Summary of Study ST003191

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 PR001987. The data can be accessed directly via it's Project DOI: 10.21228/M8WB25 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.

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Study IDST003191
Study TitleFructose 1,6-bisphosphate quantification in HepG2 liver cancer cell line.
Study TypeLC/MS Quantitative Analysis
Study SummaryQuantification of specific fructose 1,6-bisphosphate (FBP) concentrations in HepG2 cells. A minimum of 1 million cells per replicate and condition will be grown and treated. Glucose-starved cells will be either treated with 10 mM glucose, 2.5 μM Oligomycin, 50 mM 2-deoxy-D-glucose (2-DG), or not treated. Cells will be lysed and processed for FBP quantification using an isotope FBP standard by LC/MS.
Institute
Vrije Universiteit Brussel
DepartmentVIB-VUB Center for Structural Biology
LaboratoryRedOx Laboratory
Last NamePerez Chavez
First NameIsrael
AddressPleinlaan 2, building E, 4th floor
Emailisrael.perez.chavez@vub.be
Phone+32 474160756
Submit Date2024-05-04
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-08-05
Release Version1
Israel Perez Chavez Israel Perez Chavez
https://dx.doi.org/10.21228/M8WB25
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001987
Project DOI:doi: 10.21228/M8WB25
Project Title:Fructose 1,6-bisphosphate quantification in HepG2 liver cancer cell line
Project Type:LC/MS Quantitative Analysis
Project Summary:Quantification of specific fructose 1,6-bisphosphate (FBP) concentrations in HepG2 cells. A minimum of 1 million cells per replicate and condition will be grown and treated. Glucose-starved cells will be either treated with 10 mM glucose, 2.5 μM Oligomycin, 50 mM 2-deoxy-D-glucose (2-DG), or not treated. Cells will be lysed and processed for FBP quantification using an isotope FBP standard by LC/MS.
Institute:Vrije Universiteit Brussel
Department:VIB-VUB Center for Structural Biology
Laboratory:RedOx Laboratory
Last Name:Perez Chavez
First Name:Israel
Address:Boulevard de la Plaine 2
Email:israel.perez.chavez@vub.be
Phone:+32 474160756

Subject:

Subject ID:SU003310
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male
Cell Strain Details:HepG2 Cells

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Treatment
SA347888MCF001881_IP04Liver Cancer Cell Line 10 mM Glucose
SA347889MCF001881_IP06Liver Cancer Cell Line 10 mM Glucose
SA347890MCF001881_IP05Liver Cancer Cell Line 10 mM Glucose
SA347891MCF001881_IP09Liver Cancer Cell Line 2.5 µM Oligomycin
SA347892MCF001881_IP08Liver Cancer Cell Line 2.5 µM Oligomycin
SA347893MCF001881_IP07Liver Cancer Cell Line 2.5 µM Oligomycin
SA347894MCF001881_IP12Liver Cancer Cell Line 50 mM 2-Deoxy-D-Glucose
SA347895MCF001881_IP11Liver Cancer Cell Line 50 mM 2-Deoxy-D-Glucose
SA347896MCF001881_IP10Liver Cancer Cell Line 50 mM 2-Deoxy-D-Glucose
SA347897MCF001881_IP02Liver Cancer Cell Line Control
SA347898MCF001881_IP03Liver Cancer Cell Line Control
SA347899MCF001881_IP01Liver Cancer Cell Line Control
Showing results 1 to 12 of 12

Collection:

Collection ID:CO003303
Collection Summary:Cells were trypsinized, washed, counted, centrifuged, resuspended in extraction buffer, centrifuged, and the supernatant stored at -80°C.
Collection Protocol Filename:FBPquantificationMethod.pdf
Sample Type:HepG2 cells

Treatment:

Treatment ID:TR003319
Treatment Summary:Cells were glucose starved for 1 h. Then, it involved the addition of 10 mM glucose, 2.5 μM of oligomycin, and 50 mM of 2-DG.

Sample Preparation:

Sampleprep ID:SP003317
Sampleprep Summary:The cell pellet was resuspended in 100 µL of extraction buffer (80% Methanol/20% mQ water + 2 µM Fructose-1,6-bisphosphate (U-¹³C₆). Cells were then incubated for 3 min on ice and then spun at 20.000 x g 4°C for 20 min. The supernatant was collected and stored at -80°C until metabolomics analysis. This procedure was performed in control, after glucose addition, oligomycin and 2-DG addition.

Combined analysis:

Analysis ID AN005239
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000
Column Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode NEGATIVE
Units µM

Chromatography:

Chromatography ID:CH003966
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:40℃
Flow Gradient:0-13 min: 0% B; 13-14 min: 33.33% B; 14-25 min: 36.4% B
Flow Rate:0.25 mL/min
Solvent A:95% milliQ Water, 5% Methanol; 10 mM Tertiary Butyl Alcohol and 15 mM acetic acid
Solvent B:100% methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS004972
Analysis ID:AN005239
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The mass spectrometer operated in full scan (range [70.0000-1050.0000]) and AGC target was set at 3.0E+006 using a resolution of 140000. Data collection was performed using the Xcalibur software (Thermo Scientific). The data analyses were performed by integrating the peak areas (El-Maven – Polly - Elucidata).
Ion Mode:NEGATIVE
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