Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology
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ABSTRACT:
PROVIDER: PRJNA674824 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12992430_1.fastq.gz | Fastqsanger.gz | |||
| SRR12992430_2.fastq.gz | Fastqsanger.gz | |||
| SRR12992431_1.fastq.gz | Fastqsanger.gz | |||
| SRR12992431_2.fastq.gz | Fastqsanger.gz | |||
| SRR12992432_1.fastq.gz | Fastqsanger.gz |
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Project description:Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals, for example, flatworms, newts, salamanders, and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately, the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues, and even cause serious loss of function or death. However, the research on regeneration mechanisms is limited and incomplete so far. Here, we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d, 3d, and 7d after caudal fin removal, and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change, especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa (blastema outgrowth stage) were dramatically enriched in 20 Biological Processes (FDR < 0.05), three of which were cell cycle (GO:0007049), mitotic cell cycle (GO:0000278), and cell cycle process (GO:0022402), one was response to wounding (GO:0009611), etc. Conclusion: Taken together, the results revealed that the DEGs were enriched in numerous biological processes, molecular function, cellular component, and signaling pathways, suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism.
2022-04-04 | GSE160909 | GEO
Project description:The study analysed proteomic changes during zebrafish caudal fin tissue regeneration post small molecule treatment.
2025-11-24 | PXD060144 | Pride
Project description:Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Small RNA and mRNA gene expression profiling during 0 and 4 days post amputation.
2016-06-01 | E-GEOD-74415 | biostudies-arrayexpress
Project description:Adult zebrafish are able to regenerate many organs such as their caudal fin in only few days post amputation. To explore the landscape and dynamic of the genes involed in regeneration, we performed a global transcriptomic analysis using RNA-seq during zebrafish caudal fin regeneration.
2019-08-13 | GSE112498 | GEO
Project description:Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing.
2016-06-01 | GSE74415 | GEO
Project description:Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single-molecule-based sequencing technology for high-throughput profiling of both intact (uncut) and regenerating caudal fin samples (cut) at 24hpA. We confirmed the presence of macrophage subsets, previously described by our group to govern zebrafish fin regeneration, and identified a novel blastemal cell population.
2021-07-17 | GSE158851 | GEO
Project description:single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell-type-specific genetic program during regeneration
2020-08-12 | GSE137971 | GEO
Project description:Aim: In this study, we aim to establish a diabetic zebrafish model and examine the effects of high glucose on inflammation and tissue regeneration. Materials and Methods: Tübingen strain zebrafish (wild type, WT), Tg (mpo: EGFP), and Tg (coro1a: EGFP) zebrafish were employed. Caudal fin amputation was performed to study tissue regeneration and inflammation. Results: Our results showed that high glucose increased the recruitment of neutrophils and macrophages after amputation. Most importantly, limb regeneration was severely impaired after amputation in zebrafish larvae exposed to 222 mM glucose for 14 days. In addition, inflammatory factors IL-1β, IL-6, TNF-α, VCAM-1, and MCP-1, which are closely related to the development of diabetic wound, increased significantly in caudal fin amputation after glucose exposure. The p38 inhibitor SB203580 can reduce the expression of inflammatory factors and promote regeneration in high glucose. It showed that caudal fin amputation after glucose exposure resulted in genes enrichment of several pathways involved in amino acid metabolism, lipid metabolism, and inflammation based on high-throughput transcriptome sequencing. Conclusions: Overall, this experimental system using zebrafish larvae provides a wide spectrum of genetic and molecular profile recapitulating human diabetes which will be beneficial for basic research of inflammation and regeneration in diabetic background and promote translational research for diabetes therapy.
2025-09-01 | GSE260718 | GEO
Project description:Tissue regeneration relies on precise molecular mechanisms controlling cell fate transitions, with cell metabolism emerging as a key regulator. Lactate-derived histone lactylation has recently been identified as an important epigenetic modification involved in the regulation of gene expression across various biological processes. In this study, we report an increase in global histone lactylation and H3K18Lac levels in the mesenchyme and osteoblasts of the zebrafish caudal fin, during the early stages of regeneration. Our findings demonstrate that this epigenetic modification is functionally regulated by increased lactate levels, while inhibition of glycolysis and lactate production significantly reduces histone lactylation. These results suggest that metabolic reprogramming, in response to caudal fin injury, regulates histone lactylation, potentially modulating gene expression essential for cell plasticity and proliferation. This study expands our understanding of how metabolic-epigenetic interactions influence regenerative processes, providing valuable insights for the development of novel therapeutic strategies to enhance tissue repair.
2026-01-19 | GSE311919 | GEO
Project description:RNA-seq data from adult zebrafish caudal fin regeneration
| PRJNA447984 | ENA