Summary of Study ST003132
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 PR001945. The data can be accessed directly via it's Project DOI: 10.21228/M89M7J 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 | ST003132 |
| Study Title | Untargeted Metabolomics on Mouse colonic mucosa |
| Study Type | Mouse |
| Study Summary | While there is strong evidence for interactions between the microbiota-gut-brain axis and host physiology in the context of chronic stress, limited research has investigated the role of the microbiome in host response to acute stress. Determining the underlying mechanisms by which stress-induced microbiota changes may provoke functional changes in the gut and brain is critical for developing future therapeutics to alleviate the adverse consequences of traumatic stress. Here, we aimed to identify a biological signature of gut metabolites that are significantly altered following exposure to acute restraint stress. Adult male C57Bl/6 conventional, germ-free and colonized germ-free mice underwent a 15-minute restraint stress exposure. Caecal contents were collected from naïve mice and stressed mice, either immediately or 45 minutes following stress. Colonic mucosa underwent untargeted metabolomics analysis. |
| Institute | University College Cork |
| Department | Psychiatry |
| Laboratory | Microbiota-Gut-Brain Axis Group |
| Last Name | Clarke |
| First Name | Gerard |
| Address | Gaol Walk, Cork |
| G.Clarke@ucc.ie | |
| Phone | +353-21-4901408 |
| Submit Date | 2024-03-19 |
| Num Groups | 9 |
| Total Subjects | 63 |
| Num Males | 63 |
| Analysis Type Detail | Other |
| Release Date | 2024-03-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001945 |
| Project DOI: | doi: 10.21228/M89M7J |
| Project Title: | The microbiota drives diurnal rhythms in tryptophan metabolism in the stressed gut |
| Project Type: | Untargeted metabolomics by Metabolon |
| Project Summary: | Adult male C57Bl/6 conventional, germ-free and colonized germ-free mice underwent a 15-minute restraint stress exposure. Caecal contents and colonic mucosal scrapings were collected from naïve mice and stressed mice, either immediately or 45 minutes following stress. Caecal contents and colonic mucosal scrapings underwent untargeted metabolomics analysis. |
| Institute: | University College Cork |
| Department: | Psychiatry |
| Laboratory: | Microbiota-Gut-Brain Axis Group |
| Last Name: | Clarke |
| First Name: | Gerard |
| Address: | Gaol Walk, Cork |
| Email: | G.Clarke@ucc.ie |
| Phone: | +353-21-4901408 |
| Funding Source: | The research was conducted in the APC Microbiome Ireland which is funded by Science Foundation Ireland (SFI/12/RC/2273). This project in part is a collaborative agreement (FA9550-17-1-0016) funded by European Office of Aerospace Research and Development, Air Force Office of Scientific Research and 711 Human Performance Wing, Air Force Research Laboratory. |
Subject:
| Subject ID: | SU003249 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl/6J |
| Age Or Age Range: | 8-10 weeks |
| Weight Or Weight Range: | 20-29g |
| Gender: | Male |
| Animal Animal Supplier: | Taconic |
| Animal Housing: | Gnotobiotic isolators/conventional housing |
| Animal Light Cycle: | 12/12 |
| Animal Feed: | RM1A (P) and RM3A (P) from Special Diet Services |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Factor |
|---|---|---|---|
| SA339239 | ColGF8.5 | Colonic mucosa | ColGF_0min |
| SA339240 | ColGF8.6 | Colonic mucosa | ColGF_0min |
| SA339241 | ColGF8.4 | Colonic mucosa | ColGF_0min |
| SA339242 | ColGF8.2 | Colonic mucosa | ColGF_0min |
