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 ID	ST001338
Study Title	Global profiling for cecal contents
Study 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 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 Name	DONG
First Name	FANGCONG
Address	314 Life Sciences Building, University Park, PA 16802
Email	fxd93@psu.edu
Phone	8148637610
Submit Date	2020-03-26
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2020-10-13
Release Version	1

Select appropriate tab below to view additional metadata details:

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
SA097557	Cecal content_GF3	germ-free
SA097558	Cecal content_GF4	germ-free
SA097559	Cecal content_GF2	germ-free
SA097560	Cecal content_GF1	germ-free
SA097561	Cecal content_C2	wild-type
SA097562	Cecal content_C3	wild-type
SA097563	Cecal content_C4	wild-type
SA097564	Cecal content_C1	wild-type

Showing results 1 to 8 of 8

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.

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