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Pre-division TCF1 downregulation determines long-term effector and memory CD8 T cell fates [ATAC-Seq]

GSE306736 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 15 samples Submitted 2026/04/10 Platform GPL21103
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 15 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
15 samples: 5 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.
Paper
Pre-division TCF1 drop determines long-term CD8 T cell fatesbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
ATAC-SEQ analysis of antigen-specific CD8 T cells sorted from the spleens of Listeria-infected mice at different early timepoints following activation. As a control, we sequenced naive CD8 T cells prior to transfer into infected hosts.
Published in
Pre-division TCF1 drop determines long-term CD8 T cell fates
Favret NR, Astorkia M, Wolf MM et al. · bioRxiv : the preprint server for biology 2025 · PMID 41279579 · doi:10.1101/2025.10.06.680655
This dataset
Open GSE306736 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 GSE306736_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 PRJNA1312000 and SRA study SRP613928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41279579) ↗
Study design
5 conditions, mostly in triplicate
CD8+CD90.1+CD69+CFSE+ transgenic TCRTAG CD8 T… ×3 CD8+CD90.1+P4-6CD25low transgenic TCRTAG CD8 … ×3 CD8+CD90.1+P4-6CD25high transgenic TCRTAG CD8… ×3 CD8+CD90.1+CD44- transgenic TCRTAG CD8 T cell… ×2 CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T cells… ×2 Sort-purified (live CD8+CD90.1+CD44-) transge… ×1 live CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T … ×1

Supports a between-group comparison across 13 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 13 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
Datasets on a similar topic

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