STRIPE-seq captures the yeast initiation landscape. (A) Plot of the fraction of unique TSSs that are promoter-proximal (−250 to +100 bp relative to an annotated gene start) at or above the indicated read threshold. Dot color is indicative of the number of genes with a promoter-proximal TSS. Corresponding plots for all STRIPE-seq samples are presented in Supplemental Figure S6. (B) Hierarchically clustered heatmap of Pearson's r values for pairwise comparisons between TSSs identified in STRIPE-seq samples. Before clustering, samples were thresholded such that each TSS had to have at least 3 raw counts in one sample, and then counts were TMM normalized. (C) Genomic distribution of TSSs in 100-ng STRIPE-seq replicate 1 broken into quintiles by TSS strength. The “promoter” annotation indicates −250 to +100 relative to an annotated gene start and “downstream” refers to the 3 kb downstream from a 3′ gene end. Genomic distributions of TSSs for all STRIPE-seq samples are presented in Supplemental Figure S7. (D) Density plot of 100-ng STRIPE-seq replicate 1 unique TSS positions relative to annotated gene starts. (E) Genome browser tracks showing CPM-normalized STRIPE-seq (replicate 1 for each input amount) and poly(A)+ RNA-seq (replicate 1) at two representative regions of the yeast genome. (F) Sequence logos of TSSs detected in 100-ng STRIPE-seq replicate 1 broken into quintiles by TSS strength. Sequence logos of TSSs in all STRIPE-seq samples are presented in Supplemental Figure S9. (G) Nucleotide color plot of the sequence context of TSSs detected in 100-ng STRIPE-seq replicate 1. TSSs are ranked descending by read count. (H) Dinucleotide frequencies at TSSs detected in 100-ng STRIPE-seq replicate 1. Dinucleotide frequencies at TSSs in all STRIPE-seq samples are presented in Supplemental Figure S10.
