal disease patients undergoing iliac arteriovenous fistula creation using solution state NMR spectroscopy. Blood samples were obtained prior to surgery and again 6-weeks after AVF creation.
Institute:University of Florida
Department:Applied Physiology and Kinesiology
Laboratory:Rm 42 and Rm 43
Last Name:Khattri
First Name:Ram
Address:1864 Stadium RD, Gainesville, FL, 32611, USA
Email:rbk11@ufl.edu
Phone:3307856045
Funding Source:R01HL148597 and K23HL115673 (PI: Salvatore T. Scali)
Project Comments:Study of the serum metabolome in patients with end stage kidney disease before and 6-weeks after iliac arteriovenous fistula creation via 1H NMR
Contributors:Ram B. Khattri, Kyoungrae Kim, Erik M. Anderson, Salvatore T. Scali, Terence E. Ryan

Subject:

Subject ID:SU002506
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:67.47+/-13.50 years
Gender:Male and female
Human Race:Black(17), White(27), Other(1)
Human Ethnicity:Black(17), White(27), Other(1)
Human Medications:Allopurinol, Asprin,Atenolol, Atorvastatin calcium, calcitriol, Clopidogrel, Codeine, Gabapentin, Levothyroxine, Losartan, Alprostadil, Carbamide peroxide, Cinacalcet HCL, Diltiazem HCL, Exetimibe, Glipizide, Rosuvastatin CA, Valsartan

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA242085Terence_AVF_33022-6wk_Aq6-wk post op.
SA242086Terence_AVF_33020-6wk_Aq6-wk post op.
SA242087Terence_AVF_33017-6wk_Aq6-wk post op.
SA242088Terence_AVF_33023-6wk_Aq6-wk post op.
SA242089Terence_AVF_33018-6wk_Aq6-wk post op.
SA242090Terence_AVF_33024-6wk_Aq6-wk post op.
SA242091Terence_AVF_33029-6Wk_Aq6-wk post op.
SA242092Terence_AVF_33028-6wk_Aq6-wk post op.
SA242093Terence_AVF_33026-6wk_Aq6-wk post op.
SA242094Terence_AVF_33016-6wk_Aq6-wk post op.
SA242095Terence_AVF_33014-6wk_Aq6-wk post op.
SA242096Terence_AVF_33006-6wk_Aq6-wk post op.
SA242097Terence_AVF_33005-6wk_Aq6-wk post op.
SA242098Terence_AVF_33004-6wk_Aq6-wk post op.
SA242099Terence_AVF_33003-6wk_Aq6-wk post op.
SA242100Terence_AVF_33007-6wk_Aq6-wk post op.
SA242101Terence_AVF_33010-6wk_Aq6-wk post op.
SA242102Terence_AVF_33030-6wk_Aq6-wk post op.
SA242103Terence_AVF_33012-6wk_Aq6-wk post op.
SA242104Terence_AVF_33011-6wk_Aq6-wk post op.
SA242105Terence_AVF_33015-6wk_Aq6-wk post op.
SA242106Terence_AVF_33031-6wk_Aq6-wk post op.
SA242107Terence_AVF_33050-6wk_Aq6-wk post op.
SA242108Terence_AVF_33048-6wk_Aq6-wk post op.
SA242109Terence_AVF_33047-6wk_Aq6-wk post op.
SA242110Terence_AVF_33046-6wk_Aq6-wk post op.
SA242111Terence_AVF_33051-6wk_Aq6-wk post op.
SA242112Terence_AVF_33052-6wk_Aq6-wk post op.
SA242113Terence_AVF_33057-6wk_Aq6-wk post op.
SA242114Terence_AVF_33056-6wk_Aq6-wk post op.
SA242115Terence_AVF_33054-6wk_Aq6-wk post op.
SA242116Terence_AVF_33044-6wk_Aq6-wk post op.
SA242117Terence_AVF_33043-6wk_Aq6-wk post op.
SA242118Terence_AVF_33035-6wk_Aq6-wk post op.
SA242119Terence_AVF_33033-6wk_Aq6-wk post op.
SA242120Terence_AVF_33032-6wk_Aq6-wk post op.
SA242121Terence_AVF_33037-6wk_Aq6-wk post op.
SA242122Terence_AVF_33039-6wk_Aq6-wk post op.
SA242123Terence_AVF_33042-6wk_Aq6-wk post op.
SA242124Terence_AVF_33041-6wk_Aq6-wk post op.
SA242125Terence_AVF_33040-6wk_Aq6-wk post op.
SA242126Terence_AVF_33002-6wk_Aq6-wk post op.
SA242127Terence_AVF_33001-6wk_Aq6-wk post op.
SA242128Terence_AVF_33022B_AqBaseline
SA242129Terence_AVF_33020B_AqBaseline
SA242130Terence_AVF_33018B_AqBaseline
SA242131Terence_AVF_33017B_AqBaseline
SA242132Terence_AVF_33023B_AqBaseline
SA242133Terence_AVF_33024B_AqBaseline
SA242134Terence_AVF_33029B_AqBaseline
SA242135Terence_AVF_33028B_AqBaseline
SA242136Terence_AVF_33026B_AqBaseline
SA242137Terence_AVF_33016B_AqBaseline
SA242138Terence_AVF_33015B_AqBaseline
SA242139Terence_AVF_33005B_AqBaseline
SA242140Terence_AVF_33004B_AqBaseline
SA242141Terence_AVF_33003B_AqBaseline
SA242142Terence_AVF_33002B_AqBaseline
SA242143Terence_AVF_33006B_AqBaseline
SA242144Terence_AVF_33007B_AqBaseline
SA242145Terence_AVF_33014B_AqBaseline
SA242146Terence_AVF_33012B_AqBaseline
SA242147Terence_AVF_33010B_AqBaseline
SA242148Terence_AVF_33030B_AqBaseline
SA242149Terence_AVF_33031B_AqBaseline
SA242150Terence_AVF_33050B_AqBaseline
SA242151Terence_AVF_33048B_AqBaseline
SA242152Terence_AVF_33047B_AqBaseline
SA242153Terence_AVF_33046B_AqBaseline
SA242154Terence_AVF_33051B_AqBaseline
SA242155Terence_AVF_33052B_AqBaseline
SA242156Terence_AVF_33056B_AqBaseline
SA242157Terence_AVF_33054B_AqBaseline
SA242158Terence_AVF_33053B_AqBaseline
SA242159Terence_AVF_33044B_AqBaseline
SA242160Terence_AVF_33043B_AqBaseline
SA242161Terence_AVF_33037B_AqBaseline
SA242162Terence_AVF_33035B_AqBaseline
SA242163Terence_AVF_33033B_AqBaseline
SA242164Terence_AVF_33032B_AqBaseline
SA242165Terence_AVF_33038B_AqBaseline
SA242166Terence_AVF_33039B_AqBaseline
SA242167Terence_AVF_33042B_AqBaseline
SA242168Terence_AVF_33041B_AqBaseline
SA242169Terence_AVF_33040B_AqBaseline
SA242170Terence_AVF_33001B_AqBaseline
Showing results 1 to 86 of 86

