Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Ebbs and Flows of Marine Biodiversity: Navigating Spatio-Temporal Patterns of Environmental DNA in a Coastal Tidal Ecosystem

PROVIDER: PRJNA1090157 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28400600_1.fastq.gz	Fastqsanger.gz
	SRR28400600_2.fastq.gz	Fastqsanger.gz
	SRR28400700_1.fastq.gz	Fastqsanger.gz
	SRR28400700_2.fastq.gz	Fastqsanger.gz
	SRR28400800_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 996

Similar Datasets

Project description:Fresh insights into Mediterranean biodiversity: Environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily

| PRJEB45583 | ENA

Gene Expression in Prokaryotic Microbial Assemblages Across Salinity Gradients in the Columbia River Coastal Margin

Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212). Total RNA was isolated from 64 filtered environmental water samples collected in the Columbia River coastal margin during 4 research cruises (14 from August, 2007; 17 from November, 2007; 18 from April, 2008; and 16 from June, 2008), and analyzed using microarray hybridization with the CombiMatrix 4X2K format. Microarray targets were prepared by reverse transcription of total RNA into fluorescently labeled cDNA. All samples were hybridized in duplicate, except samples 212 and 310 (hybridized in triplicate) and samples 336, 339, 50, 152, 157, and 199 (hybridized once). Sample location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; AST and HAM, Columbia River estuary locations near Astoria (river mile 7-9) and Hammond (river mile 5), respectively; TID, Columbia River estuary locations in the tidal basin (river mile 22-23); BA, river location at Beaver Army Dock (river mile 53) near Quincy, Oregon; UP, river location at mile 74.

2010-09-10 | E-GEOD-18303 | biostudies-arrayexpress

H1N1 influenza A/New Caledonia/20/1999 time series in monocyte-derived dendritic cells

Project description:Genome-wide gene expression patterns were measured in human monocyte-derived dendritic cells (DCs) infected in vitro with seasonal H1N1 influenza A/New Caledonia/20/1999. To provide a mechanistic explanation for the timing of gene expression changes over the first 12 hours post-infection, we developed a statistically rigorous enrichment approach integrating genome-wide expression kinetics and time-dependent promoter analysis. Our approach, TI me-Dependent Activity Linker (TIDAL), generates a regulatory network that connects transcription factors associated with each temporal phase of the response into a coherent linked cascade. TIDAL infers 12 transcription factors and 32 regulatory connections that drive the antiviral response to influenza. To demonstrate the generality of this approach, TIDAL was also used to generate a network for the DC response to measles infection.

2012-10-01 | GSE41067 | GEO

Complementary effects of above- and belowground biodiversity on ecosystem functions across global grasslands

Project description:biodiversity ecosystem functioning

| PRJEB53575 | ENA

Project description:Study on microeukaryotic biodiversity of coastal aquatic ecosystem in seaweed farming

| PRJNA1045086 | ENA

Project description:biodiversity and ecosystem multifunctionality

| PRJNA862865 | ENA

Arabidopsis thaliana strain:Col-0 Epigenomics

Project description:Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. We performed whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in Arabidopsis grown under phosphate starvation.

2015-05-02 | E-MTAB-4211 | biostudies-arrayexpress

Effect of Hypercapnia on Murine Ventilator-Induced Lung Injury

Project description:Addition of CO2 to the inspired gas can ameliorate lung injury during high tidal volume mechanical ventilation in animal models. Although some effects of hypercapnia on physiology and cell signaling have been characterized, we hypothesized that assessment of genome-wide gene expression patterns would reveal novel pathways of protection. We subjected male C57BL/6J mice to non-injurious low stretch (tidal vol = 10 mL/kg, PEEP = 2 cm H2O) or injurious high stretch (tidal volume approx 35 mL/kg, PEEP = 0 cm H2O) mechanical ventilation for 3 hours under normocapnia (FiCO2 = 0) or hypercapnia (FiCO2 = 0.12).

2017-02-22 | GSE86229 | GEO

Project description:Monitoring of spatio-temporal habitat occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA

| PRJNA616325 | ENA

Local adaptation of Avicennia schaueriana to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches

Project description:Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.

2020-05-15 | GSE116060 | 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