(A) Fragments per kilobase per million reads were summed for all mRNAs derived from the global stability profiling, normalized to the spike control and the time = 0 value, plotted and fit for half-life determination. (B) Numbers of transcripts that were successfully fit to the model and numbers of transcripts that failed to be measured for listed reasons. (C) Two biological replicates of the global mRNA stability profiling of wild-type cells (KWY165) were collected and transcript half-lives are plotted against each other. Red portions of the plot represent areas with dense datapoints and blue portions of the plot represent areas with sparse datapoints. (D) Distribution of efficiency parameters for the experiment described in Figure 1C. Each bin is 0.01 units wide. (E) Distribution of R2 values for the experiment described in Figure 1C. Each bin is 0.002 units wide. (F) Scatter plot of half-life values measured in this study compared to the values reported in Munchel et al. (2011). Colors represent density of datapoints as in Figure 1—figure supplement 1C. (G) Functional enrichment of long-lived transcripts as defined as transcripts having a half-life longer than one standard deviation greater than the mean half-life. (H) Half-life distributions of all 137 ribosomal protein-encoding mRNA half-lives (yellow) compared to the entire transcriptome (blue) normalized to the size of each transcript group. Each bin is 0.5 min wide. (I) Spearman correlation coefficients were computed for pairs of mRNA stability datasets and plotted. Orange represents positive correlation and blue represents negative correlation. Text background colors represents experimental methodology: metabolic labeling in dark gray, transcriptional shutoff in light gray and other in white. The datasets were hierarchically clustered based on Euclidian distances. The datasets were derived from the following: Gresham (Neymotin et al., 2014), Weis (2) [this study], Cramer (Shyu et al., 1991; Miller et al., 2011), Cramer (Muhlrad and Parker, 1992; Sun et al., 2012), Brown (1) and (Muhlrad and Parker, 1992; Wang et al., 2002), Peltz (Duttagupta et al., 2005), Coller (1) and (Muhlrad and Parker, 1992; Presnyak et al., 2015), Hughes (Grigull et al., 2004), Young (Holstege et al., 1998), Struhl (Geisberg et al., 2014), Pilpel (Shalem et al., 2008), Weis (Shyu et al., 1991; Munchel et al., 2011), Perez-Ortin (Pelechano and Pérez-Ortín, 2010).