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Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis.

GSE224832 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 104 samples Submitted 2024/12/18 Platform GPL30173Platform GPL21626Platform GPL24247Platform GPL21697Platform GPL24676Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 104 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
104 samples: 23 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.
Paper
Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesisNature genetics · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis
Lim B, Kamal A, Gomez Ramos B et al. · Nature genetics 2025 · PMID 39948437 · doi:10.1038/s41588-025-02081-w
This dataset
Open GSE224832 in finder → Find more ChIP / ATAC / CUT&Tag 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 GSE224832_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA932757 and SRA study SRP424215. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39948437) ↗
Study design
23 conditions, mostly in triplicate
Liver Prox1 ×5 Liver IgG ×5 Akt_Notch OE ×3 HCC day 16 EV ×3 HCC day 16 OE ×3 Hep3B cell line Day7 control ×3 Hep3B cell line Day7 Prox1 OE ×3 Hep3B Control ×3 +56 more

Supports a case/control comparison: 4 samples read as cases, 8 as controls.

How we read this: 23 replicated groups read from 104 sample titles; they account for 63 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

+ 64 more — browse all 104 samples with per-sample file links →

Datasets on a similar topic

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