Additional file 1: of What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

Table S1. Statistics from the de novo assembly of unmapped reads from DNA sequencing. Table S2. Statistics from the de novo assembly of unmapped reads from RNA sequencing. Table S3. Summary of all significant alignments from pairwise alignment of de novo assembled contigs from DNA unmapped reads to the nt database. Table S4. Number of significant alignments per tissue from pairwise alignment of de novo assembled contigs from unmapped RNA-seq reads to the nt database. Table S5. Summary of all significant alignments from pairwise alignment of de novo assembled contigs from unmapped RNA-seq reads to the nt database. Table S6. DNA sequencing metadata. Table S7. Genes represented in alignments of de novo assembled contigs from unmapped RNA-seq reads to Bos taurus. Table S8. Genes represented in alignments of de novo assembled contigs from unmapped RNA-seq reads to Bison bison bison, Bubalus bubalis, or Bos mutus. (XLSX 731 kb

Additional file 2: of What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

Note 1: The Onchocerca ochengi reference assembly is contaminated with bovine genomic sequence. Note 2: Estimation of the number of protein coding genes missing or misassembled in the UMD3.1 bovine reference assembly. (DOCX 41 kb

Numbers of Up- and Down-Regulated Differentially Expressed Genes and Isoforms for each Challenge Group in Contrast to Controls.

<p>Numbers of Up- and Down-Regulated Differentially Expressed Genes and Isoforms for each Challenge Group in Contrast to Controls.</p

Differentially Expressed Genes with the Largest Expression Variances by Challenge Group.

<p>Differentially Expressed Genes with the Largest Expression Variances by Challenge Group.</p

Heatmap for 200 differentially expressed genes with the greatest fold differences from all pathogen challenges using hierarchical clustering analysis.

<p>Hierarchical clustering of gene expression profiles in all samples. Each row represents a gene and each column an animal. The extent of expression of each gene in each sample is indicated by a color code. The color key ranges from saturated red for log_<b>2</b> ratios less or equal to -5.0 to saturated yellow for log_<b>2</b> ratios greater than or equal to 10. Red indicates an increased gene expression in the challenged animals. Legend: bact_0, bact_1 and bact_2 are <i>M</i>. <i>bovis</i> challenged; bact_3, bact_4, bact_5 and bact_6 are <i>P</i>. <i>multocida</i> challenged; bact_7, bact_8, bact_9 and bact_10 are <i>M</i>. <i>haemolytica</i> challenged; virus_0, virus_1, virus_2 and virus_3 are BRSV challenged; virus_4, virus_5, virus_6 and virus_7 are BVDV challenged and virus_8, virus_9, virus_10 and virus_11 are IBR challenged.</p

Principal component analysis for gene-level features.

<p>Principal component analysis for gene-level features.</p

Multidimensional scaling plot of samples based on all genes.

<p>Legend: bact_0, bact_1 and bact_2 are <i>M</i>. <i>bovis</i> challenged; bact_3, bact_4, bact_5 and bact_6 are <i>P</i>. <i>multocida</i> challenged; bact_7, bact_8, bact_9 and bact_10 are <i>M</i>. <i>haemolytica</i> challenged; virus_0, virus_1, virus_2 and virus_3 are BRSV challenged; virus_4, virus_5, virus_6 and virus_7 are BVDV challenged and virus_8, virus_9, virus_10 and virus_11 are IBR challenged animals.</p

Differentially expressed genes enriched within the toll-like receptor pathway.

<p><b>A</b>. IBR challenged animals. <b>B</b>. <i>M</i>. <i>haemolytica</i> challenged animals. Red stars indicate the differentially expressed genes in each pathway.</p

Transcript Classifications Reported by Cuffmerge for the Merged Assemblies.

<p>Transcript Classifications Reported by Cuffmerge for the Merged Assemblies.</p

Heatmap showing the Jensen–Shannon (JS) divergence between challenge groups estimated from FPKM values for all genes.

<p>Heatmap showing the Jensen–Shannon (JS) divergence between challenge groups estimated from FPKM values for all genes.</p