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Arid3b suppresses CD8+ T cell infiltration and function in microsatellite stable colorectal cancer via Runx3 [RNA-seq]

GSE304750 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/04/14 Platform GPL34328
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × CD8+ T cells, Arid3b-KO, co-cultured with CMT93-OVA cells, vs 3 × CD8+ T cells,Control, co-cultured with CMT93-OVA cells, vs 3 × CD8+ T cells, Arid3b-KO, untreat, vs 3 × CD8+ T cells, Control, untreat,Groups 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
Arid3b suppresses CD8 + T cell infiltration and function in microsatellite-stable colorectal cancer via Runx3Nature communications · 2026
Summary (written by the submitters)
Microsatellite stable/proficient mismatch repair (MSS/pMMR) colorectal cancer (CRC) is characterized by a cold tumor microenvironment, marked by sparse CD8⁺ T cell infiltration and resistance to immune checkpoint inhibitors (ICIs). To uncover regulators that limit CD8⁺ T cell infiltration in MSS CRC, we conducted an in vivo CRISPR/Cas9 screen targeting genes in CD8⁺ T cells using a CMT93 cell-derived tumor model.
Read the full summary ↓
This screen identified Arid3b as a key negative regulator of CD8⁺ T cell tumor infiltration and antitumor activity. Genetic ablation of Arid3b in CD8⁺ T cells significantly enhanced their intratumoral accumulation and mediated robust tumor control. Mechanistically, Arid3b deficiency upregulated Runx3, promoting a tissue-resident memory phenotype and effector function. Notably, the benefits conferred by Arid3b knockout were abrogated by Runx3 deletion, indicating a Runx3-dependent mechanism. In summary, targeting ARID3B could offer a promising strategy to reshape the tumor microenvironment and sensitize MSS CRC to immunotherapy.
Published in
Arid3b suppresses CD8 + T cell infiltration and function in microsatellite-stable colorectal cancer via Runx3
Wang S, Hou S, Luo C et al. · Nature communications 2026 · PMID 42140952 · doi:10.1038/s41467-026-73241-7
This dataset
Open GSE304750 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 GSE304750_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 PRJNA1302450 and SRA study SRP607026. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42140952) ↗
Study design
3 × CD8+ T cells, Arid3b-KO, co-cultured with CMT93-OVA cells, vs 3 × CD8+ T cells,Control, co-cultured with CMT93-OVA cells, vs 3 × CD8+ T cells, Arid3b-KO, untreat, vs 3 × CD8+ T cells, Control, untreat,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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