Summary of Study ST003120
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 PR001938. The data can be accessed directly via it's Project DOI: 10.21228/M86T69 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 | ST003120 |
| Study Title | Mannose is crucial for mesoderm specification and symmetry breaking in gastruloids. |
| Study Summary | Patterning and growth are fundamental features of embryonic development that must be tightly coordinated. To understand how metabolism impacts early mesoderm development, we used mouse embryonic stem cell-derived gastruloids, that co-expressed glucose transporters with the mesodermal marker T/Bra. While the glucose mimic, 2-deoxy-D-glucose (2-DG), blocked T/Bra expression and abolished axial elongation in gastruloids, removal of glucose did not phenocopy 2-DG treatment despite a decline in glycolytic intermediates occurring under both conditions. As 2-DG could also act as a competitive inhibitor of mannose in protein glycosylation, we added mannose together with 2-DG and found that it could rescue the mesoderm specification both in vivo and in vitro. We further showed that blocking production and intracellular recycling of mannose abrogated mesoderm specification. Proteomics analysis revealed that mannose reversed glycosylation of the Wnt pathway regulator, Secreted Frizzled Receptor, Frzb. Our study showed how mannose is crucial for mesoderm specification in gastruloids. |
| Institute | Dept of Genetics, University of Cambridge |
| Last Name | Dingare |
| First Name | Chaitanya |
| Address | Downing Site, Cambridge, Cambridgeshire, CB2 3EH, United Kingdom |
| cd705@cam.ac.uk | |
| Phone | +447916677460 |
| Submit Date | 2024-02-24 |
| Publications | https://doi.org/10.1101/2023.06.05.543730 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-03-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005114 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Vanquish UHPLC |
| Column | Atlantis Premier BEH Z-HILIC (100 x 2.1 mm, 1.7 um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Fisher Scientific Orbitrap Exploris 240 |
| Ion Mode | NEGATIVE |
| Units | counts per second (cps) |
MS:
| MS ID: | MS004851 |
| Analysis ID: | AN005114 |
| Instrument Name: | Thermo Fisher Scientific Orbitrap Exploris 240 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Analytes were recorded via a full scan with a mass resolving power of 120,000 over a mass range from 60 – 900 m/z (scan time: 100 ms, RF lens: 70%). To obtain MS/MS fragment spectra, data-dependant acquisition was carried out (resolving power: 15,000; scan time: 22 ms; stepped collision energies [%]: 30/50/70; cycle time: 900 ms). Ion source parameters were set to the following values: spray voltage: 4100 V (positive mode) / -3500 V (negative mode), sheath gas: 30 psi, auxiliary gas: 5 psi, sweep gas: 0 psi, ion transfer tube temperature: 350°C, vaporizer temperature: 300°C. All experimental samples were measured in a randomized manner. Pooled quality control (QC) samples were prepared by mixing equal aliquots from each processed sample. Multiple QCs were injected at the beginning of the analysis in order to equilibrate the analytical system. A QC sample was analyzed after every 5th experimental sample to monitor instrument performance throughout the sequence. For determination of background signals and subsequent background subtraction, an additional processed blank sample was recorded. Data was processed using MS-DIAL and raw peak intensities for relative metabolite quantification. Feature identification was based on accurate mass, isotope pattern, MS/MS fragment scoring and retention time matching to an inhouse library. (Data was acquired on both the positive and the negative modes and the respective raw files are deposited. However, we have processed the data acquired only on the negative mode.) |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | LC_MS_MS_Full_Protocol.pdf |
