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Higher basal tumor immune activity coupled with a systemic immune response improves liver cancer outcomes

GSE325237 Mus musculus (mouse) RNA-seq (gene expression) 116 samples Submitted 2026/04/12 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 116 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
116 samples: 116 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.
Paper
Bile acids mediate liver-bone marrow crosstalkiScience · 2026
Summary (written by the submitters)
This study examines how systemic immune responses and liver immune activity influence liver tumor development. In a diethylnitrosamine (DEN)‑induced mouse model of hepatocellular carcinoma, mice were fed different diets for 26 weeks to assess the impact of metabolic and inflammatory conditions on tumor progression. Tumor burden varied across diets, with increased tumor formation in some diets and a diet with combined cholesterol and cholic acid showing tumor burdens similar to controls.
Read the full summary ↓
Flow cytometry revealed that mice on the combined diet exhibited the strongest expansion and activation of bone marrow hematopoietic stem and progenitor cells (HSPCs). RNA‑seq was performed on tumor and non‑tumor liver tissues to profile diet‑associated transcriptional changes, and weighted gene co‑expression network analysis (WGCNA) identified conserved immune‑related gene expression modules. Enhanced systemic hematopoietic responses were associated with stronger liver immune gene expression and increased innate immune cell infiltration, correlating with reduced tumor burden. These findings highlight a link between systemic hematopoietic activation, hepatic immune responses, and liver tumor outcomes.
Published in
Bile acids mediate liver-bone marrow crosstalk
Vitale D, Azardaryany MK, Alipour Talesh G et al. · iScience 2026 · PMID 42389593 · doi:10.1016/j.isci.2026.116462
This dataset
Open GSE325237 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 GSE325237_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 PRJNA1439239 and SRA study SRP684793. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42389593) ↗
Study design
116 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 116 sample titles: 116 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

+ 76 more — browse all 116 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.