Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circadian cycles are the dominant transcriptional rhythm in the intertidal mussel Mytilus californianus

ABSTRACT: Gene expression profiles associated with periods of tidal submergence and aerial emergence

ORGANISM(S): Mytilus californianus

SUBMITTER: Andrew Gracey

PROVIDER: E-MTAB-777 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Circadian cycles are the dominant transcriptional rhythm in the intertidal mussel Mytilus californianus.

Connor Kwasi M KM Gracey Andrew Y AY

Proceedings of the National Academy of Sciences of the United States of America 20110912 38

Residents in the marine intertidal, the zone where terrestrial and marine habitats converge, inhabit an environment that is subject to both the 24-h day and night daily rhythm of the terrestrial earth and also the 12.4-h ebb and flow of the tidal cycle. Here, we investigate the relative contribution of the daily and tidal cycle on the physiology of intertidal mussels, Mytilus californianus, by monitoring rhythms of gene expression in both simulated and natural tidal environments. We report that ...[more]

PMID: 21911390

Similar Datasets

RNA-seq data from the blue mussel (Mytilus edulis) gill samples in response to salinity and temperature

Project description:This project is aiming to examine the molecular response of the blue mussel (Mytilus edulis) to increased air temperatures and reduced salinity under laboratory conditions. There are 5 treatment groups (n=5), with group A representing the control (salinity 23percent salinity and temperature 5 degree celsius), group B ( 23percent salinity 30 degree celsius), group C (23percent salinity 33 degree celsius), group D (15percent salinity 5 degree celsius), group E (15percent salinity 30 degree celsius), group F (15percent salinity33 degree celsius), group G (5percent salinity 5 degree celsius).

2021-12-04 | E-MTAB-11178 | biostudies-arrayexpress

iTRAQ Manatee

Project description:In 2013, two large-scale Florida manatee (Trichechus manatus latirostris) mortality episodes were reported on separate coasts of Florida. The east coast mortality episode was associated with an unknown etiology in the Indian River Lagoon (IRL). The west coast mortality episode was attributed to a persistent Karenia brevis algal bloom or ‘red tide’ centered in Southwest Florida. To investigate these two mortality episodes, proteomic experiments using two-dimensional difference gel electrophoresis (2D-DIGE) followed by protein identification using liquid chromatography-tandem mass spectrometry (LC-MS/MS) were conducted, along with a separate gel-free analysis using isobaric tags for relative and absolute quantification (iTRAQ) LC-MS/MS. In comparison to the control group, manatees from the IRL, an area associated with an unknown mortality episode, displayed increased levels of several proteins in their serum samples. These increased proteins, which were identified in the iTRAQ experiment, included kininogen-1 isoform 1 (average ratio 1.38), protein AMBP (1.38), histidine-rich glycoprotein (1.34), properdin (1.30), and complement C4-A isoform 1 (1.25). In the red tide group, ceruloplasmin (2.32), pyruvate kinase isozymes M1/M2 isoform 3 (2.29), angiotensinogen (2.08), complement C4-A isoform 1 (1.83), and complement C3 (1.42) were increased. The proteins kininogen-1 isoform 1, histidine-rich glycoprotein, complement C4-A isoform 1, angiotensinogen, and complement C3 were also identified in increased levels in the 2D-DIGE experiment (Table 2b). These proteins are associated with acute-phase response, amyloid formation and accumulation, copper and iron homeostasis, the complement cascade pathway, and other important cellular functions. The increased level of complement C4 protein observed in both the red tide and unknown mortality episode groups was confirmed through the use of Western Blot.

2021-08-30 | PXD002470 | Pride

Transcription profiling of flounders (Platichthys flesus) exposed to polybrominated diphenyl ethers (pentamix)

Project description:A Platichthys flesus cDNA microarray (GENIPOL) comprised of 12,700 clones, was used to determine and characterize gene expression profiles of flounders (Platichthys flesus) exposed to polybrominated diphenyl ethers (pentamix).

2013-02-01 | E-MTAB-1255 | biostudies-arrayexpress

The Expression Profiles of Zebra Mussel Byssus Genes along Byssogenesis

Project description:To identify the expression profiles of zebra mussel byssus unique genes with the regeneration of the byssal threads, a time-course study was performed. The RNA samples from the feet of fully attached zebra mussels (maintained attachment for more than 4 weeks) were extracted as common reference. The detached mussels were allowed to re-attach on underwater surface. Then the RNA samples from feet of the mussels at different time points post detachment were taken, namely, 12 hours, 1 day, 2 days, 3 days, 4 days, 7 days, and 21 days post detachment. The comparisons of the genes expression profiles were made between different time points and reference, as well as the any two connected time points (expect for 7 days and 21 days). The dual-channel microarray hybridizations were performed as following: 12hâR, 12hâR, 1DâR, 1DâR, 2DâR, 2DâR, 3DâR, 3DâR, 4DâR 4DâR, 7DâR, 7DâR, 21DâR, 21DâR, 12hâ1D, 12hâ1D, 1Dâ2D, 1Dâ2D, 2Dâ3D, 2Dâ3D, 3Dâ4D, 3Dâ4D, 4Dâ7D, 4Dâ7D, 7Dâ21D, 7Dâ21D. The direction of the arrows stand for the way of labeling: Alexa555âAlexa647. Six biological replicates of 1D, 2D, 3D, 4D, and 7D were used; four biological repllicates of 12h and 21D were taken; fourteen biological replicates of reference were applied. The whole experiment includes 26 microarray slide hybridizations.

