Can the loading order be modified? For multiple samples, can each chip be loaded individually?

Answer:
No. The loading order (cells → barcoded beads → carrier oil) must be strictly followed, and samples should be loaded by row across chips, not one chip at a time.

Underlying rationale:

• Premature cell lysis risk:
  Barcoded beads typically contain lysis components. If beads or oil are loaded before cells, subsequently added cells may contact lysis reagents prematurely within the microfluidic channels.
  This can lead to early cell lysis, resulting in: 
  • Non-specific binding of released mRNA to barcodes 
  • RNA degradation or dilution prior to droplet formation 
  • Increased background noise and reduced usable data 

• Droplet formation mechanism:
  Carrier oil serves as the continuous phase and is essential for forming stable water-in-oil droplets.
  If oil is loaded first, aqueous phases (cells and beads) may not be properly encapsulated, leading to unstable or failed droplet generation. 
• Batch consistency in multi-chip workflows:
  Single-cell experiments are highly time-sensitive.
  If chips are processed sequentially, the time gap between the first and last chip may introduce variability in cell viability, RNA integrity, and overall data quality. Loading by row ensures that all samples are processed under nearly identical conditions, minimizing batch effects and improving comparability.