Table 1:
Steps to follow when starting with a new cell type
| Step | Questions to address | Refer to: | ||
|---|---|---|---|---|
| 1. | Genome editing | • What delivery method are you using? • Is genome editing successful at the on-target site? |
Box 1 | |
| 2. | Sonication | • What are the correct sonication settings (intensity, number of cycles) to obtain 200–500 bp fragments of sheared chromatin? → this should be optimized on crosslinked cells |
Box 3 | |
| 3. | Timing | • Using your delivery method, what is the right time point to do DISCOVER-Seq? • Suggested time points: |
Box 2 | |
| RNP electroporation | ∼ 8–16 h | |||
| Adenovirus injection (in vivo) | ∼ 24 h | |||
| RNP lipofection | Determine experimentally | |||
| Plasmid electroporation/lipofection | Determine experimentally | |||
| Lentiviral transduction | Determine experimentally | |||
| AAV delivery (in vitro & in vivo) | Determine experimentally | |||