Summary of study ST001633

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.

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Study IDST001633
Study TitleAromatic amino acid metabolism by the anaerobic gut bacterium Clostridium sporogenes (part-II)
Study SummaryGerm-free MCAD-/- mice or MCAD+/+ controls were mono-colonized with wild-type Clostridium sporogenes. Urine was collected for untargeted LC-QTOF analysis.
Institute
Stanford University
LaboratoryDodd
Last NamePruss
First NameKali
Address300 Pasteur Drive, Lane 235
Emailkmpruss@stanford.edu
Phone6507212961
Submit Date2020-12-11
Raw Data AvailableYes
Raw Data File Type(s).d
Analysis Type DetailLC-MS
Release Date2021-01-26
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:SU001710
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 Mouse_Genotype Treatment
SA13818536MCAD-/- Cs
SA13818635MCAD-/- Cs
SA13818737MCAD-/- Cs
SA13818839MCAD-/- Cs
SA13818934MCAD-/- Cs
SA13819024MCAD-/- Cs
SA13819138MCAD-/- Cs
SA13819215MCAD-/- Cs
SA13819333MCAD-/- Cs
SA13819414MCAD-/- Cs
SA13819513MCAD-/- Cs
SA13819623MCAD-/- Cs
SA13816018MCAD+/+ Cs
SA13816117MCAD+/+ Cs
SA13816216MCAD+/+ Cs
SA13816319MCAD+/+ Cs
SA13816420MCAD+/+ Cs
SA13816522MCAD+/+ Cs
SA13816621MCAD+/+ Cs
SA13816712MCAD+/+ Cs
SA13816811MCAD+/+ Cs
SA13816910MCAD+/+ Cs
SA1381709MCAD+/+ Cs
SA13819748MCAD-/- GF
SA13819849MCAD-/- GF
SA13819952MCAD-/- GF
SA13820047MCAD-/- GF
SA13820151MCAD-/- GF
SA13820250MCAD-/- GF
SA13820344MCAD-/- GF
SA1382046MCAD-/- GF
SA1382055MCAD-/- GF
SA1382067MCAD-/- GF
SA1382078MCAD-/- GF
SA13820845MCAD-/- GF
SA13820943MCAD-/- GF
SA13821046MCAD-/- GF
SA13817131MCAD+/+ GF
SA13817232MCAD+/+ GF
SA13817340MCAD+/+ GF
SA13817441MCAD+/+ GF
SA13817530MCAD+/+ GF
SA13817629MCAD+/+ GF
SA13817727MCAD+/+ GF
SA1381781MCAD+/+ GF
SA13817925MCAD+/+ GF
SA13818028MCAD+/+ GF
SA13818126MCAD+/+ GF
SA1381824MCAD+/+ GF
SA1381833MCAD+/+ GF
SA1381842MCAD+/+ GF
Showing results 1 to 51 of 51

Collection:

Collection ID:CO001703
Collection Summary:MCAD-/- mice were re-derived as germ-free (GF) for the purpose of this study. MCAD-/- mice or MCAD+/+ controls were maintained in sterile gnotobiotic isolators or cages with HEPA-filtered air supply. Urine from GF MCAD-/- and MCAD+/+ mice was collected under sterile conditions. Seven days subsequent, mice were mono-colonized with wild-type C. sporogenes (Cs) by gavage of 200 µL saturated overnight culture. Urine was collected one week after colonization. C. sporogenes colonization was verified with serial dilution plating. Urine samples were immediately frozen on dry ice and stored under -80 oC until analysis.
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001723
Treatment Summary:MCAD-/- mice were re-derived as germ-free (GF) for the purpose of this study. MCAD-/- mice or MCAD+/+ controls were maintained in sterile gnotobiotic isolators or cages with HEPA-filtered air supply. Urine from GF MCAD-/- and MCAD+/+ mice was collected under sterile conditions. Seven days subsequent, mice were mono-colonized with wild-type C. sporogenes (Cs) by gavage of 200 µL saturated overnight culture. Urine was collected one week after colonization. C. sporogenes colonization was verified with serial dilution plating.

Sample Preparation:

Sampleprep ID:SP001716
Sampleprep Summary:. Mouse urine samples (2.5 μL) were diluted with LC-MS grade water (5 μL) and mixed with internal standard (7.5 μL, d3-creatinine,1 mM; d9-phenylpropionic acid, 0.2 mM; 2,2-d2-hippuric acid, 0.2 mM), then 60 μL of extraction solvent containing reference standards (d7-glucose, d3-methionine, L-4-hydroxyphenyl-d4-alanine, d5-hippuric acid, d5-tryptophan, d3-leucine, di-n-octyl phthalate-3,4,5,6-d4, d19-decanoic acid, d15-octanoic acid, d27-tetradecanoic acid, 2-flurophenylglycine, d9-carnitine in methanol) was added to precipitate proteins. The solution was vortexed, then the plate was centrifuged at 15,000 x g for 5 min at 4 C. Supernatant (60 μL) was transferred to a new plate and 20 μL of each was diluted with 60 μL LC-MS grade water. Three procedure blanks were included using the same preparation method with LC-MS water (2.5 μL) instead of urine sample. Quality controls (QC) were pooled from each LC-MS ready sample.

Combined analysis:

Analysis ID AN002669
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290 Infinity II UPLC
Column Waters BEH C18 (2.1 × 100 mm, 1.7μm)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6545XT QTOF
Ion Mode UNSPECIFIED
Units peak height normalized with creatinine

Chromatography:

Chromatography ID:CH001964
Instrument Name:Agilent 1290 Infinity II UPLC
Column Name:Waters BEH C18 (2.1 × 100 mm, 1.7μm)
Chromatography Type:Reversed phase

MS:

MS ID:MS002468
Analysis ID:AN002669
Instrument Name:Agilent 6545XT QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Acquisition was done in All-Ions fragmentation mode using collision energies of 0, 20, and 40 eV. Suspect screening was performed with MS-DIAL (version 4.24) and MS-CleanR. Peak height was normalized with creatinine
Ion Mode:UNSPECIFIED
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