Fig 2: Transcriptome and translatome changes in the UPR at the total reads analysis. (A) MA plot of cytosolic RNA-seq, P-TRAP-seq and L10a-TRAP-seq data from thapsigargin (TPG)-treated versus DMSO-treated HEK293 cells. Differentially expressed genes (adjusted P-value < 0.05 and log2 fold change > |1.5|) are highlighted in red (up-regulated) or blue (down-regulated). (B) Counts per million (CPM) values of selected ER stress response genes (HSPA5, DDIT3, PDIA4, DNAJC3 and HERPUD1) and a control gene (GAPDH) in the cytosolic RNA-seq (RNA), P-TRAP-seq (P0) and L10a-TRAP-seq (L10a) in response to DMSO- (black) or TPG- (red) treatments. The means and standard deviations of three replicates are shown. (C) Cumulative distributions of the log2 fold changes of selected gene categories (preferentially translated by polysome upon eIF2α phosphorylation) compared to all genes, together with P-values of Mann–Whitney U test. (D) Venn diagrams overlapping DEGs detected by the cytosolic RNA-seq (red), P-TRAP-seq (blue), and L10a-TRAP-seq (yellow) in the total reads analysis.