Figure 2: RNA-seq data quality and visualization.

(a). Bulk-population RNA-seq FastQC quality scores across read position, shown for a representative sample (D0 hESC). (b). PCA plot of bulk-population RNA-seq data, based on the top 500 genes by variance across all samples, and using log₂ TPM values. (c). Single-cell RNA-seq FastQC quality scores across read position, shown for a representative sample (D2.25 somitomeres). (d). PCA plot of single-cell RNA-seq data, based on the top 500 genes by variance across all cells, and using log₂ TPM values. (e). Black: Plot of density against standardized log₂ TPM for single-cell RNA-seq data across all genes in all cells, after removing zeroes. Red: Fitted normal distribution. (f). Plot of single-cell variability (s.d.) against mean expression value for each gene, shown for a representative cell type (paraxial mesoderm).