GEO series

Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [ChIP-seq]

GSE275722 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 37 samples Submitted 2025/09/18 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 37 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)
Samples: 37 samples: 37 samples, each with a distinct title — no replicated groupsGroups 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: Extrachromosomal DNA associates with nuclear condensates and reorganizes chromatin structures to enhance oncogenic transcriptionCancer cell · 2025

Summary (written by the submitters)

Extrachromosomal, circular DNA (ecDNA) is a prevalent and significant oncogenic alteration in cancer genomes. Its frequency is associated with aggressive tumor behavior and poor patient outcome. To understand how ecDNA promotes oncogenesis, we map ecDNA-associated chromatin complexes at single-molecule resolution in three well-characterized ecDNA+ cancer models that harbor different oncogenes.

Read the full summary ↓

Using a suite of 3D genome mapping and imaging analyses, we determined ecDNA nuclear organization and uncovered that ecDNA hubs are part of MED1-mediated condensates that can be rapidly disrupted by agents perturbing liquid-liquid phase separation (LLPS). The functional relevance of ecDNA condensates was demonstrated by inhibition of LLPS which led to hub dispersal, the reduction of MED1 co-activator binding, inhibition of oncogenic transcription and selectively increase cell death of ecDNA-containing cells across a broad range of cancer models. Robust epigenetically silencing of the regulatory modules within ecDNAs effectively disrupts ecDNA’s mode of actions and demonstrates the causality between ecDNA enhancer function, chromosomal contacts, transcription and cellular proliferation, which directly corroborate ecDNA’s trans-activator activity. Our findings reveal that ecDNA drives tumor promotion activity through nuclear condensate and suggests that exploiting these nuclear structures may serve as a universal strategy against malignant tumors. Our work elucidates the structures, functions and regulation of ecDNA which is expected to transform the paradigm for studying cancer genomes and expand the current views of how oncogenes are regulated, from which new clinical strategies can be realized.

Published in

Extrachromosomal DNA associates with nuclear condensates and reorganizes chromatin structures to enhance oncogenic transcription

Taghbalout A, Tung CH, Clow PA et al. · Cancer cell 2025 · PMID 40972571 · doi:10.1016/j.ccell.2025.08.008

This dataset

Open GSE275722 in finder → Find more human 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 GSE275722_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 PRJNA1152633 and SRA study SRP528748. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40972571) ↗

Study design

37 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 37 sample titles: 37 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

GSM8483402 PC3DM_Input
GSM8483403 PC3DM_RNAPII-ChIP-seq
GSM8483404 PC3DM_H3K27ac-ChIP-seq
GSM8483405 PC3DM_MED1-ChIP-seq
GSM8483406 PC3DM-mock-rep1_Input
GSM8483407 PC3DM-mock-rep1_MED1-ChIP
GSM8483408 PC3DM-mock-rep2_MED1-ChIP
GSM8483409 PC3DM-3%HD-30min-rep1_MED1-ChIP
GSM8483410 PC3DM-3%HD-30min-rep2_MED1-ChIP
GSM8483411 PC3DM-3%HD-1h-rep1_MED1-ChIP
GSM8483412 PC3DM-3%HD-1h-rep2_MED1-ChIP
GSM8483413 COLO320DM_Input
GSM8483414 COLO320DM_RNAPII-ChIP-seq
GSM8483415 COLO320DM_H3K27ac-ChIP-seq
GSM8483416 COLO320DM_MED1-ChIP-seq
GSM8483417 COLO320DM-mock-rep1_Input
GSM8483418 COLO320DM-mock-rep1_MED1-ChIP
GSM8483419 COLO320DM-mock-rep2_MED1-ChIP
GSM8483420 COLO320DM-3%HD-30min-rep1_MED1-ChIP
GSM8483421 COLO320DM-3%HD-30min-rep2_MED1-ChIP
GSM8483422 COLO320DM-3%HD-1h-rep1_MED1-ChIP
GSM8483423 COLO320DM-3%HD-1h-rep2_MED1-ChIP
GSM8483424 COLO320DM-3%HD-2h-rep1_MED1-ChIP
GSM8483425 COLO320DM-3%HD-2h-rep2_MED1-ChIP
GSM8483426 COLO320DM-3%HD-3h-rep1_MED1-ChIP
GSM8483427 COLO320DM-3%HD-3h-rep2_MED1-ChIP
GSM8483428 GBM171DM_Input
GSM8483429 GBM171DM_RNAPII-ChIP-seq
GSM8483430 GBM171DM_H3K27ac-ChIP-seq
GSM8483431 GBM171DM_MED1-ChIP-seq
GSM8483432 GBM171DM-mock-rep1_Input
GSM8483433 GBM171DM-mock-rep1_MED1-ChIP
GSM8483434 GBM171DM-mock-rep2_MED1-ChIP
GSM8483435 GBM171DM-3%HD-1h-rep1_MED1-ChIP
GSM8483436 GBM171DM-3%HD-1h-rep2_MED1-ChIP
GSM8483437 GBM171DM-3%HD-2h-rep1_MED1-ChIP
GSM8483438 GBM171DM-3%HD-2h-rep2_MED1-ChIP

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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.