Summary of Study ST001028
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 PR000686. The data can be accessed directly via it's Project DOI: 10.21228/M80Q2W 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 | ST001028 |
| Study Title | Metabolic profiling of identified single cells in Xenopus laevis embryos |
| Study Type | Metabolic profiling of single cells |
| Study Summary | Single D11 cells were identified in 16-cell embryos of Xenopus laevis. Metabolites were extracted, and the extracts were analyzed using a custom-built capillary electrophoresis electrospray ionization platform coupled to a quadrupole time-of-flight mass spectrometer. The resulting metadata was analyzed by Trace, a custom-design software, designed to extract molecular feautres from trace-sensitive metabolomics experiments. The results were validated against molecular features that were extracted by manual curation of the same raw mass spectrometer files. |
| Institute | University of Maryland |
| Department | Department of Chemistry & Biochemistry |
| Laboratory | Nemes Laboratory |
| Last Name | Nemes |
| First Name | Peter |
| Address | 0107 Chemistry Building, 8051 Regents Dr, College Park, MD 20742 |
| nemes@umd.edu | |
| Phone | 3014050373 |
| Submit Date | 2018-07-25 |
| Num Groups | 5 biological replicates (different cells from different embryos) + 1-to-3 technical replicates (same extract analyzed multiple times) |
| Total Subjects | 5 different D11 cells were analyzed, each from a different embryo |
| Publications | Trace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-09-23 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Collection:
| Collection ID: | CO001061 |
| Collection Summary: | Cells were identified based on morphology, pigmentation, and location in the embryo in comparision to established cell-fate maps for 16-cell Xenopus laevis embryos. A portion of the identified D11 cell was microaspirated using a fabricated microcapillary. |
| Collection Protocol ID: | Liu 2018 Metabolomics Workbench Protocol.pdf |
| Sample Type: | Embryonic cells |
| Collection Method: | Microaspiration of cell content |
| Collection Frequency: | 1 collection per cell |
| Collection Duration: | 5 s for aspiration |
| Volumeoramount Collected: | Ca. 10 nL per aspiration |
| Storage Conditions: | -80℃ |
| Collection Tube Temp: | chilled on ice |
