Figure 2

Validation of CIRS-seq data. (a) Distribution of transcripts with at least one RT stop on average per base. (b) Scatter plot of normalized reactivities in the two biological replicates of CIRS-seq. Reactivities are averaged in 10-nucleotide windows, with an offset of 5 nucleotides (PearsoN's correlation coefficient = 0.90. (c) Normalized reactivity profiles for the glutamic acid tRNA and overlay of reactivity data on the phylogenetically derived secondary structure. Yellow arrows indicate highly reactive positions (reactivity >0.7). Bases are color coded according to their reactivity. (c) Normalized reactivity profiles for the U5 snRNA and overlay of reactivity data on phylogenetically derived secondary structure. The structure of the U5 human homolog is also shown, with superimposed DMS/CMCT-reactive positions from [55]. The colors correspond to different degrees of chemical modification (purple, strong; yellow, medium; green, weak). Yellow arrows indicate highly reactive positions (reactivity >0.7). Bases are color coded according to their reactivity.