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Mapping breakome of multiple cancer cell-lines

GSE290558 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 62 samples Submitted 2025/12/21 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 62 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
62 samples: 21 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
Superenhancers shape the landscape and repair dynamics of transcription-associated DNA breaks in cancerScience advances · 2026
Summary (written by the submitters)
Cancer is characterized by uncontrolled proliferation accompanied by the hypertranscription of oncogenes, leading to transcription stress, a key source of DNA double-strand breaks (DSBs) that jeopardize genomic stability. Yet, transcription stress is still underexplored. In this study, we utilized maps of DSBs identified through in-suspension break labeling in situ and sequencing (sBLISS), along with transcription stress markers, revealing that transcription stress regions coincide with the super-enhancer regulatory landscape.
Read the full summary ↓
Notably, γH2AX mapping indicates its enrichment at transcription stress sites while not all DSB-enriched genes show equal γH2AX marking, but those with DSBs tied to transcription stress are distinctly marked. Intriguingly, genes with high-DSBs marked by γH2AX exhibited significantly higher DSB turnover and repair than those with γH2AX-low genes, manifesting vulnerability to mutagenesis. These findings underscore super-enhancer activity as a determinant of the transcription stress landscape in cancer, posing a threat to the genomic stability of oncogenes in cancer.
Published in
Superenhancers shape the landscape and repair dynamics of transcription-associated DNA breaks in cancer
Hidmi O, Shatleh D, Flayshman SO et al. · Science advances 2026 · PMID 41564182 · doi:10.1126/sciadv.aeb6379
This dataset
Open GSE290558 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 GSE290558_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 PRJNA1228613 and SRA study SRP566479. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41564182) ↗
Study design
21 conditions, mostly in triplicate
HMLE ×4 A4098 ×3 HEK_293 ×3 HeLa_CDK9i ×3 HeLa_dBET6 ×3 HeLa_DMSO ×3 MCF7_ATMi_ve ×3 MCF7_CDK9i ×3 +16 more

Supports a between-group comparison across 59 samples.

How we read this: 21 replicated groups read from 62 sample titles; they account for 59 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

+ 22 more — browse all 62 samples with per-sample file links →

Datasets on a similar topic

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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