Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RAD-seq of 96 Nassau Grouper (Epinephelus striatus)

ABSTRACT: sbfI single-end RAD sequencing of Nassau Grouper

PROVIDER: PRJEB36904 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3950790.fastq.gz	Fastqsanger.gz
	ERR3950800.fastq.gz	Fastqsanger.gz
	ERR3950810.fastq.gz	Fastqsanger.gz
	ERR3950820.fastq.gz	Fastqsanger.gz
	ERR3950830.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 96

Similar Datasets

Profiling transcriptome and proteome of orange-spotted grouper (Epinephelus coioides) after nervous necrosis virus infection

Project description:Grouper is an important commercial maricultural fish, which suffer viral nervous necrosis (VNN) disease at the larval and juvenile stages, but the changes of transcriptomics and proteomics during viral infection remain unknown. In this study, we applied RNA-seq and label-free mass spectrum for the first time to depict the map of transcriptomics and proteomics in non-infected, susceptible-infected and tolerate-infected grouper in larval stage. Further analyses showed that the transcriptome and proteome change dramatically among 3 distinct groups, indicating that different immune response for infected and perststent grouper in larval stage. These valuable transcriptomics and proteomics datasets enable the investigation of molecular mechanism in nervous necrosis (VNN) virus infection, thus helps the further development of molecular breeding and marine fishery

2019-05-15 | PXD012763 | Pride

Identification of host microRNAs potentially related to SGIV infection in grouper Epinephelus coioides

Project description:microRNAs (miRNAs) are an evolutionarily conserved class of non-coding RNA molecules, which regulate kinds of biological processes at post-transcriptional level. Investigation of miRNAs expression profiles using high-throughput strategies is efficiently conductive to identify and characterize miRNAs. In this study, through Solexa deep sequencing approach, we obtained 115 orange spotted grouper (Epinephelus coioides) encoded miRNAs. Among them, 107 miRNAs shared high similarity with miRNAs encoded by zebrafish (Danio rerio) and other four vertebrates, indicating that cellular miRNAs are highly conserved between species. 18-26 nt small RNAs from GS cells were sequenced in one Solexa lane

2015-01-01 | E-GEOD-64445 | biostudies-arrayexpress

Identification of host microRNAs potentially related to SGIV infection in grouper Epinephelus coioides

2015-01-01 | GSE64445 | GEO

Population structure and phylogeography in Nassau grouper (Epinephelus striatus), a mass-aggregating marine fish.

Project description:To address patterns of genetic connectivity in a mass-aggregating marine fish, we analyzed genetic variation in mitochondrial DNA (mtDNA), microsatellites, and single nucleotide polymorphisms (SNPs) for Nassau grouper (Epinephelus striatus). We expected Nassau grouper to exhibit genetic differentiation among its subpopulations due to its reproductive behavior and retentive oceanographic conditions experienced across the Caribbean basin. All samples were genotyped for two mitochondrial markers and 9 microsatellite loci, and a subset of samples were genotyped for 4,234 SNPs. We found evidence of genetic differentiation in a Caribbean-wide study of this mass-aggregating marine fish using mtDNA (FST?=?0.206, p<0.001), microsatellites (FST?=?0.002, p?=?0.004) and SNPs (FST?=?0.002, p?=?0.014), and identified three potential barriers to larval dispersal. Genetically isolated regions identified in our work mirror those seen for other invertebrate and fish species in the Caribbean basin. Oceanographic regimes in the Caribbean may largely explain patterns of genetic differentiation among Nassau grouper subpopulations. Regional patterns observed warrant standardization of fisheries management and conservation initiatives among countries within genetically isolated regions.

| S-EPMC4022523 | biostudies-literature

Solexa sequencing of small RNAs in Singapore grouper iridovirus (SGIV)-infected grouper cells

Project description:We applied Solexa sequencing technology to identify Singapore grouper iridovirus (SGIV) encoded microRNAs during its infection. A small RNA library arising from SGIV infected grouper cells (GP) was constructed and sequenced. We recovered 6,802,977 usable reads, of which 34,400 reads represented the small RNA sequences encoded by SGIV. Among them, 16 novel SGIV encoded miRNAs were identified by a computational pipeline. Generally, these 16 miRNAs are dispersed throughout the SGIV genome, while three of them are located within open reading frame 057L (ORF057L) region. Meanwhile, We identified 138 conserved microRNA genes between grouper fish and zebrafish.

2011-01-29 | GSE26909 | GEO

Solexa sequencing of small RNAs in Singapore grouper iridovirus (SGIV)-infected grouper cells

2011-01-29 | E-GEOD-26909 | biostudies-arrayexpress

Epinephelus fuscoguttatus, Jinhu grouper

Project description:Transcriptome data of brain, pituitary and gonad from Jinhu grouper and Epinephelus fuscoguttatus

| PRJNA955319 | ENA

Recovery of critically endangered Nassau grouper (<i>Epinephelus striatus</i>) in the Cayman Islands following targeted conservation actions.

Project description:Many large-bodied marine fishes that form spawning aggregations, such as the Nassau grouper (Epinephelus striatus), have suffered regional overfishing due to exploitation during spawning. In response, marine resource managers in many locations have established marine protected areas or seasonal closures to recover these overfished stocks. The challenge in assessing management effectiveness lies largely in the development of accurate estimates to track stock size through time. For the past 15 y, the Cayman Islands government has taken a series of management actions aimed at recovering collapsed stocks of Nassau grouper. Importantly, the government also partnered with academic and nonprofit organizations to establish a research and monitoring program (Grouper Moon) aimed at documenting the impacts of conservation action. Here, we develop an integrated population model of 2 Cayman Nassau grouper stocks based on both diver-collected mark-resight observations and video censuses. Using both data types across multiple years, we fit parameters for a state-space model for population growth. We show that over the last 15 y the Nassau grouper population on Little Cayman has more than tripled in response to conservation efforts. Census data from Cayman Brac, while more sparse, show a similar pattern. These findings demonstrate that spatial and seasonal closures aimed at rebuilding aggregation-based fisheries can foster conservation success.

| S-EPMC6983384 | biostudies-literature

Epinephelus coioides strain:orange-spotted grouper

Project description:orange-spotted grouper Epinephelus coioides genetic linkage maps construction

| PRJDB1493 | ENA

Single-cell RNA sequencing reveals the gonadal dynamic changes of sex differentiation in hermaphroditic protogynous orange-spotted grouper, Epinephelus coioides

Project description:Sex differentiation is a complex process that requires many factors to regulate proliferation, differentiation, development, and organization of the gonads. In teleosts, the molecular mechanisms of sex differentiation are diverse and unclear, especially in hermaphrodite fish. In the present study, 15 cell types, including germ cells, follicle cells, and theca cells, and so on, were identified using single-cell RNA sequencing (scRNA-seq) in the gonads during sex differentiation in a hermaphrodite fish, orange-spotted grouper (Epinephelus coioides). Two pre-follicle cell types were defined, and the differentiating trajectories of the follicle cells were outlined. Notably, both pre-follicle and follicle cells highly expressed male-related genes synchronously, such as amh, sox9, and dmrt3 in pre-follicle cells, as well as dmrt1 in follicle cells. Oocyte possessed two distinct states, with high expression of oocyte development related genes in one state and spermatogenesis related genes in the other state, respectively. Our results provide novel insights into cell types and lineage tracing in the gonads during sex differentiation in hermaphrodite species.

2024-07-26 | GSE218835 | 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