scRNA-seq libraries were generated using a Drop-seq protocol or the Chromium Single Cell 3’ Reagent Kit (10x Genomics). Drop-seq was performed as described earlier (5). For Drop-seq, single-cell suspensions were prepared in 1× PBS-BSA at a concentration of 100,000 cells/ml. Barcoded beads (ChemGenes) were resuspended in lysis buffer at concentration of 120,000 beads/ml. Syringes loaded with suspension of beads, suspension of cells, and oil were connected to a custom-built microfluidics chip (FlowJEM), and monodispersed droplets were generated. Droplets were lysed, complementary DNA (cDNA) was generated and amplified, and quality was assessed using the TapeStation (Agilent 2200). Thereafter, the cDNA was tagmented and amplified using the Nextera XT DNA Sample Prep Kit (Illumina) using primers described previously (Drop-seq Laboratory Protocol, version 3.1; http://mccarrolllab.com/dropseq/). The library was purified and sequenced using custom Read1 primer on the Illumina NextSeq 500 platform (using High Output v2 kit, Illumina) as follows: 20 base pairs (bp) (Read1) and 60 bp (Read2). For 10x scRNA-seq, the procedure was performed according to the manufacturer’s instruction using Chromium Single Cell 3’ Reagents Kits V2 (10x Genomics). The library was sequenced on Illumina HiSeq 2500 platform as follows: 26 bp (Read1) and 98 bp (Read2).

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