List of SI Figures and Tables

SI Figure 1: Contrast of clusters

Flank steepness of exonic (A) and intronic (B) read clusters varied markedly. A minor shift towards a higher contrast for exonic clusters was noted.

SI Figure 2: Pathway analysis

The example of a “pathway” activated in the L4 DRG after L5 SNL is shown. Genes or gene products are represented as nodes, and the biological relationship between two nodes is represented as an edge (line). The intensity of the node color indicates the degree of up- (red) or down- (green) regulation found by mRNA-seq data. Pathway depictions such as this may help to identify key events but imply a degree of linearity, which may not accurately reflect the complexity of interdependence likely underlying complex transcriptome reprogramming.

SI Figure 3: qPCR validation of mRNA-seq

Relative differences (fold-change) of 755 transcripts between two quality control mRNA samples. Results determined by mRNA-seq correlated highly with qRT-PCR (as detailed in the methods section).

SI Table 1: UMR counts mapping to known protein coding genes

Ensembl gene ID is given in the first column; sample type and time point in the subsequent column. Raw UMR counts are provided for all Ensembl genes classified as known protein-coding genes. (Genes with a UMR count of 0 omitted.)

SI Table 2: Correlation of raw read counts between biological replicates

Pairwise comparison of primary data was performed by calculating Pearson correlation coefficients for the 10,367 known protein coding genes quantified in the study. Biological replicates correlated very highly. As shown, the Pearson correlation coefficient for all control-control sample pairs was r=0.99. Correlation coefficients for SNL-SNL sample pairs at each time point was also r=0.99, while correlation of SNL-SNL pairs between 2 wk and 2 mo time points was nearly as high, r=0.98 on average (range 0.97-0.99). For comparison, the mean correlation for SNL-control sample pairs was 0.82 reflecting expression changes in a substantial subset of genes as laid out in Results.

SI Table 3: Most strongly induced and suppressed genes

Genes induced or suppressed by a factor of 4 fold or greater (at 2 wk or 2 mo) are listed.

SI Table 4: Overview of published microarray findings and mRNA-seq results

Expression changes in the DRG that were reported for 330 genes in the microarray literature were also quantified in our experiments as shown here. () up regulated; () down-regulated; () unchanged. The chi-square test comparing microarray and mRNA-seq results (reported in the main text) was performed on this contingency table.

SI Table 5: Detailed comparison of published microarray findings and mRNA-seq results

A gene-by-gene comparison of our mRNA-seq results with five microarray based DRG studies is provided. The published studies used different nerve injury models and pooling of DRG from several anatomical levels and animals as discussed in the text.

SI Table 6: Validation of ELAND alignments

The alternative alignment program Bowtie was used to process 106 random reads resulting in the expected high rate of agreement.

SI Table 7: ROC curve

This table contains the sensitivity and 1-specificity value for each tested density.

SI Table 8: UMR clusters

Each line contains a cluster ID (using the coding scheme: UW = all clusters in present study, RN = Rattus Norvegicus, CR = Cluster of Reads, 2 digit number = chromosome ID where 91 = X chromosome, 12 digit number = primary key in UW database), start and end positions on the chromosome, length of the cluster, number of reads falling inside the cluster, read density and the covered Ensembl exons.

SI Table 9: Splice junction clusters

Each line contains a splice junction cluster (SJC) ID (using the following coding scheme: UW = all SJC in present study, RN = Rattus Norvegicus, CS = Cluster of Splice Reads, 2 digit number = chromosome ID were 91 equals X chromosome, 12 digit number = primary key in UW database), chromosome, splice junction boundary positions and the number of splice junction reads supporting this splice site.

SI Table 10: Splice junction connectivity

List of splice junction clusters (SJC) including the read clusters that are connected with each other. Each line contains the SJC-ID (as explained in the legend to SI table 9), followed by read cluster ID 1 and read cluster ID 2.

SI Table 11: Read cluster groups (de novo gene discovery)

This table lists groups of two or more UMR clusters (from SI Table 8), which are connected by SJC (from SI Table 9 and 10). Each line provides a group ID; chromosome (where 91 stands for the X chromosome); start position of the first cluster in the group; end position of the last cluster in the group; group type (<KNOWN>, <UNKNOWN>, <MIXED>); number of clusters in the group; and the UMR clusters contributing to the group. The 421 groups marked as <UNKNOWN> correspond to the novel gene candidates discussed in the main text. Their UW ID’s provided in this table will be used as alias in the rat genome database (RGD), to which the data was submitted.

SI Table 12: Annotations to sample pathway genes

Column A-D = Gene abbreviation, synonyms, family, and subcellular function. E-H = Entrez gene name and ID for human, mouse, and rat.

SI Table 13: Non-canonical splice sites

Relative frequency of sequences of non-canonical splice site motifs identified by a small minority (3%) of sjUMR reads.