Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Freshwater cyanophages

PROVIDER: PRJNA451519 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7059769_1.fastq.gz	Fastqsanger.gz
	SRR7059769_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Genome-wide DNA methylation profiling reveals epigenetic adaptation of stickleback to sea and freshwater conditions

Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment.

2017-05-30 | GSE82310 | GEO

Epigenetic adaptation of stickleback to sea and freshwater conditions: RNA-seq

2021-11-03 | GSE186925 | GEO

Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress [set1]

Project description:We use RNA-Seq to investigate gene expression differences in response to saltwater exposure by the larval stages of the obligate freshwater mosquito Anopheles coluzzii (formerly An. gambiae "M" form), and the euryhaline An. merus. After rearing in freshwater, both young and old larval instars of each species were briefly (6 h) exposed to either saltwater (SW) or freshwater (FW) conditions to test the impact of salinity on mRNA levels.

2016-03-09 | E-GEOD-59632 | biostudies-arrayexpress

Transcriptomic analysis of trout gill ionocytes in freshwater and seawater using laser capture microdissection combined with microarray analysis

Project description:Fish gills represent a complex organ that perform multiple physiological functions and is composed of several cell types. Among these cells, ionocytes are implicated in the maintenance of ion homeostasis. However, because the ionocyte represents only a small percent of whole gill tissue, its specific transcriptome can be overlooked among the numerous cell types included in the gill. The objective of this study is to better understand ionocyte functions by comparing the RNA expression of this cell type in freshwater and seawater adapted rainbow trout. To realize this objective, ionocytes were captured from gill cryosections using laser capture microdissection after immunohistochemistry. Then, transcriptome analyses were performed on an Agilent trout oligonucleotide microarray. Gene expression analysis identified 108 unique annotated genes differentially expressed between freshwater and seawater ionocytes, with a gene fold higher than 3. Most of these genes were up regulated in freshwater cells. Interestingly, several genes implicated in ion transport, extracellular matrix and structural cellular proteins appeared up regulated in freshwater ionocytes. Among them, several ion transporters, such as CIC2, SLC26A6, and NBC, were validated by qPCR and/or in situ hybridization. The latter technique allowed us to localize the transcripts of these ion transporters in only ionocytes and more particularly in the freshwater cells. Genes involved in metabolism and also several genes implicated in transcriptional regulation, cell signaling and the cell cycle were also over-expressed in freshwater ionocytes. In conclusion, laser capture microdissection combined with microarray analysis allowed for the determination of the cell signature of scarce cells in fish gills, such as ionocytes, and aided characterization of the transcriptome of these cells in freshwater and seawater adapted trout.

2015-10-08 | GSE69409 | GEO

Marine and freshwater three-spined stickleback (Gasterosteus aculeatus) gene expression differences

Project description:In order to identify gene expression difference between marine and freshwater stickleback populations, we compared the transcriptomes of seven adult tissues (eye, gill, heart, hypothalumus, liver, pectoral muscle, telencephalon) between a marine population sampled from the mouth of the Little Campbell river in British Columbia (LITC) and a freshwater population (Fishtrap Creek, FTC) from northern Washington. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents.

2011-12-30 | GSE34783 | GEO

Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach [miRNA-Seq]

Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs.

2016-06-01 | GSE72417 | GEO

Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach [miRNA microarray analysis]

2016-06-01 | GSE72416 | GEO

Transcriptome sequencing of two Baikal (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) amphipod species exposed to 1.5 and 12 degree Celsius

Project description:This project aims to find the molecular changes driving the cold stress response of freshwater amphipods with different overwintering strategies

2020-09-09 | GSE157288 | GEO

Transcription profiling of gill, kidney and brain from Atlantic salmon at different developmental stages to identify genes involved in freshwater to salt water adaptation

Project description:Identification of the genes involved in the freshwater to saltwater adaptation of the Atlantic salmon.

2008-09-19 | E-MEXP-1267 | biostudies-arrayexpress

RNA-seq reveals potential gene biomarkers in Pimephales promelas for exposure to treated wastewater effluent

Project description:We investigated the impacts of wastewater effluent exposure on gene expression in adult fathead minnows, a freshwater fish commonly used as an ecotoxicological model.

2022-08-31 | GSE180719 | 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