Additional file 1: Figure S1. of Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

The tissues used in this study. Figure S2. Reproducibility of RNA-seq data. Figure S3. Randomised distributions of features over genomic regions within the uniquely mappable part of the genome. Figure S4. (A) The size distributions of the different features in base pairs and (B) the distributions of the gene expression levels in the two tissues. Figure S5. Characteristics of enhancer-overlapping TEs. Figure S6. Examples of (A, B) enhancers that contain TEs and (C, D) TEs that contain an enhancer. Figure S7. Example of data on tb1 enhancer. Figure S8. Asymmetric H3K9ac enrichment at candidate DHSs. Figure S9. Average profiles of the enhancer candidates in V2-IST and husk for each category. Figure S10. Heatmaps of chromatin, DNA and transcript features at TSSs. Figure S11. Average profiles of randomly selected TSSs in V2-IST and husk for each category. Figure S12. Comparison of expression levels between genes and enhancer candidates in V2-IST and husk. Figure S13. Heatmaps and average profiles of H3K9ac and H3K4me3 at (A, B, D) candidates and (A, C, E) TSSs. Figure S14. ChIP-qPCR data on H3K9ac and H3K4me1 enrichment at enhancer candidate regions. Figure S15. DNase I experiments resulting in the libraries sequenced and analysed in this study. Table S1. Sequencing datasets generated in this study. Table S2. Number of DHSs that overlap between replicates. Table S3. Number of H3K9ac peaks that overlap between replicates. Table S4. Number of TEs (for RLG family with and without candidates) and enhancers that carried the GGCCCA motif. Supplemental Methods. (PDF 2730 kb)