Summary of Study ST002418
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.
| Study ID | ST002418 |
| Study Title | Serum metabolomics and lipidomics profiling in iliac arteriovenous fistula creation in clinical patients: part 2 |
| Study 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 |
| Study 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. It was hypothesized that after 6-weeks of AVF creation, these patients would present with altered serum metabolite features. |
| 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 |
| rbk11@ufl.edu | |
| Phone | 3307856045 |
| Submit Date | 2022-12-22 |
| Num Groups | 2 |
| Total Subjects | 45 subjects, 2 samples per subject, total of 90 samples |
| Num Males | 36 |
| Num Females | 9 |
| Study 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 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2023-12-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | SU002507 |
| 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 |
|---|---|---|
| SA242171 | Terence_AVF_33022-6wk_Org | 6-wk post op. |
| SA242172 | Terence_AVF_33020-6wk_Org | 6-wk post op. |
| SA242173 | Terence_AVF_33017-6wk_Org | 6-wk post op. |
| SA242174 | Terence_AVF_33023-6wk_Org | 6-wk post op. |
| SA242175 | Terence_AVF_33018-6wk_Org | 6-wk post op. |
| SA242176 | Terence_AVF_33024-6wk_Org | 6-wk post op. |
| SA242177 | Terence_AVF_33029-6Wk_Org | 6-wk post op. |
| SA242178 | Terence_AVF_33028-6wk_Org | 6-wk post op. |
| SA242179 | Terence_AVF_33026-6wk_Org | 6-wk post op. |
| SA242180 | Terence_AVF_33016-6wk_Org | 6-wk post op. |
| SA242181 | Terence_AVF_33014-6wk_Org | 6-wk post op. |
| SA242182 | Terence_AVF_33006-6wk_Org | 6-wk post op. |
| SA242183 | Terence_AVF_33005-6wk_Org | 6-wk post op. |
| SA242184 | Terence_AVF_33004-6wk_Org | 6-wk post op. |
| SA242185 | Terence_AVF_33003-6wk_Org | 6-wk post op. |
| SA242186 | Terence_AVF_33007-6wk_Org | 6-wk post op. |
| SA242187 | Terence_AVF_33010-6wk_Org | 6-wk post op. |
| SA242188 | Terence_AVF_33030-6wk_Org | 6-wk post op. |
| SA242189 | Terence_AVF_33012-6wk_Org | 6-wk post op. |
| SA242190 | Terence_AVF_33011-6wk_Org | 6-wk post op. |
| SA242191 | Terence_AVF_33015-6wk_Org | 6-wk post op. |
| SA242192 | Terence_AVF_33031-6wk_Org | 6-wk post op. |
| SA242193 | Terence_AVF_33050-6wk_Org | 6-wk post op. |
| SA242194 | Terence_AVF_33048-6wk_Org | 6-wk post op. |
| SA242195 | Terence_AVF_33047-6wk_Org | 6-wk post op. |
| SA242196 | Terence_AVF_33046-6wk_Org | 6-wk post op. |
| SA242197 | Terence_AVF_33051-6wk_Org | 6-wk post op. |
| SA242198 | Terence_AVF_33052-6wk_Org | 6-wk post op. |
| SA242199 | Terence_AVF_33057-6wk_Org | 6-wk post op. |
| SA242200 | Terence_AVF_33056-6wk_Org | 6-wk post op. |
| SA242201 | Terence_AVF_33054-6wk_Org | 6-wk post op. |
| SA242202 | Terence_AVF_33044-6wk_Org | 6-wk post op. |
| SA242203 | Terence_AVF_33043-6wk_Org | 6-wk post op. |
| SA242204 | Terence_AVF_33035-6wk_Org | 6-wk post op. |
| SA242205 | Terence_AVF_33033-6wk_Org | 6-wk post op. |
| SA242206 | Terence_AVF_33032-6wk_Org | 6-wk post op. |
| SA242207 | Terence_AVF_33037-6wk_Org | 6-wk post op. |
| SA242208 | Terence_AVF_33039-6wk_Org | 6-wk post op. |
| SA242209 | Terence_AVF_33042-6wk_Org | 6-wk post op. |
| SA242210 | Terence_AVF_33041-6wk_Org | 6-wk post op. |
| SA242211 | Terence_AVF_33040-6wk_Org | 6-wk post op. |
| SA242212 | Terence_AVF_33002-6wk_Org | 6-wk post op. |
| SA242213 | Terence_AVF_33001-6wk_Org | 6-wk post op. |
| SA242214 | Terence_AVF_33022-B_Org | Baseline |
| SA242215 | Terence_AVF_33020-B_Org | Baseline |
| SA242216 | Terence_AVF_33018-B_Org | Baseline |
| SA242217 | Terence_AVF_33017-B_Org | Baseline |
| SA242218 | Terence_AVF_33023-B_Org | Baseline |
| SA242219 | Terence_AVF_33024-B_Org | Baseline |
| SA242220 | Terence_AVF_33029-B_Org | Baseline |
