Additional file 2 of Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

Additional file 2: Fig. S1. The analysis process and characteristics of peaks. (a) and (b) The ATAC-seq signal enrichment around TSSs and insert size distribution of ATAC-seq for 2 samples (brain_sample1 and brain_sample2). (c) Proportion of tissue-specific peaks that were distal peaks or proximal peaks. (d) Distribution of peak size obtained in this study. Fig. S2. Identifying the functional pathway and tissue specificity via RNA-seq. (a) Hierarchical clustering using gene expression. (b) Functional enrichment of tissue-specific expression genes for each tissue based on Gene Ontology (GO) biological processes (left). Distribution of the number of tissue-specific genes (right). (c) Representative examples of heart specific gene which is highly expressed in heart tissue. (d) Bar plot showing representative biological processes enriched in target genes of the system specific peaks and conserved peaks. Different colors refer to different systems, and light yellow indicates biological processes enriched in target genes of conserved peaks. (e) Bar plot showing peak intensity of liver specific peaks which located close to ARG1 (a protein coding gene expressed primarily in the liver and involved in the urea cycle). (f) Functional enrichment of genes for each tissue based on GO biological processes. The columns represent 20 tissues. The rows represent GO terms in each tissue (upper). Representative examples of enriched biological processes in target genes of heart specific peaks (bottom). Fig. S3. Hierarchical clustering inferred from peak intensity and gene expression. (a) Hierarchical clustering using peak intensity. The top 100,000 peaks with high intensity were used for the analysis. (b) Hierarchical clustering using gene expression. The top 5000 highly variable genes were used for the analysis. Fig. S4. The flowchart and outcomes from the correlation between peak intensity and gene expression.