Summary of Study ST002947
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 | ST002947 |
| Study Title | Hepatic lipid profiles of wild type and Cgref1-depleted mice of C57BL/6 strain obtained by an untargeted LC-MS/MS analysis |
| Study Summary | Among the range of experiments and observations recorded, we compared the lipid expression in the liver tissues between wild type and Cgref1-knockout mice of C57BL/6 strain using untargeted LC-MS/MS (n=3 per group). Particularly, the results revealed that Cgref1-knockout (KO) mice overall have lower levels of triglyceride and diglyceride species. Such finding provides supportive evidence that Cgref1 may promote de novo lipogenesis in the liver and increase the risk of fatty liver development. |
| 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) | raw(Thermo) |
| Analysis Type Detail | LC-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: | SU003060 |
| 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 |
|---|---|---|
| SA320898 | CG3 | Cgref1-knockout |
| SA320899 | CG2 | Cgref1-knockout |
| SA320900 | CG1 | Cgref1-knockout |
| SA320901 | WT2 | Wild-type |
| SA320902 | WT3 | Wild-type |
| SA320903 | WT1 | Wild-type |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO003053 |
| 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: | untargeted_protocol.pdf |
| Sample Type: | Liver |
| Storage Conditions: | On ice |
Treatment:
| Treatment ID: | TR003069 |
| Treatment Summary: | Samples did not receive any treatment. |
Sample Preparation:
| Sampleprep ID: | SP003066 |
| Sampleprep Summary: | As described in the provided protocol (see attached file): - "2mL chloroform:methanol (2:1, v/v) was added to user provided tissue. The sample was then sonicated under ice chilled probe sonicator for 20 sec, cooled down for 10 sec and another sonication for 20 sec. The sample was then centrifuged at 3000 g for 5 min. Supernatant was aliquot out and dried under nitrogen.The sample was then reconstituted with IPA:MeOH:chloroform (1:1:0.2, v/v) in 1mg to 5uL. Then, 3 μL was injected into the LC-MS/MS system." |
| Sampleprep Protocol Filename: | untargeted_protocol.pdf |
Combined analysis:
| Analysis ID | AN004832 | AN004833 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C30 (150 x 2.1mm,2.6um) | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Orbitrap Exploris 120 | Orbitrap Exploris 120 |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak Area | Peak Area |
Chromatography:
| Chromatography ID: | CH003652 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| Column Temperature: | 45°C |
| Flow Gradient: | The gradient started at 30% B and was increased to 43% B in 2 min, then increased to 55% B in 2.1 min, 65 % B in 12 min, 85% B in 18 min and 100 % B in 20 min, then held for 5min, and decreased linearly to 30% B for re-equilibration time at starting conditions. |
| Flow Rate: | 0.26 mL min−1 |
| Solvent A: | 10mM ammonium formate with 0.1% formic acid in acetonitrile and water, v/v 6:4 |
| Solvent B: | 10mM ammonium formate with 0.1% formic acid in acetonitrile and IPA 1:9 |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004578 |
| Analysis ID: | AN004832 |
| Instrument Name: | Orbitrap Exploris 120 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometry analysis was processed using an Orbitrap Exploris 120 mass spectrometer Thermo Fisher (Waltham, MA, USA) equipped with a HESI II probe in polar switching mode with source parameters set as follows: sheath gas flow rate, 60; auxiliary gas flow rate, 17; sweep gas flow rate, 1; spray voltage,+3.5/-3.0 kV; capillary temperature, 275 oC; S-lens RF level, 70; and heater temperature, 325 °C. Data was collected at dd-MS2 mode. Data analysis was performed using Lipidsearch (Thermofisher Scientific/Mitsui Knowledge Industries) with the default parameters for Orbitrap MS Product Search and Alignment. After alignment, raw peak areas for all identified lipids were exported to Excel files. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004579 |
| Analysis ID: | AN004833 |
| Instrument Name: | Orbitrap Exploris 120 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometry analysis was processed using an Orbitrap Exploris 120 mass spectrometer Thermo Fisher (Waltham, MA, USA) equipped with a HESI II probe in polar switching mode with source parameters set as follows: sheath gas flow rate, 60; auxiliary gas flow rate, 17; sweep gas flow rate, 1; spray voltage,+3.5/-3.0 kV; capillary temperature, 275 oC; S-lens RF level, 70; and heater temperature, 325 °C. Data was collected at dd-MS2 mode. Data analysis was performed using Lipidsearch (Thermofisher Scientific/Mitsui Knowledge Industries) with the default parameters for Orbitrap MS Product Search and Alignment. After alignment, raw peak areas for all identified lipids were exported to Excel files. |
| Ion Mode: | NEGATIVE |
