Summary of Study ST003452
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 PR002126. The data can be accessed directly via it's Project DOI: 10.21228/M8T52T 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 | ST003452 |
Study Title | Integrated Proteomic and Lipidomic Analysis |
Study Summary | GNB1 and SCARB2 genes were knocked down in human subcutaneous adipocytes using RNA interference. Both proteomic and lipidomic analyses were performed using mass spectrometry. The proteomic results revealed significant changes in the expression levels of key proteins involved in lipid metabolism and adipogenesis. The lipidomic analysis identified significant changes in lipid species, including phosphatidylcholines, ceramides, and cholesterol esters. This integrated analysis provides insights into the molecular pathways and lipid metabolism regulated by GNB1 and SCARB2 in adipocyte function. |
Institute | Hamamatsu University School of Medicine |
Last Name | Kitamoto |
First Name | Takuya |
Address | 1-20-1 Handayama, Chuo-ku, Hamamatsu 431-3192, Japan |
t.ktmt@hama-med.ac.jp | |
Phone | +81-53-435-2987 |
Submit Date | 2024-08-05 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2024-12-27 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR002126 |
Project DOI: | doi: 10.21228/M8T52T |
Project Title: | Integrative proteomic and lipidomic analysis of GNB1 and SCARB2 knockdown in human subcutaneous adipocytes |
Project Type: | Multi-omics (Proteomics and Lipidomics) |
Project Summary: | This project focuses on the knockdown of two candidate genes, GNB1 and SCARB2, identified through a comprehensive integration of genome-wide association studies (GWAS) related to BMI and proteomics data from previous studies using human subcutaneous adipocytes before and after fat accumulation. We aim to understand the regulatory roles of these genes in fat accumulation by performing an integrated analysis of changes in the proteome and lipidome using mass spectrometry following gene knockdown. |
Institute: | Hamamatsu University School of Medicine |
Last Name: | Kitamoto |
First Name: | Takuya |
Address: | 1-20-1 Handayama, Chuo-ku, Hamamatsu 431-3192, Japan |
Email: | t.ktmt@hama-med.ac.jp |
Phone: | +81-53-435-2987 |
Subject:
Subject ID: | SU003579 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 38 |
Gender: | Female |
Cell Biosource Or Supplier: | Zen-Bio, Inc. (Research Triangle Park, NC, USA) |
Subject Comments: | The cell line was derived from abdominal subcutaneous adipose tissue |
Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | Sample source | Gene Knockdown Target |
---|---|---|---|
SA380956 | lipidome_GNB1_3 | Human subcutaneous adipocytes | GNB1 |
SA380957 | proteome_GNB1_1 | Human subcutaneous adipocytes | GNB1 |
SA380958 | proteome_GNB1_2 | Human subcutaneous adipocytes | GNB1 |
SA380959 | proteome_GNB1_3 | Human subcutaneous adipocytes | GNB1 |
SA380960 | lipidome_GNB1_2 | Human subcutaneous adipocytes | GNB1 |
SA380961 | lipidome_GNB1_1 | Human subcutaneous adipocytes | GNB1 |
SA380962 | lipidome_nc_2 | Human subcutaneous adipocytes | Negative Control |
SA380963 | lipidome_nc_3 | Human subcutaneous adipocytes | Negative Control |
SA380964 | proteome_nc_1 | Human subcutaneous adipocytes | Negative Control |
SA380965 | proteome_nc_2 | Human subcutaneous adipocytes | Negative Control |
SA380966 | proteome_nc_3 | Human subcutaneous adipocytes | Negative Control |
SA380967 | lipidome_nc_1 | Human subcutaneous adipocytes | Negative Control |
SA380968 | proteome_SCARB2_3 | Human subcutaneous adipocytes | SCARB2 |
SA380969 | proteome_SCARB2_2 | Human subcutaneous adipocytes | SCARB2 |
SA380970 | proteome_SCARB2_1 | Human subcutaneous adipocytes | SCARB2 |
SA380971 | lipidome_SCARB2_1 | Human subcutaneous adipocytes | SCARB2 |
