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 CoverageUNLIMITED and hypothesis-freeLIMITED by probe design
Risk of Cross-HybridzationNoneBetween closely related elements
MultiplexingYESNO
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.

Learn More:

Ordering Information

Sku Name Size Price Qty
K182000 PureLink® Genomic DNA Mini Kit 10 preps USD 55.00
K182001 PureLink® Genomic DNA Mini Kit 50 preps USD 138.00
K182002 PureLink® Genomic DNA Mini Kit 250 preps USD 604.00
4449640 SOLiD™ ChIP-Seq Kit 1 kit USD 2,595.00
4449638 SOLiD™ ChIP-Seq Kit, with ChIP magnet 1 kit USD 2,920.00
492024 MAGnify™ Chromatin Immunoprecipitation System 24 reactions USD 518.00

Ordering Information

Sku Name Size Price Qty
4463592 AB Library Builder™ System, self installation 1 instrument Request a Quote  
4463794 AB Library Builder™ System, service installation 1 instrument Request a Quote  
4465657 AB Library Builder™ Barcode Reader 1 instrument Request a Quote  
4463776 AB Library Builder™ Tip and Tube Rack 1 unit USD 1,294.00
4463762 Library Builder™ Fragment Core Kit for the SOLiD™ 4 System 1 kit USD 1,312.00
4465602 AB Library Builder™ Builder D-Rings 1 unit USD 48.90
4465603 AB Library Builder™ Builder D-Ring Tool 1 unit USD 91.75
4463763 Library Builder™ Fragment Core Kit for 5500 Genetic Analysis Systems 1 kit USD 1,312.00
4464412 5500 SOLiD™ Fragment Library Core Kit 1 kit USD 1,100.00
4464404 5500 SOLiD™ Fragment Library Barcode Adaptors 1ndash;96 1 kit USD 5,090.00
4464405 5500 SOLiD™ Fragment Library Barcode Adaptors 1-16 1 kit USD 1,018.00
4464406 5500 SOLiD™ Fragment Library Barcode Adaptors 17ndash;32 1 kit USD 1,018.00
4464407 5500 SOLiD™ Fragment Library Barcode Adaptors 33ndash;48 1 kit USD 1,018.00
4464408 5500 SOLiD™ Fragment Library Barcode Adaptors 49ndash;64 1 kit USD 1,018.00
4464409 5500 SOLiD™ Fragment Library Barcode Adaptors 65ndash;80 1 kit USD 1,018.00
4464410 5500 SOLiD™ Fragment Library Barcode Adaptors 81ndash;96 1 kit USD 1,018.00
4464411 5500 SOLiD™ Fragment Library Standard Adaptors 1 kit USD 458.00
4453093 SOLiD™ EZ Bead™ E10 System Consumables 4 packs USD 2,645.00
4453094 SOLiD™ EZ Bead™ E20 System Consumables 4 pack USD 3,340.00
4453095 SOLiD™ EZ Bead™ E80 System Consumables 4 pack USD 3,915.00
4465571 SOLiD™ EZ Bead™ E120 System Consumables 4 packs USD 5,940.00
4452720 SOLiD™ EZ Bead™ Emulsifier E10 Reagents Kit 1 kit USD 96.75
4452721 SOLiD™ EZ Bead™ Emulsifier E20 Reagents Kit 1 kit USD 184.00
4452722 SOLiD™ EZ Bead™ Emulsifier E80 Reagents Kit 1 kit USD 504.00
4465555 SOLiD™ EZ Bead™ Emulsifier E120 Reagents Kit 1 each USD 790.00
4453065 SOLiD™ EZ Bead™ Emulsifier E10 Accessories Kit 1 kit USD 102.00
4453076 SOLiD™ EZ Bead™ Emulsifier E20 Accessories Kit 1 kit USD 102.00
4453070 SOLiD™ EZ Bead™ Emulsifier E80 Accessories Kit 1 kit USD 112.00
4465569 SOLiD™ EZ Bead™ Emulsifier E120 Accessories Kit 1 each USD 112.00
4457185 SOLiD™ EZ Bead™ Emulsifier Oil Pack Kit 1 kit USD 81.50
4453071 SOLiD™ EZ Bead™ Amplifier E10 Accessories Kit 4 packs USD 112.00
4453077 SOLiD™ EZ Bead™ Amplifier E20 Accessories Kit 4 packs USD 112.00
4453072 SOLiD™ EZ Bead™ Amplifier E80 Accessories Kit 4 packs USD 143.00
4452723 SOLiD™ EZ Bead™ Enricher E10 Reagent Kit 1 kit USD 102.00
4452724 SOLiD™ EZ Bead™ Enricher E20 Reagent Kit 1 kit USD 189.00
4452725 SOLiD™ EZ Bead™ Enricher E80 Reagent Kit 1 kit USD 534.00
4465564 SOLiD™ EZ Bead™ Enricher E120 Reagents Kit 1 each USD 1,068.00
4444140 SOLiD™ EZ Bead™ Enricher Buffer Reagent Kit 1 kit USD 117.00
4453073 SOLiD™ EZ Bead™ Enricher Accessories Kit 1 kit USD 204.00
4449639 SOLiD™ Library TaqMan® Quantitation Kit 250 reactions USD 1,086.00
A12127 SOLiD™ Library TaqMan® qPCR Module 250 reactions USD 810.00
A12126 SOLiD™ Library qPCR Standard 10 µL USD 307.00
4449640 SOLiD™ ChIP-Seq Kit 1 kit USD 2,595.00
4449638 SOLiD™ ChIP-Seq Kit, with ChIP magnet 1 kit USD 2,920.00
4444836 SOLiD™ Fragment Library Barcoding Kit Module 1-16 16 barcodes USD 1,208.00
4449636 SOLiD™ Fragment Library Barcoding Kit Module 17-32 16 barcodes USD 1,208.00
4449635 SOLiD™ Fragment Library Barcoding Kit Module 33-48 16 barcodes USD 1,208.00
4449641 SOLiD™ Fragment Library Barcoding Kit Module 49-64 16 barcodes USD 1,208.00
4449642 SOLiD™ Fragment Library Barcoding Kit Module 65-80 16 barcodes USD 1,208.00
4449643 SOLiD™ Fragment Library Barcoding Kit Module 81-96 16 barcodes USD 1,208.00
4443471 SOLiD™ Fragment Library Construction Kit, with size selection gels 10 preps USD 1,986.00
4443713 SOLiD™ Fragment Library Construction Reagents 10 preps USD 1,862.00
4443473 SOLiD™ Fragment Library Construction Kit 10 preps USD 1,928.00
4385612 Fast SYBR® Green Master Mix 1 x 5 mL USD 403.20
4352042 TaqMan® Fast Universal PCR Master Mix (2X), no AmpErase® UNG 250 reactions USD 242.00

