Search

Additional file 15: Activity-dependent splicing of Homer1 in primary cultured hippocampal neurons. pdf. a Homer1 expression in primary cultured hippocampal neurons of control mice or 3 h after KCl treatment detected by RNA sequencing. Shown are coverage plots (blue) from paired-end reads for the two sample groups. The reference gene track is depicted below (green). b Sashimi plot of RNA sequencing data for Homer1. Numbers indicate the counts of RNA sequencing reads that span the respective exon junctions. RNA-seq data was generated by Quesnel et al. and deposited in the GEO database under ID code GEO: GSE89984.

Additional file 2: Temporal cluster analysis of activity-regulated genes. pdf. Activity-regulated genes identified on the whole gene level were assigned to clusters based on their differential regulation over four time points (0, 1, 4, 8 h after seizure onset). Similar expression kinetics were grouped and the thick black line represents mean expression profiles.

Additional file 7: Products of RT-PCR. pdf

Additional file 3: Genes with activity-dependent splice variation identified through time-dependent ANOSVA. pdf. pValueBH, minimal adjusted p-value derived by Bonferoni and Holm method. DE, differentially expressed, indicates whether the whole gene was identified as induced by neuronal activity in our initial analysis (Additional file 1).

Additional file 4: Genes with activity-dependent exon usage identified through the FIRMA method. pdf. FIRMA (F) scores represent the discrepancy of one probeset from the other probesets in the same gene and were calculated for every probeset and sample. fSscore, corresponds to samples collected after seizure compared to controls and samples. f0 score, corresponds to samples collected after vehicle treatment compared to controls. FDR, False discovery Rate calculated from F scores for the alternative and the null model. DE, differentially expressed, indicates whether the whole gene was identified as induced by neuronal activity in our initial analysis (Additional file 1).

Additional file 8: Alternative splice variants of Krt75. pdf. a Exons of murine Krt75 according to the Ensembl database. Boxes represent exons (not to scale), black boxes correspond to coding sequence, white boxes to untranslated regions. Numbers indicate exon size (upper row) and intron size (lower row). A corresponding cDNA was cloned from skin in this study (Genebank accession number NM_133357). b An alternatively spliced and previously undescribed cDNA was cloned in this study from skin (Genebank accession number MN037882). The internal alternative splice site (arrowhead) in exon 7 is indicated. The usage of this alternative splice site results in a frameshift and premature stop in the sequence corresponding to exon 8. c A truncated splice variant was cloned in this study from hippocampus of mice 4 h after seizure onset (Genebank accession number MN124092). It starts with exon 4. d Schematic of the protein domain structure of Krt75 corresponding to the canonical variant depicted in a. 1A, 1B, 2A and 2B are coiled-coil subdomains and L1, L12 and L2 are intervening linkers. The orange box indicates 10–20 amino acid segments that are highly conserved among keratin and other interfilament proteins. e Schematic of the protein domain structure of Krt75 corresponding to the new splice variant from skin depicted in b. f Schematic of the protein domain structure of Krt75 corresponding to the activity-regulated splice variant expressed in the hippocampus depicted in c.

Additional file 9: Gene expression profile of Rcan1. pdf. Analysis and visualization of the microarray data obtained for Rcan1. The upper 3 plots show the log2 transformed expression values of Rcan1 over the course of its probes and probesets per exon. While the red lines show the intensity values of the control samples (vehicle and untreated), the 3 shades of green represent the expression intensities in the samples at the three different time points after seizures. The upper plot shows raw probe level intensities and grey bins stand for the individual probes. The middle plot shows the normalized intensities summarized to probeset level (probes divided by grey bins) for every sample. The lower plot shows the log2 ratio calculated from the mean of the intensities seen in the second plot, each line represents one of the 3 time points after seizure. At the bottom 3 types of exon models are depicted. The dark blue boxes represent the probesets per exons, which were included in the microarray analysis. The yellow boxes and track correspond to genomic sequence and each box indicates an exon. The light blue tracks and boxes represent the annotated transcripts present in the Ensembl database.

Additional file 5: Gene expression profile of Krt75. pdf. Analysis and visualization of the microarray data obtained for Krt75. The upper 3 plots show the log2 transformed expression values of Krt75 over the course of its probes and probesets per exon. While the red lines show the intensity values of the control samples (vehicle and untreated), the 3 shades of green represent the expression intensities in the samples at the three different time points after seizures. The upper plot shows raw probe level intensities and grey bins stand for the individual probes. The middle plot shows the normalized intensities summarized to probeset level (probes divided by grey bins) for every sample. The lower plot shows the log2 ratio calculated from the mean of the intensities seen in the second plot, each line represents one of the 3 time points after seizure. At the bottom, 3 types of exon models are depicted. The dark blue boxes represent the probesets per exons, which were included in the microarrays. The yellow boxes and track correspond to genomic sequence and each box indicates an exon. The light blue tracks and boxes represent the only so far annotated transcript present in the Ensembl database. Note that exons 5 and 8 are not represented by probesets.

Additional file 6: Exon spanning primers. pdf

Nature Communications 9(1), 20 (2018). doi:10.1038/s41467-017-02391-6