Oncorhynchus mykiss
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA312486 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3185640.fastq.gz | Fastqsanger.gz | |||
| SRR3185650.fastq.gz | Fastqsanger.gz | |||
| SRR3185660.fastq.gz | Fastqsanger.gz | |||
| SRR3185670.fastq.gz | Fastqsanger.gz | |||
| SRR3185641.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.
2024-04-01 | GSE262612 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.
2024-04-16 | GSE263547 | GEO
Project description:Rainbow trout is a typical cold-water fish, with the intensification of global warming, high temperatures severely restrict the development of aquaculture in summer. Understanding the molecular regulation mechanisms of rainbow trout in response to heat stress will be salutary to alleviate heat stress-related damage. In the present study, we performed transcriptome analysis of liver tissues in rainbow trout under heat stress (24℃) and control (18℃) conditions to identify induced lncRNAs and pathways by heat stress. More than 658 million clean reads and 5,916 lncRNAs were identified from six liver libraries. A total of 927 novel lncRNAs were generated and 428 differentially expressed lncRNAs were screened through stringent thresholds. The RNA-seq results were verified by RT-qPCR. In addition, the regulatory network of important functional lncRNA-mRNA were constructed. GO and KEGG enrichment analysis of target gene of differentially expressed lncRNAs were performed. Many target genes involved in maintaining homeostasis or adapting to stress and stimuli were highly induced under heat stress. Several important regulatory pathways were involved in heat stress, including thyroid hormone signaling pathway, PI3K-Akt signaling pathway, estrogen signaling pathway, etc. This result broadens our understanding of lncRNA associated with heat stress and provides new insights into lncRNA-mediated regulation of rainbow trout heat stress.
2019-08-11 | GSE135668 | GEO
Project description:Purpose:Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout Methods:miRNAs of rainbow trout were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries of the kidney tissues under control (18℃) and heat-treated (24℃) conditions Results:high-throughput sequencing was performed to identify miRNAs responsive to heat stress. We obtained 41,991,119 and 43,882,123 raw reads and 39,756,736 and 42,538,331 clean reads from under control (18℃) and heat-treated (24℃) .A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. In addition to, including 393 negative correlation miRNA-target gene pairs Conclusions:through high-throughput sequencing of the six libraries from head kidney tissue of rainbow trout, the expression level of miRNA has significant changes after heat stress.
2018-03-16 | GSE111816 | GEO
Project description:Hypoxia negatively affects the behavior, growth, reproduction, and survival of fish, causing serious economic losses to aquaculture. Rainbow trout (Oncorhynchus mykiss), an important economic fish worldwide, belongs to a hypoxia-sensitive fish species. However, the regulatory mechanisms of miRNAs under hypoxia stress response of rainbow trout remains unclear. In this study, rainbow trout were subjected to hypoxia stress (DO: 3.5 mg/L) for 3 h (H3h_L), 12 h (H12h_L), 24 h (H24h_L) and 3 h reoxygenation (R3h_L) to systemically evaluate the changes of miRNA expression profiles in liver, and the functions of sha-miR-92a_L+2R+4 were investigated. We found 17, 144, 57 and 55 differentially expressed (DE) miRNAs in H3h_L vs. control (N_L), H12h_L vs. N_L, H24h_L vs. N_L and R3h_L vs. N_L comparisons, respectively. Enrichment analysis revealed that the targets of these DE miRNAs were significantly enriched in HIF signaling pathway, VEGF signaling pathway, FoxO signaling pathway and glycolysis/gluconeogenesis. Through miRNA-mRNA nteraction and weighted gene co-expression network analysis (WGCNA), five key DE miRNAs (sha-miR-92a_L+2R+4, ssa-miR-128-3p, ssa-miR-101b-3p_R+1, ola-miR-199a-5p_R+2 and tni-miR-199_1ss18CG) were identified, which can target at least two hypoxia-responsive genes, such as vegfaa, ho, glut1a and junb. Functional analysis found that sha-miR-92a_L+2R+4 directly regulated vegfaa expression by targeting its 3′-UTR, overexpression of sha-miR-92a_L+2R+4 significantly decreased vegfaa expression in rainbow trout liver cells, while opposite results were obtained after transfection of sha-miR-92a_L+2R+4 inhibitor. Furthermore, overexpression of sha-miR-92a_L+2R+4 promoted rainbow trout liver cell proliferation and inhibited apoptosis. These results deepen our understanding of the crucial roles of miRNAs under hypoxia stress in rainbow trout, and provide valuable information for further studying the regulatory mechanisms of key hypoxia-responsive miRNAs and breeding hypoxia-tolerant rainbow trout species.
