Integrated Epigenetic and Genetic Programming of Primary Human T Cells

Overview

This repository contains the code and data analysis for the manuscript "Integrated Epigenetic and Genetic Programming of Primary Human T Cells" by Goudy et al.

Project Structure

RNA-seq Analysis

• Cas9_KO_vs_CRISPRoff_KD/: RNA-seq data from multiple donors comparing CRISPRoff vs CRISPR-Cas9 knockout
• CRISPRoff_KO_MED12/: Comparison of MED12 silencing between CRISPRoff and CRISPR-Cas9
• CRISPRoff_surface_markers/: Comparison of different Cas9 effector proteins on surface marker expression

Methylation Analysis

• WGBS/: Bisulfite sequencing analysis for methylation profiling

Key Analyses

1. CRISPRoff vs CRISPR-Cas9 Comparison

Demonstrates comparable gene silencing efficiency between epigenetic (CRISPRoff) and genetic (CRISPR-Cas9) approaches.

2. Multi-target Analysis

Evaluates CRISPRoff performance across multiple therapeutically relevant genes including:

• FAS
• MED12
• PTPN2
• RASA2
• RC3H1
• SUV39H1

3. Surface Marker Analysis

Compares different Cas9 variants for targeting T cell surface markers:

• CD55
• CD81
• CD151

Dependencies

• R (v4.3+)
• DESeq2
• edgeR
• methylKit
• bsseq
• ggplot2
• tidyverse

Data Availability

Raw sequencing data and processed files are organized in respective subdirectories.

Contact

For questions regarding this repository, please contact the corresponding authors:

• justin.eyquem [at] ucsf.edu
• brian.shy [at] ucsf.edu
• alexander.marson [at] ucsf.edu
• luke [at] arcinstitute.org