Fig. 5

Activity dependent alternative splicing of Cda and Errfi1. a Cda is encoded by 4 exons (yellow boxes, not to scale). Transcript 1 comprises all 4 exons, transcript 2 only exon 3 and 4 and exon 3 has a 5′ extension. b Visualization of the microarray data. The plot shows the log2 ratio calculated from the mean normalized intensities of transformed expression values over the course of probesets per exon. Green lines represent expression kinetics of one time point after seizure onset. Blue boxes represent probesets per exon present on the microarrays. c Validation of Cda variant expression in hippocampus of control mice or 1, 4 or 8 h after seizure onset by RNA sequencing. Shown are coverage plots (blue) from paired-end reads for the four sample groups. The reference gene track is depicted below (black). d Sashimi plot of RNA sequencing data. Numbers indicate the counts of RNA sequencing reads that span the respective exon junctions. e Validation of splicing events by RT-PCR. Numbers indicate exons. Exon-spanning primers (arrows) were used to assess expression of exons in total RNA of hippocampi of control mice (−) and of mice sacrificed 4 h after seizure onset (+). Note that the forward primer corresponds to the 5′-UTR of exon 3 that is specific for transcript 2. The reverse primers correspond to 5′- or 3′-terminal sequence in exon 4. f Errfi1 is encoded by 6 exons. The first two exons are mutually exclusive and their alternative usage results in transcript 1 or 3. Transcript 2 comprises no open reading frame. g Visualization of the microarray data. h Validation of Errfi1 variant expression by RNA sequencing. i Sashimi plot of RNA sequencing data for Errfi1. j Validation of splicing events by RT-PCR. Note that no product was amplified by using Exon 1 and 4 specific primers