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The Ddx21 mutant peptide is a potent neoantigen in preventive lung cancer vaccines and can activate long-term immune function

GSE270091 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2025/02/26 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 48 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
48 samples: 12 conditions, mostly with about 4 replicates eachGroups 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
Ddx21 mutant peptide is an effective neoantigen in prophylactic lung cancer vaccines and activates long-term anti-tumor immunityFrontiers in immunology · 2025
Summary (written by the submitters)
Preventive vaccine is an important means of tumor prevention. Our previous study showed that the lung cancer cell lines KPL160302S and KPL160424S obtained from the primary culture of lung cancer mice were prepared into preventive vaccines. After inoculation with KPL160302S, the survival period of lung cancer mice was significantly prolonged and the anti-tumor immunity of mice was enhanced.
Read the full summary ↓
Significantly increased the number of CD8+CD4+T cells, while KPL160424S failed to extend survival and had limited effects on the immune system. In order to explore the cause of this difference, two mutant peptides Ddx21 and Zfp760 were screened as potential neoantigens by bioinformatics method. The results showed that Ddx21MT immunization could significantly up-regulate central memory T cells (TCM) and activate long-term immune function in mice. The magnetic bead sorting of spleen CD4+ and CD8+T cells after enhanced immunization was performed by transcriptome sequencing to explore the differences.
Published in
Ddx21 mutant peptide is an effective neoantigen in prophylactic lung cancer vaccines and activates long-term anti-tumor immunity
Zhang Z, Xia Y, Wang Z et al. · Frontiers in immunology 2025 · PMID 39981234 · doi:10.3389/fimmu.2025.1500417
This dataset
Open GSE270091 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 GSE270091_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1124976 and SRA study SRP514446. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39981234) ↗
Study design
12 conditions, mostly with about 4 replicates each
CD4 Tcells,Ddx21MT,DMCD ×4 CD4 Tcells,Ddx21WT,DWCD ×4 CD4 Tcells,Zfp760MT,ZMCD ×4 CD4 Tcells,Zfp760WT,ZWCD ×4 CD4 Tcells,PolyIC,PoCD ×4 CD4 Tcells,PBS,PBCD ×4 CD8 Tcells,Ddx21MT,DMCD ×4 CD8 Tcells,Zfp760MT,ZMCD ×4 +6 more

Supports a between-group comparison across 46 samples.

How we read this: 12 replicated groups read from 48 sample titles; they account for 46 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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