Supplementary Figure 9: RNA-seq and ChIP-seq analysis of WID and EID.

(a) RNA-seq mapping and quantification statistics. Genomic reads are reads mapping to the genome. Genomic reads mapping uniquely are classified in three classes: intronic reads are reads mapping entirely within a gene but not entirely within annotated exons; exonic reads are reads mapping entirely within exons; and intergenic reads are reads not mapping entirely within genes. Junction reads are reads mapping to splice junctions but not to the genome. (b) Number of genes and transcripts expressed at different expression cutoffs. (c) Mapping statistics for the ChIP-seq experiments on histone modifications. The genome-wide Pearson correlation between the WID and EID epigenomes is very high: 0.90 for H3, 0.84 for H3K4me3, 0.94 for H3K9ac, 0.96 for H3K36me3, 0.92 for H3K4me1 and 0.92 for H3K27ac when computed on the number of reads mapping to 1,000-bp windows. (d,e) Join distribution in WID and EID of gene and transcript expression. Expression is measured in log(RPKM). (f) Gene Ontology term enrichment of 628 genes preferentially expressed in EID and 184 genes preferentially expressed in WID.