Quality control and further analyses were done in R v3.4.2, using Seurat package v2.0.1 [fig. S1D; (26)]. To discard doublets, cells were ordered by their number of UMIs, and the top (N/1000) percentage of cells per sample were filtered out, where N is the total number of called cell barcodes identified per sample (20). To discard broken cells (lysed cells with retained mitochondrial RNA), cells with more than 5% UMIs mapped to mitochondrial DNA were filtered out (61). The numbers of cells per sample filtered out by the different criteria appear in table S1. Together, 24,007 cells were kept for further analysis after quality control. Within each cell, the expression level of each gene was normalized cell-wise, by using the NormalizeData function of Seurat. This function divides the expression level of a gene by the total expression of all genes in that cell, multiplies the quotient by a scale factor of 10,000, and log-transforms the product (base e) after the addition of a pseudocount of 1.

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