GEO series

T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms [Multi-omics]

GSE342312 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 40 samples Submitted 2026/08/04 Platform GPL28330Platform GPL21103

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 40 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 40 samples: 12 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Effector CD8+ T cells must rapidly acquire cytotoxic functions while maintaining lineage fidelity and suppressing alternative fates. T-bet and Runx3 are key transcription factors that drive this process, yet their integrated regulatory logic has remained unclear due to the lack of comprehensive binding and chromatin accessibility data.

Read the full summary ↓

Here, we systematically dissect the cooperative and distinct roles of T-bet and Runx3 in shaping the transcriptional and epigenetic landscape of antiviral CD8+ T cells. Using CUT&RUN, ATAC-seq, RNA-seq and scRNA-seq across single and double knockout models, we reveal that T-bet and Runx3 coordinate effector differentiation through both chromatin remodeling-dependent and -independent mechanisms. T-bet preferentially binds promoters and restrains Th17-like programs, while Runx3 targets distal elements to suppress Tfh-associated genes and sustain cytotoxic identity. Our findings uncover a cis-regulatory logic wherein these factors act combinatorially to balance activation of effector programs with repression of alternative lineages, ensuring functional precision during antiviral responses. This work establishes a comprehensive framework for understanding lineage enforcement by transcription factors in effector T cells. This SuperSeries is composed of the SubSeries listed below.

This dataset

Open GSE342312 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE342312_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1507333 and SRA study SRP600682. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 conditions, mostly in triplicate

RNA-seq of Cpntrol ×3 RNA-seq of Runx3 KO ×3 RNA-seq of Tbet and Runx3 KO ×3 RNA-seq of Tbet KO ×3 ATAC-seq of Cpntrol ×3 ATAC-seq of Runx3 KO ×3 ATAC-seq of Tbet and Runx3 KO ×3 ATAC-seq of Tbet KO ×3 +8 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 40 sample titles; they account for 36 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM9105434 RNA-seq of Cpntrol 1 RNA-seq of Cpntrol
GSM9105435 RNA-seq of Cpntrol 2 RNA-seq of Cpntrol
GSM9105436 RNA-seq of Cpntrol 3 RNA-seq of Cpntrol
GSM9105437 RNA-seq of Runx3 KO 1 RNA-seq of Runx3 KO
GSM9105438 RNA-seq of Runx3 KO 2 RNA-seq of Runx3 KO
GSM9105439 RNA-seq of Runx3 KO 3 RNA-seq of Runx3 KO
GSM9105440 RNA-seq of Tbet and Runx3 KO 1 RNA-seq of Tbet and Run…
GSM9105441 RNA-seq of Tbet and Runx3 KO 2 RNA-seq of Tbet and Run…
GSM9105442 RNA-seq of Tbet and Runx3 KO 3 RNA-seq of Tbet and Run…
GSM9105443 RNA-seq of Tbet KO 1 RNA-seq of Tbet KO
GSM9105444 RNA-seq of Tbet KO 2 RNA-seq of Tbet KO
GSM9105445 RNA-seq of Tbet KO 3 RNA-seq of Tbet KO
GSM9105446 ATAC-seq of Cpntrol 1 ATAC-seq of Cpntrol
GSM9105447 ATAC-seq of Cpntrol 2 ATAC-seq of Cpntrol
GSM9105448 ATAC-seq of Cpntrol 3 ATAC-seq of Cpntrol
GSM9105449 ATAC-seq of Runx3 KO 1 ATAC-seq of Runx3 KO
GSM9105450 ATAC-seq of Runx3 KO 2 ATAC-seq of Runx3 KO
GSM9105451 ATAC-seq of Runx3 KO 3 ATAC-seq of Runx3 KO
GSM9105452 ATAC-seq of Tbet and Runx3 KO 1 ATAC-seq of Tbet and Ru…
GSM9105453 ATAC-seq of Tbet and Runx3 KO 2 ATAC-seq of Tbet and Ru…
GSM9105454 ATAC-seq of Tbet and Runx3 KO 3 ATAC-seq of Tbet and Ru…
GSM9105455 ATAC-seq of Tbet KO 1 ATAC-seq of Tbet KO
GSM9105456 ATAC-seq of Tbet KO 2 ATAC-seq of Tbet KO
GSM9105457 ATAC-seq of Tbet KO 3 ATAC-seq of Tbet KO
GSM9105458 Chip-seq of Runx3 1 Chip-seq of Runx3
GSM9105459 Chip-seq of Runx3 2 Chip-seq of Runx3
GSM9105460 Chip-seq of Runx3 3 Chip-seq of Runx3
GSM9105461 Chip-seq of Tbet with Runx3 KO 1 Chip-seq of Tbet with R…
GSM9105462 Chip-seq of Tbet with Runx3 KO 2 Chip-seq of Tbet with R…
GSM9105463 Chip-seq of Tbet with Runx3 KO 3 Chip-seq of Tbet with R…
GSM9105464 Chip-seq of Tbet 1 Chip-seq of Tbet
GSM9105465 Chip-seq of Tbet 2 Chip-seq of Tbet
GSM9105466 Chip-seq of Tbet 3 Chip-seq of Tbet
GSM9105467 Chip-seq of Runx3 with Tbet KO 1 Chip-seq of Runx3 with …
GSM9105468 Chip-seq of Runx3 with Tbet KO 2 Chip-seq of Runx3 with …
GSM9105469 Chip-seq of Runx3 with Tbet KO 3 Chip-seq of Runx3 with …
GSM9903219 single cell RNA-seq of Control
GSM9903220 single cell RNA-seq of Runx3 KO
GSM9903221 single cell RNA-seq of Tbet KO
GSM9903222 single cell RNA-seq of Tbet and Runx3 KO

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