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MB Sample ID: SA219161
| Local Sample ID: | SN_GP61_1_2 |
| Subject ID: | SU002373 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002373 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SN_GP61_1_2 | SA219161 | FL026595 | SN | sample_site |
| SN_GP61_1_2 | SA219161 | FL026595 | GP61 | strain |
| SN_GP61_1_2 | SA219161 | FL026595 | 1 | biologial_rep |
| SN_GP61_1_2 | SA219161 | FL026595 | 2 | technical_rep |
Collection:
| Collection ID: | CO002366 |
| Collection Summary: | The different E. coli strains were grown in LB media and subcultured to OD600 = 0.5. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR002385 |
| Treatment Summary: | E.coli strains were either wild type (MG1655), were deficient in outer membrane porin (OmpC KO) or had a viral epitope from LCMV in place of the OmpC (GP61) |
Sample Preparation:
| Sampleprep ID: | SP002379 |
| Sampleprep Summary: | Metabolites from supernatant were extracted in 100% methanol, precipitated at -20°C for 1 hour, centrifuged and diluted into a linear range (1:20 final dilution) with 50% methanol. To extract intracellular metabolites, bacterial pellet was snap-frozen in liquid nitrogen, resuspended in cell lysis buffer (1M Tris, 5M NaCL, 0.5M EDTA, 10% SDS in H2O) and sonicated. Metabolites were extracted as described above |
Combined analysis:
| Analysis ID | AN003739 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Thermo Syncronis HILIC (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | NEGATIVE |
| Units | AUC |
Chromatography:
| Chromatography ID: | CH002770 |
| Methods Filename: | protocol.docx |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Syncronis HILIC (100 x 2.1mm,1.7um) |
| Column Temperature: | 30C |
| Flow Gradient: | 2 stage linear gradient |
| Flow Rate: | 600uL/min |
| Solvent A: | 100% water; 20 mM ammonium formate, pH 3 |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003487 |
| Analysis ID: | AN003739 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | 50-750 m/z, peak integration and assignment using El-Maven software matching to authentic standard library (~150 compounds). |
| Ion Mode: | NEGATIVE |
