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.

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Study IDST001606
Study TitleAromatic amino acid metabolism by the anaerobic gut bacterium Clostridium sporogenes
Study SummaryGerm-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
LaboratoryDodd
Last NamePruss
First NameKali
Address300 Pasteur Drive, Lane 235
Emailkmpruss@stanford.edu
Phone6507212961
Submit Date2020-11-20
Raw Data AvailableYes
Raw Data File Type(s).cdf
Analysis Type DetailGC-MS
Release Date2020-12-01
Release Version1
Kali Pruss Kali Pruss
https://dx.doi.org/10.21228/M8F39C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA1360141 - Cecal Contents_fldC-5_038Cecal Contents fldC
SA1360151 - Cecal Contents_fldC-4_037Cecal Contents fldC
SA1360161 - Cecal Contents_fldC-2_035Cecal Contents fldC
SA1360171 - Cecal Contents_fldC-1_034Cecal Contents fldC
SA1360181 - Cecal Contents_fldC-3_036Cecal Contents fldC
SA1360091 - Cecal Contents_WT-1_014Cecal Contents WT
SA1360101 - Cecal Contents_WT-5_018Cecal Contents WT
SA1360111 - Cecal Contents_WT-4_017Cecal Contents WT
SA1360121 - Cecal Contents_WT-2_015Cecal Contents WT
SA1360131 - Cecal Contents_WT-3_016Cecal Contents WT
SA1360242 - Feces_fldC-4_032Feces fldC
SA1360252 - Feces_fldC-5_033Feces fldC
SA1360262 - Feces_fldC-3_031Feces fldC
SA1360272 - Feces_fldC-1_029Feces fldC
SA1360282 - Feces_fldC-2_030Feces fldC
SA1360192 - Feces_WT-5_013Feces WT
SA1360202 - Feces_WT-4_012Feces WT
SA1360212 - Feces_WT-3_011Feces WT
SA1360222 - Feces_WT-1_009Feces WT
SA1360232 - Feces_WT-2_010Feces WT
SA1360343 - Serum_fldC-5_023Serum fldC
SA1360353 - Serum_fldC-4_022Serum fldC
SA1360363 - Serum_fldC-3_021Serum fldC
SA1360373 - Serum_fldC-1_019Serum fldC
SA1360383 - Serum_fldC-2_020Serum fldC
SA1360293 - Serum_WT-5_005Serum WT
SA1360303 - Serum_WT-4_004Serum WT
SA1360313 - Serum_WT-3_003Serum WT
SA1360323 - Serum_WT-2_002Serum WT
SA1360333 - Serum_WT-1_001Serum WT
SA1360424 - Urine_fldC-5_028Urine fldC
SA1360434 - Urine_fldC-4_027Urine fldC
SA1360444 - Urine_fldC-1_024Urine fldC
SA1360454 - Urine_fldC-2_025Urine fldC
SA1360464 - Urine_fldC-3_026Urine fldC
SA1360394 - Urine_WT-5_008Urine WT
SA1360404 - Urine_WT-4_007Urine WT
SA1360414 - Urine_WT-1_006Urine 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, 0.25μm)
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, 0.25μm)
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
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