RNA from lysed cells was barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne Silane Beads (Invitrogen, 37002D). Single-cell RNA-seq libraries were prepared using Single Cell 3′ Library Gel Bead Kit V2 (10x Genomics, 120237). Sequencing was performed with using multiple NextSeq 500/550 High Output Kit v2 on an Illumina NextSeq with pair end 150bp (PE150). On average, sequencing generated 100-200K reads per cell on average over the libraries.