Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1193778 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31593878.fastq.gz | Fastqsanger.gz |
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Project description:In order to explore the regulatory information of the two different color associations in crucian carp, we identified the differential miRNAs of gold and greenish grey by smallRNA sequencing, and analyzed their functional and pathway enrichment.
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Project description:The freshwater fish crucian carp (Carassius carassius) are able to survive chronic anoxia for several months at low temperatures. Consequently, anoxia-related physiological and biochemical adaptations in this species have been studied for more than half a century. Still, despite for the well-known role of protein phosphorylation in regulating cellular processes, no studies have comprehensively characterized the phosphoproteome in crucian carp. In this study, we report the global phosphoproteome in crucian carp brain and liver during anoxia and reoxygenation. By applying a bottom-up proteomic approach on enriched phosphopeptides we found that the brain phosphoproteome show surprisingly few changes during anoxia-reoxygenation exposure with 110 out of 4316 phosphopeptides being differentially regulated. By contrast, in the liver 395 out of 1293 phosphopeptides were regulated. Although most changes occurred in the liver phosphoproteome, we found evidence for metabolic depression and decreased translation in both brain and liver. We also found regulated phosphoproteins involved in apoptotic regulation and reactive oxygen species handling in both tissues. In the brain, some of the most regulated phosphopeptides belonged to proteins involved in central nervous system development and neuronal activity at the synaptic cleft. Regulated phosphoproteins specific for liver tissue were related to glucose metabolism, including glycolytic flux and glycogenolysis, and the ubiquitin-proteasome system.
2024-05-29 | PXD033061 | Pride
Project description:In order to explore the regulatory information of the two different color associations in crucian carp, we identified the differential mRNAs of gold and greenish grey by transcriptome sequencing, and analyzed their functional and pathway enrichment.
2022-12-25 | GSE212495 | GEO
Project description:Hypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. In this study, we detected the changes of biochemical parameters after hypoxia stress (3 h (H3h), H12h, and H24h) and reoxygenation (reoxygenation for 3 h after hypoxia 24 h (R3h)), mRNA and miRNA expression profiles under H12h compared to the control, and key hypoxia-related genes expression patterns in the liver of crucian carp through biochemical methods, RNA-seq, and qRT-PCR. Compared with the control, increased T-SOD, CAT, GSH-Px, T-AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress, and LDH activity increased only in the H12h and H24h groups. Based on RNA-seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif-1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrc3, nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre-miR-125c-3p/novel_173, dre-miR-181b-5p, and dre-miR-338-5p/dre-miR-128-3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, NOD−like receptor signaling pathway, and cytokine-cytokine receptor interaction. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp, which are of great significance for genetics and breeding of other fishes tolerant to hypoxia.
2022-10-18 | GSE215752 | GEO
Project description:Hypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. In this study, we detected the changes of biochemical parameters after hypoxia stress (3 h (H3h), H12h, and H24h) and reoxygenation (reoxygenation for 3 h after hypoxia 24 h (R3h)), mRNA and miRNA expression profiles under H12h compared to the control, and key hypoxia-related genes expression patterns in the liver of crucian carp through biochemical methods, RNA-seq, and qRT-PCR. Compared with the control, increased T-SOD, CAT, GSH-Px, T-AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress, and LDH activity increased only in the H12h and H24h groups. Based on RNA-seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif-1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrc3, nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre-miR-125c-3p/novel_173, dre-miR-181b-5p, and dre-miR-338-5p/dre-miR-128-3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, NOD−like receptor signaling pathway, and cytokine-cytokine receptor interaction. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp, which are of great significance for genetics and breeding of other fishes tolerant to hypoxia.
2022-10-15 | GSE215372 | GEO
Project description:llotetraploid hybrids of Red Crucian Carp and common Carp are a new species bred by distant hybridization. SWATH-MS was applied for quantitative proteomics profiling in liver tissue of allotetraploid，Red Crucian Carp and Common Carp respectively.
2020-11-26 | PXD022748 |
Project description:SWATH-MS based quantitative proteomic profiling was performed on the liver tissues from triploid crucian carp（TCC） and its parents Red Crucian Carp (RCC) and allotetraploid (4nAT)
2021-05-12 | PXD025964 |
Project description:The freshwater fish crucian carp (Carassius carassius) can survive complete oxygen depletion (anoxia) for several months at low temperatures, achieved by a combination of reduced energy demand and increased glycolysis fueled by large hepatic glycogen stores. In crucian carp, the energy-requiring protein synthesis is controlled in a tissue-specific manner when oxygen levels decrease. During anoxia, translational rates are maintained at almost normoxic levels in brain, while heart and liver translation rates are strongly reduced. However, little is known about how the global proteome of these tissues are affected by oxygen variations. By applying mass spectrometry-based proteomics, 3304 proteins in brain, 3004 proteins in heart and 2516 proteins in liver were detected, of which 66 brain proteins, 243 cardiac proteins and 162 hepatic proteins were differentially expressed during the course of anoxia-reoxygenation compared to normoxic control. The brain proteome showed few differences in response to oxygen variations, indicating that anoxic survival is not regulated through protein expression in this tissue. Cardiac and hepatic adaptions to anoxia included enrichment of mitochondrial proteins involved in aerobic respiration and mitochondrial membrane integrity. We show that enzymes in the electron transport system (ETS) are regulated in a tissue-specific manner since no ETS components were regulated in brain, but were downregulated in heart and upregulated in liver during anoxia and reoxygenation. Furthermore, complement system activation was enriched in heart during anoxia. During reoxygenation, proteins involved in the cristae junction organization were regulated in the heart, possibly explaining how reactive oxygen species can be avoided when oxygen returns in this master of anoxic survival.
2023-01-27 | PXD032830 | Pride