Lipidomic data uncover extensive heterogeneity in phosphatidylcholine structural variants in HepG2 cells

Abstract

The data contain information related to the research article entitled "Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNF alpha response in human hepatoma cells" (DOI: 10.1093/nar/gkv858). In the article alluded to, we reported that tumor necrosis factor alpha (TNF alpha) increases notably the cellular content of the major glycerolipid phosphatidylcholine (PC). Here, accompanying lipidomic data determine the PC structural variants that have been identified in human hepatoma HepG2 cells and those whose relative abundance is modified by TNF alpha. We used ultrahigh performance liquid chromatography (UHPLC) coupled to electrospray ionization (ESI) tandem mass spectrometry (MS/MS)-based lipidomic profiling to analyze lipid extracts of control and TNF alpha-treated HepG2 cells. The identity of PC individual species was elucidated using the values of the retention time and molecular weight in addition to the fragmentation patterns. MS data were then processed and analyzed for the characterization of statistically significant differences in detected structural variants. We have annotated the dataset of PC species that characterize HepG2 cells' phenotype, both under normal and pro-inflammatory conditions.