Genomic features and expression levels of DNA, LNA and RNA-based libraries. (A) Percentage of reads that align to known genomic features (promoter, intron, exon), for the libraries comparing the template-switching (TS) oligonucleotides R3, L3, L2, L1, and D3. Technical triplicates were averaged and error bars represent standard deviations. (B): Genomic representation of the R3, L3 and D3 libraries on the Myl1 locus (11 kbp). Aligned CAGE tags are represented as horizontal bars colored in purple for the sense strand and in green for the antisense strand, where the height is proportional to the number of tags in a given genomic bin, after normalizing tag counts per million (TPM) and averaging the triplicates. The highest peaks have the same size in the three tracks, representing 5717, 1665 and 180 TPM values for R3, L3 and D3 respectively. (C) Pairwise comparisons between the D3, L1, L2, L3 and R3 libraries. Each square provides data for the pair of libraries defined by the horizontal and vertical intersections with the diagonal. Upper part: Expression plots (logarithmic scale), where each dot represents the normalized number of reads aligning to a reference gene model (same strand only). Technical triplicates were averaged. Lower part: Pearson correlation coefficients before (left) and after (right) removal of strand-invasion artifacts. (D) Influence of temperature (indicated by grey labels) on TS with the R3, L3, and D3 TS oligonucleotides. Technical triplicates prepared on random-primed HeLa RNA.