Figure 3

Example of a genome graph for the Cacna2d1 gene (Calcium channel, voltage-dependent, alpha2/delta subunit 1). A) The genomic location of the Cacna2d1 gene on chromosome 4, highlighted in red. B) The exonic/intronic structure of the gene; brown squares represent exons, the black links between them represent introns. C) A zoomed-in region of the gene, showing the positions where the sequenced reads align to the exons and introns of the gene (grey bricks), for a given RNA-seq sample (in this example, an SNT sample is shown, sequenced to a depth of 50 M reads). D) A further zoomed in region of the gene, showing the individual reads and the positions to which they align in greater detail. E) The genome graphs for all of the samples (shown for sequencing depth 50 M). Each row represents a different sample. When calculating fold change, the reads aligning to each exon are summed to produce the raw expression value for each sample, and then DESeq is used to compare these values between SNT and naive samples. Some reads align outside of known exons, this is explored further in the section “Intronic expression and its effect on fold change calculation”.