Summary of Study ST003356
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 PR002086. The data can be accessed directly via it's Project DOI: 10.21228/M8025G This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003356 |
| Study Title | Noninvasive multiomic measurement of cell type repertoires in human urine |
| Study Summary | Background: Early detection of the cell type changes underlying several genitourinary tract diseases largely remains an unmet clinical need, whereas existing assays, if available, lack the cellular resolution afforded by an invasive biopsy. While messenger RNA in urine could reflect dynamic signal that facilitates early detection, current measurements primarily detect single genes and thus do not capture the full spectrum of cell type specific contributions. Methods: We isolated and sequenced the cellular and cell-free RNA from urine samples (n = 6 healthy controls and n = 12 kidney stones) alongside the metabolome. We analyzed the resulting urine transcriptomes and metabolomes by comparing the bulk gene expression, deconvolving the noninvasively measurable cell type contributions, and comparing to the plasma cell-free transcriptome. Results: We primarily observed signal originating from genitourinary tract cell types in addition to cell types from high-turnover solid tissues beyond the genitourinary tract. Integration of urinary transcriptomic and metabolomic measurements identified various metabolic pathways involved in amino acid metabolism overlap with metabolic subsystems associated with proximal tubule function. Conclusions: Noninvasive whole transcriptome measurements of human urine reflect signal from hard-to-biopsy tissues exhibiting low representation in the blood at cell type resolution. |
| Institute | CZ Biohub |
| Last Name | DeFelice |
| First Name | Brian |
| Address | 1291 Welch Rd., Rm. G0821 (SIM1), Stanford CA, California, 94305, USA |
| bcdefelice@ucdavis.edu | |
| Phone | 5303564485 |
| Submit Date | 2024-07-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005497 | AN005498 |
|---|---|---|
| Chromatography ID | CH004180 | CH004180 |
| MS ID | MS005223 | MS005224 |
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak height | Peak height |
