Extended Data Fig. 7: Optimized SiR UltraSelex ranking, taking into account mock-bead binding.
From: Single-step discovery of high-affinity RNA ligands by UltraSelex
a, Chemical structure of the SiR original (blue and black part) and mock (black part only) compound for RNA aptamer selection. b, High correlation of the normalized AUC values among the UltraSelex experimental replicates against the SiR mock target. The AUC values from the top 2000 species of each replicate were analyzed. The raw AUC values were normalized by the min–max method using (AUC − min_AUC)/(max_AUC − min_AUC). Each species is denoted by a blue dot, and the reference line x = y = z is represented by the dashed gray line. c, Fraction of identical sequences between the triplicate UltraSelex datasets from b with increasing top rank of aptamers. d, Comparison of the rank order distribution of turn-on ('On') and non-turn-on ('Non') SELEX RNA aptamers in the UltraSelex libraries before (w/o mock) and after (mock) computational filtering for mock-bead binding. The RNA species were ranked by the ratio of the normalized AUC in SiR-B to SiR mock target. The y axis represents the rank order of the RNA aptamer in the specified UltraSelex library. The group of turn-on and non-turn-on RNA aptamers are shown with a purple box and a gray box, respectively. SiR-A (n = 39), SiR-B (n = 37) and SiR-C (n = 38). The box pots are defined as in Fig. 2f. e, Venn diagram showing the intersection of the 25 top-ranked RNA aptamers derived from the three mock-bead-optimized UltraSelex experiments SiR-A, SiR-B and SiR-C.
