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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 provides enough reagents to support up to 24 DNA sequencing libraries, and must be used in combination with the DNA Library Prep Kit for Illumina Systems (ChIP-Seq, CUT&RUN) #56795.

    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, CUT&RUN Assay Kit #86652, and CUT&RUN Assay Kit (with Drosophila Spike-In Control) #84647. This product is not compatible with CUT&Tag Assay Kit #77552, 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).

    Alternate Names

    Barcode; ChIP; ChIP Kit; ChIP-seq; ChIP-sequencing; Chromatin Immunoprecipitation; Chromatin IP; CnR; CUT & RUN; cut and run; CUT and RUN; cutandrun; DNA library; DNA library construction; DNA library preparation; next gen sequencing; NG-sequencing; Oligo; Oligos; Sequencing; Sequencing primer

    Limited Uses

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    Products are labeled with For Research Use Only or a similar labeling statement and have not been approved, cleared, or licensed by the FDA or other regulatory foreign or domestic entity, for any purpose. Customer shall not use any Product for any diagnostic or therapeutic purpose, or otherwise in any manner that conflicts with its labeling statement. Products sold or licensed by CST are provided for Customer as the end-user and solely for research and development uses. Any use of Product for diagnostic, prophylactic or therapeutic purposes, or any purchase of Product for resale (alone or as a component) or other commercial purpose, requires a separate license from CST. Customer shall (a) not sell, license, loan, donate or otherwise transfer or make available any Product to any third party, whether alone or in combination with other materials, or use the Products to manufacture any commercial products, (b) not copy, modify, reverse engineer, decompile, disassemble or otherwise attempt to discover the underlying structure or technology of the Products, or use the Products for the purpose of developing any products or services that would compete with CST products or services, (c) not alter or remove from the Products any trademarks, trade names, logos, patent or copyright notices or markings, (d) use the Products solely in accordance with CST Product Terms of Sale and any applicable documentation, and (e) comply with any license, terms of service or similar agreement with respect to any third party products or services used by Customer in connection with the Products.

    For Research Use Only. Not for Use in Diagnostic Procedures.
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