Transcriptomic analysis of the transition from preantral to early antral bovine ovarian follicles

Our ongoing research aims to identify key factors and pathways involved in the preantral (PM, PF, and SF) to EA transition in the bovine model that can be targeted to develop efficient and reliable culture protocols for assisted reproduction. PM, PF, and SF were previously collected in-house (GSE283263 and GSE309360). For this study, EA and SF were mechanically isolated from the ovarian cortex of dairy cows aged 15 to 31 months, and bulk RNA sequencing was performed. PM, PF, SF, and EA samples were batch-corrected and normalized. The data were analyzed to investigate the overall relationships within the sample. Differential gene expression analysis was performed, and genes significantly associated with increasing follicle diameter were used to build gene co-expression modules via WGCNA. Additionally, candidate biomarkers involved in the preantral-to-EA transition were identified through an integrative analysis using other publicly available NCBI datasets (refer to the paper). Moreover, the reliability of candidate biomarkers was evaluated using machine learning-based models. Our results demonstrated the robustness of the in-house datasets, which were consistent with each other and with external datasets, enabling the identification of reliable biomarkers. These biomarkers hold the potential for providing qualitative checkpoints to monitor preantral follicle progression to the antral stage during in vitro culture, in the future.