biostudies-literatureDelley CLSwiss National Science FoundationNIBIB NIH HHSNHGRI NIH HHSNIAMS NIH HHS2465-2472https://www.ebi.ac.uk/biostudies/studies/S-EPMC7978498biostudies-literatureUnknown20(14)Current encapsulation approaches control the number of particles encapsulated per droplet, but not the particle types; consequently, they are unable to generate droplets containing combinations of distinct particle types, limiting the reactions that can be performed. We describe a microfluidic particle zipper that allows the number and types of particles encapsulated in every droplet to be controlled. The approach exploits self-ordering to generate repeating particle patterns that allow controlled encapsulation in droplets. We use the method to combine barcode particles with gel encapsulated cells to profile multiple disease relevant genomic loci with single cell sequencing. Particle zippers can operate in series to generate complex particle compositions in droplets.Lab on a chipMicrofluidic particle zipper enables controlled loading of droplets with distinct particle types.PMC7978498183853175086R01 EB019453DP2 AR068129R01 HG008978Delley CLAbate ARfalseMicrofluidic particle zipper enables controlled loading of droplets with distinct particle types.Current encapsulation approaches control the number of particles encapsulated per droplet, but not the particle types; consequently, they are unable to generate droplets containing combinations of distinct particle types, limiting the reactions that can be performed. We describe a microfluidic particle zipper that allows the number and types of particles encapsulated in every droplet to be controlled. The approach exploits self-ordering to generate repeating particle patterns that allow controlled encapsulation in droplets. We use the method to combine barcode particles with gel encapsulated cells to profile multiple disease relevant genomic loci with single cell sequencing. Particle zippers can operate in series to generate complex particle compositions in droplets.2020-01-01T00:00:00Z2020 Jul2022-02-10T19:32:41.594Z2022-02-10T19:32:41.594ZS-EPMC79784983253100410.1039/d0lc00339e