Omics · study · 2026
A side-by-side comparison of commercial CUT&RUN kits
Listed in NCBI GEO
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.
Description
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.
Methods
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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). ATAC-seq data was integrated to assess the accuracy of peaks generated with each CUT&RUN kit.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE306nnn/GSE306141 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE306141 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1309578 ncbi.nlm.nih.gov/bioproject/PRJNA1309578 ↗
project · from NCBI GEO
- PubMed 42088458 pubmed.ncbi.nlm.nih.gov/42088458 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Genome binding/occupancy profiling by high throughput sequencing · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- Genetics 70% · Sequencing 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE306141 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].anzsrc:group:3105 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (70%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:genome-binding-occupancy-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |