Guide for ChIP and ChIP-seq

Sonication and Enzymatic Protocols.

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Sonication or Enzymatic Digestion: We have kits to support both experimental methods

Sonication is a popular choice for preparing chromatin for ChIP. However, most protocols require subjecting the chromatin to harsh, denaturing conditions (i.e., high heat, detergent, and shearing force) that can damage both antibody epitopes and the integrity of the chromatin.

CST provides multiple options for avoiding the problems of traditional sonication protocols:

  • Sonication: Our sonication protocol uses specially formulated cell and nuclear lysis buffers. This approach protects chromatin integrity and antibody epitopes, resulting in increased ChIP efficiency and making it more compatible for use with transcription factors and cofactors, which are labile and have less stable DNA interactions.
  • Enzymatic digestion: Enzymatic digestion is an alternative method of chromatin fragmentation that is compatible with all target types and highly amenable to the immunoprecipitation of transcription factors and cofactors. This approach uses micrococcal nuclease to cut the linker region between nucleosomes. Additionally, it is simple to control and protects chromatin and antibody epitopes from shearing or denaturation, making it an ideal option for users who are new to performing ChIP.

The CST SimpleChIP kits for sonication or enzymatic digestion, work as well as traditional sonication for assessing histones, and both outperform traditional sonication when assessing either transcription factors or cofactors.

Traditional Sonication vs. CST-optimized Sonication and Enzymatic Digestion

Chromatin was cross-linked and then fragmented with micrococcal nuclease (CST-enzymatic; blue track), CST sonication buffer (red track) or traditional sonication buffer (green track) and immunoprecipitated using the indicated antibodies. DNA was prepared for sequencing as outlined in the protocol for the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005.

No. Name Applications Cells/Tissue
#56383 SimpleChIP® Plus Sonication Chromatin IP Kit (Magnetic Beads) ChIP, ChIP-seq Cells and Tissue
#9005 SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) ChIP, ChIP-seq Cells and Tissue
#9003 SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) ChIP, ChIP-seq Cells
#9004 SimpleChIP® Plus Enzymatic Chromatin IP Kit (Agarose Beads) ChIP Cells and Tissue
#9002 SimpleChIP® Enzymatic Chromatin IP Kit (Agarose Beads) ChIP Cells
#81804 SimpleChIP® Sonication Cell and Nuclear Lysis Buffers ChIP, ChIP-seq Cells and Tissue
#14282 SimpleChIP® Enzymatic Cell Lysis Buffers A & B ChIP, ChIP-seq Cells and Tissue
#14231 SimpleChIP® Chromatin IP Buffers ChIP, ChIP-seq Cells and Tissue
#14209 SimpleChIP® DNA Purification Buffers and Spin Columns ChIP, ChIP-seq Cells and Tissue