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PROVIDER: PRJNA1293109 | ENA |
REPOSITORIES: ENA
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Project description:Purpose:Salinity is an important environmental factor that affects the physiological activities of fish. The goals of this study are investigating the effect of different saline-alkali stress on grass carp (Ctenopharyngodon idella). Methods: Grass carp individuals, averaging 12 cm in body length, were obtained from Duofu fish farm (Wuhan, China) and cultured at recirculating aquaculture system for 2 weeks before the experiment began. For the challenge, all grass carp were randomly divided into three groups, and then cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰. After 30 days, some grass crap cultured at 3‰ and 6‰ saline-alkali water were injured. At the same time, gill samples of grass carp were collected from 0, 3‰ (grass carp was not injured), 3‰ (grass carp was injured), 6‰ (grass carp was not injured) and 6‰ (grass carp was injured)saline-alkali groups. Total RNA of all samples was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's introduction. RNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, USA). Samples with RNA integrity numbers (RINs) ≥ 7.5 were subjected to cDNA library construction using TruseqTM RNA sample prep Kit (Illumina). Results:A total of 15 were processed for transcriptome sequencing, generating 94.99Gb Clean Data. At least 5.76Gb clean data were generated for each sample with minimum 91.87% of clean data achieved quality score of Q30. Clean reads of each sample were mapped to specified reference genome. Mapping ratio ranged from 88.59% to 92.84%. The expression of genes was quantified and differentially expressed genes were identified based on their expression.Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.05. Fold change(FC) refers to the ratio of gene expression in two samples. These DEGs were further processed for functional annotation and enrichment analysis. Conclusions: Our study represents Effects and molecular regulation mechanisms of saline-alkali stress on the healthy grass carp by using RNA-seqtechnology. Our results show that saline-alkali stress will impair the immune system of grass carp.
2021-12-31 | GSE185170 | GEO
Project description:Effect of High Temperature on Immune Response of Grass Carp (Ctenopharyngodon idellus) by Transcriptome Analysis To understand the immune response mechanisms of this fish in high temperature circumstance, the transcriptomic profiles of the spleens from grass carp groups undergoing heat stress and normal temperature were investigated.
2016-03-16 | E-GEOD-79265 | biostudies-arrayexpress
Project description:This dataset contains raw and processed TMT-based quantitative proteomic data generated from gill tissues of grass carp (Ctenopharyngodon idella) subjected to chronic salinity stress. Fish were gradually acclimated from freshwater (0‰) to elevated salinities (7‰ and 14‰) under controlled conditions. After stable acclimation, gill tissues were collected, pooled, and proteins were extracted, reduced, alkylated, and digested with trypsin. Peptides were labeled using TMT reagents and analyzed by nano LC–MS/MS on an Orbitrap Fusion Lumos mass spectrometer operated in data-dependent acquisition mode. The resulting MS/MS data were processed using Proteome Discoverer for protein identification and quantification. This proteomic dataset supports an integrated multi-omics analysis of gill adaptive responses to long-term salinity stress in grass carp.
2025-12-16 | PXD072032 |
Project description:Purpose:Salinity is an important environmental factor that affects the physiological activities of fish. Flavobacterium cloumnare is a major aquaculture pathogen infecting various saltwater and freshwater fish. The goals of this study are investigating the mechanism of the immune responses to Flavobacterium cloumnare in grass carp under saline-alkali stress. Methods: Grass carp individuals, averaging 12 cm in body length, were obtained from Duofu fish farm (Wuhan, China) and cultured at recirculating aquaculture system for 2 weeks before the experiment began. For the challenge, all grass carp were randomly divided into three groups, and then cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰. After 30 days, Groups of grass carp were were infected with 2 × 105 CFU/mL Flavobacterium cloumnare G4 strains for 3 h .Gills from each group at 24 hpi, 3dpi and 6dpi were collected. Total RNA of all samples was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's introduction. gill per group at 24 hpi and 48 hpi were rinsedRNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, USA). Samples with RNA integrity numbers (RINs) ≥ 7.5 were subjected to cDNA library construction using TruseqTM RNA sample prep Kit (Illumina). Results:A total of 27 were processed for transcriptome sequencing, generating 177.79Gb Clean Data. At least 5.73Gb clean data were generated for each sample with minimum 93.70% of clean data achieved quality score of Q30. Clean reads of each sample were mapped to specified reference genome. Mapping ratio ranged from 88.11% to 92.33%. The expression of genes was quantified and differentially expressed genes were identified based on their expression.Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.05. Fold change(FC) refers to the ratio of gene expression in two samples. These DEGs were further processed for functional annotation and enrichment analysis. Conclusions: Our study represents the immune response of zebrafish against Flavobacterium cloumnare infection in saline-alkali stress conditions, and reveal the discrepant expression pattern of NOD-like pattern recognition receptors in the gills.
