GEO DataSets

(Submitter supplied) Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. more...

Organism:

Ciona intestinalis; Tetraodon nigroviridis; Chlorella variabilis; Physcomitrium patens; Phycomyces blakesleeanus; Drosophila melanogaster; Apis mellifera; Laccaria bicolor; Uncinocarpus reesii; Selaginella moellendorffii; Postia placenta; Volvox carteri; Coprinopsis cinerea; Bombyx mori; Oryza sativa; Tribolium castaneum; Nematostella vectensis

Type:

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

17 related Platforms

33 Samples

Download data: GFF, TXT

(Submitter supplied) Cytosine methylation, a common form of DNA modification that antagonizes transcriptional initiation, is found at transposons and repeats in vertebrates, plants, and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within about 20% of Arabidopsis genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL3371

5 Samples

Download data: GFF, TXT

(Submitter supplied) To gain insights into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase II and histone modifications at 24.000 promoters in primary human soma and germline cells. Keywords: DNA methylation, MeDIP

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array

Platform:

GPL3497

11 Samples

Download data

(Submitter supplied) Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.

Organism:

Magallana gigas

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13986

2 Samples

Download data: TXT

(Submitter supplied) Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas

Organism:

Magallana gigas

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13986

112 Samples

Download data: BEDGRAPH

(Submitter supplied) Extensive gene methylation correlated strongly with transcriptional silencing and differential expression under specific conditions. DNA methylation and its role in gene regulation is conserved in stramenopile.

Organism:

Phaeodactylum tricornutum

Type:

Methylation profiling by genome tiling array

Platform:

GPL17291

3 Samples

Download data: PAIR, TXT

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

Organism:

Glycine max

Type:

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

Platform:

GPL15087

12 Samples

Download data: TXT

(Submitter supplied) Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposon mobility during plant developmental processes. Recently, the variation of DNA methylation has been described between wild type and DNA methylation-related mutants in Arabidopsis thaliana. However, the elaborate representation of soybean DNA methylomes remains lacking. Here, we described the epigenome maps of soybean root, stem, leaf, and cotyledon of developing seed at a single-base resolution. more...

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15087

4 Samples

Download data: TXT

(Submitter supplied) Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposon mobility during plant developmental processes. Recently, the variation of DNA methylation has been described between wild type and DNA methylation-related mutants in Arabidopsis thaliana. However, the elaborate representation of soybean DNA methylomes remains lacking. Here, we described the epigenome maps of soybean root, stem, leaf, and cotyledon of developing seed at a single-base resolution. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15087

4 Samples

Download data: TXT

(Submitter supplied) Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposon mobility during plant developmental processes. Recently, the variation of DNA methylation has been described between wild type and DNA methylation-related mutants in Arabidopsis thaliana. However, the elaborate representation of soybean DNA methylomes remains lacking. Here, we described the epigenome maps of soybean root, stem, leaf, and cotyledon of developing seed at a single-base resolution. more...

Organism:

Glycine max

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15087

4 Samples

Download data: TXT

(Submitter supplied) DNA methylation is a widely conserved epigenetic modification that is established and maintained by the cooperative activity of DNA methyltransferases. While the complement of DNA methyltransferase genes can vary substantially between animal species, whole-genome methylation analyses have suggested that major features of animal methylomes are widely conserved. We have now used genome-scale bisulfite sequencing to analyze the methylome of the desert locust, Schistocerca gregaria, which represents an economically important pest with a high degree of phenotypic plasticity. more...

Organism:

Schistocerca gregaria

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16114

2 Samples

Download data: BEDGRAPH

(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) Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. While DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here, we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. more...

Organism:

Chlamydomonas reinhardtii; Oryza sativa; Danio rerio; Arabidopsis thaliana; Ciona intestinalis; Mus musculus; Populus trichocarpa; Apis mellifera

Type:

Methylation profiling by high throughput sequencing

9 related Platforms

14 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL11180

8 Samples

Download data: BED, CEL

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

Organism:

Nasonia vitripennis

Type:

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

Platforms:

GPL16488 GPL16489

3 Samples

Download data: TXT

(Submitter supplied) The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. more...

Organism:

Nasonia vitripennis

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL16488 GPL16489

2 Samples

Download data: TXT

(Submitter supplied) The expression level in the parasitoid Nasonia vitripennis adult female samples was profiled and compared with the methylation pattern. Methylated and non-methylated genes showed markedly different patterns. The expression level was higher for methylated than non-methylated genes. non-nmethylated genes account for 99% of the genes that were not found to be expressed in the adult female RNA-seq data (FPKM < 0.1). more...

Organism:

Nasonia vitripennis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16488

1 Sample

Download data: TXT

(Submitter supplied) To profile the Daphnia species methylome and to achieve a better understanding of the level of variations in the methylome of Daphnia species, we performed whole genome bisulfite sequencing (WGBSeq) of adult Daphnia magna Bham2 strain and Daphnia pulex Eloise Butler strain (EB45 and EB31 strains). We also analysed the correlation between gene expression and methylation in the two species, using data generated in this study and RNA-seq data from Orsini, et al. more...

Organism:

Daphnia pulex; Daphnia magna

Type:

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

Platforms:

GPL24022 GPL23821 GPL24021

41 Samples

Download data: TXT, VCF

(Submitter supplied) Kelp are the largest photosynthetic organisms in the ocean with tissue differentiation and complex life cycles. Other multicellular organisms with similar complexity such as plants and animals are well known to posses epigenetic mechanisms such as DNA methylation to control development and morphogenesis. Despite plant-like body plans and the presence of different life-cycle stages, the kelp species Saccharina japonica has only a very low level of DNA methylation, yet we have found strong evidence for differential methylation of regulatory elements and protein-coding genes which seem to contribute to the formation of life-cycle stages, tissue differentiation, growth and halogen metabolism. more...

Organism:

Saccharina japonica

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL25337

9 Samples

Download data: BW, TXT

(Submitter supplied) Cytosine methylation is a conserved base modification, but explanations for its interspecific variation remain elusive. Only through taxonomic sampling of disparate groups can unifying explanations for interspecific variation be thoroughly tested. Here we leverage phylogenetic resolution of cytosine DNA methyltransferases (DNA MTases) and genome evolution to better understand widespread interspecific variation across 40 diverse fungal species. more...

Organism:

Plenodomus lingam; Candida albicans; Coemansia reversa; Postia placenta; Coemansia spiralis; Kirkomyces cordensis; Metarhizium robertsii; Pseudogymnoascus destructans; Agaricus bisporus; Mixia osmundae; Sporobolomyces roseus; Cordyceps militaris; Wolfiporia cocos; Spinellus fusiger; Hesseltinella vesiculosa; Microbotryum lychnidis-dioicae; [Candida] auris; Heterobasidion irregulare; Saccharomyces cerevisiae; Aspergillus flavus; Coprinopsis cinerea; Clavispora lusitaniae; Lobosporangium transversale; Radiomyces spectabilis; Flammula alnicola; Cryptococcus neoformans var. grubii; Pyricularia oryzae KJ201; Syncephalis fuscata; Podospora anserina; Phanerodontia chrysosporium; Phycomyces blakesleeanus; Fusarium fujikuroi; Neurospora crassa; Pleurotus ostreatus; Aureobasidium pullulans; Laccaria bicolor; Uncinocarpus reesii; Parasitella parasitica; Botrytis cinerea; Tilletiopsis washingtonensis

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

29 related Platforms

31 Samples

Download data: TSV, TXT, XLS