Learn More:

 

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.

Ordering Information

Sku Name Size Price Qty
4460730 5500xl Genetic Analyzer 1 instrument Request a Quote  
4452865 5500 Genetic Analyzer 1 instrument Request a Quote  
4461826 SOLiD™ 6-Lane FlowChip 1 kit USD 678.00
4463011 SOLiD™ FWD1 SP Kit 1 kit USD 167.00
4463012 SOLiD™ FWD2 SP Kit 1 kit USD 167.00
4463019 SOLiD™ REV1 (RNA) SP Kit 1 kit USD 209.00
4463020 SOLiD™ REV1 (DNA) SP Kit 1 kit USD 209.00
4463013 SOLiD™ Small RNA SP Kit 1 kit USD 167.00
4463030 SOLiD™ REV SR Kit, Double 1 kit USD 3,225.00
4463032 SOLiD™ FWD ECC Module, Double 1 kit USD 1,146.00
4461840 SOLiD™ Run Cycle Buffer Kit, Double 1 kit USD 642.00
4459193 SOLiD™ FWD Buffer, Double 1 kit USD 78.50
4463027 SOLiD™ REV Buffer, Double 1 kit USD 78.50
4458935 SOLiD™ Buffer D, Double 1 kit USD 78.50

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

Learn more

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.