GEO DataSets

(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; Phycomyces blakesleeanus; Fusarium fujikuroi; Neurospora crassa; Pleurotus ostreatus; Aureobasidium pullulans; Laccaria bicolor; Uncinocarpus reesii; Parasitella parasitica; Botrytis cinerea; Tilletiopsis washingtonensis; Agaricus bisporus; Mixia osmundae; Sporobolomyces roseus; Cordyceps militaris; Wolfiporia cocos; Spinellus fusiger; Hesseltinella vesiculosa; Microbotryum lychnidis-dioicae; Heterobasidion irregulare; Saccharomyces cerevisiae; Aspergillus flavus; Coprinopsis cinerea; Clavispora lusitaniae; Lobosporangium transversale; Radiomyces spectabilis; Flammula alnicola; Cryptococcus neoformans var. grubii; Candidozyma auris; Pyricularia oryzae KJ201; Syncephalis fuscata; Podospora anserina; Phanerodontia chrysosporium

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

29 related Platforms

31 Samples

Download data: TSV, TXT, XLS

(Submitter supplied) Background DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. Whilst vertebrate genomes are hypermethylated, in most invertebrates, 5mC concentrates on constantly and highly transcribed genes (gene body methylation; GbM) and, in some species, on transposable elements (TEs), a pattern known as ‘mosaic’. more...

Organism:

Owenia fusiformis; Capitella teleta; Dimorphilus gyrociliatus

Type:

Methylation profiling by high throughput sequencing

6 related Platforms

35 Samples

Download data: BED, CGMAP, TXT

(Submitter supplied) Owenia fusiformis has a unique mitraria larvae form which is different to other marine spiralians. we utilize RNA-seq and ATAC-seq to profile the gene expression and chromatin accessibility dynamics to understand their development and evolution.

Organism:

Owenia fusiformis

Type:

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

Platform:

GPL30632

11 Samples

Download data: NARROWPEAK, TXT

(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:

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

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) Aberrant DNA methylation is common in cancer. To associate DNA methylation with gene function, we performed RNAseq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients. To quantify 5mC and 5hmC level in each CG site at genome-wide level, we performed BS-seq and TAB-seq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients, respectively.

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) DNA methylation and gene expression in response to the loss of care for 30 generations in N. Vespilloides

Organism:

Nicrophorus vespilloides

Type:

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

Platform:

GPL20831

60 Samples

Download data: COV, CSV

(Submitter supplied) The study provides new insights into how 5mC/5hmC vary across different part of brain, and the association and distinct roles of 5mC/5hmC in regulating tissue identity and specification.

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL21273

22 Samples

Download data: BW, FPKM_TRACKING, TXT

(Submitter supplied) 5-methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. However, in many eukaryotes 5mC has gained complex roles in gene regulation beyond parasite control. Animals are a paradigmatic case for 5mC evolution, as they show widespread variability across lineages, ranging from gene regulation and transposable element control to loss of this base modification. Here we show that the protist animal relative Amoebidium appalachense displays both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. more...

Organism:

Creolimax fragrantissima; Amoebidium appalachense; Ichthyosporea sp. XGB-2017a; Amoebidium parasiticum; Sphaeroforma arctica

Type:

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

5 related Platforms

50 Samples

Download data: CGMAP, TSV, TXT

(Submitter supplied) Analysis of genome-wide hydroxymethylation within infant placental tissue collected at term. These samples have been collected from the RhodeIsland Child Health Study (RICHS) cohort.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

46 Samples

Download data: IDAT, TXT

(Submitter supplied) Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in transfer RNAs of all three sub-cellular transcriptomes across six diverse species that include, the single-celled algae Nannochloropsis oculata, the macro algae Caulerpa taxifolia and multi-cellular higher plants Arabidopsis thaliana, Brassica rapa, Triticum durum and Ginkgo biloba.

Organism:

Nannochloropsis oculata; Brassica rapa; Caulerpa taxifolia; Arabidopsis thaliana; Triticum turgidum subsp. durum; Ginkgo biloba

Type:

Other; Non-coding RNA profiling by high throughput sequencing

6 related Platforms

14 Samples

Download data: XLS, XLSX

(Submitter supplied) Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs of all three sub-cellular transcriptomes across six diverse species that included, the single-celled algae Nannochloropsis oculata, the macro algae Caulerpa taxifolia and multi-cellular higher plants Arabidopsis thaliana, Brassica rapa, Triticum durum and Ginkgo biloba. more...

Organism:

Nannochloropsis oculata; Ginkgo biloba; Arabidopsis thaliana; Brassica rapa; Triticum turgidum subsp. durum; Caulerpa taxifolia

Type:

Other; Non-coding RNA profiling by high throughput sequencing

6 related Platforms

13 Samples

Download data: XLSX

(Submitter supplied) Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in transfer RNAs of all three sub-cellular transcriptomes of Arabidopsis thaliana. 5-methylcytosine sites in tRNAs were also determined in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5 and NOP2A.

Organism:

Arabidopsis thaliana

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17970

11 Samples

Download data: XLS, XLSX

(Submitter supplied) Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in ribosomal RNAs of all three sub-cellular transcriptomes in Arabidopsis thaliana. m5C sites in rRNAs were also anlyzed in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5, NOP2A, NOP2B and NOP2C.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL17970

25 Samples

Download data: XLS, XLSX

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

Organism:

Oxytricha trifallax; mixed culture metagenome; Escherichia coli; Helicobacter pylori

Type:

Methylation profiling by high throughput sequencing; Other

4 related Platforms

22 Samples

Download data: CSV, TXT

(Submitter supplied) DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. more...

Organism:

Oxytricha trifallax; Escherichia coli

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL30646 GPL21222

10 Samples

Download data: CSV, TXT

(Submitter supplied) DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. more...

Organism:

Helicobacter pylori; Escherichia coli; mixed culture metagenome

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL30645 GPL21222 GPL30644

14 Samples

Download data: CSV