| SA242221 | Terence_AVF_33028-B_Org | Baseline |
| SA242222 | Terence_AVF_33026-B_Org | Baseline |
| SA242223 | Terence_AVF_33016-B_Org | Baseline |
| SA242224 | Terence_AVF_33015-B_Org | Baseline |
| SA242225 | Terence_AVF_33005-B_Org | Baseline |
| SA242226 | Terence_AVF_33004-B_Org | Baseline |
| SA242227 | Terence_AVF_33003-B_Org | Baseline |
| SA242228 | Terence_AVF_33002-B_Org | Baseline |
| SA242229 | Terence_AVF_33006-B_Org | Baseline |
| SA242230 | Terence_AVF_33007-B_Org | Baseline |
| SA242231 | Terence_AVF_33014-B_Org | Baseline |
| SA242232 | Terence_AVF_33012-B_Org | Baseline |
| SA242233 | Terence_AVF_33010-B_Org | Baseline |
| SA242234 | Terence_AVF_33030-B_Org | Baseline |
| SA242235 | Terence_AVF_33031-B_Org | Baseline |
| SA242236 | Terence_AVF_33050-B_Org | Baseline |
| SA242237 | Terence_AVF_33048-B_Org | Baseline |
| SA242238 | Terence_AVF_33047-B_Org | Baseline |
| SA242239 | Terence_AVF_33046-B_Org | Baseline |
| SA242240 | Terence_AVF_33051-B_Org | Baseline |
| SA242241 | Terence_AVF_33052-B_Org | Baseline |
| SA242242 | Terence_AVF_33056-B_Org | Baseline |
| SA242243 | Terence_AVF_33054-B_Org | Baseline |
| SA242244 | Terence_AVF_33053-B_Org | Baseline |
| SA242245 | Terence_AVF_33044-B_Org | Baseline |
| SA242246 | Terence_AVF_33043-B_Org | Baseline |
| SA242247 | Terence_AVF_33037-B_Org | Baseline |
| SA242248 | Terence_AVF_33035-B_Org | Baseline |
| SA242249 | Terence_AVF_33033-B_Org | Baseline |
| SA242250 | Terence_AVF_33032-B_Org | Baseline |
| SA242251 | Terence_AVF_33038-B_Org | Baseline |
| SA242252 | Terence_AVF_33039-B_Org | Baseline |
| SA242253 | Terence_AVF_33042-B_Org | Baseline |
| SA242254 | Terence_AVF_33041-B_Org | Baseline |
| SA242255 | Terence_AVF_33040-B_Org | Baseline |
| SA242256 | Terence_AVF_33001-B_Org | Baseline |
| Showing results 1 to 86 of 86 |
Collection:
| Collection ID: | CO002500 |
| 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_Lipid_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. |
| Storage Conditions: | -80℃ |
| Collection Vials: | cryovials |
| Storage Vials: | cryovials |
Treatment:
| Treatment ID: | TR002519 |
| 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: | SP002513 |
| 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_Lipid_Phase_Procedures.docx |
| Processing Method: | Lyophilization and Homogenization |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Modified FOLCH extraction for lipid phase samples |
| Extract Storage: | -80℃ |
| Sample Resuspension: | In 700 microliter of CDCl3 with 10 mM of pyrazine as internal standard for lipid phase samples |
| Sample Spiking: | 10 mM of TSP for urine samples |
Analysis:
| Analysis ID: | AN003939 |
| Laboratory Name: | McKnight Brain Institute |
| Analysis Type: | NMR |
| Analysis Protocol File: | AVF-NMR_Lipid_Phase_Procedures.docx |
| Acquisition Date: | 08/02/2022 |
| Software Version: | Topspin |
| Operator Name: | Ram Khattri |
| Detector Type: | Bruker 600 MHz |
| Data Format: | fid, 1r |
| Num Factors: | 2 |
| Num Metabolites: | 19 |
| Units: | Peak intensity |
NMR:
| NMR ID: | NM000260 |
| Analysis ID: | AN003939 |
| Instrument Name: | Bruker 600 MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Field Frequency Lock: | CDCl3 |
| Standard Concentration: | 10 mM TSP |
| Spectrometer Frequency: | 600 MHz |
| NMR Probe: | 5mm TXI CryoProbe |
| NMR Solvent: | 700 uL of CDCl3 with 10 mM pyrazine |
| NMR Tube Size: | 5 mm O.D. |
| Shimming Method: | Topshim |
| Pulse Sequence: | noesy1d |
| Water Suppression: | none |
| Pulse Width: | 90-degree |
| Receiver Gain: | 106.7 |
| Chemical Shift Ref Cpd: | TPS |
| 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: | 7.26 ppm for CDCl3 |
| Binned Increment: | NA |
| Binned Data Protocol File: | NA |
| Binned Data Excluded Range: | NA |
