Summary of Study ST000241
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 PR000194. The data can be accessed directly via it's Project DOI: 10.21228/M89W2D 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.
Download additional data: Pos mode data | Neg mode data
| Study ID | ST000241 |
| Study Title | Cyclobutene- and cyclobutane-functionalized fatty acids as novel biochemical probes of structure and function in HepG2 cells |
| Study Type | Lipid analysis novel C18 fatty acid anologues in complex lipids |
| Study Summary | Human hepatoma HepG2 cells (American Type Culture Collection; HB-8065) were grown in 75 ml tissue cell culture flasks in Eagle's minimal essential medium (EMEM) augmented with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO2. For treatment with fatty acids or analogues, the cells were seeded at a density of 2 × 106 cells in a T25-cm2 flask for 24 h. Each FA or analogue was added to the culture medium as a fatty acid-bovine serum albumin (BSA) complex (2.5:1, FA:BSA) to give the desired final concentration. The controls in these experiments were HepG2 cells with BSA alone. After 24 h treatment, the media was collected, cells were rinsed twice with PBS and cells were harvested for analysis. To each cell suspension prior to lipid extraction a standard mixture of 25 µg C15:0 PE, C17:0 PC and C71:1 TAG was added as standards. Extraction of lipids was performed according to the Folch method. For metabolomics analysis, the lipid extracts were resuspended in chloroform/methanol, 2:1 (v/v).All analyses were carried out using an Agilent 1200 Series HPLC, ACE 5 C8-300 column (2.1 x 100 mm) and linear gradient elution at a flow rate of 0.1 mL/min. Mobile phase A and B consisted of 0.1% formic acid; 10 mM ammonium acetate in H2O and 0.1% formic acid; 10 mM ammonium acetate in ACN/isopropanol (50/50; v/v), respectively. The injection volume was 4 µL. Separation of metabolites was achieved at the following gradient: T=0 min: 30% B; T=1 min: 30% B; T=25 min: 100% B; T=45 min: 100% B; T=47 min: 30% B; and T=60 min: 30% B (re-equilibration). The HPLC system was directly coupled to a Bruker Soalrix 70 Hybrid FTMS instrument equipped with electrospray ionization source (ESI) (Bruker Daltonics). The system was controlled by HyStar v.3.4.8.0 software. MS data was collected with resolving power of 78,000 (at m/z 400) in positive or negative mode under following conditions: a capillary voltage of (+/-) 4,500 V and an end plate offset of -500 V. The dry temperature was set at 180°C. Dry gas flow was maintained 4 L/min. Acquisition range was 244-1,800 m/z with 0.2 s ion accumulation time. LC-MS data was converted into mzXML format using CompassXport v. 3.0.6 and processed by mzMine v.2.10 [25] or XCMS data analysis software. Data processing involved mass detection, chromatographic peak detection and deconvolution, isotopic peaks grouping, normalization and peak alignment. Metabolite data were mean-centered and unit-variance scaled to remove the offsets and adjust the importance of high and low abundance metabolites to an equal level. Significantly altered metabolites were defined by a fold change (FC) >2 and p<0.05. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) of signature metabolites altered in compounds treated cells compared to control were performed in the Metaboanalyst web portal (www.metaboanalyst.ca). |
| Institute | University of Nebraska-Lincoln |
| Department | Biochemistry |
| Laboratory | DiRusso Black FATTT Lab |
| Last Name | DiRusso |
| First Name | Concetta |
| Address | Department of Biochemistry, University of Nebraska-Lincoln, N241 Beadle Center 1901 Vine St. |
| cdirusso2@unl.edu | |
| Phone | 402-472-6504 or 402-613-9293 |
| Submit Date | 2015-09-09 |
| Num Groups | 8 |
| Total Subjects | 24+24=48 |
| Study Comments | 8 groups in triplicate ran in both negative and positive mode |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2017-07-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN000373 | AN000374 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1200 | Agilent 1200 |
| Column | ACE 5 C8-300 (100 x 2.1mm) | ACE 5 C8-300 (100 x 2.1mm) |
| MS Type | ESI | ESI |
| MS instrument type | FT-ICR-MS | FT-ICR-MS |
| MS instrument name | Bruker SolariX FT-ICR-MS | Bruker SolariX FT-ICR-MS |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH000270 |
| Methods Filename: | jac8lipidneg.m |
| Chromatography Comments: | jalcms1lipneg.m |
| Instrument Name: | Agilent 1200 |
| Column Name: | ACE 5 C8-300 (100 x 2.1mm) |
| Flow Rate: | 0.1 mL/min |
| Internal Standard: | 25 g C15:0 PE, C17:0 PC and C71:1 TAG |
| Solvent A: | 100% water; 0.1% acetic acid; 2 mM ammonium acetate |
| Solvent B: | 50% acetonitrile/50% isopropanol; 0.1% formic acid; 10 mM ammonium acetate |
| Analytical Time: | 60 min |
| Chromatography Type: | Reversed phase |
