Summary of Study ST002908
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 PR001808. The data can be accessed directly via it's Project DOI: 10.21228/M80X4Q 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 | ST002908 |
| Study Title | Rumenomics: Evaluation of rumen metabolites content on phenotypical features of sheep |
| Study Summary | Study the link between the gut microbiome and glycosaminoglycan (GAG) production and turnover in synovial joint tissues using cell culture, tissue biomechanics, and studies in mice and sheep. Gut-Joint Axis. Here we evaluate the functional linkages between 510 metabolites collected from rumen compartment in sheep and identified from Metabolomics with phenotypic features such as weight, sex, age and breed. The associations between metabolites and phenotypic features were established by principal component analysis, partial least squares regression, univariate linear modeling and multiple hypothesis testing. With these results, we extract association insights that reveal the most influential metabolites per each phenotypic feature. |
| Institute | Purdue University |
| Department | Biomedical Engineering-Veterinary Clinical Sciences |
| Last Name | Munoz-Briones |
| First Name | Javier |
| Address | 610 Purdue Mall, West Lafayette, IN 47907 |
| munoz99@purdue.edu | |
| Phone | 7657469102 |
| Submit Date | 2023-09-30 |
| Total Subjects | 16 |
| Num Males | 9 |
| Num Females | 7 |
| Analysis Type Detail | Other |
| Release Date | 2025-09-30 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001808 |
| Project DOI: | doi: 10.21228/M80X4Q |
| Project Title: | Rumenomics: Evaluation of rumen metabolites content on phenotypical features of sheep |
| Project Type: | Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC-MS/MS) |
| Project Summary: | Study the link between the gut microbiome and glycosaminoglycan (GAG) production and turnover in synovial joint tissues using cell culture, tissue biomechanics, and studies in mice and sheep. Gut-Joint Axis. Here we evaluate the functional linkages between 510 metabolites collected from rumen compartment in sheep and identified from Metabolomics with phenotypic features such as weight, sex, age and breed. The associations between metabolites and phenotypic features were established by principal component analysis, partial least squares regression, univariate linear modeling and multiple hypothesis testing. With these results, we extract association insights that reveal the most influential metabolites per each phenotypic feature. |
| Institute: | Purdue University |
| Department: | Biomedical Engineering - Veterinary Clinical Sciences |
| Last Name: | Munoz-Briones |
| First Name: | Javier |
| Address: | 610 Purdue Mall, West Lafayette, IN 47907 |
| Email: | munoz99@purdue.edu |
| Phone: | 7657469102 |
| Funding Source: | DARPA |
| Contributors: | Smrutiti Jena, Brendan Ball, Tim Lescun, Deva Chan, Doug Brubaker, Javier Munoz Briones |
Subject:
| Subject ID: | SU003021 |
| Subject Type: | Mammal |
| Subject Species: | Ovis aries |
| Taxonomy ID: | 9940 |
| Age Or Age Range: | 8-61 |
| Weight Or Weight Range: | 44-95 |
| Gender: | Male and female |
| Animal Animal Supplier: | West Lafayette, Indiana, United States |
| Animal Housing: | West Lafayette, Indiana, United States |
| Animal Feed: | Aad libitum hay (75% grass, 25% alfalfa) |
| Animal Water: | Free access to water |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Ovis aries (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sex | Breed |
|---|---|---|---|
| SA315975 | B1S9 | Female | Cross.bred |
| SA315976 | B1S8 | Female | Cross.bred |
| SA315977 | B1S13 | Female | Cross.bred |
| SA315978 | B1S12 | Female | Dorset |
| SA315979 | B1S5 | Female | Hampshire |
| SA315980 | B1S2 | Female | Hampshire |
| SA315981 | B1S10 | Female | Ramboilette |
| SA315982 | B3S1 | Male | Cross.bred |
| SA315983 | B3S7 | Male | Cross.bred |
| SA315984 | B3S2 | Male | Cross.bred |
| SA315985 | B3S9 | Male | Cross.bred |
| SA315986 | B3S4 | Male | Cross.bred |
| SA315987 | B3S6 | Male | Cross.bred |
| SA315988 | B3S8 | Male | Cross.bred |
| SA315989 | B3S3 | Male | Dorset |
| SA315990 | B3S5 | Male | Dorset |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO003014 |
| Collection Summary: | Rumenomics. Rumen fluid was collected post morten in a necropsy laboratory from rumen. Samples were filtered using cheese cloth and were transported at 4°C at the laboratory to be preprocessed. Samples were centrifuged at 25000 rpm for 15 min, then syringe filters 0.45 um pore size were used to remove solids and storage at 20 °C while they were sent to Metabolon. |
| Sample Type: | Sheep Rumen Fluid |
| Collection Location: | West Lafayette, Indiana, United States |
| Collection Frequency: | One-time |
| Collection Duration: | 10 minutes |
| Collection Tube Temp: | -80°C |
Treatment:
| Treatment ID: | TR003030 |
| Treatment Summary: | Sheep were healthy by their age and weight. They were not under treatment |
Sample Preparation:
| Sampleprep ID: | SP003027 |
| 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. |
Chromatography:
| Chromatography ID: | CH003603 |
| Chromatography Summary: | Low pH polar (LC/MS Pos early) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 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: | CH003604 |
| Chromatography Summary: | Low pH Lipophilic (LC/MS Pos late) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 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: | CH003605 |
| Chromatography Summary: | High pH (LC/MS Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 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: | CH003606 |
| 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 |
Analysis:
| Analysis ID: | AN004771 |
| Analysis Type: | MS |
| Chromatography ID: | CH003603 |
| Num Factors: | 6 |
| Num Metabolites: | 194 |
| Units: | Batch normalized peak area |
| Analysis ID: | AN004772 |
| Analysis Type: | MS |
| Chromatography ID: | CH003604 |
| Num Factors: | 6 |
| Num Metabolites: | 12 |
| Units: | Batch normalized peak area |
| Analysis ID: | AN004773 |
| Analysis Type: | MS |
| Chromatography ID: | CH003605 |
| Num Factors: | 6 |
| Num Metabolites: | 213 |
| Units: | Batch normalized peak area |
| Analysis ID: | AN004774 |
| Analysis Type: | MS |
| Chromatography ID: | CH003606 |
| Num Factors: | 6 |
| Num Metabolites: | 91 |
| Units: | Batch normalized peak area |
