Extended Data Fig. 2: Quality control of Live-seq data, relative to Fig. 2.

(a) Number of input reads (input reads), the rate of reads uniquely mapped to the genome (uniquely mapped reads), the fraction of reads mapped to exons (Reads mapped in exon), total counts of all genes (nCount), number of detected genes (nGene) and the percentage of counts from mitochondrial genes (percent MT) are shown per cell type/state for Live-seq samples/libraries passing the quality control. N = 5 replicates, a total of 294 cells. (b) tSNE-based visualization of clusters, cell types/states, cell lines, replicates, number of genes (nGene), and number of counts (nCount) of the Live-seq data. The Adjusted Rand Index (ARI) between the clustering and cell type/state classification is indicated. (c) Clustering tree of the Seurat-based clustering results of the Live-seq data. It visualizes the relationship between clustering at increasing resolutions (top to bottom). The size of the circles represents the number of cells in that cluster, while the opacity of the arrows shows the proportion of the cells passing from one cluster to another at a different resolution. Note that the ASPCs do not split by treatment due to batch effect. The clustering was therefore independently adapted for the clustered ASPCs to correctly capture their state difference (see Methods). (d) Barplot showing the overlap in number of cells between the clustering (x-axis) and the ground truth, i.e., cell type/state, displayed in (b). (e-f) tSNE-based visualization of cell type/state, nGene, Clustering, nCount and batch for (e) ASPCs and (f) RAW cells. The ASPCs only contain one batch.