Extended Data Fig. 2: Comparative proteomic analysis of WT and Padi6^Null oocytes.

(a) Venn diagram illustrating the overlap and unique proteins identified in WT and Padi6^Null oocytes. (b) Principal component analysis (PCA) of proteomic profiles demonstrates clear clustering of WT (blue) and Padi6^Null (red) oocytes. (c) Bar plot illustrating the number of significantly upregulated (blue) and downregulated (red) proteins in Padi6^Null oocytes compared to WT. Differential expression was assessed using an unpaired Student’s t-test (two-sided). Proteins with log2 (fold change) > 0.5 or log2 (fold change) < −0.5 and P < 0.05 were considered significantly upregulated or downregulated, respectively. (d) Volcano plot illustrating the differentially expressed proteins in Padi6^Null compared to WT oocytes. Differential expression was assessed using an unpaired Student’s t-test (two-sided); proteins meeting log2 (fold change) > 0.5 or log2 (fold change) < −0.5 with P < 0.05 were highlighted as significantly upregulated (blue) or downregulated (red), respectively. Key proteins are labeled as indicated. (e-g) Venn diagrams showing the overlap of quantified proteins (e), downregulated proteins (f), and upregulated proteins (g) in Padi6^Null oocytes between this study (MII stage) and Jentoft et al. (GV stage). (h) Scatter plot comparing fold changes of differentially expressed proteins from the MII stage in the GV stage. Proteins are categorized as showing consistent or inconsistent trends, and as significant or insignificant in the GV stage. (i, j) GO molecular function enrichment analysis of downregulated (i) and upregulated (j) proteins in Padi6^Null oocytes at the MII stage (this study, red) and GV stage (Jentoft et al., blue). GO enrichment was performed using clusterProfiler::enrichGO (hypergeometric test), with P < 0.05 as the significance threshold. No adjustments for multiple comparisons were applied. (k) Heatmap showing the expression of shared downregulated proteins between MII- and GV-stage Padi6^Null oocytes. (l) GO molecular function enrichment analysis of shared downregulated proteins between the MII and GV stages. GO enrichment was performed using clusterProfiler::enrichGO (hypergeometric test), with P < 0.05 as the significance threshold. No adjustments for multiple comparisons were applied.