Summary of Study ST000336
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 PR000268. The data can be accessed directly via it's Project DOI: 10.21228/M84S4K This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000336 |
| Study Title | Targeted LC/MS of urine from boys with DMD and controls |
| Study Type | Natural History |
| Study Summary | Quantify the urine levels of amino acids and organic acids in patients with DMD both with and without steroid treatment. Track the progression of DMD in patients who have provided multiple urine samples. |
| Institute | University of Florida |
| Department | SECIM |
| Laboratory | Sanford Burnham |
| Last Name | Lee |
| First Name | Brittany |
| Address | - |
| balm22@ufl.edu | |
| Phone | - |
| Submit Date | 2016-01-14 |
| Num Groups | 2 |
| Total Subjects | 58 |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-08-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000268 |
| Project DOI: | doi: 10.21228/M84S4K |
| Project Title: | Urine metabolomics to track disease progression in DMD |
| Project Summary: | Duchenne Muscular Dystrophy (DMD) is an X-linked recessive form of muscular dystrophy that affects males via a mutation in the gene for the muscle protein, dystrophin. Progression of the disease results in severe muscle loss, ultimately leading to paralysis and death. Steroid therapy has been a commonly employed method for reducing the severity of symptoms. This study aims to quantify the urine levels of amino acids and organic acids in patients with DMD both with and without steroid treatment. Track the progression of DMD in patients who have provided multiple urine samples. |
| Institute: | University of Florida |
| Department: | Physiology and Functional Genomics |
| Last Name: | Walter |
| First Name: | Glenn |
| Address: | - |
| Email: | glennw@ufl.edu |
| Phone: | - |
Subject:
| Subject ID: | SU002842 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 5-14 |
| Gender: | Males |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Diagnosis | steroid_status |
|---|---|---|---|
| SA288627 | SA009 | Controls | - |
| SA288628 | SA011 | Controls | - |
| SA288629 | SA012 | Controls | - |
| SA288630 | SA008 | Controls | - |
| SA288631 | SA001 | Controls | - |
| SA288632 | SA010 | Controls | - |
| SA288633 | SA003 | Controls | - |
| SA288634 | SA007 | Controls | - |
| SA288635 | SA004 | Controls | - |
| SA288636 | SA002 | Controls | - |
| SA288637 | SA005 | Controls | - |
| SA288638 | SA006 | Controls | - |
| SA288639 | SA024 | DMD | - |
| SA288640 | SA025 | DMD | - |
| SA288641 | SA026 | DMD | - |
| SA288642 | SA028 | DMD | - |
| SA288643 | SA023 | DMD | - |
| SA288644 | SA029 | DMD | - |
| SA288645 | SA027 | DMD | - |
| SA288646 | SA022 | DMD | - |
| SA288647 | SA016 | DMD | - |
| SA288648 | SA014 | DMD | - |
| SA288649 | SA013 | DMD | - |
| SA288650 | SA017 | DMD | - |
| SA288651 | SA015 | DMD | - |
| SA288652 | SA018 | DMD | - |
| SA288653 | SA021 | DMD | - |
| SA288654 | SA020 | DMD | - |
| SA288655 | SA019 | DMD | - |
| SA288656 | SA050 | DMD | 1 |
| SA288657 | SA051 | DMD | 1 |
| SA288658 | SA049 | DMD | 1 |
| SA288659 | SA046 | DMD | 1 |
| SA288660 | SA052 | DMD | 1 |
| SA288661 | SA047 | DMD | 1 |
| SA288662 | SA048 | DMD | 1 |
| SA288663 | SA057 | DMD | 1 |
| SA288664 | SA045 | DMD | 1 |
| SA288665 | SA058 | DMD | 1 |
| SA288666 | SA056 | DMD | 1 |
| SA288667 | SA055 | DMD | 1 |
| SA288668 | SA054 | DMD | 1 |
| SA288669 | SA053 | DMD | 1 |
| SA288670 | SA030 | DMD | 1 |
| SA288671 | SA035 | DMD | 1 |
| SA288672 | SA036 | DMD | 1 |
| SA288673 | SA034 | DMD | 1 |
| SA288674 | SA033 | DMD | 1 |
| SA288675 | SA031 | DMD | 1 |
| SA288676 | SA032 | DMD | 1 |
| SA288677 | SA037 | DMD | 1 |
| SA288678 | SA038 | DMD | 1 |
| SA288679 | SA042 | DMD | 1 |
| SA288680 | SA043 | DMD | 1 |
| SA288681 | SA041 | DMD | 1 |
| SA288682 | SA040 | DMD | 1 |
| SA288683 | SA039 | DMD | 1 |
| SA288684 | SA044 | DMD | 1 |
| Showing results 1 to 58 of 58 |
Collection:
| Collection ID: | CO002835 |
| Collection Summary: | Subjects are consented and given a bag containing a urine collection cup, antiseptic wipes and directions of how to give a clean catch urine sample. They are then lead to a restroom where they collect their own urine sample using a clean catch method (direction provided). Urine samples are then placed on ice and brought to the UF CTSI Biorepository. There, samples are transferred into 500uL aliquots and stored at -80C. Samples will remain there until samples will be removed and ran on the NMR for this study. |
| Sample Type: | Urine |
Treatment:
| Treatment ID: | TR002851 |
| Treatment Summary: | No treatment, samples are from a Natural History Clinical Trial. Samples are either boys with DMD or control boys all within the ages 5-14. Unaffected, control boys are moderately active (less than 3 low to moderate exercise bouts per week) |
Sample Preparation:
| Sampleprep ID: | SP002848 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | SB_AA_Assay.pdf, SB_OA_Assay.pdf |
Combined analysis:
| Analysis ID | AN004436 | AN004437 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Other | Reversed phase |
| Chromatography system | Agilent 1290 Infinity HPLC | Dionex UltiMate 3000 HPLC |
| Column | AccQ·Tag 2 x 100 mm, 1.7 µm column, Waters Corp | Acquity UPLC BEH C18 2.1 x 100 mm, 1.7 µm column, Waters Corp |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ | Thermo Quantiva QQQ |
| Ion Mode | POSITIVE | POSITIVE |
| Units | umol/mg Creatinine | umol/mg creatinine |
Chromatography:
| Chromatography ID: | CH003332 |
| Chromatography Summary: | Amino acid assay |
| Methods Filename: | SB_AA_Assay.pdf |
| Instrument Name: | Agilent 1290 Infinity HPLC |
| Column Name: | AccQ·Tag 2 x 100 mm, 1.7 µm column, Waters Corp |
| Column Temperature: | - |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | Other |
| Chromatography ID: | CH003333 |
| Chromatography Summary: | Organic Acids assay |
| Methods Filename: | SB_OA_Assay.pdf |
| Instrument Name: | Dionex UltiMate 3000 HPLC |
| Column Name: | Acquity UPLC BEH C18 2.1 x 100 mm, 1.7 µm column, Waters Corp |
| Column Temperature: | - |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004183 |
| Analysis ID: | AN004436 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | AA assay ESI |
| Ion Mode: | POSITIVE |
| MS ID: | MS004184 |
| Analysis ID: | AN004437 |
| Instrument Name: | Thermo Quantiva QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | OA assay- HESI |
| Ion Mode: | POSITIVE |
