EpiCypher has specific recommendations for control antibodies and spike-ins controls in CUT&RUN experiments, outlined below. Note that these controls are included in the CUTANA™ CUT&RUN Kit; for DIY CUT&RUN protocol users, links to relevant products are provided.
Control antibodies paired with SNAP-CUTANA™ K-MetStat Panel
Reactions using negative control (IgG) and positive control (H3K4me3, H3K27me3) antibodies should be included in every experiment to validate protocols and examine assay background. When paired with the SNAP-CUTANA Spike-in K-MetStat Panel of nucleosome spike-in controls, control reactions can assist in validating and troubleshooting your workflow.
H3K4me3, EpiCypher 13-0060
H3K27me3, EpiCypher 13-0055
IgG, EpiCypher 13-0042
SNAP-CUTANA K-MetStat Panel, EpiCypher 19-1002
E. coli Spike-in DNA for sequencing normalization
E. coli DNA (EpiCypher 18-1401) is spiked in prior to library prep to aid in library prep and sequencing troubleshooting as well as normalization. For more information on how to use E. coli spike-in DNA for normalization, see this article.
Spike-in nucleosome controls for experimental targets
SNAP-CUTANA Spike-in Controls are the only control that uses purified recombinant nucleosomes, replicating the physiological target of CUT&RUN assays. These panels of on- and off-target spike-ins can be used to validate antibodies to experimental targets, including lysine methylation PTMs and epitope-tagged proteins. For more information visit the SNAP-CUTANA Spike-in section or navigate to specific articles on:
What are SNAP-CUTANA Spike-in Controls and how do they work?
Using SNAP-CUTANA Spike-in Controls to determine CUT&RUN success
Using SNAP-CUTANA Spike-in Controls to troubleshoot workflows or validate histone PTM antibodies