Supplementary Information for

Tables

• Supplementary Table 1    Summary of Illumina libraries and alignments.
• Supplementary Table 2    Poised genes by species.
• Supplementary Table 3    Two-way poised gene overlaps.
• Supplementary Table 4    Core poised genes and assigned protein function categories.
• Supplementary Table 5    GO category enrichments.
• Supplementary Table 6    Genes poised in only one of five mammalian species.
• Supplementary Table 7    Motifs gained in promoters of genes poised in only one of five mammalian species.
• Supplementary Table 8    Poised gene set overlaps among five mammalian species.
• Supplementary Table 9    Poised genes in chicken male germ cells and gene set overlaps among six amniote species.

Files

• Supplementary Text and Figures Includes:
  • Figure S1: Assessment of sample purity and quality.
  • Figure S2: Correspondence between H3K4me3, H3K27me3, and expression levels.
  • Figure S3: Correlations between biological replicates.
  • Figure S4: Principal-component and clustering analysis of H3K4me3, H3K27me3, and RNA-seq data.
  • Figure S5: Effect of changing ChIP and expression thresholds on the number of poised genes called.
  • Figure S6: Effect of changing ChIP and expression thresholds on the number of poised genes called in only one of five mammalian species.
  • Figure S7: ChIP signal at sequential ChIP–qPCR targets.
  • Figure S8: Characteristics of core poised genes.
  • Figure S9: Additional examples of genes poised specifically in only one of five mammalian species.
  • Figure S10: Poised genes in Drosophila germ cells and in human and mouse spermatozoa.
  • Supplementary Note: Evolution of histone modification states in pachytene spermatocytes and round spermatids
  • Supplementary References
  • Supplementary Table 10: Primer sequences used for qPCR.

Supplementary Data:

• SuppData1_hs1
• SuppData2_hs2
• SuppData3_hs3
• SuppData4_rh1
• SuppData5_rh2
• SuppData6_mm1
• SuppData7_mm2
• SuppData8_bt1
• SuppData9_md1
• SuppData10_md2
• SuppData11_gg1
• SuppData12_fiveway_orthologs
• SuppData13_sixway_orthologs

Supplementary Code:

• divergencePlots
• findIntersections
• heatmaps
• pairwiseOverlaps
• README
• varyThresholds