Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diatoms metabarcoding - karstic river case

ABSTRACT: Diatom eDNA metabarcoding in the peryphyton of a karstic river using the rbcl gene marker

PROVIDER: PRJEB48565 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR9660060_1.fastq.gz	Fastqsanger.gz
	ERR9660060_2.fastq.gz	Fastqsanger.gz
	ERR9660070_1.fastq.gz	Fastqsanger.gz
	ERR9660070_2.fastq.gz	Fastqsanger.gz
	ERR9660080_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 62

Similar Datasets

Diatoms eDNA metabarcoding of a tufa-depositing river

Project description:The Diatom Diversity and Ecological Status of a Tufa-Depositing River through eDNA Metabarcoding vs. a Morphological Approach—A Case Study of the Una River (Bosnia and Herzegovina)

| PRJEB75497 | ENA

benthic diatom metabarcoding

Project description:benthic diatom metabarcoding

| PRJNA421862 | ENA

Investigation of Coastal Benthic Diatom Communities Using rbcL Marker

Project description:Investigation of Diatom Diversity by rbcL marker

| PRJEB78716 | ENA

Phytoplankton community composition and gene expression involved in carbon and nitrogen assimilation

Project description:A functional gene microarray was developed and used to investigate phytoplankton community composition and gene expression in the English Channel. Genes encoding the CO2 fixation enzyme RuBisCO (rbcL) and the nitrate assimilation enzyme nitrate reductase (NR) representing several major groups of phytoplankton were included as oligonucleotide probes on the 'phytoarray'. Five major groups of eukaryotic phytoplankton that possess the Type 1D rbcL gene were detected, both in terms of presence (DNA) and activity (rbcL gene expression). Changes in relative signal intensity among the Type 1D rbcL probes indicated a shift from diatom dominance in the spring bloom to dominance by haptophytes and flagellates later in the summer. Because of the limitations of a smaller database, NR probes detected fewer groups, but due to the greater diversity among known NR sequences, NR probes provided higher phylogenetic resolution than did rbcL probes, and identified two uncultivated diatom phylotypes as the most abundant (DNA) and active (NR gene expression) in field samples. Unidentified chlorophytes and the diatom Phaeodactylum tricornutum were detected at both the DNA and cDNA (gene expression) levels. The reproducibility of the array was evaluated in several ways and future directions for further improvement of probe development and sensitivity are outlined. The phytoarray provides a relatively high resolution, high throughput approach to assessing phytoplankton community composition in marine environments. Keywords: seawater natural assemblages, functional gene expression

2008-09-12 | GSE12742 | GEO

Towards functional profiling for eDNA based monitoring in coastal environments: a comparison of three approaches

Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.

2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress

Phytoplankton community composition and gene expression involved in carbon and nitrogen assimilation

2010-06-19 | E-GEOD-12742 | biostudies-arrayexpress

Groundwater eDNA metabarcoding

Project description:Groundwater eDNA metabarcoding Raw sequence reads

| PRJNA905821 | ENA

eDNA metabarcoding across oceans, habitats and time

Project description:eDNA metabarcoding (marker: COI) of reef and mangrove habitats in Honduras and Kenya

| PRJEB49866 | ENA

eDNA metabarcoding in Honduras and Kenya (Marine habitats)

Project description:eDNA metabarcoding (marker: COI) of reef and mangrove habitats in Honduras and Kenya

| PRJEB45038 | ENA