| SA339243 | ColGF8.1 | Colonic mucosa | ColGF_0min |
| SA339244 | ColGF8.7 | Colonic mucosa | ColGF_0min |
| SA339245 | ColGF8.3 | Colonic mucosa | ColGF_0min |
| SA339246 | ColGF9.6 | Colonic mucosa | ColGF_45min |
| SA339247 | ColGF9.7 | Colonic mucosa | ColGF_45min |
| SA339248 | ColGF9.5 | Colonic mucosa | ColGF_45min |
| SA339249 | ColGF9.4 | Colonic mucosa | ColGF_45min |
| SA339250 | ColGF9.3 | Colonic mucosa | ColGF_45min |
| SA339251 | ColGF9.1 | Colonic mucosa | ColGF_45min |
| SA339252 | ColGF9.2 | Colonic mucosa | ColGF_45min |
| SA339253 | ColGF7.3 | Colonic mucosa | ColGF_Pre |
| SA339254 | ColGF7.1 | Colonic mucosa | ColGF_Pre |
| SA339255 | ColGF7.4 | Colonic mucosa | ColGF_Pre |
| SA339256 | ColGF7.2 | Colonic mucosa | ColGF_Pre |
| SA339257 | ColGF7.6 | Colonic mucosa | ColGF_Pre |
| SA339258 | ColGF7.5 | Colonic mucosa | ColGF_Pre |
| SA339259 | ColGF7.7 | Colonic mucosa | ColGF_Pre |
| SA339260 | Conv5.3 | Colonic mucosa | Conv_0min |
| SA339261 | Conv5.2 | Colonic mucosa | Conv_0min |
| SA339262 | Conv5.5 | Colonic mucosa | Conv_0min |
| SA339263 | Conv5.7 | Colonic mucosa | Conv_0min |
| SA339264 | Conv5.1 | Colonic mucosa | Conv_0min |
| SA339265 | Conv5.6 | Colonic mucosa | Conv_0min |
| SA339266 | Conv5.4 | Colonic mucosa | Conv_0min |
| SA339267 | Conv6.3 | Colonic mucosa | Conv_45min |
| SA339268 | Conv6.2 | Colonic mucosa | Conv_45min |
| SA339269 | Conv6.4 | Colonic mucosa | Conv_45min |
| SA339270 | Conv6.6 | Colonic mucosa | Conv_45min |
| SA339271 | Conv6.7 | Colonic mucosa | Conv_45min |
| SA339272 | Conv6.1 | Colonic mucosa | Conv_45min |
| SA339273 | Conv6.5 | Colonic mucosa | Conv_45min |
| SA339274 | Conv4.3 | Colonic mucosa | Conv_Pre |
| SA339275 | Conv4.1 | Colonic mucosa | Conv_Pre |
| SA339276 | Conv4.7 | Colonic mucosa | Conv_Pre |
| SA339277 | Conv4.6 | Colonic mucosa | Conv_Pre |
| SA339278 | Conv4.2 | Colonic mucosa | Conv_Pre |
| SA339279 | Conv4.4 | Colonic mucosa | Conv_Pre |
| SA339280 | Conv4.5 | Colonic mucosa | Conv_Pre |
| SA339281 | GF2.4 | Colonic mucosa | GF_0min |
| SA339282 | GF2.5 | Colonic mucosa | GF_0min |
| SA339283 | GF2.6 | Colonic mucosa | GF_0min |
| SA339284 | GF2.3 | Colonic mucosa | GF_0min |
| SA339285 | GF2.7 | Colonic mucosa | GF_0min |
| SA339286 | GF2.2 | Colonic mucosa | GF_0min |
| SA339287 | GF2.1 | Colonic mucosa | GF_0min |
| SA339288 | GF3.5 | Colonic mucosa | GF_45min |
| SA339289 | GF3.7 | Colonic mucosa | GF_45min |
| SA339290 | GF3.1 | Colonic mucosa | GF_45min |
| SA339291 | GF3.4 | Colonic mucosa | GF_45min |
| SA339292 | GF3.6 | Colonic mucosa | GF_45min |
| SA339293 | GF3.3 | Colonic mucosa | GF_45min |
| SA339294 | GF3.2 | Colonic mucosa | GF_45min |
| SA339295 | GF1.3 | Colonic mucosa | GF_Pre |
| SA339296 | GF1.2 | Colonic mucosa | GF_Pre |
| SA339297 | GF1.4 | Colonic mucosa | GF_Pre |
| SA339298 | GF1.1 | Colonic mucosa | GF_Pre |
| SA339299 | GF1.7 | Colonic mucosa | GF_Pre |
| SA339300 | GF1.6 | Colonic mucosa | GF_Pre |
| SA339301 | GF1.5 | Colonic mucosa | GF_Pre |
| Showing results 1 to 63 of 63 |
Collection:
| Collection ID: | CO003242 |
| Collection Summary: | Upon entering the cull room, mice were immediately decapitated, trunk blood collected, and tissues harvested. Caecal contents and intestinal samples were manually dissected and stored in PCR-grade microfuge tubes at -80°C until analyses. |
| Sample Type: | Colon |
| Storage Conditions: | -80? |
Treatment:
| Treatment ID: | TR003258 |
