Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Linking Ecology, Behavior, and Immunology to Spatio-Temporal Variation in Helminth Transmission - PRJ5

ABSTRACT: Samples of livers from stickleback fish captured from 47 lakes on Vancouver Island, with associated data on parasite infection status, immune traits, diet, and morphology. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).

INSTRUMENT(S): Orbitrap Exploris 240

ORGANISM(S): Gasterosteus Aculeatus (ncbitaxon:69293)

SUBMITTER: Daniel Bolnick

PROVIDER: MSV000095784 | GNPS |

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - Bolnick Alaska Experimental Evolution (2024) - PRJ7

Project description:Livers preserved in Ethanol from threespine stickleback (Gasterosteus aculeatus). Thirty per lake from 15 lakes in Alaska. Seven of the lakes are native populations, and eight of the lakes are experimentally introduced populations founded in 2019. Samples were collected by Dan Bolnick and colleagues in 2024. We are tracking evolution of stickleback as the newly founded populations adapt to their lake environments. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).

2024-08-07 | MSV000095540 | GNPS

GNPS - Bolnick Alaska Experimental Evolution (2023) - PRJ1

Project description:Livers preserved in Ethanol from threespine stickleback (Gasterosteus aculeatus). Thirty per lake from 16 lakes in Alaska. Seven of the lakes are native populations, and nine of the lakes are experimentally introduced populations founded in 2019. Samples were collected by Dan Bolnick and colleagues in June 2023. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).

2024-08-27 | MSV000095708 | GNPS

Proteomic analysis of the secretome of Schistocephalus solidus LC-MS/MS

Project description:Schistocephalus solidus is a cestode parasite that is thought to manipulate the behaviour of its threespine stickleback host Gasterosteus aculeatus. It has been hypothesized that the worm could liberate in its external environment “manipulation factors” that would ultimately interfere with the host’s physiology and behaviour. The objective of this project is to describe the whole proteomic content of the proteome and of the secretome of a putative manipulative parasite, Schistocephalus solidus, with the aim to identify proteins that could be involved in the behavioural perturbations of the threespine stickleback.

2021-09-09 | PXD016844 | Pride

GNPS - Fish-Tapeworm co-metabolomics (Fish Livers) - PRJ6_LIVERS

Project description:We have pairs of fish and their tapeworms, from Merril (MER), Vernon (VER), Nimpkish (NIM), and Woss (WOS) Lakes on Vancouver Island. The fish samples are livers, preserved in ethanol. The parasite samples are a third of each individual tapeworm. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).

| MSV000095773 | GNPS

GNPS - Immune activation in lab-raised stickleback - PRJ3

Project description:Lab-raised stickleback from Echo and Gosling and Boot Lakes on Vancouver Island (and their F1 hybrids) were given intraperitoneal injections with alum or saline to induce a fibrotic immune response (or, controls). We flash-froze stomachs and intestines from each fish for metabolomics. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).

2024-08-15 | MSV000095620 | GNPS

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

Project description:stickleback gut microbiota depended on parasite exposure

| PRJNA495340 | ENA

Standing genetic variation in Atlantic stickleback

Project description:Standing genetic variation in Atlantic stickleback

| PRJEB42736 | ENA

Microarray transcriptional profiling of three-spined stickleback (Gasterosteus aculeatus) exposed to 10 different model toxicants and 26 mixtures of these toxicants

Project description:Adult female three-spined stickleback fish (Gasterosteus aculeatus) were exposed to 10 individual chemicals, 26 mixtures of these chemicals, or control conditions in a flow-through system for 4 days. Transcriptomics was performed on liver samples by microarray. The main aims were to determine molecular signatures induced by these chemicals in the three-spined stickleback, discover whether these persisted in chemical mixtures and identify non-additive molecular responses in chemical mixtures exposures.

2018-03-01 | E-MTAB-5581 | biostudies-arrayexpress

Assessing the Potential Ecological Impacts of Perfluorinated Chemicals (PFCs) in the liver and testis of male largemouth bass (Micropterus salmoides) in Minnesota Lakes

Project description:This study used an emerging analytical technology (cDNA microarrays) to assess the potential effects of PFC exposure on largemouth bass in TCMA lakes. Microarrays simultaneously measure the expression of thousands of genes in various tissues from organisms exposed to different environmental conditions. From this large data set, biomarkers (i.e., genes that are expressed in response to an exposure to known stressors) and bioindicators (e.g., suites of genes that correspond to changes in organism health) can be simultaneously measured to clarify the relationship between contaminant exposure and organism health. Based on current scientific literature, we hypothesized that gene expression patterns would be altered in fish exposed to PFCs (as compared with fish from reference lakes), and that the magnitude of these changes would correspond to the concentrations of PFCs present throughout TCMA lakes. Patterns of gene expression in largemouth bass observed across the TCMA lakes corresponded closely with PFC concentration. Concentrations of PFCs in largemouth bass varied significantly across the sampled lakes, where the lowest concentrations were found in Steiger and Upper Prior Lakes and the highest concentrations were found in Calhoun and Twin Lakes. Patterns of gene expression were most different (relative to controls) in fish with the highest PFC tissue concentrations, where fish from Twin and Calhoun Lakes were observed to have between 5437 and 5936 differentially expressed genes in liver and gonad tissues. Although gene expression patterns demonstrated a high degree of correlation with PFC concentrations, microarray data also suggest there are likely additional factors influencing gene expression patterns in largemouth bass in TCMA lakes.

2014-07-31 | GSE57684 | 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