🧬 Treg Foxp3 Degradation — High-Throughput Genomics Analysis

This repository contains a collection of Jupyter notebooks and associated datasets for the comprehensive analysis of regulatory T cells (Tregs) undergoing acute Foxp3 degradation, across diverse biological contexts for the following publication: (link TBD). Leveraging both single-cell and bulk RNA-sequencing technologies, these analyses uncover dynamic transcriptional changes following the targeted loss of Foxp3.

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📁 Repository Structure

The repository is organized into single-cell, bulk transcriptomics, and shared utility code, each addressing a distinct role in the analysis workflow.

🔬 Single-Cell RNA-seq Analyses

These notebooks explore the effects on transcription in diverse Treg contexts following Foxp3 degradation:

• Foxp3 Degradation in Adult Secondary Lymphoid Organs (SLO)

  • scrna-filter-d0.ipynb (Initial filtering of D0 cells)
  • scrna-postfilter.ipynb (Complete analysis)

• Foxp3 Degradation Across Multiple Organs

  • scrna-organ.ipynb

• Foxp3 Degradation in the Tumor Microenvironment

  • scrna-tumor.ipynb

• Foxp3 Degradation in Adoptive Transfer Settings

  • scrna-transfer.ipynb

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🧪 Bulk RNA-seq Analyses

Bulk RNA-seq analyses include both newly generated and reanalyzed datasets:

• bulk_rna_data/

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📊 Cross-Modality Figures

Plots combining multiple modalities (e.g., single-cell and bulk RNA-seq data) can be found in:

• final-figures.ipynb

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🧰 Reusable Functions and Utilities

• code/
  A collection of shared functions and modules used across the notebooks, including:
  • Data loading and preprocessing utilities
  • Plotting functions
  • Statistical tests and helper methods

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📣 Questions & Feedback

For questions, feedback, or other concerns, feel free to reach out via e-mail or by posting a GitHub issue.