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Figure S1. Comparison of ChIP-seq data with published ChIP–chip data.

Figure S2. Identification of genes associated with histone modifications using various maximum intervals between peaks and gene boundaries.

Figure S3. Re-ChIP analysis of the physical co-localizations of histone modifications for H3K4me3 monovalent genes and putative K4/K27me3 bivalent genes.

Figure S4. Pearson correlation coefficient matrix for chromatin modifications corresponding to the heatmap in Figure 1(b).

Figure S5. Chromatin state and expression analysis of locus types.

Figure S6. Comparison of NAT-associated genes identified by RNA-seq and genome-wide tiling array experiments.

Figure S7. State-specific effects analysis (SSEA) for chromatin modifications.

Figure S8. ANCORP analyses between chromatin states and sense or antisense transcripts.

Figure S9. Quantification of sense transcripts and histone modifications for chromatin states defined in Figure 5(c).

Figure S10. Strand-specific RT-PCR assays for quantification of NATs.

Figure S11. Quantities of sense mRNA for NAT-producing loci in mutant backgrounds.

Figure S12. Mis-regulation of NATs in the elf8-1 background.

Figure S13. Analyses of histone modifications for NAT-associated loci in various genetic backgrounds.

Figure S14. Quantification of DNA methylation in various genetic backgrounds with the McrBC/quantitative PCR assays.

Figure S15. Determination of nuclear enrichment for NATs.

Figure S16. Sense and antisense transcripts associated with the TAF4 (AT5G43130) locus.

tpj12017-sup-0002-TableS1.xlsapplication/msexcel32KTable S1. Summary of ChIP-seq and RNA-seq experiments.
tpj12017-sup-0003-TableS2.xlsapplication/msexcel3913KTable S2. Chromatin states defined by 10 chromatin modifications.
tpj12017-sup-0004-TableS3.xlsapplication/msexcel221KTable S3. List of genes associated with the putative H3K4me3/H3K27me3 bivalent chromatin state.
tpj12017-sup-0005-TableS4.xlsapplication/msexcel343KTable S4. GO term and locus type enrichment analysis for chromatin states.
tpj12017-sup-0006-TableS5.xlsapplication/msexcel2506KTable S5. NAT identifications using the stringent definition.
tpj12017-sup-0007-TableS6.xlsapplication/msexcel1005KTable S6. NAT identifications using the relaxed definition.
tpj12017-sup-0008-TableS7.xlsapplication/msexcel66KTable S7. Analysis of sense and antisense transcript abundances for chromatin states.
tpj12017-sup-0009-TableS8.xlsapplication/msexcel109KTable S8. Loci associated with intronic antisense tags.
tpj12017-sup-0010-TableS9.xlsapplication/msexcel39KTable S9. Sequences of primers used.
tpj12017-sup-0011-AppendixS1.pdfapplication/PDF86KAppendix S1. Supplementary experimental procedures.

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