Troubleshooting and FAQs
The most commonly asked questions
- Troubleshooting overview
- What antibody should I use?
- Can I use my ChIP antibody for CUT&RUN?
- How do I know if my cell sample is good enough for CUT&RUN?
- What should I expect when using frozen cell samples for CUT&RUN?
- How should nuclei look for CUT&RUN?
- How should I optimize my workflow for new targets or cell types?
- How should I optimize my workflow for reduced cell inputs?
- What controls should I use?
- Why should I use SNAP-CUTANA Spike-ins to troubleshoot my workflows?
- Are my ConA beads okay to use?
- How do I know ConA bead binding was successful?
- Why are my ConA beads sticky? Does it matter?
- How do I prevent ConA beads from becoming sticky?
- Can I do qPCR or Bioanalyzer/TapeStation to evaluate raw CUT&RUN DNA?
- What should I do if I have low CUT&RUN yields (below 5ng)?
- My yields from the H3K4me3 positive control are low (i.e. below 5 ng), about the same as the IgG negative control. Did my experiment fail?
- What are considerations for library prep and sequencing from low yields?
- Why are there no peaks in my Bioanalyzer/TapeStation results?
- Do I need to adjust the protocol to map transcription factors or other chromatin-associated proteins?