MOESM2 of Deciphering targeting rules of splicing modulator compounds: case of TG003

Additional file 2: Figure S1. A RNA-seq data visualization of CLK1 exon 4 in both human and mouse.RNA-seq data was visualized by sashimi-plot. Numbers of junction reads shown are calculated by our method. B Experimental validation by RT-PCR

MOESM9 of Deciphering targeting rules of splicing modulator compounds: case of TG003

Additional file 9: Table S5. Values used in decision tree analysis.Table to accompany Figure 6

MOESM10 of Deciphering targeting rules of splicing modulator compounds: case of TG003

Additional file 10: Table S6. Comparison result of skip-enhanced exons between TG003 treated cells and U2AF65-KD cells

MOESM6 of Deciphering targeting rules of splicing modulator compounds: case of TG003

Additional file 6: Table S4. Exon feature scores of all 2335 control exon pairs. Ensembl IDs, genomic coordinates and all information used to draw Figure 5 box plots (column 1 and 2) are provided with in this table. Some SVM-BP scores are not given because SVM-BP did not find any branch point that satisfies the required conditions of a branch point

Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding

Non-coding RNAs are emerging targets for drug development because they are involved in various cellular processes. However, there are a few reliable design strategies for small molecules that can target RNAs. This paper reports a simple and efficient method to comprehensively analyze RNA motifs that can be bound by a specific small molecule. The method involves Dicer-mediated pre-miRNA cleavage and subsequent analysis of the reaction products by high-throughput sequencing. A pre-miRNA mutant library containing a randomized region at the Dicer cleavage site was used as the substrate for the reaction. Sequencing analysis of the products of the reaction carried out in the presence or absence of a synthetic small molecule identified the pre-miRNA mutants whose Dicer-mediated cleavage was significantly altered by the addition of the small molecule. The binding of the small molecule to the identified pre-miRNA mutants was confirmed by surface plasmon resonance, demonstrating the feasibility of our method

Additional file 1 of PDIVAS: Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing

Additional File 1: Supplementary Figure S1-6

Additional file 3: of SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology

Table S1. Quality control of SINC-seq samples. (XLSX 21 kb

Additional file 4: of SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology

Movie S2. Experimental run #55 with unsuccessful fractionation. (MP4 1372 kb

Additional file 5: of SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology

Movie S3. Experimental run #69 with unsuccessful fractionation. (MP4 1116 kb

Additional file 1: of SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology

Supplementary information and Figures S1–S12. (DOCX 4587 kb