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Rationalistic Modulation of Immune Mechanisms Synergizes the Anti-Tumor Effects of Targeted Radiation Therapy in Pre-clinical Models

GSE294347 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/10/15 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 14 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
14 samples: 4 × TILs from B16F10 tumors 6 days after 12 Gy treatment vs 4 × TILs from CT26 tumors 6 days after 12 Gy treatment vs 3 × TILs from B16F10 tumors 6 days after sham treatment vs 3 × TILs from CT26 tumors 6 days after sham treatmentGroups 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)
In this study, we employed a diverse set of pre-clinical syngeneic murine tumor models with varying immune profiles to investigate the immunological impact of radiotherapy. We observed that immunologically 'hot' tumors demonstrated stronger tumor growth inhibition (TGI) following RT compared to 'cold' tumors. Additionally, RT induced both pro- and anti-inflammatory shifts within the tumor immune microenvironment, with significant changes noted in the spleen and tumor-draining lymph nodes.
Read the full summary ↓
Importantly, radiotherapy led to an intratumoral increase in proliferating CD8 T cells, while the population of proliferating macrophages was notably reduced. Our findings also reveal that STING deficiency compromises TGI, particularly in tumors with a high baseline population of macrophages expressing an interferon response signature. Moreover, we identified a synergistic tumor growth control effect when combining HPK1 deficiency with RT. Collectively, these results provide insights into the complex interplay between RT and the immune response, offering potential avenues for novel therapeutic combination strategies.
This dataset
Open GSE294347 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 GSE294347_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 PRJNA1249074 and SRA study SRP578114. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × TILs from B16F10 tumors 6 days after 12 Gy treatment vs 4 × TILs from CT26 tumors 6 days after 12 Gy treatment vs 3 × TILs from B16F10 tumors 6 days after sham treatment vs 3 × TILs from CT26 tumors 6 days after sham treatment

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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

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.