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Human-correlated genetic HCC and HCC-organoid models identify combination therapy for precision medicine

GSE275444 Mus musculus (mouse) RNA-seq (gene expression) 216 samples Submitted 2024/12/02 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 216 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
216 samples: 33 conditions, mostly with about 7 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
Human-correlated genetic models identify precision therapy for liver cancerNature · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Human-correlated genetic models identify precision therapy for liver cancer
Müller M, May S, Hall H et al. · Nature 2025 · PMID 39972137 · doi:10.1038/s41586-025-08585-z
This dataset
Open GSE275444 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 GSE275444_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 PRJNA1150922 and SRA study SRP523846. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39972137) ↗
Study design
33 conditions, mostly with about 7 replicates each
Mouse Liver Ctnnb1-tmtMmt, MYC, Tumou ×13 DEN + ALIOS; liver; Male; DP ×9 Bcatex3 HET, R26myc HOM; AAV-Cre low dose; li… ×7 Bcatex3 HET, R26myc HOM, p53fl HET; AAV-Cre l… ×7 Bcatex3 HET, R26myc HOM, p53fl HOM; AAV-Cre l… ×7 Bcatex3 HET, R26myc HOM, p16KO HOM; AAV-Cre l… ×7 Bcatex3 HET, R26myc HOM, p16KO HOM, PTENfl HO… ×7 Bcatex3 HET, p16KO HOM, PTENfl HOM; AAV-Cre l… ×7 +36 more

Supports a between-group comparison across 205 samples.

How we read this: 33 replicated groups read from 216 sample titles; they account for 205 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

+ 176 more — browse all 216 samples with per-sample file links →

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.