Drop microfluidics has driven innovations
for high throughput,
low input analysis techniques such as single-cell RNA-seq. However,
the instability of single emulsion (SE) drops occasionally causes
significant merging during drop processing, limiting most applications
to single-step reactions in drops. Here, we show that double emulsion
(DE) drops address this critical limitation and completely prevent
drop contents from mixing. DEs show excellent stability during thermal
cycling. More importantly, DEs undergo rupture into the continuous
phase instead of merging, preventing content mixing and eliminating
unstable drops from the downstream analysis. Due to the lack of drop
merging, the monodispersity of drops is maintained throughout a workflow,
enabling the deterministic manipulation of drops downstream. We also
developed a simple, one-layer DE drop maker compatible with simple
surface treatment using a plasma cleaner. The device allows for the
robust production of single-core DEs at a wide range of flow rates
and better control over the shell thickness, both of which have been
significant limitations of conventional two-layer devices. This approach
makes the fabrication of DE devices much more accessible, facilitating
its broader adoption. Finally, we show that DE droplets eliminate
content mixing and maintain compartmentalization of single virus genomes
during PCR-based amplification and barcoding, while SEs mixed contents
due to merging. With their resistance to content mixing, DE drops
have key advantages for multistep reactions in drops, which is limited
in SEs due to merging and content mixing.