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Get High-Resolution ChIP-Exo-Seq Results for your Publication

Stop wasting precious samples and research time. 

Our HPA-validated antibodies deliver superior specificity and reproducibility for chromatin immunoprecipitation applications.

 

Find ChIP-Validated Antibodies →

97%

Specificity Rate 

500+

Chip-Validated Antibodies

88%

Reduced Time-to-Results

1450+

ChIP Citations

 

ChIP Challenges: What’s Slowing You Down?

 

 

1. Non-Specific Binding

Generic antibodies often bind to off-target proteins, creating misleading signals and confounding your data interpretation. This leads to inconclusive or false results that can't be published.

2. Batch-to-Batch Variability

Inconsistent antibody performance between lots forces constant re-validation and protocol adjustments. Just when you optimize your workflow, the next batch fails.

3. Limited Sample Yield

Poor antibody efficiency means you need more starting material for successful ChIP experiments. This is particularly problematic with rare or patient-derived samples.

4. Unknown Epitope Accessibility

Many antibodies recognize epitopes that become inaccessible in crosslinked chromatin, resulting in weak or absent signals despite the target being present.

5. High Background Noise

Excessive background signal in ChIP-seq data creates analytical challenges and reduces peak detection confidence. This often requires complex bioinformatic correction.

6. Time-Consuming Optimization

Without validated ChIP antibodies, you might spend weeks or months adjusting conditions before getting usable data, delaying publications and discoveries.

 

The Atlas Antibodies ChIP-Exo-Seq Solution

 

1

HPA-Designed Antibodies

Our antibodies are engineered from the Human Protein Atlas project.

2

Functional Enrichment

Our antibodies are tested in ChIP assays to confirm enrichment at known binding sites.

3

Cross-Platform Testing

Validation across standard ChIP and next-gen ChIP-seq/Exo-seq.

4

Batch Consistency

Our antibodies are ISO-certified for reliable lot-to-lot performance.

 

Download the Application Note

 

 

 

 

 

ChIP-Exo-Seq by Atlas Antibodies

✅ Higher Resolution 

Achieves near single-base precision for mapping binding sites.

✅ Reduced Noise 

Exonuclease trimming eliminates background DNA, leading to cleaner data.

✅ Precise Localization 

Provides more accurate mapping of transcription factor binding sites or other protein-DNA interactions

Establishing a Higher Benchmark for Antibodies Performance

Our antibodies demonstrate exceptional specificity and reproducibility in ChIP-Exo-Seq assays.

This ensures sharper, more accurate peak detection, marking exact protein-DNA binding sites. 

Image: ChIP-Exo-Seq composite graph for Anti-ELF1 (HPA001755, Lot R00715) tested in K562 cells. Strand-specific reads (blue: forward, red: reverse) and IgG controls (black: forward, grey: reverse) are plotted against the distance from a composite set of reference binding sites. Plots are smoothed by a 21 bp moving average across 460 sites. The antibody exhibits robust target enrichment compared to a non-specific IgG control and precisely reveals its structural organization around the binding site. Data generated by Prof. B. F. Pugh´s Lab at Cornell University, Ithaca, NY, USA.

 

Ready to Elevate Your Chromatin Research?

Say goodbye to unreliable antibodies, inconsistent enrichment, and low-resolution data. Our ChIP-Exo–Seq-validated antibody collection delivers high specificity and reproducibility for precise mapping of protein-DNA interactions—saving your samples and your time.

Select from over 500 of expertly designed, ChIP-grade targets tailored for chromatin research.

 

Start Today!

 

 

🔬 Expert Support

Protocol optimization and technical guidance from ChIP specialists—our scientists at Atlas Antibodies and the Human Protein Atlas provide expert support and guidance to help you achieve reliable, reproducible results. From experiment design to troubleshooting, we're here to assist every step of the way.

 

Need Help? Contact Us!

 

Anti-GTF2A1 Antibody
Anti-GTF2A1 Antibody

Anti-GTF2A1 Antibody

HPA000869
In Stock (10+)
4 570,0 kr
Anti-ZNF148 Antibody
Anti-ZNF148 Antibody

Anti-ZNF148 Antibody

HPA001656
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4 570,0 kr
Anti-CEBPE Antibody
Anti-CEBPE Antibody

