Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and for disease research.

ChIP-Seq technology can simplify your process for identifying and characterizing protein–DNA interactions.

ChIP (the capture specific DNA-bound proteins) followed by next-generation DNA sequencing allows you to map where proteins bind across the genome.

ChIP-Seq combines the quantification advantage afforded by high numbers of reads with the single-base resolution of sequencing.

Benefits Over Microarrays

Microarrays are restricted to the number of queried sequences and to the sequence content of the probes on a given array.

Direct sequencing of enriched fragments is more effective in determining protein binding sites in an unbiased, hypothesis-free manner.

Feature 5500 Genetic Analyzers Microarrays
Resolution > 700 million sequence tags/run ~ 6.5 million oligos/array
Genome Coverage UNLIMITED and hypothesis-free LIMITED by probe design
Risk of Cross-Hybridzation None Between closely related elements
Multiplexing YES NO
Comparison of ChIP Detection Platforms

ChIP-Seq With the MAGnify™ ChIP Kit, 5500 Fragment Library Reagent Kit, and the 5500xl Genetic Analyzer

Enlarge Image
Figure 1: DNA enrichment by chromatin immunoprecipitation(ChIP)
and SOLiD® fragment library construction.

Optimized, end-to-end system for genome-wide ChIP analysis

Includes ChIP preparation reagents and library generation reagents for 12 samples.

Significantly simplified sample prep:

  • Dynabeads® immunoprecipitation allows rapid isolation of protein:DNA complexes
  • Novel magnetic MAGnify™ ChIP DNA Kit purification beads allow rapid isolation of DNA fragments and eliminate the need for lengthy phenol:chloroform precipitation or column purification
  • ChIP washes are optimized with two wash buffers instead of four, minimizing handling and time
  • Reduced input cell number means you can finally perform ChIP with high-impact, publication-worthy samples alongside standard samples with one kit
  • Run 16 ChIPs simultaneously
  • Best-in-class reagents from the 5500xl Genetic Analyzer.

Together, the MAGnify™ ChIP Kit, 5500 Fragment Library Reagent Kit, and the Ultra–High-Throughput 5500xl Genetic Analyzer Enable:

  • Hypothesis-free analysis—unbiased characterization of protein–DNA interactions across the genome without spacing limitations imposed by predetermined microarray probes
  • Increased sensitivity—high numbers of uniquely mapping reads coupled with superior accuracy provide precise binding site localization and quantification
  • Low sample input—perform genome-wide ChIP analysis from as little as 167 µg of fresh frozen tissue or 10,000 primary cells, with library construction requiring only 1 to 10 ng of DNA
  • Multiplexing—the SOLiD® Fragment Library Barcoding Kits allow you to sequence up to 50 ChIP-Seq libraries simultaneously in a single lane, reducing per-sample analysis cost and allowing you to analyze both normal and diseased research samples in a single run
  • Faster sample prep—perform the ChIP workflow typically in just 5 hours, compared to 2 to 3 days for traditional ChIP. The MAGnify ChIP Kit is highly optimized using magnetic bead capture technology, and is compatible with multichannel pipetting, simplifying the workflow and improving reproducibility
  • Simplified workflows—clear, optimized protocols and kits guide you from sample preparation through analysis, so you get results sooner

Step-by-Step Guide to Chromatin Immunoprecipitation Sequencing (ChIP-Seq)

Antibody quality has a significant impact on results. Order ChIP qualified antibodies for your protein of interest or qualify the antibodies yourself. When designing your experiment, consider important parameters such as the target number of tags to be sequenced, sensitivity, controls, and multiplexing.

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User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub.

The tools you need for each step in the ChIP-Seq data analysis workflow:

Data Analysis Step Applied Biosystems Software 3rd-Party Software***
1. Align reads to reference in color space
  • ICS
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
2. Generate quality metrics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
3. Generate sequencing and alignment statistics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
4. Format data and call peaks
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
5. Translate color space to base space  
6. Visualize in context of annotation
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
7. Convert SRF for publishing    
*** Need XSQ --> csfasta/qual converter

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