ChIC/CUT&RUN equipment

CUT&RUN relies on gentle handling of intact nuclei and precise control of enzymatic reactions. The following equipment is typically required to ensure consistent performance and reproducible results:

Core laboratory equipment

• Microcentrifuge with a cooling function (4°C) for pelleting nuclei and bead‑bound samples.
• Magnetic rack for 1.5 mL or 2 mL tubes to enable rapid separation of Concanavalin A (ConA) beads during wash and binding steps.
• Benchtop vortex mixer for gentle resuspension of beads and nuclei.
• Tube rotator or end‑over‑end mixer for consistent antibody incubation and MNase/tagmentation binding steps.
• Thermomixer or heat block capable of maintaining temperatures between 0–55°C, depending on protocol requirements.
• Ice bucket or cold block for maintaining low temperatures during nuclei preparation, permeabilization, and MNase binding.

Temperature‑controlled workstations

• Refrigerated microcentrifuge and cold room or 4°C workstation for steps requiring cold handling (nuclei isolation, antibody incubation).
• 37°C incubator or heat block may be required for adapter‑ligation steps during library prep (protocol‑dependent).

Pipettes and low‑retention consumables

• Standard P2, P20, P200, and P1000 pipettes with low‑retention tips to prevent loss of nuclei and small DNA fragments.
• Low‑DNA‑binding microcentrifuge tubes (1.5 mL or 2 mL) to minimize sample loss during fragment recovery.
• Optional: wide‑bore filtered tips for gentle handling of nuclei or primary cells.

Quality control and quantification

• Fluorometer (eg Qubit) for low‑input DNA quantification.
• Bioanalyzer, TapeStation, or Fragment Analyzer for assessing library size distribution.
• Nanodrop or spectrophotometer for concentration checks during clean‑up steps.

Specialised supplies (assay‑specific)

• Concanavalin A–coated magnetic beads, essential for immobilizing nuclei and enabling efficient wash steps.
• Chilled metal block for controlled Ca²⁺ activation of MNase, if performing CUT&RUN.
• PCR thermocycler for library amplification.

Optional equipment

Depending on sample type or workflow:

• Automated liquid‑handling platform for high‑throughput CUT&RUN or CUT&Tag workflows.
• Flow cytometer for confirming nuclei quality or gating rare populations before CUT&RUN.
• Cell counter for accurate input quantification, especially for low‑cell‑number samples.