MethBank - Plants

MethBank-Plants

MethBank-Plants is a repository of whole-genome single-base nucleotide methylomes for economically important species based on NGS bisulfite-sequencing data. It features genome-wide profiling of methylation distributions across chromosomes, identification of differentially methylated promoters (DMPs) between a range of conditions and visualization of methylation patterns for genes and CpG islands across multiple different samples. Ongoing developments are continuous integration of more high-quality single-base nucleotide methylomes from a wide range of species, with the aim to serve as an important resource for epigenetic studies throughout the world.

Data sources

Species Project ID Project Name Platform Submitter Year Experiment No.
Soybean SRP016593 Single-base resolution DNA methylomes of soybean recombinant inbred lines reveals heritability patterns of natural methylation variants Illumina HiSeq 2000 Schmitz RJ,Ecker JR 2015 2
Soybean SRP012991 Methylation changes in soybean early maturation seed parts Illumina HiSeq 2000 Goldberg RB, Le BH 2012 3
Soybean SRP015838 Methylation changes in soybean mid-maturation seed parts Illumina HiSeq 2000 Goldberg RB, Le BH 2013 3
Soybean SRP042052 Methylation Changes in Soybean Cotyledon Stage Seed Parts Illumina HiSeq 2000 Goldberg RB, Le BH 2014 3
Soybean SRP012990 Methylation Changes in Soybean Early Maturation Seed Compartments Using LCM Illumina HiSeq 2000 Goldberg RB, Hur J 2014 2
Soybean SRP010037 Methylation Changes During Soybean Seed Development Illumina HiSeq 2000 Goldberg RB, Le BH 2012 15
Cassava SRP064404 Genome-wide methylome study in cassava Illumina HiSeq 2000 Wang H, Jacobsen S 2015 3
Rice PRJCA000239 Methylation changes during rice seed development Illumina Genome Analyzer II Li R 2016 6
Rice SRP043447 Oryza sativa Raw sequence reads/methylome of homozygote,heterozygote and WT Illumina HiSeq 2000 Hu L, Liu B 2015 3
Rice SRP017256 Plants regenerated from tissue culture contain stable epigenome changes in rice Illumina HiSeq 2000 Stroud H, Jacobsen SE 2013 18
Rice SRP032765 DNA methylation in rice in response to phosphate stress Illumina HiSeq 1000 Secco D, Lister R 2015 64
Rice SRP013556 Transcriptome and methylome interactions in rice hybrids Illumina Genome Analyzer II Chodavarapu RK, Pellegrini M 2013 1
Common bean SRP049211 Single-base resolution DNA methylomes of two legume species, Glycine max (soybean) and Phaseolus vulgaris (common bean) Illumina HiSeq 2000/Illumina HiSeq 2500 Kim KD, Jackson SA 2015 2
Tomato SRP008329 whole genome shotgun bisulfite sequencing of tomato fruits Illumina HiSeq 2000/Illumina Genome Analyzer II Zhong S, Giovannoni JJ 2011 8
Soybean SRP010103 Glycine max Epigenomics Illumina Genome Analyzer IIx Zhang JS 2012 4
Cassava SRP072226 Widespread natural variation of DNA methylation within angiosperms Illumina HiSeq 2000 Schmitz RJ 2016 1
Rice SRP061969 Cooperation between H3K27me3 and non-CG methylation in epigenetic regulation of genes in rice. Illumina HiSeq 2000 Zhou SL 2016 1
Tomato SRP082267 Tomato methylomes during chilling Illumina HiSeq 2500 Boyce Thompson Institute 2016 3
Soybean SRP049211 Single-base resolution DNA methylomes of two legume species, Glycine max (soybean) and Phaseolus vulgaris (common bean) Illumina HiSeq Illumina HiSeq 2000/Illumina HiSeq 2500 University of Georgia 2015 6