Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Shotgun metagenomes from productive urban lakes in Sweden

ABSTRACT: Shotgun metagenomes from productive urban lakes in Sweden Other

PROVIDER: PRJNA1021391 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Shotgun metagenomes from productive lakes in an urban region of Sweden.

Project description:Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Mälaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Mälaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.

| S-EPMC10656542 | biostudies-literature

Regional Epigenetic Variation in Asexual Snail Populations among Urban and Rural Lakes

Project description:Epigenetic variation has the potential to control environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the responsiveness of epigenetic variation, which should be even more important when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2 and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. Observations suggest there is no effect of geographic distance or any consistent pattern of DMRs between urban and rural lakes. Environmental factors may influence epigenetic response.

2019-09-27 | GSE133502 | GEO

Metagenomes of Swedish lakes

Project description:Metagenomes of Swedish lakes

| PRJEB54817 | ENA

Canadian high-arctic lakes metagenomes

Project description:Canadian high-arctic lakes metagenomes Raw sequence reads

| PRJNA1074374 | ENA

Temporal Dynamics of Cyanobacterial Bloom Community Composition and Toxin Production from Urban Lakes

Project description:These data are raw mass spec files and corresponding mzXML files for time series mass spec data from three urban lakes at Roger Williams Park in Providence, RI. Data files are described by lake location (Pleasure, Polo, Cunliff) and date of sample collection. The Microcystis _Cells file is a positive control of a cultivated strain from the UTEX culture collection (M. aeruginosa UTEX #LB2385) - a known microcystin-LR producer. Information on LC-MS/MS method can be found in the published work.

2023-12-16 | MSV000093676 | MassIVE

Metagenomes of lakes Alalay taken in January 2018

Project description:Metagenomes of a contaminated urban lake

| PRJEB41039 | 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

Freshwater metagenomes from different European and Asian lakes

Project description:Freshwater metagenomes from different European and Asian lakes

| PRJEB35640 | ENA

Metaproteomes of phototrophic mats from four soda lakes found in the Cariboo Plateau region of British Columbia, Canada

Project description:In this study we used metaproteomics to discern the metabolism and physiology of the microorganisms occurring in the phototrophic mats of four soda lakes in the interior of British Columbia, Canada. Binned and assembled metagenomes were used as the database for protein identification.

2019-07-29 | PXD011230 | Pride

Tissue Contaminants and Associated Transcriptional Response in Trout Liver from High Elevation Lakes of Washington

Project description:The consistent cold temperatures and large amount of precipitation in the Olympic and Cascade ranges of Washington State are thought to increase atmospheric deposition of contaminants in these high elevation locations. Total mercury and 28 organochlorine compounds were measured in composite, whole fish samples collected from 14 remote lakes in the Olympic, Mt. Rainer, and North Cascades National Parks. Mercury was detected in fish from all lakes sampled and ranged in concentration from 17 to 262 ug/kg wet weight. Only two organochlorines, total polychlorinated biphenyls (tPCB) and dichlorodiphenyldichloroethylene (DDE), were detected in fish tissues (concentrations <25 ug/kg wet weight). No organochlorines were detected in sediments (MRL ≈1-5 ug/kg), while median total and methyl mercury in sediments were 30.4 and 0.34 ug/kg (dry weight), respectively. Using a targeted rainbow trout cDNA microarray with known genes, we detected significant differences in liver transcriptional responses, including metabolic, endocrine, and immune-related genes, in fish collected from a contaminated lake compared to a lake with a lower contaminant load. Overall, our results suggest that local urban areas are contributing to the observed contaminant patterns, while the transcriptional changes point to a biological response associated with exposure to these contaminants in fish. Specifically, the gene expression pattern leads us to hypothesize a role for mercury in disrupting the metabolic and reproductive pathways in fish from high elevation lakes in western Washington. Keywords: High altitude lakes, mercury, salmonids, organochlorines

2007-05-01 | GSE6886 | 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