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A side-by-side comparison of commercial CUT&RUN kits [Cut&Run]

GSE306233 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 72 samples Submitted 2026/05/15 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 72 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
72 samples: 72 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
A side-by-side comparison of commercial CUT&RUN kitsJournal of biomolecular techniques : JBT · 2026
Summary (written by the submitters)
Introduction: CUT&RUN (Cleavage Under Targets and Release Using Nuclease) followed by next-generation sequencing is a powerful method increasingly used in place of ChIP-seq to profile genome-wide protein-DNA interactions including those of transcription factors, histone modifications and chromatin remodelers. Although the choice of antibody is well known to affect data quality, we found that enrichment chemistry and protocol significantly affect data quality as well.
Read the full summary ↓
Methods: In this study, we evaluated the performance of three commercially available CUT&RUN kits (Active Motif - ChIC/CUT&RUN Assay Kit, Cell Signaling Technology (CST) – CUT&RUN Assay Kit, EpiCypher - CUTANA™ ChIC/CUT&RUN Kit) on two target histone marks to represent sharp peaks (H3K4me3) and broad domains (H3K27me3). We compared data quality from libraries generated with fresh and frozen cells as well as with cell numbers that represent the low and high ends of the recommended input. Results and Discussion: Our results show that all three chemistries generate high-quality libraries. Our data revealed that despite generating libraries with fewer H3K4me3 peaks than the EpiCypher and Active Motif workflows did, the CST protocol generated libraries with superior signal and higher accuracy. Compared with the H3K4me3 libraries, the H3K27me3 libraries presented a lower percentage of shared peaks across all libraries and lower reproducibility between technical replicates. Compared with the CST protocol, the Active Motif and EpiCypher protocols generated H3K27me3 libraries with higher peak numbers, and the EpiCypher chemistry scored highest in accuracy. Libraries from cryopreserved cells generated data of similar quality as libraries from fresh cells; libraries generated with 100,000 cells had higher concordance between technical replicates than did libraries made with 500,000 cells.
Published in
A side-by-side comparison of commercial CUT&RUN kits
Pham K, Rodriquez V, Tokcan E et al. · Journal of biomolecular techniques : JBT 2026 · PMID 42088458 · doi:10.7171/001c.154138
This dataset
Open GSE306233 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 GSE306233_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 PRJNA1309724 and SRA study SRP610875. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42088458) ↗
Study design
72 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 72 sample titles: 72 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

+ 32 more — browse all 72 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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