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 |
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. |
Combined analysis:
| Analysis ID | AN002695 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 6890N |
| Column | DB-5MS (J&W Scientific) 60m |
| MS Type | EI |
| MS instrument type | Single quadrupole |
| MS instrument name | Agilent 5973 |
| Ion Mode | POSITIVE |
| Units | Intensity |
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 |
MS:
| MS ID: | MS002493 |
| Analysis ID: | AN002695 |
| Instrument Name: | Agilent 5973 |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | Agilent Chem Station software used for data acquisition, Enhanced Data Analysis software used for converting data to .cdf file, AMDIS was used for peak deconvolution and NIST17 GCMS library was used for compound identification. |
| Ion Mode: | POSITIVE |
| Helium Flow: | 1mL/min |
| Ion Source Temperature: | 230C |
| Ionization Energy: | 70ev |
| Reagent Gas: | Helium |
| Source Temperature: | 230C |
| Dataformat: | .d |
