Extended Data Fig. 1: Development of Ezra-seq.
From: Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation
(a) The top panels show the comparison of Ezra-seq and two ligation-based Ribo-seq procedures. The bottom panels show in-frame ratio (IFR) of reads at codons with 1.0 indicating complete in-frame. The inserted bar plots show the fraction of reads in different reading frames. (b) An outline of Ezra-seq procedure (see Materials and Methods for the detail). (c) Aggregation plots show the ribosome density across the transcriptome. Transcripts are aligned to start and stop codons, respectively. Both 5’ end (green) and 3’ end (orange) of footprints are used for plotting. The heatmap shows the density of ribosome footprints with different length. (d) Aggregation plots show the ribosome density across the transcriptome in different cell lines and tissues. Transcripts are aligned to start and stop codons, respectively. Both 5’ end (green) are 3’ end (orange) of footprints are used for plotting. The right panel shows the range of codon IFR with 1.0 indicating complete in-frame reads. The inserted bar plot shows the fraction of reads in different reading frames. (e) Mean ribosome reads on individual triple-motifs. The top 10 motifs with the highest occupancy were listed. (f) Aggregation plots show ribosome densities around the motif PPD (left) and PPE (right). The 5’ end of the reads was used. (g) Variance analysis of ribosome density at individual P-sites when different offset values were considered. The pie chart shows the fraction of P-sites that have variation of ribosome density (12-nt offset) higher (red) or lower (blue) than the variation of ribosome density with random offset.
