Subtracks⇓  Description⇓  Histone modification Track Settings
 
Histone modification sites derived from PlantTFDB   (All Expression and Regulation tracks)

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Histone modification
H3K23ac 
H3K36me3 
H3K4me2 
H4K12ac 
H4K16ac 
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 leaf H3K23ac  Histone modification for H3K23ac in leaf leaf   schema 
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 leaf H4K16ac  Histone modification for H4K16ac in leaf leaf   schema 
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 seedling H3K36me3  Histone modification for H3K36me3 in seedling ChIP-H3K36me3   schema 
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 seedling H3K4me2  Histone modification for H3K4me2 in seedling ChIP-H3K4me2   schema 
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 seedling H4K12ac  Histone modification for H4K12ac in seedling ChIP-H4K12ac   schema 

Description

The HM track is the histone modification regions inferred from ChIP-seq experiment. Data were collected from GEO datasets.

Method

Reads were mapped to unmasked genomes using bowtie2 (v2.2.8) and at most 1 mismatch in seed alignment was allowed (-N 1). Macs2 (v2.1.1.20160309) was used for peak calling. For histone modification, this process was performed with options of "--broad".

Reference

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods, 9(4), 357-359. doi:10.1038/nmeth.1923

Feng, J., Liu, T., Qin, B., Zhang, Y., & Liu, X. S. (2012). Identifying ChIP-seq enrichment using MACS. Nat Protoc, 7(9), 1728-1740. doi:10.1038/nprot.2012.101

Data Source

Accession number Pubmed ID
GSE26734 22110044
GSE66537 25886904
GSE69426 26646900
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