Gene expression and translation efficiency (TE) differences in RP haploinsufficient mutants. (A) RNA and TE log₂ ratio estimates for the top five most significant genes for all RP haploinsufficient mutants were plotted. The y-axis shows the log₂ fold change predictions, with TE and RNA levels for each mutant labeled in distinct colors. Superscript numbers denote the specific balancers compared between an RP mutant and its wild type counterpart. Balancer chromosomes are denoted as follows: +¹ = tmC20, +² = tmC5, +³ = mIn1, +⁴ = nT1. (B) Heatmap depicting the log₂ fold change of each RP gene expression at the RNA, TE, and protein levels for all four different mutants. The heatmap scale on the left represents non-scaled log₂ fold ratio estimates. (C) The 28S/18S rRNA ratio was calculated based on area measurements from Bioanalyzer RNA results. The top chart represents an example of a Bioanalyzer result. In the bottom plot, the y-axis shows the 28S/18S ratios, with each point representing a biological replicate. Each RP haploinsufficient mutant sample was compared to stage-matched wild-type control sample using a Student’s t test. All P values were >0.5, indicating no significant differences in the ratios were observed. Data distribution was assumed to be normal but this was not formally tested. (D) RNA expression and TE differences were plotted along the y-axis for all ribosomal protein genes that belong to large subunit (top) and small subunit (bottom) were plotted for shRPL5 and shRPS19 knockdown in hematopoietic cells (Khajuria et al., 2018). For statistical analysis of changes in expression of large and small subunit ribosomal protein genes at RNA and TE level, ROAST multivariate gene expression analysis was conducted (Wu et al., 2010).