Figure 1.

Lipidome overview in isogenic control and E12-KO H1299 cells. (A). Schematic of lipidomic and metabolomic analysis workflow in isogenic control and E12^−/− H1299 cells. (B). Class-level overview of metabolites annotated by LC-MS/MS and GC-MS analysis in isogenic control and E12^−/− H1299 cells. 897 individual metabolites were identified using accurate mass and in-silico libraries (top). Number of metabolites in each class are indicated in the parentheses (bottom). Classes with less than 10 identified lipids or metabolites were grouped together and denoted “Other (lipids)” or “Other (primary metabolites)”. (C). Principal component analysis (PCA) of isogenic control, E12^−/− H1299 cells and pooled quality control samples. (D). Volcano plot of isogenic control compared to E12^−/− H1299 cells. Up indicates lipids and metabolites higher in isogenic control cells. (E). Chemical similar enrichment analysis (ChemRICH) of all lipids identified in isogenic control and E12^−/− H1299 cells. Y-axis represents statistical significance assessed by Kolmogorov-Smirnov test and node size represents total number of lipids per cluster. Classes with less than 10 identified lipids were grouped together and denoted “Other”. TG: triacylglycerols; PC: phosphatidylcholines; CER: ceramides; CL: cardiolipins; FA: fatty acids; DG: diacylglycerols; LPE: lysophosphatidylethanolamines; LPC: lysophosphatidylcholines; PE: phosphatidylethanolamines; PI: phosphatidylinositols; PG: phosphatidylglycerols; PS: phosphatidylserines; SM: sphingomyelins. (F). Heatmap of all annotated lipids clustered by class in isogenic control and E12^−/− H1299 cells. Color intensity indicates z-score values of peak heights. CER: ceramides; CL: cardiolipins; DG: diacylglycerols; FA: fatty acids; LPC: lysophosphatidylcholines; LPE: lysophosphatidylethanolamines; PC: phosphatidylcholines; PE: phosphatidylethanolamines; PG: phosphatidylglycerols; PI: phosphatidylinositols; PS: phosphatidylserines; SM: sphingomyelins; TG: triacylglycerols.