Summary of Study ST000603
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 PR000440. The data can be accessed directly via it's Project DOI: 10.21228/M85W25 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000603 |
| Study Title | Urinary Volatile Compound, Associated with Chronic Inflammation In Interstitial Cystitis |
| Study Summary | Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a clinical condition that manifests as a sensory hypersensitivity of unknown cause and is characterized by urinary frequency, bladder discomfort, and pelvic pain. In the present volatolomic study, we have analyzed the VOCs unique to urine specimens obtained from interstitial cystitis patients, in compassion to healthy controls.This is the novel finding from comprehensive and unbiased metabolomics analysis that urinary menthol is decreased in urine specimens from IC patients, and that the reduced menthol level in IC is potentially linked to the chronic inflammation, which is often observed in IC patients |
| Institute | University of California, Davis |
| Department | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | Health Sciences Drive, Davis, California, 95616, USA |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2017-05-09 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2017-07-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000440 |
| Project DOI: | doi: 10.21228/M85W25 |
| Project Title: | Urinary Volatile Compound, Associated with Chronic Inflammation In Interstitial Cystitis |
| Project Summary: | Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a clinical condition that manifests as a sensory hypersensitivity of unknown cause and is characterized by urinary frequency, bladder discomfort, and pelvic pain. In the present volatolomic study, we have analyzed the VOCs unique to urine specimens obtained from interstitial cystitis patients, in compassion to healthy controls.This is the novel finding from comprehensive and unbiased metabolomics analysis that urinary menthol is decreased in urine specimens from IC patients, and that the reduced menthol level in IC is potentially linked to the chronic inflammation, which is often observed in IC patients |
| Institute: | Cedars-Sinai Medical Center |
| Last Name: | Kim |
| First Name: | Jayoung |
| Address: | 8700 Beverly Blvd. Davis Research Building Ste 5071 Los Angeles, CA 90048 |
| Email: | jayoung.kim@cshs.org |
| Phone: | 310-423-7168 |
Subject:
| Subject ID: | SU000626 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA033304 | 160427blvsa19_1 | control |
| SA033305 | 160427blvsa08_1 | control |
| SA033306 | 160427blvsa09_1 | control |
| SA033307 | 160427blvsa10_1 | control |
| SA033308 | 160427blvsa15_1 | control |
| SA033309 | 160427blvsa14_1 | control |
| SA033310 | 160427blvsa13_1 | control |
| SA033311 | 160427blvsa18_1 | control |
| SA033312 | 160427blvsa05_1 | control |
| SA033313 | 160427blvsa17_1 | control |
| SA033294 | 160427blvsa04_1 | IC |
| SA033295 | 160427blvsa02_1 | IC |
| SA033296 | 160427blvsa12_1 | IC |
| SA033297 | 160427blvsa11_1 | IC |
| SA033298 | 160427blvsa03_1 | IC |
| SA033299 | 160427blvsa06_1 | IC |
| SA033300 | 160427blvsa16_1 | IC |
| SA033301 | 160427blvsa20_1 | IC |
| SA033302 | 160427blvsa07_1 | IC |
| SA033303 | 160427blvsa01_1 | IC |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO000620 |
| Collection Summary: | First morning urine specimens were obtained using clean catch methods, and sent to clinical laboratory. After a 10 min centrifugation to remove cell debris, urine specimens were stored at −80◦C until further analysis. |
| Sample Type: | Urine |
Treatment:
| Treatment ID: | TR000640 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP000633 |
| Sampleprep Summary: | 1. Vortex the urine samples for about 10s to obtain a homogenized sample using the MiniVortexer VWR. 2. Aliquot 15-30ul and add 1ml extraction solution. The extraction solution has to be pre-chilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. 3. Vortex the sample for about 10s and shake for 5min at 4°C using the Orbital Mixing Chilling/Heating plate. If you are using more than one sample, keep the rest of the samples on ice (chilled at <0°C with NaCl). 4. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 5. Aliquot 2X 0.5ml supernatant. One for analysis and one for backup. Store 2nd aliquot in -20°C freezer. 6. Evaporate 0.5ml aliquots of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 7. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Urine.pdf |
Combined analysis:
| Analysis ID | AN000923 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC Ion Trap |
| MS instrument name | Varian 210-MS GC Ion Trap |
| Ion Mode | POSITIVE |
| Units | Counts |
Chromatography:
| Chromatography ID: | CH000659 |
| Instrument Name: | Agilent |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Column Pressure: | 7.7 PSI (initial condition) |
| Column Temperature: | 50 - 330°C |
| Flow Rate: | 1 ml/min |
| Injection Temperature: | 50°C ramped to 250°C by 12°C/s |
| Sample Injection: | 0.5µl |
| Oven Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min |
| Transferline Temperature: | 230°C |
| Washing Buffer: | Ethyl Acetate |
| Sample Loop Size: | 30 m length x 0.25 mm internal diameter |
| Randomization Order: | Excel generated |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000821 |
| Analysis ID: | AN000923 |
| Instrument Name: | Varian 210-MS GC Ion Trap |
| Instrument Type: | GC Ion Trap |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 250°C |
| Ionization Energy: | 70eV |
| Mass Accuracy: | Nominal |
| Source Temperature: | 250°C |
| Scanning Cycle: | 17 Hz |
| Scanning Range: | 85-500 |
| Skimmer Voltage: | 1850 V |
