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Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade [ATAC-Seq]

GSE285308 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 33 samples Submitted 2025/01/27 Platform GPL34328
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 33 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
33 samples: 11 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
Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockadebioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Immune checkpoint blockade can facilitate tumor clearance by T cells, resulting in long term patient survival. However, the capacity of exhausted CD8+ T cells (Tex), present during chronic antigen exposure, to form memory after antigen clearance remains unclear. Here, we performed longitudinal single cell RNA/T cell receptor sequencing and ATAC-sequencing on antigen-specific T cells after the peripheral clearance of chronic lymphocytic choriomeningitis virus infection.
Read the full summary ↓
These data revealed the formation of a robust population of memory CD8+ T cells that transcriptionally, epigenetically, and functionally resemble central memory T cells (Tcm) that form after clearance of acute infection. To lineage trace the origin and memory recall response of Tex-derived memory clones, we utilized T cell receptor sequencing over the course of primary infection and rechallenge. We show that chronic Tcm are a clonally distinct lineage of Tex derived from progenitor exhausted cells, persist long-term in the absence of antigen, and undergo rapid clonal expansion during rechallenge. Finally, we demonstrate that αPD-L1 immune checkpoint blockade selectively expands clones which form Tcm after clearance. Together, these data support the concept that chronically stimulated T cells form bona fide functional memory T cells through an analogous differentiation pathway to acutely stimulated T cells, which may have significant implications for enhancing immune memory to cancer through checkpoint blockade and vaccination.
Published in
Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade
Raposo CJ, Yan PK, Chen AY et al. · bioRxiv : the preprint server for biology 2025 · PMID 39990338 · doi:10.1101/2025.02.10.637523
This dataset
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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 GSE285308_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 PRJNA1202197 and SRA study SRP556592. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39990338) ↗
Study design
11 conditions, mostly in triplicate
ATACseq_028dpi_Cl13_TexInt ×3 ATACseq_028dpi_Cl13_TexKLR ×3 ATACseq_028dpi_Cl13_TexProg ×3 ATACseq_028dpi_Cl13_TexProg62L ×3 ATACseq_028dpi_Cl13_TexTerm ×3 ATACseq_167dpi_Arm_Tcm ×3 ATACseq_167dpi_Arm_Tem ×3 ATACseq_167dpi_Cl13_Tcm ×3 +3 more

Supports a between-group comparison across 33 samples.

How we read this: 11 replicated groups read from 33 sample titles; they account for 33 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
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