Fig. 4
The method of RNA extraction has little effect on differential expression analysis. Hierarchical clustering of median-centered log2-fold TPM changes for 4232 transcripts that were differentially expressed in response to heat (FDR < 0.01) in at least one set of samples (P = phenol, R = RNeasy, D = Direct-zol). The left portion of the heat map displays gene expression changes during heat shock across the four biological replicates, with red indicating genes induced by heat shock, and blue indicating genes repressed by heat shock. The right portion shows differences in abundance in pairwise comparisons between each RNA isolation method, with brown indicating higher expression than the comparison group, and violet indicating lower expression than the comparison group. The Venn Diagram depicts overlap between differentially expressed genes in the Phenol, RNeasy, and Direct-zol isolated samples