GEO DataSets

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL17639 GPL13222

15 Samples

Download data: TSV

(Submitter supplied) DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell type specific patterns of DNA methylation, especially in the CHH sequence context. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TSV

(Submitter supplied) DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell type specific patterns of DNA methylation, especially in the CHH sequence context. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL13222 GPL17639

9 Samples

Download data: TSV

(Submitter supplied) Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from the most heterochromatic transposons to euchromatic genes determines the requirement of DDM1 for methylation maintenance in all sequence contexts. more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL9302 GPL13222 GPL11221

33 Samples

Download data: GFF

(Submitter supplied) DNA methylation and nucleosome densities play a critical role in the regulation of gene expression. While much is known about the mechanisms of transcriptional control that are mediated by these, less is known about the degree to which they are tissue-specific. By comparing DNA methylation, nucleosome densities and transcriptional levels in different tissue types we can gain a clearer understanding of the extent to which these mechanisms influence gene expression in a tissue-specific manner. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL9302

3 Samples

Download data: BEDGRAPH

(Submitter supplied) In this work, we studied function of rice DDM1 in coordinating DNA methylation, expression of small (sRNA) and long noncoding (lncRNA) RNAs, and nucleosome positioning by high throughput approaches.We show that the ddm1a/1b mutation resulted in ectopic CHH methylation of transposable elements (TE) and repeats. The ectopicCHH methylationwas dependent on DRM2, a DNA methyltransferase involved in sRNA-dependent DNA-methylation (RdDM). more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL13834

3 Samples

Download data: BW

(Submitter supplied) The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeller DDM1 causes hundreds of genomic regions to switch from CMT2-dependency to RdDM-dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). 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; Genome variation profiling by high throughput sequencing

Platforms:

GPL23157 GPL17639

42 Samples

Download data: BW, TDF, TSV, WIG

(Submitter supplied) DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize. Here, we characterized the function of DDM1 in regulating genome-wide DNA methylation in maize. Two homologs of ZmDDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. more...

Organism:

Zea mays

Type:

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

Platform:

GPL17628

8 Samples

Download data: BED, TXT

(Submitter supplied) Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: methylcytosine ChIP-chip on tiling array

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10977

4 Samples

Download data: CEL, TXT

(Submitter supplied) Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput transcriptome sequencing

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT

(Submitter supplied) Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput small RNA sequencing

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT

(Submitter supplied) Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT

(Submitter supplied) Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0. more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL9062 GPL10977

16 Samples

Download data: CEL, TXT

(Submitter supplied) DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hy- brids displayed nonadditive DNA methylation levels, termed meth- ylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differ- entially methylated regions in parents. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL13222

16 Samples

Download data: WIG

(Submitter supplied) Ecotype-specific differences in genome methylation were assayed in Arabidopsis Col and Ler variations using genomic tiling microarrays. Comparative genome hybridization was also performed so that the contribution of ecotype-specific amplifications and deletions could be estimated and integrated into the analysis of differential DNA methylation. Keywords: methylation analysis and comparative genome hybridization

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Methylation profiling by array

Platform:

GPL5116

3 Samples

Download data

(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 used a two-component transgene system to study the RNA-dependent DNA methylation (RdDM) and transcriptional gene silencing (TGS) in Arabidopsis. By profiling the small RNA population in  mutants defected in RdDM or RNA polymerase II-transcribed trigger for generating silencing siRNA, we investigated how repetitive loci such as tandem repeats were regulated transcriptionally through the action of RNA polymerase IV.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TXT

(Submitter supplied) In plants, RNA polymerase II (Pol II) transcription of inverted DNA repeats produces hairpin RNAs that are processed by several DICER-LIKE enzymes into siRNAs that are 21-24-nt in length. When targeted to transcriptional regulatory regions, the 24-nt size class can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS). In a forward genetic screen to identify mutants defective in RdDM of a target enhancer leading to TGS of a downstream GFP reporter gene in Arabidopsis thaliana, we recovered a structurally mutated silencer locus, named SΔ35S, in which the 35S promoter driving transcription of an inverted repeat of target enhancer sequences had been specifically deleted. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

1 Sample

Download data: TXT

(Submitter supplied) We uncover distinct DNA methylation dynamics over genes and repeat sequences during early plant life in Arabidopsis. While gene body methylation, which is restricted to CG sites and concerns 20-30% of all genes is detected at all stages examined, it typically fluctuates over a few CGs, with no coherent pattern. In contrast, transposable elements and their relics as well as other repeat sequences, have consistently high methylation levels at CGs and show increasing CHG and especially CHH methylation during embryogenesis. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL13222

5 Samples

Download data: BEDGRAPH, GFF

(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; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

25 Samples

Download data: BEDGRAPH, TXT, WIG