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MB Sample ID: SA203981
| Local Sample ID: | CID4 |
| Subject ID: | SU002204 |
| Subject Type: | Fish |
| Subject Species: | Danio rerio |
| Taxonomy ID: | 7955 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002204 |
| Subject Type: | Fish |
| Subject Species: | Danio rerio |
| Taxonomy ID: | 7955 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| CID4 | SA203981 | FL025045 | CID661578 | Treatment |
Collection:
| Collection ID: | CO002197 |
| Collection Summary: | zebrafish larvae were treated with DMSO or CID661578 for 24 hours prior to global metabolomics analysis (n=6). Metabolites were extracted from pools of 10 zebrafish larvae at 5 dpf using a 80% methanol/water-based extraction method. Detailed metabolite extraction was described previously using 80% methanol/water as solvent (PMID: 24410464, PMID: 24894601, PMID: 25795660) and dry pellets were stored in -80 °C freezer until ready for LC-MS analysis. Pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v), and 5 μL was injected into the LC-MS. |
| Sample Type: | new |
Treatment:
| Treatment ID: | TR002216 |
| Treatment Summary: | Chemicals (DMSO orCID661578) were added to the E3 medium for larvae to reach final concentration of 10 uM. Pools of 10 wild-type (WT) larvae at 5 dpf were used for each of the 6 independent biological replicates for DMSO or CID661578 treatment from 4-5 dpf. |
Sample Preparation:
| Sampleprep ID: | SP002210 |
| Sampleprep Summary: | Intracellular metabolites were harvested as described previously using 80% methanol/water as solvent (PMID: 24410464, PMID: 24894601, PMID: 25795660) and dry pellets were stored in -80 °C freezer until ready for LC-MS analysis. For metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v), and 5 μL was injected into the LC-MS. |
Combined analysis:
| Analysis ID | AN003467 | AN003468 | AN003469 | AN003470 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | HILIC | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters Xbridge amide (100 x 2.1mm,3.5um) | Waters Xbridge amide (100 x 2.1mm,3.5um) | Waters Xbridge amide (100 x 2.1mm,3.5um) | Waters Xbridge amide (100 x 2.1mm,3.5um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | ion counts | ion counts | ion counts | ion counts |
Chromatography:
| Chromatography ID: | CH002561 |
| Chromatography Summary: | HILIC method is for general metabolomics analysis. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters Xbridge amide (100 x 2.1mm,3.5um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003228 |
| Analysis ID: | AN003467 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | It was operated in the full-scan mode (positive/negative switching) with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003229 |
| Analysis ID: | AN003468 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | It was operated in the full-scan mode (positive/negative switching) with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003230 |
| Analysis ID: | AN003469 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | It was operated in the full-scan mode (positive ion mode only) with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003231 |
| Analysis ID: | AN003470 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | It was operated in the full-scan mode (negative ion mode only) with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch. |
| Ion Mode: | NEGATIVE |
