Extended presentation of RNA-seq and ChIP-seq data. (A) Full spread of individual genes from RNA-seq along with their binned averages from Fig. 3 C. (B) Change in spike-in normalized gene expression (TxPG) plotted against and binned by expression level in control, with and without removal of genes involved in stress response or cell cycle. Each bin represents 5% of genes. Genes were excluded before binning. (C–F) Scatter plots comparing different parameters calculated from RNA-seq and Pol II ChIP-seq data sets, as indicated by axes. The occupancy around the transcription start site (TSS) was quantified over a region from 100 bp upstream to 200 bp downstream of the annotated TSS. Each dot represents one gene, lines show best fit linear models. Correlation values are reported above each plot. (G) PCA plots of RNA-seq and Pol II ChIP-seq experiments showing variation between biological replicates (dots). (H) Full spread of individual genes along with their binned averages from Fig. 3 E. (I) Representative metagene profiles showing the average occupancy of a bin of genes at each base pair, relative to the TSS. Each color represents a bin of 2% of genes, binned by their expression level (TxPG) in control, and the height indicates the average Pol II occupancy of genes in the bin. (J) Change in Pol II occupancy plotted against and binned by Pol II occupancy in control. Each bin represents 5% of genes, colored dots represent mean fold change within the bin, and error bars represent a 99% confidence interval.