ChIP-exo Services
The ChIP-exo service includes chromatin fragmentation, performance of the ChIP-exo assay, next-gen sequencing, and standard bioinformatics analysis. ChIP-exo identifies protein binding sites across a genome down to near single base pair resolution, compared to resolutions of 100-500 base pairs (bp) for current ChIP-chip and ChIP-seq technology. By combining a superior laboratory method with user-friendly bioinformatics analysis, we produce significantly improved results over ChIP-seq services in the market.
ChIP-exo assay services from Peconic provide researchers with:
Superior ResolutionProtein binding sites identified to near base pair resolution and significantly reduced background noise
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Easy-to-Use BioinformaticsStandard ChIP-exo bioinformatics analysis and data presentation in an easy-to-interpret and use format
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Reduced Risk and CostOur technical expertise combined with competitive pricing reduces research risk and cost
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ChIP-exo Procedure
Chromatin immunoprecipitation, or “ChIP”, is a means by which the genomic binding locations for a protein can be identified. This involves formaldehyde-based crosslinking of proteins to DNA to covalently trap proteins at their physiologically-bound locations in vivo. Genomic binding sites are separated from other sites by sonication, which shears chromosomes into small fragments of ~200-1000 bp. The protein of interest is then purified using immobilized antibodies directed against the protein. The random cleavage of DNA by the sonication process limits mapping resolution to about ±100 bp. To improve this resolution, ChIP-exo employs lambda exonuclease to trim the randomly cleaved ends up to the point of where the protein is crosslinked to DNA, thereby diminishing the uncertainty to about a few base pairs. Since the trimming is exclusively in the 5’- 3’ direction, DNA sequences downstream (more 3’) of the exonuclease block site remain intact, and thus are sufficiently long to allow unique identification by deep sequencing.
Details of the method can be found in a publication by H.S. Rhee and B.F. Pugh in Cell 2011, 147(6):1408-1419 titled “Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.” It should be noted that ChIP-exo is an experimental method with many complicated steps that may fail for technical reasons, or because the protein of interest may not "ChIP" very well.
ChIP-exo Services from Peconic
Peconic provides comprehensive ChIP-exo services to researchers interested in using the methodology to support their core research objectives. Our core service offering includes chromatin fragmentation, performance of the ChIP-exo assay, next-gen sequencing, and standard bioinformatics analysis to provide you with high quality data in an easy-to-use format. ChIP-exo results are available 6 to 8 weeks after receipt of the samples.
Chromatin immunoprecipitation, or “ChIP”, is a means by which the genomic binding locations for a protein can be identified. This involves formaldehyde-based crosslinking of proteins to DNA to covalently trap proteins at their physiologically-bound locations in vivo. Genomic binding sites are separated from other sites by sonication, which shears chromosomes into small fragments of ~200-1000 bp. The protein of interest is then purified using immobilized antibodies directed against the protein. The random cleavage of DNA by the sonication process limits mapping resolution to about ±100 bp. To improve this resolution, ChIP-exo employs lambda exonuclease to trim the randomly cleaved ends up to the point of where the protein is crosslinked to DNA, thereby diminishing the uncertainty to about a few base pairs. Since the trimming is exclusively in the 5’- 3’ direction, DNA sequences downstream (more 3’) of the exonuclease block site remain intact, and thus are sufficiently long to allow unique identification by deep sequencing.
Details of the method can be found in a publication by H.S. Rhee and B.F. Pugh in Cell 2011, 147(6):1408-1419 titled “Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.” It should be noted that ChIP-exo is an experimental method with many complicated steps that may fail for technical reasons, or because the protein of interest may not "ChIP" very well.
ChIP-exo Services from Peconic
Peconic provides comprehensive ChIP-exo services to researchers interested in using the methodology to support their core research objectives. Our core service offering includes chromatin fragmentation, performance of the ChIP-exo assay, next-gen sequencing, and standard bioinformatics analysis to provide you with high quality data in an easy-to-use format. ChIP-exo results are available 6 to 8 weeks after receipt of the samples.
Specific steps in our process include:
To increase the likelihood of success, we also offer an antibody validation service to assess the ChIP-exo compatibility of a chosen antibody. Click here for a list of antibodies that have already been ChIP-exo validated. If your antibody is not on this list, we recommend validating it before running it through the ChIP-exo assay with samples.
- Receipt of your frozen formaldehyde-crosslinked cell pellets and antibodies (we highly recommend including a negative control)
- Chromatin fragmentation of your samples (includes DNA fragmentation check)
- ChIP of your samples
- Exonuclease treatment and library construction with positive (included) and negative controls
- Library gel check
- Deep sequencing of the library using the Illumina NextSeq 500 (paired-end)
- Mapping of the reads to a reference genome
- Peak calling, peak-pair matching, and other standard analyses - see Results for more details
To increase the likelihood of success, we also offer an antibody validation service to assess the ChIP-exo compatibility of a chosen antibody. Click here for a list of antibodies that have already been ChIP-exo validated. If your antibody is not on this list, we recommend validating it before running it through the ChIP-exo assay with samples.
How to Begin
We ask all customers to fill out and submit an electronic sample submission form prior to sending samples, so that we may inspect it for completeness and errors. Complete submittal instructions will be provided with the form. To begin the process, please Contact Us.
We ask all customers to fill out and submit an electronic sample submission form prior to sending samples, so that we may inspect it for completeness and errors. Complete submittal instructions will be provided with the form. To begin the process, please Contact Us.