Additional file 1 of Dysregulated lipid metabolism in a retinal pigment epithelial cell model and serum of patients with age-related macular degeneration
Creators: name: Álvarez-Barrios, Ana
name: Álvarez, Lydia
name: Sáenz de Santa María, Pilar
name: García, Montserrat
name: Álvarez-Buylla, Jorge R.
name: Pereiro, Rosario
name: González-Iglesias, Héctor
Publisher: name: figshare
Year: 2025
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 1: Supporting information. Table S1 Enriched biological processes with time in culture. SCGs identified in RPE cell cultures through linear or quadratic regression models were compared to genes annotated to GO biological processes database using ShinyGO 0.81. Statistical significance was monitored as false discovery rate (FDR) and adjusted for multiple comparisons through Benjamini–Hochberg method. The analyses included data from three biological replicates of cell cultures at 4, 12, and 17 weeks, as well as two additional replicates at 25 weeks. Fig. S1 Enrichment of biological processes according to GO database between 4, 12, 17, and 25 weeks’ comparisons. Bubble chart of the 20 most significantly enriched biological processes when comparing (A) 4 weeks (n = 3) vs 12 weeks (n = 3), (B) 4 weeks (n = 3) vs 17 weeks (n = 3), (C) 12 weeks (n = 3) vs 17 weeks (n = 3), (D) 12 weeks (n = 3) vs 25 weeks (n = 2), and (E) 17 weeks (n = 3) vs 25 weeks (n = 2). Each process is represented by a bubble and indicated in the Y-axis. The size of the bubble shows the number of DEGs annotated to that GO term and its color, the significance of its enrichment (q value). X-axis represents the enrichment ratio of each process (ratio between the number of DEGs annotated to the GO term and the total number of genes annotated to that GO term). Fig. S2 Expression of RPE-specific genes over time. (A) DEGs identified between 4 (n = 3), 12 (n = 3), 17 (n = 3), and 25 (n = 2) time points. Fold-changes and statistical significance were obtained by DESeq2 method. ns: q value &gt; 0.05; *: q value &lt; 0.05; **: q value &lt; 0.01; ***: q value &lt; 0.001. (B) SCGs identified through linear and quadratic regression models. Equation of the regression curve is shown together with the associated coefficient of determination (R2) and p value adjusted by Benjamini–Hochberg method. Fig. S3 Heatmap of hierarchical clustering analysis of differential molecular features in 25-week-old (n = 3 biological replicates, each measured 3 times) RPE cells versus 4- (n = 3 biological replicates, each measured 3 times), 12- (n = 3 biological replicates, each measured 3 times), and 17-week-old (n = 3 biological replicates, each measured 3 times) cells, (A) in positive ionization mode and, (B) in negative ionization mode. Significantly different compounds were identified using the Kruskal–Wallis test with Benjamini–Hochberg correction (adjusted p value &lt; 0.05 and fold-change &gt; 2).