Can vortexing damage cells/nuclei when generating emulsions in the Illumina Single Cell workflow?

Is there potential for damaging cells during the vortexing steps used to generate the emulsions in the Illumina Single Cell workflow?

The presence of hydrogel particles during emulsification is highly protective of the cells or nuclei compared to vortexing in a tube without particles. The hydrogel slurry effectively increases the viscosity in the system to minimize shear near the surface of the template particles. This method minimizes wall shear stress compared to using a microfluidic device. Microscopy experiments have confirmed the cells are not lysed during the vortexing steps to generate the emulsions.

As fluid flows through a microfluidic device channel, it creates a greater shear force on the cells that are close to the channel walls. This stress can impact cell behavior and morphology. Shear stress is greatly reduced when the flow of fluid is more evenly distributed, as with emulsions generated via vortexing within a single tube using hydrogel particles.

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