2021-10-13 | GSE185641 | GEO
Project description:Few studies reported for obtaining the grass carp resistant to hemorrhagic disease via gene editing in commercial fish. Here, we demonstrate that the expression and activity of grass carp PI4KB (gcPI4KB) are vital for GCRV-I and GCRV-II replication. Due that obvious cytopathic effect (CPE) in the present available cell lines is only caused by GCRV-I, but GCRV-II is the current popular and fatal strain in grass carp, GCRV-I and GCRV-II are used in cell lines and in grass carp, respectively. The in vitro studies in CIK cells revealed that gcPI4KB interacted with NS80 and VP3 of GCRV-I, and that gcPI4KB was recruited by NS80 for promoting the generation of GCRV VIBs. Since the negative regulatory role of gcPI4KB in GCRV infection was confirmed by in vitro data,we performed gene editing of gcPI4KB in grass carp. We found that PI4KB F0 crispants juvenile grass carp have obvious advantages in promoting growth and in resisting GCRV-II infection. Compared with uninfected WT grass carp, the uninfected PI4KB F0 crispants juvenile grass carp exhibit a higher expression level of many genes involved in growth- and development-related metabolic pathways such as the FoxO signaling pathway and insulin signaling pathway. Compared with WT grass carp without infection, PI4KB F0 crispants juvenile grass carp without infection or WT grass carp infected with GCRV-II, higher expression levels for many genes involved in metabolic diseases and viral infection were observed in the liver from PI4KB F0 crispants juvenile grass carp infected with GCRV-II. Altogether, the present study suggests the mechanism of gcPI4KB in facilitating GCRV replication, the signaling pathways regulated by gcPI4KB, and the possibility to obtain the grass carp resistant to hemorrhagic disease via gene editing of PI4KB.
2025-09-30 | GSE273923 | GEO
Project description:Animals often face food scarcity in nature. In order to survive, some animals store substantial fat when food is available. However, the physiological mechanism by which they store substantial fat and maintain metabolic health in the short term is poorly understood. Here, using the grass carp (Ctenopharyngodon idellus) as a model, which exhibits remarkable fat storage capacity, we found that adipose tissue responded to energy overload first and expanded through adipocyte hypertrophy and hyperplasia. Mechanistically, hypoxia inducible factor-1αa (hif-1αa) was activated in mature adipocytes after short-term high-energy intake, thereby bidirectionally regulating adipose triglyceride lipase (atgl) to drive healthy expansion of adipose tissue in grass carp: (1) Hif-1αa downregulates atgl protein levels via the ubiquitin-proteasome pathway, promoting adipocyte hypertrophy; (2) Hif-1αa upregulates atgl transcription to sustain basal lipolysis, releasing free fatty acids that activate peroxisome proliferator-activated receptor γ (pparγ) in preadipocytes to promote adipocyte hyperplasia. This crosstalk-mediated rapid adipocyte hyperplasia prevents detrimental excessive hypertrophy and significantly boosts the overall energy storage capacity. Taken together, our study reveals how grass carp utilize hypoxia signals (a signal often associated with metabolic disorders in mammals) to coordinate the pattern of adipose tissue expansion, achieving rapid and healthy lipid storage. Our findings redefine hypoxia's role as a metabolic orchestrator rather than a stress indicator, suggesting potential implications for a theoretical basis for addressing obesity-related diseases in humans and farmed animals caused by excessive energy intake.