2023-05-10 | GSE231752 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is a typical cold-water fish, the development of rainbow trout aquaculture was severely hampered via the high temperature in summer. Understanding the regulatory mechanism of rainbow trout response to chronic heat stress can provide a theoretical basis for formulating measures to relieve heat stress. In the study, changes in the biochemical parameters revealed that a strong stress response occurred in rainbow trout at 24 °C, the organisms stress defense system was activated, and the immune system was also affected. Proteome of rainbow trout liver tissues under heat stress (24 °C) and control conditions (18 °C) were performed using DIA/SWATH. A total of 390 DEPs were identified by strict threshold (q-value <0.05 and fold changes >1.5), among them 175 were up-regulated and 225 were down-regulated. Some proteins related to HSP, metabolism and immunity were identified. GO analysis showed that some proteins that were highly induced to express at high temperature were involved in the regulation of cell homeostasis, metabolism, adaptive stress and stimulation. KEGG analysis shows that some pathways play an important role in the regulation of heat stress, such as metabolic pathway, protein processing in endoplasmic reticulum pathway, PPAR signaling pathway and complement and coagulation cascades pathway, etc. PPI network analysis shows HSP90b1 and C3 maybe cooperative to protect the integrity of cell membrane function under heat stress. Our finding provide a comprehensive review of protein expression of rainbow trout liver under heat stress, which helps to formulate strategies for rainbow trout to relieve heat stress during high temperature in summer.
2020-07-06 | PXD020206 |
Project description:Transcriptome profiling of rainbow trout liver under moderate heat stress
| PRJNA352601 | ENA
Project description:With the intensification of global warming, rainbow trout is suffering from varying degrees thermal stimulation, heat stress may cause pathological signs or diseases by reducing the immune roles and then lead to mass mortality, so high temperatures severely restrict the development of its aquaculture. Understanding the molecular regulation mechanism of rainbow trout under heat stress is used to take measures to relieve symptoms. We performed multiple transcriptomic analysis of liver tissues from rainbow trout under heat stress (24 °C) and control conditions (18 °C) to identify circRNAs, miRNAs and mRNAs. Changes of non-specific immune parameters revealed that strong stress response of rainbow trout is caused in 24 °C. A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified from six libraries, and ceRNA regulatory network is constructed. 301 circRNA–miRNA and 51 miRNA–mRNA negative correlation pairs were screened from ceRNA regulatory network, and predicted three regulatory correlation pairs that novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some genes involved in metabolic process, biological regulation or response to stimulus are highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as Protein processing in endoplasmic reticulum (ER), Estrogen signaling pathway, HIF-1 signaling pathway, etc. These results extend our understanding of the molecular mechanisms of heat stress response and expected to provide a novel insight into develop strategies for relieve heat stress.
2019-11-08 | GSE140112 | GEO
Project description:Transcriptome profiling of rainbow trout head kidney under moderate heat stress
| PRJNA448020 | ENA
Project description:Dissolved oxygen (DO) has an important impact on fish survival and reproduction, and is also one of the keys limiting conditions for healthy fish life. Rainbow trout (Oncorhynchus mykiss), an economically significant cold-water fish globally, are highly susceptible to hypoxia stress. However, the physiological changes and molecular mechanisms of rainbow trout under different hypoxic conditions are still unknown. In the present study, we used RNA-seq analysis and measurement of biochemical parameters at different time points (0-, 4-, 8-, 12-, 24 h) under acute (3.0 ± 0.1 mg/L), chronic (4.5 ± 0.1 mg/L) hypoxic stress and reoxygenation (R12-, R24 h) to reveals the physiological changes and molecular mechanism of the hypoxic stress response in rainbow trout. The transcriptome results showed that a total of 424 differentially expressed genes (DEGs) were identified in the CM-vs-Tm12M, CM-vs-Ts12M and Tm12M-vs-Ts12M groups and the genes for FOXO signaling pathway, p53 signaling pathway, Adipocytokine signaling pathway, Autophagy, Glycine, serine and threonine metabolism, etc. were significantly enriched under hypoxic stress, as shown by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes enrichment analyses (KEGG) and Gene Set Enrichment Analysis (GSEA). Based on DEGS expression trend analysis, the most significant 2 clusters were selected to construct protein-protein interaction (PPI) networks, which resulted in the prediction of ddit4, txnip, slc3a2 and p4ha1 as the hypoxia-induced hub genes in cluster 7. fgg, f7, serpina1 and serpinf2 are the hypoxia-induced hub genes of cluster 3. This study preliminarily elucidated the adaptive mechanism of rainbow trout in response to hypoxic stress and provide a basis for the study of the molecular mechanism of fish adaptation to different hypoxic stresses.
2024-01-18 | GSE253274 | GEO