Fig. 2

Transcriptome analysis during human fetal ovary development. (a) Principal component analysis of all 47 tissue samples included in this study (19 ovaries, 20 testes, 8 controls). The plot shows individual samples positioned according to the first and second principal components. RNA was extracted from each individual sample and RNA sequencing undertaken without pooling. Individual samples were grouped together as described for bioinformatic analysis. CS, Carnegie stage; PC, principal component; wpc, weeks post conception. (b) Overlay between three differential gene expression analyses: ovary v control (data from all stages combined); testis v control (data from all stages combined); ovary v testis (data from all stages combined)(log₂FC > 2, p.adj < 0.05). The total numbers of positively differentially-expressed genes (DEGs) are shown above the Venn diagrams. Total numbers and names of the top ten genes within the ovary-specific (red), testis-specific (green), gonad-specific (violet), and highly ovary-specific (pink) DEGsets are shown within the Venn diagram. “Highly ovary-specific” refers to DEGset in both the ovary v control and ovary v testes datasets. The top ten differentially expressed genes within the gonad-specific and highly ovary-specific genesets are shown in boxes. (c) Volcano plots demonstrating four differential gene expression analyses comparing ovary v testis samples at CS22/23 (both n = 5), 9/10wpc (both n = 5), 11/12wpc (both n = 5), 15/16wpc (ovary n = 4, testis n = 5). Each dot represents a single gene. Genes that were differentially expressed with a log₂FC > 2 and p.adj < 0.05 are coloured cyan; those coloured red did not meet these significance thresholds. A max value of log₁₀(p.adj) is displayed on the y-axis of the graph. Total numbers of positively and negatively DEGs are shown in violet. Gene names of the top ten positively and negatively DEGs across each developmental timepoint are displayed, based on log₂FC. (d) Heatmap showing normalized gene expression values for the top 30 differentially expressed highly ovary-specific genes identified in (b) across the entire count matrix. Genes are ordered according to descending log₂FC values. Samples are ordered according to tissue and stage (supervised). A color scale represents gene expression intensity (violet, lowest; yellow, neutral; red, highest). A p.adj value of < 0.05 was used throughout this analysis.