2026-03-04 | GSE315218 | GEO
Project description:Grass carp is the most produced freshwater fish species in China. However, frequent outbreaks of bacterial diseases caused by Aeromonas ssp. have led to huge economic losses in grass carp farming. Various omics technologies have been used to study the response of grass carp to these pathogens. For instance, the transcriptional profile of the spleen from grass carp challenged with A. hydrophila, which revealed significant enrichment of gene clusters, including phagocytosis, complement system, cytokines, antigen processing and presentation, pattern recognition receptors, cell adhesion molecules, apoptosis, and antioxidant enzymes. Furthermore, a large number of differentially expressed genes related to inflammation were identified in the intestinal transcriptome of grass carp infected with A. hydrophila. However, the immune response of grass carp infected with A. veronii remains unresolved at the multi-omics level. In the present study, an intestinal infection model was established in grass carp using the isolated A. veronii strain EL07, and the differentially expressed genes and proteins in the intestinal and differentially expressed metabolites in serum were analyzed. The results may contribute to a better understanding of the pathogenesis of grass carp enteritis caused A. veronii.
2026-04-30 | GSE329120 | GEO
Project description:Grass carp (Ctenopharyngodon idellus), the world’s largest aquaculture fish species, exhibits superior growth in females compared to males. However, the lengthy sexual maturation period of four to five years poses a significant obstacle to the genetic reproduction and breeding of grass carp. Consequently, classical methods such as gonadogenesis or sex reversal through steroid treatment, employed for breeding all-female grass carp, demand considerable time and effort. In this study, we developed an super-fast breeding strategy for generating all-female grass carp in a total of half a year, using a surrogate production method. We first characterized grass carp female germline stem cells (GSCs) from genetic female juveniles at three months post-fertilization (mpf). The female GSCs with XX chromosomes were then transplanted into germ cell-depleted zebrafish larvae at five days post-fertilization (dpf). The transplanted grass carp XX germ cells underwent rapid spermatogenesis in the zebrafish recipient. At three months after transplantation, all zebrafish recipients had developed into males capable of producing the all-X sperm of the grass carp. By using these sperm to fertilize wildtype grass carp eggs, we successfully produced an all-female grass carp offspring. This groundbreaking achievement highlights the potential of surrogate production in the genetic breeding of valuable fish species, and opens a new avenue for advancing genetic breeding in aquaculture.
2025-03-01 | GSE261835 | GEO
Project description:The invasive marine mussel Mytilus galloprovincialis has displaced the native congener Mytilus trossulus from central and southern California, but the native species remains dominant at more northerly sites that have high levels of freshwater input. To determine the extent to which interspecific differences in physiological tolerance to low salinity might explain limits to the invasive species’ biogeography, we used an oligonucleotide microarray to compare the transcriptional responses of these two species to an acute decrease in salinity. Among 6,777 genes on the microarray, 117 genes showed significant changes that were similar between species, and 12 genes showed significant species-specific responses to salinity stress. Osmoregulation and cell cycle control were important aspects of the shared transcriptomic response to salinity stress, whereas the genes with species-specific expression patterns were involved in mRNA splicing, polyamine synthesis, exocytosis, translation, cell adhesion, and cell signaling. Forty-five genes that changed expression significantly during salinity stress also changed expression during heat stress, but the direction of change in expression was typically opposite for the two forms of stress. These results (i) provide insights into the role of changes in gene expression in establishing physiological tolerance to acute decreases in salinity, and (ii) indicate that transcriptomic differences between M. galloprovincialis and M. trossulus in response to salinity stress are subtle and involve only a minor fraction of the overall suite of gene regulatory responses.
2011-01-10 | GSE25111 | GEO