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Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples

GSE261351 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 278 samples Submitted 2025/01/16 Platform GPL30173Platform GPL30172Platform GPL11154
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 278 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
278 samples: 278 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
RNA polymerase II at histone genes predicts outcome in human cancerScience (New York, N.Y.) · 2025
Summary (written by the submitters)
Hypertranscription occurs at targets of oncogene transcription factors in aggressive human cancers. However, detection relies on mRNAs which are heavily processed and have variable half-lives, and on accurate cell number estimations. Here we apply FFPE-CUTAC on slides and curls to quantify hypertranscription at regulatory elements and replication-coupled histone genes.
Published in
RNA polymerase II at histone genes predicts outcome in human cancer
Henikoff S, Zheng Y, Paranal RM et al. · Science (New York, N.Y.) 2025 · PMID 39946483 · doi:10.1126/science.ads2169
This dataset
Open GSE261351 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 GSE261351_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 PRJNA1086538 and SRA study SRP494607. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39946483) ↗
Study design
278 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 138 samples read as cases, 105 as controls.

How we read this: Read from 278 sample titles: 278 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

+ 238 more — browse all 278 samples with per-sample file links →

Datasets on a similar topic

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

Share this dataset

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.