What controls should I use?

CUTANA™ CUT&RUN workflows contain multiple quality control checks to help ensure assay success. This includes the control reactions and spike-in controls outlined below, as well as key cell sample quality checks, confirmation of cell binding to ConA beads, examination of CUT&RUN DNA yields, and fragment distribution analysis of purified sequencing libraries. Find a summary of CUTANA CUT&RUN quality control steps here.

Control antibodies

Reactions using negative control (IgG) and positive control (H3K4me3) antibodies should be included in every experiment to validate protocols and examine assay background. When used with SNAP-CUTANA™ Spike-in controls (below), control antibodies can assist in validating and troubleshooting your workflow.

Spike-in nucleosome controls

SNAP-CUTANA™ Spike-in Controls are the only control that uses purified recombinant nucleosomes, replicating the physiological target of CUT&RUN assays.

SNAP-CUTANA Spike-in Controls are essential controls for any CUT&RUN experiment. When combined with negative and positive control antibodies, SNAP-CUTANA Spike-in Controls give users the best chance of CUT&RUN success. For more information on SNAP-CUTANA Spike-in Controls, visit their section or navigate to specific articles on:

• What are SNAP-CUTANA Spike-in Controls and how do they work?
• Analyzing SNAP-CUTANA Spike-in Controls
• Using SNAP-CUTANA Spike-in Controls to determine CUT&RUN success
• Using SNAP-CUTANA Spike-in Controls to troubleshoot workflows or validate select histone post-translational modification antibodies

E. coli Spike-in DNA

E. coli DNA 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.