Summary of Study ST002953
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 PR001832. The data can be accessed directly via it's Project DOI: 10.21228/M8X144 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 | ST002953 |
| Study Title | Comparisons of hepatic medium & long chain fatty acids expression between wild type and Cgref1-depleted mice of C57BL/6 strain by targeted GC-MS/MS |
| Study Summary | In this study, we performed a targeted analysis on the expression of hepatic medium & long chain fatty acids between wild type (n=3) and Cgref1-knockout mice (n=2) using targeted GC-MS/MS. The results, however, did not reveal significant differences between the two groups of mice. In the future, a larger sample size and optimization of normalization methods may be helpful to provide more meaningful insights. |
| Institute | The University of Hong Kong |
| Department | School of Biomedical Sciences |
| Laboratory | L3-53 |
| Last Name | Chan |
| First Name | Pearl |
| Address | 21 Sassoon Road, Pokfulam, Hong Kong |
| pearl20@connect.hku.hk | |
| Phone | +85239176812 |
| Submit Date | 2023-10-26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS |
| Release Date | 2024-10-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001832 |
| Project DOI: | doi: 10.21228/M8X144 |
| Project Title: | A study of the physiological functions and impact of secretory protein Cgref1 |
| Project Summary: | Cell Growth Regulator with EF-Hand Domain 1 (Cgref1) is a secretory protein with limited information on its functions. Our group has performed an extensive study using both in-vitro and in-vivo models. Particularly, we used transgenic mice in which the Cgref1 gene is deleted to enable loss-of-function studies. Cgref1-knockout (KO) mice are generally leaner and metabolically healthier compared to wild type mice. To gain evidence of certain parameters, metabolomics studies have been performed for this project. |
| Institute: | The University of Hong Kong |
| Department: | School of Biomedical Sciences |
| Laboratory: | L3-53 |
| Last Name: | Chan |
| First Name: | Pearl |
| Address: | 21 Sassoon Road, Pokfulam, Hong Kong, HKSAR, NA, Hong Kong |
| Email: | pearl20@connect.hku.hk |
| Phone: | +85239176812 |
Subject:
| Subject ID: | SU003066 |
| 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 |
|---|---|---|
| SA321826 | CG3 | Cgref1-knockout |
| SA321827 | CG2 | Cgref1-knockout |
| SA321828 | CG1 | Cgref1-knockout |
| SA321829 | WT2 | Wild-type |
| SA321830 | WT3 | Wild-type |
| SA321831 | WT1 | Wild-type |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO003059 |
| Collection Summary: | Mouse liver tissues were extracted, kept on ice and sent immediately to the the Centre of Panoromic Sciences (The University of Hong Kong) for testing |
| Collection Protocol Filename: | targeted_protocol.pdf |
| Sample Type: | Liver |
| Storage Conditions: | On ice |
Treatment:
| Treatment ID: | TR003075 |
| Treatment Summary: | Samples did not receive any treatment. |
Sample Preparation:
| Sampleprep ID: | SP003072 |
| Sampleprep Summary: | As described in the provided protocol (see attached file): Sample homogenization and metabolite extraction 100 μl of chloroform with 20 μg C19:0 fatty acid internal standard was spiked to the sample. The sample was extracted with 5 rounds of 2:1 Chloroform/Methanol, followed by sonication. After centrifugation, the supernatant was further cleaned by liquid-liquid extraction in 0.73% NaCl and Methanol. The resultant mixture was dried under a fume of N2 at 45°C before transesterification. Transesterification 1 ml of methanol and 50 μl of concentrated hydrochloric acid (35%, w/w) were added to the sample. The solution was overlaid with nitrogen and the tube was tightly closed. After vortexing, the tube was heated at 100°C for 1.5 h. Once cooled to room temperature, 1 ml of hexane and 1 ml of water were added for FAMEs extraction. The tube was vortexed and after phase separation, 1 μl the hexane phase was injected for GC-MS analysis. |
Combined analysis:
| Analysis ID | AN004850 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890B |
| Column | Agilent DB-23 (60m × 0.25mm, 0.15um) |
| MS Type | EI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 7010 |
| Ion Mode | POSITIVE |
| Units | nmol/g |
Chromatography:
| Chromatography ID: | CH003662 |
| Methods Filename: | targeted_protocol.pdf |
| Instrument Name: | Agilent 7890B |
| Column Name: | Agilent DB-23 (60m × 0.25mm, 0.15um) |
| Column Temperature: | N/A |
| Flow Gradient: | N/A |
| Flow Rate: | N/A |
| Solvent A: | N/A |
| Solvent B: | N/A |
| Chromatography Type: | GC |
MS:
| MS ID: | MS004596 |
| Analysis ID: | AN004850 |
| Instrument Name: | Agilent 7010 |
| Instrument Type: | Triple quadrupole |
| MS Type: | EI |
| MS Comments: | GC/MS chromatogram was acquired in SCAN and SIM mode in an Agilent 7890B GC - Agilent 7010 Triple Quadrapole Mass Spectrometer system. The sample was separated through an Agilent DB-23 capillary column (60 m × 0.25 mm ID, 0.15 μm film thickness) under constant pressure of helium at 33.4 psi. The GC oven program started at 50°C (hold time 1 min) and was increased to 175°C at a ramp rate of 25°C/min. The temperature was then raised to 190°C (hold time 5 min) at a ramp rate of 3.5°C/min. Finally the temperature was raised to 220°C (hold time 4 min) at a ramp rate of 2°C/min. Inlet temperature and transfer line temperature were 250°C and 280°C respectively. Characteristic fragment ions (m/z 55, 67, 69, 74, 79, 81, 83, 87, 91, 93, 95, 96, 97, 115, 127, 143) were monitored in SIM mode throughout the run. Mass spectra from m/z 50-350 were acquired in SCAN mode. Data analysis was performed using the Agilent MassHunter Workstation Quantitative Analysis Software. Linear calibration curves for each analyte were generated by plotting peak area ratio of external/internal standard against standard concentration at different concentration level. Analytes were confirmed by comparing the ratio of characteristic fragment ions in the sample and standard. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | targeted_protocol.pdf |
