Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Effect of environmental DNA sampling resolution compared to capture surveys in detecting marine biodiversity

PROVIDER: PRJNA1051585 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27397600_1.fastq.gz	Fastqsanger.gz
	SRR27397600_2.fastq.gz	Fastqsanger.gz
	SRR27398000_1.fastq.gz	Fastqsanger.gz
	SRR27398000_2.fastq.gz	Fastqsanger.gz
	SRR27398100_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1436

Similar Datasets

Project description:Sea semester samples 2020 - optimizing marine eDNA sampling at sea towards standardized marine biodiversity surveys

| PRJNA777358 | ENA

Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre

Project description:Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities.

2018-09-03 | GSE109218 | GEO

Project description:Biodiversity surveys in coastal and offshore marine environments

| PRJNA740347 | ENA

Project description:Biodiversity Monitoring in Remote Marine Environments: Advancing Purpose-Built Environmental DNA/RNA Sampling Workflows

| PRJNA1138772 | ENA

Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream

Project description:eRNA metabarcoding for biodiversity surveys

| PRJEB64868 | ENA

Project description:eRNA metabarcoding for biodiversity surveys

| PRJEB72883 | ENA

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

Project description:Environmental meta-omics is rapidly expanding as sequencing capabilities improve, computing technologies become more accessible, and associated costs are reduced. The in situ snapshots of marine microbial life afforded by these data provide a growing knowledge of the functional roles of communities in ecosystem processes. Metaproteomics allows for the characterization of the dynamic proteome of a complex microbial community. It has the potential to reveal impacts of microbial metabolism on biogeochemical transport, storage and cycling (for example, Hawley et al., 2014), while additionally clarifying which taxonomic groups perform these roles. Previous work illuminated many of the important functions and interactions within marine microbial communities (for example, Morris et al., 2010), but a review of ocean metaproteomics literature revealed little standardization in bioinformatics pipelines for detecting peptides and inferring and annotating proteins. As prevalence of these data sets grows, there is a critical need to develop standardized approaches for mass spectrometry (MS) proteomic spectrum identification and annotation to maximize the scientific value of the data obtained. Here, we demonstrate that bioinformatics decisions made throughout the peptide identification process are as important for data interpretation as choices of sampling protocol and bacterial community manipulation experimental design. Our analysis offers a best practices guide for environmental metaproteomics.

2019-01-25 | PXD006688 | Pride

Project description:Marine vertebrate biodiversity and distribution within the central California Current using environmental DNA (eDNA) metabarcoding and ecosystem surveys

| PRJNA525068 | ENA

seawater metagenome

Project description:Biomolecular surveys of marine biodiversity in the Northern Salish Sea, British Columbia

| PRJNA1141475 | ENA

seawater metagenome

Project description:Optimizing the sampling effort for detecting fish environmental DNA in the open ocean

| PRJDB14220 | ENA