Comparative analysis of protein aggregates isolated from SETX-depleted U2OS and differentiated SH-SY5Y cells. (A) Spearman correlation coefficients for shControl and shSETX pellet values normalized by lysates (three biological replicates each); 1,580 proteins present in all samples. See Table S1. (B) Enriched Gene Ontology groups are shown from analysis of significantly aggregated proteins in U2OS cells with the number of proteins and FDR values in parentheses. (C) Enriched Gene Ontology groups and fold enrichment of proteins identified in aggregates from SETX-depleted SH-SY5Y cells as in B, number of genes and FDR values in parentheses. (D and E) Aggregates and total lysates from three replicates of SETX shRNA depletion were analyzed by mass spectrometry. Aggregate values (normalized by lysate, log₂ transformed) for each protein (mean of three replicates) were plotted: (D) SETX-depleted cells (X axis) versus ATM shRNA-treated cells (Y axis) (Lee et al., 2021), 310 proteins, Spearman correlation coefficient = 0.51; (E) Mre11-depleted cells (X axis) versus ATM shRNA-treated cells (Y axis) (Lee et al., 2021), 1,424 proteins, Spearman correlation coefficient = 0.978. (F) SETX-depleted cells (X axis) versus insoluble protein log₂ fold change in ATM KO U2OS cells (Huiting et al., 2022) (Y axis), 1,044 proteins, Spearman correlation coefficient = 0.002. (G) SETX-depleted cells (X axis) versus insoluble protein log₂ fold change in CPT-treated U2OS cells (Huiting et al., 2022) (Y axis), 818 proteins, Spearman correlation coefficient = 0.01. For each comparison, only proteins with measurements in both datasets are plotted.