Fig. 2: Superovulation disrupts the expression of genes involved in oocyte maturation.

Differentially expressed genes and enriched functional pathways between naturally ovulated (NY) and superovulated young (SY) oocytes (OCs) (a) and granulosa cells (GCs) (b) (n = 3 NY, 4 SY mice). The bars are colored based on the proportion of genes in the pathways that are up- or downregulated in SY compared to NY. Differential gene expression was performed using a two-tailed Wald test with multiple testing correction as implemented in DESeq2. Over-representation of pathways was done using a one-tailed hypergeometric test and p values were corrected for multiple testing. c Schematic representation of gene expression expectation in mature (M) and immature (I) oocytes between poly-A biased (SMART-seq2) and unbiased protocols (total RNA-seq) for genes involved in oocyte transcriptional remodeling during maturation (re-poly-adenylation, de-adenylation, and degradation). Expectation of upregulation is represented in light red, downregulation in light blue. d Comparison of gene expression between naturally and superovulated oocytes using SMART-seq2 (n = 15 NY, 31 SY) and total RNA-seq (n = 25 NY, 22 SY). For each technology, the fold change is computed between the two groups (“Methods”). Each row represents gene expression in an individual oocyte (randomly subsampled set). Full heatmap with additional genes available in Supplementary Fig. 1e. e Expression of genes involved in spindle assembly checkpoint (SAC) machinery in naturally and superovulated oocytes (n = 15 NY, black, 31 SY, gray, oocytes). P values were computed using a two-tailed Wilcoxon test. Center line—median, box limits—first and third quartiles, whiskers—maximum and minimum or 1.5 times interquartile range if outliers, dots—outliers. f Expression of genes involved in the cGMP pathway in naturally and superovulated granulosa cells (n = 18 NY, 31 SY granulosa cells). P values were computed using a two-tailed Wilcoxon test. Center line—median, box limits—first and third quartiles, whiskers—maximum and minimum or 1.5 times interquartile range if outliers, dots—outliers. Source data are provided as a Source Data file.