Summary of Study ST001649
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 PR001055. The data can be accessed directly via it's Project DOI: 10.21228/M8B70D 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 | ST001649 |
| Study Title | Urinary microbiota and metabolome in pediatric vesicoureteral reflux and scarring |
| Study Type | Observational/cross-sectional |
| Study Summary | We enrolled girls and boys aged zero to nine years presenting to a pediatric urologist for recurrent urinary tract infection (UTI) or renal scarring (decreased uptake on a nuclear renal scan) or grade 3-5 vesico ureteral reflux (VUR). Exclusion criteria included other urogenital abnormalities, medical renal disease, immunodeficiency, syndromes associated with VUR, acute UTI, persistent UTI (ongoing positive urine culture 1-3 weeks after completing a treatment course), or global renal atrophy on imaging. At one patient visit, a urine specimen was collected for 16S and metabolomic analysis. |
| Institute | University of Missouri-Columbia |
| Department | MU Metabolomics Center |
| Last Name | Sarma |
| First Name | Saurav |
| Address | 1201 Rollins street, Bond Life Science Center |
| sarmas@missouri.edu | |
| Phone | 5738825596 |
| Submit Date | 2021-01-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2021-01-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001055 |
| Project DOI: | doi: 10.21228/M8B70D |
| Project Title: | Urinary microbiota and metabolome in pediatric vesicoureteral reflux and scarring |
| Project Type: | Observational/cross-sectional |
| Project Summary: | Experiment to analyze the changes in the urinary microbiota and metabolome related to pediatric veicoureteral reflux with special attention to the differences related to renal scarring. |
| Institute: | University of Missouri-Columbia |
| Department: | Surgery |
| Last Name: | Malm-Buatsi |
| First Name: | Elizabeth |
| Address: | 1 Hospital Dr, MC 301, Columbia, MO 65212 |
| Email: | malmbuatsie@health.missouri.edu |
| Phone: | (573) 817-3311 |
Subject:
| Subject ID: | SU001726 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 4.14 to 8.86 years |
| Weight Or Weight Range: | 4.5 to 41.3 kg |
| Height Or Height Range: | 56.0 to 143.1 inch |
| Gender: | Male and female |
| Human Race: | white |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | race | sex | category |
|---|---|---|---|---|
| SA151663 | A12 | Black | F | No scarring |
| SA151664 | A17 | Other | F | VUR |
| SA151680 | A15 | White | F | No scarring |
| SA151681 | A23 | White | F | No scarring |
| SA151682 | A27 | White | F | No scarring |
| SA151683 | A26 | White | F | No scarring |
| SA151684 | B18 | White | F | No scarring |
| SA151685 | A24 | White | F | No scarring |
| SA151686 | A22 | White | F | No scarring |
| SA151687 | B8 | White | F | No scarring |
| SA151688 | A9 | White | F | No scarring |
| SA151689 | A14 | White | F | No scarring |
| SA151690 | A5 | White | F | No scarring |
| SA151691 | A3 | White | F | No scarring |
| SA151692 | A10 | White | F | No scarring |
| SA151693 | A13 | White | F | No scarring |
| SA151694 | A11 | White | F | No scarring |
| SA151665 | B10 | White | F | No VUR |
| SA151666 | B16 | White | F | No VUR |
| SA151667 | B17 | White | F | No VUR |
| SA151668 | B14 | White | F | No VUR |
| SA151669 | B15 | White | F | No VUR |
| SA151670 | A16 | White | F | No VUR |
| SA151671 | A1 | White | F | No VUR |
| SA151672 | B5 | White | F | No VUR |
| SA151673 | B13 | White | F | No VUR |
| SA151674 | B7 | White | F | No VUR |
| SA151675 | B4 | White | F | No VUR |
