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MB Sample ID: SA055511
| Local Sample ID: | CD_12hr_5 |
| Subject ID: | SU000969 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
| Age Or Age Range: | 5-8 |
| Gender: | Male and female |
| Animal Light Cycle: | 12 hr cycle of light and darkness |
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Subject:
| Subject ID: | SU000969 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
| Age Or Age Range: | 5-8 |
| Gender: | Male and female |
| Animal Light Cycle: | 12 hr cycle of light and darkness |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| CD_12hr_5 | SA055511 | FL010171 | 12 | Hours |
Collection:
| Collection ID: | CO000963 |
| Collection Summary: | Cecal content was collected from mice at the time of necropsy and flash frozen in liquid nitrogen until later metabolomics analysis. |
| Sample Type: | Cecum |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR000983 |
| Treatment Summary: | Mice were treated with cefoperazone in their drinking water for 5 days with a two day washout before being challenged with C. difficile spores. Mice were euthanized at time 0hr, prior to C. difficile challenge, and post challenge at 12, 24, and 30 hr. The cecum of mice was collected, flash frozen and stored in the -80C until processing. |
Sample Preparation:
| Sampleprep ID: | SP000976 |
| Sampleprep Summary: | Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis. |
Combined analysis:
| Analysis ID | AN001524 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters Acquity BEH C8 (100 x 2mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | scaled intensity |
Chromatography:
| Chromatography ID: | CH001074 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C8 (100 x 2mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001404 |
| Analysis ID: | AN001524 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | UNSPECIFIED |
