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:
Sample Preparation:
| Sampleprep ID: | SP003244 |
| Sampleprep Summary: | Sample preparation: Metabolite extraction was performed by addition of 200 µL 80 % methanol (including 2 % (v/v) internal standards) and subsequent homogenization on dry ice via a bead beater (FastPrep-24; MP Biomedicals, CA, USA) at 6.0 m/s (5 x 30 s, 5 min pause time) using 1.0 mm zirconia/glass beads (Biospec Products, OK, USA). After centrifugation for 10 min at 15,000 g and 4 °C with a 5415R microcentrifuge (Eppendorf, Hamburg, Germany), supernatants were transferred and the remaining sample residues were reextracted with 200 µL acetonitrile:methanol:water (2:2:1, v/v) containing 1 % (v/v) formic acid using identical settings for homogenization and centrifugation. Corresponding supernatants of both extraction steps were combined and dried under a stream of nitrogen. Dried samples were reconstituted in 60 µL acetonitrile:methanol:water (2:2:1, v/v), vortexed for 5 min, centrifuged, and transferred to analytical glass vials. The LC-MS/MS analysis was initiated within one hour after the completion of the sample preparation. |
| Sampleprep Protocol Filename: | Sample_Collection_CD.pdf |
| Processing Storage Conditions: | Described in summary |
| Extract Storage: | Described in summary |
