Fig. 1: Overview of data collection and splicing analysis.
From: Alternative splicing across the C. elegans nervous system
A Schematic of the experimental procedure. B–E Four methods to analyze alternative splicing, applied to the gene ric-4/SNAP25 in the neurons NSM and PVM. B Raw data visualization. Top track: Gene model of ric-4 (along with non-coding RNAs 21ur-13262 and Y22F5A.10). Bottom tracks: Read coverage and junction counts. Numbers denote junction-spanning reads for the splice junctions of interest. Blue and orange boxes indicate alternative first exons. C Local Splicing Variation (LSV) visualization. Top: Gene model of ric-4, highlighting the alternative first exons corresponding to ric-4a (blue) and ric-4b (orange). Bottom: Posterior mPSI (MAJIQ-defined Percent Selected Index) estimates displayed as violin plots. Numbers indicate the posterior expected mPSI (summing to one in each neuron, as the orange and blue junctions are mutually exclusive). D Transcript-level quantification. Top: Average transcript TPM across all sequenced neurons. Middle: Relative transcript usage (in proportion to the total TPM for the gene, in each neuron), in NSM and PVM. Bottom: Transcript quantification, indicating the mean +/- standard deviation of TPM across samples for each transcript in each neuron. E Neuron-wise comparison between PVM and NSM. Top: The application returns a list of splice junctions with differential usage between the two neurons, including two junctions belonging to the same LSV in the gene ric-4. Bottom: Visualization of junction usage for this LSV in neurons PVM and NSM.