| SA151676 | B1 | White | F | No VUR |
| SA151677 | B9 | White | F | No VUR |
| SA151678 | B6 | White | F | No VUR |
| SA151679 | B12 | White | F | No VUR |
| SA151695 | A2 | White | F | Scarring |
| SA151696 | A4 | White | F | Scarring |
| SA151697 | A6 | White | F | Scarring |
| SA151698 | A7 | White | F | Scarring |
| SA151699 | A20 | White | F | Scarring |
| SA151700 | A8 | White | F | Scarring |
| SA151701 | A25 | White | F | VUR |
| SA151703 | B11 | White | M | No scarring |
| SA151702 | B3 | White | M | No VUR |
| SA151704 | A18 | White | M | Scarring |
| Showing results 1 to 42 of 42 |
Collection:
| Collection ID: | CO001719 |
| Collection Summary: | Urine was collected from eligible children at clinic visits to a pediatric urologist |
| Sample Type: | Urine |
| Collection Method: | Clean catch or catheterized |
| Collection Location: | Pediatric urology clinic |
| Collection Frequency: | Once |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001739 |
| Treatment Summary: | No treatments |
Sample Preparation:
| Sampleprep ID: | SP001732 |
| Sampleprep Summary: | 100 µL of freshly prepared 1 mg/mL urase solution was added to 100 µL of each of the urine samples then vortexed for 20 seconds and allowed to stand at -20 oC for 1 h. Next, 20 µL of 1 mg/mL of ribitol in water was added to each sample followed by addition of 1 mL of MeOH that was precooled to -20 ºC. The solution was again vortexed for 20 seconds and allowed to stand at -20 ºC for another 2 hours. The samples were centrifuged at 13000g for 15 minutes, and 1 ml of the supernatant from each sample was transferred to an autosampler vial and dried under gaseous nitrogen stream. Additionally, a pooled sample was prepared by combining 200 µL of supernatants from each sample and dried under nitrogen. Dried extracts were stored at -20 C until derivatization. |
| Processing Storage Conditions: | -20℃ |
| Extraction Method: | For GCMS-polar analysis samples were extracted with water, containing 1 mg/ml ribitol, and 1 ml methanol. |
| Extract Enrichment: | 1 mL each of supernatant was collected from each sample for GCMS-polar analysis. |
| Extract Storage: | -20℃ |
| Sample Resuspension: | For GCMS analysis extracts dried under nitrogen flow and storred at -20C then resuspended in 25 μl of pyridine containing 15 mg/ml methoxyamine hydrochloride |
| Sample Derivatization: | GCMS samples were derivatized with 25 μl MSTFA (N-methyl-N-(trimethyl-silyl)trifluoroacetamide) + 1% TMCS (chlorotrimethylsilane) |
| Sample Spiking: | Ribitol was used as internal standard for GCMS-polar analysis. |
Chromatography:
| Chromatography ID: | CH001988 |
| Chromatography Summary: | Gas chromatography integrated to mass spectrometer |
| Chromatography Comments: | 1:1 split injection with 1uL injection volume |
| Instrument Name: | Agilent 6890N |
| Column Name: | DB-5MS (J&W Scientific) 60m |
| Column Pressure: | variable |
| Column Temperature: | 80 0C for 2 minutes, then ramped at 5 0C /min to 315 ºC and held at 315 ºC for 12 minutes |
| Flow Rate: | 1mL/Min of Helium gas |
| Injection Temperature: | 280C |
| Internal Standard: | Ribitol |
| Retention Time: | 9 to 61 min |
| Analytical Time: | 61 min |
| Oven Temperature: | 80C to 315C |
| Chromatography Type: | GC |
Analysis:
| Analysis ID: | AN002695 |
| Laboratory Name: | MU Metabolomics Center |
| Analysis Type: | MS |
| Operator Name: | Saurav Sarma |
| Detector Type: | Mass Spectrometer |
| Data Format: | .d |
| Chromatography ID: | CH001988 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST001649_AN002695_Results.txt |
| Units: | Intensity |
