This site contains the scripts used for the analyses performed in our research paper, entitled "Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy". This paper is the process of peer review. For details on using the scripts, refer to RScripts/README_Analysis_Scripts.md.
Title: Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy
Changes in DNA methylation and gene expression play a major role in the epileptogenic process that turns a healthy brain into an epileptic brain. The goal of this investigation was to identify shared and distinct changes in gene expression and methylation in two widely used but mechanistically distinct rat models of temporal lobe epilepsy: intrahippocampal electrical kindling and systemic kainic acid. RNA sequencing and reduced-representation bisulfite sequencing were used to assess differences in gene expression and DNA methylation. Considering the distinct histopathological features of the electrical kindling and kainic acid models, we anticipated that gene expression and DNA methylation changes during epileptogenesis would be largely non-overlapping, but that areas of overlap would highlight generalizable, model-independent epileptogenesis pathways. Five genes (Fcgbp1, Loxhd1, Nedd9, Ptpre, and Adcy4) were differentially methylated and expressed in both models. Identifying these genes in different epilepsy models suggests a common methylation-regulated dysregulation in epileptogenesis, highlighting potential targets for future therapeutic interventions.
If you use these scripts, please cite the original paper:
[Your Publication]
- Study: Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy
- Authors: Benton Purnell*, Junguk Hur*, David Ruskin, Madhuvika Murugan, Fabio Tescarollo, Riddhimaa Sinha, Nikhil Ramavenkat, Susan Masino, Jonathan D. Geiger, and Detlev Boison
- Journal: Scientific Reports
- Status: Accepted as of 01/08/2026
- DOI: Pending
For questions or issues with these scripts:
- GitHub Issues: https://github.com/hurlab/EpilepsyEpigenetics/issues
- Email: junguk.hur@med.und.edu
[Specify license - e.g., MIT, GPL-3, etc.]
- Rutgers University Genomics Center for sequencing
- This study was funded through grants NS127846 and NS065957.
- R/Bioconductor community for software tools