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MB Sample ID: SA069159
Local Sample ID: | V1E2T1N |
Subject ID: | SU001071 |
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 |
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Subject:
Subject ID: | SU001071 |
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 |
---|---|---|---|---|
V1E2T1N | SA069159 | FL011032 | WT | Embryo Type |
Collection:
Collection ID: | CO001065 |
Collection Summary: | Cells were identified based on morphology, pigmentation, and location in the embryo in comparison to established cell-fate maps for Xenopus laevis embryos. A portion of the identified V1 cell was microaspirated using a fabricated microcapillary. |
Collection Protocol ID: | Portero 2018 Metabolomics Workbench Protocols FINAL 2018-08-08 |
Collection Protocol Filename: | nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf |
Sample Type: | embryonic cell |
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℃ |
Treatment:
Treatment ID: | TR001085 |
Treatment Summary: | All protocols related to the handling and manipulation of animals were approved by the University of Maryland, College Park (College Park, MD). Embryos were dejellied using 2% cystine solution, cultured in 100% Steinberg's solution (media), and used without further treatment. |
Treatment Protocol ID: | IACUC # R-DEC-17-57 |
Treatment Protocol Filename: | nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf |
Sample Preparation:
Sampleprep ID: | SP001078 |
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 Filename: | nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf |
Processing Method: | On ice, then extracts stored at -80 degC until analysis. |
Processing Storage Conditions: | On ice |
Extraction Method: | In cold aqueous mixture of 40% acetonitrile and 40% methanol. |
Extract Enrichment: | none |
Extract Cleanup: | none |
Extract Storage: | -80℃ |
Subcellular Location: | Unknown |
Combined analysis:
Analysis ID | AN001692 | AN001693 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | CE | CE |
Chromatography system | Custom-built CE system | Custom-built CE system |
Column | Bare fused silica capillary | Bare fused silica capillary |
MS Type | ESI | ESI |
MS instrument type | QTOF | QTOF |
MS instrument name | Bruker Impact HD | Bruker Impact HD |
Ion Mode | POSITIVE | NEGATIVE |
Units | peak area | peak area |
Chromatography:
Chromatography ID: | CH001191 |
Chromatography Summary: | Metabolites were separated in a custom-built capillary electrophoresis (CE) system. |
Instrument Name: | Custom-built CE system |
Column Name: | Bare fused silica capillary |
Column Temperature: | Room temperature |
Injection Temperature: | Room temperature |
Sample Injection: | Ca. 10 nL |
Solvent A: | 100% water; 1% formic acid |
Analytical Time: | 45 min of separation |
Capillary Voltage: | During cationic separation, +19,000-20,000 V was applied on the inlet end of the CE capillary. |
Preconditioning: | Sodium hydroxide solution |
Sheath Liquid: | During cationic analysis, the electrospray sheath solution was 50% methanol with 0.1% formic acid. |
Chromatography Type: | CE |
Chromatography ID: | CH001192 |
Chromatography Summary: | Metabolites were separated in a custom-built capillary electrophoresis (CE) system. |
Instrument Name: | Custom-built CE system |
Column Name: | Bare fused silica capillary |
Column Temperature: | Room temperature |
Injection Temperature: | Room temperature |
Sample Injection: | Ca. 10 nL |
Solvent A: | 100% water; 20 mM ammonium bicarbonate |
Analytical Time: | 45 min of separation |
Capillary Voltage: | During anionic, +19,000-20,000 V was applied on the inlet end of the CE capillary. |
Preconditioning: | Sodium hydroxide solution |
Sheath Liquid: | During cationic analysis, the electrospray sheath solution was 0.2 mM ammonium bicarbonate in 50% isopropanol. |
Chromatography Type: | CE |
MS:
MS ID: | MS001567 |
Analysis ID: | AN001692 |
Instrument Name: | Bruker Impact HD |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | POSITIVE |
Capillary Temperature: | 100 degC |
Capillary Voltage: | +1700 V during cationic analysis |
Mass Accuracy: | <5 ppm |
Dataformat: | mzML |
Scanning Cycle: | 2 Hz |
Scanning Range: | mz 50-550 |
MS ID: | MS001568 |
Analysis ID: | AN001693 |
Instrument Name: | Bruker Impact HD |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | NEGATIVE |
Capillary Temperature: | 150 degC |
Capillary Voltage: | -2100 during anionic analysis |
Mass Accuracy: | <5 ppm |
Dataformat: | mzML |
Scanning Cycle: | 2 Hz |
Scanning Range: | mz 50-550 |