Additional file 2.

Figures S1 to 11. Figure S1: Mean levels of exons and introns in shoots and roots of reciprocal hybrids. Figure S2: Distribution of H3K36me3 levels within and around differentially expressed genes. Figure S3: Experimental validation of methylated DNA regions by genomic bisulfite sequencing. Figure S4: A representative genomic region on maize chromosome 1 showing integrated maps of transcription and epigenetic modifications. Figure S5: Tree view of hierarchical clustering of H3K9ac and H3K36me3 levels. Figure S6: Relationships of variations in H3K36me3 and gene expression between organs and between genotypes. Figure S7: Functional categories of genes upregulated in shoots and roots of hybrids. Figure S8: Correlation of allelic expression bias between shoots and roots of Mo17 ยด B73. Figure S9: Coverage of 21 nt, 22 nt, and 24 nt siRNA clusters in and around protein-coding genes. Figure S10: Distribution of 21 nt and 22 nt siRNA clusters on maize chromosome 1. Figure S11: Correlation between 22 nt siRNAs and DNA-methylation levels at the same genomic loci.

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He et al. Genome Biology 2013 14:R57   doi:10.1186/gb-2013-14-6-r57