The quality of each cell was assessed by examining the total number of reads, total reads aligned to hg19, total reads aligning to genes (pre-UMI correction), total transcript counts, and total genes with at least one detected transcript. Cells were excluded from downstream analyses if the total number of transcripts was not twofold greater than the total background-level transcripts detected in the empty well negative control on each plate (fig. S3). Cells were also excluded from downstream analyses if there was a weak Pearson correlation (r < 0.7) between detected ERCC RNA Spike-In transcript counts (log10) and ERCC input concentration (log10) (amol/ml) (fig. S3). All non–protein-coding genes and genes with less than two transcript counts in five cells were removed from the dataset. The remaining 7680 genes measured across 796 cells were used for subsequent analyses.

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