SA380972 | lipidome_SCARB2_2 | Human subcutaneous adipocytes | SCARB2 |
SA380973 | lipidome_SCARB2_3 | Human subcutaneous adipocytes | SCARB2 |
Showing results 1 to 18 of 18 |
Collection:
Collection ID: | CO003572 |
Collection Summary: | Primary cultured human preadipocytes were obtained from Zen-Bio, Inc., derived from the abdominal subcutaneous adipose tissue of a 38-year-old Caucasian woman. The cells were grown, differentiated, and collected as mature adipocytes on day 14. All experiments were performed in three independent replicates. |
Sample Type: | White adipose |
Treatment:
Treatment ID: | TR003588 |
Treatment Summary: | siRNA transfection was performed to knock down the expression of GNB1 and SCARB2 genes in differentiated human subcutaneous adipocytes. Three rounds of transfection were carried out over a period of 14 days. Following the final transfection, cells were harvested for both proteomic and lipidomic analyses. |
Sample Preparation:
Sampleprep ID: | SP003586 |
Sampleprep Summary: | Proteomics: Cells were lysed, proteins were extracted, and concentrations were determined using the BCA assay. Proteins were precipitated, reduced, alkylated, and digested with trypsin. Peptides were purified using a MonoSpin C18 column and analyzed using an EASY-nLC 1200 and a Q-Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific). Data were processed using Proteome Discoverer 2.2 software (Thermo Fisher Scientific). Lipidomics: Lipids were extracted using the Bligh and Dyer method, dissolved in methanol, and analyzed using an Ultimate 3000 and a Q-Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific). Data were processed using LipidSearch software version 5.1.9 (Thermo Fisher Scientific). |
Combined analysis:
Analysis ID | AN005668 | AN005669 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
Column | Thermo Acclaim (150 x 2.1mm, 3um) | Thermo Acclaim (150 x 2.1mm, 3um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE | NEGATIVE |
Units | Relative abundance (isotope normalized) | Relative abundance (isotope normalized) |
Chromatography:
Chromatography ID: | CH004305 |
Chromatography Summary: | HPLC lipidome analysis. C18 column (Acclaim 120 C18 column (3 μm, 2.1 mm × 150 mm), gradient elution with aqueous and organic solvents containing ammonium formate and formic acid. Flow rate: 300 μL/min, column at 50°C. 70-min gradient. Solvent A: 5 mM ammonium formate in water/methanol/acetonitrile (2:1:1) with 0.1% formic acid; Solvent B: 5 mM ammonium formate in isopropanol/acetonitrile (9:1) with 0.1% formic acid |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Thermo Acclaim (150 x 2.1mm, 3um) |
Column Temperature: | 50℃ |
Flow Gradient: | 20% to 100% B over 50 min, 100% B for 10 min, then return to 20% B |
Flow Rate: | 300 μL/min |
Solvent A: | 50% water/25% methanol/25% acetonitrile; 5 mM ammonium formate; 0.1% formic acid |
Solvent B: | 90% isopropanol/10% acetonitrile; 5 mM ammonium formate; 0.1% formic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS005392 |
Analysis ID: | AN005668 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | MS acquisition Comments: Full scan MS followed by data-dependent MS/MS Data processing Comments: Raw data processed using LipidSearch for lipidomics Software/procedures used for feature assignments: LipidSearch for lipid identification |
Ion Mode: | POSITIVE |
MS ID: | MS005393 |
Analysis ID: | AN005669 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | MS acquisition Comments: Full scan MS followed by data-dependent MS/MS Data processing Comments: Raw data processed using LipidSearch for lipidomics Software/procedures used for feature assignments: LipidSearch for lipid identification |
Ion Mode: | NEGATIVE |