Integrity of total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies). Copy RNA synthesis, hybridization to HG U133 plus 2.0 microarrays (Affymetrix), and subsequent steps were performed according to the manufacturers’ protocol. Data analysis was performed in R version 3.6.3. The Affy package (93 (link)), version 1.64.0, was used for Robust Multichip Average (RMA) normalization. All +dox samples (n = 9) were compared with the –dox samples (n = 9), using the Limma package (94 (link)), version 3.42.2. Upregulated (log2 fold change > 0.6, P < 0.05, and q < 0.1) and downregulated (log2 fold change < –0.6, P < 0.05, and q < 0.1) probe sets were collapsed to genes. The gene names were used for GO term analysis in the web version of PANTHER (released 20200407, ref. 95 (link)), using the human data set with default settings. Heatmaps were created using Pheatmap package in R.
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