Anti-CEBPE Antibody

HPA002928
In Stock (10+)
4 311,0 kr
Anti-GABPA Antibody
Anti-GABPA Antibody

Anti-GABPA Antibody

HPA003258
In Stock (10+)
4 570,0 kr
Anti-UBE2B Antibody
Anti-UBE2B Antibody

Anti-UBE2B Antibody

HPA003875
In Stock (10+)
4 570,0 kr
Anti-SMARCD1 Antibody
Anti-SMARCD1 Antibody

Anti-SMARCD1 Antibody

HPA004101
In Stock (10+)
4 570,0 kr
Anti-ZBTB17 Antibody
Anti-ZBTB17 Antibody

Anti-ZBTB17 Antibody

HPA005789
In Stock (10+)
4 570,0 kr
Anti-ZNF445 Antibody
Anti-ZNF445 Antibody

Anti-ZNF445 Antibody

HPA006678
In Stock (10+)
4 570,0 kr
Anti-MEF2D Antibody
Anti-MEF2D Antibody

Anti-MEF2D Antibody

HPA007114
In Stock (10+)
4 311,0 kr
Anti-NMI Antibody
Anti-NMI Antibody

Anti-NMI Antibody

HPA008588
In Stock (10+)
4 570,0 kr
Anti-ZNF134 Antibody
Anti-ZNF134 Antibody

Anti-ZNF134 Antibody

HPA009064
In Stock (10+)
4 570,0 kr
Anti-ZNF599 Antibody
Anti-ZNF599 Antibody

Anti-ZNF599 Antibody

HPA014701
In Stock (10+)
4 570,0 kr
Anti-NSD3 Antibody
Anti-NSD3 Antibody

Anti-NSD3 Antibody

HPA018893
In Stock (10+)
4 570,0 kr
Anti-HAND2 Antibody
Anti-HAND2 Antibody

Anti-HAND2 Antibody

HPA019591
In Stock (10+)
4 570,0 kr
Anti-ING2 Antibody
Anti-ING2 Antibody

Anti-ING2 Antibody

HPA021517
In Stock (10+)
4 570,0 kr
Anti-ZBTB2 Antibody
Anti-ZBTB2 Antibody

Anti-ZBTB2 Antibody

HPA023487
In Stock (10+)
4 570,0 kr
Anti-ZSCAN2 Antibody
Anti-ZSCAN2 Antibody

Anti-ZSCAN2 Antibody

HPA024331
In Stock (10+)
4 570,0 kr
Anti-GTF2I Antibody
Anti-GTF2I Antibody

Anti-GTF2I Antibody

HPA026638
In Stock (10+)
4 311,0 kr
Anti-NAB2 Antibody
Anti-NAB2 Antibody

Anti-NAB2 Antibody

HPA027464
In Stock (10+)
4 570,0 kr
Anti-MYOG Antibody
Anti-MYOG Antibody

Anti-MYOG Antibody

HPA028336
In Stock (10+)
4 311,0 kr
Anti-ELK4 Antibody
Anti-ELK4 Antibody

Anti-ELK4 Antibody

HPA028863
In Stock (10+)
4 570,0 kr
Anti-SUPT5H Antibody
Anti-SUPT5H Antibody

Anti-SUPT5H Antibody

HPA029273
In Stock (10+)
4 570,0 kr
Anti-EGR1 Antibody
Anti-EGR1 Antibody

Anti-EGR1 Antibody

HPA029938
In Stock (10+)
4 311,0 kr
Anti-ZNF30 Antibody
Anti-ZNF30 Antibody

Anti-ZNF30 Antibody

HPA030400
In Stock (10+)
4 570,0 kr

 

FAQs: Your Questions Answered

 

  • What is ChIP-Exo-Seq, and how does it differ from ChIP-Seq?

    ChIP-exo seq is a refinement of ChIP-seq that uses exonuclease digestion to improve the resolution of protein-DNA interaction mapping. The exonuclease trims DNA in a 5' to 3' direction, stopping at the protein-DNA crosslink. This results in single-base resolution of binding sites, compared to the broader peaks typical of ChIP-seq. It reduces background noise and provides more precise localization of binding sites.

  • What are the key advantages of ChIP-Exo-Seq over traditional ChIP-Seq?

     

    • Single-base resolution: ChIP-exo seq provides near-base-pair precision for mapping binding sites.
    • Reduced noise: Exonuclease digestion eliminates nonspecific DNA, leading to cleaner data.
    • More accurate peak calling: Peaks are sharper and better defined compared to ChIP-seq.
    • Higher reproducibility: The improved precision leads to better reproducibility across experiments.
  • What types of applications can benefit from ChIP-Exo-Seq?

    ChIP-exo seq is particularly useful for:

    • Identifying transcription factor binding sites with high precision.
    • Mapping histone modifications or other epigenetic markers at single-base resolution.
    • Understanding cis-regulatory elements in gene regulation.
    • Enhancing functional studies in comparative genomics or between different cell states.
  • How does the data analysis for ChIP-Exo-Seq differ from ChIP-Seq?

    In ChIP-exo seq, the data consists of sharp peaks marking the exonuclease stop points, requiring specialized analysis tools.

    The analysis pipeline involves:

    Mapping sequencing reads to the reference genome.
    Calling precise peaks using algorithms that account for single-base resolution.
    Comparing sharp peaks to motifs or regulatory elements for functional interpretation. Unlike ChIP-seq, the narrower peak width makes false positives less likely.

  • ChIP-Exo-Seq Protocol

    Protocol Overview:
    The method combines chromatin immunoprecipitation (ChIP) with next-generation sequencing to identify binding sites of DNA-associated proteins across the genome.

    Steps in the Protocol:

    Crosslink and shear DNA 
    Proteins of interest are crosslinked to DNA to preserve protein-DNA interactions.
    The DNA is fragmented into smaller pieces using shearing methods (e.g., sonication).
    Chromatin immunoprecipitation (ChIP)
    Specific antibodies are used to bind the protein of interest, isolating the DNA-protein complex.
    Immunoprecipitation is performed to pull down these complexes.
    Adaptor ligation
    A first adaptor is ligated to the ends of the sheared DNA fragments.
    The ends are filled in to create blunt ends for downstream steps.
    Exonuclease digestion (5' to 3')
    An exonuclease enzyme digests the DNA in a 5' to 3' direction.
    Digestion stops precisely at the point where the protein is crosslinked to DNA, leaving single-stranded DNA ends.
    Reverse crosslinking and adaptor addition
    The protein-DNA crosslinks are reversed, freeing the DNA.
    The DNA is extended using primer extension, and a second adaptor is ligated to the opposite end.
    High-throughput sequencing analysis
    The processed DNA is subjected to high-throughput sequencing to map the protein-DNA binding sites.
    The resulting sequencing data identifies sharp peaks, representing precise protein-DNA interaction sites at single-base resolution.