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.

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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 IDST003452
Study TitleIntegrated Proteomic and Lipidomic Analysis
Study SummaryGNB1 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 NameKitamoto
First NameTakuya
Address1-20-1 Handayama, Chuo-ku, Hamamatsu 431-3192, Japan
Emailt.ktmt@hama-med.ac.jp
Phone+81-53-435-2987
Submit Date2024-08-05
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-12-27
Release Version1
Takuya Kitamoto Takuya Kitamoto
https://dx.doi.org/10.21228/M8T52T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA380956lipidome_GNB1_3Human subcutaneous adipocytes GNB1
SA380957proteome_GNB1_1Human subcutaneous adipocytes GNB1
SA380958proteome_GNB1_2Human subcutaneous adipocytes GNB1
SA380959proteome_GNB1_3Human subcutaneous adipocytes GNB1
SA380960lipidome_GNB1_2Human subcutaneous adipocytes GNB1
SA380961lipidome_GNB1_1Human subcutaneous adipocytes GNB1
SA380962lipidome_nc_2Human subcutaneous adipocytes Negative Control
SA380963lipidome_nc_3Human subcutaneous adipocytes Negative Control
SA380964proteome_nc_1Human subcutaneous adipocytes Negative Control
SA380965proteome_nc_2Human subcutaneous adipocytes Negative Control
SA380966proteome_nc_3Human subcutaneous adipocytes Negative Control
SA380967lipidome_nc_1Human subcutaneous adipocytes Negative Control
SA380968proteome_SCARB2_3Human subcutaneous adipocytes SCARB2
SA380969proteome_SCARB2_2Human subcutaneous adipocytes SCARB2
SA380970proteome_SCARB2_1Human subcutaneous adipocytes SCARB2
SA380971lipidome_SCARB2_1Human subcutaneous adipocytes SCARB2
SA380972lipidome_SCARB2_2Human subcutaneous adipocytes SCARB2
SA380973lipidome_SCARB2_3Human 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
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