Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: dinoflagellate cyst 28S sequencing

PROVIDER: PRJNA1100815 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28746100.fastq.gz	Fastqsanger.gz
	SRR28746101.fastq.gz	Fastqsanger.gz
	SRR28746102.fastq.gz	Fastqsanger.gz
	SRR28746059.fastq.gz	Fastqsanger.gz
	SRR28746060.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 44

Similar Datasets

Project description:Dinoflagellate 28s rDNA sequencing

| PRJNA901253 | ENA

Project description:Dinoflagellate cyst in surface sediment of Tongyeong, Korea

| PRJNA397358 | ENA

Project description:18S-V4 amplification of dinoflagellate cyst communities in the South China Sea

| PRJNA421045 | ENA

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

Project description:Dinoflagellate sequencing

| PRJNA608149 | ENA

The identification of Stat92E target genes in Drosophila testis by ChIP-seq [Stat-ChIP]

Project description:To identify the target genes of Stat92E in adult Drosophila testis cyst cells, the testes of c587ts;UAS-Stat92E were dissected and cross-linked to conduct chromatin immunoprecipitation(ChIP) assay and ChIP-high throughput sequencing.

2024-09-23 | GSE241608 | GEO

The identification of Stat92E target genes in Drosophila testis by ChIP-seq [CG-ChIP]

Project description:To identify the target genes of Stat92E in adult Drosophila testis cyst cells, the testes of control (c587ts) and c587ts;UAS-upd were dissected and cross-linked to conduct chromatin immunoprecipitation(ChIP) assay and ChIP-high throughput sequencing.

2024-09-23 | GSE241607 | 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

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

rRNA cleavage ensures translational cessation in the mature sperm

Project description:We report how unique RNA seq profiles of ribosomal RNA (18S, 28S) present in sperm indicate specific cleavage sites. Additionally, these sequencing results reveal how overall character of RNA (GC content) can significantly affect overall distribution of mapped reads.

2013-03-11 | GSE29160 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data