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MB Sample ID: SA378166
| Local Sample ID: | 12 11 TVB-2640 40 uM 2 |
| Subject ID: | SU003562 |
| Subject Type: | Fish |
| Subject Species: | Danio rerio |
| Taxonomy ID: | 7955 |
| Gender: | Pooled |
| Species Group: | Fish |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003562 |
| Subject Type: | Fish |
| Subject Species: | Danio rerio |
| Taxonomy ID: | 7955 |
| Gender: | Pooled |
| Species Group: | Fish |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 12 11 TVB-2640 40 uM 2 | SA378166 | FL043637 | Zebrafish | Sample source |
| 12 11 TVB-2640 40 uM 2 | SA378166 | FL043637 | Zebrafish embryo metabolite extract | Sample Type |
| 12 11 TVB-2640 40 uM 2 | SA378166 | FL043637 | 40 uM TVB-2640 | Drug Treatment |
Collection:
| Collection ID: | CO003555 |
| Collection Summary: | For intracellular metabolite samples, the medium was aspirated, and cells were washed with PBS volume matching the volume of the medium. Metabolites were extracted with ice-cold 80% methanol. The volume of the solvent was 500 µl per 6-cm Petri dish (scaled according to the ratio of surface areas for other cell containers). After adding the methanol solution, cells were scraped from the plates, and all the content was transferred to Eppendorf tubes. |
| Collection Protocol Filename: | DM_metabolomics_samples.txt |
| Sample Type: | Media, Metabolite extract |
| Collection Method: | 80% methanol extraction |
| Storage Conditions: | -80℃ |
| Collection Vials: | 1.5 ml plastic centrifuge tubes |
| Storage Vials: | 1.5 ml plastic centrifuge tubes |
Treatment:
| Treatment ID: | TR003571 |
| Treatment Summary: | The zebrafish research was approved by the University of Pennsylvania Institutional Animal Care and Use Committee. Husbandry was performed in accordance with institutional animal welfare guidelines. Embryos from wild type, Tübingen zebrafish were collected within 15 minutes of fertilization. Embryos between 2 and 3 crosses were equally pooled and allocated to treatment conditions for all experiments. Embryos were reared at 28 °C in E3 medium (4 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4, no methylene blue) until treatment. Pharmacological agents were diluted from stocks at room temperature in E3 for 15 minutes before treatment. For treatment at 48 h post-fertilization, embryos in their chorions were transferred to clean plates with the inhibitor-supplemented E3 and incubated for 6 hours. |
| Treatment Compound: | Rotenone, Fasnall, TVB-2640, and GSK2194069 |
| Treatment Route: | Drugs were dissolved in the medium |
| Treatment Vehicle: | DMSO |
Sample Preparation:
| Sampleprep ID: | SP003569 |
| Sampleprep Summary: | Zebrafish embryos were combined by eight per Eppendorf tube, washed with PBS twice, and snap-frozen on dry ice. Frozen samples were ground at the temperature of liquid nitrogen by Retsch Cryomill. To each tube, 300 µl of 80% methanol were added. |
| Sampleprep Protocol Filename: | DM_metabolomics_samples.txt |
| Processing Storage Conditions: | 4℃ |
| Extraction Method: | 80% methanol |
| Extract Enrichment: | None |
| Extract Cleanup: | None |
| Extract Storage: | -80℃ |
| Sample Resuspension: | None |
| Sample Derivatization: | None |
| Sample Spiking: | None |
| Subcellular Location: | Intracellular metabolites and medium metabolites |
Combined analysis:
| Analysis ID | AN005643 | AN005644 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Shimadzu 20AD | Shimadzu 20AD |
| Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 5500 QTrap | ABI Sciex 5500 QTrap |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | Counts per second (cps) | Counts per second (cps) |
Chromatography:
| Chromatography ID: | CH004284 |
| Instrument Name: | Shimadzu 20AD |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Pressure: | 900-3000 psi |
| Column Temperature: | 40 |
| Flow Gradient: | 0-12.5 min, 80-30% B; 12.5-15 min, 30% B; 15-15.2 min, 30-80% B; 15.2-22.5 min, 80% B |
| Flow Rate: | 0-20 min, 0.2 ml/min; 20-21 min 0.2-0.3 ml/min; 21-22 min, 0.3 ml/min; 22-22.1 min, 0.2 ml/min; 22.1-22.5 min, 0.2 ml/min |
| Injection Temperature: | 4 |
| Sample Injection: | 1-5 ul |
| Solvent A: | 100% Water; 0.01% ammonium hydroxide; 20 mM ammonium bicarbonate |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005367 |
| Analysis ID: | AN005643 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Data were analyzed with SCIEX Multiquant 3.0.3. |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 500 °C |
| Capillary Voltage: | -4500 |
| Dry Gas Flow: | 70 |
| Dry Gas Temp: | 500 °C |
| Ion Source Temperature: | 500 °C |
| Ion Spray Voltage: | -4500 |
| Mass Accuracy: | UNIT |
| Source Temperature: | 500 °C |
| Spray Voltage: | -4500 |
| Desolvation Gas Flow: | 70 |
| Desolvation Temperature: | 500 °C |
| MS ID: | MS005368 |
| Analysis ID: | AN005644 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Data were analyzed with SCIEX Multiquant 3.0.3. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 500 °C |
| Capillary Voltage: | 4500 |
| Dry Gas Flow: | 70 |
| Dry Gas Temp: | 500 °C |
| Ion Source Temperature: | 500 °C |
| Ion Spray Voltage: | 4500 |
| Mass Accuracy: | UNIT |
| Source Temperature: | 500 °C |
| Spray Voltage: | 4500 |
| Desolvation Gas Flow: | 70 |
| Desolvation Temperature: | 500 °C |
