Fig. 3.

Phenol preferentially extracts mRNAs that encode for membrane proteins. a Hierarchical clustering of unstressed samples (P = Phenol, R = RNeasy, D = Direct-zol). Clustering on relative transcript abundance (TPMs) reveals differences depending upon RNA isolation method, while clustering on sample identity shows that the Phenol method diverges from both Kits. Red indicates higher than average transcript abundance within a sample, and blue indicates lower than average transcript abundance. b Hierarchical clustering of 3127 transcripts with significantly differential abundance (FDR < 0.01) in any pairwise comparisons between each RNA isolation method. Brown indicates higher expression than the comparison group (e.g. Phenol in the P v. R column) and violet indicates lower expression than the comparison group (e.g. RNeasy in the P v. R column). Enriched Gene Ontology (GO) categories (Bonferroni-corrected P < 0.01) are shown on the right. Complete GO enrichments for each cluster can be found in Supplementary File 3. c Overlap between transcripts with significantly differential abundance (FDR < 0.01) in the Phenol v. RNeasy and Phenol v. Direct-zol comparisons