| Treatment Summary: | All animal work carried was approved by the Animal Experimentation Ethics Committee of University College Cork and Health Products Regulatory Authority (HPRA) before beginning this study. All experimentation was carried out in accordance with European Directive 2010/63/EU and was approved by both the Animal Experimentation Ethics Committee of University College Cork (Project Authorization AE19130/P160) and United States Air Force Surgeon General's Office of Research Oversight and Compliance. C57/BL6 mice breeding pairs were acquired from Taconic Biosciences, and F1-generation male and female offspring were used in all experiments. Germ-free, ex-germ-free, and conventional mice were housed 2-4 mice/cage under a 12-hour light/dark cycle and maintained on ad libitum autoclaved water and autoclaved, pelleted diet (Special Diet Services). Housing conditions for germ-free, conventional, and colonized germ-free adhered to the same environmental conditions of temperature (21 ± 1°C) and humidity (55%-60%). Germ-free mice were housed in gnotobiotic flexible-film isolators. Colonized germ-free mice were born and maintained as germ-free mice in gnotobiotic flexible-film isolators until postnatal day 21 when they were removed from the isolators and, for the remaining duration of this study, re-located to the standard animal facility and housed in wire-top cages that contained used-bedding from age- and sex-matched conventional mice. The acute restraint stress procedure was performed using a clean perforated polypropylene screw-cap 50 mL conical tubes. Cages were randomly assigned to either non-stress or stress groups. Each mouse that underwent stress was placed into the 50 mL tube and restrained for 15 minutes. |
Sample Preparation:
| Sampleprep ID: | SP003256 |
| Sampleprep Summary: | Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis. |
Combined analysis:
| Analysis ID | AN005139 | AN005140 | AN005141 | AN005142 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) | Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) | Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Raw Peak Area | Raw Peak Area | Raw Peak Area | Raw Peak Area |
Chromatography:
| Chromatography ID: | CH003889 |
| Chromatography Summary: | Low pH polar (LC/MS Pos early) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Solvent B: | 100% methanol; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003890 |
| Chromatography Summary: | Low pH Lipophilic (LC/MS Pos late) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes. |
| Flow Rate: | 0.60 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Solvent B: | 50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003891 |
| Chromatography Summary: | High pH (LC/MS Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 6.5 mM ammonium bicarbonate, pH 8 |
| Solvent B: | 95% methanol/5% water; 6.5 mM ammonium bicarbonate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003892 |
| Chromatography Summary: | HILIC (LC/MS Polar Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes. |
| Flow Rate: | 0.50 mL/min |
| Solvent A: | 15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with NH4OH) |
| Solvent B: | 50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with NH4OH) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004875 |
| Analysis ID: | AN005139 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos early) |
| Ion Mode: | POSITIVE |
| MS ID: | MS004876 |
| Analysis ID: | AN005140 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos late) |
| Ion Mode: | POSITIVE |
| MS ID: | MS004877 |
| Analysis ID: | AN005141 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Neg) |
| Ion Mode: | NEGATIVE |
| MS ID: | MS004878 |
| Analysis ID: | AN005142 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Polar) |
| Ion Mode: | NEGATIVE |
