Quantitative Chromatin Profiling for Regulatory Discovery

Epigenome Technologies runs validated ChIP-seq, CUT&Run, and CUT&Tag assays so your project teams receive gold-standard protein-DNA interaction maps, histone modification landscapes, and transcription factor occupancy data. We align method selection to sample constraints and deliver ideal data for your experiment.

ChIP-seq

Gold Standard

Robust immunoprecipitation for abundant targets and established benchmarks.

CUT&Run

Low Background

In situ enzyme cleavage for high signal-to-noise and scarce samples.

CUT&Tag

Ultra-Low-Input

Antibody-guided tagmentation for single-cell compatibility and minimal handling.

Speak with a Scientist Request a Project Brief Get a Quote

Choose the right chromatin profiling method

Service Cat. No Input Requirements Background Best For Inquiry
ChIP-seq EGT-CS-310 ≥1M cells Established Gold standard, abundant targets, benchmarking Request Quote
CUT&Run EGT-CR-105 100K-250K cells Reduced Scarce samples, difficult targets, lower sequencing Request Quote
CUT&Tag EGT-CT-201 5,000–50,000 cells Minimal Ultra-low-input, single-cell, high-throughput Request Quote
H3K4me3 TSS enrichment heatmap
H3K4me3 signal enrichment at transcription start sites across chromatin profiling methods.

Chromatin profiling for mechanistic discovery

ChIP-seq, CUT&Run, and CUT&Tag map protein-DNA interactions and histone modifications to define regulatory states. We emphasize when each modality delivers optimal signal-to-noise, resolution, and sample efficiency for specific biological questions.

Common applications

  • Transcription factor binding site identification and regulatory network mapping
  • Histone modification profiling for chromatin state annotation
  • Enhancer and silencer element mapping for therapeutic targeting
  • Drug response screens tracking chromatin remodeling
  • Single-cell epigenetic heterogeneity in disease and development
  • FFPE and archival specimen rescue for retrospective analysis

Included with every engagement

Boxplot comparison of fragments-in-peaks
ChIP, CUT&Run, and CUT&Tag differ in input requirements, and signal-to-noise.
  • Joint design sessions align sample availability, antibody validation, method selection, and controls
  • Project scientists embedded through QC reviews, peak calling, and interpretation
  • Peak calling and replicate concordance benchmarked to established standards
  • Optional differential occupancy analysis and motif discovery for regulatory insights

ChIP-seq: Gold-Standard Chromatin Immunoprecipitation

For legacy comparisons or antibody panels best suited to immunoprecipitation, our ChIP-seq service offers full project management from chromatin preparation through sequencing and analysis. Established benchmark for mapping protein-DNA interactions through cross-linking, immunoprecipitation, and sequencing.

ChIP-seq multi-target tracks in K562 cells
Multiple histone modifications profiled by ChIP-seq in K562 cells.

Best for

  • High-input samples (≥1 million cells typical)
  • Abundant transcription factors and histone marks
  • Benchmarking and method validation studies
  • Broad antibody compatibility requirements
  • Cross-linked or native chromatin from diverse tissues and cell lines

QC metrics

  • FRiP (Fraction of Reads in Peaks) ≥ 0.15
  • NSC (Normalized Strand Coefficient) ≥ 1.05
  • RSC (Relative Strand Correlation) ≥ 0.8
  • Replicate correlation > 0.90
ChIP-seq profile comparison
Comparative ChIP-seq profiles across multiple targets.

Workflow

  1. Plan

    Experiment design review, antibody sourcing guidance, and sample batching strategy.

  2. Prepare chromatin

    Cross-linking, chromatin shearing, and immunoprecipitation with QC on fragment distribution.

  3. Library construction

    Adapter ligation, size selection, and amplification with complexity assessment.

  4. Sequence & analyze

    Paired-end sequencing, peak calling, and integrated analysis connecting occupancy to gene regulation.

Deliverables

  • Library QC metrics and sequencing-ready material or FASTQ delivery
  • Peak calls, coverage tracks, and replicate concordance reports
  • Detailed processing report with QC, coverage metrics, and call parameters
  • Optional downstream integration with CUT&Tag or RNA outputs

Advantages

  • Gold-standard methodology with extensive literature validation
  • Broad antibody compatibility across targets
  • Robust for abundant targets with established protocols
  • Established QC benchmarks for quality assurance

CUT&Run: Low-Background, High-Resolution Mapping

CUT&Run delivers precise protein-DNA maps with minimal background by cleaving chromatin only at antibody-bound loci. In situ chromatin profiling using antibody-tethered enzyme cleavage eliminates cross-linking artifacts and reduces non-specific background. The assay is ideal for transcription factor discovery, enhancer validation, and studies limited by sample quantity.

