ChIP-seq crosslinks chromatin with formaldehyde, sonicates it, and immunoprecipitates protein-DNA complexes. CUT&RUN and CUT&Tag work differently. They use an antibody bound in situ to direct a nuclease or transposase to the target. This releases or tags the adjacent DNA without bulk immunoprecipitation. Both methods need fewer cells, give lower background, and use less antibody than conventional ChIP-seq.
NGS - Next Generation Sequencing
ChIP-seq Kits and Epigenomic Profiling
CUT&RUN, CUT&Tag, ChIP-seq, Methyl-seq and Fiber-seq kits for epigenomic profiling
ChIP-seq maps histone marks and transcription factors, but the protocol takes a week and needs millions of your cells. CUT&RUN and CUT&Tag skip chromatin sonication and immunoprecipitation. Instead, an antibody directs enzymatic cleavage or tagmentation at the target site in situ, so you can work from several thousand cells with far fewer sequencing reads.
CUT&RUN suits most of your targets and cell types, including transcription factors and chromatin remodelling enzymes, and needs little optimisation. CUT&Tag works from as few as 10,000 nuclei using a direct-to-PCR workflow that goes from your cells to library in two days. It gives you the strongest results for histone marks and rewards labs with chromatin mapping experience. ChIP-seq remains useful when continuity with established datasets, validated in-house workflows, or specific crosslinking-based experimental designs is important. For many new chromatin-mapping projects, CUT&RUN or CUT&Tag can reduce input, hands-on time and sequencing requirements.
For DNA methylation, meCUT&RUN maps 5-methylcytosine genome-wide without bisulfite conversion, avoiding the DNA damage bisulfite chemistry causes. Standard library preparation needs only 10,000 of your cells and 15 million reads to provide enrichment profiles at approximately 150 bp resolution; adding enzymatic conversion gives you base-resolution 5mC calls at higher sequencing depth. Bisulfite sequencing kits remain available when your lab is standardised on PBAT or high-sensitivity bisulfite workflows.
Fiber-seq goes further still, mapping chromatin accessibility, DNA methylation and protein footprints from single DNA molecules in one long-read run.
- Assay type first. For most histone marks, transcription factors or chromatin remodellers, a CUT&RUN kit gives you the best start. For low-input histone PTM profiling from limited nuclei, CUT&Tag suits you. A ChIP-seq kit fits when you need to match legacy datasets or a validated protocol.
- Input amount. CUT&RUN works from 5,000 to 500,000 cells with 3 to 8 million reads. CUT&Tag needs 10,000 to 100,000 of your nuclei. ChIP-seq needs millions of your cells and 20 to 60 million reads, though high-sensitivity formats bring that down to 100 cells.
- Methylation target. For genome-wide 5-methylcytosine without bisulfite conversion, meCUT&RUN gives you the direct route. If your lab is standardised on bisulfite chemistry, PBAT and high-sensitivity bisulfite-seq kits remain available. For 5-mC or 5-hmC in RNA, RNA bisulfite-seq kits cover your needs.
- Multiomic and long-read needs. When one experiment needs to capture accessibility, methylation, protein footprints and sequence-variant information together, Fiber-seq gives you all four in one long-read experiment. It reduces the need for separate ATAC-seq and methylation workflows, but does not replace target-specific chromatin profiling when a defined histone modification or protein must be mapped.
Applications
CUT&RUN chromatin mapping
CUT&RUN maps histone marks, transcription factors and remodelling enzymes from as few as 5,000 cells. Pairing it with CUT&RUN reagents and antibodies gives you antibody-guided cleavage.
CUT&Tag low-input profiling
CUT&Tag profiles histone modifications from 10,000 to 100,000 nuclei using a direct-to-PCR workflow. It suits labs with chromatin mapping experience and your single-cell studies.
meCUT&RUN DNA methylation
meCUT&RUN maps 5-methylcytosine genome-wide from 10,000 cells, without bisulfite conversion. Bisulfite and DNA methylation kits are also available as well as m6A and 5-mC RNA Methylation Kits.
Fiber-seq multiomic profiling
Fiber-seq captures chromatin accessibility, DNA methylation and protein footprints from single DNA molecules in one long-read run.
ChIP-seq histone and TF mapping
ChIP-seq remains available for labs matching legacy datasets or protocols already validated in-house. High-sensitivity formats handle your inputs down to 100 cells per reaction.
Open chromatin profiling
ATAC-seq maps open chromatin using Tn5 or Next Generation Transposase TnX transposase, from as few as 500 of your cells without an antibody. For accessibility, methylation and protein footprints in one run, Fiber-seq gives you all three instead.
Frequently asked questions
Standard ATAC-seq protocols use 50,000 cells as a starting point. Optimised versions work with 500 to 5,000 cells. Single-cell ATAC-seq captures chromatin accessibility from individual nuclei. Cell viability above 85% and immediate processing after isolation improve signal quality, by reducing mitochondrial DNA contamination and nucleosome degradation.
5-methylcytosine (5-mC) is a stable epigenetic mark linked to gene silencing. 5-hydroxymethylcytosine (5-hmC) is an oxidised derivative found at active enhancers and gene bodies. Standard bisulfite sequencing cannot tell them apart. Both read as protected cytosine. To resolve 5-mC from 5-hmC, use oxidative bisulfite sequencing or TET-assisted bisulfite methods.
For transcription factor ChIP-seq, 20 to 30 million mapped reads is usually enough for sharp-peak targets. Broad histone marks such as H3K9me3 benefit from 40 to 60 million reads. Sequence input control libraries at a comparable depth to the ChIP library. This supports accurate peak calling and background normalisation.
Product catalogs
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