Fig. 1

Transcriptome changes during NSN to SN transition. A PCA plot of scRNA-seq data of oocytes classified as NSN, SN or intermediate based on Hoechst staining. Symbol shape indicates the mouse from which the oocyte was collected. The density of NSN and SN oocyte distributions in PC1 and PC2 is also shown. The plot demonstrates that chromatin configuration is the main source of variation (PC1, 36%). B Scatterplot showing the total number of transcripts detected in each NSN and SN oocyte as a function of library read depth. Dots represent individual oocytes. A gene was considered to be expressed if it had at least 1 transcript count in any of the NSN or SN oocytes. SN oocytes express significantly fewer transcripts compared to NSN oocytes of comparable sequencing depths (when considering oocytes between the two dashed red lines; Wilcoxon P = 0.0012). C Barchart showing that genes not expressed in SN oocytes (SN missing) are lowly expressed in NSN oocytes (expression quartiles Q1 and Q2) compared to random genes, which are equally distributed among all NSN expression quartiles (Chi square p < 0.0001). Expression quartiles were determined based on all oocyte transcripts expressed in NSN oocytes. D Volcano plot showing differential expression between NSN and SN oocytes. Indicated are the log₂ shrunken fold change (LFC) and the -log₁₀ adjusted P-value (-log₁₀ Padj). Each dot represents an oocyte transcript. Differentially expressed genes (DEGs) are highlighted in blue (down) or red (up). The dashed lines indicate the LFC > |1| and Padj < 0.05 cut-offs used to further select the DEGs for downstream analysis. E Dot plot showing gene ontology results for biological processes of downregulated DEGs with LFC < -1. The size of the dots indicates the number of DEGs enriched for a category and the colour signifies the adjusted P-value (Padj). The x-axis shows the ratio of DEGs enriched for a certain category