Fig. 3

Time course scRNA-seq data analysis and reconstructing DE differentiation trajectory. a Upper panel, schematics of experimental strategy illustrating time points of scRNA-seq sampling along the differentiation from pluripotent state though mesendoderm to DE cells. Lower panel, PCA of scRNA-seq data, shown is PC1 vs. PC2. b Violin plots of selected stage-specific markers identified by SCPattern analysis. The y-axis indicates normalized expression value, Log2(expected count + 1). The x-axis indicates time points of sampling. c Reconstructed single-cell order by Wave-Crest. Shown are four of the eight genes used for temporal reconstruction. The x-axis indicates cells following Wave-Crest recovered cell order. The y-axis indicates normalized expression value. Fitted lines of gene-specific expression are shown in black. d Top 25 upregulated or downregulated genes identified by Wave-Crest at 36 h of differentiation. The x-axis indicates gene symbol, the y-axis indicates the significance value, -Log (p value) of each gene