Additional file 4 of Single-cell profiling reveals transcriptome dynamics during bovine oocyte growth

Additional file 4: Supplementary Tables. Table S1. Sample quality control analysis performed in Rstudio by selecting samples with more than 100,000 reads and 2,500 expressed genes (genes with more than 1 count). In addition, filtering for contamination with mitochondrial DNA was also performed. Additional information is from MuitQC Report. The table on the right summarizes the information by experimental groups. Table S2. Common and unique expressed genes (more than 1 count) in each oocyte size group. Enriched pathways from gene ontology analysis are shown in the panel on the right. Table S3. Common and unique lowly expressed genes (zero count in at least half of the samples for each group) in each oocyte size group. Enriched pathways from gene ontology analysis are shown in the panel on the right. Table S4. Top-100 highly expressed genes on each oocyte size group. Enriched pathways from gene ontology analysis are shown in the panels on the right. Table S5. Common and unique Top-100 highly expressed genes in each oocyte size group. Enriched pathways from gene ontology analysis are shown in the panel on the right. Table S6: Summary table of WGCNA output. GS/p.GS: gene significance for oocyte size and related p-value. The higher the absolute value, the more biologically relevant to oocyte size. MM/p.MM: Module membership and related p value. Correlation value of each gene related to gene expression profile in a module. Table S7. Trendy analysis output table to identify changes in gene expression of specific genes. Segment slope measures the rate of change of the data within that segment. The segment trend defines how the expression of each gene changes inside that segment. 1 = increase; -1 = decrease; 0/NA = no change. The p-value will indicate if the change is significant (<0.05). Breakpoints indicate the oocyte diameter at which gene expression is changing. Only the top dynamic genes are shown, defined as those whose optimal model has a high adjusted R2 (>0.5). Table S8. Differentially expressed genes between <70 and 70-79 um in diameter oocytes (up and downregulated). Significant genes were determined by FDR<0.05. Enriched pathways from gene ontology analysis are presented in the panels on the right. Table S9. Differentially expressed genes between 70-79 and 80-99 um in diameter oocytes (up and downregulated). Significant genes were determined by FDR<0.05. Enriched pathways from gene ontology analysis are presented in the panel on the right. Table S10. Differentially expressed genes between 80-89 and 100-109 um in diameter oocytes (up and downregulated). Significant genes were determined by FDR<0.05. Enriched pathways from gene ontology analysis are presented in the panels on the right. Table S11. Differencial expressed genes between 100-109 and 110-119 um in diameter oocytes (up and downregulated). Significant genes were determined by FDR<0.05. The panels on the right are showing all the enriched pathways from gene ontology analysis. Table S12. Differential expressed genes between 110-119 and >120 um in diameter oocytes (up and downregulated). Significant genes were determined by FDR<0.05. Enriched pathways from gene ontology analysis are presented in the panel on the right. Table S13. Genes with stable expression across the bovine oocyte growth phase. Respective enriched pathways are listed in the table on the right.