• Personal protective equipment (PPE; e.g., powder-free gloves, safety glasses, lab coat, sleeve protector)
• Nuclease-decontamination solution
• Nuclease-free water
• Isopropanol
• Ethanol
• Thermal cycler with block for 0.2-ml tubes
• Centrifuges and rotors for conical tubes and plates (e.g., Eppendorf 5810R with swinging plate buckets, ≥2,600g, and room temperature & 4°C operation; Kubota 3740 with rotor SF-240 for cell preparation)
• 50-ml and 15-ml conical tubes
• Nuclease-free 0.2-ml PCR tubes and nonstick 1.5-ml tubes
• Single-channel pipettes: 10 µl, 20 µl, 200 µl, and 1,000 µl
• Filter pipette tips: 2 µl, 20 µl, 200 µl, and 1,000 µl
• Wide-bore pipette tips: 200 µl and 1,000 µl
• Serological pipettes and controller
• Minicentrifuges for 1.5-ml tubes and 0.2-ml tubes or strips
• Vortex mixer
• Exhaust hood system with UV
• Two pairs of tweezers, for handling chips during imaging

• 1X PBS (no Ca²⁺, Mg²⁺, phenol red, or serum, pH 7.4; Thermo Fisher Scientific, Cat. No. 10010-023)
• ReadyProbes Cell Viability Imaging Kit, Blue/Red (contains Hoechst 33342 and propidium iodide; Thermo Fisher Scientific, Cat. No. R37610)
• TrypLE Express (Thermo Fisher, Cat. No. 12604-021)
• Molecular biology-grade/PCR-grade/nuclease-free water

• Qiagen MinElute Column (Cat. No. 28004)
• Agencourt AMPure XP PCR purification system (5 ml; Beckman Coulter, Cat. No. A63880)
  
  

  NOTES: Agencourt AMPure XP beads need to come to room temperature before the container is opened. Therefore, we strongly recommend aliquoting the beads into 1.5-ml tubes upon receipt, and then refrigerating the aliquots. Individual tubes can be removed for each experiment, allowing them to come to room temperature more quickly (~30 min). This aliquoting process is also essential for minimizing the chances of bead contamination. Immediately prior to use, vortex the beads until they are well dispersed. The color of the liquid should appear homogeneous. Confirm that there is no remaining pellet of beads at the bottom of the tube. Mix well to disperse before adding the beads to your reactions. The beads are viscous, so pipette them slowly.

• Qubit dsDNA HS Assay Kit (100 assays; Thermo Fisher Scientific, Cat. No. Q32851)
• Qubit Fluorometer (Thermo Fisher Scientific)

• Agilent 2100 Bioanalyzer: High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626)
• Bioanalyzer instrument (Agilent or similar)

• Recommended: MOXI Z Mini Automated Cell Counter Kit (ORFLO, Cat. No. MXZ001) with MOXI Z Cell Count Cassettes, Type M (25 pack; ORFLO, Cat. No. MXC001) or S (25 pack; ORFLO; Cat. No. MXC002) based on cell size.
  
  

  NOTE: Refer to a Moxi Z user manual for guidance in selecting an appropriate cassette size for the cells being analyzed.

• Alternatively: use any preferred cell counter with demonstrated, accurate cell counting.
  
  

References

Mezger, A., et al. High-throughput chromatin accessibility profiling at single-cell resolution. Nat. Commun. 9, 3647 (2018).