GEO series

KLF5 modulates epigenetic modifications driving human pancreatic ductal adenocarcinoma metastasis [Multiome]

GSE290274 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2026/02/10 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 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: 16 samples: 2 × A13Lg shCtrl-5 GEX biol vs 2 × A13Lg shCtrl-5 ATAC biol vs 2 × A13Lg shKLF5-5 GEX biol vs 2 × A13Lg shKLF5-5 ATAC biolGroups 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: CRISPR screen of human pancreatic cancer xenografts identifies a KLF5 proliferation vulnerability through epigenetic modifiers NCAPD2 and MTHFD1Molecular cancer · 2026

Summary (written by the submitters)

We previously showed that distant metastases of human pancreatic ductal adenocarcinoma (PDAC) are driven by epigenetic alterations in the primary tumor rather than by additional mutations1. However, the specific epigenetic driver genes responsible have not been identified. To identify genes modulating these changes, we performed a pooled CRISPR genetic screen and single-cell multiomics analysis using patient-derived xenograft cell lines established from a primary PDAC tumor and a distant metastasis from the same patient.

Read the full summary ↓

We identified KLF5 as the leading epigenetic modulator regulating progression in distant metastasis. Knockdown of KLF5 selectively reduced the growth of the distant metastasis and caused a large-scale increase in heterochromatin. Single-cell multiome ATAC and gene expression analysis revealed two clusters with high KLF5 expression and increased expression and chromatin accessibility of stem cell markers and genes related to migration and epithelial to mesenchymal transition. Further, we identified two epigenetic modifiers, NCAPD2 and MTHFD1, which are regulated by KLF5 and result in these increases in heterochromatin when knocked down. These data provide a sequence of epigenetic modulators, modifiers and mediators which shape the metastatic landscape of pancreatic cancer.

Published in

CRISPR screen of human pancreatic cancer xenografts identifies a KLF5 proliferation vulnerability through epigenetic modifiers NCAPD2 and MTHFD1

Maeda M, Sherman K, Zhou W et al. · Molecular cancer 2026 · PMID 41668133 · doi:10.1186/s12943-026-02575-z

This dataset

Open GSE290274 in finder → Find more human 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 GSE290274_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 PRJNA1227119 and SRA study SRP565729. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41668133) ↗

Study design

2 × A13Lg shCtrl-5 GEX biol vs 2 × A13Lg shCtrl-5 ATAC biol vs 2 × A13Lg shKLF5-5 GEX biol vs 2 × A13Lg shKLF5-5 ATAC biol

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 8 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

GSM8809630 A13Pr2 shKLF5-5 GEX
GSM8809631 A13Pr2 shKLF5-5 ATAC
GSM8809632 A13Pr2 shCtrl GEX
GSM8809633 A13Pr2 shCtrl ATAC
GSM8809634 A13Pr2 Parental GEX
GSM8809635 A13Pr2 Parental ATAC
GSM8809636 A13Lg shCtrl-5 GEX biol rep1 A13Lg shCtrl-5 GEX biol
GSM8809637 A13Lg shCtrl-5 ATAC biol rep1 A13Lg shCtrl-5 ATAC biol
GSM8809638 A13Lg Parental GEX
GSM8809639 A13Lg Parental ATAC
GSM8809640 A13Lg shCtrl-5 GEX biol rep2 A13Lg shCtrl-5 GEX biol
GSM8809641 A13Lg shCtrl-5 ATAC biol rep2 A13Lg shCtrl-5 ATAC biol
GSM8809642 A13Lg shKLF5-5 GEX biol rep1 A13Lg shKLF5-5 GEX biol
GSM8809643 A13Lg shKLF5-5 ATAC biol rep1 A13Lg shKLF5-5 ATAC biol
GSM8809644 A13Lg shKLF5-5 GEX biol rep2 A13Lg shKLF5-5 GEX biol
GSM8809645 A13Lg shKLF5-5 ATAC biol rep2 A13Lg shKLF5-5 ATAC biol

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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.