GEO DataSets

(Submitter supplied) DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. more...

Organism:

Cannabis sativa; Cucumis sativus; Prunus persica; Manihot esculenta; Panicum virgatum; Fragaria vesca; Eucalyptus grandis; Populus trichocarpa; Erythranthe guttata; Eutrema salsugineum; Beta vulgaris; Panicum hallii; Theobroma cacao; Brassica rapa; Malus domestica; Ricinus communis; Brachypodium distachyon; Lotus japonicus; Citrus x clementina; Medicago truncatula; Setaria viridis; Sorghum bicolor; Vitis vinifera

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

30 related Platforms

34 Samples

Download data: TSV

(Submitter supplied) Bisulfite treatment libraries were made to characterize DNA methylation of Norway spruce

Organism:

Picea abies

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19695

81 Samples

Download data: WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Physcomitrium patens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL29161 GPL30513 GPL30955

8 Samples

Download data: GFF

(Submitter supplied) We mutated PpDDM1 and the early land plant. Using BS-seq and RNA-seq, we here show that though DNA methylation is disrupted in all contexts development isn't and TE and gene differential expression are minute

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30513 GPL30955

6 Samples

Download data: TXT

(Submitter supplied) We mutated PpDDM1 and the early land plant. Using BS-seq and RNA-seq, we here show that though DNA methylation is disrupted in all contexts development isn't and TE and gene differential expression are minute

Organism:

Physcomitrium patens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL29161

2 Samples

Download data: GFF

(Submitter supplied) Functional genomic states are maintained by reinforcing chromatin interactions that exclude the components of other states. Plant heterochromatin features methylation of histone H3 at lysine 9 (H3K9me) and extensive DNA methylation. However, DNA methylation is also catalyzed by a mostly euchromatic small RNA-directed pathway (RdDM) thought to seek H3K9me. How RdDM is excluded from H3K9me-rich heterochromatin is unclear. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL21785 GPL19580

62 Samples

Download data: BW, GFF

(Submitter supplied) To properly regulate the genome, cytosine methylation is established by animal DNA methyltransferase 3s (DNMT3s). While altered DNMT3 homologs, DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs), have been shown to establish methylation via the RNA directed DNA methylation (RdDM) pathway, the role of true-plant DNMT3 orthologs remains elusive. Here, we profile de novo (RPS transgene) and genomic methylation in the basal plant, Physcomitrella patens, mutated in each of its PpDNMTs. more...

Organism:

Physcomitrium patens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL14798

10 Samples

Download data: GFF

(Submitter supplied) OsDDM1 and OsDRM2 display functional specificities that define distinct DNA methylation pathways in the bulk of DNA methylation of the rice genome

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13834

17 Samples

Download data: BAM, BW, CSV, GFF, WIG, XLS

(Submitter supplied) We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platforms:

GPL10977 GPL10978

24 Samples

Download data: CEL, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Manihot esculenta

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL17194

6 Samples

Download data: WIG

(Submitter supplied) Bisulfite treatment, and mRNA libraries were made to characterize DNA methylation and expression of cassava.

Organism:

Manihot esculenta

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17194

3 Samples

Download data: WIG

(Submitter supplied) Bisulfite treatment, and mRNA libraries were made to characterize DNA methylation and expression of cassava.

Organism:

Manihot esculenta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17194

3 Samples

Download data: TXT

(Submitter supplied) Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL29591 GPL18740

10 Samples

Download data: GFF3

(Submitter supplied) Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL29591

2 Samples

Download data: GFF3

(Submitter supplied) Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

6 Samples

Download data: TXT

(Submitter supplied) Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.

Organism:

Vitis vinifera

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18740

2 Samples

Download data: TAB, TXT

(Submitter supplied) Previous studies have shown that exposure to ionising radiation (IR) results in DNA methylation changes in plants. However, to the best of our knowledge, this phenomenon is yet to be studied across multiple generations. Furthermore, the exact role of these changes in the IR-induced plant response is still far from understood. Here, we study the effect of gamma radiation on DNA methylation and its effect across generations in young Arabidopsis plant. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19580

45 Samples

Download data: TXT

(Submitter supplied) In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H=A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. more...

Organism:

Eutrema salsugineum

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21150

41 Samples

Download data: BED, TSV, TXT

(Submitter supplied) In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. more...

Organism:

Brassica rapa; Arabidopsis lyrata; Brassica oleracea; Eutrema salsugineum; Arabidopsis thaliana; Capsella rubella

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

10 related Platforms

44 Samples

Download data: BED, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL21179

24 Samples

Download data