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MB Sample ID: SA151708
Local Sample ID: | KP_JS_C08.Ctrl2_010 |
Subject ID: | SU001727 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | Swiss Webster |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001727 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | Swiss Webster |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
KP_JS_C08.Ctrl2_010 | SA151708 | FL017806 | Ctrl | Colonization |
Collection:
Collection ID: | CO001720 |
Collection Summary: | Cecal contents from gnotobiotic mice were collected under sterile conditions, flash-frozen in liquid nitrogen and stored at -80 C. |
Sample Type: | Feces |
Storage Vials: | -80 |
Treatment:
Treatment ID: | TR001740 |
Treatment Summary: | Swiss Webster germ-free mice were tri-colonized with Bacteroides thetaiotaomicron, Clostridium sporogenes and Escherichia coli for 10 days. Mice were subsequently infected with wild-type Clostridium difficile R20291 (n=5), the isogenic toxin-deficient mutant TcdA-B-CDT- (n=5), or gavaged with PBS as an uninfected control (n=4). Cecal contents were colleged 5 days after C. difficile infection. |
Sample Preparation:
Sampleprep ID: | SP001733 |
Sampleprep Summary: | Metabolites were extracted according to the methodology described in Fiehn 2017 Curr Protoc Mol Biol. ; 114: 30.4.1–30.4.32. doi:10.1002/0471142727.mb3004s114. Briefly, 1 mL 3:3:2 acetonitrile:isopropanol:water was added to ~4 mg cecal contents/feces. Samples were homogenized and then shaken at 4 C for 6 min prior to centrifugation at 14,000 x g for 2 minutes. An aliquot of 475 µl supernatant was taken for subsequent analysis, evaporated, cleaned with acetonitrile and water (1:1), and fully evaporated to dryness. 10 µl MeOH and 91 µl MSTFA were added to all samples for derivatization. |
Combined analysis:
Analysis ID | AN002696 |
---|---|
Analysis type | MS |
Chromatography type | GC |
Chromatography system | Agilent 6890 GC |
Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
MS Type | EI |
MS instrument type | GC-TOF |
MS instrument name | Leco Pegasus IV TOF |
Ion Mode | UNSPECIFIED |
Units | preak area |
Chromatography:
Chromatography ID: | CH001989 |
Chromatography Summary: | Agilent 6890 GC is equipped with a Gerstel automatic liner exchange system (ALEX) that includes a multipurpose sample (MPS2) dual rail, and a Gerstel CIS cold injection system (Gerstel, Muehlheim, Germany) with temperature program as follows: 50°C to 275°C final temperature at a rate of 12 °C/s and hold for 3 minutes. Injection volume is 0.5 μl with 10 μl/s injection speed on a splitless injector with purge time of 25 seconds. Liner (Gerstel #011711-010-00) is changed after every 10 samples, (using the Maestro1 Gerstel software vs. 1.1.4.18). Before and after each injection, the 10 μl injection syringe is washed three times with 10 μl ethyl acetate A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min. |
Instrument Name: | Agilent 6890 GC |
Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
Flow Rate: | 1 ml/min |
Chromatography Type: | GC |
MS:
MS ID: | MS002494 |
Analysis ID: | AN002696 |
Instrument Name: | Leco Pegasus IV TOF |
Instrument Type: | GC-TOF |
MS Type: | EI |
MS Comments: | A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da. |
Ion Mode: | UNSPECIFIED |