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.
| Study ID | ST003191 |
| Study Title | Fructose 1,6-bisphosphate quantification in HepG2 liver cancer cell line. |
| Study Type | LC/MS Quantitative Analysis |
| Study 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 | Pleinlaan 2, building E, 4th floor |
| israel.perez.chavez@vub.be | |
| Phone | +32 474160756 |
| Submit Date | 2024-05-04 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-05 |
| Release Version | 1 |
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 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA347888 | MCF001881_IP04 | 10 mM Glucose |
| SA347889 | MCF001881_IP06 | 10 mM Glucose |
| SA347890 | MCF001881_IP05 | 10 mM Glucose |
| SA347891 | MCF001881_IP09 | 2.5 µM Oligomycin |
| SA347892 | MCF001881_IP08 | 2.5 µM Oligomycin |
| SA347893 | MCF001881_IP07 | 2.5 µM Oligomycin |
| SA347894 | MCF001881_IP12 | 50 mM 2-Deoxy-D-Glucose |
| SA347895 | MCF001881_IP11 | 50 mM 2-Deoxy-D-Glucose |
| SA347896 | MCF001881_IP10 | 50 mM 2-Deoxy-D-Glucose |
| SA347897 | MCF001881_IP02 | Control |
| SA347898 | MCF001881_IP03 | Control |
| SA347899 | MCF001881_IP01 | 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. |
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 |
Analysis:
| Analysis ID: | AN005239 |
| Analysis Type: | MS |
| Chromatography ID: | CH003966 |
| Num Factors: | 4 |
| Num Metabolites: | 1 |
| Units: | µM |
