Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1220081 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparison of the hepatic transcriptomes for two half-sib-families of European sea bass fed on vegetable and fish diet. These two half-sib-families exhibit similar growth on fish diet while significantly different on vegetable diet. The aim of the study is to point out the large panel of metabolic and physiological effects induced by total substitution of both fish meal and fish oil in the diets of European sea bass and to reveal physiological characteristics associated to the two half-sib-families.
2011-09-01 | GSE27649 | GEO
Project description:The experiment focused on the transcriptomic changes associated with gill inflammation in sea farmed Atlantic salmon (Salmo salar). To ensure the multifactorial aspect of gill inflammation, fish were sampled at three marine production sites (A on Isle of Mull, B in Shetland and C in Shetland) between October 2017 and March 2018. All fish were of strain Fanad and originated from the same egg fertilisation batch. They were reared in different hatcheries (Couldoran, Pettigo-Damph and Knock-Frisa for sites A, B and C, respectively) for one year and entered the sea in spring 2017. The resultant gill tissues (44 samples in total with 1 gill sample per fish) were first scored for proliferative gill disease (PGD), using gross morphology PGD scores from 0 with no visual pathology to 5 with severe visual pathology, and then subjected to RNA-seq and histopathological (microscopic) examination. One RNA-seq sample (fish 95) was identified as an outlier and removed from the subsequent analysis. As a result, the analysis aiming to integrate gill transcriptome, gross morphology and histopathology was performed on 43 gill samples, classified either as PGD score 1 (n = 26) or PGD score 3 (n = 17). In total, 20 gill samples originated from site A (10 with PGD1 and 10 with PGD 3, 10 samples from site B (7 with PGD1 and 3 with PGD 3) and 13 samples from site C (9 with PGD1 and 4 with PGD 3).
2020-06-01 | E-MTAB-8855 | biostudies-arrayexpress
Project description:Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.
2024-11-24 | GSE263620 | GEO
Project description:Comparison of the hepatic transcriptomes for two half-sib-families of European sea bass fed on vegetable and fish diet. These two half-sib-families exhibit similar growth on fish diet while significantly different on vegetable diet. The aim of the study is to point out the large panel of metabolic and physiological effects induced by total substitution of both fish meal and fish oil in the diets of European sea bass and to reveal physiological characteristics associated to the two half-sib-families. Fish from both two half-sib-families (G and g) were fed a a fish diet (FD) or a vegetable diet (VD) diet for 9 months. Five to eight independent experiments were performed for each experimental groups (G-FD; G-VD; g-FD; g-VD) using different fishes for each experiment.
2011-08-31 | E-GEOD-27649 | biostudies-arrayexpress
Project description:We have further tested and validated a reproduction-enriched microarray designed specifically for European sea bass providing a reliable tool to study gene expression patterns in this fish species. Results obtained by using this platform helped to increase our knowledge in the gene cascade of sex differentiation and give evidence of the complexity of the molecular processes. We described the gene expression profile of genes and pathways required to differentiate bipotential tissue to either an ovary or testis providing a deep transcriptomic analysis in the developing gonads. Resulting data may help to improve sex control in fish culture particularly in the European sea bass
2019-12-01 | GSE115841 | GEO
Project description:Japanese medaka (Oryzias latipes) embryos were exposed to two concentrations of the water accommodated fractions and chemically-enhanced water accommodated fractions of two types of diluted bitumen (dilbit). Chemical-dispersion did not significantly alter transcriptional responses to dilbit toxicity but may have acted through alternative mechanisms to give similar phenotypic responses, such as normal swim bladder development. This study identified novel biomarkers in fish with or without visual malformations exposed to dilbit that can be used to assess aquatic ecosystem health. Microarray analyses identified novel biomarkers and gene networks in dilbit-exposed malformed embryos that were not evident in unaffected dilbit-exposed fish or in controls.
2020-05-12 | GSE142734 | GEO
Project description:The Cyprinus carpio is one of the most important food fish with over hundred varieties in the world. It shows many morphological and genetic variations after selection breeding. It is also considered an alternative vertebrate fish model to zebrafish. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been suggested to have a crucial role in embryonic development. However, systemic research on the lncRNAs and miRNAs during embryonic development of C. carpio has not been reported yet. In this study, we investigated the miRNA, lncRNA and mRNA expression profiles during six main embryonic development stages (cleavage (2 hours post-fertilization hpf)), blastocyst (6 hpf), gastrulation (12 hpf), organ formation (20 hpf), hatching (64 hpf) and 1 day post-hatching). A total of 9,888,123 clean reads were obtained frommiRNA library. After filtering, 2886 miRNAs were identified. The results would open the way for future genetic, genomic, and evolutionary studies and enable better understanding of gene regulation during embryonic development of C. carpio.
2019-03-26 | GSE128806 | GEO
Project description:scRNA-seq was used in order to produce a cell type atlas of the larval and adult sea lamprey (Petromyzon marinus) brain. This resource enabled us to reveal the cell type composition and molecular organization of a representative of a lineage (i.e., the cyclostomes) that diverged from the rest of vertebrates around 500 million years ago, and lays the foundations for a better comprehension of vertebrate brain evolution
2021-12-13 | E-MTAB-11087 | biostudies-arrayexpress
Project description:Photoreception, a form of sensory experience, is essential for normal development of the mammalian visual system. Detecting photons during development is a prerequisite for visual system function - from shaping vision’s first synapse and maturation of retinal vascular networks, to transcriptional establishment and maturation of cell types within the visual cortex. Consistent with this theme, we find that the lighting environment regulates developmental rod photoreceptor apoptosis via OPN4-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs). Using a combination of genetics, sensory environment manipulations, and computational approaches, we establish a molecular pathway in which light-dependent glutamate release from ipRGCs is detected via a transiently expressed kainate receptor (GRIK3) in rod precursors localized to the inner retina. Communication between ipRGCs and nascent inner retinal rods appears to be mediated by transient hybrid neurites projecting from ipRGCs that sense light before eye-opening. These structures, previously referred to as outer retinal dendrites (ORDs), span the ipRGC-rod precursor distance over the first postnatal week and contain the machinery for sensory detection (melanopsin, OPN4) and anterograde neurotransmitter release (Synaptophysin and VGLUT2). Computational and histological assessment of human mid-gestation development reveal conservation of several hallmarks of an ipRGC-to-rod precursor pathway, including displaced rod precursors, transient GRIK3 expression in the rod lineage, and the presence of ipRGCs with putative neurites projecting deep into the developing human retina. Thus, this analysis defines a retinal retrograde signaling pathway that links the sensory environment to rod precursors via ipRGC photoreceptors, allowing the visual system to adapt to distinct lighting environments prior to eye-opening.
2024-07-04 | GSE269102 | GEO