Extended Data Fig. 3: High level of reproducibility of library variants in Pol II mutants.
(A) Histograms showing the distribution of measured efficiencies for all designed −8 to +4 TSSs for MASTER libraries in Pol II mutants. Dashed lines mark the 5% efficiency cutoff with number (N) of TSS variants shown. (B) TSS usage distributions at designed −10 to +25 TSSs for MASTER libraries in Pol II mutants. Dots represent three biological replicates. Bars are mean +/- standard deviation. (C) Hierarchical clustering of Pearson correlation coefficients of TSS efficiencies for major TSSs (designed +1 TSS for ‘AYR’ and ‘BYR’ libraries, +2 TSS for ‘ARY’ library) for WT or Pol II mutants illustrated as a heat map for three biological replicates. (D) Example correlation plots of TSS efficiency of major TSSs between representative biological replicates. Pearson r and number (N) of compared variants are shown. (E) Plots of CoV versus total RNA reads (three biological replicates) for Pol II mutants. The red dashed lines mark the CoV = 0.5 cutoff, an arbitrary cutoff for promoters with reasonable reproducibility across replicates. G1097D replicates contain outliers because this mutant is susceptible to genetic suppressors. A suppressor existing in one biological replicate generates a high CoV allowing filtering.
