Total cellular RNA was isolated using the
RNeasy kit (Qiagen). For standard reverse transcriptase-polymerase chain reaction (RT-PCR), 400 ng RNA was reverse transcribed using random hexamers and
SuperScript II Reverse Transcriptase (Life Technologies) followed by PCR with Platinum Taq PCR Polymerase (Life Technologies) according to the manufacturer's instructions. PCR product was resolved on 5% non-denaturing polyacrylamide gel and stained in ethidium bromide prior to imaging on the Kodak
Gel Logic Imaging System. The percentage of exon skipping was calculated as [exon exclusion band/ (exon inclusion band + exon exclusion band)] x 100 with a correction factor for the amount of ethidium bromide per base pair of DNA. See Supplementary Table S3 for primer sequences.
For quantitative RT-PCR, approximately 10 ng RNA was added to EXPRESS One-Step SuperScript qRT-PCR Universal (Life Technologies) with custom designed or predesigned Taqman primer and probe sets (see Supplementary Table S4 for sequences). All quantification was performed by the relative standard curve method and normalized to Ribogreen.
Ward A.J., Norrbom M., Chun S., Bennett C.F, & Rigo F. (2014). Nonsense-mediated decay as a terminating mechanism for antisense oligonucleotides. Nucleic Acids Research, 42(9), 5871-5879.