Tle3 Multiomics Analysis — Nature Immunology 2024

Analysis code for the following publication:

The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8+ T cell fates.
X. Zhao*, W. Hu*, S.R. Park*, S. Zhu, S.S. Hu, C. Zang, W. Peng, Q. Shan, H.H. Xue.
Nature Immunology, 2024. (co-first author)
https://doi.org/10.1038/s41590-023-01720-w

---

Repository Structure

tle3-multiomics-NI2024/
├── rnaseq/         # Bulk RNA-seq analysis
├── atacseq/        # ATAC-seq analysis
└── cutandrun/      # CUT&RUN analysis

---

rnaseq/

Bulk RNA-seq analysis of CD8+ T cell subsets (Tem, Tcm, Tfh-like).

Directory / File	Description
sh/	Shell scripts: trimming (Trimmomatic), alignment (STAR), feature counting
R/	DESeq2 differential expression, FPKM calculation
csv/	Input count matrices
info/	Gene marker references
RNA_seq_workflow.txt	Step-by-step pipeline overview

Key scripts:

• sh/trimming_to_featurecount.sh — End-to-end preprocessing pipeline
• R/deseq2_fpkm.r — DESeq2 analysis + FPKM normalization
• R/RNA_seq_Tfh_AYAA.2021.11.12.R — Tfh-related comparisons

---

atacseq/

ATAC-seq chromatin accessibility analysis.

Directory	Description
sh/	Alignment, peak calling (MACS2), bigwig generation
R/	DESeq2 on peaks, DiffBind differential peak analysis, PCA
macs2/	MACS2 peak calling scripts
homer/	Motif enrichment analysis
bedtools/	Intersection and coverage calculations
bw/	Bigwig normalization scripts
peak_manipulation/	Peak filtering and formatting utilities

Key scripts:

• R/Differential_Peaks_by_DESeq2.R — Differential accessibility by DESeq2
• R/Peak_analysis_using_DiffBind.R — DiffBind-based differential peak analysis
• R/Icos_Read_bed.normalization.blacklist_out.2over3_filtering.r — Peak normalization with blacklist removal

---

cutandrun/

CUT&RUN analysis for Tle3 and histone mark profiling.

Directory	Description
sh/	Alignment, peak calling, quality checks
R/	Coverage normalization, differential peak analysis, heatmaps
DESeq/	DESeq2-based differential CUT&RUN signal
motif/	Motif analysis inputs
data/	Reference genome files (mm10)

Key scripts:

• R/cutandrun_2021.11.10.dif_peak.manipulation.and.save.log.R — Differential peak calling
• R/coverage_narrowpeak_normalization.R — Signal normalization
• DESeq/DESeq_comparison.R — Statistical comparison across conditions

---

Dependencies

Tool	Version	Use
STAR	2.7.x	RNA-seq alignment
Trimmomatic	0.39	Read trimming
MACS2	2.2.x	Peak calling
HOMER	4.11	Motif analysis
R	4.x	Statistical analysis
DESeq2	1.34+	Differential analysis
DiffBind	3.x	ATAC-seq differential peaks

---

Contact

Sung Rye Park — GitHub · LinkedIn