Fig. 1

Sequencing details. A Proportion of reads mapping to rRNA and tRNA in tag-RNA-seq enriched Cappable-seq RNA for different experimental conditions (as indicated; MM, minimal medium; acid, LB + malic acid; salt, LB + sodium chloride, exp, exponential phase; stat, stationary phase). In Cappable-seq RNA (blue, TSS- and PSS-tag data combined) between 15 to 41% and in TSS-tag enriched Cappable-seq RNA (orange, TSS-tag) about 6 to 21% of the reads match to rRNA and tRNA, respectively. In contrast, total RNA contains about 94% rRNA and tRNA (gray) according to AJ Westermann, SA Gorski and J Vogel [57]. This indicates indirect rRNA and tRNA depletion by combined use of Cappable-seq and TSS-tag-RNA-seq enrichment. B Reproducibility of Cappable-seq indicated by the Pearson correlation coefficient r. All mapped reads were trimmed to the most 5’ base. For positions with reads, a relative read score was calculated and compared between replicates by calculating the Pearson correlation coefficient r. Cappable library III was sequenced twice to obtain technical replicates (IIIA and IIIB), which were merged later to data set III. Data sets I, II and III represent independent biological replicates