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.
| 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 |
| 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 |
| Species Group: | Mammals |
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 |
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 |
