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MB Sample ID: SA078066
Local Sample ID: | GF Cecal_1 |
Subject ID: | SU001188 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | C57BL/6 germ-free mice |
Animal Animal Supplier: | Taconic |
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Subject:
Subject ID: | SU001188 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | C57BL/6 germ-free mice |
Animal Animal Supplier: | Taconic |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
GF Cecal_1 | SA078066 | FL011888 | None | Inoculum |
GF Cecal_1 | SA078066 | FL011888 | None | Strain |
Collection:
Collection ID: | CO001182 |
Collection Summary: | Caecal samples from GF mice colonized with B. thetaiotaomicron WT or the ΔSPT mutant were weighed, and 20 mg of each wet-weight sample was used for lipid profiling. |
Sample Type: | Cecum |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR001203 |
Treatment Summary: | In an anaerobic chamber, bacterial cultures from frozen stocks were first plated on BHI supplemented with hemin and vitamin K, and subsequently pure cultures were selected and mixed together at a 1:1 ratio in sterile, reduced PBS. Bacterial mixtures in PBS were removed from the anaerobic chamber and immediately transported to the animal facility for gavage experiments. The volume of the mixture received per mouse was 100 μL, at a concentration of 10^9 cells/mL. The concentration of the mixture in cell/mL was determined using a UV spectrometer, and gavage doses were confirmed by back-titering the inocula. |
Sample Preparation:
Sampleprep ID: | SP001196 |
Sampleprep Summary: | 20 mg of each wet-weight cecal sample was extracted using 200 μL isopropanol + 0.1 ng/μL C24:0 PC as internal standard, incubated at RT for 1 hr, and centrifuged for 10 min at 10,000g. |
Combined analysis:
Analysis ID | AN001852 |
---|---|
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: | CH001340 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS001713 |
Analysis ID: | AN001852 |
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 |