Single-Cell CUT&Tag Kits

Advantages of droplet scCUT&Tag

• High library complexity – Equivalent or greater UMI recovery compared to scATAC-seq for abundant marks like H3K4me1 and H3K27ac.
• Robust per-cell quantification – Optimized tagmentation chemistry ensures accurate fragment capture and low background noise.
• Reproducible results – Each nucleus is barcoded during droplet encapsulation, preserving data integrity across replicates and experiments.
• Ideal for regulatory profiling – Provides precise, quantitative readouts of cell-type–specific chromatin states.

Droplet scCUT&Tag Highlights

• Distinct regulatory clustering – Active histone marks such as H3K4me1, H3K27ac, and H3K4me3 separate cleanly by lineage, defining cell-state diversity.
• Integrated analysis – Compatible with standard single-cell tools like Scanpy or Seurat for dimensionality reduction, clustering, and visualization.
• Biological applications – Reveal cell-type–specific enhancer activity, transcription factor occupancy, and regulatory heterogeneity in complex samples.
• Multiomic-ready – Easily paired with scRNA-seq or scATAC-seq for comprehensive analysis of chromatin control and gene expression.

BD Rhapsody scCUT&Tag enables large-scale mapping of epigenetic landscapes across complex tissues, developmental systems, or perturbation models. Each nucleus is barcoded during micro-well capture, allowing massively parallel profiling of histone modifications, chromatin modifiers, or transcription factors at single-cell resolution.

Key Advantages

• High cell throughput – Profile tens of thousands of nuclei in a single run for comprehensive sampling of cellular heterogeneity.
• Efficient library construction – The BD ATAC-seq chemistry ensures robust tagmentation and high UMI recovery even at large scale.
• Flexible input compatibility – Works with primary cells, cryopreserved material, or sorted populations.

BD Rhapsody scCUT&Tag data integrate smoothly into standard single-cell analysis pipelines such as Scanpy, Seurat, or ArchR, providing clustering and feature embedding directly from TF-IDF–normalized signal matrices. The approach captures cell-type–specific regulatory programs across diverse tissues, enabling researchers to connect chromatin accessibility and histone mark occupancy with transcriptional potential and cell fate.

Applications

• High-diversity tissues – Map chromatin states across immune, neural, or developmental lineages.
• Large-scale perturbation screens – Quantify regulatory responses to chemical, genetic, or environmental stimuli.
• Clinical and translational studies - Characterize patient-derived samples with limited RNA quality but intact chromatin.

PIPseq scCUT&Tag captures the regulatory complexity of chromatin landscapes at single-cell resolution without dependence on proprietary droplet or microwell systems. Barcoding and tagmentation occur within emulsified microdroplets, preserving both sensitivity and per-cell identity across a wide range of input scales.

Key advantages

• Platform-free flexibility - No 10x or BD system required; runs on standard thermocyclers and liquid handlers.
• Scalable throughput - Choose the PIPseq T2, T20, or T100 kit to balance cell numbers, sequencing depth, and cost.
• High data quality - Maintains UMI recovery and signal-to-noise comparable to droplet-based CUT&Tag for abundant marks.

Applications

• Accessible single-cell epigenetics - Extend chromatin profiling capabilities to labs without dedicated droplet instrumentation.
• Custom or pilot projects - Test new antibodies, sample types, or species without platform restrictions.
• Large-scale discovery - Scale up easily using higher-capacity kits for full tissue or organism-wide profiling.