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MB Sample ID: SA064536
| Local Sample ID: | D11cellE3T2 |
| Subject ID: | SU001067 |
| Subject Type: | Other |
| Subject Species: | Xenopus laevis |
| Taxonomy ID: | 8355 |
| Age Or Age Range: | Embryos were obtained from natural mating of frogs (Nasco) |
| Weight Or Weight Range: | Sexually mature male and female frogs |
| Gender: | Not applicable |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001067 |
| Subject Type: | Other |
| Subject Species: | Xenopus laevis |
| Taxonomy ID: | 8355 |
| Age Or Age Range: | Embryos were obtained from natural mating of frogs (Nasco) |
| Weight Or Weight Range: | Sexually mature male and female frogs |
| Gender: | Not applicable |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| D11cellE3T2 | SA064536 | FL011008 | WT | Embryo Type |
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 |
Treatment:
| Treatment ID: | TR001081 |
| Treatment Summary: | All protocols related to the handling and manipulation of animals were approved by the Institutional Animal Care and Use Committee (IACUC) of the George Washington University (Washington, DC) and the University of Maryland, College Park (College Park, MD). |
| Treatment Protocol ID: | IACUC #A311 (George Washington University) and IACUC #R-DEC-17-57 (University of Maryland, College Park) |
| Treatment Protocol Filename: | Liu 2018 Metabolomics Workbench Protocol.pdf |
| Treatment Protocol Comments: | Embryos were dejellied using 2% cystine solution, cultured in 100% Steinberg's solution (media), and used without further treatment. |
Sample Preparation:
| Sampleprep ID: | SP001074 |
| Sampleprep Summary: | Ca. 10 nL of cell content were aspirated from identified cells. The aspirated material was ejected into ~4 uL of aqueous mixture of 40% acetonitrile and 40% methanol to extract metabolites. |
| Sampleprep Protocol ID: | Cold aqueous acetonitrile-methanold extraction |
| Sampleprep Protocol Filename: | Liu 2018 Metabolomics Workbench Protocol.pdf |
| Processing Storage Conditions: | On ice |
| Extraction Method: | In cold aqueous mixture of 40% acetonitrile and 40% methanol. |
| Extract Storage: | -80℃ |
| Sample Resuspension: | None. The cells were stored in the extraction solution. The extract was not dried or processed further. |
| Subcellular Location: | Unknown |
Combined analysis:
| Analysis ID | AN001686 |
|---|---|
| Analysis type | MS |
| Chromatography type | CE |
| Chromatography system | Custom built CE system |
| Column | Bare fused silica capillary |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker Impact HD |
| Ion Mode | POSITIVE |
| Units | PeakAreaInCounts |
Chromatography:
| Chromatography ID: | CH001186 |
| Chromatography Summary: | About 10 nL of metabolite extract were injected into bare fused silica capillary filled with the background electrolyte, then potential difference was applied between the capillary ends to electrophoretically separate metabolites. |
| Instrument Name: | Custom built CE system |
| Column Name: | Bare fused silica capillary |
| Column Temperature: | Room temperature (~21 degC) |
| Flow Rate: | Electroosmoti flow rates apply in this study (~1 nL/min, estimated) |
| Injection Temperature: | Room temperature (~21 degC) |
| Retention Time: | Metabolites were separated across ~45 min. |
| Sample Injection: | 10 nL |
| Solvent A: | 100% water; 1% formic acid |
| Capillary Voltage: | Ca. +20,000 V applied to inlet end of the CE fused silica separation capillary |
| Migration Time: | Ca. 45 min total run time collected |
| Preconditioning: | Sodium hydroxide solution |
| Running Buffer: | See background electrolyte (above) |
| Sheath Liquid: | 50% methanol, 0.1% formic acid |
| Chromatography Type: | CE |
MS:
| MS ID: | MS001561 |
| Analysis ID: | AN001686 |
| Instrument Name: | Bruker Impact HD |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | Ca. 100 degC |
| Capillary Voltage: | -1700 V |
| Dry Gas Flow: | 2 L/min |
| Dry Gas Temp: | 100 degC |
| Ion Source Temperature: | 100 degC |
| Mass Accuracy: | <10 ppm |
| Dataformat: | .d (Bruker) |
| Resolution Setting: | ~45000 FWHM |
| Scanning Cycle: | 2 Hz spectral |
| Scanning Range: | m/z 50-550 |
