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Activation of RAS/MEK/ERK signaling drives biliary differentiation in primary liver cancer [112UE]

GSE236129 Mus musculus (mouse) RNA-seq (gene expression) 80 samples Submitted 2025/04/30 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 80 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
80 samples: 9 conditions, mostly in triplicateGroups 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)
RAS mutations are frequently observed in human cholangiocarcinoma (CCA), while they are relatively rare in hepatocellular carcinoma (HCC). In a genetically engineered mouse model with liver specific conditional deletion of tumor suppressors Rb and p53 together with activation of oncogenic KRAS, intrahepatic CCA develop primarily from hepatocytes.
Read the full summary ↓
CCA show activation of PI3K/AKT and MEK/ERK signaling pathways. targeted genetic inactivation of each of these downstream pathways of KRAS leads to delayed tumor growth and profound alterations in tumor differentiation. Specifically, reduced PI3K/AKT signaling promotes the formation of well-differentiated tumors, whereas the inactivation of MEK/ERK signaling induces a differentiation switch towards a more hepatocyte-like phenotype.
This dataset
Open GSE236129 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 GSE236129_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 PRJNA989115 and SRA study SRP446545. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in triplicate
RPK;AlbCreER_tumo ×8 RPK;Pdk1;AlbCreER_tumo ×7 control_live ×5 RPK_tumor_AAV ×5 control_liver_4weeks ×4 internal_control ×4 RPK_liver_4weeks ×3 RPK;Pdk1_liver_4weeks ×3 +39 more

Supports a case/control comparison: 25 samples read as cases, 22 as controls.

How we read this: 9 replicated groups read from 80 sample titles; they account for 42 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

+ 40 more — browse all 80 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.