Drop-seq
Drop-seq experiments were performed according to the original protocol (Macosko et al., 2015). Briefly, single cells (100/μl) were co-encapsulated in droplets with barcoded beads (120/μl, ChemGenes) at rates of 4000 μl/h. Droplet emulsions were collected for 10-20 min/each prior to droplet breakage by perfluorooctanol (Sigma-Aldrich). After breakage, beads were harvested and the hybridized mRNA transcripts reverse transcribed (Maxima RT, Thermo Fisher). Exonuclease digestion and PCR were carried out as described (12 PCR cycles). For each sample, 1 ng of pre-amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5-primer (Integrated DNA Technologies). Single-cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000.