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HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression

GSE245734 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 225 samples Submitted 2025/09/16 Platform GPL21103Platform GPL24676Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 225 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
Homo sapiens (human)
Topic
Pancreatic cancerThis series is part of our curated briefing on it.
Samples
225 samples: 209 distinct titles, 8 of them repeatedGroups 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
Transcription factor switching drives subtype-specific pancreatic cancerNature 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
Transcription factor switching drives subtype-specific pancreatic cancer
Rao SV, Young L, Cheeseman D et al. · Nature genetics 2025 · PMID 41168397 · doi:10.1038/s41588-025-02389-7
This dataset
Open GSE245734 in finder → Find more RNA-seq datasets → Pancreatic cancer landscape →
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 GSE245734_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 PRJNA1029626 and SRA study SRP467179. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41168397) ↗
Study design
209 distinct titles, 8 of them repeated
HPAFII-Cas-9 ×4 HPAFII-HNF4G KO ×4 KPC tumour ×4 KPC Liver mets ×4 FOXA1 KPC tumour ×2 FOXA1 KPC Liver mets ×2 HNF4G KPC tumour ×2 HNF4G KPC Liver mets ×2

Supports a case/control comparison: 46 samples read as cases, 8 as controls.

How we read this: Read from 225 sample titles: 209 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

+ 185 more — browse all 225 samples with per-sample file links →

More Pancreatic cancer datasets

Search all 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.