Fig 1: Dotplot enrichment map showing cellular pathways associated with up-regulated GDTEs from HEK293 cells knocked down of eL38. The colors of the points depend on the p.adj values, and their sizes are determined by the number of GDTEs associated with the corresponding pathways (color and dot size keys are shown on the right).
Fig 2: Gene ontology (GO) analysis performed for the up-regulated GDTEs set from HEK293 cells knocked down of eL38. Only the highest categories in the GO hierarchy (biological process, molecular function, and cellular component) with multiple enrichment values > 5 and gene numbers of at least 5 are presented.
Fig 3: The coverage plots for three representative genes with differential translational efficiencies (GDTEs) in HEK293 cells treated with specific siRNAs against eL38 mRNA and with non-targeting siRNA. The left panels show the normalized read coverage of gene regions, given in coordinates of the respective transcripts, for cells with normal eL38 level (the upper part, N) and eL38 knocked down cells (the lower part, KD). The brown and purple histograms on the plots illustrate the read densities across these regions derived from the RNA-seq and Ribo-seq data, respectively. The yellow and peach areas on the plots correspond to the coding sequences (CDSs) of transcripts and their 5'- and 3'-untranslated regions (UTRs), respectively. The right panels present the dot plots of normalized read counts obtained from the RNA-seq (“mRNA” plot) and Ribo-seq (“RPF” plot) data in three replicates. The DESeq2-derived statistics, Log2FoldChange (LFC) and p adjusted (p.adj) values, are given inside the boxes. The TE change for each gene is designated by an arrow and its statistics are shown.
Fig 4: Dotplot enrichment map showing cellular pathways associated with down-regulated GDTEs from HEK293 cells knocked down of eL38. Designations are the same as in Figure 4.
Fig 5: Ribosomal protein eL38 knockdown in HEK293 cells. (A) Western blot analysis of the levels of eL38 and GAPDH (as a reference) in cells transfected with siRNAs specific for eL38 mRNA (1) and non-targeting siRNA (2). The diagram shows triplicate western blot data as the mean of arbitrary units (a.u.) ± SEM (** p < 0.01, calculated using Mann-Whitney test). (B) Sucrose gradient polysome profiles obtained by the centrifugation of the lysates of cells transfected with non-targeting siRNA (solid line) and eL38 mRNA-specific siRNAs (dashed line); the peaks of 60S and 40S subunits, 80S ribosomes and polysomes are marked. Western blot analysis of the sucrose gradient fractions for the presence of ribosomal proteins eL38 and eS4 (as a reference).
Supplier Page from Thermo Fisher Scientific for RPL38 Antibody