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MB Sample ID: SA078052
| Local Sample ID: | WT1_4 |
| Subject ID: | SU001187 |
| Subject Type: | Bacteria |
| Subject Species: | Bacteroides thetaiotaomicron VPI-5482 |
| Taxonomy ID: | 226186 |
| Genotype Strain: | WT (VPI-5482), SPT K.O. (BT_0870) |
| Cell Biosource Or Supplier: | ATCC |
| Cell Strain Details: | Wild type Bacteroides tethaiotamicron strains and serine palmitoyltransferase (SPT) knockouts |
| Subject Comments: | Grown in Minimal Media |
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Subject:
| Subject ID: | SU001187 |
| Subject Type: | Bacteria |
| Subject Species: | Bacteroides thetaiotaomicron VPI-5482 |
| Taxonomy ID: | 226186 |
| Genotype Strain: | WT (VPI-5482), SPT K.O. (BT_0870) |
| Cell Biosource Or Supplier: | ATCC |
| Cell Strain Details: | Wild type Bacteroides tethaiotamicron strains and serine palmitoyltransferase (SPT) knockouts |
| Subject Comments: | Grown in Minimal Media |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| WT1_4 | SA078052 | FL011885 | WT (VPI-5482) | Bacterial Species / Inoculum |
Collection:
| Collection ID: | CO001181 |
| Collection Summary: | WT and ΔSPT cultures of B. thetaiotaomicron were grown in 5 mL of minimal 714 media (M9 salts (Teknova), 1% vitamin K1-hemin solution (Becton Dickinson), 1% trace mineral 715 supplement (ATCC), 1% trace vitamin supplement (ATCC), 2% lactose). |
| Sample Type: | Bacterial cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001202 |
| Treatment Summary: | In-frame deletion of the serine palmitoyl transferase gene (spt) in B. thetaiotaomicron Δtdk was generated using a counter-selectable allelic exchange procedure (Koropatkin et al., 2008). |
| Cell Storage: | -80C |
| Cell Growth Container: | anaerobic chamber (Coy Laboratory Products) with an atmosphere of 20% CO2, 5% H2, and 75% N2 at 37°C. |
Sample Preparation:
| Sampleprep ID: | SP001195 |
| Sampleprep Summary: | After 48 hrs, resulting cultures were pelleted by centrifugation at 8000 rpm for 10 min and cell density was normalized. Lipids were extracted using isopropanol and stored at -80C until ready for lipidomic analysis. |
Combined analysis:
| Analysis ID | AN001851 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Shimadzu Nexera X2 |
| Column | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Focus |
| Ion Mode | POSITIVE |
| Units | abundance |
Chromatography:
| Chromatography ID: | CH001339 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001712 |
| Analysis ID: | AN001851 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.1 (Thermo Fisher) and Progenesis QI (Nonlinear dynamics). Retention time, m/z, MS/MS fragmentation were used to confirm the identity of metabolite using authentic reference standards when available (level 1 identifications), in addition to monitoring the product ions produced and the retention time and mass of species belonging to the each lipid class (level 2-3 annotation). |
| Ion Mode: | POSITIVE |
