Rice chromatin states
About chromatin state:

We collected 100 rice epigenomic datasets, including ChIP-seq, DNase-seq, ATAC-seq and DNA methylation data. A Hidden Markov Model was applied to aggregate or collapse the multi-dimensional matrices into a small number of chromatin states. We identified 38 chromatin states located in 831,235 segments across the whole genome and different chromatin states contained different epigenetic features.

After chromatin state partition, we employed self-organization mapping (SOM) to integrate, visualize, and mine diverse epigenomic datasets, including 1,350 units that contained different chromatin signatures.

All of 38 states:
StatePreferential epigenetics marksPreferential location
State 1weak histone acetylationintron,promoter,3'UTR,intergenic
State 2H3K36me1,histone acetylationpromoter,3'UTR,intergenic
State 3H3K36me2,histone acetylation3'UTR
State 4H3K36me2,H3K36me3,H3K4me2exon
State 5H3K36me3,H3K4me2intron
State 6H3K27me3intergenic,intron,promoter
State 7H3K27me3intergenic,intron,promoter
State 8H3K27me3intergenic,intron,promoter
State 9H3K27me3,H2A.Zintergenic,intron,promoter
State 10H3K27me3,H2A.Z,H3K9ac,H3K23ac,H3K4me3,H3K4me2exon
State 11H3K9ac,H3K23ac,H3K4me3,H3K4me2,H3K27me3,H2A.Zexon,promoter
State 12H2A.Z,histone acetylation,H3K4me2,H3K4me3exon,promoter
State 13histone acetylation,H3K4me3,H3K4me2,H3K36me3,H3K36me2,H2A.Z5'UTR
State 14H3K4me3,H3K4me3,H3K36me3,H2A.Z,histone acetylationintron
State 15H3K4me3,H3K4me3,H3K36me3intron
State 16H3K4me3,histone acetylation,H2A.Zexon,promoter,5'UTR
State 17histone acetylation,acessible DNA,H3K4me2,H3K4me3promoter,exon,3'UTR
State 18histone acetylation,acessible DNA,H2A.Z,H3K4me35'UTR,promoter,intergenic
State 19DNA methylation,H3K4me3,H4K12ac,H4K16ac,OsNF-YB1,OsbZIPcentromere,intergenic
State 20accessible DNA,H2A.Z,histone acetylation,H3K27me3,DNA methylationintergenic,promoter,intron
State 21acessible DNAintergenic,promoter
State 22acessible DNAintergenic,promoter
State 23acessible DNAintergenic,promoter
State 24acessible DNAintergenic,promoter
State 25H2A.Z,H3K4me2,H3K4me3,histone acetylationpromoter,intergenic,intron,3'UTR
State 26DNA methylation,OsNF-YB1intergenic,promoter,intron
State 27H3K9me2,DNA methylation,OsNF-YB1intergenic,TE,promoter,exon
State 28H3K9me2,DNA methylation,MnaseTE,intergenic,intron,promoter,exon
State 29DNA methylation,H3K9me2,CENH3,MnaseTE,exon,promoter,intron,intergenic
State 30H3K9me2,DNA methylationTE,exon,intron,promoter,intergenic
State 31H3K9me2,CENH3,DNA methylationTE,intron,intergenic,exon,promoter,
State 32H3K9me2,CENH3,DNA methylation,MnaseTE,intergenic,intron,exon,promoter
State 33DNA methylation,H3K9me2TE,exon,intergenic,promoter,intron
State 34DNA methylation,H3K36,H3K4me2intron
State 35DNA methylation,H3K27me3,H3K36me1,H3K36me2,H3K36me3intergenic,intron,promoter
State 36DNA methylation,H3K36me1intergenic,promoter,intron
State 37DNA methylationintergenic,intron,promoter
State 38rare signalintergenic,promoter,intron
Segment counts of SOM map
Nucleotide counts of SOM map
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