Summary of Study ST003695
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 PR002293. The data can be accessed directly via it's Project DOI: 10.21228/M87F9Z 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 | ST003695 |
| Study Title | Metabolomics studies on mouse cecum samples on a Western diet |
| Study Summary | Targeted metabolomics was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS).to measure polar metabolites in both positive and negative ionization mode on cecummice tissue acquired after a 30 week dietary intervention. |
| Institute | University of Sydney |
| Department | School of Medical Sciences |
| Laboratory | Cardiometabolic Disease |
| Last Name | Liu |
| First Name | Renping |
| Address | Charles Perkins Centre |
| renping.liu@sydney.edu.au | |
| Phone | +61432953638 |
| Submit Date | 2025-01-07 |
| Num Groups | 4 |
| Total Subjects | 35 |
| Num Males | 35 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | API |
| Release Date | 2025-02-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002293 |
| Project DOI: | doi: 10.21228/M87F9Z |
| Project Title: | Investigating the role of 4-diets through multi-organ and multi-omic crosstalk |
| Project Type: | Targeted MS quantitative analysis |
| Project Summary: | Presently, dietary patterns have undergone significant shifts, and understanding the intricate interplay between diet, particularly high fat and high sucrose diets, the gut microbiome, and cardiometabolic health has become paramount. These dietary patterns have been consistently associated with heightened cardiometabolic risk factors including obesity, insulin resistance, dyslipidemia, and hypertension. High-fat diets, in particular, contribute to increased adiposity and ectopic fat deposition, exacerbating systemic inflammation and oxidative stress, thereby promoting the development of metabolic dysfunction. Similarly, high sucrose diets have been implicated in the dysregulation of glucose homeostasis, leading to insulin resistance and hyperglycemia, key hallmarks of cardiometabolic diseases such as type 2 diabetes mellitus. Amidst this, the exploration of multi-omic profiles alongside the gut microbial landscape has emerged as a pivotal avenue for unraveling the complexities of cardiometabolic health dynamics affected by the effects of high-fat and high-sucrose diets. The approach of using a multi-omic comparison between organs offers a comprehensive lens through which the intricate molecular signatures underlying the impact of dietary compositions, particularly high fat and high sucrose, on metabolic health, can be examined. |
| Institute: | University of Sydney |
| Department: | School of Medical Sciences |
| Laboratory: | Cardiometabolic Disease |
| Last Name: | Liu |
| First Name: | Renping |
| Address: | The Hub, Charles Perkins Centre, D17, The University of Sydney, NSW, 2006 |
| Email: | renping.liu@sydney.edu.au |
| Phone: | +61432953638 |
Subject:
| Subject ID: | SU003827 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 6 weeks old |
| Gender: | Male |
| Animal Animal Supplier: | Australian Resource Centre |
| Animal Housing: | 3 per cage |
| Animal Light Cycle: | 12-hour light-dark cycle |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Diet |
|---|---|---|---|
| SA403906 | C62.1 | cecum | chow |
| SA403907 | C59.2 | cecum | chow |
| SA403908 | C62.3 | cecum | chow |
| SA403909 | C62.2 | cecum | chow |
| SA403910 | C59.1 | cecum | chow |
| SA403911 | C61.3 | cecum | chow |
| SA403912 | C61.1 | cecum | chow |
| SA403913 | C59.3 | cecum | chow |
| SA403914 | C61.2 | cecum | chow |
| SA403915 | HF58.1 | cecum | hfd |
| SA403916 | HF58.2 | cecum | hfd |
| SA403917 | HF58.3 | cecum | hfd |
| SA403918 | HF65.1 | cecum | hfd |
| SA403919 | HF65.2 | cecum | hfd |
| SA403920 | HF65.3 | cecum | hfd |
| SA403921 | HF67.1 | cecum | hfd |
| SA403922 | HF67.2 | cecum | hfd |
| SA403923 | HF67.3 | cecum | hfd |
| SA403924 | HFHS66.1 | cecum | hfhsd |
| SA403925 | HFHS66.3 | cecum | hfhsd |
| SA403926 | HFHS66.2 | cecum | hfhsd |
| SA403927 | HFHS57.1 | cecum | hfhsd |
| SA403928 | HFHS57.3 | cecum | hfhsd |
| SA403929 | HFHS56.3 | cecum | hfhsd |
| SA403930 | HFHS56.2 | cecum | hfhsd |
| SA403931 | HFHS56.1 | cecum | hfhsd |
| SA403932 | HS60.1 | cecum | hsd |
| SA403933 | HS60.2 | cecum | hsd |
| SA403934 | HS60.3 | cecum | hsd |
| SA403935 | HS63.1 | cecum | hsd |
| SA403936 | HS63.2 | cecum | hsd |
| SA403937 | HS63.3 | cecum | hsd |
| SA403938 | HS64.1 | cecum | hsd |
| SA403939 | HS64.2 | cecum | hsd |
| SA403940 | HS64.3 | cecum | hsd |
| Showing results 1 to 35 of 35 |
Collection:
| Collection ID: | CO003820 |
| Collection Summary: | Mouse cecum samples were collected at the end of the experimental design (after 30-weeks on the diet) during the cull. These samples were immediately clamped with metal clamps and snap-frozen in liquid nitrogen and stored in -80 degrees Celsius until further analysis. This process was approved by the University of Sydney’s Ethics Committee (USYD # 2017/1294). |
| Sample Type: | Cecum |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003836 |
