Drop-seq libraries were prepared as previously described (Macosko et al., 2015)(Drop-seq protocol v3.1), with full details available online (http://mccarrolllab.com/dropseq/). Deviations from the original protocol are noted. Cell and bead concentrations were matched to two different sets of PDMS devices generating droplet of different volumes such that the lambda loading parameter for cells was 0.08–0.1 and for 0.09–0.13 for beads. Cell suspensions were diluted with using room temperature “Dissociation Buffer + BSA.” For device A (droplet diameter: 125 μm; droplets/μl: 980), cells were loaded at 100 cells/μl (λcell = 100/980=0.1). For device B (droplet diameter: 100 μm; droplets/μl: 2631), cells were loaded at 220 cells/μl (λcell = 220/2631=0.08). Bead concentrations of 125 beads/μl (A) and 250 beads/μl (B) achieved λbeads between or 0.09 (A) and 0.13 (B). Flow rates for cells/beads were 1.8 – 4 mL/hr, adjusted to the highest value possible while ensuring homogenous droplet sizes. Oil flow rates were between 13–15 mL/hr. Cell suspensions were split between two Drop-seq rigs to reduce runtime. Drop-seq encapsulation was performed within 2 hours after suspension preparation. Drop-seq conditions for nuclei paralleled those
