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Multiplex Oligos for Illumina Systems (Single Index Primers) (ChIP-seq, CUT&RUN)

Multiplex Oligos for Illumina Systems (Single Index Primers) (ChIP-seq, CUT&RUN) #29580

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Product Information

Storage

Store all components at -20ºC. This product is stable for 12 months if stored properly.

Protocol

Product Description

Next generation sequencing (NG-seq) is a high throughput method that can be used downstream of chromatin immunoprecipitation (ChIP) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) assays to identify and quantify target DNA enrichment across the entire genome. Multiplex Oligos for Illumina Systems (Single Index Primers) (ChIP-seq, CUT&RUN) contains adaptors and primers that are ideally suited for multiplex sample preparation for NG-seq on the Illumina Systems platform. This kit can be used to generate up to 12 distinct, barcoded ChIP-seq or CUT&RUN DNA libraries that can be combined into a single sequencing reaction.

This product is compatible with SimpleChIP Enzymatic ChIP Kit (Magnetic Beads) #9003, SimpleChIP Plus Enzymatic ChIP Kit (Magnetic Beads) #9005, SimpleChIP Plus Sonication ChIP kit #56383, and CUT&RUN Assay Kit #86652. This product is not compatible with SimpleChIP Enzymatic Chromatin IP Kit (Agarose Beads) #9002 and SimpleChIP Plus Enzymatic Chromatin IP Kit (Agarose Beads) #9004 because agarose beads are blocked with sonicated salmon sperm DNA, which will contaminate DNA library preps and NG-seq.

Specificity / Sensitivity

This kit has been validated in combination with DNA Library Prep Kit for Illumina Systems (ChIP-seq, CUT&RUN) #56795 to generate qualified DNA libraries using as little as 0.5 ng ChIP DNA or as little as 0.1 ng CUT&RUN DNA as starting materials. Libraries prepared from different starting amounts of DNA exhibit similiar Agilent Bioanalyzer System profiles, genome mapping rates, numbers of identified binding peaks, and signal-to-noise ratios across the whole genome.

Background

The chromatin immunoprecipitation (ChIP) assay is a powerful and versatile technique used for probing protein-DNA interactions within the natural chromatin context of the cell (1,2). This assay can be used to identify multiple proteins associated with a specific region of the genome, or the opposite, to identify the many regions of the genome bound by a particular protein (3-6). It can be used to determine the specific order of recruitment of various proteins to a gene promoter or to "measure" the relative amount of a particular histone modification across an entire gene locus (3,4). In addition to histone proteins, the ChIP assay can be used to analyze binding of transcription factors and co-factors, DNA replication factors and DNA repair proteins. When performing the ChIP assay, cells or tissues are first fixed with formaldehyde, a reversible protein-DNA cross-linking agent that "preserves" the protein-DNA interactions occurring in the cell (1,2). Cells are lysed and chromatin is harvested and fragmented using either sonication or enzymatic digestion. The chromatin is then immunoprecipitated with antibodies specific to a particular protein or histone modification. Any DNA sequences that are associated with the protein or histone modification of interest will co-precipitate as part of the cross-linked chromatin complex and the relative amount of that DNA sequence will be enriched by the immunoselection process. After immunoprecipitation, the protein-DNA cross-links are reversed and the DNA is purified. Standard PCR or Quantitative Real-Time PCR can be used to measure the amount of enrichment of a particular DNA sequence by a protein-specific immunoprecipitation (1,2). Alternatively, the ChIP assay can be combined with genomic tiling micro-array (ChIP on chip) techniques, high throughput sequencing, or cloning strategies, all of which allow for genome-wide analysis of protein-DNA interactions and histone modifications (5-8).

Limited Uses

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For Research Use Only. Not For Use In Diagnostic Procedures.

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