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. 2020 Mar 20;21:249. doi: 10.1186/s12864-020-6673-2

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© The Author(s). 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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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