Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenome of three deep-sea polychaete species

ABSTRACT: We provide the genome-wide methylome surveys of three species of deep-sea polychaete worms using Oxford Nanopore data: the siboglinids Paraescarpia echinospica and Ridgeia piscesae, and the alvinellid Paralvinella palmiformis. We characterised 5mCpG methylation in order to test hypotheses about the putative role of DNA methylation in these species.

ORGANISM(S): Ridgeia piscesae Paraescarpia echinospica Paralvinella palmiformis

PROVIDER: GSE217309 | GEO | 2022/11/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Nanopore DNA sequencing in a model of oxidative stress

Project description:Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human cell lineHEK 293T, before and after oxidative stress, using long-read nanopore sequencing.

2021-04-20 | GSE159582 | GEO

Nanopore DNA sequencing of a human liver progenitor-like cell line

Project description:Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human hepatocyte-like progenitor cell line HepaRG, before and after in vitro differentiation, using long-read nanopore sequencing.

2021-04-20 | GSE158224 | GEO

Clostridium sp. 'deep sea' isolate:deep sea

Project description:Clostridium sp. 'deep sea' isolate:deep sea Genome sequencing

| PRJNA668535 | ENA

Single molecule DNA methylation reveals unique epigenetic identity profiles of T helper cells

Project description:Identity and plasticity of CD4 T helper (Th) cells are regulated in part by epigenetic mechanisms. Cytosine methylation in CpG context (5mCpG) and cytosine hydroxymethylation (5hmCpG) are DNA modifications that identify stable cell phenotypes. To assess transition states in Th cells, we developed a method based on Cas9-targeted single molecule nanopore sequencing and found that 5mCpG can be used as markers of cellular identity. Targeting as few as 10 mouse selected genomic loci, we were able to distinguish major differentiated T cell subtypes as well as intermediate phenotypes by their native DNA 5mCpG patterns. Moreover, by using off-target sequences we were able to infer transcription factor activities relevant to each cell subtype. Our data highlight the potential to exploit native DNA methylation profiling to study physiological and pathological Th transition states.

2024-01-08 | GSE248540 | GEO

Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization

Project description:We identified cis-regulatory elements based on their dynamic chromatin accessibility during the gastrula-larva stages of sea urchin and sea star and studied their evolution in these echinoderm species

2021-10-24 | GSE186363 | GEO

Nanopore sequencing of K562 for DNA cytosine modification detection

Project description:Nanopore sequencing of K562 human cell line using the Oxford Nanopore GridION and R9.4.1 version chemistry

2021-09-20 | GSE173688 | GEO

Age-dependent DNA methylation characterization of the rat supraoptic nucleus (Methylation)

Project description:Our prior studies indicat age-dependent contralateral axonal sprouting following unilateral lesion of magnocellular neurons in the supraoptic nucleus. We performed Oxford Nanopore sequencing of the rat supraoptic nucleus to determine changes in DNA methylation with age.

2023-08-16 | GSE231615 | GEO

Lentisphaerae bacterium strain:deep sea | isolate:deep sea

Project description:Lentisphaerae bacterium strain:deep sea | isolate:deep sea Genome sequencing

| PRJNA704257 | ENA

Planctomycetes bacterium strain:deep sea | isolate:deep sea

Project description:Planctomycetes bacterium strain:deep sea | isolate:deep sea Genome sequencing

| PRJNA685606 | ENA

Tenericutes bacterium strain:deep sea | isolate:deep sea

Project description:Tenericutes bacterium strain:deep sea | isolate:deep sea Genome sequencing

| PRJNA728368 | ENA