Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Marine sediment metagenome

ABSTRACT: Marine sediments from the maritime Antarctic assessed using DNA metabarcoding

PROVIDER: PRJNA879780 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21537246_1.fastq.gz	Fastqsanger.gz
	SRR21537246_2.fastq.gz	Fastqsanger.gz
	SRR21537247_1.fastq.gz	Fastqsanger.gz
	SRR21537247_2.fastq.gz	Fastqsanger.gz
	SRR21537248_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Improving protein extraction for metaproteomic analysis of marine sediment with high clay content

Project description:Marine sediments harbor highly diverse microbial communities that contribute to global biodiversity and play essential roles in the ecosystem functioning. However, the metaproteome of marine sediments remains poorly understood. Extracting proteins from environmental samples can be challenging, especially in marine sediments due to their complex matrix. Few studies have been conducted on improving protein extraction methods from marine sediments. To establish an effective protein extraction workflow for clay-rich sediments, we compared, combined and improved several protein extraction methods. The presented workflow includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis via ultra-sonication, and the electro-elution and simultaneous fractionation of proteins. Using this workflow, we were able to recover 100% of the previously added Escherichia coli proteins from the sediment.

2025-05-12 | PXD054260 | Pride

Survey functional genes in Arctic marine sediment communities

Project description:The objective was to identify functional genes encoded by Fungi and fungal-like organisms to assess putative ecological roles Using the GeoChip microarray, we detected fungal genes involved in the complete assimilation of nitrate and the degradation of lignin, as well as evidence for Partitiviridae (a mycovirus) that likely regulates fungal populations in the marine environment. These results demonstrate the potential for fungi to degrade terrigenously-sourced molecules, such as permafrost and compete with algae for nitrate during blooms. Ultimately, these data suggest that marine fungi could be as important in oceanic ecosystems as they are in freshwater environments.

2020-07-14 | GSE117831 | GEO

marine sediment metagenome

Project description:Microbial Diversity in Antarctic marine sediments (Admiralty Bay and Bransfield Strait)

| PRJNA335729 | ENA

Biological effects of marine contaminated sediments on Sparus aurata juveniles

Project description:Chemical analysis of the compounds present in sediment, although informative, often is not indicative of the downstream biological effects that these contaminants exert on resident aquatic organisms. More direct molecular methods are needed to determine if marine life is affected by exposure to sediments. In this study, we used an aquatic multispecies microarray and q-PCR to investigate the effects on gene expression in juvenile sea bream (Sparus aurata) of two contaminated sediments defined as sediment 1 and 2 respectively, from marine areas in Northern Italy.

2011-01-01 | E-TABM-1146 | biostudies-arrayexpress

marine sediment metagenome

Project description:hydrocarbon marine sediments

| PRJNA383383 | ENA

Gene expression profiling as a tool for sediment risk assessment: a pilot study using Caenorhabditis elegans whole genome microarrays

Project description:Toxicity of river sediments are assessed using whole sediment toxicity tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. Moreover, natural sediment properties, such as grain size distribution and organic carbon content, can influence the test parameters by masking pollutant toxicity. The use of gene expression profiling facilitates the identification of transcriptional changes at the molecular level that are specific to the bioavailable fraction of pollutants. The nematode Caenorhabditis elegans is ideally suited for these purposes, as (i) it can be exposed to whole sediments, and (ii) its genome is fully sequenced and widely annotated. In this pilot study we exposed C. elegans for 48 h to three sediments varying in degree of contamination with e.g. heavy metals and organic pollutants. Following the exposure period, gene expression was profiled using a whole genome DNA-microarray approach.

2008-06-25 | GSE11837 | GEO

marine sediment metagenome

Project description:Metagenomic sequencing of methane-rich Antarctic sediments

| PRJNA443146 | ENA

Gene expression profiling as a tool for sediment risk assessment: a pilot study using Caenorhabditis elegans whole genome microarrays

2008-06-25 | E-GEOD-11837 | biostudies-arrayexpress

marine sediment metagenome

Project description:Coastal marine sediments Metagenome

| PRJNA207694 | ENA

marine sediment metagenome

Project description:Fungal diversity in sediments of subtropical China seas as revealed by DNA metabarcoding

| PRJNA293164 | ENA