Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Dinoflagellate sequencing

PROVIDER: PRJNA608149 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11148504_1.fastq.gz	Fastqsanger.gz
	SRR11148504_2.fastq.gz	Fastqsanger.gz
	SRR11148505_1.fastq.gz	Fastqsanger.gz
	SRR11148505_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome

Project description:In dinoflagellates, the most unique and divergent nuclear organization among the known diversity of eukaryotes has evolved. The list of highly unusual features of dinoflagellate nuclei and genomes is long -- permanently condensed liquid crystalline chromosomes, in which histones are not the main packaging component, genes organized as very long unidirectional gene arrays, general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. Most of these fascinating properties were originally identified in the 1970s and 1980s but have received very little attention in recent decades using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, and also often coincides with the boundaries between gene arrays. It is generally anti-correlated with chromatin accessibility, the levels of which are lower in those regions. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.

2023-10-19 | GSE241969 | GEO

Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides (Cp) when exposed to the algicide copper sulfate

Project description:To identify the transcripome of dinoflagellate Cochlodinium polykrikoides that responded to algicide copper sulfate

2017-02-10 | GSE75463 | GEO

Characterization of the enzyme for 5-hydroxymethyluridine production and its role in silencing transposable elements in dinoflagellates

Project description:Dinoflagellate chromosomes are extraordinary, as their organization is independent of architectural nucleosomes unlike typical eukaryotes and shows a cholesteric liquid crystal state. 5-hydroxymethyluridine (5hmU) is present at unusually high levels and its function remains an enigma in dinoflagellates chromosomal DNA for several decades. Here, we demonstrate that 5hmU contents vary among different dinoflagellates and are generated through thymidine hydroxylation. Importantly, we identified the enzyme, which is a putative dinoflagellate TET/JBP homologue, catalyzing 5hmU production using both in vivo and in vitro biochemical assays. Based on the near-chromosomal level genome assembly of dinoflagellate Amphidinium carterae, we depicted a comprehensive 5hmU landscape and found that 5hmU loci are significantly enriched in repeat elements. Moreover, inhibition of 5hmU via dioxygenase inhibitor leads to transcriptional activation of 5hmU-marked transposable elements (TEs), implying that 5hmU appears to serve as an epigenetic mark for silencing transposon. Together, our results revealed the biogenesis, genome-wide landscape and molecular function of dinoflagellate 5hmU, providing mechanistic insight into the function of this enigmatic DNA mark.

2024-09-29 | GSE248611 | GEO

Transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum [RNA-seq]

Project description:Transcriptome of D. shibae 5 h in the light after 12 days in co-culture with the dinoflagellate P. minimum. Two biological replicates.

2014-02-01 | E-GEOD-53871 | biostudies-arrayexpress

Transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum at different growth stages

Project description:Transcriptome of D. shibae 5 h in the light after 18,24 and 30 days in coculture with the dinoflagellate P. minimum two biological replicates

2014-05-01 | E-GEOD-55371 | biostudies-arrayexpress

Transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum at different growth stages

Project description:Transcriptome of D. shibae 5 h in the light after 18,24 and 30 days in coculture with the dinoflagellate P. minimum

2014-05-01 | GSE55371 | GEO

Illuminating the key biological processes during the blooming period of a marine dinoflagellate by metaproteomics

Project description:Dinoflagellate blooms are natural phenomena that have drawn global attention due to their huge negative impacts on marine ecosystems, mariculture and human health. Although the understanding of dinoflagellate blooms has been significantly improved over the past half century, little is known about the underlying mechanisms sustaining the high biomass growth rate during the bloom period which is paradoxically characterized by low dissolved CO2 and inorganic nutrients. Here, we compared the metaproteomes of non-bloom, mid-bloom and late-bloom cells of a marine dinoflagellate Prorocentrum donghaiense in the coastal East China Sea, to understand the underlying mechanisms sustaining high biomass growth rate under the typically low CO2 and inorganic nutrient conditions.

2021-01-21 | PXD018006 | Pride

Project description:dinoflagellate cyst 28S sequencing

| PRJNA1100815 | ENA

Project description:Dinoflagellate 28s rDNA sequencing

| PRJNA901253 | ENA

Transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum [RNA-seq]

Project description:Transcriptome of D. shibae 5 h in the light and dark after 12 days in co-culture with the dinoflagellate P. minimum.

2014-02-01 | GSE53871 | GEO