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Daunorubicin-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ prolifeating T cells [scRNA-Seq]

GSE269347 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2025/06/30 Platform GPL21273
At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
16 samples: 16 samples, each with a distinct title — no replicated groupsGroups 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)
We showed that chemotherapy agent doxorubicin-pretreated CD8+ proliferating T cells had enhanced cytolytic activity against tumors after anti-PD-1 treatment in vitro. Doxorubicin-plus-anti-PD-1 treatment promoted the activation and expansion of endogenous tumor-reactive CD8+ proliferating T cells and efficiently suppressed tumor growth in multiple mice tumor models.
Read the full summary ↓
The single-cell RNA-sequencing and TCR-sequencing demonstrated that doxorubicin-plus-anti-PD-1 combination altered the metabolic reprogramming and activation of CD8+ proliferating T cells and markedly elevated the clonally expansion and effector function of proliferating T cells as compared with anti-PD-1 monotherapy, presenting increased expression of genes associated with T cell activation, proliferation, cytolytic activity, memory and mitochondrial metabolism. Strikingly, doxorubicin-plus-anti-PD-1 combination promoted the expression and activity of T cell activation transcription factor Nfat, which was reduced following PD-1 blockade therapy. Together, our findings show that the novel chemoimmunotherapy remodels CD8+ proliferating T subset, improves responsiveness to anti-PD-1 therapy.
This dataset
Open GSE269347 in finder → Find more mouse RNA-seq 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 GSE269347_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1121260 and SRA study SRP512479. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
16 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 16 sample titles: 16 distinct titles with little repetition. 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

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.