Summary of Study ST001338

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 PR000913. The data can be accessed directly via it's Project DOI: 10.21228/M8P67T 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 IDST001338
Study TitleGlobal profiling for cecal contents
Study SummaryThe aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that responds to a variety of structurally diverse exogenous and endogenous small molecules. Gut microbiota utilizing tryptophan and indole metabolism as a reservoir, has been demonstrated to provide an abundant source of AHR ligands. So differential analysis was performed to find the potential candidates of AHR activator in cecal contents between conventional and germ-free mice with the help of untargeted global profiling.
Institute
Pennsylvania State University
Last NameDONG
First NameFANGCONG
Address314 Life Sciences Building, University Park, PA 16802
Emailfxd93@psu.edu
Phone8148637610
Submit Date2020-03-26
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-10-13
Release Version1
FANGCONG DONG FANGCONG DONG
https://dx.doi.org/10.21228/M8P67T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000913
Project DOI:doi: 10.21228/M8P67T
Project Title:aryl hydrocarbon receptor-related compounds studies
Project Summary:The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that responds to a variety of structurally diverse exogenous and endogenous small molecules. Gut microbiota utilizing tryptophan and indole metabolism as a reservoir, has been demonstrated to provide an abundant source of AHR ligands. So untargeted global profiling was performed to find the potential candidates of AHR activator in human feces.
Institute:Pennsylvania State University
Last Name:DONG
First Name:FANGCONG
Address:314 Life Sciences Building, University Park, PA 16802
Email:fxd93@psu.edu
Phone:8148637610

Subject:

Subject ID:SU001412
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 Genotype
SA097557Cecal content_GF3germ-free
SA097558Cecal content_GF4germ-free
SA097559Cecal content_GF2germ-free
SA097560Cecal content_GF1germ-free
SA097561Cecal content_C2wild-type
SA097562Cecal content_C3wild-type
SA097563Cecal content_C4wild-type
SA097564Cecal content_C1wild-type
Showing results 1 to 8 of 8

Collection:

Collection ID:CO001407
Collection Summary:C57BL/6J wild type mice were originally purchased from Jackson Laboratories (Bar Harbor, MN, USA). Germ-free (GF) C57BL/6J mice were from the Pennsylvania State University Gnotobiotic Animal Research Facility. Mice were bred in-house and fed on a standard animal chow diet. Animal experiments were performed after approval by the Institutional Animal Care and Use Committee. Fresh cecal contents from conventional and GF mice were collected and stored at -80 °C.
Sample Type:Cecum

Treatment:

Treatment ID:TR001427
Treatment Summary:C57BL/6J wild type mice were originally purchased from Jackson Laboratories (Bar Harbor, MN, USA). Germ-free (GF) C57BL/6J mice were from the Pennsylvania State University Gnotobiotic Animal Research Facility. Mice were bred in-house and fed on a standard animal chow diet. Animal experiments were performed after approval by the Institutional Animal Care and Use Committee. Fresh cecal contents from conventional and GF mice were collected and stored at -80 °C.

Sample Preparation:

Sampleprep ID:SP001420
Sampleprep Summary:Each mixture was homogenized with 1 mm zirconium beads using a BeadBlasterTM 24 (Benchmark Scientific, Edison, NJ, USA) homogenizer. All samples were homogenized according to the program parameters: 6500 - 1×30 - 005 (×3). After vortexing, samples were sonicated for 20 min in an ice water bath, prior to centrifugation at 20,000 × g for 20 min at 4 ℃. The supernatants were collected, dried in a Savant SpeedVac (Thermo Scientific, Waltham, MA, USA), and reconstituted in 100 μL of 3% methanol (v/v) containing 1 µM chlorpropamide (internal standard).
Sampleprep Protocol Filename:MS_protocol_for_global_profiling.pdf

Combined analysis:

Analysis ID AN002232
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Fusion Tribrid Orbitrap
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH001638
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Flow Gradient:The initial condition was 97% A and 3% B, increasing to 45% B at 10 min and 75% B at 12 min, where it was held at 75% B until 17.5 min before returning to the initial conditions.
Solvent A:100% water; 0.1% formic acid;
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS002078
Analysis ID:AN002232
Instrument Name:Thermo Fusion Tribrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Solvent A was HPLC-grade water with 0.1% formic acid, and solvent B was HPLC-grade acetonitrile with 0.1% formic acid. The initial condition was 97% A and 3% B, increasing to 45% B at 10 min and 75% B at 12 min, where it was held at 75% B until 17.5 min before returning to the initial conditions. Differential analyses were performed by the use of Compound Discoverer (Thermo Fisher Scientific, Waltham, MA, USA)
Ion Mode:POSITIVE
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