To capture transcriptomic information of hiPSCs-derived hCS and hSS (IS) single-cells, we used the BD Resolve system (BD Genomics, Menlo Park, CA) as previously reported with modifications13. Multiple hCS or hSS at day 105 of differentiation were combined and dissociated enzymatically into single cells, and processed in one batch. Single cell capture was achieved by random distribution of a single cell suspension across >200,000 microwells via a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation such that a bead was paired with a cell in a microwell. Cell lysis buffer was added such that poly-adenylated RNA molecules hybridize to the beads. Beads were collected into a single tube for reverse transcription. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (i.e., 3′ end of mRNA transcript) with a molecular index and cell label indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Resolve single cell whole transcriptome amplification workflow. Briefly, second strand cDNA was synthesized, followed by ligation of adaptor for universal amplification. Eighteen cycles of PCR were used to
