Maize chromatin states
About chromatin state:

We collected 95 maize 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 26 chromatin states located in 3,936,844 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 26 states:
StatePreferential epigenetics marksPreferential location
State 1histone acetylation,Mnase,acessible DNA3'UTR,promoter,intron
State 2H3K4me3,H3K36me3,acessible DNA3'UTR,promoter,intergenic
State 3H3K4me3,H3K36me3,acessible DNAintron,repeat_region
State 4histone acetylation,H3K4me3,H3K36me3,acessible DNApromoter,5'UTR,exon,3'UTR
State 5histone acetylation,H3K4me3,H3K36me3,acessible DNAexon,intron,promoter,5'UTR,3'UTR
State 6histone acetylation,H3K4me3,H3K27me3exon,promoter,5'UTR,3'UTR
State 7histone acetylation,Mnase,H3K4me3,H3K27me3,acessible DNApromoter,intergenic,3'UTR
State 8H3K27me3,Mnase, histone acetylationpromoter,intergenic,3'UTR,repeat_region
State 9H3K36me3,H3K9ac,H3K56acintron,exon,promoter,centromere
State 10H3K27me3intergenic,repeat_region,promoter
State 11Mnase,acessible DNA, histone acetylation,H3K9me2,CENH,DNA Methylationintergenic,repeat_region,3'UTR,promoter
State 12Mnase,ZmRAD51intergenic,repeat_region
State 13Mnase,ZmRAD51intergenic,repeat_region,promoter
State 14Mnase,CENH,DNA Methylation,H3K9me2,ZmRAD51intergenic,repeat_region,promoter
State 15Mnaseintergenic,repeat_region
State 16Mnase,H3K9me2,DNA Methylationintergenic,repeat_region,promoter
State 17Mnase,H3K9me2intergenic,repeat_region
State 18DNA Methylation,H3K9me2,Mnaseintergenic,repeat_region
State 19DNA Methylation,Mnase,H3K9me2intergenic,repeat_region
State 20CENHintergenic,repeat_region,centromere
State 21CENH,Mnase,H3K9me2,DNA Methylationintergenic,repeat_region,centromere
State 22Mnase,CENH,H3K9me2,DNA Methylationintergenic,repeat_region
State 23ZmO2intergenic,repeat_region
State 24H3K9me2,DNA Methylation,Mnase(weak signal)intergenic,repeat_region
State 25rare signalintergenic,repeat_region
State 26H3K9me2intergenic,repeat_region
Segment counts of SOM map
Nucleotide counts of SOM map
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