Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
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DNA enrichment by ChIP and SOLiD™ fragment library construction
| Feature | SOLiD™ System | Microarray |
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| Resolution | > 700 million sequence tags/run | ~ 6.5 million oligos/array |
| Genome Coverage | UNLIMITED and hypothesis free | LIMITED by probe design |
| Risk of Cross-Hybridization | None | Between closely related elements |
| Multiplexing | YES | NO |
Comparison of ChIP Detection Platforms
Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a particular protein of interest. This technique gives a picture of the protein-DNA interactions that occur inside the nucleus of living cells or tissues. Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and disease states.
Microarray-based ChIP studies are restricted to a fixed number of probes Currently, the most common method for genome-wide analysis of DNA-binding proteins is Chip-on-chip (ChIP-chip), which combines chromatin immunoprecipitation with DNA microarrays. The major limitation of this hybridization-based method is that microarrays are restricted to a fixed number of probes, thereby introducing bias.
ChIP-Seq with the SOLiD™ System
SOLiD™ System-based ChIP-Sequencing (ChIP-Seq) overcomes the limitation of microarrays by combining chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing, offering a highly sensitive, hypothesis-neutral method to accurately characterize the protein-DNA interactions of an entire genome. The SOLiD™ System’s throughput and flexible slide format allow you to analyze both normal and diseased samples in a single run.
The SOLiD™ ChIP-Seq Kit is optimized for genome-wide ChIP analysis from as little as 10,000 cells and library construction using 1-10 ng of DNA. Magnetic bead capture technology reduces ChIP workflow to just 5 hours, is compatible with multichannel pipetting and improves reproducibility.
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Products
Experimental Workflow: Find the Products You Need for Every Step
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Step 1: Design Experiment
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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Step 2: Prepare DNA
Begin your sample preparation with chromatin immunoprecipitation, in which you:
- Crosslink DNA to DNA-binding proteins.
- Isolate the DNA-protein complexes by shearing the DNA and precipitating the DNA-protein complexes using antibodies.
- Reverse the crosslinking and digest the protein so that the DNA is ready for library preparation.
Products for Step 2: Prepare DNA
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SOLiD™ ChIP-Seq Kit
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The SOLiD™ ChIP-Seq Kit is an optimized system for genome-wide ChIP analysis on the SOLiD™ System, which includes reagents for ChIP and library construction for 20 samples along with a unique optimized protocol.
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View more reagents, kits and bench-top devices on invitrogen.com
Qualified Antibodies for ChIP
Find antibodies for a broad range of applications and targets.
For research use only. Not intended for any animal or human therapeutic or diagnostic use.
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Step 3: Construct DNA Library
Once you have prepared your ChIP DNA, construct a library using the optimized SOLiD™ ChIP-Seq protocol starting with as little as 1 ng of input DNA.
Products for Step 3: Construct DNA Library
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SOLiD™ Fragment Library Oligos Kit
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A set of oligonucleotide adaptors and primers for constructing fragment libraries. The kit contains P1 and P2 adaptors (double-stranded DNA) that are ready for ligation to library DNA and PCR primers for library amplification.
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SOLiD™ ChIP-Seq Kit
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The SOLiD™ ChIP-Seq Kit is an optimized system for genome-wide ChIP analysis on the SOLiD™ System, which includes reagents for ChIP and library construction for 20 samples along with a unique optimized protocol.
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SOLiD™ Library TaqMan® Quantitation Kit
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The SOLiD™ Library TaqMan® Quantitation Kit provides a complete qPCR solution to determine the appropriate amount of library to input into emulsion PCR for all library types.
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Step 4: Amplify & Sequence
After you construct your libraries, amplify the DNA using standard emulsion PCR. Next, deposit the beads on a slide for sequencing on the SOLiD™ Analyzer.
Products for Step 4: Amplify & Sequence
Sequencing
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SOLiD™ 4 System
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The Applied Biosystems SOLiD™ 4 System is a revolutionary genetic analysis platform that enables massively parallel sequencing of clonally-amplified DNA fragments linked to beads. The sequencing methodology is based on sequential ligation with dye-labeled oligonucleotides. The SOLiD™ 4 System enables researchers to obtain higher-quality genomes at lower cost without the purchase of a new instrument.
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Fragment Library Sequencing Reagents for SOLiD™ 4 System, Main Kits
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These kits contain sequencing master mixes in an easy-to-use strip tube format for ligation sequencing of fragment libraries on the SOLiD™ 4 System. Reagent mixing is not required, minimizing tube mix ups and providing a convenient automated method for sequencing reagent handling.
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Instrument Buffers for SOLiD™ 4 System
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This kit contains a set of buffers needed for ligation sequencing on the SOLiD™ 4 System and is sufficient for 110 cycles. The product is compatible only with the SOLiD™ 4 System. Store components at ambient, 2 °C to 8 °C, and at -15 °C to -25 °C.
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Workflow Analysis Reagents for SOLID™ 4 System
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This kit is for accurate qualification and quantitation of templated beads prior to your sequencing run. Use this kit to perform a workflow analysis (WFA) run on the SOLiD™ 4 Analyzer.
Emulsion PCR (ePCR)
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SOLiD™ ePCR Kits
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The SOLiD™ ePCR Kits contain the components needed for amplifying short library inserts by emulsion PCR on beads. Each kit includes reagents for performing PCR, reagents for generating emulsions, and P1 DNA beads for clonal amplification.
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SOLiD™ Buffer Kits
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These kits contain buffers needed for emulsion PCR, bead enrichment, and bead deposition onto slides for ligation sequencing. These kits are available a 10 full-scale reaction size and a 20 mini-reaction size.
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Thermocycler Systems
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We have a full range of thermal cyclers for every budget, including our award-winning Veriti® thermal cycler series.
Bead Deposition
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SOLiD™ Bead Deposition Kits
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These kits contains components for depositing templated beads onto a slide for ligation sequencing on the SOLiD™ Analyzer. The kits contain reagents for performing a 3’ end modification and buffers. These kits are available in a 10 full-scale reaction size and a 20 mini-reaction size.
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SOLiD™ Bead Enrichment Kits
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These kits contain components to enrich templated beads amplified by emulsion PCR. The kit includes enrichment beads and reagents. These kits are available in a 10 full-scale reaction size and a 20 mini-reaction size.
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SOLiD™ Slide Kits
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These kits contain activated slides and storage buffer for ligation sequencing on the SOLiD™ Analyzer.
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Step 5: Analyze Data
Using the data analysis tools listed below:
- Align reads to a reference
- Peak calling
- Visualize data
Products for Step 5: Analyze Data
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Data Analysis Tools
The tools you need for each step in the ChIP-seq data analysis workflow: | Data Analysis Step | Applied Biosystems Tools | Applied Biosystems Software | 3rd-Party Software |
| 1. Align reads to reference in color space | | | |
| 2. Format data | | | |
| 3. Peak calling | | | |
| 4. Format data | | | |
| 5. Visualize in context of annotation | | | |
| 6. Convert to SRF for publishing | | | |
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Step 6: Validate Results
Validate with our Real Time PCR using either TaqMan® or SYBR® Green chemistries.
Products for Step 6: Validate Results
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Real-Time PCR
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For a list of recommended products, visit the Real-Time PCR section of our online catalog.
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Publications & Literature
Application Note
Publications
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.
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