Comparative Analysis of Ovarian Development

The NMR was then compared to publicly available mouse (Mus musculus) ovarian development RNAseq data^{45 (link)}. The fastq files for the mouse ovarian RNAseq data for E10.5, E13.5, P3, P14, and P28 were downloaded from https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6798/^{11 (link)}. The data were processed using the same pipeline as the NMR RNAseq data, with the exception of using the mouse genome and transcriptome annotation (Mus musculus, ftp://ftp.ensembl.org/pub/release-100/fasta/; GENCODE M25). t-SNE plots for the NMR and mouse RNAseq data were then plotted using the t-SNE wrapper function in M3C^{76 (link)} (Supplementary Fig. 4d-e). Next, a gene list was compiled consisting of the 20 qPCR genes profiled in Supplementary Fig. 5 and the 65 genes that enriched for meiotic pathways in the E56 vs. PND1 comparison (“chromosome organization involved in meiotic cell cycle”, “gamete generation”, “homologous chromosome pairing at meiosis”, “homologous chromosome segregation”, “male gamete generation”, “meiosis I cell cycle process”, “meiotic cell cycle”, “meiotic cell cycle process”, “meiotic chromosome organization” and “meiotic chromosome segregation”, and “nuclear chromosome segregation”). Nine genes overlapped between the two lists (Dmc1, Hormad1, Meiob, MeioC, Rec8, Spo11, Stra8, Sycp1, Sycp3), leaving a total of 76 genes. The gene expression (counts per million) for the gene list was then plotted in a heatmap in the NMR and mouse (Fig. 5b, respectively).