2010-05-06 | E-GEOD-16407 | biostudies-arrayexpress

Transcriptional dose-response curves for copper for the mussel Mytilus californianus

Project description:Transcriptional dose-response curves for copper for the mussel Mytilus californianus

2011-11-01 | E-MTAB-810 | biostudies-arrayexpress

Factorial Microarray Analysis of Zebra Mussel Adhesion Process under the Impact of Multiple Environmental Factors

Project description:Factorial Microarray Analysis of Zebra Mussel (Dreissena polymorpha) Adhesion Process under the Impact of Multiple Environmental Factors The expression profiles of the zebra mussel byssus unique genes in our cDNA microarray can be influenced by multiple factors. Three environmental factors plus adhesion status were considered as four main factors in this study. Two different levels in each factor were created, therefore, a 2x2x2x2 factorial experimental design was made by sixteen treatment groups with four biological replicates in each group. There were 32 dual-channel microarray slides included in this study and the effects of main factors on gene expression profiles as well as the two-way, three-way, and four-way interactions of the main factors were analyzed. Factors: temperature, water agitation, oxygen level, and adhesion status

2010-05-16 | E-GEOD-16397 | biostudies-arrayexpress

Polymer type specific microplastic effects on Dreissena bugensis’ proteome, antioxidant activity and behavior

Project description:The freshwater mussel Dreissena bugensis was exposed for nine days to different microplastic particles, in detail, to three petroleum-based polymers (polyamide (PA), polyethylene terephthalate (PET), polystyrene (PS)), to one bio-based polymer (polylactic acid (PLA)) and to ground mussel shells (MS), serving as a natural particle control (size range: 20-75 µm;1000 p ml-1). Behavior endpoints were analyzed with hall sensor based real-time valvometry. Additionally, biochemical alterations of ROS detoxifying enzymes were analyzed, and a proteomic profiling on digestive gland tissue was performed.

2022-11-11 | PXD030056 | Pride

Temporal gill transcriptome of the deep-sea mussel Bathymodiolus azoricus in situ and in the laboratory

Project description:The project was designed to explore biological rhythms in the hydrothermal vent mussel Bathymodiolus azoricus. The experiment provides the first high-resolution temporal transcriptomes of an hydrothermal species, both in situ and in the laboratory. For each condition, 5 mussels were sampled every 2h 4min for 24h 48min.

2020-06-12 | E-MTAB-8451 | biostudies-arrayexpress

How nanomolar doses of combined metal salts (Cd, Cu, Hg) induce DNA damage and transcriptional changes in the gills of Mytilus galloprovincialis.

Project description:We used a cDNA microarray previously defined for the marine sentinel organism Mytilus galloprovincialis (MytArray1.0) to evaluate the effects of nanomolar doses of combined metal salts (50, 100 and 200 nM mixtures of Cd, Cu and Hg) after 48 hours of mussel exposure. Pointing to the mussel gills, first target of toxic water contaminants and actively proliferating tissue, we found significant dose-related increases of cells with micronuclei and other nuclear abnormalities in the treated mussels, with differences in the bioconcentration of the three metals determined in the mussel pulp by atomic absorption spectrometry. Following gill RNA purification and DNA microarray analysis, individual gene expression profiles revealed some transcriptional changes at the 50 nM dose, and substantial increases of differentially expressed genes at the 100 and 200 nM doses with roughly similar amounts of up- and down-regulated signals. The functional annotation of transcripts with consistent expression trends and significantly altered at least in one dose point disclosed the complexity of the induced cell response. Three-condition experiment (50, 100 and 200 nM doses), individual treated mussel vs. pooled control mussels (N=5), 3 biological replicates with dye-swap competitive hybridization (array A and B, 2 technical replicates/array).

2013-06-30 | E-GEOD-41218 | biostudies-arrayexpress

Sequencing Greenlip Abalone - We have used the greenlip abalone draft genome (PRJNA433241) to generate basic genetic knowledge of the reproductive process with a specific focus on the key interactive processes of maturation, neural signalling, communication and the stress response.

Project description:We have used the greenlip abalone draft genome (PRJNA433241) to generate basic genetic knowledge of the reproductive process with a specific focus on the key interactive processes of maturation, neural signalling, communication and the stress response.

2019-07-16 | PXD009218 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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