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.

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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 IDST002947
Study TitleHepatic lipid profiles of wild type and Cgref1-depleted mice of C57BL/6 strain obtained by an untargeted LC-MS/MS analysis
Study SummaryAmong 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
DepartmentSchool of Biomedical Sciences
LaboratoryL3-53
Last NameChan
First NamePearl
Address21 Sassoon Road, Pokfulam, Hong Kong
Emailpearl20@connect.hku.hk
Phone+85239176812
Submit Date2023-10-26
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-10-28
Release Version1
Pearl Chan Pearl Chan
https://dx.doi.org/10.21228/M8X144
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA320898CG3Cgref1-knockout
SA320899CG2Cgref1-knockout
SA320900CG1Cgref1-knockout
SA320901WT2Wild-type
SA320902WT3Wild-type
SA320903WT1Wild-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
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