Summary of Study ST001606
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001031. The data can be accessed directly via it's Project DOI: 10.21228/M8F39C This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001606 |
| Study Title | Aromatic amino acid metabolism by the anaerobic gut bacterium Clostridium sporogenes |
| Study Summary | Germ-free mice were mono-colonized with wild-type Clostridium sporogenes or its isogenic phenyllactate dehydratase (fldC) mutant. Feces, cecal contents, serum, and urine were collected for untargeted GC-TOF analysis. |
| Institute | Stanford University |
| Laboratory | Dodd |
| Last Name | Pruss |
| First Name | Kali |
| Address | 300 Pasteur Drive, Lane 235 |
| kmpruss@stanford.edu | |
| Phone | 6507212961 |
| Submit Date | 2020-11-20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2020-12-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001031 |
| Project DOI: | doi: 10.21228/M8F39C |
| Project Title: | Metabolic interactions between gut microbiota and the mammalian host |
| Project Summary: | Untargeted metabolomics performed on various host compartments under different colonization states in gnotobiotic mice. |
| Institute: | Stanford University |
| Laboratory: | Dodd |
| Last Name: | Pruss |
| First Name: | Kali |
| Address: | 300 Pasteur Drive, Lane 235 |
| Email: | kmpruss@stanford.edu |
| Phone: | 6507212961 |
Subject:
| Subject ID: | SU001683 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | host_compartment | bacterial_genotype |
|---|---|---|---|
| SA136014 | 1 - Cecal Contents_fldC-5_038 | Cecal Contents | fldC |
| SA136015 | 1 - Cecal Contents_fldC-4_037 | Cecal Contents | fldC |
| SA136016 | 1 - Cecal Contents_fldC-2_035 | Cecal Contents | fldC |
| SA136017 | 1 - Cecal Contents_fldC-1_034 | Cecal Contents | fldC |
| SA136018 | 1 - Cecal Contents_fldC-3_036 | Cecal Contents | fldC |
| SA136009 | 1 - Cecal Contents_WT-1_014 | Cecal Contents | WT |
| SA136010 | 1 - Cecal Contents_WT-5_018 | Cecal Contents | WT |
| SA136011 | 1 - Cecal Contents_WT-4_017 | Cecal Contents | WT |
| SA136012 | 1 - Cecal Contents_WT-2_015 | Cecal Contents | WT |
| SA136013 | 1 - Cecal Contents_WT-3_016 | Cecal Contents | WT |
| SA136024 | 2 - Feces_fldC-4_032 | Feces | fldC |
| SA136025 | 2 - Feces_fldC-5_033 | Feces | fldC |
| SA136026 | 2 - Feces_fldC-3_031 | Feces | fldC |
| SA136027 | 2 - Feces_fldC-1_029 | Feces | fldC |
| SA136028 | 2 - Feces_fldC-2_030 | Feces | fldC |
| SA136019 | 2 - Feces_WT-5_013 | Feces | WT |
| SA136020 | 2 - Feces_WT-4_012 | Feces | WT |
| SA136021 | 2 - Feces_WT-3_011 | Feces | WT |
| SA136022 | 2 - Feces_WT-1_009 | Feces | WT |
| SA136023 | 2 - Feces_WT-2_010 | Feces | WT |
| SA136034 | 3 - Serum_fldC-5_023 | Serum | fldC |
| SA136035 | 3 - Serum_fldC-4_022 | Serum | fldC |
| SA136036 | 3 - Serum_fldC-3_021 | Serum | fldC |
| SA136037 | 3 - Serum_fldC-1_019 | Serum | fldC |
| SA136038 | 3 - Serum_fldC-2_020 | Serum | fldC |
| SA136029 | 3 - Serum_WT-5_005 | Serum | WT |
| SA136030 | 3 - Serum_WT-4_004 | Serum | WT |
| SA136031 | 3 - Serum_WT-3_003 | Serum | WT |
| SA136032 | 3 - Serum_WT-2_002 | Serum | WT |
| SA136033 | 3 - Serum_WT-1_001 | Serum | WT |
| SA136042 | 4 - Urine_fldC-5_028 | Urine | fldC |
| SA136043 | 4 - Urine_fldC-4_027 | Urine | fldC |
| SA136044 | 4 - Urine_fldC-1_024 | Urine | fldC |
| SA136045 | 4 - Urine_fldC-2_025 | Urine | fldC |
| SA136046 | 4 - Urine_fldC-3_026 | Urine | fldC |
| SA136039 | 4 - Urine_WT-5_008 | Urine | WT |
| SA136040 | 4 - Urine_WT-4_007 | Urine | WT |
| SA136041 | 4 - Urine_WT-1_006 | Urine | WT |
| Showing results 1 to 38 of 38 |
Collection:
| Collection ID: | CO001676 |
| Collection Summary: | Feces, cecal contents, and urine were collected under sterile conditions and snap-frozen in liquid nitrogen prior to storage at -80. Whole blood was collected via cardiac puncture and centrifuged at room temperature for 10 minutes at 2,500 x g in serum separator tubes prior to storage at -80C. |
| Sample Type: | Feces;Urine;Serum |
| Storage Vials: | -80 |
Treatment:
| Treatment ID: | TR001696 |
| Treatment Summary: | Swiss-webster germ-free mice were maintained in sterile gnotobiotic isolators for the duration of the experiment. Mice were mono-colonized with either strain (WT or fldC mutant) of Clostridium sporogenes and tissues collected four weeks thereafter. |
Sample Preparation:
| Sampleprep ID: | SP001689 |
| Sampleprep Summary: | Bacteria were grown anaerobically from glycerol stocks maintained at -80C and gavaged to individual mice in 200 µl volumes. |
Combined analysis:
| Analysis ID | AN002639 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 6890 GC |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25m) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus IV TOF |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH001949 |
| Chromatography Summary: | Injector conditions: 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. Gas Chromatography conditions: 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. |
| Chromatography Comments: | 0 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film)) |
| Instrument Name: | Agilent 6890 GC |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25m) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002451 |
| Analysis ID: | AN002639 |
| 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. Data processing: Peaks reported are normalized to average mtic for each treatment. The algorithm used was developed to replace missing values, assuming each study investigates a specific organ. When very different organs (like in this study) are tested, a compound that is found in one organ but not in others would still be yielding data through noise replacements, or sometimes by adjacent compounds. We therefore report % of positive detections for all compounds in each organ. |
| Ion Mode: | POSITIVE |
