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 signal tracks for multiple targets in K562 cells
Comparative ChIP-seq profiles across multiple targets.

ChIP-seq 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.

ChIP-seq 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 signal tracks for multiple targets in K562 cells
Comparative CUT&Run profiles across multiple targets.

CUT&RUN Workflow

  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.

CUT&RUN 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

CUT&Tag fragment insert size distribution for low-input samples
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 signal tracks for multiple targets in K562 cells
Comparative CUT&Tag profiles across multiple targets.

CUT&Tag 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.

CUT&Tag 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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