How can clogging during droplet generation be identified?

Answer:
Clogging or abnormal droplet generation should be evaluated based on a combination of emulsion appearance, recovered volume, and residual volume in chip wells.

Normal conditions:

• The emulsion should appear uniform and well-dispersed. 
• The recovered emulsion volume should be approximately 100–120 μL. 

• Emulsion color varies by assay type: 
  • 3’, 5’, and FAST-seq workflows: light pink 
  • Other workflows (e.g., spatial, ATAC multi-omics, methylation multi-omics, scMLPSeq): milky white 

Indicators of potential clogging:

• Reduced emulsion volume (<100 μL) 
• Abnormal emulsification (e.g., poor dispersion or phase inconsistency) 

In such cases, further confirmation should be performed by examining residual volumes in chip wells:

• Well 1 (cell channel): residual volume should be <10 μL 
• Well 2 (bead channel): residual volume should be <20 μL 

If residual volumes exceed these thresholds, it may indicate that one or more channels may not have properly entered the microfluidic pathway, suggesting clogging or flow obstruction. 

Common misinterpretation (important):

A transparent oil phase may settle beneath the emulsion in the collection tube. This is a normal phenomenon and does not indicate clogging or performance issues.