Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Freshwater lake metagenome

ABSTRACT: Freshwater lake metagenomes of 6 european lakes

PROVIDER: PRJNA602302 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11430612_1.fastq.gz	Fastqsanger.gz
	SRR11430612_2.fastq.gz	Fastqsanger.gz
	SRR11430613_1.fastq.gz	Fastqsanger.gz
	SRR11430613_2.fastq.gz	Fastqsanger.gz
	SRR11430614_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Freshwater metagenomes from different European and Asian lakes

Project description:Freshwater metagenomes from different European and Asian lakes

| PRJEB35640 | ENA

Freshwater metagenomes

Project description:Bacteria from european freshwater lakes

| PRJNA559862 | ENA

Freshwater Metagenomes from European Lakes and Reservoirs (including time-series metagenomes)

Project description:Freshwater Metagenomes from European Lakes and Reservoirs (including time-series metagenomes)

| PRJEB35770 | ENA

Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Heart and Blood: the beginning of a comprehensive lake trout protein database

Project description:Lake trout (Salvelinus namaycush) are a top-predator species in the Laurentian Great Lakes that are often used as bioindicators of chemical stressors in the ecosystem. Although many studies are done using these fish to determine concentrations of stressors like legacy persistent, bioaccumulative and toxic chemicals, there are currently no proteomic studies on the biological effects these stressors have on the ecosystem. This lack of proteomic studies on Great Lakes lake trout is because there is currently no complete, comprehensive protein database for this species. In this research, we aimed to use proteomic methods and established protein databases from NCBI and UniProtKB to identify potential proteins in the lake trout species. The current study utilized heart tissue and blood from two separate lake trout. Our previous published work on the lake trout liver revealed 4,194 potential protein hits in the NCBI databases and 3,811 potential protein hits in the UniProtKB databases. In the current study, using the NCBI databases we identified 838 potential protein hits for the heart and 580 potential protein hits for the blood of the first lake trout (biological replicate 1). In the second lake trout (biological replicate 2), using the NCBI databases we identified 1,180 potential protein hits for the heart and 561 potential protein hits for the blood. Similar results were obtained using the UniProtKB databases. This study builds on our previous work by continuing to build the first comprehensive lake trout protein database. Through this investigation, we are also able to make observations as to protein homology through evolutionary relationships.

2021-12-30 | PXD023970 | Pride

Freshwater metagenomes from Lake Zurich, Switzerland

Project description:Freshwater metagenomes from Lake Zurich, Switzerland

| PRJNA428721 | ENA

Freshwater lake metagenome

Project description:Freshwater lake metagenome Metagenome

| PRJNA578039 | ENA

Transcription profiling of Atlantic salmon gill epithelium from three different stocks migrating from freshwater river to lake (Saimaa stock, SS), brackish water (Neva stock, NS) or seawater (Teno stock, TS) were compared at three successive developmental stages (parr, smolt and postsmolt)

Project description:Transcripts of the gill epithelium from three different stocks of Atlantic salmon (Salmo salar) migrating from freshwater river to lake (Saimaa stock, SS), brackish water (Neva stock, NS) or seawater (Teno stock, TS) were compared at three successive developmental stages (parr, smolt and postsmolt) using the 16K GRASP cDNA microarray platform.

2010-06-01 | E-MEXP-2210 | biostudies-arrayexpress

Proteomic analysis of the lake trout (Salvelinus namaycush)

Project description:Lake trout are used as bioindicators for toxics exposure in the Great Lakes ecosystem. However, there is no knowledge about lake trout proteome. Here we performed the first lake trout (Salvelinus namaycush) liver proteomics and searched the databases against (NCBI and UniProtKB) Salvelinus, Salmonidae, Actinopterygii and the more distant Danio rerio. In the NCBI search, we identified 4371 proteins in 1252 clusters. From these proteins, we found 2175 proteins in Actinopterygii 1253 in Salmonidae, 69 in Salvelinus and 901 in Danio rerio NCBI searches. In the UniProtKB search, we identified 2630 proteins in 1100 clusters. From these proteins, we found 317 in Actinopterygii, 1653 in Salmonidae, 37 in Salvelinus and 666 in Danio rerio UniProtKB searches. A similar outcome was also obtained from a technical replicate experiment. A large number of lake trout liver proteins were not in any Salvelinus databases, suggesting that lake trout liver proteins have homologues to some proteins from the Salmonidae family and Actinopterygii class, as well as to the species Danio rerio, a more highly studied Cypriniformes fish. Therefore, our study not only builds the first comprehensive lake trout protein database, but also establishes protein homology-based evolutionary relationships between the fish within their family and class, as well as distant-related fish (lake trout and zebrafish). In addition, this study opens the possibility of identifying evolutionary relationships (i.e. adaptive mutations) between various groups (i.e. zebrafish, Salmonidae, Salvelinus and lake trout) through evolutionary proteomics

2019-10-10 | PXD011924 | Pride

freshwater lake samples

Project description:freshwater lake Metagenome

| PRJNA695572 | ENA

Diel cycles of gene expression in oligotrophic, dystrophic, and eutrophic lakes to identify new gene functions and dissect carbon cycling metabolisms

Project description:Aquatic microbial communities contain a vast amount of genetic diversity and we have much to learn about how this manifests to functional diversity. Existing long-term time series data includes 16S tags, metagenomes, single amplified genomes (SAGs), and genomes from metagenomes (GFMs). Information about functional diversity and metabolic capabilities is often unavailable. The study sites include three lakes that are the subject of intense study through the North Temperate Lakes Long Term Ecological Research site: Sparkling Lake (oligotrophic), Lake Mendota (eutrophic), and Trout Bog Lake (dystrophic). The work (proposal:https://doi.org/10.46936/10.25585/60000947) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-11-02 | MSV000093272 | MassIVE

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