Oocyte Isoform Transcriptome Analysis

This repository contains the R source code for data analysis and visualization presented in the study of human and mouse oocyte isoform landscapes. Single oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability during oocyte maturation (https://www.biorxiv.org/content/10.1101/2025.06.17.659919v1.full)

🔬 Project Summary

This project explores the transcriptomic diversity in oocytes using Long-read sequencing. Key analyses include:

• Identification of stage-specific isoforms (GV, MI, MII).
• Differential Transcript Usage (DTU) and Isoform Switching analysis.
• Characterization of Transposable Element (TE) derived transcripts.
• Multi-incoproration, ActD half-lives, Enrichment of TE-derived isoform, RBP binding prediction.

📂 Repository Structure

Script Name	Main Figures	Analysis Description
01.plot_F1.R	Fig 1	Expression fractions.
02.plot_F2.R	Fig 2	SQANTI3 classification (FSM, ISM) distribution, Coding potential analysis (CPAT).
03.plot_F3.R	Fig 3	SQANTI3 classification (FSM, ISM) distribution, Coding potential analysis (CPAT).
04.plot_F4.R	Fig 4	Isoform switching analysis via IsoformSwitchAnalyzeR.
05.plot_F5.R	Fig 5	TE-derived isoform classification of repeat class/repeat family.
06.plot_F6.R	Fig 6	Multi-incoproration, ActD half-lives, Enrichment of TE-derived isoform, RBP binding prediction.

🛠 Prerequisites

R Environment

• R Version: >= 4.3.0
• Main Packages: tidyverse, data.table, ggplot2, ggpubr, IsoformSwitchAnalyzeR, ComplexHeatmap.

📊 Data Availability

The processed source data (TPM matrices, isoform annotations, etc.) required to run these scripts are provided as Source Data files accompanying the published version of this article in Nature Communications.

Installation

install.packages(c("tidyverse", "data.table", "ggpubr", "viridis"))
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("IsoformSwitchAnalyzeR", "ComplexHeatmap"))

## 📄 Citation
If you use this code, please cite our study:

```bibtex
@article{author2025,
  title = {Single oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability during oocyte maturation},
  author = {Wang et al.},
  journal = {bioRxiv},
  year = {2025},
  doi = {https://doi.org/10.1101/2025.06.17.659919},
  url = {[https://www.biorxiv.org/content/10.1101/2025.06.17.659919v1.full](https://www.biorxiv.org/content/10.1101/2025.06.17.659919v1.full)}
}