Here we combine the published Arabidopsis epigenomic datasets (e.g. ChIP-seq, ATAC-seq, MNase-seq, BS-seq), 3D genome datasets (e.g. Hi-C, Capture Hi-C, HiChIP, ChIA-PET), and transcriptome datasets (e.g. RNA-seq and ncRNA-seq) to construct a comprehensive Arabidopsis thaliana Encyclopedia of DNA Elements Database (AraENCODE). This database contains 4,511 datasets. The Arabidopsis TAIR10 is uniformly selected as the reference genome. So, it's convenient for the display and comparison of data. AraENCODE database mainly includes seven search functions, including Histone Modification,
Transcriptome, Open Chromatin Region, DNA methylation, 3D Genome, Chromatin State and Wildtype vs Mutant, and they help database users to quickly search for targeted epigenetics. This also shows the epigenetic landscape of Arabidopsis in AraENCODE database from five aspects: histone modification, transcriptional expression, open chromatin state, DNA methylation degree and mutant difference. AraENCODE database has also equipped with WashU Epigenome Browser, it can show the standardized Arabidopsis datasets more intuitively.
AT2G18790(PHYB); AT5G10140(FLC);
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Wang Z., Liu M., Lai F., Fu Q., Xie L., Fang Y., Zhou Q., and Li G. (2023). AraENCODE: a comprehensive epigenomic database of Arabidopsis thaliana. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2023.06.005.
Guoliang's Bioinformatics Lab
Welcome to Guoliang's Lab Website of Bioinformatics at College of Informatics, Huazhong Agricultural University (HZAU).Our main research interests are in the field of three-dimensional (3D) Genomics.
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