Echinoderm metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA291441 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We identified cis-regulatory elements based on their dynamic chromatin accessibility during the gastrula-larva stages of sea urchin and sea star and studied their evolution in these echinoderm species
2021-10-24 | GSE186363 | GEO
Project description:Seawater exposure to the gram negative marine bacterium Vibrio diazotrophicus induces a robust cellular response in sea urchin larvae that includes the migration of pigment cells to the gut epithelium, changes in cell behavior and altered gut morphology (Ho et al., 2016; PMID 27192936). To investigate the transcriptional underpinnings of this response, whole transcriptome sequencing was performed on mRNA isolated from larval samples collected at 0, 6, 12 and 24 hr of exposure to V. diazotrophicus. The morphological simplicity of the sea urchin larva provides a systems-level model for identifying biologically relevant transcriptional state changes in response to dysbiosis in the gut lumen.
2017-03-24 | GSE96940 | GEO
Project description:In contrast to women, echinoderms have the amazing ability to keep producing functional gametes throughout their lifespan, in some cases exceeding 200 years. The histology and ultrastructure of echinoderm ovaries has been described but how these ovaries function and maintain the production of high-quality gametes is still a mystery. Here, we present the first single cell RNA sequencing (scRNAseq) datasets of two sea urchin species (Strongylocentrotus purpuratus and Lytechinus variegatus) and one sea star species (Patiria miniata). We find 14 cell states in the Sp ovary, 16 cell states in the Lv ovary and 13 cell states in the ovary of the sea star. This resource is essential to understand the structure and functional biology of the ovary in echinoderms, and better informs decisions in the utilization of in situ RNA hybridization probes selective for various cell types. We link key genes with cell clusters of the feature plots in validation of this approach. This resource also aids in the identification of the stem cells for prolonged and continuous gamete production, is a foundation for testing changes in the annual reproductive cycle, and is essential for understanding the evolution of reproduction of this important phylum. Highly selective gene expression revealed by this dataset also divulges gene targets of highest priority for interrogating gene activities by Cas9-targeted gene knock-out and knock-in approaches and in dissociated ovarian cell cultures to test the function of each cell type identified.
2023-11-29 | GSE246430 | GEO
Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under three different seawater CO2 concentrations 400, 800, 1200 µatm. The goal was to determine the effects of CO2, an important climate change variable, on global gene expression
2013-01-01 | GSE37522 | GEO
Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.
2017-07-19 | PXD005780 | Pride
Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under four different seawater conditions: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. The goal was to determine the effects of temperature and CO2, both important climate change variables, on gene expression
2013-01-01 | GSE39125 | GEO
Project description:Sea urchins lack proper eye organs but are photosensitive. In this study, we investigate an extraocular photoreceptor cell (PRC) system in developmental stages of the sea urchin Paracentrotus lividus.
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Project description:Using MethylC-seq we investigated single-base resolution methylomes of sea urchin during development.
2021-11-08 | GSE188333 | GEO
Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under three different seawater CO2 concentrations 400, 800, 1200 M-BM-5atm. The goal was to determine the effects of CO2, an important climate change variable, on global gene expression Larvae were cultured under three different seawater CO2 concentrations 400, 800, 1200 M-BM-5atm, each with four replicate cultures, and sampled at two developmental stages (gastrula and pluteus)
2013-01-01 | E-GEOD-37522 | biostudies-arrayexpress