CUT&Run multi-target tracks in K562 cells
Multiple histone marks profiled by CUT&Run.

Best for

  • Low-input samples (50,000–100,000 cells)
  • Targets with high non-specific background in ChIP-seq
  • Studies requiring reduced sequencing costs
  • Difficult-to-crosslink or labile protein targets
  • Optimized workflows for transcription factors, cofactors, and chromatin remodelers

QC metrics

  • FRiP ≥ 0.40 (typically higher than ChIP-seq)
  • Background signal reduction vs ChIP-seq documented per target
  • Spike-in normalization for quantitative comparisons
  • Replicate correlation > 0.92
CUT&Run profile comparison
Comparative CUT&Run profiles across multiple targets.

Workflow highlights

  1. Plan

    Sample batching, antibody validation, and controls with our scientists.

  2. In situ binding

    Cell permeabilization, antibody incubation, and protein A-MNase tethering.

  3. On-bead digestion

    Controlled chromatin cleavage at antibody-bound sites with integrated QC checks.

  4. Library & analysis

    Library prep, sequencing, and delivery of fastqs, basic analyses, and publication-ready figures.

Deliverables

  • Library QC metrics with spike-in normalization curves
  • FASTQ files and sequencing-ready material
  • Peak calls with enrichment at known regulatory elements
  • Comparative signal-to-noise analysis versus ChIP-seq
  • Optional replicates for robust differential analysis

Advantages

  • Reduced non-specific background compared to ChIP-seq
  • Lower sequencing depth requirements (cost savings)
  • Faster protocol without cross-linking steps
  • Improved signal-to-noise for difficult targets
  • Rapid turnaround for pilot validation

CUT&Tag: Ultra-Low-Input Antibody-Guided Tagmentation

CUT&Tag couples antibody targeting with tethered transposase to map histone marks or transcription factors with exceptional signal-to-noise. Direct tagmentation of antibody-bound chromatin using protein A-Tn5 fusion enables ultra-low-input profiling and single-cell compatibility. We routinely support projects with limiting input material, FFPE samples, and broad histone panels.

CUT&Tag multi-target tracks in K562 cells
Multiple histone marks profiled by CUT&Tag.

Best for

  • Ultra-low-input samples (5,000–10,000 cells)
  • Single-cell chromatin profiling
  • Studies requiring minimal sample manipulation
  • High-throughput screening with limited material

Insert size distribution
High-quality tagmentation even for low-input samples.

QC metrics

  • FRiP ≥ 0.60
  • Fragment size distribution with clear nucleosomal ladder
  • Single-cell barcode quality and cell detection rates
  • Replicate correlation > 0.90
CUT&Tag profile comparison
Comparative CUT&Tag profiles across multiple targets.

Workflow

  1. Plan

    Sample qualification, antibody validation, and histone mark or TF panel selection.

  2. Epitope binding

    Nuclear extraction, permeabilization, and antibody incubation.

  3. Tagmentation

    Protein A-Tn5 fusion targeting with direct adapter insertion at antibody-bound sites.

  4. Library & analysis

    Single-tube library generation, followed by sequencing, alignment, and peak calling.

Deliverables

  • Library QC metrics with fragment size distributions
  • Sequencing-ready material or FASTQ delivery
  • Peak calls and coverage tracks with nucleosomal resolution
  • Single-cell compatibility demonstrations when applicable
  • Joint RNA-seq integration support for multiomic interpretation

Advantages

  • Ultra-low-input and single-cell compatible
  • Simplified workflow with direct library generation
  • Minimal DNA purification or amplification artifacts
  • High sensitivity for scarce samples
  • Low background with single-fragment resolution
  • Parallel mark profiling to benchmark developmental trajectories

Partner with our scientists

Share your target list, sample availability, and study goals. We will return a scoped chromatin profiling brief outlining recommended assay mix (ChIP-seq, CUT&Run, or CUT&Tag), QC checkpoints, and downstream reporting.

  • Sample requirements: Method-specific inputs from 100 cells (CUT&Tag) to 1M cells (ChIP-seq) with low-input contingencies available.
  • Storage guidance: Fresh, cryopreserved, or FFPE submissions accepted with documented handling.
  • Data options: Raw, processed, and interpretive outputs available individually or bundled.
  • Support: Project scientists provide experimental planning and guidance, data reviews, and troubleshooting.
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