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MB Sample ID: SA078071
Local Sample ID: | MM2 |
Subject ID: | SU001189 |
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 with or without d4-alanine |
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Subject:
Subject ID: | SU001189 |
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 with or without d4-alanine |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
MM2 | SA078071 | FL011890 | WT (VPI-5482) | Strain |
Collection:
Collection ID: | CO001183 |
Collection Summary: | After 48 hrs of labeling, 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 for lipidomic analysis. |
Sample Type: | Bacterial cells |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR001204 |
Treatment Summary: | WT and ΔSPT cultures of B. thetaiotaomicron and B. ovatus were grown in 5 mL of minimal media (M9 salts (Teknova), 1% vitamin K1-hemin solution (Becton Dickinson), 1% trace mineral supplement (ATCC), 1% trace vitamin supplement (ATCC), 2% lactose), supplemented with 10μM of deuterium (D4)-labelled alanine (Sigma), or 10μM of -alanine (Sigma). |
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: | SP001197 |
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 | AN001853 |
---|---|
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 | Abundances |
Chromatography:
Chromatography ID: | CH001341 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS001714 |
Analysis ID: | AN001853 |
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 |