Fig. 1.

Reproducibility analysis of the RNA-Seq data. (A) Hierarchical clustering of gene expression profiles, showing the similarity of different treatment times. See Table 2 for details of Euclidian distance between paired libraries. h = hours. (B) Multidimensional scaling plot of different time points. Color legend is reported in the upper left corner of the plot. hrs = hours; dim = dimension; logFC = logarithm of fold change. (C) Differential expression between untreated libraries. Each comparison is run between one library and the other two (e.g. in “Rep 1 vs Rep 2 & 3” replicate 1 indicates first replicate versus the other two (second and third) replicates pulled together). up = up-regulated; down = down-regulated; both = up- and down-regulated; Rep = replicate.