Perfect your Chromatin Shearing

  • Choose a kit for your specific experimental needs
  • Obtain perfect fragment size for high quality ChIP
  • Get consistent results from different samples and runs
Chromatin Shearing Optimization kit

For ChIP-seq
Chromatin Shearing Optimization kit
Medium SDS
Chromatin Shearing Optimization kit
High SDS
SDS concentration < 0.1% 0.5% 1%
Nuclei isolation Yes Yes No
Allows for shearing of... cells 100 million cells 100 million cells 100 million cells
Compatible with iDeal ChIP-seq kit HighCell# ChIP kit LowCell# ChIP kit
  Order now the chromatin shearing optimization kit - Low SDS Order now the chromatin shearing optimization kit - Medium SDS Order now the chromatin shearing optimization kit - High SDS
Key to successful chromatin shearing

It has been widely described that detergents (e.g. SDS) are essential for successful chromatin shearing. Therefore, the right concentration of SDS has to be chosen carefully for your assay to function. Too high concentrations might lead to inaccessibility of the epitope or alter the antibody binding during ChIP. Although it is possible to dilute prior to ChIP, this might not always be compatible with your workflow (e.g. too high reaction volume, limited cell amounts available, etc.)

When you need a low SDS concentration:

  • Antibodies may be inhibited by higher SDS concentrations because of protein denaturation (epitopes are inaccessible)
  • Limited cell amounts are available and you wish to avoid the dilution of your chromatin (to reach lower SDS concentration) prior to ChIP
  • Maximum reaction volume cannot be exceeded (e.g. for SX-8G IP-Star® Automated System)

When you need a high SDS concentration:

  • Increase shearing efficiency - higher detergent concentration may be beneficial with difficult cell types
Optimal chromatin fragment size for ChIP

K562 cells (myelogenous leukemia cell line) are fixed with 1% formaldehyde (for 8 min at RT). Nuclei isolation of 1 million fresh cells are performed using buffers from Diagenode's Chromatin Shearing Optimization kit - Low SDS (Cat. No. AA-001-0100) and are then resuspended in 100 µl of Shearing Buffer iS1 prior to chromatin shearing. Samples are sheared during 1, 2 or 3 rounds of 10 cycles of 30 sec ON/ 30 sec OFF with the Bioruptor® PLUS combined with the Bioruptor® Water cooler (Cat. No. BioAcc-Cool) & Single Cycle Valve (Cat. No. VB-100-0001) at HIGH power setting (position H). For optimal results, samples are vortexed before and after performing 10 sonication cycles, followed by a short centrifugation at 4°C. All samples were treated with RNase and reverse cross-linked.
Panel A: 10 μl of DNA (equivalent to 300 ng) are analyzed on a 1.5% agarose gel.
Panel B and C:
Third sample of panel A (3x 10 min) was analyzed on Bioanalyzer 2100 using DNA High Sensitivity chip. The default log scaled Bioanalyzer output can be seen in Panel A, while Panel C represents their linear transformation for better vizualisation. Out of range fragments were not shown on this graph.

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