| Treatment Summary: | 36 male C57BL/6J mice were allocated to four different diets (n = 7-8) consisting of a control diet (Chow), a high-sucrose diet (HSD), a high-fat diet (HFD), and a high-fat high-sucrose (western) diet (HFHSD) at 8 weeks of age. Mice had ad libitum access to their food and autoclaved water. One mouse was euthanised prior to the expected experimental endpoint due to the loss of body condition and was excluded from this study. 4 samples were not collected after euthanisation making the groups (n = 7-8) |
| Treatment: | Chow, HFD, HSD, HFHSD |
Sample Preparation:
| Sampleprep ID: | SP003834 |
| Sampleprep Summary: | Approximately 50 mg of ground cecum tissue was weighed into 2 mL Eppendorf tube and subjected to a two-phase extraction protocol involving tissue, ice-cold extraction medium (methanol:water, and chloroform). Samples were then centrifuged at 14 000 x g at 4°C for 25 min. The aqueous layer was transferred into a new microfuge tube and reconstituted in the acetonitrile/methanol/formic acid (75:25:0.2; v/v/v, HPLC grade; Thermo Fisher Scientific) for the HILIC analysis, and acetonitrile/methanol (25:25; v/v/v, HPLC grade) for the AMIDE and NAD analysis. |
Combined analysis:
| Analysis ID | AN006062 | AN006063 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | AMIDE |
| Chromatography system | Agilent 1260 | Agilent 1260 |
| Column | Waters Atlantis T3 (150 x 4.6 mm, 5 µm) | Waters XBridge BEH Amide (100 x 2.1 mm, 2.5 µm) |
| MS Type | API | API |
| MS instrument type | QTRAP | QTRAP |
| MS instrument name | ABI Sciex 6500 QTrap | ABI Sciex 6500 QTrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak Area | Peak Area |
Chromatography:
| Chromatography ID: | CH004606 |
| Chromatography Summary: | Chromatographic method to detect analytes such as amino acids, endocannabinoids, fatty acid β-oxidation intermediates, gut-derived metabolites, nucleotides, neurotransmitters, cofactors and vitamins. |
| Instrument Name: | Agilent 1260 |
| Column Name: | Waters Atlantis T3 (150 x 4.6 mm, 5 µm) |
| Column Temperature: | 40°C |
| Flow Gradient: | The LC gradient program begins with an initial condition of 5% solvent A and 95% solvent B, with a flow rate of 0.25 mL/min, which is held for 0.5 minutes to establish system equilibration. The gradient then proceeds as follows: at 6 minutes, the mobile phase composition shifts to 60% solvent A and 40% solvent B for 3minutes; at 10 minutes, it changes back to 5% solvent A and 95% solvent B; at 11 minutes, the flow rate increases to 0.4 mL/min while maintaining a composition of 5% solvent A and 95% solvent B for a duration of 12.5 minutes; and at 24.5 minutes, the flow rate decreases back to 0.25 mL/min. The final condition is maintained for 1 minutes to ensure stability before subsequent analyses. |
| Flow Rate: | 0.250 – 0.400 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate (pH ~2.5) |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH004607 |
| Chromatography Summary: | Chromatographic method to detect analytes such as amino acids, endocannabinoids, fatty acid β-oxidation intermediates, gut-derived metabolites, nucleotides, neurotransmitters, cofactors and vitamins. |
| Instrument Name: | Agilent 1260 |
| Column Name: | Waters XBridge BEH Amide (100 x 2.1 mm, 2.5 µm) |
| Column Temperature: | 40°C |
| Flow Gradient: | The LC gradient program is initialized with an initial mobile phase composition of 15% solvent A and 85% solvent B at a flow rate of 0.25 mL/min. Over the course of 8 minutes, the mobile phase composition undergoes a transition to 65% solvent A and 35% solvent B. Subsequently, at 8 minutes, the composition shifts to 98% solvent A and 2% solvent B, maintained for 1 minute. The mobile phase reverts back to the initial composition of 15% solvent A and 85% solvent B at 10 minutes. At 12.5 minutes, the flow rate is increased to 0.4 mL/min, while maintaining a constant mobile phase composition of 15% solvent A and 85% solvent B for a period of 2.5 minutes. Finally, at 15 minutes, the flow rate is reduced back to 0.25 mL/min. To ensure system stability, the final condition is maintained for 1 minute prior to subsequent analyses. |
| Flow Rate: | 0.250 – 0.400 mL/min |
| Solvent A: | 95% acetonitrile/5% water; 20mM ammonium acetate; 20mM ammonium hydroxide (pH 9.0) |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | AMIDE |
MS:
| MS ID: | MS005770 |
| Analysis ID: | AN006062 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | API |
| MS Comments: | Targeted metabolite profiling was performed using MS multiple reaction-monitoring transitions. Multiple Reaction Monitoring (MRM) Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex) was performed using software MultiQuant 3.0 (ABSciex). |
| Ion Mode: | POSITIVE |
| MS ID: | MS005771 |
| Analysis ID: | AN006063 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | API |
| MS Comments: | Targeted metabolite profiling was performed using MS multiple reaction-monitoring transitions. Multiple Reaction Monitoring (MRM) Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex) was performed using software MultiQuant 3.0 (ABSciex). |
| Ion Mode: | NEGATIVE |
