Extended Data Fig. 1 ∣. Tracking cell lysis efficiencies using Cellbrite-Fix 555 and SYBR Green staining in >1000 droplets or gels in each step of the lysis protocol.

Cellbrite (CF555) stains cell membrane and cell wall components while SYBR Green stains DNA, allowing us to identify whether a cell is intact (CF555 and SYBR staining) or lysed (only SYBR staining). (a) Representative fluorescence microscopy overlay of Green Channel (SYBR staining), Red Channel (CF555 staining), and Brightfield (Droplets/Gels) as a water-in-oil emulsion, as gels before lysis (top two images) and as gels after lysis (bottom image). Arrows denote representative droplets containing cells. Scale bars represent 100 μm. (b) The percentage of droplets containing fluorescent particles (# of fluorescent particles divided by the total # of droplets or gels) by SYBR or CF555 staining for each condition. Before lysis, CF555 and SYBR fluorescent particles are approximately equal in abundance. Following lysis, CF555 particles are substantially reduced, indicating lysis of the cells. n represents total number of droplets analyzed for each condition. The discrepancy between % encapsulated cells in pre-lysis emulsion and pre-lysis gel is due to the approximate nature of the droplet counting algorithm. Since the droplet counting algorithms are imperfect, some droplets do not get counted and some get counted multiple times. Therefore, the % of stained cells are only approximate estimates. (c) The percentage of droplets containing unlysed cells at each step. Unlysed cells are defined as particles that are fluorescent in both CF555 and SYBR Green channels. Data shown are result of one independent experiment.