Figure S5.
Untargeted lipidomics data of other lipid species from APOE knockdown and APOE3 versus APOE4 experiments. (A) Comparison of the total abundance of other major lipid classes between non-targeting (NT) and APOE knockdown (KD) cells at each timepoint. Lipidomics data were collected from two independently performed experiments which each used three separate plates of cells as technical replicates. Each data point denotes a single technical replicate, and the dot colors indicate data collected from the same independently performed experiment. There is no significant difference in the total abundance of any other major lipid classes between NT and APOE KD at any timepoint. ns P > 0.05. P values were calculated using the Wilcox rank sum test and Bonferonni-corrected for multiple comparisons. ChE, cholesterol ester; DG, diacylglycerol; PC, phosphatidyl choline; PE, phosphatidyl ethanolamine; PG, phosphatidylglycerol; PI, phosphatidylinositol. (B) Heatmap of the abundance of phosphatidylethanolamine (PE) species in NT versus APOE KD cells separated by their degree of unsaturation at each timepoint of the assay. Heatmap values are derived from the means of three technical replicates from two independently performed experiments (shown as separate columns) for each condition. Means were grouped by lipid class and Z-score normalized. (C) Comparison of the total abundance of other major lipid classes between APOE3 and APOE4 cells at each timepoint. Lipidomics data were collected from two independently performed experiments which each used three separate plates of cells as technical replicates. Each data point denotes a single technical replicate, and the dot colors indicate data collected from the same independently performed experiment. Other than TG, there is no significant difference in the total abundance of any major classes between E3 and E4 at any timepoint. (D) Heatmap of the abundance of PE species in E3 versus E4 cells separated by their degree of unsaturation at each timepoint of the assay. Heatmap values were derived from the means of three technical replicates from two independently performed experiments (shown as separate columns) for each condition. Means were grouped by lipid class and Z-score normalized. The red box frames lipid species enriched in E3.

Untargeted lipidomics data of other lipid species from APOE knockdown and APOE3 versus APOE4 experiments. (A) Comparison of the total abundance of other major lipid classes between non-targeting (NT) and APOE knockdown (KD) cells at each timepoint. Lipidomics data were collected from two independently performed experiments which each used three separate plates of cells as technical replicates. Each data point denotes a single technical replicate, and the dot colors indicate data collected from the same independently performed experiment. There is no significant difference in the total abundance of any other major lipid classes between NT and APOE KD at any timepoint. ns P > 0.05. P values were calculated using the Wilcox rank sum test and Bonferonni-corrected for multiple comparisons. ChE, cholesterol ester; DG, diacylglycerol; PC, phosphatidyl choline; PE, phosphatidyl ethanolamine; PG, phosphatidylglycerol; PI, phosphatidylinositol. (B) Heatmap of the abundance of phosphatidylethanolamine (PE) species in NT versus APOE KD cells separated by their degree of unsaturation at each timepoint of the assay. Heatmap values are derived from the means of three technical replicates from two independently performed experiments (shown as separate columns) for each condition. Means were grouped by lipid class and Z-score normalized. (C) Comparison of the total abundance of other major lipid classes between APOE3 and APOE4 cells at each timepoint. Lipidomics data were collected from two independently performed experiments which each used three separate plates of cells as technical replicates. Each data point denotes a single technical replicate, and the dot colors indicate data collected from the same independently performed experiment. Other than TG, there is no significant difference in the total abundance of any major classes between E3 and E4 at any timepoint. (D) Heatmap of the abundance of PE species in E3 versus E4 cells separated by their degree of unsaturation at each timepoint of the assay. Heatmap values were derived from the means of three technical replicates from two independently performed experiments (shown as separate columns) for each condition. Means were grouped by lipid class and Z-score normalized. The red box frames lipid species enriched in E3.

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