Venn diagram of number of validated class3 lncRNA with stranded blood libraries that are found between each animal.

<p> This figure represents the number of common and unique class 3 lncRNA validated with stranded RNA-Seq from blood that are found in each animal. The green circle represents the validated lncRNA found in the cow 210004817. The orange circle represents the validated lncRNA found in the cow Y10ST0106. The blue circle represents the class 3 lncRNA found in the cow daisy. The red circle represents the validated lncRNA found in the cow Y10ST0027. In the very middle we see that 237 validated class 3 lncRNA are found in all 4 animals.</p

Tissue x tissue heat map and hierarchical clustering of gene co-expression data for putative intergenic long ncRNA.

<p>This heat map shows the number of transcripts that are co-expressed in each of the tissues in relation to another tissue along with the replicates (calculated using the package DESeq). The order of the tissues is based on their pairwise distances. The colour indicates the level of the expression correlation within tissue replicates and between tissue samples. The darker the blue colour is the higher the correlations are. A white colour indicates no similarities in the expression data.</p

Validated lncRNA from blood stranded RNA-Seq that overlap with class 3 un-stranded lncRNA.

<p>Validated lncRNA from blood stranded RNA-Seq that overlap with class 3 un-stranded lncRNA.</p

Average number of differential expressed class 3 transcripts that are either upregulated or downregulated.

<p>This graph shows us the average number of class 3 putative lncRNA transcripts that are either upregulated (blue bars) or downregulated (red bars). We see that in the tissues kidney, liver and thymus there are, on average, more upregulated transcripts, while in the tissues leg muscle, ovaries, spleen and tongue there is, on average, more downregulated transcripts.</p

Differential expression heat map of class 3 lncRNA.

<p>This heat map shows the number of transcripts that either upregulated or downregulated for each tissue. On the x-axis are the upregulated tissues. On the y-axis are the downregulated tissues. The tissues are ordered and grouped based on upregulation. Red colors indicating the most differential expression, while white colors indicate the least differential expression.</p

Total number of class 3 putative lncRNA per chromosome vs the size of each chromosome.

<p> This figure shows the correlation with the number of class 3 putative lncRNA found on each chromosome vs the actual size of our chromosome. The blue bars indicate the number of class 3 transcripts (as a percentage of the total number). The red line indicates the size of the chromosome (as a percentage of the total nucleotide size).</p

Number of unknown transcripts that pass the filtering pipeline, showing no coding potential.

<p>Number of unknown transcripts that pass the filtering pipeline, showing no coding potential.</p

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Additional file 7: of Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

Appendix 2. ANOVA testing the effects of TAD, CTCF and gene on ASE variation. TAD and CTCF remained significant when gene was fitted into a categorical variable in the ANOVA model, indicating that TAD and CTCF were independent factors from gene that were predictive of ASE variation. (ZIP 78 kb

Additional file 4: of Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

Table S3. Rank and fold change of enrichment of biological hallmarks at putative bovine TAD boundaries. This table shows the level of enrichment of each biological hallmark at putative bovine TAD boundaries. The level of enrichment for each biological signal is measured by the number of base pairs that a biological signal overlapping with the TAD boundary. Presented are two types of TAD boundaries for each TAD set, differed by whether a boundary is considered present if two neighbouring putative bovine TADs overlap each other by 1 bp. “< 0.0001” denotes the degree of overlap between the biological hallmark and TAD boundaries larger than all permuted cases. (A) The degrees of enrichment of all biological signals at the boundary of each TAD set are shown. (B) The degrees of enrichment of each pattern of CTCF binding motifs at the boundary of each TAD set are shown. Each motif pattern has a unique motif number defined by the FIMO output. Each best possible match motif is manually compared with the MEME-ChIP to assess whether the matched motif is previously reported. (XLSX 54 kb