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MB Sample ID: SA051125
| Local Sample ID: | 42_HFD Vancomycin_129Jax |
| Subject ID: | SU000914 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammal |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000914 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammal |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 42_HFD Vancomycin_129Jax | SA051125 | FL009847 | HFD | Diet |
| 42_HFD Vancomycin_129Jax | SA051125 | FL009847 | vancomycin | Treatment |
| 42_HFD Vancomycin_129Jax | SA051125 | FL009847 | 129Jax | Strain |
Collection:
| Collection ID: | CO000908 |
| Collection Summary: | The mice were fasted for 2 hours and anesthetized with isoflurane before collecting cecum and plasma. |
| Blood Serum Or Plasma: | Plasma |
Treatment:
| Treatment ID: | TR000928 |
| Treatment Summary: | Mice were maintained on normal chow containing 22% calories from fat, 23% from protein and 55% from carbohydrates (Mouse Diet 9F 5020, PharmaServ, Framingham, MA) or a high fat diet (Open Source Diet, D12492, Research Diets, New Brunswick, NJ) containing 60% calories from fat, 20% from protein and 20% from carbohydrates. For antibiotic treatment, 6-week old mice were treated with either placebo, vancomycin (1g/L) or metronidazole (1g/L) (Sigma-Aldrich, St. Louis, MO) in drinking water then started on HFD from age 7 to 11 weeks. |
Sample Preparation:
| Sampleprep ID: | SP000921 |
| Sampleprep Summary: | Cecal contents were homogenized in 10 volumes (weight:volume) of H2O using a bead beater HILIC-posLC-MS samples were prepared from cecal homogenates (10 μL) via protein precipitation with the addition of nine volumes of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples are centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were injected onto column. HILIC-neg:Cecal homogenates (30μL) were extracted using 120 μL of 80% methanol (VWR) containing 0.05 ng/μL inosine-15N4, 0.05 ng/μL thymine-d4, and 0.1 ng/μL glycocholate-d4 as internal standards (Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000 x g, 4ºC) and the supernatants (10 μL) were injected onto column.. C18-neg: Cecal homogenates (30 μL) were extracted using 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) and centrifuged (10 min, 9,000 x g, 4°C). The supernatants (10 μL) were injected onto column.. C8-pos: Lipids were extracted from cecal homogenates (10 μL) using 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL). After centrifugation (10 min, 9,000 x g, ambient temperature), supernatants (10 μL) were injected directly onto column. |
Combined analysis:
| Analysis ID | AN001433 | AN001434 | AN001435 | AN001436 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
| Chromatography system | Shimadzu Nexera X2 | Waters Acquity | Shimadzu Nexera X2 | Shimadzu Nexera X2 |
| Column | Waters Atlantis HILIC (150 x 2mm) | Phenomenex Luna NH2 (150 x 2.0mm) | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Triple quadrupole | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | ABI Sciex 5500 QTrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | NEGATIVE | POSITIVE |
| Units | Peak area | Peak area | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH001004 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Atlantis HILIC (150 x 2mm) |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001005 |
| Instrument Name: | Waters Acquity |
| Column Name: | Phenomenex Luna NH2 (150 x 2.0mm) |
| Solvent A: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide (Sigma-Aldrich) (VWR) |
| Solvent B: | 75% acetonitrile/25% methanol; 10 mM ammonium hydroxide |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001006 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001007 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
| Solvent A: | 95% water/5% methanol; 0.1% acetic acid; 10 mM ammonium acetate |
| Solvent B: | 100% methanol; 0.1% acetic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001323 |
| Analysis ID: | AN001433 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| MS ID: | MS001324 |
| Analysis ID: | AN001434 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001325 |
| Analysis ID: | AN001435 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001326 |
| Analysis ID: | AN001436 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