Collection:

Collection ID:CO002499
Collection Summary:Institutional review board (IRB) of the University of Florida reviewed and approved this study. All human subjects included in this study were fully informed about the study, and informed consent were obtained from each of them (IRB#140-2013, IRB#556-2009). Blood samples from ESKD patients were collected at different time points: baseline (pre-operation) and 6-weeks post-op from fistula creation.
Collection Protocol Filename:AVF-NMR_Aqueous_Phase_Procedures.docx
Sample Type:Blood (serum)
Collection Method:Serum samples were collected from the patients. The samples were let sit at room temperature for ~45 minutes. Later, the samples were centrifuged for 15 minutes maintaining 2180-rpm speed at 4 oC with brake on. The supernatant from each sample was transfered into a new 15 mL tube and furthermore, aliquoted into a vial (250 uL in each vial). All of the serum samples were stored at -80 oC until analysis.
Collection Location:University of Florida, Applied Physiology and Kinesiology, MBI, 1149 Newell Dr, Gainesville, FL 32610
Storage Conditions:-80℃
Collection Vials:cryovials
Storage Vials:cryovials

Treatment:

Treatment ID:TR002518
Treatment Summary:Metabolomic profile of serum from end stage kidney disease before and 6-week after AVF surgery were evaluated. After 6-week of post op., ESKD patients exhibited difference in few small-molecule environment. A total of 45 ESKD patients were included in this study, with a life expectancy greater than or equal to 9 months (in the period 2012-2015). These patients were evaluated for demographics, comorbidities, hand dominance and prior access history before and 6 weeks post operation.
Human Fasting:non-fasted
Human Endp Clinical Signs:N/A

Sample Preparation:

Sampleprep ID:SP002512
Sampleprep Summary:Serum samples are associated with binding of residual proteins with DSS signal, resulting broaden DSS peak. The presence of the residual proteins, even after performing modified FOLCH extraction, was observed for serum samples, making it un-reliable for quantitative purpose. In this study, we coupled two extraction protocols to extract metabolites from the serum samples. Modified FOLCH extraction was performed as a first step to separate out water-soluble and lipid-soluble metabolites/compounds. Furthermore, acetonitrile:isopropanol:water (3:3:2 vol/vol/vol) extraction was performed on aqueous phase samples that we obtained from modified FOLCH extraction.
Sampleprep Protocol Filename:AVF-NMR_Aqueous_Phase_Procedures.docx
Processing Method:Lyophilization and Homogenization
Processing Storage Conditions:-80℃
Extraction Method:Modified FOLCH extraction followed by acetonitrile:isopropanol:water (3:3:2 vol/vol/vol) extraction for aqueous phase samples
Extract Storage:-80℃
Sample Resuspension:In 500 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:AN003938
Laboratory Name:McKnight Brain Institute
Analysis Type:NMR
Analysis Protocol File:AVF-NMR_Aqueous_Phase_Procedures.docx
Acquisition Date:07/21/2022
Software Version:Topspin
Operator Name:Ram Khattri
Detector Type:Bruker 600 MHz
Data Format:fid, 1r
Num Factors:2
Num Metabolites:42
Units:mM

NMR:

NMR ID:NM000259
Analysis ID:AN003938
Instrument Name:Bruker 600 MHz
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Field Frequency Lock:Deuterium
Standard Concentration:0.5mM DSS
Spectrometer Frequency:600 MHz
NMR Probe:5mm 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:5 mm O.D.
Shimming Method:Topshim
Pulse Sequence:noesypr1d
Water Suppression:presat
Pulse Width:90-degree
Receiver Gain:202.2
Offset Frequency:4.77 ppm
Chemical Shift Ref Cpd:DSS
Temperature:298.2 oK
Number Of Scans:128
Dummy Scans:8
Acquisition Time:4s
Relaxation Delay:1s
Spectral Width:9578.5
Num Data Points Acquired:38313
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:NA
Binned Data Protocol File:NA
Binned Data Excluded Range:NA
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