Bulk RNA sequencing analysis of gene expression in staged mouse ovarian follicles

Authors

Sophia E. Meytin, The Thayer School of Engineering and Quantitative Biomedical Sciences, Dartmouth CollegeFollow
Yu-Ying Chen, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University
Daniela Russo, The Broad Institute, Harvard University and MIT
Teresa K. Woodruff, Department of Obstetrics and Gynecology, Michigan State University
Alex K. Shalek, The Broad Institute, Harvard University and MIT; Ragon Institute of MGH, MIT and Harvard; Department of Chemistry and Institute for Medical Engineering and Science MIT
Francesca Duncan, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University
Brittany A. Goods, The Thayer School of Engineering and Quantitative Biomedical Sciences, Dartmouth CollegeFollow

Files

Student Class

2026

Author ORCID Identifier

https://orcid.org/0000-0003-0428-228X

Sophia Meytin (0000-0003-0428-228X) - ORCID

First Advisor

Brittany A. Goods

First Advisor Department

Department of Engineering Sciences—Thayer School of Engineering

Description

This project aimed to employ bulk RNA sequencing analysis to quantify the differences in gene expression between staged follicles in ovarian mouse models. The follicles of interest—cortical and medullary—differ by location, activation time, and impact on fertility, indicating potential differences in expression. A dataset of 97 primordial ovarian follicles was curated and sequenced to obtain gene expression readouts. Of these, 82 contained unambiguous metadata; subsequent filtering yielded 44 analyzable follicles. Principal component analysis (PCA) was conducted on the filtered data, revealing a heavy batch effect. Two avenues were explored to rectify this—batch correction using the ComBat-seq method and isolation of a single batch, Batch 5. Batch correction proved largely ineffective, as a batch effect was still observed within corrected data; isolation of a single batch was effective. The PCA of Batch 5 did not reveal a clear impact on gene expression by follicle location within the first two Principal Components. This was corroborated by a Pearson Correlation Plot. Future work focuses on improving batch correction methods, analyzing other Principal Components within Batch 5, and conducting Differential Expression (DE) analysis on both subsets of data to formally quantify differences in gene expression. This approach will thus create opportunities for more targeted exploration of genes which may impact fertility.

Publication Date

2024

Keywords

RNA, fertility, follicles, ovary, cortical, medullary, RNAseq

Disciplines

Computational Biology | Genomics | Urogenital System

Dartmouth Digital Commons Citation

Meytin, Sophia E.; Chen, Yu-Ying; Russo, Daniela; Woodruff, Teresa K.; Shalek, Alex K.; Duncan, Francesca; and Goods, Brittany A., "Bulk RNA sequencing analysis of gene expression in staged mouse ovarian follicles" (2024). Wetterhahn Science Symposium Posters 2024. 19.
https://digitalcommons.dartmouth.edu/wetterhahn_2024/19