Extended Data Fig. 6: Alternative views of global bulk transcriptome.
From: The changing mouse embryo transcriptome at whole tissue and single-cell resolution
a, Bulk tissue transcriptome is organized on a 2D t-SNE plane, with colour code as in Fig. 1. n = 156 bulk RNA-seq libraries b, Two-way hierarchical clustering of differential genes in bulk data using Pearson correlation. c, Normalized principal component scores of the top 20 components. Tissue identities and stages are labelled at the bottom following colour codes in Fig. 1. d, e, One-way hierarchical clustering (d) and PCA projection (PC scores are labelled at the bottom and loading coefficients are on the right) (e) of whole transcriptome with forebrains, hindbrains and neural tubes removed to test robustness. n = 112 bulk RNA-seq libraries. Colour codes as in Fig. 1. f, g, One-way hierarchical clustering (f) and PCA projection (similar to e) (g) of whole transcriptome quantified by TPM instead of FPKM. n = 156 bulk RNA-seq libraries. Colour codes as in Fig. 1.
