The BD Resolve analysis pipeline was used to process sequencing data (fastq files). Cell labels and molecular indices were identified, and gene identity was determined by alignment against the gencode comprehensive hg19 reference. A table containing molecule counts per gene per cell was output. 7,663 and 4,983 cells were identified for hCS and hSS, respectively, with an average number of reads of ~14,800, an average of ~3,710 molecules and ~1,700 number genes detected per cell with an average molecular index coverage (i.e. number of times a molecule was sequenced) of ~2. A total of 34,242 genes were detected across all cells. Cells with mitochondrial gene (with gene symbol starting with MT) content > 25%, were discarded retaining 7,126 and 4,712 cells for hCS and hSS (IS), respectively. Pseudogenes were removed. The distribution of reads per single cell is shown in Extended Data Fig. 2m. For visualization and clustering, the data tables of the two libraries were concatenated, and the combined table was further reduced to retain only the most variable genes using the method outlined in Macosko et al49, yielding
