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:
When you need a high SDS concentration:
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.