IL-9 as a naturally orthogonal cytokine with optimal JAK/STAT signaling for engineered T cell therapy

This repository contains scripts for analyzing scRNA-seq and bulk RNA-seq data from the manuscript.

Data Availability

Data can be accessed from Zenodo (https://zenodo.org/records/14537359)

Repository Contents

This repository includes the following scripts:

• Data processing: data processing.R - Initial processing and preparation of scRNA-seq data
• RNA-Seq analysis: RNASeq.R - Initial processing and preparation of RNA sequencing data
• SCENIC analysis: SCENIC.R - Script for single-cell regulatory network inference and clustering using the SCENIC workflow
• Transcription factor analysis: TFonBulkRNAseq.R - Analysis of transcription factor activity on bulk RNA-seq data
• Correlation analysis: correlation_plotting.R - Script for generating correlation plots and analyses
• Phosphoproteomics: phosphoproteomics_volcanoplot.R - Creates volcano plots for phosphoproteomics data visualization

Citation

https://www.biorxiv.org/content/10.1101/2025.01.15.633105v1