Additional file 5 of Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits

Additional file 5: Figure S1. Associations between immune cell global methylation and DNA methyltransferase (DNMT) expression. Moderate negative and positive correlations were observed between global methylation and normalized transcript abundance of DNMT1 (A) and DNMT3A (B), respectively. Normalized DNMT3B abundance was significantly negatively correlated with global DNA methylation (C). Considering abundance of all DNMTs, the normalized abundances of DNMT1 and DNMT3B subtracted from DNMT3A abundance were significantly positively correlated with global methylation (D). Figure S2. Methylation rates across immune cell marker genes CD19 (A), SIRPA (B), and TBX21 (C), and CD4 (D) for expressing and non-expressing cell types. Gray boxes indicate cell differentially methylated regions (cDMRs) within each gene locus, and black dots indicate CpG coordinates. Figure S3. (A) Dot plot of average methylation at CD8A TSS-proximal cell differentially methylated regions (cDMRs). (B) Dot plot of CD8A transcript abundance as percentage of maximum transcripts per kilobase million (TPM) across samples. Letters indicate statistically significant differences between means (p < 0.05). Figure S4. Positive methylation:expression correlations are associated with more lowly expressed genes and highly methylated regions. (A) Transcripts per kilobase million (TPM) of genes overlapping cDMRs negatively and positively correlated with gene expression, separated by gene feature. (B) Methylation levels of cDMRs negatively and positively correlated with gene expression, separated by gene feature. **=p